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https://openalex.org/W4368617919
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http://www.thieme-connect.de/products/ejournals/pdf/10.1055/a-2072-5740.pdf
|
English
| null |
Rare complications related to lumen-apposing metal stent placement, successfully treated by endoscopic hand-suturing device.
|
Endoscopy
| 2,023
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cc-by
| 1,365
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Article published online: 2023-05-04 Article published online: 2023-05-04 Article published online: 2023-05-04 Rare complications related to lumen-apposing metal stent placement,
successfully treated by endoscopic hand-suturing device. E-Videos
cle published online: 2023-05-04 E-Videos Rare complications related to lumen-apposing metal stent placement,
successfully treated by endoscopic hand-suturing device. Rare complications related to lumen-apposing metal stent placement,
successfully treated by endoscopic hand-suturing device. ▶Fig. 1 Steps to close the fistula associated with the placement of a lumen-apposing metal stent using an endoscopic hand-suturing device. a Computed tomography revealed the presence of the walled-off necrosis (WON) (green arrow). b Fluoroscopy revealed a colonic fistula asso-
ciated with WON (yellow triangle) at the sigmoid colon (red triangle). c A plastic stent was placed to improve the relapsed WON and to close
the fistula. d The gastric mucosa around the fistula was cauterized circumferentially using an electrical device. e A suture needle with thread was
introduced into the stomach using an endoscopic hand-suturing device. f An endoscopic hand-suturing device and a suture needle with thread
were applied to close the fistula. g The fistula was completely sutured with thread. h One month after endoscopic suturing, the fistula was
completely fixed with a normal covered mucosa. A 56-year-old man with a walled-off
necrosis (WON) underwent endoscopic
necrosectomy using a lumen-apposing
metal stent (LAMS) (Hot Axios; Boston
Scientific, Boston, Massachusetts, USA)
(▶Fig. 1 a), which improved the abdomi-
nal inflammation within 1 month. How-
ever, 1 year after removal of the LAMS,
the WON relapsed with abdominal pain
and elevated C-reactive protein (CRP)
levels. Gastroscopy revealed that the fis-
tula caused by the LAMS placement
persisted, with leakage of necrotic mate-
rial. Fluoroscopy also revealed a colonic
fistula associated with the WON in the
sigmoid colon (▶Fig. 1 b). An ileostomy,
in combination with drainage using a
plastic stent into the WON and adminis-
tration of antibiotics, failed to improve
abdominal symptoms and normalize CRP Usually,
LAMS-associated
fistulas
are
closed in their natural course [1–3]. We
encountered a rare case in which a long-
term remaining fistula resulted in WON
relapse, which was successfully treated
by closing the fistula using a new endo-
scopic suturing device. This hand-sutur-
ing device is a good option for closing
LAMS-associated fistulas. levels; this was suggested to be attribut-
ed to the two fistulas. After percutaneous
drainage of the WON, an over-the-scope
(OTS) clip was applied to close these fistu-
las. Although there is no conflict of interest for
this paper, Y. Minoda has an research and de-
velopment consulting agreement with Olym-
pus Corporation. Article published online: 2023-05-04 However, the colon and gastric tis-
sues around the fistula were too rigid to
be pulled in the OTS clip. In this situation,
we attempted to close the gastric fistula
using a new endoscopic hand-suturing
device (SutuArt; Olympus, Tokyo, Japan)
and a suture needle with thread (V-lock;
Medtronic, Dublin, Ireland) after cauteri-
zation of the gastric mucosa surrounding
the fistula to promote wound healing
(▶Fig. 1 c–g, ▶Video 1). One month la-
ter, the fistula was completely fixed with
a normal covered mucosa (▶Fig. 1 h). This led to an improvement in abdominal
pain and CRP levels. A 56-year-old man with a walled-off
necrosis (WON) underwent endoscopic
necrosectomy using a lumen-apposing
metal stent (LAMS) (Hot Axios; Boston
Scientific, Boston, Massachusetts, USA)
(▶Fig. 1 a), which improved the abdomi-
nal inflammation within 1 month. How-
ever, 1 year after removal of the LAMS,
the WON relapsed with abdominal pain
and elevated C-reactive protein (CRP)
levels. Gastroscopy revealed that the fis-
tula caused by the LAMS placement
persisted, with leakage of necrotic mate-
rial. Fluoroscopy also revealed a colonic
fistula associated with the WON in the
sigmoid colon (▶Fig. 1 b). An ileostomy,
in combination with drainage using a
plastic stent into the WON and adminis-
tration of antibiotics, failed to improve
abdominal symptoms and normalize CRP Endoscopy_UCTN_Code_CPL_1AH_2AG Endoscopy_UCTN_Code_CPL_1AH_2AG ▶Fig. 1 Steps to close the fistula associated with the placement of a lumen-apposing metal stent using an endoscopic hand-suturing device.
a Computed tomography revealed the presence of the walled-off necrosis (WON) (green arrow). b Fluoroscopy revealed a colonic fistula asso-
ciated with WON (yellow triangle) at the sigmoid colon (red triangle). c A plastic stent was placed to improve the relapsed WON and to close
the fistula. d The gastric mucosa around the fistula was cauterized circumferentially using an electrical device. e A suture needle with thread was
introduced into the stomach using an endoscopic hand-suturing device. f An endoscopic hand-suturing device and a suture needle with thread
were applied to close the fistula. g The fistula was completely sutured with thread. h One month after endoscopic suturing, the fistula was
completely fixed with a normal covered mucosa. ENDOSCOPY E-VIDEOS
https://eref.thieme.de/e-videos E-Videos is an open access online
section of the journal Endoscopy,
reporting on interesting cases
and new techniques in gastroenterological
endoscopy. All papers include a high-quality
video and are published with a Creative
Commons CC-BY license. Endoscopy
E-Videos qualify for HINARI discounts and
waivers and eligibility is automatically
checked during the submission process. We grant 100% waivers to articles whose
corresponding authors are based in Group
A countries and 50% waivers to those
who are based in Group B countries as
classified by Research4Life (see: https://
www.research4life.org/access/eligibility/). Video 1 Steps to close the fistula associated with the placement of a lumen-apposing
metal stent using an endoscopic hand-suturing device. The authors [1] Karstensen JG, Novovic S, Hansen EF et al. EUS-guided drainage of large walled-off
pancreatic necroses using plastic versus
lumen-apposing metal stents: a single-cen-
tre randomised controlled trial. Gut 2022. doi:10.1136/gutjnl-2022-328225 Yosuke Minoda1, 2 , Nao Fujimori1, Mitsuru
Esaki1 , Shuzaburo Nagatomo1, Yasuhiro
Komori1, Keijiro Ueda1, Eikichi Ihara1, 3
1
Kyushu University Faculty of Medicine
Graduate School of Medical Science,
Department of Medicine and Bioregulatory
Science, Fukuoka, Fukuoka, Japan
2
Kyushu University, Department of
Endoscopic Diagnostics Therapeutics,
Fukuoka, Fukuoka, Japan
3
Kyushu University Faculty of Medicine
Graduate School of Medical Science,
Department of Gastroenterology and
Metabolism, Japan [2] Gkolfakis P, Chiara Petrone M, Tadic M et al. Efficacy and safety of endoscopic drainage
of peripancreatic fluid collections: a retro-
spective multicenter European study. Ann
Gastroenterol 2022; 35: 654–662 This section has its own submission
website at This section has its own submission
website at https://mc.manuscriptcentral.com/e-videos [3] Zhu H, Xie P, Wang Y et al. The role of solid
debris in endoscopic ultrasound-guided
drainage of walled-off necrosis: A large co-
hort study. J Gastroenterol Hepatol 2020;
35: 2103–2108 [2] Gkolfakis P, Chiara Petrone M, Tadic M et al.
Efficacy and safety of endoscopic drainage
of peripancreatic fluid collections: a retro-
spective multicenter European study. Ann
Gastroenterol 2022; 35: 654–662 [1] Karstensen JG, Novovic S, Hansen EF et al.
EUS-guided drainage of large walled-off
pancreatic necroses using plastic versus
lumen-apposing metal stents: a single-cen-
tre randomised controlled trial. Gut 2022.
doi:10.1136/gutjnl-2022-328225 Competing interests E692 Minoda Yosuke et al. Rare complications related … Endoscopy 2023; 55: E692–E693 | © 2023. The Author(s). Video 1 Steps to close the fistula associated with the placement of a lumen-apposing
metal stent using an endoscopic hand-suturing device. Minoda Yosuke et al. Rare complications related… Endoscopy 2023; 55: E692–E693 | © 2023. The Author(s). [3] Zhu H, Xie P, Wang Y et al. The role of solid
debris in endoscopic ultrasound-guided
drainage of walled-off necrosis: A large co-
hort study. J Gastroenterol Hepatol 2020;
35: 2103–2108 Yosuke Minoda1, 2 , Nao Fujimori1, Mitsuru
Esaki1 , Shuzaburo Nagatomo1, Yasuhiro
Komori1, Keijiro Ueda1, Eikichi Ihara1, 3
1
Kyushu University Faculty of Medicine
Graduate School of Medical Science,
Department of Medicine and Bioregulatory
Science, Fukuoka, Fukuoka, Japan
2
Kyushu University, Department of
Endoscopic Diagnostics Therapeutics,
Fukuoka, Fukuoka, Japan
3
Kyushu University Faculty of Medicine
Graduate School of Medical Science,
Department of Gastroenterology and
Metabolism, Japan Bibliography Bibliography Yosuke Minoda, MD
Department of Medicine and Bioregulatory
Science , Kyushu University Hospital, 3-1-1
Maidashi, Higashi-ku, Fukuoka 812-8582,
Japan
Fax: +81-92-642-5287
minoda.yosuke.633@m.kyushu-u.ac.jp Yosuke Minoda, MD
Department of Medicine and Bioregulatory
Science , Kyushu University Hospital, 3-1-1
Maidashi, Higashi-ku, Fukuoka 812-8582,
Japan
Fax: +81-92-642-5287
minoda.yosuke.633@m.kyushu-u.ac.jp Endoscopy 2023; 55: E692–E693
DOI 10.1055/a-2072-5740
ISSN 0013-726X
© 2023. The Author(s). E693 Minoda Yosuke et al. Rare complications related… Endoscopy 2023; 55: E692–E693 | © 2023. The Author(s).
|
https://openalex.org/W4384693630
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https://www.preprints.org/manuscript/202306.1507/v1/download
|
English
| null |
Absorption and Distribution of Imidacloprid and Its Metabolites in Goldfish (Carassius auratus Linnaeus)
|
Toxics
| 2,023
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cc-by
| 9,115
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Article Not peer-reviewed version Absorption and Distribution of
Imidacloprid and Its Metabolites in
goldfish(Carassius Auratus
Linnaeus) Wanghui Xu , Lulu Zhang , Jiayin Hou , Xiaohua Du , Liezhong Chen * Article
Absorption and Distribution of Imidacloprid and Its
Metabolites in Goldfish (Carassius auratus Linnaeus)
Wanghui Xu 1, Lulu Zhang 2, Jiayin Hou 3 and Xiaohua Du 1and Liezhong Chen 3,*
1 College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China;
2 College of Food and Pharmaceutical Science, Ningbo University, Zhejiang Ningbo 315800, China;
3 State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-
Products, Zhejiang Academy of Agricultural Sciences，Hangzhou 310021 China;.
* Correspondence: zwsclz@163.com; Tel.: 86-571-86419163 Abstract: Imidacloprid is the first-generation neonicotinoid insecticide. But, the long-term use of
imidacloprid as a pesticide has caused severe water pollution. Recently, the toxicity of imidacloprid
to aquatic organisms has received increasing attention. This study aimed to investigate the
absorption and distribution of imidacloprid in various tissues (gills, intestine, liver, muscle, brain,
and gonads) of goldfish through short-term and continuous exposure tests for 28 days. The results
of short-term exposure indicated that the concentration of imidacloprid and its metabolites in
tissues at the transfer stage decreased steadily after 1 day of 40 mg/l imidacloprid water treatment
and was below the detection limit after 3 days. Continuous exposure for 28 days at various treatment
concentrations showed that the concentrations of imidacloprid and its metabolites differed
significantly among the different tissues of the goldfish. In the 20 mg/l treatment group (S1), the
highest concentration of imidacloprid was found in the liver (12.04 μg /gtissue), followed by the
intestine (9.91 μg /gtissue), muscle (6.20 μg /gtissue), gill (6.11 μg /gtissue), gonads (5.22 μg /gtissue), and
brain (2.87 μg /gtissue). In the 40 mg/l treatment group (S2), the order of tissue concentrations was
similar to that of the S1 group, with the highest concentration observed in the liver (12.04 μg/gtissue),
followed by the intestine (9.91 μg/gtissue), muscle (6.20 μg/gtissue), gill (6.11 μg/gtissue), gonads (5.22
μg/gtissue), and brain (2.87 μg/gtissue). Furthermore, the study detected 5-hydroxyimidacloprid,
imidacloprid urea, and 6-chloronicotinic acid in imidacloprid metabolites in all tissues, while
imidacloprid was detected only in the intestine and liver. Overall, the results of this study contribute
to a better understanding of the metabolic behavior of imidacloprid in organisms and provide new
data to support the assessment of imidacloprid toxicity in fish. Keywords: Imidacloprid; Goldfish; Metabolites; Tissue Distribution; Toxicity Preprints.org is a free multidiscipline platform providing preprint service that
is dedicated to making early versions of research outputs permanently
available and citable. Preprints posted at Preprints.org appear in Web of
Science, Crossref, Google Scholar, Scilit, Europe PMC.
Copyright: This is an open access article distributed under the Creative Commons
Attribution License which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited. Preprints.org is a free multidiscipline platform providing preprint service that
is dedicated to making early versions of research outputs permanently
available and citable. Preprints posted at Preprints.org appear in Web of
Science, Crossref, Google Scholar, Scilit, Europe PMC. Copyright: This is an open access article distributed under the Creative Commons
Attribution License which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited. Disclaimer/Publisher’s Note: The statements, opinions, and data contained in all publications are solely those of the individual author(s) and
contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting
from any ideas, methods, instructions, or products referred to in the content. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 doi:10.20944/preprints202306.1507.v1 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 2 worldwide [5]. Struger et al. conducted three consecutive years of sampling and detection in the
surrounding surface waters of 15 agricultural active areas in southwestern Ontario, Canada, from
2012 to 2014, and the results showed that the detection rate of imidacloprid exceeded 90% in more
than half of the areas. In 75% of samples collected in two regions, the concentration of imidacloprid
exceeded the local legal limit level (230ng/l) [6]. In California, Starner Keith et al. collected and tested
75 surface water samples from rivers, creeks and drains around farmland, and the results showed
that imidacloprid was detected in 67 samples, with the maximum residue of 3.29μg/l and the average
concentration of 0.77μg/l [7]. Similarly, imidacloprid residues have been detected in water bodies of
various basins in China, such as the Yangtze River and the Yellow River, with detection
concentrations ranging between 2.08 ng/l and 121.71 ng/l and an average detection concentration of
41.89 ng/l [8]. In conclusion, imidacloprid has been detected in lakes, rivers, groundwater and other
water bodies at home and abroad to varying degrees, and some areas even exceed the standard
seriously. The contamination of imidacloprid in aquatic environment may cause potential health
hazards to aquatic organisms. Fish are an important part of aquatic life, so it is necessary to assess
the potential harm of imidacloprid to fish. Researchers previously believed that imidacloprid had low toxicity to nontarget organisms and
lacked teratogenic, carcinogenic and mutagenic effects [9]. Until Whitehorn et al. discovered that the
use of imidacloprid could significantly inhibit the reproductive ability of bumblebee populations,
bringing attention to the safety of imidacloprid on nontarget organisms [10]. Subsequently, more and
more studies have shown that imidacloprid has certain effects on non-target organisms. For example,
low concentration of imidacloprid can induce intestinal histological damage and intestinal oxidative
stress in zebrafish, significantly increase the levels of superoxide dismutase (SOD) and catalase
(CAT), and slightly induce intestinal flora imbalance and specific bacterial changes [11]. Topal et al. studied the neurotoxicity of imidacloprid on the brain tissue of rainbow trout. The results showed
that under the treatment of 10mg/l and 20mg/l imidacloprid, the activity of acetylcholinesterase
(AChE) decreased and the activity of 8-hydroxy-2-deoxyguanosine (8-OHdG)(a marker related to
cellular oxidative stress) increased in the brain tissue of rainbow trout. Moreover, oxidative stress
parameters of rainbow trout were changed, thus showing neurotoxicity to rainbow trout [12]. Lonare
et al. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 found that imidacloprid was hepatotoxic to rats and could also cause damage to the
reproductive system of male rats. In addition, studies have shown that imidacloprid can also slow
down the growth rate [13], reduce activity [14], damage DNA [15] and other effects on non-target
organisms. Goldfish (Carassius auratus Linnaeus), a Chinese species of Cyprinidae, was selected for this study
to better reflect the impact of imidacloprid on environmental organisms. Previous research has
identified the metabolites of imidacloprid in goldfish, including imidacloprid-urea, imidacloprid-
olefin, 5-hydroxyimidacloprid, and 6-chloronicotinic acid [16]. This study aims to investigate the
tissue distribution of imidacloprid and its metabolites in goldfish after exposure, providing new data
support for the toxicity study of imidacloprid and a better understanding of its metabolic behavior
in organisms. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.150 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 1. Introduction Imidacloprid is the first-generation neonicotinoid insecticide developed by Bayer Crop Science,
Germany [1]. It is mainly used for the control of aphids, leaf hoppers, thrips and other stinging
mouthparts pests. The mechanism of its insecticidal action is to act on the nicotinic acetylcholine
receptors in the postsynaptic membrane of the insect nervous system and its surrounding nerves, so
that the insects can maintain continuous excitement, paralysis and then die [2,3]. The effect of
imidacloprid is relatively fast, and it will have a strong control effect on pests 1 day after the drug. Compared with traditional pesticides, imidacloprid has the advantages of high efficiency, high
selectivity and lasting effect on target pests, and it has been widely used all over the world soon after
its launch. However, in the application process of imidacloprid, only a small amount of the effective
components is absorbed by crops (about 5%), most of which will enter the soil and eventually enter
the water environment with infiltration, runoff and other methods [4]. Due to the water solubility,
stability, and persistence of imidacloprid, their residues have been detected in water bodies © 2.2. Exposure experiment For the short-term exposure test, 60 domesticated goldfish were placed into a 20 L culture barrel
with 15 L of test water containing 40 mg/l imidacloprid. After one day of exposure, the goldfish were
transferred to clean water for purification, with breeding density maintained at 4 tails/L and test
water renewed daily. Uneaten food and feces were removed from the tank shortly after feeding to
prevent food absorption and adsorption. Five goldfish were randomly selected from the experimental
group at 0 h, 0.5 d, 1 d, 1.5 d, and 3 d after transfer for dissection, with each fish as an independent
sample. The goldfish were anesthetized on ice, and the liver, intestine, muscle, gill tissue, brain tissue,
and gonad were dissected and stored at -80°C until analysis. In the continuous exposure experiment, domesticated goldfish were randomly divided into a
control group and two treatment groups with imidacloprid concentrations of 20 mg/l and 40 mg/l. The treatment concentrations were determined based on the LC50 value of imidacloprid on goldfish
obtained in an earlier stage. The feeding conditions were consistent with the short-term exposure test. Goldfish were sampled and dissected before the start of the experiment and at 2 h, 6 h, 1 d, 3 d, 5 d,
7 d, 14 d, and 28 d of exposure, with the sampling process being identical to that of the exposure test. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 3 The instruments utilized in the experiment included an Albrecht sciex5500+ high-performance
liquid phase triple quadrupole tandem mass spectrometer, a Sartorius BSA124S one ten-thousandth
scale from Sedolis, Germany, and an LC-DCY-12SF water bath nitrogen blowing instrument from
Shanghai Lichen Instrument Technology Co., Ltd. The instruments utilized in the experiment included an Albrecht sciex5500+ high-performance
liquid phase triple quadrupole tandem mass spectrometer, a Sartorius BSA124S one ten-thousandth
scale from Sedolis, Germany, and an LC-DCY-12SF water bath nitrogen blowing instrument from
Shanghai Lichen Instrument Technology Co., Ltd. The test organism for the experiment was 3-month-old goldfish purchased from Hangzhou
Fengqi Flower and Bird Market. The goldfish were domesticated in the laboratory for over a week
prior to the formal experiment, with tap water treated by aeration dechlorination and meeting the
provisions of the fishery water quality standard (GB11607-1989) used as the test water [17]. The
goldfish were examined for the absence of imidacloprid and its metabolites in their bodies before
exposure. The domestication conditions were maintained at a pH of 7.0-8.5, temperature of 20.9 ±
0.4°C, and dissolved oxygen of 6.9 ± 0.2 mg/l. 2.3. Sample pretreatment Goldfish tissue samples were placed into a 20 ml centrifuge tube and mixed with 12 ml ethyl
acetate aqueous solution (v/v=2/1). The mixture was vortexed for 1 minute, and then 1 g anhydrous
MgSO4 and 0.5 g diatomite were added, followed by another vortex and mixing for 1 minute. The
sample was sonicated at room temperature for 10 minutes and then centrifuged at 4000 r/min at 4°C
for 10 minutes. The upper layer supernatant was collected, dried using nitrogen gas, reconstituted
with 1 ml of methanol, and subjected to membrane analysis. 2.1. Chemicals, instruments and animals Reagents used in the experiment included imidacloprid (purity 95.00%) from Shanghai Yuanye
Biotechnology Co., Ltd, imidacloprid standard (purity 98.00%) from Shanghai Anpu Experimental
Technology Co., Ltd, and imidacloprid-urea methanol standard solution (100.00 mg/l), imidacloprid-
olefin methanol standard solution (100.00 mg/l), 5-hydroxyimidacloprid methanol standard solution
(100.00 mg/l), and 6-chloronicotinic acid methanol standard solution (100.00 mg/l) from Tianjin Alta
Technology Co., Ltd. Chromatographic grade methanol and ethyl acetate were obtained from
Millipore, and purified water was provided by Watson Co., Ltd. Anhydrous magnesium sulfate
(analytical grade) was sourced from China Pharmaceutical Group Co., Ltd, and diatomite was from
Shanghai McLean Biochemical Technology Co., Ltd. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 4 Mass spectrometry was performed using an electrospray ion source (ESI) in positive ion mode,
and select ion reaction monitoring mode (SRM) was used for scanning. The spray voltage was set at
4000 V, and the temperature was maintained at 200℃. High-purity nitrogen was used as both the
sheath gas and auxiliary gas at a pressure of 60 psi, while the ion transport capillary temperature was
set at 450℃. The collected fragments are summarized below(Table 2). Table 2. Fragment parameters were collected by mass spectrometry. Detection object
Parent ion
Daughter ion
Imidacloprid
256.2
175.3
Imidacloprid- urea
212.2
128.1
Imidacloprid- olefin
254.2
171.0
5-hydroxyimidacloprid
272.2
225.3
6-chloronicotinic acid
155.9
112.1
2.5. Detection limit, precision and recovery Table 2. Fragment parameters were collected by mass spectrometry. The method used in this study was evaluated for its detection limit, limit of quantification,
precision, and recovery, and the results showed that it met the detection requirements with good
reproducibility and high precision (Table 3). Table 3. Detection limit, precision and recovery of imidacloprid and its metabolites. Table 3. Detection limit, precision and recovery of imidacloprid and its metabolites. object
LOD(limit of
detection) （μg/l）
LOQ(limit of
quantitation) （
μg/l）
precision/% recovery/% RSD/%
Imidacloprid
0.001
0.00334
3.41
96.08
6.523
Imidacloprid- urea
0.0099
0.032907
1.98
99.77
4.172
Imidacloprid- olefin
0.0011
0.003519
3.79
85.25
7.355
5-hydroxyimidacloprid
0.0068
0.022718
2.84
87.24
8.825
6-chloronicotinic acid
0.0056
0.018682
2.64
100.23
2.805
2.6. Data analysis 2.6. Data analysis Data analysis was performed using Microsoft Excel 2019 software, and the mean value and
standard deviation were calculated and analyzed by T-test. 2.4. Instrument Conditions The HPLC column used was an Eclipse C18 column (1.8 μm, 3.0 × 100 mm, Agilent, USA) with a
column temperature of 40°C, injection volume of 2 μL, and flow rate of 5 μL/s. The mobile phase
consisted of 0.1% formic acid water (aqueous phase) and methanol (organic phase) using gradient
elution. The elution procedure was as follows (Table 1). Table 1. Gradient elution procedure. Time/min
aqueous phase %
organic phase /%
0-5
80
20
5
60
40
6
40
60
7
80
20
8
80
20 Table 1. Gradient elution procedure. 3. Results 3.1. Concentration changes of imidacloprid and its metabolites in goldfish under short-term exposure Figure 1 illustrates the concentration changes of imidacloprid and its metabolites in goldfish
tissues under short-term exposure. Imidacloprid accumulated in goldfish after one day of exposure,
with the highest concentration in the liver (23.411 μg/gtissue), followed by the intestine (16.20 μg/gtissue),
muscle (8.61 μg/gtissue), gill (7.36 μg/gtissue), gonads (7.41 μg/gtissue), and brain (7.15 μg/gtissue). After
transfer to clean water, the concentration of imidacloprid and its metabolites in all tissues showed a
decreasing trend, and after 3 days, the content in all tissues was lower than the detection limit. Figure 1 illustrates the concentration changes of imidacloprid and its metabolites in goldfish
tissues under short-term exposure. Imidacloprid accumulated in goldfish after one day of exposure,
with the highest concentration in the liver (23.411 μg/gtissue), followed by the intestine (16.20 μg/gtissue),
muscle (8.61 μg/gtissue), gill (7.36 μg/gtissue), gonads (7.41 μg/gtissue), and brain (7.15 μg/gtissue). After
transfer to clean water, the concentration of imidacloprid and its metabolites in all tissues showed a
decreasing trend, and after 3 days, the content in all tissues was lower than the detection limit. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 5 5 0.0
0.5
1.0
1.5
2.0
2.5
3.0
0
5
10
15
20
25
Tissue concentration
（μg/g）
Time（d）
intestine
liver
muscle
brain
gills
gonads
A
0.0
0.5
1.0
1.5
2.0
2.5
3.0
0
300
600
900
1200
1500
1800
Treatment concentration
（ng/g）
Time（d）
intestine
liver
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Figure 1. Concentration changes of imidacloprid and its metabolites in goldfish under short-term
exposure(treatment concentration: 40mg/l), a: imidacloprid, b: imidacloprid-urea, c: 6-chloronicotinic
acid, d: 5-hydroxyimidacloprid. 3. Results 0.0
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C Figure 1. Concentration changes of imidacloprid and its metabolites in goldfish under short-term
exposure(treatment concentration: 40mg/l), a: imidacloprid, b: imidacloprid-urea, c: 6-chloronicotinic
acid, d: 5-hydroxyimidacloprid. 3.3.1. Concentration changes in imidacloprid metabolites in gill tissues Figure 3 illustrates the presence of imidacloprid-urea, 6-chloronicotinic acid, and 5-
hydroxyimidacloprid in the gill tissue of goldfish following exposure to imidacloprid. In the high
concentration treatment group, the concentration of imidacloprid urea increased in the gill tissue,
ultimately reaching 435.59 ng/g tissue at 28 days. The accumulation of imidacloprid urea was relatively
gradual during the first 3 days, with a rapid increase to 374.30 ng/g tissue at day 5, followed by a slow
increase to its maximum concentration between days 5-28. The concentration of 6-chloronicotinic acid
initially decreased, subsequently increased, and then decreased again in the gill tissue. At days 0-3,
its concentration declined from 6.85 ng/g tissue to 3.40 ng/g tissue, followed by an increase to a maximum
of 10.92 ng/g tissue at day 5, which then decreased to 4.47 ng/g tissue by day 28. The maximum
accumulation of 5-hydroxyimidacloprid was observed at 761.24 ng/g tissue at 6 hours, followed by a
downward trend until day 28, with a final concentration of 140.48 ng/g tissue. 0
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Figure 3. Concentration changes in imidacloprid metabolites in gill tissues(Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. 0
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（a） Figure 3. Concentration changes in imidacloprid metabolites in gill tissues(Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. In the low concentration treatment group, the accumulation of imidacloprid urea exhibited a
similar trend as observed in the high concentration group, with a slight increase from 0-3 d, followed
by a decline after peaking at 278.26 ng/g tissue in 3-7 d. The accumulation of imidacloprid urea was
167.51 ng/g tissue at 28 d. 3.3.1. Concentration changes in imidacloprid metabolites in gill tissues In the 0-28 d period, the content of 6-chloronicotinic acid exhibited two peaks
at 6 h and 5 d posttreatment, with concentrations of 3.18 ng/g tissue and 8.37 ng/g tissue, respectively. The
final accumulation was 1.57 ng/g tissue at 28 d. The maximum accumulation of 5-hydroxyimidacloprid
reached 148.22 ng/g tissue at 6 h and showed a downward trend from 6 h-5 d. Once it decreased to a
certain concentration, the content of 5-hydroxyimidacloprid suddenly increased on the 7th day and
then began to decline. Ultimately, the concentration of 5-hydroxyimidacloprid was 37.69 ng/g tissue on
the 28th day. 3.3.2. Dynamic changes in imidacloprid metabolites in the intestine 3.3. Dynamic changes in imidacloprid metabolites in different tissues of goldfish under continuous exposure 3.3. Dynamic changes in imidacloprid metabolites in different tissues of goldfish under continuous exposure 3.3.1. Concentration changes in imidacloprid metabolites in gill tissues Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 6 Figure 2. Concentration changes imidacloprid in goldfish under continuous exposure(Treatment
concentration: S1:20mg/l; S2:40mg/l). Figure 2. Concentration changes imidacloprid in goldfish under continuous exposure(Treatment
concentration: S1:20mg/l; S2:40mg/l). Figure 2. Concentration changes imidacloprid in goldfish under continuous exposure(Treatment
concentration: S1:20mg/l; S2:40mg/l). 3.2. Concentration changes of imidacloprid in goldfish under continuous exposure The changes in imidacloprid concentration in different tissues of goldfish with exposure time
are presented in Figure 2 during the continuous exposure treatment test. There were significant
differences in the distribution of imidacloprid in muscle, liver, intestine, brain tissue, muscle, and
gonad (P < 0.05). In the high concentration treatment group, imidacloprid accumulation increased
rapidly in each tissue at the beginning of the treatment, reaching a peak on day 5. Subsequently, from
day 5 to day 28, the accumulation rate of imidacloprid in each tissue declined and eventually reached
a steady state. The intestinal tract and muscle even showed a downward trend between days 5 and
14. Finally, after 28 days of exposure, the accumulation of imidacloprid in goldfish tissues from high
to low was liver (12.040 μg/g tissue), intestine (9.91 μg/g tissue), muscle (6.20 μg/g tissue), gill (6.11 μg/g
tissue), gonads (5.22 μg/g tissue), and brain (2.87 μg/g tissue). In the low concentration treatment group, the
accumulation of imidacloprid was similar to that in the high concentration treatment group. It
accumulated rapidly in tissues from 0 to 5 days and gradually decreased from 5 to 28 days. The
amount of imidacloprid accumulated in various tissues from high to low was intestine (6.93 μg/g
tissue), liver (6.10 μg/g tissue), muscle (4.20 μg/g tissue), gonads (3.93 μg/g tissue), gill (2.81 μg/g tissue), and
brain (2.30 μg/g tissue). 0
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S1 3.3.2. Dynamic changes in imidacloprid metabolites in the intestine 3.3.2. Dynamic changes in imidacloprid metabolites in the intestine Figure 4 illustrates that in addition to imidacloprid urea, 5-hydroxyimidacloprid and 6-
chloronicotinic acid, imidacloprid was detected in the intestine after imidacloprid exposure. The
maximum accumulation of these metabolites, from high to low, was observed for 5-
hydroxyimidacloprid, imidacloprid urea, 6-chloronicotinic acid, and IMI imidacloprid. In the high
concentration treatment group, imidacloprid urea showed an increasing trend until 1 day, reaching
a maximum value of 422.77 ng/g tissue, followed by a gradual decline, and finally stabilized at a
concentration of 249.23 ng/g tissue. The dynamics of accumulation of 6-chloronicotinic acid were more
complex, with an initial increase and subsequent decrease observed in 2 h-1 d, 1-7 d, and 7-28 d,
respectively. The maximum accumulation was observed at 14 d (30.37 ng/g tissue), while the final
concentration was 2.67 ng/g tissue at 28 d. The content of 5-hydroxyimidacloprid peaked value of 999.02
ng/g tissue at 6 h, followed by a declining trend, reaching a certain level at 3 d, then increasing to 461.78 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 7 ng/g tissue at 3-5 d, and finally stabilizing at a concentration of 149.23 ng/g tissue at 28 d. The content of
imidacloprid-olefin ene increased until 3 days, then decreased to 6.05 ng/g tissue on the 5th day, and
then gradually increased again. Finally, the content of imidacloprid-olefin was 9.23 ng/g tissue at 28 d. 0
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Figure 4. Concentration changes in imidacloprid metabolites in intestine (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid, d:
imidacloprid-olefin. 3.3.2. Dynamic changes in imidacloprid metabolites in the intestine 0
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（d） Figure 4. Concentration changes in imidacloprid metabolites in intestine (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid, d:
imidacloprid-olefin. In the low concentration treatment group, the accumulation of imidacloprid urea was
comparable to that in the high concentration treatment group, with an accumulation of 183.54 ng/g
tissue observed at 28 days. The concentration of 6-chloronicotinic acid demonstrated an overall increase
within the first 5 days, with a maximum of 12.24 ng/g tissue on day 5, followed by a decline. The final
concentration of 6-chloronicotinic acid was 5.49 ng/g tissue at 28 days, which was higher than that
observed in the high concentration treatment group. The concentration of 5-hydroxyimidacloprid
was similar to that in the high concentration treatment group, with a maximum accumulation of
488.64 ng/g tissue and a final concentration of 83.54 ng/g tissue at 28 days. The accumulation dynamics of
imidacloprid were similar to those of 6-chloronicotinic acid, with a maximum accumulation of 3.53
ng/g tissue. 3.3.3. Dynamic changes in imidacloprid metabolites in the liver 3.3.3. Dynamic changes in imidacloprid metabolites in the liver The results depicted in Figure 5 indicate that the metabolites of imidacloprid in the liver are
consistent with those in the intestine. In the high concentration treatment group, the maximum
content of each metabolite was in the following order: imidacloprid-urea, 5-hydroxyimidacloprid,
imidacloprid-olefin, and 6-chloronicotinic acid. The accumulation dynamics of imidacloprid urea
and 5-hydroxyimidacloprid were similar, with their concentrations reaching a maximum at 6 h after
exposure, 952.38 ng/g tissue and 653.13 ng/g tissue, respectively, and then reaching a relative equilibrium
state from 6 h to 28 d. Finally, the concentration distribution was 206.33 ng/g tissue and 156.27 ng/g tissue
at 28 d. The content of 6-chloronicotinic acid showed a zigzag upward trend within 0-7 d, reached a
maximum accumulation of 18.79 ng/g tissue at 7 d, and began to decline. The final concentration was
12.24 ng/g tissue at 28 d, which was lower than that of the low concentration treatment group. The
concentration of imidacloprid increased from 0 to 3 days, reaching a maximum of 49.65 ng/g tissue at 3
days and remaining relatively stable after the concentration decreased at 5 days. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 8 8 0
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Figure 5. Concentration changes in imidacloprid metabolites in intestine (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid, d:
imidacloprid-olefin. 0
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（d） Figure 5. 3.3.3. Dynamic changes in imidacloprid metabolites in the liver Concentration changes in imidacloprid metabolites in intestine (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid, d:
imidacloprid-olefin. In the low concentration treatment group, the metabolites of imidacloprid in the liver were
found to follow the same pattern as that of the high concentration treatment group. The maximum
accumulation amounts of each metabolite in the low concentration group were 5-
hydroxyimidacloprid, imidacloprid urea, imidacloprid-olefin, and 6-chloronicotinic acid, in
descending order. The concentration changes of imidacloprid-urea and 5-hydroxyimidacloprid were
similar to those in the high concentration group, with maximum accumulation amounts of 271.29
ng/g tissue and 423 ng/g tissue, respectively, at 6 h. The content of 6-chloronicotinic acid showed an
increasing trend before 14 days, reaching a maximum of 13.76 ng/g tissue at 14 days and then decreasing
at 28 days. The concentration of imidacloprid showed an upward trend in the first day, accumulated
to the maximum value of 28.32 ng/g tissue, and began to decrease in the following 1-5 days. The
concentration then stabilized at 24.32 ng/g tissue from 7-28 days. 3.3.5. Dynamic changes in imidacloprid metabolites in brain tissue 3.3.5. Dynamic changes in imidacloprid metabolites in brain tissue Figure 7 presents the accumulation dynamics of imidacloprid metabolites in goldfish brain
tissue. Three metabolites of imidacloprid were detected in the brain tissue, with 5-
hydroxyimidacloprid, imidacloprid urea, and 6-chloronicotinic acid being the metabolites with the
highest accumulation. In the high concentration treatment group, imidacloprid urea showed an
increasing trend within 0-5 d, reaching a maximum accumulation of 314.76 ng/g tissue at 5 d, and then
decreased to a lower level at 14 d and 28 d. The concentration of 6-chloronicotinic acid peaked at
10.51 ng/g tissue on the first day and then decreased to a stable level. The maximum accumulation of 5-
hydroxyimidacloprid was 640.83 ng/g tissue at 6 h, and its concentration then decreased, with a final
concentration of 249.21 ng/g tissue at 28 d. In the low concentration treatment group, the three
metabolites showed a trend of increasing first and then decreasing. The maximum content of
imidacloprid urea was 121.91 ng/g tissue on the 7th day, after which its concentration decreased. 6-
Chloronicotinic acid reached a maximum of 5.28 ng/g tissue on the 5th day, and the maximum
accumulation of 5-hydroxyimidacloprid was 386.76 ng/g tissue at 6 h. 0
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Figure 7. Concentration changes in imidacloprid metabolites in brain tissue (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. 0
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（a） Figure 7. Concentration changes in imidacloprid metabolites in brain tissue (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. 3.3.6. Dynamic changes in imidacloprid metabolites in gonads 3.3.4. Dynamic changes in imidacloprid metabolites in muscle Figure 6 illustrates the accumulation dynamics of three metabolites of imidacloprid in goldfish
brain tissue. The metabolites' maximum content in the brain tissue was 5-hydroxyimidacloprid,
imidacloprid urea, and 6-chloronicotinic acid, in descending order. In the high concentration
treatment group, the concentration of imidacloprid urea in goldfish muscle tissue fluctuated, with a
maximum accumulation of 289.50 ng/g tissue at 28 d. The concentration of 6-chloronicotinic acid in
muscle tissue ranged between 3.06-18.86 ng/g tissue. The concentration of 5-hydroxyimidacloprid
reached its maximum of 650.35.45 ng/g tissue at 6 h, then decreased to a certain level and remained
relatively stable, with a final concentration of 189.50 ng/g tissue at 28 d. In the low concentration
treatment group, the accumulation dynamics of imidacloprid urea and 5-hydroxyimidacloprid were
similar to those in the high concentration treatment group. However, in the low concentration
treatment group, the concentration of 6-chloronicotinic acid first increased and then decreased,
reaching a maximum accumulation of 14.03 ng/g tissue. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 9 0
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Figure 6. Concentration changes in imidacloprid metabolites in muscle (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. 0
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（a） Figure 6. Concentration changes in imidacloprid metabolites in muscle (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. 4. Discussion In the short-term exposure experiment, it was observed that the content of imidacloprid and its
metabolites in all tissues was below the detection limit three days after transfer, which is consistent
with the degradation rate of imidacloprid in rats. After oral administration of imidacloprid to rats, it
was found that the initial half-life of imidacloprid was approximately 3 hours, while the final half-
life ranged from 26 to 118 hours, and the residual amount of imidacloprid in tissues was less than 1%
after 48 hours. Similarly, Poliserpi et al. reported that the concentration of imidacloprid in the tissues
of Agelaioides badius was below the detection limit after 48 hours of oral administration of
imidacloprid in the United States [18]. These findings suggest that imidacloprid undergoes rapid
degradation in organisms. The accumulation of chemicals in organisms is often dependent on their
solubility, where better water solubility leads to poorer accumulation ability [19]. Due to its better
water solubility, imidacloprid and its metabolites have a faster degradation rate in goldfish. In
contrast, the concentration of imidacloprid in gills increased at 1-1.5 days. The gill is the primary
sensing organ of fish for pollutants in water, and due to the lack of metabolic enzymes around it, the
concentration of imidacloprid in gill tissue should increase with increasing exposure time [20]. Subsequently, water samples were collected at 1-1.5 days, and a certain amount of imidacloprid was
detected in the water samples at 1.5 days (unpublished data). This could be due to imidacloprid
absorbed by goldfish being excreted through the intestine and then reabsorbed by the gills, resulting
in a transient rise in the concentration of imidacloprid in the gills. The continuous exposure test revealed that goldfish accumulated the highest concentration of
imidacloprid in their intestine and liver. This result is consistent with previous studies, such as Yi
Yang et al.'s research, which found that after thiamethoxam exposure, zebrafish had the highest
concentration of thiamethoxam in their liver and intestine, suggesting that the hepatointestinal
system is a primary site of accumulation for exogenous drugs [21]. Similarly, Yang Bin IHM's study
reported that the highest accumulation of imidacloprid in crucian carp was found in the liver [22]. Therefore, it can be inferred that the accumulation pathway through hepatointestinal recycling may
play an important role in imidacloprid absorption in fish. 3.3.6. Dynamic changes in imidacloprid metabolites in gonads 3.3.6. Dynamic changes in imidacloprid metabolites in gonads In the gonads of goldfish, the concentration of imidacloprid urea is significantly lower than that
of other tissues, with its maximum content amounting to only one-tenth of that observed in other
tissues. In the high concentration treatment group, imidacloprid urea exhibited a steady rise before
0-5 d, followed by a sharp increase to a maximum value of 37.97 ng/g tissue on the 7th day, and
subsequently returned to normal levels between the 14th and 28th days. 6-Chloronicotinic acid
showed two peaks of 15.98 ng/g tissue and 17.98 ng/g tissue at 6 h and 7 d, respectively. The concentration
of 5-hydroxyimidacloprid increased initially and then decreased, reaching a maximum accumulation
of 385.21 ng/g tissue at 7 days. In the low concentration treatment group, the concentrations of
imidacloprid urea, 6-chloronicotinic acid, and 5-hydroxyimidacloprid reached their maximum levels
at 6 h, with concentrations of 12.22 ng/g tissue, 12.22 ng/g tissue, and 183.07 ng/g tissue, respectively. Subsequently, the concentrations of these three metabolites decreased from 6 h to 28 d. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 10 10 0
5
10
15
20
25
30
0
10
20
30
40
50
Tissue concentration
（ng/g）
Time（d）
S1
S2
（a）
0
5
10
15
20
25
30
0
5
10
15
20
25
Tissue concentration
（ng/g）
Time（d）
S1
S2
（b）
0
5
10
15
20
25
30
0
100
200
300
400
Tissue concentration
（ng/g）
Time（d）
S1
S2
（c）
Figure 8. Concentration changes in imidacloprid metabolites in gonads (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. 0
5
10
15
20
25
30
0
5
10
15
20
25
Tissue concentration
（ng/g）
Time（d）
S1
S2
（b） 0
5
10
15
20
25
30
0
10
20
30
40
50
Tissue concentration
（ng/g）
Time（d）
S1
S2
（a） 0
5
10
15
20
25
30
0
100
200
300
400
Tissue concentration
（ng/g）
Time（d）
S1
S2
（c） Figure 8. Concentration changes in imidacloprid metabolites in gonads (Treatment concentration:
S1:20mg/l; S2:40mg/l), a: imidacloprid urea, b: 6-chloronicotinic acid, c: 5-hydroxyimidacloprid. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 11 present in the liver and intestine. This distribution indicated that imidacloprid urea and 5-
hydroxyimidacloprid were the primary metabolites of imidacloprid in goldfish, while 6-
chloronicotinic acid and imidacloprid were secondary metabolites. This differs from Suchail et al.'s
research on the distribution and metabolism of imidacloprid in bees, where imidacloprid-urea and
6-chloronicotinic acid were the main metabolites, especially in the midgut and rectum. imidacloprid-
olefin and 4,5-dihydroxyimidacloprid were preferentially produced in the head, chest, and abdomen,
which are rich in acetylcholine receptors [23]. The differences in this experiment's distribution may
be attributed to the concentration of imidacloprid used in the treatment and the differences in
metabolic pathways between vertebrates and nonvertebrates. Byren and Nishiwaki's research
showed that the primary metabolites of imidacloprid after metabolism in houseflies and bees were
5-hydroxyimidacloprid, 4,5-dihydroxyimidacloprid, 6-chloronicotinic acid, imidacloprid-olefin, and
imidacloprid urea. See Figure 9 for the metabolic pathways [24,25]. y
y
p
y
y
p
p
imidacloprid urea. See Figure 9 for the metabolic pathways [24,25]. Table 4. The metabolites of imidacloprid. Metabolite
Maximum accumulation
Time
Ratio
Intestine
Imidacloprid- urea
432.34
24h
7.47%
Imidacloprid- olefin
9.37
28d
0.10%
6-chloronicotinic acid
31.27
14d
0.32%
5-hydroxyimidacloprid
1021.25
6h
35.64%
liver
Imidacloprid- urea
952.38
6h
25.81%
Imidacloprid- olefin
38.28
28d
0.32%
6-chloronicotinic acid
18.79
14d
0.18%
5-hydroxyimidacloprid
653.13
6h
23.60%
gill
Imidacloprid- urea
430.67
28d
9.72%
6-chloronicotinic acid
10.97
5d
0.23%
5-hydroxyimidacloprid
784.34
6h
42.68%
Muscle
Imidacloprid- urea
298.39
28d
3.99%
6-chloronicotinic acid
18.85
1d
0.16%
5-hydroxyimidacloprid
758.45
6h
19.34%
Brain
Imidacloprid- urea
319.24
5d
7.30%
6-chloronicotinic acid
10.74
1d
0.06%
5-hydroxyimidacloprid
654
6h
21.80%
gonad
Imidacloprid- urea
38.92
7d
0.41%
6-chloronicotinic acid
18.34
6h
0.59%
5-hydroxyimidacloprid
389.56
7d
5.58%
Figure 9. Metabolic pathways of imidacloprid in housefly (a) and honeybee (b). Table 4. The metabolites of imidacloprid. Metabolite
Maximum accumulation
Time
Ratio
Intestine
Imidacloprid- urea
432.34
24h
7.47%
Imidacloprid- olefin
9.37
28d
0.10%
6-chloronicotinic acid
31.27
14d
0.32%
5-hydroxyimidacloprid
1021.25
6h
35.64%
liver
Imidacloprid- urea
952.38
6h
25.81%
Imidacloprid- olefin
38.28
28d
0.32%
6-chloronicotinic acid
18.79
14d
0.18%
5-hydroxyimidacloprid
653.13
6h
23.60%
gill
Imidacloprid- urea
430.67
28d
9.72%
6-chloronicotinic acid
10.97
5d
0.23%
5-hydroxyimidacloprid
784.34
6h
42.68%
Muscle
Imidacloprid- urea
298.39
28d
3.99%
6-chloronicotinic acid
18.85
1d
0.16%
5-hydroxyimidacloprid
758.45
6h
19.34%
Brain
Imidacloprid- urea
319.24
5d
7.30%
6-chloronicotinic acid
10.74
1d
0.06%
5-hydroxyimidacloprid
654
6h
21.80%
gonad
Imidacloprid- urea
38.92
7d
0.41%
6-chloronicotinic acid
18.34
6h
0.59%
5-hydroxyimidacloprid
389.56
7d
5.58%
Figure 9. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.15 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 4. Discussion Furthermore, the accumulation dynamics
of imidacloprid in the intestine, liver, gill tissue, and brain tissue were relatively straightforward,
with their content increasing with the duration of exposure. In contrast, the accumulation in muscle
and gonad was more complex. Previous research has indicated that imidacloprid accumulates in the
muscle tissue of Procambarus clarkii, likely due to the high lipid content of the muscle composition
and imidacloprid's lipophilicity. The presence of metabolic enzymes in muscle tissue leads to the
degradation of imidacloprid into low-toxicity metabolites, which enter the bloodstream and are
excreted from the body [20]. The gonad is located on the dorsal wall of the body cavity of goldfish,
near the end of the intestine. The accumulation of imidacloprid in the gonad may be affected by
multiple factors, including the intestine and blood, resulting in complex accumulation dynamics. Subsequently, we analyzed the timing of the maximum accumulation of imidacloprid
metabolites in each tissue and the ratio between the maximum accumulation and absorbed
imidacloprid. The results are presented in Table 4. It is evident that 5-hydroxyimidacloprid had the
highest concentration in all tissues, followed by imidacloprid urea. Only a small amount of
imidacloprid was detected as 6-chloronicotinic acid and imidacloprid-olefin, with the latter only Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 12 In this study, the highest ratio of the total content of metabolites detected in the liver to
imidacloprid was observed at 6 h after exposure, indicating that the liver is likely the earliest
metabolic site for imidacloprid in goldfish. The intestine was also found to be an important site for
imidacloprid metabolism. These findings are consistent with a previous study by Yang et al., which
showed that the metabolism of thiamethoxam in zebrafish occurred in both the liver and intestine
and that its metabolic pathway involved N-demethylation and nitro reduction [26]. After exogenous
drugs enter the organism, phase I and phase II metabolism occur under the action of catalytic
enzymes in the body. Phase I metabolism mainly involves hydroxylation, desaturation, dealkylation,
and nitro reduction, among other reactions. The cytochrome CYP450 enzyme, which exists in the
liver, is an important oxidative metabolic enzyme that catalyzes these reactions [27]. The structure of
imidacloprid, shown in Figure 10, contains chemical reaction sites located on the methylene bridge
chain (I structure), the pharmacophore nitroimine (II structure), and the six-membered ring (III
structure), which can undergo a series of metabolic reactions under the action of catalytic enzymes in
vivo. Based on these observations, we hypothesize that the possible metabolic pathway of
imidacloprid in goldfish involves a dehydrogenation reaction in the I structure to generate
imidacloprid-olefin, followed by hydroxylation and nitro reduction reactions to generate 5-
hydroxyimidacloprid, imidacloprid urea, and 6-chloronicotinic acid, as shown in Figure 11. These
metabolites enter tissues through the circulatory system for enrichment or exclusion. Figure 10. Structure of imidacloprid. Figure 10. Structure of imidacloprid. Figure 10. Structure of imidacloprid. Figure 11. Possible metabolic pathways of imidacloprid in goldfish. Figure 11. Possible metabolic pathways of imidacloprid in goldfish. Upon detoxification and metabolism, the biological activity of imidacloprid metabolites will
decrease, but in some cases, imidacloprid may produce more active metabolites. For instance,
Suchail's study revealed that the two secondary metabolites of imidacloprid in bees, imidacloprid
alkenyl and 5-hydroxyimidacloprid, may have a greater relationship with the toxicity of
imidacloprid. The toxicity of imidacloprid alkenyl is twice that of imidacloprid and 10 times that of
5-hydroxyimidacloprid [28]. Additionally, studies have reported that the toxicity of imidacloprid-
olefin to Bemisia tabaci and Myzus persicae is approximately 10 times and 16 times higher than that
of imidacloprid, respectively, indicating that imidacloprid alkenyl has higher toxicity than the parent
compound [29]. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 Metabolic pathways of imidacloprid in housefly (a) and honeybee (b). Table 4. The metabolites of imidacloprid. Table 4. The metabolites of imidacloprid. Table 4. The metabolites of imidacloprid. Metabolite
Maximum accumulation
Time
Ratio
Intestine
Imidacloprid- urea
432.34
24h
7.47%
Imidacloprid- olefin
9.37
28d
0.10%
6-chloronicotinic acid
31.27
14d
0.32%
5-hydroxyimidacloprid
1021.25
6h
35.64%
liver
Imidacloprid- urea
952.38
6h
25.81%
Imidacloprid- olefin
38.28
28d
0.32%
6-chloronicotinic acid
18.79
14d
0.18%
5-hydroxyimidacloprid
653.13
6h
23.60%
gill
Imidacloprid- urea
430.67
28d
9.72%
6-chloronicotinic acid
10.97
5d
0.23%
5-hydroxyimidacloprid
784.34
6h
42.68%
Muscle
Imidacloprid- urea
298.39
28d
3.99%
6-chloronicotinic acid
18.85
1d
0.16%
5-hydroxyimidacloprid
758.45
6h
19.34%
Brain
Imidacloprid- urea
319.24
5d
7.30%
6-chloronicotinic acid
10.74
1d
0.06%
5-hydroxyimidacloprid
654
6h
21.80%
gonad
Imidacloprid- urea
38.92
7d
0.41%
6-chloronicotinic acid
18.34
6h
0.59%
5-hydroxyimidacloprid
389.56
7d
5.58% Figure 9 Metabolic pathways of imidacloprid in housefly (a) and honeybee (b) Figure 9. Metabolic pathways of imidacloprid in housefly (a) and honeybee (b). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 13 metabolites, from high to low, are olefinic imidacloprid, imidacloprid, 4-hydroxyimidacloprid, 5-
hydroxyimidacloprid, and 4,5-dihydroxyimidacloprid. Thus, the biological activity of imidacloprid
is produced by the interaction of parent and metabolites. In-depth studies on the differences in the
metabolic pathways of imidacloprid in target and nontarget organisms, as well as its metabolic
differences in different parts of the same organism, can provide a better understanding of its toxic
mechanism and provide ideas and references for the standardized use of imidacloprid. Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. Informed Consent Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: The data presented in this study are available on request from the corresponding
author. 5. Conclusion In this study, HPLC‒MS was used to investigate the tissue distribution of imidacloprid and its
metabolites in goldfish after short-term and continuous exposure. The results of the short-term
exposure experiments indicated that after transferring the exposed goldfish to an imidacloprid-free
aqueous solution, the concentrations of imidacloprid and its metabolites in various tissues decreased
and were below the detection limit after 3 days. The concentrations of imidacloprid and its
metabolites varied among different treatment concentrations in the continuous exposure
experiments. Among the imidacloprid metabolites, 5-hydroxyimidacloprid and imidacloprid urea
accumulated in equivalent amounts in various tissues, followed by 6-chloronicotinic acid. imidacloprid-olefin was detected only in the intestine and liver. These results allowed us to propose
a possible metabolic pathway of imidacloprid in goldfish. This study contributes to our
understanding of the metabolic behavior of imidacloprid in organisms and provides new data to
support the investigation of its toxicity. Author Contributions: Conceptualization, Liezhong Chen; methodology, Wanghui Xu; software, Wanghui Xu,
Lulu Zhang; validation, Jiayin Hou; resources, Wanghui Xu, Lulu Zhang and Jiayin Hou; data curation, Lulu
Zhang; writing—original draft preparation, Wanghui Xu; writing—review and editing, Liezhong Chen;
supervision, Xiaohua Du; funding acquisition, Liezhong Chen. All authors have read and agreed to the
published version of the manuscript. Funding: This work was supported by the National Key R&D Program of China, 2018YFD0200100,
2021YFD1700103, and 2022YFD1700304. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 In this study, a small amount of imidacloprid-olefin was detected in the intestine and
liver of goldfish, and further exploration of its subsequent effects on the intestine and liver can help
clarify the toxicity mechanism of imidacloprid-olefin. Moreover, metabolites with nitroimine
pharmacophores, such as hydroxylated imidacloprid and alkenylimidacloprid, are toxic to bees,
while
imidacloprid
urea
and
6-chloronicotinic
acid,
which
are
metabolites
without
pharmacodynamic groups, are nontoxic to bees [30]. The biological activities of imidacloprid and its Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 doi:10.20944/preprints202306.1507.v1 14 . Zhang Qi, Zhao Cheng, Lu Xiaoxia, Yu Bo, Huang Yuting, Advances in Research on Toxic Effect
Neonicotinoid Insecticides on Non-target Organisms [J]. Asian Journal of Ecotoxicology, 2019,15:(1)56-71 10. Penelope R. Whitehorn; Stephanie O’Connor; Felix L. Wackers; Dave Goulson, Neonicotinoid Pesticide
Reduces Bumble Bee Colony Growth and Queen Production [J]. Science, 2012,336:(6079)351-352. y
[ ]
(
)
11. Ting Luo, Xiaoyu Wang, Yuanxiang Jin, Low concentrations of imidacloprid exposure induced gut toxicity
in adult zebrafish (Danio rerio) [J]. Comp Biochem Physiol C Toxicol Pharmacol, 2021,241:108972. 12. Ahmet Topal, Gonca Alak, Mustafa Ozkaraca, Ash Cilingir Yeltekin, Selim Comakli, Gurdal Acil, Mine
Kokturk, Muhammed Atamanalp, Neurotoxic responses in brain tissues of rainbow trout exposed to
imidacloprid pesticide: Assessment of 8-hydroxy-2-deoxyguanosine activity, oxidative stress and
acetylcholinesterase activity [J]. Chemosphere, 2017,175:186-191. 13. Swapnil S. Phugare, Jyoti P. Jadhav, Biodegradation of Acetamiprid by Isolated Bacterial Strain
Rhodococcus sp. BCH2 and Toxicological Analysis of Its Metabolites in Silkworm ( Bombax mori ) [J]. CLEAN – Soil, Air, Water, 2015,43:(2) 14. Decourtye Axel, Devillers James, Cluzeau Sophie, Charreton Mercedes, Pham-Delègue Minh-Hà, Effects
of imidacloprid and deltamethrin on associative learning in honeybees under semi-field and laboratory
conditions [J]. Ecotoxicology and environmental safety, 2004,57:(3) 15. Weili Ge, Saihong Yan, Jinhua Wang, Lusheng Zhu, Aimei Chen, Jun Wang, Oxidative stress and DNA
damage induced by imidacloprid in zebrafish (Danio rerio) [J]. Journal of Agricultural and Food Chemistry,
2015,63:(6)1856-62. 16. Xu Wanghui, Hou Jiayin, Zhou Zhongjing, Yu Jianzhong, Zhang Lulu, Du Xiaohua, Chen Liezhong， A
method for detection of imidacloprid and its metabolites in Carassius auratus Linnaeus [J]. Modern
Agrochemicals 2023,phrase indicating stage of publication(in press). 17. Fisheries Water Quality Standards Revision Section, Water quality standard for fisheries GB 11607-1989
[S]. China National Environmental Protection Bureau,1989. 18. Poliserpi María Belén, Cristos Diego, PérezIglesias Juan Manuel, Brodeur Julie Céline, Tissue distribution
and sublethal effects of imidacloprid in the South American grayish baywing (Agelaioides badius) [J]. Chemosphere, 2021,284: 19. Jin H.J., Yang R., shuihuanjing zhong huaxuepin de shengwu jilei yu jiance（Bioaccumulation and
monitoring of chemicals in the water environment） [J]. Huanjing jiance guanli yu jishu, 1990,(04)12-18. 20. Li Siqi.Evaluation of The Safety Of Imidacloprid And Its Metabolites Under The Integrated R
Procambarus Clarkii Breeding Model [D]. Huazhong Agricultural University,2020 21. Yi Yang, Limin Su, Ying Huang, Xiao Zhang, Chao Li, Jia Wang, Lingyun Fan, Shuo Wang, Yuan H. Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those
of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s)
disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or
products referred to in the content. References 1. Peter Jeschke, Ralf Nauen, Michael Schindler, Alfred Elbert, Overview of the Status and Global Strategy
for Neonicotinoids [J]. Journal of Agricultural and Food Chemistry, 2011,59:(7)2897-2908. 2. Dave Goulson, David Kleijn, REVIEW: An overview of the environmental risks posed by neonicotinoid
insecticides [J]. Journal of Applied Ecology, 2013,50:(4)977-987. 3. John E. Casida, Neonicotinoids and Other Insect Nicotinic Receptor Competitive Modulators: Progress and
Prospects, in: M.R. Berenbaum (Ed.), Annual Review of Entomology, Vol 632018, pp. 125-144 4. Michelle L. Hladik, Anson R. Main, Dave Goulson, Environmental Risks and Challenges Associated with
Neonicotinoid Insecticides [J]. Environmental Science & Technology, 2018,52:(6)3329-3335. 5. J. C. Anderson, C. Dubetz, V. P. Palace, Neonicotinoids in the Canadian aquatic environment: A literature
review on current use products with a focus on fate, exposure, and biological effects [J]. Science of the Total
Environment, 2015,505:409-422. 6. J. Struger, J. Grabuski, S. Cagampan, E. Sverko, D. McGoldrick, C. H. Marvin, Factors influencing the
occurrence and distribution of neonicotinoid insecticides in surface waters of southern Ontario, Canada [J]. Chemosphere, 2017,169:516-523. 6. J. Struger, J. Grabuski, S. Cagampan, E. Sverko, D. McGoldrick, C. H. Marvin, Factors influencing the
occurrence and distribution of neonicotinoid insecticides in surface waters of southern Ontario, Canada [J]. Chemosphere, 2017,169:516-523. p
7. Starner Keith, Goh Kean S, Detections of the neonicotinoid insecticide imidacloprid in surface waters of
three agricultural regions of California, USA, 2010-2011 [J]. Bulletin of environmental contamination and
toxicology, 2012,88:(3) 8. Xu Meijia, Huang Huiting, Li Na, Li Fang, Wang Donghong, Luo Qian, Occurrence and ecological risk of
pharmaceuticals and personal care products (PPCPs) and pesticides in typical surface watersheds, China
[J]. Ecotoxicology and Environmental Safety, 2019,175:289-298. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2023 Zhao,
Bio-uptake, tissue distribution and metabolism of a neonicotinoid insecticide clothianidin in zebrafish [J]. Environmental Pollution, 2022,292: 22. Yang Bin Ihm, Chan Sub Kim, Hee Dong Lee, Mihye Jeong, Dae Kyu Kim, Kee Sung Kyung, Behavior of
the Insecticide Imidacloprid in Crucian Carp (Carassius auratus L.) and Its Toxic Effects on Organs [J]. The
Korean Journal of Pesticide Science, 2006,10:(4) 23. Séverine Suchail, Georges de Sousa, Roger Rahmani, Luc Belzunce, In vivo distribution and metabolisation
of
14C-imidacloprid in different compartments of Apis mellifera L [J]. Pest Management Science,
2004,60:(11)1056-1062. (
)
24. F. J. Byrne, S. Castle, N. Prabhaker, N. C. Toscano, Biochemical study of resistance to imidacloprid in B
biotype Bemisia tabaci from Guatemala [J]. Pest Management Science, 2003,59:(3)347-52. 25. S Suchail, L. Debrauwer, L. P. Belzunces, Metabolism of imidacloprid in Apis mellifera [J]. Pest Management
Science, 2004,60:(3)291-6. 26. Y. Yang, L. Su, Y. Huang, X. Zhang, C. Li, J. Wang, L. Fan, S. Wang, Y. H. Zhao, Bio-uptake, tissue
distribution and metabolism of a neonicotinoid insecticide clothianidin in zebrafish [J]. Environ Pollut,
2022,292:(Pt A)118317. 27. Wang Rui, Xiang Qian, Chen Kun, Fang Yi, Advance in search for influence of CYP450 genetic
polymorphism to drugmetabolism [J]. The Chinese Journal of Clinical Pharmacology, 2004,20:(2)134-138. 28. Séverine Suchail, David Guez, Luc P. Belzunces, Characteristics of imidacloprid toxicity in twoApis
melliferasubspecies [J]. Environmental Toxicology and Chemistry, 2000,19:(7)1901-1905. p
gy
y
9. Fan Yinjun, Shi Xueyan, Gao Xiwu, Research progresses on the metabolism of neonicotinoids imidaclo
and thiamethoxam [J]. Chinese Journal of Pesticide Science, 2012,14:(6)587-596. [J]
J
f
,
,
( )
30. Ralf Nauen, Klaus Tietjen, Klaus Wagner, Alfred Elbert, Efficacy of Plant Metabolites of Imidacloprid
against Myzus persicae and Aphis gossypii (Homoptera: Aphididae) [J]. Pesticide Science, 1998,52:(1)53-57. Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those
of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s)
disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or
products referred to in the content.
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Computing and data management for SABRE South
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,023
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cc-by
| 2,091
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Computing and Data Management for SABRE South J. McKenzie
ARC Centre of Excellence for Dark Matter Particle Physics
On behalf of the SABRE South Collaboration 1
Introduction The SABRE experiment aims to search for an annual modulation arising from dark matter
interactions in ultra-high purity NaI(Tl) crystals in order to provide a model-independent test
of a signal observed by DAMA/LIBRA[1]. SABRE is a dual-site experiment located in the
northern and southern hemispheres, with SABRE North located at Laboratori Nazionali del
Gran Sasso (LNGS) in Italy and SABRE South at the Stawell Underground Physics Laboratory
(SUPL) in Australia. SABRE South anticipates generating to the order of 100 terabytes of raw
and uncompressed physics data annually. Effectively managing this data is of high importance. The recent opening of SUPL, 1024m underground at an active gold mine, brings numerous chal-
lenges for efficient data management and resource allocation for the SABRE South expriment. This conference proceeding addresses critical data management issues that need to be addressed
with the opening of a new lab and outlines the computing systems for SABRE South that
will be used to support the data acquisition and analysis. Challenges include balancing data
processing and resources, developing computing and data management systems, and addressing
bottlenecks in the system such as data acquisition rates, transfer speeds, and storage limitations. Balancing the use of computing resources in the lab is of particular interest as SABRE is the
first experiment at SUPL and will be pioneering the technology used. 2
Striking a Balance To strike an optimal balance between data processing and resource allocation, the SABRE South
Collaboration will make use of powerful and widely available cloud-computing resources to min-
imise resources required in SUPL. With close proximity and strong affiliation to the University
of Melbourne, SABRE South is able to leverage a range of cutting-edge resources available to
researchers, including high-performance computing, cloud-based computing architecture, and
robust storage capabilities. While we acknowledge the value of this connection and its potential
advantages, the primary focus of our collaboration is on developing effective data processing
strategies and robust systems capable of efficiently handling the substantial data generated at
SUPL. We aim to streamline data transfer to Melbourne, where ample resources are available for
further processing, analysis, and storage. This cloud-computing approach ensures that we can
adapt to evolving environments and leverage additional enhancements offered by the University
of Melbourne as part of our flexible system design. Please refer to Figure 1 for an illustration
of the relationship between our available resources and possible data reduction methods. Figure 1: Striking a balance: here, the orange represents what is possible in the DAQ, yellow is what SABRE
South envisage for SUPL, and green is available through cloud-computing resources at Melbourne Figure 1: Striking a balance: here, the orange represents what is possible in the DAQ, yellow is what
South envisage for SUPL, and green is available through cloud-computing resources at Melbour Abstract The SABRE (Sodium iodide with Active Background REjection) experiment
aims to detect an annual rate modulation from dark matter interactions in ultra-
high purity thallium-doped sodium-iodide (NaI(Tl)) crystals in order to provide a
model independent test of the signal observed by DAMA/LIBRA. SABRE South is
located at the Stawell Underground Physics Laboratory (SUPL), in regional Victo-
ria, Australia. ,
SABRE South is designed to detect the signals generated by radiation and cos-
mic rays using both a 12kL liquid scintillator detector which will be contained in
a steel vessel, and a plane of plastic scintillator modules located above the vessel
to more reliably detect muons from cosmic-rays. In addition the crystal detector
can host seven NaI(Tl) crystals to detect potential dark matter signals. As both
the backgrounds from the outer detectors and potential signals from the crystal
detectors are of interest the data taking strategy for SABRE South is to apply a
minimal sustainable selection in DAQ to ensure no data of interest is lost. This is
then followed by dedicated event building, a final software trigger step and further
data reduction using the main SABRE South computing systems. SUPL is a newly
constructed facility and as the first experiment, the SABRE computing infrastruc-
ture also needs to manage the data transfer to the main data centre in Melbourne
serving as a template for future experiments. This proceeding will present details
of the computing systems for SABRE South and how they will be used to support
the experimental data taking and analysis. CC-BY-4.0 licence 31st International Symposium on Lepton Photon Interactions at High Energies 3
Data Flow When discussing data flow, our primary concerns encompass data acquisition, processing, both
short-term and long-term storage, computing on the cloud, ensuring high availability, and im-
plementing backup procedures. See figure 2 for the data flow diagram between SUPL and
Melbourne. Page 2 of 5 31st International Symposium on Lepton Photon Interactions at High Energies SABRE SOUTH DATA FLOW DIAGRAM
SUPL
SABRE South
NaI(Tl)
system
SABRE
Conditions
system
SABRE South
Liquid
Scintillator
system
SABRE South
Plastic
Scintillator
system
SABRE
control
systems
Laboratory
Users
D1
Storage Computer
Melbourne
PMT
Waveforms
1.0
Processing for
data reduction
PMT
waveforms
PMT
Waveforms
2.0
Simple DAQ &
dedicated
monitoring
PMT
Waveforms
Request
Plots
End Users
Conditions
metadata
Conditions
metadata
3.0
Equipment
control
Control Input
Digital
Control
D2
Data transfer buffer
D3
Database
PMT
Waveforms
Conditions
metadata
7.0
Simulation
D4
Long term data
storage
5.0
Data
(re)processing
& event building
Offsite
backup
4.0
Software trigger
and data
reduction
PMT
Waveforms
Reduced PMT
Waveforms
Simulated
Data
Metadata
Additional
metadata
Additional
metadata
Computer status
& configuration
metadata
6.0
User interface
& monitoring
Plots
Control
Input
Metadata
Metadata
Figure 2: Data Flow Diagram: depicting the main flow of data from the experiment and associated metadata. The dashed line indicates the divide between SUPL based systems and those at the University of Melbourne. Melbourne Figure 2: Data Flow Diagram: depicting the main flow of data from the experiment and associated metadata. The dashed line indicates the divide between SUPL based systems and those at the University of Melbourne. 3.1
Data Acquisition SABRE South is expected to generate O(100 TB/y) of mostly unfiltered and uncompressed
data, mainly composed of Photomultiplier Tube (PMT) waveforms and conditions metadata
such as pressure, temperature, and other sensor readings. There are three main systems that
acquire the experimental data; the NaI(Tl) crystal, liquid scintillator, and plastic scintillator
systems. Additionally, there will be a stream of conditions data from various sensors. Between
the main systems, there are six digitisers connected via optical links to three data acquisition
(DAQ) computers, one for each of the main systems. Each digitiser can transfer up to 85 MB/s,
leading to a limit of 510 MB/s[2]. SABRE South will aim to keep a sustained rate of 10% (51
MB/s) of this limit to allow for large spikes. 3.2
Initial Data Processing and Short-term Storage For initial data processing and storage between the digitisers and DAQ computers at SUPL,
SABRE South uses custom programs to store the acquired data locally and apply data reduction
methods. These programs will employ elementary data reduction techniques, with a focus
on threshold configuration, coincidence checking, zero suppression, and simple filtering. The
anticipated outcome of the methods is a substantial reduction in annual data intake, from
O(100 TB/y) down to O(20 TB/y). SUPL will be linked to cloud computing services for data storage and processing in Melbourne
via a 1 Gb/s optical link. In the case of connection failure, there is also a backup 4G connection. However, this 4G connection will not be used for experimental data transfer but for continued
remote control and monitoring of SUPL based systems. As a consequence it is important to Page 3 of 5 31st International Symposium on Lepton Photon Interactions at High Energies have a sufficiently large storage buffer for the experiment in SUPL. The DAQ computers at SUPL have a local storage capacity totalling 60 TB. This allocation
of resources ensures the resilience of SABRE South computing systems in the face of potential
disruptions to its connectivity with cloud computing infrastructure at Melbourne, providing a
safeguarded operational buffer of up to three years. The DAQ computers at SUPL have a local storage capacity totalling 60 TB. This allocation
of resources ensures the resilience of SABRE South computing systems in the face of potential
disruptions to its connectivity with cloud computing infrastructure at Melbourne, providing a
safeguarded operational buffer of up to three years. 4
Conclusion This conference proceeding has delved into managing the vast amount of data expected to be
generated by the SABRE South Experiment at the Stawell Underground Physics Laboratory in
Australia. The unfiltered and uncompressed data will primarily be composed of PMT waveforms
and conditions metadata. Data reduction methods are expected to bring the initial size of O(100
TB/y) down to O(20 TB/y). There are many challenges in this endeavour, however, SABRE
South’s affiliation with the University of Melbourne, and its ability to leverage cutting-edge
cloud-computing resources eliminates the need for extensive computing infrastructure at SUPL,
allowing us to focus on developing efficient strategies and robust systems for data processing,
compression, and seamless transfer to Melbourne. SABRE South’s data acquisition, processing,
storage, and backup procedures have been outlined. Furthermore, the crucial role of cloud-
computing, long-term storage, and backup systems ensuring the integrity and availability of our
data has been highlighted. With a strong emphasis on high availability and system automation,
the foundation has been laid for a comprehensive and resilient data management infrastructure. 3.3
Cloud Computing, Long-term Storage, and Backup Page 4 of 5 Page 4 of 5 31st International Symposium on Lepton Photon Interactions at High Energies 3.3
Cloud Computing, Long-term Storage, and Backup The SABRE South cloud computing services are centred around a highly available PostgreSQL[3]
database management system, which serves as the core foundation for computing and data
management for the experiment. In conjunction with the database, there will be a user interface
(UI), high-performance computing (HPC), and task automation. The database will store a wide range of metadata, including conditions, status, configuration,
calibration, and other related experimental data. The experimental data from SUPL undergoes
a final software trigger step and a more complex data reduction process than what is applied
at SUPL, ensuring it is ready for long term storage. Once in long term storage, it becomes the
primary experimental dataset and metadata for the datasets is also stored in the database. The database for SABRE South will be configured for high availability to facilitate load bal-
ancing and query management. A highly available database is achieved by creating streaming
replications of the database and if the master fails or is under too much load, connections and
requests are redirected to another available copy of the database. To provide a good user experience, end user access to the database is facilitated with a user
interface. Various tools are employed to collectively form the interface for system monitoring
and database query management, the most notable being: • Prometheus[4]: collects and stores metrics from all systems as time series data • Grafana[5]: enables you to query, visualize, alert on, and explore your metrics and logs • Django[6]: a high-level Python web application framework that simplifies web application
development • Django[6]: a high-level Python web application framework that simplifies web application
development These tools integrate with each other and connect to and monitor both SUPL and cloud com-
puting systems. These tools integrate with each other and connect to and monitor both SUPL and cloud com-
puting systems. For analysis and simulation using the SABRE South experimental dataset, high-performance
computing (HPC) is available through the cloud-computing service. HPC includes specialist
high memory resources that are designed for processing large datasets and running multiple
computing tasks simultaneously. Task automation throughout the SABRE South computing systems will be managed using
Apache Airflow[7]. Some examples of automation include transferring data from SUPL to Mel-
bourne, inserting data into the PostgreSQL database, and backing up the database to an offsite
location. References [1]
R. Bernabei et al. “The DAMA project: Achievements, implications and perspectives”. In: Progress in Particle and Nuclear Physics 114 (2020), p. 103810. issn: 0146-6410. doi:
https://doi.org/10.1016/j.ppnp.2020.103810. url: https://www.sciencedirect. com/science/article/pii/S0146641020300570. [2]
SABRE South Collaboration. “The SABRE South Technical Design Report”. In: (July
2023). url: https://darkmatteraustralia.atlassian.net/wiki/spaces/SABREPUBLIC/
pages/973209623/Publications. [3]
PostgreSQL Global Development Group. PostgreSQL. en. https://www.postgresql.org/. Sept. 2023. [4]
Prometheus. Prometheus - Monitoring system & time series database. https://prometheus. io/. Sept. 2023. [5]
Grafana Labs. Grafana: the open observability platform. https://grafana.com/. Sept. 2023. [6]
Django Project. Django. https://www.djangoproject.com/. Sept. 2023. [7]
The Apache Software Foundation. Apache Airflow. https://airflow.apache.org/. Sept. 2023. Page 5 of 5 Page 5 of 5
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Standardized measurement of coronary inflammation using cardiovascular computed tomography: integration in clinical care as a prognostic medical device
|
Cardiovascular research
| 2,021
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cc-by
| 10,972
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Standardized measurement of coronary
inflammation using cardiovascular computed
tomography: integration in clinical care as a
prognostic medical device Evangelos K. Oikonomou
1,2†, Alexios S. Antonopoulos1†, David Schottlander
3,
Mohammad Marwan4, Chris Mathers
3, Pete Tomlins3, Muhammad Siddique3,
Laura V. Klu¨ner
1, Cheerag Shirodaria
3, Michail C. Mavrogiannis
1,
Sheena Thomas
5, Agostina Fava6, John Deanfield7, Keith M. Channon
1,8,9,
Stefan Neubauer
1,8,9, Milind Y. Desai
6, Stephan Achenbach4, and
Charalambos Antoniades
1,5,8,9* Evangelos K. Oikonomou
1,2†, Alexios S. Antonopoulos1†, David Schottlander
3,
Mohammad Marwan4, Chris Mathers
3, Pete Tomlins3, Muhammad Siddique3,
Laura V. Klu¨ner
1, Cheerag Shirodaria
3, Michail C. Mavrogiannis
1,
Sheena Thomas
5, Agostina Fava6, John Deanfield7, Keith M. Channon
1,8,9,
Stefan Neubauer
1,8,9, Milind Y. Desai
6, Stephan Achenbach4, and
Charalambos Antoniades
1,5,8,9* 1Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK; 2Section of
Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510, USA; 3Caristo Diagnostics, 1st Floor, New Barclay House, 234
Botley Rd, OX2 0HP, Oxford, UK; 4Department of Cardiology, Friedrich-Alexander-Universita¨t Erlangen-Nu¨rnberg, Maximilianspl 2, 91054 Erlangen, Germany; 5Acute Vascular Imaging
Centre, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK; 6Department of Cardiovascular Medicine,
Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH44195, USA; 7Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, Gower Street,
London WC1E 6BT; 8British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK; and 9National Institute of Health
Research (NIHR), Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK Received 7 June 2021; editorial decision 23 August 2021; accepted 27 August 2021; online publish-ahead-of-print 27 August 2021 Aims Coronary computed tomography angiography (CCTA) is a first-line modality in the investigation of suspected
coronary artery disease (CAD). Mapping of perivascular fat attenuation index (FAI) on routine CCTA enables the
non-invasive detection of coronary artery inflammation by quantifying spatial changes in perivascular fat composi-
tion. We now report the performance of a new medical device, CaRi-HeartV
R, which integrates standardized FAI
mapping together with clinical risk factors and plaque metrics to provide individualized cardiovascular risk
prediction. The study included 3912 consecutive patients undergoing CCTA as part of clinical care in the USA (n = 2040)
and Europe (n = 1872). * Corresponding author. Tel: þ44 1865 228340; fax: þ44 1865 740352, E-mail: antoniad@well.ox.ac.uk
† These authors contributed equally to this work.
V
C The Author(s) 2021. Published by Oxford University Press on behalf of the European Society of Cardiology.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse,
distribution, and reproduction in any medium, provided the original work is properly cited. Cardiovascular Research (2021) 117, 2677–2690
doi:10.1093/cvr/cvab286 Cardiovascular Research (2021) 117, 2677–2690
doi:10.1093/cvr/cvab286 Cardiovascular Research (2021) 117, 2677–2690
doi:10.1093/cvr/cvab286 Standardized measurement of coronary
inflammation using cardiovascular computed
tomography: integration in clinical care as a
prognostic medical device Standardized measurement of coronary
inflammation using cardiovascular computed
tomography: integration in clinical care as a
prognostic medical device
Evangelos K. Oikonomou
1,2†, Alexios S. Antonopoulos1†, David Schottlander
3,
Mohammad Marwan4, Chris Mathers
3, Pete Tomlins3, Muhammad Siddique3,
Laura V. Klu¨ner
1, Cheerag Shirodaria
3, Michail C. Mavrogiannis
1,
Sheena Thomas
5, Agostina Fava6, John Deanfield7, Keith M. Channon
1,8,9,
Stefan Neubauer
1,8,9, Milind Y. Desai
6, Stephan Achenbach4, and
Charalambos Antoniades
1,5,8,9*
1Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK; 2Section of
Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510, USA; 3Caristo Diagnostics, 1st Floor, New Barclay House, 234
Botley Rd, OX2 0HP, Oxford, UK; 4Department of Cardiology, Friedrich-Alexander-Universita¨t Erlangen-Nu¨rnberg, Maximilianspl 2, 91054 Erlangen, Germany; 5Acute Vascular Imaging
Centre, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK; 6Department of Cardiovascular Medicine,
Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH44195, USA; 7Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, Gower Street,
London WC1E 6BT; 8British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK; and 9National Institute of Health
Research (NIHR), Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX39DU, Oxford UK
Received 7 June 2021; editorial decision 23 August 2021; accepted 27 August 2021; online publish-ahead-of-print 27 August 2021
Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/635 Methods
and results Standardized measurement of coronary
inflammation using cardiovascular computed
tomography: integration in clinical care as a
prognostic medical device These cohorts were used to generate age-specific nomograms and percentile curves as
reference maps for the standardized interpretation of FAI. The first output of CaRi-HeartV
R is the FAI-Score of each
coronary artery, which provides a measure of coronary inflammation adjusted for technical, biological, and anatomi-
cal characteristics. FAI-Score is then incorporated into a risk prediction algorithm together with clinical risk factors
and CCTA-derived coronary plaque metrics to generate the CaRi-Heart
V
R Risk that predicts the likelihood of a fatal
cardiac event at 8 years. CaRi-Heart
V
R Risk was trained in the US population and its performance was validated
externally in the European population. It improved risk discrimination over a clinical risk factor-based model
[D(C-statistic) of 0.085, P = 0.01 in the US Cohort and 0.149, P < 0.001 in the European cohort] and had a
consistent net clinical benefit on decision curve analysis above a baseline traditional risk factor-based model across
the spectrum of cardiac risk. ...................................................................................................................................................................... Mapping of perivascular FAI on CCTA enables the non-invasive detection of coronary artery inflammation by quan-
tifying spatial changes in perivascular fat composition. We now report the performance of a new medical device,
CaRi-HeartV
R, which allows standardized measurement of coronary inflammation by calculating the FAI-Score of 2678 E.K. Oikonomou et al. each coronary artery. The CaRi-Heart
V
R device provides a reliable prediction of the patient’s absolute risk for a fatal
cardiac event by incorporating traditional cardiovascular risk factors along with comprehensive CCTA coronary pla-
que and perivascular adipose tissue phenotyping. This integration advances the prognostic utility of CCTA for indi-
vidual patients and paves the way for its use as a dual diagnostic and prognostic tool among patients referred for
CCTA. each coronary artery. The CaRi-Heart
V
R device provides a reliable prediction of the patient’s absolute risk for a fatal
cardiac event by incorporating traditional cardiovascular risk factors along with comprehensive CCTA coronary pla-
que and perivascular adipose tissue phenotyping. This integration advances the prognostic utility of CCTA for indi-
vidual patients and paves the way for its use as a dual diagnostic and prognostic tool among patients referred for
CCTA. phical Abstract ............................................................................................................................................................................................ words
Fat attenuation index • Pericoronary • Perivascular • Atherosclerosis • Coronary artery disease
hical Abstract hical Abstract Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Graphical Abstract .......................................................................................................................................................................... 2.2 CaRi-HeartV
R device description
V However, the clinical interpretation of a given FAI value depends
on a range of technical factors (e.g. tube voltage, contrast media etc.),
local anatomical characteristics of the coronary artery under investiga-
tion (e.g. the coronary artery segment where it is measured), and bio-
logical factors including patient demographics (e.g. age, gender, and
obesity).1 This limits the clinical value of uncorrected perivascular fat
attenuation measurement, and calls for the development of standard-
ized metrics to quantify the degree of coronary inflammation based
on FAI mapping, to enable effective integration into the clinical
workflow.11 CaRi-HeartV
R is a cloud-based CE-marked medical device (Caristo
Diagnostics Ltd, Oxford UK) that provides information about vascular-
related inflammation from CCTA images, and calculates measures
related to the risk of cardiac mortality due to coronary-related inflamma-
tion, coronary atherosclerosis, and other clinical risk factors. CT scan
data can be sent electronically to the system from hospital picture archiv-
ing and communication systems (PACS) using a gateway appliance
installed in the healthcare provider’s network. Reports are electronically
sent back to originating PACS or by email. Although the segmentation of
epicardial adipose tissue and the perivascular space is done using a deep
learning network, the device includes a quality control step by a trained
analyst,
who
checks
and
edits
the
segmentations
accordingly. Segmentation and quantification of the perivascular FAI around the right
coronary artery (RCA), left anterior descending artery (LAD), and left
circumflex artery (LCX) were performed according to previously de-
scribed protocols.2,9 Three appropriately trained analysts, members of
the Oxford Academic Cardiovascular CT Core Lab (OXACCT) at the
University of Oxford were involved in the analysis of the present dataset,
and the between-reader variability for FAI and FAI-Score are excellent
(intra-class correlation coefficient ICC: 0.980, P < 0.001 for the RCA,
0.990 P < 0.001 for the LAD, and 0.992, P < 0.001 for the LCX). Traditional models of primary prevention rely on the use of clinical
risk factor-based prediction tools (e.g. the ESC-SCORE),12 which do not
capture information about the presence, extent, or nature of coronary
atherosclerosis. Although imaging-derived metrics, such as CCS can be
used to further stratify cardiovascular risk,13 CCS predominantly reflects
the presence of calcified plaques and is often increased by statin treat-
ment.14 Newer plaque interpretation scores (e.g. Standardized measurement of coronary
inflammation using cardiovascular computed
tomography: integration in clinical care as a
prognostic medical device ords
Fat attenuation index • Pericoronary • Perivascular • Atherosclerosis • Coronary artery disease Keywords Quantification of coronary inflammation by CT 2679 2. Methods The recognition of perivascular adipose tissue (PVAT) as an in vivo molec-
ular sensor of vascular inflammation has led to the development of new
imaging technologies that can detect phenotypic changes in PVAT com-
position, thereby allowing the non-invasive quantification of coronary in-
flammation.1,2 Fat attenuation index (FAI) mapping, first described in
2017, was derived from studies which demonstrated that inflammatory
molecules released from the human vascular wall inhibit adipogenesis
and stimulate lipolysis in the adjacent PVAT. These changes modify
PVAT composition from a greater lipophilic to a greater aqueous con-
tent in a spatial relationship with the inflamed vascular wall.2 Since coro-
nary computed tomography angiography (CCTA) is now a first-line
investigation in the assessment of chest pain,3–5 and with the prospect of
using CCTA as a screening tool in high-risk asymptomatic individuals,6–8
FAI provides a method to extract functional information from an existing
‘anatomical’ test with no additional scanning time or radiation exposure
for the patient. (1)
The FAI for the proximal segments of each of the major coronary
arteries. 2.1 Study population This study included two independent cohorts of patients as part of the
CRISP-CT study,9 now part of the broader Oxford Risk Factors and
Non-Invasive Imaging Study. The study population consisted of 3912
patients undergoing clinically indicated CCTA for evaluation of stable
coronary disease in two large academic centres in Europe and the USA. The US cohort included 2040 patients undergoing CCTA at Cleveland
Clinic, Cleveland, Ohio, between 2008 and 2016 [1126 (55.2%) males,
median age of 53 (range: 19–87) years]. The European cohort consisted
of 1872 patients [1178 (62.9%) males, median age of 62 (range: 17–89)
years] who underwent CCTA between 2005 and 2009 at the Erlangen
University Hospital (Erlangen, Germany). The key characteristics, pre-
senting symptoms, and indications for the study population are summa-
rized in Table 1. Definitions of risk factors as well as adjudicated endpoints have been
described elsewhere.9 Briefly, cardiac mortality was defined as any death
due to proximate cardiac causes (e.g. myocardial infarction, low-output
heart failure, and fatal arrhythmia). Deaths fulfilling the criteria of sudden
cardiac death were also included in this group.16,17 Several clinical studies have now assessed the diagnostic and prognos-
tic utility of FAI in a range of clinical scenarios. In the largest of these stud-
ies, which included 3912 patients undergoing clinically indicated CCTA
(CRISP-CT study), FAI mapping improved the prediction of adverse car-
diac events beyond traditional risk factors and CCTA metrics, such as
the extent of coronary atherosclerosis, coronary calcium score (CCS),
and presence of high-risk plaque features.9 Further studies have shown
that PVAT attenuation can identify culprit lesions in patients presenting
with acute myocardial infarction,2 and reliably identify areas of microcal-
cification and inflammation.10 The study was approved by the respective institutional review boards
(ORFAN study: South Central—Oxford C Research Ethics Committee
15/SC/0545) and local ethics committees (Cleveland Clinic IRB 17-915 &
ethics committee of the Friedrich-Alexander University Erlangen-
Nu¨rnberg) and conformed to the principles outlined in the Declaration
of Helsinki. (2)
The FAI-Score for each of the major coronary arteries, representing
the FAI weighted for technical scan parameters (e.g. tube voltage), ana-
tomical factors related with the fat distribution around the arteries and (1)
The FAI for the proximal segments of each of the major coronary
arteries.
(2)
The FAI-Score for each of the major coronary arteries, representing
the FAI weighted for technical scan parameters (e.g. tube voltage), ana-
tomical factors related with the fat distribution around the arteries and 2.2 CaRi-HeartV
R device description
V the Coronary Artery
Disease—Reporting and Data System)15 exist but are limited to quantify-
ing the extent of coronary atherosclerotic disease and do not capture
underlying clinical and biological risk factors, such as measures of coro-
nary inflammation. In this context, quantifying the degree of vascular in-
flammation through perivascular FAI mapping may introduce further
confusion. A new medical device, CaRi-Heart
V
R (Caristo Diagnostics,
Oxford, UK), was developed to integrate such information on clinical
risk factors, coronary plaques, and the degree of coronary inflammation
in a way that enables individualized estimation of a patient’s cardiac risk. We now evaluate the performance of CaRi-HeartV
R in a multinational co-
hort of patients undergoing CCTA. The principal outputs of the CaRi-Heart
V
R medical device are: (2)
The FAI-Score for each of the major coronary arteries, representing
the FAI weighted for technical scan parameters (e.g. tube voltage), ana-
tomical factors related with the fat distribution around the arteries and 2680 E.K. Oikonomou et al. .............................................................................................................................................................................................................................. Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Duration in months (median [range]) All-cause mortality, n (%) Cardiac mortality, n (%) Values presented as median (25th–75th percentile) or number (percentages, %); maximum missingness in the European cohort: *9.2%, **13.9%. ACEi, Angiotensin-converting enzyme inhibitors; ARBs, angiotensin-II-receptor blockers; CAD, coronary artery disease; CT, computed tomography. P-values are derived from Mann–Whitney U test (continuous variables) and Pearson’s v2 test (categorical variables) comparisons between the two cohorts. were imputed using the multiple imputation by chained equations
method (package mice in R) with a bootstrapped logistic regression
model for categorical (binary) variables and mean imputation for contin-
uous variables. basic demographics (age, sex); FAI-Score is also accompanied by vessel-
specific nomograms for each coronary territory to allow individualized
interpretation of the degree of local coronary inflammation. (3) (3)
The CaRi-Heart
V
R Risk representing the individualized patient risk of a
fatal cardiac event at 8 years. This metric incorporates the FAI-Score
values into a prognostic model that includes information about athero-
sclerotic plaque burden [as described through the modified Duke
coronary artery disease (CAD) index]18 and clinical risk factors
(diabetes, smoking, hyperlipidaemia, and hypertension). (3)
The CaRi-Heart
V
R Risk representing the individualized patient risk of a
fatal cardiac event at 8 years. This metric incorporates the FAI-Score
values into a prognostic model that includes information about athero-
sclerotic plaque burden [as described through the modified Duke
coronary artery disease (CAD) index]18 and clinical risk factors
(diabetes, smoking, hyperlipidaemia, and hypertension). (3)
The CaRi-Heart
V
R Risk representing the individualized patient risk of a
fatal cardiac event at 8 years. This metric incorporates the FAI-Score
values into a prognostic model that includes information about athero-
sclerotic plaque burden [as described through the modified Duke
coronary artery disease (CAD) index]18 and clinical risk factors
(diabetes, smoking, hyperlipidaemia, and hypertension). The prognostic value of FAI-Score of each coronary artery against
fatal cardiac events was then validated by using both univariate analysis as
well as Cox-regression model, after inclusion of the patient risk factors
into the models. The prognostic value of FAI-Score of each coronary ar-
tery is graphically summarized by plotting the log[hazard ratio (HR)]
against FAI-Score, using the median FAI-Score value as reference, and
the results from the Cox-regression analysis are presented as HR [95%
confidence interval (95% CI)] per unit change (or standard deviation
increments) of FAI-Score. 2.2 CaRi-HeartV
R device description
V Table 1 Cohort demographics and clinical characteristics
American cohort
European cohort
P-value
Location
Cleveland,
Erlangen,
OH, USA
Germany
Eligible subjects included in the study, n (%)
2040 (100)
1872 (100)
–
Age in years (median [range])
53 [43–62]
62 [52–68]
<0.001
Male sex, n (%)
1126 (55.2)
1178 (62.9)
<0.001
Risk factors* (n, valid %)
Hypertension
949 (46.5)
1068 (62.0)
<0.001
Hypercholesterolaemia
1126 (55.2)
930 (54.7)
0.78
Diabetes mellitus
219 (10.7)
215 (12.4)
0.11
Smoking
465 (22.8)
221 (12.8)
<0.001
Reason for referral
Assessment of coronary artery disease
1761 (86.4)
1790 (95.6)
<0.001
Symptoms prior to scan
<0.001
Chest pain
1184 (58.0)
764 (43.4)
Dyspnoea
452 (22.2)
193 (10.8)
Medications at baseline** (n, valid %)
Antiplatelets (aspirin/clopidogrel/ticagrelor)
987 (48.4)
606 (37.6)
<0.001
Statins
813 (39.9)
557 (34.6)
0.001
ACEi or ARBs
599 (29.4)
696 (43.1)
<0.001
Beta-blockers
303 (14.9)
721 (44.8)
<0.001
Modified Duke prognostic CAD index, n (%)
<50% stenosis
1044 (55.8)
1690 (82.8)
<0.001
>_2 mild stenoses with proximal CAD in 1 artery or 1 moderate stenosis
518 (27.7)
212 (10.4)
2 moderate stenoses or 1 severe stenosis
66 (3.5)
100 (4.9)
3 moderate stenoses, 2 severe stenoses, or severe stenosis in the proximal LAD
152 (8.1)
9 (0.4)
3 severe stenoses or 2 severe stenoses in the proximal LAD
18 (1.0)
14 (0.7)
>_50% stenosis in left main coronary artery
74 (3.9)
15 (0.7)
Prospective follow-up
Duration in months (median [range])
53.8 [4–105]
72 [51–109]
<0.001
All-cause mortality, n (%)
85 (4.2)
114 (6.1)
–
Cardiac mortality, n (%)
48 (2.4)
26 (1.4)
Values presented as median (25th–75th percentile) or number (percentages, %); maximum missingness in the European cohort: *9.2%, **13.9%. ACEi, Angiotensin-converting enzyme inhibitors; ARBs, angiotensin-II-receptor blockers; CAD, coronary artery disease; CT, computed tomography. P-values are derived from Mann–Whitney U test (continuous variables) and Pearson’s v2 test (categorical variables) comparisons between the two cohorts. 2.3 Statistical analysis Participant demographics are summarized as numbers (percentages) or
median (range or 25th–75th percentile as specified) for categorical and
continuous variables, respectively (unless specified otherwise). Between-
group comparisons were performed using Pearson’s v2 for categorical
variables and Mann–Whitney’s test or unpaired Student’s t-test (as ap-
propriate) for continuous variables. Correlations between continuous
predictors were assessed using Spearman’s rho coefficient. Missing data In the second part of the study, we evaluated the performance of
CaRi-HeartV
R Risk in the USA (training) and European (testing) study
populations. For validation purposes, a range of metrics are presented,
including Nagelkerke’s R2, the discrimination index D, the unreliability in-
dex U, the overall quality index Q (=D-U), the C-index (concordance) 2681 Quantification of coronary inflammation by CT and Somer’s Dxy [=2(C-0.5)], and the calibration slope, all with
optimism-adjustment and 95% CI calculated using bootstrapping with
200 replications. Finally, CaRi-HeartV
R Risk was compared to a baseline
cardiac risk prediction tool consisting of age, sex, hypertension, hyper-
cholesterolaemia, diabetes mellitus, and smoking (both with or without
inclusion of CAD presence and extent)18 to better understand the incre-
mental prognostic value of comprehensive CCTA-phenotyping in this
patient population. Improvement in discrimination was assessed by com-
paring the time-dependent C-statistic of the two models across different
follow-up times, as well as by calculating the net reclassification improve-
ment (NRI), integrated discrimination improvement (IDI), and median
improvement at 8 years (95% CI calculated using bootstrapping with 200
replications).16 over 8 years of follow-up). The probability threshold describes the mini-
mum probability of disease at which further intervention would be war-
ranted. This threshold tends to be lower for interventions with high
efficacy and low cost, though higher for minimally effective treatments or
those associated with significant morbidity. Conversely, the net benefit
reflects the difference between the expected benefit (number of patients
truly at risk who will receive an intervention using the proposed strategy)
and harm [number of patients without the disease who would be treated
unnecessarily (false positives)], weighted by the odds of the risk thresh-
old. This graphical method enables the comparison of the net
clinical benefit of different approaches across different levels of estimated
risk. 2.3 Statistical analysis Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Statistical analysis was performed in the R environment (R 4.0.2, The R
Foundation for Statistical Computing, http://www.R-project.org) using R
studio (version 4.0.2) and the following packages: rms, survival,
riskRegression, survIDINRI, timeROC, survivalROC, caret. Hmisc, Design, rmda. Finally, the net benefit of using CaRi-Heart
V
R Risk over a baseline
clinical risk model was assessed using a decision curve analysis.19 In this
analysis, the y axis reflects the net benefit, while the x axis reflects varying
probability thresholds (for the outcome of interest, i.e. cardiac mortality ure 1 FAI-Score nomograms across different age groups based on two international cohorts from Europe and the USA. Estimated nomograms with
entile curves for FAI-Score across different age strata for each one of the main coronary territories [LAD, left anterior descending artery (A); RCA, right
nary artery (B); LCX, left circumflex coronary artery (C)]. FAI, fat attenuation index. N = 3912 participants per panel. p.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Figure 1 FAI-Score nomograms across different age groups based on two international cohorts from Europe and the USA. Estimated nomograms with
percentile curves for FAI-Score across different age strata for each one of the main coronary territories [LAD, left anterior descending artery (A); RCA, right
coronary artery (B); LCX, left circumflex coronary artery (C)]. FAI, fat attenuation index. N = 3912 participants per panel. 2682 E.K. Oikonomou et al. 0
1
2
3
4
5
6
0.1
3.3
19.0 38.0 75.7
−1
0
1
2
3
4
5
0.1
6.7
24.0 48.0
−1
0
1
2
3
4
0.2
3.8
15.0 30.0 60.7
0
2
4
6
0.3
6.9
21.0 42.0 84.2
−1
0
1
2
3
4
5
0.2
4.2
12.0
24.0
48.0
0
2
4
0.4
7.5
15.0
30.0
59.2
A
B
C
D
E
F
Ln(hazard ration) for cardiac mortality
Ln(hazard ration) for cardiac mortality
Ln(hazard ration) for cardiac mortality
Right coronary artery (RCA) FAI score
Right coronary artery (RCA) FAI score
Left anterior descending (LAD) FAI score
Left anterior descending (LAD) FAI score
Left circumflex artery (LCX) FAI score
Left circumflex artery (LCX) FAI score
American cohort
European cohort
96.0
RCA
RCA
LAD
LAD
LCX
LCX
gure 2 Prognostic value of vessel-specific FAI-Scores for cardiac mortality. 2.3 Statistical analysis Association between FAI-Score calculated around the RCA (A and B)
and D) and LCX (E and F) in the American (A, C, and E, n = 2040 participants) and European cohorts (B, D, and F, n = 1872 participants). FAI: fat attenu
dex. 0
1
2
3
4
5
6
0.1
3.3
19.0 38.0 75.7
A
Ln(hazard ration) for cardiac mortality
Right coronary artery (RCA) FAI score
American cohort
RCA −1
0
1
2
3
4
5
0.1
6.7
24.0 48.0
B
Right coronary artery (RCA) FAI score
European cohort
96.0
RCA B A Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 24.0 48.0 96.0 6.7
24.0 48
Right coronary artery (RCA) FAI score Right coronary artery (RCA) FAI score −1
0
1
2
3
4
0.2
3.8
15.0 30.0 60.7
C
Ln(hazard ration) for cardiac mortality
Right coronary artery (RCA) FAI score
Left anterior descending (LAD) FAI score
LAD C 0
2
4
6
0.3
6.9
21.0 42.0 84.2
D
Left anterior descending (LAD) FAI score
LAD D Left anterior descending (LAD) FAI score Left anterior descending (LAD) FAI score −1
0
1
2
3
4
5
0.2
4.2
12.0
24.0
48.0
E
Ln(hazard ration) for cardiac mortality
Left circumflex artery (LCX) FAI score
LCX 0
2
4
0.4
7.5
15.0
30.0
59.2
F
Left circumflex artery (LCX) FAI score
LCX F E Left circumflex artery (LCX) FAI score Left circumflex artery (LCX) FAI score Left circumflex artery (LCX) FAI score Figure 2 Prognostic value of vessel-specific FAI-Scores for cardiac mortality. Association between FAI-Score calculated around the RCA (A and B), LAD
(C and D) and LCX (E and F) in the American (A, C, and E, n = 2040 participants) and European cohorts (B, D, and F, n = 1872 participants). FAI: fat attenuation
index. Quantification of coronary inflammation by CT 2683 3. Results deaths of unknown cause out of a total of 114 deaths. Patient demo-
graphics are presented in Table 1. deaths of unknown cause out of a total of 114 deaths. Patient demo-
graphics are presented in Table 1. Within the US cohort of 2040 patients with a median follow-up of
53.8 months (range: 4–105 months), a total of 85 deaths were reported,
48 of which were cardiac. In the European cohort of 1872 patients with a
median follow-up period of 72months (range: 51–109months), a total
of 26 deaths were attributed to confirmed cardiac causes and 16 were 3.1 Standardizing FAI through the
FAI-Score To better understand how to interpret FAI-Score at an individual patient
level, we calculated nomograms and percentile curves for FAI-Score
around each one of the coronary vessels in a pooled analysis (Figure 1). As shown, FAI-Score increases with age. The associated percentile
curves represent estimates of the distribution of FAI-Score in a represen-
tative sample of patients undergoing clinically indicated CCTA. Of note,
FAI-Scores around the RCA, LAD, and LCX retain their prognostic value
in both independent datasets, with higher scores linked to a higher subse-
quent risk of fatal cardiac events (Figure 2). This was preserved when
FAI-Score for each coronary artery was used as a continuous variable in
both
univariate
and
multivariable
Cox-regression
(Table
2
and
Supplementary material online, Table S1), whereas a graded (dose–
response) relationship was noted between a patient’s age- and sex-stan-
dardized FAI-Score percentile and the relative risk of cardiac mortality
(Supplementary material online, Table S2). Notably, there was no Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 ...................................................................................................... Table 2 HR (and 95% CI) for risk of fatal cardiac events in
the USA and European cohorts
US cohort
(n 5 2040)
European cohort
(n 5 1872)
FAI-score RCA
1.17 (1.13–1.21), P < 0.001 1.06 (1.04–1.08), P < 0.001
FAI-score LAD
1.11 (1.07–1.15), P < 0.001 1.07 (1.05–1.09), P < 0.001
FAI-score LCx
1.19 (1.14–1.25), P < 0.001 1.08 (1.04–1.12), P < 0.001
CaRi-Heart
V
R risk 1.10 (1.07–1.12), P < 0.001 1.06 (1.04–1.08), P < 0.001
HR calculated per 1 unit increment in FAI-score or CaRi-Heart
V
R risk. Unadjusted
hazard ratios are reported. 95% CI, 95% confidence interval; FAI, fat attenuation index; LAD, left anterior
descending; LCx, left circumflex. ...................................................................................................... Table 2 HR (and 95% CI) for risk of fatal cardiac events in
the USA and European cohorts
US cohort
(n 5 2040)
European cohort
(n 5 1872)
FAI-score RCA
1.17 (1.13–1.21), P < 0.001 1.06 (1.04–1.08), P < 0.001
FAI-score LAD
1.11 (1.07–1.15), P < 0.001 1.07 (1.05–1.09), P < 0.001
FAI-score LCx
1.19 (1.14–1.25), P < 0.001 1.08 (1.04–1.12), P < 0.001
CaRi-Heart
V
R risk 1.10 (1.07–1.12), P < 0.001 1.06 (1.04–1.08), P < 0.001
HR calculated per 1 unit increment in FAI-score or CaRi-Heart
V
R risk. Unadjusted
hazard ratios are reported. 3.1 Standardizing FAI through the
FAI-Score and extent of coronary atherosclerosis).18 To derive an integrated risk
score that encompasses all the above information for patients undergo-
ing CCTA, the CaRi-HeartV
R Risk was developed to represent risk of the
individual for a fatal cardiac event (at 8 years, to mirror the length of
follow-up in the included cohorts). A model including all above variables
was fitted in the US cohort, where it was validated internally using boot-
strapping with n = 100 repetitions and found to have excellent discrimi-
nation [C-statistic 0.809 (95% CI 0.805–0.814)] (Figure 3A) for prediction
of cardiac mortality at 8 years. Subgroup analysis across different
race and ethnicity groups is provided in Supplementary material online,
Table S3. The negative predictive value of a CaRi-HeartV
R Risk >10% for a association between CCS and FAI-Score around any coronary artery
(Supplementary material online, Figure S1). association between CCS and FAI-Score around any coronary artery
(Supplementary material online, Figure S1). 3.1 Standardizing FAI through the
FAI-Score 95% CI, 95% confidence interval; FAI, fat attenuation index; LAD, left anterior
descending; LCx, left circumflex. Table 2 HR (and 95% CI) for risk of fatal cardiac events in
the USA and European cohorts ................................. 0.70
0.75
0.80
0.85
0.90
0.95
1.00
0.70
0.75
0.80
0.85
0.90
0.95
1.00
Black: observed
Gray: ideal
Blue: optimism-corrected
Freedom from fatal cardiac event
at 8 years
Estimated probability of freedom from fatal cardiac event at 8 years
B
Validation and calibration of the CaRi model
Original Training
Testing Optimism-corrected (95% CI)
Somer’s Dxy
0.667
0.685
0.636
0.617 (0.610-0.628)
0.146
0.164
0.130
0.112 (0.107-0.116)
Slope
1.000
1.000
0.873
0.873 (0.861-0.890)
Discrimination index D
0.126
0.142
0.112
0.095 (0.091-0.099)
Unreliability index U
-0.003
-0.003
0.006
0.006 (0.004-0.006)
Overall quality index Q (D-U) 0.129
0.145
0.105
0.089 (0.086-0.095)
G-index
1.457
1.642
1.393
1.208 (1.203-1.264)
AUC
0.833
0.843
0.818
0.809 (0.805-0.814)
A
R2
gure 3 Validation of the CaRi-Heart
V
R risk. (A) Internal validation metrics in the American cohort of the CaRi-Heart
V
R Risk describing the model’s discrim-
ion and calibration. (B) Calibration curve of the CaRi-Heart
V
R Risk reflecting the model-based estimated probability of cardiac mortality at 8years vs. the
ual (observed) probability across different levels of risk in our population (n = 2040). AUC, area under the curve; 95% CI, 95% confidence interval. Validation and calibration of the CaRi model
A A 0.70
0.75
0.80
0.85
0.90
0.95
1.00
0.70
0.75
0.80
0.85
0.90
0.95
1.00
Black: observed
Gray: ideal
Blue: optimism-corrected
Freedom from fatal cardiac event
at 8 years
Estimated probability of freedom from fatal cardiac event at 8 years
B B Figure 3 Validation of the CaRi-Heart
V
R risk. (A) Internal validation metrics in the American cohort of the CaRi-Heart
V
R Risk describing the model’s discrim-
ination and calibration. (B) Calibration curve of the CaRi-Heart
V
R Risk reflecting the model-based estimated probability of cardiac mortality at 8years vs. the
actual (observed) probability across different levels of risk in our population (n = 2040). AUC, area under the curve; 95% CI, 95% confidence interval. 2684 2684 E.K. Oikonomou et al. Figure 4 Incremental discriminatory value of CaRi-Heart
V
R Risk above clinical risk predictors. Incremental discriminatory value of the CaRi-Heart
V
R Risk for
cardiac mortality (t = 8 years) above a clinical risk prediction model consisting of age, sex, hypertension, hypercholesterolaemia, diabetes mellitus, and smok-
ing in the USA (A, n = 2040 participants) and European cohorts (B, n = 1872 participants). The thick black line represents events, whereas the thin black line
represents non-events. The difference between the black dots represents the continuous NRI, the difference between the grey dots represents the median
improvement, whereas the shaded area reflects the IDI. (C) Reclassification table for discrete cardiac risk groups in the two study cohorts comparing CaRi-
based risk stratification against a baseline clinical risk prediction model. 3.2 Evaluating the prognostic value of the
CaRi-HeartV
R device Although FAI-Score was developed as a standardized metric of coronary
inflammation in each coronary artery (allowing between-subject com-
parisons), its prognostic value should be evaluated in the context of addi-
tional traditional risk factors (i.e. hypertension, hypercholesterolaemia,
and diabetes mellitus smoking) and other CCTA features (i.e. presence Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 −0.3
−0.2
−0.1
0.0
0.1
0.2
0.3
0.0
0.2
0.4
0.6
0.8
1.0
0.0
0.2
0.4
0.6
0.0
0.2
0.4
0.6
0.8
1.0
Pr(D≤s)
Median improvement:
0.021
95% CI [0.003 - 0.107],
p=0.03
NRI: 0.420
95% CI [0.117 - 0.582],
p=0.01
IDI: 0.052
95% CI [0.019 - 0.179],
p=0.01
Median improvement: 0.034
95% CI [0.004 - 0.158],
p=0.01
NRI: 0.550
95% CI [0.345 - 0.800],
p=0.01
IDI: 0.092
95% CI [0.025 - 0.280],
p<0.001
s
s
C Reclassification table
Pr(D≤s)
A American cohort
B European cohort 0.0
0.2
0.4
0.6
0.0
0.2
0.4
0.6
0.8
1.0
Median improvement: 0.034
95% CI [0.004 - 0.158],
p=0.01
NRI: 0.550
95% CI [0.345 - 0.800],
p=0.01
IDI: 0.092
95% CI [0.025 - 0.280],
p<0.001
s
Pr(D≤s)
B European cohort −0.3
−0.2
−0.1
0.0
0.1
0.2
0.3
0.0
0.2
0.4
0.6
0.8
1.0
Pr(D≤s)
Median improvement:
0.021
95% CI [0.003 - 0.107],
p=0.03
NRI: 0.420
95% CI [0.117 - 0.582],
p=0.01
IDI: 0.052
95% CI [0.019 - 0.179],
p=0.01
s
A American cohort C Reclassification table C Reclassification table Figure 4 Incremental discriminatory value of CaRi-Heart
V
R Risk above clinical risk predictors. Incremental discriminatory value of the CaRi-Heart
V
R Risk for
cardiac mortality (t = 8 years) above a clinical risk prediction model consisting of age, sex, hypertension, hypercholesterolaemia, diabetes mellitus, and smok-
ing in the USA (A, n = 2040 participants) and European cohorts (B, n = 1872 participants). The thick black line represents events, whereas the thin black line
represents non-events. The difference between the black dots represents the continuous NRI, the difference between the grey dots represents the median
improvement, whereas the shaded area reflects the IDI. (C) Reclassification table for discrete cardiac risk groups in the two study cohorts comparing CaRi-
based risk stratification against a baseline clinical risk prediction model. Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 2685 Quantification of coronary inflammation by CT 500
1000
1500
2000
2500
3000
0.5
0.6
0.7
0.8
0.9
1.0
Time post-CCTA (days)
AUC(t)
500
1000
1500
2000
2500
3000
−0.10 −0.05 0.00
0.05
0.10
0.15
0.20
Time post-CCTA (days)
ΔAUC(t)
500
1000
1500
2000
2500
3000
0.5
0.6
0.7
0.8
0.9
1.0
Time post-CCTA (days)
AUC(t)
500
1000
1500
2000
2500
3000
−0.1
0.0
0.1
0.2
0.3
0.4
0.5
Time post-CCTA (days)
ΔAUC(t)
C
D
A
B
European cohort
American cohort
American cohort
European cohort
CaRi-HEART model
Traditional model
95% confidence intervals
95% confidence bands
Figure 5 Incremental discriminatory value of the CaRi-Heart
V
R Risk across different follow-up intervals. In panel (A) the orange line reflects the calculated
‘Area under the Curve (AUC)’ (C-statistic) of a model consisting of baseline cardiovascular risk predictors (age, sex, hypertension, hypercholesterolaemia
diabetes mellitus, and smoking) at 1-year intervals post-CCTA in the American cohort (n = 2040 participants). This is compared to the AUC for the inte-
grated CaRi-Heart
V
R Risk at the same follow-up times (blue line), with the difference of the AUC [D(AUC)] between the two models graphically presented in
panel (B). Panels (C) and (D) present the results of the same analyses in the European cohort (n = 1872 participants). CCTA, coronary computed tomogra-
phy angiography. Dashed lines denote 95% CI, whereas dotted lines denote confidence bands. 500
1000
1500
2000
2500
3000
0.5
0.6
0.7
0.8
0.9
1.0
Time post-CCTA (days)
AUC(t)
A
American cohort
CaRi-HEART model
Traditional model 0
500
1000
1500
2000
2500
3000
−0.10 −0.05 0.00
0.05
0.10
0.15
0.20
Time post-CCTA (days)
ΔAUC(t)
B
American cohort
95% confidence intervals
95% confidence bands B B A Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 ΔAUC(t) Time post-CCTA (days)
0
500
1000
1500
2000
2500
3000
−0.1
0.0
0.1
0.2
0.3
0.4
0.5
Time post-CCTA (days)
ΔAUC(t)
D
European cohort Time post-CCTA (days)
500
1000
1500
2000
2500
3000
0.5
0.6
0.7
0.8
0.9
1.0
Time post-CCTA (days)
AUC(t)
C
European cohort C D ΔAUC(t) AUC(t) Figure 5 Incremental discriminatory value of the CaRi-Heart
V
R Risk across different follow-up intervals. Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 In panel (A) the orange line reflects the calculated
‘Area under the Curve (AUC)’ (C-statistic) of a model consisting of baseline cardiovascular risk predictors (age, sex, hypertension, hypercholesterolaemia,
diabetes mellitus, and smoking) at 1-year intervals post-CCTA in the American cohort (n = 2040 participants). This is compared to the AUC for the inte-
grated CaRi-Heart
V
R Risk at the same follow-up times (blue line), with the difference of the AUC [D(AUC)] between the two models graphically presented in
panel (B). Panels (C) and (D) present the results of the same analyses in the European cohort (n = 1872 participants). CCTA, coronary computed tomogra-
phy angiography. Dashed lines denote 95% CI, whereas dotted lines denote confidence bands. Across the entire study population, 611 (15.6%) patients were reclas-
sified to a higher risk category and 662 (16.9%) were reclassified to a
lower risk category by using the CaRi-HeartV
R Risk, compared to using a
clinical risk factor-based approach (Figure 4C). The incremental value of
CaRi-Heart
V
R Risk-based approach became evident in both cohorts within
3 years of follow-up after CCTA and persisted throughout the duration
of follow-up (at least until 8 years post-CCTA, Figure 5). In subgroup
analysis, the CaRi-Heart
V
R Risk retained its predictive value across all pop-
ulation subgroups (Figure 6). In a head-to-head comparison, CaRi-Heart
V
R
Risk significantly outperformed the predictive performance of CCS for
cardiac mortality among patients that underwent both non-contrast CT
and CCTA imaging (Supplementary material online, Figure S3). fatal cardiac event at 8 years was 99.3%. The CaRi-Heart
V
R-derived risk
predictions moderately overestimated risk at higher levels of pre-
dicted risk in the model calibration data (Figure 3B). When compared
to a baseline risk model consisting of age, sex, hypertension, hypercho-
lesterolaemia, diabetes mellitus, and smoking, the CaRi-Heart
V
R Risk sig-
nificantly improved risk discrimination [D(C-statistic) of 0.085, P = 0.01
in the US Cohort and 0.149, P < 0.001 in the European cohort] and clas-
sification (as assessed by the continuous NRI, IDI, and median improve-
ment index, Figure 4) in both independent cohorts of the study. Moreover, its incremental prognostic value for prediction of cardiac
mortality at 8 years persisted even after adding the modified Duke CAD
index in the baseline model (Supplementary material online, Figure S2). ................................. 2686 E.K. Oikonomou et al. Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Figure 6 Subgroup analysis for population subgroups. Predictive value of the CaRi-HeartV
R Risk model was retained across all population subgroups. 95% CI, 95% confidence interval; HR, hazard ratio. stratification of the entire study population based on traditional risk factors
forming the core of most cardiovascular risk stratification tools, including
age, sex, hypertension, hypercholesterolaemia, diabetes mellitus, and
smoking. The second CCTA-based approach utilized CaRi-HeartV
R device-
driven stratification. As shown in Figure 7, CaRi-Heart
V
R-based risk stratifi-
cation consistently exhibited a higher net clinical benefit across a range of
threshold probabilities, therefore maximizing the identification of true pos-
itives and negatives in our population to assist with improved targeting of
any preventive strategies that may be indicated. Figure 7 Decision curve analysis of CaRi-Heart
V
R Risk compared to a
clinical prediction model. Use of the integrated CaRi-Heart
V
R Risk is
associated with consistently higher net benefit compared to a baseline
risk model consisting of traditional cardiovascular risk factors (age, sex,
hypertension, hypercholesterolaemia, diabetes mellitus, and smoking)
across a wide range (1–10%) of cardiac mortality risk probabilities (at
t = 8 years). Provided as a reference, the dotted line reflects the net
benefit of ‘treating’ all individuals, whereas the continuous black line
reflects the net benefit of treating no patients (equal to zero). 4. Discussion We validate the performance of a new medical device, CaRi-Heart
V
R, that
calculates a standardized metric of each coronary artery (FAI-Score, cor-
rected for technical and anatomical factors as well as age and gender)
and integrates these readings into a prognostic model for prediction of
future fatal cardiac events, considering a patient’s atherosclerotic plaque
burden and as well as clinical cardiovascular risk profile. FAI-Score for
each coronary artery has significant prognostic value for 8-year cardiac
mortality, providing a more standardized metric of coronary inflamma-
tion than FAI as previously described.2,20 The use of this metric of coro-
nary inflammation, in combination with a patient’s atherosclerotic plaque
burden and clinical cardiovascular risk profile may provide a superior
method to define a personalized risk for fatal cardiac events compared
to clinical risk factors-based models, contributing to improved patient
risk reclassification. Figure 7 Decision curve analysis of CaRi-Heart
V
R Risk compared to a
clinical prediction model. Use of the integrated CaRi-Heart
V
R Risk is
associated with consistently higher net benefit compared to a baseline
risk model consisting of traditional cardiovascular risk factors (age, sex,
hypertension, hypercholesterolaemia, diabetes mellitus, and smoking)
across a wide range (1–10%) of cardiac mortality risk probabilities (at
t = 8 years). Provided as a reference, the dotted line reflects the net
benefit of ‘treating’ all individuals, whereas the continuous black line
reflects the net benefit of treating no patients (equal to zero). Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Coronary calcium score
n/a
≥300
<300
1872
457
262
1153
465
1407
467
1405
1178
694
985
887
1.05 (1.03, 1.06)
1.03 (1.02, 1.05)
1.04 (1.02, 1.07)
1.06 (1.03, 1.09)
1.05 (1.02, 1.08)
1.05 (1.03, 1.06)
1.03 (1.01, 1.05)
1.07 (1.04, 1.09)
1.04 (1.03, 1.06)
1.05 (1.03, 1.07)
1.04 (1.02, 1.05)
1.07 (1.04, 1.11)
1
High risk plaque features
Obstructive CAD
Sex
Age (years)
Subgroup
Overall
Yes
No
Yes
No
Male
Female
≥60
<60
No pts. 2040
458
1582
286
1754
1126
914
573
1467
HR (95% CI)
1.06 (1.04, 1.08)
1.05 (1.03, 1.08)
1.06 (1.04, 1.08)
1.04 (1.02, 1.06)
1.08 (1.05, 1.10)
1.06 (1.04, 1.08)
1.05 (1.03, 1.08)
1.05 (1.03, 1.06)
1.08 (1.04, 1.12)
HR for cardiac death per unit increase in CaRi-Heart® Risk
1
US Cohort
European Cohort
No pts. HR (95% CI)
0.9
1.1
n/a
1.2
1.1
Figure 6 Subgroup analysis for population subgroups. Predictive value of the CaRi-HeartV
R Risk model was retained across all population subgroup
95% CI, 95% confidence interval; HR, hazard ratio. Coronary calcium score
n/a
≥300
<300
1872
457
262
1153
465
1407
467
1405
1178
694
985
887
1.05 (1.03, 1.06)
1.03 (1.02, 1.05)
1.04 (1.02, 1.07)
1.06 (1.03, 1.09)
1.05 (1.02, 1.08)
1.05 (1.03, 1.06)
1.03 (1.01, 1.05)
1.07 (1.04, 1.09)
1.04 (1.03, 1.06)
1.05 (1.03, 1.07)
1.04 (1.02, 1.05)
1.07 (1.04, 1.11)
1
High risk plaque features
Obstructive CAD
Sex
Age (years)
Subgroup
Overall
Yes
No
Yes
No
Male
Female
≥60
<60
No pts. 2040
458
1582
286
1754
1126
914
573
1467
HR (95% CI)
1.06 (1.04, 1.08)
1.05 (1.03, 1.08)
1.06 (1.04, 1.08)
1.04 (1.02, 1.06)
1.08 (1.05, 1.10)
1.06 (1.04, 1.08)
1.05 (1.03, 1.08)
1.05 (1.03, 1.06)
1.08 (1.04, 1.12)
HR for cardiac death per unit increase in CaRi-Heart® Risk
1
US Cohort
European Cohort
No pts. HR (95% CI)
0.9
1.1
n/a
1.2
1.1
Figure 6 Subgroup analysis for population subgroups. Predictive value of the CaRi-HeartV
R Risk model was retained across all population subgroup
95% CI, 95% confidence interval; HR, hazard ratio. 3.3 Net clinical benefit of the CaRi-HeartV
R
i k In the presence of arterial inflammation, cytokines and other mediators
produced in the vascular wall by infiltrating inflammatory and other residing
cells are released locally and block adipocyte differentiation in the adjacent
PVAT, while stimulating lipolysis and impairing adipogenesis. This results in a Given the limitation of traditional statistical metrics, such as calibration and
discrimination, in assessing clinical value and decision analytic approaches,
we performed a decision curve analysis of two alternative methods of risk
stratifying individuals at risk of CAD. The first approach relied on risk Quantification of coronary inflammation by CT 2687 CCTA
Clinical factors
Arficial Intelligence powered -
Integrated cloud device
Internaonal datasets for re-
calibraon and re-training of
algorithms
Risk predicon algorithms
+
Demographics
Clinical risk factors
AI-powered segmentaon/analysis
Plaque analysis
Perivascular Fat Aenuaon Index
Fat Aenuaon Index maps
Harmonised FAI-Score & nomograms
Paent’s absolute risk for fatal cardiac events
Plaque analysis
Clinical decision making
RCA
LCX
LAD
Figure 8 The CaRi-HeartV
R platform. CaRi-HeartV
R is an automated cloud-based medical device that has been trained through deep learning to automate
the segmentation of heart structures, identify the PVAT, calculate the FAI and integrate its value with scan technical details and patient demographics to
provide metrics of atherosclerotic/inflammatory effects around each coronary vessel (FAI-Score), as well as an integrated cardiac risk stratification tool
(CaRi-HeartV
R Risk). Internaonal datasets for re-
calibraon and re-training of
algorithms Downloaded from https://academic.oup.com/cardiovascres/article/117/13/2677/6358671 by University College London user on 20 December 2021 Figure 8 The CaRi-HeartV
R platform. CaRi-HeartV
R is an automated cloud-based medical device that has been trained through deep learning to automate
the segmentation of heart structures, identify the PVAT, calculate the FAI and integrate its value with scan technical details and patient demographics to
provide metrics of atherosclerotic/inflammatory effects around each coronary vessel (FAI-Score), as well as an integrated cardiac risk stratification tool
(CaRi-HeartV
R Risk). Clinically-Indicated CCTA
Minor CAD
No CAD
Obstrucve CAD
≥ 5% and < 10%
< 5%
Absolute Risk
< 75th cenle for LAD or RCA
OR
< 95th cenle for LCX
75th -89th cenle for LAD or RCA
OR
≥95th cenle for LCX
≥ 10%
CaRi-Heart® Risk*
* 8-year risk of cardiac death : incorporates personalised FAI-Score with clinical risk factors, demographics, and plaque burden
Management based
on Current Clinical
Guidelines
Inflammaon-guided
management
(using FAI-Score)
Consider addional treatments
(e.g. 3.3 Net clinical benefit of the CaRi-HeartV
R
i k On CT imag-
ing, this shift can be detected as spatial changes in PVAT attenuation from
lower (closer to -190 HU) to higher (closer to -30 HU) attenuation values. Pericoronary FAI mapping applies this concept around standardized coro-
nary segments on CCTA, where it calculates weighted attenuation changes
linked to the inflammatory status of the adjacent vessel wall.2 European cohort. Indeed, CaRi-HeartV
R Risk reclassifies 16% of the sub-
jects undergoing CCTA to a higher risk category, and 17% to lower
risk category compared to a clinical risk factor-based model, when ap-
plied in the European cohort i.e. nearly a third of the total population. Our analysis also shows that, for both low and high-risk individuals, CaRi-
Heart-guided risk stratification consistently provides a higher level of net
clinical benefit (compared to standard clinical risk models) across a range
of thresholds probabilities for clinical decision making (Figure 8). Following its initial description, several clinical studies have explored
the diagnostic and prognostic implications of FAI mapping. The first and
largest of these studies (CRISP-CT study) showed that higher pericoro-
nary FAI values (reflective of a higher inflammatory/atherosclerotic bur-
den) were associated with a higher incidence of cardiac-specific adverse
outcomes as well as all-cause mortality among patients undergoing
CCTA in two large centres in Europe and the USA.9 Statistical analyses
revealed that the residual risk detected through FAI mapping was not ad-
equately explained by age, sex, traditional risk factors, coronary calcium,
high-risk plaque features, or the extent of coronary atherosclerosis on
CCTA. This highlighted how FAI provided an effective way to extract
meaningful prognostic information from a common non-invasive imaging
modality already performed as part of routine clinical care, at no in-
creased cost or radiation exposure. Subsequent studies have shown that
pericoronary fat attenuation is closely linked to coronary inflammation
and microcalcification as measured by 18F-NaF uptake on PET-CT,10
predicts the progression of coronary atherosclerosis,21 can track the
presence of culprit lesions among patients presenting with acute
myocardial infarction,22,23 stratifies the cardiac risk associated with a
high-risk plaque phenotype,24 and is modifiable through targeted
anti-inflammatory treatments.25,26 Further to the calculation of the individualized absolute risk for cardiac
mortality as a means to guide deployment of appropriate cardiovascular
risk reduction strategies, FAI-Score provides a standalone, standardized
metric of coronary inflammation. 3.3 Net clinical benefit of the CaRi-HeartV
R
i k This information may be particularly
useful in select patient groups, such as young individuals with evidence of
inflammation but no other traditional risk factors, who despite being at
low absolute risk are nonetheless at high relative risk compared to indi-
viduals of similar age and sex. In such patients, the decision to initiate
therapy may be driven by the presence of a strong biological risk factor,
such as elevated LDL cholesterol levels in young patients with familial
hypercholesterolaemia, independent of the absolute risk score calculated
through standard tools (Figure 9). Newer prospectively designed cohorts
within the ORFAN study are also underway to further examine the value
of CaRi-HeartV
R in more ethnically diverse cohorts and when added to
quantitative circulating biomarkers. ................................................................................................... -
e
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s
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t
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-
t
-
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-
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-
c Supplementary material Supplementary material is available at Cardiovascular Research online. A new medical device, CaRi-HeartV
R, now calculates the adjusted
FAI-Score for each coronary artery, projected in nomograms according to
age. Indeed, the percentile curves provided in this study may be used in in-
dependent studies to harmonize the reporting of pericoronary FAI map-
ping across different patient and investigator groups. We now validate FAI-
Score, and we demonstrate a strong prognostic value for cardiac mortality. Unlike FAI (which was previously shown to lose its prognostic value when
measured around the LCX),9 FAI-Score around each one of the major
coronary arteries is consistently associated with future cardiac mortality
risk. However, clinical interpretation of FAI-Score can only be undertaken
in a standardized way, and we now provide nomograms to allow interpre-
tation of the results across patients of different ages. 3.3 Net clinical benefit of the CaRi-HeartV
R
i k colchicine)
Lifestyle changes
Start or intensify treatment
(e.g. stans)
≥ 90th cenle
for LAD or RCA
Consider addional treatments
(e.g. colchicine)
Lifestyle changes
Start or intensify treatment
(e.g. stans)
+/- Revascularisaon Clinically-Indicated CCTA * 8-year risk of cardiac death : incorporates personalised FAI-Score with clinical risk factors, demographics, and plaque burden Figure 9 Vision for incorporating FAI-Score into current clinical workflows. Among patients undergoing clinically indicated CCTA CaRi-HeartV
R Risk
provides the individualized absolute risk for cardiac mortality based on the patient’s clinical profile (i.e. demographics and traditional risk factors), CCTA
plaque burden metrics and FAI-Score. The information on absolute risk for cardiac mortality can guide lifestyle and/or pharmacological changes as per clinical
guidelines. FAI-Score provides an additional piece of information which reflects the levels of vascular inflammation, which is considered a new cardiovascular
risk factor, accounting for the residual (inflammatory) cardiovascular risk. For instance, a young individual with no traditional risk factors may be at low abso-
lute risk for a fatal cardiac event; however, a high FAI-Score may indicate increased relative risk for cardiac events in the long-term as a result of subclinical
vascular inflammation. Hence, age- and sex-adjusted cut-offs in FAI-Score centiles may be used to guide interventions to lower vascular inflammation. Figure 9 Vision for incorporating FAI-Score into current clinical workflows. Among patients undergoing clinically indicated CCTA CaRi-HeartV
R Risk
provides the individualized absolute risk for cardiac mortality based on the patient’s clinical profile (i.e. demographics and traditional risk factors), CCTA
plaque burden metrics and FAI-Score. The information on absolute risk for cardiac mortality can guide lifestyle and/or pharmacological changes as per clinical
guidelines. FAI-Score provides an additional piece of information which reflects the levels of vascular inflammation, which is considered a new cardiovascular
risk factor, accounting for the residual (inflammatory) cardiovascular risk. For instance, a young individual with no traditional risk factors may be at low abso-
lute risk for a fatal cardiac event; however, a high FAI-Score may indicate increased relative risk for cardiac events in the long-term as a result of subclinical
vascular inflammation. Hence, age- and sex-adjusted cut-offs in FAI-Score centiles may be used to guide interventions to lower vascular inflammation. 2688 E.K. Oikonomou et al. phenotypic shift in the adipose tissue composition, from a greater to a lesser
lipophilic content and therefore a higher aqueous/lipid ratio. 5. Conclusion CaRi-Heart
V
R, a novel CCTA-based risk stratification medical device, inte-
grates the recently described FAI mapping with traditional cardiovascular
risk factors and multi-dimensional, comprehensive CCTA coronary pla-
que analysis. The prognostic output produced by CaRi-Heart
V
R demon-
strates significant net clinical benefit in two large and independent CCTA
populations over and above traditional cardiovascular risk factors. Integration of CaRi-HeartV
R analyses into current clinical pathways has
the potential to advance the prognostic utility of CCTA analysis in the in-
vestigation and management of CAD risk. As the use and application of pericoronary fat mapping continues to
expand, there is an urgent need to standardize its reporting, while ac-
knowledging potentially important confounders. While the process of
perivascular fat attenuation analysis can be easily done by different oper-
ators and platforms (with consistent prognostic value across different
age, sex, and race groups)9,27,28 the interpretation of a given PVAT at-
tenuation value ultimately relies on the patient’s age, sex, cardiometa-
bolic status, and technical variables related with the actual scan
aquisition.1,29 While the CRISP-CT study proposed a cut-off of -70.1
HU as a critical threshold to identify high-risk individuals,9 generalization
of this cut-off may be limited by the fact that this has not been adjusted
for the above-mentioned factors in other independent studies. References 1. Antoniades C, Antonopoulos AS, Deanfield J. Imaging residual inflammatory cardio-
vascular risk. Eur Heart J 2020;41:748–758. 1. Antoniades C, Antonopoulos AS, Deanfield J. Imaging residual inflammatory cardio-
vascular risk. Eur Heart J 2020;41:748–758. 19. Vickers AJ, Elkin EB. Decision curve analysis: a novel method for evaluating prediction
models. Med Decis Making 2006;26:565–574. 2. Antonopoulos AS, Sanna F, Sabharwal N, Thomas S, Oikonomou EK, Herdman L,
Margaritis M, Shirodaria C, Kampoli AM, Akoumianakis I, Petrou M, Sayeed R,
Krasopoulos G, Psarros C, Ciccone P, Brophy CM, Digby J, Kelion A, Uberoi R,
Anthony S, Alexopoulos N, Tousoulis D, Achenbach S, Neubauer S, Channon KM,
Antoniades C. Detecting human coronary inflammation by imaging perivascular fat. Sci Transl Med 2017;9:eaal2658. 2. Antonopoulos AS, Sanna F, Sabharwal N, Thomas S, Oikonomou EK, Herdman L,
Margaritis M, Shirodaria C, Kampoli AM, Akoumianakis I, Petrou M, Sayeed R,
Krasopoulos G, Psarros C, Ciccone P, Brophy CM, Digby J, Kelion A, Uberoi R,
Anthony S, Alexopoulos N, Tousoulis D, Achenbach S, Neubauer S, Channon KM,
Antoniades C. Detecting human coronary inflammation by imaging perivascular fat. Sci Transl Med 2017;9:eaal2658. 20. Oikonomou EK, Antoniades C. The role of adipose tissue in cardiovascular health
and disease. Nat Rev Cardiol 2019;16:83–99. 21. Goeller M, Tamarappoo BK, Kwan AC, Cadet S, Commandeur F, Razipour A, Slomka PJ, 21. Goeller M, Tamarappoo BK, Kwan AC, Cadet S, Commandeur F, Razipour A, Slomka PJ,
Gransar H, Chen X, Otaki Y, Friedman JD, Cao JJ, Albrecht MH, Bittner DO, Marwan M,
Achenbach S, Berman DS, Dey D. Relationship between changes in pericoronary adipose
tissue attenuation and coronary plaque burden quantified from coronary computed to-
mography angiography. Eur Heart J Cardiovasc Imaging 2019;20:636–643. cle/117/13/26 Antoniades C. Detecting human coronary inflammation by imaging perivascular fat. Sci Transl Med 2017;9:eaal2658. 3. National Institute for Health and Care Excellence (NICE). Chest Pain of Recent
Onset: Assessment and diagnosis. Clinical guideline [CG95], 2016. 3. National Institute for Health and Care Excellence (NICE). Chest Pain of Recent
Onset: Assessment and diagnosis. Clinical guideline [CG95], 2016. 4. Moss AJ, Williams MC, Newby DE, Nicol ED. The updated NICE guidelines: cardiac
CT as the first-line test for coronary artery disease. Curr Cardiovasc Imaging Rep 2017;10:
15. 22. Goeller M, Achenbach S, Cadet S, Kwan AC, Commandeur F, Slomka PJ, Gransar H,
Albrecht MH, Tamarappoo BK, Berman DS, Marwan M, Dey D. References Pericoronary adipose
tissue computed tomography attenuation and high-risk plaque characteristics in acute
coronary syndrome compared with stable coronary artery disease. JAMA Cardiol
2018;3:858–863. 677/6358671 5. Knuuti J, Wijns W, Saraste A, Capodanno D, Barbato E, Funck-Brentano C, Prescott
E, Storey RF, Deaton C, Cuisset T, Agewall S, Dickstein K, Edvardsen T, Escaned J,
Gersh BJ, Svitil P, Gilard M, Hasdai D, Hatala R, Mahfoud F, Masip J, Muneretto C,
Valgimigli M, Achenbach S, Bax JJ, Group ESCSD. 2019 ESC Guidelines for the diag-
nosis and management of chronic coronary syndromes. Eur Heart J 2019;41:407–477. 23. Oikonomou EK, Williams MC, Kotanidis CP, Desai MY, Marwan M, Antonopoulos
AS, Thomas KE, Thomas S, Akoumianakis I, Fan LM, Kesavan S, Herdman L, Alashi A,
Centeno EH, Lyasheva M, Griffin BP, Flamm SD, Shirodaria C, Sabharwal N, Kelion A,
Dweck MR, Van Beek EJR, Deanfield J, Hopewell JC, Neubauer S, Channon KM,
Achenbach S, Newby DE, Antoniades C. A novel machine learning-derived radiotran-
scriptomic signature of perivascular fat improves cardiac risk prediction using coro-
nary CT angiography. Eur Heart J 2019;40:3529–3543. by University Colle 6. Bergstrom G, Berglund G, Blomberg A, Brandberg J, Engstrom G, Engvall J, Eriksson M,
de Faire U, Flinck A, Hansson MG, Hedblad B, Hjelmgren O, Janson C, Jernberg T,
Johnsson A, Johansson L, Lind L, Lofdahl CG, Melander O, Ostgren CJ, Persson A,
Persson M, Sandstrom A, Schmidt C, Soderberg S, Sundstrom J, Toren K, Waldenstrom
A, Wedel H, Vikgren J, Fagerberg B, Rosengren A. The Swedish CArdioPulmonary
BioImage Study: objectives and design. J Intern Med 2015;278:645–659. 24. Oikonomou EK, Desai MY, Marwan M, Kotanidis CP, Antonopoulos AS, Schottlander
D, Channon KM, Neubauer S, Achenbach S, Antoniades C. Perivascular fat attenua-
tion index stratifies cardiac risk associated with high-risk plaques in the CRISP-CT
study. J Am Coll Cardiol 2020;76:755–757. ege Londo 7. Scot-Heart investigators. CT coronary angiography in patients with suspected angina
due to coronary heart disease (SCOT-HEART): an open-label, parallel-group, multi-
centre trial. Lancet 2015;385:2383–2391. 25. Elnabawi YA, Oikonomou EK, Dey AK, Mancio J, Rodante JA, Aksentijevich M, Choi
H, Keel A, Erb-Alvarez J, Teague HL, Joshi AA, Playford MP, Lockshin B, Choi AD,
Gelfand JM, Chen MY, Bluemke DA, Shirodaria C, Antoniades C, Mehta NN. Association of biologic therapy with coronary inflammation in patients with psoriasis
as assessed by perivascular fat attenuation index. JAMA Cardiol 2019;4:885–891. n user on 20 8. References Newby DE, Adamson PD, Berry C, Boon NA, Dweck MR, Flather M, Forbes J,
Hunter A, Lewis S, MacLean S, Mills NL, Norrie J, Roditi G, Shah ASV, Timmis AD,
van Beek EJR, Williams MC, Scot-Heart Investigators. Coronary CT angiography and
5-year risk of myocardial infarction. N Engl J Med 2018;379:924–933. 9. Oikonomou EK, Marwan M, Desai MY, Mancio J, Alashi A, Hutt Centeno E, Thomas
S, Herdman L, Kotanidis CP, Thomas KE, Griffin BP, Flamm SD, Antonopoulos AS,
Shirodaria C, Sabharwal N, Deanfield J, Neubauer S, Hopewell JC, Channon KM,
Achenbach S, Antoniades C. Non-invasive detection of coronary inflammation using
computed tomography and prediction of residual cardiovascular risk (the CRISP CT
study): a post-hoc analysis of prospective outcome data. Lancet 2018;392:929–939. 26. Dai X, Yu L, Lu Z, Shen C, Tao X, Zhang J. Serial change of perivascular fat attenua-
tion index after statin treatment: insights from a coronary CT angiography follow-up
study. Int J Cardiol 2020;319:144–149. Decemb 27. Tzolos E, McElhinney P, Williams MC, Cadet S, Dweck MR, Berman DS, Slomka PJ,
Newby DE, Dey D. Repeatability of quantitative pericoronary adipose tissue attenua-
tion and coronary plaque burden from coronary CT angiography. J Cardiovasc Comput
Tomogr 2021;15:81–84. ber 2021 10. Kwiecinski J, Dey D, Cadet S, Lee SE, Otaki Y, Huynh PT, Doris MK, Eisenberg E, Yun
M, Jansen MA, Williams MC, Tamarappoo BK, Friedman JD, Dweck MR, Newby DE,
Chang HJ, Slomka PJ, Berman DS. Peri-coronary adipose tissue density is associated
with (18)F-sodium fluoride coronary uptake in stable patients with high-risk plaques. JACC Cardiovasc Imaging 2019;12:2000–2010. 28. Goeller M, Rahman Ihdayhid A, Cadet S, Lin A, Adams D, Thakur U, Yap G, Marwan
M, Achenbach S, Dey D, Ko B. Pericoronary adipose tissue and quantitative global
non-calcified plaque characteristics from CT angiography do not differ in matched
South Asian, East Asian and European-origin Caucasian patients with stable chest
pain. Eur J Radiol 2020;125:108874. 11. Antoniades C, Shirodaria C. Detecting coronary inflammation with perivascular fat at-
tenuation imaging: making sense from perivascular attenuation maps. JACC Cardiovasc
Imaging 2019;12:2011–2014. 29. Ma R, Ties D, van Assen M, Pelgrim GJ, Sidorenkov G, van Ooijen PMA, van der
Harst P, van Dijk R, Vliegenthart R. Towards reference values of pericoronary adi-
pose tissue attenuation: impact of coronary artery and tube voltage in coronary com-
puted tomography angiography. Eur Radiol 2020;30:6838–6846. 12. Funding Endorsed Lipid Lowering with EBT Scanning). J Am Coll Cardiol 2013;61:1956–1961. 15. Cury RC, Abbara S, Achenbach S, Agatston A, Berman DS, Budoff MJ, Dill KE, Jacobs 15. Cury RC, Abbara S, Achenbach S, Agatston A, Berman DS, Budoff MJ, Dill KE, Jacobs
JE, Maroules CD, Rubin GD, Rybicki FJ, Schoepf UJ, Shaw LJ, Stillman AE, White CS,
Woodard PK, Leipsic JA. CAD-RADS(TM) Coronary Artery Disease - Reporting and
Data System. An expert consensus document of the Society of Cardiovascular
Computed Tomography (SCCT), the American College of Radiology (ACR) and the
North American Society for Cardiovascular Imaging (NASCI). Endorsed by the
American College of Cardiology. J Cardiovasc Comput Tomogr 2016;10:269–281. This work was supported by the British Heart Foundation (FS/16/15/
32047, TG/16/3/32687, TG/19/2/34831 and RG/F/21/110040 to CA),
the National Institute for Health Research Oxford Biomedical Research
Centre (Oxford, United Kingdom) and Innovate UK. M.Y.D. is supported
by the Haslam Family endowed chair in cardiovascular medicine. Portions of this research were funded by a generous philanthropic gift by
the Holekamp family. The study was supported by Caristo Diagnostics,
who has provided the CaRi-HeartV
R analyses. Data System. An expert consensus document of the Society of Cardiovascular North American Society for Cardiovascular Imaging (NASCI). Endorsed by the
American College of Cardiology. J Cardiovasc Comput Tomogr 2016;10:269–281. 16. Cutlip DE, Windecker S, Mehran R, Boam A, Cohen DJ, van Es GA, Steg PG, Morel
MA, Mauri L, Vranckx P, McFadden E, Lansky A, Hamon M, Krucoff MW, Serruys
PW, Academic Research Consortium. Clinical end points in coronary stent trials: a
case for standardized definitions. Circulation 2007;115:2344–2351. case for standardized definitions. Circulation 2007;115:2344–2351. 17. Hicks KA, Tcheng JE, Bozkurt B, Chaitman BR, Cutlip DE, Farb A, Fonarow GC,
Jacobs JP, Jaff MR, Lichtman JH, Limacher MC, Mahaffey KW, Mehran R, Nissen SE,
Smith EE, Targum SL. 2014 ACC/AHA Key Data Elements and Definitions for
Cardiovascular Endpoint Events in Clinical Trials: a Report of the American College
of Cardiology/American Heart Association Task Force on Clinical Data Standards
(Writing Committee to Develop Cardiovascular Endpoints Data Standards). J Am Coll
Cardiol 2015;66:403–469. p Data availability Supporting data for this manuscript will be made available by the corre-
sponding author upon reasonable request. 18. Min JK, Shaw LJ, Devereux RB, Okin PM, Weinsaft JW, Russo DJ, Lippolis NJ, Berman
DS, Callister TQ. Prognostic value of multidetector coronary computed tomographic an-
giography for prediction of all-cause mortality. J Am Coll Cardiol 2007;50:1161–1170. Authors’ contributions Effect of intensive versus moderate lipid-lowering therapy on epicardial adipose tissue
in hyperlipidemic post-menopausal women: a substudy of the BELLES trial (Beyond Authors’ contributions E.K.O and A.S.A. contributed to the study design, image/data analysis, sta-
tistical analysis, and writing of the manuscript; D.S. contributed to the sta-
tistical analysis. L.V.K. contributed to image analysis. C.S, S.N., K.M.C.,
M.Y.D., S.A., and J.D. provided scientific direction and contributed to writ-
ing the manuscript; M.M., S.A., and M.Y.D. co-ordinated the collection of
clinical data and CT scans; M.S., P.T., and C.M. coordinated the technical
development of the CaRi-Heart Medical Device; C.A designed the study,
raised the funding for image and data analysis, coordinated and directed
the project, supervised the image analysis and wrote the manuscript. Furthermore, integrating the above information into a prognostic
model that also accounts for a patient’s demographics, risk factors, and
atherosclerotic plaque burden, would provide a meaningful clinical tool
to guide deployment of primary or secondary prevention treatments. CaRi-Heart
V
R provides the CaRi-Heart
V
R Risk, which is the patient’s
8-years individualized risk for a fatal cardiac event. The algorithm was
originally trained in the American cohort and then validated in the Conflict of interest: The methods for analysis of the perivascular
FAI described in this report are subject to patent PCT/GB2015/052359
and patent applications PCT/GB2017/053262, GB2018/1818049.7,
GR20180100490, and GR20180100510, licenced through exclusive li-
cence to Caristo Diagnostics. C.A., K.M.C, C.S. and S.N. are founders,
shareholders, and directors of Caristo Diagnostics, a CT image analysis 2689 Quantification of coronary inflammation by CT company. J.D. and E.K.O. are shareholders and consultants at Caristo
Diagnostics. A.S.A declares consultancy with Caristo Diagnostics. J.D. and M.Y.D. are members of the advisory board of Caristo Diagnostics. C.S., P.T., M.S., C.M., and D.S. are employees of Caristo Diagnostics. The
remaining authors have nothing to disclose. Estimation of ten-year risk of fatal cardiovascular disease in Europe: the SCORE proj-
ect. Eur Heart J 2003;24:987–1003. ect. Eur Heart J 2003;24:987–1003. 13. Greenland P, LaBree L, Azen SP, Doherty TM, Detrano RC. Coronary artery calcium
score combined with Framingham score for risk prediction in asymptomatic individu-
als. JAMA 2004;291:210–215. 14. Alexopoulos N, Melek BH, Arepalli CD, Hartlage GR, Chen Z, Kim S, Stillman AE, Raggi
P. Effect of intensive versus moderate lipid-lowering therapy on epicardial adipose tissue
in hyperlipidemic post-menopausal women: a substudy of the BELLES trial (Beyond
Endorsed Lipid Lowering with EBT Scanning). J Am Coll Cardiol 2013;61:1956–1961. P. References Conroy RM, Pyorala K, Fitzgerald AP, Sans S, Menotti A, De BG, De BD,
Ducimetiere P, Jousilahti P, Keil U, Njolstad I, Oganov RG, Thomsen T, Tunstall PH,
Tverdal A, Wedel H, Whincup P, Wilhelmsen L, Graham IM, SCORE project group.
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English
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A ranking framework based on interval self and cross-efficiencies in a two-stage DEA system
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A RANKING FRAMEWORK BASED ON INTERVAL SELF AND
CROSS-EFFICIENCIES IN A TWO-STAGE DEA SYSTEM os Dominikos Kremantzis1,* , Patrick Beullens2 and Jonathan s Kremantzis1,* , Patrick Beullens2 and Jonathan Klein3 Marios Dominikos Kremantzis1,* , Patrick Beullens2 an Abstract. The evaluation of the performance of a decision-making unit (DMU) can be measured by
its own optimistic and pessimistic multipliers, leading to an interval self-efficiency score. While this
concept has been thoroughly studied with regard to single-stage systems, there is still a gap when it
is extended to two-stage tandem structures, which better correspond to a real-world scenario. In this
paper, we argue that in this context, a meaningful ranking of the DMUs is obtained; this outcome
simultaneously considers the optimistic and pessimistic viewpoints within the self-appraisal context,
and the most favourable and unfavourable weight sets of each of the other DMUs in a peer-appraisal
setting. We initially extend the optimistic-pessimistic Data Envelopment Analysis (DEA) models to
the specifications of such a two-stage structure. The two opposing self-efficiency measures are merged
to a combined self-efficiency measure via the geometric average. Under this framework, the DMUs
are further evaluated in a peer setting via the interval cross-efficiency (CE). This methodological tool
is applied to evaluate the target DMU in relation to the most favourable and unfavourable weight
profiles of each of the other DMUs, while maintaining the combined self-efficiency measure. We, thus,
determine an interval individual CE score for each DMU and flow. By treating the interval CE matrix
as a multi-criteria decision making problem and by utilising several well-established approaches from
the literature, we delineate its remaining elements; we show how these lead us to a meaningful ultimate
ranking of the DMUs. A numerical example about the efficiency evaluation of ten bank branches in
China illustrates the applicability of our modelling approaches. Mathematics Subject Classification. 90B10, 90C05, 90C90, 91B06. Mathematics Subject Classification. 90B10, 90C05, 90C90, 91B06. Received July 1, 2021. Accepted April 20, 2022. RAIRO Operations Research
www.rairo-ro.org RAIRO Operations Research
www.rairo-ro.org RAIRO-Oper. Res. 56 (2022) 1293–1319
https://doi.org/10.1051/ro/2022056 RAIRO-Oper. Res. 56 (2022) 1293–1319
https://doi.org/10.1051/ro/2022056 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. eywords. Data envelopment analysis, network, interval self-efficiency, interval cross-efficiency, ranking. 1 School of Management, University of Bristol, Bristol, UK. 3 Southampton Business School and CORMSIS, University of Southampton, Southampton, UK.
*C
di
h Mathematical Sciences, Southampton Business School and CORMSIS, University of Southampton, Sou uthampton Business School and CORMSIS, University of Southampton, Southampton, UK.
responding author: marios.kremantzis@bristol.ac.uk *Corresponding author: marios.kremantzis@bristol.ac.uk *Corresponding author: marios.kremantzis@bristol.ac.uk Received July 1, 2021. Accepted April 20, 2022. uthampton Business School and CORMSIS, University of Southampton, Southampton, UK.
responding author: marios.kremantzis@bristol.ac.uk 1. Introduction Data Envelopment Analysis (DEA) is a benchmarking technique for comparing the relative efficiency of a
Decision Making Unit (DMU) with the best observed efficiency [7]. The evaluation of a DMU is based on the
comparison between the amount of input(s) consumed and the amount of output(s) produced [8] by DMUs. One of the undeniably attractive features of DEA is its weight flexibility. This allows each DMU to be allocated
its most favourable set of weights to be assigned to inputs and outputs for determining its relative efficiency. *Corresponding author: marios.kremantzis@bristol.ac.uk c○The authors. Published by EDP Sciences, ROADEF, SMAI 2022 c○The authors. Published by EDP Sciences, ROADEF, SMAI 2022 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1294 M.D. KREMANTZIS ET AL. Hence, in the conventional DEA, the overall assessment of a DMU is based on the optimistic viewpoint and
on the concept of the efficiency frontier [56]. On the other hand, if the performance of a DMU is based on the
pessimistic viewpoint, then an inefficiency frontier is defined. Hence, in the conventional DEA, the overall assessment of a DMU is based on the optimistic viewpoint and
on the concept of the efficiency frontier [56]. On the other hand, if the performance of a DMU is based on the
pessimistic viewpoint, then an inefficiency frontier is defined. Optimistic and pessimistic perspectives illustrate two extreme cases for each DMU. Taking only one scenario
into account limits the examination of the performance of a unit. The obtained results might be unreasonable
[3]. Therefore, it is thought to be valuable to consider the two distinctive efficiencies together. [ ]
Research on exploring both aspects of viewing the efficiency of a DMU within a single-stage structure is
relatively extensive. Wang and Luo [48] evaluated each DMU in terms of the optimistic and pessimistic viewpoint,
by introducing an input-oriented virtual Ideal DMU (IDMU) and an output-oriented virtual Anti-ideal DMU
(ADMU). The two separate efficiencies were combined into the Relative Closeness (RC) index to obtain a
unique ranking order. Wu [51] identified a weakness in Wang and Luo’s [48] paper dealing with the ADMU for
DEA modelling. Wu argued that it is inconsistent to aggregate an input-oriented IDMU and an output-oriented
ADMU into the RC index. 1. Introduction Wang and Yang [49] proposed an alternative way of measuring the performance of DMUs. The efficiencies of
DMUs are measured within the range of an interval, in which the upper bound is 1 and the lower bound equals to
the performance of a virtual ADMU, which is the worst among all DMUs. This approach, which only considers
the performance of the lower bound, was extended by Azizi and Jahed [4], who suggested a pair of improved
bounded models for the target DMU. Wang et al. [50] combined optimistic and pessimistic efficiencies into a
geometric average efficiency to measure the overall performance of a DMU. The geometric average efficiency
was deemed effective, as it was simultaneously an efficiency measure and a ranking index. Toloo and Tichy [45]
proposed a multiplier model to identify the maximum efficiency scores and applied the envelopment model to
attain the maximum discrimination among efficient DMUs . Khodabakhshi and Aryavash [23] used a double
frontier DEA procedure to introduce a new cross-efficiency method; the merit of their approach lied on the non-
use of any alternative secondary goal. Based on the ideal and anti-ideal DMUs, Liu and Wang [29] developed
the normalised efficiency metric and then formulated two DEA models to obtain its lower and upper bounds. ¨Orkc¨u et al. [35] proposed a non-cooperative game like iterative optimistic-pessimistic DEA approach to fully
rank the DMUs. Badiezadeh et al. [5] were, to our knowledge, the first to conceive the idea of considering
optimistic-pessimistic DEA models under a network DEA context to evaluate the performance of a sustainable
supply-chain management. With the exception of Badiezadeh et al. [5], the majority of the existing studies on the double frontier DEA
models are concerned with a system handled as a whole unit, ignoring its internal structure. Several studies
illustrate that this condition might produce misleading results [22]. In reality, systems can be composed of
two sub-stages operating interdependently. In this paper, we will extend our selected optimistic-pessimistic
ranking procedure to a two-stage tandem system to not only measure the efficiency of the overall system and
its individual stages’ efficiencies; thus, the stage that causes inefficiencies can be identified. The optimistic and pessimistic self-efficiency scores can be unified via the geometric average efficiency. As
shown in Wang et al. [50], this score has a better discriminating power than either of the opposing efficiencies. 1. Introduction The aggressive and benevolent models of this process were, however, keeping only
the optimistic self-efficiency value of each DMU fixed. In summary, this paper adapts an optimistic-pessimistic DEA approach in the light of the two-stage tandem
system, in order to then support the interval CE method in such a network system. Using the proposed framework
as shown in Figure 1, a meaningful evaluation and ranking of the considered DMUs is attained. Decision makers
will be enabled to simultaneously consider: (i) both the optimistic and the pessimistic viewpoints within the
self-appraisal context, and (ii) the most favourable and unfavourable weight sets of each of the other DMUs in
a peer-appraisal setting. We believe that the combination of the methods that compose our framework has not
been considered before in the literature; in our view, this could lead to a meaningful ranking in addition to it
being adjusted to a two-stage tandem DEA structure. The procedures implemented in the first three steps of our proposed framework (Fig. 1) have been applied
in several studies (e.g., [50]) that focus on double frontier DEA models to evaluate DMUs in a self-appraisal
context in a single-stage structure. As for these steps, our study differs in that our optimistic-pessimistic DEA
models, which are inspired by the studies of Wang and Luo [48] and Wu [51], are built towards the two-stage
tandem (network) system. The remaining steps of the proposed framework pursue to support the peer-evaluation of the considered
DMUs via the customisation of the interval CE method to the specifications of the two-stage tandem structure
while embedding the respective combined self-efficiency measure (that considers the effects of both opposing
standpoints). To rank the DMUs in the interval CE matrix of the corresponding flow, this paper views this
matrix as a multi-criteria decision-making problem. To solve this problem, we implement the goal programming
method of Wang and Elhag [47] to obtain the interval local weight of each criterion. To delineate the interval
global weight of each alternative, we suggest a pair of linear programming models, introduced by Entani and
Tanaka [13]. Finally, we apply the grey relational analysis [25] for ranking the interval global weights. To our
knowledge, the aforementioned well-established approaches have not been previously considered for extracting
valuable information from an interval CE matrix. 1. Introduction Yet, this feature has not been explored in a network environment, implying the possible existence of a non-unique
ranking. It also considers the effects of the optimistic and pessimistic standpoints only within the self-appraisal
context. The integration of the geometric average score in a peer-appraisal context would contribute to the
assessment of a DMU in terms of the weight sets of other players, leading to a more logical ranking. These
points make us infer that this framework could be further extended by the use of the cross-efficiency (CE) to
ensure more fairness in the evaluation outcomes. The CE concept is based on the peer-evaluation notion [42]. As stressed by Anderson et al. [1], CE improves
the probability of obtaining a unique ranking. A shortcoming of the CE is the non-uniqueness of DEA optimal
weights, leading to the non-uniqueness of cross-efficiencies. Remedial actions have been suggested towards the
adoption of secondary goals in an aim to select unique optimal multipliers [10,26–28,52,57]. The non-uniqueness
issue is also critical in a two-stage (network) system [18,22,32–34]. Kao and Liu [22], for instance, developed an
aggressive CE model to measure the efficiency in two basic network structures. ¨Orkc¨u et al. [34] came up with A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 1295 a neutral CE model in a two-stage system, which is indifferent to the preference choice between the aggressive
and benevolent formulations. Doyle and Green [10] introduced an aggressive and a benevolent secondary goal model to remedy the non-
uniqueness of the optimal weights. The former ensures the minimisation and the latter the maximisation of the
cross-efficiencies of all other DMUs, whilst both maintaining the optimistic self-efficiency of the target DMU. The use of any formulation of the two may be subject to an individual judgement, possibly leading to an
irrational selection of either model. There is also no confirmation that these formulations will result in the same
ranking or that their optimal set of multipliers are unique [46]. To alleviate these deficiencies, Yang et al. [53] suggested the “interval CE” for the exploration of the cross-
efficiencies in a weight space considering all the weight profiles, within the single-stage DEA structure. In such a
peer-appraisal setting, the base DMU is assessed regarding the most unfavourable and favourable weight profiles
of each of the other DMUs. 1. Introduction We have also shown that our proposed framework offers
a more informative assessment of the units under consideration than particular existing methods in network
DEA-relevant literature. The remainder of the paper is organised as follows. Section 2 shortly describes the preliminaries and the
methodological background. Section 3 proposes the framework to meaningfully rank DMUs. Section 4 illustrates
the methods with a numerical example. Section 5 presents conclusions and further research. 2. Methodological background We assume that each DMU𝑗(𝑗= 1, 2, . . ., 𝑛) uses 𝑚inputs (𝑖= 1, 2, . . ., 𝑚) to produce 𝑠outputs (𝑟=
1, 2, . . ., 𝑠). Let 𝑋𝑖𝑗be the input value of 𝑖∈𝑀for DMU 𝑗∈𝑁and 𝑌𝑟𝑗be the output value of 𝑟∈𝑆for DMU
𝑗∈𝑁. We estimate the optimistic self-efficiency for each DMU, based on determining an optimal set of the
most favourable input and output weights. The conventional input-oriented CCR DEA model [7], that assesses 1296 M.D. KREMANTZIS ET AL. F
1 Th
d f
k Table 1. Cross-efficiency matrix [10]. Table 1. Cross-efficiency matrix [10]. Target
DMU𝑗
Evaluator DMU𝑘
1
2
. . . 𝑛
1
𝐸11
𝐸12
. . . 𝐸1𝑛
2
𝐸21
𝐸22
. . . 𝐸2𝑛
. . . . . . . . . . . . . . . 𝑛
𝐸𝑛1
𝐸𝑛2
. . . 𝐸𝑛𝑛 Figure 1. The proposed framework. Figure 1. The proposed framework. the efficiency of the target DMU𝑘, is illustrated as follows: the efficiency of the target DMU𝑘, is illustrated as follows: 𝐸𝑘𝑘= Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝜇𝑟𝑘, 𝜈𝑖𝑘≥0,
∀𝑟, 𝑖,
(2.1) 𝐸𝑘𝑘= Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝜇𝑟𝑘, 𝜈𝑖𝑘≥0,
∀𝑟, 𝑖,
(2.1) ∀𝑟, 𝑖,
(2.1) ︁
𝑟
1︁
𝑖
1
𝜇𝑟𝑘, 𝜈𝑖𝑘≥0,
∀𝑟, 𝑖,
(2.1) (2.1) where 𝜇𝑟𝑘, 𝜈𝑖𝑘are the 𝑟th output and the 𝑖th input weights for DMU𝑘, respectively. If the optimal (optimistic)
self-efficiency 𝐸*
𝑘𝑘= 1, then DMU𝑘is called DEA efficient; otherwise it is said to be DEA inefficient. where 𝜇𝑟𝑘, 𝜈𝑖𝑘are the 𝑟th output and the 𝑖th input weights for DMU𝑘, respectively. If the optimal (optimistic)
self-efficiency 𝐸*
𝑘𝑘= 1, then DMU𝑘is called DEA efficient; otherwise it is said to be DEA inefficient. 1297 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Table 2. Interval cross-efficiency matrix [53]. Table 2. Interval cross-efficiency matrix [53]. Target
DMU𝑗
Evaluator DMU𝑘
1
2
. . . 𝑛
1
[𝐸11, 𝐸11]
[︀
𝐸L
12, 𝐸U
12
]︀
. . . [︀
𝐸L
1𝑛, 𝐸U
1𝑛
]︀
2
[︀
𝐸L
21, 𝐸U
21
]︀
[𝐸22, 𝐸22]
. . . [︀
𝐸L
2𝑛, 𝐸U
2𝑛
]︀
. . . . . . . . . . . . . . . 𝑛
[︀
𝐸L
𝑛1, 𝐸U
𝑛1
]︀
[︀
𝐸L
𝑛2, 𝐸U
𝑛2
]︀
. . . [𝐸𝑛𝑛, 𝐸𝑛𝑛] Model (2.3) is a benevolent-based model to obtain an optimal set of weights and thus to determine the maximum
individual cross-efficiency of DMU𝑗based on DMU𝑘. Max
𝐸U
𝑘𝑗=
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗
(2.3) (2.3) ︁
subject to the same constraints as in model (2.2). In the above two models, the optimistic self-efficiency score 𝐸*
𝑘𝑘, derived from model (2.1), remains fixed;
this keeps one of the basic properties of the traditional CE concept intact. Overall, in this peer-evaluation
procedure an interval individual cross-efficiency score of DMU𝑗in terms of DMU𝑘is formed and lies in the
range
[︁
𝐸L
𝑘𝑗, 𝐸U
𝑘𝑗
]︁
. 𝐸L
𝑘𝑗is the lower bound and is found from model (2.2), whereas 𝐸U
𝑘𝑗is the upper bound
obtained from model (2.3). Table 2 depicts the individual cross-efficiencies as interval numbers, boosting the
DM’s uncertainty. The elements in the diagonal column of Table 2 show the special case of the self-efficiency
scores, for which 𝐸𝑘𝑘= 𝐸L
𝑘𝑘= 𝐸U
𝑘𝑘, ∀𝑘∈{1, 2, . . ., 𝑛}. Models (2.2) and (2.3) make use of unfavourable and favourable multipliers, respectively, to identify the
individual cross-efficiencies towards the single-stage structure. In either case, only the optimistic self-efficiency
measure is involved to accommodate their purpose. In Section 3.1, a combined self-efficiency score is obtained indicating the merger of the optimistic and pes-
simistic self-efficiencies. That score is embedded to the adjusted cross-efficiency models (Sect. 3.2) to explore the
effect of both opposing viewpoints. The above-mentioned processes are part of a broader framework presented
herein to reasonably rank DMUs towards the two-stage tandem structure. 2.1. Cross-efficiency & interval cross-efficiency in single-stage structures A significant challenge of the conventional single-stage DEA model, is to distinguish the efficient DMUs
and thus to acquire a unique ranking of the DMUs. A potential remedy to overcome this inability is the
implementation of the CE concept [42]. Let 𝜇*
𝑟𝑘and 𝜈*
𝑖𝑘be the optimal set of multipliers of model (2.1). Then,
𝐸*
𝑘𝑘= ∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘is the optimal self-efficiency score of DMU𝑘and reflects its desire to be assessed only on the
basis of its own most favourable weights. On the other hand, CE, in which peer-appraisal is the main notion,
evaluates each DMU, considering the weight profiles of all DMUs. The ratio 𝐸𝑘𝑗= ∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑗/ ∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑗
denotes the individual cross-efficiency of DMU𝑗, based on the optimal weight scheme of DMU𝑘. A CE matrix
(Tab. 1) can be a valuable tool to integrate both the peer-efficiency scores 𝐸𝑘𝑗(𝑘, 𝑗= 1, 2, . . ., 𝑛) and the self-
efficiency scores 𝐸𝑘𝑘(in the leading diagonal column). The ultimate cross-efficiency can be defined by averaging
all individual cross-efficiencies of the corresponding DMU being evaluated. The ultimate score in this case is
ˆ𝑒𝑗= 1
𝑛· ∑︀𝑛
𝑘=1 𝐸𝑘𝑗, ∀𝑗[2]. ︀
The existence of multiple optimal weights from model (2.1) can deteriorate the theoretical usefulness of the
results obtained via the cross-efficiency concept. To tackle this issue, Doyle and Green [10] proposed two opposed
secondary goals to choose their weights, favourable or unfavourable, among the optimal solutions. Considering the DEA-related literature, there is not a well-established methodological approach to guide the
decision-maker in reasonably selecting either the benevolent or the aggressive strategy. In addition, the selection
of either the former or the latter model might not provide the same ranking or a unique optimal set of weights. To overcome these obstacles, Yang et al. [53] suggested the simultaneous use of the two extreme cases in the
context of a single-stage structure. Model (2.2) is an aggressive-based model to obtain an optimal set of multipliers and thus to identify the
minimum individual cross-efficiency value of DMU𝑗based on DMU𝑘. Min 𝐸L
𝑘𝑗=
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗= 1,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘−𝐸*
𝑘𝑘
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 0,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗; 𝑗̸= 𝑘,
𝜇𝑟𝑘, 𝜈𝑖𝑘≥0,
∀𝑟, 𝑖. (2.2) (2.2) 1298 M.D. KREMANTZIS ET AL. Table 2. Interval cross-efficiency matrix [53]. 3. Models development At optimality of model (3.1), the system efficiency is estimated as 𝐸𝑠
𝑘= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), the effi-
ciency of stage 1 as 𝐸1
𝑘=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), and the efficiency of stage 2 as 𝐸2
𝑘= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
. It is obvious that the overall efficiency is the product of the efficiencies of the stage efficiencies. ︁︀︁︀︀
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
. It is obvious that the overall efficiency is the product of the efficiencies of the stage efficiencies. 3. Models development The exploration of the internal processes taking place in the core of a DMU sets the foundation for the
transition from a single-stage to a two-stage DEA structure. Each DMU𝑗(𝑗= 1, 2, . . ., 𝑛) consumes 𝑚inputs (𝑖=
1, 2, . . ., 𝑚) in the first stage to generate 𝐷intermediate products (𝑑= 1, 2, . . ., 𝐷). The outputs (intermediate
measures) of the first stage are converted into inputs in the second stage to produce 𝑠final outputs (𝑟=
1, 2, . . ., 𝑠). Let 𝑋𝑖𝑗be the input value of 𝑖∈𝑀, 𝑍𝑑𝑗be the intermediate product of 𝑑∈𝐷, and 𝑌𝑟𝑗be the
output value of 𝑟∈𝑆, for DMU 𝑗∈𝑁[21]. The above process is illustrated in the exploratory Figure 2. According to the relational model of Kao and Hwang [21], to measure the performance of the overall system
it is necessary to consider not only its operations, but also the operations of its individual sub-stages. In model
(3.1) these operations are described by the constraints, which indicate that the aggregate output can not exceed
the aggregate input. 1299 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Figure 2. Typical two-stage tandem DEA structure. Figure 2. Typical two-stage tandem DEA structure. Figure 2. Typical two-stage tandem DEA structure. 𝐸𝑠
𝑘= Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗≤0,
∀𝑗,
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. (3.1) ∀𝑟, 𝑖, 𝑑. (3.1) (3.1) ︁︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, At optimality of model (3.1), the system efficiency is estimated as 𝐸𝑠
𝑘= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), the effi-
ciency of stage 1 as 𝐸1
𝑘=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), and the efficiency of stage 2 as 𝐸2
𝑘= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/︁︀︁ At optimality of model (3.1), the system efficiency is estimated as 𝐸𝑠
𝑘= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), the effi-
ciency of stage 1 as 𝐸1
𝑘=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), and the efficiency of stage 2 as 𝐸2
𝑘= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
. It is obvious that the overall efficiency is the product of the efficiencies of the stage efficiencies. 3.1. Optimistic & pessimistic models in basic two-stage structure The above model can set the basis for the exploration of the optimistic and pessimistic self-efficiencies and,
in turn, their integration into a geometric average efficiency score within the two-stage tandem system. Sub-stage 1 consumes inputs to generate intermediate products. The following input-oriented CCR model
(3.2) [21] examines the performance of sub-stage 1: The above model can set the basis for the exploration of the optimistic and pessimistic self-efficiencies and,
in turn, their integration into a geometric average efficiency score within the two-stage tandem system. Sub-stage 1 consumes inputs to generate intermediate products. The following input-oriented CCR model
(3.2) [21] examines the performance of sub-stage 1: 𝐸1
𝑘= Max
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑖, 𝑑. (3.2) ∀𝑖, 𝑑. (3.2) (3.2) ∀𝑖, 𝑑. ︁︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑖, 𝑑. (3.2) ︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, ︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, With reference to sub-stage 1 of a basic two-stage DEA structure, two fundamental concepts, the IDMU and
the ADMU, are introduced, following the principles of Wang and Luo [48]. IDMU is a hypothetical DMU
that utilises the least amount of inputs to generate the most intermediate products. An ADMU, on the other
side, uses the most inputs to produce the least intermediate products. The IDMU can be expressed with the
vectors (𝑋min, 𝑍max), where 𝑋min
𝑖
= min𝑘{𝑋𝑖𝑘} and 𝑍max
𝑑
= max𝑘{𝑍𝑑𝑘}, ∀𝑖, 𝑑. The ADMU can be determined
with the vectors (𝑋max, 𝑍min), where 𝑋max
𝑖
= max𝑘{𝑋𝑖𝑘} and 𝑍min
𝑑
= min𝑘{𝑍𝑑𝑘}, ∀𝑖, 𝑑. As stressed in 1300 M.D. KREMANTZIS ET AL. Hatami-Marbini et al. [16], the performance of the IDMU cannot be worse than any of the actual DMUs, and
the performance of the ADMU cannot be better than that of the worst performing actual DMU. Hatami-Marbini et al. [16], the performance of the IDMU cannot be worse than any of the actual DMUs, and
the performance of the ADMU cannot be better than that of the worst performing actual DMU. 3.1. Optimistic & pessimistic models in basic two-stage structure (3.5) (3.5) 1301 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES The efficiency of the ADMU for the entire system can be illustrated as 𝐸ADMU(𝑠) =
(︀∑︀𝑠
𝑟=1 𝜇𝑟𝑌min
𝑟
)︀
/
(∑︀𝑚
𝑖=1 𝜈𝑖𝑋max
𝑖
). The associated optimisation model is formulated as follows: 𝐸ADMU(𝑠) = Min
𝑠
∑︁
𝑟=1
𝜇𝑟𝑌min
𝑟
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋max
𝑖
= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋𝑖𝑗≤0,
∀𝑗,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍𝑑𝑗≤0,
∀𝑗,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑌max
𝑟
−𝐸IDMU(𝑠)*
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋min
𝑖
≥0,
𝜇𝑟, 𝜈𝑖, 𝜂𝑑≥0,
∀𝑟, 𝑖, 𝑑. (3.6) ∀𝑟, 𝑖, 𝑑. (3.6) (3.6) ︁︁
𝜇𝑟, 𝜈𝑖, 𝜂𝑑≥0,
∀𝑟, 𝑖, 𝑑. (3.6) ︁
𝜇𝑟, 𝜈𝑖, 𝜂𝑑≥0, Model (3.6) aims to minimise the pessimistic efficiency measure of the ADMU, while keeping the optimistic
efficiency of the IDMU for the overall system no less than 𝐸IDMU(𝑠)*. It should be noted that the second and
third sets of constraints in both models imply that the overall efficiency of DMU cannot exceed 1. Model (3.6) aims to minimise the pessimistic efficiency measure of the ADMU, while keeping the optimistic
efficiency of the IDMU for the overall system no less than 𝐸IDMU(𝑠)*. It should be noted that the second and
third sets of constraints in both models imply that the overall efficiency of DMU cannot exceed 1. The next point to focus on in this paper is the examination of the highest and the lowest relative efficiency
of each DMU, considering their self-evaluation. In model (3.7), the optimistic relative efficiency of DMU𝑘for
the sub-stage 1 is examined while 𝐸IDMU(1)* is kept fixed; it is related to Wang and Luo’s [48] framework: 𝐸IDMU(1)
𝑘
= Max
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍max
𝑑
−𝐸IDMU(1)*
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋min
𝑖
= 0,
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑖, 𝑑. (3.7) ∀𝑖, 𝑑. (3.7) ︁
𝑑
1︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑖, 𝑑. (3.7) (3.7) ︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, ︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, In the same manner, we construct the counterpart model for measuring the highest relative efficiency of DMU𝑘
for the sub-stage 2, considering 𝐸IDMU(2)* as the fixed parameter. IDMU( )︀ The overall optimistic efficiency score of DMU𝑘can be determined as 𝐸IDMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇𝑟𝑘𝑌𝑟𝑘)/
(∑︀𝑚
𝑖=1 𝜈𝑖𝑘𝑋𝑖𝑘). 3.1. Optimistic & pessimistic models in basic two-stage structure The best and worst relative efficiency scores in terms of sub-stage 1 can be defined by the following two CCR
models, respective to the IDMU and the ADMU; they are related to Wang and Luo [48] and Wu’s [51] models: 𝐸IDMU(1) = Max
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍max
𝑑
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋min
𝑖
= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋𝑖𝑗≤0,
∀𝑗, ∀𝑗, (3.3) ︁
𝜈𝑖, 𝜂𝑑≥0, 𝐸ADMU(1) = Min
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍min
𝑑
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋max
𝑖
= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋𝑖𝑗≤0,
∀𝑗,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍max
𝑑
−𝐸IDMU(1)*
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋min
𝑖
≥0,
𝜈𝑖, 𝜂𝑑≥0,
∀𝑖, 𝑑,
(3.4) (3.4) ︁
𝜈𝑖, 𝜂𝑑≥0, where 𝐸IDMU(1)* is the optimal optimistic score of IDMU in terms of sub-stage 1, obtained in model (3.3). Model (3.4) ensures that the best relative efficiency of sub-stage 1 is fixed at a value greater than or equal to
𝐸IDMU(1)*. where 𝐸IDMU(1)* is the optimal optimistic score of IDMU in terms of sub-stage 1, obtained in model (3.3). Model (3.4) ensures that the best relative efficiency of sub-stage 1 is fixed at a value greater than or equal to
𝐸IDMU(1)*. By the same token, we establish the definitions as well as formulate the appropriate optimisation models for
the IDMU and the ADMU, regarding sub-stage 2 of the basic two-stage structure. Note that sub-stage 2 focuses
on the consumption of intermediate products for the generation of the final outputs. The next stage concerns the determination of the optimistic and pessimistic efficiency scores of the IDMU
and the ADMU, respectively, in terms of the overall system. The reference model is the relational two-
stage DEA model (3.1). The efficiency of the IDMU for the entire system can be defined as 𝐸IDMU(𝑠) =
(∑︀𝑠
𝑟=1 𝜇𝑟𝑌max
𝑟
)/
(︀∑︀𝑚
𝑖=1 𝜈𝑖𝑋min
𝑖
)︀
. The factor weights 𝜇𝑟and 𝜈𝑖are assigned to the 𝑟th output and the 𝑖th input,
respectively. We thus construct the following LP model that aims to maximise the efficiency of the IDMU. 𝐸IDMU(𝑠) = Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑌max
𝑟
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋min
𝑖
= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑋𝑖𝑗≤0,
∀𝑗,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑍𝑑𝑗≤0,
∀𝑗,
𝜇𝑟, 𝜈𝑖, 𝜂𝑑≥0,
∀𝑟, 𝑖, 𝑑. (3.5 ︁︁
𝜇𝑟, 𝜈𝑖, 𝜂𝑑≥0,
∀𝑟, 𝑖, 𝑑. 3.1. Optimistic & pessimistic models in basic two-stage structure It is clear that this measure is the product of the optimistic efficiencies of the DMU𝑘of the
two sub-stages, adopting the principle of the multiplicative efficiency decomposition approach [21]. Thus, we
propose model (3.8), that maximises the above ratio. 𝐸IDMU(𝑠)
𝑘
= Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1, 1302 M.D. KREMANTZIS ET AL. 𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗≤0,
∀𝑗,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍max
𝑑
−𝐸IDMU(1)*
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋min
𝑖
= 0,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌max
𝑟
−𝐸IDMU(2)*
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍min
𝑑
= 0,
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. ∀𝑟, 𝑖, 𝑑. (3.8) (3.8) ︁︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. (3.8) ︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, ︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, The fourth and fifth constraints indicate that 𝐸IDMU(1)* and 𝐸IDMU(2)*, respectively, remain unchanged. Let
𝜈*
𝑘= (𝜈*
1𝑘, 𝜈*
2𝑘, . . ., 𝜈*
𝑚𝑘), 𝜂*
𝑘= (𝜂*
1𝑘, 𝜂*
2𝑘, . . ., 𝜂*
𝐷𝑘), 𝜇*
𝑘= (𝜇*
1𝑘, 𝜇*
2𝑘, . . ., 𝜇*
𝑠𝑘), be an optimal solution to model
(3.8). For DMU𝑘, 𝐸IDMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), 𝐸IDMU(1)
𝑘
=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), and
𝐸IDMU(2)
𝑘
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
, which are referred to as optimistic self-efficiency measures with
respect to the overall system and its sub-stages, respectively. The fourth and fifth constraints indicate that 𝐸IDMU(1)* and 𝐸IDMU(2)*, respectively, remain unchanged. Let
𝜈*
𝑘= (𝜈*
1𝑘, 𝜈*
2𝑘, . . ., 𝜈*
𝑚𝑘), 𝜂*
𝑘= (𝜂*
1𝑘, 𝜂*
2𝑘, . . ., 𝜂*
𝐷𝑘), 𝜇*
𝑘= (𝜇*
1𝑘, 𝜇*
2𝑘, . . ., 𝜇*
𝑠𝑘), be an optimal solution to model
(3.8). For DMU𝑘, 𝐸IDMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), 𝐸IDMU(1)
𝑘
=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), and
𝐸IDMU(2)
𝑘
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
, which are referred to as optimistic self-efficiency measures with
respect to the overall system and its sub-stages, respectively. The fourth and fifth constraints indicate that 𝐸IDMU(1)* and 𝐸IDMU(2)*, respectively, remain unchanged. Let
𝜈*
𝑘= (𝜈*
1𝑘, 𝜈*
2𝑘, . . ., 𝜈*
𝑚𝑘), 𝜂*
𝑘= (𝜂*
1𝑘, 𝜂*
2𝑘, . . ., 𝜂*
𝐷𝑘), 𝜇*
𝑘= (𝜇*
1𝑘, 𝜇*
2𝑘, . . 3.1. Optimistic & pessimistic models in basic two-stage structure However, we should consider that it sheds light on the effects of the optimistic and pessimistic standpoints
only within the self-appraisal context. In other words, each DMU is assessed, based on its own most favourable
and unfavourable weights, without considering the weight scheme of each of the other DMUs. This score also
ensures a better discriminating power than either of the optimistic and pessimistic efficiencies [50]. Yet, this
feature has not been explored in a more complex network structure. To this end, in the next section, the double
frontier DEA models are further extended by the use of the interval CE within a two-stage tandem system, to
ensure a more logical ranking order. 3.1. Optimistic & pessimistic models in basic two-stage structure For DMU𝑘, 𝐸ADMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇∼
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈∼
𝑖𝑘𝑋𝑖𝑘), 𝐸ADMU(1)
𝑘
=
(︁∑︀𝐷
𝑑=1 𝜂∼
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈∼
𝑖𝑘𝑋𝑖𝑘),
and 𝐸ADMU(2)
𝑘
= (∑︀𝑠
𝑟=1 𝜇∼
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂∼
𝑑𝑘𝑍𝑑𝑘
)︁
, which are referred to as pessimistic self-efficiency measures
with respect to the overall system and its constituent parts, respectively. Let 𝜈∼
𝑘= (𝜈∼
1𝑘, 𝜈∼
2𝑘, . . ., 𝜈∼
𝑚𝑘), 𝜂∼
𝑘= (𝜂∼
1𝑘, 𝜂∼
2𝑘, . . ., 𝜂∼
𝐷𝑘), 𝜇∼
𝑘= (𝜇∼
1𝑘, 𝜇∼
2𝑘, . . ., 𝜇∼
𝑠𝑘), be an optimal solution to model
(3.10). For DMU𝑘, 𝐸ADMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇∼
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈∼
𝑖𝑘𝑋𝑖𝑘), 𝐸ADMU(1)
𝑘
=
(︁∑︀𝐷
𝑑=1 𝜂∼
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈∼
𝑖𝑘𝑋𝑖𝑘),
and 𝐸ADMU(2)
𝑘
= (∑︀𝑠
𝑟=1 𝜇∼
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂∼
𝑑𝑘𝑍𝑑𝑘
)︁
, which are referred to as pessimistic self-efficiency measures
with respect to the overall system and its constituent parts, respectively. ︀︀
Consequently, in a two-stage DEA structure, a self-efficiency interval is formulated for each DMU under
consideration, both for the overall system and its constituent stages. For instance, considering the overall system,
an efficiency interval denoted by
[︁
𝐸ADMU(𝑠)*
𝑘
, 𝐸IDMU(𝑠)*
𝑘
]︁
is shaped, where 𝐸ADMU(𝑠)*
𝑘
(lower bound) represents
the worst relative efficiency of DMU𝑘and 𝐸IDMU(𝑠)*
𝑘
(upper bound) illustrates the best relative efficiency of
DMU𝑘, obtained via models (3.10) and (3.8), respectively. There is a clear need to integrate both optimistic and pessimistic self-efficiency measures to provide an
overall assessment of the performance of each DMU in a two-stage DEA process. This study adopts the ge-
ometric average efficiency measure, proposed and verified by Wang et al. [50], to meet this requirement. Let
𝐸comb(𝜖)*
𝑘
=
√︁
𝐸ADMU(𝜖)*
𝑘
· 𝐸IDMU(𝜖)*
𝑘
be the combined self-efficiency measure of DMU𝑘, where 𝜖= 𝑠(over-
all system) or 1 (sub-stage 1) or 2 (sub-stage 2). We easily prove that the combined self-efficiency score
of DMU𝑘for the overall system is the product of the combined self-efficiency measures of DMU𝑘for the
two sub-stages: 𝐸𝑐𝑜𝑚𝑏(𝑠)*
𝑘
=
√︁
𝐸ADMU(𝑠)*
𝑘
· 𝐸IDMU(𝑠)*
𝑘
=
√︁
𝐸ADMU(1)*
𝑘
· 𝐸ADMU(2)*
𝑘
· 𝐸IDMU(1)*
𝑘
· 𝐸IDMU(2)*
𝑘
=
√︁
𝐸ADMU(1)*
𝑘
· 𝐸IDMU(1)*
𝑘
·
√︁
𝐸ADMU(2)*
𝑘
· 𝐸IDMU(2)*
𝑘
= 𝐸𝑐𝑜𝑚𝑏(1)*
𝑘
· 𝐸𝑐𝑜𝑚𝑏(2)*
𝑘
. √︁
√︁
The geometric average efficiency is an approachable efficiency measure that leads to a fairer ranking index
[50]. 3.1. Optimistic & pessimistic models in basic two-stage structure ., 𝜇*
𝑠𝑘), be an optimal solution to model
(3.8). For DMU𝑘, 𝐸IDMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), 𝐸IDMU(1)
𝑘
=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑘), and
𝐸IDMU(2)
𝑘
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑘)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑘
)︁
, which are referred to as optimistic self-efficiency measures with
respect to the overall system and its sub-stages, respectively. ︀︁︀︁
Then, model (3.9) evaluates the worst relative efficiency of DMU𝑘, in terms of sub-stage 1, while the parameter
𝐸ADMU(1)* takes the value as determined previously from model (3.4). This model is related to Wu’s [51]
framework. 𝐸ADMU(1)
𝑘
= Min
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍min
𝑑
−𝐸ADMU(1)*
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋max
𝑖
= 0,
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑖, 𝑑. (3.9) ∀𝑖, 𝑑. (3.9) (3.9) ︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, ︁
𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, Similarly, we formulate the counterpart model for measuring the lowest relative efficiency of DMU𝑘for the
sub-stage 2, considering 𝐸ADMU(2)* as the unchanged parameter. ADMU( )︀︀ Similarly, we formulate the counterpart model for measuring the lowest relative efficiency of DMU𝑘for the
sub-stage 2, considering 𝐸ADMU(2)* as the unchanged parameter. ADMU( )︀︀ The overall pessimistic score of DMU𝑘can be determined as 𝐸ADMU(𝑠)
𝑘
= (∑︀𝑠
𝑟=1 𝜇𝑟𝑘𝑌𝑟𝑘)/(∑︀𝑚
𝑖=1 𝜈𝑖𝑘𝑋𝑖𝑘) and
denotes the product of the pessimistic efficiencies of the DMU𝑘of the two sub-stages. Thus, we suggest model
(3.10), whose purpose is to minimise the above ratio. 𝐸ADMU(1)* and 𝐸ADMU(2)* are maintained. 𝐸ADMU(𝑠)
𝑘
= Min
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 1,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗, ∀𝑗, A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 1303 𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗≤0,
∀𝑗,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍min
𝑑
−𝐸ADMU(1)*
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋max
𝑖
= 0,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌min
𝑟
−𝐸ADMU(2)*
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍max
𝑑
= 0,
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. (3.10) ∀𝑗, ∀𝑟, 𝑖, 𝑑. (3.10) ︁︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. (3.10) (3.10) ︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, Let 𝜈∼
𝑘= (𝜈∼
1𝑘, 𝜈∼
2𝑘, . . ., 𝜈∼
𝑚𝑘), 𝜂∼
𝑘= (𝜂∼
1𝑘, 𝜂∼
2𝑘, . . ., 𝜂∼
𝐷𝑘), 𝜇∼
𝑘= (𝜇∼
1𝑘, 𝜇∼
2𝑘, . . ., 𝜇∼
𝑠𝑘), be an optimal solution to model
(3.10). 3.2. Interval cross-efficiencies in basic two-stage structure Model (3.11) pursues to minimise the cross-efficiency value
of DMU𝑗under the condition that the combined self-efficiency scores for the overall system and its constituent In model (3.11), 𝐸comb(𝑠)*
𝑘
and 𝐸comb(2)*
𝑘
are the crisp combined self-efficiency measures of the system and
the sub-stage 2 for DMU𝑘, respectively, obtained from Section 3.1. The second and third constraint maintain
combined system and sub-stage efficiencies for DMUs. Model (3.11) pursues to minimise the cross-efficiency value
of DMU𝑗under the condition that the combined self-efficiency scores for the overall system and its constituent
parts remain unchanged. At optimality, the minimum individual cross-efficiencies of DMU𝑗based on DMU𝑘(𝑗̸=
𝑘) for the overall system, the stage 1, and the stage 2, are determined as 𝐸𝐿(𝑠)
𝑘𝑗
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑗)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑗),
𝐸𝐿(1)
𝑘𝑗
=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑗
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑗), and 𝐸𝐿(2)
𝑘𝑗
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑗)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑗
)︁
, respectively. By the same In model (3.11), 𝐸comb(𝑠)*
𝑘
and 𝐸comb(2)*
𝑘
are the crisp combined self-efficiency measures of the system and
the sub-stage 2 for DMU𝑘, respectively, obtained from Section 3.1. The second and third constraint maintain
combined system and sub-stage efficiencies for DMUs. Model (3.11) pursues to minimise the cross-efficiency value
of DMU𝑗under the condition that the combined self-efficiency scores for the overall system and its constituent
parts remain unchanged. At optimality, the minimum individual cross-efficiencies of DMU𝑗based on DMU𝑘(𝑗̸=
𝑘) for the overall system, the stage 1, and the stage 2, are determined as 𝐸𝐿(𝑠)
𝑘𝑗
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑗)/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑗),
𝐸𝐿(1)
𝑘𝑗
=
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑗
)︁
/(∑︀𝑚
𝑖=1 𝜈*
𝑖𝑘𝑋𝑖𝑗), and 𝐸𝐿(2)
𝑘𝑗
= (∑︀𝑠
𝑟=1 𝜇*
𝑟𝑘𝑌𝑟𝑗)/
(︁∑︀𝐷
𝑑=1 𝜂*
𝑑𝑘𝑍𝑑𝑗
)︁
, respectively. By the same
token, a benevolent strategy is implemented to construct the following maximisation model: 𝐸𝑈(𝑠)
𝑘𝑗
= Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘· 𝑌𝑟𝑗 𝐸𝑈(𝑠)
𝑘𝑗
= Max
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘· 𝑌𝑟𝑗
(3.12) (3.12) ︁
subject to the same constraints as in model (3.11). This model seeks to maximise the cross-efficiency of DMU𝑗given that the combined self-efficiency measures are
kept fixed for the overall system and its sub-stages. Similarly, we define the maximum individual cross-efficiencies
of DMU𝑗for the system and its stages. 3.2. Interval cross-efficiencies in basic two-stage structure In terms of 𝜖, where 𝜖= 𝑠(overall system), 1 (stage 1) or 2 (stage 2), for DMU𝑗, its cross-efficiency rated by
DMU𝑘lies in
[︁
𝐸L(𝜖)
𝑘𝑗, 𝐸U(𝜖)
𝑘𝑗
]︁
, where 𝐸L(𝜖)
𝑘𝑗
is the lower bound and 𝐸U(𝜖)
𝑘𝑗
is the upper bound. Therefore, three
generalised interval CE matrices (based on the concept of Tab. 2) are shaped for the 𝑛DMUs, in regard to
the overall system, the stage 1, and the stage 2, respectively. The diagonal column in each of these matrices
demonstrates the special case in which 𝐸L(𝜖)*
𝑗𝑗
= 𝐸U(𝜖)*
𝑗𝑗
= 𝐸comb(𝜖)*
𝑗
∀𝑗, where 𝜖= 𝑠, 1 or 2. 𝑗𝑗
𝑗𝑗
𝑗
The recently created interval CE matrices can be viewed as MCDM problems. Taking that into consideration,
we will set the scene for the determination of the interval local weights of criteria and the interval global weights
of alternatives (ultimate cross-efficiencies) to fully rank the DMUs, in a basic two-stage DEA structure. 3.2. Interval cross-efficiencies in basic two-stage structure In this section, we will propose the customisation and simultaneous use of the traditional aggressive and
benevolent secondary models in the context of the basic two-stage DEA structure with combined self-efficiencies,
obtained in Section 3.1. Their purpose is the determination of the minimum and maximum individual cross-
efficiencies of DMU𝑗, with respect to the optimal weight scheme of DMU𝑘(𝑘, 𝑗= 1, 2, . . ., 𝑛), respectively. A fruitful aspect we believe, is the integration of the combined self-efficiency score for the corresponding sys-
tem/stage within the CE process. This is irrespective of the type of multipliers, favourable for a benevolent or
unfavourable for an aggressive strategy, that are used to capture the cross-efficiencies. 1304 M.D. KREMANTZIS ET AL. We initially adopt an aggressive strategy to establish the following minimisation model:︁ We initially adopt an aggressive strategy to establish the following minimisation model:︁ 𝐸𝐿(𝑠)
𝑘𝑗
= Min
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗= 1,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘−𝐸comb(𝑠)*
𝑘
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 0,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘−𝐸comb(2)*
𝑘
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑘= 0,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
∀𝑗,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗≤0,
∀𝑗,
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. (3.1 𝐸𝐿(𝑠)
𝑘𝑗
= Min
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗
subject to
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗= 1,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘−𝐸comb(𝑠)*
𝑘
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑘= 0,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑘−𝐸comb(2)*
𝑘
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑘= 0,
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗−
𝑚
∑︁
𝑖=1
𝜈𝑖𝑘𝑋𝑖𝑗≤0,
𝑠
∑︁
𝑟=1
𝜇𝑟𝑘𝑌𝑟𝑗−
𝐷
∑︁
𝑑=1
𝜂𝑑𝑘𝑍𝑑𝑗≤0,
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, ∀𝑟, 𝑖, 𝑑. (3.11) (3.11) ︁︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0,
∀𝑟, 𝑖, 𝑑. (3.11) ︁︁
𝜇𝑟𝑘, 𝜈𝑖𝑘, 𝜂𝑑𝑘≥0, In model (3.11), 𝐸comb(𝑠)*
𝑘
and 𝐸comb(2)*
𝑘
are the crisp combined self-efficiency measures of the system and
h
b
f
DMU
i
l
b
i
d f
S
i
Th
d
d hi d
i
i
i In model (3.11), 𝐸comb(𝑠)*
𝑘
and 𝐸comb(2)*
𝑘
are the crisp combined self-efficiency measures of the system and
the sub-stage 2 for DMU𝑘, respectively, obtained from Section 3.1. The second and third constraint maintain
combined system and sub-stage efficiencies for DMUs. 3.3. Interval cross-efficiencies and MCDM context We will provide their optimisation model as we would apply this within the basic 2-stage series
structure: Ω= Min
𝑛
∑︁
𝑘=1
(︀
𝛿+
𝑘+ 𝛿−
𝑘+ 𝛾+
𝑘+ 𝛾−
𝑘
)︀
subject to (𝐸L −𝐼)𝑊U −(𝑛−1)𝑊L −∆+ + ∆−= 0,
(𝐸U −𝐼)𝑊L −(𝑛−1)𝑊U −Γ+ + Γ−= 0,
𝑤L
𝑘+
𝑛
∑︁
𝜔=1,𝜔̸=𝑘
𝑤U
𝜔≥1,
∀𝑘,
𝑤U
𝑘+
𝑛
∑︁
𝜔=1,𝜔̸=𝑘
𝑤L
𝜔≤1,
∀𝑘,
𝑊U −𝑊L ≥0,
𝑊U 𝑊L ∆+ ∆−Γ+ Γ−≥0 Ω= Min
𝑛
∑︁
𝑘=1
(︀
𝛿+
𝑘+ 𝛿−
𝑘+ 𝛾+
𝑘+ 𝛾−
𝑘
)︀
subject to (𝐸L −𝐼)𝑊U −(𝑛−1)𝑊L −∆+ + ∆−= 0,
(𝐸U −𝐼)𝑊L −(𝑛−1)𝑊U −Γ+ + Γ−= 0,︁ 𝑤L
𝑘+
𝑛
∑︁
𝜔=1,𝜔̸=𝑘
𝑤U
𝜔≥1,
∀𝑘, ︁
𝑤U
𝑘+
𝑛
∑︁
𝜔=1,𝜔̸=𝑘
𝑤L
𝜔≤1,
∀𝑘, ︁
𝑊U −𝑊L ≥0,
𝑊U, 𝑊L, ∆+, ∆−, Γ+, Γ−≥0, ︁
𝑊U −𝑊L ≥0,
𝑊U, 𝑊L, ∆+, ∆−, Γ+, Γ−≥0,
(3.13) 𝑊U
𝑊L ≥0,
𝑊U, 𝑊L, ∆+, ∆−, Γ+, Γ−≥0,
(3.13)︀︀︀︀︀︀︀ U
L ≥,
𝑊U, 𝑊L, ∆+, ∆−, Γ+, Γ−≥0, (3.13) where ∆+ =
(︀
𝛿+
1 , . . ., 𝛿+
𝑛
)︀𝑇, ∆−=
(︀
𝛿−
1 , . . ., 𝛿−
𝑛
)︀𝑇, Γ+ =
(︀
𝛾+
1 , . . ., 𝛾+
𝑛
)︀𝑇, Γ−=
(︀
𝛾−
1 , . . ., 𝛾−
𝑛
)︀𝑇, 𝑊U =︀
U
U)︀𝑇
(︀
L
L)︀𝑇 where ∆+ =
(︀
𝛿+
1 , . . ., 𝛿+
𝑛
)︀𝑇, ∆−=
(︀
𝛿−
1 , . . ., 𝛿−
𝑛
)︀𝑇, Γ+ =
(︀
𝛾+
1 , . . ., 𝛾+
𝑛
)︀𝑇, Γ−=
(︀
𝛾−
1 , . . ., 𝛾−
𝑛
)︀𝑇, 𝑊U =
(︀
𝑤U
1 , . . ., 𝑤U
𝑛
)︀𝑇, 𝑊L =
(︀
𝑤L
1 , . . ., 𝑤L
𝑛
)︀𝑇, 𝐼is a 𝑛⊗𝑛unit matrix whose elements on the diagonal are 1, and
𝐸L and 𝐸U are the minimum and maximum individual cross-efficiency matrices, whose elements are in the form
of 𝐸L(𝜖)
𝑘𝑗
and 𝐸U(𝜖)
𝑘𝑗
respectively. The deviation vectors ∆+, ∆−, Γ+, Γ−, that appear in the first two constraint
sets, pursue to eliminate the uncertainty and connect the lower level criteria 𝑊L with the upper level criteria 𝑊U. The third and fourth sets of constraints ensure the normalisation of the local interval weights, whereas the fifth
constraint set determines their lower and upper bounds. 3.3. Interval cross-efficiencies and MCDM context Each generalised interval CE matrix (see Sect. 3.2) can be treated as a multi-criteria decision making (MCDM)
problem with 𝑗= 1, 2, . . ., 𝑛DMUs that act as alternatives. Each DMU𝑗is assessed considering the weight profile A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 1305 of 𝑘= 1, 2, . . ., 𝑛DMUs that act as criteria. Interestingly, the former intuition is attributed to the novel study
of Cook et al. [8], according to which each DEA-related problem could be viewed as a multi-criteria evaluation
problem. This has also been consolidated by Rakhshan [37], who argues that the combination of the MCDM
and the DEA tools could mitigate their drawbacks when applied as stand-alone techniques. g
pp
q
Our primary target is to estimate the interval ultimate cross-efficiency scores, which are the interval global
weights for the evaluated DMUs. To this end, our approach is twofold as it requires not only the local weights
of alternatives with respect to a certain criterion, but also the local weights of criteria. The former are the
elements 𝐸L(𝜖)
𝑘𝑗
and 𝐸U(𝜖)
𝑘𝑗
, which act as lower-level and upper-level local weights of alternative 𝑗in reference
to criterion 𝑘for 𝜖= 𝑠, 1 or 2, respectively, and overall compose
[︁
𝐸L(𝜖)
𝑘𝑗, 𝐸U(𝜖)
𝑘𝑗
]︁
. These elements have been
obtained in Section 3.2. The latter illustrates the local weight of criterion 𝑘, that is manifested as an interval
value with lower bound 𝑤L
𝑘and upper bound 𝑤U
𝑘. The existence of this interval value is due to dealing with two
diametrically opposed strategies for the overall system and its constituent stages. Wang and Elhag [47] suggest a goal programming (GP) method to elicit normalised interval local weights
from an interval comparison matrix. In our scenario, the interval CE matrix is committed to undertaking the
role of the interval comparison matrix. Their method captures the lower and upper limits of the local weight of
criterion 𝑘(𝑘= 1, 2, . . ., 𝑛) without ignoring the interval individual cross-efficiencies and the potential existence
of uncertainty. Table 3. Synthesis of interval cross-efficiencies. Target
DMU𝑗
Evaluator DMU𝑘
1
2
. . . 𝑛
1
[︁
𝑤L(𝜖)
1
, 𝑤U(𝜖)
1
]︁
[︁
𝐸L(𝜖)
11 , 𝐸U(𝜖)
11
]︁
[︁
𝐸L(𝜖)
12 , 𝐸U(𝜖)
12
]︁
. . . [︁
𝐸L(𝜖)
1𝑛, 𝐸U(𝜖)
1𝑛
]︁
2
[︁
𝑤L(𝜖)
2
, 𝑤U(𝜖)
2
]︁
[︁
𝐸L(𝜖)
21 , 𝐸U(𝜖)
21
]︁
[︁
𝐸L(𝜖)
22 , 𝐸U(𝜖)
22
]︁
. . . [︁
𝐸L(𝜖)
2𝑛, 𝐸U(𝜖)
2𝑛
]︁
. . . . . . . . . . . . . . . 𝑛
[︁
𝑤L(𝜖)
𝑛
, 𝑤U(𝜖)
𝑛
]︁
[︁
𝐸L(𝜖)
𝑛1 , 𝐸U(𝜖)
𝑛1
]︁
[︁
𝐸L(𝜖)
𝑛2 , 𝐸U(𝜖)
𝑛2
]︁
. . . [︁
𝐸L(𝜖)
𝑛𝑛, 𝐸U(𝜖)
𝑛𝑛
]︁
Ultimate cross-efficiencies
[︁
𝐸L.B.(𝜖)
1
, 𝐸U.B.(𝜖)
1
]︁
[︁
𝐸L.B.(𝜖)
2
, 𝐸U.B.(𝜖)
2
]︁
. . . [︁
𝐸L.B.(𝜖)
𝑛
, 𝐸U.B.(𝜖)
𝑛
]︁ Taking the interval local weight for each criterion 𝑘and the interval local weight of each alternative 𝑗with
respect to criterion 𝑘into account, we determine the interval ultimate cross-efficiencies for the alternatives. We
recommend using the practical method of Entani and Tanaka [13] that is based on a pair of linear programming
(LP) models. Their approach treats the local weights of criteria as decision variables to be optimised and intends
to determine the global weights for each DMU. The pair of LP models is described as follows: 𝐸L.B.(𝜖)
𝑗
= Min
𝑛
∑︁
𝑘=1
𝑤(𝜖)
𝑘𝐸L(𝜖)
𝑘𝑗
subject to
𝑛
∑︁
𝑘=1
𝑤(𝜖)
𝑘
= 1,
𝑤L(𝜖)
𝑘
≤𝑤(𝜖)
𝑘
≤𝑤U(𝜖)
𝑘
,
∀𝑘,
(3.14) (3.14) and 𝐸U.B.(𝜖)
𝑗
= Max
𝑛
∑︁
𝑘=1
𝑤(𝜖)
𝑘𝐸U(𝜖)
𝑘𝑗 𝐸U.B.(𝜖)
𝑗
= Max
𝑛
∑︁
𝑘=1
𝑤(𝜖)
𝑘𝐸U(𝜖)
𝑘𝑗
(3.15) (3.15) ︁
subject to the same constraints as in model (3.14), ︁
subject to the same constraints as in model (3.14), where 𝑤(𝜖)
𝑘
is the decision variable of the 𝑘th local criterion weight (𝑘= 1, 2, . . ., 𝑛) for 𝜖= 𝑠(overall system),
1 (stage 1) or 2 (stage 2). The above pair of LP models (3.14) and (3.15) results in the interval global weight
for each alternative 𝑗(𝑗= 1, 2, . . ., 𝑛), denoted by
[︁
𝐸L.B.(𝜖)
𝑗
, 𝐸U.B.(𝜖)
𝑗
]︁
for the entire system and its sub-stages. Table 3 illustrates the synthesis of the interval cross-efficiencies. where 𝑤(𝜖)
𝑘
is the decision variable of the 𝑘th local criterion weight (𝑘= 1, 2, . Table 3. Synthesis of interval cross-efficiencies. . ., 𝑛) for 𝜖= 𝑠(overall system),
1 (stage 1) or 2 (stage 2). The above pair of LP models (3.14) and (3.15) results in the interval global weight
for each alternative 𝑗(𝑗= 1, 2, . . ., 𝑛), denoted by
[︁
𝐸L.B.(𝜖)
𝑗
, 𝐸U.B.(𝜖)
𝑗
]︁
for the entire system and its sub-stages. Table 3 illustrates the synthesis of the interval cross-efficiencies. 3.3. Interval cross-efficiencies and MCDM context Model (3.13) should, in effect, run three times, based
on the investigation of the interval CE matrix of the respective system and stage to compose
[︁
𝑤L(𝜖)
𝑘
, 𝑤U(𝜖)
𝑘
]︁
. [︁
]︁
Their approach might make sense in our study for two reasons. It has a greater scope for action due to
its compatibility with any interval comparison matrix, and involves less constraints than other methods such
as that of Sugihara et al. [43]. This enables it as an easier-to-use method for the DM. The fewer number of
constraints was owed to its practice, putting more emphasis on the matrix as a whole rather than on each
element individually. Wang and Elhag’s [47] technique has, to our knowledge, not received attention on eliciting
interval local weights from an interval CE matrix. Therefore, this section intends to use their approach to achieve
this goal. 1306 M.D. KREMANTZIS ET AL. Table 4. Interval ultimate cross-efficiencies. DMU𝑗
1 (L.B.)
2 (U.B.)
1
𝐸L.B.(𝜖)
1
𝐸U.B.(𝜖)
1
2
𝐸L.B.(𝜖)
2
𝐸U.B.(𝜖)
2
. . . . . . . . . 𝑛
𝐸L.B.(𝜖)
𝑛
𝐸U.B.(𝜖)
𝑛 performance of all alternatives into comparability sequence. According to the comparability sequence, an ideal
target sequence (reference sequence) is defined in the reference sequence definition (second step). In a third step,
a grey relational coefficient is calculated to illustrate the distance between the comparability and the reference
sequence. In a final step, the GRG between the reference and every comparability sequence is calculated, based
on the grey relational coefficient. If the comparability sequence of an alternative has the highest grey relational
grade, then this alternative is deemed as the most desirable one [25]. Below, we will provide an overview of the
GRA as we would apply this to ranking interval ultimate cross-efficiencies. performance of all alternatives into comparability sequence. According to the comparability sequence, an ideal
target sequence (reference sequence) is defined in the reference sequence definition (second step). In a third step,
a grey relational coefficient is calculated to illustrate the distance between the comparability and the reference
sequence. In a final step, the GRG between the reference and every comparability sequence is calculated, based
on the grey relational coefficient. If the comparability sequence of an alternative has the highest grey relational
grade, then this alternative is deemed as the most desirable one [25]. Below, we will provide an overview of the
GRA as we would apply this to ranking interval ultimate cross-efficiencies. To start with, we collect the data to be evaluated from the mathematical viewpoint. The interval ultimate
cross-efficiency scores, defined in Section 3.3, are gathered into a 𝑛⊗2 matrix, setting out the appropriate
conditions for translating the DMUs into alternatives and the two extreme cases (lower bound, upper bound)
into criteria. Hence, we form another MCDM problem with 𝑗= 1, 2, . . ., 𝑛alternatives that are assessed by
𝑖= 1, 2 attributes. Table 4 depicts what we described above.︁︁ The 𝑗th alternative can be expressed as 𝐸(𝜖)
𝑗
=
(︁
𝐸L.B.(𝜖)
𝑗
, 𝐸U.B.(𝜖)
𝑗
)︁
, where 𝐸𝑖(𝜖)
𝑗
is the ultimate cross-efficiency
of attribute 𝑖of alternative 𝑗and where 𝜖= 𝑠(overall system), 1 (stage 1) or 2 (stage 2). 3.4. Grey relational analysis for ranking DMUs In Section 3.3, we obtained an interval ultimate cross-efficiency score for DMU𝑗(𝑗= 1, 2, . . ., 𝑛). It is apparent
that there is a significant need to identify a simple yet efficient ranking approach for comparing and ranking
different DMUs, whose performance is expressed in the form of interval values. In this study, the Grey Relational
Analysis (GRA) is applied to obtain a unique ranking order for the DMUs, whose ultimate cross-efficiencies
are illustrated within certain boundaries, and thus to determine the most desirable alternative. GRA is based
on the grey system theory proposed by Julong [20]. It has proved to be a worthy methodological tool when
uncertain information emerges. GRA has fruitfully examined complex interconnections among several factors
[6] as well as obtained the optimal alternative among several alternatives [25,41]. GRA consists of four main steps: grey relational generating, reference sequence definition, grey relational
coefficient calculation, and grey relational grade (GRG) calculation. In a first step, GRA translates the existing 1307 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Table 4. Interval ultimate cross-efficiencies. The term 𝐸(𝜖)
𝑗
is
translated into the comparability sequence
¯
𝐸(𝜖)
𝑗
=
(︁
¯
𝐸L.B.(𝜖)
𝑗
,
¯
𝐸U.B.(𝜖)
𝑗
)︁
by use of one of the following equations: ︁︁
¯
𝐸𝑖(𝜖)
𝑗
=
𝐸𝑖(𝜖)
𝑗
−min
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁
max
{︁
𝐸𝑖(𝜖)
𝑗
, 𝑗
}︁
−min
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁,
∀𝑗, 𝑖,
(3.16)
¯
𝐸𝑖(𝜖)
𝑗
=
max
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁
−𝐸𝑖(𝜖)
𝑗
max
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁
−min
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁,
∀𝑗, 𝑖,
(3.17)
¯
𝐸𝑖(𝜖)
𝑗
=
⃒⃒⃒𝐸𝑖(𝜖)
𝑗
−𝐸𝑖(𝜖)
𝑑𝑒𝑠
⃒⃒⃒
max
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁
−min
{︁
𝐸𝑖(𝜖)
𝑗
, ∀𝑗
}︁,
∀𝑗, 𝑖. (3.18) (3.16) (3.17) (3.18) ︁︁︁︁
Equation (3.16) is used for the greater-the-better attributes, equation (3.17) is used for the smaller-the-better
attributes, and equation (3.18) is used for the closer-to-the-desired-value- 𝐸𝑖(𝜖)
𝑑𝑒𝑠-the-better. (︁
( ))︁ We proceed to calculating the grey relation distance between the reference sequence
(︁
𝐸𝑖(𝜖)
𝑗
)︁
and the com-
parability sequence
(︁¯
𝐸𝑖(𝜖)
𝑗
)︁
, which is ∆𝑖(𝜖)
𝑗
=
⃒⃒⃒𝐸𝑖(𝜖)
𝑗
−
¯
𝐸𝑖(𝜖)
𝑗
⃒⃒⃒, ∀𝑗, 𝑖. As stressed in Kuo et al. [25], the reference
sequence 𝐸𝑖(𝜖)
𝑗
=
(︁
𝐸1(𝜖)
𝑗
, 𝐸2(𝜖)
𝑗
)︁
= (1, 1). (︁
¯ )︁ ︁︁
Then, we compute the grey relational coefficient 𝛾
(︁
𝐸𝑖(𝜖)
𝑗
,
¯
𝐸𝑖(𝜖)
𝑗
)︁
. It is used to determine how close 𝐸𝑖(𝜖)
𝑗
is to
¯
𝐸𝑖(𝜖)
𝑗
. The larger the coefficient, the closer 𝐸𝑖(𝜖)
𝑗
and
¯
𝐸𝑖(𝜖)
𝑗
are. Let 𝛾
(︁
𝐸𝑖(𝜖)
𝑗
,
¯
𝐸𝑖(𝜖)
𝑗
)︁
= Δ(𝜖)
min +𝜁·Δ(𝜖)
max
Δ𝑖(𝜖)
𝑗
+𝜁·Δ(𝜖)
max , ∀𝑗, 𝑖where ︁︁
Then, we compute the grey relational coefficient 𝛾
(︁
𝐸𝑖(𝜖)
𝑗
, 𝐸𝑖(𝜖)
𝑗
)︁
. It is used to determine how close 𝐸𝑖(𝜖)
𝑗
is to
¯
𝐸𝑖(𝜖)
𝑗
. The larger the coefficient, the closer 𝐸𝑖(𝜖)
𝑗
and
¯
𝐸𝑖(𝜖)
𝑗
are. Let 𝛾
(︁
𝐸𝑖(𝜖)
𝑗
,
¯
𝐸𝑖(𝜖)
𝑗
)︁
= Δ(𝜖)
min +𝜁·Δ(𝜖)
max
Δ𝑖(𝜖)
𝑗
+𝜁·Δ(𝜖)
max , ∀𝑗, 𝑖where 1308 M.D. KREMANTZIS ET AL. Table 5. The numerical application of Zhou et al. [55]. Table 5. The numerical application of Zhou et al. [55]. Table 4. Interval ultimate cross-efficiencies. DMU
𝑋1
𝑋2
𝑋3
𝑍1
𝑍2
𝑌1
𝑌2
1
0.526
0.478
0.385
49.917
5.461
34.990
0.843
2
0.713
1.236
0.555
37.495
4.083
20.601
0.486
3
0.443
0.446
0.342
20.985
0.690
8.633
0.129
4
0.638
1.248
0.457
45.051
1.724
9.235
0.302
5
0.575
0.705
0.404
38.163
2.249
12.017
0.314
6
0.432
0.645
0.401
30.168
2.335
13.813
0.377
7
0.510
0.724
0.371
26.539
1.342
5.096
0.145
8
0.322
0.336
0.233
16.124
0.489
5.980
0.093
9
0.423
0.668
0.347
22.185
1.177
9.235
0.200
10
0.256
0.342
0.159
13.436
0.406
2.533
0.006 ∆(𝜖)
min = min
{︁
∆𝑖(𝜖)
𝑗
, ∀𝑗, 𝑖
}︁
, ∆(𝜖)
max = max
{︁
∆𝑖(𝜖)
𝑗
, ∀𝑗, 𝑖
}︁
, and 𝜁denotes the distinguishing coefficient, 𝜁∈[0, 1]. 𝜁is used to expand or squeeze the range of the grey relational coefficient. ( ) ∆(𝜖)
min = min
{︁
∆𝑖(𝜖)
𝑗
, ∀𝑗, 𝑖
}︁
, ∆(𝜖)
max = max
{︁
∆𝑖(𝜖)
𝑗
, ∀𝑗, 𝑖
}︁
, and 𝜁denotes the distinguishing coefficient, 𝜁∈[0, 1]. 𝜁is used to expand or squeeze the range of the grey relational coefficient. ( ) ︁︁︁︁
Finally, the GRG Γ(𝜖)
𝑗, which is the weighted average of the grey relational coefficients, is estimated as
Γ(𝜖)
𝑗
= ∑︀2
𝑖=1 𝑤𝑖· 𝛾𝑖(𝜖)
𝑗
, ∀𝑗, where 𝑤𝑖is the weight of the criterion 𝑖and can be more prone to subjective
modifications by a DM. Nevertheless, it is possible to delineate it with the use of an objective method [19]. Besides, ∑︀2
𝑖=1 𝑤𝑖= 1. We should emphasise that GRG only ranks the alternatives; thus, it is not an efficiency
measure. The DMU with the highest GRG is placed first. Finally, the GRG Γ(𝜖)
𝑗, which is the weighted average of the grey relational coefficients, is estimated as
Γ(𝜖)
𝑗
= ∑︀2
𝑖=1 𝑤𝑖· 𝛾𝑖(𝜖)
𝑗
, ∀𝑗, where 𝑤𝑖is the weight of the criterion 𝑖and can be more prone to subjective
modifications by a DM. Nevertheless, it is possible to delineate it with the use of an objective method [19]. Besides, ∑︀2
𝑖=1 𝑤𝑖= 1. We should emphasise that GRG only ranks the alternatives; thus, it is not an efficiency
measure. The DMU with the highest GRG is placed first. ︀
To conclude, GRA is considered as an efficient ranking tool not only for traditional MCDM problems [25],
but also for efficiency evaluation DEA problems as a MCDM context in disguise [41]. Table 4. Interval ultimate cross-efficiencies. Nevertheless, GRA has, to
our knowledge, not yet received explicit attention on ranking interval values and, in particular, interval ultimate
cross-efficiencies within an interval CE matrix. Hence, this section has aspired to attain this target, in the light
of a meaningful prioritisation of the DMUs. ︀
To conclude, GRA is considered as an efficient ranking tool not only for traditional MCDM problems [25],
but also for efficiency evaluation DEA problems as a MCDM context in disguise [41]. Nevertheless, GRA has, to
our knowledge, not yet received explicit attention on ranking interval values and, in particular, interval ultimate
cross-efficiencies within an interval CE matrix. Hence, this section has aspired to attain this target, in the light
of a meaningful prioritisation of the DMUs. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. 𝐸IDMU(1)
2.41405
𝐸ADMU(1)
0.05162
𝐸IDMU(2)
10.92813
𝐸ADMU(2)
0.00550
𝐸IDMU(s)
2.41405
𝐸ADMU(s)
0.00469 presented in Table 6. These scores are also accompanied by the combined self-efficiency ratings for each DMU
and system/stage. The numbers in parentheses illustrate the rankings of the corresponding bank branches for
each type of efficiency measure. presented in Table 6. These scores are also accompanied by the combined self-efficiency ratings for each DMU
and system/stage. The numbers in parentheses illustrate the rankings of the corresponding bank branches for
each type of efficiency measure. In Table 7, no matter what point of view efficiency is measured from, DMU 1 is certainly the best unit and
DMU 10 is the worst unit, in terms of the entire system (second expanded column). Considering stage 1, regard-
less of the viewpoint, DMU 1 and DMU 3 are the most and least desirable units, respectively (third expanded
column). In stage 2 (fourth expanded column), DMU 10 is deemed as the least promising unit. However, there
is no correspondence between the optimistic and pessimistic perspectives regarding the best unit. Notably, none
of the 10 bank branches perform efficiently in both stages and viewpoints. This is, for instance, seen in the
non-efficient overall optimistic self-efficiency scores
(︁
𝐸IDMU(𝑠)
𝑘
)︁
, where the highest score is 0.8132 occurring at
DMU 1, followed by 0.3490 occurring at DMU 6. ︁︁
The next focal point of the framework is the geometric aggregation of the optimistic and pessimistic perspec-
tives, to build a combined self-efficiency measure for each DMU, with respect to the system
(︁
𝐸comb(𝑠)
𝑘
)︁
, the
stage 1
(︁
𝐸comb(1)
𝑘
)︁
, and the stage 2
(︁
𝐸comb(2)
𝑘
)︁
. In Table 7, DMU 1 has the best performance among all units,
reflecting the two opposed standpoints. This is completely verified by the consistent results of the overall system
and the stage 1. Nevertheless, regarding stage 2, there is a significant inconsistency between the optimistic and
the pessimistic efficiency. In detail, DMU 1 receives a moderate rating (0.8132) with respect to the optimistic
aspect. This rating is compensated by its exceptional pessimistic performance (0.0760). The overall performance
of bank branch 1 is also grievously higher than the corresponding performance of all others. A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 1309 4. Numerical application This section illustrates the use of the mathematical models presented in Section 3 to meaningfully evaluate
and rank the DMUs. There are two salient factors that evaluate each DMU within the two-stage tandem
structure herein: (i) the optimistic and pessimistic efficiency scores within a self-evaluation context, and (ii)
the most favourable and unfavourable weight sets of each of the other DMUs, in a peer-appraisal setting that
integrates the combined self-efficiency measure. The numerical example drawn from Zhou et al. [55] is used for illustrative purposes. In Table 5, ten bank
branches of China Construction Bank in Anhui are assessed within the two-stage tandem structure (see Fig. 2). The employee (𝑋1), the fixed assets (𝑋2), and the expenses (𝑋3) are the input resources of the first stage to be
consumed to produce the intermediate products; the credit (𝑍1) and the inter-bank loans (𝑍2). The latter are
used as inputs in the second stage to generate the final outputs; the loan (𝑌1) and the profit (𝑌2). For modelling,
running, and analysing our data, we have utilised the programming language Python 3.7.6 and in particular
the version 2.1 of PuLP as the free linear programming library. The experiment ran on a computer with 16GB
RAM. In our framework, we first consider determining the best and worst relative efficiencies of the IDMU and the
ADMU, respectively, for the overall system and its individual stages. Table 6 exhibits the corresponding scores
from solving models (3.3)–(3.6), introduced in Section 3.1. Then, models (3.7)–(3.10) are used to obtain the highest and the lowest relative efficiency scores of the target
DMU𝑘in terms of the overall system, the stage 1, and the stage 2. These scores are given in Table 7. Recall that
these relative self-efficiency scores indicate their distance from the respective IDMU and ADMU efficiencies, Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. For instance, in
stage 1 the combined self-efficiency score of DMU 1 approximates 0.51, whereas the corresponding rating of
DMU 2 (in the second place) equals to 0.2733. The geometric average efficiency also indicates that DMU 10 has
the worst performance in terms of the overall system and the stage 2. p
y
g
The combined self-efficiencies calculated for every DMU, satisfy the sound mathematical property that the
overall system combined self-efficiency score is the product of the two sub-stages, as discussed in Section 3.1. As an example, the combined self-efficiencies calculated for DMU 1 satisfy 0.1267 = 0.5099 * 0.2486. Since this
property is satisfied, every 𝐸comb(𝑠)
𝑘
is no greater than its corresponding 𝐸comb(1)
𝑘
and 𝐸comb(2)
𝑘
. Another point
to be noted is that most bank branches have a smaller 𝐸comb(2)
𝑘
than 𝐸comb(1)
𝑘
. Only DMUs 3, 8, and 9 have a
smaller 𝐸comb(1)
𝑘
than 𝐸comb(2)
𝑘
. However, after implementing the Wilcoxon’s matched-pairs signed-ranks test [9]
we found that there is not sufficient evidence to say that the average efficiency measures of these two sub-stages
are not equal. This may be due to the limited sample under examination. In addition, it is noteworthy that the
difference between ratings and ranks of the combined self-efficiency measures in all stages is quite significant
for several bank branches. For instance, the rank of DMU 3 for the overall system, the stage 1, and the stage
2, is 8, 10, and 2, respectively, indicating that at least 6 ranks difference exists. A large difference may reveal
the source that causes the inefficiency of the overall system. For example, DMUs 2 and 5 perform satisfactorily
in stage 1 (as compared to stage 2) whereas DMUs 3 and 8 perform satisfactorily in stage 2 (as compared to
stage 1). Decomposing the overall system combined self-efficiency score into the product of its two sub-stages,
may assist the respective bank branch in identifying the sub-stage that triggers inefficiency. 1310 M.D. KREMANTZIS ET AL. The combined self-efficiency measures obtained with our proposed method (see the respective columns of
Tab. 7) are also compared with the respective scores (Tab. 8) obtained with Kao and Hwang’s [21] approach. As mentioned in Section 3, the latter approach aims to explore the efficiency decomposition in a two-stage
production process by taking into consideration the series relationship of the two sub-stages. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. As a matter of fact, there is no absolute discrimination of some inefficient
DMUs considering the combined self-evaluation results at each stage, presented in Table 7. In particular, in the
overall system the DMUs 2 and 6 tied (0.0528) in the second place. Similarly, at stage 2 the DMUs 3 and 6 also
tied (0.2094), sharing the second place. In such results, each DMU is self-assessed ignoring the weight profile of
each of the other DMUs. Embedding the geometric average score into a peer context, would possibly contribute
to a more comprehensive ranking. To this end, the proposed framework is further extended by the use of the
interval CE. The next step in our proposed approach concerns the implementation of the interval CE towards the evaluated
network structure, as discussed in Section 3.2. Tables 9–11 showcase the interval individual cross-efficiencies of
DMU𝑗based on the optimal weight scheme of DMU𝑘for the overall system, the stage 1, and the stage 2,
respectively. In this case, each DMU is evaluated considering simultaneously an aggressive (model (3.11)) and
a benevolent (model (3.12)) strategy; this originally creates an atmosphere of neutrality. (
(
))
gy;
g
y
p
y
To make the content of Tables 9–11 comprehensible to the reader, it should be ideal to present a few examples. In the second column of Table 9, DMU 1 is assessed based on the weight profile of all other DMUs, except its
own weight set. The minimum and maximum individual cross-efficiencies of DMU 1 based on the optimal weight
scheme of DMU 2 are 0.1216 and 0.2371, respectively, for the overall system. In the fifth column of Table 10,
DMU 4 is also peer-appraised with respect to the weight profile of all other DMUs. The minimum and maximum
individual cross-efficiencies of DMU 4 based on the weight profile of DMU 10 are 0.1475 and 0.2281, respectively,
for sub-stage 1. Table 11 determines in a similar manner the individual cross-efficiencies for each DMU, for the
sub-stage 2. The diagonal leading column in each of these three matrices demonstrates the special case in which
𝐸L(𝜖)*
𝑗𝑗
= 𝐸U(𝜖)*
𝑗𝑗
= 𝐸comb(𝜖)*
𝑗
∀𝑗, where 𝜖= 𝑠(overall system), 1 (stage 1) or 2 (stage 2). These are the combined
self-efficiency scores. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. Their relational
model (see model (3.1)) was found to be reliable in terms of measuring overall and division efficiencies along
with the better identification of the causes of inefficiency. Our study has applied their relational model to further
analyse and validate the dataset provided in Table 5, by measuring the efficiencies of the whole process and
its constituent sub-stages for the ten DMUs. In Table 8, the self-efficiency scores along with their ranks of the
overall system, the stage 1, and the stage 2, are depicted in the second, third, and fourth column, respectively. The rankings of the two models with respect to the overall system are quite similar, showing that the largest
difference is 1 occurring at the bank branches 2, 3, and 8. The rankings of the two models with respect to
sub-stage 1 are also quite close to each other. In the latter case, the largest difference occurs at DMU 7 with a
rank difference of 4. The second largest difference occurs at DMUs 9 and 10 with a rank difference of 2. For the
remaining 7 bank branches, their rank differences are less than 2. The rank differences look very similar even
with the case of sub-stage 2. Correlation analysis suggests that there is a highly strong association between the
ranks of these two approaches, as indicated by the Spearman coefficients [9] of 0.985 (overall system), 0.806
(stage 1), and 0.841 (stage 2), which are significant at the 0.01 level (two-tailed). This can be demonstrated
even by the fact that both our method and Kao and Hwang’s method identify DMU 1 as the best performer. However, our approach is more informative within the self-appraisal context, in that it not only considers the
most favourable self-efficiency scores (as in [21]), but also the most unfavourable ones to obtain a more accurate
and less misleading overall assessment for each DMU and flow. As a result, it puts emphasis on both sides of
the same coin simultaneously. The above points further validate the rationale of our approach. As discussed in Section 1, the geometric average efficiency is an easy-to-use measure with a good discriminating
power amongst the evaluated DMUs. However, it may not be sufficiently strong in terms of leading to a unique
ranking in this two-stage process. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. DMU
𝐸𝑠
𝑘(Rank)
𝐸1
𝑘(Rank)
𝐸2
𝑘(Rank)
1
1.00 (1)
1.00 (1)
1.00 (1)
2
0.43 (3)
0.55 (2)
0.79 (8)
3
0.29 (7)
0.29 (9)
1.00 (1)
4
0.30 (6)
0.32 (7)
0.94 (4)
5
0.35 (4)
0.43 (4)
0.83 (7)
6
0.54 (2)
0.54 (3)
1.00 (1)
7
0.18 (9)
0.28 (10)
0.62 (9)
8
0.28 (8)
0.31 (8)
0.92 (5)
9
0.33 (5)
0.38 (5)
0.85 (6)
10
0.17 (10)
0.37 (6)
0.47 (10) Table 9. Interval cross-efficiencies for the overall system. Table 9. Interval cross-efficiencies for the overall system. DMU
1
2
3
4
5
6
7
8
9
10
1
0.1267 0.1267
0.0282 0.0550
0.0207 0.0371
0.0127 0.0381
0.0294 0.0449
0.0370 0.0690
0.0121 0.0226
0.0198 0.0357
0.0215 0.0415
0.0011 0.0221
2
0.1216 0.2371
0.0528 0.0528
0.0225 0.0613
0.0234 0.0397
0.0382 0.0597
0.0489 0.0785
0.0182 0.0269
0.0223 0.0563
0.0347 0.0438
0.0017 0.0234
3
0.0970 0.1738
0.0244 0.0667
0.0284 0.0284
0.0108 0.0498
0.0250 0.0587
0.0314 0.0854
0.0103 0.0295
0.0261 0.0300
0.0203 0.0463
0.0016 0.0178
4
0.1018 0.3039
0.0407 0.0691
0.0175 0.0802
0.0307 0.0307
0.0354 0.0707
0.0437 0.0888
0.0182 0.0292
0.0184 0.0737
0.0268 0.0573
0.0014 0.0307
5
0.1192 0.1819
0.0374 0.0585
0.0205 0.0480
0.0183 0.0366
0.0423 0.0423
0.0489 0.0677
0.0174 0.0220
0.0216 0.0441
0.0285 0.0442
0.0015 0.0225
6
0.0966 0.1801
0.0354 0.0568
0.0175 0.0475
0.0181 0.0369
0.0329 0.0455
0.0528 0.0528
0.0164 0.0219
0.0173 0.0437
0.0269 0.0407
0.0013 0.0243
7
0.1161 0.2161
0.0407 0.0600
0.0199 0.0571
0.0218 0.0349
0.0397 0.0502
0.0498 0.0664
0.0208 0.0208
0.0210 0.0524
0.0305 0.0453
0.0016 0.0240
8
0.1012 0.1825
0.0267 0.0675
0.0270 0.0310
0.0118 0.0473
0.0273 0.0557
0.0343 0.0864
0.0112 0.0282
0.0285 0.0285
0.0221 0.0468
0.0017 0.0176
9
0.1105 0.2136
0.0437 0.0551
0.0222 0.0507
0.0194 0.0415
0.0347 0.0538
0.0469 0.0708
0.0166 0.0246
0.0220 0.0466
0.0363 0.0363
0.0017 0.0216
10
0.0357 0.6610
0.014 0.1913
0.0099 0.1081
0.0062 0.1326
0.0117 0.1666
0.0135 0.2448
0.0053 0.0798
0.0100 0.1033
0.0104 0.1327
0.0062 0.0062
ultim. CE
0.1000 0.2611
0.0323 0.0755
0.0197 0.0579
0.0158 0.0508
0.0305 0.0673
0.0394 0.0953
0.0140 0.0316
0.0198 0.0540
0.0246 0.0554
0.0015 0.0227 Recalling the discussion in Section 3.3, we view each interval CE matrix as a MCDM problem. In Tables 9–11,
the ten DMUs (alternatives) located in their last 11 columns, are evaluated by the weight profiles of the ten
DMUs (criteria) presented in their first column. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. Clearly, the property of maintaining the combined self-efficiency measure for each DMU
is satisfied both for the overall system and its individual stages; this accomplishes our efforts towards a more
reasoned peer-appraisal setting that entails the effects of the optimistic and pessimistic viewpoints. A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 1311 Table 7. Self-efficiency ratings and ranks of the overall system, the stage 1, and the stage 2,
with the proposed method. DMU 𝐸IDMU(s)
𝑘
𝐸ADMU(s)
𝑘
𝐸comb(s)
𝑘
𝐸IDMU(1)
𝑘
𝐸ADMU(1)
𝑘
𝐸comb(1)
𝑘
𝐸IDMU(2)
𝑘
𝐸ADMU(2)
𝑘
𝐸comb(2)
𝑘
1
0.8132 (1)
0.0197 (1)
0.1267 (1)
1.0000 (1)
0.2600 (1)
0.5099 (1)
0.8132 (6)
0.0760 (1)
0.2486 (1)
2
0.3255 (3)
0.0086 (2)
0.0528 (2) 0.5186 (2)
0.1441 (5)
0.2733 (2)
0.6277 (8)
0.0595 (2)
0.1933 (6)
3
0.1398 (9)
0.0058 (6)
0.0284 (8)
0.1421 (10) 0.1298 (10) 0.1358 (10) 0.9838 (2)
0.0446 (5)
0.2094 (2)
4
0.2450 (5)
0.0038 (8)
0.0307 (6)
0.2655 (5)
0.1731 (3)
0.2144 (5)
0.9227 (3)
0.0222 (8)
0.1432 (8)
5
0.2886 (4)
0.0062 (4)
0.0423 (4)
0.3927 (4)
0.1818 (2)
0.2672 (3)
0.7350 (7)
0.0341 (7)
0.1584 (7)
6
0.3490 (2)
0.0080 (3)
0.0528 (2) 0.4101 (3)
0.1549 (4)
0.2521 (4)
0.8509 (5)
0.0515 (3)
0.2094 (2)
7
0.1454 (8)
0.0030 (9)
0.0208 (9)
0.2549 (6)
0.1425 (7)
0.1906 (6)
0.5706 (9)
0.0208 (9)
0.1090 (9)
8
0.1476 (7)
0.0055 (7)
0.0285 (7)
0.1476 (9)
0.1372 (8)
0.1423 (9)
1.0000 (1)
0.0402 (6)
0.2005 (5)
9
0.2141 (6)
0.0061 (5)
0.0363 (5)
0.2389 (7)
0.1362 (9)
0.1804 (7)
0.8963 (4)
0.0451 (4)
0.2011 (4)
10
0.0133 (10) 0.0029 (10) 0.0062 (10) 0.1796 (8)
0.1438 (6)
0.1607 (8)
0.0739 (10) 0.0204 (10) 0.0389 (10)
Table 8. Self-efficiency ratings and ranks of the overall system, the stage 1, and the stage 2,
with Kao and Hwang’s [21] method. Table 8. Self-efficiency ratings and ranks of the overall system, the stage 1, and the stage 2,
with Kao and Hwang’s [21] method. Table 10. Interval cross-efficiencies for the stage 1. Table 11. Interval cross-efficiencies for the stage 2. and stage 2, respectively. The interval weights are obtained via the GP model (3.13), and the interval global
weights, according to the pair of optimisation models (3.14) and (3.15), as stated in Section 3.3. For instance, in the second column of the last row of Table 9, we obtain the interval ultimate CE of DMU 1:
[0.1000, 0.2611], where 0.1000 is the minimum and 0.2611 is the maximum CE score. The minimum score of
DMU 1 for the overall system is estimated via solving model (3.14). The basic prerequisites of this model are to
recognise the minimum individual cross-efficiencies of DMU 1 based on the weight profile of all ten DMUs (left
side of column 2 of Tab. 9) and the interval weights per criterion for the overall system (column 2 of Tab. 12). The maximum ultimate cross-efficiency of DMU 1 for the overall system is estimated via solving model (3.17). The basic prerequisites of this model are to identify the maximum individual cross-efficiencies of DMU 1 based
on the weight profile of all 10 DMUs (right side of column 2 of Tab. 9) and the interval weights per criterion
for the overall system (column 2 of Tab. 12). The final step of our methodological approach seeks for a unique and reasonable prioritisation of the interval
ultimate cross-efficiencies via the established GRA, as discussed in Section 3.4. This step continues to allow
the DMUs, located in the columns of the interval CE matrices mentioned above, to act as alternatives and
to be assessed by two attributes; the first attribute concerns the minimum (worst condition) and the second
attribute is pertinent to the maximum (best condition) ultimate CE of each DMU, towards the corresponding
system/stage. The interval ultimate cross-efficiencies (last row of each of the Tabs. 9–11) form the appropriate
matrix, as shown in Table 4. The data of performance values of the two attributes are subsequently normalised through the greater-the-
better equation (3.16); this choice reflects the necessity of pushing up the peer-efficiency of each DMU. The
results are depicted in the second column of Appendix A for the overall system, of Appendix B for stage 1,
and of Appendix C for stage 2. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. To designate the interval global weights (interval ultimate cross-
efficiencies) in the last row of each of these matrices, it is required to determine the interval weight per criterion
except the known interval individual cross-efficiencies. To start with, the interval weight of each criterion is
determined in the second, third, and fourth column of Table 11, with respect to the overall system, stage 1, 1312 M.D. KREMANTZIS ET AL. Table 10. Interval cross-efficiencies for the stage 1. DMU
1
2
3
4
5
6
7
8
9
10
1
0.5099 0.5099
0.1472 0.2811
0.0689 0.0764
0.0615 0.1353
0.1422 0.2002
0.1615 0.2654
0.0826 0.1299
0.0648 0.0752
0.0785 0.1366
0.0530 0.0915
2
0.4956 0.9466
0.2733 0.2733
0.0743 0.1279
0.1143 0.1399
0.1867 0.2640
0.2161 0.2998
0.1255 0.1533
0.0724 0.1203
0.1258 0.1458
0.0757 0.0984
3
0.9056 0.9999
0.2887 0.4994
0.1358 0.1358
0.1211 0.2537
0.2793 0.3751
0.3170 0.4715
0.1623 0.2435
0.1277 0.1410
0.1543 0.2426
0.1044 0.1716
4
0.8073 1.0000
0.4186 0.2893
0.1147 0.2665
0.2144 0.2144
0.3103 0.3785
0.3311 0.3713
0.2057 0.2407
0.1191 0.2653
0.1928 0.2223
0.1259 0.2174
5
0.6804 0.9578
0.2765 0.3911
0.0967 0.1295
0.1156 0.1845
0.2672 0.2672
0.2790 0.3692
0.1552 0.1796
0.1004 0.1217
0.1475 0.1900
0.0995 0.1222
6
0.4923 0.8093
0.2336 0.3241
0.0738 0.1094
0.0977 0.1659
0.1855 0.2454
0.2521 0.2521
0.1247 0.1593
0.0720 0.1028
0.1246 0.1493
0.0752 0.1122
7
0.7478 1.0000
0.2889 0.4148
0.1062 0.1828
0.1547 0.1985
0.2834 0.3151
0.3067 0.3917
0.1906 0.1906
0.1100 0.1773
0.1786 0.2015
0.1150 0.1343
8
0.9640 0.9999
0.2887 0.5365
0.1370 0.1496
0.1310 0.2559
0.2898 0.3785
0.3227 0.5066
0.1706 0.2465
0.1423 0.1423
0.1615 0.2606
0.1164 0.1731
9
0.6732 1.0000
0.2889 0.3915
0.1009 0.1858
0.1568 0.2005
0.2536 0.3173
0.3097 0.3378
0.1705 0.1924
0.0984 0.1803
0.1804 0.1804
0.1029 0.1356
10
0.2473 0.6610
0.1239 0.2484
0.1170 0.1958
0.1475 0.2281
0.1802 0.2651
0.1433 0.2834
0.1364 0.1816
0.1317 0.1961
0.1218 0.1858
0.1607 0.1607
ultim. CE
0.6083 0.7509
0.2172 0.3407
0.0892 0.1257
0.1018 0.1754
0.2013 0.2661
0.2260 0.3277
0.1245 0.1705
0.0880 0.1230
0.1195 0.1731
0.0808 0.1240
Table 11. Interval cross-efficiencies for the stage 2. Table 6. Highest and lowest relative efficiency scores for the overall system, stage 1, and stage 2. DMU
1
2
3
4
5
6
7
8
9
10
1
0.2486 0.2486
0.1918 0.1957
0.3007 0.4856
0.2078 0.2820
0.2072 0.2246
0.2294 0.2600
0.1473 0.1743
0.3056 0.4745
0.2739 0.3044
0.0225 0.2417
2
0.2454 0.2504
0.1933 0.1933
0.3030 0.4795
0.2052 0.2842
0.2046 0.2263
0.2265 0.2620
0.1455 0.1757
0.3080 0.4686
0.2760 0.3006
0.0227 0.2387
3
0.1072 0.1738
0.0848 0.1336
0.2094 0.2094
0.0897 0.1964
0.0896 0.1564
0.0993 0.1811
0.0636 0.1214
0.2045 0.2128
0.1316 0.1908
0.0157 0.1042
4
0.1261 0.3039
0.0973 0.2389
0.1526 0.3012
0.1432 0.1432
0.1140 0.1867
0.1320 0.2393
0.0885 0.1213
0.1551 0.2779
0.1390 0.2580
0.0114 0.1413
5
0.1752 0.1899
0.1352 0.1495
0.2119 0.3710
0.1588 0.1988
0.1584 0.1584
0.1753 0.1833
0.1126 0.1229
0.2154 0.3626
0.1931 0.2326
0.0159 0.1847
6
0.1963 0.2225
0.1515 0.1753
0.2375 0.4348
0.1861 0.2228
0.1775 0.1856
0.2094 0.2094
0.1319 0.1377
0.2414 0.4249
0.2164 0.2726
0.0178 0.2165
7
0.1553 0.2161
0.1409 0.1447
0.1878 0.3122
0.1410 0.1762
0.1403 0.1595
0.1625 0.1696
0.1090 0.1090
0.1909 0.2959
0.1711 0.2251
0.0141 0.1787
8
0.1050 0.1825
0.0925 0.1258
0.1972 0.2075
0.0905 0.185
0.0943 0.1473
0.1065 0.1706
0.0661 0.1143
0.2005 0.2005
0.1373 0.1797
0.0148 0.1021
9
0.1641 0.2136
0.1512 0.1408
0.2207 0.2732
0.1237 0.2070
0.1368 0.1697
0.1515 0.2095
0.0973 0.1280
0.2243 0.2585
0.2011 0.2011
0.0165 0.1596
10
0.1444 1.0000
0.1132 0.7699
0.0847 0.5521
0.0422 0.5815
0.0649 0.6285
0.0943 0.8637
0.0395 0.4397
0.0764 0.5268
0.0858 0.7140
0.0389 0.0389
ultim. CE
0.1606 0.2970
0.1310 0.2247
0.2055 0.3782
0.1354 0.2522
0.1349 0.2235
0.1540 0.2722
0.0977 0.1644
0.2071 0.3656
0.1770 0.2904
0.0168 0.1773 Table 10. Interval cross-efficiencies for the stage 1. Table 10. Interval cross-efficiencies for the stage 1. The unique final rank in Table 13 reflects the improvement of the discriminating power, as compared
to the original rank derived from the combined self-efficiency measures in Table 7. This practically means that
the non-dominated bank branches, which cannot be fully discriminated by the self-evaluation notion, can be
discriminated by the methodologies followed in peer notion. In detail, DMU 10 is without a doubt the least
desirable unit in all three cases. DMU 1 is also considered to be the most promising bank branch for the overall
system and stage 1, while DMU 3 is the best unit according to stage 2. Generally, one can deduce that the ranking
results for all branches (except DMU 10) are not consistent and may show a higher degree of uncertainty and
inefficiency in specific stages. The GRG grades obtained with our proposed framework (see Tab. 13) are also compared with the respective
ultimate cross-efficiency ratings (Tab. 14) obtained via the Kao and Liu’s [21] approach. In their study, they
applied the concept of cross-evaluation to measure the efficiency of basic (parallel & series) network structures. Their proposed aggressive-based secondary goal model was particularly able to decompose the cross-efficiency
score of the overall system into the product of those of the internal sub-stages for the series structure. Our study
has applied their aggressive-based model under the two-stage tandem series structure and the peer-appraisal
setting to further analyse the dataset provided in Table 5. In Table 14, the peer-efficiency scores along with
their ranks of the overall system, the stage 1, and the stage 2, are respectively presented in the second, third,
and fourth column. Firstly, we have noticed that the multiplicative mathematical relationship between the
overall system and its sub-stage efficiencies is indeed satisfied. For example, the ultimate cross-efficiency score
of DMU 6 (0.446) is equal to the product of its sub-stage 1 (0.574) and sub-stage 2 (0.778) efficiencies. Secondly,
the rankings of the two methods with respect to the overall system and the stage 1 are not significantly different
based on a Spearman rank order correlation test with statistics of 0.964 and 0.830, respectively. These are
significant at the 0.01 level (two-tailed). However, it is worthwhile to mention that DMU 10 has a difference of
3 ranks in terms of the evaluation of stage 1. Thirdly, as for the stage 2, the rankings from the two methods are
not so close. Table 10. Interval cross-efficiencies for the stage 1. The grey relational distance calculation is also utilised to measure the distance
between the reference sequence and the comparability sequence (normalised values), see the third column of
each of the appendices. In addition, we compute the grey relational coefficient to explore how close the reference
and the comparability sequences are. In this formula, the value of 𝜁may affect the size of the correlation degree
distribution interval, thereby affecting the results of the correlation analysis. The value of 𝜁can be determined
considering the DMU’s tendency towards optimism-pessimism. Following [21], we have set 𝜁= 0.5 implying 1313 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Table 12. Interval weights per criterion for the overall system, the stage 1, and the stage 2. Criteria
(DMUs)
Interval weights
per criterion
(overall system)
Interval weights per
criterion (stage 1)
Interval weights per
criterion (stage 2)
1
0.0000
0.1111
0.4502
0.4726
0.0134
0.1198
2
0.0000
0.1111
0.0286
0.0510
0.0133
0.1197
3
0.0000
0.1111
0.0506
0.0730
0.0016
0.1080
4
0.0000
0.1111
0.0479
0.0703
0.0023
0.1088
5
0.0000
0.1111
0.0390
0.0613
0.0068
0.1132
6
0.0000
0.1111
0.0283
0.0507
0.0091
0.1156
7
0.0000
0.1111
0.0433
0.0657
0.0052
0.1117
8
0.0000
0.1111
0.0538
0.0761
0.0017
0.1081
9
0.0000
0.1111
0.0394
0.0618
0.0060
0.1125
10
0.0000
0.1111
0.0170
0.0394
0.0000
0.0887 12. Interval weights per criterion for the overall system, the stage 1, and the stage 2. that the DMU has neither an optimistic nor a conservative attitude. The respective results are portrayed in the
last column of each of the appendices. that the DMU has neither an optimistic nor a conservative attitude. The respective results are portrayed in the
last column of each of the appendices. that the DMU has neither an optimistic nor a conservative attitude. The respective results are portrayed in the
last column of each of the appendices. The GRG and the rank for each DMU with respect to the overall system, the stage 1, and the stage 2,
are illustrated in the second, third, and fourth column of Table 13, respectively. It is important to make two
remarks about the process of obtaining the GRG: firstly, the relative importance weights of the two performance
attributes were assumed to be equal (𝑤1 = 𝑤2 = 0.5) illustrating that the two extremes are of the same
importance, and secondly, the GRG is just an index that only captures the rank rather than an efficiency
measure. Table 10. Interval cross-efficiencies for the stage 1. The bank branch 2 is the extreme case with a rank difference of 6. The second largest difference
occurs at DMU 8 with a rank difference of 4. All the remaining bank branches have a rank difference of no 1314 M.D. KREMANTZIS ET AL. Table 13. Grey Relational Grade and ranks of the overall system, the stage 1, and the stage 2. DMU
GRG
Γ(𝑠)
𝑗
Rank over-
all system
GRG
Γ(1)
𝑗
Rank
stage 1
GRG
Γ(2)
𝑗
Rank
stage 2
1
1.0000
1
1.0000
1
0.6199
4
2
0.4062
3
0.4181
2
0.4830
8
3
0.3750
6
0.3356
8
0.9916
1
4
0.3655
8
0.3477
7
0.5145
6
5
0.3978
4
0.3931
4
0.4886
7
6
0.4333
2
0.4171
3
0.5719
5
7
0.3530
9
0.3519
5
0.3992
9
8
0.3729
7
0.3349
9
0.9471
2
9
0.3811
5
0.3512
6
0.6543
3
10
0.3333
10
0.3335
10
0.3403
10
Table 14. Peer-efficiency ratings and ranks of the overall system, the stage 1, and the stage
2, with Kao and Liu’s [22] method. Table 13. Grey Relational Grade and ranks of the overall system, the stage 1, and the stage 2. 3. Grey Relational Grade and ranks of the overall system, the stage 1, and the stage 2. Table 14. Peer-efficiency ratings and ranks of the overall system, the stage 1, and the stage
2, with Kao and Liu’s [22] method. Table 14. Peer-efficiency ratings and ranks of the overall system, the stage 1, and the stage
2, with Kao and Liu’s [22] method. DMU
System CE (Rank)
Stage 1 CE (Rank)
Stage 2 CE (Rank)
1
1.000 (1)
1.000 (1)
1.000 (1)
2
0.416 (3)
0.534 (4)
0.780 (2)
3
0.239 (7)
0.315 (10)
0.760 (4)
4
0.251 (6)
0.488 (5)
0.513 (8)
5
0.330 (4)
0.573 (3)
0.576 (7)
6
0.446 (2)
0.574 (2)
0.778 (3)
7
0.160 (9)
0.420 (6)
0.381 (9)
8
0.238 (8)
0.336 (9)
0.710 (6)
9
0.297 (5)
0.392 (8)
0.756 (5)
10
0.072 (10)
0.397 (7)
0.182 (10) DMU
System CE (Rank)
Stage 1 CE (Rank)
Stage 2 CE (Rank) more than 3. Statistically, this situation is even further validated by the Spearman coefficient of 0.503, which
implies a moderate association between the rankings of the two methods. 5. Conclusions & future research This paper has provided new insight into the attainment of a meaningful and unique ranking of DMUs under a
two-stage tandem (network) structure. In particular, it extends the selected optimistic-pessimistic DEA models
into the two-stage tandem system, to then complement the interval CE method within such a system. Decision
makers are offered with the chance of evaluating the performance of the DMUs by considering: (i) the optimistic
and pessimistic self-efficiency scores, and (ii) the most favourable and unfavourable weight profiles of each of the
other DMUs in a peer-appraisal setting. In this study, we have introduced a 7-step methodological approach, as
shown in Figure 1, which combines existing methods from the literature in a novel way. This approach supports
the aforementioned conditions and ensures more multi-dimensional evaluation outcomes. The procedures implemented in the first three steps of our framework indicate how the optimistic and
pessimistic DEA models, which are inspired by the studies of Wang and Luo [48] and Wu [51], are built
towards the more realistic two-stage tandem system that better reflects the complex interconnections among its
internal sub-systems. The DMUs are initially evaluated, based on their own most favourable (optimistic) and
unfavourable (pessimistic) optimal multipliers, and then are aggregated into a combined self-efficiency measure
via the geometric average. The remaining steps of our framework ensure the peer-evaluation of the DMUs via the customisation of the
interval CE method to the specifications of the two-stage tandem structure while keeping the combined self-
efficiency measure unchanged. To rank all DMUs in the interval CE matrix of the corresponding flow, the study
introduces an alternative novel use of the GP method of Wang and Elhag [47], the LP models by Entani and
Tanaka [13], and the GRA of Kuo et al. [25]. The combination of such well-established techniques for extracting
valuable insights from an interval CE matrix has not been considered before. This combination underpins the
wider MCDM context to which the elements of the interval CE matrix belong. We envisage that our study could be applicable in several areas. In the non-life insurance industry [21],
for example, operations consist of the insurance service and the capital investment. Customers pay direct
written and reinsurance premiums, which are then invested in a portfolio to earn underwriting profit. A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 1315 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Table 10. Interval cross-efficiencies for the stage 1. Finally, Kao and Liu’s [22] approach
only considers the most unfavourable weight sets of each of the other DMUs, while keeping the optimistic
self-efficiency score constant. However, our study is more multi-dimensional since it simultaneously takes into
account the most favourable and unfavourable weight sets of each of the other players, while integrating the
respective combined self-efficiency measure. Finally, it can be statistically inferred that the rankings of the DMUs obtained from the combined self-
efficiency measures (self-appraisal), and the grey relational grades after showing peer-appraisal, are similar
with respect to the overall system and its sub-stages. As an example, for the overall system, according to the
Spearman correlation test [9], the 𝑟𝑠= 0.948. This indicates that under the significance level of 0.01, there is
a strong positive association between the ranking values of the DMUs obtained by the two separate conditions
(self-appraisal & peer-appraisal), confirming the validity of our framework. Exceptions are considered the DMUs
1, 6, and 8 within the evaluation of the second sub-stage, where there is a larger rank difference of 3. This could
be justified by the nature of the self-appraisal setting to let each bank branch to be evaluated based only on its
own (favourable and unfavourable) standpoint, while the peer-appraisal setting expects the bank branches to
be evaluated from the (favourable and unfavourable) standpoint of all branches. 5. Conclusions & future research Finally, further study could focus on
the testing of the proposed models and frameworks with empirical data. In the shipping industry, for example,
it could be deployed to compare the efficiency of potential designs of a particular type of vessel, including the
selection of the right mixture of maintenance policies. interval CE matrix and, thus, our paper has worked towards this direction. Finally, further study could focus on
the testing of the proposed models and frameworks with empirical data. In the shipping industry, for example,
it could be deployed to compare the efficiency of potential designs of a particular type of vessel, including the
selection of the right mixture of maintenance policies. g
p
The models in this study were developed under the assumption of the constant returns-to-scale. A direction
for future research could be their advancement to variable returns-to-scale DEA models. In addition, current
research studies the evaluation of the performance of several DMUs with a two-stage tandem structure in a
self and in a peer-appraisal setting, only when the data (i.e., the input and output factors) are accurate and
unambiguous, and the DEA models are based on this condition. Future research could relax this assumption
by allowing the data points to be imprecise (e.g., to be expressed as linguistic terms) and lie in an interval. Other cases to be investigated concern missing data or intervals, where some values are more likely to occur
over other values. In the latter case, since there is no information of the probability distributions, fuzzy numbers
and mathematical operations [58] could be used as an ideal alternative option. For example, there is a growing
body of literature [11,17,36,40] surrounding the development of novel fuzzy DEA approaches and models char-
acterised by intuitionistic fuzzy data, applied possibility, necessity, credibility, general fuzzy measures, and/or
trapezoidal fuzzy numbers. Some of these models were solved with the aid of either a linear programming with
an intuitionistic fuzzy objective function and an alphabetical technique, a chance-constrained programming, a
lexicographic multi-objective linear programming, or a fuzzy linear programming. The network double-frontier
DEA models introduced in this study could be adjusted to the specifications of such an uncertain (fuzzy)
environment adopting the most suitable formulation and solution techniques. Finally, it would be worthwhile to adjust the modelling approaches, introduced in our study, ensuring that
they will be taking into consideration the decision maker’s preferences. 5. Conclusions & future research Another
promising area would be the evaluation of the performance of the high-technology industry that is decomposed
into the technology development and the economic application [54]. In this two-stage tandem network, raw
data and knowledge are processed into technological achievements, which are then transformed into economic
development. A third application connects our study’s methodological framework with the operational activities
of the international shipping industry; these could be divided into the supervision of the ship dispatching
management and the control of the working time in the port [15]. Finally, the efficiency evaluation of two-stage
(food) supply chains of different factories or farming communities [24] could also serve the goals of our paper. For instance, the process of the refinement of selected cocoa beans into milk/dark chocolate and the production
of black tea through withering, fermentation, drying, and sieving across a number of specialised factory branches
could further highlight the importance of our evaluation and ranking framework. This paper treats the two sub-stages of a DMU equally. In reality, however, there might be a certain degree
of leader-follower relationship between the upstream and downstream of a particular DMU. We acknowledge
this as a limitation of our study and we believe that the introduction of relative weights for the different stages
when calculating overall efficiency could accommodate such an issue. In addition, one of the main steps of the
grey relational analysis methodology, used to rank the interval ultimate cross-efficiencies within an interval
cross-efficiency matrix, is the calculation of the grey relational grade. It is defined as the weighted average of
the grey relational coefficients, where the weight of the respective criterion is subjectively determined by the
decision maker. To better reflect the reality, we would have taken advantage of an existing powerful multi-criteria
decision-making method, such as the analytic network process [39] or the best-worst method [38], to identify in
an objective manner the weights. We have also recognised that the grey relational grade is just an index that can
only capture the rank rather than an efficiency measure. In other words, there is no sufficient information that
would allow the identification of the DEA-efficient DMUs that constitute the best-practice frontier. However, we
acknowledge that the GRA technique has not received attention on ranking interval cross-efficiencies within an 1316 M.D. KREMANTZIS ET AL. interval CE matrix and, thus, our paper has worked towards this direction. 5. Conclusions & future research Relevant literature has already focused
on this aspect by combining DEA and multiple-objective linear programming [12,30,31,44]. Appendix B. Stage 1 and grey relational analysis Table B.1. Normalisation of data, calculation of grey relational distance and grey relational
coefficient for the stage 1. DMU
Normalisation of data
Grey relational distance
Grey relational coefficient
C1
C2
C1
C2
C1
C2
1
1.0000
1.0000
0.0000
0.0000
1.0000
1.0000
2
0.2585
0.3467
0.7415
0.6533
0.4028
0.4335
3
0.0159
0.0043
0.9841
0.9957
0.3369
0.3343
4
0.0397
0.0834
0.9603
0.9166
0.3424
0.3529
5
0.2284
0.2278
0.7716
0.7722
0.3932
0.3930
6
0.2753
0.3259
0.7247
0.6741
0.4083
0.4259
7
0.0827
0.0756
0.9173
0.9244
0.3528
0.3510
8
0.0135
0.0000
0.9865
1.0000
0.3364
0.3333
9
0.0732
0.0797
0.9268
0.9203
0.3504
0.3520
10
0.0000
0.0015
1.0000
0.9985
0.3333
0.3337
Reference value
1.0000
1.0000
–
–
–
– Appendix C. Stage 2 and grey relational analysis Table C.1. Normalisation of data, calculation of grey relational distance and grey relational
coefficient for the stage 2. DMU
Normalisation of data
Grey relational distance
Grey relational coefficient
C1
C2
C1
C2
C1
C2
1
0.7556
0.6199
0.2444
0.3801
0.6717
0.5681
2
0.6000
0.2820
0.4000
0.7180
0.5555
0.4105
3
0.9915
1.0000
0.0085
0.0000
0.9833
1.0000
4
0.6230
0.4104
0.3770
0.5896
0.5701
0.4589
5
0.6204
0.2765
0.3796
0.7235
0.5685
0.4087
6
0.7209
0.5041
0.2791
0.4959
0.6418
0.5021
7
0.4250
0.0000
0.5750
1.0000
0.4651
0.3333
8
1.0000
0.9409
0.0000
0.0591
1.0000
0.8942
9
0.8417
0.5893
0.1583
0.4107
0.7596
0.5491
10
0.0000
0.0602
1.0000
0.9398
0.3333
0.3473
Reference value
1.0000
1.0000
–
–
–
– Acknowledgements. The work was supported by the Engineering and Physical Sciences Research Council (Industrial
CASE award) under grant 5162031105656, and BAE Systems. Appendix A. Overall system and grey relational analysis Table A.1. Normalisation of data, calculation of grey relational distance and grey relational
coefficient for the overall system. le A.1. Normalisation of data, calculation of grey relational distance and grey relationa
fficient for the overall system. DMU
Normalisation of data
Grey relational distance
Grey relational coefficient
C1
C2
C1
C2
C1
C2
1
1.0000
1.0000
0.0000
0.0000
1.0000
1.0000
2
0.3132
0.2217
0.6868
0.7783
0.4213
0.3911
3
0.1851
0.1477
0.8149
0.8523
0.3803
0.3697
4
0.1456
0.1181
0.8544
0.8819
0.3692
0.3618
5
0.2941
0.1872
0.7059
0.8128
0.4146
0.3809
6
0.3847
0.3046
0.6153
0.6954
0.4483
0.4183
7
0.1267
0.0376
0.8733
0.9624
0.3641
0.3419
8
0.1861
0.1313
0.8139
0.8687
0.3806
0.3653
9
0.2349
0.1372
0.7651
0.8628
0.3952
0.3669
10
0.0000
0.0000
1.0000
1.0000
0.3333
0.3333
Reference value
1.0000
1.0000
–
–
–
– 1317 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES [2] L. Angulo-Meza and M.P.E. Lins, Review of methods for increasing discrimination in data envelopment analysis. Ann. Oper.
Res. 116 (2002) 225–242. [1] T.R. Anderson, K. Hollingsworth and L. Inman, The fixed weighting nature of a cross-evaluation model. J. Prod. Anal. 17
(2002) 249–255. References [1] T.R. Anderson, K. Hollingsworth and L. Inman, The fixed weighting nature of a cross-evaluation model. J. Prod. Anal. 17
(2002) 249–255. [1] T.R. Anderson, K. Hollingsworth and L. Inman, The fixed weighting nature of a cross-evaluation model. J. Prod. Anal. 17
(2002) 249–255. [2] L. Angulo-Meza and M.P.E. Lins, Review of methods for increasing discrimination in data envelopment analysis. Ann. Oper. [1] T.R. Anderson, K. Hollingsworth and L. Inman, The fixed weighting nature of a cross-evaluation m
(2002) 249–255. [2] L. Angulo-Meza and M.P.E. Lins, Review of methods for increasing discrimination in data envelopment analysis. Ann. Oper. Res. 116 (2002) 225–242. 1318 M.D. KREMANTZIS ET AL. [4] H. Azizi and R. Jahed, Improved data envelopment analysis models for evaluating interval efficiencies of decision-making units. Comput. Ind. Eng. 61 (2011) 897–901. (
)
[5] T. Badiezadeh, R.F. Saen and T. Samavati, Assessing sustainability of supply chains by double frontier network DEA: a big
data approach. Comput. Oper. Res. 98 (2018) 284–290. [6] A.Y. Chang, Prioritising the types of manufacturing flexibility in an uncertain environment. Int. J. Prod. Res. 50 (2012)
2133–2149. [7] A. Charnes, W.W. Cooper and E. Rhodes, Measuring the efficiency of decision-making units. Eur
429–444. k, K. Tone and J. Zhu, Data envelopment analysis: prior to choosing a model. Omega 44 (2014) 1–4. [8] W.D. Cook, K. Tone and J. Zhu, Data envelopment analysis: prior to choosing a model. Omega [9] W.W. Daniel, Applied Nonparametric Statistics. Houghton Mifflin, Boston (1978). [10] J. Doyle and R. Green, Efficiency and cross-efficiency in DEA: derivations, meanings and uses. J. Oper. Res. Soc. 45 (1994)
567–578. [11] A. Ebrahimnejad, Cost efficiency measures with trapezoidal fuzzy numbers in data envelopment analysis based on ranking
functions: application in insurance organization and hospital. Int. J. Fuzzy Syst. App. (IJFSA) 2 (2012) 51–68. [12] A. Ebrahimnejad and F.H. Lotfi, Equivalence relationship between the general combined-oriented CCR model and the weighted
minimax MOLP formulation. J. King Saud Univ.-Sci. 24 (2012) 47–54. (
)
naka, Interval estimations of global weights in AHP by upper approximation. Fuzzy Sets Syst. 158 (2007 13] T. Entani and H. Tanaka, Interval estimations of global weights in AHP by upper approximation. Fu
1913–1921. [14] T. Entani, Y. Maeda and H. Tanaka, Dual models of interval DEA and its extension to interval data. Eur. J. Oper. Res. 136
(2002) 32–45. [15] G. Gan, H.S. Lee, L. Lee, X. Wang and Q. References Wang, Network hierarchical DEA with an application to international shipping
industry in Taiwan. J. Oper. Res. Soc. 71 (2020) 991–1002. [16] A. Hatami-Marbini, S. Saati and M. Tavana, An ideal-seeking fuzzy data envelopment analysis framework. Appl. Soft Comput. 10 (2010) 1062–1070. [17] A. Hatami-Marbini, A. Ebrahimnejad and S. Lozano, Fuzzy efficiency measures in data envelopmen
multiobjective approach. Comput. Ind. Eng. 105 (2017) 362–376. [18] Y. Huang, Y.M. Wang and J. Lin, Two-stage fuzzy cross-efficiency aggregation model using a fuzzy information retrieval
method. Int. J. Fuzzy Syst. 21 (2019) 2650–2666. [19] A. Jahan, F. Mustapha, S.M. Sapuan, M.Y. Ismail and M. Bahraminasab, A framework for weighting of criteria in ranking
stage of material selection process. Int. J. Adv. Manuf. Technol. 58 (2012) 411–420. g
p
f
(
)
[20] D. Julong, Introduction to grey system theory. J. Grey Syst. 1 (1989) 1–24. tion to grey system theory. J. Grey Syst. 1 (1989) 1 [21] C. Kao and S.N. Hwang, Efficiency decomposition in two-stage data envelopment analysis: an application to non-life insurance
companies in Taiwan. Eur. J. Oper. Res. 185 (2008) 418–429. [21] C. Kao and S.N. Hwang, Efficiency decomposition in two-stage data envelopment analysis: an
companies in Taiwan. Eur. J. Oper. Res. 185 (2008) 418–429. [22] C. Kao and S.T. Liu, Cross efficiency measurement and decomposition in two basic network syste [22] C. Kao and S.T. Liu, Cross efficiency measurement and decomposition in two basic network systems. Omega 83 (2019) 70–79. [23] M. Khodabakhshi and K. Aryavash, The cross-efficiency in the optimistic–pessimistic framework. Oper. Res. 17 (2017) 619–632. [24] M.D. Kremantzis, P. Beullens and J. Klein, A fairer assessment of DMUs in a generalised two-stage DEA structure. Expert
Syst. App. 187 (2022) 115921. [
]
,fi
y
p
y
g
(
)
[23] M. Khodabakhshi and K. Aryavash, The cross-efficiency in the optimistic–pessimistic framework. Oper. Res. 17 (2017) 619–632. [24] M.D. Kremantzis, P. Beullens and J. Klein, A fairer assessment of DMUs in a generalised two-stage DEA structure. Expert [23] M. Khodabakhshi and K. Aryavash, The cross-efficiency in the optimistic–pessimistic framework. Oper. Res. 17 (2017) 619–632. [
] 3] M. Khodabakhshi and K. Aryavash, The cross-effic [24] M.D. Kremantzis, P. Beullens and J. Klein, A fairer assessment of DMUs in a generalised two-s
Syst. App. 187 (2022) 115921. [25] Y. Kuo, T. Yang and G.W. Huang, The use of grey relational analysis in solving multiple attribute decision-making problems. Comput. Ind. Eng. [37] S.A. Rakhshan, Efficiency ranking of decision making units in data envelopment analysis by using TOPSIS-DEA method.
J. Oper. Res. Soc. 68 (2017) 906–918. A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Li, J. Wu and J. Sun, Cross-efficiency evaluation in data envelopment analysis based on the perspective of fairness
utility. Comput. Ind. Eng. 151 (2021) 106926. y
p
g
(
)
[58] H.J. Zimmermann, Fuzzy Set Theory – And Its Applications. Springer Science & Business Media (2011). y
p
g
(
)
[58] H.J. Zimmermann, Fuzzy Set Theory – And Its Applications. Springer Science & Business Media (2011). This journal is currently published in open access under a Subscribe-to-Open model (S2O). S2O is a transformative
model that aims to move subscription journals to open access. Open access is the free, immediate, online availability of
research articles combined with the rights to use these articles fully in the digital environment. We are thankful to our
subscribers and sponsors for making it possible to publish this journal in open access, free of charge for authors. Please help to maintain this journal in open access! A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES [38] J. Rezaei, Best-worst multi-criteria decision-making method: some properties and a linear model. Omega 64 (2016) 126–130. [
] J. Rezaei, Best-worst multi-criteria decision-making method: some properties and a linear model. Omeg [38] J. Rezaei, Best-worst multi-criteria decision-making method: some properties and a linear model [38] J. Rezaei, Best-worst multi-criteria decision-making method: some properties and a linear model. Omega 64 (2016) 126–130. [39] T.L. Saaty and L.G. Vargas, The analytic network process. In: Decision Making with the Analytic Network Process. Springer,
Boston, MA (2013) 1–40. [
]
,
g
p
p
g
(
)
[39] T.L. Saaty and L.G. Vargas, The analytic network process. In: Decision Making with the Analytic Network Process. Springer,
Boston, MA (2013) 1–40. A. Ebrahimnejad and A. Zabihi, A new approach for solving intuitionistic fuzzy data envelopment analysi
im. Model. J. 2 (2021) 46–56. [40] F.J. Santos Arteaga, A. Ebrahimnejad and A. Zabihi, A new approach for solving intuitionistic fuz
problems. Fuzzy Optim. Model. J. 2 (2021) 46–56. [41] F. Sarraf and S.H. Nejad, Improving performance evaluation based on balanced scorecard with grey relational analysis and
data envelopment analysis approaches: case study in water and wastewater companies. Eval. Program Planning 79 (2020)
101762. [42] T.R. Sexton, R.H. Silkman and A.J. Hogan, Data envelopment analysis: critique and extensions. New Directions Program
Eval. 1986 (1986) 73–105. (
)
[43] K. Sugihara, H. Ishii and H. Tanaka, Interval priorities in AHP by interval regression analysis. Eur. J. Oper. Res. 158 (2004)
745–754. [44] M. Tavana, A. Ebrahimnejad, F.J. Santos-Arteaga, S.M. Mansourzadeh and R.K. Matin, A hybrid DEA-MOLP model for
public school assessment and closure decision in the City of Philadelphia. Soc. Econ. Planning Sci. 61 (2018) 70–89. vana, A. Ebrahimnejad, F.J. Santos-Arteaga, S.M. Mansourzadeh and R.K. Matin, A hybrid DEA-MO
h
l
t
d
l
d
i i
i
th
Cit
f Phil d l hi
S
E
Pl
i
S i 61 (2018) 44] M. Tavana, A. Ebrahimnejad, F.J. Santos-Arteaga, S.M. Mansourzadeh and R.K. Matin, A hybrid
public school assessment and closure decision in the City of Philadelphia. Soc. Econ. Planning Sci. 6 [45] M. Toloo and T. Tich´y, Two alternative approaches for selecting performance measures in data
surement 65 (2015) 29–40. T. Tich´y, Two alternative approaches for selecting performance measures in data envelopment analys
(2015) 29–40. [46] Y.M. Wang and K.S. Chin, A neutral DEA model for cross-efficiency evaluation and its extension. Expert Syst. App. A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES 37 (2010)
3666–3675. [47] Y.M. Wang and T.M. Elhag, A goal programming method for obtaining interval weights from an interval comparison matrix. Eur. J. Oper. Res. 177 (2007) 458–471. [48] Y.M. Wang and Y. Luo, DEA efficiency assessment using ideal and anti-ideal decision-making units. Appl. Math. Comput. 173 (2006) 902–915. (
)
[49] Y.M. Wang and J.B. Yang, Measuring the performances of decision-making units using interval e
Math. 198 (2007) 253–267. Yang, Measuring the performances of decision-making units using interval efficiencies. J. Comput. App
3–267. [50] Y.M. Wang, K.S. Chin and J.B. Yang, Measuring the performances of decision-making units using geometric average efficiency. J. Oper. Res. Soc. 58 (2007) 929–937. (
)
[51] D. Wu, A note on DEA efficiency assessment using ideal point: an improvement of Wang and Luo’s model. Appl. Math. Comput. 183 (2006) 819–830. [52] J. Wu, J. Chu, J. Sun, Q. Zhu and L. Liang, Extended secondary goal models for weights selection in DEA cross-efficiency
evaluation. Comput. Ind. Eng. 93 (2016) 143–151. 53] F. Yang, S. Ang, Q. Xia and C. Yang, Ranking DMUs by using interval DEA cross efficiency matrix w
Eur. J. Oper. Res. 223 (2012) 483–488. Xia and C. Yang, Ranking DMUs by using interval DEA cross efficiency matrix with acceptability analysis
23 (2012) 483–488. [54] L. Zhang and K. Chen, Hierarchical network systems: an application to high-technology industry in China. Omega 82 (2019)
118–131. [54] L. Zhang and K. Chen, Hierarchical network systems: an application to high-technology industry in China. Omega 82 (2019)
118–131. [55] Z. Zhou, L. Sun, W. Yang, W. Liu and C. Ma, A bargaining game model for efficiency decomposition in the centralized model
of two-stage systems. Comput. Ind. Eng. 64 (2013) 103–108. [55] Z. Zhou, L. Sun, W. Yang, W. Liu and C. Ma, A bargaining game model for efficiency decomposition in the centralized model
of two-stage systems. Comput. Ind. Eng. 64 (2013) 103–108. (
)
J. Zhu, Data Envelopment Analysis: A Handbook of Models and Methods. Vol. 221. Springer (2015). Q Zh
F Li J W
d J S
C
ffi i
l
ti
i
d t
l
t
l
i b
d
th (
)
J. Zhu, Data Envelopment Analysis: A Handbook o [57] Q. Zhu, F. Li, J. Wu and J. Sun, Cross-efficiency evaluation in data envelopment analysis based on the perspective of fairness
utility. Comput. Ind. Eng. 151 (2021) 106926. [57] Q. Zhu, F. References 55 (2008) 80–93. p
g
(
)
[26] F. Li, Q. Zhu, Z. Chen and H. Xue, A balanced data envelopment analysis cross-efficiency evaluation approach. Expert Syst. App. 106 (2018) 154–168. [27] F. Li, H. Wu, Q. Zhu, L. Liang and G. Kou, Data envelopment analysis cross efficiency evaluation with reciprocal behaviors. Ann. Oper. Res. 302 (2021) 173–210. 28] L. Liang, J. Wu, W.D. Cook and J. Zhu, Alternative secondary goals in DEA cross-efficiency evalua
113 (2008) 1025–1030. D. Cook and J. Zhu, Alternative secondary goals in DEA cross-efficiency evaluation. Int. J. Prod. Econ
0. [29] W. Liu and Y.M. Wang, Ranking DMUs by using the upper and lower bounds of the normalized efficiency in data envelopment
analysis. Comput. Ind. Eng. 125 (2018) 135–143. y
p
g
(
)
[30] F.H. Lotfi, G.R. Jahanshahloo, A. Ebrahimnejad, M. Soltanifar and S.M. Mansourzadeh, Target setting in the general
combined-oriented CCR model using an interactive MOLP method. J. Comput. Appl. Math. 234 (2010) 1–9. [31] F.H. Lotfi, G.R. Jahanshahloo, M. Soltanifar, A. Ebrahimnejad and S.M. Mansourzadeh, Relationship between MOLP and
DEA based on output-orientated CCR dual model. Expert Syst. App. 37 (2010) 4331–4336. hou, W. Zhao and W. Liu, Game cross efficiency for systems with two-stage structures. J. Appl. Math 32] C. Ma, D. Liu, Z. Zhou, W. Zhao and W. Liu, Game cross efficiency for systems with two-stage st
2014 (2014) 8. [33] F. Meng and B. Xiong, Logical efficiency decomposition for general two-stage systems in view of cross efficiency. Eur. J. Oper. Res. 294 (2022) 622–632. [34] H.H. ¨Orkc¨u, V.S. ¨Ozsoy, M. ¨Orkc¨u and H. Bal, A neutral cross efficiency approach for basic two stage production systems. Expert Syst. App. 125 (2019) 333–344. [35] H.H. ¨Orkc¨u, V.S. ¨Ozsoy, M. ¨Orkc¨u and H. Bal, An optimistic-pessimistic DEA model based on game cross efficiency approach. RAIRO: Oper. Res. 54 (2020) 1215–1230. [36] P. Peykani, F. Hosseinzadeh Lotfi, S.J. Sadjadi, A. Ebrahimnejad and E. Mohammadi, Fuzzy chance-constrained data envelop-
ment analysis: a structured literature review, current trends, and future directions. Fuzzy Optim. Decision Making 21 (2022)
197–261 [37] S.A. Rakhshan, Efficiency ranking of decision making units in data envelopment analysis by using TOPSIS-DEA method. J. Oper. Res. Soc. 68 (2017) 906–918. 1319 A RANKING FRAMEWORK BASED ON INTERVAL SELF AND CROSS-EFFICIENCIES Please help to maintain this journal in open access! Check that your library subscribes to the journal, or make a personal donation to the S2O programme, by contacting
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ISSN 2181-9297
Doi Journal 10.26739/2181-9297
TОШКЕНТ-2022
1
№2 (2022) DOI http://dx.doi.org/10.26739/2181-9297-2022-2
Бош муҳаррир:
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“ЗУЛМАТ” ҚИРОЛЛИГИДА СУКУТ ХАВФИ………………………………………………….5
2. Худойбердиева А.Х.
ТЕОРЕТИЧЕСКИЕ ОСНОВЫ ФОРМИРОВАНИЯ ОБРАЗНО-КРЕАТИВНОГО
МЫШЛЕНИЯ У ШКОЛЬНИКОВ………………………………………………………………..12
3. Asadov To’lqin Hamroyevich
O’ZBEK TILIDA SO’Z YASALISHI TADQIQI VA RIVOJI XUSUSIDA………………………18
4. Fayziyeva Aziza Anvarovna
METAFORALAR TARJIMASINING LINGVOMADANIY XUSUSIYATLARI………………..26
5. Sultanova Muxabbat Shamsiyevna, Mardanova Firuza Subhonovna
CHET TILLARNI O'RGANISHNING INTERFAOL USULLARI………………………………..31
6. Максумова Фарида Абдуразаковна
СТИЛЕВЫЕ ОСОБЕННОСТИ ДЕКОРАТИВНО-ПРИКЛАДНОЕ
ИСКУССТВО ТУРЦИИ…………………………………………………………………………...36
7. Ахмедова Азиза Хусеновна
ПРИРОДА СЕМАНТИЧЕСКОЙ ДЕРИВАЦИИ В МОЛОДЕЖНОМ СЛЕНГЕ
(НА МАТЕРИАЛЕ СЛОВАРЕЙ МОЛОДЕЖНОГО СЛЕНГА)………………………………..43
8. Туракулова Зарина Мардонкуловна
МНОГООБРАЗИЕ ТЕМАТИЧЕСКИХ ГРУПП УСТАРЕВШИХ
ЛЕКСИЧЕСКИХ И ФРАЗЕОЛОГИЧЕСКИХ ЕДИНИЦ РУССКОГО ЯЗЫКА,
ОБРАЗУЮЩИХ РАЗЛИЧНЫЕ ЛЕКСИКО-СЕМАНТИЧЕСКИЕ ПОЛЯ…………………….50
9. Сулайманова Нилуфар Жаббаровна
ДИОЛОГИК НУТҚДА БАҲО НУТҚИЙ АКТЛАРИ БАЖАРИЛИШИНИНГ
ПРАГМАТИК ВА СОЦИОЛИНГВИСТИК ШАРТЛАРИ……………………………………...56
10. Umarova Feruzabonu Bobir qizi
TARBIYACHILARNING KASBIY MADANIYATINI SHAKLLANTIRISHDA
INNOVATSION PEDAGOGIK TEXNOLOGIYALARDAN FOYDALANISH…………………68
11. Shahnoza Izbosarova
HALIMA XUDOYBERDIYEVA IJODIDA O‘XSHATISHLARNING
LINGVOPOETIK XUSUSIYATLARI……………………………………………………………..72
12. Рашидова Умида Мансуровна
БАДИИЙ МАТНДА УСЛУБИЙ ХОСЛАНГАН ПОЛИСЕМАНТИК
ФРАЗЕОЛОГИЗМЛАРНИНГ ФУНКЦИОНАЛ-СТИЛИСТИК ХУСУСИЯТЛАРИ…………78
13. Назарова Нуржаҳон Баҳодировна
ЭРТАКНИНГ ДИСКУРСИВ БЕЛГИЛАРИ……………………………………………………..83
14. Дўстова Сурайё Савроновна
“ТАЗКИРАИ ШУАРО”ДА БЕРИЛГАН ҒАЗАЛЛАРДАГИ МАТНИЙ ФАРҚЛАР………….87
15. Юсуфжонова Шахло Мухторовна
ТАРЖИМА МУАММОЛАРИНИНГ УМУМЛАШТИРИЛГАН ТАВСИФИ…………………93
16. Шахноза Акрамовна Қўлдашева
ЎЗБЕК ТИЛИ ТАЛАФФУЗ ТИЗИМИДА УМУМТУРКИЙ ДИВЕРГЕНТ
ВА КОНВЕРГЕНТ БЕЛГИЛАР ЭВОЛЮЦИЯСИ………………………………………………99
3
17. To’rayeva Maftuna Akbar qizi
SEMANTIK NEOLOGIZMLARNING LINGVOMADANIY TAHLILI......................................108
18. Феруз Ражабов Умарқулович
ЗАҲИРИДДИН МУҲАММАД БОБУР ЛИРИК АСАРЛАРИДАГИ
АНТРОПОНИМЛАРНИНГ ЛИНГВОПОЭТИК ХУСУСИЯТЛАРИ........................................113
19. Amirova Zohida Oripovna
LINGVOKULTUROLOGIYA KONTEKSIDA “TIL” TUSHUNCHASI TALQINI……………120
20. Nizomova Mohinur Baratboyevna
PEDAGOGIKAGA OID TERMINLARNING ETIMOLOGIK KOMPONENTI
ASOSIDA ILMIY MATNLARNI TARJIMA QILISHNI O‘RGATISH
MODELINI AMALGA OSHIRISH………………………………………………………….…...124
21. Ҳамраев Фозилбек Йўлдошевич
ТИЛ ТАРАҚҚИЁТИДА НЕОЛОГИЗМЛАРНИНГ ЎРНИ……………………………………130
22. Jumaniyozova Nuriya Axmedovna
O’ZBEK TILIDA YURIDIK DISKURS NOMINATIV BIRLIKLARI…………………….……136
23. Насиба Раимназарова
ШЕВАГА ОИД СЎЗЛАРНИНГ ГЕНЕТИК-ЭТИМОЛОГИК ХУСУСИЯТЛАРИ ВА
УЛАРНИНГ ЛЕКСИКОГРАФИК ТАВСИФИ МАСАЛАСИ………………………………....141
24. Tugba Yilmaz
ABDULLA ORIPOV SHE’RLARIDA TASAVVUR VA OBRAZ…………….………………..146
25. Ibodullayeva Maftuna Habibullayevna, Yunusova Bahora Axtamjonovna
THE USE OF SUPERSTITIONS IN THE LIFE OF ENGLISH SPEAKING COUNTRIES
AND THEIR TYPES ACCORDING TO SITUATIONS…………………………………….…...153
26. Ҳамраев Фозилбек Йўлдошевич
ТИЛ ТАРАҚҚИЁТИДА НЕОЛОГИЗМЛАРНИНГ ЎРНИ……………………………….……161
27. Джураев Ботир Илхомович
СЕМЕЛЬФАКТИВ ФЕЪЛЛАР ТИПОЛОГИЯСИ………………………………………….….167
28. Vosiljonov Azizbek Boxodirjon o’g’li
O‘ZBEK TILI ELEKTRON KORPUSIDA DIALEKTAL KORPUS
YARATISHNING NAZARIY MASALALARI……………………………………………….….172
29. Abduraxmonova Nilufar Zaynobiddin qizi, Qodirova Zebo Gulboyevna
TABIIY TILLAR JARAYONI UCHUN SEMANTIK MUNOSABATLAR TAHLILIDA
ONTOLOGIYANING O‘RNI…………………………………………………………………..…177
30. Emrah Yilmaz
MAXTUMQULI FIROG‘IY DEVONIDAGI FRAZEOLOGIZMLARNING
LEKSIKOLOGIK XUSUSIYATLARI…………………………………………………………....184
31. A. Bozorbekov
LOGISTIKA TERMINOLOGIYA TIZIMINING XUSUSIYATLARI…………………….……191
32. Насима Саидбурхоновна Қодирова
ОЛИМНИНГ ИЛМИЙ-АДАБИЙ ОЛАМИ (И.Ҳаққул ижоди мисолида)……………….…..197
33. Ulikova Mavluda
CRITERIA FOR THE SELECTION OF TERMS DENOTING FAMILY TIES………………...206
4
Назарова Нуржаҳон Баҳодировна
Самарқанд давлат чет тиллари институти
таянч докторанти
E-mail: nurjahonn@gmail.ru
ЭРТАКНИНГ ДИСКУРСИВ БЕЛГИЛАРИ
https://doi.org/10.5281/zenodo.6634057
АННОТАЦИЯ
Ушбу мақолада эртак жанри матнини ўрганишнинг долзарблиги ҳамда дискурс тушунчаси ва
унинг категориал белгилари, қолаверса ушбу дискурс категориал белгиларининг эртак
жанрига алоқадорлик жиҳатлари тўғрисида сўз юритилади. Бугунги кунда эртак жанрини
ўрганиш долзарб масала бўлиб бормоқда. Бугунга қадар бу жанр ҳақида кўплаб олимларимиз
ўрганган бўлса-да, улар тадқиқот хусусиятига эга эмас. Муаллиф фикрича, бунинг сабаби
дискурс ҳодисаси ва дискурсив таҳлил ҳақида бирон бир якдил хулосага келинмаганлиги
билан боғлиқ.
Калит сўзлар: эртак, дискурс, дискурсив белги, тил, нутқ, матн антропоцентриклик,
вазиятлилик, адреслилик, очиқлик, процессуаллик.
Nazarova Nurjahon Bahodirovna
PhD Student of Samarkand State
Institute of Foreign Languages
Email: nurjahonn@gmail.ru
DISCURSIVE SIGNS OF A FAIRY TALE
ANNOTATION
This article discusses the relevance of the study of the text of the fairy tale genre and the concept of
discourse and its categorical features, as well as aspects of the relevance of these discourse categorical
features to the fairy tale genre. Today, the study of the fairy tale genre is becoming a topical issue.
Although many of our scientists have studied this genre so far, they are not of a research nature.
According to the author, this is due to the fact that no consensus has been reached on the discourse
phenomenon and discursive analysis.
Key words: Fairy tale, discourse, discoursive sign, language, speech, text, anthropocentricity,
situationally, addressability, openness
Назарова Нуржаҳон Баҳодировна
Докторант Самаркандского государственного
института иностранных языков
Электронная почта: nurjahonn@gmail.ru
83
ДИСКУРСИВНЫЕ ПРИЗНАКИ СКАЗКИ
АННОТАЦИЯ
В данной статье рассматривается актуальность изучения текста жанра сказки и понятия
дискурса и его категориальных признаков, а также аспекты соотнесения этих категориальных
признаков дискурса с жанром сказки. На сегодняшний день изучение жанра сказки становится
актуальным вопросом. Хотя до сих пор многие наши ученые изучали этот жанр, они не носят
исследовательского характера. По мнению автора, это связано с тем, что не достигнуто
единого мнения о феномене дискурса и дискурсивном анализе.
Ключевые слова: Сказка, дискурс, дискурсивный знак, язык, речь, текст,
антропоцентричность, ситуативность, адресность, открытость
Фольклор асарлари орасида тадқиқотчилар диққатини энг кўп жалб қилиб келаётган
жанр эртакдир. Филология соҳасида эртак кўпроқ фольклоршунослар томонидан ўрганилган
бўлса-да, лекин бу жанрдаги асарлар адабиётшунослик, матншунослик каби фан соҳаларининг
ҳам тадқиқ объектига айланиб улгурган. Тилшунослар узоқ пайтлардан буён эртакларнинг
лисоний хусусиятлари, уларнинг матн тузилиши каби масалалар билан шуғулланиб
келмоқдалар. Эртакларнинг просодик хусусиятлари, луғат таркиби, синтактик тузилиши,
генетик асослари, бадиияти бирмунча батафсил ўрганилган ( Сахарова 1981; Печерникова
1962; Плохова 2007; Дўстхўжаева 1999; Содиқова 2003; Усмонова 1999 ва бошқалар). Бироқ
эртакларнинг дискурсив хусусиятлари, уларнинг алоҳида турдаги дискурс сифатида мулоқот
жараёнида бажарадиган вазифалари мукаммал даражада ўрганилмаган.
Машҳур фольклоршунос В.Я Пропп ўз пайтида эртакнинг матн сифатида
ўрганилишига кам аҳамият берилаётганидан ташвишланиб қуйдагиларни ёзган эди: “....асосан
эртаклар матнлари нашр қилиниб, у ёки бу масалаларга бағишланган ишлар ҳам кўп, аммо
умумий характердаги тадқиқотлар жуда кам. Бундай ишлар мавжуд бўлса-да, лекин улар тўла
маънодаги тадқиқот хусусиятига эга эмас.....Эртак ҳақидаги фаннинг боши берк кўчага кириб
қолишининг сабаби нимада экан ?”(Пропп 1998:7). Орадан шунча йиллар ( В.Я.Пропп ўтган
асрнинг 20-йиллари назарда тутилмоқда) ўтган бўлса-да, аммо олимнинг қўйган саволига
жавоб топиш ва “ боши берк кўчадан” чиқиб кетишнинг йўлини топиш борасидаги
изланишлар давом этмоқда.
Бизнингча, юқорида эслатилган муаммонинг пайдо бўлиш сабабларидан бири
тилшунослик фанида дискурс ҳодисаси ва дискурсив таҳлил ҳақида бирон бир якдил хулосага
келинмаганлиги билан боғлиқ. Жаҳон фанида дискурс тушунчаси табора оммавийлашиб
бораётгани ҳамда ушбу ҳодисанинг мукаммал, кўпжиҳатли тавсир-таърифлари
берилаётганига қарамасдан, баъзилар ҳануз дискурсни алоҳида тадқиқ объекти сифатида тан
олишдан тортиниб турганлари ҳам маълум (Партин 1996; Ревзина 1999). Турли гуманитар
интегратив муносабатлар асосида шаклланаётган янги йўналишнинг худудий чегараси аниқ
эмаслиги, дискурс ҳодисаси талқинида катта қийинчиликлар туғдирмоқда. Нидерландиялик
олим Т. ван Дейк бундай ноқулайликлар пайдо бўлишининг асосий сабабини “дискурс”
тушунчасининг кўп маънолигида кўради. Унинг фикрича, дискурс тушунчаси тил
тушунчасидек дудмалдир. “ Биламизки,-деб ёзади олим,- дудмал ва таърифлаш қийин бўлган
тушунчалар кўпинча оммавийлашади. Дискурс тушунчаси худди шундайлардан
биридир”(Дейк Т.А.ван 1988).
Ҳозирги пайтда турли манбаларда дискурс ҳодисасига берилаётган ўнлаб тарифларни
учратиш мумкин. Ғарбдаги олимларнинг баъзилари матн ва дискурсни гап ҳодисаси билан
қиёслашга одатланишган. Жумладан, инглиз адабиётшуноси Р.Фаулер “Linguistics and the
Novel” китобида “матн” тушунчасини нутқий тузилмаларининг сиртқи қатлами билан
тенглаштиради. Матн, олимнинг талқини бўйича, гаплар бирикишидан ҳосил бўладиган
тузилма ва ўқувчи гаплар кетма кетлигидан маънони англаб етади. Дискурс эса “нуқтаи-назар”
(point of view), “муносабат” (attitude), “дунёқараш” (world view) каби модал омиллардан иборат
ва мазмун жиҳатидан муаллифнинг воқеликка муносабатини акс эттиради (Fowler 1983:49).
84
“Дискурс таҳлили” (Discourse analysis) асарида матн ва дискурс тушунчалари тил ва
нутқ қарама қаршилигида тавсифланади.Ушбу китоб муаллифларининг фикрича, дискурс
“қўлланишдаги тил”(language in use) бўлса, матн эса коммуникатив ҳаракатнинг лисоний
қайдидир (Brown, Yule 1983:1-6).
Ҳақиқатдан ҳам, матн маъно шаклланишини бошлаб бeрувчи восита бўлса, дискурс
худди шу жараённинг ўзидир (Наberland 1999:915). Шу сабаб, матн ва дискурс ҳодисалари
муносабати талқинида охиргисини лисоний шахс фаолияти доирасида тавсифлаш лозим
бўлади. Матн эса шу фаолият маҳсулидир.
Ҳозирги пайтда дискурс назарияси соҳасида кўплаб тадқиқотлар амалга
оширилганини эътироф этиш лозим. Дискурс таҳлили тилдан ижтимоий-маданий муҳитда
фойдаланиш билан боғлиқ ҳолда олиб борилмоқда. Л.М.Макаров ёзишича, дискурс таҳлилида
лисоний мулоқотнинг ижтимоий-маданий ва инерактив жиҳатлари ўрганилади, “лекин бундан
унинг ҳудуди фақат оғзаки диалог билан чегараланиши ҳақида хулосага келмаслик керак:
лисоний мулоқотнинг ҳар қандай кўриниши....шу нуқтаи назардан таҳлилга тортилиши
мумкин” (Макаров 2003: 88).
Дискурснинг кенг маънода талқин қилиниши унинг категориал белгиларини
аниқлашни тақоза этади. Ушбу ҳодисанинг структур-семантик, коммуникатив-прагматик,
когнитив ва эстетик-маданий хусусиятларини эътиборга олиш лозимлигини уқтирган
тадқиқотчилар унинг категориал белгилари антропоцентриклик, вазиятлилик, адреслилик,
очиқлик, процессуаллик, миллий узига хослик кабилардан иборат эканини қайд этадилар
(Нормуродова 2020: 16-17).
Эртакнинг дискурсив табиатини аниқлашга қийналаётган матншунослар юқорида
санаб ўтилган категориал белгиларнинг баъзилари фақат оғзаки нутқ ёки бадиий матнга хос
деб ҳисоблайдилар. Бинобарин, М.Я.Дымарский матн талқинига бағишланган семинарда
ўқиган маърузасида “процесуаллик” белгисини воқелик кечаётган давр билан боғлайди. Унинг
фикрича, қўлланилаётган сўзлар, иборалар, медиаматнларда, маърузаларда, турли фикрлар
алмашинувида даврнинг кечиш давомийлигини акс эттиради (М.Я.Дымарский 1998:19). Аммо
давомийлик дискурснинг категориал белгиси сифатида кенгроқ маънода англашинилади.
Ушбу аспектуал маънога ўтган ва келаси замон шакллари ҳам эга бўлиши мумкинлиги
исботланган ҳақиқатдир ( Анзаев 1999; Мирсанов 2018).
Фольклорга қарашли ҳар қандай жанр оғзаки дискурс шаклига эга.Ушбу турдаги
асарлар ҳар бир кўринишида қайта яратилаётгандек туюлади.Ёзиб олинган эртакда ҳам табиий
нутққа хос хусусиятлар сақланиб қолади, унда мулоқот жараёни учун хос бўлган хислатлар
намоён бўлади. Эртак дискурсининг ёзма шакли воситасида узатилаётган ахборот тингловчига
тезроқ етиб боради. Демак, эртак дискурсида процессуаллик доимий белгидир.
Дискурснинг яна бир муҳим категориал белгиларидан бири интертекстуалликдир.
Маълумки, тил фақат тайёр хабарни узатиш билан чекланмасдан, янги хабарларни ифодалаш
имконига ҳам эга.Тилнинг мазкур ижодкорлик вазифаси айнан матнлар дискурслар яратишида
намоён бўлади. Янгидан шаклланётган матн эса бошқа матнлар билан диалогик муносабатга
киришади. Шу муносабат доирасида янги матннинг мазмуни шаклланади (Кузьмина 2009: 1920). Шундай экан, интертекстуалликни эртак дискурсининг ажралмас белгиси эканлигини
эътироф этмасликнинг иложи йўқ. Зеро, эртак тилида табиий тилнинг ижодкорлик вазифаси
яққол намоён бўлади.
“Эртак дискурсининг пайдо бўлиши ижтимоий эҳтиёт талаб натижасидир ва унинг
дастлабки намуналарида вазиятлилик белгиси аниқ кўзга ташланган.Чунки бу ҳолатда
дискурсив фаолиятнинг асосий иштирокчилар эртак айтувчи ва тинловчи бўлган. Аммо оғзаки
мулоқотнинг ёзма шакл олиши давомида вазиятлиликнинг таъсир кучи камайиб бориб,
эртакнинг эстетик қиймати ошиб боради. Шунинг билан биргаликда, эртак ҳикоячиси
қандайдир мавҳум, эркин ижод шахси бўлмасдан, балки унинг ижоди замон ва муҳит билан
боғлиқ ҳолда кечади. Бироқ, давр ва муҳит доимий бўлмагандек, эртакнинг вазиятлилик
хусусияти ҳам ўзгариб туради.(Пропп 2000: 373).
85
Хуллас, онгли фаолият маҳсули бўлган эртак матнида ташқи олам манзараси ўзига хос
равишда акс топади. Ушбу турдаги дискурс умумлашган, оммавий характерга эга бўлиб, унинг
баёнида оддийлик, жозибалик, тингловчилар диққатини доимий равишда жалб қилади. Эртак
матни эса жамиятда муҳим вазифа бажаради
Адабиётлар
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
Brown G., Discourse analysis. -Cambridge: Cambridge University Press,1983. -P.1-6.
Haberland H. Text, discourse, discourse: The latest report the terminology vice Squad //Journal
of pragmatics,1999. N 31.-P.901-922.
Макаров М.Я. Основы теории дискурса-М : Гнозис, 2003.-88 с.
Нормуродова Н.З.
Инглиз бадиий дискурсида антропосентризмнинг
вербал
экспликацсияси. Филол. фан. докт. дисс. Автореферати.- Т.2020.-16-17 б.
Арурюнова Н.Д. Дискурс //Лингвистический энциклопедический словарь.-М: Советская
энциклопедия, 1990.-С. 136-137.
Дымарский
М.Я. Текст-дискурс-художественный текст// Текст как объект
многоаспектного исследования: Сборник статей научно-методического семинара
“Техтиs”. Вып.З.-СПБ.,1998-192 с.
Ризаев Б.Х.Проблемы аспектной семантики временных форм немецкого языка.
Аспектная семантика претерита.-Т.: Фан, 1999.-121 с.
Мирсанов Ғ.Дискурс таркибида аспектуал ва терминологик мазмун ифодаси.-Т.: Наврўз,
2018.-156 б.
Кузьмина Н.А.Интертекст и его роль в процессах эволюции поэтического текста –М. Л
И Б К О Р М, 2009.-272 с.
Пропп В.Я.Русская сказка // собрание трудов В.Я.Проппа.-М.: Лабиринт, 2000.-373 с.
Галиева М.Р.Теолингвистика: истоки, направления, перспиктива .-Т.: VneshInvest Prom,
2018.-260 c.
Пропп В.Я. Морфология волшебного сказка.-М.: Лабиринт, 2011.-128 с.
86
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Mechanism of Action of Veverimer: A Novel, Orally Administered, Nonabsorbed, Counterion-Free, Hydrochloric Acid Binder under Development for the Treatment of Metabolic Acidosis in Chronic Kidney Disease
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The journal of pharmacology and experimental therapeutics/The Journal of pharmacology and experimental therapeutics
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cc-by
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Gerrit Klaerner, Jun Shao, Kalpesh Biyani, Matthew Kade, Paul Kierstead, Randi Gbur,
Scott Tabakman, Son Nguyen, and Jerry Buysse
Tricida, Inc., South San Francisco, California (G.K., J.S., K.B., M.K., P.K., R.G., S.T., S.N.) and FFV Consulting, Los Altos,
California (J.B.) Gerrit Klaerner, Jun Shao, Kalpesh Biyani, Matthew Kade, Paul Kierstead, Randi Gbur,
Scott Tabakman, Son Nguyen, and Jerry Buysse
Tricida, Inc., South San Francisco, California (G.K., J.S., K.B., M.K., P.K., R.G., S.T., S.N.) and FFV Consulting, Los Altos,
California (J.B.) at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
Downloaded from Received June 30, 2020; accepted August 31, 2020 Received June 30, 2020; accepted August 31, 2020 Received June 30, 2020; accepted August 31, 2020 SIGNIFICANCE STATEMENT Metabolic acidosis is a complication of chronic kidney disease
(CKD) as well as a cause of CKD progression. Veverimer is
a high-capacity, selective, nonabsorbed, hydrochloric acid–
binding polymer being developed as a treatment for meta-
bolic acidosis. Veverimer binds and removes hydrochloric
acid from the gastrointestinal tract, resulting in increased
serum bicarbonate and the correction of metabolic acidosis. Veverimer is not an ion-exchange resin and does not deliver
sodium or other counterions, and so it may be appropriate
for patients with CKD with and without sodium-sensitive
comorbidities. This work was supported in its entirety by Tricida, Inc.
The authors report the following disclosures regarding their relationship
and roles at Tricida, Inc. G.K. is a full-time Tricida employee and a member of
the Tricida Board of Directors and has stock and stock options in Tricida; G.K.
is listed on granted and pending Tricida patents. J.B. reports consulting fees
and stock and stock options from Tricida during and outside this work; J.B. is
listed on granted and pending Tricida patents. J.S., K.B., M.K., P.K., R.G., S.T.,
and S.N. are full-time Tricida employees and have stock and stock options in
Tricida along with listings on granted and pending Tricida patents.
Primary laboratory of origin: Tricida, Inc. (South San Francisco, CA).
The work was partially published in abstract form at American Society of
Nephrology, Kidney Week 2019 (Washington, D.C.).
https://doi.org/10.1124/jpet.120.000190. ABBREVIATIONS: CAS, Chemical Abstract Service; CKD, chronic kidney disease; CTAB, cetyltrimethylammonium bromide; GCTA, GI
compartment transit assay; GI, gastrointestinal; HCl, hydrochloric acid; IC, ion chromatography; p/n, catalog number; SGF, simulated
gastric fluid; SIB, simulated intestine inorganic buffer; SOB, simulated intestine organic and inorganic buffer; wt%, weight percent. ABSTRACT Current management of metabolic acidosis in patients with
chronic kidney disease (CKD) relies on dietary intervention to
reduce daily endogenous acid production or neutralization of
retained acid with oral alkali (sodium bicarbonate, sodium
citrate). Veverimer is being developed as a novel oral treatment
for metabolic acidosis through removal of intestinal acid, result-
ing in an increase in serum bicarbonate. Veverimer is a free-
amine polymer that combines high capacity and selectivity to
bind and remove hydrochloric acid (HCl) from the gastrointes-
tinal (GI) tract. In vitro studies demonstrated that veverimer had
a binding capacity of 10.7 6 0.4 mmol HCl per gram of polymer
with significant binding capacity (.5 mmol/g) across the range of
pH values found in the human GI tract (1.5–7). Upon protonation,
veverimer bound chloride with high specificity but showed little
or no binding of phosphate, citrate, or taurocholate (,1.5 mmol/
g), which are all anions commonly found in the human GI tract. Administration of veverimer to rats with adenine-induced CKD
and metabolic acidosis resulted in a significant increase in fecal
chloride excretion and a dose-dependent increase in serum
bicarbonate to within the normal range compared with untreated controls. Absorption, distribution, metabolism, and excretion
studies in rats and dogs dosed with 14C-labeled veverimer
showed that the polymer was not absorbed from the GI tract
and was quantitatively eliminated in the feces. Acid removal by
veverimer, an orally administered, nonabsorbed polymer, may
provide a potential new treatment for metabolic acidosis in
patients with CKD. Primary laboratory of origin: Tricida, Inc. (South San Francisco, CA).
The work was partially published in abstract form at American Society of
Nephrology, Kidney Week 2019 (Washington, D.C.).
https://doi.org/10.1124/jpet.120.000190. 1521-0103/375/3/439–450$35.00
THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS
Copyright ª 2020 The Author(s).
This is an open access article distributed under the CC BY Attribution 4.0 International lic 1521-0103/375/3/439–450$35.00
THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS
Copyright ª 2020 The Author(s). This is an open access article distributed under the CC BY Attribution 4.0 International lic https://doi.org/10.1124/jpet.120.000190
J Pharmacol Exp Ther 375:439–450, December 2020 Materials and Methods Chemicals and Reagents. Veverimer, which was previously
designated TRC101 (Bushinsky et al., 2018), was synthesized at
Tricida, Inc. (South San Francisco, CA). Veverimer is a highly
crosslinked, aliphatic amine polymer with the chemical structure
presented in Fig. 1; the chemical name for veverimer is poly(allyl-
amine-co-N,N9-diallyl-1,3-diaminopropane-co-1,2-diaminoethane). Veverimer was synthesized by first copolymerizing two monomers:
allylamine hydrochloride [Chemical Abstract Service (CAS) Regis-
try
Number
10017-11-5]
and
N,N9-diallyl-1,3-diaminopropane
dihydrochloride (CAS Registry Number 205041-15-2), followed by
crosslinking of the polymer with 1,2-dichloroethane (CAS Registry
Number 107-06-2). Veverimer has an intrinsic high binding capac-
ity and selectivity for chloride. The hydrochloric acid binding
capacity derives from the high amine content of the monomer
components comprising the polymer, and the extensive crosslinking
in veverimer provides size-exclusion properties and selectivity for
binding chloride over larger anions. Acid binding and removal through the gastrointestinal
(GI) tract using an amine-based nonabsorbed polymer,
which results in an increase in serum bicarbonate, is a novel
approach to treat metabolic acidosis without introduc-
ing deleterious counterions (e.g., sodium or potassium) or
attempting long-term dietary changes. This approach mimics
the physiologic response to acid removal observed in patients
with persistent vomiting or during nasogastric suction, each of
which results in an elevated serum bicarbonate level (Khanna
and Kurtzman, 2006; Gennari and Weise, 2008; Valeur and
Julsrud, 2013). The polymer restores the ability to excrete acid
from the body, a function that is impaired during chronic
kidney disease. Physicochemical Characterization of Veverimer. The parti-
cle size distribution of veverimer was determined via laser light
diffraction with a Malvern Mastersizer 3000 particle size analyzer
(Malvern Instruments, Malvern, UK). In each measurement, a vever-
imer sample (250 6 20 mg) was weighed into a closable 15-ml plastic
tube, and 5 ml of methanol was added while vortexing at low speed. The tube was closed tightly, and vortexing continued at a higher speed
for an additional 30 seconds. An aliquot of this suspension was then
used to measure the particle size. The average for d(0.1), d(0.5), and
d(0.9) of three sample preparations as a whole number (in micro-
meters) was recorded. To achieve the desired clinical effect of increasing serum
bicarbonate through acid removal in the GI tract, the amine-
based nonabsorbed polymer requires specific chemical and
physical properties that promote high capacity and selectivity
for hydrochloric acid (HCl) binding. Introduction Dietary interventions in patients with CKD
and metabolic acidosis comprising increased intake of fruits
and vegetables or reduced animal protein intake have been
shown to be effective in raising serum bicarbonate and slowing
kidney disease progression (Goraya et al., 2014; Garneata
et al., 2016). Additionally, oral alkali supplementation (so-
dium bicarbonate, sodium citrate) in patients with CKD and
metabolic acidosis has also been shown to increase serum
bicarbonate and slow kidney disease progression (de Brito-
Ashurst et al., 2009; Phisitkul et al., 2010; Di Iorio et al., 2019;
Dubey et al., 2020). These approaches reduce dietary acid
intake or neutralize endogenous acid with oral bicarbonate
but have the disadvantage of potentially increasing serum
potassium (dietary approaches) or introducing significant
sodium (oral alkali) in patients with CKD who are prone to
hyperkalemia and sodium-sensitive comorbidities (Goraya
and Wesson, 2019). digestion of proteins from the diet (Szerlip, 2005; Scialla and
Anderson, 2013; Hamm et al., 2015). The daily production of
these endogenous nonvolatile acids is approximately 0.7–1
mEq per kg of body weight or ∼50 to .70 mEq/day in healthy
adults eating typical Western acid-producing diets (Alpern
and Sakhaee, 1997; Scialla and Anderson, 2013; Goraya and
Wesson, 2017). Dietary interventions in patients with CKD
and metabolic acidosis comprising increased intake of fruits
and vegetables or reduced animal protein intake have been
shown to be effective in raising serum bicarbonate and slowing
kidney disease progression (Goraya et al., 2014; Garneata
et al., 2016). Additionally, oral alkali supplementation (so-
dium bicarbonate, sodium citrate) in patients with CKD and
metabolic acidosis has also been shown to increase serum
bicarbonate and slow kidney disease progression (de Brito-
Ashurst et al., 2009; Phisitkul et al., 2010; Di Iorio et al., 2019;
Dubey et al., 2020). These approaches reduce dietary acid
intake or neutralize endogenous acid with oral bicarbonate
but have the disadvantage of potentially increasing serum
potassium (dietary approaches) or introducing significant
sodium (oral alkali) in patients with CKD who are prone to
hyperkalemia and sodium-sensitive comorbidities (Goraya
and Wesson, 2019). demonstrated a high capacity and selectivity for HCl binding
and removal in the GI tract, leading to an increase in serum
bicarbonate. Veverimer binds and removes HCl without
exchanging the proton for a cation, thus representing a novel
means of increasing acid excretion in patients with CKD and
metabolic acidosis. Introduction (CKD) and is caused by the inability of the diseased kidney
to quantitatively remove daily endogenous acid production
(Alpern and Sakhaee, 1997; Hamm et al., 2015; Kraut and
Madias, 2016). The result of this imbalance is that acid
accumulates in the body and serum bicarbonate, the major
extracellular acid buffer, and pH both fall from their normal
ranges of 22–29 mEq/l and 7.36–7.44, respectively (Wesson
et al., 2020). Chronic metabolic acidosis is recognized clinically
as a persistent reduction of serum bicarbonate to less than the
lower limit of normal, which is generally 22 mEq/l, in a pa-
tient with CKD and normal pulmonary function (Kraut and
Madias, 2018; Raphael, 2018). Metabolic acidosis is a common disorder in patients with
non–dialysis-dependent, stage 3–5 chronic kidney disease pp
y
y
The authors report the following disclosures regarding their relationship
and roles at Tricida, Inc. G.K. is a full-time Tricida employee and a member of
the Tricida Board of Directors and has stock and stock options in Tricida; G.K. is listed on granted and pending Tricida patents. J.B. reports consulting fees
and stock and stock options from Tricida during and outside this work; J.B. is
listed on granted and pending Tricida patents. J.S., K.B., M.K., P.K., R.G., S.T.,
and S.N. are full-time Tricida employees and have stock and stock options in
Tricida along with listings on granted and pending Tricida patents. i
l b
f
i i
d
(S
h S
CA) The human body continually generates acid through me-
tabolism of the daily diet. Sources of acid include amino acids
and nucleic acids, incomplete oxidation of carbohydrates, and ABBREVIATIONS: CAS, Chemical Abstract Service; CKD, chronic kidney disease; CTAB, cetyltrimethylammonium bromide; GCTA, GI
compartment transit assay; GI, gastrointestinal; HCl, hydrochloric acid; IC, ion chromatography; p/n, catalog number; SGF, simulated
gastric fluid; SIB, simulated intestine inorganic buffer; SOB, simulated intestine organic and inorganic buffer; wt%, weight percent. 439 440 Klaerner et al. digestion of proteins from the diet (Szerlip, 2005; Scialla and
Anderson, 2013; Hamm et al., 2015). The daily production of
these endogenous nonvolatile acids is approximately 0.7–1
mEq per kg of body weight or ∼50 to .70 mEq/day in healthy
adults eating typical Western acid-producing diets (Alpern
and Sakhaee, 1997; Scialla and Anderson, 2013; Goraya and
Wesson, 2017). Materials and Methods First, the polymer should
have an amine capacity to bind at least 5 mEq of proton per
gram of polymer with a convenient daily dose of less than
10 g/day (Bushinsky et al., 2018). Once protonated, the acid-
binding polymer should selectively bind chloride to ensure net
acid removal from the GI tract (Turnberg et al., 1970). Additionally, the polymer should minimize binding and re-
moval of other anions in the GI tract, such as fatty acids and
bile acids, which represent precursors metabolized by the liver
to bicarbonate (den Besten et al., 2013; Ríos-Covián et al.,
2016). Fig. 1. Chemical structure of veverimer. Veverimer is a highly crosslinked
aliphatic amine polymer that is synthesized by first copolymerizing two
monomers, allylamine hydrochloride and N,N9-diallyl-1,3-diaminopropane
dihydrochloride, followed by crosslinking the polymer with 1,2-dichloroethane. a = residue of N,N9-diallyl-1,3-diaminopropane dihydrochloride (monomer
and crosslinker), b = residue of allylamine (monomer), and c = residue of
1,2-dichloroethane (ethylene crosslink between two amines); an ethylene
linkage between two allylamine groups is shown as an example of one
of many possible linkages between amines, and m = a large number
indicating an extended polymer network. In this report, we provide the initial in vitro and in vivo
characterization of veverimer, a nonabsorbed HCl-binding
polymer under development for the treatment of metabolic
acidosis and slowing of kidney disease progression in patients
with CKD (Bushinsky et al., 2018; Wesson et al., 2019a,b). Veverimer is composed of low-swelling, spherical polymeric
beads that are approximately 100 mm in diameter. Size
exclusion built into the three-dimensional structure of the
polymer enables preferential binding of chloride versus larger
inorganic and organic anions, such as phosphate, citrate, fatty
acids, and bile acids. Using a rat model of CKD, veverimer Fig. 1. Chemical structure of veverimer. Veverimer is a highly crosslinked
aliphatic amine polymer that is synthesized by first copolymerizing two
monomers, allylamine hydrochloride and N,N9-diallyl-1,3-diaminopropane
dihydrochloride, followed by crosslinking the polymer with 1,2-dichloroethane. a = residue of N,N9-diallyl-1,3-diaminopropane dihydrochloride (monomer
and crosslinker), b = residue of allylamine (monomer), and c = residue of
1,2-dichloroethane (ethylene crosslink between two amines); an ethylene
linkage between two allylamine groups is shown as an example of one
of many possible linkages between amines, and m = a large number
indicating an extended polymer network. Fig. 1. Chemical structure of veverimer. Materials and Methods The general procedure for the GCTA assay comprised the following
steps: 2.5 mg/ml of the polymer was incubated in SGF buffer at 37°C
for 1 hour, and after incubation, the polymer was isolated and washed
with 10 ml of deionized water. The recovered polymer was next
incubated in SOB buffer at 37°C for 2 hours; after incubation, the
polymer was isolated and washed with 10 ml of deionized water. Finally, the recovered polymer was incubated in retention buffer
(50
mM
N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic
acid,
100 mM acetate, 17 mM chloride, 2.0 mM phosphate, 3 mM sulfate,
30 mM bicarbonate, pH 7.0) at 37°C for 42 hours; after incubation, the
polymer was isolated and washed with 10 ml deionized water. After
this final wash, the polymer was incubated in 0.20 M sodium
hydroxide solution at 37°C for 18 hours to elute anions, which were
quantitated by IC analysis. pH-Dependent Equilibrium Chloride Binding. To determine
the pH-dependent equilibrium chloride binding, veverimer (4 mg/ml)
was incubated for 18 hours in 100 mM sodium chloride solution
(i.e., test solution). The sample was continuously stirred during the
incubation, and the pH of the solution was maintained at a predeter-
mined value by slowly adding 0.1 N HCl using an automatic titrator
(T50; Mettler Toledo). The pH values maintained in the individual test
solutions ranged from 1.5 to 7.0. After incubation, the chloride content
in the supernatant was measured by IC (ICS-1600; Thermo Scientific). Equilibrium chloride binding to veverimer was calculated by de-
termining the difference between the amount of chloride added during
the experiment and the amount remaining in the supernatant at the
end of the study. In Vitro Hydrochloric Acid Binding Assays. The in vitro
chloride binding capacity and specificity of veverimer were assessed
in three biologic matrices mimicking the environment of different GI
compartments: 1) simulated gastric fluid (SGF) that mimics the acidic
environment of the stomach (pH 1.2) and reflects an optimal condition
for binding of hydrochloric acid; 2) simulated intestine inorganic buffer
(SIB) with a pH (5.5) resembling the human proximal intestine and
containing a high concentration of phosphate as a potential competing
anion; and 3) simulated intestine organic and inorganic buffer (SOB)
with a pH (6.2) and anion content that correspond to the human distal
intestine and provide additional potential competing anions (Table 2). Materials and Methods Veverimer was tested in duplicate at a concentration of 2.5 mg/ml at
37°C for 16 hours in SGF, 1 hour in SIB, or 24 hours in SOB. After
incubation at 37°C with shaking, samples were kept at room Animal and Ethics Approval. All animal experiments were
conducted in accordance with the Guide for the Care and Use of
Laboratory Animals from the Institute for Laboratory Animal Re-
search, National Research Council and as adopted and promulgated
by US National Institutes of Health and approved by the vendor Materials and Methods aNegative and zero results are reported as zero. Water as a test medium also represented high pH (i.e., the equilibrium
pH of water during the solubility test was approximately 9). The
solution of 0.1 N HCl and buffers at pH 4.5 and 6.8 were used to
simulate the physiologic pH range that exists along the GI tract. In
addition, the buffers at pH 4.5 and 6.8 were evaluated with three types
of surfactants at 2 weight percent (wt%) each: the anionic surfactant
SDS (Catelog Number [p/n] 74255, CAS Registry Number 151-21-3;
Sigma-Aldrich), the cationic surfactant cetyltrimethylammonium
bromide (CTAB) (p/n ARK2188, CAS Registry Number 57-09-0;
Sigma-Aldrich), and the nonionic surfactant polyoxyethylene sorbitan
mono-oleate (Tween 80, p/n BP388, CAS Registry Number 9005-65-6;
Fisher Scientific). To conduct the solubility tests, approximately 1 g of
veverimer in 1 l solvent was shaken at 37°C in the test medium for 7
days. The insoluble veverimer was recovered by filtering, and this was
followed by washing and drying the insoluble polymer collected on the
filter. The dry weight of the insoluble polymer was determined
gravimetrically (ML204; Mettler Toledo) and corrected for total
amount of residual counterions when applicable. The solubility was
calculated as a weight loss (initial dry weight of veverimer minus dry
weight of insoluble veverimer). The results were expressed as the
amount of veverimer (milligram) dissolved in 1 l of test medium and
reported as an average value (Table 1). The general procedure for the GCTA assay comprised the following
steps: 2.5 mg/ml of the polymer was incubated in SGF buffer at 37°C
for 1 hour, and after incubation, the polymer was isolated and washed
with 10 ml of deionized water. The recovered polymer was next
incubated in SOB buffer at 37°C for 2 hours; after incubation, the
polymer was isolated and washed with 10 ml of deionized water. Finally, the recovered polymer was incubated in retention buffer
(50
mM
N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic
acid,
100 mM acetate, 17 mM chloride, 2.0 mM phosphate, 3 mM sulfate,
30 mM bicarbonate, pH 7.0) at 37°C for 42 hours; after incubation, the
polymer was isolated and washed with 10 ml deionized water. After
this final wash, the polymer was incubated in 0.20 M sodium
hydroxide solution at 37°C for 18 hours to elute anions, which were
quantitated by IC analysis. Materials and Methods Veverimer is a highly crosslinked
aliphatic amine polymer that is synthesized by first copolymerizing two
monomers, allylamine hydrochloride and N,N9-diallyl-1,3-diaminopropane
dihydrochloride, followed by crosslinking the polymer with 1,2-dichloroethane. a = residue of N,N9-diallyl-1,3-diaminopropane dihydrochloride (monomer
and crosslinker), b = residue of allylamine (monomer), and c = residue of
1,2-dichloroethane (ethylene crosslink between two amines); an ethylene
linkage between two allylamine groups is shown as an example of one
of many possible linkages between amines, and m = a large number
indicating an extended polymer network. 441 Mechanism of Action of Veverimer TABLE 1
Solubility of veverimer in various aqueous and organic solvents TABLE 1 temperature for 2 minutes without agitation, which was enough to
clear the supernatant of polymer particles for sampling. Supernatant
samples were then filtered and transferred to chromatography vials
for ion chromatography (IC) (ICS-2100; Thermo Scientific) analysis to
quantify concentrations of anions present in the supernatant before
and after incubation with each of the polymers. Test Medium
Solubility
(mg/l)a
Water
0
0.1 N HCl
3
Methanol
0
n-Heptane
0
50 mM acetate buffer (pH 4.5)
0
50 mM acetate buffer (pH 4.5) with 2 wt% SDS
0
50 mM acetate buffer (pH 4.5) with 2 wt% CTAB
2
50 mM acetate buffer (pH 4.5) with 2 wt% Tween 80
0
50 mM phosphate buffer (pH 6.8)
0
50 mM phosphate buffer (pH 6.8) with 2 wt% SDS
0
50 mM phosphate buffer (pH 6.8) with 2 wt% CTAB
0
50 mM phosphate buffer (pH 6.8) with 2 wt% Tween
80
0
Tween 80, polyoxyethylene sorbitan mono-oleate. aNegative and zero results are reported as zero. The chloride binding capacity of veverimer was calculated using the
following equation: Where : C1 ¼ chloride concentration present at the beginning mmol=l
ð
Þ
C2 ¼ chloride concentration present after the incubation mmol=l
ð
Þ GI Compartment Transit Assay. An in vitro GI compartment
transit assay (GCTA) was used to measure the binding and retention
of various anions to veverimer under conditions simulating the
passage of the polymer through various compartments of the GI tract. Sequential incubation in three different matrices simulated the pH,
ionic environment, and residence times associated with transit
through three different GI compartments (i.e., stomach, distal small
intestine/cecum, and colon). After incubation in each the three
matrices, all remaining bound ions were eluted from veverimer and
quantitated by IC (ICS-2100; Thermo Scientific). Tween 80, polyoxyethylene sorbitan mono-oleate. TABLE 2 Samples were analyzed for serum bicarbonate levels and pH
values. In addition, a 24-hour fecal sample was obtained from each
animal in the control and high-dose groups during weeks 4 and 6 of
part 1 of the study and weeks 9 and 11 of part 2 of the study. Anions
were extracted from lyophilized and homogenized fecal samples by
incubating the samples with NaOH for 18 hours at 37°C. Sample
supernatants were analyzed for chloride and phosphate by IC (ICS-
2100; Thermo Scientific). Veverimer Proof-of-Concept Efficacy Study in Rats. Vever-
imer was evaluated in vivo in an adenine-induced rat model of CKD
and metabolic acidosis (Diwan et al., 2018). The study was designed in
two parts (Fig. 2). In both parts, male Sprague-Dawley rats (N = 10/
group) were first administered adenine (0.75 wt% in casein diet
[Research Diets, New Brunswick, NJ]) for 2 weeks to induce chronic
kidney disease. Part 1 of the study investigated the effect of early
treatment with veverimer administered to rats on a casein diet with
0.25 wt% adenine for the 4 weeks after the 2-week induction period. Part 2 of the study investigated the effect of delayed treatment with
veverimer; in this part, after the 2-week induction period, rats were
maintained on a casein diet containing 0.25 wt% adenine for 5 weeks
prior to initiation of veverimer administration and through the dosing
phase with veverimer. During the veverimer treatment periods, rats
were fed diets admixed with 0, 1.5, 3.0, and 4.5 wt% veverimer. After
correcting for body weight and food consumption, the 1.5, 3.0, and 4.5 at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
wnloaded from Bioavailability Assessment. The bioavailability of veverimer
was assessed in pharmacokinetic studies conducted in Wistar Han
rats and Beagle dogs by administering [14C]-radiolabeled veverimer as
a single oral dose to male and female animals at 0.0735 g/kg. The
target radioactive dose was 100 mCi/kg. Absorption was characterized
by measuring levels of radioactivity in the blood. The doses used in the
absorption studies were selected to be representative of doses that will Fig. 2. In vivo evaluation of veverimer
efficacy in the treatment of acidosis in an
adenine-induced model of chronic kidney
disease in rats. The study was designed in
two parts. In both parts, male Sprague-
Dawley rats (N = 10/group) were first
administered adenine (0.75 wt% in casein
diet) for 2 weeks to induce chronic kidney
disease. TABLE 2 institutions’ Animal Care and Use Committee prior to the initia-
tion of the studies. Rat studies testing the mechanism of action and
pharmacology of veverimer in the adenine-induced rat model of
CKD and metabolic acidosis were carried out at Murigenics, Inc. (Vallejo, CA). Study parts 1 and 2 both assessed the effect of withdrawing
veverimer after the end of the treatment phase, with a 2-week
withdrawal phase in which veverimer was discontinued in the low
(1.5 wt%) and high (4.5 wt%) veverimer dose groups but was continued
in the mid-dose group (3.0 wt%). All animals received a casein diet
with 0.25 wt% adenine during the withdrawal phase. Male Sprague-Dawley rats (7 to 8 weeks, 260–280 g) were obtained
from Charles River Laboratories (Hollister, CA) for the purposes of
this study and used to evaluate the pharmacodynamics of veverimer in
the CKD model with respect to fecal chloride binding and effect on
serum bicarbonate. The animals were pair-housed in a temperature-
controlled facility under a 12-hour light/12-hour dark regimen. Diet
and water were provided ad libitum. Adult Wistar Han rats and
Beagle dogs as well as juvenile Sprague-Dawley rats were used for
bioavailability assessments of [14C]-veverimer absorption, distribution,
metabolism, and excretion and were tested and housed at MPI/Charles
River (Mattawan, MI). Male Sprague-Dawley rats (7 to 8 weeks, 260–280 g) were obtained
from Charles River Laboratories (Hollister, CA) for the purposes of
this study and used to evaluate the pharmacodynamics of veverimer in
the CKD model with respect to fecal chloride binding and effect on
serum bicarbonate. The animals were pair-housed in a temperature-
controlled facility under a 12-hour light/12-hour dark regimen. Diet
and water were provided ad libitum. Adult Wistar Han rats and
Beagle dogs as well as juvenile Sprague-Dawley rats were used for
bioavailability assessments of [14C]-veverimer absorption, distribution,
metabolism, and excretion and were tested and housed at MPI/Charles
River (Mattawan, MI). Animals were randomized based on serum bicarbonate levels at
baseline (i.e., after adenine induction of nephropathy and before
initiation of the dosing period) so that mean baseline serum bi-
carbonate levels were comparable across all dose groups. Body weights
and food consumption were determined weekly, allowing calculation
of actual administered dose. For both part 1 and part 2 of the study,
blood samples were obtained from the rats before initiation of
veverimer dosing, then weekly during the dosing and withdrawal
phases. TABLE 2 TABLE 2
Anion concentration of in vitro test matrices designed to mimic GI tract compartments
Matrix
Acetate (mM)
Chloride (mM)
Phosphate (mM)
Citrate (mM)
Taurocholate (mM)
Oleic Acid (mM)
SGFa
0
98.0
0
0
0
0
SIBb
0
36.0
20.0
0
0
0
SOBc
50.0
36.0
7.0
1.5
5.0
30.0
aSGF, pH = 1.2; it mimics the acidic environment of the fasted stomach and reflects an optimal condition for binding of HCl. bSIB, pH = 5.5; pH is representative of the human proximal small intestine (duodenum and early jejunum), and that contains chloride and a high concentration of
phosphate as a potential competing anion to chloride. The solution was buffered by 2-(N-morpholino)ethanesulfonic acid. cSOB, pH = 6.2; pH and competing anion content (bile acid, citrate, oleic acid, and acetate) represent components of the human distal small intestine (late jejunum, ileum)
and cecum. The solution was buffered by N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid. Anion concentration of in vitro test matrices designed to mimic GI tract compartments aSGF, pH = 1.2; it mimics the acidic environment of the fasted stomach and reflects an optimal condition for binding of HCl. bSIB, pH = 5.5; pH is representative of the human proximal small intestine (duodenum and early jejunum), and that contains chloride and a high concentration of
phosphate as a potential competing anion to chloride. The solution was buffered by 2-(N-morpholino)ethanesulfonic acid. cSOB, pH = 6.2; pH and competing anion content (bile acid, citrate, oleic acid, and acetate) represent components of the human distal small intestine (late jejunum, ileum)
and cecum. The solution was buffered by N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid. 442 Klaerner et al. wt% veverimer treatment groups received mean veverimer doses of
0.8, 1.5, and 2.4 g/kg per day, respectively, in part 1 of the study and
0.7, 1.4, and 2.3 g/kg per day, respectively, in part 2 of the study. wt% veverimer treatment groups received mean veverimer doses of
0.8, 1.5, and 2.4 g/kg per day, respectively, in part 1 of the study and wt% veverimer treatment groups received mean veverimer doses of
0.8, 1.5, and 2.4 g/kg per day, respectively, in part 1 of the study and institutions’ Animal Care and Use Committee prior to the initia-
tion of the studies. Rat studies testing the mechanism of action and
pharmacology of veverimer in the adenine-induced rat model of
CKD and metabolic acidosis were carried out at Murigenics, Inc. (Vallejo, CA). TABLE 2 Three in vitro assessments of the chloride binding
capacity of veverimer were conducted in test matrices that
mimicked various GI compartments with respect to pH and
anion composition (Table 2). Competing anions (e.g., phosphate,
citrate, and taurocholate) were included in the two matrices
simulating intestinal fluid (SIB and SOB). Table 3 summarizes
the matrices used, the incubation times, the competing anions,
and the binding of chloride and competing anions by veverimer. Binding studies in the test matrices demonstrated that vever-
imer bound chloride with high capacity and selectivity. Vever-
imer bound 10.7 6 0.4 mmol of chloride per gram of polymer in
SGF. In the SIB matrix, veverimer preferentially bound
chloride over phosphate with binding capacities of 4.3 6 0.1
mmol of chloride and 1.5 6 0.3 mmol of phosphate per gram of
polymer, respectively. In the most complex SOB matrix,
veverimer preferentially bound chloride (3.8 6 0.3 mmol/g of
polymer) in the presence of various competing inorganic and
organic anions such that the polymer essentially did not bind
phosphate, citrate or taurocholate. To examine distribution of veverimer, adult Wistar Han rats (n = 7/
sex per group) received a single oral administration of [14C]-veverimer
at a target dose level of 0.0735 g/kg (100 mCi/kg). At each time point
evaluated (0.5, 1, 6, 24, 48, 120, and 168 hours postdose), rats (n = 1/sex
per time point) were euthanized, and carcasses were subjected to
quantitative whole-body autoradiography using a Fuji FLA-5100
fluorescent image analyzer (Fuji Photo Film Co., Ltd., Japan). To determine excretion of veverimer, adult Wistar Han rats (n = 3/
sex) and adult Beagle dogs (n = 3/sex) received a single oral adminis-
tration (via gavage) of [14C]-veverimer at 0.0735 g/kg (100 mCi/kg). Animals were placed in metabolic cages immediately after dosing, and
urine, feces, expired air (rat only), and cage washings were collected
predose and at the following postdose time intervals: at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
oaded from An in vitro GCTA was used to measure the binding and
retention of various anions to veverimer under conditions
simulating the passage of the polymer through distinct
compartments of the GI tract. Sequential incubation in three
different matrices simulated the pH, ionic environment and
residence times associated with transit through the stomach
(SGF buffer), distal small intestine/cecum (SOB buffer), and
colon (retention buffer). TABLE 2 In
addition, to determine whether bioavailability differed between
juvenile and adult animals because of different stages of GI maturity
an oral absorption study was conducted in juvenile Sprague-Dawley
rats. Rat pups on postnatal days 7 and 11 (n = 18/sex per group) were
administered [14C]-radiolabeled veverimer at a total labeled/unla-
beled combined veverimer dose of 0.15 g/kg (target radioactive dose =
100 mCi/kg). Serial blood samples were taken from each animal before
dosing and at 0.5, 1, 2, 4, 6, 24, and 48 hours postdose in the adult rat
before dosing and at 0.5, 1, 2, 4, 6, 12, 24, 48, 72, 120, and 168 hours
postdose in the dog and 1, 2, 4, 8, and 24 hours postdose in the juvenile
rat. Absorption was characterized by measuring levels of radioactivity
in whole blood (dog and juvenile rat) and/or plasma (dog, adult rat, and
juvenile rat) using liquid scintillation counting (Packard 2300TR;
PerkinElmer, Waltham, MA). be administered to human subjects, including pediatric subjects. In
addition, to determine whether bioavailability differed between
juvenile and adult animals because of different stages of GI maturity
an oral absorption study was conducted in juvenile Sprague-Dawley
rats. Rat pups on postnatal days 7 and 11 (n = 18/sex per group) were
administered [14C]-radiolabeled veverimer at a total labeled/unla-
beled combined veverimer dose of 0.15 g/kg (target radioactive dose =
100 mCi/kg). Serial blood samples were taken from each animal before
dosing and at 0.5, 1, 2, 4, 6, 24, and 48 hours postdose in the adult rat
before dosing and at 0.5, 1, 2, 4, 6, 12, 24, 48, 72, 120, and 168 hours
postdose in the dog and 1, 2, 4, 8, and 24 hours postdose in the juvenile
rat. Absorption was characterized by measuring levels of radioactivity
in whole blood (dog and juvenile rat) and/or plasma (dog, adult rat, and
juvenile rat) using liquid scintillation counting (Packard 2300TR;
PerkinElmer, Waltham, MA). is determined to be insoluble in aqueous and organic solvents
and in media encompassing the physiologic pH range with and
without surfactant. is determined to be insoluble in aqueous and organic solvents
and in media encompassing the physiologic pH range with and
without surfactant. Characterization of Veverimer Hydrochloric Acid
Binding
In
Vitro
at
Physiologically
Relevant
pH
Values. TABLE 2 Veverimer bound an average of 8.1
mmol of chloride per gram of polymer under simulated gastric
conditions (pH 1.2, 1 hour, 37°C) and retained most of the
bound chloride (7 mmol/g of polymer; approximately 85%)
after being challenged by conditions designed to mimic the
environment of the distal small intestine and cecum (pH 6.2,
2 hours, 37°C). After the third incubation under conditions
representing the colon (pH 7.0, 42 hours, 37°C), approximately
60% of initially bound chloride (approximately 5 mmol
chloride/per gram of polymer) was retained. Release of
chloride was attributed to the pH-dependent decrease in the
total binding capacity of the veverimer polymer. Veverimer
bound very little or no measurable amounts of the other
competing anions (i.e., acetate, phosphate, citrate, taurocholate,
oleic acid, sulfate, and bicarbonate) present in the simulated
human distal small intestine/cecum and colon matrices. Urine (Rat and Dog): 0–6 (rat) or 0–12 (dog), 6–24 (rat) or 12–24
(dog), 24–48, 48–72, 72–96, 96–120, 120–144 and 144–168 hours. Feces (rat and dog): 0–24, 24–48, 48–72, 72–96, 96–120, 120–144,
and 144–168 hours. Expired air (rat): 0–24, 24–48, and 48–72 hours. Expired air (rat): 0–24, 24–48, and 48–72 hours. Cage washings (dog): 24, 48, 72, 96, 120, 144, and 168 hours. Cage washings (dog): 24, 48, 72, 96, 120, 144, and 168 hours. Cage washings (rat): 168 hours. Cage washings (rat): 168 hours. Rats were euthanized after the 168-hour sample collection, and
additional samples for radioactivity measurements were taken from
carcasses. All rat and dog samples were analyzed using liquid
scintillation counting (Packard 2300TR; PerkinElmer). TABLE 2 Part 1 of the study investigated
the effect of early treatment with vever-
imer administered to rats on a casein diet
with 0.25 wt% adenine for the 4 weeks
after the 2-week chronic kidney disease
induction period. In contrast, part 2 of the
study investigated the effect of delayed
treatment with veverimer after the 2-
week induction period, in which rats were
maintained on a casein diet containing
0.25 wt% adenine for 5 weeks prior to
initiation of veverimer administration
and through the dosing phase with vever-
imer. During the veverimer treatment
periods, rats were fed diets admixed with
0, 1.5, 3.0, and 4.5 wt% veverimer. After
correcting for body weight and food con-
sumption, the 1.5, 3.0, and 4.5 wt% vever-
imer treatment groups received mean
veverimer doses of 0.8, 1.5, and 2.4 g/kg per
day, respectively, in part 1 of the study and
0.7, 1.4, and 2.3 g/kg per day, respectively,
in part 2 of the study. Fig. 2. In vivo evaluation of veverimer
efficacy in the treatment of acidosis in an
adenine-induced model of chronic kidney
disease in rats. The study was designed in
two parts. In both parts, male Sprague-
Dawley rats (N = 10/group) were first
administered adenine (0.75 wt% in casein
diet) for 2 weeks to induce chronic kidney
disease. Part 1 of the study investigated
the effect of early treatment with vever-
imer administered to rats on a casein diet
with 0.25 wt% adenine for the 4 weeks
after the 2-week chronic kidney disease
induction period. In contrast, part 2 of the
study investigated the effect of delayed
treatment with veverimer after the 2-
week induction period, in which rats were
maintained on a casein diet containing
0.25 wt% adenine for 5 weeks prior to
initiation of veverimer administration
and through the dosing phase with vever-
imer. During the veverimer treatment
periods, rats were fed diets admixed with
0, 1.5, 3.0, and 4.5 wt% veverimer. After
correcting for body weight and food con-
sumption, the 1.5, 3.0, and 4.5 wt% vever-
imer treatment groups received mean
veverimer doses of 0.8, 1.5, and 2.4 g/kg per
day, respectively, in part 1 of the study and
0.7, 1.4, and 2.3 g/kg per day, respectively,
in part 2 of the study. 443 Mechanism of Action of Veverimer be administered to human subjects, including pediatric subjects. Results The suspended
monomer droplets were converted to cross-
linked polymer particles that allowed for
control of particle size. Veverimer beads
were characterized using laser diffrac-
tion, and a monomodal distribution was
detected, wherein greater than 90% of the
volume was composed of beads with a par-
ticle size diameter larger than 40 mm. Fig. 3. Veverimer beads and monomodal
particle size distribution. The particle
size of veverimer was controlled in the
first step of the drug substance synthetic
process. Veverimer polymer beads were
synthesized by a polymerization process
that maintained monomer droplets in the
suspension medium before initiation of
the polymerization step. The suspended
monomer droplets were converted to cross-
linked polymer particles that allowed for
control of particle size. Veverimer beads
were characterized using laser diffrac-
tion, and a monomodal distribution was
detected, wherein greater than 90% of the
volume was composed of beads with a par-
ticle size diameter larger than 40 mm. adenine (0.75 wt% in casein diet) for 2 weeks to induce CKD
(Fig. 2). The veverimer-related effects on serum bicarbonate
and fecal excretion of chloride and phosphate are summarized
in Figs. 5 and 6. Animals were randomized based on serum
bicarbonate levels at baseline (i.e., after adenine induction of
CKD and before initiation of the dosing period) so that mean
baseline serum bicarbonate levels were similar across all dose
groups. Endpoints evaluated in the study included serum
bicarbonate and pH (weekly measurements) and fecal chloride
and phosphate (24-hour samples measured at weeks 4 and 6 of
part 1 and weeks 9 and 11 of part 2). The part 1 and part 2 rat
studies were designed to accommodate a withdrawal period,
with one group (3.0 wt%) maintained on continuous dosing as
an internal control for the withdrawal groups tested (1.5 and
4.5 wt%). retention and removal of HCl from the body through the feces),
and the CKD model provides proof-of-concept that veverimer
administration results in restoration of serum bicarbonate to
the normal range in a dose-dependent manner. at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
Downloaded from Veverimer
Absorption,
Distribution,
Metabolism,
and Excretion. The physicochemical properties of veverimer,
including its insolubility in aqueous and organic solvents and
particle size distribution, suggested that the polymer would not
be absorbed from the GI tract. Results Veverimer Particle Size Distribution and Solubility
in Aqueous and Organic Solvents. The physical form of
veverimer is that of a free-flowing powder composed of low-
swelling, spherical beads (Fig. 3). Each bead is a single,
high–molecular weight, crosslinked polyamine molecule. The
particle size of veverimer was primarily controlled by the stir
rate during the suspension polymerization reaction in which
the beads are first formed to generate an average particle
diameter of approximately 100 mm. Particle size distribution
analysis showed a monomodal particle size distribution,
wherein greater than 90% of the volume was composed of
particles with a diameter larger than 40 mm (Fig. 3). pH-dependent equilibrium chloride binding of veverimer
(4 mg/ml) was determined in 100 mM sodium chloride
solutions (i.e., test solution) in which the pH of the solution
was maintained at a predetermined value by slowly adding
0.1 N HCl. The pH values maintained in the individual test
solutions ranged from 1.5 to 7.0. Although the chloride binding
capacity for veverimer decreased with increasing pH, which
was considered related to a decrease in veverimer protonation,
veverimer maintained significant chloride binding capacity
(i.e., .5 mmol/g of polymer) over a range of pH values (1.5–7.0)
that are physiologically relevant for the GI tract (Fig. 4). The solubility of veverimer was evaluated in a variety of
aqueous and organic solvents and expressed as the amount of
veverimer (milligram) dissolved in 1 l of solvent (Table 1). Apart from the 0.1 N HCl (veverimer solubility of 3 mg/l) and
50 mM acetate buffer (pH 4.5) with 2 wt% CTAB (veverimer
solubility of 2 mg/l) matrices, veverimer was uniformly
insoluble in the aqueous and organic solvents tested. In
accordance with USP (General Notices and Requirements),
the descriptive term of insoluble or practically insoluble is
applied to any material wherein 10,000 or more parts of
solvent are required for one part of solute, and thus veverimer Veverimer Effects on Serum Bicarbonate and Fecal
Chloride Excretion in Rats with CKD and Metabolic
Acidosis. Veverimer was evaluated in a two-part in vivo
study in male Sprague-Dawley rats (n = 10/group) administered 444 Klaerner et al. Fig. 3. Veverimer beads and monomodal
particle size distribution. The particle
size of veverimer was controlled in the
first step of the drug substance synthetic
process. Veverimer polymer beads were
synthesized by a polymerization process
that maintained monomer droplets in the
suspension medium before initiation of
the polymerization step. ,
pp
aSGF, pH = 1.2; it mimics the acidic environment of the fasted stomach and reflects an optimal condition for binding of HCl.
bSIB, pH = 5.5; pH is representative of the human proximal small intestine (duodenum and early jejunum), and that contains Results To test this hypothesis, the
absorption, distribution, metabolism, and excretion of an
administered pharmaceutical compound within an organism
of [14C]-veverimer after oral administration of a single dose in
both Wistar Han rats and Beagle dogs was assessed. Absorption of [14C]-veverimer into the blood was not detect-
able in any adult rat plasma, dog blood, or juvenile rat blood or
plasma sample. Radioactivity was detected in only one dog
plasma sample at a single time point but was not considered to
indicate absorption since the detectable level was close to the
limit of detection, fell within the range of background sample
radioactivity values, and was not observed in this dog at time
points bracketing the sample. The results of the radiolabeled
absorption studies indicated that veverimer was not system-
ically absorbed from the GI tract after oral administration to
the juvenile or adult rat or the dog. Serum bicarbonate was elevated to within the normal range
(23.0–31.1 mEq/l based on values for five age-matched rats) in
veverimer-dosed rats but remained below normal in untreated
CKD control rats. Serum bicarbonate levels generally remained
within the normal range with continued veverimer dosing,
whereas withdrawal of veverimer was associated with a decline
in serum bicarbonate within 2 weeks to values that were
generally less than those observed in control animals. The
effect of veverimer on blood pH reflected the results observed for
serum bicarbonate (unpublished data). A significant increase in
fecal chloride was observed in veverimer-dosed rats relative to
untreated controls. Although veverimer also significantly in-
creased fecal phosphate excretion, the effect was notably less
than that observed for chloride. The study results support the
proposed veverimer mechanism of action (i.e., selective binding, Distribution of veverimer was assessed by quantitative
whole-body autoradiography in the adult rat. Radioactivity
was not detectable in any tissue or organ other than within
the GI tract, and therefore, tissue distribution could not
be quantitated. The intestinal transit of the radiolabel
was effectively complete by approximately 120 hours after TABLE 3 As the pH of the
incubation solution was increased, the equilibrium chloride binding
capacity of veverimer decreased but still bound .5.0 mmol/g of chloride
under physiologically relevant conditions (i.e., pH 5.0–7.0). at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
nloaded from Evaluation of veverimer metabolism in the rat and dog was
not conducted based on the absence of systemic exposure. The
in vivo pharmacology studies (summarized above) demon-
strating binding and removal of chloride after oral adminis-
tration of veverimer along with the significant 10-fold increase administration of [14C] -veverimer. The lack of radioactivity in
tissues or organs outside of the GI tract demonstrated that
radiolabeled veverimer was not absorbed from the gut after
oral administration to rats. Fig. 5. Effect of veverimer on serum
bicarbonate and fecal excretion of chlo-
ride and phosphate in part 1 of proof-of-
concept rat study. (A) Effect of veverimer
on serum bicarbonate in part 1. Mean 6
S.D. from blood samples collected at week
6 (treatment phase) and week 8 (with-
drawal phase). The 3.0 wt% veverimer
treatment group remained on veverimer,
whereas 1.5 and 4.5 wt% veverimer treat-
ment groups were withdrawn from drug
during the withdrawal phase (weeks 7
to 8). Horizontal dotted lines mark the
normal serum bicarbonate range for male
at ASPET Journals on October 23, 2024
rg Fig. 5. Effect of veverimer on serum
bicarbonate and fecal excretion of chlo-
ride and phosphate in part 1 of proof-of-
concept rat study. (A) Effect of veverimer
on serum bicarbonate in part 1. Mean 6
S.D. from blood samples collected at week
6 (treatment phase) and week 8 (with-
drawal phase). The 3.0 wt% veverimer
treatment group remained on veverimer,
whereas 1.5 and 4.5 wt% veverimer treat-
ment groups were withdrawn from drug
during the withdrawal phase (weeks 7
to 8). Horizontal dotted lines mark the
normal serum bicarbonate range for male
Sprague-Dawley rats of the same age. Statistical
analysis:
two-way
ANOVA
with Dunnett’s multiple comparisons test
vs. untreated group; N = 10 rats per
group. (B) Fecal chloride excretion in rats
during part 1 of the study. Mean 6 S.D. from fecal samples collected at week 4 and
week 6. Statistical analysis: unpaired,
two-tailed t test; N = 10 rats per group. (C) Fecal phosphate excretion in rats
during part 1 of the study. Mean 6 S.D. from fecal samples collected at week 4 and
week 6. TABLE 3 The lack of radioactivity in
tissues or organs outside of the GI tract demonstrated that
radiolabeled veverimer was not absorbed from the gut after
oral administration to rats. Excretion of veverimer was predominantly through the feces
(Tables 4 and 5). Approximately 95%–97% of the administered
radioactive dose in the rat and 96%–99% in the dog was
recovered in the feces. Excretion of radioactivity was relatively
rapid with most of the radioactivity (approximately 90%)
excreted within the first 24 hours postdose in both species. In general, radioactivity was not detectable in any fecal or
urine sample after 72 hours postdose in the rat or after
120 hours in the dog. Very small amounts of radioactivity were
detected over the first 24-hour postdose period in rat urine and
expired air (mean #0.02% of the administered dose, each
matrix) and dog urine (mean = 0.02% of the administered
dose). The amount in urine and/or expired air for both the rat
and dog corresponded within the variability of the study to the
unincorporated radiolabel remaining in the administered
material [14C]-veverimer. In addition, some degree of cross-
contamination of urine by feces was likely to have contributed
to the very low levels of radiolabel detected in the urine of both
species because complete separation of urine and feces is
rarely completely achieved despite the use of metabolic cages. Thus, excretion data together with blood and plasma data
demonstrated that veverimer was not systemically absorbed
in rats and dogs after oral administration, with almost 100% of
the recovered radioactivity in the feces. Evaluation of veverimer metabolism in the rat and dog was
not conducted based on the absence of systemic exposure. The
in vivo pharmacology studies (summarized above) demon-
strating binding and removal of chloride after oral adminis-
tration of veverimer along with the significant 10-fold increase
Fig. 4. Veverimer chloride binding through a range of pH values. Equilibrium chloride binding was assessed at different pH values for
veverimer as described. Veverimer had a chloride binding capacity of
10.1 mmol/g under highly acidic conditions (i.e., pH 1.5) in which all the
available free amine groups (primary, secondary, and tertiary) were
protonated and bound to chloride as a counterion. As the pH of the
ncubation solution was increased, the equilibrium chloride binding
capacity of veverimer decreased but still bound .5.0 mmol/g of chloride
under physiologically relevant conditions (i.e., pH 5.0–7.0). Mechanism of Action of Veverimer
445 Fig. TABLE 3 4. Veverimer chloride binding through a range of pH values. Equilibrium chloride binding was assessed at different pH values for
veverimer as described. Veverimer had a chloride binding capacity of
10.1 mmol/g under highly acidic conditions (i.e., pH 1.5) in which all the
available free amine groups (primary, secondary, and tertiary) were
protonated and bound to chloride as a counterion. As the pH of the
incubation solution was increased, the equilibrium chloride binding
capacity of veverimer decreased but still bound .5.0 mmol/g of chloride
under physiologically relevant conditions (i.e., pH 5.0–7.0). 445 Mechanism of Action of Veverimer Excretion of veverimer was predominantly through the feces
(Tables 4 and 5). Approximately 95%–97% of the administered
radioactive dose in the rat and 96%–99% in the dog was
recovered in the feces. Excretion of radioactivity was relatively
rapid with most of the radioactivity (approximately 90%)
excreted within the first 24 hours postdose in both species. In general, radioactivity was not detectable in any fecal or
urine sample after 72 hours postdose in the rat or after
120 hours in the dog. Very small amounts of radioactivity were
detected over the first 24-hour postdose period in rat urine and
expired air (mean #0.02% of the administered dose, each
matrix) and dog urine (mean = 0.02% of the administered
dose). The amount in urine and/or expired air for both the rat
and dog corresponded within the variability of the study to the
unincorporated radiolabel remaining in the administered
material [14C]-veverimer. In addition, some degree of cross-
contamination of urine by feces was likely to have contributed
to the very low levels of radiolabel detected in the urine of both
species because complete separation of urine and feces is
rarely completely achieved despite the use of metabolic cages. Thus, excretion data together with blood and plasma data
demonstrated that veverimer was not systemically absorbed
in rats and dogs after oral administration, with almost 100% of
the recovered radioactivity in the feces. Fig. 4. Veverimer chloride binding through a range of pH values. Equilibrium chloride binding was assessed at different pH values for
veverimer as described. Veverimer had a chloride binding capacity of
10.1 mmol/g under highly acidic conditions (i.e., pH 1.5) in which all the
available free amine groups (primary, secondary, and tertiary) were
protonated and bound to chloride as a counterion. TABLE 3 TABLE 3 TABLE 3
Chloride binding by veverimer in matrices mimicking the GI tract TABLE 3
Chloride binding by veverimer in matrices mimicking the GI tract
Matrix
Incubation Time (h)
Anion Bound (mmol/g Polymer)
Chloride
Phosphate
Citrate
Taurocholate
SGFa
16
10.7 6 0.4
N/A
N/A
N/A
SIBb
1
4.3 6 0.1
1.5 6 0.3
N/A
N/A
SOBc
24
3.8 6 0.3
0.1 6 0.1d
,0.1e
,0.1e
N/A, not applicable. aSGF, pH = 1.2; it mimics the acidic environment of the fasted stomach and reflects an optimal condition for binding of HCl. bSIB, pH = 5.5; pH is representative of the human proximal small intestine (duodenum and early jejunum), and that contains chloride and a high conc. of phosphate as
a potential competing anion to chloride. The solution was buffered by 2-(N-morpholino)ethanesulfonic acid. cSOB, pH = 6.2; pH and competing anion content (bile acid, phosphate, citrate, oleic acid, and acetate) represent components of the human distal small intestine (late
jejunum, ileum) and cecum. The solution was buffered by N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid. dPhosphate conc. used to calculate phosphate binding capacity of veverimer lots were estimated by calculating the change in the phosphate peak area before and after
incubating the polymer in SOB. eCitrate and taurocholate peaks for veverimer lots were not well separated in the IC chromatogram because of method limitations. Combined peak area was used to
estimate conc. of these anions before and after incubating the polymer in SOB. Oleic acid was not determined because it was not detected by the IC method used. TABLE 3
Chloride binding by veverimer in matrices mimicking the GI tract
Matrix
Incubation Time (h)
Anion Bound (mmol/g Polymer)
Chloride
Phosphate
Citrate
Taurocholate
SGFa
16
10.7 6 0.4
N/A
N/A
N/A
SIBb
1
4.3 6 0.1
1.5 6 0.3
N/A
N/A
SOBc
24
3.8 6 0.3
0.1 6 0.1d
,0.1e
,0.1e
N/A not applicable TABLE 3
Chloride binding by veverimer in matrices mimicking the GI tract g
p
y
eCitrate and taurocholate peaks for veverimer lots were not well separated in the IC chromatogram because of method limitations. Combined peak area was used to
estimate conc. of these anions before and after incubating the polymer in SOB. Oleic acid was not determined because it was not detected by the IC method used. administration of [14C] -veverimer. TABLE 3 Statistical
analysis: two-way ANOVA with Dun-
nett’s multiple comparisons test vs. untreated group; N = 10 rats per group. (B) Fecal chloride excretion during part
2 of the study. Mean 6 S.D. from fecal
samples collected at week 9 and week
11. Statistical analysis: unpaired, two-
tailed t test; N = 10 rats per group. (C)
Fecal phosphate excretion during part 2
of the study. Mean 6 S.D. from fecal
samples collected at week 9 and week
11. Statistical analysis: unpaired, two-
tailed t test; N = 10 rats per group. Fig. 6. Effect of veverimer on serum
bicarbonate and fecal excretion of chlo-
ride and phosphate in part 2 of proof-of-
concept rat study. (A) Effect of veverimer
in part 2 of the study. Mean 6 S.D. from
blood samples collected at week 11 (treat-
ment phase) and week 13 (withdrawal
phase). The 3.0 wt% veverimer treatment
group remained on veverimer, whereas
1.5 and 4.5 wt% veverimer treatment
groups were withdrawn from drug during
the withdrawal phase (weeks 12 to 13). Horizontal dotted lines mark the normal
serum bicarbonate range for male Sprague-
Dawley rats of the same age. Statistical
analysis: two-way ANOVA with Dun-
nett’s multiple comparisons test vs. untreated group; N = 10 rats per group. (B) Fecal chloride excretion during part
2 of the study. Mean 6 S.D. from fecal
samples collected at week 9 and week
11. Statistical analysis: unpaired, two-
tailed t test; N = 10 rats per group. (C)
Fecal phosphate excretion during part 2
of the study. Mean 6 S.D. from fecal
samples collected at week 9 and week
11. Statistical analysis: unpaired, two-
tailed t test; N = 10 rats per group. at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
Downloaded from at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
om in fecal chloride but only a 2-fold increase in phosphate fecal
excretion relative to controls in rats with adenine-induced
nephropathy administered veverimer suggested that the poly-
mer retained its functional integrity (i.e., high capacity,
selective chloride binding) and, therefore, structural integrity
during transit through the GI tract after oral administration,
supporting a lack of veverimer metabolism or degradation
within the GI tract. no change of these serum cations during the animal studies. Serum magnesium was not measured during the animal
studies. TABLE 3 Statistical analysis: unpaired,
two-tailed t test; N = 10 rats per group. Fig. 5. Effect of veverimer on serum
bicarbonate and fecal excretion of chlo-
ride and phosphate in part 1 of proof-of-
concept rat study. (A) Effect of veverimer
on serum bicarbonate in part 1. Mean 6
S.D. from blood samples collected at week
6 (treatment phase) and week 8 (with-
drawal phase). The 3.0 wt% veverimer
treatment group remained on veverimer,
whereas 1.5 and 4.5 wt% veverimer treat-
ment groups were withdrawn from drug
during the withdrawal phase (weeks 7
to 8). Horizontal dotted lines mark the
normal serum bicarbonate range for male
Sprague-Dawley rats of the same age. Statistical
analysis:
two-way
ANOVA
with Dunnett’s multiple comparisons test
vs. untreated group; N = 10 rats per
group. (B) Fecal chloride excretion in rats
during part 1 of the study. Mean 6 S.D. from fecal samples collected at week 4 and
week 6. Statistical analysis: unpaired,
two-tailed t test; N = 10 rats per group. (C) Fecal phosphate excretion in rats
during part 1 of the study. Mean 6 S.D. from fecal samples collected at week 4 and
week 6. Statistical analysis: unpaired,
two-tailed t test; N = 10 rats per group. 446 Klaerner et al. Klaerner et al. in fecal chloride but only a 2-fold increase in phosphate fecal
excretion relative to controls in rats with adenine-induced
nephropathy administered veverimer suggested that the poly-
mer retained its functional integrity (i e
high capacity
no change of these serum cat
Serum magnesium was not
studies. Fig
bica
ride
con
in p
bloo
men
pha
gro
1.5
gro
the
Hor
seru
Daw
ana
net
unt
(B)
2 o
sam
11. tail
Fec
of t
sam
11. tail
446
Klaerner et al. Fig. 6. Effect of veverimer on serum
bicarbonate and fecal excretion of chlo-
ride and phosphate in part 2 of proof-of-
concept rat study. (A) Effect of veverimer
in part 2 of the study. Mean 6 S.D. from
blood samples collected at week 11 (treat-
ment phase) and week 13 (withdrawal
phase). The 3.0 wt% veverimer treatment
group remained on veverimer, whereas
1.5 and 4.5 wt% veverimer treatment
groups were withdrawn from drug during
the withdrawal phase (weeks 12 to 13). Horizontal dotted lines mark the normal
serum bicarbonate range for male Sprague-
Dawley rats of the same age. oactivity not detectable.
s time sampling was discontinued as per plan because of radioactivity not being detectable in the 24248 and 48272-h collections. lculable; ND, radioactivity not detectable.
h postdose, as this time sampling was discontinued as per plan because of radioactivity not being detectable in the 24248 and 482
postdose only. Discussion Veverimer is an orally administered, nonabsorbed, counterion-
free HCl binder under development for the treatment of
metabolic acidosis in patients with CKD. The mechanism of
action of veverimer relies on highly specific binding and
retention of proton and chloride as the polymer traverses the
GI tract (Fig. 7). In the first step of this process, veverimer
becomes protonated after ingestion, with high-capacity proton
binding occurring across the pH range (pH = 1.5–7.0) found in Treatment with veverimer did not cause diarrhea in the
rats or dogs used in the absorption, distribution, metabolism,
and excretion of an administered pharmaceutical compound
within an organism assessment or in the rat model of
metabolic acidosis associated with CKD. In addition, analy-
sis of serum data for sodium, potassium, and calcium showed TABLE 4
Recovery of administered [14C]-veverimer in excreta and carcasses of male and female Wistar Han rats NC, not calculable; ND, radioactivity not detectable.
aUp to 72 h postdose, as this time sampling was discontinued as per plan because of radioactivity not being detectable in the 24248 and 48272-h collections.
bAt 168 h postdose only. aUp to 72 h postdose, as this time sampling was discontinued as per plan because of radioactivity not being detectable in th
bAt 168 h postdose only. TABLE 4 Dosing with veverimer initiated imme-
diately after the 2-week adenine CKD-induction period or
7 weeks after initiation of adenine exposure at doses of
0.7–2.4 g/kg per day by dietary admixture resulted in a signif-
icant, dose-dependent increase in serum bicarbonate within 1
week, a dose-dependent increase in blood pH, and a significant,
concomitant increase in fecal chloride excretion relative to
untreated controls (Figs. 5 and 6). The pharmacological
activity of veverimer—specifically maintenance of serum
bicarbonate levels within the normal range—was shown to
be durable through at least 6 weeks of dosing. Discontinuation
of dosing was associated with a decrease in serum bicarbonate
and pH values that were below the normal range for age-
matched rats, confirming the treatment effect of veverimer. The physicochemical analysis of veverimer along with the
nonclinical pharmacology studies reported here illustrate
various aspects of the proposed mechanism of action for
veverimer. Veverimer is a free-flowing powder composed of
highly crosslinked, low-swelling, spherical polymeric beads
(Fig. 3). Particle size analysis showed a monomodal particle
size distribution, wherein greater than 90% of the volume was
composed of particles with a diameter .40 mm and an average
diameter of approximately 100 mm. These size parameters
were carefully selected to prevent systemic absorption from
the GI tract while being small enough to optimize oral
administration and tolerability (Bushinsky et al., 2018). The particle size distribution of the polymer beads is
primarily controlled by the stir rate during the suspension
polymerization in which the beads are first formed. Solu-
bility tests in a variety of organic and aqueous solvents
showed no significant solubility of the polymer. In vitro
measurement of chloride binding in a range of intestinal
mimics and pHs demonstrated that the extensive cross-
linking promoted high capacity and selective HCl binding,
particularly in the most complex matrix mimicking the
lower GI tract, in which veverimer preferentially bound
chloride (3.8 mmol/g polymer) in the presence of various
competing anions, some of which provide precursors for
bicarbonate production (Table 3). Furthermore, the reten-
tion of chloride, which was evaluated with GCTA that
simulated the passage of the polymer through various
compartments of the GI tract, showed approximately
60% of initially bound chloride (approximately 5 mmol/g
polymer) was retained. TABLE 4 TABLE 4 TABLE 4
Recovery of administered [14C]-veverimer in excreta and carcasses of male and female Wistar Han rats
Sample
% of Administered Dose
Males (n = 3)
Females (n = 3)
Mean
S.D. Mean
S.D. Total feces
97.09
1.72
95.05
4.38
Total urine
0.02
0.01
0.02
0.01
Total expired aira
0.02
0.01
0.01
0.01
Cage washb
ND
NC
ND
NC
Carcassb
ND
NC
ND
NC
Total recovery
97.13
1.72
95.08
4.38
NC, not calculable; ND, radioactivity not detectable. aUp to 72 h postdose, as this time sampling was discontinued as per plan because of radioactivity not being detectable in the 24248 and 48272-h collections. bAt 168 h postdose only. administered [14C]-veverimer in excreta and carcasses of male and female Wistar Han rats 447 Mechanism of Action of Veverimer TABLE 5
Recovery of administered [14C]-veverimer in excreta and carcasses of male and female Beagle dogs TABLE 5
Recovery of administered [14C]-veverimer in excreta and carcasses of male and female Beagle dogs TABLE 5
Recovery of administered [14C]-veverimer in excreta and carcasses of male and female Beagle dogs
Sample
% of Administered Dose
Males (n = 3)
Females (n = 3)
Mean
S.D. Mean
S.D. Total feces
98.98
3.35
96.72
7.28
Total urine
0.02
0.01
0.02
,0.01
Total cage wash
0.01
0.01
0.01
0.01
Total recovery
99.01
3.36
96.74
7.28 the GI lumen (Fig. 4; Table 3). The concurrent binding and
retention of chloride by the protonated polymer facilitated by
the highly crosslinked polymer backbone that restricts the
binding of larger anions effectively removes HCl from the GI
tract, which is then eliminated with the polymer in the feces
(Figs. 5 and 6). HCl removal in this manner results in an
elevation of serum bicarbonate (Figs. 5 and 6). In patients with
CKD and metabolic acidosis, in which kidney-mediated acid
excretion is reduced resulting in acid retention (Wesson et al.,
2020), veverimer can restore an important acid excretion
capacity and so is distinguished from other metabolic acidosis
interventions that either reduce acid intake or neutralize
systemic acidity. Proof-of-concept data for veverimer were provided by a rat
model of adenine-induced CKD (Diwan et al., 2018) that is
characterized by low serum bicarbonate (,23.0 mEq/l) and
acidemia (pH , 7.4). TABLE 4 Indeed, to raise serum bicarbonate
by 3–4 mEq/l in an 80-kg patient, 6–8 g/day of sodium
bicarbonate is required, delivering 1.722.2 g/day of sodium
in addition to normal dietary sodium intake (Abramowitz
et al., 2013), thus exceeding the published guidelines for daily
sodium intake in patients with CKD (Wright and Cavanaugh, 2010). This additional sodium has the potential to aggravate
sodium-sensitive comorbidities, such as hypertension, conges-
tive heart failure, and edema, in patients with CKD (Bush-
insky, 2019; Navaneethan et al., 2019). The additional sodium
load from sodium-based oral alkali may also diminish the
effect of renoprotective agents, such as renin-angiotensin-
aldosterone system inhibitors (Lambers Heerspink et al.,
2012; Vegter et al., 2012), and lead to worsening albuminuria
(Raphael et al., 2020), thereby counteracting the benefits of
treating metabolic acidosis. To avoid these challenges, veverimer removes acid through
the GI tract, thus reducing the overall acid accumulation that
is the hallmark of chronic metabolic acidosis, and in so doing
introduces bicarbonate into the circulation without the addi-
tion of deleterious counterions. This mechanism of acid re-
moval has similarities to the physiologic response to prolonged
vomiting, chloride-losing diarrhea, or nasogastric suction,
each of which removes HCl from the stomach and leads to
a rapid increase in serum bicarbonate levels that may result in
hypochloremic metabolic alkalosis (Kassirer and Schwartz,
1966; Niv and Fraser, 2002; Khanna and Kurtzman, 2006;
Valeur and Julsrud, 2013). It is fundamentally different from
these responses in persons with normal kidney function, at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
Downloaded from Fig. 7. Mechanism of action of veverimer in the gastrointestinal tract. The mechanism of action of veverimer involves binding of proton and chloride,
resulting in a net reduction and removal of HCl from the GI tract and an increase in serum bicarbonate. This physiologic effect of veverimer is the result
of several steps (1–6) that occur concurrently throughout the gastrointestinal tract but are illustrated here with a focus on the gastric lumen. The initial
step in this cascade involves the oral administration of veverimer as a nonabsorbed, free-amine polymer. Within the parietal cell, H2O plus CO2 is
converted under the influence of carbonic anhydrase into H+ and HCO3
2 (Yao and Forte, 2003). H+ is secreted from the gastric parietal cell into the GI
lumen in exchange for K+ through the action of the H+/K+ ATPase (Shin et al., 2009). TABLE 4 restoring acid-base balance in the body under the conditions of
metabolic acidosis. As kidney function declines, generation of
metabolic acids continues, but their excretion is compromised,
leading to acid retention. Current treatment options to
attenuate this acid retention include dietary interventions
with very low-protein diets (Garneata et al., 2016), base-
producing fruits and vegetables (Goraya et al., 2013, 2014,
2019), or oral alkali supplementation (de Brito-Ashurst et al.,
2009; Phisitkul et al., 2010; Di Iorio et al., 2019; Dubey et al.,
2020). Although dietary interventions are effective in elevat-
ing serum bicarbonate and reducing kidney function decline,
adherence to dietary interventions can be difficult to achieve
(Garneata et al., 2016) and necessarily involves the consump-
tion of foods high in dietary potassium (Goraya and Wesson,
2019). Oral alkali supplementation introduces a significant
amount of sodium into the body, along with the neutralizing
bicarbonate or citrate equivalents, increasing overall sodium
load in patients with CKD. Indeed, to raise serum bicarbonate
by 3–4 mEq/l in an 80-kg patient, 6–8 g/day of sodium
bicarbonate is required, delivering 1.722.2 g/day of sodium
in addition to normal dietary sodium intake (Abramowitz
et al., 2013), thus exceeding the published guidelines for daily
sodium intake in patients with CKD (Wright and Cavanaugh, restoring acid-base balance in the body under the conditions of
metabolic acidosis. As kidney function declines, generation of
metabolic acids continues, but their excretion is compromised,
leading to acid retention. Current treatment options to
attenuate this acid retention include dietary interventions
with very low-protein diets (Garneata et al., 2016), base-
producing fruits and vegetables (Goraya et al., 2013, 2014,
2019), or oral alkali supplementation (de Brito-Ashurst et al.,
2009; Phisitkul et al., 2010; Di Iorio et al., 2019; Dubey et al.,
2020). Although dietary interventions are effective in elevat-
ing serum bicarbonate and reducing kidney function decline,
adherence to dietary interventions can be difficult to achieve
(Garneata et al., 2016) and necessarily involves the consump-
tion of foods high in dietary potassium (Goraya and Wesson,
2019). Oral alkali supplementation introduces a significant
amount of sodium into the body, along with the neutralizing
bicarbonate or citrate equivalents, increasing overall sodium
load in patients with CKD. TABLE 4 The highly crosslinked structure of
veverimer confers a marked size-exclusion selectivity to the
negatively charged moieties that bind to the protonated
polymer, strongly favoring binding of the smallest anions
and restricting binding of larger anions. Based on the
physicochemical characteristics of veverimer and the results
from in vitro and human studies, veverimer is unlikely to have
significant drug-drug interactions (Shao et al., 2020). The results from the rat model of CKD are consistent with
clinical findings in patients with CKD and metabolic acidosis
treated with veverimer (Bushinsky et al., 2018; Wesson et al.,
2019a,b). The veverimer doses at which an effect on serum
bicarbonate was observed in both phase 3 clinical trials
(0.05–0.15 g/kg per day) were lower than the doses used in
the nonclinical study (0.7–2.4 g/kg per day) reported here, but
rats produce approximately 7.5-fold more acid per kg of body
weight than humans (Toto and Alpern, 1996; Lin et al., 1998). Correcting the rat dose by this factor (7.5) results in a dose
(0.1–0.32 g/kg per day) that is consistent with the pharmaco-
logically active dose in humans. In addition, it is noted that the
limited phosphate binding detected in the in vitro matrix
experiments (Table 3) and the in vivo treatment experiments
(Figs. 5C and 6C) did not translate into physiologic changes in
serum or urinary phosphate in either animal studies or human
clinical studies (Bushinsky et al., 2018; Wesson et al., 2019a,b). Lack of veverimer absorption from the GI tract was demon-
strated in both rats and dogs administered a single oral dose of
[14 C]-veverimer. The mean bead size of approximately 100 mm
with a narrow particle size distribution likely restricted
absorption of particles from the GI tracts of the test animals,
which was consistent with literature reports showing that
particles larger than 0.5 mm are not systemically absorbed
(Jung et al., 2000). Because radioactivity was not observed in
the plasma of either species, metabolism was not evaluated. The lack of absorption in conjunction with the pharmacological
effects on serum bicarbonate and fecal chloride excretion in rats
supports that veverimer is not metabolized or degraded but
maintains functional and, therefore, structural integrity during
transit through the GI tract after oral administration. Veverimer has a distinct mechanism of action that removes
rather than neutralizes endogenous acid as a means of 448 Klaerner et al. TABLE 4 Chloride and potassium ions within the parietal cell are transported
into the gastric lumen via apical membrane conductance channels (potassium voltage-gated channel subfamily E member 2 and potassium voltage-gated
channel subfamily Q member 1 K+ channels, and chloride voltage-gated channel 2 Cl2 channels) (Heitzmann and Warth, 2007) so that the exchange of
K+ and H+ effectively recycles the potassium cation. Veverimer binds H+ with high capacity in the GI lumen, and every bound H+ results in an HCO3
2
entering the blood via basolateral exchange with serum Cl2 (Petrovic et al., 2003). Veverimer binds Cl2 with high selectivity in the GI lumen, excluding
larger organic anions from the protonated polymer. HCl-bound veverimer is excreted in the feces, and the resulting increase in HCO3
2 in the blood leads
to a correction of metabolic acidosis. References Raphael KL, Isakova T, Ix JH, Raj DS, Wolf M, Fried LF, Gassman JJ, Kendrick C,
Larive B, Flessner MF, et al. (2020) A randomized trial comparing the safety,
adherence, and pharmacodynamics profiles of two doses of sodium bicarbonate in
CKD: the BASE pilot trial. J Am Soc Nephrol 31:161–174. Raphael KL, Isakova T, Ix JH, Raj DS, Wolf M, Fried LF, Gassman JJ, Kendrick C,
Larive B, Flessner MF, et al. (2020) A randomized trial comparing the safety,
adherence, and pharmacodynamics profiles of two doses of sodium bicarbonate in Abramowitz MK, Melamed ML, Bauer C, Raff AC, and Hostetter TH (2013) Effects of
oral sodium bicarbonate in patients with CKD. Clin J Am Soc Nephrol 8:714–720. Alper SL and Sharma AK (2013) The SLC26 gene family of anion transporters and Abramowitz MK, Melamed ML, Bauer C, Raff AC, and Hostetter TH (2013) Effects of
oral sodium bicarbonate in patients with CKD. Clin J Am Soc Nephrol 8:714–720. Alper SL and Sharma AK (2013) The SLC26 gene family of anion transporters and
channels. Mol Aspects Med 34:494–515. oral sodium bicarbonate in patients with CKD. Clin J Am Soc Nephrol 8:714–720. Alper SL and Sharma AK (2013) The SLC26 gene family of anion transporters and
channels. Mol Aspects Med 34:494–515. CKD: the BASE pilot trial. J Am Soc Nephrol 31:161–174. p
channels. Mol Aspects Med 34:494–515. Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de Los Reyes-Gavilán
CG, and Salazar N (2016) Intestinal short chain fatty acids and their link with diet
and human health. Front Microbiol 7:185. Alpern RJ and Sakhaee K (1997) The clinical spectrum of chronic metabolic acidosis:
homeostatic mechanisms produce significant morbidity. Am J Kidney Dis 29:
291–302. Schultheis PJ, Clarke LL, Meneton P, Miller ML, Soleimani M, Gawenis LR,
Riddle TM, Duffy JJ, Doetschman T, Wang T, et al. (1998) Renal and intestinal
absorptive defects in mice lacking the NHE3 Na+/H+ exchanger. Nat Genet 19:
282–285. Bushinsky DA (2019) Tolerance to sodium in patients with CKD-induced metabolic
acidosis: does the accompanying anion matter? Am J Kidney Dis 73:858–865. p
y
g
y
Bushinsky DA, Hostetter T, Klaerner G, Stasiv Y, Lockey C, McNulty S, Lee A,
Parsell D, Mathur V, Li E, et al. (2018) Randomized, controlled trial of TRC101 to Bushinsky DA, Hostetter T, Klaerner G, Stasiv Y, Lockey C, McNulty S, Lee A,
Parsell D, Mathur V, Li E, et al. Mechanism of Action of Veverimer Mechanism of Action of Veverimer de Brito-Ashurst I, Varagunam M, Raftery MJ, and Yaqoob MM (2009) Bicarbonate
supplementation slows progression of CKD and improves nutritional status. J Am
Soc Nephrol 20:2075–2084. however, in that veverimer only binds HCl and does not induce
the loss of fluid, sodium, and potassium that are hallmarks of
hypochloremic metabolic alkalosis (Khanna and Kurtzman,
2006). p
den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, and Bakker BM
(2013) The role of short-chain fatty acids in the interplay between diet, gut
microbiota, and host energy metabolism. J Lipid Res 54:2325–2340. The selective binding and removal of HCl by veverimer
allows for the excretion of acid while generating bicarbonate
in the blood by the mechanisms described in the process of
parietal cell HCl secretion (summarized in Fig. 7). In the
process of facilitating the excretion of HCl through the gut in
this manner, veverimer can be seen as supplementing and
replacing the deficiency of acid excretion in the diseased
kidney, thus extending the known structural and functional
aspects of the gut epithelium that often mimic epithelial cells
of the kidney nephrons (Coudrier et al., 1988; Schultheis et al.,
1998; Wang et al., 2002; Alper and Sharma, 2013; Soleimani,
2013). ,
gy
p
Di Iorio BR, Bellasi A, Raphael KL, Santoro D, Aucella F, Garofano L, Ceccarelli M, Di Iorio BR, Bellasi A, Raphael KL, Santoro D, Aucella F, Garofano L, Ceccarelli M,
Di Lullo L, Capolongo G, Di Iorio M, et al.; UBI Study Group (2019) Treatment of
metabolic acidosis with sodium bicarbonate delays progression of chronic kidney
disease: the UBI Study. J Nephrol 32:989–1001. Diwan V, Brown L, and Gobe GC (2018) Adenine-induced chronic kidney disease in
rats. Nephrology (Carlton) 23:5–11. p
gy
Dubey AK, Sahoo J, Vairappan B, Haridasan S, Parameswaran S, and Priyamvada
PS (2020) Correction of metabolic acidosis improves muscle mass and renal func- Dubey AK, Sahoo J, Vairappan B, Haridasan S, Parameswaran S, and Priyamvada
PS (2020) Correction of metabolic acidosis improves muscle mass and renal func-
tion in chronic kidney disease stages 3 and 4: a randomized controlled trial. Nephrol Dial Transplant 35:121–129. tion in chronic kidney disease stages 3 and 4: a randomized controlled trial. Nephrol Dial Transplant 35:121–129. Garneata L, Stancu A, Dragomir D, Stefan G, and Mircescu G (2016) Ketoanalogue-
supplemented vegetarian very low-protein diet and CKD progression. J Am Soc
Nephrol 27:2164–2176. Mechanism of Action of Veverimer Jung T, Kamm W, Breitenbach A, Kaiserling E, Xiao JX, and Kissel T (2000) Bio-
degradable nanoparticles for oral delivery of peptides: is there a role for polymers degradable nanoparticles for oral delivery of peptides: is there a role for polymers
to affect mucosal uptake? Eur J Pharm Biopharm 50:147–160. g
p
y
p p
p
y
to affect mucosal uptake? Eur J Pharm Biopharm 50:147–160. to affect mucosal uptake? Eur J Pharm Biopharm 50:147–160. Kassirer JP and Schwartz WB (1966) The response of normal man to selective de-
pletion of hydrochloric acid Factors in the genesis of persistent gastric alkalosis Kassirer JP and Schwartz WB (1966) The response of normal man to selective de-
pletion of hydrochloric acid. Factors in the genesis of persistent gastric alkalosis. Am J Med 40:10–18. Khanna A and Kurtzman NA (2006) Metabolic alkalosis. J Nephrol 19 (Suppl 9):
S86–S96. Acknowledgments Kraut JA and Madias NE (2016) Metabolic acidosis of CKD: an update. Am J Kidney
Dis 67:307–317. The authors would like to acknowledge the helpful discussions,
editing, and insightful comments provided by David Bushinsky (Uni-
versity of Rochester), Dawn Parsell (Tricida, Inc.), and Christopher
Waldapfel (Tricida, Inc.) in the course of the work and in the preparation
of this report. Kraut JA and Madias NE (2018) Re-evaluation of the normal range of serum total
CO2 concentration. Clin J Am Soc Nephrol 13:343–347. Lambers Heerspink HJ, Holtkamp FA, Parving HH, Navis GJ, Lewis JB, Ritz E, de
Graeff PA, and de Zeeuw D (2012) Moderation of dietary sodium potentiates the
renal and cardiovascular protective effects of angiotensin receptor blockers. Kidney
Int 82:330–337. Lin SH, Cheema-Dhadli S, Chayaraks S, Chen CB, Gowrishankar M, and Halperin
ML (1998) Physiological disposal of the potential alkali load in diet of the rat: steps
to achieve acid-base balance. Am J Physiol 274:F1037–F1044. Authorship Contributions Participated in research design: Klaerner, Shao, Biyani, Kierstead,
Tabakman, Nguyen, Buysse. Participated in research design: Klaerner, Shao, Biyani, Kierstead,
Tabakman, Nguyen, Buysse. Navaneethan SD, Shao J, Buysse J, and Bushinsky DA (2019) Effects of treatment of
metabolic acidosis in CKD: a systematic review and meta-analysis. Clin J Am Soc
Nephrol 14:1011–1020. Conducted experiments: Shao, Biyani, Kade, Kierstead, Gbur,
Tabakman, Nguyen. Niv Y and Fraser GM (2002) The alkaline tide phenomenon. J Clin Gastroenterol 35:
5–8. Contributed new reagents or analytic tools: Biyani, Kade, Kier-
stead, Gbur, Tabakman, Nguyen. Petrovic S, Ju X, Barone S, Seidler U, Alper SL, Lohi H, Kere J, and Soleimani M
(2003) Identification of a basolateral Cl-/HCO3- exchanger specific to gastric pa-
rietal cells. Am J Physiol Gastrointest Liver Physiol 284:G1093–G1103. Petrovic S, Ju X, Barone S, Seidler U, Alper SL, Lohi H, Kere J, and Soleimani M
(2003) Identification of a basolateral Cl-/HCO3- exchanger specific to gastric pa-
rietal cells. Am J Physiol Gastrointest Liver Physiol 284:G1093–G1103. Performed data analysis: Klaerner, Shao, Biyani, Kade, Kierstead,
Gbur, Tabakman, Nguyen, Buysse. g
p
rietal cells. Am J Physiol Gastrointest Liver Physiol 284:G1093– Phisitkul S, Khanna A, Simoni J, Broglio K, Sheather S, Rajab MH, and Wesson DE
(2010) Amelioration of metabolic acidosis in patients with low GFR reduced kidney
endothelin production and kidney injury, and better preserved GFR. Kidney Int 77:
617–623. Wrote or contributed to the writing of the manuscript: Klaerner,
Shao, Biyani, Kade, Kierstead, Gbur, Tabakman, Nguyen, Buysse. Raphael KL (2018) Metabolic acidosis and subclinical metabolic acidosis in CKD. J Am Soc Nephrol 29:376–382. Fig. 7. Mechanism of action of veverimer in the gastrointestinal tract. The mechanism of action of veverimer involves binding of proton and chloride,
resulting in a net reduction and removal of HCl from the GI tract and an increase in serum bicarbonate. This physiologic effect of veverimer is the result
of several steps (1–6) that occur concurrently throughout the gastrointestinal tract but are illustrated here with a focus on the gastric lumen. The initial
step in this cascade involves the oral administration of veverimer as a nonabsorbed, free-amine polymer. Within the parietal cell, H2O plus CO2 is
converted under the influence of carbonic anhydrase into H+ and HCO3
2 (Yao and Forte, 2003). H+ is secreted from the gastric parietal cell into the GI
lumen in exchange for K+ through the action of the H+/K+ ATPase (Shin et al., 2009). Chloride and potassium ions within the parietal cell are transported
into the gastric lumen via apical membrane conductance channels (potassium voltage-gated channel subfamily E member 2 and potassium voltage-gated
channel subfamily Q member 1 K+ channels, and chloride voltage-gated channel 2 Cl2 channels) (Heitzmann and Warth, 2007) so that the exchange of
K+ and H+ effectively recycles the potassium cation. Veverimer binds H+ with high capacity in the GI lumen, and every bound H+ results in an HCO3
2
entering the blood via basolateral exchange with serum Cl2 (Petrovic et al., 2003). Veverimer binds Cl2 with high selectivity in the GI lumen, excluding
larger organic anions from the protonated polymer. HCl-bound veverimer is excreted in the feces, and the resulting increase in HCO3
2 in the blood leads
to a correction of metabolic acidosis. 449 Mechanism of Action of Veverimer p
Gennari FJ and Weise WJ (2008) Acid-base disturbances in gastrointestinal disease. Clin J Am Soc Nephrol 3:1861–1868. Goraya N, Munoz-Maldonado Y, Simoni J, and Wesson DE (2019) Fruit and
vegetable treatment of chronic kidney disease-related metabolic acidosis
reduces cardiovascular risk better than sodium bicarbonate. Am J Nephrol 49:
438–448. In conclusion, the studies reported here demonstrate that
the chemical structure and design of veverimer are translated
into a potent and selective binding of HCl, as measured with
in vitro matrices mimicking various aspects of the GI tract and
in animal studies that measure chloride removal through the
feces with a polymer that is nonabsorbed and stable through-
out GI transit. The physiologic consequence of specific HCl
removal is the elevation of serum bicarbonate. The polymer
does not introduce counterions nor does it remove organic
anions in the GI tract that provide sources of bicarbonate
precursors once absorbed. Veverimer treatment in an animal
model of CKD with metabolic acidosis demonstrated that HCl
binding and removal by the polymer increased serum bi-
carbonate, which was consistent with completed studies in
human subjects that demonstrate the potential for veverimer
to treat chronic metabolic acidosis in patients with CKD. Goraya N, Simoni J, Jo CH, and Wesson DE (2013) A comparison of treating meta-
bolic acidosis in CKD stage 4 hypertensive kidney disease with fruits and vege-
tables or sodium bicarbonate. Clin J Am Soc Nephrol 8:371–381. at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
Downloaded from Goraya N, Simoni J, Jo CH, and Wesson DE (2014) Treatment of metabolic acidosis
in patients with stage 3 chronic kidney disease with fruits and vegetables or oral
bicarbonate reduces urine angiotensinogen and preserves glomerular filtration
rate. Kidney Int 86:1031–1038. y
Goraya N and Wesson DE (2017) Management of the metabolic acidosis of chronic
kidney disease. Adv Chronic Kidney Dis 24:298–304. Goraya N and Wesson DE (2019) Clinical evidence that treatment of metabolic aci-
dosis slows the progression of chronic kidney disease. Curr Opin Nephrol Hypertens
28:267–277. Hamm LL, Nakhoul N, and Hering-Smith KS (2015) Acid-base homeostasis. Clin
J Am Soc Nephrol 10:2232–2242. Heitzmann D and Warth R (2007) No potassium, no acid: K+ channels and gastric
acid secretion. Physiology (Bethesda) 22:335–341. References (2018) Randomized, controlled trial of TRC101 to
increase serum bicarbonate in patients with CKD. Clin J Am Soc Nephrol 13:
26–35. Scialla JJ and Anderson CA (2013) Dietary acid load: a novel nutritional target in
chronic kidney disease? Adv Chronic Kidney Dis 20:141–149. Shao J, Parsell D, Guttendorf R, Wu YS, Tsao L, Tabakman S, Stasiv Y, Lee A,
Biyani K, and Klaerner G (2020) P0009 Evaluation of the potential for drug
interactions with veverimer. Nephrol Dial Transplant 35 (Suppl 3):2. Coudrier E, Kerjaschki D, and Louvard D (1988) Cytoskeleton organization and
submembranous interactions in intestinal and renal brush borders. Kidney Int 34:
309–320. 450 Klaerner et al. Address correspondence to: Jun Shao, Tricida, Inc., 7000 Shoreline Ct.,
Suite 201, South San Francisco, CA 94080. E-mail: jshao@tricida.com Klaerner et al. Wesson DE, Buysse JM, and Bushinsky DA (2020) Mechanisms of metabolic
acidosis-induced kidney injury in chronic kidney disease. J Am Soc Nephrol
31:469–482. Shin JM, Munson K, Vagin O, and Sachs G (2009) The gastric HK-ATPase: structure,
function, and inhibition. Pflugers Arch 457:609–622. Soleimani M (2013) SLC26 Cl-/HCO3- exchangers in the kidney: roles in health and
disease. Kidney Int 84:657–666. Wesson DE, Mathur V, Tangri N, Stasiv Y, Parsell D, Li E, Klaerner G,
and Bushinsky DA (2019a) Long-term safety and efficacy of veverimer in patients
with metabolic acidosis in chronic kidney disease: a multicentre, randomised,
blinded, placebo-controlled, 40-week extension. Lancet 394:396–406. Szerlip HM (2005) Metabolic acidosis, in National Kidney Foundation’s Primer on
Kidney Diseases (Gilbert SJ and Weiner DE eds) pp 130–143, Elsevier Inc.,
Philadelphia. blinded, placebo-controlled, 40-week extension. Lancet 394:396 Toto RD and Alpern RJ (1996) Metabolic acid-base disorders, in Fluids and Elec-
trolytes (Kokko JP and Tannen RL eds) pp 201–266, Saunders, Philadelphia. Wesson DE, Mathur V, Tangri N, Stasiv Y, Parsell D, Li E, Klaerner G,
and Bushinsky DA (2019b) Veverimer versus placebo in patients with metabolic
acidosis associated with chronic kidney disease: a multicentre, randomised, double-
blind, controlled, phase 3 trial. Lancet 393:1417–1427. Turnberg LA, Bieberdorf FA, Morawski SG, and Fordtran JS (1970) Interrelation-
ships of chloride, bicarbonate, sodium, and hydrogen transport in the human il-
eum. J Clin Invest 49:557–567. Wright JA and Cavanaugh KL (2010) Dietary sodium in chronic kidney disease:
a comprehensive approach. Semin Dial 23:415–421. Valeur J and Julsrud J (2013) Vomiting: a physiological response to acidosis? Scand
J Gastroenterol 48:1103–1104. Yao X and Forte JG (2003) Cell biology of acid secretion by the parietal cell. Annu Rev
Physiol 65:103–131. (
Physiol 65:103–131. Vegter S, Perna A, Postma MJ, Navis G, Remuzzi G, and Ruggenenti P (2012) So-
dium intake, ACE inhibition, and progression to ESRD. J Am Soc Nephrol 23:
165–173. Address correspondence to: Jun Shao, Tricida, Inc., 7000 Shoreline Ct.,
Suite 201, South San Francisco, CA 94080. E-mail: jshao@tricida.com Address correspondence to: Jun Shao, Tricida, Inc., 7000 Shoreline Ct.,
Suite 201, South San Francisco, CA 94080. E-mail: jshao@tricida.com Wang Z, Petrovic S, Mann E, and Soleimani M (2002) Identification of an apical Cl(-
)/HCO3(-) exchanger in the small intestine. Am J Physiol Gastrointest Liver Physiol
282:G573–G579. at ASPET Journals on October 23, 2024
jpet.aspetjournals.org
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ROLE OF HYPOTHYROIDISM & PCOD IN FEMALE INFERTILITY
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International journal of advanced research
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ROLE OF HYPOTHYROIDISM & PCOD IN FEMALE INFERTILITY. Manuscript Info
……………………. Manuscript History
Received: 18 February 2017
Final Accepted: 14 March 2017
Published: April 2017 Copy Right, IJAR, 2017,. All rights reserved. …………………………………………………………………………………………………….... Introduction:-
Infertility is defined as the inability to become pregnant after 12 months of regular, unprotected intercourse. Among
couples 15-44 years of age, nearly 7 million attend infertility clinics Chandra et al. Etiology of infertility –
combined factors -40%, male factors-26-30%, ovulatory dysfunction 21-25%, tubal factors-14-20%, uterine,
cervical, peritoneal factors-10-13%, unexplained 25-28% Thonnaeu et al. …………………………………………………………………………………………………….... Introduction:-
Infertility is defined as the inability to become pregnant after 12 months of regular, unprotected intercourse. Among
couples 15-44 years of age, nearly 7 million attend infertility clinics Chandra et al. Etiology of infertility –
combined factors -40%, male factors-26-30%, ovulatory dysfunction 21-25%, tubal factors-14-20%, uterine,
cervical, peritoneal factors-10-13%, unexplained 25-28% Thonnaeu et al. Prevalence of PCOS has been established to be 15-20 % globally(Diamanti et al, Simrans ). Patients present with a
wide spectrum of clinical signs & symptoms of reproductive function - irregular menses, chronic anovulation,
oligomenorrhea, amenorrhea, hirsuitism, metabolic-weight gain(Motta ,Gambineri et al ), pigmentation around
neck, arm pits or thighs, oily skin, excess facial hair, insulin resistance in skeletal muscles Rezzonico et al, impaired
glucose tolerance, type 2 DM, cardio vascular disorders etc.,& psychological features including increased anxiety,
depression Legro et al. Defect in Hypothalamo pituitary axis, dysfunction and anatomic abnormalities of the Thyroid and hypersensitivity
of adrenal and ovarian tissue to Insulin seems to be adversely affected by associated Thyroid dysfunction. Polycystic Ovarian Syndrome is the most common endocrinopathy of women in the reproductive age group which is
associated with Thyroid dysfunction. Subclinical Hypothyroidism ( SCH) characterised by elevated serum levels of
Thyroid stimulating hormone ( TSH ) is considered as an important risk factor for many endocrine disorders Surks
et al. Abnormalities in the supply of the Thyroid hormone to the peripheral tissues are associated with alteration in a
number of metabolic processes. Early stages of Thyroid dysfunction before symptoms are obvious can lead to subtle
change in ovulation and endometrial receptivity, which may have profound effect on fertility. In Primary
Hypothyroidism , secondary depression of pituitary function may lead to ovarian atrophy and amenorrhoea. A typical PCOS ovaries has multiple cysts with a chain of pearl manifestations which leads to hormonal imbalances
resulting in infertility. Aim And Objectives:- Corresponding Author:- Dr. L. Santhanalakshmi. ISSN: 2320-5407 ISSN: 2320-5407 Int. J. Adv. Res. 5(4), 1982-1985 Journal Homepage: - www.journalijar.com
Article DOI: 10.21474/IJAR01/4041
DOI URL: http://dx.doi.org/10.21474/IJAR01/4041 Statistical Analysis:- Statistical Analysis:
was done using Chi Square test using appropriate software ( SPSS 16version ) and sigma stat 3.5version. Inclusion Criteria:- Women in reproductive age group living with their spouse with unprotected coitus, anxious to conceive .Infertile
women with menstrual irregularities. Exclusion criteria:- Women on medications for Hyperprolactinemia, Hypothyroidism, Androgen excess, Cushing’s syndrome, oral
contraceptives for cycle regulation were excluded. Materials And Methods:- After getting Ethical Committee approval from Institution, informed consent obtained from all participants after
detailed explanation. Height in centimetres measured with stadiometer and weight of the subjects in kilograms by the weighing machine
were used for calculating BMI. BMI calculated using Quetelet ‘s Formula and the results expressed in kg/m2. 10 ml of venous blood samples were collected from all participants. Serum thus separated used for assessing TSH
levels by Elisa method according to standard protocol Wistom GB. For around 50 patients transabdominal pelvic ultrasound was done to detect the presence of cystic ovaries. USG
proven PCOD attending Infertility clinic in Obstetrics Department of Government Rajaji Hospital attached to
Madurai Medical College participated as study group and another 50 parous women of the same age group attending
Endocrinology Department with problems unrelated to PCOS or Thyroid dysfunction and with normal menses were
considered as control group. Aim And Objectives:- 1982
Aim And Objectives:-
1. To correlate TSH on age and BMI matched infertile PCOD patients with general population. 2. To correlate duration of marital status with Thyroid function
Corresponding Author:- Dr. L. Santhanalakshmi. 2. To correlate duration of marital status with Thyroid function 2. To correlate duration of marital status with Thyroid function Corresponding Author:- Dr. L. Santhanalakshmi. 1982 ISSN: 2320-5407 Int. J. Adv. Res. 5(4), 1982-1985 Observations and Results:- 1. Menstrual abnormalities like Amenorrhoea ( no cycles in the past 6 months ) 1. Menstrual abnormalities like Amenorrhoea ( no cycles in 2. Oligomenorrhoea ( long cycles with scanty menses ) 3. Ultra sound appearance of polycystic ovaries ( multiple cysts > 12 in number of 2-9 mm in size. Bibliography:- g
p y
1. Simrans SM, Pate KA. Epidemilogy, diagnosis & management of PCOD. Clini. Epidemiol.201 1. Simrans SM, Pate KA. Epidemilogy, diagnosis & management of PCOD. Clini. Epidemiol.2013 Dec 18;6;1.13. 2. Motta AB. The role of obesity in the development of PCOD. Current Pharm Des.2012;18(17) ;2482-91. 1. Simrans SM, Pate KA. Epidemilogy, diagnosis & management of PCOD. Clini. Epidemiol.2013 Dec 18;6;1.13. 2. Motta AB. The role of obesity in the development of PCOD. Current Pharm Des.2012;18(17) ;2482-91. 2. Motta AB. The role of obesity in the development of PCOD. Current Pharm Des.2012;18(17) ;2482-91. y
p
(
)
3. Gambineri A, Pelusi c, Viceennati V, Pagotto U, Pasquali R.Obesity & PCOS . Int.J Obs Relat Metabolic
Disorder.2002 July;26 (7);883-96. 3. Gambineri A, Pelusi c, Viceennati V, Pagotto U, Pasquali R.Obesity & PCOS . Int.J Obs Relat Metabolic
Disorder.2002 July;26 (7);883-96. 4. Battaglia C, Mancini F, Persico N, Zaccaria V, De Aloysio D. Ultrasound evaluat ion of PCO,PCOS and OHSS
( Review). Reprod Biomed Online 2004;9;614-9. 4. Battaglia C, Mancini F, Persico N, Zaccaria V, De Aloysio D. Ultrasound evaluat ion of PCO,PCOS and OHSS
( Review). Reprod Biomed Online 2004;9;614-9. p
p
y
prevalence of PCOS in unselected Caucasian women from Spain. J Clin Endocrino Metab 2000;85;2434-2438. 6. Chandra a, Copen CE, Stephen EH. Infertility service use in US; data from the National Survey of Family
Growth, 1982-2010.National Health Stat Report.2014; (73);1-21. p
p
;
;
6. Chandra a, Copen CE, Stephen EH. Infertility service use in US; data from the National Survey of Family
Growth, 1982-2010.National Health Stat Report.2014; (73);1-21. p
(
)
7. Practice Committee of American Society for Reproductive Medicine. Diagnostic evaluation of the infertile
female; a committee opinion. Fertility Steril. 2012;98 (2); 302-307. p
7. Practice Committee of American Society for Reproductive Medicine. Diagnostic evaluation of the infertile
female; a committee opinion. Fertility Steril. 2012;98 (2); 302-307. p
y
8. Thonneau P, Marchand S, Tallec A et al. Incidence and main causes of infertility in a residential population of 3
French regions(1988-1989 ). Hum Repro. 1991; 6 (6 ); 811-816. 9. Vause TD, Cheung AP, Sierras et al. Ovulation induction in PCOS. J Obs Gyn Canada.2011;33 (1 );12 and J
Obs Gyn Canada.2010;32 (5 ); 495-502. 10. Clark AM, Thornley B, Tomlinson L, Galletley C, Norman RJ. Weight loss in obese infertile women results in
improvement in reproductive outcome for all forms fertility treatment. ISSN: 2320-5407 Int. J. Adv. Res. 5(4), 1982-1985 Int. J. Adv. Res. 5(4), 1982-1985 Int. J. Adv. Res. 5(4), 1982-1985 ISSN: 2320-5407 Int. J. Adv. Res. 5(4), 1982-1985 ISSN: 2320-5407 Adipose tissue is a major endocrine gland secreting and releasing adipokines which have metabolic and / or
inflammatory effects on many tissues Rondinone CM. Thyroid hormone enhances insulin sensitivity, reduce
hyperglycemia and hyperinsulinemia. Disturbed Thyroid function is associated with ovarian dysfunction which
results in infertility, early pregnancy loss and morbidity during pregnancy Poppe et al. Severe Hypothyroidism may
be associated with diminished libido and failure of ovulation. Wasim et al, hypothesised that Hypothyroidism
worsens PCOS by decreasing sex hormone binding Globulin levels, increases the conversion of androstenedione to
testosterone and aromatisation to estradiol and reduces the metabolic clearance rates of androstenedione and estrone. Since thyroid hormones are involved in the Gonadotropin induced estradiol and progesterone secretion by the
human granulosa cells, Hypothyroidism would interfere with ovarian function and fertility. Conclusion:- Thyroid disorders in PCOS patient can initiate, maintain or worsen the syndrome Sridhar et al. Ghosh et al
suggested that Hypothyroidism led to lowering of sex hormone binding globulin level and increment of Testosterone
level but not oestriol overproduction. Women in WHO group II, who are overweight and have PCOD, can benefit from weight loss, Life style correction,
regular exercise, avoiding junk foods, hormone fed chicken, processed food, regularising healthy sleep pattern,
medication to lower insulin resistance etc., to restore ovulatory cycles and achieve pregnancy Vause TD et al. Aiming for a BMI less than 30 kg / m2 to improve their chances of natural conception or using assisted reproductive
technology Clark AM et al. Mother is the most sweetest word in the universe. Hence PCOS demands immediate attention & improving insulin
sensibility, lowering triglycerides , intervention to get ovulatory cycles, improving ovulation, egg quality &
conceive for safe pregnancy. Early correction of Hypothyroidism in the management of Infertility associated with PCOD is recommended. If left
unattended & untreated, may lead to Infertility, Diabetes & Endometrial cancers in the years to come. Results:- Results:
This case control study revealed statistically that mean age in years was 28.2 for cases and 26.8 for controls with p
value 0.247, with BMI 0.720 and duration of marital status had 0.451which is insignificant. This case control study revealed statistically that mean age in years was 28.2 for cases and 26.8 for controls with p
value 0.247, with BMI 0.720 and duration of marital status had 0.451which is insignificant. It showed a significant p values of < 0.001for menstrual cyclical irregularities and also abnormalities in menstrual
cycles. There was a 0.005 significant p value for TSH. At the same time, Hypothyroidism with PCOD revealed a non
significant p value of 0.452. In the age group of 26-30 years, the number of cysts showed a 0.003 significant p value. Discussion:-
PCOS is the most common cause for female infertility characterised by a combination of hyperandrogenism,
chronic anovulation and irregular menstrual cycles ( Asuncion M et al). Discussion:
PCOS is the most common cause for female infertility characterised by a combination of hyperandrogenism,
chronic anovulation and irregular menstrual cycles ( Asuncion M et al). Prevalence of Hypothyroidism in adults is around 10.95 % in India. 8.02 % of these patients are diagnosed to have
subclinical Hypothyroidism with TSH > 5.50 µiu / ml. Untreated hypothyroidism contributes to Hypertension,
Infertility, Dyslipidemia, Cognitive impairment & neuromuscular dysfunction Garber J.R. et al. Women with
Hypothyroidism have significant higher BMI which influence Thyroid hormone concentration with high TSH levels
in obese women Reinehr et al. 1983 14. Wistom GB. Enzyme- immunoassay. Clin Chem 1976; 1243;22. Bibliography:- Human Repro 1998; 13 (6) 1502-1505. 11. Diamanti-Kandarakis E, Kouli CR, Bergiele AT, et al. A survey of the PCOS in the Greek island of Lesbos;
hormonal and metabolic profile. J Clin Endocrinol Metb 1999; 84; 4006-4011. 12. Legro RS , Driscoll D, Strauss JF et al. Evidence for a genetic basis for hyperandrogenemia in PCOS. Proc
Natl Acad Scie 1977;95; 14956-14960. 13. 13.Surks MI, Ortiz E, Danids GH. Subclinical Thyroid disease; Scientific Review and guideli
and management. J Am Med Assoc 2004;291;228-238. 14. Wistom GB. Enzyme- immunoassay. Clin Chem 1976; 1243;22. 1984 ISSN: 2320-5407 Int. J. Adv. Res. 5(4), 1982-1985 15. Reinehr T, Isa A, de Sousa G, et al. Thyroid hormone and their relation to weight status. Hormone Res 2008;
70; 50-57. 16. Rondinone CM. Adipocyte derived hormones, cytokines and mediators. Endocrine 2006; 29 p
y
y
17. Rezzonico J, Rezzonico M, Pusiol E et al. Introducing Thyroid gland as another victim of the insulin resistance
syndrome. Thyroid 2008; 18;461-464. 18. Poppe K, Velke niers B, G linoer D. Thyroid disease and female reproduction. Clin Endocrin 2007; 66; 309-
321. 19. Garber J.R. et al. Clinical Practice Guidelines for Hypothyroidismin adults cosponsored by the American Asso. Clinical Endocrinologists and American Thyroid Association. Thyroid 2012. Dec. (12 ) 1200-35. 20. Ghosh S, Kabir SN, Pakrashi A, Chatterjee S, Chakravarty B. Subclinical Hypothyroidism. A determinant of
PCOS. Horm Res.1993;39;61-6. (Pubmed ) 21. Wasim AN,Polizotto SL, Burholt DR. Augmentation by Thyroxine of human granulosa ce
induced steroidogenesis. Hum Reprod. 1995; 10; 2845-8 Pub Med. 22. Sridhar GR, Nagamani G. Hypothyroidism presenting with PCOS. J Assos Physicians India . 1993;41;88-90. Pub Med. 1985
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The Workshop in the Multilayered Peer Coaching Model for Tertiary EFL Teachers’ In-Service Professional Development
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English language teaching
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cc-by
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English Language Teaching; Vol. 6, No. 8; 2013
ISSN 1916-4742
E-ISSN 1916-4750
Published by Canadian Center of Science and Education
The Workshop in the Multilayered Peer Coaching Model for Tertiary
EFL Teachers’ In-Service Professional Development
Junyi Meng1 & Songphorn Tajaroensuk1
1
School of Foreign Languages, Institute of Social Technology, Suranaree University of Technology, Thailand
Correspondence: Junyi Meng, Room 3015, Surasammanakhan Hotel, Suranaree University of Technology, 111
University Avenue, Muang District, Nakhon Ratchasima 30000, Thailand. Tel: 86-138-0943-8270. E-mail:
jymeng66@hotmail.com
Received: May 15, 2013
Accepted: June 3, 2013
Online Published: July 4, 2013
doi:10.5539/elt.v6n8p44
URL: http://dx.doi.org/10.5539/elt.v6n8p44
Abstract
When English becomes the international language with the globalization of the world, it is not surprising that
EFL teachers are pushed to the front of TEFL (Teaching English as a Foreign Language) because teacher quality
is thought to be the factor that matters most for student learning. EFL teachers are expected to be more
knowledgeable and competent. So their in-service professional development seems to be indispensable to help
them reach higher professionalism. This study aimed at investigating the activities and effectiveness of the
workshop that is an important element of the Multilayered Peer Coaching Model (the MPC Model) developed
for tertiary EFL teachers’ in-service professional development. Twelve EFL teachers from Guiyang University in
China participated in this study, and such instruments as observation, teachers’ log and interview were employed
for data collection. The results showed that this workshop was effective and could smoothly lead the participants
to the follow-up teaching practice which is another critical element of the MPC Model.
Keywords: in-service professional development, tertiary EFL teachers, the Multilayered Peer Coaching Model,
workshop
1. Introduction
The global spread of English has affected all the domains of human activity from language in education to
international relationship (Kachru, 2011). The situation that “400 million people speak English as their first
language and 750 million people speak English as their second language” (Herther, 2009) has expected better
quality of the English instruction. Apart from it, the increasing number of people learning English as a foreign
language has upgraded the professionalism of Teaching English as a Foreign Language (TEFL). DarlingHammond (1998) once argued that teacher quality is the factor that matters most for student learning. Therefore,
EFL teachers are confronted with the challenge from their profession. TEFL in China is also in its reform for
keeping pace with the requirements of the rapid economic development of China. New standards and regulations
have been updated or issued for English language learning and teaching at the tertiary level, for example, the
“Syllabus for English Majors of Colleges or Universities” (revised in 2001) and the new “College English
Curriculum Requirement” (issued in 2006). For such higher professionalism, EFL teachers working at colleges
or universities are greatly encouraged to have their in-service professional development.
However, it is not easy for tertiary EFL teachers to have their in-service professional development. Many factors
have been found to be the contributors, and one of them is their heavy workload. The tertiary EFL teachers in
China can be a case in point. Generally speaking, tertiary EFL teachers in China are generally put into two
sectors: one is for non-English majors and the other is for English majors. The former sector teaches general
English skills, exactly, listening, speaking, reading, writing, and translating; the latter sector teaches both general
English and specialized courses such as English linguistics, American and British literature, translation between
Chinese and English, culture studies, English teaching methodology, etc. Since the year of 1998, China has
increased its college enrollment, during the 1996-2000 period there was a total enrollment of over 11 million,
from 2001 to 2005 the number of university students would be up to 16 million (CERNET, 2001), so the
workload for both sectors has increasingly been heavier. Likewise, another factor hindering the EFL teachers’
in-service professional development is the lack of effective programs. Tsui (2003) once claimed that EFL
profession is facing two problems, the lack of teacher training programs and the dissatisfaction with
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conventional training models. Ono and Ferreira (2010) have also affirmed that many models of professional
development do not achieve their ambitious learning goals.
Based on these factors and the needs analysis of the tertiary EFL teachers who participated in the experiment
conducted by the researcher of this present study, the Multilayered Peer Coaching Model (the MPC Model) was
developed for tertiary EFL teachers’ in-service professional development. (Note 1) A workshop was designed as
an important element of the MPC Model.
As it is defined, a workshop is an intensive, short-term learning activity that is designed to provide an
opportunity to obtain the specific knowledge and skill (Richards & Farrell, 2005). It is one of the most common
and useful forms of professional development activities for teachers (Richards, Gallo, & Ranendya, 2001).
However, not every teacher has experienced effective workshops during their careers, many of them find the
workshops they attended are less effective (Dickey, 2008). Workshops have even been criticized as being brief,
fragmented, incoherent encounters that are decontextualised and isolated from real classroom situations (e.g.
Fullan & Hargreaves, 1996; Collinson & Ono, 2001; Schwille & Dembélé, 2007). As a matter of fact, the
hit-or-miss of a workshop depends on a great deal of preliminary thought or planning, and as the name implies, it
is a place where work is accomplished, directed to the collaborative exploration and resolution of problems
(Richards & Farrell, 2005).
Therefore, this study aimed at investigating the effectiveness of this workshop that is an important element of the
MPC Model, and identifying the activities of this workshop for tertiary EFL teachers’ in-service professional
development. This study provided the answers to the following research questions:
1. What activities are conducted in the workshop of the MPC Model?
2. Does the workshop of the MPC Model help to train the tertiary EFL teachers to update their professional
knowledge and skills? If yes, to what extent? If not, why not?
2. The Multilayered Peer Coaching Model
The Multilayered Peer Coaching Model (the MPC Model) was developed for tertiary EFL teachers’ in-service
professional development. It can be defined as “the practice of peer coaching within a team teaching context in
the TEFL setting which can offer teachers more opportunities to support one another in their work.” In this
practice, teachers may experience two layers of collaboration. The first layer is team teaching in which four
teachers can be involved as a team so that common issues and problems will be discussed and solved by pooling
the ideas of the team members. The second layer is peer coaching where two dyads will be formed within the
team so that the two peer teachers in each dyad will work together to reflect on current practices, expand, refine,
and build new skills, share ideas; teach each other; conduct classroom research; or solve problems in the
workplace.
The MPC Model was developed on the basis of the ADDIE Model, which is one of the most popular
instructional system design (ISD) theories and has withstood the test of time and use. The acronym “ADDIE”
stands for Analysis, Design, Development, Implementation, and Evaluation, which represents an arrangement of
resources and procedures used to promote learning (Gagné & Wager, 1988) or a dynamic, flexible guideline for
building effective training and performance support tools (See Figure 1).
Revision
Analysis
Revision
Implementation
Evaluation
Design
Revision
Developemnt
Revision
Figure 1. The ADDIE Model (Source: http://en.wikipedia.org/wiki/ADDIE_Model)
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The MPC Model had its conceptual framework which intended to display the operationalization of the ISD
theory the MPC Model followed in its development. In order to show the relationship between each phase of the
MPC Model and that of ADDIE, the figure “the ADDIE correspondence with the MPC Model” was made. The
bottom part of this figure was the ADDIE’s phases, and the rest part was the MPC Model’s conceptual
framework. The dotted lines showed the match between the phases of these two models. The detail was
presented in Figure 2 as follows:
Developing the
Conceptual
Framework of
the Model
Selecting
Content
Identifying
Developing and
Assembling
Content Assets
Trainees
Investigating
Problems,
Suggestions and
Needs
Allocating
Time and
Space
Organizing
Teams and
Dyads
Specifying
Determining
Training
Strategies
Selecting
Resources
Trying out the
Model
Identifying
Assessment
Instruments
Conducting the
Workshop
Evaluating
Performance
Conducting the
Follow-up
Practice
Objectives
Analysis
Drafting the
Model
Design
Development
Implementation
Evaluation
Figure 2. The ADDIE Correspondence of the MPC Model
In addition, the MPC Model also had its research procedure including five phases (See Figure 3) and 15 steps.
Each of the five phases with its own elements displayed the detailed process for developing the MPC Model.
Phase I
Needs Analysis
Phase II
Design of the Model
Phase III Development of the Model
Phase IV Implementation of the Model
Phase V
Evaluation of the Model
Figure 3. The Process of Developing the MPC Model
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“Phase I: Needs Analysis” was for the tertiary EFL teachers’ problems and suggestions on their in-service
professional development, and their needs for the MPC Model. “Phase II: Design of the model” was a
systematic and specific phase, in which trainees, training objectives, environment, content, methods, and
assessment instruments were identified. “Phase III: Development of the model” was a critical phase, in which
such steps were followed: a) the conceptual framework was developed; b) the content of instruction was
developed; c) the content of the training lessons was evaluated by the experts in the field of TEFL; 4) the MPC
Model was drafted; 5) the MPC Model was tried out; 6) the model was finalized. The in-service tertiary EFL
teachers’ feedback and suggestions were considered.
It terms of “Phase IV: Implementation of the model”, it is a practical phase, in which the experiment was
conducted, and the workshop is one of the important elements (See Figure 4 below for the details of this phase).
First, on the day before the experiment, the 12 teacher participants were pre-tested on their knowledge of both
TEFL and the required teaching materials. Second, the teachers were grouped into three teams with two dyads in
each based on their teaching duration. Third, the teachers received the training in the 3-day workshop by an
external expert and the researcher. The training started with the expert’s lecture on the new concept and updated
knowledge of TEFL, and then the MPC Model was introduced by the researcher, after that, the teachers practiced
the collaborative approach they had just learned. As soon as the workshop was over, the teachers moved on to
the follow-up teaching by practicing the multilayered peer coaching in the intact classes for 15 weeks. Fourth,
after each lesson, the teachers wrote the teacher’s logs to show their procedure and feedback. Meanwhile, the
researcher observed the teachers’ classroom teaching and cooperation, and kept her field notes after each lesson.
Fifth, after the experiment, a post-test was given to the teachers. Sixth, the questionnaires were conducted to find
out the students’ opinions on the instruction given by the teachers involved in the MPC Model and the teachers’
opinions on the MPC Model. Finally, the interview was adopted to obtain the in-depth information about the
teachers’ attitudes towards the MPC Model.
Phase IV Implementation of the Model
Knowledge of EFL teaching
methodology
Pre-test
Knowledge of the required
teaching materials
Experiment
Follow-up Practice
Workshop
Team teaching
Peer coaching
Presentation of an external expert
Presentation of the researcher
Teachers’ logs
Researcher’s field notes
Post-test
Interview
Questionnaire
Teachers’ log
Researcher’s field notes
Observation
Questionnaire for students
To implement the MPC Model after developing it for tertiary EFL teacher in-service development
Figure 4. The Research Procedure in Phase IV of the MPC Model
Phase V: Evaluation of the model was an indispensable phase, in which the Model’s effectiveness and the
teachers’ performance were measured. Actually, the evaluation was conducted throughout the entire instruction
design process, whether within phases, or between phases, or after the implementation.
To conclude, the MPC Model served as an effective training support tool for tertiary EFL teachers’ in-service
professional development. With the multilayered peer coaching practice, the teachers could have and sustain
their professional development in their daily teaching, which contributed a lot to the continuity of their in-service
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professional development.
3. The Workshop of the Multilayered Peer Coaching Model
In the implementation phase of the MPC Model, a 3-day workshop was designed for the beginning of the
experiment. The teachers received the training in this workshop with the help of an external expert and the
researcher of this present study. The workshop offered the teacher updated professional knowledge and skills,
which would be further reinforced in the follow-up teaching practice with the intact classes for 15 weeks. The
details of this workshop were as follows:
3.1 Workshop Rationale
This workshop provided a framework for organizing a tertiary EFL teachers’ training program via the MPC
Model, with a focus on its contribution to tertiary EFL teachers’ in-service professional development. The drivers
of this workshop included the following aspects:
a) the higher level of professionalism in TEFL today than previously;
b) the release of the new curriculum requirements by China’s Ministry of Education;
c) the situation in Chinese universities whose EFL teachers can not sustain their professional development;
d) recognition that in-service professional development can help EFL teachers to meet the expectation of this
profession;
e) recognition that there is the gap in a review of the academic literature on in-service professional development
for tertiary EFL teachers, especially on peer coaching or team teaching.
3.2 Workshop Objectives
This workshop focused on the principle that the best way to improve teachers’ in-service professional
development was by their active involvement in the cooperation with colleagues, and their contributions to the
teamwork mattered. So the objectives of this workshop were
a) to provide EFL teachers with an opportunity to learn new knowledge and skills via the MPC Model;
b) to facilitate EFL teachers to update their professional knowledge and competence by cooperating with their
colleagues;
c) to present a concentrated but integrated discussion of effective innovations in English curriculum and delivery
of instruction to support program implementation.
For such objectives, this meant giving teachers ample time and space to stay together to plan, teach and reflect
on what they were doing for the course, and giving evidence that they were growing and changing as an EFL
teacher in their professional knowledge and competence.
3.3 Workshop Approaches
In terms of the approaches or methods, this workshop was process-oriented, so group work, pair work, oral
presentation, self-reflection, and lecture were applied in this workshop. All the methods took the following four
parts as the guidance for the activities of the participants.
a) Problem Discussion
They discussed the problems existing in the their EFL teaching, and the problems existing in their professional
development, and then their related suggestions, which led to further discussion on the updated English language
competence and TEFL methodology in practice.
b) Direct Instruction Presentation
They were involved in the lectures given by the expert, and practiced what they had learned later in this
workshop. Meanwhile, the participants themselves also presented their mini lessons in this workshop.
c) Cooperative Practice
They practiced the mini EFL lessons in group work, in peer coaching where a dyad worked together, and in team
teaching where all the dyads worked together, and then gave their reflections on what they had done, which
inductively helped to draw their ideas of cooperative teaching, to have a better understanding of the definitions
and natures of peer coaching and team teaching.
d) Multilayered Peer Coaching Practice
They implemented the MPC Model in this workshop, and their reflections contributed to the measurement of this
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model. Then they got to know the model by keeping practicing it and gradually had their conceptualization of
this model.
3.4 Workshop Participants and Length
Twelve tertiary EFL teachers, one expert in the field of TEFL, and the researcher of this present study
participated in this workshop. It was conducted for three days, with 8 hours or 4 sessions per day.
3.5 Workshop Expected Outcomes
This workshop structure attempted to model the practice in multilayered peer coaching by having expected
outcomes as follows. Each participant would
a) get a better understanding of the importance of cooperative teaching and its contribution to in-service
professional development;
b) learn how to effectively lead his or her peer within their own professional abilities and personality styles;
c) learn how to effectively collaborate under the same tasks by making his or her own contribution;
d) learn more on how to effectively solve problems and respectfully work out issues with the help of their peers
and team members;
e) learn how to create more effective working relationships;
f) learn how to be more service oriented.
3.6 Workshop Session
This workshop lasted three days with eight hours per day. Four 2-hour sessions are arranged in the morning and
afternoon respectively each day with coffee/tea break and lunch in between. So there are twelve sessions in this
workshop in total. In each session, the training had its specific topic and practice, with the cooperation of the
teacher participants in dyads and teams.
To conclude, this workshop, which served as an important part of the MPC Model, helped to train the teachers
with new knowledge and skills of TEFL. Meanwhile, it also offered the platform to them for cooperating with
each other so that they know how to work together for their in-service professional development.
4. Research Methodology
4.1 Participants
Twelve tertiary EFL teachers from the School of Foreign Languages at Guiyang University in China participated
in this study. They teach the “Comprehensive English Course”. They were grouped into 6 dyads in 3 teams, with
2 dyads in a team according to their teaching duration. The participants were selected on the basis of
purposiveness and availability.
4.2 Instruments
Three instruments were employed for data collection, namely, non-participant observation, teacher’s log and
semi-structured interview. The observation checklist was designed, or exactly, modified on the Waston’s
activities (Waston et al, 1998, cited in Richards & Farrell, 2005) to find out the activities that this workshop
offered and those the teacher participants conducted in this workshop; the teacher’s log was used for the teacher
participants to record their learning, teaching and cooperation, and to keep their reflection as well; a
semi-structured interview was employed to find more in-depth information about the teacher participants’
opinions on the workshop of the MPC Model. Some related questions were offered, which were checked by the
experts for validity and reliability.
4.3 Data Collection and Data Analysis
While collecting the data, the workshop was video recorded, and the researcher filled out the observation
checklists based on both on-the-spot observation and video-recordings. The teacher participants were asked to
fill in the teacher’s logs to record their training, in which the content of the lecture, the team discussion, the
procedure of their peer coaching, especially the application of the new strategies by the peer teachers of each
dyad before, during, and after the mini lessons, and the log also offered the space to have the teachers’ reflection
on this workshop. Besides, the 12 teacher participants were interviewed at the end of this workshop, the
questions consisted of the teacher participants’ opinions on this workshop.
While analyzing the data, frequency and content analysis were employed. The data from the checklists were
analyzed by the frequency for the occurrence of the activities. The data from the teacher’s logs and interview
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were analyzed by content analysis. For the data from the teacher’s logs, they were already the written texts and
then could be directly progressed according to the steps of content analysis; for the data from the interview, the
audio-taped data were firstly transcribed, and then the transcribed data followed the other steps of content
analysis.
5. Results
After the data were analyzed, the researcher tried to relate the results to the research questions in this study. The
responses to the two research questions were presented respectively based on the instruments.
5.1 Results of Research Question One
5.1.1 Data from the Observation
Table 1. The Results of Observation Checklist for the Workshop’s Activities
Observation
Items
Sessions
1. Direct Instruction Presentation
2. Trainee’s Presentation
3. Discussion
4. Partner Work
5. Co-planning Activities
6. Role-play/ Practice
7. Reflection
Day 1
Day 2
2
2
4
4
4
4
4
1
4
4
4
4
4
4
Day 3
0
4
4
4
4
4
4
M
SD
1.00
3.33
4.00
4.00
4.00
4.00
4.00
1.00
1.15
0.00
0.00
0.00
0.00
0.00
As shown in Table 1, this workshop offered 7 activities during the 12 sessions in 3 days, on average, 4 sessions a
day. The seven activities were conducted in different frequencies. For example, item No. 3, 4, 5, 6, and 7 were
most conducted with the mean score of 4.00 and the standard deviation of 0.00, which explained that the
activities of Discussion, Partner Work, Co-planning, Role-play, and Reflection took place in each session. Item
No. 1 was conducted the least (the mean score of 1.00 and the standard deviation of 1.00), which meant that the
trainer’s Direct Instruction Presentation was quite limited, and item No. 2 had its the mean score of 3.33 and the
standard deviation of 1.15 showed that the trainee’s Presentation was conducted more and more especially on
the last two days. This implied this workshop was very practice-based and focused on the cooperation of the
participants.
Table 2. The Results of Observation Checklist for the Teachers’ Activities in the Workshop
Teacher
Lecture
Q&A
Discussion
Observation Items
Presentation
Peer
Attendance
Co-planning
Work
Role-play/
Reflection
Practice
T1
T2
T3
T4
T5
T6
T7
T8
T9
T10
T11
T12
Mean
3
3
3
3
3
3
3
3
3
3
3
3
3.00
12
12
11
12
12
12
12
10
12
12
12
12
11.90
12
12
12
12
12
12
12
12
12
12
12
12
12.00
10
9
10
10
10
9
10
10
8
10
10
8
9.50
12
12
12
12
12
12
12
12
12
12
12
12
12.00
12
12
12
12
12
12
12
12
12
12
12
12
12.00
12
12
12
12
12
12
12
12
12
12
12
12
12.00
12
12
12
12
12
12
12
12
12
12
12
12
12.00
SD
0.00
0.28
0.00
0.79
0.00
0.00
0.00
0.00
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Table 2 showed that the teacher participants went through the workshop with the help of the activities that they
conducted. The activities that were done in each session included Discussion, Peer Work, Co-planning, Role-play,
and Reflections with the mean scores of 12.00 and the standard deviation of 0.00. The activity of Questions &
Answers was also conducted very frequently with the mean score of 11.90 and the standard deviation of 0.28.
Meanwhile, the teacher participants’ presentation was made in most cases of this workshop, which had the mean
score of 9.50 and the standard deviation of 0.79. Likewise, they attended the lectures offered in this workshop
three times in total with the mean score of 3.00 and the standard deviation of 0.00. The results indicated that the
teacher participants conducted the activities in high frequency. Because of being rooted in the cooperation within
a dyad and a team and putting emphasis on the practice, these activities contributed to their good command of
professional knowledge and skills.
5.2 Results of Research Question Two
5.2.1 Data from the Teacher’s Log
The results from the teacher’s logs showed that the teacher participants kept their logs about the steps they
followed, the activities they conducted, the cooperation they made during this workshop, and their refection on
them. The results were presented based on two themes: activity and reflection.
For their activities, the logs showed that, first, they attended the trainer’s lectures in the first, third and fifth
session about some EFL teaching theories or principles, such as Task-Based Language Teaching (TBLT),
Communicative Language Teaching (CLT), and then they applied what they learned to the practice; second, they
were grouped into the team and dyad. With their team members and peer teacher, they began to make the
cooperation according to the directions; third, they did the group discussions on the pro and con of TBLT, CLT,
etc. and how to select the teaching materials was also a focus in their discussion; fourth, they did team
co-planning and peer work for their mini lessons from preparation to presentation. For their reflections, they
thought that: a) this workshop was very interesting and helpful. Fewer lectures and more practice made them feel
less bored, and they could use what they learned immediately, which helped to keep them in mind; b) this
workshop was more supportive by implementing the MPC Model. They felt stronger and more confident by
working with both peer teachers and team members; c) this workshop offered them the chance to know their
colleagues better. They enjoyed working with friends, as they said “more heads are better than one”. Therefore,
the results implied that this workshop trained the teacher participants with updated professional knowledge and
skills for their in-service professional development.
5.2.2 Data from the Interview
The results from the interview presented their positive opinions on this workshop. To the questions they were
asked, all of the 12 teachers gave their responses. 1) Regarding their general feeling on this workshop, they said
they seemed to be very excited about their work all the time in this 3-day workshop. Although they attended
some workshops before, it was the first time to have such a feeling. 2) In terms of their updated professional
knowledge and skills, they said they had more exposure to the new information in the workshop. They learned
new TEFL knowledge and skills, and practiced them immediately in peers and teams. The peer teachers’ idea
sometimes helped them reconsider their own plan or design, which led them back to the theories to find the
support to convince the others. 3) About the lectures, they said that the lectures they attended in this workshop
were wonderful because the content was what they needed. (The researcher developed the teaching contents
based on their needs in her preliminary study). 4) As for their cooperation, they said they learned how to work
with the colleagues in this workshop. They thought each of them had some specific skill in classroom teaching
and research, working with others meant to a kind of study. 5) When asked if they liked the MPC Model at this
level, they said they liked this model because it not only provided the cooperation in the dyads and teams, but
also offered a follow-up teaching practice session after the workshop, in which they could reinforce and sustain
their profession development. As one of them said, “This workshop refreshed my understanding of the workshop.
To tell you the truth, I do not know what a workshop really is although I attended it many times. I don’t know the
difference between the workshop and other academic meeting, until I came to this workshop. It is really a
‘workshop’ because I practiced how to teach with team members, just like an apprentice. I know the workshop
refers not only to what it is, but also how to do it.” Therefore, the results revealed that the workshop helped to
train the teacher participants with what they wanted for updating their professional knowledge and skills in their
in-service professional development.
6. Discussion
According to the results presented above, this workshop’s contribution to tertiary EFL teachers’ in-service
professional development and the teachers’ attitudes towards this workshop were discussed as follows.
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6.1 Contributions of this Workshop’s Activities to Tertiary EFL Teachers’ In-service Professional Development
Based on the results of this study, the activities that this workshop planned were conducted by the teacher
participants in a high frequency. Meanwhile, the teachers had their reflections which showed their satisfaction
with these activities for their in-service professional development. This happened because all the activities were
designed on a basis of the characteristics that a workshop should have for teacher training, and played the proper
roles in teachers’ professional development. These results were in consistent with some other studies. Richards
and Farrell (2005) have stated that in a workshop the participants are expected to learn something that they can
later apply in the classroom and get the hands-on experience with the topic. Usha Rani (2012) claimed that
applied linguists cite eleven different approaches that promote professional development, and workshop is one of
them and is listed as top one. Hands-on workshops typically involve the participants doing work on a particular
issue during the program. The promise is that when they leave, they will have at least a rough plan or tools in
place to address the challenge. Therefore, this implied that the workshop of the MPC Model could help the EFL
teachers have their in-service professional development.
6.2 Factors Leading to the Satisfaction of the EFL teachers with the Workshop of the MPC Model
From the results of this study, the teachers thought that this workshop was very supportive and they felt stronger
and more confident by working with peer teachers and team members. This happened because this workshop
was rooted in the MPC Model which intended to put the practice of peer coaching within a team teaching context
so as to offer teachers more opportunities to support one another in their work. Some other researchers have
found the similar results in their studies. Darling-Hammond and Richardson (2009) reviewed 20 years of
research on effective teacher learning and professional development, examining the content, context, and design
of high quality professional development. They concluded that teachers learn most effectively and easily when
learning is collaborative and collegial, and professional development is intensive and sustained over time.
Colbert et al (2008) pointed out that when teachers collaborate, research indicates an increase in their academic
content knowledge, and an increasing number of studies identify the importance of collaboration as a key
characteristic of effective professional development.
The teachers also thought that this workshop offered them the chance to know their colleagues better, and to
know how to work with each other. They enjoyed working with friends for their in-service professional
development. This happened because the MPC Model equipped its workshop with a cooperative platform in
which the teachers in the same schools or university spent lots of time working together for what they learned
and their application to the mini lessons. Friendship made in their cooperation could encourage their learning
interest. This was just consistent with some previous studies. Colbert et al (2008) claimed that collaboration
should include groups within the same school or department so that teachers can work together in a focused
environment while dealing with issues of common interest. Dove and Honigsfeld (2010) pointed out that when
teachers engage in collaborative practices, they experience a reduction in isolation, enjoy more occasions to
share their expertise, and appreciate the opportunity to shape the way the ESL program operates in their schools.
This implied that the teachers in such a context were willing to have their in-service professional development.
7. Conclusion
This study has been conducted to investigate the effectiveness of the workshop in the MPC Model, and identify
the activities that this workshop offered for tertiary EFL teachers’ in-service professional development. The
results from this study have contributed to the field of research on EFL teachers’ professional development. It
was found that the workshop in the MPC Model could help the teachers obtain the hands-on experiences
effectively and then help them move on to the follow-up teaching practice in the real teaching context smoothly.
The teachers had positive opinions on the workshop of the MPC Model because they had their professional
knowledge and competence updated with effect in it. So they were willing to apply this workshop for their
in-service professional development. Furthermore, further research can be conducted to help tertiary EFL
teachers focus on the follow-up teaching practiced after the workshop so that their in-service professional
development will be sustained via the MPC Model.
Acknowledgements
The authors wish to thank the experts who helped to evaluate the MPC Model and the instruments. They also
want to thank the EFL teachers from Guiyang University in China, who were the main participants of this study.
References
CERNET. (2001). Chinese universities enroll 2.6 million freshmen. Education in China. Retrieved February 2,
2013, from http://www.edu.cn/200108_1470/20060323/t20060323_5346.shtml
52
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English Language Teaching
Vol. 6, No. 8; 2013
Colbert, J. A., Brown, R. S., Choi, H. S., & Thomas, S. (2008). An investigation of the impacts of teacher-driven
professional development on pedagogy and student learning. Teacher Education Quarterly, Spring,
135-154.
Collinson, V., & Ono, Y. (2001). Professional development of teachers in United States and Japan. European
Journal of Teacher Education, 24, 223-248. http://dx.doi.org/10.1080/02619760120095615
Darling-Hammond, L., & Richardson, N. (2009). Teacher learning: What matters? Educational Leadership,
66(5), 46-53.
Darling–Hammond, L., & Berry, B. (1998). Investing in teaching, Education Week. Retrieved May 27, 2012,
from http://www.edweek.org/ew/vol17/37darlin.h17
Dickey, R. J. (2006). Review on professional development for language teachers: Strategies for teacher learning
– Jack C. Richards and Thomas S. C. Farrell. Korea TESOL Journal, 8(1), 99-102. Retrieved 12 May, 2013,
from http://www.koreatesol.org/content/korea-tesol-journal-8
Dove, M., & Honigsfeld, A. (2010). ESL coteaching and collaboration: Opportunities to develop teacher
leadership
and
enhance
student
learning.
TESOL
Journal,
1(1),
3-22.
http://dx.doi.org/10.5054/tj.2010.214879
Fullan, M., & Hargreaves, A. (1996). What’s worth fighting for in your school. New York: Teachers College
Press.
Gagné, R. M., Briggs, L. J., & Wager, W. W. (1988). Principle of instructional design. Fort Worth: Holt,
Rinehart, and Winston.
Herther, N. K. (2009). The changing language of search. Searcher: The Magazine for Database Professionals,
February, 40-50.
Kachru, Y. (2011). World Englishes: Contexts and relevance for language education. In E. Hinkel (Eds.),
Handbook of research in second language teaching and learning (pp. 155-172), New York: Routledge.
Ono, Y., & Ferreira, J. (2010). A case study of continuing teacher professional development through lesson study
in South Africa. South African Journal of Education, 30, 59-74.
Richards, J. C., & Farrell, T. S. C. (2005). Professional development for language teachers. New York:
Cambridge University Press.
Richards, J. C., Gallo, P. B., & Renandya, W. A. (2001). Exploring teachers’ beliefs and the processes of change.
PAC Journal, 1, 41-58.
Schwille, J., & Dembélé, M. (2007). Global perspectives on teacher learning: Improving policy and practice.
Paris: UNESCO International Institute for Educational Planning.
Tsui, A. B. M. (2003). Understanding expertise in teaching. New York: Cambridge University Press.
UshaRani, P. M. (2012). Self-monitoring – A strategy for teacher development. MAJL, 4(1), Winter, 36-42.
Retrieved May 13, 2013, from http://www.mjal.org/Journal/3.Self-Monitoring.pdf
Notes
Note 1. The detailed information about the development of the MPC Model was in another academic paper
written by the same authors.
Copyrights
Copyright for this article is retained by the author(s), with first publication rights granted to the journal.
This is an open-access article distributed under the terms and conditions of the Creative Commons Attribution
license (http://creativecommons.org/licenses/by/3.0/).
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A review on diclofenac degradation, transformation products and their fate in the environment
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Abstract Diclofenac has been one of the widely consumed pharmaceuticals for
human and veterinary purposes. The research studies are devoted to
investigating its removal from wastewater since its adverse effect on the
environment and the organisms have been revealed. Despite its
microgram level concentrations in the wastewater or water bodies, it
could disrupt the endocrine system, which leads to problems in the
metabolism of the higher-level organisms and, thereby, the ecosystem. Therefore, urgent measures should be taken to control diclofenac
starting from its consumption and extending to the efficient diclofenac
treatment, determination of discharge standards, or the high-level
protection of aquatic life. Another problem with diclofenac is the
degradation end-products that form through photolysis, or biological
reactions remain in the wastewater treatment plants' effluent. These
transformation products create further threats for the organisms. This
review paper aims to emphasize the adverse effects of diclofenac on the
environment, the primary diclofenac sources, its endocrine disrupting
effects on the animals, metabolism in the human body, treatment
approaches, type of biological and chemical degradation metabolites,
or transformation products. Diklofenak, insan ve veterinerlik amaçlı yaygın kullanılan ilaçlardan
biri olmuştur. Diklofenak’ın çevre ve organizmalar üzerindeki olumsuz
etkilerinin ortaya çıkmasıyla, araştırma çalışmaları atıksudan
uzaklaştırılmasına yönelmiştir. Atıksu ya da yüzeysel suda mikrogram
düzeyindeki derişimlerine rağmen, endokrin sistemini bozabilir, bu da
üst düzey organizmaların metabolizmasında dolayısıyla ekosistemde
sorunlara yol açabilir. Bu nedenle diklofenakın tüketiminden
başlayarak
etkin
diklofenak
arıtımına,
deşarj
standartlarının
belirlenmesine ve su yaşamının üst düzeyde korunmasına kadar uzanan
bir yelpazede diklofenak kontrolü için acil önlemler alınmalıdır. Diklofenak ile ilgili diğer bir problem ise, fotoliz ve biyolojik
reaksiyonları ile oluşan bozunma ürünlerinin atıksu arıtma tesislerinin
çıkışında bulunmasıdır. Bu dönüşüm ürünleri organizmalar için daha
fazla tehdit oluşturmaktadır. Dolayısıyla, bu derleme makalesi
diklofenakın çevre üzerindeki olumsuz etkilerini, birincil diklofenak
kaynaklarını, hayvanlar üzerindeki endokrin bozucu etkilerini, insan
vücudundaki metabolizmasını, arıtma yaklaşımlarını, biyolojik ve
kimyasal bozunma metabolitlerinin türünü veya dönüşüm ürünlerini
vurgulamayı amaçlamaktadır. Keywords:
Diclofenac,
Endocrine
disrupting
chemicals,
Pharmaceuticals, Transformation products, Treatment. Anahtar kelimeler: Diklofenak, Endokrin bozucu kimyasal,
Farmasötikler, Dönüşüm ürünleri, Arıtma. Anahtar kelimeler: Diklofenak, Endokrin bozucu kimyasal,
Farmasötikler, Dönüşüm ürünleri, Arıtma. Keywords:
Diclofenac,
Endocrine
disrupting
chemicals,
Pharmaceuticals, Transformation products, Treatment. endocrine-disrupting effect, which has received worldwide
research
attention. Industrial
chemicals,
pesticides,
pharmaceuticals, and personal-care products are now
classified as endocrine-disrupting compounds. *Corresponding author/Yazışılan Yazar Diklofenak’ın bozunması, dönüşüm ürünleri ve çevresel akıbeti üzerine
inceleme Serenay Ceren TÜZÜN1
, Ilgi KARAPINAR1* 1Department of Environmental Engineering, Engineering of Faculty, Dokuz Eylul University, İzmir, Turkey. serenay.tuzun@deu.edu.tr, ilgi.karapinar@deu.edu.tr Revision/Düzeltme Tarihi: 02.04.2022
doi: 10.5505/pajes.2022.71363
Review Article/Derleme Makalesi Received/Geliş Tarihi: 15.11.2021
Accepted/Kabul Tarihi: 18.05.2022 Received/Geliş Tarihi: 15.11.2021
Accepted/Kabul Tarihi: 18.05.2022 doi: 10.5505/pajes.2022.71363
Review Article/Derleme Makalesi Revision/Düzeltme Tarihi: 02.04.2022 Revision/Düzeltme Tarihi: 02.04.2022 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022 1 Introduction Therefore, the possible adverse effects of DCF and its
TPs on aquatic organisms have been a significant concern in
environmental research subjects. Numerous scientific studies
regarding its toxicity and health effects on aquatic animals were
conducted [3]-[6]. Through extensive research, it was
discovered that DCF has endocrine-disrupting properties even
at an environmentally relevant concentration around µg/L and
even at ng/L [7],[8]. The toxicity studies encouraged the
community to do more occurrence and fate studies of DCF to
investigate the concentration levels in WWTPs [9]-[11] and
surface water [12]-[14]. DCF removal studies in WWTPs
revealed a wide range of efficiencies between less than 50% to
higher than 90% [15],[16]. Figure 1. Chemical Structure of DCF (2-[2-(2,6-
dichloroanilino)phenyl]acetic acid). DCF’s low air-water distribution coefficient (log Daw=-12.21)
and low octanol-water distribution coefficient (log Dow=1.79)
ensure that it stays in the dissolved phase. The pKa of 4.15 value
of DCF also indicates that it will present as its dissociated form. Moreover, volatilization and sorption to solid-phase are
considered insignificant processes [30]. Buser et al. showed
that light enhances degradation of DCF, chemical and biological
degradation in the dark is negligible [31], and no adsorption on
sediment due to its low sorption ability [31]. DCF’s low air-water distribution coefficient (log Daw=-12.21)
and low octanol-water distribution coefficient (log Dow=1.79)
ensure that it stays in the dissolved phase. The pKa of 4.15 value
of DCF also indicates that it will present as its dissociated form. Moreover, volatilization and sorption to solid-phase are
considered insignificant processes [30]. Buser et al. showed
that light enhances degradation of DCF, chemical and biological
degradation in the dark is negligible [31], and no adsorption on
sediment due to its low sorption ability [31]. The DCF metabolites in wastewaters or WWTPs effluents is
another problem affecting WWTP design and water quality. DCF is metabolized in the human body, and then different types
of metabolites at varying concentrations are released through
urine and bile [17],[18]. Therefore, the primary need is to
understand the fate of DCF and its TPs in the environment after
chemical oxidation, photolysis, aerobic, anaerobic, or anoxic
treatment approaches. The primary degradation mechanism
could be natural sunlight or photolysis due to the
photosensitive nature of DCF [19],[20]. The end products
regarding photolysis degradation were carbazole derivatives,
which were determined as a possible reason for phototoxicity
of DCF TPs [19],[21]-[23]. 1 Introduction Water pollutants have been known as heavy metals, nitrogen,
phosphorus, or organic ones named chemical oxygen demand
(COD) and biological oxygen demand (BOD). The wastewater
treatment plants were designed and constructed for the
removal of these well-known conventional pollutants. However, the need to protect the environment and organisms
from pollutants has changed recently. The term “pollutant” is
now knowns as “conventional pollutants" and "specific
pollutants." The advanced scientific background knowledge
and engineering experiences are available about conventional
pollutant control, though economical and more efficient
treatment approaches are still under development. The
discharge standards are well established for them, and existing
wastewater treatment plants have been designed and
constructed accordingly. The specific pollutants, which are
recognized as micropollutants, have become the primary
concern in the environment due to their unknown effects on
organisms, including humans. Their carcinogenic effect was
presumable, but surprisingly, they realized that they have the Pharmaceuticals include antibiotics, anti-inflammatory drugs,
pain killers, etc. Diclofenac (DCF) is a non-steroidal anti-
inflammatory drug (NSAID) that is used widely throughout the
world, with the estimation of 1443 tons consumption globally
in 2015 [1]. The risk of DCF is not only the amount consumed
by the human, but it is also a pharmaceutical used for
veterinary purposes. Human consumption residues can be
somehow managed or controlled before they reach the natural
water bodies through treatment processes. However, it is hard
to contain veterinary residues, which might be the most
significant risk for the deposition of DCF in soil and natural
waters, especially in groundwater. A study conducted by de
Voogt et al. [2] about the development of a common priority list
of pharmaceuticals relevant for the water cycle indicated that
DCF is within Class I with ten high priority pharmaceuticals
based on its resistance to treatment, high occurrence in the
water, high consumption, physical properties, toxicity and 937 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Figure 1. Chemical Structure of DCF (2-[2-(2,6-
dichloroanilino)phenyl]acetic acid). persistence. It means that it has got a high potential to reach
surface waters through wastewater treatment plants (WWTPs)
discharges in the form of the parent compound and its
transformation products (TPs) if a proper treatment
technology or strict discharges standards are not applied in the
countries. 1 Introduction Properties
Reference
Water Solubility
2.37 mg/L
[32]
Vapor pressure
6.14 x 10-8 mm
Hg (25 0C)
www.pubchem.n
cbi.nlm.nih.gov
Henry’s Law
Constant
4.79 x 10-7 Pa
m3/mol (25 ℃)
[33]
Melting point
283-285 ℃ at
760 mm Hg
(predicted)
[32]
Boiling point
412 ℃ at 760
mm Hg
[32]
pKa
4.15
[34]
logKow
4.51
[34]
logKoc
2.20-3.42
[35]
Half-life in the body
~2 h
[33],[36]
Half-life in the
atmosphere
0.8 h
[37]
Half-life in water
(photolysis)
8 d-21 d
[30],[38],[39]
Half-life in soil
<5 d
[40] It is evident that DCF received considerable research interests. These studies' results lightened the further studies that helped
eliminate DCF from the environment to provide a sustainable
world. This review paper was designed to do a detailed analysis
of DCF, including its chemistry, which affects its removal, global
consumption, its toxicity or adverse effect on the organisms, the
main
DCF
contamination
routes,
the
observed
DCF
concentrations in surface water and wastewater, the applied
treatment technologies and their effectiveness on the DCF
removal. The review mainly concentrates on the TPs generated
after applied treatment technologies to emphasize their
potential risks and devote the research interest to complete
removal of DCF from wastewater without leaving its dangerous
end products. The octanol-water partition coefficient value of DCF is logPow
of 0.7, which means high water solubility. DCF can accumulate
in the organs such as the liver, kidney, gills. Bioconcentration
factors have been determined inversely proportional to the
exposure concentration, which indicates a complete saturation
of tissues by DCF in the highest concentration group [6]. Histopathological results revealed significant concentrations in
the gills and kidneys responsible for the excretion of DCF. However, the highest concentration was found to be in the liver,
where the cytochrome P450-dependent metabolism of DCF
occurs. The exposure of 1 µg/L DCF caused an activated hepatic
metabolism in the rainbow trout’s liver [6]. 1 Introduction Aerobic bacterial degradation of DCF
is limited, but high removal can be achieved through sludge
adaptation [24]. The degradation can be enhanced by using
special bacterial stains [25],[26] and white-rot fungi [27],[28]. But, partial degradation and hydroxylated end-product
formation are observed [25],[26],[29]. Table 1. Chemical and physical properties of DCF. Table 1. Chemical and physical properties of DCF. Properties
Reference
Water Solubility
2.37 mg/L
[32]
Vapor pressure
6.14 x 10-8 mm
Hg (25 0C)
www.pubchem.n
cbi.nlm.nih.gov
Henry’s Law
Constant
4.79 x 10-7 Pa
m3/mol (25 ℃)
[33]
Melting point
283-285 ℃ at
760 mm Hg
(predicted)
[32]
Boiling point
412 ℃ at 760
mm Hg
[32]
pKa
4.15
[34]
logKow
4.51
[34]
logKoc
2.20-3.42
[35]
Half-life in the body
~2 h
[33],[36]
Half-life in the
atmosphere
0.8 h
[37]
Half-life in water
(photolysis)
8 d-21 d
[30],[38],[39]
Half-life in soil
<5 d
[40]
The octanol-water partition coefficient value of DCF is logPow
of 0.7, which means high water solubility. DCF can accumulate
in the organs such as the liver, kidney, gills. Bioconcentration
factors have been determined inversely proportional to the
exposure concentration, which indicates a complete saturation
of tissues by DCF in the highest concentration group [6]. Histopathological results revealed significant concentrations in
the gills and kidneys responsible for the excretion of DCF. However, the highest concentration was found to be in the liver,
where the cytochrome P450-dependent metabolism of DCF
occurs. The exposure of 1 µg/L DCF caused an activated hepatic
metabolism in the rainbow trout’s liver [6]. The half-life of DCF in the body is around 2 hours [33],[36]. On
the other hand, the half-life in the water phase when exposed to
sunlight is about 8 days [38]. A longer half-life up to 23 days in
the field experiment in springtime, has been reported [39]. The
temperature and irradiation variations depending on the
season regional climate and latitude are the main reasons for Table 1. Chemical and physical properties of DCF. 2 Physical and chemical properties of
diclofenac the gills and kidneys responsible for the excretion of DCF. However, the highest concentration was found to be in the liver,
where the cytochrome P450-dependent metabolism of DCF
occurs. The exposure of 1 µg/L DCF caused an activated hepatic
metabolism in the rainbow trout’s liver [6]. The physical and chemical properties of a pollutant determine
its fate and transport in the environment. These properties
specify the persistency, biodegradability, treatability, toxicity,
and bioaccumulation in the organisms. The physical and
chemical properties of DCF is given in Table 1 and its chemical
structure is shown in Figure 1. The IUPAC name of DCF is 2-[2-
(2,6-dichloroanilino)phenyl]acetic acid. The half-life of DCF in the body is around 2 hours [33],[36]. On
the other hand, the half-life in the water phase when exposed to
sunlight is about 8 days [38]. A longer half-life up to 23 days in
the field experiment in springtime, has been reported [39]. The
temperature and irradiation variations depending on the
season, regional climate, and latitude are the main reasons for 938 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar the wide range of half-life through photolysis [30],[39]. Controlling the temperature decreased half-life to the range of
0.2-1.7 h [41]. The half-life of DCF in the soil is less than five
days, as shown in Table 1. Xu et al. [42] reported that DCF has
high mobility in the soil, in turn relatively low adsorption
affinity. The microbial community in the earth is the significant
parameter that determines the half-life of DCF. Although most
of the studies concluded that the primary DCF degradation
mechanism is photolysis in the natural waters, Radke et al. [43]
claimed that photolysis is not important for even easily
photodegradable compounds like DCF in real conditions, which
indicates that DCF needs an efficient treatment before it is
discharged into the water body. [48]. The biosolids from wastewater treatment plants could be
used as a soil conditioner, which creates another risk for
surface water and groundwater contamination [49]. The source
from veterinary or DCF treated animals could be a significant
concern for water and soil contamination. Finally, the dermal
application is another source of DCF in the aquatic
environment. 3 Global diclofenac consumption The consumption can vary depending on the economics,
medical and cultural differences of the countries. It is not
possible to find accurate data about its consumption in all
countries. Therefore, Zhang et al. [33] proposed a simple
calculation method based on the average dose per capita of
countries where this data is avaliable. Then they constituted the
Equation (1) and 𝐴𝑣𝑒𝑟𝑎𝑔𝑒 𝐷𝑃𝐶 𝑜𝑓 𝑑𝑒𝑣𝑒𝑙𝑜𝑝𝑒𝑑 𝑐𝑜𝑢𝑛𝑡𝑟𝑖𝑒𝑠 × (𝑤𝑜𝑟𝑙𝑑 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛 × 0.2)
0.8 (1) Table 2. The observed DCF removal efficiencies, influent and
effluent of concentrations in different countries. Table 2. The observed DCF removal efficiencies, influent and
effluent of concentrations in different countries. 0.8 effluent of concentrations in different countries. Location
WWTP
Influent
(ng/L)
WWTP
Effluent
(ng/L)
Removal
Efficiency
(%)
Ref. USA
140-280
<10
51-80
[51]
Canada
50-2450
70-250
-
[52]
Mexico
2325-
2470
1865-2180
<46
[53]
China
13-445
2-72
<0->90
[54]
14.8-71.8
17.7-69.2
<0-25
[55]
South
Korea
59-243
13-49
81.4
[56]
India
3100-
5300
1100-2300
56-64
[57]
Singapore
318-390
271-394
<0-28.5
[58]
South
Africa
22300
19000
14
[12]
6200-
53000
2600-
15000
4-88
[9]
Spain
414-1080
189-1150
<0-54
[59]
400-1500
ND-900
<24-60
[15]
1660
430
74
[11]
400-1500
-
-
[11]
Greece
ND-4869
ND-2668
45
[11]
77.8-5164
ND-382.5
<0-65
[60]
Turkey
295-1376
119-1012
12-65
[61]
United
Kingdom
26-1161
6-496
<0
[62]
Austria
905-4114
780-1680
0-70
[63]
Poland
2251-
4477
1597-5630
<0-40
[64]
Sweden
1550-
2250
40-36
~97
[16]
Finland
250-750
1000-2250
<0
[65]
250-500
200-400
9-60
[66]
Similar to DCF concentration in wastewater, the observed
concentrations in the countries' surface waters vary estimated the annual global consumption for the year 2007. It
was reported that the possible global DCF utilization all over
the world is around 940 tons. The estimated consumption was
parallel with the available data from Intercontinental
Marketing Statistics (IMS) Health company. Altman et al. [36]
were able to find data regarding DCF consumption in the USA. It was stated that the prescription of DCF exceeded 10 million
in 2012. Among those prescriptions, DCF sodium as topical gel
accounted for 3% of the total annual prescriptions for NSAIDs. Lonappan et al. [32] compiled the information in the review
article, and it was concluded that the estimated numbers could
be higher due to unavailable data about veterinary
consumption. According to DCF consumption records in 2001
in the European Union, Germany is the biggest consumer with
86 tons/ year [44]. 3 Global diclofenac consumption The annual consumption in England and
France were 26 tons and 16 tons, respectively [45],[46]. Another estimation done in 2015 showed that the consumption
increased to 1443 tons globally [32] since the amount reported
by Zhang et al. in the year 2007 [33]. estimated the annual global consumption for the year 2007. It
was reported that the possible global DCF utilization all over
the world is around 940 tons. The estimated consumption was
parallel with the available data from Intercontinental
Marketing Statistics (IMS) Health company. Altman et al. [36]
were able to find data regarding DCF consumption in the USA. It was stated that the prescription of DCF exceeded 10 million
in 2012. Among those prescriptions, DCF sodium as topical gel
accounted for 3% of the total annual prescriptions for NSAIDs. Lonappan et al. [32] compiled the information in the review
article, and it was concluded that the estimated numbers could
be higher due to unavailable data about veterinary
consumption. According to DCF consumption records in 2001
in the European Union, Germany is the biggest consumer with
86 tons/ year [44]. The annual consumption in England and
France were 26 tons and 16 tons, respectively [45],[46]. Another estimation done in 2015 showed that the consumption
increased to 1443 tons globally [32] since the amount reported
by Zhang et al. in the year 2007 [33]. In conclusion, there is limited information in the literature
regarding the consumption of DCF for individual countries or
global consumption. Moreover, the data that can be found in the
literature do not include veterinary usage. Nevertheless, the
DCF utilization is increasing day by day, which will end up in
the natural waters. The cautions should be taken to protect the
water resources against DCF contamination. 2 Physical and chemical properties of
diclofenac It has a low absorption rate to the skin, around
6% of applied DCF, and the rest (94%) is washed away to the
sewage system. Therefore, the dermal treatment gels end up in
the form of the parent compound in the domestic effluents
rather than its metabolites [18],[50]. Table 2 depicts some of the reported DCF concentrations in the
influents and effluents with removal efficiencies of the WWTPs
around the world. The large amount of DCF in domestic
wastewaters is encountered due to the heavy consumption of
DCF by the human in some regions. The influent concentrations
for Europe, Asia, and America do not differ from each other. The
reported DCF concentration is less than the minimum
quantification limit (MQL) and could reach up to 5300 ng/L. An
exceptional concentration between 6200-53000 ng/L was
encountered in South Africa. The removal efficiency of DCF is
usually lower than 50%, but it could be as high as 97% as it was
reported in Sweden [16]. Similar to DCF concentration in wastewater, the observed
concentrations in the countries' surface waters vary
substantially (Table 3). 5 The adverse effects of diclofenac on
organisms Global consumption of DCF indicates that its utilization is
already very high even though veterinary purpose is not
included. Its adverse effects on aquatic animals is a problem
from an environmental point of view. However, there are
shreds of evidence of its impact on human health. For example,
DCF treatment was associated with the development of acute
kidney injury (AKI). A meta-analysis study showed that
individuals treated with DCF appeared to have a 77% increased
risk of developing AKI. DCF treatment during pregnancy
adversely affects the renal function of the newborn. Briefly, it
can cause toxicity in kidneys in adults while children and older
people can have renal complications due to DCF [77]. The adverse effect of DCF on animals is more concerning due to
its endocrine disrupting compound (EDC) potential, which may
cause a population shift from male to female. The change in the
population may result in the permanent destruction of the
ecosystem. Some of the studies on animals revealed its effects
on organs, its bioaccumulative, and EDC features. The survey
done by McRae et al. [4] focused on the impact of
environmentally relevant (0.17 µg/L) and high (763 µg/L)
concentrations on galaxiid fish, inanga (Galaxias maculatus),
which is an essential fish species for Southern Hemisphere. Inanga was exposed to DCF for 96-h. Bioaccumulation in the
inanga exposed to 763 µg/L was significantly higher (1811
µg/kg) than the inanga exposed to 0.17 µg/L (14.9 µg/kg). The
calculated bioconcentration factor (BCF) of 2.1±1.2 from 763
µg/L was significantly lower than the BCF value of 87±55 from
0.17 µg/L. The results showed that inanga's human
consumption exposed to the environmentally relevant
concentration of 0.17 µg/L would lead to 4.25 µg of DCF per
serving. Schwaiger et al. [6] stated that four weeks of exposure
to environmentally relevant concentrations of DCF caused
histopathological changes in the kidney and the gills of rainbow
trout. The concentration which causes renal lesions and
alterations of the gills has been determined as 5 µg/L. It was
concluded that 1 µg/L was no observed effect concentration
(NOEC). The concentration range in surface waters for Asia and South
America could be less than 0.058 ng/L and could reach up to
3000 ng/L as observed in the Red Sea and Paraopeba River. In
Europe, the concentrations are in the range of <0.25-475 ng/L. 5 The adverse effects of diclofenac on
organisms Implementation of EU Water Framework Directive and
Environmental Quality Standards for controlling hazardous
and specific pollutants, including DCF, in EU surface waters
could be the main reason for the low concentration of DCF in
European surface waters. The highest surface water
concentrations were observed in South Africa due to, probably,
a high level of DCF discharge of 8000 ng/L from the WWTP
(Table 2). Another very high concentration of 15087 ng/L in
wastewater discharge point was observed in Antarctica [74]. The surface water or streamline in Seymour/Marambio Island
receives direct liquid effluent discharges. The concentration
measured in the surface water was 7761 ng/L. The high DCF
concentration was reasoned by the population increase in the
summer months due to touristic or military activities. The discovery of decline of the vulture population in Asia due
to DCF has enlightened the science community about the
bioaccumulation in the food chain considering the utilization of
DCF in veterinary application has been limited to cattle, pigs,
and horses [75]. Since then, the utilization of DCF for veterinary
purposes, was banned in India, Nepal, Pakistan, Bangladesh,
Spain, Italy, and Slovenia. Instead, Dolofenac and Diclovet,
which contain DCF-sodium, were approved for swine, cattle,
and horse treatment [76]. Eades and Waring [78] focused on the effects of substantially
low concentration of DCF (10 ng/L and 100 ng/L) at two
salinity levels (35 and 17.5 psu) to the green shore crab
Carcinus maenas. The study was about the effect of DCF on the
osmoregulatory capacity (OC), which means regulation to
balance the fluid and the concentration of electrolyte in the
metabolism of the organisms. It maintains the homeostasis of
the organism’s water content, and a disruption in the OC could
cause a detrimental effect on the organisms. Therefore, it is
used as an indicator of early warning of any potential
environmental problems that are not immediately apparent
[79]. The crabs exposed to both 10 ng/L and 100 ng/L of DCF
showed an increase in the OC at both salinities. The results
indicated that DCF significantly impairs the OC balance of carbs
in marine and estuarine environments. This result also shows It is evident that DCF has multiple routes that contaminate the
environment. Its concentration in the different environmental
phases depends on the amount of consumption, the
effectiveness of wastewater treatment plants, and the control
measures taken or established discharge standards of the
countries. 4 Diclofenac contamination routes The main routes of DCF contamination in the environment are
through wastewater discharges and solid wastes. The drug
disposal could be the most dangerous DCF contamination route
in the surface, groundwater, and soil. Percolation from landfills
to groundwater and surface water poses a significant risk
[32],[47]. It was shown that among 400 households in the UK,
63.2% of people threw away their unfinished drugs as waste,
and 11.5% threw them away through a sink or toilet [47]. The
pharmaceutical industry and hospital effluents are the other
possible entry routes for DCF to find its way into surface waters 939 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Table 3. The observed DCF concentrations in surface waters
around the world. Location
Concentration
(ng/L)
Type of surface
water
Ref. Mexico
988-1398
River
[53]
France
35
Lake
[67]
Brazil
136-2625.7
Paraopeba River
[14]
19000-193000
River
[68]
South
Africa
600-8170
River
[12]
Finland
20-475
Lake
[65]
Greece and
Turkey
<LOQ (2.0)-9.7
Aegean Sea
[69]
Turkey
<28-1300
Sea of Marmara
[70]
Poland
<LOD (0.25)-
92.6
Baltic Sea
[71]
Saudi
Arabia
<LOD (1.6)-
>3000
Red Sea
[13]
China
<LOD (0.058)-
843
Yangtze River
Estuary
[51]
Antarctica
<LOD (4.3)-
7761
Northern
Antarctic
Peninsula
[67]
Finland
2-35
River
[66]
South
Africa
900-5300
River
[9]
Pakistan
100-4400
River
[72]
Malaysia
ND-15.49
River
[73]
LOQ: Limit of Quantification; LOD: Limit of Detection; ND: Not detected. Table 3. The observed DCF concentrations in surface waters
around the world. itself. The metabolites and TPs that form during human
metabolism, photodegradation or biodegradation are not taken
into account. The DCF treatment efficiency in WWTPs is
available only for the parent compound. The metabolites and
TPs could pose more health risks. In other words, the
awareness about the adverse effect of DCF and its fate in the
environment could be the main starting point to control DCF
contamination. 6 Diclofenac treatment and transformation
products that the effect of DCF on the organisms could be observed even
at ng/L concentrations [78]. The adverse effects of DCF can be observed through the food
chain, which could cause further threats for the endangered
species. The case was observed in Pakistan and India where
three vulture populations, namely; Gyps bengalensis, Gyps
indicus, and Gyps tenuirostris unexpectedly, but severely
declined (95%) the last decade. The investigations indicated
that DCF poisoning of wild vultures is thought to occur when
they feed on carcasses treated with DCF [3]. A similar study was
conducted by Oaks et al. in the year 2004. They investigated the
correlation between exposure to DCF and death from renal
failure in vulture species. The experiment included 20 vultures
fed with DCF-treated animals and six control vultures fed with
untreated animals. 13 vultures out of 20 (65%) exposed group
died due to renal failure. In contrast, none of the vultures in the
control group died. A significant correlation between renal
failure and DCF exposure is apparent [5]. These findings
emphasize the risk of DCF through the food chain. DCF is either partially degraded through natural physical and
chemical reactions or degraded biologically in wastewater
treatment plants and metabolized in humans/animals' body. So, DCF may not be observed as itself in the water, but its
degradation products may still exist in the environment. The
metabolites and TPs that occur as a result of these reactions
may cause a detrimental impact on the organism. Therefore, the
studies on the removal of DCF and its toxicity should include
TPs, and metabolites. Micropollutants have received extensive research attention for
the past two decades since their effects on the organisms have
been revealed. DCF is one of the most studied micropollutants
in the literature. There are many studies regarding its fate in
WWTPs and the aquatic environment. The recent studies
confirmed the presence of TPs of micropollutants in WWTPs
devoted attention to occurrence and fate studies of DCF
together with its TPs. The studies without considering TPs
could result in a false narrative that may give the impression of
good removal when, in reality, they could be transforming into
their TPs, which later could deconjugate into the parent
compounds again. Therefore, fate studies should include
monitoring TPs as well as parent micropollutants. 5 The adverse effects of diclofenac on
organisms Besides, the reported studies consider only the DCF 940 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar 6 Diclofenac treatment and transformation
products In brief, any
wastewater treatment process used for DCF removal should
consider both DCF and its transformation products to ensure
non-toxic water discharges. The adverse effect of DCF is not limited to the failure of organs
and then death. Another problem with DCF is its endocrine-
disrupting effect, which could destroy the ecosystem
irreversibly and increase species extinction risk. As it is well
known, EDCs constitute a significant concern regarding both
environmental and human health. Shortly, EDCs can be natural
or synthetic compounds that can interfere with the hormonal
system; they can mimic or block hormones, alter the pattern of
hormone synthesis or metabolism and modify the hormone
receptor levels [80]. They can create deviations in the
population from male to female by affecting the aquatic
organisms' reproducibility. A good indicator of the endocrine
disruption for a chemical in the organism is the level of
vitellogenin (VTG). It is a naturally synthesized egg protein in
females, and it is inactive in males. Increased alkali-labile
phosphate (ALP) concentration produced by VTG alkali
hydrolysis can be used as an indicator of the endocrine-
disrupting (ED) effect of a chemical. Gonzalez-Rey and
Bebianno [7] exposed female and male mussels M. galloprovincialis gonads to 250 ng/L of DCF for 15 days. The
result was a 3-fold increase in females' ALP concentrations
while males showed consistent ALP concentrations during 15
days of experiments. This study showed that 250 ng/L of DCF
for 15 days affected female mussels more than male mussels. The increased vitellogenin gene expression in Oreochromis
niloticus was observed at 1μg/L DCF [81]. In another study, the
effects of DCF and its major metabolite 4’-hydroxydiclofenac
(4’-OH-DCF) were investigated [82]. The results showed that
both DCF and 4'-OH-DCF have anti-estrogenic and anti-
androgenic effects, meaning that they block estrogen and
androgen binding receptors. On the other hand, 4’-OH-DCF
itself can mimic the estrogens and androgens in the receptors,
and it has weak estrogenic and androgenic activity. Hong et al. [8] showed that WWTP effluent and surface water samples
contain over 1000 ng/L DCF concentration, which could induce
an increase in vitellogenin production in fish, and thereby, it
could cause deviation in the population. Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Table 4. Identified human metabolites of DCF. Metabolite
Molecular Structure
Ref. 4’-OH-DCF
[86],[88]
5-OH-DCF
[86],[88]
3’-OH-DCF
[86],[88]
4’,5-DiOH-
DCF
[86],[88]
3’-OH-4’-
OCH3-DCF
[84],[86]
4’-OH-DCF-
dehydrate
[85]
DCF-AG
[86]
The amount of metabolite and the types of metabolite depend
on the DCF application. The metabolites in the urine for DCF
administered orally were 4'-OH-DCF (16.0%), 5-OH-DCF
(6.1%), 3'-OH-DCF (2.0%), and 3'-OH-4'-OCH3-DCF (<0.01%). Approximately 6.2% of DCF remains unchanged. However, if
there is declined renal function, 3’-OH-DCF, 5-OH-DCF, 3’-OH-
4’-OCH3-DCF, and DCF constitute less than 2% of the dose. The
amount of 4’,5-DiOH-DCF in urine was 9.4% of the dose [18]. Oral administration of DCF resulted in 6.5% DCF, 18.1% 4’-OH-
DCF, 8.2% 5-OH-DCF, 1.4% 3’-OH-DCF, and 15.4% 4’,5-DiOH-
DCF of urine samples. DCF and its metabolites in human bile
were mainly 10-20% 4’-OH-DCF, 5-10% 5-OH-DCF and less
than 5% unchanged DCF [85]. Table 4. Identified human metabolites of DCF. Metabolite
Molecular Structure
Ref. 4’-OH-DCF
[86],[88]
5-OH-DCF
[86],[88]
3’-OH-DCF
[86],[88]
4’,5-DiOH-
DCF
[86],[88]
3’-OH-4’-
OCH3-DCF
[84],[86]
4’-OH-DCF-
dehydrate
[85]
DCF-AG
[86]
The amount of metabolite and the types of metabolite depend covalent bonds and transforms organic pollutants into more
biodegradable and hydrolyzable compounds. There are
multiple factors affecting photodegradation, such as the
mechanism of degradation (direct or indirect), the chemical
structure of pollutant, temperature, pH, depth of surface water,
cloud coverage, altitude, latitude, and time of day [20],[89]. The photodegradation of DCF is related to the concentration of
DCF in the wastewater. Zhang et al. [90] stated that the
degradation rate is affected by the concentration due to
competition in the absorption of a limited number of photons
by DCF. Dissolved oxygen plays a significant role in the
photooxidation of DCF. The mechanism of indirect DCF
photooxidation in the presence of dissolved oxygen in the water
has two stages. First, direct photodegradation occurs through
exciting DCF by solar radiation. Later, dissolved oxygen can
absorb the energy of excited DCF, resulting in reactive oxygen
species, which induces photooxidation of DCF. On the other
hand, direct photodegradation, which is known as the primary
mechanism for DCF, is inhibited in the presence of dissolved
oxygen due to suppression of excited DCF. DCF
[86],[88 OH-DCF
[86],[88] [86],[88] The presence of other pollutants could adversely affect
photodegradation. The rate will be more affected by increasing
the concentration of these pollutants. Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Approximately 6.2% of DCF remains unchanged. However, if
there is declined renal function, 3’-OH-DCF, 5-OH-DCF, 3’-OH-
4’-OCH3-DCF, and DCF constitute less than 2% of the dose. The
amount of 4’,5-DiOH-DCF in urine was 9.4% of the dose [18]. Oral administration of DCF resulted in 6.5% DCF, 18.1% 4’-OH-
DCF, 8.2% 5-OH-DCF, 1.4% 3’-OH-DCF, and 15.4% 4’,5-DiOH-
DCF of urine samples. DCF and its metabolites in human bile
were mainly 10-20% 4’-OH-DCF, 5-10% 5-OH-DCF and less
than 5% unchanged DCF [85]. The amount of metabolite and the types of metabolite depend Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar The organic matter in the
water could enhance the target compound's oxidation through
the free radical formation of existing other organic ones. However, in the case of DCF, the rate could decrease due to
competition in receiving photons from UV irradiation [23]. Nitrogen in the form of NO3, NO2, and ammonia are the common
pollutants in domestic wastewater. Therefore, their effects on
photodegradation must be considered. Zhang et al. [90]
reported that the inhibition effect of NO2 is more potent than
that of NO3, but ammonia has no effect. The absorption
wavelength of NO2 and DCF are almost the same, which sets a
competition to receive the photon that caused decreasing in the
degradation rate of DCF. On the other hand, Sokól et al. [91]
claimed that NO3 and NO2 ions positively affected the DCF
decomposition rate due to photosensitizing properties of these
ions. 3’-OH-4’-
OCH3-DCF
[84],[86] [84],[86] OH-DCF-
ehydrate AG
[86] [86] Sokól et al. [91] investigated the influence of pH, humic
substances, and complex matrixes on the photodegradation of
DCF. It was observed that acidic conditions (pH=2 and 4)
enhances the degradation rate implying that H+ ions could be
the catalyst for the photochemical reactions. Similarly, Zhang et
al. [92] claimed that the reaction rate increased when pH was
between 3 and 5 but decreased when the pH was around 5-8. Further increase in the reaction for the alkaline range (pH=8-
12) was observed. Sokól et al. [91] concluded that the humic
acids have photosensitizing properties that lead to the
increased rate. Zhang et al. [92], reported an opposed
conclusion to Sokól et al. [91]. His experience was hindering in
DCF photodegradation rate in the presence of humic acid. Three
mechanisms were suggested to reveal the effect of humic
substance on DCF degradation. The first one was the
competition between DCF and humic acid to absorb photons in
the emission spectrum resulting in decreasing in the rate. The
second one provides an increase in DCF degradation under UV
irradiation by forming reactive oxygen species through exited
humic acid. However, UV irradiation was not enough under
simulated sunlight to support this mechanism. The third
mechanism suggests that humic acid can be a scavenger
towards DCF [92]. The amount of metabolite and the types of metabolite depend
on the DCF application. The metabolites in the urine for DCF
administered orally were 4'-OH-DCF (16.0%), 5-OH-DCF
(6.1%), 3'-OH-DCF (2.0%), and 3'-OH-4'-OCH3-DCF (<0.01%). 6.1
Metabolites of diclofenac in human DCF is subjected to aromatic hydroxylation and conjugation
through hepatic metabolism in humans and animals [84]. The
identified metabolites of DCF in the human body are shown in
Table 4. These metabolites are found in humans/animals’
excreta and blood at varying percentages. 4’-hydroxydiclofenac
(4’-OH-DCF),
5-hydroxydiclofenac
(5-OH-DCF),
4’,5-
dihydroxydiclofenac (4’,5-diOH-DCF), 3’-hydroxydiclofenac
(3’-OH-DCF) and 3’-hydroxy-4’-methoxydiclofenac (3’-OH-4’-
OCH3-DCF) were discovered in human urine, plasma, and in bile
[17]. Stülten et al. [85] identified a new minor metabolite in
human urine called lactam-dehydrate of 4'-OH-DCF. Stierlin
and Faigle [86] identified 1-O-acyl-glucuronide-DCF (DCF-AG),
which can form through direct conjugation of DCF or
hydroxylation followed by conjugation. DCF-AG is found to be
unstable in bile and possibly hydrolyzes in the gastrointestinal
tract to form DCF which, then enters the circulation again. A
study about DCF-AG showed that after 50 mg DCF
administration, the mean Cmax of DCF and DCF-AG in plasma
were comparable and Cmax ratio of DCF-AG/DCF was 0.62 [87]. The enzymes responsible for specific metabolites were studied
to investigate the DCF metabolism in detail. Bort et al. [17]
incubated DCF in human hepatocytes, human liver microsomes
and genetically engineered cytochrome P450 (CYP)-expressing
cells. The results suggested that 4’-OH-DCF is entirely formed
by CYP2C9 enzyme (>99.5%) while CYP2C9 had >97%
participation in forming 5-OH-DCF in the human liver. The
isoforms; CYP2C8, CYP2C19, CYP2C18, and CYP2B6 were also
suggested in the formation of 5-OH-DCF. CYP2C9 was the only
one to initiate the formation of 3’-OH-DCF. It is now known that DCF has endocrine-disrupting properties,
and its metabolites and TPs could pose the same risk. DCF has
been put watch-list of EU in 2015 based on toxicity results of
DCF [83]. Therefore, it is vital to determine the effects of
environmentally relevant concentrations of DCF. 941 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar 6.2
Photodegradation and transformation products Photodegradation of organic pollutants in the aquatic
environment occurs by two mechanisms: direct absorption of
solar radiation and reaction with photosensitized species. Direct photodegradation occurs via non-reversible bond
cleavage or re-arrangement of organic molecules with the
energy coming from sunlight. Indirect photodegradation is the
degradation of molecules by chromophoric compounds which
are brought to a higher level of energy by solar radiation. In
both mechanisms, energy gained from solar radiation breaks 942 942 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Buser et al. [31] investigated the elimination pathway of DCF in
the lake. The results showed that adsorption onto lake
sediment was negligible while there was no evidence of
chemical and biological degradation. However, sunlight-
exposed DCF resulted in a rapid degradation in 4 days. A high
concentration (36 mg/L) of DCF was exposed to sunlight to
discover photodegradation TPs. Three TPs of photolysis called
PH1, PH2, and PH3 were observed. PH1 was the most abundant,
and it was identified as an unchlorinated product of DCF. PH2
was suggested to be chloro analog of PH1. Both of them were
observed as the initial TPs of photolysis. PH1 was identified as
methyl esters of carbazole-1-acetic acid, and PH2 was 8-chloro
derivative of PH1. The chemical structure of PH3 was not
identified. Scheurell et al. [72] studied DCF and its several TPs
in two river waters. The TPs detected in the samples were
reported as new in the literature in the year 2009 namely 8-
chlorocarbazole-1-yl-ethanoic
acid
at
0.08-0.3
µg/L
concentration. The others were the product of photolysis as 3’-
OH-DCF, 4’-OH-DCF, 5-OH-DCF and 1-(2,6-dichlorophenyl)-1,3-
dihydro-2H-indole-2-one with the concentrations of, 0.03-0.4
µg/L, 0.4-1.8 µg/L, 0.01-0.3 µg/L and 0.02-0.2 µg/L,
respectively. transformation of DCF to D2 was the main degradation
mechanism, and TPs other than D2 were transformed into
other unknown compounds. Iovino et al. [19] carried out DCF
photodegradation experiments under UV-light at 254 nm
wavelength. The concentration of DCF was 20 mg/L, and over
98% removal of DCF was observed after 5 min UV treatment. A
very stable and colored dimer carbazole formed at the end of
the reaction. This product was named carbazole-1-acetic acid. However, further photolysis of dimer carbazole showed that
this TP was persistent under UV treatment. 6.3.1 Biodegradation of diclofenac by isolated and mixed
cultures Biodegradation of DCF is generally low (<50%) in conventional
wastewater treatment systems due to mainly resistance of DCF
to biological degradation and also limited survival of the
microbial community in the DCF containing water [26],[94]. Therefore, the isolation of bacterial strains that are capable of
biodegrading DCF ultimately is a real challenge. A bacterial
strain Raoultella sp KDF8 isolated from contaminated soil was
able to degrade 91% of DCF. This removal efficiency was
achieved within 72 h at 28 ℃, pH 7, and 1 g/L DCF
concentration. The end product identified after degradation
was 4’-OH-DCF [26]. Labrys portucalensis F11 is another
isolated bacterial strain used for DCF degradation. The results
showed that the removal of 70% of DCF was achievable when
DCF was the sole carbon source. On the other hand, if co-
substrate such as acetate was supplied to the isolate, DCF was
removed entirely within six days and 25 days of batch
cultivation for DCF concentrations 1.7 and 34 µM, respectively. Two main metabolites, namely 4’-OH-DCF and 5-OH-DCF
produced nine other intermediate metabolites formed through
hydroxylation, methylation, decarboxylation, and oxidation
reactions. The metabolites accumulated when there was no co-
substrate. In the case of acetate addition, the metabolite
generation was faster, but they were further degraded without
accumulating in the media [25]. Nitratireductor, Asticcacaulis,
and Pseudoxanthomonas were observed in fed-batch operated
activated sludge exposed to 50-5000 µg/L DCF [94]. The
removal of DCF by abiotic reactions was defined as hydrolysis,
volatilization, photolysis, and adsorption with the removal
efficiencies of 2.3 %, 2.5%, 3.2 %, 6.5%, respectively, while
biodegradation was about 21.3%. The depth of surface water can affect the photochemical
reaction. The deeper the water, the slower the reaction. Bartels
and Tümpling Jr. [22] examined the effects of surface depth by
determining the relative fluence rate (photosynthetically active
radiation [PAR]). The results showed decreased relative
fluence rate with increasing depth. The identification of end products through photolysis of DCF
was studied under direct UV light. The reported end products
of DCF through photodegradation could vary depending on the
reaction condition. Buser et al. [31] stated that DCF showed
affinity toward direct photolysis. This behavior was explained
as the UV spectrum of DCF shows high-intensity adsorption at
275 nm to >290 nm. Roscher et al. [20] observed that although
DCF disappears in 3 minutes, eleven different possible TPs
formed
similar
to
DCF
in
structure. 6.2
Photodegradation and transformation products Semi-laboratory
and field experiment carried out for the photodegradation of
[22] resulted in three new UV-decomposition products, namely
2-chloroaniline, 2,6-dichlorophenol, and 2,6-dichloroaniline
beside
to
other
four
products
2-Chloro-
and
2,6-
Dichlorodiphenylamine derivatives, and 8-Hydroxy- and 8-
Chlorocarbazole derivatives [21],[93]. 6.3.1 Biodegradation of diclofenac by isolated and mixed
cultures DCF degradation by white-rot fungus Phanerochaete
sordida YK-624 was studied by Hata et al. [27] and 90% of DCF
was removed within three days, and then complete degradation
was achieved in 6 days. Three different metabolites, namely, 4'-
OH-DCF, 5'-OH-DCF and, 4',5-diOH-DCF were observed, and 4’-
OH-DCF was the major one. Another well-known white-rot
fungi, Trametes versicolor, was used for degradation of DCF by
Marco-Urrea et al. [28]. The metabolites 4’-OH-DCF and 5-OH-
DCF formed disappeared after 24 hr [28]. White-rot fungi could be very talented in the degradation of
recalcitrant substances. However, the organism's behavior in
real wastewater, in the presence of other microorganisms with
different optimal growth conditions and growth requirements,
could be a limitation in the degradation ability of WFR. Yang et
al. [106] investigated the use of bacteria and WRF T. versicolor
ATCC 7731 to degrade DCF in a membrane bioreactor (MBR). It
was observed that the removal efficiency in the presence of
bacteria is lower than that of T. versicolor alone. The low
removal in the co-culture was explained as the bacterial
damage on fungal mycelium or enzymes, inactivation of
ligninolytic enzymes, and competition between bacteria and
fungi for organic substance resulting in inhibition on the fungal
degradation. The TPs of DCF from various degradation
processes were summarized in Table 5 and the chemical
structures of metabolites and transformation products are
given in Table S1. Barbieri et al. [97] focused on the especially anoxic condition or
denitrification in groundwater to emphasize the danger of this
pollutant and its TPs in the natural water resources. The batch
anoxic degradation test resulted in DCF removal, initially, but
then the recovery of DCF to its initial concentration at the end
of the reaction. In comparison to the most common TP, nitro-
DCF was the main TP under anoxic conditions. The DCF
disappearance and TP formation were directly related to the
presence of nitrate. The conversion of nitrite to nitrogen
resulted in the recovery of DCF concentration. There are a limited number of studies about the anaerobic
degradation of DCF and its TPs. Photodegradation is the initial
step of DCF degradation. Anaerobic conditions are light-free
media, and therefore, the initial degradation can not be
achieved, which makes the anaerobic removal of DCF more
difficult. 6.3.1 Biodegradation of diclofenac by isolated and mixed
cultures The relationship of DCF and DP1 was inversely
proportional, indicating that DP1 was an intermediate TP of
DCF directly. DP3, identified as C14H10NOCl2, was reported as
the other biodegradation TP, although it may form through
thermal decomposition of DCF or due to free OH radicals. Other
identified TPs were DP4 and DP7 formed as a result of
dehydrogenation. They had the same molecular weight, and it
was reported as isomers with the proposed chemical structure
of C13H10NCl2. The TPs DP2, DP5, and DP6 were not identified
due to their low concentration and weak fragmentation
patterns [95]. Poirier-Larabie et al. [96] studied with the mixed
culture from an aerobic wastewater treatment plant. The
biodegradation rate was slow, and no degradation was
observed for 24 hours. After 14 days, three TPs were identified
as TP311 (C14H11Cl2NO3), TP265 (C13H9Cl2NO), and TP324,
which is nitroso-DCF. All three TPs stayed in the system for 57
days indicating that they are resistant to biodegradation. formed from DCF. Only four of the TPs were properly identified. DP1 (C14H11NO2Cl2) was found to be the product of only
biological degradation since there was no DP1 in the abiotic
control. The relationship of DCF and DP1 was inversely
proportional, indicating that DP1 was an intermediate TP of
DCF directly. DP3, identified as C14H10NOCl2, was reported as
the other biodegradation TP, although it may form through
thermal decomposition of DCF or due to free OH radicals. Other
identified TPs were DP4 and DP7 formed as a result of
dehydrogenation. They had the same molecular weight, and it
was reported as isomers with the proposed chemical structure
of C13H10NCl2. The TPs DP2, DP5, and DP6 were not identified
due to their low concentration and weak fragmentation
patterns [95]. Poirier-Larabie et al. [96] studied with the mixed
culture from an aerobic wastewater treatment plant. The
biodegradation rate was slow, and no degradation was
observed for 24 hours. After 14 days, three TPs were identified
as TP311 (C14H11Cl2NO3), TP265 (C13H9Cl2NO), and TP324,
which is nitroso-DCF. All three TPs stayed in the system for 57
days indicating that they are resistant to biodegradation. intracellular cytochrome P450 system, which takes place in the
oxidation of these recalcitrant substances [28]. The use of WRF
for the removal of pharmaceuticals from polluted water is
rather a new concept. It has been shown that they can degrade
ibuprofen, ketoprofen, carbamazepine, atenolol, etc. [107]-
[110]. 6.3.1 Biodegradation of diclofenac by isolated and mixed
cultures On the other hand, DCF sorption onto the sludge is
possible and anaerobic digestion (AD) of treatment sludges is
one of the most widely used sludge stabilization methods. Therefore, the fate of DCF under anaerobic conditions is a
research subject. Carballa et al. [35] studied the removal of DCF
in AD and discovered that DCF could be removed (80%) after
the sludge adaptation period, and there is no influence of sludge
retention time (SRT) and temperature on the removal of DCF. Lahti and Oikari [98] investigated the removal of DCF from
sewage treatment plant sludge under anaerobic conditions. The
reduction in DCF was only 26% after 161 days for the initial
concentration of 100 µg/L, and the degradation mechanism
was reported as mainly abiotic but not anaerobic. Poirier-
Larabie et al. [96] identified only TP324 (nitroso-DCF) under
anaerobic degradation. This TP was the common one
encountered under aerobic degradation. However, the
concentration
of
TP324
was
lower
under
anaerobic
degradation due to low DCF biodegradation efficiency by
anaerobic microorganisms. 6.3.1 Biodegradation of diclofenac by isolated and mixed
cultures The
complete
mineralization of DCF to CO2 and water through UV irradiation
wasn’t achieved. Dechlorination and oxygenation were
presented as the dominant mechanisms in TP formation. Aguera et al. [21] provided extensive research on the possible
photodecomposition pathway and TP formation reactions. The
most important pathway to initiate the phototransformation of
DCF is the photocyclization of DCF to carbazole derivatives
(C-1), which starts the other reactions that affect the alkyl-
chain. In the first route reported by Aguera et al. [21], chlorine
atom was the most common product. The replacement of
chlorine atom in the hydroxyl-group can occur, resulting in C-6
formation, namely 8-hydroxy-9,9a-dihydro-4 aH-carbazol-1-yl-
acetic acid, which is highly reactive and the precursor of dimer
formation. This route has been the focus of the research since
carbazole formation is linked to the phototoxicity of DCF. Route
2 is initiated with decarboxylation of DCF (C-8) and oxidation
of the alkyl-chain (C-9 to C-13). The compounds in this pathway
showed persistence under photolysis. The study with the mixed aerobic bacterial culture was
conducted by Jewell et al. [29] for DCF degradation. DCF-lactam,
4’-OH-DCF, 5-OH-DCF, and DCF-benzoic acid were the main
metabolites. The secondary metabolites were formed from
these main ones. For example, 4’-OH-DCF had six TPs that
disappeared during treatment, meaning that they were either
entirely oxidized to CO2 or transformed to other tertiary
products. On the other hand, 5-OH-DCF produced nine
identified TPs in which some of them were intermediates
leading to unidentified other TPs. DCF-lactam was transformed
into 4’-OH-DCF-quinone imine and DCF-benzoic acid. Another
aerobic DCF degradation study by mixed culture was carried
out by Kosjek et al. [95]. The study showed seven TPs that Salgado et al. [23] reported four different TPs which were more
polar than DCF and two new products formed through
dechlorination, hydroxylation, oxygenation, decarboxylation
reactions. Carbazol formation was observed in some end
products. However, extending the UV irradiation up to 20 min
provided the disappearance of all products apart from the end
product
(E)-6-[2,6-dichlorophenyl)-imino]-3-oxocyclohexa-
1,4-dienecarbaldehyde
(D2). It
was
stated
that
the 943 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar formed from DCF. Only four of the TPs were properly identified. DP1 (C14H11NO2Cl2) was found to be the product of only
biological degradation since there was no DP1 in the abiotic
control. 6.3.2 The
effects
of
wastewater
treatment
plant
operation conditions in diclofenac removal and
metabolite formation Biological WWTPs are mainly designed to remove conventional
organic pollutants and nutrients. However, it has been realized
that the micropollutants end up in biological wastewater
treatment plants where they have to be removed. Many
researchers are investigating the removal of DCF and its
degradation products since these pollutants have become an
emerging concern for the environment. The reported studies
showed that the removal of DCF varies widely from no
reduction (0%) to 75% as given in Table 2. The wide range of
treatment efficiency can be explained by the operating
conditions employed in the process. DCF removal under
anaerobic-aerobic or anoxic conditions, the relationship
between SRT or hydraulic retention time (HRT) and
environmental conditions such as temperature can affect the
DCF removal. Therefore, it is crucial to define the role of process
conditions in the biodegradation of DCF and its TP. SRT is one of the factors that affect the treatment performance
of a suspended growth wastewater treatment systems. The
effect of SRT on DCF removal is not apparent. Jelic et al. [15]
stated that SRT has no influence on removing DCF in plants with
only secondary treatment. Instead, WWTP with tertiary
treatment including microfiltration and chlorination resulted in
60% DCF removal. Anumol et al. [57] drew the same conclusion
as Jelic et al. [15] that chlorination after secondary treatment
significantly improved the reduction. It was also observed that
aerated lagoon before secondary treatment could help the
degradation [57]. The other microorganism with its well-known ability in the
degradation of recalcitrant substances is white-rot fungi
(WRF). They have been widely used for the degradation of
textile dyestuff [99]-[101], PAH [102]-[104], and the other
several pollutants such as BPA, 17-β-estradiol, ethinylestradiol
[105],[106]. White-rot fungi can produce high redox potential
peroxidases (lignin peroxidase, manganese peroxidase, and
versatile peroxidase) and laccase, which are capable of
oxidizing a wide variety of pollutants. They have an 944 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Table 5. DCF metabolites and TPs from different degradation
processes. Process
Metabolites and TPs
Ref. 6.3.2 The
effects
of
wastewater
treatment
plant
operation conditions in diclofenac removal and
metabolite formation Human
4’-hydroxydiclofenac,
5-hydroxydiclofenac,
4’,5-dihydroxydiclofenac,
3’-hydroxydiclofenac,
3’-hydroxy-4’-methoxydiclofenac
[18],[84],
[86],[88]
Photodegradation
2-(8-hydroxy-3-oxo-3H-carbazol-1-
yl)acetic acid
(E)-6-[2,6-dichlorophenyl)-imino]-
3-oxocyclohexa-1,4-
dienecarbaldehyde)
2-(8-hydroxy-3-oxo-9,9a-dihydro-
3H-carbazol-1-yl)acetic acid
(E)-2-[3-(2,6-dichloro-?-
hydroxyphenylimino)-6-
oxocyclohexa-1,4-dienyl]acetic acid
2-[2-(phenylamino]phenyl)acetic
acid
2-(8-chloro-9H-carbazol-1-yl)acetic
acid
[23]
PH1: methyl esters of carbazole-1-
acetic acid
PH2: 8-chloro derivative of
carbazole-1-acetic acid
PH3: unknown
[31]
carbazole-1-acetic acid. [19]
2-chloroaniline
2,6-dichloroaniline
2,6-dichlorophenol
1-(2,6-dichlorophenyl)indolin-2-one
2-(2-
chlorophenylamino)benzaldehyde
2,6-dichloro-N-o-tolybenzenamine
9H-carbazole-1-carbaldehyde
8-chloro-9H-carbazole-1-
carbaldehyde
2-(2,6-
dichlorophenylamino)benzaldehyde
[22]
8-chlorocarbazole-1-yl-ethanoic
acid
3’-hydroxydiclofenac,
4’-hydroxydiclofenac,
5-hydroxydiclofenac
1-(2,6-dichlorophenyl)-1,3-dihydro-
2H-indole-2-one
[72]
Biodegradation
4’-hydroxydiclofenac
[26]
Raoultella sp KDF8
Labrys portucalensis
F11
4’-hydroxydiclofenac
5-hydroxydiclofenac
[25]
Mixed culture-
Aerobic
DCF-lactam,
4’-hydroxydiclofenac
5-hydroxydiclofenac
DCF-benzoic acid
[29]
C14H11NO2Cl2
1-(2,6-dichlorophenyl)-1,3-dihydro-
2H-indol-2-one
Contains structural fragment “2,6-
dichloro-N-(phenyl)aniline”
[95]
Phanerochaete
sordida YK-624
4’-hydroxydiclofenac
5-hydroxydiclofenac
4’,5-dihydroxydiclofenac
[27]
Trametes versicolor
4’-hydroxydiclofenac
5-hydroxydiclofenac
[28]
WWTPs
4’-hydroxydiclofenac
5-hydroxydiclofenac
carboxydiclofenac (C-DCF)
[16]
4’-hydroxydiclofenac
DCF-lactam
[111]
Anoxic
Nitro-Diclofenac (NO2-DCF)
[97]
Tran and Gin [58] emphasized that higher biomass
concentration, longer SRT, and better adsorption ability of
sludge could be the reason for better removal of DCF in high
biomass holding process such as membrane bioreactor (MBR) Table 5. DCF metabolites and TPs from different degradation
processes. was also concluded that one of the other reasons for low DCF
removal is the absence of electron-donating groups in DCF. Clara et al. [63] investigated the effect of SRT on DCF removal
efficiency in three different conventional activated sludge
wastewater treatment plants. A pilot-scale membrane reactor
was installed in one of the WWTPs. No DCF removal was
observed in two conventional WWTPs operated at SRT=2 days
and SRT=46 days. MBR reactor had a positive effect on DCF
removal in the system. Complete removal of DCF was achieved
in MBR at SRT=10 days and HRT=0.5 days. The contribution of
conventional WWTP removed about 50% of DCF. Increasing
SRT to 27 days resulted in 50% DCF removal in MBR and 20%
in WWTP with a total removal efficiency of 70%. Extending SRT
and HRT in MBR to 55 days and four days, respectively, did not
provide further improvement in DCF for the total of the system. The mechanism of DCF removal in this two-stage combined
system was not clearly explained. But, the operation
temperature was almost ideal (16.8- 22.1 ℃) for the biological
activity when 50% and 70% removal efficiency was obtained. Besides, long SRT combined with high temperature was
explained as the reason for improved removal efficiency [63]. Suarez et al. [24] studied the removal of DCF in a full-scale
WWTP working under sequential denitrifying and nitrifying
conditions. 7 Conclusions The studies on DCF reveals that DCF threatens ecological
balance. Photolysis through direct and indirect UV initiates the
DCF destruction, and biodegradation depends on the microbial
cultures, environmental conditions, and WWTPs operation. Photolysis or biological DCF degradation mechanisms end up
with the TPs, which need further treatment. The wastewater
treatment plants are insufficient for the complete removal of
DCF. The degradation of DCF by pure culture could give an idea
about the TPs, degradation rates, or environmental conditions
required. Nevertheless, the real wastewater conditions could
be different due to inhibitors, readily biodegradable
substances, or other toxic non-biodegradable ones in the water. Therefore, monitoring studies in WWTP should be conducted
to understand the nature of degradation or transformation
mechanisms in real conditions. The formation of various TPs
and the lack of information about their ecotoxicological effects
are the problems. Therefore, the transformation of DCF in a full-
scale wastewater treatment plant should be questioned in
detail to protect the natural water bodies. Larsson et al. [16] monitored DCF with its TPs, 4'-OH-DCF, 5-
OH-DCF, and carboxydiclofenac (C-DCF) in a full-scale WWTP
included primary treatment, conventional activated sludge,
pre-denitrification, and phosphate precipitation with ferric
chloride. The influent wastewater contained DCF itself as well
as human metabolites as 4'-OH-DCF, 5-OH-DCF, and C-DCF. Primary treatment provided only 8-20% DCF and metabolite
removal with only 1% adsorption on primary sludge. Secondary treatment resulted in 40% to 90% removal of DCF
and its metabolites with 5 to 10 % adsorption on biological
sludge. The tertiary treatment employed for phosphorus
removal did not reduce the concentrations further. It was
concluded that the secondary treatment is efficient enough for
DCF and metabolites removal. The low amounts of metabolites
detected in the effluent suggested that they are quickly
transformed even if they are formed in biological treatment
[16]. Further research about DCF can be addressed as follows; rther research about DCF can be addressed as follows;
The toxicity of the DCF metabolites can be
investigated, Lindholm-Lehto et al. [65] touched upon a subject that might
answer why there are negative removals of DCF in the
literature. It was stated that DCF is excreted as conjugates,
which can deconjugate to the parent compound later in the
treatment system, causing higher DCF concentration in the
effluent than in the influent. This phenomenon occurs in the
summertime, so no removal is obtained. 8 Author contribution statements In the scope of this study, Serenay Ceren TUZUN and Ilgi
KARAPINAR, in the formation of the idea, literature review,
writing and editing the article, were contributed. 6.3.2 The
effects
of
wastewater
treatment
plant
operation conditions in diclofenac removal and
metabolite formation DCF removal at the denitrification unit was only 2%,
suggesting
resistance
to
biodegradation
under
anoxic
conditions. The nitrification unit provided an increase in the
removal efficiency from 0% to 25%, which was explained as the
initial adaptation (~170 d) with the washout of heterotrophic
organisms. Further increase in the removal efficiency to 74%
was explained as the full adaptation of microorganisms in
relation to SRT and temperature. In another study conducted
by Suarez et al. [112] in the single sludge denitrification and
nitrification process, the removal of DCF was below 20%, which
was explained by the long half-life of DCF. The biological
degradation of DCF was determined as pseudo-first-order with
degradation constant below 0.1 L.g/SS.d. The half-life of DCF in
a plant with a biomass concentration of 2-4 g/L was calculated
as 2-3.5 d, from which it was concluded that only WWTPs with
high HRT (in the order of days) could achieve biodegradation of
DCF to some extend. It is evident that DCF is biotransformed to other products that
may not be degraded further in WWTP, and then they are
directly discharged into surface waters. The biotransformation
of DCF is initiated by cytochrome P450 (CYP2C9) oxidation to
hydroxylated metabolites, mainly 4'-OH-DCF, 5-OH-DCF and
DCF-lactam
[28],[29],[113]. Some
researchers
have
investigated the metabolite types and their concentrations in
existing full-scale wastewater treatment plants. Jewell et al. [29] monitored a domestic wastewater treatment plant in a
three-stage process as denitrification (anoxic), aerobic, and
nitrification with high aeration and hybrid moving bed
bioreactor (MBBR) to evaluate DCF removal and degradation
products. DCF-lactam was the most dominant metabolite
encountered in the process. The human metabolites such as 4’-
OH-DCF and 5-OH-DCF were detected in WWTP influent, but
not in the effluent due to probably fast transformation. No
evidence for the formation of these TPs during the treatment
process was observed. DCF-BA concentration was 23±8 ng/L in
WWTP effluent, although it was not detected in the influent,
showing that it formed at a low fraction. The major reactions in
DCF
removal
were
explained
as
hydroxylation,
decarboxylation, oxidation amide formation, ring-opening, and
reductive dechlorination. The DCF removal was mainly 945 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar achieved in MBBR [29]. Schmidt et al. 6.3.2 The
effects
of
wastewater
treatment
plant
operation conditions in diclofenac removal and
metabolite formation [111] monitored the
concentrations of DCF and its metabolites 4’-OH-DCF and DCF-
lactam in water samples taken from two Berlin WWTPs and a
canal receiving wastewater. No DCF removal was observed in
one of the WWTPs while it was around 50% in the other. A
slight increase in the metabolite concentration of both WWTP
effluent occurred. DCF-lactam concentration was below LOD
while it was 1 ng/L in WWTP effluents, although there was no
DCF removal in one of them. Interestingly, lower DCF and
metabolite concentrations were detected in the effluent
receiving water. benzotriazole (6122 ng/g TS), carbamazepine (2106 ng/g TS),
DCF (1935 ng/g TS), and heavy metal iron (18.9 mg/g TS). The
dewatered sludge was unlikely to create an acute toxicity
response, while S1 could harm soil invertebrates and
freshwater organisms (plants and crustacean). Kummerova et
al. [115] reported the impact of DCF on a duckweed plant,
Lemna minor. The results indicated that the environmentally
relevant concentrations of DCF could affect the plant's
biochemical process by producing reactive oxygen species
(ROS) and reactive nitrogen species. The production of these
species created different effects such as increased lipid
peroxidation, loss of plasma membrane integrity, etc. Another study was conducted by Kolecka et al. [64] in a WWTP
with nitrification and denitrification units. The effluent DCF
concentration was either higher or lower than the influent one
depending
on
the
sampling
time
and
wastewater
characteristics. On the other hand, the most common
metabolites 5-OH-DCF and 4’-OH-DCF were removed in the
WWTP. The maximum efficiencies were 40.6% for DCF and
between 58.6-78.6% for the metabolites. 7 Conclusions In the wintertime, DCF
consumption increases, but the deconjugation reduces due to
low temperature. Lower effluent DCF concentration can be
observed with limited removal efficiency. Moreover, photolysis
is an important elimination mechanism of DCF. Therefore, the
decreased UV light in winter could influence the removal as
well [65]. Finally, Lindqvist et al. [66] explained that industrial
wastewater entering the system could have toxic effects on the
biomass resulting in lower efficiencies.
The degradation pathway can be studied in detail,
Veterinary sources and the DCF concentrations can be
monitored,
DCF disposal through unused pills and its fate in solid
waste disposal areas or landfills can be monitored.
The fate and degradation of DCF in leachate can be
studied. 10 References [1]
Acuña V, Ginebreda A, Mor JR, Petrovic M, Sabater S,
Sumpter J, Barceló D. "Balancing the health benefits and
environmental risks of pharmaceuticals: Diclofenac as an
example". Environment International, 85(12), 327-333,
2015. [14] de Barros ALC, Schmidt FF, de Aquino SF, Afonso R. "Determination of nine pharmaceutical active compounds
in surface waters from Paraopeba River Basin in Brazil by
LTPE-HPLC-ESI-MS/MS". Environmental Science Pollution
Research, 25(20), 19962-19974, 2018. [2]
de Voogt P, Janex-Habibi ML, Sacher F, Puijker L, Mons M. "Development
of
a
common
priority
list
of
pharmaceuticals
relevant
for
the
water
cycle". Water Science and Technology, 59(1), 39-46, 2009. [15] Jelic A, Gros M, Ginebreda A, Cespedes-Sánchez R, Ventura
F, Petrovic M, Barcelo D. "Occurrence, partition and
removal of pharmaceuticals in sewage water and sludge
during
wastewater
treatment". Water
Research,
45(3), 1165-1176, 2011. [3]
Green RE, Newton IAN, Shultz S, Cunningham AA, Gilbert
M, Pain DJ, Prakash V. "Diclofenac poisoning as a cause of
vulture
population
declines
across
the
Indian
subcontinent". Journal of Applied Ecology, 41(5), 793-800,
2004. [16] Larsson E, Al-Hamimi S, Jonsson JA. "Behaviour of
nonsteroidal anti-inflammatory drugs and eight of their
metabolites during wastewater treatment studied by
hollow fibre liquid phase microextraction and liquid
chromatography mass spectrometry". Science of the Total
Environment, 485-486(13), 300-308, 2014. [4]
McRae NK, Glover CN, Burket SR, Brooks BW, Gaw S. "Acute
exposure
to
an
environmentally
relevant
concentration of diclofenac elicits oxidative stress in the
culturally important galaxiid fish Galaxias maculatus". Environmental Toxicology and Chemistry, 37(1), 224-235,
2018. [17] Bort R, Macé K, Boobis A, Gómez-Lechón Ma-J, Pfeifer A,
Castell J. "Hepatic metabolism of diclofenac: role of human
CYP in the minor oxidative pathways". Biochemical
Pharmacology, 58(5), 787-796, 1999. [5]
Oaks JL, Gilbert M, Virani MZ, Watson RT, Meteyer CU,
Rideout BA, Shivaprasad HL, Ahmed S, Iqbal Chaudhry MJ,
Arshad M, Mahmood S, Ali A, Ahmed Khan A. "Diclofenac
residues as the cause of vulture population decline in
Pakistan". Nature, 427(1), 630-633, 2004. [18] Stülten D, Zühlke S, Lamshöft M, Spiteller M. "Occurrence
of diclofenac and selected metabolites in sewage
effluents". Science
of
the
Total
Environment,
405(1), 310-316, 2008. [6]
Schwaiger J, Ferling H, Mallow U, Wintermayr H, Negele
RD. "Toxic effects of the non-steroidal anti-inflammatory
drug diclofenac. Part I: histopathological alterations and
bioaccumulation in rainbow trout". Aquatic Toxicology,
68(2), 141-150, 2004. [19] Iovino P, Chianese S, Canzano S, Prisciandaro M,
Musmarra D. "Photodegradation of diclofenac in
wastewaters". 6.4
Diclofenac in soil and wastewater treatment sludges Wastewater treatment sludge can be used for energy
production, fertilizer, or soil conditioner. It is declared that
53% of sludge produced in the European Union is used in
agriculture directly or after composting [114]. However, heavy
metals and other organic pollutants such as pharmaceuticals on
sludge make its application to soil very dangerous due to its
possible toxic effects on biota. Rastetter and Gerhardt [49]
studied the toxicity of non-dewatered bio-P sludge (S1) and
dewatered sludges (S2 and S3). The results showed that S1 was
more toxic than S2 and S3 due to the high concentrations of There is no need to obtain permission from the ethics
committee for the article prepared. There is no conflict of interest with any person/institution in
the article prepared. 946 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar [13] Ali AM, Rønning HT, Alarif W, Kallenborn R, Al-Lihaibi SS. "Occurrence of pharmaceuticals and personal care
products in effluent-dominated Saudi Arabian coastal
waters of the Red Sea". Chemosphere, 175(10), 505-513,
2017. 10 References [32] Lonappan L, Brar SK, Das RK, Verma M, Surampalli RY. "Diclofenac
and
its
transformation
products:
Environmental occurrence and toxicity-A review". Environment International, 96(9), 127-138, 2016. [33] Zhang Y, Geissen SU, Gal C. "Carbamazepine and
diclofenac: removal in wastewater treatment plants and
occurrence
in
water
bodies". Chemosphere,
73(8), 1151-1161, 2008. [48] Patel M, Kumar R, Kishor K, Mlsna T, Pittman CU, Mohan
D. "Pharmaceuticals of emerging concern in aquatic
systems: chemistry, occurrence, effects, and removal
methods". Chemical Reviews, 119(6), 3510-3673, 2019. [34] Vieno N, Sillanpää M. "Fate of diclofenac in municipal
wastewater treatment plant-a review". Environment
International, 69(8), 28-39, 2014. [49] Rastetter N, Gerhardt A. "Toxic potential of different types
of
sewage
sludge
as
fertiliser
in
agriculture:
ecotoxicological effects on aquatic, sediment and soil
indicator species". Journal of Soils and Sediments,
17(1), 106-121, 2017. [35] Carballa M, Fink G, Omil F, Lema JM, Ternes T. "Determination of the solid–water distribution coefficient
(Kd) for pharmaceuticals, estrogens and musk fragrances
in digested sludge". Water Research, 42(1), 287-295,
2008. [50] Heberer T, Feldmann D. "Contribution of effluents from
hospitals and private households to the total loads of
diclofenac and carbamazepine in municipal sewage
effluents--modeling versus measurements". Journal of
Hazardous Materials, 122(3), 211-218, 2005. [36] Altman R, Bosch B, Brune K, Patrignani P, Young C. "Advances in NSAID development: evolution of diclofenac
products
using
pharmaceutical
technology". Drugs, 75(8), 859-877, 2015. [51] Yang Y, Fu J, Peng H, Hou L, Liu M, Zhou JL. "Occurrence
and phase distribution of selected pharmaceuticals in the
Yangtze Estuary and its coastal zone". Journal of
Hazardous Materials, 190(1), 588-596, 2011. [37] Meylan WM, Howard PH. "Computer estimation of the
Atmospheric
gas-phase
reaction
rate
of
organic
compounds
with
hydroxyl
radicals
and
ozone". Chemosphere, 26(12), 2293-2299, 1993. [52] Lee H-B, Peart TE, Svoboda ML. "Determination of
endocrine-disrupting phenols, acidic pharmaceuticals,
and personal-care products in sewage by solid-phase
extraction and gas chromatography–mass spectrometry". Journal of Chromatography A, 1094(1), 122-129, 2005. [38] Tixier C, Singer HP, Oellers S, Muller SR. "Occurrence and
fate
of
carbamazepine,
clofibric
acid,
diclofenac,
ibuprofen, ketoprofen, and naproxen in surface waters". Environmental Science and Technology, 37(6), 1061-1068,
2003. [53] Rivera-Jaimes JA, Postigo C, Melgoza-Aleman RM, Acena J,
Barcelo D, Lopez de Alda M. "Study of pharmaceuticals in
surface and wastewater from Cuernavaca, Morelos,
Mexico: Occurrence and environmental risk assessment". Science of the Total Environment, 613-614(3), 1263-1274,
2018. [39] Zou H, Radke M, Kierkegaard A, McLachlan MS. 10 References 947 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar [26] Palyzova A, Zahradnik J, Maresova H, Sokolova L,
Kyslikova E, Grulich M, Stepanek V, Rezanka T, Kyslik P. "Potential of the strain Raoultella sp. KDF8 for removal of
analgesics". Folia Microbiologica, 63(3), 273-282, 2018. [41] Poiger T, Buser H-R, Müller MD. "Photodegradation of the
pharmaceutical drug diclofenac in a lake: Pathway, field
measurements,
and
mathematical
modeling". Environmental Toxicology and Chemistry, 20(2), 256-263,
2001. [27] Hata T, Kawai S, Okamura H, Nishida T. "Removal of
diclofenac and mefenamic acid by the white rot fungus
Phanerochaete sordida YK-624 and identification of their
metabolites after fungal transformation". Biodegradation,
21(5), 681-689, 2010. [42] Xu J, Wu L, Chang AC. "Degradation and adsorption of
selected pharmaceuticals and personal care products
(PPCPs)
in
agricultural
soils". Chemosphere,
77(10), 1299-1305, 2009. [43] Radke M, Ulrich H, Wurm C, Kunkel U. "Dynamics and
Attenuation of Acidic Pharmaceuticals along a River
Stretch". Environmental
Science
&
Technology,
44(8), 2968-2974, 2010. [28] Marco-Urrea E, Perez-Trujillo M, Cruz-Morato C, Caminal
G, Vicent T. "Degradation of the drug sodium diclofenac by
Trametes versicolor pellets and identification of some
intermediates by NMR". Journal of Hazardous Materials,
176(1-3), 836-842, 2010. ( )
[44] Huschek G, Hansen PD, Maurer HH, Krengel D, Kayser A. "Environmental risk assessment of medicinal products
for human use according to European Commission
recommendations". Environmental
Toxicology,
19(3), 226-240, 2004. [29] Jewell KS, Falas P, Wick A, Joss A, Ternes TA. "Transformation of diclofenac in hybrid biofilm-activated
sludge processes". Water Research, 105(18), 559-567,
2016. [30] Zou H, Radke M, Kierkegaard A, MacLeod M, McLachlan
MS. "Using chemical benchmarking to determine the
persistence
of
chemicals
in
a
swedish
lake". Environmental Science & Technology, 49(3), 1646-1653,
2015. [45] Ferrari Bt, Paxéus N, Giudice RL, Pollio A, Garric J. "Ecotoxicological impact of pharmaceuticals found in
treated wastewaters: study of carbamazepine, clofibric
acid, and diclofenac". Ecotoxicology and Environmental
Safety, 55(3), 359-370, 2003. [31] Buser H-R, Poiger T, Müller MD. "Occurrence and fate of
the pharmaceutical drug diclofenac in surface waters:
rapid photodegradation in a lake". Environmental Science
& Technology, 32(22), 3449-3456, 1998. [46] Jones
OAH,
Voulvoulis
N,
Lester
JN. "Aquatic
environmental assessment of the top 25 English
prescription
pharmaceuticals". Water
Research,
36(20), 5013-5022, 2002. (
)
[47] Bound Jonathan P, Voulvoulis N. "Household disposal of
pharmaceuticals as a pathway for aquatic contamination
in
the
United
Kingdom". Environmental
Health
Perspectives, 113(12), 1705-1711, 2005. 10 References Desalination
and
Water
Treatment,
61(3), 293-297, 2017. [7]
Gonzalez-Rey M, Bebianno MJ. "Effects of non-steroidal
anti-inflammatory drug (NSAID) diclofenac exposure in
mussel Mytilus galloprovincialis". Aquatic Toxicology,
148(3), 221-230, 2014. [20] Roscher J, Vogel M, Karst U. "Identification of ultraviolet
transformation products of diclofenac by means of liquid
chromatography and mass spectrometry". Journal of
Chromatography A, 1457(31), 59-65, 2016. [8]
Hong HN, Kim HN, Park KS, Lee S-K, Gu MB. "Analysis of
the effects diclofenac has on Japanese medaka (Oryzias
latipes)
using
real-time
PCR". Chemosphere,
67(11), 2115-2121, 2007. [21] Aguera A, Perez Estrada LA, Ferrer I, Thurman EM, Malato
S, Fernandez-Alba AR. "Application of time-of-flight mass
spectrometry to the analysis of phototransformation
products of diclofenac in water under natural sunlight". Journal of Mass Spectrometry, 40(7), 908-915, 2005. [9]
Madikizela LM, Chimuka L. "Occurrence of naproxen,
ibuprofen, and diclofenac residues in wastewater and
river water of KwaZulu-Natal Province in South Africa". Environmental
Monitoring
and
Assessment,
189(7), 348-359, 2017. [22] Bartels P, von Tümpling W. "Solar radiation influence on
the decomposition process of diclofenac in surface
waters". Science
of
the
Total
Environment,
374(1), 143-155, 2007. [10] Tran NH, Reinhard M, Gin KY-H. "Occurrence and fate of
emerging
contaminants
in
municipal
wastewater
treatment plants from different geographical regions-a
review". Water Research, 133(6), 182-207, 2018. [23] Salgado R, Pereira VJ, Carvalho G, Soeiro R, Gaffney V,
Almeida C, Vale Cardoso V, Ferreira E, Benoliel MJ, Ternes
TA, Oehmen A, Reis MA, Noronha JP. "Photodegradation
kinetics and transformation products of ketoprofen,
diclofenac and atenolol in pure water and treated
wastewater". Journal
of
Hazardous
Materials,
244-245(1), 516-527, 2013. [11] Yang YY, Liu WR, Liu YS, Zhao JL, Zhang QQ, Zhang M,
Zhang J-N, Jiang Y-X, Zhang L-J, Ying G-G. "Suitability of
pharmaceuticals and personal care products (PPCPs) and
artificial sweeteners (ASs) as wastewater indicators in the
Pearl River Delta, South China". Science of the Total
Environment, 590-591(14), 611-619, 2017. [24] Suarez S, Lema JM, Omil F. "Removal of pharmaceutical
and personal care products (PPCPs) under nitrifying and
denitrifying
conditions". Water
Research,
44(10), 3214-3224, 2010. [12] Agunbiade FO, Moodley B. "Occurrence and distribution
pattern of acidic pharmaceuticals in surface water,
wastewater, and sediment of the Msunduzi River,
Kwazulu-Natal, South Africa". Environmental Toxicology
and Chemistry, 35(1), 36-46, 2016. [25] Moreira IS, Bessa VS, Murgolo S, Piccirillo C, Mascolo G,
Castro PML. "Biodegradation of Diclofenac by the
bacterial strain Labrys portucalensis F11". Ecotoxicology
and Environment Safety, 152(6), 104-113, 2018. 10 References "Temporal
Variation of Chemical Persistence in a Swedish Lake
Assessed by Benchmarking". Environmental Science &
Technology, 49(16), 9881-9888, 2015. [40] Al-Rajab AJ, Sabourin L, Lapen DR, Topp E. "The non-
steroidal anti-inflammatory drug diclofenac is readily
biodegradable in agricultural soils". Science of the Total
Environment, 409(1), 78-82, 2010. 948 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar [66] Lindqvist N, Tuhkanen T, Kronberg L. "Occurrence of
acidic pharmaceuticals in raw and treated sewages and in
receiving waters". Water Research, 39(11), 2219-2228,
2005. [54] Yang Y, Ok YS, Kim K-H, Kwon EE, Tsang YF. "Occurrences
and removal of pharmaceuticals and personal care
products (PPCPs) in drinking water and water/sewage
treatment plants: A review". Science of the Total
Environment, 596-597(18), 303-320, 2017. [67] Vulliet
E,
Cren-Olivé
C,
Grenier-Loustalot
M-F. "Occurrence of pharmaceuticals and hormones in
drinking
water
treated
from
surface
waters". Environmental Chemistry Letters, 9(1), 103-114, 2011. [55] Sun Q, Li M, Ma C, Chen X, Xie X, Yu CP. "Seasonal and
spatial variations of PPCP occurrence, removal and mass
loading in three wastewater treatment plants located in
different
urbanization
areas
in
Xiamen,
China". Environmental Pollution, 208(1), 371-381, 2016. [68] Veras TB, Luiz Ribeiro de Paiva A, Duarte MMMB,
Napoleão DC, da Silva Pereira Cabral JJ. "Analysis of the
presence of anti-inflammatories drugs in surface water: A
case study in Beberibe river- PE, Brazil". Chemosphere,
222(9), 961-969, 2019. [56] Behera SK, Kim HW, Oh JE, Park HS. "Occurrence and
removal of antibiotics, hormones and several other
pharmaceuticals in wastewater treatment plants of the
largest industrial city of Korea". Science of the Total
Environment, 409(20), 4351-4360, 2011. [69] Nödler
K,
Voutsa
D,
Licha
T. "Polar
organic
micropollutants in the coastal environment of different
marine systems". Marine Pollution Bulletin, 85(1), 50-59,
2014. [57] Anumol T, Vijayanandan A, Park M, Philip L, Snyder SA. "Occurrence and fate of emerging trace organic chemicals
in wastewater plants in Chennai, India". Environment
International, 92-93(6), 33-42, 2016. [70] Korkmaz NE, Savun-Hekimoğlu B, Aksu A, Burak S, Caglar
NB. "Occurrence, sources and environmental risk
assessment of pharmaceuticals in the Sea of Marmara,
Turkey". Science of the Total Environment, 819(18), 1-13,
2022. [58] Tran NH, Gin KY. "Occurrence and removal of
pharmaceuticals, hormones, personal care products, and
endocrine disrupters in a full-scale water reclamation
plant". Science
of
the
Total
Environment,
599-600(20), 1503-1516, 2017. 10 References [71] Borecka M, Siedlewicz G, Haliński ŁP, Sikora K, Pazdro K,
Stepnowski P, Białk-Bielińska A. "Contamination of the
southern Baltic Sea waters by the residues of selected
pharmaceuticals: Method development and field studies". Marine Pollution Bulletin, 94(1), 62-71, 2015. [59] Osorio V, Imbert-Bouchard M, Zonja B, Abad JL, Perez S,
Barcelo D. "Simultaneous determination of diclofenac, its
human metabolites and microbial nitration/nitrosation
transformation products in wastewaters by liquid
chromatography/quadrupole-linear
ion
trap
mass
spectrometry". Journal
of
Chromatography
A,
1347(25), 63-71, 2014. [72] Scheurell M, Franke S, Shah RM, Huhnerfuss H. "Occurrence of diclofenac and its metabolites in surface
water and effluent samples from Karachi, Pakistan". Chemosphere, 77(6), 870-876, 2009. (
)
[60] Kosma CI, Lambropoulou DA, Albanis TA. "Investigation
of PPCPs in wastewater treatment plants in Greece:
Occurrence,
removal
and
environmental
risk
assessment". Science
of
the
Total
Environment,
466-467(1), 421-438, 2014. [73] Praveena SM, Shaifuddin SNM, Sukiman S, Nasir FAM,
Hanafi
Z,
Kamarudin
N,
Ismail
THT,
Aris
AZ. "Pharmaceuticals residues in selected tropical surface
water bodies from Selangor (Malaysia): Occurrence and
potential risk assessments". Science of the Total
Environment, 642(24), 230-240, 2018. [61] Sari S, Ozdemir G, Yangin-Gomec C, Zengin GE, Topuz E,
Aydin E, Pehlivanoglu-Mantas E, Okutman Tas D. "Seasonal variation of diclofenac concentration and its
relation with wastewater characteristics at two municipal
wastewater treatment plants in Turkey". Journal of
Hazardous Materials, 272, 155-164, 2014. [74] González-Alonso S, Merino LM, Esteban S, López de Alda
M, Barceló D, Durán JJ, López-Martínez J, Aceña J, Pérez S,
Mastroianni N, Silva A, Catalá M, Valcárcel Y. "Occurrence
of pharmaceutical, recreational and psychotropic drug
residues in surface water on the northern Antarctic
Peninsula
region". Environmental
Pollution,
229(11), 241-254, 2017. [62] Kasprzyk-Hordern B, Dinsdale RM, Guwy AJ. "The
removal of pharmaceuticals, personal care products,
endocrine disruptors and illicit drugs during wastewater
treatment and its impact on the quality of receiving
waters". Water Research, 43(2), 363-380, 2009. [75] Abu-Seida AM. "Efficacy of diclofenac sodium, either alone
or together with cefotaxime sodium, for control of
postoperative
pain,
in
dogs
undergoing
ovariohysterectomy". Asian Journal of Animal and
Veterinary Advances, 7(2), 180-186, 2012. [63] Clara M, Strenn B, Gans O, Martinez E, Kreuzinger N,
Kroiss
H. "Removal
of
selected
pharmaceuticals,
fragrances and endocrine disrupting compounds in a
membrane bioreactor and conventional wastewater
treatment plants". Water Research, 39(19), 4797-4807,
2005. [76] Camiña A, Aguilera J, Sarrazin F, Duriez O. "Potential
exposure to diclofenac in Spain of European vultures". 10 References "Commission
Implementing
Decision (EU) 2015/495 of 20 March 2015 establishing a
watch list of substances for Union-wide monitoring in the
field of water policy pursuant to Directive 2008/105/EC
of the European Parliament and of the Council (notified
under document C(2015) 1756) Text with EEA
relevance". http://data.europa.eu/eli/dec_impl/2015/495/oj
(08.03.2022). [95] Kosjek T, Heath E, Pérez S, Petrović M, Barceló D. "Metabolism studies of diclofenac and clofibric acid in
activated sludge bioreactors using liquid chromatography
with quadrupole-time-of-flight mass spectrometry". Journal of Hydrology, 372(1), 109-117, 2009. [96] Poirier-Larabie S, Segura PA, Gagnon C. "Degradation of
the pharmaceuticals diclofenac and sulfamethoxazole and
their
transformation
products
under
controlled
environmental
conditions". Science
of
the
Total
Environment, 557-558(15), 257-267, 2016. [84] Stierlin H, Faigle JW, Sallmann A, Kung W, Richter WJ,
Kriemler HP, Alt KO, Winkler T. "Biotransformation of
diclofenac sodium (Voltaren®) in animals and in man". Xenobiotica, 9(10), 601-610, 1979. [97] Barbieri M, Carrera J, Ayora C, Sanchez-Vila X, Licha T,
Nödler K, Osorio V, Pérez S, Köck-Schulmeyer M, López de
Alda M, Barceló D. "Formation of diclofenac and
sulfamethoxazole reversible transformation products in
aquifer material under denitrifying conditions: Batch
experiments". Science
of
the
Total
Environment,
426(11), 256-263, 2012. (
)
[85] Stülten D, Lamshoft M, Zuhlke S, Spiteller M. "Isolation
and characterization of a new human urinary metabolite
of diclofenac applying LC-NMR-MS and high-resolution
mass analyses". Journal of Pharmaceutical and Biomedical
Analysis, 47(2), 371-376, 2008. [98] Lahti M, Oikari A. "Microbial transformation of
pharmaceuticals naproxen, bisoprolol, and diclofenac in
aerobic and anaerobic environments". Archives of
Environment
Contamination
and
Toxicology,
61(2), 202-210, 2011. [86] Stierlin H, Faigle JW. "Biotransformation of diclofenac
sodium (Voltaren) in animals and in man. II. Quantitative
determination of the unchanged drug and principal
phenolic metabolites, in urine and bile". Xenobiotica,
9(10), 611-621, 1979. [87] Zhang Y, Han YH, Putluru SP, Matta MK, Kole P, Mandlekar
S, Furlong MT, Liu T, Iyer RA, Marathe P, Yang Z, Lai Y,
Rodrigues AD. "Diclofenac and Its Acyl Glucuronide:
Determination of In Vivo Exposure in Human Subjects and
Characterization as Human Drug Transporter Substrates
In
Vitro". Drug
Metabolism
and
Disposition,
44(3), 320-328, 2016. [99] Jayasinghe C, Imtiaj A, Lee GW, Im KH, Hur H, Lee MW,
Yang HS, Lee TS. "Degradation of three aromatic dyes by
white rot fungi and the production of ligninolytic
enzymes". Mycobiology, 36(2), 114-120, 2008. 10 References Vulture News, 75(2), 1-20, 2018. [77] Borghi SM, Fattori V, Ruiz-Miyazawa KW, Bertozzi MM,
Lourenco-Gonzalez Y, Tatakihara RI, Bussmann AJC,
Mazzuco TL, Casagrande R, Verri WA, Jr. "Pyrrolidine
dithiocarbamate inhibits mouse acute kidney injury
induced by diclofenac by targeting oxidative damage,
cytokines and NF-kappaB activity". Life Sciences,
208(17), 221-231, 2018. [64] Kołecka K, Gajewska M, Stepnowski P, Caban M. "Spatial
distribution
of
pharmaceuticals
in
conventional
wastewater treatment plant with Sludge Treatment Reed
Beds technology". Science of the Total Environment,
647(2), 149-157, 2019. [65] Lindholm-Lehto PC, Ahkola HS, Knuutinen JS, Herve SH. "Widespread occurrence and seasonal variation of
pharmaceuticals in surface waters and municipal
wastewater treatment plants in central Finland". Environmental
Science
Pollution
Research,
23(8), 7985-7997, 2016. (
)
[78] Eades C, Waring CP. "The effects of diclofenac on the
physiology of the green shore crab Carcinus maenas". Marine Environment Research, 69 (Supplement 1), 46-48,
2010. 949 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar [79] Bamber SD, Depledge MH. "Responses of shore crabs to
physiological challenges following exposure to selected
environmental
contaminants". Aquatic
Toxicology,
40(1), 79-92, 1997. [91] Sokół A, Borowska K, Karpińska J. "Investigating the
ınfluence of some environmental factors on the stability
of paracetamol, naproxen, and diclofenac in simulated
natural conditions". Polish Journal of Environmental
Studies, 26(1), 293-302, 2017. [80] Sonnenschein C, Soto A. "An updated review of
environmental estrogen and androgen mimics and
antagonists". The Journal of Steroid Biochemistry and
Molecular Biology, 65(1-6), 143-150, 1998. [92] Zhang
N,
Li
JM,
Liu
GG,
Chen
XL,
Jiang
K. "Photodegradation of diclofenac in aqueous solution by
simulated sunlight irradiation: kinetics, thermodynamics
and
pathways". Water
Science
and
Technology,
75(9), 2163-2170, 2017. [81] Gröner F, Höhne C, Kleiner W, Kloas W. "Chronic
diclofenac exposure affects gill integrity and pituitary
gene expression and displays estrogenic activity in nile
tilapia
(Oreochromis
niloticus)". Chemosphere,
166(1), 473-481, 2017. [93] Moore DE, Roberts-Thomson S, Zhen D, Duke CC. "Photochemical studies on the antiinflammatory drug
diclofenac". Photochemistry
and
Photobiology,
52(4), 685-690, 1990. [82] Klopčič I, Markovič T, Mlinarič-Raščan I, Sollner Dolenc M. "Endocrine disrupting activities and immunomodulatory
effects in lymphoblastoid cell lines of diclofenac, 4-
hydroxydiclofenac and paracetamol". Toxicology Letters,
294(13), 95-104, 2018. [94] Nguyen LN, Nghiem LD, Pramanik BK, Oh S. "Cometabolic
biotransformation and impacts of the anti-inflammatory
drug
diclofenac
on
activated
sludge
microbial
communities". Science
of
the
Total
Environment,
657(12), 739-745, 2019. (
)
[83] European
Commission. 10 References [100] McMullan G, Meehan C, Conneely A, Kirby N, Robinson T,
Nigam P, Banat I, Marchant R, Smyth W. "Microbial
decolourisation and degradation of textile dyes". Applied
Microbiology and Biotechnology, 56(1), 81-87, 2001. [88] Wiesenberg-Boettcher I, Pfeilschifter J, Schweizer A,
Sallmann A, Wenk P. "Pharmacological properties of five
diclofenac metabolites identified in human plasma". Agents Actions, 34(1-2), 135-137, 1991. [101] Swamy J, Ramsay JA. "The evaluation of white rot fungi in
the decoloration of textile dyes". Enzyme and Microbial
Technology, 24(3), 130-137, 1999. [102] Bhatt M, Cajthaml T, Šašek V. "Mycoremediation of PAH-
contaminated soil". Folia Microbiologica, 47(3), 255-258,
2002. [89] Wilkinson J, Hooda PS, Barker J, Barton S, Swinden J. "Occurrence, fate and transformation of emerging
contaminants in water: An overarching review of the
field". Environmental Pollution, 231(1), 954-970, 2017. [103] Field JA, de Jong E, Feijoo Costa G, de Bont JA. "Biodegradation of polycyclic aromatic hydrocarbons by
new
isolates
of
white
rot
fungi". Applied
and
Environmental Microbiology, 58(7), 2219-2226, 1992. [90] Zhang N, Liu G, Liu H, Wang Y, He Z, Wang G. "Diclofenac
photodegradation under simulated sunlight: Effect of
different forms of nitrogen and Kinetics". Journal of
Hazardous Materials, 192(1), 411-418, 2011. 950 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar [104] Zhang H, Zhang S, He F, Qin X, Zhang X, Yang Y. "Characterization of a manganese peroxidase from white-
rot fungus Trametes sp.48424 with strong ability of
degrading different types of dyes and polycyclic aromatic
hydrocarbons". Journal
of
Hazardous
Materials,
320(20), 265-277, 2016. [110] Rodarte-Morales AI, Feijoo G, Moreira MT, Lema JM. "Degradation of selected pharmaceutical and personal
care products (PPCPs) by white-rot fungi". World Journal
of Microbiology and Biotechnology, 27(8), 1839-1846,
2011. [111] Schmidt S, Hoffmann H, Garbe LA, Schneider RJ. "Liquid
chromatography-tandem mass spectrometry detection of
diclofenac and related compounds in water samples". Journal of Chromatography A, 1538(8), 112-116, 2018. [105] Shreve MJ, Brockman A, Hartleb M, Prebihalo S, Dorman
FL, Brennan RA. "The white-rot fungus Trametes
versicolor reduces the estrogenic activity of a mixture of
emerging contaminants in wastewater treatment plant
effluent". International
Biodeterioration
&
Biodegradation, 109(4), 132-140, 2016. [112] Suarez S, Reif R, Lema JM, Omil F. "Mass balance of
pharmaceutical and personal care products in a pilot-
scale single-sludge system: influence of T, SRT and
recirculation ratio". Chemosphere, 89(2), 164-171, 2012. & [106] Yang S, Hai FI, Nghiem LD, Nguyen LN, Roddick F, Price
WE. 10 References "Removal of bisphenol A and diclofenac by a novel
fungal membrane bioreactor operated under non-sterile
conditions". International
Biodeterioration
&
Biodegradation, 85(10), 483-490, 2013. [113] Bouju H, Nastold P, Beck B, Hollender J, Corvini PFX,
Wintgens T. "Elucidation of biotransformation of
diclofenac and 4′hydroxydiclofenac during biological
wastewater treatment". Journal of Hazardous Materials,
301(1), 443-452, 2016. [107] Asif MB, Hai FI, Singh L, Price WE, Nghiem LD. "Degradation of Pharmaceuticals and Personal Care
Products by White-Rot Fungi-a Critical Review". Current
Pollution Reports, 3(2), 88-103, 2017. [114] Zhou H, Liu J, Chen X, Ying Z, Zhang Z, Wang M. "Fate of
pharmaceutically active compounds in sewage sludge
during anaerobic digestions integrated with enzymes and
physicochemical
treatments". Waste
Management,
78, 911-916, 2018. [108] Marco-Urrea E, Pérez-Trujillo M, Cruz-Morató C, Caminal
G, Vicent T. "White-rot fungus-mediated degradation of
the
analgesic
ketoprofen
and
identification
of
intermediates
by
HPLC-DAD–MS
and
NMR". Chemosphere, 78(4), 474-481, 2010. [115] Kummerová M, Zezulka Š, Babula P, Tříska J. "Possible
ecological risk of two pharmaceuticals diclofenac and
paracetamol demonstrated on a model plant Lemna
minor". Journal of Hazardous Materials, 302(2), 351-361,
2016. [109] Marco-Urrea E, Pérez-Trujillo M, Vicent T, Caminal G. "Ability
of
white-rot
fungi
to
remove
selected
pharmaceuticals and identification of degradation
products
of
ibuprofen
by
Trametes
versicolor". Chemosphere, 74(6), 765-772, 2009. [109] Marco-Urrea E, Pérez-Trujillo M, Vicent T, Caminal G. "Ability
of
white-rot
fungi
to
remove
selected
pharmaceuticals and identification of degradation
products
of
ibuprofen
by
Trametes
versicolor". Chemosphere, 74(6), 765-772, 2009. Appendix A Appendix A pp
Table S1. The chemical structures of metbolites and transformation products of Diclofenac
Transformation
Products
Chemical Structure
Transformation Products
Chemical Structure
4’-hydroxydiclofenac
(4’-OH-DCF)
DCF-benzoic acid
5-hydroxydiclofenac (5-
OH-DCF)
Contains structural fragment “2,6-
dichloro-N-(phenyl)aniline
Position of CH2 group not defined
4’,5-
dihydroxydiclofenac
(4’,5-diOH-DCF)
Carboxydiclofenac (C-DCF)
3’-hydroxy-4’-
methoxydiclofenac (3’-
OH-4’-OCH3-DCF)
2-(2,6-
dichlorophenylamino)benzaldehyde Table S1. The chemical structures of metbolites and transformation products of Diclofenac Table S1. The chemical structures of metbolites and transformation products of Diclofenac Contains structural fragment “2,6-
dichloro-N-(phenyl)aniline
Position of CH2 group not defined Contains structural fragment “2,6-
dichloro-N-(phenyl)aniline Carboxydiclofenac (C-DCF) Carboxydiclofenac (C-DCF) 4’,5-
dihydroxydiclofenac
(4’,5-diOH-DCF) 2-(2,6-
dichlorophenylamino)benzaldehyde 3’-hydroxy-4’-
methoxydiclofenac (3’-
OH-4’-OCH3-DCF) 2 (2,6
dichlorophenylamino)benzaldehyde 951 Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Pamukkale Univ Muh Bilim Derg, 28(6), 937-952, 2022
S.C Tüzün, I. Karapınar Table S1. Continued. Transformation Products
Chemical Structure
Transformation Products
Chemical Structure
2-(8-hydroxy-3-oxo-3H-
carbazol-1-yl)acetic acid
8-chlorocarbazole-1-yl-ethanoic
acid
(E)-6-[2,6-dichlorophenyl)-
imino]-3-oxocyclohexa-1,4-
dienecarbaldehyde)
1-(2,6-dichlorophenyl)-1,3-
dihydro-2H-indole-2-one
2-(8-hydroxy-3-oxo-9,9a-
dihydro-3H-carbazol-1-
yl)acetic acid
DCF-lactam
(E)-2-[3-(2,6-dichloro-?-
hydroxyphenylimino)-6-
oxocyclohexa-1,4-
dienyl]acetic acid
8-chloro-9H-carbazole-1-
carbaldehyde
3’-hydroxydiclofenac (3’-
OH-DCF)
Nitro-Diclofenac (NO2-DCF)
2-[2-
(phenylamino]phenyl)acetic
acid
2-chloroaniline
2-(8-chloro-9H-carbazol-1-
yl)acetic acid
2,6-dichloroaniline
methyl 2-(9H-carbazol-9-
yl)acetate
2,6-dichlorophenol
9H-carbazole-1-
carbaldehyde
2,6-dichloro-N-o-
tolybenzenamine
2-(8-chloro-9H-carbazol-1-
yl)acetic acid
1-(2,6-dichlorophenyl)indolin-2-
one
carbazole-1-acetic acid
2-(2-
chlorophenylamino)benzaldehyde Chemical Structure
Transformation Products
Chemical Structure 8-chlorocarbazole-1-yl-ethanoic
acid (E)-6-[2,6-dichlorophenyl)-
imino]-3-oxocyclohexa-1,4-
dienecarbaldehyde) 1-(2,6-dichlorophenyl)-1,3-
dihydro-2H-indole-2-one 2-(8-hydroxy-3-oxo-9,9a-
dihydro-3H-carbazol-1-
yl)acetic acid (E)-2-[3-(2,6-dichloro-?-
hydroxyphenylimino)-6-
oxocyclohexa-1,4-
dienyl]acetic acid 8-chloro-9H-carbazole-1-
carbaldehyde Nitro-Diclofenac (NO2-DCF) Nitro-Diclofenac (NO2-DCF) 3’-hydroxydiclofenac (3’-
OH-DCF) 2-[2-
(phenylamino]phenyl)acetic
acid 2-chloroaniline 2,6-dichloroaniline 2,6-dichloroaniline 2-(8-chloro-9H-carbazol-1-
yl)acetic acid 2,6-dichlorophenol methyl 2-(9H-carbazol-9-
yl)acetate 2,6-dichloro-N-o-
tolybenzenamine 1-(2,6-dichlorophenyl)indolin-2-
one 2-(8-chloro-9H-carbazol-1-
yl)acetic acid 2-(2-
chlorophenylamino)benzaldehyde (
chlorophenylamino)benzaldehyde 952
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https://openalex.org/W4300336837
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6225f8b97c13f448ef6a29d3/original/multiscale-simulations-identify-origins-of-differential-carbapenem-hydrolysis-by-the-oxa-48-b-lactamase.pdf
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English
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Multiscale simulations identify origins of differential carbapenem hydrolysis by the OXA-48 β-lactamase
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Multiscale simulations identify origins of differential carbapenem
hydrolysis by the OXA-48 β-lactamase Viivi H. A. Hirvonen,a, b, † Tal Moshe Weizmann,a, ‡ Adrian Mulholland,b James Spencerc and Marc W. van der Kamp a, b, * a School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK, corresponding
author email: marc.vanderkamp@bristol.ac.uk a School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK, corresponding
author email: marc.vanderkamp@bristol.ac.uk a School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK, corresponding
author email: marc.vanderkamp@bristol.ac.uk
b Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close,
Bristol BS8 1TS, UK
c School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD,
UK
† Present address: Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius
väg 16, 10691 Stockholm, Sweden
‡ Present address: Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences,
Coventry University, Coventry CV1 5FB, UK Introduction The World Health organization describes antibiotic resistance as “...one of the biggest threats to
global health, food security, and development today.”2 Antibiotic resistance arises naturally and
evolved long ago,3 but its emergence and dissemination have been considerably accelerated by the
current excessive use of antibacterial drugs.4, 5 This evolving resistance not only complicates
standard medical practices, but also has additional expensive implications e.g. for the global
economy and food production.6-8 Moreover, we are currently living in the so-called antibiotic
discovery void9 where discovering new and safe antibacterials, especially for Gram-negative
bacteria, is difficult, time-consuming, and often unprofitable for big pharmaceutical companies.10,
11 β-Lactam antibiotics offer broad-spectrum antibacterial activity against Gram-negative bacteria
and remain the most prescribed drugs in clinical practice.12 The importance of β-lactams in
healthcare has been highlighted by the World Health Organization, which includes multiple
different β-lactam antibiotics in their Model List of Essential Medicine.13 All of these antibiotics
contain a four-membered β-lactam ring, which ensures antibiotic binding to penicillin-binding
proteins and consequently inhibition of bacterial cell wall biosynthesis.14, 15 Clinically used β-lactam
compounds can be divided into four different groups: penicillins, cephalosporins, carbapenems, and
monobactams, of which carbapenems play a critical role as potent antibiotics reserved for the most
serious Gram-negative infections where alternatives are limited.16 Emerging resistance against β-lactams is evident, and especially in Gram-negative bacteria, β-
lactamase enzymes are the main resistance mechanism against these drugs. 17 β-Lactamases block
antibiotic action by hydrolysing the β-lactam ring, which impairs efficient antibiotic binding to their
ultimate target in cells. The Ambler sequence-based classification divides β-lactamases into four
major subgroups: serine-β-lactamases (SBLs) comprising classes A, C, and D; and metallo-β-
lactamases (MBLs), class B.18 The hydrolysis mechanism differs between SBLs and MBLs, as
SBLs utilise a nucleophilic serine residue and MBLs employ zinc cofactors. 17 Class D SBLs are
referred to as OXA (oxacillinase) enzymes, stemming from their activity against the isoxazolyl
penicillin oxacillin,19 and they are currently of interest due to their wide distribution and the ability
of many members of the group to inactivate carbapenems. Abstract OXA-48 β-lactamases are frequently encountered in bacterial infections caused by carbapenem-resistant
Gram-negative bacteria. Due to the importance of carbapenems in treatment of healthcare-associated
infections, and the increasingly wide dissemination of OXA-48-like enzymes on plasmids, these β-
lactamases are of high clinical significance. Notably, OXA-48 hydrolyses imipenem more efficiently than
other commonly used carbapenems, such as meropenem. Here, we use extensive multiscale simulations of
imipenem and meropenem hydrolysis by OXA-48 to dissect the dynamics and to explore differences in
reactivity of the possible conformational substates of the respective acylenzymes. QM/MM simulations of
the deacylation reaction for both substrates demonstrate that deacylation is favoured when the 6α-
hydroxyethyl group is able to hydrogen bond to the water molecule responsible for deacylation, but
disfavoured by increasing hydration of either oxygen of the carboxylated Lys73 general base. Differences
in free energy barriers calculated from the QM/MM simulations correlate well with the experimentally
observed differences in hydrolytic efficiency between meropenem and imipenem. We conclude that the
impaired breakdown of meropenem, compared to imipenem, which arises from a subtle change in the
hydrogen bonding pattern between the deacylating water molecule and the antibiotic, is most likely induced
by the meropenem 1β-methyl group. In addition to increased insights into carbapenem breakdown by OXA
β-lactamases, which may aid in future efforts to design of antibiotics or inhibitors, our approach exemplifies
the combined use of atomistic simulations in determining the possible different enzyme-substrate substates,
and their influence on enzyme reaction kinetics. Introduction The OXA enzymes include five
subgroups of recognised carbapenemases: the OXA-23, OXA24/40, OXA-51, and OXA-58 β-
lactamases are mainly found in Acinetobacter baumannii, while OXA-48-like β-lactamases are
mostly encountered in Enterobacterales.20 In Enterobacterales, OXA-48 β-lactamases are among the most commonly present
carbapenemases in clinical samples.21 Their activity is relatively specific towards imipenem, but
other carbapenem substrates (such as meropenem and ertapenem) are also hydrolysed, albeit slowly.22 The specific origin of this imipenemase activity is not well established, even though
variations in measured hydrolysis rates between point variants of OXA-48 hint at structural moieties
contributing to specific hydrolytic phenotypes (Figure 1). In OXA-163, a partial deletion of the β5-
β6 loop (Arg214-Pro217) and one amino acid substitution (Ser212Asp) expands the hydrolysis
profile to accommodate expanded-spectrum oxyimino cephalosporins (such as ceftazidime) at the
expense of efficient imipenem breakdown.23 Further studies show that the β5-β6 loop plays a role
in acquired carbapenemase activity, as engineering the OXA-48 β5-β6 loop into the non-
carbapenemase OXA-10 enhances its carbapenemase activity.24 Conversely, replacing the β5-β6
loop in OXA-48 with that of OXA-18 also alters the measured carbapenemase activity (lower kcat
values).25 Site-directed mutagenesis studies of OXA-48 variants indicate that residue 214 (arginine
in the wildtype OXA-48) is essential for efficient carbapenem hydrolysis.26 In recent years,
structural studies have yielded a variety of crystal structures of OXA-48 in complex with
carbapenems, which shed new light on the acylenzyme (AC) intermediate state. 1, 27-30 Intriguingly,
although the β5-β6 loop is suggested to influence carbapenem activity, the only interaction observed
between the substrate and residues within this loop (Thr213-Lys218) is a water-mediated contact
between the imipenem 6α-hydroxyethyl hydroxyl and Thr213.1, 30 Furthermore, bound carbapenem Figure 1. Crystal structures of OXA-48 complexed with carbapenems. Acylenzyme structures of OXA-48 with
imipenem (PDB ID 6P97, green sticks) and meropenem (PDB ID 6P98, light pink sticks) show a highly similar
binding pose for both substrates, where main differences lie in the orientation of carbapenem C2 “tail” group.1
The Ω-loop is highlighted in orange, the β5-β6-loop in yellow, and relevant active site interactions with dashed
black lines. The carbapenem pyrroline ring is modelled as the Δ2-tautomer in both structures. Figure 1. Crystal structures of OXA-48 complexed with carbapenems. Introduction Acylenzyme structures of OXA-48 with
imipenem (PDB ID 6P97, green sticks) and meropenem (PDB ID 6P98, light pink sticks) show a highly similar
binding pose for both substrates, where main differences lie in the orientation of carbapenem C2 “tail” group.1
The Ω-loop is highlighted in orange, the β5-β6-loop in yellow, and relevant active site interactions with dashed
black lines. The carbapenem pyrroline ring is modelled as the Δ2-tautomer in both structures. tail groups (C2 substituents) seem to be dynamic and able to adopt multiple conformations, which
suggests they do not form strong, specific interactions with the enzyme active site. 29 The generalized β-lactam hydrolysis mechanism for SBLs consists of acylation followed by
deacylation (Scheme 1).17 Both acylation and deacylation reactions include the formation of a short-
lived tetrahedral intermediate (TI) through a nucleophilic attack; the respective TI species collapses
to yield either a covalent AC structure (after acylation), or the final hydrolyzed product (after
deacylation). In both reactions, the nucleophile (conserved serine (Ser70) in acylation and a water
molecule (deacylating water, DW) in deacylation) is activated via proton abstraction by a general
base. For OXA enzymes, this general base is a carboxylated lysine residue (Lys73). 31, 32 Notably,
Lys73 needs to be carboxylated for optimal activity; this carboxylation is reversible and pH
dependent, i.e. more carboxylation is observed at higher pH values.31 At lower pH values,
protonation of the Lys73:Nζ would lead to decarboxylation.33 Based on pH dependence studies of
the reaction between OXA-10 and penicillin or nitrocefin, the pKa of the carboxylated Lys73 is
expected to be ~5.8-6.2.31 For carbapenems, the pyrroline ring can undergo Δ2 → Δ1
tautomerization in the AC state, the Δ1 tautomer also having two stereoisomers (R and S). For class
A SBLs, the Δ2 tautomer has been suggested to be the catalytically competent form, whereas the
Δ1 form would essentially inhibit the enzyme.34 For OXA-48 enzymes, all three tautomers have Scheme 1. Top: Structures of meropenem and imipenem (with atoms numbered), the 6α-hydroxyethyl group is
highlighted in red. Bottom: Deacylation mechanism in OXA-48 with a carbapenem substrate (Δ2 tautomer). Starting from the acylenzyme, the antibiotic is deacylated via tetrahedral intermediate formation (1 2), which
collapses to yield the hydrolysed antibiotic (3). Introduction been observed in AC crystal structures,1, 28-30 but, based on NMR studies, the hydrolysis product is
suggested to be either the Δ2 or R-Δ1 tautomer.35 Kinetic measurements suggest that for OXA-48-like β-lactamases, deacylation is the rate-
limiting step in carbapenem breakdown.30 These authors suggested that the impaired imipenemase
activity in the ESBL-like OXA-163, compared to OXA-48, is due to a larger active site, which
would not constrain the substrate in deacylation-compatible conformations. Molecular dynamics
(MD) simulations of the non-covalent complexes of OXA-48 and OXA-163 with meropenem and
imipenem suggested some differences between the substrates in mobility. However, the measured
KM values for OXA-48 with imipenem and meropenem are very similar (according to one assay, 11
and 13 μM, respectively)22, which indicates that there is unlikely to be any significant difference in
the stabilities of the respective Michaelis complexes. The difference in the inactivation efficiency
of imipenem compared to meropenem is thus primarily related to differences in the rate of the
deacylation step, and it is therefore essential to consider this reaction when seeking to understand
and explain activity differences. To analyse differences in activity for carbapenems in atomistic
detail, we here simulate TI formation in deacylation, i.e. the expected rate-limiting step, of both
imipenem and meropenem by OXA-48 using combined quantum mechanics/molecular mechanics
(QM/MM) simulations. Our simulations support the hypothesis that the AC state arising from
carbabenem acylation is dynamic in nature. Further, we identify conformations of the 6α-
hydroxyethyl group that allow for efficient deacylation. Additionally, active site hydration around
the carboxylated Lys73 is observed to affect the calculated free energy barriers for deacylation, as
we previously observed hydrolysis of the expanded-spectrum oxyimino cephalosporin ceftazidime
by OXA-48 enzymes.36 Analysis of the reaction simulations shows that efficient carbapenem
breakdown results both from a decrease in hydration around carboxy-Lys73, and from subtle
changes in hydrogen bonding between the substrate and the catalytic water molecule. These results
provide detailed insight into the causes of differences in enzyme activity against different
antibiotics, information potentially useful in understanding and combating antimicrobial resistance. Methods Computational methods and details of the system setup are described in detail in the Supporting
Information (SI). To summarise, models of OXA-48 with imipenem and meropenem were prepared based
on corresponding acylenzyme (AC) crystal structures (PDB IDs 6P971 and 6P981 for imipenem and
meropenem, respectively). The ff14SB parameter set was used for the protein,37 parameters and partial
charges for non-standard residues (acylated carbapenems and carboxylated lysine) were derived with the
R.E.D. Server.38 Both systems were energy minimised, heated from 50 K to 300 K (in 20 ps), and their dynamics in the AC state were simulated for 200 ns using Langevin dynamics (collision frequency 0.2 ps–
1) with a 2 fs timestep. Five independent simulations for each AC system were run. All bonds involving
hydrogens were restrained using the SHAKE algorithm. Starting structures for QM/MM39 modelling were
chosen from MD simulations based on visual inspection of the active site hydration pattern and the 6α-
hydroxyethyl orientation; this orientation was kept from changing during subsequent QM/MM US MD by
applying a weak dihedral restraint (except in the case of orientation I). Free energy barriers for the first
(rate-limiting) step of deacylation for the different active site conformations were determined from three
separate QM/MM umbrella sampling (US) calculations for each conformation.40 Two reaction coordinates
were employed in US, one for the nucleophilic attack and one for the proton transfer, as in previous
simulations of deacylation in serine β-lactamases.36, 41-43 Sampling time in each window was 2 ps, and
DFTB2 (SCC-DFTB)44-46 was used as the QM method for regions consisting of 43 and 46 atoms (including
link atoms) for imipenem and meropenem, respectively (Figure S1). Free energy surfaces (FESs) were
constructed from 399 individual US windows. The weighted histogram analysis method (WHAM)47, 48 was
used to construct the free energy surfaces, and the minimum energy paths were analysed using the Minimum
Energy Path Surface Analysis (MEPSA) program49. All simulations and trajectory analyses were done using
the Amber18 software package50 (pmemd.cuda51-53 for MM MD, and sander for QM/MM calculations). Conformational Dynamics of Carbapenem:OXA-48 Acylenzymes AC dynamics for both imipenem and meropenem complexed with OXA-48, each in the 2
(enamine) configuration, were explored by running five 200 ns MM MD simulations for each
complex. The first 50 ns were excluded from trajectory analysis to allow time for equilibration. For
both carbapenems, the salt bridge between the C3 carboxylate and Arg250 was preserved during
simulations, and the C7 carbonyl stayed in the oxyanion hole formed by the backbone amides of
Ser70 (nucleophile) and Tyr211. The carbapenem C2 (tail) substituents sampled a range of
conformations during the simulations, consistent with previous suggestions based on structural
analysis.29 Clustering the substrate poses based on their heavy atom RMSD yielded four distinct
clusters per substrate, which differ by 0.8-1.8 Å and 1.7-2.5 Å for imipenem and meropenem,
respectively, from the poses in the corresponding crystal structures (Figure S2, Table S1 and SI
section Acylenzyme Clustering). The main deviations between cluster centroids and the crystal
structure coordinates are due to the positions of the C2 tail groups, as the pyrroline ring and its
substituents are anchored in place by hydrogen bonds to the oxyanion hole and the salt bridge with
Arg250. However, for the crystal structures 6P97 and 6P98 there is only limited electron density beyond the sulfur atom for both imipenem and meropenem, so the deposited coordinates may not
completely reliably depict the actual substrate binding poses. Additional clustering on the active Figure 2. Conformational behaviour of the carbapenem 6α-hydroxyethyl group. Left: The 6α-
hydroxyethyl group can assume three different orientations, which can be distinguished by the C7-
C6-C-O dihedral angle values. When the dihedral is around 50° (orientation I), the hydroxyl group
is hydrogen bonded with the DW, and in the 180° orientation (II) the hydroxyl group can only
interact with solvent. In the 290° orientation (III), the hydroxyl group is donating a hydrogen bond
to the carboxylated Lys73. Right: The distribution of sampled dihedral values during MM MD
simulations of the imipenem (IME) and meropenem (MER) acylenzymes (5x150 ns per
carbapenem). Figure 2. Conformational behaviour of the carbapenem 6α-hydroxyethyl group. Left: The 6α-
hydroxyethyl group can assume three different orientations, which can be distinguished by the C7-
C6-C-O dihedral angle values. When the dihedral is around 50° (orientation I), the hydroxyl group
is hydrogen bonded with the DW, and in the 180° orientation (II) the hydroxyl group can only
interact with solvent. Conformational Dynamics of Carbapenem:OXA-48 Acylenzymes The free energy difference between the different
orientations of the 6α-hydroxyethyl group was estimated by calculating the ratio of MD trajectory
frames corresponding to each orientation (Z), and using ΔG=RTln(Z), where R is the molar gas
constant and T the simulation temperature (300 K). For imipenem, the lowest free energy state is
orientation II, with slightly higher relative energies of 0.6 and 0.2 kcal/mol for orientations I and
III, respectively. For meropenem, orientation I has the lowest free energy, orientation II is slightly
higher (0.6 kcal/mol) but orientation III is significantly higher (2.2 kcal/mol). The presence of a
methyl group in the 1β-position in meropenem (instead of a 1β-proton in imipenem) may explain
the relatively higher penalty for orientation III, as in this orientation the 1β-substituent is located
directly next to the 6α-hydroxyethyl moiety. Previously, our QM/MM simulations indicated that Leu158 may play an important role in
modulating active site hydration in the deacylation of ceftazidime by OXA-48-like enzymes.36 The
orientation of Leu158 also differed initially between the two OXA-48/carbapenem systems, as the
Cβ - Cγ bond has rotated by 180° in the meropenem structure. To study if Leu158 has a similar
effect on carbapenem hydrolysis as observed for ceftazidime, its rotamers were first investigated
by measuring the χ1 dihedral (N-Cα-Cβ-Cγ) in MM MD simulations. The distribution of sampled
rotamers is presented in Figure S4. After the heating phase, Leu158 essentially always rotates away
from the crystallographic g- orientation (χ1 ≈ 290°) to the t orientation (χ1 ≈ 180°) to allow space for
the 6α-hydroxyethyl moiety, which in turn also permits for two water molecules to form hydrogen
bonds with Lys73:OQ1. As the cephalosporin scaffold lacks a functional group similar to the 6α-
hydroxyethyl group of carbapenems, typically bearing larger substituents in the β orientation at the
equivalent 7-position, it is likely that Leu158 does not possess a similar role in carbapenem
hydrolysis to that suggested for cephalosporins. Conformational Dynamics of Carbapenem:OXA-48 Acylenzymes In the 290° orientation (III), the hydroxyl group is donating a hydrogen bond
to the carboxylated Lys73. Right: The distribution of sampled dihedral values during MM MD
simulations of the imipenem (IME) and meropenem (MER) acylenzymes (5x150 ns per
carbapenem). site residues (explained in further detail in the SI) implies that there may be slight differences also
in the positions of active site residues Lys73, Tyr157, as well as of the substrate (Figure S3 and
Table S2). During MM MD, the carbapenem 6α-hydroxyethyl group was able to rotate to occupy three
different orientations, which can be distinguished by the value of the C7-C6-C-O dihedral angle:
around 50°, 180°, or 290°, henceforth referred to as orientations I, II, and III, respectively (Figure
3). The 6α-hydroxyethyl orientation affects interactions in the active site, because its hydroxyl
group can hydrogen bond either with the DW (I), or with the Lys73 carboxylate (III), or stay close
to the crystallographically observed pose, in which its methyl group is positioned next to the DW
and points towards Leu158 (II, Figure 2). The starting orientation of the 6α-hydroxyethyl for both
carbapenems is II, as in the crystal structures used in model construction. During MD simulations,
this sidechain is free to move and sample all three orientations. For meropenem, orientation I is
sampled more than II, while III is sampled only minimally (Figure 2). Conversely, both orientations II and III are sampled more than I for imipenem. The free energy difference between the different
orientations of the 6α-hydroxyethyl group was estimated by calculating the ratio of MD trajectory
frames corresponding to each orientation (Z), and using ΔG=RTln(Z), where R is the molar gas
constant and T the simulation temperature (300 K). For imipenem, the lowest free energy state is
orientation II, with slightly higher relative energies of 0.6 and 0.2 kcal/mol for orientations I and
III, respectively. For meropenem, orientation I has the lowest free energy, orientation II is slightly
higher (0.6 kcal/mol) but orientation III is significantly higher (2.2 kcal/mol). The presence of a
methyl group in the 1β-position in meropenem (instead of a 1β-proton in imipenem) may explain
the relatively higher penalty for orientation III, as in this orientation the 1β-substituent is located
directly next to the 6α-hydroxyethyl moiety. II and III are sampled more than I for imipenem. Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group Because the interactions of the 6α-hydroxyethyl group in the active site have been suggested to
play a role in modulating β-lactamase activity towards carbapenems,32 deacylation free energy
barriers were calculated separately for all three orientations of both imipenem and meropenem
acylenzymes observed in MD simulations. Starting structures for US were chosen from the 200 ns
MM MD simulations following two criteria: that a potential DW was at a suitable distance for
nucleophilic attack, and the 6α-hydroxyethyl orientation was that desired. For orientations II and
III, the sidechain dihedral was restrained close to the reference values to avoid the substrate
changing between orientations during the reaction (no restraints were needed for I, as no sidechain
rotation was observed during US). Overall barriers for deacylation were determined by combining sampling from three separate US calculations for each AC conformation (with different starting
structures), with standard deviations calculated between the free energy barriers for individual US
simulations (Table S3). More details of the US setup and analysis are available in the SI. (
)
p
y
Calculated deacylation free energy barriers for the ACs formed by imipenem and meropenem
with the 6α-hydroxyethyl in each of the three orientations are shown in Figure 3. For all orientations,
two barriers are shown, corresponding to two different hydration states around the general base. The lower barrier (in colour) corresponds to a state with only one water molecule hydrogen bonded
to Lys73:OQ2, and one or two waters hydrogen bonded to Lys73:OQ1 while the higher barrier
corresponds to a state with two water molecules hydrogen bonded to both carboxylate oxygens
(Figure 4, carboxylate oxygens labelled in Scheme 1). For all hydration states, the calculated
barriers follow the same trend of I < II < III, i.e. the lowest barriers are calculated for orientation I. Notably, the barriers are consistently underestimated due to the QM method used (DFTB2), as is
generally found for this method for similar reactions.42, 43 This underestimation likely also causes
an underestimation of the stability of the TI compared to the TS (see e.g. the small molecule
benchmark calculations the SI section “Benchmarking”), but TI minima were still located in our
free energy surfaces (likely due to stabilization by the enzyme environment). Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group As the overall shape
of the QM/MM PES is consistent when using DFTB2 or M06-2X/def2-TZVP as the QM method,
it is reasonable to expect that the underestimation of TI stability with DFTB2 does not affect trends
in reaction barriers (SI section “Benchmarking”). Taking into account an underestimation of ~8
kcal/mol, as indicated by comparison of DFTB2 to SCS-MP2/aug-cc-pVTZ (SI section
“Benchmarking”), the lowest barriers are in good agreement with experiment (see further the
section “Comparison with experimental data”). Importantly, we expect our protocol for obtaining
free energy barriers using semi-empirical QM methods to be a reliable indicator of relative energetic
trends between different enzyme active site conformations; we have demonstrated this previously
in studies of deacylation of β-lactam acylenzymes for both class A (with meropenem) and D
SBLs.36, 43 Figure 3. Free energy barriers for deacylation of carbapenem acylenzymes with the 6α-hydroxyethyl
group in the three different orientations. Each bar includes the barrier obtained with a single water
molecule hydrogen bonded to Lys73:OQ2 (lowest barrier, in colour; see Figure 4 for depiction of OQ2)
and the barrier obtained with two water molecules hydrogen bonded to Lys73:OQ2 (highest barrier, in
grey). Each barrier is derived from three individual US simulations, with standard deviations in
parenthesis. Imipenem: green, meropenem: pink. Figure 3. Free energy barriers for deacylation of carbapenem acylenzymes with the 6α-hydroxyethyl
group in the three different orientations. Each bar includes the barrier obtained with a single water
molecule hydrogen bonded to Lys73:OQ2 (lowest barrier, in colour; see Figure 4 for depiction of OQ2)
and the barrier obtained with two water molecules hydrogen bonded to Lys73:OQ2 (highest barrier, in
grey). Each barrier is derived from three individual US simulations, with standard deviations in
parenthesis. Imipenem: green, meropenem: pink. Figure 3. Free energy barriers for deacylation of carbapenem acylenzymes with the 6α-hydroxyethyl
group in the three different orientations. Each bar includes the barrier obtained with a single water
molecule hydrogen bonded to Lys73:OQ2 (lowest barrier, in colour; see Figure 4 for depiction of OQ2)
and the barrier obtained with two water molecules hydrogen bonded to Lys73:OQ2 (highest barrier, in
grey). Each barrier is derived from three individual US simulations, with standard deviations in
parenthesis. Imipenem: green, meropenem: pink. As discussed above and in ref. 36, increased hydration around the proton-accepting Lys73:OQ1
impairs deacylation in ceftazidime hydrolysis. Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group A similar phenomenon was observed for
carbapenems, with the additional observation that hydration around the second carboxylate oxygen
(Lys73:OQ2) also affects reactivity. In orientation I, the average number of hydrogen bonds
Lys73:OQ1 accepts during the reaction is 2.4 (± 0.1 standard deviation, calculated from the US
minimum free energy path trajectories), which aligns with OQ1 being hydrogen bonded to two
water molecules, and partly to Trp157. The two subpopulations with different deacylation barriers
arise from a change in hydration around Lys73:OQ2. For the lower barriers in Figure 3, the number
of hydrogen bonds to OQ2 is 1.3 (± 0.1) and for the higher barriers 2.2 (±0.1) for orientation I. The
lowest calculated deacylation barrier, 8.4 kcal/mol, is for imipenem in orientation I with one water
molecule hydrogen bonded to OQ2 and two to OQ1 (Figure 4). The barrier increases by 2.0
kcal/mol when another solvent molecule donates a hydrogen bond to OQ2. For meropenem, the
barrier is raised by 4.1 kcal/mol upon introduction of an additional water molecule close to OQ2. The hydration effect around Lys73:OQ2 indicated here has an apparently smaller effect on the
calculated barriers than that of hydration around Lys73:OQ1, since the presence of an additional water molecule hydrogen bonded to OQ1 raised the barrier for ceftazidime deacylation by
approximately 5 kcal/mol.36 Orientation II (corresponding to a dihedral angle of between 147°-192° depending on the
structure and protein chain) is observed in most OXA-48:carbapenem AC crystal structures. In this
orientation, no part of the 6α-hydroxyethyl moiety interacts with either the DW or with Lys73, so
the antibiotic may possibly not interfere with the reactive atoms. However, calculated deacylation
barriers are increased by 2.1 kcal/mol for imipenem, and by 2.4 kcal/mol for meropenem, when
comparing orientation II against I (in which only one water molecule is hydrogen bonded to OQ2). Having two water molecules donating hydrogen bonds to both OQ1 and OQ2 further raises the
calculated barriers to 13.6 and 16.0 kcal/mol for imipenem and meropenem, respectively. Therefore, our simulations suggest that II is not the most deacylation-competent AC orientation. Additionally, orientation II might hinder the positioning of the DW in the active site in proximity
to the electrophilic acyl carbon. Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group The g- rotamer of Leu158
allows space only for the DW positioned near Lys73:OQ1, which was inserted into the active site
in the starting model. Further, only one water molecule is donating a hydrogen bond to OQ2. Upon
MD equilibration, Leu158 rotates, allowing for active site hydration to change to two water
molecules hydrogen bonding to both carboxylate oxygens each. Subsequently, only the ‘high
barrier’ hydration state is sampled. This explains the large increase in activation free energy when
comparing the two hydration substates for orientation III, as two water molecules are located near
Lys73, as opposed to only one water molecule close to Lys73:OQ2 (as for orientations I and II). Therefore, our simulations indicate that III is the AC orientation that is the least competent for
deacylation for the equilibrated system (in which Leu158 has rotated). Experimentally, this AC
orientation is seen in the crystal structure of OXA-48 with hydrolyzed, non-covalently bound
imipenem (PDB ID 6PK0)28, where the hydroxyethyl hydroxyl donates a hydrogen bond to the
newly-formed carboxylate group. In our MM MD simulations of the AC, the exchange between 6α-
hydroxyethyl dihedral orientations is frequent (indicating a low energy barrier). This is probably
true also for the hydrolyzed antibiotic, suggesting that rotation of this moiety can occur post-
deacylation. Further analysis of the US trajectories reveals that hydration around Lys73:OQ2 correlates with
the rotamer of Val120. Valine has three rotamers for the χ1 dihedral (N-Cα-Cβ-Cγ1): the g+ rotamer
around 50°, t around 180°, and g- around 300° (Figure 4, Figure S6). In the starting structures for
simulations, Val120 is in the t orientation for both carbapenems (for meropenem, partial occupancy
for both t and g– rotamers was observed in the deposited structure, but only the t rotamer was used
in the computational model building).1 The rotameric state can switch to either g+ or g- during MD
simulations (Figure S6). For the g+ rotamer, one of the methyl groups points directly towards
Lys73, which only leaves space for a single water molecule next to Lys73:OQ2; this water is
positioned to accept a hydrogen bond from Gln124 and to donate one to Lys73. Conversely, the t
rotamer allows for a second water molecule to occupy the space between Lys73 and Val120, and
this water molecule is able to donate hydrogen bonds to both Lys73:OQ2 and the Val120 backbone
carbonyl. Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group For 93% and 87%, respectively, of the simulation times for the
imipenem and meropenem acylenzymes in orientation II, the distance between the AC electrophilic
carbon and the closest water molecule falls beyond 4 Å (an arbitrary threshold distance for a feasible
nucleophilic attack; Figure S5). This is likely due to the 6α-hydroxyethyl methyl group partly
occupying the space in the binding pocket for the deacylating water molecule, and thereby forcing
this water further away from the AC. This is reflected in deposited crystal structures, as a DW
candidate that is suitably positioned for nucleophilic attack is not observed in any OXA-
48/carbapenem complex.1, 27-30 In a previous study (mainly based on molecular dynamics),
orientation II was observed to obstruct the positioning of the DW in the active site. 32 Docquier et
al. concluded that only a slight repositioning of the methyl group of the 6α-hydroxyethyl sidechain
is needed to better accommodate a water molecule at a suitable distance for nucleophilic attack. However, these conclusions are based on a single 10 ns MD simulation, which likely gives
insufficient time to sample all available substrate orientations. Based on our MM MD simulations,
as well as the calculated free energy barriers, orientation II is less likely to contribute to efficient
deacylation of the carbapenem ACs. This is due both to an increase in energy required for
deacylation, as well as to a lack of sampling of active site configurations that would be suitable for
the AC carbonyl to undergo nucleophilic attack by an incoming water molecule. The largest increase in energetics between the two hydration states is calculated for orientation The largest increase in energetics between the two hydration states is calculated for orientation
III, where the barriers increase by 9.6 and 5.6 kcal/mol for imipenem and meropenem, respectively,
when the hydration state is changed. For the lower barriers, OQ1 and OQ2 form on average 2.0 (±
0.1) and 1.4 (± 0.1) hydrogen bonds, respectively, for the imipenem and meropenem complexes,
while for the higher barriers the equivalent numbers are 2.8 (± 0.1) and 2.1 (± 0.2, data not shown). For the lower barriers, Leu158 has not (yet) rotated from the g- to the t rotamer (Figure S4), as the
starting structures were chosen almost directly after the heating phase. Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group Val120 is part of motif II, which is formed by residues Ser118 - Val120 and is conserved
across class D β-lactamases.32 Together with Leu158, it forms the so-called ‘deacylating water
channel’ in the vicinity of Lys73; this hydrophobic patch partly shields the active site from bulk
solvent.1 For other OXA enzymes, a similar water channel has been proposed to open upon substrate
binding to allow for water ingress into the active site and therefore for efficient deacylation. 54, 55 For
OXA-48, previous comparison of apoenzyme and acylenzyme structures shows that substrate binding shifts Val120 and Leu158 only slightly, and that the water channel is more open than e.g. in OXA-23.1 Access of water into the catalytic position next to the substrate and Lys73 is necessary
for antibiotic hydrolysis, but as we indicate above, any additional solvent in the active site will
impair reactivity. In OXA-48, it appears that Val120 (and the specific rotamers that it samples) is
an important gateway residue controlling approach of bulk solvent to Lys73:OQ2. Our previous
work (on ceftazidime hydrolysis in OXA-48-like enzymes) indicates that Leu158 modulates
hydration around Lys73:OQ1.36 Notably, Val120 is mutated to a leucine in OXA-519, a single point
mutant of OXA-48; this mutation results in an increase in measured hydrolysis for some 1β-methyl
carbapenems, such as meropenem and ertapenem, but decreased imipenemase activity. Compared
to OXA-48, OXA-519 also increases the proportion of β-lactone reaction products, rather than
conventionally formed ring-opened species, hydrolysis products of meropenem.56 Further, the
Val120Leu mutation increases both kcat and KM for meropenem, indicating opposite effects on
binding and hydrolysis.57 The exact effect of the Val120Leu mutation on carbapenem hydrolysis on
the molecular level is therefore complex and remains to be determined. Figure 4. Alternative hydrogen bond configurations found with the 6α-hydroxyethyl in orientation I. Left: Active site
of OXA-48 with imipenem in hydrogen bond configuration 1. Val120 adopts the g+ rotamer, and consequently only
one water molecule is forming a hydrogen bond with Lys73:OQ2. The 6α-hydroxyethyl is in orientation I and donates
a hydrogen bond to a water lodged between the Tyr211 backbone and Thr213. Right: Active site interactions of OXA-
48 with meropenem in hydrogen bond configuration 2. Val120 is in its t rotameric state, which allows for two waters
to hydrogen bond with both Lys73 carboxylate oxygens. The 6α-hydroxyethyl is in orientation I but donating a
hydrogen bond to the DW. Figure 4. Deacylation efficiencies for different orientations of the 6α-hydroxyethyl group Alternative hydrogen bond configurations found with the 6α-hydroxyethyl in orientation I. Left: Active site
of OXA-48 with imipenem in hydrogen bond configuration 1. Val120 adopts the g+ rotamer, and consequently only
one water molecule is forming a hydrogen bond with Lys73:OQ2. The 6α-hydroxyethyl is in orientation I and donates
a hydrogen bond to a water lodged between the Tyr211 backbone and Thr213. Right: Active site interactions of OXA-
48 with meropenem in hydrogen bond configuration 2. Val120 is in its t rotameric state, which allows for two waters
to hydrogen bond with both Lys73 carboxylate oxygens. The 6α-hydroxyethyl is in orientation I but donating a
hydrogen bond to the DW. Comparison of carbapenem deacylation in orientation I As presented above, orientation I of the 6α-hydroxyethyl moiety is calculated to give the
overall lowest deacylation free energy barriers for both carbapenems. The combined FESs for the
hydration state with lower free energy barriers are presented in Figure S7 for all three substrate orientations. In this section, we focus further on orientation I and the ‘reactive’ active site
configuration in which only one water molecule is hydrogen bonded to Lys73:OQ1, and two to
Lys73:OQ2 (unless otherwise stated). For this AC conformation, two different hydrogen bonding
arrangements in the active site are possible: the DW can donate a hydrogen bond to the 6α-
hydroxyethyl hydroxyl group (named configuration 1), or the hydroxyl group can donate a
hydrogen bond to the DW (configuration 2), see Figure 4. In MM MD, configuration (1) is sampled
for 87% and 86% of simulation time for imipenem and meropenem, respectively. In addition to
donating a hydrogen bond to the DW as in (2), the 6α-hydroxyethyl hydroxyl group can also donate
a hydrogen bond directly to Lys73:OQ1 if the DW is displaced. This orientation of the carbapenem
6α-hydroxyethyl group may be the relevant one for β-lactone formation, which has been
characterized as a side product for OXA-48-catalysed carbapenem turnover, particularly of 1β-
methyl carbapenems (such as meropenem).56, 58 The β-lactone product has been proposed to form
via intramolecular cyclisation, where the hydroxyl group acts as a nucleophile and donates a proton
to Lys73. If the reaction occurs without a bridging water molecule, i.e. by a direct proton transfer
between -OH and Lys73, lactonization is most likely lower in energy in orientation I than in III,
based on the trends observed for deacylation energetics. For imipenem deacylation, both configurations (1) and (2) were observed in umbrella
sampling. The lowest free energy barrier of 8.4 kcal/mol was calculated for configuration (1), and
the barrier was increased by 2.0 kcal/mol for configuration (2). In addition to raising the free energy
barriers, changing from (1) to (2) shifts the location of the transition state on the FES. For (1), the
TS is located approximately at values –0.1 Å and 1.7 Å for the proton transfer and nucleophilic
attack reaction coordinates, respectively (Figure 5, left). However, for (2), the TS location on the
FES shifts to around –0.5 Å and 2.0 Å Figure S8). Comparison of carbapenem deacylation in orientation I Possible reasons
for this may include the presence of a 1β-methyl group in meropenem, as this may hinder the
rotation of the 6α-hydroxyethyl group to better optimise further hydrogen bonds between active site
residues and water molecules nearby. Such hindrance of 6α-hydroxyethyl rotation may also explain
the preference observed for configuration 2 as the DW approaches the acyl carbon. A water
molecule lodged between Tyr211 and Thr213 accepts a hydrogen bond from the carbapenem -OH
moiety in configuration (1) or donates a hydrogen bond to it in configuration (2) (Figure 5 and
Figure S8). The 1β-methyl group occupies the space above this water and may therefore induce its
displacement or the re-organization of the surrounding water molecules to optimise hydrogen bonds
between them, which could subsequently lead to a change from configuration (1) to (2). Additionally, the initial nucleophilic approach of the DW (from 3.5 Å to 2.2 Å) with the 6α-
hydroxyethyl moiety in orientation I and hydrogen bond configuration (1) is calculated to be slightly
lower in energy for imipenem (Figure S9). The DW remains hydrogen bonded to the hydroxyethyl
oxygen during this approach, with the average distance to the hydroxyethyl methyl carbon reducing
to about 3.3 Å. Notably, the initial approach between the DW and the carbapenem is also slightly
higher in energy in orientations II and III than in orientation I, which may contribute to their overall
energetics being less favorable for deacylation. However, the reasons for the preference for the
imipenem, but not the meropenem, complex to adopt configuration (1) during deacylation are likely
subtle and can result from small structural changes between the active site, substrate, and solvent
molecules. For meropenem, the lowest calculated deacylation barrier is 11.2 kcal/mol with an average
of 2.4 (± 0.1) and 1.4 (± 0.0) hydrogen bonds accepted by K73:OQ1 and OQ2, respectively. This
barrier is 2.8 kcal/mol higher than the lowest calculated barrier for imipenem, or 2.2 kcal/mol
including the free energy penalty (derived from MM MD for imipenem) for orientation I. In contrast
to imipenem, the hydroxyl of the 6α-hydroxyethyl moiety in meropenem always rotates during
unrestrained US sampling to hydrogen bond configuration (2), donating a hydrogen bond to the
DW. This rotation occurs before the TS is reached even when configuration (1) is present in the
starting structure. Enforcing the donation of a hydrogen bond from DW to the 6α-hydroxyethyl -
OH, i.e. Comparison of carbapenem deacylation in orientation I With active site configuration (2), the proton
transfer has progressed further at the TS, whereas the approach of the DW oxygen to the acyl carbon
is less advanced. This is potentially due to the additional hydrogen bond from the 6α-hydroxyethyl
moiety hydroxyl decreasing the nucleophilicity of the DW, requiring the proton transfer reaction to
have progressed further from the starting structure in the TS. Notably, a similar shift in the TS
position on the FES is observed also in orientation III, where a water molecule is donating a
hydrogen bond to the DW instead of the 6α-hydroxyethyl group (Figure S7). Mulliken charge
analysis of the key QM atoms does not reveal many significant differences for the calculated
charges along the reaction when comparing US calculations with either configuration (1) or (2)
(Tables S5-S8). The main difference is observed at the TS, where for Lys73:OQ1 the charge is more
positive and for DW:O the charge is more negative for configuration (2), as expected by the shift
in the TS location towards the TI. For meropenem, the lowest calculated deacylation barrier is 11.2 kcal/mol with an average
of 2.4 (± 0.1) and 1.4 (± 0.0) hydrogen bonds accepted by K73:OQ1 and OQ2, respectively. This
barrier is 2.8 kcal/mol higher than the lowest calculated barrier for imipenem, or 2.2 kcal/mol
including the free energy penalty (derived from MM MD for imipenem) for orientation I. In contrast
to imipenem, the hydroxyl of the 6α-hydroxyethyl moiety in meropenem always rotates during
unrestrained US sampling to hydrogen bond configuration (2), donating a hydrogen bond to the
DW. This rotation occurs before the TS is reached even when configuration (1) is present in the
starting structure. Enforcing the donation of a hydrogen bond from DW to the 6α-hydroxyethyl -
OH, i.e. restraining the reaction simulations to configuration (1), affects the location of the TS in a
similar manner to that observed with imipenem. TS locations for configurations (1) and (2) are at –
0.2/1.8 Å and –0.5/2.0 Å (proton transfer/nucleophilic attack), respectively. However, changing the
hydrogen bonding pattern between configurations has only a minimal effect on the energetics, as
the barrier for (1) is 11.9 kcal/mol. Therefore, the decrease in activation energy for configuration
(1) vs. (2) does not follow the same trend for meropenem as it does for imipenem. Comparison of carbapenem deacylation in orientation I The DW is donating a hydrogen bond to the carbapenem hydroxyl group. Right:
Free energy surface for meropenem deacylation with the lowest calculated barrier in orientation I (configuration
2). The carbapenem hydroxyl group donates a hydrogen bond to the DW. AC=acylenzyme, TS=transition state
(marked by a red circle), TI=tetrahedral intermediate. Figure 5. Free energy surfaces and transition state structures for alternative active site hydrogen bond
configurations. Left: Free energy surface for imipenem deacylation for the lowest calculated barrier in
orientation I (configuration 1). The DW is donating a hydrogen bond to the carbapenem hydroxyl group. Right:
Free energy surface for meropenem deacylation with the lowest calculated barrier in orientation I (configuration
2). The carbapenem hydroxyl group donates a hydrogen bond to the DW. AC=acylenzyme, TS=transition state
(marked by a red circle), TI=tetrahedral intermediate. Comparison of carbapenem deacylation in orientation I restraining the reaction simulations to configuration (1), affects the location of the TS in a
similar manner to that observed with imipenem. TS locations for configurations (1) and (2) are at –
0.2/1.8 Å and –0.5/2.0 Å (proton transfer/nucleophilic attack), respectively. However, changing the
hydrogen bonding pattern between configurations has only a minimal effect on the energetics, as
the barrier for (1) is 11.9 kcal/mol. Therefore, the decrease in activation energy for configuration
(1) vs. (2) does not follow the same trend for meropenem as it does for imipenem. Possible reasons
for this may include the presence of a 1β-methyl group in meropenem, as this may hinder the
rotation of the 6α-hydroxyethyl group to better optimise further hydrogen bonds between active site
residues and water molecules nearby. Such hindrance of 6α-hydroxyethyl rotation may also explain
the preference observed for configuration 2 as the DW approaches the acyl carbon. A water
molecule lodged between Tyr211 and Thr213 accepts a hydrogen bond from the carbapenem -OH
moiety in configuration (1) or donates a hydrogen bond to it in configuration (2) (Figure 5 and
Figure S8). The 1β-methyl group occupies the space above this water and may therefore induce its
displacement or the re-organization of the surrounding water molecules to optimise hydrogen bonds
between them, which could subsequently lead to a change from configuration (1) to (2). Additionally, the initial nucleophilic approach of the DW (from 3.5 Å to 2.2 Å) with the 6α-
hydroxyethyl moiety in orientation I and hydrogen bond configuration (1) is calculated to be slightly
lower in energy for imipenem (Figure S9). The DW remains hydrogen bonded to the hydroxyethyl
oxygen during this approach, with the average distance to the hydroxyethyl methyl carbon reducing
to about 3.3 Å. Notably, the initial approach between the DW and the carbapenem is also slightly
higher in energy in orientations II and III than in orientation I, which may contribute to their overall
energetics being less favorable for deacylation. However, the reasons for the preference for the
imipenem, but not the meropenem, complex to adopt configuration (1) during deacylation are likely
subtle and can result from small structural changes between the active site, substrate, and solvent
molecules. Figure 5. Free energy surfaces and transition state structures for alternative active site hydrogen bond
configurations. Left: Free energy surface for imipenem deacylation for the lowest calculated barrier in
orientation I (configuration 1). Comparison with experimental data Most of the variants in the OXA-48 family are carbapenemases, with elevated imipenem
hydrolysis rates when compared against other carbapenems.59 For OXA-48, experimental
measurements of kcat values for imipenem hydrolysis vary between 1.5 and 22.5 s–1, which can be
converted to free energy barriers for activation (Δ‡G) of 15.7 to 17.3 kcal/mol, using the Eyring
equation. For meropenem, the measured kcat values range between 0.07 - 0.16 s–1, which converts to
barriers of 18.7-19.2 kcal/mol. Using these figures as experimental estimates of free energies of
activation, the difference (ΔΔ‡G) between imipenem and meropenem hydrolysis is between 1.4-3.5
kcal/mol, which is approximately the same magnitude as the strength of a single hydrogen bond (1- 3 kcal/mol).60 Hence, structural factors contributing to more efficient breakdown of imipenem,
compared to 1β-methyl carbapenems, are most likely to be subtle. Our QM/MM simulations suggest
that orientation I of the 6α-hydroxyethyl group is the most likely AC orientation to undergo
deacylation, when this exists in a state with decreased hydration around Lys73:OQ2 (i.e., with only
one water molecule donating a hydrogen bond to this carboxylate oxygen). When comparing the
lowest free energy barriers calculated in orientation I for imipenem and meropenem (Figure 3), the
difference (ΔΔ‡G) for the two substrates is 2.8 kcal/mol; including the free energy penalty for the
imipenem 6α-hydroxyethyl moiety adopting orientation I (0.6 kcal/mol, as determined from our
MM MD simulations), the obtained ΔΔ‡G value drops to 2.2 kcal/mol. This is in excellent
agreement with the experimentally determined range of ΔΔ‡G values. This strongly supports our
assumption that TI formation is the rate-limiting process for carbapenem hydrolysis by OXA-48,
consistent with similar findings for ceftazidime breakdown by OXA-48-like enzymes35 and
carbapenem breakdown by a range of class A serine β-lactamases.41,42 The agreement further
implies that the difference between imipenem and meropenem deacylation in OXA-48 may indeed
be caused by the subtle difference in the preferred hydrogen bonding patterns involving the DW
and the 6α-hydroxyethyl sidechain reported here. In turn, the presence of the meropenem 1β-methyl
group apparently contributes to this difference by influencing both the orientation of the 6α-
hydroxyethyl group and the organization of water molecules in the near vicinity. (We further note
that the underestimation of the absolute barriers can be fully accounted for by comparison of DFTB2
to higher level QM calculations, which indicates DFTB2 underestimates barriers by ~6.3-8
kcal/mol, see Table S4 & Figure S11. Comparison with experimental data Thus, combined with the free energy penalty of 0.6 kcal/mol
noted above, the corrected lowest barriers would be 15.3-17.0 and 17.5-19.2 kcal/mol for imipenem
and meropenem, respectively.) Based on our MD simulations, the carbapenem tail groups are highly
flexible and are thus unlikely to directly affect deacylation efficiency. Differences in kcat (reflecting
the rate-limiting deacylation step) for carbapenems might therefore be explained similarly to our
findings here, with differences largely caused by the presence or absence of the 1β-methyl group. This is consistent with experimental data for OXA-48, which show higher kcat values for imipenem
and panipenem vs. 1β-methyl containing carbapenems.32, 61 Overall, our analysis of the effects of active site conformations on carbapenem hydrolysis
activity highlights the importance of controlling water access to the active site. On the one hand, it
is crucial for the enzyme active site to support the binding of the deacylating water (through the
aforementioned water channel). On the other hand, partial desolvation of the catalytic base
(carboxylated Lys73) is required for efficient reaction. Such intricate control of active site solvation
is a common feature of enzyme activity. For example, in ketosteroid isomerase, additional water molecules hydrogen bonding to the catalytic aspartate raise the barrier of reaction significantly. 62
Notably, this increased solvation occurs through water molecules hydrogen bonding to the
carboxylate oxygen that is not receiving the proton, similar to what is observed here (difference
between high and low barriers in Figure 3), but different from what we observed for ceftazidime
hydrolysis.36 Such additional hydrogen bonding will decrease the pKa of the catalytic carboxylate
base,63-65 weakening its proton affinity and thereby leading to higher barriers for the reaction. To
avoid or limit the occurrence of additional hydrogen bonding to catalytic bases, enzymes have
evolved active site architectures that can promote desolvation to increase carboxylate reactivity. Such desolvation can for example be achieved by loop closure (as in triosephosphate isomerase and
dihydrofolate reductase)66, 67 or closure of the substrate binding cleft (as in ketosteroid synthase). Here, subtle control of the solvation around the carboxylated Lys73 is related to nearby hydrophobic
residues (Val120 and Leu158), which can adopt conformations that allow the presence of the
deacylating water but avoid more extensive solvation of the catalytic carboxylate. Conclusions We have modelled carbapenem hydrolysis by the OXA-48 β-lactamase using QM/MM
reaction simulations. The deacylation reaction was modelled for two carbapenem substrates,
imipenem and meropenem, to deduce the origin of the higher activity towards imipenem compared
to other carbapenems. MM MD simulations of the acylenzyme complexes demonstrate that the
carbapenem tail (C2) groups are able to adopt many different conformations. In contrast, the
carbapenem 6α-hydroxyethyl group is able to rotate and to adopt three specific different
orientations, where it either interacts with the DW (I), Lys73 (III), or is rotated so that the methyl
group is oriented towards Leu158 (II). Subsequently, deacylation was modelled using QM/MM for
both substrates in these three orientations to investigate the effect of orientation upon deacylation
efficiency. Our calculated free energy barriers indicate that the most deacylation-competent
orientation is I, where the hydroxyl group interacts with the DW, and that the orientation III has the
highest free energy barriers. Detailed comparison of the simulations revealed two factors that significantly affect the
reaction energetics: hydration around Lys73, and the hydrogen bonding pattern between the DW
and substrate, specifically the 6α-hydroxyethyl group. Hydration around the general base has been
proposed to affect the predicted hydrolysis rates for other β-lactam substrates;36 here, we show that
this is affected by hydration around both Lys73 carboxylate oxygens (not only the oxygen
participating in proton transfer). Increased hydration around the non-reactive oxygen (Lys73:OQ2)
correlates with higher calculated barriers; in turn, the orientation of Val120 correlates with the number of water molecules near this oxygen. Another aspect influencing deacylation efficiency is
the pattern of hydrogen bonds in the active site that involve the DW and the carbapenem 6α-
hydroxyethyl sidechain. Imipenem shows a preference for a configuration in which the DW donates
hydrogen bonds to Lys73 and the 6α-hydroxyethyl hydroxyl group; the free energy barrier is higher
when the hydroxyl group instead rotates to donate a hydrogen bond to the DW. This preference is
not observed for meropenem: simulations with both hydrogen bond configurations have comparable
energy barriers, which are similar to that calculated for imipenem in the less favorable orientation. Therefore, we can conclude that the difference between hydrolytic activities for the two carbapenem
substrates stems from subtle differences in the active site hydrogen bonding patterns, which affect
the reactivity of the DW. Conclusions Furthermore, our results indicate that active site hydration is an important
determinant of catalysis in OXA-48 enzymes: increasing hydration around the general base impairs
carbapenem hydrolysis. Our study highlights the importance of detailed atomistic modelling in
addition to experimental research to determine the exact origins of catalytic activity. Simulation
protocols such as those employed here can extend information from crystallographic studies to
enable investigation of the strength and dynamics of specific active site interactions during the
catalytic cycle and directly investigate determinants of activity in situ. Corresponding Author *Marc W. van der Kamp, marc.vanderkamp@bristol.ac.uk Present Addresses † Present address: Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius
väg 16, 10691 Stockholm, Sweden. ‡ Present address: Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences,
Coventry University, Coventry CV1 5FB, UK. Author Contributions The manuscript was written through contributions of all authors. VHAH and MWK designed the study,
VHAH performed all simulations, assisted by TMW. All authors analyzed the results, participated in
writing the manuscript and have given their approval to the final version. Funding Sources VHAH and this research were supported by the UK Medical Research Council (MR/N0137941/1 for the
GW4 Biomed DTP awarded to the Universities of Bath, Bristol, Cardiff and Exeter). MWK further thanks
BBSRC for support (BB/M0626280/1). AJM thanks EPSRC for support (EP/M013219/1, EP/M022609/1,
EP/R026939/1). AJM and JS thank MRC for funding (MR/T016035). This work was conducted using the
computational facilities of the Advanced Computing Research Centre, University of Bristol. References 1. Smith, C. A.; Stewart, N. K.; Toth, M.; Vakulenko, S. B., Structural Insights into the
Mechanism of Carbapenemase Activity of the OXA-48 β-Lactamase. Antimicrob. Agents
Chemother. 2019, 63 (10), e01202-19. 2. WHO Antibiotic Resistance. https://www.who.int/news-room/fact-
sheets/detail/antibiotic-resistance (accessed 01/19/2021). 3. D’Costa, V. M.; King, C. E.; Kalan, L.; Morar, M.; Sung, W. W. L.; Schwarz, C.;
Froese, D.; Zazula, G.; Calmels, F.; Debruyne, R.; Golding, G. B.; Poinar, H. N.; Wright, G. D., Antibiotic Resistance is Ancient. Nature 2011, 477 (7365), 457-461. 4. Wang, J.; Wang, P.; Wang, X.; Zheng, Y.; Xiao, Y., Use and Prescription of Antibiotics
in Primary Health Care Settings in China. JAMA Intern. Med. 2014, 174 (12), 1914-1920. 5. Davies, J.; Davies, D., Origins and Evolution of Antibiotic Resistance. Microbiol. Mol. Biol. Rev. 2010, 74 (3), 417-433. 6. Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a Crisis for the
Health and Wealth of Nations.; 2014. 7. Lammie, S. L.; Hughes, J. M., Antimicrobial Resistance, Food Safety, and One Health:
The Need for Convergence. Annu. Rev. Food Sci. Technol. 2016, 7, 287-312. 8. Ahmed, S. A.; Barış, E.; Go, D. S.; Lofgren, H.; Osorio-Rodarte, I.; Thierfelder, K.,
Assessing the Global Poverty Effects of Antimicrobial Resistance. World Dev. 2018, 111, 148-
160. 9. Silver, L. L., Challenges of antibacterial discovery. Clin. Microbiol. Rev. 2011, 24 (1),
71-109. 71-109. 10
Lewis K The Science of Antibiotic Discovery Cell 2020 181 (1) 29-45 10. Lewis, K., The Science of Antibiotic Discovery. Cell 2020, 181 (1), 29-45. 11. Harbarth, S.; Theuretzbacher, U.; Hackett, J., Antibiotic Research and Development:
Business as Usual? J. Antimicrob. Chemother. 2015, 70 (6), 1604-1607. 12. Klein, E. Y.; Van Boeckel, T. P.; Martinez, E. M.; Pant, S.; Gandra, S.; Levin, S. A.;
Goossens, H.; Laxminarayan, R., Global Increase and Geographic Convergence in Antibiotic
Consumption Between 2000 and 2015. Proc. Natl. Acad. Sci. U S A 2018, 115 (15), E3463-
E3470. 13. World Health Organization Model List of Essential Medicines, 21st List, 2019; World
Health Organization: Geneva, 2019. 14. Sauvage, E.; Kerff, F.; Terrak, M.; Ayala, J. A.; Charlier, P., The Penicillin-Binding
Proteins: Structure and Role in Peptidoglycan Biosynthesis. FEMS Microbiol. Rev. 2008, 32 (2),
234-258. 15. Tipper, D. J.; Strominger, J. L., Mechanism of Action of Penicillins: a Proposal Based on
Their Structural Similarity to AcyL-D-Alanyl-D-Alanine. Proc. Natl. Acad. Sci. U S A 1965, 54,
1133-1141. 16. Papp-Wallace, K. M.; Endimiani, A.; Taracila, M. A.; Bonomo, R. ABBREVIATIONS SBL, serine β-lactamase; MBL, metallo-β-lactamase; AC, acylenzyme; TS, transition state; TI, tetrahedral
intermediate; QM/MM, quantum mechanics/molecular mechanics; US, umbrella sampling; FES, free
energy surface Supporting Information. Further details concerning simulation set-up and analysis; cluster analysis of
AC structures; Leu158 and V120 rotamer sampling; full results of FESs in different conformations;
analysis of DW approach; benchmarking details; Mulliken charge analysis (in PDF). Simulation
parameter files, input files, starting structures and TS structures/ensembles (included in ZIP file). 19.
Evans, B. A.; Amyes, S. G., OXA β-lactamases. Clin. Microbiol. Rev. 2014, 27, 241-63. References A., Carbapenems:
Past, Present, and Future. Antimicrob. Agents Chemother. 2011, 55 (11), 4943-4960. 17. Tooke, C. L.; Hinchliffe, P.; Bragginton, E. C.; Colenso, C. K.; Hirvonen, V. H. A.;
Takebayashi, Y.; Spencer, J., β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J. Mol. Biol. 2019, 431 (18), 3472-3500. 18. Ambler, R. P., The Structure of β-Lactamases. Phil. Trans. R. Soc. Lond. B 1980, 289,
321-331. 19. Evans, B. A.; Amyes, S. G., OXA β-lactamases. Clin. Microbiol. Rev. 2014, 27, 241-63. 20. Pitout, J. D. D.; Peirano, G.; Kock, M. M.; Strydom, K. A.; Matsumura, Y., The Global
Ascendency of OXA-48-Type Carbapenemases. Clin. Microbiol. Rev. 2019, 33 (1), e00102-19. 21. Thomson, K. S.; Munson, E., In Vitro Activity of Imipenem against Carbapenemase-
Positive Enterobacteriaceae Isolates Collected by the SMART Global Surveillance Program from
2008 to 2014. J. Clin. Microbiol. 2017, 55 (6), 1608-1611. ( )
22. Oueslati, S.; Nordmann, P.; Poirel, L., Heterogeneous Hydrolytic Features for OXA-48-
like β-lactamases. J. Antimicrob. Chemother. 2015, 70 (4), 1059-1063. 23. Poirel, L.; Castanheira, M.; Carrer, A.; Rodriguez, C. P.; Jones, R. N.; Smayevsky, J.;
Nordmann, P., OXA-163, an OXA-48-related Class D β-lactamase with Extended Activity
Toward Expanded-spectrum Cephalosporins. Antimicrob. Agents Chemother. 2011, 55 (6), 2546-
2551. 24. De Luca, F.; Benvenuti, M.; Carboni, F.; Pozzi, C.; Rossolini, G. M.; Mangani, S.;
Docquier, J. D., Evolution to Carbapenem-hydrolyzing Activity in Noncarbapenemase Class D
β-lactamase OXA-10 by Rational Protein Design. Proc. Natl. Acad. Sci. U S A 2011, 108 (45),
18424-18429. 25. Dabos, L.; Zavala, A.; Bonnin, R. A.; Beckstein, O.; Retailleau, P.; Iorga, B. I.; Naas,
T., Substrate Specificity of OXA-48 after β5-β6 Loop Replacement. ACS Infect. Dis. 2020, 6 (5),
1032–1043. 26. Oueslati, S.; Retailleau, P.; Marchini, L.; Berthault, C.; Dortet, L.; Bonnin, R. A.;
Iorga, B. I.; Naas, T., Role of the Arginine 214 in the Substrate Specificity of OXA-48. Antimicrob. Agents Chemother. 2020, 64 (5), e02329-19. 27. Akhter, S.; Lund, B. A.; Ismael, A.; Langer, M.; Isaksson, J.; Christopeit, T.; Leiros,
H. S.; Bayer, A., A Focused Fragment Library Targeting the Antibiotic Resistance Enzyme -
Oxacillinase-48: Synthesis, Structural Evaluation and Inhibitor Design. Eur. J. Med. Chem. 2018, 145, 634-648. 28. Akhtar, A.; Pemberton, O. A.; Chen, Y., Structural Basis for Substrate Specificity and
Carbapenemase Activity of OXA-48 Class D β-Lactamase. ACS Infect. Dis. 2020, 6 (2), 261-
271. 29. Papp-Wallace, K. M.; Kumar, V.; Zeiser, E. T.; Becka, S. References A.; van den Akker, F.,
Structural Analysis of The OXA-48 Carbapenemase Bound to A "Poor" Carbapenem Substrate,
Doripenem. Antibiotics (Basel) 2019, 8 (3), 145. p
(
)
( )
30. Stojanoski, V.; Hu, L.; Sankaran, B.; Wang, F.; Tao, P.; Prasad, B. V. V.; Palzkill, T.,
Mechanistic Basis of OXA-48-like β-Lactamases' Hydrolysis of Carbapenems. ACS Infect. Dis. 2021, 7 (2), 445-460. 31. Golemi, D.; Maveyraud, L.; Vakulenko, S.; Samama, J.-P.; Mobashery, S., Critical
Involvement of a Carbamylated Lysine in Catalytic Function of Class D β-lactamases. Proc. Natl. Acad. Sci. U S A 2001, 98 (25), 14281-14285. 32. Docquier, J. D.; Calderone, V.; De Luca, F.; Benvenuti, M.; Giuliani, F.; Bellucci, L.;
Tafi, A.; Nordmann, P.; Botta, M.; Rossolini, G. M.; Mangani, S., Crystal Structure of the
OXA-48 β-lactamase Reveals Mechanistic Diversity Among Class D Carbapenemases. Chem. Biol. 2009, 16, 540-547. 33. Birck, C.; Cha, J. C.; Cross, J.; Schulze-Briese, C.; Meroueh, S. O.; Schlegel, H. B.;
Mobashery, S.; Samama, J.-P., X-ray Crystal Structure of the Acylated β-Lactam Sensor Domain
of BlaR1 from Staphylococcus aureus and the Mechanism of Receptor Activation for Signal
Transduction. J. Am. Chem. Soc. 2004, 126, 13945-13947. 34. Fonseca, F.; Chudyk, E. I.; Van der Kamp, M. W.; Correia, A.; Mulholland, A. J.;
Spencer, J., The Basis for Carbapenem Hydrolysis by Class A β-lactamases: a Combined
Investigation Using Crystallography and Simulations. J. Am. Chem. Soc. 2012, 134, 18275-
18285. 35. Lohans, C. T.; Freeman, E. I.; Groesen, E. V.; Tooke, C. L.; Hinchliffe, P.; Spencer,
J.; Brem, J.; Schofield, C. J., Mechanistic Insights into β-Lactamase-Catalysed Carbapenem
Degradation Through Product Characterisation. Sci. Rep. 2019, 9 (1), 13608. 36. Hirvonen, V. H. A.; Mulholland, A. J.; Spencer, J.; Van der Kamp, M. W., Small
Changes in Hydration Determine Cephalosporinase Activity of OXA-48 β-Lactamases. ACS
Catal. 2020, 10 (11), 6188-6196. 37. Maier, J. A.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K. E.; Simmerling,
C., ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from
ff99SB. J. Chem. Theory Comput. 2015, 11, 3696-3713. 38. Vanquelef, E.; Simon, S.; Marquant, G.; Garcia, E.; Klimerak, G.; Delepine, J. C.;
Cieplak, P.; Dupradeau, F. Y., R.E.D. Server: a Web Service for Deriving RESP and ESP
Charges and Building Force Field Libraries for New Molecules and Molecular Fragments. Nucleic Acids Res. 2011, 39, W511-7. 39. Kästner, J., Umbrella Sampling. WIREs Comput. Mol. Sci. 2011, 1, 932-942 39. Kästner, J., Umbrella Sampling. References WIREs Comput. Mol. Sci. 2011, 1, 932-942. 40. Walker, R. C.; Crowley, M. F.; Case, D. A., The Implementation of a Fast and Accurate
QM/MM Potential Method in Amber. J. Comput. Chem. 2008, 29 (7), 1019-1031. 40. Walker, R. C.; Crowley, M. F.; Case, D. A., The Implementation of a Fast and Accurate
QM/MM Potential Method in Amber J Comput Chem 2008 29 (7) 1019 1031 41. Hermann, J. C.; Ridder, L.; Holtje, H. D.; Mulholland, A. J., Molecular Mechanisms of
Antibiotic Resistance: QM/MM Modelling of Deacylation in a Class A β-lactamase. Org. Biomol. Chem. 2006, 4 (2), 206-210. 42. Chudyk, E. I.; Limb, M. A.; Jones, C.; Spencer, J.; Van der Kamp, M. W.; Mulholland,
A. J., QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases. Chem. Commun. 2014, 50 (94), 14736-14739. 43. Hirvonen, V. H. A.; Hammond, K.; Chudyk, E. I.; Limb, M. A. L.; Spencer, J.;
Mulholland, A. J.; Van der Kamp, M. W., An Efficient Computational Assay for β-Lactam
Antibiotic Breakdown by Class A β-Lactamases. J. Chem. Inf. Model. 2019, 59 (8), 3365-3369. 44. Seabra, G. d. M.; Walker, R. C.; Elstner, M.; Case, D. A.; Roitberg, A. E.,
Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber
Molecular Dynamics Package. J. Phys. Chem. A 2007, 111 (26), 5655-5664. ,
;
,
;
,
;
,
;
g,
,
Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber
Molecular Dynamics Package. J. Phys. Chem. A 2007, 111 (26), 5655-5664. 45. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, M.; Haugk, M.; Frauenheim, T. H.;
Suhai, S.; Seifert, G., Self-Consistent-Charge Density-Functional Tight-Binding Method for
Simulations of Complex Materials Properties. Phys. Rev. B 1998, 58 (11), 7260-7268. 46. Niehaus, T. A.; Elstner, M.; Frauenheim, T. H.; Suhai, S., Application of an
Approximate Density-Functional Method to Sulfur Containing Compounds. J. Mol. Struct. THEOCHEM 2001, 541, 185-194. 47. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M., The
Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. I. The
Method. J. Comput. Chem. 1992, 13, 1011-1021. 48. Grossfield, A. WHAM: an Implementation of the Weighted Histogram Analysis Method. http://membrane.urmc.rochester.edu/content/wham/ (accessed 08/01/2020). 49. Marcos-Alcalde, I.; Setoain, J.; Mendieta-Moreno, J. I.; Mendieta, J.; Gomez-Puertas,
P., MEPSA: Minimum Energy Pathway Analysis for Energy Landscapes. Bioinformatics 2015,
31, 3853-3855. 50. Case, D. A.; Ben-Shalom, I. Y.; Brozell, S. R.; Cerutti, D. References S.; Cheatham, T. E. I.;
Cruzeiro, V. W. D.; Darden, T. A.; Duke, R. E.; Ghoreishi, D.; Giambasu, G.; Giese, T. J.;
Gilson, H.; Gohlke, H.; Goetz, A. W.; Greene, D.; Harris, R.; Homeyer, N.; Huang, Y.;
Izadi, S.; Kovalenko, A.; Krasny, R.; Kurtzman , T.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.;
Liu, J.; Luchko, T.; Luo, R.; Man, V.; Mermelstein, D.; Merz, K. M.; Miao, Y.; Monard, G.;
Nguyen, C.; Nguyen, H.; Onufriev, A.; Pan, F.; Qi, R.; Roe, D. R.; Roitberg, A.; Sagui, C.;
Schott-Verdugo, S.; Shen, J.; Simmerling, C. L.; Smith, J.; Swails, J.; Walker, R. C.; Wang,
J.; Wei, H.; Wilson, L.; Wolf, R. M.; Wu, X.; Xiao, L.; Xiong, Y.; M., Y. D.; P.A., K. AMBER 2019, University of California: San Francisco, 2019. 51. Salomon-Ferrer, R.; Gotz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C., Routine
Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent
Particle Mesh Ewald. J. Chem. Theory Comput. 2013, 9, 3878-3888. 52. Le Grand, S.; Götz, A. W.; Walker, R. C., SPFP: Speed Without Compromise—A
Mixed Precision Model for GPU Accelerated Molecular Dynamics Simulations. Comput. Phys. Commun. 2013, 184, 374-380. 53. Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C., Routine
Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent
Particle Mesh Ewald. J. Chem. Theory Comput. 2012, 8 (5), 1542-1555. 54. Smith, C. A.; Antunes, N. T.; Stewart, N. K.; Toth, M.; Kumarasiri, M.; Chang, M.;
Mobashery, S.; Vakulenko, S. B., Structural Basis for Carbapenemase Activity of the OXA-23 β-
lactamase from Acinetobacter baumannii. Chem. Biol. 2013, 20, 1107-1115. 55. Toth, M.; Smith, C. A.; Antunes, N. T.; Stewart, N. K.; Maltz, L.; Vakulenko, S. B.,
The Role of Conserved Surface Hydrophobic Residues in the Carbapenemase Activity of the
Class D β-lactamases. Acta Crystallogr. 2017, C73 (8), 692-701. 56. Aertker, K. M. J.; Chan, H. T. H.; Lohans, C. T.; Schofield, C. J., Analysis of β-lactone
Formation by Clinically Observed Carbapenemases Informs on a Novel Antibiotic Resistance
Mechanism. J. Biol. Chem. 2020, 295 (49), 16604-16613. 57. Dabos, L.; Bogaerts, P.; Bonnin, R. A.; Zavala, A.; Sacre, P.; Iorga, B. I.; Huang, D. T.; Glupczynski, Y.; Naas, T., Genetic and Biochemical Characterization of OXA-519, a Novel
OXA-48-Like β-Lactamase. Antimicrob. Agents Chemother. 2018, 62 (8), e00469-18. 58. Lohans, C. T.; van Groesen, E.; Kumar, K.; Tooke, C. References L.; Spencer, J.; Paton, R. S.;
Brem, J.; Schofield, C. J., A New Mechanism for β-Lactamases: Class D Enzymes Degrade 1β-
Methyl Carbapenems through Lactone Formation. Angew. Chem. Int. Ed. 2018, 57 (5), 1282-
1285. 59. Hirvonen, V. H. A.; Spencer, J.; Van der Kamp, M. W., Antimicrobial Resistance
Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding. Antimicrob. Agents Chemother. 2021, 65 (6), e00184-21. g
,
( )
60. Berg, J. M.; Tymoczko, J. L.; Stryer, L., Biochemistry. 5th edition. W. H. Freeman: New
York, 2002. 61. Antunes, N. T.; Lamoureaux, T. L.; Toth, M.; Stewart, N. K.; Frase, H.; Vakulenko, S. B., Class D β-lactamases: are they all carbapenemases? Antimicrob. Agents Chemother. 2014, 58
(4), 2119-2125. 62. Van der Kamp, M. W.; Chaudret, R.; Mulholland, A. J., QM/MM modelling of
ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis. FEBS J. 2013, 280 (13), 3120-3131. 63. Shan, S.; Daniel Herschlag, D., Energetic Effects of Multiple Hydrogen Bonds. Implications for Enzymatic Catalysis. J. Am. Chem. Soc. 1996, 118 (24), 5515-5518. 63. Shan, S.; Daniel Herschlag, D., Energetic Effects of Multiple Hydrogen Bonds
Implications for Enzymatic Catalysis. J. Am. Chem. Soc. 1996, 118 (24), 5515-5518. 64. Porter, M. A.; Hall, J. R.; Locke, J. C.; Jensen, J. H.; Molina, P. A., Hydrogen bonding
is the prime determinant of carboxyl pKa values at the N-termini of alpha-helices. Proteins 2006,
63 (3), 621-635. 65. Tao, L.; Han, J.; Tao, F., Correlations and Predictions of Carboxylic Acid pKa Values
Using Intermolecular Structure and Properties of Hydrogen-Bonded Complexes. J. Phys. Chem. A 2008, 112, 775-782. 66. Mhashal, A. R.; Pshetitsky, Y.; Cheatum, C. M.; Kohen, A.; Major, D. T., Evolutionary
Effects on Bound Substrate pKa in Dihydrofolate Reductase. J. Am. Chem. Soc. 2018, 140 (48),
16650-16660. 67. Liao, Q.; Kulkarni, Y.; Sengupta, U.; Petrovic, D.; Mulholland, A. J.; Van der Kamp,
M. W.; Strodel, B.; Kamerlin, S. C. L., Loop Motion in Triosephosphate Isomerase Is Not a
Simple Open and Shut Case. J. Am. Chem. Soc. 2018, 140 (46), 15889-15903.
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Automated Model Construction for Combined Sewer Overflow Prediction Based on Efficient LASSO Algorithm
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IEEE transactions on systems, man, and cybernetics. Systems
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cc-by
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Automated Model Construction for Combined
Sewer Overflow Prediction Based on
Efficient LASSO Algorithm Wanqing Zhao, Member, IEEE, Thomas H. Beach, and Yacine Rezgui from precipitation events and sewage/wastewater from domes-
tic, industrial, commercial and municipal release together in
the same sewer [1]–[3]. The wastewater gathered in the CSS
is then directed to wastewater treatment plants (WWTPs),
usually driven by gravity through paved inclined sewers
together with a small number of lift pumping stations to
assist water transportation between sewers. It should be noted
the fact that in dry weather conditions and during light to
moderate rainfall, CSSs are usually designed to be capable of
conveying all the flows to WWTPs [4]. Besides, a compelling
feature of CSSs is that the system is equipped with com-
bined sewer overflow (CSO) structures [5]–[7] to discharge
combined untreated wastewater and stormwater runoff to
receiving water bodies (via a consent from governing bodies),
in order not to overload the maximum capacity of CSSs in
case of heavy rainfall (sometimes even moderate rainfall in
reality) [4], [8]. The occurrence of CSO spillages, especially
unexpected ones can potentially lead to environmental pol-
lution [9]. A variety of research has therefore been devoted
to identifying various pollutants, the possible impact on the
environment and drinking water quality and correspondingly
coping strategies [10], [11]. Since the actual use of CSOs is
stringently regulated by environmental agencies, unexpected
spillages can also incur fines and damage public relations of
water utilities. Whilst the release of diluted wastewater via
CSO structures has potential adverse effects, it can, however,
help avoid overloading of CSSs and reduce the risk of sewer
flooding on properties and streets [8], [12]. Therefore, the
real-time CSO status should be adequately monitored and
predicted to support the waste network management process. Abstract—The prediction of combined sewer overflow (CSO)
operation in urban environments presents a challenging task
for water utilities. The operation of CSOs (most often in heavy
rainfall conditions) prevents houses and businesses from flood-
ing. However, sometimes, CSOs do not operate as they should,
potentially bringing environmental pollution risks. Therefore,
CSOs should be appropriately managed by water utilities, high-
lighting the need for adapted decision support systems. This
paper proposes an automated CSO predictive model construc-
tion methodology using field monitoring data, as a substitute
for the commonly established hydrological-hydraulic modeling
approach for time-series prediction of CSO statuses. It is a
systematic methodology factoring in all monitored field vari-
ables to construct time-series dependencies for CSO statuses. 1254 1254 IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 Automated Model Construction for Combined
Sewer Overflow Prediction Based on
Efficient LASSO Algorithm The model construction process is largely automated with lit-
tle human intervention, and the pertinent variables together
with their associated time lags for every CSO are holistically
and automatically generated. A fast least absolute shrinkage
and selection operator solution generating scheme is proposed
to expedite the model construction process, where matrix inver-
sions are effectively eliminated. The whole algorithm works in a
stepwise manner, invoking either an incremental or decremental
movement for including or excluding one model regressor into, or
from, the predictive model at every step. The computational com-
plexity is thereby analyzed with the pseudo code provided. Actual
experimental results from both single-step ahead (i.e., 15 min)
and multistep ahead predictions are finally produced and ana-
lyzed on a U.K. pilot area with various types of monitoring data
made available, demonstrating the efficiency and effectiveness of
the proposed approach. Index Terms—Combined sewer overflows (CSOs), efficient
model construction, hydraulics, prediction, wastewater. To gain insight into CSO behaviors, typically, physical
hydrological-hydraulic models of the large-scale catchment
of interest must be developed and elaborately calibrated, in
connection with the actual CSO level formation process (i.e.,
the hydrological-hydraulic process of forming CSO levels,
from rainfall through to runoff and network flows) [13]–[15]. The whole model development process is time-consuming and
associated with high costs. Sufficient spatial and temporal res-
olution of rainfall data [16] monitored from either rain-gauge
stations or weather radar and flow survey data are needed
to delicately calibrate such physical models. In this regard,
Schellart et al. [17] discussed different sources of errors that
might be presented in rain-gauge (e.g., blockages, wetting, and
evaporation) and radar (e.g., spurious echoes and attenuation)
approaches. Currently, dedicated commercial products, such as
InfoWorks ICM [18], SWMM [19], and MOUSE [20], can be Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/licenses/by/3.0/ This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/licenses/by/3.0/ is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecommons.org/li I. INTRODUCTION In addition to the CSO and rainfall data, other
field variables such as wet well levels and pumped flows are
also examined in the model construction. All field variables
are dealt with simultaneously in a global manner during the
model construction process, set by the criteria of L1 norm
regularization, without considering each correlation separately
and independently. Specifically, given the overall methodology,
each CSO predictive model also captures its interrelationships
with other pertinent CSOs in the field. used to build these physical models. A list of weaknesses faced
by this conventional model building approach is summarized
in Section II. Alternatively,
the
control-oriented
modeling
approach [21], [22] using the “virtual tank” concept can
be adopted to approximate the field model. It is a simplified
mathematical processing of a number of subcatchments
divided from the whole catchment of interest, where the
network
topology
and
some
conversion
and
absorption
coefficients
need
to
be
specified
and
estimated. Such
modeling process requires the involvement of field experts,
which can be viewed as a lighter version of the traditional
physical modeling approach. It also includes manual analysis
processes, such as model structure determination based on
the provision of network topology and division of catchment. With such simplified model, model-based predictive control
techniques can then be adopted to control the sewerage
network, for example, with the implementation of detention
tanks and actuation of retention/diversion gates. Unlike the above model designed for control problems,
recent research has begun to study employing data-driven
approaches to tackle the time-series prediction of CSOs for
warning of future problems within the sewerage network,
such as the use of artificial neural networks [23]–[25]. Their
methodologies have been found favorable for modeling the
water hydrological-hydraulic behaviors without the need for
an in-depth understanding of the underlying sewer system. Of these studies, the cross-correlation between the CSO and
rainfall variables, and the serial-correlation within the CSO,
are manually analyzed for various time lags in order to find
an appropriate range of lags to be considered as data-driven
model’s inputs. Though promising results have been demon-
strated, there is still a lack of systematic work. Some research
questions are still open to be addressed for the data-driven
approach. This paper is organized as follows. The preliminary rel-
evant domain knowledge and mathematical formulation of
CSO predictive models are given in Section II. Section III
presents the LASSO concept and its stepwise solutions. I. INTRODUCTION W W
ITHIN
the
water
infrastructure
of
an
urban
environment, combined sewer systems (CSSs) are
commonly employed to collect and convey both stormwater Manuscript received February 22, 2017; revised April 30, 2017; accepted
June 22, 2017. Date of publication August 21, 2017; date of current ver-
sion May 14, 2019. This work was supported by the EU Seventh Framework
Programme under Grant 619795 (WISDOM) involving 11 partners, includ-
ing universities/institutes, local authorities, water utilities, and ICT companies. This paper was recommended by Associate Editor K. T. Seow. (Corresponding
author: Wanqing Zhao.) The authors are with the School of Engineering, Cardiff University, Cardiff
CF24 3AA, U.K. (e-mail: zhaow9@cardiff.ac.uk; beachth@cardiff.ac.uk;
rezguiy@cardiff.ac.uk). Color versions of one or more of the figures in this paper are available
online at http://ieeexplore.ieee.org. Color versions of one or more of the figures in this paper are available
online at http://ieeexplore.ieee.org. Digital Object Identifier 10.1109/TSMC.2017.2724440 This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://creativecom This work is licensed under a Creative Commons Attribution 3.0 License. For more information, see http://cre ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1255 without the need of human intervention and network topology. The problem is defined on top of the field under investi-
gation and the current practice of network operation (e.g.,
using predictive control or local control techniques). In light
of the aforementioned considerations, this paper proposes a
systematic and automated approach for CSO predictive model
construction. The whole model construction process is largely
automated based on monitored field variables, in the catchment
of interest. The least absolute shrinkage and selection opera-
tor (LASSO) is employed to perform field variable and the
associated time lag selection, as well as model construction in
a stepwise manner under the well-known L1 norm regulariza-
tion. With the adjustment of the regularization parameter, the
overall model size is controllable, enabling the determination
of pertinent field variables and lags for a particular CSO. To
improve the computational efficiency of model construction,
an efficient LASSO solution generating scheme is proposed
based on least angle regression (LAR). The matrix inversions
are thereby eliminated and different model sizes in the LASSO
sense can be produced in sequence. A real catchment is stud-
ied as part of this paper with more than 20 CSOs with good
data availability. I. INTRODUCTION The
efficient LASSO solution generating scheme for CSO model
construction is then given in Section IV. The mathematical
derivations, algorithm and computational complexity are all
detailed therein. The experimental results from a U.K. pilot
area are presented in Section V, where a description of the
catchment and the detailed analysis of model construction
results are given. Finally, Section VI concludes this paper. 1) The whole model construction process needs a certain
degree of human intervention (e.g., the manual correla-
tion analysis and model trial processes vary from site to
site) and is not fully automated, limiting the transferabil-
ity of CSO model construction in different catchments
and urban configurations. 2) The quantity of CSOs being analyzed is limited where
only one or several CSOs are studied within a catchment
for predictive model construction. II. PRELIMINARIES AND CSO MODEL FORMULATION A conventional modeling approach can therefore be used
to predict CSO statuses given the predicted/calibrated meteo-
rology rainfall and wastewater release information. However,
the whole model construction process is time-consuming and
costly. The developed model also needs to be carefully exam-
ined and calibrated. Some key restrictions for use of such
conventional approach to develop CSO predictive models are
as follows. complexity of the CSO behavior (e.g., seasonal variations). Practically, the model can be reconstructed every month to
improve accuracy before the required historical data has been
made available. Within the data-driven approach, the nonlin-
ear dynamic time-series relationships between input/process
variables and the CSO status are then artificially established
exploring the measured data. Considering the general avail-
ability of data, the field variables presented in the problem
can be categorized as system input variables, system pro-
cess variables, and CSO outputs, which are in turn defined
as follows. 1) In-depth expert knowledge in the wastewater domain. 2) Sophisticated modeling skills in terms of using various
modeling software packages. 3) Detailed information gathered about the catchment and
sewer network. 4) Lack of model transportability (site specific). 1) System Input Variables: Specifying the external infor-
mation that can be generally considered as the inputs to
the sewer system. 5) Low model adaptability to change (e.g., modification
and aging of network). 6) Long model development cycle. a) Rainfall Data: This involves real-time rainfall
information which is envisaged to have large
impact on CSO level formation. Rain-gauge and
radar measurements are both acceptable with suf-
ficient spatial (e.g., 1–5 km) and temporal (e.g.,
5–15 min) resolutions [16], [17], [26], [27] for the
catchments of interest. 7) High model development expenses. 8) Time-consuming model simulation process. 9) Complicated model calibration process. Although the advantage of using a hydrological-hydraulic
approach lies in the ability to provide accurate and reli-
able CSO time-series predictions, its wide applications are
inevitably limited by the above restrictions. Hence, as an
alternative to conventional models, in the sense of provid-
ing time-series predictions for a number of time-steps, the
data-driven approach relying on the monitoring data from the
field is to be investigated in this paper. The intention is not
to completely replace the often-needed hydrological-hydraulic
model, as the latter is essential to support a number of
stormwater management functionalities, such as the modeling
of drainage networks for real-time control and water behav-
ior analysis. II. PRELIMINARIES AND CSO MODEL FORMULATION To predict CSO statuses, the conventional approach uses
a first-principle mechanism by constructing a physical model
conceptualizing the actual process of CSO level formation. It
usually involves the development of two submodels that cor-
respond to the two subprocesses of the CSO level formation,
i.e., hydrological process and hydraulic process, each briefly
described below. 3) Only pairwise correlation between a CSO and a vari-
able is considered sequentially with distinct time lags
when determining appropriate variable lags, while the
global relationship across all field variables is not fully
analyzed and utilized. 4) Only CSO and rainfall data are included in the model
construction, rarely are other field variables investigated. 4) Only CSO and rainfall data are included in the model
construction, rarely are other field variables investigated. 5) The interrelationships between different CSOs are not
captured in the model construction process. 1) The hydrological process that takes place in the catch-
ment, where rainfall is the input of the process and
the runoff hydrograph is the output. It consists of
the calculation of effective precipitation and then the
calculation of runoff hydrographs, factoring in param-
eters, such as evaporation, infiltration, wetting, and
surface storage [13]. Through this submodel construc-
tion, a hydrological rainfall-runoff relationship can be
established. 5) The interrelationships between different CSOs are not
captured in the model construction process. 6) The whole model construction process is still time-
consuming. The research problem in this paper, therefore, is to achieve
the real-time prediction of future CSO statuses [single-
step (i.e., 15 min) and multistep ahead predictions] using
the previously observed statuses of pertinent field variables IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1256 Fig. 1. CSO data-driven model prediction framework. 2) The hydraulic process that takes place inside the under-
ground sewer network, where the above runoff hydro-
graph together with the sewage/wastewater released
from residents and businesses is the input of the process,
leading to the generation of network flows and CSO lev-
els. The diluted wastewater in the network is conveyed
either to WWTPs for treatment before being discharged
or to CSO structures for direct discharge into the envi-
ronment (e.g., following a heavy rainfall). Through this
submodel construction, a hydraulic relationship between
runoff/wastewater and network flows/CSO statuses can
be established. Fig. 1. CSO data-driven model prediction framework. II. PRELIMINARIES AND CSO MODEL FORMULATION , y(t −ly)] ∈ℜM (M = NIPlu + NCSOly), i,m
is the corresponding model coefficient for the ith regressor,
and m is the number of selected model regressors. Assuming
that the full set of φ(t) is employed at the beginning of model
construction while N training samples are provided, (2) can
be reformulated as the following generic matrix form: where pi(t) (i = 1, . . . , m) is the ith model regressor selected
from the set φ(t) = [ϕ1(t), . . . , ϕM(t)] = [u(t −1), . . . , u(t −
lu), y(t −1), . . . , y(t −ly)] ∈ℜM (M = NIPlu + NCSOly), i,m
is the corresponding model coefficient for the ith regressor,
and m is the number of selected model regressors. Assuming
that the full set of φ(t) is employed at the beginning of model
construction while N training samples are provided, (2) can
be reformulated as the following generic matrix form: To efficiently solve the LASSO problem, Efron et al. [38]
proposed a novel approach based on LAR. Interestingly, the
LAR approach operates in a stepwise selection manner. This
means that it is able to locate the global optimum model
regressors in different sizes in a stepwise manner, in corre-
spondence to different values of λ in the LASSO sense. This
is an important property as the traditional forward/backward
stepwise selection has historically been only able to search for
suboptimal subsets of regressors in the least-squares sense. In
detail, every step, say at the kth step, a submodel k ˆθk is
introduced to explain the remaining model error ek−1 result-
ing from the previous step, where ˆθk = γk(T
k k)−1T
k ek−1,
k = [p1, . . . , pk] and γk are, respectively, the submodel
coefficients, selected model regressors and step size. As γk
increases from zero, the next model regressor (pk+1) to be
selected is determined such that the largest absolute correlation
between those unselected regressors (say ϕi, i = k+1, . . . , M)
and the resulting model error ek is first found just equal
to the absolute correlation incurred by any selected regres-
sors. This will make the absolute correlations exhibited for
selected regressors always equal to one another and no smaller
than those for unselected ones. II. PRELIMINARIES AND CSO MODEL FORMULATION It is worth noting that the aim of this paper is
to predict future CSO statuses (e.g., the future statuses of
the next 15–60 min) in real-time for the purpose of daily
network management under given catchment, network and
operational configurations, rather than performing predictions
between different constructions of network and catchment
infrastructure. The low model adaptability comment above,
therefore, refers to the fact that, in order to provide such
CSO time-series predictions after the change of catchment
and network, the physical network modeling approach would
need a high level of human intervention and calibration
work. In contrast, the data-driven approach just requires an
execution of the automated model reconstruction based on
new monitoring data. However, sufficient quantity of new
data, say one year, should be collected to reflect the full b) Consumer’s Discharge: It provides another channel
of input to the sewer system from the domes-
tic release of sewage as well as other forms of
discharge such as industrial wastewater. This is
deemed to have considerably smaller impact to the
occurrence of CSO spillage. 2) 2) System Process Variables: Specifying the internal infor-
mation originating from the operation of sewer systems. 2) System Process Variables: Specifying the internal infor-
mation originating from the operation of sewer systems. a) Flow variables, such as those monitored from
pumps, sewers, treatment works, and inlets and
outlets of temporary storage tanks. a) Flow variables, such as those monitored from
pumps, sewers, treatment works, and inlets and
outlets of temporary storage tanks. b) Level variables, such as those monitored from wet
wells and manholes. c) Pump running statuses. c) Pump running statuses. 3) CSO Statuses: Specifying the actual levels/flows in CSO
structures. As CSO statuses are of particular interest to
the underlying research question, these are treated differ-
ently to other system process variables described above
and thus taken as the output variable from the sewer
system. Given the above discussion, the following well-known time-
series prediction model (as depicted in Fig. 1), the nonlinear
autoregressive model with exogenous inputs [28]–[30], is ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1257 employed to cope with the data-driven prediction of CSOs
in the waste sector where λ is a tradeoff parameter controlling the degree of
L1 regularization. II. PRELIMINARIES AND CSO MODEL FORMULATION , yNCSO(t)] defines the CSO output variables
with a maximal time lag of ly, and NCSO is the total number of
CSO structures, fi(·) and ei(t) are, respectively, the predictive
model and model residual to be identified for the ith CSO. As
shown in Fig. 1, the CSO prediction problem lies in the iden-
tification of a data-driven model that relates the future CSO
status to the past status of field variables. It should be noted
that though the next step (the next 15 min for the pilot area to
be given in Section V-A) prediction is formulated in (1) and
primarily pursued in this paper, multistep predictions can sim-
ply be achieved by replacing yi(t) and ei(t) with yi(t+tm) and
ei(t + tm) therein (where tm + 1 ≥2 is the number of multiple
steps predicted ahead). For simplicity, the subscript i in yi(t),
fi(·) and ei(t) will be omitted from now on to generally refer
to any CSO quantity. Through deducing the gradient and subgradient of the
objective function (4) with respect to the model coefficient
vector , the following Karush–Kuhn–Tucker optimal condi-
tions [34] can be obtained for deriving an LASSO solution for
a given λ: Te = λs
(5)
where s = [s1, . . . , sM]T and
si ∈
⎧
⎪⎨
⎪⎩
{1},
ˆi,M > 0
(6)
{−1},
ˆi,M < 0
(7)
[−1, 1],
ˆi,M = 0. (8) (5) The task then involves extracting a proper set of field
variables associated with certain time lags to construct the
following model for each CSO identity: (8) Therefore, an LASSO solution ( ˆi,M, i = 1, . . . , M) is
considered to satisfy (5)–(8), simultaneously. This leads to
a quadratic programming problem and there is no general
analytical solution available [37]. Therefore, an LASSO solution ( ˆi,M, i = 1, . . . , M) is
considered to satisfy (5)–(8), simultaneously. This leads to
a quadratic programming problem and there is no general
analytical solution available [37]. y(t) =
m
i=1
pi(t)i,m + e(t)
(2) (2) where pi(t) (i = 1, . . . , m) is the ith model regressor selected
from the set φ(t) = [ϕ1(t), . . . , ϕM(t)] = [u(t −1), . . . , u(t −
lu), y(t −1), . . . II. PRELIMINARIES AND CSO MODEL FORMULATION Based on this property and to
find successive sets of LASSO solutions, the following two
quantities of γk (k = 1, . . . , M −1) need to be computed: y = + e
(3) y = + e (3) where
y
=
[y(1), . . . , y(N)]T
∈
ℜN
and
e
=
[e(1), . . . , e(N)]T ∈ℜN are, respectively, the actual CSO
output and model error vectors,
=
[ϕ1, . . . , ϕM]
∈
ℜN×M formulates the initial CSO regression matrix (ϕi =
[ϕi(1), . . . , ϕi(N)]T,
1
≤
i
≤
M),
and
=
[1,M, . . . , M,M]T is the model parameter vector. where
y
=
[y(1), . . . , y(N)]T
∈
ℜN
and
e
=
[e(1), . . . , e(N)]T ∈ℜN are, respectively, the actual CSO
output and model error vectors,
=
[ϕ1, . . . , ϕM]
∈
ℜN×M formulates the initial CSO regression matrix (ϕi =
[ϕi(1), . . . , ϕi(N)]T,
1
≤
i
≤
M),
and
=
[1,M, . . . , M,M]T is the model parameter vector. II. PRELIMINARIES AND CSO MODEL FORMULATION Noting that the L1 regularization possesses
better shrinking properties compared to the well-known L2
ridge regularization (||||2
2), in terms of being able to force
part model coefficients exactly to zeros [36]. However, the
objective function is no longer quadratic though still con-
vex; the corresponding solutions become nonlinear and no
closed form expression is thus available. As λ varies from
0 to larger values, the resultant coefficients generally move
from the least-squares estimate to partial zeros, until complete
zeros (meaning that different sizes of optimal model regressors
can be selected in the LASSO sense). yi(t) = fi
u(t −1), . . . , u(t −lu), y(t −1), . . . ,
y
t −ly
+ ei(t), i = 1, . . . , NCSO (1) where u(t) = [u1(t), . . . , uNIP(t)] denotes the actual sewer
system’s input and process variables (with the total number
being NIP) at time sequence t with a maximal time lag of lu,
y(t) = [y1(t), . . . , yNCSO(t)] defines the CSO output variables
with a maximal time lag of ly, and NCSO is the total number of
CSO structures, fi(·) and ei(t) are, respectively, the predictive
model and model residual to be identified for the ith CSO. As
shown in Fig. 1, the CSO prediction problem lies in the iden-
tification of a data-driven model that relates the future CSO
status to the past status of field variables. It should be noted
that though the next step (the next 15 min for the pilot area to
be given in Section V-A) prediction is formulated in (1) and
primarily pursued in this paper, multistep predictions can sim-
ply be achieved by replacing yi(t) and ei(t) with yi(t+tm) and
ei(t + tm) therein (where tm + 1 ≥2 is the number of multiple
steps predicted ahead). For simplicity, the subscript i in yi(t),
fi(·) and ei(t) will be omitted from now on to generally refer
to any CSO quantity. where u(t) = [u1(t), . . . , uNIP(t)] denotes the actual sewer
system’s input and process variables (with the total number
being NIP) at time sequence t with a maximal time lag of lu,
y(t) = [y1(t), . . . III. LASSO AND ITS STEPWISE SOLUTIONS Given (3), a relevant set of field variables together with
appropriate time lags must be identified in order to con-
struct the predictive model of a particular CSO. In this
paper, LASSO [31]–[34] is adopted to perform such vari-
able selection. Compared with other model selection methods,
such as forward/backward stepwise selection and ridge regres-
sion [28], LASSO is able to perform both variable selection
and regularization with enhanced generalization ability, while
also possessing geometric and Bayesian interpretations [35]. Essentially, the objective function of LASSO is to minimize ⎧
⎪⎪⎪⎨
⎪⎪⎪⎩
γ ⋆
k =
M
min
i=k+1
±ϕT
i ek−1 −
pT
k ek−1
±ϕT
i k(T
k k)−1T
k ek−1 −
pT
k ek−1
+
(9)
γ ◦
k =
k−1
min
i=1 [−ˆi,k−1/ ˆθi,k]+
(10) ⎧
⎪⎪⎪⎨γ ⋆
k =
M
min
i=k+1
±ϕT
i ek−1 −
pT
k ek−1
±ϕT
i k(T
k k)−1T
k ek−1 −
pT
k ek−1
+
(9) (9) (10) J(λ, ) = 1
2eTe + λ||||1
(4) J(λ, ) = 1
2eTe + λ||||1 (4) IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1258 the following main properties [39], [40]: where “[]+” denotes retrieving the minimum but positive value
for the above two quantities of γk, “±” means that the cor-
responding values in the denominator and numerator of (9)
should be chosen as either positive or negative simultaneously,
ˆi,k−1 is the accumulated coefficient for the ith model regres-
sor until the previous step with k −1 regressors selected, and
[ ˆθ1,k, . . . , ˆθk,k]T = (T
k k)−1T
k ek−1. ⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎩
Rk = Rk−1 −
Rk−1pkpT
k RT
k−1
pT
k Rk−1pk
,
k = 1, . . . , M
(11)
Rkpi = 0; Rkei = Rky,
i = 1, . . . , k
(12)
pT
i Ri−1ej = pT
i Ri−1y
j
l=i
(1 −γl)
i ≤j ≤k −1, 1 ≤i ≤k −1. (13) k
k
Here, on the one hand, if 0 < γ ◦
k ≤γ ⋆
k is not met, then
γk = γ ⋆
k and the (k + 1)th regressor pk+1 = arg γ ⋆
k is selected
to form the new regression matrix, i.e., k+1 = [k, pk+1]. III. LASSO AND ITS STEPWISE SOLUTIONS The LASSO conditions (5)–(8) are all satisfied simply because
the absolute correlations as stated in (5)–(7) for the selected
regressors are the same (being the value of the tradeoff param-
eter λ) and greater than that for any candidate regressors as
indicated in (5) and (8). On the other hand, if 0 < γ ◦
k ≤γ ⋆
k
is met, then γk = γ ◦
k and the rth regressor pr = arg γ ◦
k
is to be removed from the current regression matrix, result-
ing in the new one ˜k−1 = [˜p1, . . . , ˜pk−1]. This is because
if the selection proceeds using γ ⋆
k and thus the model size
increases, the model coefficient sign for regressor pr is going
to be changed and thus different to the sign of this term’s
correlation, breaking the LASSO sign condition (6) or (7). To continue meeting the LASSO conditions, pr is required to
be removed from the model, through adjusting the step size
(i.e., γk = γ ◦
k ) accordingly to just make the corresponding
model coefficient equal to zero. Therefore, as the controlling
parameter λ (equally the absolute correlation for the selected
regressors) decreases, it can be found that though the num-
ber of nonzero model coefficients overall increases it does not
increase in a monotonic fashion. (13) To facilitate continuous computation of (9), a set of
variables including scalars, vectors and matrices have been
used and updated throughout the model construction process. Assuming that a total of k regressors have just been added
into the model while deciding the size of γ ⋆
k , those variables
are expressed as follows (ρk ∈ℜ, ck) ∈ℜM−k, dk) ∈ℜM−k,
Ak) ∈ℜk×M, and bk) ∈ℜk), which can later be extended in
the decremental movement where removal of model regressor
occurs: ⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩
ρk =
pT
i ek−1
,
i = 1, . . . , k
(14)
ck)
i = ϕT
i ek, k = 0, . . . , M −1; i = k + 1, . . . , M
(15)
dk)
i = ϕT
i k(T
k k)−1T
k ek−1
k = 1, . . . , M −1; i = k + 1, . . . , M
(16)
ak,i = pT
k Rk−1ϕi,
k = 1, . . . , M; i = k, . . . III. LASSO AND ITS STEPWISE SOLUTIONS , M
(17)
bk = pT
k Rk−1y,
k = 1, . . . , M. (18) The step size in (9) is now computed as γ ⋆
k =
M
min
i=k+1
±ck−1)
i
−ρk
±dk)
i −ρk
+
,
k = 1, . . . , M −1. (19) (19) B. Decremental Movement Assuming that now we are going to determine the step size
γk (where an error vector ek−1 and a total of k selected model
regressors are given) and γ ⋆
k is computed as in the previous
section as if the (k + 1)th regressor is to be added into the
predictive model, the value of γ ◦
k is taken as the smallest pos-
itive one that drives an existing model coefficient to zero, given
by (10). First of all, ˆθi,k can be computed as ˆθ1,k, . . . , ˆθk,k
T
=
T
k k
−1T
k ek−1
=
T
k k
−1T
k
y −k−1 ˆk−1
=
T
k k
−1T
k y −
ˆ
T
k−1, 0
T
=
ˆϑ1,k −ˆ1,k−1, . . . , ˆϑk−1,k −ˆk−1,k−1, ˆϑk,k
T
(20) ˆθ1,k, . . . , ˆθk,k
T
=
T
k k
−1T
k ek−1
=
T
k k
−1T
k
y −k−1 ˆk−1
=
T
k k
−1T
k y −
ˆ
T
k−1, 0
T
=
ˆϑ1,k −ˆ1,k−1, . . . , ˆϑk−1,k −ˆk−1,k−1, ˆϑk,k
T
(20) IV. EFFICIENT LASSO ALGORITHM FOR AUTOMATED
CSO MODEL CONSTRUCTION Therefore, whilst only the increase of model size is consid-
ered, the aforementioned (11)–(19) give the rationales for fast
computation of its step size. The full algorithm, computational
complexity and relevant derivations can be referred to [39]. Based on these, the efficient removal of model regressors to
obtain LASSO solutions when triggering condition (10) will
be given based on the further adjustment of (14)–(18). As presented in the previous section, the key task now is
to determine the size γk successively in order to derive dif-
ferent sets of LASSO solutions. This in turn lies in how to
efficiently compute γ ⋆
k and γ ◦
k based on (9) and (10). An
efficient LASSO solution generating scheme is proposed in
this section to relax the heavy computation requirements of
performing matrix inversions and vector correlations. As men-
tioned previously, the model construction process guided by
the LASSO criterion involves the bidirectional movement of
model regressors for either including or excluding a regres-
sor at every step, i.e., incremental movement and decremental
movement. The incremental movement performs the same as
in the original LAR and its efficient solution was recently
introduced by Zhao et al. [39], where a regression framework
was given for forward selection in LAR. To enable the efficient
derivation of LASSO solutions, the incremental movement
is briefly introduced first, followed by the decremental
movement. A. Incremental Movement To perform efficient computations in the case that only the
increase of model size is allowed, a new efficient LAR algo-
rithm has recently been presented in [39]. In detail, a so-called
residue matrix is defined as Rk = I −k(T
k k)−1T
k , with (20) ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1259 where Rky = y −k(T
k k)−1T
k y = y −(p1 ˆϑ1,k + · · · +
pk ˆϑk,k) and the following can be obtained for i = k, . . . , 1: On the other hand, the associated parameters ˆθi,k−1 (i =
1, . . . , k −1) for the newly added submodel are given
by [ ˆθ1,k−1, . . . , ˆθk−1,k−1]T
=
( ˜
T
k−1 ˜k−1)−1 ˜
T
k−1ek. As
described at the beginning of this section, in order to pro-
ceed with the algorithm and determine the value of γ ◦
k−1 and
γ ⋆
k−1 based on the reduced set of selected regressors, the term
˜dk−1) ∈ℜM−k+1 in (27) and the term ˆθi,k−1 (i = 1, . . . , k−1)
need computed. By using (11), the direction vector ˜dk−1)
i ˆϑi,k = pT
i Ri−1y −k
l=i+1 pT
i Ri−1pl ˆϑl,k
pT
i Ri−1pi
= bi −k
l=i+1 ai,l ˆϑl,k
ai,i
. (21) ai,i Given that ˆk−1 is already known from the previous pro-
cess, the corresponding model regressor pr = arg mink−1
i=1
[−ˆi,k−1/ ˆθi,k]+ will be removed from the selected regression
matrix k in the case that 0 < γ ◦
k ≤γ ⋆
k . Otherwise, the
selection procedure proceeds as described in the previous sec-
tion, where the regression matrix expands by adding one more
regressor. p
y
g
(i = k, . . . , M) can be calculated as (i = k, . . . , M) can be calculated as ˜dk−1)
k
= ck−1)
k
−pT
r ˜Rk−1ek
= ck−1)
k
−pT
r ˜Rk−1
y −˜k−1 ˆk−1
= ck−1)
k
−pT
r ˜Rk−1y (28) and for i = k + 1, . . . , M and for i = k + 1, . . . A. Incremental Movement , M ˜dk−1)
i
= (1 −γ ◦
k )dk)
i −ϕT
i ˜Rk−1prpT
r ˜Rk−1ek
pTr ˜Rk−1pr
= (1 −γ ◦
k )dk)
i −ϕT
i ˜Rk−1prpT
r ˜Rk−1y
pTr ˜Rk−1pr
(29) Now, consider that the removal of some selected regressor
pr from the regression matrix is required at the kth step, first
of all, the entries of the correlation vector ck−1) ∈ℜM−k+1
for the remaining regressors are updated as (29) ck−1)
i
=
pT
r ek =
1 −γ ◦
k
ρksr,
i = k
ϕT
i ek = ck−1)
i
−γ ◦
k dk)
i ,
i = k + 1, . . . , M
(22) (22) where ˜Rk−1 = I −˜k−1( ˜
T
k−1 ˜k−1)−1 ˜
T
k−1 denotes the
residue matrix resulted from excluding pr from the regres-
sion matrix k. Similar as in (20), the following can also be
easily obtained: where sr denotes the sign of the correlation for pr. Moreover,
the absolute correlation for selected regressors is simply
updated as ρk−1 = (1−γ ◦
k )ρk. The resulted model coefficients
from adding the current submodel can be computed as [ ˆθ1,k−1, . . . , ˆθk−1,k−1]T
= ( ˜
T
k−1 ˜k−1)−1 ˜
T
k−1ek
= ( ˜
T
k−1 ˜k−1)−1 ˜
T
k−1y −ˆk−1
= [ ˆϑ1,k−1 −ˆ1,k−1, . . . , ˆϑk−1,k−1 −ˆk−1,k−1]T
(30)
where
˜Rk−1y = y −˜k−1( ˜
T
k−1 ˜k−1)−1 ˜
T
k−1y = y −
(˜p1 ˆϑ1,k−1 + · · · + ˜pk−1 ˆϑk−1,k−1) and the following holds for
i = k −1, . . . , 1:
ˆϑi,k−1 = ˜pT
i ˜Ri−1y −k−1
l=i+1 ˜pT
i ˜Ri−1 ˜pl ˆϑl,k−1
˜pT
i ˜Ri−1 ˜pi
. (31) ˆi,k = ˆi,k−1 + γ ◦
k ˆθi,k,
i = 1, . . . , k −1; i ̸= r
(23) and ˆk,k = γ ◦
k ˆθk,k, where ˆr,k = 0 together with the cor-
responding regressor pr is going to be removed from the
coefficient vector and the regression matrix. The size of the
resulted overall model coefficient vector remains unchanged,
i.e., ˆk−1 ∈ℜk−1. (30) At the next step, the model error resulted by adding a new
submodel to the overall model can be written as ˆϑi,k−1 = ˜pT
i ˜Ri−1y −k−1
l=i+1 ˜pT
i ˜Ri−1 ˜pl ˆϑl,k−1
˜pT
i ˜Ri−1 ˜pi
. C. Algorithm The efficient successive LASSO solution generating scheme
for CSO model construction is now summarized, the pseudo
code being given in Algorithm 1. In consideration of all the
field monitoring variables with the designated maximum time
lags, a number of candidate regressors ϕi, say i = 1, . . . , M,
can be first obtained. For each CSO identity, a predictive
model can then be automatically constructed based on such
candidate regressors and the proposed efficient LASSO algo-
rithm. To get a predictive model with a size of one, the
correlations between these candidate regressors and the CSO
output are used to initialize the two vectors c0) and b1);
consequently, the regressor leading to the largest absolute
correlation is selected and added into the predictive model. Correspondingly, the variables ρ1, 1, A1), b1), d1), k, ˆθ1,1,
and γ ⋆
1 are computed in sequence (where γ ◦
1 is assigned
with zero in order to initiate the model learning process) to
prepare the computing framework for locating the next LASSO
solution. d . Compute ˆθi,k (i = 1, . . . , k). ˆ
ˆ p
i,k (
,
, )
Find γ ◦
k ←mink
i=1 [ −ˆi,k/ ˆθi,k]+. k) Find γ ⋆
k ←minM
i=k+1 [(±ck)
i −ρk)/(±dk)
i −ρk)]+. else Assign pk+1 ←arg γ ⋆
k . :
Assign pk+1 ←arg γ ⋆
k . ˆ p
+
22:
Update Ak), bk), and dk). ˆ p
Compute ˆθi,k (i = 1, . . . , k). k 1
ˆ As the regularization parameter decreases, the following
procedure is then performed efficiently to find the correspond-
ing LASSO solutions. In the case that 0 < γ ◦
k ≤γ ⋆
k is not
met, the next regressor pk+1 = arg γ ⋆
k to be added into the
predictive model is determined together with variables ˆi,k
(i = 1, . . . , k), ck)
i
(i = k + 2, . . . , M), ρk+1 and k+1. The
model size k will then increase by one and variables Ak),
bk), dk), and ˆθi,k (i = 1, . . . , k) are updated subsequently
to compute γ ◦
k and γ ⋆
k for use in pursuing the next LASSO
solution. Algorithm
1 Pseudo Code for CSO Predictive Model
Construction 1: Generate candidate CSO predictive model regressors
ϕ1, . . . , ϕM from field variables associated with time lags. 0)
1)
T
T (33) 1
M
g
2: Initialize items {c0), b1)} ←[ϕT
1y, . . . , ϕT
My], ρ1
←
maxM
i=1 |c0)
i |, p1 ←arg ρ1, 1 ←p1, A1), b1), d1), and
k ←1 in sequence. ˆ The model learning process is then repeated by determining
whether an incremental or decremental movement is required
at each step to search for successive LASSO solutions until
some stopping criterion is satisfied. 3: Compute ˆθ1,1 ←b1/a1,1. M
0)
1) 3: Compute ˆθ1,1 ←b1/a1,1. M
0)
1) 4: Find γ ⋆
1
←
minM
i=2 [(±c0)
i −ρ1)/(±d1)
i −ρ1)]+ and
γ ◦
1 ←0. 4: Find γ ⋆
1
←
minM
i=2 [(±c0)
i −ρ1)/(±d1)
i −ρ1)]+ and
γ ◦
1 ←0. 1
5: while k ≤m do
6:
if 0 < γ ◦
k ≤γ ⋆
k then
7:
Assign pr ←arg γ ◦
k . 8:
Update ˆi,k (i = 1, . . . , k) and ck−1)
i
(i = k, . . . , M). 9:
Update ρk−1 ←(1 −γ ◦
k )ρk. 10:
Compute ˜k ←[˜p1, . . . , ˜pk−1, pr], ˜Ak), and ˜bk). 11:
Update ˜dk−1)
i
(i = k, . . . , M). 12:
Update k ←k −1. 13:
Assign k ←˜k, Ak) ←˜Ak), bk) ←˜bk), and dk) ←
˜dk). A. Incremental Movement , M
(32 (27) (32) IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1260 and ˆθi,k−1 = ˆϑi,k−1 −ˆi,k−1 (i = 1, . . . , k −1), where
ˆϑi,k−1 =
˜bi −k−1
l=i+1 ˜ai,l ˆϑl,k−1
˜ai,i
. (33) Algorithm
1 Pseudo Code for CSO Predictive Model
Construction
1: Generate candidate CSO predictive model regressors
ϕ1, . . . , ϕM from field variables associated with time lags. 2: Initialize items {c0), b1)} ←[ϕT
1y, . . . , ϕT
My], ρ1
←
maxM
i=1 |c0)
i |, p1 ←arg ρ1, 1 ←p1, A1), b1), d1), and
k ←1 in sequence. 3: Compute ˆθ1,1 ←b1/a1,1. 4: Find γ ⋆
1
←
minM
i=2 [(±c0)
i −ρ1)/(±d1)
i −ρ1)]+ and
γ ◦
1 ←0. 5: while k ≤m do
6:
if 0 < γ ◦
k ≤γ ⋆
k then
7:
Assign pr ←arg γ ◦
k . 8:
Update ˆi,k (i = 1, . . . , k) and ck−1)
i
(i = k, . . . , M). 9:
Update ρk−1 ←(1 −γ ◦
k )ρk. 10:
Compute ˜k ←[˜p1, . . . , ˜pk−1, pr], ˜Ak), and ˜bk). 11:
Update ˜dk−1)
i
(i = k, . . . , M). 12:
Update k ←k −1. 13:
Assign k ←˜k, Ak) ←˜Ak), bk) ←˜bk), and dk) ←
˜dk). 14:
Compute ˆθi,k (i = 1, . . . , k). 15:
Find γ ◦
k ←mink
i=1 [ −ˆi,k/ ˆθi,k]+. 16:
Find γ ⋆
k ←minM
i=k+1 [(±ck)
i −ρk)/(±dk)
i −ρk)]+. 17:
else
18:
Assign pk+1 ←arg γ ⋆
k . 19:
Update ˆi,k (i = 1, . . . , k) and ck)
i (i = k+2, . . . , M). 20:
Assign ρk+1 ←(1−γ ⋆
k )ρk and k+1 ←[k, pk+1]. 21:
Update k ←k + 1. 22:
Update Ak), bk), and dk). ˆ A. Incremental Movement (31) (31) ˜ek−1 = ek −γk−1 ˜k−1
˜
T
k−1 ˜k−1
−1 ˜
T
k−1ek
(24) (24) Here, it can be found that if pr was the last selected regres-
sor in the regression matrix, i.e., ˜k = [ ˜k−1, pr], then
the corresponding matrix ˜A and vector ˜b can be used to
solve (28)–(31). This can be achieved by restarting the process
with the newly selected sequence of regressors, though obvi-
ously it would be computationally expensive. Instead, a com-
putationally friendly solution [41] can be readily employed
here, by each time swapping two neighboring regressors in k
(starting at which pr is located) and updating the correspond-
ing matrix and vector, for a number of times until pr has been
shifted to the last position of the regression matrix. Therefore,
after a total of k −r swaps, the selected regression matrix
will become ˜k = [˜p1, . . . , ˜pk−1, ˜pk], in which pr is moved
to the last position of ˜k, i.e., pr = ˜pk. The intermediate
regression matrix ˜A and vector ˜b are thus obtained. Given
this, the direction vector ˜dk−1)
i
and coefficients ˆθi,k−1 can now
be computed as where ˜k−1 is the reduced set of selected regressors by remov-
ing pr, i.e., ˜k−1 = [˜p1, . . . , ˜pk−1]. On the one hand, it can
be seen that the new correlation for the remaining regressors
after introducing this submodel becomes ˜ck−1)
i
=
⎧
⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎩
pT
r ek −γk−1pT
r ˜k−1
˜
T
k−1 ˜k−1
−1 ˜
T
k−1ek
i = k
ϕT
i ek −γk−1ϕT
i ˜k−1
˜
T
k−1 ˜k−1
−1 ˜
T
k−1ek
i = k + 1, . . . , M. (25) Combining (22), this can be equivalently formulated as Combining (22), this can be equivalently formulated as ˜ck−1)
i
= ck−1)
i
−γk−1˜dk−1)
i
,
i = k, . . . , M (26) where where ˜dk−1)
i
=
⎧
⎪⎪⎨
⎪⎪⎩
pT
r ˜k−1
˜
T
k−1 ˜k−1
−1 ˜
T
k−1ek,
i = k
ϕT
i ˜k−1
˜
T
k−1 ˜k−1
−1 ˜
T
k−1ek
i = k + 1, . . . , M. ˜dk−1)
i
=
ck−1)
k
−˜bk,
i = k
(1 −γ ◦
k )dk)
i −˜ak,i˜bk/˜ak,k, i = k + 1, . . . ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1261 (a)
(b)
Fig. 2. Schematic of the pilot area. (a) Field map. (b) Monitoring variables. pilot area are solely owned by Welsh Water (also known as (a) V. EXPERIMENTS In this section, the effectiveness of the proposed methodol-
ogy to automate the CSO predictive model construction and
the efficiency of the proposed algorithm are demonstrated. As
part of an ongoing research, a pilot area was chosen with the
presence of multiple CSOs and various field monitoring vari-
ables already in existence. The experiments were all performed
on a Intel Core2 Duo Processor P8600 2.40 GHz, with pro-
grams executed by MATLAB. A range of model performance
and results are provided. (b) Fig. 2. Schematic of the pilot area. (a) Field map. (b) Monitoring variables. pilot area are solely owned by Welsh Water (also known as
DCWW or D ˆwr Cymru Cyfyngedig). The pilot area has been
chosen due to the fact that it contains a typical CSS with
certain complexities of catchment and topography, and the
network operator already has the network closely monitored
which would provide the opportunity of applying a data-driven
approach. 1) The obtained model structure, and training/test time,
error and accuracy for CSO predictive model construc-
tion terminated by both designated number of model
regressors and AIC criterion [see (34)–(38)]. g
2) The consideration of modeling results for imbalanced
dataset. After an in-depth analysis of the quality of the data collected
by the existing sensing infrastructure, a total of 73 monitoring
variables were considered, including 24 CSO level variables
(percent), six rainfall variables (mm/h), nine flow variables (l/s,
e.g., pumped flows, treatment flows, and storm flows), and 34
other level variables (m or percent, e.g., wet well levels, sump
levels, and screen levels). A CSO level with a percent value
larger than 100% indicates the occurrence of CSO spillages. These monitoring variables can be seen from Fig. 2(b), where
one of the weather stations for monitoring rainfall information
is located to the west just outside the trial area. The field
variables are monitored via Welsh Water’s proprietary systems. 3) The comparisons of the proposed algorithm with neural
network and fuzzy approaches. y
4) The integration of multistep ahead predictions. D. Computational Complexity Based on the proposed algorithm described in the previous
section, the computational complexity comprises a fixed ele-
ment arising from successive inclusion of model regressors
without removal, and a varied element taking into account the
removal plus again inclusion of new regressors. Given that
N data samples and M candidate model regressors are made
available at the beginning of the training process, the fixed
amount of computational complexity resulted from m model
regressors being first generated is Cfixed = mN(2M −m + 1) + (2N −1)M
+ mM(m + 9) −m(2m2 −3m + 49)/6. (39) (39) On the other hand, the computational complexity for remov-
ing a selected model regressor and adding another varies with
the underlying model size being considered (say k) and the
position of the regressor being removed from the regression
matrix (say δk), yielding (a) (b) (b)
Fig. 2. Schematic of the pilot area. (a) Field map. (b) Monitoring variables. Cvaried = 2(k −δk)(2M −k −δk + 6) + (2N + 2k + 19)
× (M −k + 1) + 2(k + 2)2 −28. (40) Given the CSO predictive problem, it usually holds that δk <
k < m ≪M ≪N. The computational complexity involved
in (39) and (40) then mainly relies on terms 2mMN and 2MN,
respectively. The actual computational burden will therefore
depend on the number of decremental movements during the
LASSO solution searching process, and when and where they
occur. In addition, if AIC is applied to terminate the training
process, a fixed additional amount of 2N+13m+1 complexity
will be incurred, together with an extra of 18 computations
added to the varied complexity Cvaried. C. Algorithm On the contrary, if 0 < γ ◦
k ≤γ ⋆
k is met, the term
pr = arg γ ◦
k is removed from the current regression matrix, the
value of ˆi,k (i = 1, . . . , k) and ck−1)
i
(i = k, . . . , M) being,
respectively, updated according to (23) and (22) together with
ρk−1 = (1 −γ ◦
k )ρk. Then, through consecutively swapping a
series of two neighboring selected regressors in k (starting
with pr) to update items ˜k = [˜p1, . . . , ˜pk−1, pr], ˜Ak) and
˜bk), upon which the value of ˜dk−1)
i
(i = k, . . . , M) is thus
obtained by using (32). As a result, the size of the regres-
sion matrix is reduced by one (k = k −1) together with
k = ˜k, Ak) = ˜Ak), bk) = ˜bk), and dk) = ˜dk) updated. The parameter ˆθi,k (i = 1, . . . , k), γ ◦
k = mink
i=1 [−ˆi,k/ ˆθi,k]+,
and γ ⋆
k = minM
i=k+1 [(±ck)
i −ρk)/(±dk)
i −ρk)]+, are thereby
calculated and ready for use in searching for the next
LASSO solution. The whole algorithm can be terminated
by designating a specified number of model regressors first
reached during the model learning process or using other
criteria such as Akaike information criterion (AIC); thereby
the selected model regressors and associated coefficients are
retrieved. p
i,k (
)
nd γ ◦
k ←mink−1
i=1 [ −ˆi,k−1/ ˆθi,k]+. nd γ ⋆
k ←minM
i=k+1 [(±ck−1)
i
−ρk)/(±dk)
i −ρk)]+. if 29: Output k and ˆk. As for using the AIC criterion, it is expressed as [42] AIC = N log(SSE/N) + 2k
(34) (34) where N, k, and SSE refer to the sample number, model size,
and sum of squared errors. In correspondence to the incre-
mental and decremental movements of the proposed algorithm,
SSE can be recursively computed as: ⎧
⎪⎪⎪⎨
⎪⎪⎪⎩
eT
k ek
= (1 −γk)2eT
k−1ek−1 + γk(2 −γk)eT
k−1Rkek−1
(35)
˜eT
k−1˜ek−1
= (1 −γk−1)2eT
k ek + γk−1(2 −γk−1)eT
k ˜Rk−1ek
(36) (35) where where
eT
k−1Rkek−1 = eT
k−2Rk−1ek−2 −b2
k/ak,k
(37)
eT
k ˜Rk−1ek = eT
k−1Rkek−1 + ˜b2
k/˜ak,k. (38) ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 It is apparent that
the proposed algorithm possesses significant computational
advantage over the original algorithm. The elapsed time for
constructing CSO predictive models using the proposed algo-
rithm compared with the original one is expected to decrease
by around two times, especially so when more model regres-
sors are included. It should be noted that in case of large-scale
sewer networks and associated datasets, the time needed for
each CSO model construction can increase significantly due to
the increased number of field variables (also see Section IV-D
for computational complexity analysis), so does the average
model construction time using AIC criterion to be given in
Table II. As model size (the number of model regressors,
i.e., the number of field variables associated with time lags)
increases, the training root mean squared error (RMSE) is
consistently decreased as expected, by optimizing the updated
LASSO objective function where the weighting of the L1 norm
of model parameters decreases and correspondingly the impor-
tance of L2 norm of model errors increases. On the other
hand, the test RMSE generally decreases first, then stabilizes
and increases again (where overfitting appears). Reflecting on
this, the test R2 generally increases first, then stabilizing and
decreasing again as the number of model regressors increases. IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1262 TABLE I
AVERAGE MODEL CONSTRUCTION RESULTS OVER ALL THE CSOS
PRODUCED BY THE ORIGINAL AND PROPOSED ALGORITHMS
WITH VARYING NUMBER OF MODEL REGRESSORS The monitoring data from various field variables was col-
lected from April 1, 2014 to March 1, 2016 at a time resolution
of 15 min (thus also being considered as the prediction time-
step). In principle, the total amount of samples for each
variable would be 67 205. In the case where missing values
exist, they were simply estimated using linear interpolation
methods. However, given that the proposed predictive method-
ology is independent of the data preprocessing, it would not
hinder the use of other (complex) data imputation techniques
though there is no consensus on the best approach to do
this. As a matter of fact, having reliable monitoring system
is required in order to avoid the long periods of missing data
as it would be very difficult to accurately infer the missing
values using imputation techniques. The negative and hugely
positive values together with other abnormal values resulting
from sensor reading errors were also regarded as missing val-
ues and processed in the same manner. It was found that an
average of 2.28% missing data existed over the various field
variables, where for some individual variables this can reach
as high as 20%. Specifically, for the variable with a high level
of missing data, if the missing data comprises a small number
of long periods, it makes little difference whether consider-
ing such a variable at the beginning of model construction
as the methodology can hardly relate this variable’s behav-
ior (resulting from the interpolated low quality of data) to the
CSO behavior of interest. Therefore, this variable would not
be selected in the resulting CSO predictive model. Whilst in
the case that the missing data is continuously accumulated (say
one missed in every five measurements), the behavior exhibited
by this variable can still be somewhat recovered by interpola-
tion and potentially considered for being related to the CSO
behavior. Finally, a data partition of 60% (from April 1, 2014
to May 26, 2015) of the entire collection period was used to
train the CSO predictive models, while the remaining 40%
(from May 26, 2015 to March 1, 2016) was employed for
model testing. the model size (similarly for other tables in their respec-
tive settings as presented in this paper). A. Pilot Area Description and Data Gathering A U.K. pilot area depicted in Fig. 2(a) is employed to repre-
sent various features related to wastewater collection networks
and the corresponding catchments. The associated sensing
variables are shown in Fig. 2(b), with the entire area serv-
ing around 52 000 residents. The network assets within this IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS comparatively accurate predictions, as more field monitoring
variables are distributed therein. Whilst some CSO models
obtained relatively low level of accuracy, others can achieve
extremely high accuracy with a test R2 value larger than
0.90. This demonstrates the effectiveness of the proposed data-
driven methodology for tackling the CSO prediction problem,
provided that high quality and resolution field data is made
available. While the averaged test RMSE (6.0505) is a bit larger
than the training one (4.7871), notably, the averaged test R2
(0.8453) over all the CSO models is better than the training
one (0.7975), demonstrating the good generalization ability of
the constructed models. Though it maybe often seen that the
model generalization performance is worse than the training
one, this is not always the case as it is highly dependent on the
performance measure, the type of model and training algorithm
(e.g., using regularization, subset selection and local learning
techniques) as well as the differing data quality between the
training and test dataset. Looking through the eighth to tenth
columns, each CSO tends to exhibit a relationship with a rela-
tively higher proportion of the weather stations and the CSOs
than with the other 43 field variables. size increasing, other pertinent field variables would then have
more chance of getting selected to further improve model
performance. After a certain number of model regressors being
included (can be otherwise determined using the AIC crite-
rion), say around 30, the test performance becomes steady,
whereby the expansion of model size does not improve much
(or maybe reduce) the model performance. In this situation,
adding more field variables into predictive models would not
help improve prediction accuracy. In addition, from the model
complexity point of view, a simpler model in small size is
usually preferred. It may be interesting to see the selected field variables with
time lags for the constructed models. Due to the large number
of CSOs involved, here, CSO model #9 is simply taken as an
example to illustrate the resultant model structure. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS It is found
that the following variables are presented in the predictive
model: y2(t−1), y3(t−1), y4(t−1), y9(t−1), y9(t−4), y9(t−
5), y9(t−7), y9(t−10), y11(t−1), y15(t−1), y18(t−1), w29(t−
1), w30(t −1), w30(t −2), l48(t −5), l48(t −9), l51(t −1),
l54(t−1), l54(t−9), l54(t−10), where y, w, and l denote the cor-
responding CSO, rainfall, and level variables, respectively. In
order to predict future statuses for CSO #9, it can be seen that
the model captures the previous statuses of seven CSO vari-
ables (including itself #9), two rainfall variables (#29 and #30),
and three level variables (#48, #51, and #54). The variable #54
is monitored at the same location as #34. These variables are
considered as the most important determined by the LASSO
criterion and the time-series pattern exhibited in the monitor-
ing data. Under the current catchment/network configuration
and given the monitored data, the surrounding critical CSOs,
weather stations and level variables together with their time
lags are thus identified, leading to a total of 12 field variables
included in this model and a model size of 20 including the
various lags. Alternatively, through using the AIC criterion, the model
construction results for all the CSOs produced by the orig-
inal and proposed algorithms are given in Table II. It is
again shown that the proposed algorithm reduces dramati-
cally the computational time compared to the original for
all the CSO models; in this case, roughly 50% reductions
are achieved. The difference between the training and test
RMSEs is acceptable and indicates well-trained models with
good generalization ability. To facilitate direct comparisons
across different CSO models, the training and test R2 val-
ues (the percentage/proportion of the CSO behavior/variation
that is predicted/explained by the model) are given for every
model, where those exhibiting a larger value represent a better
constructed predictive model (a maximum value of 1.0 indi-
cates that the underlying CSO dynamic behavior is completely
explained and predicted by the model). Due to the distinct data
quality of each CSO and field constraints (e.g., some CSOs
might lack monitoring of close neighbor or correlated field
variables), it shows that different levels of model goodness-of-
fit are presented amongst these CSO models. B. Results and Analysis The maximum time lag of the field variables was assigned
with a value of 10 (ten time-steps, i.e., 150 min of prior data)
followed by a preliminary site trial (determined by trial-and-
error as usual in time-series prediction), amounting to a total
of 730 potentially available model regressors at the beginning
of the model construction. It is worth mentioning that, as the
maximum lag increases, more time is needed to construct the
CSO model as the number of initial model regressors gets
larger for the model learning. In this case, it was found that
a value larger than 10 would not help improve the model
performance significantly. The original algorithm as well as
its realization [43] (followed by the modification of LAR) for
deriving LASSO solutions as described in Section III, was also
examined to verify the computational advantage of our algo-
rithm. To evaluate the efficiency of the proposed algorithm as
well as the effectiveness of the overall methodology of CSO
model construction, Table I lists the average modeling results
over all the CSOs produced by both original and proposed
algorithms with varying number of selected model regres-
sors. The model structure is expressed in terms of the number
of selected weather stations, CSOs and field variables and To examine the importance of weather rain-gauge stations
and the existence of interrelationships amongst different CSOs,
the average number of weather stations and CSOs contained
over all constructed CSO models for each subset of model
regressors are listed in the eighth and ninth columns of Table I,
while the last column gives the average amount of total
selected field variables also including other measures such
as pumped flows and wet well levels. Overall, the selected
field variables play an important role in constructing the CSO
predictive models. It can be found that the CSO plus rainfall
variables account for the major contributing factors when a
small number of model regressors are required to construct
the predictive models (where the summation of numbers of
selected weather stations and CSOs, over the total number of
selected variables is very high). Notably, in addition to the
involvement of weather stations, as many CSO variables are
also picked up for model construction, a clear interrelation-
ship between distinct CSOs is thus evident. With the model ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1263 TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS Specifically, it
can be seen from Table II, there is a clear relationship between
the CSO and rainfall, whilst particularly, no correspondingly
existing rainfall stations were found important for explaining
the behavior of CSO #23, which potentially led to the less
accurate predictions. In this regard, improved spatial resolution
of rainfall data can be approached to enhance the model accu-
racy. Overall, the upper middle part of the pilot area received To visualize the model performance, Fig. 3 depicts one
of the best obtained CSO models (model #10) with a train-
ing and test R2 of 0.9912 and 0.9822, respectively. It can
be found that the majority of CSO levels were distributed in
the range between 20 and 60, resulting in the dense plot of
data in the bottom part of Fig. 3(a). Compared with the mea-
sured values, both trained and predicted CSO levels are well
modeled for the whole period starting from April 1, 2014 to
March 1, 2016. It is worth noting that the missing data for
this CSO variable is mainly between October 10, 2014 and
November 12, 2014 (accounting for less than 5% of the entire
data collection period), and linear interpolation was applied
as indicated in Section V-A. Considering the large number
of monitoring variables and that different variables can have 1264
IEEE TRANSACTIONS
(a)
(b)
(c)
Fig. 3. One of the best constructed CSO predictive models (#10). (a) Measured and modeled CSO levels for the whole period between
April 1, 2014 and March 1, 2016. Zoomed-in view of measured and (b) trained
CSO levels in August 2014 and (c) predicted CSO levels in August 2015. (The
red sign “x” denotes the sensor reading and the blue dashed line depicts the
model output.)
different periods of missing data, the overall usable amount IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1264 (a) illustrated here) where the missing values could be due to
accumulation from many small periods or one/several long
periods. Notwithstanding, given the focus of this paper (i.e.,
the proposed methodology) is independent of the handling
of missing values, other imputation techniques can also be
used. Here, the historical data from three weather stations and
ten CSO variables were found to be relevant to construct the
underlying model, while a total of 41 model regressors were
selected also including various degrees of time lags from these
variables. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS In order to see a more detailed comparison between
the model output and the system output, the modeled and mea-
sured CSO levels in August 2014 (training dataset) and August
2015 (test dataset), are illustrated in Fig. 3(b) and (c), respec-
tively. Out of these, the underlying complexity of the CSO
behavior including large and small instances has been clearly
learned and predicted by the developed model. In this case,
though the instances monitored are imbalanced in terms of
huge amount of small levels of CSOs and considerably less
quantity of large measurements, the learning algorithm was
still able to cope with it appropriately. (a) (b) It should be mentioned that the mechanism for the CSO
time-series prediction is to predict future CSO statuses based
on the input of a number of previously observed statuses of
field monitoring variables. During the model training period,
the modeled CSO levels try to fit all those contained in the
training dataset including both monitored and interpolated
(where missing values occur) data. However, due to the input
of less accurate (or even incorrect) interpolated values for the
previous network statuses, the model can thereby infer wrong
predictions at that specific moment (the period in which miss-
ing values occur). This would not be a problem for model
training as it is just a way of maximizing the overall length
of training dataset. In short, though the model is constructed
to explain the CSO behavior with the selected field variables
and associated time lags, however, the actual prediction is also
dependent on the quality of the monitoring data that feeds into
the model. Once the model is constructed, in the worst case
scenario, the model will not be able to produce any predictions
if there are persistent missing values from the field monitor-
ing data. In the case of missing data (which can be detected
directly from the sensing system, not from the model), both
predicted and monitored values do not exist for comparison. The comparison between the predicted and monitored CSO
statuses can therefore be made under the normal running of
sensing system to indicate if there is a malfunction with the
sewer network. (b) (c) (c) Fig. 3. One of the best constructed CSO predictive models (#10). (a) Measured and modeled CSO levels for the whole period between
April 1, 2014 and March 1, 2016. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS (The red sign x denotes the sensor
reading and the blue dashed line depicts the model output.)
for each CSO model construction, as long as the total number TABLE III
AVERAGE MODEL CONSTRUCTION RESULTS OVER ALL THE CSOS
PRODUCED BY THE ORIGINAL AND PROPOSED ALGORITHMS
WITH VARYING NUMBER OF MODEL REGRESSORS
(UPSAMPLING CASE) (a) (a) (b) TABLE IV
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR THOSE SERIOUSLY
IMBALANCED CSOS (UPSAMPLING CASE) (b) Fig. 4. CSO data is seriously imbalanced in terms of relatively few large
CSO levels measured. (a) Predictive models constructed without upsampling
(large CSO levels not well fitted). (b) Predictive models constructed with
upsampling (large CSO levels well fitted). (The red sign x denotes the sensor
reading and the blue dashed line depicts the model output.) acceptable. The large difference between the training and test
R2 values is because the CSO levels in the training dataset
are very closely distributed around its mean value (giving the
low training R2), whereas it is not the case in the test dataset. Finally, Fig. 4(b) illustrates a better predictive model in the
sense of well-fitted large CSO levels compared with Fig. 4(a). To continue examining the performance of the con-
structed models, neural networks and fuzzy systems were also
employed to learn the CSO behavior based on the selected field
variables and associated time lags produced by our method-
ology, envisaging the potential of improving model predictive
accuracy. Here, the well-known feed-forward backpropagation
network (optimized by Levenberg–Marquardt method) and
Sugeno-type fuzzy system (optimized by the hybrid of least-
squares and gradient descent methods) were used employing
MATLAB neural network (feedforwardnet and train) and
fuzzy logic (genfis3 and anfis) toolboxes, respectively. During
the model training process, 20% of the training data was
used for validation purposes in order to mitigate overfitting. The training and test time/RMSE/R2 are shown in Fig. 5
based on the nonupsampled data. It once again shows that
our approach required significantly less training and test times
as in Fig. 5(a) and (b). Though the training RMSE and R2
[Fig. 5(c) and (e)] of the proposed models were slightly
increased and decreased, compared to that of the neural and
fuzzy models, more importantly, our model’s generalization
performance indicated by test RMSE and R2 [Fig. 5(d) and (f)] acceptable. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS The large difference between the training and test
R2 values is because the CSO levels in the training dataset
are very closely distributed around its mean value (giving the
low training R2), whereas it is not the case in the test dataset. Finally, Fig. 4(b) illustrates a better predictive model in the
sense of well-fitted large CSO levels compared with Fig. 4(a). for each CSO model construction, as long as the total number
of large instances for the CSO of interest is less than a partic-
ular proportion (say a threshold of 2%) amongst the training
dataset, these large instances together with the corresponding
instances of input variables will be replicated up to this propor-
tion for model training. By using the upsampling techniques,
the average model construction results under varying num-
ber of model regressors and the updated model construction
results for these CSOs seriously suffered from this imbalance
issue are, respectively, shown in Tables III and IV. This again
confirms the computational superiority of the proposed algo-
rithm in comparison with the original one by looking at the
second and third columns of both tables. The overall train-
ing RMSE/R2 is slightly reduced as the training process was
forced to fit more onto the rarely occurring large CSO values at
the expense of partially sacrificing fitting the absolute majority
of low CSO values. Moreover, as expected, the involvement
of rainfall information in the constructed models is seen gen-
erally enhanced, as these large CSO values are intrinsically
more driven by heavy rainfall. Specifically, it is worth not-
ing that the training and test RMSEs for CSO #21 as well
as the small difference between them indicate the model is for each CSO model construction, as long as the total number
of large instances for the CSO of interest is less than a partic-
ular proportion (say a threshold of 2%) amongst the training
dataset, these large instances together with the corresponding
instances of input variables will be replicated up to this propor-
tion for model training. By using the upsampling techniques,
the average model construction results under varying num-
ber of model regressors and the updated model construction
results for these CSOs seriously suffered from this imbalance
issue are, respectively, shown in Tables III and IV. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS Zoomed-in view of measured and (b) trained
CSO levels in August 2014 and (c) predicted CSO levels in August 2015. (The
red sign “x” denotes the sensor reading and the blue dashed line depicts the
model output.) On a different note, it was found that for some CSOs, e.g.,
#24, the imbalanced data issue can be extremely serious, i.e.,
the number of monitored large instances (e.g., larger than 90%)
of CSO level readings is dramatically less than the number
of monitored small instances (e.g., less than 90%) of CSO
level readings. As shown in Fig. 4(a), though the model was
trained well to predict the majority of small levels of CSOs,
the large levels were not fully modeled. Given the imbalanced
dataset, the training procedure tended to learn dynamics more
exhibited by the small instances. This issue can be simply
addressed using the common upsampling technique (i.e., repli-
cating instances from the minority) [44] to increase the amount
of instances from those that are under-represented. In detail, different periods of missing data, the overall usable amount
of data can be dramatically reduced if such durations of miss-
ing data are removed directly (every removal of a sensing
period due to one field variable can cause a correspondingly
overall size reduction of useful dataset given its a time-series
problem). On the other hand, the model will also need to have
certain level of anti-noise ability regarding data quality (as well ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1265 TABLE III
AVERAGE MODEL CONSTRUCTION RESULTS OVER ALL THE CSOS
PRODUCED BY THE ORIGINAL AND PROPOSED ALGORITHMS
WITH VARYING NUMBER OF MODEL REGRESSORS
(UPSAMPLING CASE)
TABLE IV
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR THOSE SERIOUSLY
IMBALANCED CSOS (UPSAMPLING CASE) (a)
(b)
Fig. 4. CSO data is seriously imbalanced in terms of relatively few large
CSO levels measured. (a) Predictive models constructed without upsampling
(large CSO levels not well fitted). (b) Predictive models constructed with
upsampling (large CSO levels well fitted). C. Discussion (f) (e) The main aim of this paper is to propose an automated
predictive model construction methodology to address the
future CSO status prediction problem. The requirements for
developing CSO predictive models were elicited as part of
an EU FP7 water project (WISDOM) involving a multi-
disciplinary consortium from the water value chain across
Europe, and mainly attributed to our water utility partner
(DCWW). It is an important research topic that has attracted
interest of a number of previous studies [23]–[25]. In gen-
eral, the predictive model can provide data for the construction
of an online decision support tool that can be used to
consistently. Fig. 5. Comparisons between the proposed, neural, and fuzzy models for
all the CSOs. (a) Training time. (b) Test time. (c) Training RMSE. (d) Test
RMSE. (e) Training R2. (f) Test R2. was even better as fundamentally desired. Some CSO models
(e.g., #11 and #21) produced by neural networks and fuzzy
systems give very poor test R2 values. Therefore, the out-
standing performance of our algorithm, in terms of both model
accuracy and computational time, has been demonstrated
owing to the regularization and fast training. Furthermore, given the proposed methodology, it is also
straightforward to develop multistep CSO predictive mod-
els where needed, by using the CSO status at the required
prediction step as the model output. The training and test
RMSE/R2 across the 24 CSOs for five prediction steps
are illustrated in Fig. 6. As expected, with the increase of
prediction steps, the prediction accuracy generally reduces
due to less recent information about the system being avail-
able (uncertainty increases) and considered by the model. However, as for the CSOs with high accuracy at single-
step prediction, they still possess very good performance at
multistep prediction where large accuracy reduction was not
seen. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS (other than that in CSOs) can be predicted in the same way
as CSO statuses using the proposed approach; this, however,
is out of the scope of this paper. C. Discussion
The main aim of this paper is to propose an automated
predictive model construction methodology to address the
future CSO status prediction problem. The requirements for
developing CSO predictive models were elicited as part of
EU FP7
j
(WISDOM) i
l i
l i (a)
(b)
(c)
(d)
(e)
(f)
Fig. 5. Comparisons between the proposed, neural, and fuzzy models for
all the CSOs. (a) Training time. (b) Test time. (c) Training RMSE. (d) Test
RMSE. (e) Training R2. (f) Test R2. (b) (a)
(b)
(c)
(d)
Fig. 6. Multistep ahead predictions for all the CSOs. (a) Training RMSE. (b) Test RMSE. (c) Training R2. (d) Test R2. (a) (a) (b) (b) (b) (a) (a) (d) (c) (c) (d) (d) (c) (d) (c) (f) (e) Fig. 6. Multistep ahead predictions for all the CSOs. (a) Training RMSE. (b) Test RMSE. (c) Training R2. (d) Test R2. (other than that in CSOs) can be predicted in the same way
as CSO statuses using the proposed approach; this, however,
is out of the scope of this paper. TABLE II
MODEL CONSTRUCTION RESULTS BY THE ORIGINAL AND PROPOSED
ALGORITHMS USING AIC FOR ALL THE CSOS This again
confirms the computational superiority of the proposed algo-
rithm in comparison with the original one by looking at the
second and third columns of both tables. The overall train-
ing RMSE/R2 is slightly reduced as the training process was
forced to fit more onto the rarely occurring large CSO values at
the expense of partially sacrificing fitting the absolute majority
of low CSO values. Moreover, as expected, the involvement
of rainfall information in the constructed models is seen gen-
erally enhanced, as these large CSO values are intrinsically
more driven by heavy rainfall. Specifically, it is worth not-
ing that the training and test RMSEs for CSO #21 as well
as the small difference between them indicate the model is g
p
g
( )
To continue examining the performance of the con-
structed models, neural networks and fuzzy systems were also
employed to learn the CSO behavior based on the selected field
variables and associated time lags produced by our method-
ology, envisaging the potential of improving model predictive
accuracy. Here, the well-known feed-forward backpropagation
network (optimized by Levenberg–Marquardt method) and
Sugeno-type fuzzy system (optimized by the hybrid of least-
squares and gradient descent methods) were used employing
MATLAB neural network (feedforwardnet and train) and
fuzzy logic (genfis3 and anfis) toolboxes, respectively. During
the model training process, 20% of the training data was
used for validation purposes in order to mitigate overfitting. The training and test time/RMSE/R2 are shown in Fig. 5
based on the nonupsampled data. It once again shows that
our approach required significantly less training and test times
as in Fig. 5(a) and (b). Though the training RMSE and R2
[Fig. 5(c) and (e)] of the proposed models were slightly
increased and decreased, compared to that of the neural and
fuzzy models, more importantly, our model’s generalization
performance indicated by test RMSE and R2 [Fig. 5(d) and (f)] IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1266 (a)
(b)
(c)
(d)
(e)
(f)
Fig. 5. Comparisons between the proposed, neural, and fuzzy models for
all the CSOs. (a) Training time. (b) Test time. (c) Training RMSE. (d) Test
RMSE. (e) Training R2. (f) Test R2. (a)
(b)
(c)
(d)
Fig. 6. Multistep ahead predictions for all the CSOs. (a) Training RMSE. (b) Test RMSE. (c) Training R2. (d) Test R2. C. Discussion The
efficient model selection algorithm developed in this paper can
be employed or integrated in various model training and struc-
ture determination tasks including that for polynomial models,
artificial neural networks, support vector machines and fuzzy
systems, where high computational burden and model com-
plexity are usually a concern as experienced in model learning,
understanding and reasoning processes. Finally, the proposed data-driven approach does not need to
know the network topology or detailed information about the
drainage network, thus to reduce the effort and time spent
in collecting and analyzing the corresponding information
related to a particular network and also to improve the gen-
eral applicability of the algorithm across different networks. However, given that the aim of the data-driven model is to
predict CSO statuses in a number of future steps, it cannot
be used to analyze the actual propagation of a malfunc-
tion within the network. Our methodology is systematically
based on the global optimization of LASSO criterion fur-
ther enhanced by computational advantage, without testing
all the possible combinations (i.e., exhaustive approach) of
model regressors resulting from the monitoring variables and
their associated lags. It is widely recognized that an exhaus-
tive approach guarantees the optimality of the solution, but it
can take years or even be practically impossible to complete. Other approaches such as relying on expert knowledge (per-
haps together with simplified mathematical processing) with
the aid of network topology information, and performing for-
ward/backward stepwise selection can be employed to reduce
the model development time but at the expense of reduced
solution quality. In this regard, our approach enjoys both
global optimality in the LASSO sense as well as computational
efficiency. As the aim of the research is to develop a predictive model
for real-time prediction of the future state of CSOs, based on
the current composition and operation of the sewer network
and catchment, therefore, similar to using the hydrological-
hydraulic model, the data-driven model usually does not
change once constructed. However, the developed model does
need the continuous provision (update) of new field monitor-
ing data to produce consecutive predictions as time moves
forward. C. Discussion More specifically, both single-step
and multistep ahead predictions can be generated in real-time
but with different level of accuracies (the prediction accuracy
improves with the decrease in number of forward prediction
steps), as more recent field information (leading to less uncer-
tainty) is collected and processed by the model for fewer
step ahead predictions. Thus, the multistep ahead prediction
can be used in the control room for the preliminary/coarse
decision making (e.g., to put field teams and resources on
standby), while more recent predictions (especially next step
predictions) can be adopted for more precise decision mak-
ing (e.g., to examine specific CSO structures and determining
solutions to fix issues). Moreover, the proposed data-driven
approach for CSO time-series predictions (e.g., statuses of the
next 15–60 min) also helps reduce the cost and time associated
with model development and calibration in comparison with
the hydrological-hydraulic modeling approaches, while meet-
ing regulatory obligations imposed by environment agencies
and/or local authorities. the network, the model can be reconstructed say every month
before the whole year data is made available. In addition,
though independent of the proposed methodology, techniques
of data validation and reconciliation can be employed to
improve the quality (i.e., accuracy and reliability) of field mea-
surements. Notably, the model is not able to respond to the
actual intervention, but to alert when a remedial intervention
is required; however, whenever such an intervention occasion-
ally alters the sewer network an update of the model is needed
as indicated above. Moreover, the time saving achieved for model construc-
tion can have both practical and methodological meanings. The practical implications lie in the algorithmic ability to
not only accurately but also quickly (re)construct the CSO
predictive models for their subsequent use and integration in
the water utility’s network management process. This is espe-
cially important when dealing with large-scale networks and
data where substantial model construction time can be experi-
enced. On the other hand, the methodological meanings from
a wider research community perspective provide contributions
to an important research topic: development of low-complexity
machine learning algorithms for fast model construction. C. Discussion 1) Predict future CSO statuses (especially those indicat-
ing a spillage event) in advance (using either single or
multiple step predictions), thus enabling network oper-
ators to take corrective actions (e.g., getting the excess
CSO spillages properly treated/processed) as early as
possible in order to mitigate the potential adverse effects,
or alerting customers/authorities; 2) As a secondary benefit, inform network operators about
abnormal CSO performance by comparing the predicted
with monitored statuses and detecting if there is a sig-
nificant discrepancy between them, thus allowing timely
CSO performance restoration from asset malfunctions
such as that originated from failed pumping and sewer
blockages. Based on the aforementioned facts including the obtained
performance in a variety of settings and comparisons with
other approaches, in conclusion, the proposed methodology is
confirmed capable of quickly and effectively automating the
entire CSO predictive model construction process. It is worth
mentioning that other field variables such as flows and levels In the latter case, if at some point, it is found that there
is a significant discrepancy starting to appear between the
predicted and actual monitored CSO statuses, this can poten-
tially indicate part of malfunctions (e.g., blockages) that have
occurred within the sewer network if such malfunctions can ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1267 lead to the CSO behavior change. In this case, the predicted
CSO statuses can (dramatically) either rise above or drop
below the monitored statuses depending on the actual mal-
function, as the predictive model no longer represents the
CSO behavior given the malfunction. The CSO predictive
model for normal conditions in the sewer network therefore
gives predicted CSO statuses different from the monitored
ones resulting from the network with malfunctions. It should
be noted that rather than prediction of malfunctions, here it
considers to inform network operators timely whenever such
a malfunction has occurred. Therefore, our model can help
improve the management of CSOs and network assets, for
example, in the development of an online warning system
underpinned by some rules that can be triggered based on the
real-time predicted and monitored values of CSOs, to alert
water utilities enabling them to react with remedial actions
proactively or timely, thus reducing the volume or quantity of
unexpected CSO spillages. C. Discussion If there is a significant change in the field network
or the catchment, then the data-driven model can be recon-
structed automatically using the new sensing data after the
change, a simpler process compared with utilizing and updat-
ing the hydrological-hydraulic model (where a tedious manual
process is involved to modify, test and calibrate the model). In
order to acquire an accurate data-driven model, the field data
collected for model learning should be representative and of
sufficient quantity to reflect the full complexity of the CSO
behavior. Roughly, a year’s worth of data was utilized in this
paper to cover any seasonal effects on the CSO behavior. The requirement of the relatively long time-series data some-
what constitutes a drawback of the data-driven approach if the
model needs to be reconstructed. In practice, to improve model
accuracy while also providing predictions after a change to REFERENCES [1] A. Montserrat, L. Bosch, M. A. Kiser, M. Poch, and L. Corominas,
“Using data from monitoring combined sewer overflows to assess,
improve, and maintain combined sewer systems,” Sci. Total Environ.,
vol. 505, pp. 1053–1061, Feb. 2015. [2] B. Joseph-Duran, C. Ocampo-Martinez, and G. Cembrano, “Output-
feedback control of combined sewer networks through receding horizon
control with moving horizon estimation,” Water Resources Res., vol. 51,
no. 10, pp. 8129–8145, Oct. 2015. [3] W. Zhao, T. H. Beach, and Y. Rezgui, “Optimization of potable water
distribution and wastewater collection networks: A systematic review
and future research directions,” IEEE Trans. Syst., Man, Cybern., Syst.,
vol. 46, no. 5, pp. 659–681, May 2016. [4] Combined Sewer Overflow Management Fact Sheet (Sewer Separation),
document EPA 832-F-99-041, United States Environ. Protect. Agency,
Washington, DC, USA, Sep. 1999. [5] L. García et al., “Modeling and real-time control of urban drainage
systems: A review,” Adv. Water Resources, vol. 85, pp. 120–132,
Nov. 2015. [6] H. Baek, J. Ryu, J. Oh, and T.-H. Kim, “Optimal design of multi-storage
network for combined sewer overflow management using a diversity-
guided, cyclic-networking particle swarm optimizer—A case study in
the Gunja subcatchment area, Korea,” Expert Syst. Appl., vol. 42, no. 20,
pp. 6966–6975, Nov. 2015. p
g
Given this is a data-driven approach, it is worth highlighting
that the model construction requires availability and access to
reliable field monitoring data which can present a substan-
tial effort and challenge to network operators. Despite the
regulatory and operational requirements, it is also recognized
that the quality and availability of sensing data in drainage
networks can vary with different sites and network operators. With the overall improvement of the situation in the future, the
chance of providing better CSO predictions using the proposed
data-driven methodology can be correspondingly increased. Moreover, it is known that the use of gray or green infras-
tructure (e.g., storage and attenuation) can reduce the amount
of CSO spills through moving the stormwater runoff outside
the catchment or absorbing/leveraging the runoff across the
catchment (utilizing natural cycles and ecological systems). The data-driven model is able to predict CSO statuses in catch-
ments with existing gray or green infrastructure as the model
is constructed to learn such particular catchment and network
behaviors. VI. CONCLUSION VI. CONCLUSION This paper has proposed a systematic and automated data-
driven methodology to construct CSO predictive models. IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS: SYSTEMS, VOL. 49, NO. 6, JUNE 2019 1268 Various field monitored variables can be holistically taken into
account by the proposed approach. Little human involvement
is needed given the fact that the proposed approach is able
to collectively search for the relevant field variables and their
time lags associated to a particular CSO model. The model
training solutions provided are directly under the global opti-
mization of L1 regularization, making it more convenient and
effective than performing the pairwise correlation analysis for
a CSO as previously used. Computational efficiency was also
achieved by the proposal of a successive LASSO solution
generating scheme without matrix inversions. Given the field
investigation where many CSOs were involved, it is evident
that most CSOs exhibited a clear interrelationship with other
CSOs and field variables, in addition to the relationship with
the rainfall data as previously studied. Experimental results
showed that the proposed approach was able to automatically
construct CSO predictive models with good generalization
capability. For some CSOs with good spatial availability and
quality of surrounding data, the prediction accuracy can be
extraordinarily high, where more than 90% (R2 value) of
the underlying CSO behavior (variation) has been predicted
by the model. The superiority of the proposed approach
in terms of computational efficiency and model generaliza-
tion performance was also illustrated in comparison with
neural networks and fuzzy models. Furthermore, in addi-
tion to single-step ahead predictions (i.e., 15 min), multistep
ahead predictions were examined to demonstrate the promising
potential of the proposed methodology though the accuracy
decreases as the number of prediction steps increases. Such
CSO predictive models are easily constructed and run online,
by simply connecting a computing platform to the network’s
existing sensing framework. It can then be used to pro-
vide decision support to network operators as discussed in
Section V-C, in order to alleviate the impact of unexpected
CSO spillages. near future but cannot deduce the effect in the planning phase. In that respect, our proposed model addresses a specific use
case aiming at the prediction of future outcomes, as opposed
to the testing/assessing of hypotheses. VI. CONCLUSION Finally, future work
within this paper will involve increasing prediction time-steps
and conducting online model learning while also considering
acceptable model accuracies by leveraging the advanced model
and algorithm development, in order to allow more response
time for network operators to react with remedial actions. ACKNOWLEDGMENT The authors would like to thank the editors, the review-
ers, and Welsh Water for their constructive comments for
improving the quality of this paper. ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM Friedman, T. Hastie, and R. Tibshirani, “Regularization paths for gen-
eralized linear models via coordinate descent,” J. Stat. Softw., vol. 33,
no. 1, pp. 1–22, Jan. 2010. Yacine Rezgui received the M.Sc. degree from
University Paris 6, Paris, France, in 1991, and the
Ph.D. degree from Ecole Nationale des Ponts et
Chaussees, Paris, in 1994, both in construction
informatics. [33] M. McClelland and M. Campbell, “Probabilistic modeling of antici-
pation in human controllers,” IEEE Trans. Syst., Man, Cybern., Syst.,
vol. 43, no. 4, pp. 886–900, Jul. 2013. pp
[34] J. D. Lee, D. L. Sun, Y. Sun, and J. E. Taylor, “Exact post-selection
inference, with application to the lasso,” Ann. Stat., vol. 44, no. 3,
pp. 907–927, 2016. informatics. He is a Professor of building systems and
informatics with Cardiff University, Cardiff, U.K.,
and the Founding Director of the Building Research
Establishment
(BRE)
Centre
for
Sustainable
Engineering, Watford, U.K., sponsored by the BRE. In 1995, he joined Salford University, Lancashire,
U.K., as a Research Fellow, where he was a Lecturer in 1996, a Senior
Lecturer in 1998, a Professor in 2001, and the Founding Director of the 5*
(RAE 2001) rated Informatics Research Institute, from 2003 to 2007. He has
successfully completed over 40 research and development projects at national
(U.K. Engineering and Physical Sciences Research Council and Technology
Strategy Board) and international (European Framework Programs 5–7)
levels. His current research interests include informatics, covering ontology
engineering and artificial intelligence applied to the built environment. He
has over 150 refereed publications in the above areas, which appeared in
international journals, such as the IEEE TRANSACTIONS ON SERVICES
COMPUTING, Information Sciences, Data and Knowledge Engineering, and
Computer-Aided Design. pp
[35] T. Hastie, R. Tibshirani, and J. Friedman, The Elements of Statistical
Learning: Data Mining, Inference, and Prediction. New York, NY, USA:
Springer-Verlag, 2009. p
g
g
[36] C. Xiao and W. A. Chaovalitwongse, “Optimization models for feature
selection of decomposed nearest neighbor,” IEEE Trans. Syst., Man,
Cybern., Syst., vol. 46, no. 2, pp. 177–184, Feb. 2016. y
y
pp
[37] S. Boyd and L. Vandenberghe, Convex Optimization. Cambridge, U.K.:
Cambridge Univ. Press, 2009. [38] B. Efron, T. Hastie, I. Johnstone, and R. Tibshirani, “Least angle
regression,” Ann. Stat., vol. 32, no. 2, pp. 407–451, 2004. [39] W. Zhao, T. H. Beach, and Y. Rezgui, “Efficient least angle regression
for identification of linear-in-the-parameters models,” Proc. Roy. Soc. A,
vol. 473, no. ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM He is currently a Research Fellow with the School
of Engineering, Cardiff University, Cardiff, U.K. He
was a Research Associate with the Department of
Computer Science, Loughborough University, Loughborough, U.K. His cur-
rent research interests include machine learning, computational intelligence,
automatic control, autonomous systems, water resource management, and built
environment resilience. [24] A. Kurth, A. Saul, S. Mounce, W. Shepherd, and D. Hanson,
“Application of artificial neural networks (ANNs) for the prediction of
CSO discharges,” in Proc. 11th Int. Conf. Urban Drain., Edinburgh,
U.K., 2008. [25] S. R. Mounce, W. Shepherd, G. Sailor, J. Shucksmith, and A. J. Saul,
“Predicting combined sewer overflows chamber depth using artificial
neural networks with rainfall radar data,” Water Sci. Technol., vol. 69,
no. 6, pp. 1326–1333, Mar. 2014. pp
[26] A. Berne, G. Delrieu, J.-D. Creutin, and C. Obled, “Temporal and spa-
tial resolution of rainfall measurements required for urban hydrology,”
J. Hydrol., vol. 299, nos. 3–4, pp. 166–179, Dec. 2004. Thomas H. Beach received the Ph.D. degree in
computer science from Cardiff University, Cardiff,
U.K., in 2011. [27] C. Charlton-Perez, H. L. Cloke, and A. Ghelli, “Rainfall: High-resolution
observation and prediction,” Meteorol. Appl., vol. 22, no. 1, pp. 1–127,
Jan. 2015. He is currently a Lecturer of construction infor-
matics with Cardiff University. His current research
interests include application of computing technolo-
gies to the built environment, specification and
implementation of building/district/city data storage,
the Internet of Things and its application to the mon-
itoring and control of the built environment, data
analytics covering machine learning and artificial
intelligence, application of cloud/distributed computing to data storage and
processing for built environment applications, and the semantics of data within
the built environment. [28] E. M. A. M. Mendes and S. A. Billings, “An alternative solution to the
model structure selection problem,” IEEE Trans. Syst., Man, Cybern. A,
Syst., Humans, vol. 31, no. 6, pp. 597–608, Nov. 2001. y
pp
[29] S. A. Billings, Nonlinear System Identification: NARMAX Methods in
the Time, Frequency, and Spatio-Temporal Domains. Chichester, U.K.:
Wiley, 2013. [30] A. A. Adeniran and S. E. Ferik, “Modeling and identification of nonlin-
ear systems: A review of the multimodel approach—Part 1,” IEEE Trans. Syst., Man, Cybern., Syst., vol. 47, no. 7, pp. 1149–1159, Jul. 2017. y
y
y
pp
[31] R. Tibshirani, “Regression shrinkage and selection via the lasso,” J. Roy. Stat. Soc. B, vol. 58, no. 1, pp. 267–288, 1996. [32] J. ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 1269 [41] K. Li, J.-X. Peng, and E.-W. Bai, “A two-stage algorithm for iden-
tification of nonlinear dynamic systems,” Automatica, vol. 42, no. 7,
pp. 1189–1197, Jul. 2006. [16] N. A. Mancipe-Munoz, S. G. Buchberger, M. T. Suidan, and T. Lu,
“Calibration of rainfall-runoff model in urban watersheds for stormwater
management assessment,” J. Water Resources Plan. Manag., vol. 140,
no. 6, Jun. 2014, Art. no. 05014001. pp
[42] K. Aho, D. Derryberry, and T. Peterson, “Model selection for ecologists:
The worldviews of AIC and BIC,” Ecology, vol. 95, no. 3, pp. 631–636,
Mar. 2014. [17] A. N. A. Schellart, W. J. Shepherd, and A. J. Saul, “Influence of rainfall
estimation error and spatial variability on sewer flow prediction at a
small urban scale,” Adv. Water Resources, vol. 45, pp. 65–75, Sep. 2012. [43] K. Sjöstrand, MATLAB Implementation of LASSO, LARS, the Elastic
Net and SPCA. Lyngby, Denmark: Informat. Math. Model., Jun. 2005. [Online]. Available: http://www2.imm.dtu.dk/pubdb/p.php?3897 [18] Innovyze. InfoWorks ICM. Accessed on Aug. 9, 2017. [Online]. Available: http://www.innovyze.com/products/infoworks_icm/ [44] B. Krawczyk, “Learning from imbalanced data: Open challenges and
future directions,” Progress Artif. Intell., vol. 5, no. 4, pp. 221–232,
Nov. 2016. [19] U.S. Environmental Protection Agency. Storm Water Management
Model (SWMM). Accessed on Aug. 9, 2017. [Online]. Available:
https://www.epa.gov/water-research/storm-water-management-model-
swmm [20] Danish
Hydraulic
Institute. Modelling
Urban
Drainage
Systems
With MOUSE. Accessed on Aug. 9, 2017. [Online]. Available:
http://www.crwr.utexas.edu/gis/gishyd98/dhi/mouse/mousmain.htm [21] V. Puig et al., “Predictive optimal control of sewer networks using
CORAL tool: Application to Riera Blanca catchment in Barcelona,”
Water Sci. Technol., vol. 60, no. 4, pp. 869–878, Apr. 2009. Wanqing Zhao (M’13) received the B.Eng. degree
in automation from Anhui Polytechnic University,
Anhui, China, in 2006, the M.Eng. degree in con-
trol theory and control engineering from Shanghai
University, Shanghai, China, in 2009, and the Ph.D. degree from the Intelligent Systems and Control
Group, Queen’s University Belfast, Belfast, U.K., in
2012. [22] C. Ocampo-Martinez,
V. Puig,
G. Cembrano,
and
J. Quevedo,
“Application of predictive control strategies to the management of com-
plex networks in the urban water cycle,” IEEE Control Syst., vol. 33,
no. 1, pp. 15–41, Feb. 2013. [23] A. K. Fernando, X. Zhang, and P. F. Kinley, “Combined sewer
overflow forecasting with feed-forward back-propagation artificial neu-
ral network,” Enformatika Trans. Eng. Comput. Technol., vol. 12,
pp. 58–64, Mar. 2006. REFERENCES However, on the other hand, it cannot be used to
predict the potential benefit (effect) of using an envisaged
gray/green infrastructure though this particular problem is out-
side the scope of this paper. The same conclusion can also
be drawn on other options of stormwater management, e.g.,
the model can be trained to predict the CSO behavior in the [7] A.-S. Madoux-Humery et al., “The effects of combined sewer over-
flow events on riverine sources of drinking water,” Water Res., vol. 92,
pp. 218–227, Apr. 2016. [8] D ˆwr Cymru Welsh Water (DCWW). What is a Combined Sewer
Overflow? Accessed
on
Aug. 9,
2017. [Online]. Available:
https://www.dwrcymru.com/_library/leaflets_publications_english/comb-
ined_sewer_overflow.pdf [9] C. Henriques et al., “The future water environment—Using scenar-
ios to explore the significant water management challenges in England
and Wales to 2050,” Sci. Total Environ., vols. 512–513, pp. 381–396,
Apr. 2015. [10] J. Gasperi et al., “Priority pollutants in urban stormwater: Part 2—
Case of combined sewers,” Water Res., vol. 46, no. 20, pp. 6693–6703,
Dec. 2012. [11] I. Jalliffier-Verne et al., “Cumulative effects of fecal contamination from
combined sewer overflows: Management for source water protection,”
J. Environ. Manag., vol. 174, pp. 62–70, Jun. 2016. J. Environ. Manag., vol. 174, pp. 62–70, Jun. 2016. [12] U.K. Environmental Law Association. Types of Flooding. Accessed on
Aug. 9, 2017. [Online]. Available: http://www.environmentlaw.org.uk/
rte.asp?id=100 [13] D. Sempere-Torres, C. Corral, J. Raso, and P. Malgrat, “Use of weather
radar for combined sewer overflows monitoring and control,” J. Environ. Eng., vol. 125, no. 4, pp. 372–380, Apr. 1999. [14] L. S. Nanía, A. S. León, and M. H. García, “Hydrologic-hydraulic model
for simulating dual drainage and flooding in urban areas: Application
to a catchment in the metropolitan area of Chicago,” J. Hydrol. Eng.,
vol. 20, no. 5, May 2015, Art. no. 04014071. [15] V. M. Morales, J. M. Mier, and M. H. Garcia, “Innovative modeling
framework for combined sewer overflows prediction,” Urban Water J.,
vol. 14, no. 1, pp. 97–111, 2017. ZHAO et al.: AUTOMATED MODEL CONSTRUCTION FOR CSO PREDICTION BASED ON EFFICIENT LASSO ALGORITHM 2198, 2017, Art. no. 20160775. [40] K. Li, J.-X. Peng, and G. W. Irwin, “A fast nonlinear model identification
method,” IEEE Trans. Autom. Control, vol. 50, no. 8, pp. 1211–1216,
Aug. 2005.
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The Itinerant Curriculum as an Alternative Pathway for Responsiveness in African Higher Education in the Era of the Fourth Industrial Revolution
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African journal of inter-multidisciplinary studies
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cc-by-sa
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al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 The
Itinerant
Curriculum
as
an
Alternative
Pathway
for
Responsiveness in African Higher Education in the Era of the Fourth
Industrial Revolution Kehdinga George Fomunyam1 Abstract The Fourth Industrial Revolution is upon us, and it has serious implications for education globally. The educational curricula used in the first, second, and third industrial revolutions may not
necessarily be useful in this era of the Fourth Industrial Revolution (4IR), as societal and
organisational demands have changed. Curricula in African higher education needs therefore to
adapt to the changing demands of the Fourth Industrial Revolution, or else students may be
unprepared for the demands of future organisations and the society. Therefore, to enhance the
responsiveness of the curriculum in Africa, this paper examines the itinerant curriculum as an
alternative pathway to other highlighted curricula in the literature. The study posits how the
itinerant curriculum can be used to achieve curriculum responsiveness, economically, culturally,
disciplinarily, and in learning. The study concludes that the itinerant curriculum is an important
tool that can help African higher education achieve curriculum responsiveness in the era of the
Fourth Industrial Revolution. Keywords: African higher education; curriculum responsiveness; itinerant curriculum Introduction The challenge for schools is how to
prepare students well for the coming prolific job automation. Higher education in Africa must
urgently respond to the power of the Fourth Industrial Revolution technologies as such, either
positive social impacts will follow, or devastating environmental damage is upon us (Penprase,
2018). Substantial change is needed to the curriculum currently used, as the current curriculum
precludes students from developing capacities required for the new era of genomics, data science,
artificial intelligence, robotics, nanomaterials, and 3D printing. Hence, educational curricula in
Africa must prepare to change in accordance with technology. The Fourth Industrial Revolution have a great impact on education, as graduates of today will, in
a short space of time, face a future in an uncertain and technology-driven labour market. The
Fourth Industrial Revolution will favour automated job activities. McKinsey, as cited in Schwab
(2016) predicts that 800 million workers or a third of the workforce could be displaced in 42
countries, through the 4IR. However, Carruthers (2018) argues that graduates equipped with the
correct skills in this era will enjoy endless job opportunities. The challenge for schools is how to
prepare students well for the coming prolific job automation. Higher education in Africa must
urgently respond to the power of the Fourth Industrial Revolution technologies as such, either
positive social impacts will follow, or devastating environmental damage is upon us (Penprase,
2018). Substantial change is needed to the curriculum currently used, as the current curriculum
precludes students from developing capacities required for the new era of genomics, data science,
artificial intelligence, robotics, nanomaterials, and 3D printing. Hence, educational curricula in
Africa must prepare to change in accordance with technology. Schleicher (2019) points out that students will need skills for future job and labour markets, and
they will need the ability to navigate the increasing uncertainty and potential precariousness of
the gig economy. According to Carruthers (2018), little has been done to prepare future workers
through school curricula, as the currently used curriculum is obsolete, and does not meet the
demands of the Fourth Industrial Revolution workplace. The itinerant curriculum may be a
pathway that will ensure that the curriculum in Africa responds to this current era of rapid
globalisation. The itinerant curriculum is a destabilising epistemology that aims to defamiliarize
the canonical tradition of monocultures of ‘scientific’ knowledge, crucial to the ecology of
knowledge (Paraskeva, 2018). Introduction The itinerant curriculum does not abolish the past but assumes
and redeems the past by swerving from it. The itinerant curriculum will push educators and
students to think in the light of the future, and not in the light of the past. This paper, therefore,
proposes the itinerant curriculum as the superlative alternative in making African higher
education responsive to the Fourth Industrial Revolution. To achieve this objective, this paper is divided into four parts. The first part of the paper focuses
on the drawbacks of African higher education, while the second part centres on curriculum
responsiveness and its dimensions, and why the curriculum in Africa must be responsive in light
of such dimensions of curriculum responsiveness. The third part of the paper discusses
extensively the itinerant curriculum and the itinerant curriculum theory. The fourth part of the
paper explains how the itinerant curriculum can be used to achieve the dimensions of
responsiveness in the Fourth Industrial Revolution. This part presents in detail the processes or
steps that will encourage higher education in Africa to achieve responsiveness to this
technological era using the itinerant curriculum. Introduction The world is undergoing a technological revolution that is fundamentally altering the way we live,
work, and relate to one another. The transformation that will come alongside this technological
revolution will be so drastic that it will be unlike anything humankind has experienced before. Schwab (2016) propounds that we do not yet know just how the revolution will unfold, but one
thing is clear: the response to it must be integrated and comprehensive, involving all stakeholders
of the global polity, from the public and private sectors to academia and civil society. The Fourth
Industrial Revolution is upon us; therefore, it needs a response from academia. The Fourth
Industrial Revolution is the current and developing environment in which disruptive
technologies and trends such as the internet of things (IoT), robotics, virtual reality (VR), and
artificial intelligence (AI), are changing the way we live and work (Ayentimi and Burgess, 2019). Since the way we live and work is a product of how we are trained and socialised both in school
and in the society, higher education needs to respond to changing times. The Fourth Industrial
Revolution comes with implementation of smart technologies in our factories and workplaces,
connected machines will interact, visualising the entire production chain, and making decisions
autonomously (Marr, 2018). The Fourth Industrial Revolution is expected to impact all spheres
of human life, from various disciplines to industries, economies and very importantly, the sphere
of education. This is happening at an exponential rate. Therefore, governments, educators, and
parents alike must ask how they can prepare both present and future generations to thrive in
this transforming world (Brown-Martin, 2018). 1Durban University of Technology, GeorgeK@dut.ac.za 1Durban University of Technology, GeorgeK@dut.ac.za 1Durban University of Technology, GeorgeK@dut.ac.za African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 The Fourth Industrial Revolution have a great impact on education, as graduates of today will, in
a short space of time, face a future in an uncertain and technology-driven labour market. The
Fourth Industrial Revolution will favour automated job activities. McKinsey, as cited in Schwab
(2016) predicts that 800 million workers or a third of the workforce could be displaced in 42
countries, through the 4IR. However, Carruthers (2018) argues that graduates equipped with the
correct skills in this era will enjoy endless job opportunities. African Higher Education African higher education needs strong collaboration and partnership among concerned
stakeholders to address the multiple challenges confronting higher education in the continent. Mba (2017) points out that Africa has an estimated 1,650 higher-education institutions, many of
which face challenges that require the intervention of various stakeholders, national
governments, and development partners. Such interventions he continues would allow students
to maximise their learning outcomes, and contribute effectively to the workforce, especially in
this era of the Fourth Industrial Revolution. One of the issues facing higher education in Africa,
according to Mba (2017), is the current pattern of skills production in Africa that does not match
the labour market demand or development needs. Higher institutions of learning in Africa
produce millions of graduates annually. Despite this, many graduates remain unemployed
because they have a substantial shortage of skills (particularly certain soft skills needed within
this era of the 4IR, as well as other hard skills particularly relating to the use of computers)
needed for the current work environment. This happens because there is a disconnect between
the skills African graduates have, and the skills needed to flourish in the Fourth Industrial 142 er/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 rican Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/aji Revolution work setting (Fomunyam, 2019). Higher education in Africa suffers mostly from poor
content, outdated curriculum, inadequate materials, and untrained teachers. Ayentimi and Burgess (2019) argue that most countries in Africa still compel students to
memorise facts and figures from overloaded curricula with outdated content. This leaves
students insufficiently skilled to meet the demands of the workplace. Hence, Kayembe and Nel
(2019) assert that there is a danger that African young people – half the continent’s population –
could become frustrated with their education systems, especially at the post-primary level. Providing a solution to this, Rehorn (2017) states that Africa must launch a new education model
to meet the current technological advancements. Thus, there is an urgent need for curriculum
reform among African countries, as this will expand access to and democratise education, while
ensuring quality learning opportunities through relevant and pertinent curricula for this era of
globalisation. A few countries in Africa have started reforming their curricula by moving away
from those which are overloaded and outdated. Countries are trying to move in line with recent
changes in the world. Curriculum and Curriculum Responsiveness Much has been said about curriculum and curriculum responsiveness. What does this actually
mean? Fomunyam (2014) argues that curriculum is often understood as a framework that sets
expectations for students’ learning, and it serves as a guide for teachers, establishing standards
for student performance and teacher accountability. He goes further to articulate what he thinks
is a more accurate definition of curriculum by seeing it as a series of potential experiences
organised in a school for disciplining students in ways of thinking and acting. A curriculum not
only provides students with the knowledge required; it shapes the way they behave and view
scenarios. The fundamental purpose of an educational curriculum is to ensure that students
receive integrated, coherent learning experiences that contribute towards their personal,
academic, and professional learning and development (Wedekind 2019). The curriculum
therefore extends beyond the classroom, because it affects the personal lives of students by
developing them, making them a better version of themselves. According to Linda (2009) and George (2009), there are four basic types of curricula used by
educators. These are the traditional, thematic, programmed, and classical curricula. Linda (2009)
asserts that the traditional curriculum is the traditional workbook/textbook approach; it is
grade-specific and may be expensive. The traditional curriculum focuses on a specific body of
knowledge to be transmitted to students; and relies heavily on memorization and drilling of facts
and formulas. The curriculum does not take into consideration the specific needs of students, as
the curriculum ensures that all students are taught the same content in the same time frame. No
adjustments are made for students who have difficulty with the material, or for those who find
the material easy and are ready to move on ahead of the rest of the class. The traditional
curriculum is not a responsive curriculum; nevertheless, it is regarded as the most widely used
curriculum in African higher education (Bleazby, 2015). Bleazby supports this when he says that
the traditional curriculum favours the same course content being taught to students from one
decade to the next, without any modifications. This implies that the curriculum is old, and
irrelevant; it does not, and cannot prepare African students for the demands of the future
workplace. This therefore calls for enormous changes to the curriculum being used in Africa. Conversely, the thematic curriculum is the organisation of a curriculum using themes. African Higher Education South Africa, Rwanda, Tunisia, Gambia, and Ethiopia are favouring curricula
that focus on competencies in key knowledge and skills areas (Kayembe and Nel, 2019). Despite
such changes by these countries, they are yet to seriously consider how the Fourth Industrial
Revolution will shape the workplace; and the effect it will have on future workers. Curriculum and Curriculum Responsiveness Thematic
instruction integrates basic disciplines like reading, mathematics, and science with the
exploration of a broad subject such as communities, rain forests, river basins and the use of
energy (Tessier and Tessier, 2015). Ashokan (2014) explains that a thematic approach is a way
of teaching and learning, in which many areas of the curriculum are connected and integrated 143 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 within a theme. The idea of thematic curriculum is that students will acquire more knowledge
when they can connect what they are being taught in the classroom with real-world events. Educators, instructors, and teachers often try to connect themes used in lessons to students’
everyday lives. Therefore, a thematic curriculum will allow learning to be more natural and less
fragmented, unlike the traditional curriculum in which a school day is time-divided into various
subject areas. Children practise exercises frequently related to nothing other than what the
teacher has decided on while writing on the chalk board (Ashokan, 2014). Although the thematic
curriculum has a few benefits, it has certain drawbacks. First, some students could lose interest
in the theme, which means less motivation to participate. Second, a student missing a day is
missing a major connection, becoming lost in class when a different topic is introduced. Most
important, the thematic curriculum focuses mainly on the needs of students, ignoring societal
needs (Pirinen, 2009). Right now, the societal need is for the development of students that will
be able to function in this era of the Fourth Industrial Revolution. The thematic curriculum does
not guarantee this. Therefore, higher education in Africa must move away from the use of a
thematic curriculum. Such a curriculum leads to mass-producing graduates that will struggle to
operate in the current technological era. American behavioural psychologist, B. F. Skinner, is the major contributor to programmed
learning. Programmed learning is an educational technique characterised by self-paced, self-
administered instruction presented in logical sequence, and with much repetition of concepts
(Rolandsson, 2015). Therefore, programmed learning can be said to be an individualised and
systematic instructional strategy for classroom learning and self-learning (Seel, 2012). The basic
requirement of programmed learning is breaking up study material into small steps, giving
immediate feedback and confirmation of every step. This is achieved by means of information
presentation, questions, and learners’ response (Hošková-Mayerová and Rosicka, 2012). Curriculum and Curriculum Responsiveness 144 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 rican Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/aji No matter the kind of curriculum used in a particular region, curricula must be responsive to the
needs of students and the society in which these students find themselves (Fomunyam and
Teferra, 2017). Moll (2004) explains that curriculum responsiveness is the ability of curricula
taught in schools or universities to address students’ needs as well as societal circumstances. For
a curriculum to be responsive, students should be able to become productive members of the
society when they graduate, by continually solving societal problems with relative ease. In the
context of this study, curriculum responsiveness means the ability of the higher-education
curriculum in Africa to produce students with the capacity to be productive in the era of the
Fourth Industrial Revolution. Fomunyam and Teferra (2017) relate that, for a curriculum to
achieve full responsiveness in this Fourth Industrial Revolution era, it must be economically
responsive, classroom or culturally responsive, disciplinarily responsive, and learning
responsive. Fomunyam and Teferra (2017) see economic responsiveness as dealing with the ability of a
curriculum to train skilled professionals in the various sectors of the economy. Therefore, a
curriculum is said to be economically responsive when graduates are highly skilled and ready for
the job market. Being ready for the job market means that students can develop long-lasting
solutions to organisational problems. An economically responsive curriculum will not just satisfy
the current job market but will be able to proffer solutions to anticipated organisational
problems, contributing immensely to the development of the general economy (Wedekind, 2019). It becomes imperative that the African higher-education curriculum become economically
responsive to the Fourth Industrial Revolution. This is because, in this era of technological
advancement, organisations will be confronted by new technological challenges that will
threaten, affect, and change their business processes from less automated to highly automated
business processes. This will make organisations yearn for employees that are highly skilled and
that have the capacity to operate within automated organisations. On the other hand, cultural responsiveness is the curriculum’s ability to access and respond to
the cultural dissonance in the classroom (Moll, 2004). A classroom is always divided along
cultural lines: this could be in the form of race, ethnicity, religion, age, and sometimes gender. Curriculum and Curriculum Responsiveness Lessons
are broken into various smaller sections containing information. Each smaller section is followed
immediately by comprehension questions to be answered by students. Immediate feedback is
then received from students on the correctness of the answers. Seel (2012) avers that
programmed learning is a small step, self-pacing, and a kind of learning that gives immediate
feedback. Some of the textbooks being used by students recently are structured in a programmed
learning format. Despite its usefulness, it is very difficult to develop instructional materials using
programmed learning. Only cognitive objectives can be achieved; there is no chance for students’
creativity, as their responses are highly structured. It is important to note that programmed
learning cannot be applied at higher-education level. Programmed curriculum cannot work in
higher education, therefore is not an option for African higher education in this era of
globalisation. The classical curriculum is a complete classical Christian curriculum that emphasises the
traditional liberal arts of language and mathematics and the cultural heritage of the Christian
West, as expressed in the great works of history and literature (George, 2009)). The curriculum
focuses on basic skills of reading, writing, and arithmetic laying special emphasis on Latin. The
classical curriculum is designed to develop students, both academically and spiritually, training
students to think critically, and teaching them to speak and write persuasively. According to
Boutin and Rodgers (2011), the classical curriculum serves several purposes. It focuses on the
highest spiritual, literary, and artistic achievements of Western civilization, elevating the mind
and soul; it introduces students to the greatest books in their original sources, not biased textbook
summaries; it integrates the study of various subjects, showing the interrelationships that exist
among them; and provides a solid grounding in the basics, emphasising the technique of learning
by memorization in the lower grades. The major drawback of the classical curriculum as far as
this paper is concerned, is that it focuses mainly on languages and history, hence, classical
education tends to be a bit weak on science (Witmond, 2008), and science is the order of the day
in the Fourth Industrial Revolution. This means that classical education will not help prepare
African students for the Fourth Industrial Revolution. Moreover, Africa is a secular continent. A
curriculum with Christian roots, therefore, may not be favoured in some parts of the continent. Curriculum and Curriculum Responsiveness Ladson-Billings (1995) argues that culturally responsive pedagogy is a student-centred approach
to teaching that includes cultural references. It recognises the importance of students’ cultural
backgrounds and experiences in all aspects of learning. A culturally responsive classroom will
promote engagement by embracing classroom diversity, nurturing students’ cultural strengths. Brown-Jeffy and Cooper (2011) explain that culturally responsive teaching is concerned with
using cultural knowledge, prior experiences, frames of reference, and performance styles of
ethnically diverse students to make learning more relevant and effective for students. Thus, a
culturally responsive classroom will see diversity and cultural differences as assets and values; it
will challenge racial and cultural stereotypes, prejudices, racism, injustice, and oppression; and it
will promote social justice and academic equity. Globalisation and internalisation have made the
classroom more culturally diverse than ever before. Classrooms must therefore be culturally
responsive: researchers have discovered that culturally responsive classrooms motivate students
to learn and help them become effective learners. A disciplinarily responsive curriculum offers a type of responsiveness cogent to this era of the
Fourth Industrial Revolution. Ferdinand (2009) states that disciplinarily responsiveness is the
ability of a curriculum document to be up to date with the research in the field, while promoting
new discoveries within the discipline. For a curriculum to be disciplinarily responsive, it must
continually incorporate new knowledge of the field into the curriculum. A disciplinarily
responsive curriculum allows for specialization, depth of content knowledge; it is specific,
current, factual, and it develops skills in students as it emerges from experts in the discipline
(Fomunyam and Teferra, 2017). As a result of the current technological advancement, there is the
need for new knowledge to be continually embedded into the curriculum, for it to remain
responsive to the drastic changes in the workplace caused by technological advancement. Moja 145 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 (2004) posits that disciplinarily responsiveness will ensure that what is happening locally and
internationally, as far as any discipline is concerned, is duly embedded into the curriculum. This
will encourage students to think globally, and act locally, to develop the discipline, and to solve
current and anticipated organisational problems. Finally, learning responsiveness, otherwise called pedagogy, is the curriculum’s ability to respond
to the needs of the student (Fomunyam and Teferra, 2017). Curriculum and Curriculum Responsiveness Pedagogy must take into serious
consideration the individual needs of students, because, without this, students may find it difficult
to learn. Here, the idea is helping students to develop their academic, social, and emotional skills
in a learning environment that is developmentally responsive to their strengths and needs. In this
age of technological advancement, it is important that learning becomes responsive to the
respective needs of students, so that students do not become uninterested in class lessons. Students need to be excited and keen to learn the rudiments of becoming successful employees
in the workplace. The ultimate question therefore is: how can the African higher-education curriculum in Africa
achieve economic responsiveness, cultural responsiveness, disciplinarily responsiveness and
learning responsiveness to prepare students in Africa for the Fourth Industrial Revolution? Earlier studies proposed some alternative pathways to achieve curriculum responsiveness in
African higher education during this fourth era of globalisation. However, this study proposes the
itinerant curriculum as the alternative to make African higher education responsive to the
demands of the workplace in this era of the Fourth Industrial Revolution. The Itinerant Curriculum Theory African colonial masters thus, epistemised African epistemology by
making Africans believe their language to be inferior, complicated, and impractical in institutions 146 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 of learning. African governments are also reluctant to radically change the curriculum used in
Africa, because there is still a strong belief in the curriculum that the colonial masters left behind
(Fomunyam and Teferra, 2017) and African nations would have to articulate their own path and
ensure that they create an alternate future for themselves. This is particularly critical because the
curriculum left behind for African higher-education institutions generally dismisses the intrinsic
value of African culture, customs, and practices, favouring mostly Western culture, customs, and
practices, not minding the suitability of the curriculum to the African environment (Fomunyam
and Teferra, 2017). This has made learning in Africa stationary, non-progressive, redundant, and
irrelevant. The African continent only transfers technology, and mostly never produces globally
acceptable innovations in biology, technology, mathematics, and medicine. Hoskins (1992)
rightly argued that Africa’s contribution to the body of knowledge has been denied altogether
with the dominant culture presented as the only authentic producer of knowledge. The ICT is an incredible method of winning the battle against African curriculum epistemicide. It
is a clarion call to challenge curriculum epistemicide by completely engaging in the mind-boggling
battle for social and cognitive justice. Paraskeva (2016) adds that the ICT likewise cautions on the
need to challenge any type of indigeneity or the romanticising of the indigenous societies and
knowledges. This is not confined to any dichotic skeleton of West–Rest. Masaka (2018) adding to
this stated that this will allow the people of Africa to tell their own story from their own
standpoint, thereby contributing to knowledge production. The ICT pushes the field of curriculum
studies along a totally different, creative, inter-, and transnational path (Oliveira, 2017). Oliveira
(2017) demands that curriculum studies solidly draw epistemologies and scholarly customs that,
until now, has been totally overlooked. In this sense, curriculum developers in Africa are expected
to fine-tune the already existing curriculum, to ensure its relevance to the African continent and
its relevance to the Fourth Industrial Revolution. Süssekind (2014b) argues that the ICT drives a post-abyssal, non-abyssal and non-territorial
curriculum for the benefit of all. The Itinerant Curriculum Theory The ICT therefore emphasises that to destroy epistemicide in
Africa, the current curriculum used in the continent must be abolished. A new curriculum devoid
of epistemicide which would encourage forward thinking should be developed. From the
foregoing, it can be concluded that the major objective of the ICT is to fight against epistemicide
and ensure curriculum relevance. The major objectives of this research are considered very
significant to the Fourth Industrial Revolution and to students and graduates studying or
graduating within this era. To prepare African students for the future workplace, there is need
for curriculum change in line with the demands of today’s world of high automation and
globalisation. With these, the major objectives of the ICT (i.e., fighting against epistemicide and
ensuring curriculum relevance) will be achieved in African higher education. There is no single
accepted method of adopting and using the ICT in ensuring that its objectives are achieved. Sloterdjik (2013) articulates that the ICT does not come with an endorsed formula nor prescribed
recipe. It challenges the scripted nature of our curriculum crisis and emergency driven by the
standardization momentum. Sloterdjik (2013) further adds that the ICT is not an assault or attack
on specific epistemologies, but rather a procedure of mindfulness that challenges epistemicide. Assaults and attacks are pre-planned; they have a prescribed recipe, an endorsed formula, and a
programme of events. However, the ICT is not an assault, nor an attack; it does not have a
programme of events nor a standardised global process. It is based on contingency. The ICT is
usually applied based on the situation, and the objectives it is hoping to achieve. This study
proposes the ICT as an effective pathway to making African higher education responsive to the
demands of the Fourth Industrial Revolution. The Itinerant Curriculum Theory The Itinerant Curriculum Theory (ICT) attempts to create an itinerant path to address a problem
(Paraskeva, 2017). Paraskeva (2017) defines an itinerant as a person who moves from place to
place, typically for work, such as the itinerant preacher who moves to a new community every
few years. An itinerant person could be a labourer or an employee who moves from place to place
as demanded by employment. However, an itinerant curriculum is a deliberate disrespecting of
the canon (Süssekind, 2014b). The itinerant curriculum is a radical means of changing the archaic
curriculum used in African higher education developed by their colonial masters. The ICT, according to Paraskeva (2016: 16), is “a new path that is sentient of the functionalism of
both dominant and counter-dominant Western Eurocentric positions, of the richness of non-
Western epistemological platforms, of the fallacy of the history fabricated by Western Eurocentric
dominant and specific dominant traditions, of the fascism of the Western Eurocentric
epistemological coloniality that failed, and it failed greatly, not only because of its crude
limitations and fallacies but also given the immense power of non-Western epistemological ways
of reading and being in the world that always challenge Western Eurocentric dominant position”. The ICT will produce curricula in Africa driven by emancipatory epistemologies of contrasting
and reverberating otherness, and this according to Paraskeva (2016) will give us the space in
which to (re)imagine, what we do, change the unbending, and reductive philosophies that plague
our education and our lives. Thus, through such emancipatory labour in African schools and
communities, Africans will open themselves and their students to new possibilities for working
across their differences, as they name, resist, and disrupt old ways of knowing, that formerly
rendered their lives silent and invisible. Hence, the ICT is a radical way of changing the Western-
centric curriculums used by Africans. The ICT is influenced by the importance of non-Western
curricula in the struggle for a more relevant and socially committed education and curriculum. African colonial masters epistemised Africa, meaning that they killed off African knowledge
systems. For example, most countries in Africa adopted the language of colonial masters as their
lingua franca. Students are mandated to speak either English or French, undermining African
indigenous languages. Itinerant Curriculum as a Panacea for Curriculum Responsiveness The importance of achieving curriculum responsiveness in African higher education in this
current era has been earlier discussed and cannot be overemphasised. As pointed out earlier, a
curriculum will only afford responsiveness if it achieves economic responsiveness, classroom or 147 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 cultural
responsiveness,
disciplinary
responsiveness,
and
learning
or
pedagogical
responsiveness. This section of the paper details how the itinerant curriculum can be used as an
alternative pathway in achieving these four types of responsiveness to the Fourth Industrial
Revolution. Advances in technology, biology, and medicine have improved quality of life, yet it
has made life more complex. Recent developments in technology around the globe have affected
and will continue to affect organisations and society at large (Penprase, 2018). Schleicher (2018)
that organisational processes and procedures will continually be modified to adapt to these
changes and developments in technology. Even society at large will be affected, as artificial
intelligence is unleashing a whole new level of productivity and augmenting our lives in many
ways. According to Schleicher (2019), these changes and developments mean that workers with
less education and fewer skills are at a disadvantage as the Fourth Industrial Revolution
progresses. How then can the itinerant curriculum make learning in African higher education
become economically responsive in this era? As earlier explained, economic responsiveness involves not only satisfying the job market but
creating sustainable solutions to future challenges, while growing the economy (Fomunyam and
Teferra, 2017). Spector (2021: 78) argues that there is “critical need for curriculum to become
more responsive and proactive, perhaps even refocusing curricular time away from traditional
school subjects towards timely topics, which would be informed by traditional school subjects”. This is to say that most of the curricula in use especially on the African continent needs immediate
attention if they are to effectively prepare students for this era. Fomunyam and Teferra (2017)
confirms this when they argue that if a change is not made, African graduates may become
redundant in the current and future organisational work settings. Business processes are now
being gradually automated, and in no distant time, business processes and procedures may well
become fully automated. Itinerant Curriculum as a Panacea for Curriculum Responsiveness Speaking on education in Africa before colonialism, Abdi (2012: 12)
posits that the African system of knowledge exposes a “particular philosophy of education, a
sagacity that was less doctrinaire than, say the specialized categories of the philosophy of 148 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 education (e.g., idealism, realism, analytic, or behaviourist), but was based on needs identified for
that given situation. That is, precolonial African philosophies of education were focused on the
real lives of Africans and were not responsive [to] the problematic elaborations of Eurocentrism
and the perforce peripheralization of the rest of the world”. This education was relevant and
adequate and spoke to responsiveness and particularly economic responsiveness. Abdi (2012:
19) categorically states that, “an education that is not relevant for people’s cultures and needs is
an inadequate education” and colonialism as well as its vestiges which lies at the heart of the rise
of Europe, sucked as much as it could from this humanistic system and dismantled it, making it
irrelevant (Paraskeva, 2016). The propositions of the ICT can be used to create this change. Although, the ICT is a radical theory,
it has shown itself to be effective. First, the current curriculum used in most of Africa need review
or change to ensure it does not continue slowing down the growth of the continent in this era of
the Fourth Industrial Revolution. Schleicher (2018) posits that critical engagement on content
around Big Data, Creative Studies, and Decision Sciences should be included in all curricula,
irrespective of the course of study. These contents are enormously important and will expose
students to basic knowledge they need in this current era. Background knowledge in technology
by students will ensure they have the capacity and necessary skills to operate in future
workplaces. Paraskeva (2016: 195) argues that “the task, therefore, is to think of education in
general and curriculum in particular from a diametric perspective, …for there is no greater crime
than facing current intellectual challenges with the equipment of the past. We must deal with
issues of interest, rather than with issues of fact, because reality is not just defined by issues of
fact”. A change in approach, focus and content is needed to ensure we do not face current challenges
with equipment from the past. Itinerant Curriculum as a Panacea for Curriculum Responsiveness The curriculum in most parts of Africa still favours the analogue
methods of carrying out business operations, which in a few years will be totally out of place. Many traditional courses, such as Biology, Business studies, and Accounting are still taught in
higher institutions of learning without incorporating new courses relevant to this era of
globalisation and the Fourth Industrial Revolution (Spector, 2021). Many graduates from Africa may become totally irrelevant in the workplace. If curriculum review
and or change is not initiated swiftly to correct this anomaly, multinationals may, in no distant
time, resist employing graduates from Africa, who lack the capacity and skills to operate in
Fourth-era organisations. There are already complaints about some graduates from Africa:
multinationals believe that they are not properly trained to fit into the world of work in terms of
desirable knowledge and skills to operate in an automated organisational setting (Iruonagbe and
Egharevba, 2015). The curriculum in Africa is plagued by several challenges and this has slowed
the growth and development of the region, while other regions like Asia and South Africa which
are largely made up of third world countries have enjoyed steady growth and development. They
have developed technologies that suit their environments perfectly. On the contrary, Iruonagbe
and Egharevba (2015) argue that most African countries only wait for the transfer of technology,
instead of being committed to a system in which they can copy, adapt, and fabricate foreign
technology through an inward-looking strategy to suit their own cultures, environment, and
needs. Africa hardly develops her own technologies, rather, technologies are being transferred to
the continent, not regarding its suitability to the environment. This happens because the higher-
education curriculum does not favour technology development, but rather technology imitation. To buttress this point, till 2022, Africa was unable to manufacture a single dose of the Covid-19
vaccine and had to wait for Europe and America to provide the vaccine. It was not until 2022 that
the president of South Africa announced the first vaccine manufacturing plant in South Africa. A
change in curriculum would improve capacity and ability on the continent to ensure that Africa
can meet its own needs. Itinerant Curriculum as a Panacea for Curriculum Responsiveness However,
most researchers and scholars are of the view that the additive and transformation approaches
are most effective. Harmon (2012) explains that the additive approach will see books and
materials added to the existing curriculum in an attempt to add multicultural content, while the
concepts and objectives of lessons are unchanged. However, this approach is not radical since
lessons, objectives and concepts will remain un-tampered with. On the other hand, a more radical
approach is the transformation approach that will see curriculum, concepts, and objectives
changed to include voices that have previously been distorted or excluded (Harmon, 2012). This
will sometimes make students examine and challenge their own sets of beliefs and values. The transformation approach is in line with ICT and seeks a more radical solution to problems. Based on the purpose and the assumptions of the ICT, multicultural education, using the
transformation approach, should inform the core curriculum of the African higher-education
curriculum. This will achieve curriculum responsiveness and relevance; and will also make the
classroom responsive to the growing cultural diversity in this era of globalisation and
internationalization. By doing this, Africa will not only be critiquing dominant traditional
positivist curriculum, but will also be countering dominant critical curriculum theories,
denouncing how both perspectives were/are functionalistic (Paraskeva, 2016). Each discipline in African higher education must be continually updated to make it responsive to
the discipline itself, and relevant to society in this technological era. Fomunyam and Teferra
(2017) state that for a curriculum to be disciplinarily responsive, it must respond to new
knowledge produced according to the dictates of the discipline by the community of scholars in
that discipline. Using ICT as the lens for this will mean to radically change the curriculum content
of each of the disciplines studied in higher institutions of Africa, contextually, thereby, ensuring
it is deterritorialised and previously epistemicide knowledge are included. This will be a step in
the right direction, and the denunciation of the epistemicide within the epistemicide (Paraskeva,
2016). The curriculum used in higher education by the Western world is gradually changing
because of the present globalisation (Schleicher, 2018). Many universities in the Western world
have been introducing new and relevant contents to various disciplines that align with the
current and future demands of the workplace. Itinerant Curriculum as a Panacea for Curriculum Responsiveness This will also make certain that African students develop their own
environmentally friendly technology, thereby reducing the transfer of technology from the
Western world. By doing this, one of the major objectives of the ICT (i.e., opposing epistemicide,
and ensuring curriculum relevance) will be achieved. It is imperative that the curriculum in Africa
be culturally responsive to the Fourth Industrial Revolution. In this age, globalisation and
internalization have made classrooms more culturally divided. Classrooms in Africa nowadays
are filled with students from various parts of the continent, especially in higher-education
classrooms. Culture must therefore be given serious consideration, since a culturally responsive
classroom will make students comfortable to learn. On the contrary, a less culturally responsive
classroom will dissuade students from learning, and hence, reduce students’ performance (Lee,
2007). Of what use will an economically responsive curriculum be to the Fourth Industrial
Revolution, if students are uninterested in learning? As earlier highlighted, the current curriculum is not culturally responsive and must be changed
significantly, in order to allow the curriculum to achieve relevance. Howard and Terry (2011)
posit that a culturally responsive pedagogy is situated in a framework that recognises the rich
and varied cultural wealth, knowledge, and skills that diverse students bring to schools. A
culturally responsive pedagogy seeks to develop dynamic teaching practices, multicultural
content, multiple means of assessment, and a philosophical view of teaching dedicated to
nurturing students’ academic, social, emotional, cultural, psychological, and physiological well-
being. Therefore, to achieve this in this era, Harmon (2012) proposes that teachers draw on
African culture and history; locate ‘self’ in a historical and cultural context; enable students to
create new knowledge based upon life experiences; and view knowledge as reciprocal. Ladson-
Billing (2010) asserts that to ensure a culturally responsive classroom, teachers should create a
community of learners much like an extended family, perceiving teaching as a calling, and having
high expectations for the success of all students. Multicultural education should be part of the curriculum in African higher education. Harmon
(2012) states that this will provide opportunities for students to view issues through multiple
lenses; it will improve their problem-solving skills and help address issues of social justice. 149 rican Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/aji According to Banks (1999), multicultural content has four approaches that ensure high
curriculum responsiveness − contribution, additive, transformation, and social action. Itinerant Curriculum as a Panacea for Curriculum Responsiveness Africa needs to tap into the itinerant approach and
deterritorialise curriculum “to address some dead ends with the radical critical platform and to
lead the struggle against the epistemicides” (Janson and Silva, 2017: 1). The curriculum in Africa must be learning responsive, because, if a curriculum is economically
responsive, culturally responsive, and disciplinarily responsive, but it is not learning responsive,
no serious learning will take place. Fomunyam and Teferra (2017) contend that without the
curriculum responding to the needs of individual learners, no meaningful learning can take place. The curriculum can therefore be relevant and have content that will prepare students for the
Fourth Industrial Revolution. Slonimsky, Lynne and Shalem (2006) posit that if students become
disengaged during class lessons, the curriculum becomes redundant and irrelevant. This clearly
depicts the importance of making lessons learning responsive. Ogude, Nel and Oosthuizen (2005)
in this light outline a framework for pedagogical or learning responsive. The authors assert that
responding to student needs through the curriculum entails specific approaches to the design of
curricula, instructional systems, methods of assessment, techniques for appraisal, and
approaches to student support. To them, such approaches take the characteristics and context of target student groups seriously. Putting this in place will make learning responsive to the specific needs of students. This will
ensure that students become interested in class lessons. It will motivate them to learn how to
become better employees in the technological age. Janson and Silva (2017: 1) concomitantly state
that within ICT, we need to “to redefine the struggle for social justice as a struggle for cognitive
justice… and produce a new language that promotes new endless meanings for the field”. This
will create endless possibilities for pedagogical or learning responsiveness as new meanings or 150 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 al of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 solutions to old and new challenges would be developed by fighting for a different research
platform, one that pushes research to a “level of instability, not stability, generating concepts also,
in itself, unstable” (Paraskeva 2016: 196). It is important that the African higher education
achieve all four dimensions of responsiveness. This is because all the dimensions play important
roles in preparing students for the demands of the Fourth Industrial Revolution. Conclusion The changing times in which we currently are, demand for a change in curriculum to meet the
demands of the times and seasons. Graduates sent out by African universities are struggling in
the job market be it in the drive to find employment or create one for themselves. As stated by
Zavale, and Schneijderberg (2022: 199) between 1980 and 2019 just about 6483 research articles
have been published on higher education in Africa and these articles can be grouped into four
communities of researchers, “the community researching teaching and learning issues, the
community focusing on structural transformation of HE, the community focusing on the internal
organisation of HE and the community focusing on societal engagement of HE”. They further state
that a total of 22 African countries are home to less than 2% of the authors with institutional
affiliations and conclude that scholars studying African higher education in Africa come from 34
out of 54 countries. This means that a total of 20 countries are not represented. As stated earlier (Paraskeva 2016),
ICT demands different research platforms which would push research to the point of instability
especially because without new and alternative research, an itinerant curriculum cannot be
developed. The absence of curriculum amongst the communities is also troubling and explains or
speaks to the question of epistemicide which ICT seeks to destroy. The itinerant curriculum
informed by the itinerant curriculum theory would work towards the production of graduates
who are ready for the changing times. Curriculum responsiveness in this era can only be achieved
if the African curriculum is economically, culturally, disciplinarily, and learning responsive. Many
alternatives have been proposed in the literature to achieve this. However, this study examined
this issue from a unique angle. That is, using the itinerant curriculum to achieve these dimensions
of curriculum responsiveness. This research therefore recommends that, for higher education in Africa to achieve economic
responsiveness in this era, the current curriculum must be radically engaged with immediate
effect. If a change is not affected, African students will find it impossible to solve organisational
and societal problems. New content, relevant to this present age should be included in the
curriculum. This will provide students with necessary skills and knowledge imperative for this
era of technological revolution. Multicultural education is needed in the curriculum for the
curriculum to become culturally responsive. Conclusion African voices that were once conspicuously
removed by the colonial masters should be added to the course contents and curricula. Itinerant Curriculum as a Panacea for Curriculum Responsiveness The ICT can play
a major role in enabling the curriculum in Africa to achieve responsiveness. Therefore, to make
the curriculum in African higher education responsive in this era of the Fourth Industrial
Revolution, learning authorities must combat epistemicide, and make the curriculum relevant. Ayentimi, D. T. and Burgess, J. 2019. Is the Fourth Industrial Revolution relevant to sub-Sahara
Africa? Technology Analysis and Strategic Management, 31(6): 641-652. Ashokan, V. 2014. Thematic approach for effective communication in early childhood education.
International Journal of Education and Psychological Research, 3(3): 49-51. Abdi, A. 2012. Eurocentric discourses and African philosophies and epistemologies in education.
In: Wright, H. K. and Abdi, A. A. eds. The Dialectics of African Education and Western Discourses.
New York: Peter Lang, 12–26. References Abdi, A. 2012. Eurocentric discourses and African philosophies and epistemologies in education. In: Wright, H. K. and Abdi, A. A. eds. The Dialectics of African Education and Western Discourses. New York: Peter Lang, 12–26. Ashokan, V. 2014. Thematic approach for effective communication in early childhood education. International Journal of Education and Psychological Research, 3(3): 49-51. Ayentimi, D. T. and Burgess, J. 2019. Is the Fourth Industrial Revolution relevant to sub-Sahara
Africa? Technology Analysis and Strategic Management, 31(6): 641-652. 151 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 Banks, J. A. 1999. An Introduction to Multicultural Education. 2nd ed. Boston: Allyn and Bacon. Bleazby, J. 2015. Why some school subjects have a higher status than others: The epistemology of
the traditional curriculum hierarchy. Oxford Review of Education, 41(5): 671-689. Boutin, S. and Rodgers, J. B. 2011. Jefferson's classical curriculum: An examination of the classical
influences on Thomas Jefferson's educational philosophies. American Educational History Journal,
38(1/2): 399. Brown-Jeffy, S. and Cooper, J. E. 2011. Toward a conceptual framework of culturally relevant
pedagogy: An overview of the conceptual and theoretical literature. Teacher Education Quarterly,
38(1): 65-84. Brown-Martin, G. 2018. Education and the Fourth Industrial Revolution. Available:
https://cdn.lgseta.co.za/resources/research_and_reports/4IR%20Resources/Education%20an
d%20the%204IR_Graham%20Brown-Martin_2017.pdf (Accessed 3 February 2022). Carruthers, H. 2018. Education in the Fourth Industrial Revolution: Relocate Global Online. Available:
https://www.relocatemagazine.com/articles/education-schools-relocate-global-
international-guide-education-in-the-fourth-industrial-revolution (Accessed 2 February 2022). Ferdinand, D. S. 2009. Workforce Education and Development Curriculum Responsiveness to
Culturally and Internationally Diverse Graduate Students: A Mixed Methods Study. Carbondale:
Carbondale Southern Illinois University. Fomunyam, K. G. 2014. Curriculum theorizing and individualism: An exploration of the
curriculum’s relation to the social, personal, and political dimensions of schooling. Mevlana
International Journal of Education, 4: 122–131. Fomunyam, K. G. and Teferra, D. 2017. Curriculum responsiveness within the context of
decolonisation in South African higher education. Perspectives in Education, 35(2): 196-207. Fomunyam, K. G. 2019. Education and the fourth industrial revolution: Challenges and
possibilities for engineering education. International Journal of Mechanical Engineering
Technology, 10(8): 23-25. George, J. W. 2009. Classical curriculum design. Arts and Humanities in Higher Education, 8(2):
160-179. Harmon, D. A. 2012. Culturally responsive teaching though a historical lens: Will history repeat
itself? Interdisciplinary Journal of Teaching and Learning, 2(1): 12-22. Hoskin, L. A. 1992. Eurocentrism vs. Afrocentrism: A geopolitical linkage analysis. Journal of Black
Studies, 23: 247-253. Hošková-Mayerová, Š. and Rosická, Z. References 2012. Programmed learning. Procedia - Social and
Behavioral Sciences, 31: 782-787. Iruonagbe, C. T. and Egharevba, M. E. 2015. Higher education in Nigeria and the emergence of
private universities. International Journal of Education and Research, 3(2): 49-64. Janson, E. and Silva, C. M. 2017. Itinerant curriculum theory: Navigating the waters of power,
identity, and praxis. Journal of the American Association for the Advancement of Curriculum
Studies, 12(1): 1-16. Kayembe, C. and Nel, D. 2019. Challenges and opportunities for education in the Fourth Industrial
Revolution. African Journal of Public Affairs, 11(3): 79-94. Ladson-Billings, G. 1995. But that’s just good teaching: The case for culturally relevant pedagogy. Theory into Practice, 34(3): 159-165. 152 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 Linda,
P. 2009. Five
basic
types
of
curriculums. Available:
https://theeducationcafe.wordpress.com/2009/11/12/five-basic-types-of-curriculum/
(Accessed 12 November 2019). Marr, B. 2018. The 4th Industrial Revolution is here - Are you Ready? Available:
https://www.forbes.com/sites/bernardmarr/2018/08/13/the-4th-industrial-revolution-is-
here-are-you-ready/#27596d5b628b/ (Accessed 12 November 19). Masaka, D. 2018. The prospects of ending epistemicide in Africa: Some thoughts. Journal of Black
Studies, 49(3): 284-301. Mba, J. C. 2017. Challenges and prospects of Africa’s higher education. Available:
https://www.globalpartnership.org/blog/challenges-and-prospects-africas-higher-education
(Accessed 3 February 2022). Moja, T. 2004. Globalisation: A challenge for curriculum responsiveness. In: Griesel, H. ed. Curriculum Responsiveness: Case Studies in Higher Education. Pretoria: South African Universities
Vice-Chancellors Association, 21-38. Moll, I. 2004. Curriculum responsiveness: The anatomy of a concept. In: Griesel, H. ed. Curriculum
Responsiveness: Case Studies in Higher Education. Pretoria: South African Universities Vice-
Chancellors Association, 1-19. Ogude, N., Nel, H. and Oosthuizen, M. 2005. The Challenge of Curriculum Responsiveness in South
African Higher Education. Pretoria: Council on Higher Education. Oliveira, I. B. 2017. Itinerant curriculum theory against epistemicides: A dialogue between the
thinking of Santos and Paraskeva. Journal of the American Association for the Advancement of
Curriculum Studies, 12(1): 1-22. Paraskeva, J. M. 2016. Curriculum Epistemicide: Toward an Itinerant Curriculum Theory. New York:
Routledge. Paraskeva, J. M. 2017. Against the epistemicide: Itinerant curriculum theory and the reiteration
of an epistemology of liberation. In: Uljens, M. and Ylimaki, R. eds. Bridging Educational
Leadership, Curriculum Theory and Didaktik. Cham: Springer, 199-213. Paraskeva, J. M. 2018. Against the scandal: itinerant curriculum theory as subaltern momentum. Qualitative Research Journal, 18(2): 128-143. Penprase B. E. 2018. The Fourth Industrial Revolution and Higher Education. In: Gleason, N. W. ed. Higher Education in the Era of the Fourth Industrial Revolution. Singapore: Palgrave Macmillan,
978-981. References Pirinen, R. 2009. Thematic curriculum. Proceedings of the 8th WSEAS International Conference on
Education and Educational Technology, 61-66. Rehorn, L. 2017. Five ways to improve education in developing countries. Available:
https://www.borgenmagazine.com/education-in-developing-countries/ (Accessed 2 February
2022). Rolandsson, L. 2015. Programmed or not: A study about programming teachers’ beliefs and
intentions in relation to curriculum. Doctoral dissertation, KTH Royal Institute of Technology. Schleicher, A. 2018. The Future of Education and Skills Education 2030. Paris: OECD. Schleicher, A. 2019. What the Fourth Industrial Revolution could mean for Education and Jobs. Paris: OECD. 153 African Journal of Inter/Multidisciplinary Studies 2022 | Volume 4(1): 141-154 | DOI: https://doi.org/10.51415/ajims.v4i1.989 Schwab, K. 2016. The Fourth Industrial Revolution: What it means, how to Respond. Geneva: World
Economic Forum. Seel N. 2012. Programmed learning. In: Seel, N. M. ed. Encyclopaedia of the Sciences of Learning. Boston: Springer, 1310-1313. Slonimsky, L. and Shalem, Y. 2006. Pedagogic responsiveness for academic depth. Journal of
Education, 40(1): 37-58. Spector, H. 2021. The significance of sense in the time of plagues: Curricular responsiveness to
the Covid-19 crisis. Prospects, 51: 77-93. Sussekind, M. L. 2014. Why a Deterritorialized Curriculum? Transnational Curriculum Inquiry,
11(2): 67-75. Tessier, L. and Tessier, J. 2015. Theme-based courses foster student learning and promote
comfort with learning new material. Journal of Learning through the Arts, 11(1): 1-10. Wedekind, V. 2019. Curriculum responsiveness and student employability: An institutional
analysis. In: Kruss, G., Wildschut, A. and Petersen, I. eds. Skills for the Future: New Research
Perspectives. Cape Town: HSRC Press, 79-90. Witmond, L. 2008. The classical education method of home-schooling: What it entails, and the
pros
and
cons
of
a
Latin-centred
curriculum. Available:
https://www.brighthubeducation.com/homeschool-methodologies/11604-classical-education-
overview-plus-advantages-and-disadvantages/ (Accessed 12 November 2019). Zavale, N.C. and Schneijderberg, C. 2022. Mapping the field of research on African higher
education: A review of 6483 publications from 1980 to 2019. Higher Education, 83: 199-233. 154 154
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ӨГҮҮЛЭЛ / ARTICLE ӨГҮҮЛЭЛ / ARTICLE Unlegalized activities and practice of political parties to raise funds to support
women candidates Unlegalized activities and practice of political parties to raise funds to support
women candidates Tuguldur Yanjiv
Doctor (Ph.D), associated professor
Division of Social Science
Mongolian University of Science and Technology
Ulaanbaatar, Mongolia
tugul@must.edu.mn Эмэгтэй нэр дэвшигчдийг дэмжих хөрөнгө босгоход чиглэсэн улс төрийн
намуудын хуульчлагдаагүй арга хэмжээ ба туршлагууд Янживын Төгөлдөр1
Доктор (Ph.D), дэд профессор
Шинжлэх Ухааны Технологийн Их Сургуулийнм
Нийгмийн ухааны салбар
Улаанбаатар, Монгол Улс
tugul@must.edu.mn Хураангуй Монгол Улс шийдвэр гаргах түвшинд жендерийн тэгш байдлын хангах, тэр дундаа
эмэгтэйчүүдийн оролцоог нэмэгдүүлэхэд чиглэсэн бодлого, хэрэгжилт, хууль эрх зүйн
шинэчлэл хийж байгаа ч ахиц дэвшил удаашралтай хэвээр байна. Иймд шийдвэр гаргах
түвшинд эмэгтэйчүүдийн оролцоо, төлөөллийг хангахад нөлөөлөх гол хүчин зүйл болох
санхүүжилтийн асуудлыг эмэгтэй нэр дэвшигчдэд чиглэсэн улс төрийн намуудын сайн
дурын санаачилга, хөрөнгө босгож байгаа арга замуудыг судлахад чиглүүлсэн болно. Мөн
судлагдахууны хүрээнд суурь ойлголтуудыг тодруулахыг хичээлээ. Tүлхүүр үгс: эмэгтэй нэр дэвшигч, улс төрийн намууд, санхүүжилтийн
хуульчлагдаагүй арга хэмжээ, сайн туршлагууд Unlegalized activities and practice of political parties to raise funds to support
women candidates Unlegalized activities and practice of political parties to raise funds to suppo
women candidates Studia Philosophiae Et Juris - XXXVIII Studia Philosophiae Et Juris - XXXVIII https://doi.org/10.5564/spej.v38i1.3164 Abstract: Mongolia is making policy, implementation, and legal reforms aimed at ensuring gender equality
at the decision-making level, including increasing the participation and representation of women,
however progress is still slow. It is still ranked below the Asian and global average in the Global
Gender Cap Index. Therefore, the issue of financing, which is the main factor affecting the
participation and representation of women at the decision-making level, is directed to the study
of the voluntary initiatives of political parties aimed at female candidates and the ways in which https://orcid.org/0000-0002-5701-5647 © The Author(s) 2023
https://creativecommons.org/licenses/by/4.0/ © The Author(s) 2023
https://creativecommons.org/licenses/by/4.0/ Received: 26 August 2023
Accepted: 27 September 2023 Received: 26 August 2023
Accepted: 27 September 2023 - 80 - Философи, эрх зүйн судлал - XXXVIII funds are raised. Also, the researcher tried to give a clear understanding and terms in the scope
of the study. funds are raised. Also, the researcher tried to give a clear understanding and terms in the scope
of the study. Keywords: female candidates, political parties, illegal financing special events and good
practices. II.Судалгааны арга зүй Судалгааны зорилго нь эмэгтэй нэр дэвшигчийг дэмжсэн хөрөнгө босгож буй
улс төрийн намуудын санаачилга, туршлагуудыг судалж, улс төрийн практикт
хэрэгжүүлэх боломжийн талаар судлахад чиглэсэн болно. Судалгааны өгүүллийг бичихдээ нийгмийн шинжлэх ухааны чанарын
судалгааны баримт бичгийн шинжилгээ, бенчмаркингийн арга, анализ, сентизийн
аргыг ашигласан. Өгүүллийн
хүрээнд
эмэгтэй
нэр
дэвшигчдийг
дэмжихэд
чиглэсэн
санхүүжилтийн талаарх улс орнуудын туршлага, үр дүнг хуваалцах зорилгоор
судалгааны бенчмаркингийн аргыг түлхүү ашиглав. Бенчмаркингийн арга нь
судлагдахууны талаарх хамгийн сайн туршлагуудыг харьцуулан судлах практик ач
холбогдолтой шинжилгээний арга юм. Мөн баримт бичгийн шинжилгээний аргаар
улс орнуудын эрх зүйн орчны шинжилгээ хийж, холбогдох эрх зүйн зохицуулалт
байгаа эсэхийг тодрууллаа. Үүнээс гадна сонгуулийн эмэгтэй нэр дэвшигчдийн онцлог, гарааны тэгш
байдал, санхүүжилтийн зарчим, хуульчлагдсан болон хуульчлагдаагүй зохицуулалт,
нөөц, арга хэмжээнүүд гэсэн суурь ойлголтуудыг судалж, судалгааны цар хүрээг уг
судлагдахуунаар хязгаарлах оролдлого хийлээ. I. Оршил Улс төрийн шийдвэр гаргах түвшний эмэгтэйчүүдийн оролцоо, төлөөллийн
индексээрээ манай улс дэлхийн дунджаас доогуур эрэмбэлэгдсээр байна. Дэлхийн
эдийн засгийн форумын жил бүр гаргадаг тайланд Монгол Улс шийдвэр гаргах
түвшин буюу улс төрийн эрх мэдлийн индексийн үзүүлэлтээрээ нийт 146 орноос
121-д жагсаж байна. Уг үзүүлэлтийн дэлхийн дундаж нь 22.1 хувь байгаа бөгөөд
манайх 17.1 хувьтай доогуур байна. Түүнчлэн УИХ-ын сүүлийн 2 удаагийн сонгуульд нэр дэвшигчдийн дунд
эмэгтэйчүүдийн эзлэх байр суурь, төлөөлөл буурсаар байна. 2012 оны УИХ-ын
сонгуулийн нийт нэр дэвшигчдээс эмэгтэйчүүдийн тоо 174 бөгөөд 32 хувьтай
байсан бол 2016 онд 129 эмэгтэйчүүд ба 25,9 хувь, 2020 онд 478 ба 21.1 болж
буурсан үзүүлэлтэй байна. Шийдвэр гаргах түвшинд эмэгтэйчүүдийн оролцоо, төлөөллийг хангахад
нөлөөлөх хүчин зүйлс олон байх боловч, эдгээрээс санхүүжилтийн асуудлыг
нарийвчлан судалсан, зорилтот судалгаа шинжилгээ цөөн байна. Тиймээс эмэгтэй
нэр дэвшигчдэд чиглэсэн улс төрийн намуудын санхүүжилтийн сайн дурын
санаачилга, хөрөнгө босгож байгаа дэлхий улс орнуудын туршлага, хэрэгжилтийн
арга замуудыг судлах хэрэгцээ шаардлагын дагуу судалгааны зорилгыг дэвшүүллээ. Эмэгтэй нэр дэвшигчдэд нийтлэг тулгардаг гол бэрхшээлүүдийн нэг
нь санхүүжилт босгох явдал. Жил ирэх тусам сонгуулийн өртөг нэмэгдэж,
шаардлагатай санхүүжилтийн хэмжээ сонгуулиас сонгуульд өсөж байна. Иймд
улс орнуудад эмэгтэйчүүд, залуучууд зэрэг нийгмийн төлөөллийг хангахуйц
улс төрийн өрсөлдөөний тэгш боломжийг бий болгох зорилгоор зорилтот нэр
дэвшигчийг дэмжсэн санхүүжилтийн шинэ бодлого боловсруулах, хэрэгжилтийг
хангахад анхаарах болжээ. Мөн холбогдох судалгаа шинжилгээг хийх, туршлага хуваалцах, шинэ
санаачилга, боломжуудыг бий болгох замаар улс төрийн сайн дурын болон
төрийн бодлого, шийдвэрийн дагуу тусгай арга хэмжээнүүд ч идэвхжиж байна. Ялангуяа өмнөд, хойд Америкийн орнуудад эмэгтэйчүүдийг улс төрд дэмжих гол
хөшүүрэг болж байгаа хөрөнгө босгох хамтын арга хэмжээнүүдийн талаар судлах,
бенчмаркингийн шинжилгээ хийж, сайн туршлагуудаас суралцах нь ардчилсан улс
орнуудын хамтын зорилго болж байна. Гэсэн хэдий ч Ази, Африк, Латин Америкийн орнуудад эмэгтэйчүүд эдийн
засгийн янз бүрийн шалтгааны улмаас нэр дэвшигч болохоос татгалздаг болохыг
судлаачид тэмдэглэсээр байна (Women’s Environment and Development Organization
2007, 4-7). Манай улсын хувьд ч уг шалтгаанаар эмэгтэйчүүд нэр дэвшихээс эргэлзэх,
татгалзах үндэслэл болдог нь практикаас тодорхой харагддаг. Учир нь эмэгтэй нэр
дэвшигч гэр бүлийн өмч хөрөнгөө сонгуулийн зардалд зарцуулах, зээл хүсэх, өмч
хөрөнгөө эрсдэлд оруулах, эрхэлсэн ажлаа болон ээж, эхнэрийн бусад асрах үүргээ - 81 - Studia Philosophiae Et Juris - XXXVIII орхих зэрэг нийгэм, эдийн засгийн асуудлууд нь тэднийг сонгуульд оролцохоос
татгалзах шалтгаанууд болдог. Иймд улс орнууд эмэгтэйчүүд, жендерийн тэгш
байдлыг дэмжсэн санхүүжилтийн талаарх бодлого, хөтөлбөрийг санаачлах, сайн
үр дүнг хуваалцаж, нөлөөллийн арга хэмжээнүүдийг авч хэрэгжүүлэхийг уриалж
байна. I. Оршил орхих зэрэг нийгэм, эдийн засгийн асуудлууд нь тэднийг сонгуульд оролцохоос
татгалзах шалтгаанууд болдог. Иймд улс орнууд эмэгтэйчүүд, жендерийн тэгш
байдлыг дэмжсэн санхүүжилтийн талаарх бодлого, хөтөлбөрийг санаачлах, сайн
үр дүнг хуваалцаж, нөлөөллийн арга хэмжээнүүдийг авч хэрэгжүүлэхийг уриалж
байна. III. Судалгааны үр дүн 1.Эмэгтэй нэр дэвшигчдийг дэмжих хөрөнгө босгох арга хэмжээ ба суурь
ойлголтууд. Цаг хугацааны хувьд 2000 оноос хойш улс орнуудад Жендерийн тэгш байдлыг
дэмжсэн санхүүжилтийн бодлого, төлөвлөлт, хэрэгжилт, үнэлгээний талаарх
судалгаа, шинжилгээний ажил эрчимжсэн байна. Харин Жендерийн тэгш байдлыг
хангахад чиглэсэн төрийн шууд болон шууд бус санхүүжилт, хөрөнгө босгох,
намуудын санаачилгын талаарх хууль тогтоомж, хэрэгжилт шинэлэг хэвээр байна. Эмэгтэй нэр дэвшигчдэд чиглэсэн хөрөнгө босгож буй туршлагаас үзэхэд
дараахь үндсэн хоёр арга хэмжээ, санаачилгын хүрээнд судлагдаж байна (ННХ ба
АСДҮОУХ 2020, 409). Үүнд: Эмэгтэй нэр дэвшигчдэд чиглэсэн хөрөнгө босгож буй туршлагаас үзэхэд
дараахь үндсэн хоёр арга хэмжээ, санаачилгын хүрээнд судлагдаж байна (ННХ ба
АСДҮОУХ 2020, 409). Үүнд: 1) Хуульчилсан арга хэмжээ: Төрийн санхүүжилт хэлбэрээр улс төрийн нам,
эмэгтэй нэр дэвшигчдэд санхүүжилт хуваарилдаг. Үүнд: • Жендерийн хувьд төвийг сахисан загвартай, харин практикт Жендерийн
үр дагавартай байх, • Загвар болон хэрэгцээ талаасаа Жендерт чиглэсэн ба эмэгтэйчүүдийн улс
төрийн оролцоог төрийн санхүүжилтээр ил тод дэмжсэн байх. - 82 -
2) Хуульчлагдаагүй арга хэмжээ: Энэ нь улс төрийн нам сайн дурын үндсэн Хуульчлагдаагүй арга хэмжээ: Энэ нь улс төрийн нам сайн дурын үндсэн - 82 - Философи, эрх зүйн судлал - XXXVIII дээр авч хэрэгжүүлдэг үйл ажиллагаанууд багтдаг. Үүнд: дээр авч хэрэгжүүлдэг үйл ажиллагаанууд багтдаг. Үүнд: • Сайн дурын, зөвхөн асуудлыг хөндөж буй тухайн намд үйлчлэх улс
төрийн арга хэмжээнүүд; • Сайн дурын, зөвхөн асуудлыг хөндөж буй тухайн намд үйлчлэх улс
төрийн арга хэмжээнүүд; • Эмэгтэй нэр дэвшигчдэд шууд санхүүжилт босгоход нь зориулагдсан
иргэний нийгмийн арга хэмжээ, бусад санаачилгууд хамаарна. • Эмэгтэй нэр дэвшигчдэд шууд санхүүжилт босгоход нь зориулагдсан
иргэний нийгмийн арга хэмжээ, бусад санаачилгууд хамаарна. Энэ өгүүллийн хүрээнд хуульчлагдаагүй арга хэмжээнүүдийн нэг болох
эмэгтэй нэр дэвшигчдэд зориулсан улс төрийн намын сайн дурын санхүүгийн
дэмжлэг, хөрөнгө босгож буй санаачилга, туршлагуудыг авч үзсэн. Мөн судлаачийн
зүгээс шинжилгээг улс төрийн намаас сонгуульд нэр дэвших гурван үе шаттай
холбож, эмэгтэйчүүдэд тулгардаг санхүүжилтийн асуудлыг улс орнуудад хэрэгжиж
буй сайн туршлагын хамт судлахыг хичээлээ. Сонгуульд нэр дэвших нь нэр дэвшихээр шийдэх, нэр дэвших, сонгуулийн
кампанит ажил явуулах (Women’s Environment and Development Organization
2007, 3, 4) гэсэн гурван өөр үе шатаас бүрддэг бөгөөд эмэгтэйчүүдийн хувьд
нэр дэвшихэд энэ гуравт нөлөөлөхүйц санхүүжилтийн нөөцийг шаарддаг. Харин
эмэгтэйчүүд санхүүгийн нөөц бололцоо хязгаарлагдмал бол сонгуульд ялах
магадлал буурч, намууд ч эмэгтэйчүүдийг нэр дэвшүүлэхийг дэмжих нь бага
болохыг практикаас харж болно. Нэмж дурдахад сонгуулийн кампанит ажлын үед ашиглагддаг шууд болон
шууд бус санхүүгийн нөөцийн талаарх ойлголтыг дээрх нэр дэвших үе шатуудад
ангилан авч үзлээ. III. Судалгааны үр дүн Уг асуудалд хамаарах улс орнуудын санхүүгийн шууд болон шууд бус
дэмжлэгийн талаар дурдвал: Намын хураамж, татвар, дэнчин: Нэр дэвшин сонгуульд оролцохын
өмнө хэд хэдэн хураамж, түүний дотор намын гишүүнчлэлийн татвар,
нэр дэвшигчийн бүртгэлийн хураамж төлөх шаардлага байдаг. Намын
гишүүнчлэлийн татвар нь улс төрийн намуудын орлогын нийтлэг эх үүсвэр
бөгөөд намын үйл ажиллагаа болон намын аппаратыг санхүүжүүлэхэд
ашигладаг. Түүнчлэн нэр дэвшихийн тулд намдаа эсвэл Сонгуулийн төв
байгууллагад бүртгэлийн хураамжаа нэр дэвшигч өөрөө төлөхийг намууд
шаарддаг улс орнууд байна. Эдгээр хураамжийн хэмжээ янз бүр байгаа ч
зарим эмэгтэй нэр дэвшигчийн хувьд хэт өндөр байх магадлалтай юм. Эмэгтэйчүүдийг албан тушаалд өрсөлдөх явдлыг дэмжих зорилгоор зарим
улс төрийн нам тэдний гишүүнчлэлийн татвар, нэр дэвшигчийн бүртгэлтэй
холбоотой хураамжийг сайн дураараа багасган, эсвэл чөлөөлсөн туршлагууд
байна. Жишээлбэл, Гана Улсад бараг бүх намууд нь эмэгтэйчүүд нэр
дэвшихээр бүртгүүлэхэд төлдөг хураамжийг 50 хувь хөнгөлж өгснийг нэгэн
эмэгтэй парламентын гишүүн тэмдэглэжээ (ННХ ба АСДҮОУХ 2020). Намын хураамж, татвар, дэнчин: Нэр дэвшин сонгуульд оролцохын
өмнө хэд хэдэн хураамж, түүний дотор намын гишүүнчлэлийн татвар,
нэр дэвшигчийн бүртгэлийн хураамж төлөх шаардлага байдаг. Намын
гишүүнчлэлийн татвар нь улс төрийн намуудын орлогын нийтлэг эх үүсвэр
бөгөөд намын үйл ажиллагаа болон намын аппаратыг санхүүжүүлэхэд
ашигладаг. Түүнчлэн нэр дэвшихийн тулд намдаа эсвэл Сонгуулийн төв
байгууллагад бүртгэлийн хураамжаа нэр дэвшигч өөрөө төлөхийг намууд
шаарддаг улс орнууд байна. Эдгээр хураамжийн хэмжээ янз бүр байгаа ч
зарим эмэгтэй нэр дэвшигчийн хувьд хэт өндөр байх магадлалтай юм. Эмэгтэйчүүдийг албан тушаалд өрсөлдөх явдлыг дэмжих зорилгоор зарим
улс төрийн нам тэдний гишүүнчлэлийн татвар, нэр дэвшигчийн бүртгэлтэй
холбоотой хураамжийг сайн дураараа багасган, эсвэл чөлөөлсөн туршлагууд
байна. Жишээлбэл, Гана Улсад бараг бүх намууд нь эмэгтэйчүүд нэр
дэвшихээр бүртгүүлэхэд төлдөг хураамжийг 50 хувь хөнгөлж өгснийг нэгэн
эмэгтэй парламентын гишүүн тэмдэглэжээ (ННХ ба АСДҮОУХ 2020). Шууд бус санхүүгийн эх үүсвэрийн хувьд авч үзвэл: Хондураст депутатаар
сонгогдсон Гуильям Гуифарро (Women’s Environment and Development
Organization 2007) эмэгтэйчүүд зөвхөн олон нийтийн хүрээнд кампанит
ажил бэлтгэх зардлыг тооцдог төдийгүй гэр бүлдээ ч зарцуулах хөрөнгө
мөнгө шаардагддаг болохыг хэлжээ. Тэрээр хүүхэд асрах, эцэг эхээ асран
халамжлах, гэрийн ажил гэх мэт зардлыг эмэгтэйчүүд кампанит ажлынхаа үе
шатуудад бүхэлд нь хариуцах ёстой байдаг бөгөөд үүнийг кампанит ажлын
зардал болгож оруулах санаачилгыг эхлүүлсэн. Энэ нь эмэгтэйчүүдэд нэр
дэвшихээр шийдэх чухал хөшүүрэг болно гэж үзжээ. Суринамын ерөнхийлөгчийн сонгуульд нэр дэвшигч Моник Эссед-
Фернандес /Monique Essed-Fernandes/ хэлэхдээ (Cigane ба Ohman 2014,
17-21): “Нэр дэвшиж буй эмэгтэйчүүд нэг бол ганц бие, хүүхэдгүй, том
хүүхэдтэй эсвэл хүүхэд асрах дэмжлэгтэй байдаг. III. Судалгааны үр дүн Эмэгтэй, эрэгтэй нэр дэвшигчид хоёулаа сонгуулийн кампанит
ажилдаа шууд болон шууд бус нөөцийг ашигладаг. Нэр дэвшигчийн кампанит
ажилд шууд ба шууд бус нөөцийг ялгах нь чухал гэж үздэг (Women’s Environment
and Development Organization 2007, 3, 4). (Мөнгөн ба мөнгөн бус гэж бас ойлгож
болно) Шууд нөөц гэдэг нь хувийн хандивлагчид, улс төрийн намуудын хөрөнгө,
улсын төсвийн санхүүжилт, татаас, эсвэл нэр дэвшигчийн хувийн нөөцөөс гардаг
бэлэн мөнгө гэж тодорхойлж болно. Шууд бус санхүүгийн нөөцийг бэлэн мөнгөөр бус, улс төрийн үйл ажиллагаа,
кампанит ажилд тустай материаллаг эдийн засгийн хувь нэмэр гэж тодорхойлдог. Шууд бус эх үүсвэрийг ихэвчлэн нэр дэвшигчийн нэрийн өмнөөс цалингүй
хөдөлмөрөө хандивласан хувь хүмүүс, улс төрийн намын гишүүд, дэмжигчид,
сайн дурын байгууллагуудын дэмжлэг, тойргийн дэмжигч нар хийдэг. Эдгээрээс
хамгийн түгээмэл арга замууд нь кампанит ажлын үйл ажиллагааг явуулахад
шаардлагатай холбооны хэрэгсэл, сайн дурынхан, тэдний дэд бүтэц, оффисын
дэмжлэг, танил талын сүлжээ зэрэг материаллаг нөөц байж болно. Эмэгтэй нэр дэвшигчдийн хувьд санхүүгийн эх үүсвэр нь хязгаарлагдмал байх
магадлалтай тул эдийн засгийн янз бүрийн шууд бус эх үүсвэрт найдах нь илүү үр
дүнтэй юм. Эмэгтэйчүүдийн улс төрийн карьерын дээрх гурван үе шатуудад шууд
болон шууд бус нөөцийг ашиглах нь чухал бөгөөд сонгуульд өрсөлдөх шийдвэрт
ихээхэн нөлөөлнө гэж үздэг. Эхний буюу нэр дэвшихээр шийдэх үе шат: Энэ үед эмэгтэйчүүдэд татвар,
хураамж, дэнчин босгох зэрэг санхүүгийн асуудлууд гарч ирдэг. Уг асуудалд - 83 - Studia Philosophiae Et Juris - XXXVIII чиглэсэн улс төрийн намуудын дэмжлэгүүдийг авч үзвэл эмэгтэйчүүдийн нэр
дэвших үеийн намын дотоод сонгууль болон сонгон шалгаруулалтын үед тулгардаг
дэнчин, татвар, хураамжийг багасгах эсвэл бүр чөлөөлсөн туршлагууд байна. Мөн эмэгтэй нэр дэвшигчдэд шууд бус санхүүгийн нөөцөөр дэмжлэг үзүүлэх
хандлагууд нэмэгдэх болжээ. Шууд бус нөөцийн дэмжлэгт улс төрд оролцоход
шаардагдах хувь хүний хөгжлийн ур чадварууд, хөрөнгө босгох стратеги болон
холбоо харилцаагаа ашиглах арга зам, сонгуулийн кампанит ажлын менежмент
зэрэгт арга зүйн дэмжлэг үзүүлэх сургалт, хөтөлбөр, арга хэмжээнүүдийг улс
төрийн намууд түлхүү хэрэгжүүлж байна. чиглэсэн улс төрийн намуудын дэмжлэгүүдийг авч үзвэл эмэгтэйчүүдийн нэр
дэвших үеийн намын дотоод сонгууль болон сонгон шалгаруулалтын үед тулгардаг
дэнчин, татвар, хураамжийг багасгах эсвэл бүр чөлөөлсөн туршлагууд байна. Мөн эмэгтэй нэр дэвшигчдэд шууд бус санхүүгийн нөөцөөр дэмжлэг үзүүлэх
хандлагууд нэмэгдэх болжээ. Шууд бус нөөцийн дэмжлэгт улс төрд оролцоход
шаардагдах хувь хүний хөгжлийн ур чадварууд, хөрөнгө босгох стратеги болон
холбоо харилцаагаа ашиглах арга зам, сонгуулийн кампанит ажлын менежмент
зэрэгт арга зүйн дэмжлэг үзүүлэх сургалт, хөтөлбөр, арга хэмжээнүүдийг улс
төрийн намууд түлхүү хэрэгжүүлж байна. III. Судалгааны үр дүн Хүүхэд харах үйлчилгээ
гэдэг бол нэр дэвшихээс өмнө эхэлдэг асуудал, учир нь амьдрал дээр хүүхэд
асрах асуудалтай хүмүүс энэ тогтолцооноос хасагддаг, эсвэл өөрсдийгөө
хасдаг” гэжээ. Иймд сонгуулийн санхүүжилтийн зардалд оруулах заалтыг
дэмжихийг уриалсан. Мөн ийм ажиглалтыг судлаач Уолш /Walsh/ дэвшүүлж, АНУ-д эмэгтэйчүүд Мөн ийм ажиглалтыг судлаач Уолш /Walsh/ дэвшүүлж, АНУ-д эмэгтэйчүүд - 84 - Философи, эрх зүйн судлал - XXXVIII өөрсдийгөө ялах чадвартай нэр дэвшигч болно гэдгийг итгүүлэх нь нэр
дэвшихийн өмнөх үе шатанд чухал юм. Үүний тулд эмэгтэйчүүдээс “та нэр
дэвших үү?” гэж асуух хэрэгтэй, учир нь тэдний хувьд сэтгэл зүйн хүч чадлыг
нэмэгдүүлэх дасгал ажил болно. Үгүй бол тэд цаашид тулгарах эдийн засаг,
соёл, мэдээллийн зэрэг бусад саад тотгорыг даван туулах итгэлгүй болно гэж
тэмдэглэжээ (Women’s Environment and Development Organization 2007). Эхний бөгөөд эмэгтэйчүүдийн нэр дэвшихээс өмнөх үе шатанд тэдний нэр
дэвшигч болох итгэл үнэмшлийг бэхжүүлэхэд улс төрийн намын үүрэг, оролцоо
чухал байна. Намын зүгээс эмэгтэйчүүдэд чиглэсэн сэтгэл зүйн болоод санхүүгийн
хөшүүргээр дэмжих сайн дурын санаачилга, тусгай арга хэмжээнүүдийг
тогтвортой хэрэгжүүлэх нь нэр дэвшигчийн хувьд өөртөө итгэлтэй, хүчтэй
байх сэдэл, чадварыг нэмэгдүүлэх суурь нөхцөл нь юм. Ийм учраас эмэгтэй нэр
дэвшигчдэд тулгардаг эдийн засгийн дарамт, “санхүүгийн саад”-ыг бууруулах арга
хэмжээнүүдийг улс төрийн нам, мөн эмэгтэйчүүдийн өөрсдийн санал, шаардлагаар
эхэлж, зөв хандлагыг бэхжүүлэх хэрэгцээ байна. Хоёр дахь буюу эмэгтэйчүүдийн нэр дэвших үе шат: Энэ үед эмэгтэйчүүд
нэр дэвших эрхээ авсан байх бөгөөд сонгуулийн сурталчилгааны кампанит ажлаа
эхлүүлэх санхүүжилт тулгардаг. Ихэнх эмэгтэй нэр дэвшигчдийн хувьд энэ үе
шатанд улс төрийн намын дэмжлэг чухал байхаас гадна Жендерийн тэгш байдлыг
дэмжих “зөөлөн хувилбар” (Ohman 2018, 10) гэж нэрлэдэг төрийн санхүүжилтийн
дэмжлэг гол үүрэгтэй болно. Иймд улс төрийн намууд Жендерийн тэгш байдлыг
дэмжих иргэний боловсролыг дээшлүүлэх, улс төрд оролцох сонирхолтой
эмэгтэйчүүдийг урамшуулах, зөвлөх, дэмжих зэрэг хуульчилсан ба хуульчлагдаагүй
олон арга хэмжээнүүдийг хэрэгжүүлж буй туршлагууд нэмэгдэж байна. Хуульчилсан арга хэмжээ бол төрийн санхүүжилт хэлбэрээр улс төрийн нам,
эмэгтэй нэр дэвшигчдэд санхүүжилт хуваарилдаг ойлголт юм. Улс орнуудын
туршлагаас үзэхэд Сонгуулийн тухай хууль болон Улс төрийн намуудын тухай
хуульд намуудын хүлээн авах төрийн санхүүжилтийн хэмжээ, түүний хуваарилалт
нь Жендертэй холбоотой заалтууд, эсвэл төрийн санхүүжилтийн зарим хэсгийг
Жендерт чиглэсэн хуулийн зохицуулалтаар холбосон эрх зүйн шинэчлэл хийгдэж
байна Гэхдээ энэ үе шатанд эмэгтэйчүүдийн нэр дэвшихэд тулгардаг санхүүжилтийн
хуульчлагдаагүй сайн дурын арга хэмжээнүүдийг авч үзэх учраас хуулийн
зохицуулалт, төрийн санхүүжилтийг дурдагдахгүй юм. Эмэгтэйчүүдийн хувьд нэр дэвших эрхээ аваад сонгуулийн сурталчилгааны
зардлаа урьдчилан эрт олж чадвал цаашид сонгогдох эмэгтэйчүүдийн тоог нэмэх
стратегийн ач холбогдолтой юм. III. Судалгааны үр дүн Сонгуулийн сурталчилгааны зардлыг хоёр ба
түүнээс дээш жилийн хугацаанд тогтмол хөрөнгө босгож байхаар төлөвлөж чадвал
үр өгөөжтэй гэж үзэж байна. Учир нь тойрог, намын гишүүдийн дунд тэдний
нэр хүнд, байр сууриа олж авахад нэр дэвшигчдээс маш их цаг хугацаа, хөрөнгө
мөнгө зарцуулж, тасралтгүй ажиллах шаардлага тулгардаг. Тухайлбал, харилцаа
холбооны зардал болох утас, шуудан, тээвэр, нүүр тулсан ярилцлага хийх,
өөрийгөө таниулах арга хэмжээнд тойргийн иргэдтэй уулзах зардал, олон нийтийн
арга хэмжээ, ярилцлагад орох, бусад зардал буюу хувцас, буудал, хоол гэх мэт далд - 85 - Studia Philosophiae Et Juris - XXXVIII хэлбэрийн гэр бүлтэй холбоотой олон үйл ажиллагааны зардлууд эмэгтэйчүүдэд
нэмэгддэг байна. Эдийн засгийн эдгээр хэрэгцээг хангахын тулд улс орнуудад эмэгтэй нэр
дэвшигчдийг дэмжих зорилгоор нэгдэж, амжилттай санаачилгуудыг хэрэгжүүлсээр
иржээ. Тухайлбал, хамгийн анхдагч санаачилга нь EMILY’s List мөн WISH List
гэх мэт мөнгө босгох механизмыг хэрэгжүүлсэн туршлага онцлон дурдагддаг. Эмэгтэйчүүдэд урьдчилж эрт мөнгө, хандив босгох нь сонгуулийн сурталчилгааны
үеэр илүү их мөнгө цуглуулах магадлалыг нэмэгдүүлдэг гэж үздэг. Иймд уг
туршлагыг баримтжуулж, хэрэгжүүлэх санаачилгууд улс орнуудад өргөжин тэлж
байна. Уг агуулгыг тусад нь дэлгэрүүлэн авч үзсэн тул энд санааг товчлон дурдлаа. Гурав дахь ба сонгуулийн кампанит ажлын үе шат: Сонгуулийн кампанит
ажлын сурталчилгаа нь тухайн улсын сонгуулийн системийн онцлог, улс төрийн
санхүүжилтийн бодлого, эрх зүйн зохицуулалт, намын дотоод дүрэм, журам
зэргээс хамаараад өөр өөр байдаг. Энэ үе шатанд эмэгтэй нэр дэвшигчдэд чиглэсэн
сонгуулийн сурталчилгааны хөнгөлөлт, урамшуулал, хязгаарлалт, хориг зэрэг
хуульчилсан арга хэмжээнүүдийг төрийн санхүүжилттэй уялдуулсан зохицуулалт
улс орнуудад нийтлэг хэрэгжиж байна. Малави Улсын нэгэн эмэгтэй парламентын гишүүний тэмдэглэснээр (Cigane
and Ohman 2014, 21): Нэр дэвших эрхээ намаасаа авсны дараа нэр дэвшигчид
сурталчилгаа явуулахын тулд тухайн сонгуулийн жилдээ хоёр дахь удаагаа
санхүүжилт олох шаардлагатай тулгардаг гэжээ. Уг асуудлыг шийдвэрлэхэд
заримдаа шууд бус санхүүгийн эх үүсвэрийг ашиглах, кампанит ажилд зарцуулах
мөнгө, цаг хугацааны хязгаарыг тогтоох зэрэг сонгуулийн хуулийн хязгаарлалтууд
эмэгтэй нэр дэвшигчдийн кампанит ажилд эергээр нөлөөлж байгааг дурджээ. Үүнтэй төстэй өөр жишээг дурдвал: Зүүн Тиморын 2001 оны сонгуулиар эмэгтэй нэр дэвшигчдэд болон
эмэгтэйчүүдийг “ялах” магадлалтай нэр дэвшигчдийн жагсаалтад оруулсан
намуудад телевизийн сурталчилгааны нэмэлт цаг гаргаж өгч байсан. Бразилд
2009 онд хийсэн шинэчлэлээр эмэгтэй нэр дэвшигчдэд ашиглуулах зорилгоор улс
төрийн намуудад хэвлэл мэдээллийн цагийг 10 хувь нэмэгдүүлж өгдөг болжээ. Хэвлэл мэдээллийн тухай хууль тогтоомжид эрэгтэй, эмэгтэй нэр дэвшигчдэд
хэвлэл мэдээлэл ашиглах тэгш боломж олгосон, эсвэл намуудад илүү олон
эмэгтэйчүүд (ялалт байгуулах магадлалтай газар нь) нэр дэвшүүлэх сонирхлыг
төрүүлсэн заалтууд тусгаж байна. III. Судалгааны үр дүн Афганистанд хэдийгээр хэвлэл мэдээллийн цагийг хэрхэн хуваарилах талаар
сонгуулийн тухай хуульдаа заагаагүй боловч 2005 оны сонгуулиар эмэгтэй
нэр дэвшигчдийн 76 хувь нь хэвлэл мэдээллийг хөнгөлөлттэй үнээр ашиглах
боломжийг олгожээ. Харин нийт эмэгтэй нэр дэвшигчдийн 55 хувь нь л үүнийг
ашиглажээ. Зарим судалгаагаар эмэгтэйчүүд сонгуулийн кампанит ажилд зориулж
хөрөнгө босгохдоо эрэгтэйчүүдээс дутахгүй амжилттай байдаг нь нотлогддог
бол зарим судалгаанд эмэгтэй нэр дэвшигчид өрсөлдөх чадвартай байхын тулд
эрэгтэйчүүдээс хамаагүй их хөрөнгө босгох шаардлага тулгарч, ингэснээр хөрөнгө
босгоход зарцуулдаг цаг хугацаа ч нэмэгддэг гэж үзжээ(Sanbonmatsu 2017). - 86 - Философи, эрх зүйн судлал - XXXVIII Канад улсад явуулсан судалгаагаар эмэгтэй нэр дэвшигчид эрэгтэйчүүдээсээ
10 хувиар илүү мөнгө зардаг болохыг тооцоолон гаргасан (Sidhu and Meena 2007,
31). Мөн сонгуульд нэр дэвших нь улсын Ерөнхийлөгчөөс илүү хэцүү байдаг тул
албан тушаалд ажиллаж байгаа нэр дэвшигчийн олон давуу талуудыг хязгаарлаж,
тэгш бус байдлыг авч үзэх хэрэгтэй гэжээ (Women’s Environment and Development
Organization 2007). АНУ-д хийсэн судалгаагаар сонгогчид эрэгтэй нэр дэвшигчдээс
илүү эмэгтэйчүүдэд илүү өндөр шаардлага тавьдаг бөгөөд эмэгтэй нэр дэвшигч
сонгуулийн сурталчилгааны үеэр алдаа гаргасан тохиолдолд уучлах чадвар
багатай байдаг (Barbara Lee Family Foundation and Lake Research Partners 2012)
гэх зэрэг олон асуудлуудыг нэрлэж болно. Харин үүнийг хязгаарлах, тэгшитгэх
боломжуудыг улс орнууд сонгуулийн тухай хуульдаа тусгаж, хязгаарлалтын
зохицуулалтыг нийтлэг хийдэг. Дээрх агуулгаас үзэхэд сонгуулийн кампанит ажлын нийт зардлын
дээд хязгаарыг тогтоох, тодорхой төрлийн сурталчилгааг хориглох, төрийн
санхүүжилтийн хуваарилалт зэрэг элементүүдээр сонгуулийн өрсөлдөөнийг
тэгшитгэхийг оролдож, ялангуяа эмэгтэй нэр дэвшигчдийн сонгуулийн кампанит
ажлыг дэмжих шууд ба шууд бус хэлбэрийн арга замууд нэлээд идэвхжиж буй нь
харагдаж байна. 2. Улс төрийн намуудын эмэгтэй нэр дэвшигчид чиглэсэн санхүүжилт босгох
дотоод механизм арга замууд Нэр дэвшиж буй эмэгтэйчүүдэд тулгардаг санхүүгийн олон сорилтуудыг
хүлээн зөвшөөрсний үндсэн дээр улс төрийн намууд санаачилгаараа эмэгтэй нэр
дэвшигчдэд санхүүжилт босгох механизм бий болгож байна. Санхүүжилт босгох
механизм нь намын дотоод бүтцэд байх бөгөөд төрийн санхүүжилтээс ялгаатай
ойлголт юм. Эмэгтэй нэр дэвшигчдийг дэмжих энэ төрлийн санаачилга нь цөөхөн
ч сонгуулийн кампанит ажлыг амжилттай болгоход нөлөөлөхүйц хөрөнгө босгосон
үр дүн сайтай туршлага болж байна. Иймд улс орнуудад хэрэгжиж буй эмэгтэй нэр дэвшигчдэд чиглэсэн төрийн
санхүүжилтээс үл хамаарах хөрөнгө босгох зорилготой улс төрийн намуудын
дэргэдэх сан, хөтөлбөр, арга хэмжээнүүдийг доор нэгтгэн авч үзлээ. Үүнд: 1. АНУ-ын Ардчилсан Намын “Эмилигийн жагсаалт” (EMILY’s LIST) 2. Австрали Улсын Хөдөлмөрийн Намын “Эмилигийн жагсаалт” 3. АНУ-ын Бүгд Найрамдах Намын “Хүслийн жагсаалт” (WISH LIST) 4. Канадын Либерал Намын дэргэдэх “Жюди ЛаМарш сан” (Judy LaMarsh Fun 5. Ирландын Хөдөлмөрийн Намын эмэгтэйчүүдийн бүлгийн “5-Си” хөтөлбөр (“5-
C” program) 6. Гана Улсын “Эмэгтэйчүүдийн сан” (улс төрийн намуудаас сонгуульд оролцох
эрмэлзэлтэй эмэгтэйчүүдийг дэмжих зорилготой) 6. Гана Улсын “Эмэгтэйчүүдийн сан” (улс төрийн намуудаас сонгуульд оролцох
эрмэлзэлтэй эмэгтэйчүүдийг дэмжих зорилготой) 7. Эль-Сальвадор Улсын Фарабундо Мартигийн Үндэсний чөлөөлөх фронт (олон
намын институт байгуулж, эмэгтэйчүүдэд сургалт явуулдаг) 8. Камбож Улсын Сам Рэнси Намын сонгуулийн сурталчилгааны дэмжлэг хөтөлбөр
9
И Б
У
К
Н
“W
2Wi ” 8. Камбож Улсын Сам Рэнси Намын сонгуулийн сурталчилгааны дэмжлэг хөтөлбөр
9. Их Британи Улсын Консерватив Намын дэргэдэх “Women2Win” Их Британи Улсын Консерватив Намын дэргэдэх “Women2Win” - 87 - Studia Philosophiae Et Juris - XXXVIII 1. Эмилигийн жагсаалт (EMILY’S LIST). АНУ-ын Ардчилсан Намын
“EMILY’S LIST” нь сонгуулийн сурталчилгааны ажлын санхүүжилт босгох тод
жишээ юм. “EMILY’S List” гэдэг нэр нь зуурсан гурилыг өсгөдөг хөрөнгө гэсэн утгатай
юм. Улс төрийн өрсөлдөөний эхэн үед их хэмжээний хандив босгох нь дараа үеийн
хандивлагчдыг татах гол стратегийг баримтлан хөрөнгө босгодог байгууллага юм. (цаашид EMILY-ийн жагсаалт гэх) EMILY-ийн жагсаалт нь эмэгтэйчүүдийн кампанит ажилд гарааны мөнгө олгох
замаар улс төрийн тэгш бус өрсөлдөөнийг өөрчлөх зорилгоор үйл ажиллагаагаа
эхлүүлсэн. EMILY-ийн жагсаалтаар дэмжлэг авсан анхны нэр дэвшигчдийн нэг нь
Сенатын гишүүн Барбара Микулски байв. Тэрээр 1986 онд өөрийн кампанит ажлын
нийт санхүүжилтийн 20% болох 60,000 ам.долларыг EMILY-ийн жагсаалтаас
сонгуулийн сурталчилгааны ажлынхаа хугацааны эхэн үед авчээ. Тэрээр Конгресст
хамгийн удаан ажиллаж байгаа, Сенатын хүчирхэг хорооны нэг болох Санхүүгийн
хорооны даргаар ажилласан анхны эмэгтэй гишүүн юм. 2011 онд тэрээр хэлэхдээ
“EMILY байгаагүй бол, EMILY яг цагаа олж туслаагүй бол бас намайг тохирсон
нэг дэвшигч гэдгийг харуулахад хэрэгтэй туслалцаа үзүүлээгүй бол би АНУ-ын
Сенатад байхгүй байлаа” гэсэн байна. 2. Улс төрийн намуудын эмэгтэй нэр дэвшигчид чиглэсэн санхүүжилт босгох
дотоод механизм арга замууд Тус хөдөлгөөнийг 1996 онд
өрнүүлэх үед нам доторх барууны чиг баримжаатай хэсэг нь тухайн хөдөлгөөнийг
зүүний үзэл баримтлалын арга зам хэмээн эсэргүүцэн тэмцэж байв. Австралийн
EMILY-ийн жагсаалт аажмаар бие даасан байгууллага болж үүсгэн байгуулагдсан
бөгөөд гишүүдийн 40 хувь нь Австралийн Хөдөлмөрийн Нам бус хүмүүсээр
өргөжсөн. Гэхдээ улс төрийн санхүүжилтийн ил тод байдлын үүднээс Австралийн
Хөдөлмөрийн Намын дэргэдэх байгууллага хэмээн үздэг. 3. WISH LIST хөдөлгөөн (ННХ and АСДҮОУХ 2020, 416-419)нь Бүгд
Найрамдах Намын ирээдүйтэй гэгдэх эмэгтэй нэр дэвшигчдэд санхүүжилт босгох,
дэмжлэг үзүүлэх зорилгоор 1992 онд байгуулагджээ. Бүгд Найрамдах Намын
сонгуулийн ажилд санхүүжилт босгох энэхүү бүлэг нь ЭМИЛИ-ийн жагсаалтын
нэгэн адил сонгож авсан өрсөлдөгчдөд санхүүгийн туслалцаа үзүүлэх, хөрөнгө
мөнгө босгох, сонгуулийн сурталчилгааны менежмент, хэвлэл мэдээллийн арга
техник зэрэг чиглэлээр зөвлөгөө, стратегийн дэмжлэг үзүүлэхэд илүү чиглэж
ажилладаг. 3. WISH LIST хөдөлгөөн (ННХ and АСДҮОУХ 2020, 416-419)нь Бүгд
Найрамдах Намын ирээдүйтэй гэгдэх эмэгтэй нэр дэвшигчдэд санхүүжилт босгох,
дэмжлэг үзүүлэх зорилгоор 1992 онд байгуулагджээ. Бүгд Найрамдах Намын
сонгуулийн ажилд санхүүжилт босгох энэхүү бүлэг нь ЭМИЛИ-ийн жагсаалтын
нэгэн адил сонгож авсан өрсөлдөгчдөд санхүүгийн туслалцаа үзүүлэх, хөрөнгө
мөнгө босгох, сонгуулийн сурталчилгааны менежмент, хэвлэл мэдээллийн арга
техник зэрэг чиглэлээр зөвлөгөө, стратегийн дэмжлэг үзүүлэхэд илүү чиглэж
ажилладаг. Үүсэн байгуулагдсанаасаа хойш WISH жагсаалтын хүчин чармайлтаар Бүгд
Найрамдах Намын эмэгтэй нэр дэвшигчдэд зориулан 3.5 сая ам.доллар босгож
чадсан бөгөөд Сенат дахь тус намын эмэгтэйчүүдийн тоог дөрөв дахин өсгөж,
Төлөөлөгчдийн танхим дахь тус намын эмэгтэйчүүдийн тоог хэвээр хадгалахад
хувь нэмрээ оруулж чаджээ. 4. Жюди ЛаМарш сан: Канадын Либерал нам эмэгтэй нэр дэвшигчдэд дэмжлэг
үзүүлэх мөнгө босгох зарцуулах зорилгоор Жюди ЛаМарш сан байгуулжээ (Judy
LaMarsh Fund 2023). Сангийн санхүүжилтийг хэрхэн зарцуулах нь аль эмэгтэй
нэр дэвшигчид эн тэргүүнд санхүүжилт өгөх зэрэг асуудлыг тус нам шууд мэдэж
шийддэг аж. Дээрх сан Канадын санхүүжилтийн эрх зүйн зохицуулалтын хүрээнд
гол төлөв хөрөнгө санхүүжилт босгох арга хэмжээ зохион байгуулан захидал
явуулах, интернэт ашиглах замаар санхүүжилтээ босгодог. Энэ арга нь сонгуулийн
ажлаа амжилттай явуулахад нь эмэгтэйчүүдэд мөнгөн ба мөнгөн бус хандив өгөхөд
чиглэсэн шинэчлэл болсон. Гол санаачилга нь эмэгтэйчүүдийн нуруун дээр байдаг
бусдыг халамжлах, хүүхэд асрах зэрэг хариуцлагуудыг сонгуулийн сурталчилгааны
үед хослуулах үндэслэлийг гаргаж, шийдвэрлэж чадсан. Тодруулбал, Канадын
Либерал намаас нэр дэвшүүлэх үеэр эмэгтэйчүүдэд хүүхэд асрах үйлчилгээ авахад
нь 500 хүртэлх канад доллар ($440) –ын нөхөн олговор олгож, газар зүйн хувьд
өргөн уудам сонгуулийн тойргоор явахад нь нэмэлт санхүүжилт хуваарилдаг
болжээ. Хүүхэд асрах үйлчилгээний төлбөрийг буцаан олгох, эсвэл мөнгөн бус
дэмжлэг үзүүлэх зэрэг өөр бусад санаачилгууд ч бий болжээ. 5. 2. Улс төрийн намуудын эмэгтэй нэр дэвшигчид чиглэсэн санхүүжилт босгох
дотоод механизм арга замууд Эндээс уг байгууллагын ач холбогдол,
дэмжлэгийн талаарх нотолгоог харж болно. EMILY-ийн жагсаалт улс төрийн өрсөлдөөний тэгш бус, зөрүүтэй байдлыг
өөрчлөхийн тулд зөвхөн гарааны мөнгө олгох анхны зорилгоосоо хальж, нэр
дэвшигч болох ирээдүйтэй эмэгтэйчүүд, сонгуулийн багийнханд зориулсан арга
барил суулгах сургалт явуулах янз бүрийн төсөл хөтөлбөр, мөн сонгогчид саналаа
өгөх явдлыг нэмэгдүүлэхэд чиглэсэн үйл ажиллагааг авч хэрэгжүүлэх болжээ. Сонгуулийн үйл явцын туршид санхүүжилт босгох явдал EMILY-ийн жагсаалтын
хамгийн чухал ажлын нэг хэвээр байгаа бөгөөд сайтар сонгож авсан Ардчилсан
намын ирээдүйтэй эмэгтэй нэр дэвшигчдэд зориулж санхүүжилт босгох хэлбэрээр
ажилладаг. 1992-2006 онд цуглуулсан хандивын хэмжээгээрээ EMILY-ийн жагсаалт нь
хамгийн их хөрөнгө босгосон ба одоо ч тэргүүн эгнээнд байсаар ирсэн. 1985 онд
үүсэн байгуулагдсанаасаа хойш 100 гаруй эмэгтэйд Конгрессын сонгуульд ялалт
байгуулахад нь дэмжлэг үзүүлсэн бөгөөд орон нутгийн сонгуульд ч олон зуун
эмэгтэйд тусалжээ. EMILY-ийн жагсаалт эмэгтэй нэр дэвшигчдийг дэмжихэд
нийтдээ 350 гаруй сая ам.доллар босгосон нь тус орны кампанит ажлын хөрөнгө
босгох бүлгүүд дотор хамгийн их амжилттай ажилласанд тооцогдож байна. EMILY-ийн жагсаалтын амжилт олон улсын хэмжээнд ч анхаарал татаж нэлээдгүй
оронд энэ загвараар мөнгө босгох кампанит ажлууд хийгдэх болжээ. /EMILY-ийн
жагсаалт түүний он цагийн товч түүхийг Хавсралт 1-д оруулав./ Ийнхүү 1985 онд байгуулагдсан эмэгтэй нэр дэвшигчдэд чиглэсэн хөрөнгө
босгох зорилготой хэсэг бүсгүйчүүдийн санаачилга нь одоо уриа лоозон биш,
бодит үр дүн туршлага болж бусад улс орнуудад салбарлан тархаж байна. Тухайлбал, Австралийн EMILY-ийн жагсаалт, Английн Хөдөлмөрийн Намын
Эмэгтэйчүүдийн сүлжээ зэрэг байгууллагууд нь эмэгтэй нэр дэвшигчдийг дэмжих - 88 - Философи, эрх зүйн судлал - XXXVIII 2. Австралийн EMILY-ийн жагсаалт Австралийн Викториа муж улсын
тэргүүн асан Жоан Кирнер АНУ дахь EMILY-ийн жагсаалтын амжилтыг анзаарч,
Австралийн Хөдөлмөрийн Нам (ALP)-ын эмэгтэйчүүдийг дэмжин хандив
хуримтлуулах зарчимд тулгуурласан ижил төстэй байгууллага байгуулах ажил
эхлүүлжээ (ННХ and АСДҮОУХ 2020, 414-416). Тус хөдөлгөөнийг 1996 онд
өрнүүлэх үед нам доторх барууны чиг баримжаатай хэсэг нь тухайн хөдөлгөөнийг
зүүний үзэл баримтлалын арга зам хэмээн эсэргүүцэн тэмцэж байв. Австралийн
EMILY-ийн жагсаалт аажмаар бие даасан байгууллага болж үүсгэн байгуулагдсан
бөгөөд гишүүдийн 40 хувь нь Австралийн Хөдөлмөрийн Нам бус хүмүүсээр
өргөжсөн. Гэхдээ улс төрийн санхүүжилтийн ил тод байдлын үүднээс Австралийн
Хөдөлмөрийн Намын дэргэдэх байгууллага хэмээн үздэг. 2. Австралийн EMILY-ийн жагсаалт Австралийн Викториа муж улсын
тэргүүн асан Жоан Кирнер АНУ дахь EMILY-ийн жагсаалтын амжилтыг анзаарч,
Австралийн Хөдөлмөрийн Нам (ALP)-ын эмэгтэйчүүдийг дэмжин хандив
хуримтлуулах зарчимд тулгуурласан ижил төстэй байгууллага байгуулах ажил
эхлүүлжээ (ННХ and АСДҮОУХ 2020, 414-416). 2. Улс төрийн намуудын эмэгтэй нэр дэвшигчид чиглэсэн санхүүжилт босгох
дотоод механизм арга замууд Ирландын Хөдөлмөрийн Намын “5-Си” хөтөлбөр (ННХ and АСДҮОУХ
2020): Эмэгтэйчүүдийн нийгэмд эзлэх байр суурь, нэр хүндэд нөлөөлж байгаа
(Confidence, Childcare, Cash, Candidate Selection and Culture) өөртөө итгэх итгэл, 5. Ирландын Хөдөлмөрийн Намын “5-Си” хөтөлбөр (ННХ and АСДҮОУХ
2020): Эмэгтэйчүүдийн нийгэмд эзлэх байр суурь, нэр хүндэд нөлөөлж байгаа
(Confidence, Childcare, Cash, Candidate Selection and Culture) өөртөө итгэх итгэл, - 89 - Studia Philosophiae Et Juris - XXXVIII хүүхэд асрах, бэлэн мөнгө, нэр дэвшигчийн сонголт ба соёл гэсэн таван зорилтот
сорилтуудыг шийдвэрлэх санаачилга дэвшүүлсэн. Тус нам эмэгтэй гишүүддээ
сургалт семинар хийх, сонгогч дэмжигчдэд хүрч ажиллах зэрэг арга хэмжээ зохион
байгуулж, эмэгтэй нэр дэвшигчдийн өмнөөс санхүүжилт босгодог бөгөөд шинээр
элссэн эсвэл анх удаа нэр дэвшиж буй эмэгтэйчүүдийг дэмжихэд онцгойлон
анхаардаг. хүүхэд асрах, бэлэн мөнгө, нэр дэвшигчийн сонголт ба соёл гэсэн таван зорилтот
сорилтуудыг шийдвэрлэх санаачилга дэвшүүлсэн. Тус нам эмэгтэй гишүүддээ
сургалт семинар хийх, сонгогч дэмжигчдэд хүрч ажиллах зэрэг арга хэмжээ зохион
байгуулж, эмэгтэй нэр дэвшигчдийн өмнөөс санхүүжилт босгодог бөгөөд шинээр
элссэн эсвэл анх удаа нэр дэвшиж буй эмэгтэйчүүдийг дэмжихэд онцгойлон
анхаардаг. р
6. Гана Улсын “Эмэгтэйчүүдийн сан” (ННХ and АСДҮОУХ 2020, 412)
тодорхой улс төрийн намуудаас сонгуульд оролцох эрмэлзэлтэй эмэгтэйчүүдийг
дэмжих зорилготой Эмэгтэйчүүдийн сан үүсгэн байгуулах амлалт авсан байна. 2011
онд болсон тус улсын намуудын уулзалт дээр хүлээн авсан санхүүжилтийнхээ 10
хувийг улс төрч болох эрмэлзэлтэй эмэгтэйчүүдэд шууд зарцуулах санал гаргасан
мэдэгдлийг хэд хэдэн нам хийжээ. 6. Гана Улсын “Эмэгтэйчүүдийн сан” (ННХ and АСДҮОУХ 2020, 412)
тодорхой улс төрийн намуудаас сонгуульд оролцох эрмэлзэлтэй эмэгтэйчүүдийг
дэмжих зорилготой Эмэгтэйчүүдийн сан үүсгэн байгуулах амлалт авсан байна. 2011
онд болсон тус улсын намуудын уулзалт дээр хүлээн авсан санхүүжилтийнхээ 10
хувийг улс төрч болох эрмэлзэлтэй эмэгтэйчүүдэд шууд зарцуулах санал гаргасан
мэдэгдлийг хэд хэдэн нам хийжээ. 7. Фарабундо Мартигийн Үндэсний чөлөөлөх фронт (ФМҮЧФ) (ННХ and
АСДҮОУХ 2020, 415) нам нь Эль Сальвадор Улсын эмэгтэйчүүдийн оролцоог
дэмжих зорилготой Сонгуулийн хороо байгуулсан байна. Тус хороо нь дотоодын
болон гадаадын компани, дэмжигч, гишүүдэд хандан санхүүжилт босгох арга
хэмжээ зохион байгуулсан. Тухайлбал, сурталчилгааны зардал гаргуулах
зорилгоор нэр хүндтэй бизнес эрхлэгчдийн дунд зоог барих, бусад зорилтот
бүлгүүдээс хөрөнгө босгох зэрэг нэмэлт арга хэмжээг зохион байгуулдаг. Босгосон
санхүүжилтээ бүх эмэгтэй нэр дэвшигчийг хэвлэл мэдээллээр таниулах, тэдний
нэр бүхий зурагт хуудас, өмсгөл, намын хөтөлбөрийг хэвлэн орон даяар тараах
зэрэгт зарцуулжээ. 8. Камбож Улсын “Сам Рэнси” (ННХ and АСДҮОУХ 2020, 414) нам нь
сонгуулийн ажилд шаардлагатай эд зүйлс болох сурталчилгааны үед өмсөх хувцас,
тээврийн хэрэгсэл зэргээр эмэгтэй нэр дэвшигчдийг хангадаг. 2. Улс төрийн намуудын эмэгтэй нэр дэвшигчид чиглэсэн санхүүжилт босгох
дотоод механизм арга замууд Хувцас, тээврийн
хэрэгсэл, сонгуулийн сурталчилгааны материал зэрэг мөнгөн бус эдээр өгөх
хандив нь эмэгтэй нэр дэвшигчдэд учирч болох санхүүгийн ачааллыг бууруулна
гэж үздэг. Уг байгууллага нь орон нутаг, муж, холбооны түвшинд нэр дэвшигчдээс
ур чадварын талаарх хүсэлтийг хүлээн авч, эдгээрийг холбогдох сайн дурын
мэргэжилтнүүдтэй холбож өгдөг байна (Spangler 2017). g
9. Их Британийн Women2Win (Women2 Win 2023): Women2Win-ийг 2005 онд
Кеннингтоны Баронесса Женкин /Baroness Jenkin of Kennington/, парламентын
гишүүн Рт Хон Тереза Мэй /Rt Hon Theresa May/ нар Консерватив намаас илүү
олон эмэгтэй нэр дэвшигчид болон тэдний хэрэгцээтэй кампанит ажлыг явуулж,
сурталчлах, сургалтаар хангах зорилгоор үүсгэн байгуулжээ. Women2Win нь парламент болон улс төрд консерватив үзэлтэй эмэгтэйчүүдийн
тоог нэмэгдүүлэх зорилготой бөгөөд төрийн албан тушаал, мөн сонгуульд нэр
дэвшиж буй эмэгтэйчүүдийг олонд таниулах, тэдэнд заавар, зөвлөгөө өгөх зэрэг
үйл ажиллагааг явуулдаг. 2005 онд Консерватив намаас парламентын 17 эмэгтэй
гишүүн байсан нь парламентад суудалтай намын дөнгөж 9 хувийг төлөөлдөг
байжээ. Одоо 15 жилийн дараа, дөрвөн удаагийн сонгуулийн дараа Консерватив
парламентын 87 эмэгтэй гишүүн байгаа бөгөөд энэ нь 20 гаруй хувь байна. IV. Дүгнэлт Мөн эмэгтэй нэр дэвшигчдэд чиглэсэн сонгуулийн сурталчилгааны болон
хэвлэл мэдээллийн зардалд намаас илүү дэмжлэг үзүүлдэг байх, 5. Мөн эмэгтэй нэр дэвшигчдэд чиглэсэн сонгуулийн сурталчилгааны болон
хэвлэл мэдээллийн зардалд намаас илүү дэмжлэг үзүүлдэг байх, 6. Нэр дэвшиж буй тойрог нь хол, өргөн уудам нутаг дэвсгэртэй тохиолдол
зэрэг онцлогуудыг харгалзан унаа, байр, хоол, харилцаа холбоо болон албан
томилолтын бусад зардлуудыг төрийн санхүүжилтийн эсвэл бусад намын
нөөц санхүүжилтэд тусгаж зарцуулдаг байх, 7. Дотоод болон гадаадын мөнгө босгож буй шилдэг туршлагуудыг
баримтжуулж, эмэгтэй нэр дэвшигчдэд чиглэсэн шууд ба шууд бус нөөцийг
бүрдүүлэх, ашиглах үр дүнтэй аргуудыг сургалтаар түгээн дэлгэрүүлэх, Сонгуулийн тухай хуульд өгөх санал: Сонгуулийн тухай хуульд өгөх санал: 8. Улс төрийн намуудын зардалд нэр дэвшигчдийн ялангуяа эмэгтэйчүүдийн
кампанит ажлын зардлыг нэмэхэд чиглэсэн өөрчлөлтийг сонгуулийн тухай
хуульд тусгах, тухайлбал: 8. Улс төрийн намуудын зардалд нэр дэвшигчдийн ялангуяа эмэгтэйчүүдийн
кампанит ажлын зардлыг нэмэхэд чиглэсэн өөрчлөлтийг сонгуулийн тухай
хуульд тусгах, тухайлбал: Сонгуулийн тухай хуулийн 50.2.-т “Төрийн аудитын дээд байгууллага нам,
эвсэл болон нэр дэвшигчээс сонгуульд зарцуулах зардлын дээд хэмжээг тогтоохдоо
нутаг дэвсгэрийн хэмжээ, байршил, өрхийн болон сонгогчийн тоо, мөн эмэгтэй
нэр дэвшигчийн хүйсийн онцлог болон энэ хуульд заасан бусад шаардлагыг
харгалзан Сонгуулийн ерөнхий хороо болон Монгол Улсын Ерөнхий аудитор
хамтран батална. гэж нэмэлт өөрчлөлт оруулах. Сонгуулийн тухай хуулийн 50.2.-т “Төрийн аудитын дээд байгууллага нам,
эвсэл болон нэр дэвшигчээс сонгуульд зарцуулах зардлын дээд хэмжээг тогтоохдоо
нутаг дэвсгэрийн хэмжээ, байршил, өрхийн болон сонгогчийн тоо, мөн эмэгтэй
нэр дэвшигчийн хүйсийн онцлог болон энэ хуульд заасан бусад шаардлагыг
харгалзан Сонгуулийн ерөнхий хороо болон Монгол Улсын Ерөнхий аудитор
хамтран батална. гэж нэмэлт өөрчлөлт оруулах. • Эмэгтэй нэр дэвшигчийн сонгуулийн кампанит ажлын зардалд хүүхэд асрах,
асран халамжлах зардлыг багтаана. гэж тодотгож болно. • Эмэгтэй нэр дэвшигчийн сонгуулийн кампанит ажлын зардалд хүүхэд асрах,
асран халамжлах зардлыг багтаана. гэж тодотгож болно. Жендерийн эрх тэгш байдлыг хангах тухай хуульд өгөх санал: IV. Дүгнэлт - 90 - Философи, эрх зүйн судлал - XXXVIII Улс төрийн нам нь нэр дэвшигчдийг шилж сонгох, нэр дэвшүүлэх ажлыг хариуцдаг
гол инститүц юм. Мөн намууд сонгуулийн ажлыг удирдан зохион байгуулах,
мөнгө санхүүг хянан зарцуулах хариуцлага үүрдэг учир сонгуулийн өрсөлдөөнд
эмэгтэйчүүдийг дэмжин ажиллахад чухал үүрэгтэй. Иймд намуудаас Жендерт
чиглэсэн бодлого, хөтөлбөрийг санаачлан хэрэгжүүлж нийгэмд тэгш байдлыг
хангахад тууштай улс төрийн манлайллын хэрэгцээ шаардлага үгүйлэгдэж байна. Ялангуяа эмэгтэй нэр дэвшигчдийн кампанит ажлыг дэмжих төрийн
санхүүжилтээс үл хамаарах хөрөнгө босгох сайн дурын санаачилгыг эхлүүлэх,
мөн бусад шууд бус нөөцийг бүрдүүлэх, ашиглах зэрэг тусгай арга хэмжээнүүдийг
зохион байгуулах хэрэгцээ асар их байна. Үүнээс гадна эмэгтэй нэр дэвшигчдийг
дэмжиж хөрөнгө босгож чадсан туршлага, арга замуудаас үзэхэд тэдний өөрсдийнх
нь санаачилга, оролцоотойгоор амжилттай үр дүнд хүрч, нийгэм олон нийтэд
нөлөөлөхүйц арга хэмжээ болж чадсан нь ажиглагдаж байна. Ийнхүү судалгааны үр дүнд улс төрийн намуудын дотоод санаачилгаар
хэрэгжиж буй хуульчлагдаагүй арга хэмжээнүүдийг судлахад дараахь санал,
зөвлөмжүүдийг дэвшүүлж болохоор байна. Дэвшүүлж буй саналыг улс төрийн
намд болон хуулийн заалтад гэсэн байдлаар хоёр хэсэгт хувааж бичсэн. Улс төрийн намуудад зориулсан санал, зөвлөмж: 1. Эмэгтэй нэр дэвшигчдийг сонгуульд нэр дэвшихээс эхлэн компанит ажил
дуусах хүртэлх үндсэн гурван үе шатуудад тулгарч байгаа (нэр дэвшихээр
шийдэх, нэр дэвших, сонгуулийн кампанит ажил явуулах) санхүүгийн
асуудалд тулгуурлан шууд ба шууд нөөцүүдийг бүрдүүлэх, ашиглах арга
хэмжээнүүдийг улс төрийн намууд санаачлах. Тодруулбал, • Нэр дэвшихээр шийдэх үеийн сэтгэл зүйн болоод санхүүгийн шууд ба
шууд бус дэмжлэг үзүүлэх. Жишээлбэл, нийгэм олон нийтэд танигдахад
нь туслах, чиглүүлэх, нэр дэвшихийг санал болгож, үргэлж тэдэнд боломж
байгаа гэдгийг мэдрүүлж, итгэлтэй болоход нь туслах нөлөөллийн ажил
зохион байгуулах • Улс төрийн намын дотоод аппарат болон улс төрийн шийдвэр гаргах
түвшний албан тушаалд нэр дэвшүүлж, томилон ажиллуулах гэх мэт 2. Нэр дэвшихээр тодорхой болсон эмэгтэй нэр дэвшигчдэд чиглэсэн эрт буюу
урьдчилан хандив босгох ЭМИЛИ–ийн жагсаалт, ХҮСЛИЙН жагсаалт шиг
сайн дурын хөдөлгөөн, байгууллагыг намууд санаачлан нийгэмд таниулж,
жишиг арга хэмжээ болгох: • Намын өөрсдийн санаачилгаар хийх арга хэмжээ • Эсвэл намууд нэгдэж хамтын санаачилгаар хийх тусгай арга хэмжээтэй
болох, 3. Мөн нэр дэвших эрхээ авсан эмэгтэй нэр дэвшигчдийг намын татвар,
хураамж, дэнчин зэрэг зардлуудаас чөлөөлөх эсвэл бууруулах, 4. Нэр дэвшигчийн сонгуулийн кампанит ажилд чиглэсэн дэмжлэгийн хувьд
хамтран ажиллах хүсэлтэй сайн дурынхны жагсаалтыг гаргаж, дэмжигч,
ухуулагч гэх мэт бүлгүүдэд цалингүйгээр сайн дурын хөдөлмөрөө
хандивлагчдыг татах арга хэмжээнүүдийг санаачлан зохион байгуулах, - 91 - Studia Philosophiae Et Juris - XXXVIII 5. Жендерийн эрх тэгш байдлыг хангах тухай хуульд өгөх санал: 9. Улс төрийн нам дотооддоо санхүүжилтийн нөөцөө хуваарилахдаа
эмэгтэйчүүдийн байгууллага, эмэгтэй нэр дэвшигчдэд чиглэсэн хуваарилалт,
зарцуулалт байхыг дэмжсэн бодлогын шинэчлэлийг Жендерийн эрх
тэгш байдлыг хангах тухай хууль (цаашид ЖЭТБХТ гэх) дараахь нэмэлт
өөрчлөлтийг оруулах, ЖЭТБХТ хуулийн 8.2 заалтад: “Бүх шатны сонгуульд нэр дэвшигч эрэгтэй
эмэгтэй хүний сонгуулийн сурталчилгаанд зориулан улс төрийн намаас үзүүлэх
санхүүгийн дэмжлэг ижил хэмжээтэй байна” заалт нь Жендерийн эрх тэгш
байдлыг хангах заалт гэхээсээ илүү тэгшитгэн хуваарилах зарчмыг баримталсан
хүйсийн ялгаатай байдлын онцлогийг харгалзан үзээгүй өнгөц зохицуулалт гэж
үзэж байна. Тодруулбал, хүүхэд асрах, асран халамжлах зэрэг жам ёсны үүргийг
харгалзах ёстой. Иймд дараахь өөрчлөлтийн саналыг дэвшүүлж байна. ЖЭТБХТ хуулийн 8.2 заалтад: “Бүх шатны сонгуульд нэр дэвшигч эрэгтэй
эмэгтэй хүний сонгуулийн сурталчилгаанд зориулан улс төрийн намаас үзүүлэх
санхүүгийн дэмжлэг ижил хэмжээтэй байна” заалт нь Жендерийн эрх тэгш
байдлыг хангах заалт гэхээсээ илүү тэгшитгэн хуваарилах зарчмыг баримталсан
хүйсийн ялгаатай байдлын онцлогийг харгалзан үзээгүй өнгөц зохицуулалт гэж
үзэж байна. Тодруулбал, хүүхэд асрах, асран халамжлах зэрэг жам ёсны үүргийг
харгалзах ёстой. Иймд дараахь өөрчлөлтийн саналыг дэвшүүлж байна. Жендерийн эрх тэгш байдлыг хангах тухай
хуулийн 8 дугаар зүйл. Санал болгож буй нэмэлт өөрчлөлт
8.2. Бүх шатны сонгуульд нэр дэвшигч эрэгтэй
эмэгтэй
хүний
сонгуулийн
сурталчилгаанд
зориулан улс төрийн намаас үзүүлэх санхүүгийн
дэмжлэг ижил хэмжээтэй байна. Бүх
шатны
сонгуулийн
сурталчилгаанд
зориулан улс төрийн намаас үзүүлэх санхүүгийн
дэмжлэгийг эмэгтэй нэр дэвшигчийн хүйсийн
онцлогийг харгалзан нэмэгдүүлж болно. Жендерийн эрх тэгш байдлыг хангах тухай
хуулийн 8 дугаар зүйл. Санал болгож буй нэмэлт өөрчлөлт
8.2. Бүх шатны сонгуульд нэр дэвшигч эрэгтэй
эмэгтэй
хүний
сонгуулийн
сурталчилгаанд
зориулан улс төрийн намаас үзүүлэх санхүүгийн
дэмжлэг ижил хэмжээтэй байна. Бүх
шатны
сонгуулийн
сурталчилгаанд
зориулан улс төрийн намаас үзүүлэх санхүүгийн
дэмжлэгийг эмэгтэй нэр дэвшигчийн хүйсийн
онцлогийг харгалзан нэмэгдүүлж болно. - 92 - Философи, эрх зүйн судлал - XXXVIII Ашигласан материал Women’s Environment and Development Organization. 2007. Women Candidates and
Campaign Finance. New York city: Women’s Environment and Development
Organization p
g
Campaign Finance. New York city: Women’s Environment and Development
Organization ННХ, and АСДҮОУХ. 2020. Улс төрийн намын болон сонгуулийн санхүүжилт. Улс төрийн санхүүжилтийн гарын авлага. ред. Д.Энхтуул, Б.Баттуул,
П.Эрдэнэжаргал. Уб. Cigane, Lolita, & Magnus Ohman. 2014. Political Finance and Gender Equality. IFES White
Paper. Washington, DC : International Foundation for Electoral Systems. Ohman, Magnus. 2018. Gender-targeted Public Funding for Political Parties: A comparative
analysis. International IDEA. Sanbonmatsu, Kira . 2017. Money and Women Candidates. Political Parity. October. Accessed
October 13, 2023. politicalparity.org/wp-content/inventory-money.pdf. Sidhu, Gretchen Luchsinger, and Ruth Meena. 2007. Electoral Financing to Advance
Women’sPolitical Participation: AGuide for UNDP Support. New York: United
Nations Development Programme. Barbara Lee Family Foundation , and Lake Research Partners. 2012. Pitch Perfect: Winning
Strategies for Women Candidates. Barbara Lee Family Foundation. November 8. https://www.barbaraleefoundation.org/wp-content/uploads/BLFF-Lake-Pitch-Perfect-
Wining-Strategies-for-Women-Candidates-11.08.12.pdf. 2023. Judy LaMarsh Fund. October 13. https://nwlc-clfn.liberal.ca/judy-lamarsh-fund/. Spangler, Lizzy . 2017. Political Organizations That Help Women Run for Office. Study Breaks:
Magazine. https://studybreaks.com/news-politics/women-political-organizations-run-office/. 2023. Women2 Win. https://www.women2win.com/about. 2023. Women2 Win. https://www.women2win.com/about. - 93 - - 93 -
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Features of graphic models of multioperational computing processes
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Optiko-elektronnì ìnformacìjno-energetičnì tehnologìï
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Т.Б. МАРТИНЮК, А.Г. БУДА, А.В. КОЖЕМ’ЯКО, Л.М. КУПЕРШТЕЙН
ОСОБЛИВОСТІ ГРАФІЧНИХ МОДЕЛЕЙ БАГАТООПЕРАНДНИХ
ОБЧИСЛЮВАЛЬНИХ ПРОЦЕСІВ Вінницький національний технічний університет
95, Хмельницьке шосе, Вінниця, 21021, Україна
E-mail: antbuda@vntu.edu.ua Анотація. У статті розглянуто моделі обчислювальних процесів з обробленням масивів даних за
різницевими зрізами. Запропоновано моделі у вигляді інформаційних графів для згортки та
алгебраїчного підсумовування елементів векторного масиву чисел. Наведено числові приклади
розглянутих обчислювальних процесів, які ілюструють відповідні часові співвідношення для
обчислювальних операцій багатооперандного підсумовування чисел. Ключові слова: інформаційний граф, згортка елементів векторного масиву чисел, алгебраїчне
підсумовування елементів масиву чисел. Аннотация. В статье рассмотрены модели вычислительных процессов с обработкой массивов
данных по разностным срезам. Предложены модели в виде информационных графов для свертки и
алгебраического суммирования элементов векторного массива чисел. Приведены числовые примеры
рассмотренных вычислительных процессов, которые иллюстрируют соответствующие временные
соотношения для вычислительных операций многооперандного суммирования чисел. Ключевые слова: информационный граф, свертка элементов векторного массива чисел,
алгебраическое суммирование элементов массива чисел. Abstract. The article deals with the models of computational processes with the processing of data arrays
by difference cuts. The models in the form of information graphs for the convolution and algebraic
summation of elements of a numbers vector array are proposed. The numerical examples of the
computational processes under consideration, which illustrate the corresponding time relations for
computational operations of numbers multioperand summation, are given. Key words: information graph, convolution of elements of a numbers vector array, algebraic summation of
elements of a numbers array.1 DOI: 10.31649/1681-7893-2018-35-1-5-13 1© Т.Б. МАРТИНЮК, А.Г. БУДА, А.В. КОЖЕМ’ЯКО, Л.М. КУПЕРШТЕЙН, 2018 ЗГОРТКА ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ Основну операцію у прямому лінійному дискретному перетворенні за РЗ [9] складає згортка
елементів векторного масиву або групове (багатооперандне) підсумовування. Алгоритм виконання цієї
операції можна подати таким чином [10]. 1. У кожному циклі у поточному векторному масиві аj-1 чисел (і = 1,n ), який можна подати у
вигляді n-елементного вектор-стовпця, виділяють величину qj як внутрішній поріг оброблення,
що є найменшим ненульовим числом із чисел, що входять у масив аj-1 в процесі порівняння між
його елементами, a1,j-1,...,ai,j-1, ... ,an,j-1, тобто 1. У кожному циклі у поточному векторному масиві аj-1 чисел (і = 1,n ), який можна подати у
вигляді n-елементного вектор-стовпця, виділяють величину qj як внутрішній поріг оброблення,
що є найменшим ненульовим числом із чисел, що входять у масив аj-1 в процесі порівняння між
його елементами, a1,j-1,...,ai,j-1, ... ,an,j-1, тобто
1
,
1
1
min
min
,
n
j
j
i j
q
a
a
(1) (1)
1
2. Перевіряють виконання умови
qj = 0. 2. Перевіряють виконання умови
qj = 0. (2)
Якщо ця умова не виконується то перехід до п 3 а якщо виконується то перехід до п 5 ння умови
qj = 0. (2) (2) qj = 0. і qj
Якщо ця умова не виконується, то перехід до п.3, а якщо виконується, то перехід до п.5. 3. Формують новий векторний масив аj чисел (і = 1,n ) у вигляді n-елементного вектора-стовпця
вигляду 3. Формують новий векторний масив аj чисел (і = 1,n ) у вигляді n-елементного вектора-стовпця
вигляду
,
,
1
1
1 ,
n
n
j
i j
i j
j
a
a
q
a
(3) (3) Одночасно формують поточну часткову суму Sj вигляду Одночасно формують поточну часткову суму Sj вигляду Одночасно формують поточну часткову суму Sj вигляду Одночасно формують поточну часткову суму Sj вигляду j
j
j
j
S
q
b
,
(4)
b
і
і
≥0 j
j
j
S
q
b
, j
j
j
S
q
b
,
(4) (4) j
j
j
де bj – кількість чисел аi,j ≥ 0. Виконують накопичення поточних сум вигляду
k j
де bj – кількість чисел аi,j ≥ 0. Виконують накопичення поточних сум вигляду де bj – кількість чисел аi,j ≥ 0. ВСТУП Одним із способів опису алгоритмів є форма його подання у вигляді графів [1]. При цьому
загальні графічні форми є доцільними при виборі прийнятної архітектури обчислювальних засобів, а
функціональна форма подання інформаційних графів (ІГ) дозволяє ефективно досліджувати
інформаційні структури [1]. Аналогічне графічне подання алгоритмів в роботі [2] має назву часової
паралельної граф-схеми (ЧПГС), а в роботі [3] використовуються як графо-структурні моделі, так і
широко розповсюджені ІГ. Тому для детального дослідження особливостей математичних моделей
способів оброблення за різницевими зрізами (РЗ) векторних масивів даних [4] доцільно скористатись
поданням процесів оброблення у вигляді інформаційних графів (ІГ), оскільки це робить наочним їх
структурний аналіз [5, 6]. При цьому ІГ зображують як спрямований граф [5] в ярусно-конвеєрній формі
для визначення попередніх та наступних вершин [7, 8]. Метою даної роботи є аналіз можливостей розпаралелювання обчислювальних процесів за
ими зрізами. 1© Т.Б. МАРТИНЮК, А.Г. БУДА, А.В. КОЖЕМ’ЯКО, Л.М. КУПЕРШТЕЙН, 2018 5 5 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ ЗГОРТКА ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ В 6 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ результаті ІГ для алгоритму згортки елементів векторного масиву матиме вигляд (рис. 2), на якому
видно, що використовуються тільки міжвузлові зв’язки для передачі РЗ aj та накопичених сум S′j. an,j-1
s’j-1
a1,j-1
gj
fj
qj
sj
s’j
a1,j
an,j
--
--
+
+
+
m
m
. . . . . . . . . . . . . . . . . . . . . . . . . . . j
gj
fj
aj
aj-1
s’j-1
s’j
qj
sj
а)
б)
Рис. 1 – Базовий вузол інформаційних графів оброблення за РЗ an,j-1
s’j-1
a1,j-1
gj
fj
qj
sj
s’j
a1,j
an,j
--
--
+
+
+
m
m
. . . . . . . . . . . . . . . . . . . . . . . . . . . j
gj
fj
aj
aj-1
s’j-1
s’j
qj
sj
а)
б)
Рис. 1 – Базовий вузол інформаційних графів оброблення за РЗ
'
0
S
N
a
0
N
S
1a
1
N
2
Рис. 2 – ІГ для алгоритму згортки елементів векторного масиву Рис. 1 – Базовий вузол інформаційних графів оброблення за РЗ '
0
S
N
a
0
N
S
1a
1
N
2
Рис. 2 – ІГ для алгоритму згортки елементів векторного масиву Рис. 2 – ІГ для алгоритму згортки елементів векторного масиву Для наочності за аналогією з роботою [12] наведено приклад виконання згортки елементів
векторного масиву (при n = 5) по циклах у такому вигляді (рис. 3), де векторні масиви розглядаються як
групи чисел, а формування поточних часткових сум показано як обчислення кратних мінімальних
елементів qj (4) замість їх послідовного накопичення. ЗГОРТКА ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ Виконують накопичення поточних сум вигляду
k 0
,
1,
k
k
j
j
S
S
k
N
(5) (5) j
4. Одночасно формують у вигляді n-елементних вектор-стовпців j-ті бінарні маски fj і qj з
елементами вигляду:
1
0
j
4. Одночасно формують у вигляді n-елементних вектор-стовпців j-ті бінарні маски fj і qj з
елементами вигляду:
4. Одночасно формують у вигляді n-елементних вектор-стовпців j-ті бінарні маски fj і qj з
елементами вигляду: ,
,
,
1, якщо
0,
0, якщо
0,
i j
i j
i j
a
f
a
, (6)
,
,
,
1, якщо
0,
0, якщо
0. i j
i j
i j
a
g
a
(7) (7) і порівнюють елементи a1j,...,aij,...,an,j векторного масиву аj чисел (і = 1,n ) з виділенням величини qj+1. Перехід до п. 2. 5
Завершення процесу і порівнюють елементи a1j,...,aij,...,an,j векторного масиву аj чисел (і = 1,n ) з виділенням величини qj+1. Перехід до п. 2. р
5. Завершення процесу. р
р
у
Цикл оброблення складають пп.2-4. Результатом виконання цієї операції є обчислення
остаточної суми
0
N
S
елементів вхідного векторного масиву а0: ,0
1
1
,
n
N
i
j
i
j
S
a
S
(8) (8) а також формування матриць бінарних масок F i G, які можна розглядати відповідно як матрицю
додатних ознак і матрицю нульових ознак, і вектора ваг (коефіцієнтів) q. В процесі виконання
формуються проміжні результати: різницевий зріз aj і часткова сума Sj [11]. а також формування матриць бінарних масок F i G, які можна розглядати відповідно як матрицю
додатних ознак і матрицю нульових ознак, і вектора ваг (коефіцієнтів) q. В процесі виконання
формуються проміжні результати: різницевий зріз aj і часткова сума Sj [11]. j
j
Для спрощення ІГ на рис. 1а наведено функціональну структуру його базового вузла з
врахуванням особливостей оброблення за РЗ, а рис. 1б – схематичне подання базового вузла, причому
для відмінності від позначення часткових сум Sj (4) введено позначення для накопичених сум (5) у
вигляді S′j, сформованих у j-му циклі, а для остаточної суми, сформованої в N-му циклі, введено
позначення S0
N. Крім того, на рис.1а і в подальшому використовуються такі позначення для операторів: "+" –
оператор підсумовування; "–" – оператор віднімання; m – оператор визначення мінімального елемента. ЗГОРТКА ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ 3) складає:
min
(
) (
1)
(
1)
j
j
sm
sub
T
T
T
N
t n N
,
(14) min
(
) (
1)
(
1)
j
j
sm
sub
T
T
T
N
t n N
,
(14) (14) не значення часу
max
sm
T
для цього оброблення за умови (9) дорівнює: max
2
(
)
sm
T
t n
n
. (15) max
2
(
)
sm
T
t n
n
. (15) Наведені теоретичні відомості дозволяють розглядати оброблення елементів векторного масиву
за РЗ як оброблення з використанням принципів модулярної арифметики [13]. ЗГОРТКА ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ Максимальна кількість циклів підсумовування
залежить від розмірності масиву чисел, тобто max
N
n
,
(9) (9) а часові залежності мають такий вигляд а часові залежності мають такий вигляд min
(
1),
(
1),
,
j
com
j
sm
sm
j
j
sub
sub
T
t
n
T
t
b
T
t
(10) (10) де
min,
,
j
j
j
sm
sub
T
T
T
– відповідно час визначення мінімального елемента поточного РЗ, обчислення
поточної часткової суми і формування наступного РЗ у j-му циклі;
,
,
com
sm
sub
t
t
t
– відповідно час
порівння, підсумовування і віднімання двох чисел; bj – кількість додатних елементів у РЗ aj; j = 1,N , N –
кількість циклів оброблення. 7 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ Рис. 3 – Приклад згортки елементів векторного масиву
При цьому необхідно врахувати, що При цьому необхідно врахувати, що com
sm
sub
t
t
t
t
,
(11) (11) а також можливість поєднання у часі в кожному циклі виконання операцій визначення мінімального
елемента (
min
j
T
) і віднімання (
j
sub
T
) з операціями формування поточної часткової суми (
j
sm
T
) і
накопичення часткових сум ( sm
t
). Тому середній час сt виконання кожного циклу складає: min
j
j
j
c
sub
sm
sm
t
T
T
T
t
,
(12)
причому за умови (11) ці суми дорівнюють величині
(
1)
ct
t n
t
t n
,
(13)
якщо приймемо для спрощення що
jb
n
const
. min
j
j
j
c
sub
sm
sm
t
T
T
T
t
,
(12)
і (12) орівнюють величині
(
1)
ct
t n
t
t n
,
(13)
що b
n
const
(
1)
ct
t n
t
t n
,
(13) (
1)
ct
t n
t
t n
,
(13)
о
jb
n
const
. (13) В результаті загальний час
sm
T
операції згортки (підсумовування) елементів векторного масиву
з урахуванням часу формування величини qN+1 для завершення процесу оброблення (рис. 3) складає: В результаті загальний час
sm
T
операції згортки (підсумовування) елементів векторного масиву
з урахуванням часу формування величини qN+1 для завершення процесу оброблення (рис. АЛГЕБРАЇЧНЕ ПДІСУМОВУВАННЯ ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ АЛГЕБРАЇЧНЕ ПДІСУМОВУВАННЯ ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ Особливістю оброблення за РЗ є можливість суміщення у часі оброблення додатних і від’ємних
елементів початкового масиву, тобто можливість виконання паралельного алгебраїчного підсумовування
елементів масиву [14]. Два варіанти виконання цієї операції подано у вигляді ІГ на рис. 4 і 5, а у вигляді
розгорнутого по циклах процесу на рис. 6 і рис. 7 відповідно. В обох випадках перед початком
оброблення початковий масив (початкову групу) поділяють на дві групи за знаком елементів на додатну і
від’ємну відповідно і в подальшому розглядають обидві як групу елементів з додатними знаками (рис. 6,
7) Для першого варіанта (рис. 4, 6) кінцевий результат формується за формулами [15]: 8 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ ,0
1
n
i
N
N
i
S
a
S
S
,
(16)
причому
1
1
2
2
1
1
1
1
... ,
... ,
n
N
n
j
j
n
N
n
j
j
S
S
S
S
S
S
S
S
,0
1
n
i
N
N
i
S
a
S
S
,
(16) (16) причому 1
1
2
2
1
1
1
1
... ,
... ,
n
N
n
j
j
n
N
n
j
j
S
S
S
S
S
S
S
S
де аі,0 – і-й елемент у початковій групі; n – розмірність початкової групи;
,
j
j
S
S
– поточні часткові суми у j-
му циклі оброблення відповідно для додатної та від’ємної груп; n1, n2 – розмірність відповідно додатної та
від’ємної груп; N1, N2 – кількість циклів для оброблення відповідно додатної та від’ємної груп. 1
N
2
1a
'
0
S
N
S
1
N
2
1a
N
S
'
0
S
-
S
N
a
N
a
Рис. АЛГЕБРАЇЧНЕ ПДІСУМОВУВАННЯ ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ 5, 7) кінцевий результат формується таким чином [16]: 1
N
j
j
S
R
, 1
N
j
j
S
R
,
(19) (19) де j
j
j
R
S
S
,
(20) j
j
j
R
S
S
, (20) причому поточні часткові різниці
j
R підсумовуються з урахуванням їхнього знака (рис. 5). причому поточні часткові різниці
j
R підсумовуються з урахуванням їхнього знака (рис. 5). Максимальна кількість циклів оброблення для другого варіанта співпадає з величиною Nмах (17),
а час на обчислення поточних часткових різниць Rj (20) враховано часом sm
t
(12) замість накопичення
часткових сум. Таким чином, загальний час алгебраїчного підсумовування елементів векторного масиву
має вигляд (18). д (
)
Отже, багатофункціональність підсумовування (згортки) елементів векторного масиву
жується можливістю паралельного оброблення масиву чисел з різними знаками. ВИСНОВКИ Спосіб підсумовування елементів векторного масиву даних з використанням різницевих зрізів є
альтернативним по відношенню до відомих паралельних способів підсумовування, а саме, до алгоритму
логарифмічного підсумовування, оскільки його часткові суми в кожному циклі оброблення
представляють загальну частину всіх елементів поточного різницевого зрізу, а не є сукупністю попарних
часткових сум. Це дозволяє, по-перше, розпаралелити процес згортки елементів векторного масиву
чисел, тобто реалізувати багатооперандне підсумовування елементів масиву чисел. А по-друге, сумістити
підсумовування двох векторних масивів, розділених за знаком їх елементів. Це свідчить про широкі
функціональні можливості оброблення векторних масивів даних за РЗ. фу
р
р
Крім того, відмінною особливістю підсумовування елементів масиву чисел за РЗ є не жорстко
фіксований, а "плаваючий" часовий параметр (кількість циклів), який залежить від розмірності n
вхідного масиву і характеру розподілу елементів у масиві [10, 17]. АЛГЕБРАЇЧНЕ ПДІСУМОВУВАННЯ ЕЛЕМЕНТІВ ВЕКТОРНОГО МАСИВУ ДАНИХ 4 – ІГ для алгоритму алгебраїчного підсумовування
елементів векторного масиву (варіант 1) – ІГ для алгоритму алгебраїчного підсумовування
елементів векторного масиву (варіант 1) – ІГ для алгоритму алгебраїчного підсумовування
елементів векторного масиву (варіант 1) 1
N
2
1a
1
S
1
N
2
'
0
S
+
S
+
+
-
-
-
2
S
N
S
1S
2
S
N
S
1
R
2
R
N
R
1a
N
a
N
a
Рис. 5 – ІГ для алгоритму алгебраїчного підсумовування
елементів векторного масиву (варіант 2)
При цьому максимальна кількість циклів оброблення складає
1
1
2
max( ,
)
1
N
n n
. Рис. 5 – ІГ для алгоритму алгебраїчного підсумовування
елементів векторного масиву (варіант 2) При цьому максимальна кількість циклів оброблення складає
1
1
2
max( ,
)
1
N
n n
. При цьому максимальна кількість циклів оброблення складає
1
1
2
max( ,
)
1
N
n n
. (17) 9 9 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ
Рис. 6 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 1)
Рис. 7 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 2)
Крім того, після формування накопичених часткових сум у кожній групі можна от
цеву різницю (16) як результат оброблення (рис. 4) за додатковий час
sub
t
, тобто час обро
івнює: Рис. 6 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 1) Рис. 6 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 1) р
д
р
д у
у
векторного масиву (варіант 1)
Рис. 7 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 2)
К і
і
ф
ій
і векторного масиву (варіант 1)
Рис. 7 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 2)
К і
і
ф
ій
і Рис. 7 – Приклад алгебраїчного підсумовування елементів
векторного масиву (варіант 2) р
у (
р
)
Крім того, після формування накопичених часткових сум у кожній групі можна отримати
кінцеву різницю (16) як результат оброблення (рис. 4) за додатковий час
sub
t
, тобто час оброблення
дорівнює: 10 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ (18) min
1
sm
sub
sub
Для другого варіанта (рис. СПИСОК ЛІТЕРАТУРИ 1. В.В. Воеводин, Вл. В. Воеводин. (2004). Параллельные вычисления. – СПб.: БХВ-Петербург 2. Г.А. Поляков, Ю.Д. Умрихин. (1988) Автоматизация проектирования сложных цифровых
систем коммутации и управления. М.: Радио и связь. 2. Г.А. Поляков, Ю.Д. Умрихин. (1988) Автоматизация проектирования сложных цифровых
систем коммутации и управления. М.: Радио и связь. 3. Царев А.П. (2000). Алгоритмические модели и структуры высокопроизводительных
процессоров цифровой обработки сигналов. Szczecin, Informa. 3. Царев А.П. (2000). Алгоритмические модели и структуры высокопроизводительных
процессоров цифровой обработки сигналов. Szczecin, Informa. 4. Т.Б. Мартинюк, А.В. Кожем’яко. (2001). Реалізація концепції різницевих зрізів при
обробленні зображень та розпізнаванні образів. Оптико-електронні інформаційно-енергетичні
технології, 1, 79-85. 4. Т.Б. Мартинюк, А.В. Кожем’яко. (2001). Реалізація концепції різницевих зрізів при
обробленні зображень та розпізнаванні образів. Оптико-електронні інформаційно-енергетичні
технології, 1, 79-85. , ,
5. Николайчук Я.М. (2010). Теорія джерел інформації. Тернопіль: ТзОВ "Терно-граф". 6. О.Н. Паулин, Т.И. Усова. (2010). Метод распараллеливания нелинейных задач. Проблемы
программирования, 2-3, 145-148. 7. К.Г. Самофалов, Г.М. Луцкий. (1989). Основы теории многоуровневых конвейерных
вычислительных систем. М.: Радио и связь. 8. О.Н. Паулин, Т.И. Усова. (вересень 2010) Алгоритм распараллеливания решения нелинейных
уравнений на основе ИГ. Искусственный интеллект. Интеллектуальные системы (ИИ-2010):
Междунар. науч.-техн. конф., 20-24 сентября 2010 г.: материалы. – Донецк: ИПИИ "Наука і
освіта". 9. Т.Б. Мартынюк, В.В. Хомюк (2010). Особенности математической модели дискретного SM-
преобразования. Математичні машини і системи, 4, 145-155. 10. Мартинюк Т.Б. (2000) Рекурсивні алгоритми багатооперандної обробки інформації. Вінниця:
УНІВЕРСУМ-Вінниця. 11. Т.Б. Мартинюк, В.В. Хом’юк, І.М. Савалюк, Д.В. Охрущак. (1998). Використання зрізів
різниць для багатооперандного додавання числових величин. Вісник Вінницького
політехнічного інституту, 2, 63-68. у у
12. А.с. 1119035 СССР, МКИ5 G06G7/14. Способ параллельного сложения длительностей группы 11 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ временных интервалов / В.П. Кожемяко, Л.И. Тимченко, Т.В. Головань, Н.Е. Фурдияк. Т.Б. Мартынюк: Винниц. политех. ин-т. – № 3528903/18; заявл. 24.12.82; опубл. 15.10.84,
Бюл. № 38. временных интервалов / В.П. Кожемяко, Л.И. Тимченко, Т.В. Головань, Н.Е. Фурдияк. Т.Б. Мартынюк: Винниц. политех. ин-т. – № 3528903/18; заявл. 24.12.82; опубл. 15.10.84,
Бюл. № 38. 13. Т.Б. Мартинюк, А.В. Кожем’яко, Л.М. Куперштейн. (2015) Різницево-зрізова обробка з
використанням принципів модулярної арифметики. Вісник Хмельницького національного
університету, 2, 165-168. 14. Т.Б. Мартинюк, В.В. Хом’юк. (2005) Методи та засоби паралельних перетворень векторних
масивів даних. Вінниця: УНІВЕРСУМ-Вінниця. 7 15. Пат. 5495 Україна, МПК7 G 06 G 7/14. Спосіб паралельного алгебраїчного додавання
тривалостей групи часових інтервалів / А.С. Васюра, Т.Б. Мартинюк, Л.В. Куперштейн,
І.В. Мисловський; Вінниц. нац. техн. ун-т. – № 20040604914; заявл. 21.06.2004; опубл. REFERENCES 1. V.V. Voyevodin, Vl. V. Voyevodin. (2004). Parallel'nyye vychisleniya. SPb.: BKHV-Peterburg. 2. G.A. Polyakov, YU.D. Umrikhin. (1988) Avtomatizatsiya proyektirovaniya slozhnykh tsifrovykh
sistem kommutatsii i upravleniya. – M.: Radio i svyaz'. p
y
y
3. Tsarev A.P. (2000) Algoritmicheskiye modeli i struktury vysokoproizvoditel'nykh protsessorov
tsifrovoy obrabotki signalov. Szczecin, Informa. 4. T.B. Martinyuk, A.V. Kozhem’yako (2001). ea zat ya kont e t r znit e ikh zr z ri
obrob enn zobrazhen' ta roz zna ann obraz . Optiko-ye ektronn nformat yno-yener eti hn
tekhno o , 1, 79-85. 5. Nikolaychuk YA.M. (2010) Teor ya zhere nformat . Terno ': TzOV "Terno-graf". 6. O.N. Paulin, T.I. Usova. (2010). Metod rasparallelivaniya nelineynykh zadach. Problemy
programmirovaniya, 2-3, 145-148. 7. K.G. Samofalov, G.M. Lutskiy (1989). Osnovy teorii mnogourovnevykh konveyyernyk
vychislitel'nykh sistem. M.: Radio i svyaz'. 8. O.N. Paulin, T.I. Usova ( September 2010). Algoritm rasparallelivaniya resheniya nelineynykh
uravneniy na osnove IG. Iskusstvennyy intellekt. Intellektual'nyye sistemy (II-2010): Mezhdunar. nauch.-tekhn. konf., 20-24 sentyabrya 2010 g.: materialy. – Donet k: IPII "Nauka o ta". 9. T.B. Martynyuk, V.V. Khomyuk (2010). Osobennosti matematicheskoy modeli diskretnogo SM-
preobrazovaniya. Matemati hn ma hini i temi, 4, 145-155. 10. Martinyuk T.B. (2000) ekur i n a oritmi ba atoo eran no obrobki nformat . V nnit ya:
UNÍVE SUM-V nnit ya. 11. T.B. Martinyuk, V.V. Khom’yuk, Í.M. Sa a yuk, D.V. Okhrushchak (1998). Vikori tannya zr z
r znit '
ya
ba atoo eran no o
o a annya
hi o ikh
e i hin. V nik
V nnit 'kogo
o tekhn hno o n titutu, 2, 63-68. 12. A.s. 1119035 SSSR, MKI5 G06G7/14. Sposob parallel'nogo slozheniya dlitel'nostey gruppy
vremennykh intervalov / V.P. Kozhemyako, L.I. Timchenko, T.V. Golovan', N.Ye. Furdiyak. T.B. Martynyuk: Vinnits. politekh. in-t. – № 3528903/18; zaya . 24.12.82; o ub . 15.10.84, Byu . № 38. 13. T.B. Martinyuk, A.V. Kozhem’yako, L.M. Ku er hteyn (2015). znit e o-zr zo a obrobka z
ikori tannyam rint i mo u yarno arifmetiki. V nik Khme 'nit 'ko o nat ona 'no o
un er itetu, 2, 165-168. 14. T.B. Martinyuk, V.V. Khom’yuk (2005). Metodi ta zasobi paralel'nikh peretvoren' vektornikh
ma i anikh. – V nnit ya: UNÍVE SUM-V nnit ya. y
y
15. Pat. 5495 Ukra na, MPK7 06 7/14. S o b ara e 'no o a ebra hno o o a annya tri a o tey
ru i ha o ikh nter a / A.S. Va yura, T.B. СПИСОК ЛІТЕРАТУРИ 15.03.2005, Бюл. № 3. 16. Пат. 70407 Україна, МПК7 G 06 G 7/14. Спосіб паралельного алгебраїчного додавання
тривалостей групи часових інтервалів / Т.Б. Мартинюк, В.В. Хом’юк, А.А. Яровий,
І.В. Хом’юк, О.Б. Мартинюк, Вінниц. нац. техн. ун-т. – № 2002086940; заявл. 23.08.2002;
опубл. 15.10.2004, Бюл. № 10. – 5 с. 17. Т.Б. Мартинюк, В.В. Хом’юк, Л.М. Куперштейн, Є.С. Матвєєв. (2002) Аналіз моделей
паралельного
підсумовування
елементів
числового
масиву. Вісник
Вінницького
політехнічного інституту, 6, 65-70. REFERENCES Martinyuk, L.V. Ku er hteyn, Í.V. Mi o 'kiy;
V nnit . nat . tekhn. un-t. – № 20040604914; zaya . 21.06.2004; o ub . 15.03.2005, Byu . № 3. ;
y
;
,
y
16. Pat. 70407 Ukra na, MPK7 06 7/14. S o b ara e 'no o a ebra hno o o a annya
tri a o tey ru i ha o ikh nter a / T.B. Martinyuk, V.V. Khom’yuk, A.A. Yaro iy, Í.V. 12 МЕТОДИ ТА СИСТЕМИ ОПТИКО-ЕЛЕКТРОННОЇ І ЦИФРОФОЇ ОБРОБКИ ЗОБРАЖЕНЬ ТА СИГНАЛІВ Khom’yuk, O.B. Martinyuk, V nnit . nat . tekhn. un-t. – № 2002086940; zaya . 23.08.2002; o ub . 15.10.2004, Byu . № 10. – 5 s. Khom’yuk, O.B. Martinyuk, V nnit . nat . tekhn. un-t. – № 2002086940; zaya . 23.08.2002; o ub . 15.10.2004, Byu . № 10. – 5 s. Khom’yuk, O.B. Martinyuk, V nnit . nat . tekhn. un-t. – № 2002086940; zaya . 23.08.2002; o ub . 15.10.2004, Byu . № 10. – 5 s. 18. T.B. Martinyuk, V.V. Khom’yuk, L.M. Kupershteyn, Ê.S. Matvêêv (2002). Anal z modeley
paralel'nogo
p dsumovuvannya
yelement v
chislovogo
masivu. V snik
V nnits'kogo
pol tekhn chnogo nstitutu, 6, 65-70. 18. T.B. Martinyuk, V.V. Khom’yuk, L.M. Kupershteyn, Ê.S. Matvêêv (2002). Anal z modeley
paralel'nogo
p dsumovuvannya
yelement v
chislovogo
masivu. V snik
V nnits'kogo
pol tekhn chnogo nstitutu, 6, 65-70. Надійшла до редакції 05.02.2018р. АНТОНІНА ГЕРОНІЇВНА БУДА – кандидат технічних наук, доцент кафедри системного
аналізу, комп`ютерного моніторингу та інженерної графіки, Вінницький національний
технічний університет, Вінниця, Україна АНТОНІНА ГЕРОНІЇВНА БУДА – кандидат технічних наук, доцент кафедри системного
аналізу, комп`ютерного моніторингу та інженерної графіки, Вінницький національний
технічний університет, Вінниця, Україна ТЕТЯНА БОРИСІВНА МАРТИНЮК – доктор технічних наук, професор кафедри
обчислювальної техніки, Вінницький національний технічний університет, Вінниця,
Україна ТЕТЯНА БОРИСІВНА МАРТИНЮК – доктор технічних наук, професор кафедри
обчислювальної техніки, Вінницький національний технічний університет, Вінниця,
Україна ЛЕОНИД МИХАЙЛОВИЧ КУПЕРШТЕЙН − кандидат технічних наук., доцент кафедри
захисту інформації, Вінницький національний технічний університет, Вінниця, Україна АНДРІЙ ВІКТОРОВИЧ КОЖЕМ’ЯКО − кандидат технічних наук, доцент кафедри
лазерної та опто-електронної техніки, Вінницький національний технічний університет,
Вінниця, Україна 13 13
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https://openalex.org/W2739719315
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https://zenodo.org/records/1423050/files/JDPS-4-148.pdf
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English
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Prospective clinical trial on the effectiveness of Topical Anesthetic in second stage surgeries of Dental Implants
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Journal of dental problems and solutions
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cc-by
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Abstract Objectives: The aim of this study is to evaluate the effectiveness of gel topical anaesthesia in second
surgeries of dental implants according to the different treated areas of the oral cavity, as well as the type
of oral mucosa in which is effective. Dates: Received: 19 June, 2017; Accepted: 28 June,
2017; Published: 29 June, 2017 Dates: Received: 19 June, 2017; Accepted: 28 June,
2017; Published: 29 June, 2017 *Corresponding author: Jordi Ortega-Martínez,
Faculty of Dentistry. Universitat Internacional de
Catalunya, Josep Trueta s/n 08195, Sant Cugat del
Vallès, Barcelona, Spain, E-mail: Material and methods: Thirteen partially and completely edentulous patients with 30 implants in
total were included in the study. The oral mucosa was dried and the anesthetic gel (Benzocaine 20%)
was applied with a cotton roll for 2 minutes. The effectiveness was evaluated with an exploratory probe. Those implants whose cover screw was not submerged in a depth higher than 2-4 mm were selected. In
the event of the gel topical anaesthesia not being effective, reinforcement with conventional infi ltrative
anaesthesia was made. Pain was measured with Visual Analogue Scales (VAS), and the gum thickness
with periodontal probe. A one-way Anova and a Pearson correlation were used to perform the statistical
analysis (p≤0.05). Keywords: Anaesthetics; Topical anaesthesia; Oral
mucosa; Dental implants; Second stage surgery https://www.peertechz.com Results: The 66.67% of the sample needed reinforcement through conventional anesthetic infi ltration. No statistically signifi cant differences were found in the comparison of pain with different gum thickness
(p=0.59), although a higher feeling of pain was actually observed in those patients who were fi rstly
subjected to a second-stage surgery (p=0.0335). Conclusion: The use of gel topical anaesthesia cannot be considered as the sole treatment to
eliminate the feeling of pain, but as a coadjuvant to infi ltrative anesthesia. No signifi cant differences
have been found between the different treated areas of the oral cavity, nor in the thickness or type of oral
mucosa. So far the use of topical anaesthesia in dentistry has been
more popular between those specialized in pediatric dentistry,
but the great demand of adult patients for an initial topical
anaesthesia to avoid pain produced by needle has lead to the
development by the chemical industry of gels and nebulizers
with ideal effectiveness and non-toxic for human beings
[1,6,8,9]. Topical anaesthesia acts on the terminal nervous
branches of the superfi cial mucosa [10,11]. Abstract Therefore, it can be
assumed that in an intervention affecting only this area, with
restricted depth, an unnecessary anesthetic puncture might be
avoided. Journal of Dental Problems and Solutions Jordi Ortega-Martínez1*, Elvira
Ferrés-Amat2, Eduard Ferrés-Padró3
and Federico Hernández-Alfaro4 Prospective clinical trial on the
effectiveness of Topical Anesthetic
in second stage surgeries of Dental
Implants 1Professor, Medicine, Surgery and Oral Implantology
Department, Dental School, International University
of Catalonia, Spain
2DDS, A. Professor, Medicine, Surgery and
Oral Implantology Department, Dental School,
International University of Catalonia, Spain
3Professor, Medicine, Surgery and Oral Implantology
Department, Dental School, International University
of Catalonia, Spain
4Professor and Head of Department of Medicine,
Surgery and Oral Implantology, Dental School,
International University of Catalonia, Spain 1Professor, Medicine, Surgery and Oral Implantology
Department, Dental School, International University
of Catalonia, Spain
2DDS, A. Professor, Medicine, Surgery and
Oral Implantology Department, Dental School,
International University of Catalonia, Spain
3Professor, Medicine, Surgery and Oral Implantology
Department, Dental School, International University
of Catalonia, Spain
4Professor and Head of Department of Medicine,
Surgery and Oral Implantology, Dental School,
International University of Catalonia, Spain 1Professor, Medicine, Surgery and Oral Implantology
Department, Dental School, International University
of Catalonia, Spain Clinical Group Journal of Dental Problems and Solutions https://www.peertechz.com ons
ISSN: 2394-8418
DOI
CC By Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectivenes
econd stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Inclusion and exclusion criteria Patients who were made a second surgical stage of dental
implants were included in the study. Therefore, the inclusion
criteria will be the same than the criteria of the fi rst stage. The
inclusion criteria for implant placement were the following:
patients with physical and psychical normality conditions,
partial or complete edentulous selected to be treated with
implants, non-smokers or controlled smokers (10 cigarettes
/day maximum), healthy patients or whose local or systemic
disease is controlled and does not contraindicate any type of
implantological oral surgery. Patient selection A data collection sheet was fi lled with the name, age, sex,
intervention date, implants details, gingival biotype and the
location are of the implant for every 13 patient, who also signed
an specifi c inform consent of the study. The pain perceived was recorded with the Visual Analogue
Scale (VAS), which comprises a 10 cm line representing the
continuous spectrum of the painful experience. The use of
infi ltrative anaesthesia required was also registered. The VAS
line can be vertical or horizontal terminating in right-angles
ends. Descriptions are to be found on the ends, being «no pain»
at one end and «the worst conceivable pain» at the other, with
no other description along the line [19,20]. The patient himself
indicates his personal experience of each implant by writing a
cross on the line. The specifi c inclusion criteria of the second-stage surgery
of dental implants were that of the patients who had been
subjected to a surgical treatment with implants and whose
healing screw was superfi cially submerged (up to 4 mm
measured with a periodontal probe once the topical anesthetic
has taken effect). Second-stage surgeries of dental implants are made in
implants that have been submerged placed and must be
uncovered through a second surgical act in order to conform
the surrounding mucosa and perform the prosthetic restoration
to be supported [13,14]. They are frequently made in a very thin
keratinized gum or free gingivae in which the implant cover
screw is visible, and rising up the periosteum is not necessary
to have it removed [15,16]. The patient comes from a dental
implant surgery in which has experienced several punctures. The trauma that might suffer the patient before a new puncture
to infi ltrate anaesthesia could be worse than applying topical
anaesthesia with a minimum surgical incision. All those patients who presented allergies to any type of
component of the anesthetics, pregnancy, those who had not
signed the surgery informed consent, who have had any type
of analgesic in the last 24 hours or who have had peri-implant
pathology during the healing period were excluded. Implant Location Several studies are focused on the possibility of avoiding this
second surgical act to simplify the treatment and for the sake
of convenience. Those studies compare both protocols (1 stage
vs. 2 stages), as well as its indications and contraindications,
although due to different clinical situations, such as the lack
of primary stability or absence of keratinized mucosa, second-
stage surgeries remain as an essential procedure [13,14,17,18]. Every measurement was made by the same researcher in
order to avoid discrepancies or possible bias. The evaluation
of the implant depth was visually made, whereas the probing
was carried out with a conventional exploratory probe in order
to localize the cover screw; the measurement was done with a
periodontal probe over the area, once the topical anaesthetic
had been applied and its effect checked. The aim of this study is to prove that the use of topical
anaesthesia is effective in oral surgical operations as second-
stages to uncover the cover screw of a dental implant when
it is already submerged. The null hypothesis is that topical
anaesthesia is insuffi cient to eliminate pain in second
surgeries of dental implants, and there are no differences in
the effectiveness between maxilla and mandible. The Scientifi c
Investigation Ethics Committee of the Universitat Internacional
de Catalunya has approved this study. Material and Methods In the event of pain during the measurement, an injected
anesthetic reinforcement (Ultracaín, 4% Articaine, Epinephrine
1:100.000, Laboratorios Normon S.A. Madrid, Spain) was
applied, thereby avoiding that feeling to the patient during the
treatment. Application of the anaesthetic solution A 0.12% Clorhexidine solution must be locally applied on
the area to be treated (where the dental implant is localized)
and dried with sterile gauze conventionally used in dentistry
in order to favour the diffusion of the anesthetic preparation. The preparation (Hurricaine, 20%, Benzocaine, Laboratorios
Clarben S.A. Madrid, Spain) impregnated in a cotton pellet was
applied onto the area during a period of at least 2-3 minutes. Introduction Pain is one of the most ancient worries of human being
and was considered as a natural event of human body. The
development of basic sciences allowed the control of pain to
carry out certain surgical acts [1]. In view of the need of painless dental treatments, turning to
anesthesiology becomes necessary. The percentage of patients
having fear of the anesthetic injection is especially high [1-4]. Topical anesthetic has been used for decades with certain
indications regarding intra-oral use, with the particular aim
of eliminating the painful feeling produced by the infi ltration
of other local anesthetics or the reduction of nauseas in
diagnostic procedures, which affect the pharyngeal area, such
as exploring the pharyngeal or laryngeal area or endoscopies of
high digestive via [1,2,5-7]. Currently, dental implants used in prosthetic oral
rehabilitation can be made in a surgical stage (with the healing
cap initially exposed to the oral medium) or in two surgical
stages (implant submerged under the gum and not exposed to
the oral cavity) [12-14]. 048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effe
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.00004 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectivenes
econd stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Pain vs. gingival thickness Figure 2: Differences in the degree of pain, considering if the patient had been
previously exposed to a second stage surgery. 050
017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
ttp://doi.org/10.17352/2394-8418.000048
Figure 1: Pie Chart: Percentage of the sample that needed conventional infi ltrative
anaesthetic reinforcement. Figure 2: Differences in the degree of pain, considering if the patient had been
previously exposed to a second stage surgery. Figure 1: Pie Chart: Percentage of the sample that needed conventional infi ltrative
anaesthetic reinforcement. Surgical technique If a depth higher than
2-4 mm is observed and the patient has not presented any
discomfort, we will start the incision on a surface covering the
dental implant with nº 3 fl at handle scalpel having a scalpel
blade of nº 15, 15c or 11. Once the implant was localized, its head
was released by adapting the mucosa to the abutment shape. A
circular scalpel or Punch having the diameter of the implant
head was occasionally used. After preparing the mucosa, the
cover screw is removed with a specifi c screwdriver and is placed
in the corresponding healing abutment. The intervention area
was sutured, if needed. Pain vs. First second surgery of the patient The
patient
was
not
subjected
to
any
additional
pharmacological treatment, so the only recommendations
were painkillers in case of discomfort and also following the
postoperative instructions. There were statistically signifi cant differences, since the
p-value was <0.05. Patients subjected for the fi rst time to a
second surgery felt more pain than those who had already
experienced a similar surgical act (Figure 2). Comparison of pain and different studied variables Pain was numerically considered (statistically speaking),
since it is a quantitative variable and a 0 - 9.9 range (mean
4.491) was showed according to the VAS pain measurement
scale (comprised between 0 and 10 when transformed to
numeral values). Whenever possible, the papillary regeneration technique
proposed by Palacci was made in the second-stage surgery. With this technique, a scalloped with gingival appearance and
a papillary formation is obtained since the beginning of the
surgery. It consists in pushing the keratinized gingivae from
the palate/lingual towards the buccal direction so as to increase
the tissue volume, thereby allowing the dissection and rotation
of the pedicle fl at, by falciform type incisions in the periimplant
areas, to subsequently create the interimplantar papillae [21]. The remaining studied variables were considered as feature
type due to its qualitative nature and therefore a graphic study
with a one-way Anova was carried out, comparing means,
median and standard deviations, except the gingival thickness,
because, being a quantitative value, a Pearson correlation or
multivariable analysis was carried out. Pain vs. gingival thickness Every analyzed data were moved to the Statgraphics Plus
5.1 program to carry out the statistical study. The statistical
study consisted in relating quantitative and qualitative
variables in a one-way Anova study (comparison of pain with
type of implant, gingival biotype, position in the arch, fi rst
surgery, sex and subject) and only quantitative variables, so a
correlation multivariable analysis was used (pain vs. gingival
thickness). The analysis made was multivariable or correlative,
because the nature of both variables is quantitative and tries
to group data with similar features and also observe if any of
the variables presents a p-value≤0.05. Neither statistically
signifi cant difference nor any type of relationship was found
(Figure 3). Figure 1: Pie Chart: Percentage of the sample that needed conventional infi ltrative
anaesthetic reinforcement. The percentage of patients who needed reinforcement
with conventional infi ltrative anesthetic was calculated
using tabulation and observing the bar diagram and the pie
diagram. The possible statistically signifi cant differences were
individually analyzed, between means and standard deviations. The P-value was calculated checking if it was ≤ 0.05 and the
charts were observed distinguishing between level code, means
and 95.0 percentages, LSD intervals and the box-and-whisker
plot. 050
Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048
The percentage of patients who needed reinforcement
with conventional infi ltrative anesthetic was calculated
using tabulation and observing the bar diagram and the pie
diagram. The possible statistically signifi cant differences were
individually analyzed, between means and standard deviations. The P-value was calculated checking if it was ≤ 0.05 and the
charts were observed distinguishing between level code, means
and 95.0 percentages, LSD intervals and the box-and-whisker
plot. Results
Thirteen patients were included in the present study (3 men
and 10 women, mean age 62.92±18.92), with a total amount of
30 implants. Each patient presented from 2 to 12 implants to
be rehabilitated. Every patient was treated with gel topical anesthetic
(Hurricaine, 20%, Benzocaine Laboratorios Clarben S.A. Madrid, Spain) and, in the event of not being effective, a
conventional anaesthetic technique was applied by infi ltration
(Ultracaín, 4% Articaine 1:100.000 Epinefrine, Laboratorios
Figure 1: Pie Chart: Percentage of the sample that needed conventional infi ltrative
anaesthetic reinforcement. Surgical technique Every patient underwent a previous radiographic control
(periapical radiograph or orthopantomography) to estimate
the localization, the conditions of the adjacent anatomic
structures and the osseointegration of those implants. At
the time of the surgery the implant was found visually,
radiographically and with a conventional exploratory probe. At this point of the intervention, the possible discomforts of
the patient were evaluated. Once the cover screw is localized,
we will proceed to measure the depth at which that screw is Those patients who had not signed the informed consent
of surgery and implants, those allergic to any component of
the conventional local anaesthesia (infi ltrative or topical),
having active neoplasia, uncontrolled systemic disease or
contraindicating the placement of dental implants were not
candidates for its placing and therefore a second surgery would
not be possibly done without a fi rst one. 049 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 placed with a periodontal probe (having marks which allow the
exact millimeter depth measurement). If a depth higher than
2-4 mm is observed and the patient has not presented any
discomfort, we will start the incision on a surface covering the
dental implant with nº 3 fl at handle scalpel having a scalpel
blade of nº 15, 15c or 11. Once the implant was localized, its head
was released by adapting the mucosa to the abutment shape. A
circular scalpel or Punch having the diameter of the implant
head was occasionally used. After preparing the mucosa, the
cover screw is removed with a specifi c screwdriver and is placed
in the corresponding healing abutment. The intervention area
was sutured, if needed. Normon S.A. Madrid, Spain). The 66.67% of the total amount of
implants required reinforcement with infi ltrative anaesthetic. Therefore, the data obtained in this study support the null
hypothesis, this is, that topical anesthetic is insuffi cient to
eliminate pain in second surgeries of dental implants, and
there are no differences in the effectiveness between maxilla
and mandible (Figure 1). placed with a periodontal probe (having marks which allow the
exact millimeter depth measurement). Discussion The application time of the agent on the area to be
treated has also been proved. A minimum of 2-3 minutes
and a maximum of 10-20 minutes on the area to be treated
is essential to obtain a proper effect [6,10,25]. An application
time equal or higher than 30 minutes can produce ulcerations
on the oral mucosa [28]. Pain is a defense mechanism of the human body produced
as a response in the face of an attack towards it. It is an
unpleasant subjective feeling present in our patients when
exposed to a surgical act [1]. Not only this, it is diffi cult for the
patient to exactly quantify the degree of pain suffered and also
a chronic pain, frequently related to a depressive condition of
the patient, is not valued in the same way than an acute pain
[3,19]. The palatal mucosa shows a higher resistance to the
effectiveness of local agents [6]. Topical anaesthetic does not
guarantee a pain-free treatment when it implies soft tissues
with a thickness higher than 5 mm [1,6], although other
studies note that the effectiveness does not exceed a depth of
2-3 mm [25]. Different measurement methods for rating pain have
been described with the aim of transforming the subjective
experience in an approximate objective. The subjective
measurement can be one-dimensional (intensity) or multi-
dimensional (intensity, quality, emotions). A great amount of
methods are available, such as the numerical scale described by
Downie in 1978, the simple descriptive scale by Keele in 1948
or the Visual Analogue Scale described by Huskinson in 1976
[19]. In our study, we decided to use the Visual Analogue Scale
(VAS), which is a continuous numeric one-dimension scale;
it is simple, solid, sensitive and reproducible, and therefore
useful for the reassessment of pain of the same patient but in
different moments [20]. Different studies mention the lack of alteration in the
perception of pain by some topical use anesthetics, because
it is a sensitive technical process, for the variability of pain
threshold in different patients, a poor effectiveness or an
application time lower than necessary [1,4,8]. An application of the local topical anaesthesia with the
proper dosing has not showed toxicity levels [1,9]. Results Thirteen patients were included in the present study (3 men
and 10 women, mean age 62.92±18.92), with a total amount of
30 implants. Each patient presented from 2 to 12 implants to
be rehabilitated. Every patient was treated with gel topical anesthetic
(Hurricaine, 20%, Benzocaine Laboratorios Clarben S.A. Madrid, Spain) and, in the event of not being effective, a
conventional anaesthetic technique was applied by infi ltration
(Ultracaín, 4% Articaine 1:100.000 Epinefrine, Laboratorios Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Figure 3: Multivariable analysis of pain and gingival thickness. reduce patient’s anxiety [2,8] but no study demonstrate its
effectiveness in second-stage surgeries to uncover dental
implants. It is proved that a great variety of anesthetic agents have
pharmacological effects, but there is no evidence of an ideal
topical agent [1]. 5% lidocaine is an effective topical agent and,
combined in 2.5% with 2.55% prilocaine is even more effective
[4]. The eutectic mixture of these amides, 2.5% lidocaine and
2.5% prilocaine (EMLA) is a commonly used agent [1,3,4,6]. 15% benzocaine (ester) with 1.7% amethocaine and 20%
benzocaine are also effective [6-8]. Discussion However,
they should not be applied in elderly patients, patients having
hypersensitivity to ester and amide-type anesthetics, patients
having allergy to paraminobenzoic acid, severe hypertension,
ventricular tachycardia, hyperthyroidism, bradycardia, partial
heart blocks, myocardial disease or severe arteriosclerosis [29]. The most common secondary effects are tissue irritation or
temporary taste disorders, although cases of cyanosis and even
anaphylactic shocks have been described [9]. Local anesthetics are those drugs, which act on a limited area
of the organism, depending on its application, and are divided
in topical and parenteral [1,9]. Developments of anesthetic
techniques, as well as the different application methods, have
allowed us having of a broad range of techniques available to
eliminate pain in different clinical situations. Starting from
the use of cocaine as an analgesic of choice drug, the procaine
synthesis by Alfred Einhorm in 1904 and later in 1948 the
lidocaine synthesis by Nils Löfgren, anesthetic solutions
have been evolving towards a more specifi c, scientifi c and
safe anesthesiology, thus allowing a regular use of anesthetic
techniques in medicine. Topical anesthetics are preparations of
high concentrations of local anaesthetics, which diffuse until
their arrival to the terminal nervous branches [1,9]. Dental implants inserted in the oral cavity with the aim
of being rehabilitated can be left exposed to the oral cavity in
the same surgical time or covered under the gum [14,30-32]. Several reasons justify that an implant should be left covered
and a second minor surgical act should be carried out, as
for instance, the lack of primary stability at the time of the
insertion, the presence of intra-oral factors that may lead to
premature uncontrolled or undesired loads on these implants
during the osseointegration stage, or the use of biomaterials
in the guided tissue/bone regeneration [13,14,31,32]. Another
important issue to justify a two-stage implant procedure is
the manipulation of the soft tissues around them for aesthetic
reasons or for the lack of keratinized gum around to provide
protection, facilitate hygiene and improve the long-term
prognostic [13,21]. Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Conclusions 8. Kohli K, Ngan P, Crout R, Linscott CC (2001) A survey of local and topical
anesthesia use by pediatric dentists in the United States. Pediatr Dent 23:
265-269. Link: https://goo.gl/XwDbCe The conclusions that might be extracted from this study
are: 9. Kravitz ND (2007) The use of compound topical anesthetics: a review. J Am
Dent Assoc 138: 1333-1339. Link: https://goo.gl/7mPq6g The use of gel topical anaesthesia (20% benzocaine) cannot
be considered as the sole treatment to eliminate the feeling of
pain, but as a coadjuvant to the infi ltrative anaesthesia. 66.67%
of the sample needed a conventional anaesthetic reinforcement
through puncture. 10. Bhalla J, Meechan JG, Lawrence HP, Grad HA, Haas DA (2009) Effect of
time on clinical effi cacy of topical anesthesia. Anesth Prog 56: 36-41. Link:
https://goo.gl/qNQQh9 11. Roller NW, Ship II (1975) Lidocaine topical fi lm strip for oral mucosal biopsies. J Oral Med 30: 55-58. Link: https://goo.gl/j3tUPd No signifi cant differences have been found in the
perception of pain between the different treated areas of the
oral cavity, between maxilla and mandible or between anterior
and posterior. 12. Abrahamsson I, Berglundh T, Moon IS, Lindhe J (1999) Peri-implant tissues
at submerged and non-submerged titanium implants. J Clin Periodontol 26:
600-607. Link: https://goo.gl/JVrg5T 13. Esposito M, Grusovin MG, Maghaireh H, Coulthard P, Worthington HV (2007)
Interventions for replacing missing teeth: management of soft tissues for
dental implants. Cochrane Database Syst Rev. Link: https://goo.gl/2mXZGw No statically signifi cant differences have been found in the
thickness and type of oral mucosa. 14. Esposito M, Grusovin MG, Martinis E, Coulthard P, Worthington HV (2007)
Interventions for replacing missing teeth: 1- versus 2-stage implant
placement. Cochrane Database Syst Rev. Link: https://goo.gl/krnmb1 Statistically signifi cant differences (p-value<0.05) have
been found in those patients who had not been subjected before
to this process of second-stage surgeries of implants. Patients
who had already experienced this treatment presented a lower
feeling of pain. The reason might be that those patients already
knew second-stage surgeries of implants, they were conscious
of its nature, therefore they faced the treatment more relaxed
and confi dent. Stress and anxiety could make the organism
react in a more emphasized way in the face of a treatment
unknown to the patient. 15. Oyster DK, Parker WB, Gher ME (1995) CO2 lasers and temperature
changes of titanium implants. J Periodontol 66: 1017-1024. Link:
https://goo.gl/CLe99J 16. Conclusions Yeh S, Jain K, Andreana S (2005) Using a diode laser to uncover
dental implants in second-stage surgery. Gen Dent 53: 414-417. Link:
https://goo.gl/y2RAHE 17. Fiorellini JP, Buser D, Paquette DW, Williams RC, Haghighi D, et al. (1999)
A radiographic evaluation of bone healing around submerged and non-
submerged dental implants in beagle dogs. J Periodontol 70: 248-254. Link:
https://goo.gl/RwyKpg There is a need of more clinical studies evaluating the topical
anesthetic in second-stage surgeries, however application
times should be changed, the anaesthetic agent concentration
and its absorption methods. 18. Weber HP, Buser D, Donath K, Fiorellini JP, Doppalapudi V, et al. (1996)
Comparison of healed tissues adjacent to submerged and non-submerged
unloaded titanium dental implants. A histometric study in beagle dogs. Clin
Oral Implants Res 7: 11-19. Link: https://goo.gl/Zdp82g The elimination of this second surgical act is the object
of study of many authors in order to avoid discomforts to the
patient and simplify the surgical technique. The comparison
of both protocols (1 stage vs. 2 stages), its indications and
contraindications, are also objects of different studies, without
statistically signifi cant differences so far [12-14,17,18]. If
covering the implant is unavoidable, there are different
techniques which have been studied with the aim of minimising
the disadvantages of this second surgical stage of the implants,
such as for instance the use of diode lasers, CO2 laser or the use
of punch type circular scalpel [15, 16], but there is no published
study regarding the use of a topical anesthetic agent. 4. Meechan JG, Thomason JM (1999) A comparison of 2 topical anesthetics
on the discomfort of intraligamentary injections: a double-blind, split-mouth
volunteer clinical trial. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 87:
362-365. Link: https://goo.gl/9Lc7En 5. Carr MP, Horton JE (2001) Clinical evaluation and comparison of 2 topical
anesthetics for pain caused by needle sticks and scaling and root planing. J
Periodontol 72: 479-484. Link: https://goo.gl/v123xU 6. Meechan JG (2002) Effective topical anesthetic agents and techniques. Dent
Clin North Am 46: 759-766. Link: https://goo.gl/4TQ9vY 7. Nusstein JM, Beck M (2003) Effectiveness of 20% benzocaine as a
topical anesthetic for intraoral injections. Anesth Prog 50: 159-163. Link:
https://goo.gl/tzVn6e Acknowledgement 19. Downie WW, Leatham PA, Rhind VM, Wright V, Branco JA, et al. (1978)
Studies with pain rating scales. Ann Rheum Dis 37: 378-381. Link:
https://goo.gl/wiXnJb The authors are very grateful for the valuable contribution
to this study and help from Carme Tronchoni. Discussion Scientifi c literature confi rms the effectiveness of topical
anaesthesia in superfi cial periodontal treatments [2,5,22,23],
placing the clamp in absolute isolations with rubber dam
[24], temporary orthodontic anchorages [25,26], biopsies
[3,11], decreasing painful feeling when needle insertion
[1,2,5,6,10], pediatric use [8], extraction of deciduous teeth
or abscess drainage [8], implant-abutment connection in
oral implantology [27], as well as a psychological tool to 051 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 References 20. Price DD, McGrath PA, Rafi i A, Buckingham B (1983) The validation of visual
analogue scales as ratio scale measures for chronic and experimental pain. Pain 17: 45-56. Link: https://goo.gl/umduVg 1. Meechan JG (2000) Intra-oral topical anaesthetics: a review. J Dent 28: 3-14. Link: https://goo.gl/qPamHH 21. Palacci P, Nowzari H (2008) Soft tissue enhancement around dental implants. Periodontol 2000 47: 113-132. Link: https://goo.gl/kJn9hB 2. Gunsolley JC (2005) The need for pain control during scaling and root
planing. Compend Contin Educ Dent 26: 3-5. Link: https://goo.gl/nVwhkH 2. Gunsolley JC (2005) The need for pain control during scaling and root
planing. Compend Contin Educ Dent 26: 3-5. Link: https://goo.gl/nVwhkH 22. Stoltenberg JL, Osborn JB, Carlson JF, Hodges JS, Michalowicz BS (2007)
A preliminary study of intra-pocket topical versus injected anaesthetic
for scaling and root planing. J Clin Periodontol 34: 892-896. Link:
https://goo.gl/7t6GEB 3. Meechan JG (2001) The use of EMLA for an intraoral soft-tissue
biopsy in a needle phobic: a case report. Anesth Prog 48: 32-34. Link:
https://goo.gl/ZhRxgH 052 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effe
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.0000 al. (2008) Ulceration of gingival mucosa after topical application of EMLA:
report of four cases. Br Dent J 204: 133-134. Link: https://goo.gl/5XV5sp 23. Svensson P, Petersen JK, Svensson H (1994) Effi cacy of a topical anesthetic
on pain and unpleasantness during scaling of gingival pockets. Anesth Prog
41: 35-39. Link: https://goo.gl/HQj8u3 29. Mehra P, Caiazzo A, Maloney P (1998) Lidocaine toxicity. Anesth Prog 45:
38-41. Link: https://goo.gl/HxD4jJ 29. Mehra P, Caiazzo A, Maloney P (1998) Lidocaine toxicity. Anesth Prog 45:
38-41. Link: https://goo.gl/HxD4jJ 24. Yoon RK, Chussid S (2009) Topical anesthesia for rubber dam clamp
placement in sealant placement: comparison of lidocaine/prilocaine gel and
benzocaine. Pediatr Dent 31: 377-381. Link: https://goo.gl/UM4KSm 30. Branemark PI, Hansson BO, Adell R, Breine U, Lindstrom J, et al. (1977)
Osseointegrated implants in the treatment of the edentulous jaw. References Experience
from a 10-year period. Scand J Plast Reconstr Surg Suppl 16: 1-132. Link:
https://goo.gl/QkcfVW 25. Kravitz ND, Kusnoto B (2006) Placement of mini-implants with topical
anesthetic. J Clin Orthod 40: 602-604. Link: https://goo.gl/H4ST3U 26. Reznik DS, Jeske AH, Chen JW, English J (2009) Comparative effi cacy of 2
topical anesthetics for the placement of orthodontic temporary anchorage
devices. Anesth Prog 56: 81-85. Link: https://goo.gl/Nbk2WY 31. AlKhafagy HH (2010) Infl uence of cancellous bone rigidity on stress
distribution in bone around dental implant: a fi nite element study. J Int Dent
Med Res 3: 11-14. Link: https://goo.gl/7UESDm 31. AlKhafagy HH (2010) Infl uence of cancellous bone rigidity on stress
distribution in bone around dental implant: a fi nite element study. J Int Dent
Med Res 3: 11-14. Link: https://goo.gl/7UESDm 27. Berteretche MV, Hue O (2009) Topical anesthesia for prosthetic implant
procedures. J Prosthet Dent 102: 128-129. Link: https://goo.gl/DbfR41 32. Zortuk M, Kilic E, Yildiz P, Leblebicioglu I (2011) Effect of parafunctional force
on dental implant treatment in bruxism: a case report (two year results). J Int
Dent Med Res 4: 25-29. Link: https://goo.gl/V3Y2Gm 32. Zortuk M, Kilic E, Yildiz P, Leblebicioglu I (2011) Effect of parafunctional force
on dental implant treatment in bruxism: a case report (two year results). J Int
Dent Med Res 4: 25-29. Link: https://goo.gl/V3Y2Gm 32. Zortuk M, Kilic E, Yildiz P, Leblebicioglu I (2011) Effect of parafunctional force
on dental implant treatment in bruxism: a case report (two year results). J Int
Dent Med Res 4: 25-29. Link: https://goo.gl/V3Y2Gm 28. Franz-Montan M, Ranali J, Ramacciato JC, de Andrade ED, Volpato MC, et Copyright: © 2017 Ortega-Martínez J, et al. This is an open-access article distributed under the terms of the Creative Commons At
nrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 053 Citation: Ortega-Martínez J, Ferrés-Amat E, Ferrés-Padró E, Hernández-Alfaro F (2017) Prospective clinical trial on the effectiveness of Topical Anesthetic in
second stage surgeries of Dental Implants. J Dent Probl Solut 4(3): 048-053. DOI: http://doi.org/10.17352/2394-8418.000048
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Idiopathic Ketotic Hypoglycemia
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Definitions
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Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Open Peer Review on Qeios Idiopathic Ketotic Hypoglycemia National Cancer Institute Qeios ID: P4XT69 · https://doi.org/10.32388/P4XT69 Source National Cancer Institute. Idiopathic Ketotic Hypoglycemia. NCI Thesaurus. Code
C131855. Ketotic hypoglycemia that usually occurs in young, thin children in association with
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Motor planning error in Parkinson's disease and its clinical correlates
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RESEARCH ARTICLE a1111111111
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a1111111111 Motor planning error in Parkinson’s disease
and its clinical correlates Tsubasa Kawasaki*, Kyohei Mikami¤a, Tsutomu Kamo¤a, Ryoma Aoki¤a,
Rumiko Ishiguro¤a, Hiroshi Nakamura¤b, Ryosuke Tozawa¤b, Nao Asada¤b,
Yukinobu Hiiragi¤b, Yoichi Yamada¤b, Masahiro Hirano¤b, Kazuko Katsuki¤b Tsubasa Kawasaki*, Kyohei Mikami¤a, Tsutomu Kamo¤a, Ryoma Aoki¤a,
Rumiko Ishiguro¤a, Hiroshi Nakamura¤b, Ryosuke Tozawa¤b, Nao Asada¤b,
Yukinobu Hiiragi¤b, Yoichi Yamada¤b, Masahiro Hirano¤b, Kazuko Katsuki¤b Tsubasa Kawasaki*, Kyohei Mikami¤a, Tsutomu Kamo¤a, Ryoma Aoki¤a,
Rumiko Ishiguro¤a, Hiroshi Nakamura¤b, Ryosuke Tozawa¤b, Nao Asada¤b,
Yukinobu Hiiragi¤b, Yoichi Yamada¤b, Masahiro Hirano¤b, Kazuko Katsuki¤b Institute of Sports Medicine and Science, Tokyo International University, Matoba, Kawagoe-shi, Saitama,
Japan ¤a Current address: Noborito Neurology Clinic, 434 Nobotitoshinmachi, Tama-ku, Kawasaki, Kanagawa,
Japan
¤b Current address: Department of Physical Therapy, Faculty of Health Science, Ryotokuji University, 5-8-1
Akemi, Urayasu-City, Chiba, Japan
* kawasaki.283@gmail.com ¤a Current address: Noborito Neurology Clinic, 434 Nobotitoshinmachi, Tama-ku, Kawasaki, Kanagawa,
Japan
¤b Current address: Department of Physical Therapy, Faculty of Health Science, Ryotokuji University, 5-8-1
Akemi, Urayasu-City, Chiba, Japan
* kawasaki.283@gmail.com Japan
¤b Current address: Department of Physical Therapy, Faculty of Health Science, Ryotokuji University, 5-8-1
Akemi, Urayasu-City, Chiba, Japan
* kawasaki.283@gmail.com a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 Abstract This study aimed to investigate (a) motor planning difficulty by using a two-step test in Par-
kinson’s disease (PD) compared with age-matched healthy subjects and (b) the relationship
between motor planning difficulty and clinical factors. The two-step test was performed by
58 patients with PD with Hoehn & Yahr (H&Y) stage I–IV and 110 age-matched healthy
older adult controls. In the two-step test, the participants estimated the two-step distance
with maximum effort. Subsequently, they performed the actual two-step trial to measure the
actual maximum distance. We calculated the accuracy of the estimation (estimated distance
minus actual distance). In both groups, subjects who estimated >5 cm were defined as the
overestimation group, and those who estimated <5 cm over- and underestimation were
defined as the non-overestimation group. The overestimation group consisted of 17 healthy
older adults (15.5%) and 23 patients with PD (39.7%). The number of patients with PD with
overestimation was significantly more than that of healthy controls by Chi-squared test. H&Y stage and the Unified Parkinson’s Disease Rating Scale (UPDRS) part II and III scores
in overestimation group in PD patients were significantly higher than those in overestimation
group in PD patients. Moreover, multiple regression using H&Y stage and UPDRS parts II
and III as independent variables showed that the UPDRS part II score was the only related
factor for the estimation error distance. Estimation error distance was significant correlated
with UPDRS parts II and III. Patients with PD easily have higher rates of motor-related over-
estimation than age-matched healthy controls. In addition, UPDRS parts II and III expressed
ability of activities of daily living and motor function as influences on motor-related overesti-
mation. Particularly, multiple regression indicated that UPDRS part II directly showed the
ability of daily living as an essential factor for overestimation. OPEN ACCESS Citation: Kawasaki T, Mikami K, Kamo T, Aoki R,
Ishiguro R, Nakamura H, et al. (2018) Motor
planning error in Parkinson’s disease and its
clinical correlates. PLoS ONE 13(8): e0202228. https://doi.org/10.1371/journal.pone.0202228 Editor: Wing-ho Yung, Chinese University of Hong
Kong, HONG KONG Introduction Patients with Parkinson’s disease (PD) present with motor disorders, such as resting tremor,
bradykinesia, rigidity, and postural instability [1], and other typical motor symptoms showing
abnormal gait freezing gait, and motor coordination deficits [1, 2]. Some cognitive dysfunc-
tions may be observed in addition to these motor symptoms. A representative cognitive dys-
function is decline in executive function, which is a part of frontal brain function and refers to
the cognitive control of behavior: selecting and successfully monitoring behaviors that facili-
tate the attainment of chosen goals. Lezak has stated that executive function includes goal set-
ting, motor planning, and effective motor execution [3]. Some previous studies reported that
individuals with PD have decreased brain ability in the frontal lobe and striatum [4, 5], thus
influencing their cognitive dysfunction [6–8]. In the present study, we focused on the executive function of motor prediction based on work-
ing memory and motor-related strategic thinking. In a previous study, although movement accu-
racy did not decline, they prolonged the time until movement by using the Tower of London task
[9]. Based on the results, patients with PD have been suggested to have difficulty in the motor pre-
diction of operating figures [9]. Furthermore, Owen et al. then focused on severe PD in the inves-
tigation of decreased motor prediction and reported that patients with severe PD particularly had
a difficulty in motor execution accuracy of the task in addition to motor prediction delay [10]. These results suggested that severity of PD affected motor prediction and function. e results suggested that severity of PD affected motor prediction and function. The effects of motor prediction disorder in patients with PD are shown not only in opera-
tion of figures but also in action imitation tasks. For example, using apraxia testing, Golden-
berg et al. have reported that patients with PD had impaired ability of action imitation [11]. These previous studies have shown that patients with PD had difficulty in motor prediction by
using executive function. Difficulty of motor prediction affect some actual movement disabilities. Cohen et al. reported that patients with PD frequently made a judgment error on whether they could pass
an aperture without collisions. This result showed the difficulty of motor prediction in patients
with PD, indicating that the judgment error would result in freezing gait [12]. Kameda et al. Editor: Wing-ho Yung, Chinese University of Hong
Kong, HONG KONG Copyright: © 2018 Kawasaki et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. Data Availability Statement: All Fig and Table files
are available from the Figshare database (DOI: 10. 6084/m9.figshare.6203900). Funding: The authors received no specific funding
for this work. Competing interests: The authors have declared
that no competing interests exist. Competing interests: The authors have declared
that no competing interests exist. 1 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Motor planning and clinical symptoms in Parkinson’s disease Introduction measured the amounts of discordance between motor prediction and motor execution of for-
ward reach distance (functional reach distance), reporting that overestimation (prediction
distance > actual distance) leads to a high frequency of falls in patients with PD [13]. Through
these studies, movement disabilities in patients with PD have been suggested to be related to
motor prediction error, including motor-related overestimation. However, whether a factor is associated with motor prediction error is still unclear. Identifi-
cation of the factor associated with motor prediction error would contribute in the determina-
tion of the mechanisms of movement disability (freezing gait or falling) directly affecting
activity of daily living. In the present study, we used a two-step test to measure motor predic-
tion error [14]. The reliability of the two-step test, which was developed to judge the require-
ment of nursing care in Japan, or being at risk of doing so, due to a decline in mobility,
resulting from a musculoskeletal system disorder, has been confirmed [14]. Subsequently, we tion error [14]. The reliability of the two-step test, which was developed to judge the require-
ment of nursing care in Japan, or being at risk of doing so, due to a decline in mobility,
resulting from a musculoskeletal system disorder, has been confirmed [14]. Subsequently, we
investigated whether motor prediction was related to the factors of PD (severity, duration, cog-
nitive function, or motor function). resulting from a musculoskeletal system disorder, has been confirmed [14]. Subsequently, we
investigated whether motor prediction was related to the factors of PD (severity, duration, cog-
nitive function, or motor function). Overall, 58 patients with PD (26 men and 32 women; mean age, 73.0 ± 7.4 years) and 110 age-
matched healthy elderly subjects (21 men and 89 women; mean age, 72.8 ± 6.7 years) Subjects Overall, 58 patients with PD (26 men and 32 women; mean age, 73.0 ± 7.4 years) and 110 age-
matched healthy elderly subjects (21 men and 89 women; mean age, 72.8 ± 6.7 years) 2 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Motor planning and clinical symptoms in Parkinson’s disease participated in the present study. Cognitive function was assessed using the Mini-Mental State
Examination (MMSE) and Six-item test. MMSE was used for patients with PD and elderly sub-
jects, and six-item score was used only for elderly subjects. Note that, for control subjects, the
six-item score was used as a screening for dementia. Subjects who scored fewer than three
points in the six-item test were administered the MMSE to assess details of their cognitive
function. In all patients with PD, MMSE was first used to accurately assess cognitive function
following traditional methods. The exclusion criteria were (a) cognitive impairment MMSE
score <23 [15], and six-item score <3 [16]); and (b) visual impairment influence with action. In addition to the criteria, Hoehn and Yahr (H&Y) stage >4 was excluded for patients with
PD [17]. These criteria were set to carry out a motor-prediction task exactly using a two-step-
forward task (see below for details). The tenets of the Declaration of Helsinki were followed,
and participants provided informed consent before study participation. Preliminary results and one implication Rate of female and male in overestimation group in PD patients was 60.9% (14/23) and 39.1%
(9/23) respectively. No significant gender difference was observed by the Pearson’s Chi-
squared (p = 0.12). In the same manner as PD patients, the rate of female and male in overesti-
mation group in control subjects was 70.6% (12/17) and 29.4% (5/17), respectively. No signifi-
cant gender differences were observed by the Pearson’s Chi-squared (p = 0.24). This suggests
that there was no possibility for impact of gender on overestimation. Procedure First, the subjects performed a two-step test (measuring estimation and actual distance) (Fig
1). All subjects were instructed to predict the distance that they can perform two-step forward
as far as possible with maximum effort. The subjects indicated the prediction point using a
laser pointer, and the examiner measured the predicted distance. The actual two-step distance
was subsequently measured. When the subjects performed the actual two-step performance, Fig 1. Schematic illustration of the two-step test. Participants estimated the two-step distance forward with maximum effort and indicated the distance using a laser
pointer. After the estimation, the actual distance was measured. https://doi.org/10.1371/journal.pone.0202228.g001 Fig 1. Schematic illustration of the two-step test. Participants estimated the two-step distance forward with maximum effort and indicated the distance using a laser
pointer. After the estimation, the actual distance was measured. https://doi.org/10.1371/journal.pone.0202228.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 3 / 10 Motor planning and clinical symptoms in Parkinson’s disease they were instructed to put their legs together to stand still before and after taking the two
steps forward. For each patient, we also identified Unified Parkinson’s Disease Rating Scale
(UPDRS) part I–III scores [18], H&Y stage, MMSE score, and L-dopa dose (mg/day). Statistical analyses non-overestimated control group) regarding estimation distance, actual distance,
and estimation error distance to determine details of the overestimation in patients with PD. p
For each UPDRS (I–III) score, the Mann–Whitney U test was performed to analyze the
H&Y stage, duration of PD, L-dopa dose, and MMSE. Variables showing significant difference
in the statistical analyses were used for Pearson’s correlation analysis with estimation error
and also utilized as predictor variables in multiple regression of estimation error distance. We used SPSS for Windows (version 17.0; SPSS Inc., Chicago. IL, USA) for all statistical
analyses and set the statistical significance at p < 0.05. This study was approved by the Ethics
Committee of the Japan Primary Care Association (approval, 2017–006) and Ryotokuji Uni-
versity (approval, 2829). For each UPDRS (I–III) score, the Mann–Whitney U test was performed to analyze the
H&Y stage, duration of PD, L-dopa dose, and MMSE. Variables showing significant difference
in the statistical analyses were used for Pearson’s correlation analysis with estimation error
and also utilized as predictor variables in multiple regression of estimation error distance. We used SPSS for Windows (version 17.0; SPSS Inc., Chicago. IL, USA) for all statistical
analyses and set the statistical significance at p < 0.05. This study was approved by the Ethics
Committee of the Japan Primary Care Association (approval, 2017–006) and Ryotokuji Uni-
versity (approval, 2829). Statistical analyses The estimation error (estimation distance [cm] minus actual distance [cm]) was calculated. The subjects with accuracy of estimation of >5 cm and <5 cm were classified into the overesti-
mation and non-overestimation groups, respectively. The criteria of this definition were
derived from evidence that the prediction distance using the laser pointer had a measurement
margin of error of 5 cm in our unpublished preliminary study. Exactly indicating the estima-
tion distance was difficult because of tremors in some patients with PD. That is, we believe that
some margin (±5 cm) is necessary in the judgment of overestimation or non-overestimation. For preliminary analyses, to demonstrate whether gender influences overestimation, the
number of female subjects with overestimation was analyzed using Pearson’s Chi-squared test
(X2) with Yates’ correction. This is why the gender ratio was completely different in the two
groups (patients with PD and healthy control groups); there were more females in the control
group than in the PD group. Pearson’s Chi-squared test (X2) with Yates’ correction was also conducted to examine
whether patients with PD had overestimation as compared with healthy control subjects. The
number of subjects with overestimation was analyzed in the two groups of subjects (patients
with PD vs. healthy control subjects). A one-way analysis of variance (ANOVA) followed by the Bonferroni post hoc test was con-
ducted with groups (overestimated vs. non-overestimated PD group vs. overestimated control
group vs. non-overestimated control group) regarding estimation distance, actual distance,
and estimation error distance to determine details of the overestimation in patients with PD. For each UPDRS (I–III) score, the Mann–Whitney U test was performed to analyze the
H&Y stage, duration of PD, L-dopa dose, and MMSE. Variables showing significant difference
in the statistical analyses were used for Pearson’s correlation analysis with estimation error
and also utilized as predictor variables in multiple regression of estimation error distance. We used SPSS for Windows (version 17.0; SPSS Inc., Chicago. IL, USA) for all statistical
analyses and set the statistical significance at p < 0.05. This study was approved by the Ethics
Committee of the Japan Primary Care Association (approval, 2017–006) and Ryotokuji Uni-
versity (approval, 2829). A one-way analysis of variance (ANOVA) followed by the Bonferroni post hoc test was con-
ducted with groups (overestimated vs. non-overestimated PD group vs. overestimated control
group vs. Motor planning and clinical symptoms in Parkinson’s disease esults of two-step test of control groups (non-overestimation and overestimation) and patients with PD groups (non-
± SD) Table 1. Demographic clinical details and results of two-step test of control groups (non-overestimation and overestimation) and patients with PD groups (non-
overestimation and overestimation) (mean ± SD). Controls
PD patients
Overestimation
Non-overestimation
Overestimation
Non-overestimation
Number
17
93
23
35
Age (years)
72.33 ± 6.28
75.35 ± 8.57
73.5 ± 8.26
71.72± 8.98
Gender (female)
12
77
14
14
MMSE
― §
― §
27.57 ± 2.37
28.11 ± 1.95
Hoehn-Yahr stage
―
―
2.91± 0.70 ‡
2.50± 0.70
Duration of disease(months)
―
―
7.87 ± 6.02
5.77 ± 5.75
Drugs (levodopa equivalent doses (mg)
―
―
443.18 ± 164.24
366.18 ± 154.10
UPDRS part I
―
―
2.87 ± 2.16
2.03 ± 1.76
UPDRS part II
―
―
10.87± 5.35 ‡
6.46 ± 3.97
UPDRS part III
―
―
23.65± 10.71 ‡
15.20 ± 9.90
Estimation distance (cm)
237.94 ± 33.21
179.84 ± 31.90
163.26 ± 41.69
151.86 ± 38.39 , †
Actual distance (cm)
210.53 ± 24.94
210.68 ± 30.44
139.35 ± 41.04 , †, ‡
175.14 ± 40.28 , †
Estimation error distance (cm)
27.41± 18.22
-30.84 ± 22.90
23.91 ± 16.54 †, ‡
-20.29 ± 18.19 , †
comparing with overestimation group in control subjects (p < .05)
† comparing with non-overestimation group in control subjects (p < .05)
‡ comparing with non-overestimation group in PD patients (p < .05): Bonferroni correction was applied. § Six-item score was used instead of MMSE to screen for dementia. MMSE: Mini Mental State Examination; UPDRS: Unified Parkinson’s Disease Rating Scale
https //doi org/10 1371/jo rnal pone 0202228 t001 comparing with overestimation group in control subjects (p < .05) https://doi.org/10.1371/journal.pone.0202228.t001 overestimation in patients with PD was significantly higher than that in age-matched healthy
control subjects (p = 0.005). With regard to estimation distance, a one-way ANOVA showed a significant main effect of
the group F(3, 167) = 24.72, p < 0.0001. Post-hoc analysis showed that estimation distance in
the overestimation and non-overestimation groups in patients with PD and non-overestima-
tion group in control subjects was lesser than the overestimation group in control subjects
(overestimation group in patients with PD vs. that in control subjects: t(164) = 6.69, p <
0.0001; non-overestimation group in PD patients vs. Main results The characteristics of all subjects and results of the two-step test are shown in Table 1. The
rates of overestimation in PD patients and control subjects were 39.7% (23/58) and 15.5%
(17/110), respectively. The Pearson’s Chi-squared test showed that the percentage of 4 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Motor planning and clinical symptoms in Parkinson’s disease and the non-overestimation group in control subjects: t(165) = 1.22, p = 0.23; t(164) = 2.04,
p = 0.04, respectively (Table 1). With regard to actual distance, a one-way ANOVA showed a significant main effect of the
group F(3, 167) = 31.99, p < 0.0001. Post hoc analysis showed that actual distance in the over-
estimation and non-overestimation groups of PD patients was significantly less than that in
the overestimation group in control subjects (t(164) = 6.53, p < 0.0001; t(164) = 3.51, With regard to actual distance, a one-way ANOVA showed a significant main effect of the
group F(3, 167) = 31.99, p < 0.0001. Post hoc analysis showed that actual distance in the over-
estimation and non-overestimation groups of PD patients was significantly less than that in
the overestimation group in control subjects (t(164) = 6.53, p < 0.0001; t(164) = 3.51,
p = 0.0006, respectively). The actual distance in the overestimation group in PD patients was
significantly smaller than those in the non-overestimation group in PD patients and control
subjects (t(164) = 3.91, p < 0.0001; t(164) = 8.98, p < 0.0001, respectively). The actual distance
in the non-overestimation group in PD patients was significantly smaller than that in control
subjects (t(164) = 5.25, p < 0.0001) (Table 1). There was no significant difference between
overestimation and non-overestimation groups in control subjects (t(164) = 0.02, p = 0.99). With regard to the estimation error distance, a one-way ANOVA also showed a significant
main effect of the group F(3, 167) = 69.23, p < 0.0001. Post hoc analysis showed no significant
difference between the overestimation groups in PD patients and control subjects (t(164) =
0.53, p = 0.60)) and between non-overestimation groups in PD patients and control subjects (t
(164) = 2.56, p = 0.01). On the other hand, the estimation error distances in the overestimation
groups of PD patients and control subjects were significantly larger than that in the non-over-
estimation group in control subjects (t(164) = 11.31, p < 0.0001; t(164) = 10.63, p < 0.0001,
respectively). Similarly, the estimation error differences in the overestimation groups in PD
patients and control subjects were significantly larger than that in the non-overestimation
group in PD patients (t(164) = 7.92, p < 0.0001; t(164) = 7.76, p < 0.0001, respectively). The identified data were compared between the overestimation and non-overestimation
groups in patients with PD. Table 1 also shows the result of comparisons between the overesti-
mation and non-overestimation groups. The result showed that the H&Y stage (p = 0.04) and
UPDRS parts II (p = 0.002) and III (p = 0.005) in the overestimation group were significantly
higher than those in the non-overestimation group. In contrast, no difference was found
between the two groups in MMSE (p = 0.34), duration of PD (p = 0.19), L-dopa dose
(p = 0.08), and UPDRS part I (p = 0.15). The H&Y stage and UPDRS parts II and III showed significant differences between the two
groups in patients with PD, and these were used for Pearson’s correlation analysis with estima-
tion error. Results showed that the estimation error significantly correlated with UPDRS part
II and III scores (r = 0.43 and 0.30, respectively), but not at the H&Y stage (r = 0.17) (Fig 2). Also, the three dependent variables were also used as independent variables in a linear mul-
tiple regression analysis. Results showed the regression equation obtained in the estimation
error distance (−22.689 + 2.428 × UPDRS part II score, R2 = 0.19). The UPDRS part II score
was significantly associated with the estimation error (p < 0.001). overestimation group in control subjects:
t(164) = 8.36, p < 0.0001); non-overestimation group vs. overestimation group in control sub-
jects: t(164) = 6.31, p < 0.0001). Non-overestimation group in control subjects was significant
greater than that in PD patients: t(164) = 4.04, p < 0.0001), whereas no significant differences
between the overestimation and non-overestimation groups in PD patients, and between over-
estimation group in PD patients and non-overestimation group in control subjects were
observed: t(165) = 1.22, p = 0.23; t(164) = 2.04, p = 0.04, respectively (Table 1). With regard to estimation distance, a one-way ANOVA showed a significant main effect of
the group F(3, 167) = 24.72, p < 0.0001. Post hoc analysis showed that estimation distances in
the overestimation and non-overestimation groups in patients with PD and the non-overesti-
mation group in control subjects were less than that in the overestimation group in control
subjects (overestimation group in patients with PD vs. that in control subjects: t(164) = 6.69,
p < 0.0001; non-overestimation group in PD patients vs. overestimation group in control
subjects: t(164) = 8.36, p < 0.0001); non-overestimation group vs. overestimation group in
control subjects: t(164) = 6.31, p < 0.0001). The estimation distance in the non-overestimation
group in control subjects was significantly greater than that in PD patients: t(164) = 4.04,
p < 0.0001), whereas there were no significant differences between the overestimation and
non-overestimation groups in PD patients or between the overestimation group in PD patients 5 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Discussion In the present study, we verified motor prediction error in patients with PD and the associa-
tion between the motor prediction error and clinical factors. The result showed that more
patients with PD overestimated their own motor performance compared with healthy control
subjects. This result was supported by a previous report that showed the decreased ability of
motor prediction in patients with PD: a previous study verifying motor prediction error in
patients with PD using forward reach task (functional reach task) reported that they estimated
higher motor performance than actual motor performance comparing with age-matched
healthy control subjects [13]. The results in the previous report were consistent with the pres-
ent study. This confirms that the two-step test could be available to measure the accuracy of 6 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Motor planning and clinical symptoms in Parkinson’s disease Fig 2. Scattergrams of the estimation error distance, and H&Y stage (upper left), and UPDRS part II (upper right) and III (lower). https://doi.org/10.1371/journal.pone.0202228.g002 Fig 2. Scattergrams of the estimation error distance, and H&Y stage (upper left), and UPDRS part II (upper right) and III (lower). https://doi.org/10.1371/journal.pone.0202228.g002 Fig 2. Scattergrams of the estimation error distance, and H&Y stage (upper left), and UPDRS part II (upper right) and III (lower). https://doi.org/10.1371/journal.pone.0202228.g002 motor estimation, and that patients with PD have overestimation compared with healthy con-
trol subjects. Results in accuracy of estimated distance compared among four groups (overestimation
and non-overestimation × PD patients and control subjects) showed that the estimation error
distances of overestimated PD patients and control subjects were higher than those of the
other two groups (non-overestimation groups in PD patients and control subjects). The esti-
mation distance was not significantly different among the two PD groups and the non-overes-
timation group in control subjects, whereas, the actual distance of the overestimation group in
PD patients was significantly smaller than that of non-overestimation groups in PD patients
and control subjects, i.e., the two-step performance of the overestimation group in PD patients
was significantly lower than that in the non-overestimation group. Based on the results, over-
estimation in PD patients is suggested to be caused by the decrease of motor performance. Consistent with previous studies [19, 20], overestimation was observed in healthy elderly
people; as stated above, the number of PD patients who overestimated was significantly more
than that in healthy controls. PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Discussion Taken together with these results, this suggests that overestima-
tion in PD subjects would be caused by the onset of PD in addition to the effects of natural
aging. Comparing the overestimation group with the non-overestimation group in identified data,
significant higher H&Y stage and UPDRS parts II and III were shown, whereas duration of dis-
ease, L-dopa dose, MMSE, and UPDRS part I were not different. These results suggested that
the accuracy of motor estimation was involved in the H&Y stage and UPDRS parts II and III. 7 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Motor planning and clinical symptoms in Parkinson’s disease These variables expressed the severity of PD associated with motor function. Variables that
showed no significant difference (i.e., L-dopa dose, MMSE, and UPDRS part I) were consis-
tently non-motor function-related. H&Y stage showed the severity of PD as assessed by motor
symptoms. UPDRS parts II and III expressed the ability of activity of daily living and move-
ment disorder, respectively. Considering characteristics of these variables, the accuracy of
motor estimation is associated with severity of PD involved in motor function. Although these
statements are plausible, the lack of correlation between the estimation error distance and
H&Y stage by Pearson’s correlation analysis must be considered; this distance was correlated
with only UPDRS parts II and III. This supports an association between estimation error and
ability of activity of daily living and movement disorder, whereas concluding that the degree of
estimation error correlates with the severity of PD would be premature. Future research is
needed to additionally investigate the relationship between estimation error and the H&Y
stage, i.e., the severity of PD. The reason for the association between the accuracy of motor estimation and progress of
motor-related symptoms may involve difficulty of upload (recognition). This decreases their
motor performance based on the progress of PD. Generally, progress of PD leads to low physi-
cal activity, which means that patients with PD are considered to lose their ability of uploading
their motor performance. Sakurai et al. has reported that older adults with high risk of falling
have overestimation in the step-over test, suggesting that poor physical activity might be
avoided through participation in physical activity in daily living, and these lifestyles would
limit the recognition of the current activity [20]. Discussion Taking these statements together, patients
with PD tend to maintain their own recognition of current motor performance (i.e., current
motor performance was not uploaded before onset of PD). As a result, patients with severe PD
have low motor performance and overestimation. Particularly, multiple regression analysis showed that the accuracy of motor estimation sig-
nificantly was associated with UPDRS part II. The coefficient of multiple determination (R2)
value was 0.19, which was relatively low; however, the standardized regression coefficient (β)
value was 0.43, suggesting that the accuracy of motor estimation and UPDRS part II expressed
that the ability of daily living has a medial relationship [21]. A previous study showed that the
executive function in PD was related to UPDRS part II [8]. The present study was consistent
with the previous study. This showed that executive function, including motor estimation, is
involved in UPDRS part II, which expresses the ability of activity of daily living that is required
to sequence motion based on motor planning (executive function). In the two-step test proce-
dure, the patients with PD were also instructed to execute after estimating their own perfor-
mance. Therefore, UPDRS part II would be shown as a predictor variable because this
procedure included the process of motor planning (executive function). In conclusion, the present study determined that (a) the frequency of overestimation in
patients with PD was higher than that in healthy elderly people, and (b) the overestimation in
PD was associated with motor-related severely (H&Y stage and UPDRS parts II and III). These
results suggest that overestimation (which often causes falls) may be influenced by the progress
of motor-related symptoms in patients with PD. However, whether interventions that address
motor-related symptoms directly contribute to fall prevention remains unclear. Future studies
should be conducted on the prevention effects of motor-related symptom interventions, espe-
cially with respect to falling risk in patients with PD. Writing – review & editing: Tsubasa Kawasaki. Writing – review & editing: Tsubasa Kawasaki. References 1. Jankovic J. Parkinson’s disease: clinical features and diagnosis. Journal of Neurology, Neurosurgery &
Psychiatry. 2008; 79(4):368–76. 2. Bartels AL, Leenders KL. Parkinson’s disease: the syndrome, the pathogenesis and pathophysiology. Cortex. 2009; 45(8):915–21. https://doi.org/10.1016/j.cortex.2008.11.010 PMID: 19095226 3. Lezak MD. The problem of assessing executive functions. International journal of Psychology. 1982; 17
(1–4):281–97. 4. Lewis SJ, Dove A, Robbins TW, Barker RA, Owen AM. Cognitive impairments in early Parkinson’s dis-
ease are accompanied by reductions in activity in frontostriatal neural circuitry. The Journal of Neurosci-
ence. 2003; 23(15):6351–6. PMID: 12867520 5. Ray NJ, Strafella AP. The neurobiology and neural circuitry of cognitive changes in Parkinson’s disease
revealed by functional neuroimaging. Movement Disorders. 2012; 27(12):1484–92. https://doi.org/10. 1002/mds.25173 PMID: 23038645 6. Adele D. Executive functions. Annual review of psychology. 2013; 64:135–68. https://doi.org/10.1146/
annurev-psych-113011-143750 PMID: 23020641 7. Dirnberger G, Jahanshahi M. Executive dysfunction in Parkinson’s disease: a review. Journal of neuro-
psychology. 2013; 7(2):193–224. https://doi.org/10.1111/jnp.12028 PMID: 24007368 8. Kamei S, Hara M, Serizawa K, Murakami M, Mizutani T, Ishiburo M, et al. Executive dysfunction using
behavioral assessment of the dysexecutive syndrome in Parkinson’s disease. Movement Disorders. 2008; 23(4):566–73. https://doi.org/10.1002/mds.21890 PMID: 18098279 9. Morris RG, Downes JJ, Sahakian BJ, Evenden JL, Heald A, Robbins TW. Planning and spatial working
memory in Parkinson’s disease. Journal of Neurology, Neurosurgery & Psychiatry. 1988; 51(6):757–66. 10. Owen A, James M, Leigh P, Summers B, Marsden C, Quinn Na, et al. Fronto-striatal cognitive deficits
at different stages of Parkinson’s disease. Brain. 1992; 115(6):1727–51. 11. Goldenberg G, Wimmer A, Auff E, Schnaberth G. Impairment of motor planning in patients with Parkin-
son’s disease: evidence from ideomotor apraxia testing. Journal of Neurology, Neurosurgery & Psychia-
try. 1986; 49(11):1266–72. 12. Cohen RG, Chao A, Nutt JG, Horak FB. Freezing of gait is associated with a mismatch between motor
imagery and motor execution in narrow doorways, not with failure to judge doorway passability. Neurop-
sychologia. 2011; 49(14):3981–8. https://doi.org/10.1016/j.neuropsychologia.2011.10.014 PMID:
22027173 13. Kamata N, Matsuo Y, Yoneda T, Shinohara H, Inoue S, Abe K. Overestimation of stability limits leads to
a high frequency of falls in patients with Parkinson’s disease. Clinical Rehabilitation. 2007; 21(4):357–
61. https://doi.org/10.1177/0269215507073346 PMID: 17613577 14. Ogata T, Muranaga S, Ishibashi H, Ohe T, Izumida R, Yoshimura N, et al. Development of a screening
program to assess motor function in the adult population: a cross-sectional observational study. Journal
of Orthopaedic Science. 2015; 20(5):888–95. https://doi.org/10.1007/s00776-015-0737-1 PMID:
26008771 15. Larrabee GJ. Software: Tsubasa Kawasaki. Supervision: Kyohei Mikami, Tsutomu Kamo, Hiroshi Nakamura. Visualization: Tsubasa Kawasaki. Visualization: Tsubasa Kawasaki. Writing – original draft: Tsubasa Kawasaki. Writing – original draft: Tsubasa Kawasaki. Author Contributions Conceptualization: Tsubasa Kawasaki. Formal analysis: Tsubasa Kawasaki. 8 / 10 PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 Motor planning and clinical symptoms in Parkinson’s disease Investigation: Tsubasa Kawasaki, Kyohei Mikami, Ryoma Aoki, Rumiko Ishiguro, Hiroshi
Nakamura, Ryosuke Tozawa, Nao Asada, Yukinobu Hiiragi, Yoichi Yamada, Masahiro Hir-
ano, Kazuko Katsuki. Methodology: Tsubasa Kawasaki, Kyohei Mikami. Project administration: Tsubasa Kawasaki, Kyohei Mikami, Tsutomu Kamo, Hiroshi
Nakamura. Software: Tsubasa Kawasaki. PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 References Assessment of malingered neuropsychological deficits: Oxford University Press; 2007. PLOS ONE | https://doi.org/10.1371/journal.pone.0202228
August 13, 2018 9 / 10 Motor planning and clinical symptoms in Parkinson’s disease 16. Callahan CM, Unverzagt FW, Hui SL, Perkins AJ, Hendrie HC. Six-item screener to identify cognitive
impairment among potential subjects for clinical research. Medical care. 2002; 40(9):771–81. https://
doi.org/10.1097/01.MLR.0000024610.33213.C8 PMID: 12218768 17. Goetz CG, Poewe W, Rascol O, Sampaio C, Stebbins GT, Counsell C, et al. Movement Disorder Soci-
ety Task Force report on the Hoehn and Yahr staging scale: status and recommendations the Move-
ment Disorder Society Task Force on rating scales for Parkinson’s disease. Movement disorders. 2004;
19(9):1020–8. https://doi.org/10.1002/mds.20213 PMID: 15372591 18. Martı´nez-Martı´n P, Gil-Nagel A, Gracia LM, Go´mez JB, Martı´nez-Sarrie´s J, Bermejo F. Unified Parkin-
son’s disease rating scale characteristics and structure. Movement disorders. 1994; 9(1):76–83. https://
doi.org/10.1002/mds.870090112 PMID: 8139608 19. Robinovitch SN, Cronin T. Perception of postural limits in elderly nursing home and day care partici-
pants. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences. 1999; 54
(3):124–30. 20. Sakurai R, Fujiwara Y, Ishihara M, Higuchi T, Uchida H, Imanaka K. Age-related self-overestimation of
step-over ability in healthy older adults and its relationship to fall risk. BMC geriatrics. 2013; 13(1):44. 21. Dancey CP, Reidy J. Correlational analysis: Pearson’s r. Statistics Without Maths for Psychology. USA: Prentice Hall; 2011. 10 / 10
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English
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Deformed AdS$$_4$$–Reissner–Nordström black branes and shear viscosity-to-entropy density ratio
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European physical journal. C, Particles and fields
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Received: 3 April 2019 / Accepted: 23 July 2019 / Published online: 7 August 2019
© The Author(s) 2019 Received: 3 April 2019 / Accepted: 23 July 2019 / Published online: 7 August 2019
© The Author(s) 2019 Abstract
AfamilyofdeformedAdS4–Reissner–Nordström
black branes, governed by a free parameter, is derived
using the ADM formalism, in the context of the mem-
brane paradigm. Their new event horizons, the Hawking tem-
perature and other aspects are scrutinized. AdS/CFT near-
horizon methods are then implemented to compute the shear
viscosity-to-entropy ratio for the deformed AdS4–Reissner–
Nordström metric. The Killing equation is shown to yield
new values for the free parameter and the shear viscosity-to-
entropy ratio is used to derive a reliable range for the tidal
charge. [6]. In the membrane paradigm, the AdS boundary can be
identified with a brane, in the fluid/gravity correspondence
structure [7]. As a black brane is a solution of the Einstein’s
equations in the AdS bulk, the 4D brane can be also taken
as an appropriate landscape, where black holes on the brane
are also solutions of the Einstein’s effective field equations. However, considering the 4D brane embedded in the AdS
bulk, yields the AdS Riemann tensor to be related to the
brane Riemann tensor by the Gauss–Codazzi equations. A
useful constraint to the Einstein’s effective field equations
on the brane [7] within the holographic membrane paradigm
is to demand the general-relativistic limit, consisting of a
rigid brane, meaning a brane that has infinite tension. This
condition, in fact, produces a physically correct low-energy
limit, allowing the construction of black holes on the brane
[8–12]. a e-mail: andre.juan@ufabc.edu.br
b e-mail: pedro.meert@ufabc.edu.br
c e-mail: roldao.rocha@ufabc.edu.br Deformed AdS4–Reissner–Nordström black branes and shear
viscosity-to-entropy density ratio A. J. Ferreira-Martins1,a, P. Meert1,b, R. da Rocha2,c
1 CCNH, Universidade Federal do ABC-UFABC, Santo André 09210-580, Brazil
2 CMCC, Federal University of ABC, Santo André 09210-580, Brazil Eur. Phys. J. C (2019) 79:646
https://doi.org/10.1140/epjc/s10052-019-7167-8 Regular Article - Theoretical Physics 1 Introduction The
AdS5 bulk, with electromagnetic field strength, satisfies the
Einstein’s equations, RAB −1
2 R gAB = gAB + TAB,
(3) (3) for for TAB = FAC F C
B −1
4gAB F2,
(4) (4) where F2 = FAB F AB. Projecting Eq. (3) on an AdS4 brane,
with 4 cosmological constant, and introducing Gaussian
coordinates in the bulk, xμ and w, one obtains the constraints
at w = 0: By allowing a free parameter in the AdS4–RN metric,
we expect to gain more freedom, in the sense that intrinsic
features, such as transport coefficients and thermodynamic
quantities, can be modelled – or fine tuned – according to
experimental evidence to come, or even eventually describe
unknown materials in condensed matter. at w = 0: at w = 0: Rμw = 0,
R = 4 + Eμ
μ,
(5) (5) This paper is organized as follows: in Sect. 2 the spacetime
metric, that we call deformed AdS4–RN , shall be derived and
some features considered relevant, such as the new horizon,
its associated temperature and conditions for such quantities
to be meaningful, are studied. We then proceed to describe
the process of implementing perturbations to compute the
shear viscosity-to-entropy ratio via the fluid/gravity corre-
spondence in Sect. 3. In Sect. 4 the AdS/CFT correspon-
dence is briefly reviewed for our purposes and applied for
computing the shear viscosity-to-entropy density ratio, asso-
ciated to the dual theory of the deformed AdS4–RN solution. Finally, concluding remarks and some perspectives for the
forthcoming developments regarding this type of solutions
are presented in Sect. 5. where R is the Ricci curvature scalar, 4 the brane cosmolog-
ical constant, and Eμ
ν represents the electric part of the Weyl
tensor. It mimics a Weyl fluid in the bulk [23], that illus-
trates how the brane embedding into the bulk contributes to
the brane bending, possible by the finite value of the brane
tension [9,24,25]. For static solutions, Eq. (5) emulate the Hamiltonian and
themomentumconstraints[11],intheADMformalism.Such
constraints play the important role of sorting out admissible
field configurations along manifolds of constant w [11]. The
selected field configurations thus can be propagated out the
AdS4 brane, under the residual Einstein’s effective equations
(3). The Hamiltonian constraint comprehends a weaker stip-
ulation than the 4D vacuum equations Rμν = 0. The Q
parameter is interpreted as a tidal charge [23]. 1 Introduction Applying the ADM formalism to generate a family of
deformed AdS4–RN spacetimes, let us start with the metric
(1), still considering the temporal components (2), 1 Introduction C (2019) 79 :646 ds2
4 = −r2 f (r)
L2
dt2 +
L2
r2 g(r)dr2 + r2
L2 dx2 + r2
L2 dy2,
( ds2
4 = −r2 f (r)
L2
dt2 +
L2
r2 g(r)dr2 + r2
L2 dx2 + r2
L2 dy2,
(1) regarding holographic superconductors and strange metals
[19–22]. (1) We will apply the ADM formalism to derive a family of
spacetime solutions, leading into the AdS4–RN in a very spe-
cific limit. One calls this spacetime a deformation of AdS4–
RN.Itisgovernedbyafreeparameterintheradialcomponent
of the metric. When this parameter equals to unity, the AdS4–
RN spacetime is then recovered. Although carrying similar
features, the bulk geometry of the new solution is quite dif-
ferent of the standard AdS4–RN one. The first aspect noticed
is the appearance of a coordinate singularity, which is in fact
an event horizon when certain conditions are met. This opens
new possibilities, as the horizon is an important feature when
exploring the thermodynamic properties of a black hole. It
has, thus, direct consequence in the CFT at the AdS bound-
ary. Second, this spacetime can be derived from an action
without matter terms, consisting of a vacuum in AdS/CFT,
however with a cosmological constant in an AdS5, wherein
AdS4 is embedded. This is a consequence of the formalism
implied to obtain the solution, and we use the notation Q
for the charge as mere analogy at this point, since its origin
is different and the proper terminology is to call it a tidal
charge [23], i.e., the source for this charge is the curvature of
the spacetime itself, which comes from a higher dimensional
AdS5 bulk. with f (r) = g(r) = 1 −(1 + Q2)
r0
r
3
+ Q2 r0
r
4
,
(2) (2) is a well known solution of the 4D Einstein–Maxwell the-
ory with a cosmological constant = −3/L2, where Q
denotes the black hole charge and r0 represents the event
horizon position [17,18], which is unique, as the black hole
is extremal. The AdS/CFT membrane paradigm can set the 4D brane
as the boundary of an AdS5 bulk with cosmological constant
related to the vacuum energy density of the boundary. 1 Introduction The AdS/CFT correspondence consists of a solid appara-
tus where strongly coupled QFTs can be studied. Any given
QFT, including finite temperature ones, has a hydrodynam-
ical description in the infra-red (IR) limit, corresponding
to long length scales in the theory. In the anti-de Sitter
(AdS) bulk space, a theory of gravity is dual to the CFT on
the boundary. The AdS bulk geometry can include a black
brane presenting an event horizon. The holographic duality
between the AdS bulk and its boundary then conjectures that
the CFT at the long scale regime must be ruled by a near-
horizon limit regarding dual geometries. For instance, any
general relativistic black hole presents a spurious fluid on
its horizon, consisting of the so-called membrane paradigm,
whose low-energy regime is a strongly coupled field theory
[1–3]. In the membrane paradigm, black holes were scruti-
nized [4,5], in the long wavelength limit. Transport coeffi-
cients were introduced by the duality between black branes
in the AdS bulk and fluid dynamics, in the AdS boundary Methods in AdS/CFT and the membrane paradigm were
successful derived in Refs. [13,14]. Tests of AdS/CFT have
been performed in cases for which the supergravity back-
grounds are supersymmetric [15,16]. However, a static AdS
black hole in the supersymmetric limit can have a naked
singularity, avoided when rotation is assumed, as in the
Reissner–Nordström spacetime. Exploring the precise link
between braneworld scenarios and the AdS/CFT duality,
realized through the membrane paradigm [3], provides a
transliteration of the brane models into the AdS/CFT lan-
guage. It allows to scrutinize black branes and their hydro-
dynamics using the well-known AdS/CFT methods. In this
work, we shall focus on computing transport coefficients,
including the shear viscosity-to-entropy density ratio, η/s. Thereafter, viscosity bounds will be imposed to a general-
izedblackbrane.TheReissner–Nordström–AdS(AdS4–RN)
spacetime plays a prominent role in this procedure, being
widely known in the context of AdS/CMT [17,18] for being
dual to a finite temperature CFT describing a conserved U(1)
charge in the boundary. In fact there is a comprehensive lit-
erature regarding this spacetime and the related dual theory, 12 3 3 646
Page 2 of 9 Eur. Phys. J. 2 Deformed AdS4–Reissner–Nordström spacetime The AdS4–Reissner–Nordström black hole background rep-
resents a charged, asymptotically-AdS black hole solution
with a planar horizon, described by coordinates {xμ} =
{t,r, x, y}, ds2
4 = −r2 f (r)
L2
dt2 + n(r) L2
r2 dr2 + r2
L2 dx2 + r2
L2 dy2. (6) (6) {t,r, x, y}, 123 {t,r, x, y}, 123 Page 3 of 9
646 Eur. Phys. J. C (2019) 79 :646 Page 3 of 9
646 Page 3 of 9
646 646 for for IfinsteadoneinsistsonrequiringtheAdS4–RNwitharegular
AdS4 horizon, the price to pay is to have something beyond
the vacuum in the bulk, as a field strength [17,18]. This is
not the case considered here. Considering that only the rt
component is non-zero, one can check that F2 = 2Frt Frt,
and also obtain the components of the stress–energy tensor, for for pQ = pQ(r) =
Q2 + 1
rr3
0 −Q2r4
0 −r4,
(9a)
hQ = hQ(r) = pQ −Q2r4
0
(9b)
kβ = kβ(r) = 9r −(2β + 7)r0,
(9c) (9a) (9c) where β denotes a free parameter that governs the deforma-
tion. It is free in the sense that its value is not determined a
priori, nevertheless it is taken as constant along the calcula-
tions. Hence, the solution Ttt= F r
t Frt −1
4gtt F2
(7a)
Trr= F t
r Ftr −1
4grr F2
(7b)
Txx= Tyy = −1
4gxx F2. (7c) (7a) (7b) n(r) =
1
f (r)
1 −r0
r
1 −r0
r
1 + 1
3 (β −1)
,
(10) (10) Equivalently, the electromagnetic potential reads A
=
A(r) dt, having the chemical potential and the charge den-
sity representing its components of expansion near bound-
ary, A(r) = μ −Q
r . At the horizon, r →r0, A →0. Hence
μ =
Q
r0 , in this regime. Here Q denotes the U(1) gauge
charge, then Q =
Q2 + ˜Q2, where ˜Q is the tidal charge. satisfies Eq. (8), once the temporal component is claimed to
be the same as the standard AdS4–RN, given by f (r) in Eq. (2). Notice that for β = 1, the metric (6) is precisely the RN
black hole in AdS4 background. From now on L = 1 will be
assumed for the sake of conciseness. The electromagnetic potential A = Aμdxμ is determined
from the Maxwell equations, which simply read
A family of analytic solutions of the form (6) obtained
by relaxing the condition f (r) = 1/g(r) in (1), by fixing
either f or g as in the AdS4–RN and finding the most gen-
eral solutions for the constraints (5). 123 C (2019) 79 :646 Fig. 1 Plot of Eq. (19), β(Q) × Q. It is shown that Q =
√
3 yields
β = 1. Hence, we are interested in values of Q >
√
3 if considering β
given by Eq. (19) The essential features involving the event horizon of
AdS4–RN are present in the solution (6). A closer look on
(10) reveals that 1/n(rβ) →0, i.e. grr(rβ) →0, for rβ = r0
1 + 1
3 (β −1)
,
(17) (17) Of course, this is a coordinate singularity at this point, but in
fact one can ask weather it if rβ is an event horizon or not. If
so, by inspection, it is obvious that β > 1 leads to rβ > r0,
which means that (17) is a bigger horizon than the standard
AdS4–RN outer horizon. Hence, it should be considered as
the surface for which quantities, such as temperature and
entropy of the black hole, are evaluated. Fig. 1 Plot of Eq. (19), β(Q) × Q. It is shown that Q =
√
3 yields
β = 1. Hence, we are interested in values of Q >
√
3 if considering β
given by Eq. (19) For a static space-time a sufficient condition for a surface
to be an event horizon is that it be a Killing horizon [27],
which satisfies ξμξμ = 0, where ξμ is the time-like Killing
vector. Demanding that ξμ associated to (10) satisfies such
condition, two values of β are found: at the horizon. Then once one has the Killing vector, it is
just a matter of computation. It is worth mentioning that Eq. (20) is only valid at r = rβ, or at any other horizon if such
surface exists. However, it cannot be used for other points
in spacetime [27]. The surface gravity and temperature are
closely related by β = 1,
(18)
β = −3 +
2 × 21/3
−7 −27Q2 + 3
√
3
3 + 14Q2 + 27Q4
1/3
+
7 + 27Q2 −3
√
3
3 + 14Q2 + 27Q4
1/3
21/3
. (19) (18) T = κ
2π . 123 These solutions will be
expressed in terms of the ADM mass M and the parameter β,
which is fixed but arbitrary [26]. The momentum constraints ∂μ
√−gFμν
= 0 ,
(11) (11) where Fμν = ∂μAν −∂ν Aμ is the electromagnetic field
strength. As assumed previously A = A (r) dt, the solution
to (11) is given by At =
−2Q√r −r0
√β + 2√3r −r0 (β + 2) −Qr (β −1)
π −2 arctan
√r−r0
√β+2
√3r−r0(β+2)
2
√
3r0
√β + 2r
,
(12) (12) and one can verify that and one can verify that and one can verify that are identically satisfied by the metric (6) and the Hamiltonian
constraint can be written out explicitly in terms of f (r) and
n(r). Fixing the temporal component (2), the Hamiltonian
constraint in the ADM formalism reads lim
β→1 At = Q
1
r −1
r0
,
(13) (13) which is nothing but Coulomb’s law – the solution for
the spherically symmetric case, considered in the Reissner–
Nordström scenario. Moreover one can check that −
1
324L4r14 p2
Qk3
β
×
22L4r12
Q2r4
0 −r4−r2r2
0 −rr3
0 + r3r0
+4L4r12 pQ
Q2+1
rr3
0 −3Q2r4
0 −r4
k3
β
+4L4r8r0 p2
Qk2
β
9
Q2+1
r2r2
0 + 9Q2r4
0
−9
2Q2+1
rr3
0 −2(β−1)r4
−L4r12h2
Qk3
β
+pQk2
β
9r2 −(β + 17)rr0 + (2β + 7)r2
0
+81r0(r −r0)2hQ p4
Q
r2r2
0
2β −27Q2 −29
+rr3
0
6β + (4β + 59)Q2 + 21
−4(2β + 7)Q2r4
0
+2(β −1)(r4 + r3r0)
= 0, lim
r→rβ At = 0,
(14)
lim
r→∞At ≈μ −Q
r + · · ·
(15) lim
r→rβ At = 0,
(14) (14) lim
r→∞At ≈μ −Q
r + · · ·
(15) (15) It is of no surprise that these conditions are met, since those
are the boundary conditions applied to (11). In particular,
expansion (15) at the boundary allows to obtain the chemical
potential, μ, of the CFT at the boundary. Explicitly, expand-
ing (12) gives μ = −Q
6r0
6 +
√
3 (β −1)
√2 + β
arctan
β + 2
3
. (16) (16) (8) 12 646
Page 4 of 9 646
Page 4 of 9 Eur. Phys. J. 123 (21) (21) (19) Evaluating (20) is fairly simple, and one finds immediately As expected, β = 1 is a solution, which simply confirms that
the deformed AdS4–RN contains the standard AdS4–RN, for
the previous established value of the deformation parameter. On the other hand, expression (19) fixes β according to the
value of Q, which is proportional to the charge placed inside
the event horizon when modelling the AdS4–RN spacetime. Equation (19) is not an intuitive function to picture, hence
it is more useful to present its plot and point out certain
features, useful for future arguments. Interestingly, it is seen
that for both values, (18) and (19), rβ is a Killing horizon
and, as was previously established, β is a parameter that is
not fixed a priori. Moreover, Fig. 1 shows that the range
Q >
√
3 implies β > 1, which is the region where (17), with
β given by (19), should replace r0 for calculations regarding
the horizon. As expected, β = 1 is a solution, which simply confirms that
the deformed AdS4–RN contains the standard AdS4–RN, for
the previous established value of the deformation parameter. κ2 =
2r4 + r3
0
1 + Q2
r −2Q2r4
0
2 [3r + r0 (β + 2)]
12r4 (r0 −r)2
r3 + r0r2 + r2
0r −r3
0 Q2
r=rβ
= 0. (22) (22) Hence, the temperature is identically zero. Notice that this
result does not depend on the value of β, thus it is valid in the
particular choice of β given by (19). Moreover, we emphasize
that this result is indeed expected, as we are considering an
extremal black hole [28]. Hence, the temperature is identically zero. Notice that this
result does not depend on the value of β, thus it is valid in the
particular choice of β given by (19). Moreover, we emphasize
that this result is indeed expected, as we are considering an
extremal black hole [28]. 3 Fluid/gravity preliminaries The temperature of this black hole at the horizon rβ is an
important quantity, that will be computed according to the
geometric procedure outlined in Ref. [27]. Such calculation
proceeds as follows: one evaluates the quantity This section is devoted to describe the theoretical back-
ground necessary to the computation of the shear viscosity-
to-entropy density ratio, usually denoted by η/s, for the
deformed RN–AdS4 solutions. κ2 = lim
r→rβ
−
ξμ∇μξλ
(ξν∇νξλ)
ξρξρ
. (20) (20) 3.2 Hydrodynamics and fluid dynamics The formalism of hydrodynamics provides a description of
themacroscopicbehaviour of agivensystem. Moreprecisely,
it refers to the dynamics of macroscopic variables, with main
interest to the conserved ones, that remain in the hydrody-
namic limit, characterized by a low-energy, long-wavelength
regime [30]. Thus, from the field theoretical point of view,
hydrodynamics is a legitimate effective theory. Therefore,
one cannot expect it to carry the details of a microscopic
theory, which are encoded in the transport coefficients. g(0)
μν dxμdxν = ημνdxμdxν + 2h(0)
xy (t)dxdy,
(27) (27) for ημν. for ημν. 3.1 Linear response theory and Kubo’s formula Let one consider a theory described by an action S. It is
often of interest to determine what is the response of a Then one identifies κ as the surface gravity by arguing that the
computation of such quantity leads to the same expression 123 Eur. Phys. J. C (2019) 79 :646 Page 5 of 9
646 Page 5 of 9
646 646 where the term τ μν contains dissipative effects. In the local
rest frame, it is such that given operator O, denoted by δ⟨O⟩, when one adds a cou-
pled external source, ϕ(0). Hence, the theory is altered as
S →S+
d4xϕ(0)(t, x)O(t, x) [29]. The response is deter-
mined by employing the linear response theory, establishing
that τi j = −η
∂iu j + ∂jui −2
3δi j∂kuk
−ζδi j∂kuk. (26) (26) Notice that two transport coefficients are introduced when
dissipative effects are considered: the shear, η, and bulk, ζ,
viscosities. The introduction of a constitutive equation for
the viscous fluid closes the equations of motion, yielding the
continuity and the Navier–Stokes equations. δ ⟨O(t, x)⟩:= ⟨O(t, x)⟩S −⟨O(t, x)⟩,
(23) (23) where ⟨O(t, x)⟩S denotes the ensemble average (one-point
function) of the operator O in the presence of the external
source. The method is implemented by applying the time-
dependent perturbation theory of quantum mechanics [29,
30], which yields the response, in momentum space, 3.3 Kubo’s formula for the shear viscosity 3.3 Kubo’s formula for the shear viscosity δ ⟨O(ω, q)⟩= −GO,O
R
(ω, q)ϕ(0)(ω, q),
(24) General relativity states that spacetime fluctuations bring up
fluctuations into the stress tensor [27]. In agreement with
this idea, the Kubo’s formula for the shear viscosity η can
be derived by coupling fictitious gravity to the fluid, and
then determining the response of T μν, under gravitational
perturbations. At this stage, one should see this procedure
just as a quick way to derive the Kubo’s formula, as one does
not really curve spacetime in fluid experiments. However, the
derivation presented here has a natural interpretation within
the AdS/CFT duality framework, as discussed in Sect. 4. (24) where GO,O
R
(ω, q) is the Fourier-transformed retarded
Green’s function associated to O [30]. Equation (24) shows that the response to the operator, by
a coupled external source, is narrowed down to the determi-
nation of the retarded Green’s function, which is related to a
transport coefficient through the Kubo’s formula. Hereon we
are ultimately interested in obtaining the shear viscosity η as
a transport coefficient emerging in the fluid dynamics that is
dual to the deformed RN–AdS4 family of solutions. First, one adds a gravitational perturbation to a 4D space-
time. Since we are interested in determining the shear viscos-
ity η, it is natural to consider an off-diagonal perturbation, so
that the perturbed metric g(0)
μν is, in the {t, x, y, z} coordinate
system, given by 3.2 Hydrodynamics and fluid dynamics for ημν. Since the perturbed spacetime is no longer flat, one must
extend the constitutive equation for the stress tensor to a
curved spacetime, according to T μν = (ρ + p)uμuν + Pgμν(0) + τ μν,
(28) (28) For a simple fluid, one can consider, as a macroscopic vari-
able, the energy–momentum stress tensor, T μν, along with
its conservation law, ∂μT μν = 0. In (3+1) dimensions, T μν,
a symmetric rank-(2, 0) tensor, has 10 independent compo-
nents, whilst its conservation law provides only 4 equations. In order to close the equations of motion one must introduce a
constitutive equation, which is conveniently written in terms
of the normalized fluid velocity field uμ(xν), its rest-frame
energy density ρ(xμ) and its pressure p(xμ). so that the dissipative part now reads τ μν = −ηPμσ Pνλ
∇σuλ + ∇λuσ −2
3g(0)
σλ∇kuk
−ζ Pμσ Pνλg(0)
σλ∇kuk, (29) where ∇μ represents the covariant derivative with respect to
the perturbed metric g(0)
μν . The Pμν := gμν(0) + uμuν is the
projection tensor, necessary to write the constitutive equation
in a covariant way. In general, one introduces a constitutive equation by deter-
mining the form of T μν in a derivative expansion. To first
order, dissipation effects, which are absent in the perfect fluid In general, one introduces a constitutive equation by deter-
mining the form of T μν in a derivative expansion. To first
order, dissipation effects, which are absent in the perfect fluid
– which corresponds to the zeroth order – are included. A vis-
cous fluid has stress tensor expressed as [31] Notice that the perturbation is considered to be homoge-
neous, as well as the fluid velocity field, i.e., ui = ui(t). However, parity invariance forbids motion in any direction,
so the fluid must be at rest. Therefore, the covariant derivative
of the velocity field is reads ∇μuν = ∂μuν −σ
μνuσ = t
μν. – which corresponds to the zeroth order – are included. A vis-
cous fluid has stress tensor expressed as [31] T μν = (ρ + p)uμuν + pημν + τ μν,
(25) T μν = (ρ + p)uμuν + pημν + τ μν, (25) 12 3 Eur. Phys. J. C (2019) 79 :646 646
Page 6 of 9 that is, the functions appearing in the metric coefficients (2)
and (10) are now f = f (u) and n = n(u), respectively. for ημν. (32) with the general result from lin-
ear response theory of Eq. (24), in this case, δ ⟨τ xy⟩=
−Gxy,xy
R
h(0)
xy , one obtains the Kubo’s formula, In practice, the greatest operational advantage provided
by the GKP–Witten relation is the possibility of obtaining
the generating functional of a gauge theory by the evaluation
of the classical action of a gravitational theory. As we are
interested in the response of a system in the presence of an
external source, one obtains, from the GKP–Witten relation,
the following expression for the one-point function [30], η = −lim
ω→0
1
ωℑ
Gxy,xy
R
(ω, 0)
. (33) (33) Naturally, η does depend neither on ω nor on q, which is
why one takes the ω →0 limit and set q = 0 in the Green
function, accounting to k = 0. Of course, the problem of
finding the retarded Green’s function Gxy,xy
R
remains, and
one will employ the AdS/CFT methods to this task. ⟨O⟩S = δ ¯S[ϕ(0)]
δϕ(0)
. (35) (35) Naturally, to obtain the one-point function in the absence of
the external source, one evaluates the expression above for
ϕ(0) = 0, that is, ⟨O⟩= ⟨O⟩S|ϕ(0)=0. for ημν. Calculating the response in τ xy, up to linear order in the per-
turbation, requires the covariant derivatives ∇xuy = t
xy =
t
yx = ∇yux. Notice that they are of linear order in the per-
turbation, The left-hand side of Eq. (34) is the generating functional
of the D-dimensional boundary gauge theory, when an exter-
nal source ϕ(0) is added, whilst the right-hand side of Eq. (34) is the generating functional of a (D + 1)-dimensional
bulk gravitational theory. The on-shell action is obtained by
simply evaluating the integral when the field ϕ is the solu-
tion of the equations of motion meeting certain conditions
imposed at the AdS boundary, ϕ|u=0 = ϕ(0). Now, since ϕ is
the solution of the equation of motion, ¯S reduces to a surface
term on the AdS boundary, which allows us to obtain from the
(D+1)-dimensional action a D-dimensional quantity, which
is identified with the generating functional of the boundary
theory, according to Eq. (34). This is the sense in which we
loosely say that the gauge theory lives on the boundary of the
bulk. t
xy = 1
2gtt(0)
∂xg(0)
ty +∂yg(0)
tx −∂tg(0)
xy
= 1
2∂th(0)
xy ,
(30) (30) so that the terms proportional to ∇kuk in Eq. (29) will be
second order in the perturbation. Now, since ∇xuy is already
linear in the perturbation, one can use the projection tensor in
the rest frame and in flat spacetime, Pμν = diag(0, 1, 1, 1). In fact, considering the perturbed metric contribution yields
in terms an order higher in the perturbation. Therefore, the
response in τ xy reads δ
τ xy
= −2ηt
xy = −η∂th(0)
xy ,
(31) (31) An important point to notice is that, from the (D + 1)-
dimensional point of view, ϕ is a field propagating in the bulk;
whilst ϕ(0) is an external source from the D-dimensional
point of view. Therefore, in the context of AdS/CFT, one can
say that a bulk field acts as an external source of a boundary
operator. whose Fourier transformation yields δ
τ xy(ω, 0)
= iωηh(0)
xy . (32) (32) Comparing Eq. (32) with the general result from lin-
ear response theory of Eq. (24), in this case, δ ⟨τ xy⟩=
−Gxy,xy
R
h(0)
xy , one obtains the Kubo’s formula, Comparing Eq. 4 AdS/CFT and the GKP–Witten relation ϕ
The gravitational theory to be considered is classical 4D
general relativity with negative cosmological constant, <
0, i.e., the Einstein–Hilbert action plus a matter term The core claim of the AdS/CFT duality [1,2] is that the gen-
erating functionals, or partition functions, of the gauge and
gravitational theories are equivalent, Zgauge = Z AdS, which
is realized through the (Lorentzian) GKP–Witten relation
[32,33]: S =
1
16π
d4x√−g (R −2) + Smat,
(36) (36) where Smat is chosen according to the boundary theory. Besides, as the term F2 can be included into the part Smat,
since it does not contribute for the computation of the shear
viscosity, η. Although it does contribute to the computation
of other transport coefficients, as the conductivities, which is
not our aim here. exp
i
ϕ(0)O
= exp
i ¯S[ϕ(0)]
,
(34) (34) where ⟨· ⟩denotes an ensemble average. The ϕ represent a
field in the gravitational (bulk) theory, and ¯S is the on-shell
action. Also, ϕ(0) = ϕ|u=0, in coordinates such that the AdS
boundary where the gauge theory lives is located at u = 0 –
for the spacetime we are working with, c.f. Eq. (6), one has
u = r0/r. Hereon the coordinate u will be used instead of r, The Here a massless scalar field is considered Smat =
d4x√−g
−1
2
∇μϕ
2
. (37) (37) 123 Eur. Phys. J. C (2019) 79 :646 Page 7 of 9
646 646 4.1 η/s in the deformed RN–AdS4 black brane 4.1 η/s in the deformed RN–AdS4 black brane In fact, since one is only interested in the asymptotic
behaviour, the metric (6) reads A bulk perturbation hxy can be considered, such that gμνdxμdxν ∼r2
0
u2
−dt2 + 1
r2
0
du2 + dx2 + dy2
,
(38) gμνdxμdxν ∼r2
0
u2
−dt2 + 1
r2
0
du2 + dx2 + dy2
,
(38)
ds2 = ds2
0 + 2hxydxdy. (46) ds2 = ds2
0 + 2hxydxdy. (46) (38) (46) where ds2
0 is given by (6). According to the linear response
theory, the response in the boundary energy–momentum ten-
sor is given by where ds2
0 is given by (6). According to the linear response
theory, the response in the boundary energy–momentum ten-
sor is given by which is, of course, the AdS spacetime. 1 Recall that we are concerned about the horizon given by rβ, c.f. Eq.
(17), with β given by (19). 4 AdS/CFT and the GKP–Witten relation In these coordinates
the equation of motion from Eq. (37) is 1
2u3 ϕ′
′
∼0,
(39) δ
τ xy
= iωηh(0)
xy ,
(47) (47) (39) where h(0)
xy is the perturbation added to the boundary theory,
which is asymptotically related to hxy by where the prime denotes differentiation with respect to u. Notice that the Einstein–Hilbert action does not play any role
in the calculation of ⟨O⟩S, since it is independent of the field
ϕ. Requiring the scalar field to be static and homogeneous
along the boundary direction, ϕ = ϕ (u), yields where the prime denotes differentiation with respect to u. Notice that the Einstein–Hilbert action does not play any role
in the calculation of ⟨O⟩S, since it is independent of the field
ϕ. Requiring the scalar field to be static and homogeneous
along the boundary direction, ϕ = ϕ (u), yields gxxhxy ∼h(0)
xy
1 + h(1)
xy u3
,
(48) (48) holding as long as gxxhxy obeys the equation of motion for a
massless scalar field [29,30]. Since the asymptotic behaviour
of (6) is given by (38), one can directly apply the results
discussed in this section, and treat gxxhxy as the 4D bulk
scalar field ϕ, which acts as an external source of a boundary
operator. Thus, Eq. (44) yields Smat =
d4x√−g
−1
2guu
ϕ′2
∼
dx4
−1
2
r3
0
u2
ϕ′2
. (40) (40) Theusualtechniquetoproceedisintegrationbyparts,leading
to δ
τ xy
= r3
0
16π 3h(1)
xy h(0)
xy . (49) to (49) Smat ∼
d3x
r3
0
2u2 ϕϕ′
u=0
+
d4xr3
0
1
2u3 ϕ′
′
ϕ,
(41) Comparing Eqs. (47) and (49) implies that (41) iωη =
3r3
0
16πG4
h(1)
xy . (50) (50) where it is assumed that the scalar field vanishes at the hori-
zon.ThesecondterminEq.(41)isjusttheequationofmotion
(39), which has the following asymptotic solution On the other hand, the entropy density associated to (6)
is, according to the area law, given by s = r2
β/4.1 Plugging
this result into Eq. (50) yields On the other hand, the entropy density associated to (6)
is, according to the area law, given by s = r2
β/4.1 Plugging
this result into Eq. (50) yields ϕ ∼ϕ(0)
1 + ϕ(1)u3
. (42) (42) η
s =
3r0
4π
1 + 2
9 (β −1)
2
h(1)
xy
iω . 5 Concluding remarks and perspectives Fig. 2 Plot of Eq. (57) without the factor
1
4π . We see that there is a
change of sign in the η/s ratio for Q =
√
3 The membrane paradigm was here used to derive a new fam-
ily of deformed AdS4–RN black branes. For it, the ADM
formalism was employed, assuming the temporal compo-
nent fixed, and the Hamiltonian constraint implemented a
deformation of the AdS4–RN black brane, given by Eqs. (6) and (10). The Killing equation for the Killing vector of
the deformed AdS4–RN black brane was then solved, yield-
ing the values of the β free parameter given by Eqs. (18)
and (19). Although Eq. (18) yields the standard AdS4–RN
black brane, Eq. (19) presents new solutions, encoding the
deformed AdS4–RN black brane β free parameter a func-
tion of the black brane tidal charge. The Hawking tempera-
ture was also computed in Eq. (22). Fluid/gravity methods
were then employed for computing the shear viscosity-to-
entropy ratio for the deformed AdS4–Reissner–Nordström
black branes. This ratio is used to derive a reliable range for
the tidal charge as well. Now, by imposing the incoming wave boundary condition
near the horizon and the Dirichlet boundary condition at the
AdS boundary, and proceeding as outlined in [30] to incor-
porate these conditions2 one arrives at the full solution φ = φ(0)
1 −i ω
r0
Q2 −3
|Q2 −3|
u2
√f n du
. (54) (54) Accordingly, the full time-dependent perturbation is asymp-
totically given by gxxhxy ∼e−iωtφ(0)
1 −i ω
r0
Q2 −3
|Q2 −3|
u3
3
. (55) (55) Comparing now Eq. (55) to Eq. (48), and identifying h(0)
xy =
φ(0)e−iωt, one promptly obtains It is worth to emphasize that the value of the β deforma-
tion parameter, in Eq. (18), does correspond to the standard
AdS4–RNblackbrane,asexpected.Infactbyexploringsome
features of the deformation exposed in Sect. 2, we found that
the deformation parameter is restricted to a precise value, tak-
ing us back to the conventional AdS4–RN spacetime, which
we see as an argument in favour of the unicity of this solution,
whenever the ADM formalism is utilized. h(1)
xy = −iω
3r0
Q2 −3
|Q2 −3|. (56) (56) Thus, substituting the resulting h(1)
xy above in Eq. 2 Namely: solving Eq. (53) in the limit u →1 and afterwards in a
power series of ω up to O(ω) in the hydrodynamic limit. 4 AdS/CFT and the GKP–Witten relation We see that there is a
change of sign in the η/s ratio for Q =
√
3 Therefore, the following bound for Q can be obtained 0 < Q <
√
3,
(58) (58) 0 < Q <
√
3, for the η/s ratio to assume the saturated value η/s = 1/4π
[34], as the initial action is Einstein–Hilbert. Notice that, as
defined, the tidal charge Q must be a positive quantity, so
that the −
√
3 < Q < 0 interval, which also satisfies the
3 −Q2 > 0 bound, was not considered in this result, which
is also very interesting, and worthy of further investigation. 4 AdS/CFT and the GKP–Witten relation (51) (51) For a scalar field of this form, Eq. (42), the action (41) reduces
to a surface term on the AdS boundary. Substituting (42) on
the action and evaluating the surface term, the on-shell action
reads One now must find h(1)
xy , by solving the equation of motion
for the perturbation gxxhxy ≡ϕ, which is that of a massless
scalar in a 4D background, ¯S
ϕ(0)
∼
d3x
3
2r3
0
ϕ(0)2
ϕ(1)
. (43) (43) ∂μ
√−ggμν∂νϕ
= 0
(52) (52) Thus, the one-point function from (35) is given by Taking ϕ = φ(u)e−iωt, the perturbation equation reduces to Taking ϕ = φ(u)e−iωt, the perturbation equation reduces to ⟨O⟩S = 3r3
0ϕ(1)ϕ(0). (44) (44) u2
√f n
√f n
u2 φ′
′
+ 1
f n
ω2
r2
0
φ = 0. (53) which, compared to the linear response relation of Eq. (24),
yields the Green function:
u2
√f n
√f n
u2 φ′
′
+ 1
f n
ω2
r2
0
φ = 0. (53) which, compared to the linear response relation of Eq. (24),
yields the Green function:
u2
√f n
√f n
u2 φ′
+ 1
f n
ω2
r2
0
φ = 0. (53) (53) which, compared to the linear response relation of Eq. (24),
yields the Green function: GO,O
R
(k = 0) = −3r3
0ϕ(1),
(45)
1 Recall that we are concerned about the horizon given by rβ, c.f. Eq. (17), with β given by (19). GO,O
R
(k = 0) = −3r3
0ϕ(1),
(45)
1 Recall that we are concerned about the horizon given by rβ, c.f. Eq. (17), with β given by (19). 1 Recall that we are concerned about the horizon given by rβ, c.f. Eq. (17), with β given by (19). 1 Recall that we are concerned about the horizon given by rβ, c.f. Eq. (17), with β given by (19). GO,O
R
(k = 0) = −3r3
0ϕ(1),
(45)
1 Recall that we a
(17), with β given (45) 12 646
Page 8 of 9 Eur. Phys. J. C (2019) 79 :646 Fig. 2 Plot of Eq. (57) without the factor
1
4π . 5 Concluding remarks and perspectives (51) yields Preliminary numerical analysis provide us with deforma-
tions of the AdS4–RN black brane (1, 2) without AdS5 bulk
embedding, as an exact solution of a Lee–Wick-like action of
gravity, and then more members of the family of deformed
AdS4–RN black branes might be taken into account, with
free parameter given by Eq. (19). In order to implement it,
the value of η/s cannot be conjectured to be equal to 1/4π,
and must be derived for the Lee–Wick-like action. However,
up to now we have not concluded these computations, as the
machining time employed is awkwardly long. If these calcu-
lations can be finally implemented, and if the η/s ratio allows
a value β ̸= 1, one can therefore apply the deformed AdS4–
RN black brane in the context of the AdS/CMT correspon-
dence. In fact, the standard AdS4–RN black brane is already η
s =
9
1 −2×21/3
χQ
+ χQ
21/3
2
3 −Q2
3 −Q2
,
(57) (57) for χQ =
−7 −27Q2 + 3
9 + 42Q2 + 81Q4
1/3
, where
the β parameter is written as given by Eq. (19). for χQ =
−7 −27Q2 + 3
9 + 42Q2 + 81Q4
1/3
, where
the β parameter is written as given by Eq. (19). The ratio η/s is a positive quantity, since both the shear
viscosity and the entropy density are positive. From the plot
in Fig. 2, representing Eq. (57), one sees where this condition
is met. 3 Page 9 of 9
646 Eur. Phys. J. C (2019) 79 :646 known to describe the strange metals in the holographic dual-
ity setup. By promoting the spacetime metric from the stan-
dard AdS4–RN black brane, corresponding to the particular
value in Eq. (18), to the deformed family (2, 6) studied here,
with the β parameter given by Eq. (19), we expect to gain
freedom in describing such materials. Hence this family of
deformed black branes can model a wider class of strange
metals and the β parameter in Eq. (19) can be then used to
compute other transport coefficients, or fine tune quantities
already known, like the electric conductivity and the thermal
conductivity, for example. 9. J. Ovalle, Phys. Rev. D 95, 104019 (2017). arXiv:1704.05899
(preprint) 10. A. Fernandes-Silva, A.J. Ferreira-Martins, R. da Rocha, Eur. Phys. J. C 78, 631 (2018). arXiv:1803.03336 (preprint) 11. R. arXiv:1610.01572 (preprint) Funded by SCOAP3. 26. M.C.B. Abdalla, J.M. Hoff da Silva, R. da Rocha, Phys. Rev. D 80,
046003 (2009)
Xi 0907 1321 (
i t) 26. M.C.B. Abdalla, J.M. Hoff da Silva, R. da Rocha, Phys. Rev. D 80,
046003 (2009). arXiv:0907.1321 (preprint) 26. M.C.B. Abdalla, J.M. Hoff da Silva, R. da Roc
046003 (2009). arXiv:0907.1321 (preprint) 046003 (2009). arXiv:0907.1321 (preprint) 27. R. Wald, General Relativity (University of Chicago Press, Chicago,
2010) 5 Concluding remarks and perspectives Casadio, A. Fabbri, L. Mazzacurati, Phys. Rev. D 65, 084040
(2002). arXiv:gr-qc/0111072 (preprint) 12. R. Casadio, R.T. Cavalcanti, R. da Rocha, Eur. Phys. J. C 76, 556
(2016). arXiv:1601.03222 (preprint) 13. I. Antoniadis, N. Arkani-Hamed, S. Dimopoulos, G.R. Dvali, Phy
Lett. B 436, 257 (1998). arXiv:hep-ph/9804398 (preprint) 14. I. Antoniadis, Phys. Lett. B 246, 377–384 (1990) 15. P. Meert, R. da Rocha, Eur. Phys. J. C 78, 1012 (2018). arXiv:1809.01104 (preprint) 16. L. Bonora, K.P.S. de Brito, R. da Rocha, JHEP 02, 069 (2015). arXiv:1411.1590 (preprint) Acknowledgements AJFM is grateful to FAPESP (Grants no. 2017/
13046-0 and no. 2018/00570-5) and to Coordenação de Aperfeiçoa-
mento de Pessoal de Nível Superior – Brazil. The work of PM was
financed by CAPES. RdR is grateful to CNPq (Grant no. 303293/2015-
2), to FAPESP (Grant no. 2017/18897-8), and to ICTP HE 210-V, for
partial financial support. 17. R.A. Davison, N.K. Kaplis, JHEP 12, 037 (2011). arXiv:1111.0660
(preprint) 18. M. Cadoni, G. D’Appollonio, P. Pani, JHEP 03, 100 (2010). arXiv:0912.3520 (preprint) 19. S.S. Gubser, S.S. Pufu, JHEP 11, 033 (2008). arXiv:0805.2960
(preprint) 20. S.A. Hartnoll, C.P. Herzog, G.T. Horowitz, JHEP 12, 015 (2008). arXiv:0810.1563 (preprint) Data Availability Statement This manuscript has no associated data
or the data will not be deposited. [Authors’ comment: This is a theoret-
ical study and no experimental data has been listed.] 21. N. Iqbal, H. Liu, M. Mezei, JHEP 04, 086 (2012). arXiv:1105.4621
(preprint) 22. G. Giordano, N. Grandi, A. Lugo, R. Soto-Garrido, JHEP 10, 068
(2018). arXiv:1808.02145 (preprint) Open Access This article is distributed under the terms of the Creative
Commons Attribution 4.0 International License (http://creativecomm
ons.org/licenses/by/4.0/), which permits unrestricted use, distribution,
and reproduction in any medium, provided you give appropriate credit
to the original author(s) and the source, provide a link to the Creative
Commons license, and indicate if changes were made. 23. R. Maartens, K. Koyama, Living Rev. Relativ. 13, 5 (2010) 24. R. Casadio, J. Ovalle, R. da Rocha, Class. Q
045016 (2014). arXiv:1310.5853 (preprint) 045016 (2014). arXiv:1310.5853 (preprint) 25. R. Casadio, R. da Rocha, Phys. Lett. B 763, 434–438 (2016). arXiv:1610.01572 (preprint) References 28. J. Zaanen, Y.W. Sun, Y. Liu, K. Schalm, Holographic Duality in
Condensed Matter Physics (Cambridge University Press, Cam-
bridge, 2015) 1. J.M. Maldacena, Int. J. Theor. Phys. 38, 1113 (1999) 1. J.M. Maldacena, Int. J. Theor. Phys. 38, 1113 (1999) 2. J.M. Maldacena, Adv. Theor. Math. Phys. 2, 231 (1998). arXiv:hep-th/9711200 (preprint) 29. D.T. Son, Acta Phys. Polon. B 39, 3173 (2008) 3. N. Iqbal, H. Liu, Phys. Rev. D 79, 025023 (2009). arXiv:0809.3808
(preprint) 30. M. Natsuume, Lect. Notes Phys. 903, 1 (2015). arXiv:1409.3575
(preprint) 4. R. Casadio, J. Ovalle, R. da Rocha, Class. Quantum Gravity 32,
215020 (2015). arXiv:1503.02873 (preprint) 31. M. Rangamani, Class. Quantum Gravity 26, 224003 (2009). arXiv:0905.4352 (preprint) 5. R. da Rocha, Phys. Rev. D 95, 124017 (2017). arXiv:1701.00761
(preprint) 32. E. Witten,
Adv. Theor. Math. Phys. 2,
253
(1998). arXiv:hep-th/9802150 (preprint) 6. S. Bhattacharyya, V.E. Hubeny, S. Minwalla, M. Rangamani, JHEP
02, 045 (2008). arXiv:0712.2456 (preprint) 33. S.S. Gubser, I.R. Klebanov, A.M. Polyakov, Phys. Lett. B 428, 105
(1998). arXiv:hep-th/9802109 (preprint) 7. T. Shiromizu, K.I. Maeda, M. Sasaki, Phys. Rev. D 62, 024012
(2000). arXiv:gr-qc/9910076 (preprint) 34. P. Kovtun, D.T. Son, A.O. Starinets, Phys. Rev. Lett. 94, 111601
(2005). arXiv:hep-th/0405231 (preprint) 8. R. Casadio, J. Ovalle, Gen. Relativ. Gravit. 46, 1669 (2014). arXiv:1212.0409 (preprint) 123 123
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More than a Fair Share? Principal-Principal Conflicts in Emerging Markets: Evidence from India
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Abstract The concentrated ownership structure of emerging market firms may help mitigate principal-agent conflicts;
however, the presence of two sets of principals, promoters with controlling stake and dispersed shareholders,
may give rise to principal-principal conflicts. India, where firms are largely organized as business groups, with
stock pyramids and complex cross-ownership structures, presents a distinctive venue to study the presence of
such conflicts. This paper tests if the principal-principal conflicts transpire in the form of risk aversion when
Indian bidders seek to merge or acquire. We observe that Indian bidders resort to risk-aversion only when
promoters have high cash flow rights, that is, when they hold a majority stake in the acquiring firm. We argue
that in business group firms this is likely to happen due to ‘tunnelling distortion’, whereas in standalone firms,
this is likely to occur due to ‘portfolio concentration’. However, on investigating deal-announcement returns, we
observe that firms with high promoter ownership create value. Keywords:
principal-principal
conflicts,
agency
theory,
India,
M&A,
ownership
concentration,
promoter-manager, risk-taking behaviour International Journal of Economics and Finance; Vol. 8, No. 7; 2016
ISSN 1916-971X E-ISSN 1916-9728
Published by Canadian Center of Science and Education International Journal of Economics and Finance; Vol. 8, No. 7; 2016
ISSN 1916-971X E-ISSN 1916-9728
Published by Canadian Center of Science and Education More than a Fair Share? Principal-Principal Conflicts in Emerging
Markets: Evidence from India Radha M. Ladkani1 & Ashok Banerjee2
1 Indian Institute of Management Indore, Indore, India
2 Indian Institute of Management Calcutta, Kolkata, India
Correspondence: Radha M. Ladkani, Indian Institute of Management Indore, J-205, Faculty Block–J,
Rau-Pithampur Road, Rau, Indore, Pin–453331, India. Tel. 91-731-243-9698. E-mail: radhal@iimidr.ac.in Radha M. Ladkani1 & Ashok Banerjee2
1 Indian Institute of Management Indore, Indore, India
2 Indian Institute of Management Calcutta, Kolkata, India Accepted: May 6, 2016 Online P
URL: http://dx.doi.org/10.5539/ijef.v8n7p31 Online Published: June 25, 2016 Received: March 28, 2016
doi:10.5539/ijef.v8n7p31 Received: March 28, 2016
doi:10.5539/ijef.v8n7p31 2. Literature Review and Research Objective For our study, we have borrowed heavily from the literature on managerial opportunism, which addresses the
concerns of the traditional agency problem observed in developed countries with dispersed ownership. But, we
attempt to extend the new branch of agency theory literature which considers the conflict of interest between the
majority and the minority shareholders (Dharwadkar et al., 2000), and is more relevant in the context of the
emerging economies where high ownership concentration among the promoters is a classic feature of firm
ownership (Young et al., 2008). In this study, we test the presence of principal-principal conflicts in India by
employing the established empirical approaches used to study the traditional agency problems in developed
countries, and hence we review this literature at length. A study similar to ours yet quite different in context is
undertaken by Chen and Young (2010), who have found empirical evidence supporting the principal-principal
agency concerns in Chinese state owned enterprises. In their seminal work, Amihud and Lev (1981) consider the impact of managerial ownership on the firm
diversification activity and propose the ‘employment risk’ argument to explain managerial risk-aversion. They
suggest that since a manager’s income is dependent on firm’s performance, and she bears the non-diversifiable
risk of losing her job, she is induced to reduce this risk by entering into conglomerate mergers. Literature on managerial opportunism offers several behavioural explanations like the ‘empire building’
motivation (Jensen, 1986, 1993) and the ‘hubris’ hypothesis (Roll, 1986), which also help us understand why
managers’ act against their shareholders by making value-destroying decisions. Managers driven by empire
building motivations like to have greater control over the firm’s resources to derive larger private benefits,
whereas, managers guided by their overconfidence (hubris) tend to make valuation mistakes. The empirical literature in this area primarily explores the relationship between equity ownership, including
stock option grants and other components of executive compensation, and managerial opportunistic behaviour
(including entrenchment). Empirical studies by Lloyd, Modani, and Hand (1987), Morck, Shleifer, and Vishny
(1990), and Saunders, Strock and Travlos (1990), support Amihud and Lev’s (1981) conclusions. They observe
that manager-controlled firms are more prone to diversifying their income streams, which implies risk-averse
behaviour on the part of the managers. But Lane, Cannella, and Lubatkin, (1998) present contradictory evidence
advocating that managers do not always exhibit risk aversion. In fact, they propose stewardship theory in support
of managers’ behaviour with respect to mergers and acquisitions. 1. Introduction The classic agency-theory that stems from the disharmony of interests and goals of principals and agents (Jensen
& Meckling, 1976) is well suited to address corporate governance concerns in the countries where the
stock-ownership is dispersed. However, business settings where the high concentration of ownership is
predominant, call for addressing governance issues through the lens of principal-principal conflicts (Young, Peng,
Ahlstrom, Bruton, & Jiang, 2008). In emerging markets, factors like concentrated and complex ownership structures, weak shareholder protection,
and institutional voids, give rise to conflicts between the majority and minority shareholders (Young et al., 2008). India presents a unique venue to test the presence of such conflicts. In Indian firms, promoters have high
ownership stakes, and also control the management of the firm (we label them promoter-managers). Furthermore,
the pyramidal-stock ownership structure (Note 1) enables promoters to have greater control compared to their
cash flow rights in a lower level business group firm as well (Khanna & Palepu, 2000a). As a consequence of
this phenomenon, two sets of shareholders emerge. One set of shareholders are the promoter-managers, whereas,
the other set of shareholders have a substantial yet minority stake in the firm, but are widely dispersed to have
any significant say in management’s decisions. In such a setting, there is a greater possibility for the
promoter-managers to ignore the interests of the minority shareholders, which could give rise to
principal-principals conflicts (Dharwadkar, George, & Brandes, 2000; Morck, Wolfenzon, & Yeung, 2005). The classical agency literature assumes that managers are opportunistic; and there is extant empirical evidence
that suggests that the managers have a tendency to make suboptimal risk choices (entrenchment hypothesis,
Shleifer & Vishny, 1989). A widely acknowledged reason is the non-diversifiable employment risk faced by a
manager (Amihud & Lev, 1981). Besides, making risky investments can also limit a manager’s rent seeking
ability (perquisite consumption) since it requires more prudent use of the firm’s resources (Jensen, 1986, 1993). Such managerial opportunism is addressed by effective incentive design and compensation structure that
includes equity and option holdings (based on the incentive alignment hypothesis). This approach is based on the 31 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef premise that high equity ownership of managers can help mitigate the risk-avoidance resorted to, by them. 1. Introduction Now,
since, most of the Indian firms already have promoter-managers (Note 2), that is, managers with high equity
stakes, we believe it would be interesting to study if their risk-related behaviour favours all the shareholders
including the dispersed shareholders, when they make external corporate investment decisions, or they resort to
risk aversion in the same fashion as their western counterparts. premise that high equity ownership of managers can help mitigate the risk-avoidance resorted to, by them. Now,
since, most of the Indian firms already have promoter-managers (Note 2), that is, managers with high equity
stakes, we believe it would be interesting to study if their risk-related behaviour favours all the shareholders
including the dispersed shareholders, when they make external corporate investment decisions, or they resort to
risk aversion in the same fashion as their western counterparts. In this paper, we test if the principal-principal conflicts transpire in the form of risk aversion when Indian bidders
seek to merge or acquire. Therefore, we assess the risk-taking behaviour of bidders in an emerging market, i.e. India. We observe that Indian bidders are undertaking value enhancing risky deals as long as the promoters do
not hold majority stake (i.e., more than 50 per cent shares). The Indian bidders resort to risk-aversion when
promoters hold majority stake, that is, when their cash-flow rights in a firm are more than fifty per cent. We posit
that in business group firms this is likely to happen due to ‘tunnelling distortion’ whereas in standalone firms,
this is likely to occur due to ‘portfolio concentration’. However, on investigating the announcement returns of
such deals, we observe that on an average the managers (promoter-managers) do not destroy value. The paper is organized as follows: the next section presents the literature review and research objective; the third
section presents the methodology; the fourth section presents the data and the sample selection; the fifth section
presents the results and a brief discussion, and the sixth section presents our concluding remarks. 2. Literature Review and Research Objective Similarly, Rose and Shepard (1997) show that
due to the challenges and demands of the job that the CEOs of diversified firms are able to fetch greater salaries
and bonuses than their counterparts in non-diversified firms, and not due to the entrenchment reasons. However,
a more recent study by Shekhar and Torbey (2005) found evidence hinting managerial-opportunism in Australian
M&A. They found that increased equity ownership leads to greater diversification; nevertheless, such
diversification deals are not value destroying. A strand of empirical literature on managerial opportunism explores the relationship between equity ownership
and firm value. McConnell and Servaes (1990) observe a non-linear link between equity ownership by corporate
insiders and firm value, with inflection point at the 40-50 per cent ownership level. A similar positive link is
observed in Frye (2004), but Sesil, Kroumova, Kruse, and Blasi (2007) conclude such a link only in favour of
stock options. 32 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Another strand of literature uses M&A deal announcement abnormal returns as a tool to investigate managerial
opportunism. Lewellen, Loderer, and Rosenfeld (1985) report higher abnormal returns on merger announcements
for firms with higher insider (managerial) ownership, thus, implying that agency conflicts are reduced by
increasing management’s equity ownership. Cornett, Hovakimian, Palia, and Tehranian (2003) observe the
negative investor reaction around diversification deal announcements by acquiring banks, thus, implying that
agency concerns are not completely addressed through corporate governance mechanisms like equity & option
holdings; however, Minnick, Unal, and Yang (2011) observe contradictory results for small & medium sized
banks. A considerable stream of literature on managerial opportunism investigates the risk taking behaviour of insiders
(i.e. managers) given their equity ownership and/or compensation structure. Agrawal and Mandelker (1987)
observe a positive relationship between the extent of stock & options held by the managers & their risk taking
behaviour, but Lewellen, Loderer, and Rosenfeld (1989) find very weak evidence in support of this view. The aforementioned discussion suggests that the literature in this area has evolved over the years but the final
word is yet to be said. There are conflicting evidences with regards to equity and option ownership by the
insiders/managers/executives and its impact on firm‟s long term growth strategies like acquisitions (related or
unrelated) and idiosyncratic risk. . Methodology: Risk Taking Behaviour of the Bidders: Tobit and Negative Binomial Regression To study the promoters, or managers, risk taking behaviour, we consider the ratio of post-deal risk over the
pre-deal risk (Lewellen et al., 1989, Williams & Rao, 2006). Since our dependent variable is the standard
deviation of security returns (absolute and market-adjusted), the value of this measure cannot go below zero, that
is, the response variable is bounded on the lower side. Hence, based on the characteristic of our dependent
variable, the model that we test is a corner-solution model, and the use of the ordinary least square regression
would not be appropriate, since it can give us negative predictions. Thus, we employ tobit regression analysis,
which is a hybrid of the OLS regression and the probit regression analysis (Note 3). 𝑃𝑜𝑠𝑡−𝑑𝑒𝑎𝑙 𝑅𝑖𝑠𝑘 𝑜𝑣𝑒𝑟 𝑃𝑟𝑒−𝑑𝑒𝑎𝑙 𝑅𝑖𝑠𝑘𝑖= 𝛼 + 𝛽1𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑖+ 𝑃𝑜𝑠𝑡−𝑑𝑒𝑎𝑙 𝑅𝑖𝑠𝑘 𝑜𝑣𝑒𝑟 𝑃𝑟𝑒−𝑑𝑒𝑎𝑙 𝑅𝑖𝑠𝑘𝑖= 𝛼 + 𝛽1𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑖+
𝛽2𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑂𝑛𝑠𝑖𝑑𝑒𝑟 𝑟𝑠𝑐𝑟𝑒𝑎𝑠𝑒 𝑖𝑛 𝑝𝑜𝑠𝑡 𝑣𝑖𝑜𝑟. 𝑖𝑜𝑛, 𝑎𝑡𝑖𝑜 𝑜𝑓 𝑑𝑖𝑟𝑒𝑐𝑡𝑜𝑟′𝑜 𝑢𝑠𝑒 𝑡𝑒 𝑟𝑎𝑡𝑖𝑜 𝑜𝑓 𝑎𝑛𝑑 𝑡𝑒𝑠𝑖𝑠 𝑐𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑡𝑒 𝑝𝑟𝑒𝑠𝑒𝑛𝑐𝑒 𝑜𝑓 𝑝𝑟𝑖𝑛𝑖𝑐𝑝𝑎𝑙−
𝑡𝑒𝑟2 + 𝛽𝑅𝑒𝑙𝐹𝐹+ 𝛽𝐶𝑜𝑛𝑡𝑟𝑜𝑙𝑠(𝑒𝑔𝐿𝑜𝑔𝐷𝑒𝑎𝑙𝑆𝑖𝑧𝑒𝐴𝑐𝑞𝑃𝑒𝑟𝑐𝑒𝑛𝑡𝐷𝐸𝐵𝐺𝑃𝑜𝑠𝑡1991 𝑖𝑛𝑑𝑢𝑠𝑡𝑟𝑦𝑒𝑓𝑓𝑒𝑐𝑡𝑠𝑦𝑒𝑎𝑟𝑒𝑓𝑓𝑒𝑐𝑡𝑠)
(1) 𝑃𝑜𝑠𝑡−𝑑𝑒𝑎𝑙 𝑅𝑖𝑠𝑘 𝑜𝑣𝑒𝑟 𝑃𝑟𝑒−𝑑𝑒𝑎𝑙 𝑅𝑖𝑠𝑘𝑖= 𝛼 + 𝛽1𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑖+
𝛽2𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑂𝑛𝑠𝑖𝑑𝑒𝑟 𝑟𝑠𝑐𝑟𝑒𝑎𝑠𝑒 𝑖𝑛 𝑝𝑜𝑠𝑡 𝑣𝑖𝑜𝑟. 𝑖𝑜𝑛, 𝑎𝑡𝑖𝑜 𝑜𝑓 𝑑𝑖𝑟𝑒𝑐𝑡𝑜𝑟′𝑜 𝑢𝑠𝑒 𝑡𝑒 𝑟𝑎𝑡𝑖𝑜 𝑜𝑓 𝑎𝑛𝑑 𝑡𝑒𝑠𝑖𝑠 𝑐𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑡𝑒 𝑝𝑟𝑒𝑠𝑒𝑛𝑐𝑒 𝑜𝑓 𝑝𝑟𝑖𝑛𝑖𝑐𝑝𝑎𝑙−
𝑡𝑒𝑟𝑖
2 + 𝛽3𝑅𝑒𝑙𝐹𝐹𝑖+ 𝛽4 𝐶𝑜𝑛𝑡𝑟𝑜𝑙𝑠𝑖(𝑒𝑔. 𝐿𝑜𝑔𝐷𝑒𝑎𝑙𝑆𝑖𝑧𝑒, 𝐴𝑐𝑞𝑃𝑒𝑟𝑐𝑒𝑛𝑡, 𝐷𝐸, 𝐵𝐺, 𝑃𝑜𝑠𝑡1991,𝑖𝑛𝑑𝑢𝑠𝑡𝑟𝑦𝑒𝑓𝑓𝑒𝑐𝑡𝑠, 𝑦𝑒𝑎𝑟𝑒𝑓𝑓𝑒𝑐𝑡𝑠)
(1) 𝑤𝑛𝑂𝑛𝑠𝑖𝑑𝑒𝑟 𝑟𝑠𝑐𝑟𝑒𝑎𝑠𝑒 𝑖𝑛 𝑝𝑜𝑠𝑡 𝑣𝑖𝑜𝑟. 𝑖𝑜𝑛, 𝑎𝑡𝑖𝑜 𝑜𝑓 𝑑𝑖𝑟𝑒𝑐𝑡𝑜𝑟′𝑜 𝑢𝑠𝑒 𝑡𝑒 𝑟𝑎𝑡𝑖𝑜 𝑜𝑓 𝑎𝑛𝑑 𝑡𝑒𝑠𝑖𝑠 𝑐𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑡𝑒 𝑝𝑟𝑒𝑠𝑒𝑛𝑐𝑒 𝑜𝑓 𝑝𝑟𝑖𝑛𝑖𝑐𝑝𝑎𝑙− 𝛽2𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑂𝑛𝑠𝑖𝑑𝑒𝑟 𝑟𝑠𝑐𝑟𝑒𝑎𝑠𝑒 𝑖𝑛 𝑝𝑜𝑠𝑡 𝑣𝑖𝑜𝑟. 𝑖𝑜𝑛, 𝑎𝑡𝑖𝑜 𝑜𝑓 𝑑𝑖𝑟𝑒𝑐𝑡𝑜𝑟′𝑜 𝑢𝑠𝑒 𝑡𝑒 𝑟𝑎𝑡𝑖𝑜 𝑜𝑓 𝑎𝑛𝑑 𝑡𝑒𝑠𝑖𝑠 𝑐𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑡𝑒 𝑝𝑟𝑒𝑠𝑒𝑛𝑐𝑒 𝑜𝑓 𝑝𝑟𝑖𝑛𝑖𝑐𝑝𝑎𝑙− (1) 𝑡𝑒𝑟𝑖
2 + 𝛽3𝑅𝑒𝑙_𝐹𝐹𝑖+ 𝛽4 𝐶𝑜𝑛𝑡𝑟𝑜𝑙𝑠𝑖 (𝑒𝑔. 𝐿𝑜𝑔 𝐷𝑒𝑎𝑙 𝑆𝑖𝑧𝑒, 𝐴𝑐𝑞_𝑃𝑒𝑟𝑐𝑒𝑛𝑡, 𝐷𝐸, 𝐵𝐺, 𝑃𝑜𝑠𝑡_1991,𝑖𝑛𝑑𝑢𝑠𝑡𝑟𝑦 𝑒𝑓𝑓𝑒𝑐𝑡𝑠, 𝑦𝑒𝑎𝑟 𝑒𝑓𝑓𝑒𝑐𝑡 For the pre-deal period risk calculation, we calculate the risk variable over a period of 180 days starting 30 days
before a deal, and for the post-deal risk calculation, we measure risk variable over a 180 day period starting 11
days after the completion of a deal (Williams & Rao, 2006). 𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑖 is the proxy for promoter holdings. We have used two proxies of insider owners in our analysis
on the idiosyncratic risk, and six proxies of the same variable in our analysis on M&A Activity. We have also
employed a squared variable of each of the insider ownership proxies because this variable is likely to have a
curvilinear relationship with the risk measure. This curvilinear relationship is suitably captured by introducing a
squared term of the insider ownership measure. 2. Literature Review and Research Objective Moreover, over time the authors have considered different components of
executive compensation, board structure, presence of block holders and other corporate governance mechanisms
to study the dynamics of managerial risk taking. High promoter ownership in Indian companies makes it a classic case to study the above inter-linkages from the
perspective of principal-principal agency. In the light of the above discussion, we undertake this study to test if
we observe managerial opportunism in the form of principal-principal agency in Indian companies when they
make external corporate investment decisions. Firstly, we address this inquiry by analysing the impact of high
ownership concentration on the risk-taking behaviour of its management, i.e., we test if M&A deals by highly
concentrated bidders lead to decrease in post-deal risk (idiosyncratic). Subsequently, we study the
acquisitiveness (M&A activity) of highly concentrated bidders. Our objective is to test the impact of promoter
holdings on their M&A activity. M&A activity is another proxy for risk, and it mirrors the idiosyncratic risk
proxy. And thirdly, we study if the firms with potential for the presence of principal-principal conflicts make
value-creating or value-destroying acquisitions. . Methodology: Risk Taking Behaviour of the Bidders: Tobit and Negative Binomial Regression We also employ another model to test the risk taking behaviour of insider owners. In this model, we employ the
number of M&A deals, termed as M&A activity (overall, and only diversification only, i.e., deals in unrelated
industries), by bidders in ten years prior to a given deal announcement as the dependent variable. The response
variable in this model is a count variable, and hence we employ negative binomial regression analysis to estimate
the following model: 33 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef 𝑀&𝐴 𝐴𝑐𝑡𝑖𝑣𝑖𝑡𝑦𝑖(𝑡𝑜𝑡𝑎𝑙 𝑎𝑐𝑡𝑖𝑣𝑖𝑡𝑦)= α + 𝛽1𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑖+
𝛽2𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑂𝑛𝑠𝑖𝑑𝑒𝑟 𝑟𝑠𝑐𝑟𝑒𝑎𝑠𝑒 𝑖𝑛 𝑝𝑜𝑠𝑡 𝑣𝑖𝑜𝑟. 𝑖𝑜𝑛, 𝑎𝑡𝑖𝑜 𝑜𝑓 𝑑𝑖𝑟𝑒𝑐𝑡𝑜𝑟′𝑜 𝑢𝑠𝑒 𝑡𝑒 𝑟𝑎𝑡𝑖𝑜 𝑜𝑓 𝑎𝑛𝑑 𝑡𝑒𝑠𝑖𝑠 𝑐𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑡𝑒 𝑝𝑟𝑒𝑠𝑒𝑛𝑐𝑒 𝑜𝑓 𝑝𝑟𝑖𝑛𝑖𝑐𝑝𝑎𝑙−
𝑡𝑒𝑟𝑖
2 + 𝛽3𝑅𝑒𝑙_𝐹𝐹𝑖+ 𝛽4 𝐶𝑜𝑛𝑡𝑟𝑜𝑙𝑠𝑖 (𝑒𝑔. 𝐿𝑜𝑔 𝐴𝑠𝑠𝑒𝑡𝑠, 𝐷𝐸, 𝑃𝑜𝑠𝑡_1991, 𝑖𝑛𝑑𝑢𝑠𝑡𝑟𝑦 𝑒𝑓𝑓𝑒𝑐𝑡𝑠, 𝑦𝑒𝑎𝑟 𝑒𝑓𝑓𝑒𝑐𝑡s.) (2)
𝑀&𝐴 𝐴𝑐𝑡𝑖𝑣𝑖𝑡𝑦𝑖(𝑖𝑛 𝑢𝑛𝑟𝑒𝑙𝑎𝑡𝑒𝑑 𝑖𝑛𝑑. )= α + 𝛽1𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑖+
𝛽2𝐼𝑛𝑠𝑖𝑑𝑒𝑟 𝑂𝑤𝑛𝑂𝑛𝑠𝑖𝑑𝑒𝑟 𝑟𝑠𝑐𝑟𝑒𝑎𝑠𝑒 𝑖𝑛 𝑝𝑜𝑠𝑡 𝑣𝑖𝑜𝑟. 𝑖𝑜𝑛, 𝑎𝑡𝑖𝑜 𝑜𝑓 𝑑𝑖𝑟𝑒𝑐𝑡𝑜𝑟′𝑜 𝑢𝑠𝑒 𝑡𝑒 𝑟𝑎𝑡𝑖𝑜 𝑜𝑓 𝑎𝑛𝑑 𝑡𝑒𝑠𝑖𝑠 𝑐𝑜𝑛𝑐𝑒𝑟𝑛𝑖𝑛𝑔 𝑡𝑒 𝑝𝑟𝑒𝑠𝑒𝑛𝑐𝑒 𝑜𝑓 𝑝𝑟𝑖𝑛𝑖𝑐𝑝𝑎𝑙−
𝑡𝑒𝑟𝑖
2+𝛽3𝑅𝑒𝑙_𝐹𝐹𝑖+ 𝛽4 𝐶𝑜𝑛𝑡𝑟𝑜𝑙𝑠𝑖 (eg. Log Assets, DE, Post_1991, industry effects, year effects.) (3) (2) The dependent variable in models 2 and 3 is the mirror image of the risk proxy used in the model no. 1. In these
models (2 and 3), the increase in the dependent variable would suggest risk aversion, whereas, an increase in the
dependent variable of model 1, would suggest greater risk taking. We have kept all the independent variables in
the model 1, 2 and 3 as the same; however, we have deleted some of the control variables not relevant for M&A
activity models (model no. 2 and 3). Table 1. Statistical properties of key variables (used for risk analysis)
Variable
N
Mean
Median
Stdev
Max
Min
Q1
Q3
Var Ratio
224
1.0179
0.9687
0.4043
2.8801
0.1307
0.7262
1.2722
Mkt. Adj. . Methodology: Risk Taking Behaviour of the Bidders: Tobit and Negative Binomial Regression Var Ratio
224
0.9802
0.9737
0.1763
1.5255
0.3495
0.8719
1.1011
Deal Value
224
83.292
12.708
226.646
1691.064
0.002
3.774
43.862
Percent Acq
224
0.6582
0.6767
0.3176
1.0000
0.1000
0.3925
1.0000
Percent Owned
224
0.7637
0.9107
0.2791
1.0000
0.1000
0.5105
1.0000
Insider Own Proxy1
224
0.4712
0.4625
0.1887
0.8950
0.0000
0.3419
0.6144
Insider Own Proxy2
224
0.4544
0.4522
0.2000
0.8950
0.0000
0.3182
0.6099
Insider Own Proxy3
224
0.4017
0.3977
0.2167
0.8950
0.0000
0.2628
0.5406
Insider Own Proxy4
224
0.6828
0.7016
0.1701
0.9783
0.0412
0.5714
0.8035
Insider Own Proxy5
224
0.5734
0.5745
0.1817
0.9655
0.0369
0.4612
0.7000
Insider Own Proxy6
224
0.3283
0.3377
0.2463
0.8950
0.0000
0.0797
0.5005
Debt
203
20390.04
2134.30
72740.16
739044.80
0.50
595.90
9810.90
DE
224
0.7021
0.5000
0.9540
10.2200
0.0000
0.1150
0.9500
Debt_cost
214
0.0897
0.0755
0.0839
0.6718
0.0000
0.0469
0.1057
Note. This table presents summary statistics of key variables used in the Risk analysis using regression model. The definitions of the variables
are presented in Appendix A. Table 1. Statistical properties of key variables (used for risk analysis) 3.1 Variability in Returns as a Measure of Risk In this study, we consider variability in bidder’s stock returns as one of the measures of risk. We employ two
different measures of risk, a. raw standard deviation of stock returns, and b. market adjusted standard deviation
of stock returns. The first measure is the overall variability in stock returns, whereas the second measure, that is,
the residual standard deviation of returns (market adjusted standard deviation of returns), represents an estimate
of the firm’s unsystematic risk. Lewellen et al. (1989) and Williams and Rao (2006) have employed these
measures of risk to study the impact of management’s stock ownership and options holdings on firm risk. 3.5 Age Group There are five age groups of companies reported on prowess based on the year of incorporation of the firm: a. before 1950, b. between 1951 and 1971, c. between 1972 and 1985, d. between 1986 and 1990, and e. after 1991. Each group represents a different economic environment with respect to industrial licensing, stringency of
controls over growth in size, economic reforms, etc. (Note 4). Academic research has shown younger firms are
greater risk-takers than the older firms (Fink et al., 2004). Thus, we have considered the ‘after-1991’ age group
category provided by prowess as an independent variable to identify younger firms. Table 1B. M&A Activity as per different insider ownership buckets Table 1B. M&A Activity as per different insider ownership buckets Note. This table presents the total and the average of M&A activity undertaken by all the Indian acquirers in our sample, classified as per
different Insider Ownership buckets. Our objective is to observe the M&A activity by acquirers falling in certain Insider-Ownership bucket, and
also to see if with increase / decrease in insider-ownership, the acquisitiveness of acquirers varies. M&A activity is the number of M&A deals
by an acquirer in 10 year prior to a deal announcement. Note. This table presents the total and the average of M&A activity undertaken by all the Indian acquirers in our sample, classified as per
different Insider Ownership buckets. Our objective is to observe the M&A activity by acquirers falling in certain Insider-Ownership bucket, and
also to see if with increase / decrease in insider-ownership, the acquisitiveness of acquirers varies. M&A activity is the number of M&A deals
by an acquirer in 10 year prior to a deal announcement. 3.4 Industry Relatedness Corporate diversification is the diversification of the firm specific risk, also called the idiosyncratic or the
unsystematic risk. As per modern portfolio theory, the unsystematic risk can be managed by the way of
diversification and hence should not reflect in the investor’s valuation of a firm, however, corporate strategy
research differs on this conclusion. In the words of Bettis (1983), ‘Modern financial theory suggests that the
equity markets will not reward unsystematic risk management, but unsystematic risk management lies at the
heart of strategic management’. Thus, Bettis (1983) has put forward an important conundrum faced by academic
researchers in the area of modern financial theory and corporate strategy. The empirical research in these fields is
yet to agree on a common conclusion, since some research supports the diversification discount hypothesis
(Rajan, Servaes, & Zingales, 2000; Laeven & Levine, 2007), whereas other body of work suggests that
diversification creates value (Villalonga, 2004; ref. Martin & Sayrak, 2003), for a detailed review of the
literature on this issue). We employ a dummy variable on industry relatedness to separate diversification deals from the deals in the
related industries. The diversification research has presented different ways of identifying related and unrelated
deals; the most common approach is the use of SIC codes. Researchers have looked at the first two, the first
three or the first four digits of the SIC to identify a diversification deal. We did employ this technique of
identifying the diversification deals by considering the first three digits of the SIC, but found the industry sector
segregation as provided Fama-French was a more reliable indicator of the relatedness of a deal. Thus, based on
the Fama-French forty-nine industry classification, if the deals are in different industries, then the dummy value
of relatedness for the risk analysis part (tobit regressions) is one. 3.3 Insider Ownership Insider Own Proxy1, captures the total promoter holdings, including holdings by persons acting in concert as
promoters. Insider Own Proxy2, represents the sum of holdings by all the Promoters, Indian as well as foreign. Insider Own Proxy3, captures the total of Indian Promoters and persons acting in concert as promoters. Insider
Own Proxy4, captures holdings by promoters as well as non-promoter institutions like mutual funds, UTI (Unit
Trust of India), insurance companies, etc. Insider Own Proxy 5 captures the total percentage of Promoters and
non-promoter FIIs’ holdings. Insider Own Proxy6 captures the sum of holdings by Indian promoters. Thus, we
employ different combinations of promoter and non-promoter holdings to capture the insider ownership effect. 3.2 M&A Activity as a Measure of Risk Amihud and Lev (1981) have looked at M&A activity of bidders to assess the managerial motive for
conglomerate mergers. Thus, borrowing from their paper, we have used M&A activity, that is, the number of
M&A deals by a bidder in ten years prior to a given deal, as another proxy for risk. We have also considered
M&A deals by a bidder only in unrelated industries. Increased M&A deals suggest risk-reduction behaviour on
part of the manager, and vice versa. To capture this measure we have excluded those deals where only assets
were acquired. We have also excluded the deals where the percentage of stake acquired was less than ten. In Table 1B, we have presented a summary of total deals undertaken by Indian acquirers classified as per
insider-ownership bucket they belong to. This table clearly shows that M&A activity, overall and unrelated, is
high at lower insider ownership levels, but decreases when the ownership of promoters is more than 25 per cent. This observation suggests that the classical agency problem, the principal-agent problem is mitigated by
increasing insider ownership. However, when this insider ownership is more than 50 per cent, the table suggests
that there is a slight increase in M&A activity, indicating the presence of principal-principal conflict. We
substantiate this claim by undertaking the negative binomial regression analysis, and the results are discussed in
section 5. 34 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Table 1B. M&A Activity as per different insider ownership buckets
M&A activity in 10 years
Insider Ownership (Proxy1)
Less than 10%
10% to 25%
25% to 50%
Greater than 50%
Sum of No. of deals
36
26
104
111
Average of No. of deals
5.14
2.17
0.95
1.17
Sum of No. of Unrelated Deals
22
19
44
52
Average of No. of Unrelated Deals
3.14
1.58
0.40
0.55
Note. This table presents the total and the average of M&A activity undertaken by all the Indian acquirers in our sample, classified as per
different Insider Ownership buckets. Our objective is to observe the M&A activity by acquirers falling in certain Insider-Ownership bucket, and
also to see if with increase / decrease in insider-ownership, the acquisitiveness of acquirers varies. M&A activity is the number of M&A deals
by an acquirer in 10 year prior to a deal announcement. 3.6 Other Controls Leverage: We have used debt-equity ratio as one of the control variables, since it is an important determinant of
stock return volatility (Guay, 1999). Increase in leverage leads to increase in risk. We have used the square root
of the debt-equity ratio of the acquirer, since this transformation helps us make the variable more normally
distributed. 35 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef BG: Business Group (BG) affiliation is a significant factor unique to emerging economies, and to capture the
effect of this factor on the risk taking behaviour of its affiliates we employ a dummy variable to identify the
business group affiliated firms in our model. BG: Business Group (BG) affiliation is a significant factor unique to emerging economies, and to capture the
effect of this factor on the risk taking behaviour of its affiliates we employ a dummy variable to identify the
business group affiliated firms in our model. Industry Controls: We have used control variables to isolate industry effects on the risk-taking behaviour of
bidders. We have controlled for three relevant industries, namely, a. Construction material, building/construction
and engineering, b. IT consulting and services, and software, and c. oil and gas, petrochemicals, power and other
energy and power. Year Effects: We have controlled for 2008 and 2009, because after 2007 there was a sharp drop in M&A activity
in India due to the global economic downturn. The abnormal return is captured as: The abnormal return is captured as: ARit = Rit – E (Rit)
(5) (5) The abnormal return is then aggregated over different event window, where T represents the length of the
window: 𝐶𝐴𝑅𝑖
𝑇= ∑
𝐴
𝑡𝑛
𝑡=𝑡1
𝑅𝑖𝑡
(6) (6) The 𝐸(𝑅𝑖𝑡) is the expected return from the market model for a bidder I, and 𝑅𝑚𝑡 is the return on market
portfolio for day t. 𝑅𝑖𝑡 is the actual return of the bidder i for time t. 𝐴𝑅𝑖𝑡 is the abnormal return for the event i
on the day t. 𝐶𝐴𝑅𝑖
𝑇 is the cumulative abnormal return for the event window T, from day t1 to tn. 3.7 Measuring Abnormal Returns For studying the announcement effects of deals done by firms with high promoter holdings versus the firms with
low promoter holdings, we use the event study methodology (Brown & Warner, 1985; MacKinlay, 1997). We use
the market model to estimate the returns, and observe the difference between the actual return and the expected
return as the abnormal return. We capture these abnormal returns over different event windows. The market
model that is estimated over 200 days is: E(Rit) = α + β Rmt
(4)
ARit = Rit – E (Rit)
(5) (4) E(Rit) = α + β Rmt
(4) 5. Results and Discussion A large number of Indian businesses are organized as business groups as a consequence of India’s business
history and the institutional voids that are generally observed in the emerging markets (Khanna & Palepu,
2000b). Most of these business groups are family owned with high promoter holdings, as a classic feature of
their ownership structure (Huchet & Ruet, 2006). On one hand, there is a likelihood of tunnelling in business
groups (Bertrand, Mehta, & Mullainathan, 2002, Khanna & Rivkin, 2001), that is, the expropriation of wealth
from minority shareholders and channelling them to the group affiliated under-performing firms (Shleifer &
Vishny, 1997); whereas, contrary to this, there is empirical evidence in favour of family businesses that suggests
that such firms do not destroy value on making acquisitions (Caprio, Croc, & Del Giudice, 2011). Our empirical
study sample comprises family owned business-group affiliated firms and stand-alone firms. Thus, in our
opinion, undertaking this study has helped us understand the risk-taking behaviour of these firms across different
ownership structures, and more importantly has helped us gather empirical evidence related to
principal-principal conflicts arising due to the aforementioned ownership structures. k Taking Behaviour of the Bidders: Tobit Regression Analysis, and Negative Binomial Regression Ana To understand the risk taking behaviour of bidding firms, we study the changes to firm risk after an acquisition
or a merger deal, and if these changes are related to the ownership structure of the bidder. We also look at the
past deal activity levels (M&A activity -total and in unrelated industries) by bidders as another proxy for the
risk-taking. Thus, we undertake an inquiry in to the risk-taking behaviour of insider owners which would help us
make informed conclusions on the principal-principal dynamics at play in Indian companies. As discussed in the methodology section, we have employed different proxies of insider ownership and have also
considered the squared term of each of the proxies to capture the curvilinear relationship between the risk
measure and insider ownership. The market-adjusted measure of risk is a better measure for our regression
analysis as compared to the raw measure since the same reflects the firm specific risk. 4. Data Our data set comprises mergers and acquisition deals by Indian acquirers from 2001 to 2010. The data on
mergers and acquisition deals in India and also the stock price data (for the event study) are taken from Thomson
Reuters’ Thomson One database. We have taken bidder’s company financial information from the CMIE’s
Prowess (Note 5) database. Table 2. Pairwise correlation coefficients of key variables
Variables
Var Ratio
Mkt. Adj. Var Ratio
Deal
Value
Acq_percent
Percent
Own
Insider Own
Proxy1
Executive
Director Comp
Manag-erial
Comp
Debt
DE
Mkt. Adj. Var
Ratio
0.92
1
(0.00)
Deal Value
0.12
0.09
1
(0.07)
(0.16)
Acq_percent
-0.04
-0.06
-0.09
1
(0.52)
(0.35)
(0.19)
Percent Own
-0.06
-0.06
-0.02
0.73
1
(0.40)
(0.37)
(0.71)
(0.00)
Insider Own
Proxy1
0.07
0.11
0.16
0.09
-0.03
1
(0.31)
(0.09)
(0.02)
(0.20)
(0.61)
Exec. Director
Compensation
0.01
0.01
0.37
-0.11
-0.02
0.08
1
(0.93)
(0.86)
(0.00)
(0.19)
(0.82)
(0.31)
Managerial
Compensation
-0.04
-0.04
0.35
-0.12
0.00
0.02
0.98
1
(0.58)
(0.61)
(0.00)
(0.09)
(0.98)
(0.82)
(0.00)
Debt
-0.05
-0.05
0.56
-0.20
-0.01
0.15
0.45
0.42
1
(0.50)
(0.48)
(0.00)
(0.00)
(0.90)
(0.03)
(0.00)
(0.00)
DE
0.05
0.05
-0.01
0.06
-0.01
0.07
-0.03
-0.05
0.03
1
(0.44)
(0.42)
(0.91)
(0.38)
(0.88)
(0.32)
(0.72)
(0.50)
(0.71)
Note. This table reports pairwise correlation coefficients of key variables used for Risk Analysis. p-values are reported in the parenthesis. Table 2. Pairwise correlation coefficients of key variables Table 2. Pairwise correlation coefficients of key variables 36 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef For our study, we have considered deals done by Indian acquirers; so, these deals are domestic and cross border
as well. We have filtered only the completed deals; hence the deals that were announced but were terminated, are
out of the purview of our study. We exclude the following types of deals: the acquisition of assets, buybacks, bankruptcy acquisitions, and
divestiture. We also exclude those deals where acquirer is an investor group, deals where the value of the
transaction is undisclosed or unavailable, deals by private firms, government owned enterprises and by financial
firms. There are deals that are announced in parts, i.e., the deals where the acquirer and the target is same, but the deal
value and other deal characteristics differ. In such cases of multiple announcements, we have included the deal
with the highest percentage acquired. 4. Data We have filtered out the deals where the percentage acquired is less than
ten. However, to be included in our data set, a deal must have all the required data with respect to closing stock
prices and other financial variables used in the study. 5. Results and Discussion The models III and IV (in Table 3) report results on regression models that use the overall standard deviation of
stock returns as the response variable, whereas, the models I and II report the results on regression models that
use the market-adjusted standard deviation of returns as the response variable. Table 4 and 5 report results on the
overall M&A activity and the activity in unrelated industries, respectively; different columns represent models
using different insider ownership proxies. The relationship of the insider ownership with risk is non-linear in nature; the coefficients of the insider
ownership proxy term and its squared term (Table 3) suggest that the relationship is positive up to an inflection
point, after which the relationship turns negative. Thus, the insider owners undertake risky investments up to a
certain level of their holdings, but if their holdings are more than that level, they tend to resort to risk-avoidance
(in case of the model I, this turning point is at 45.07 percentage holdings of insider owners (Note 6)). This means
that up to a level of insider holdings, principal-principal conflicts are well prevented, but if insiders own stake
beyond the majority threshold of close to 50 per cent, we can expect principal-principal conflicts to be present. We observe that the same curvilinear relationship is present in the risk models (Table 3) and also the M&A
activity models (Table 4 and 5). The signs of the coefficients of the insider-ownership proxy and its squared term
in the M&A activity model are exactly opposite to the signs in the risk model. 37 International Journal of Economics and Finance Vol. 8, No. 7; 2016 Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Table 3. Bidder risk taking and insider ownership - Tobit regression
Variables
Market Adj. Risk -Model I
Market Adj. 5. Results and Discussion Risk - Model II
Risk –Model III
Risk –Model IV
insiderown_proxy6
0.302**
0.3710
[0.017]
[0.241]
insiderown_proxy6_sqr
-0.335**
-0.4230
[0.046]
[0.328]
insiderown_proxy2
0.412**
0.6920
[0.032]
[0.121]
insiderown_proxy2_sqr
-0.380*
-0.6610
[0.071]
[0.189]
Rel_FF
0.02610
0.02410
0.03310
0.03050
[0.224]
[0.266]
[0.527]
[0.563]
Log_deal_size
0.0101**
0.0112**
0.0300**
0.0318***
[0.030]
[0.022]
[0.011]
[0.009]
Acq_percent
-0.0438
-0.0469
-0.0557
-0.0650
[0.248]
[0.209]
[0.497]
[0.429]
DE
0.0246
0.0349
0.0765
0.0876*
[0.254]
[0.104]
[0.120]
[0.071]
BG
-0.0517**
-0.0452**
-0.0852
-0.0774
[0.018]
[0.036]
[0.104]
[0.131]
Post_1991
0.0364
0.0400*
0.0664
0.0684
[0.136]
[0.098]
[0.244]
[0.229]
ConsMatBldg
0.0412
0.0497
0.1090
0.1280
[0.213]
[0.161]
[0.173]
[0.110]
ITConltServ
0.0075
0.0203
0.0329
0.0517
[0.808]
[0.521]
[0.653]
[0.492]
OilGasPow
-0.0040
-0.0084
-0.0195
-0.0212
[0.907]
[0.814]
[0.809]
[0.797]
Yr._2009
-0.183***
-0.177***
-0.391***
-0.385***
[0.000]
[0.000]
[0.000]
[0.000]
Yr._2008
0.0805***
0.0837***
0.150**
0.149**
[0.005]
[0.004]
[0.030]
[0.033]
Sigma
0.152***
0.153***
0.361***
0.361***
[0.000]
[0.000]
[0.000]
[0.000]
Pseudo R-Sq
-0.4500
-0.4430
0.2150
0.2190
F
6.5230
6.5160
5.3930
5.3720
p
0.0000
0.0000
0.0000
0.0000
LL
103.60
103.10
-89.85
-89.44
Note. This table presents the results of the tobit regression analysis on the risk taking behaviour of insider owners. We have used robust Table 3. Bidder risk taking and insider ownership - Tobit regression Note. This table presents the results of the tobit regression analysis on the risk taking behaviour of insider owners. d d
h d
hil
i
i
h
d l
𝑑
𝑙
𝑘
𝑑
𝑙
𝑘
𝛽
𝑑 + β3Rel_FFi + β4 Controlsi. P-values are in the parentheses. * p<0.1, ** p<0.05, *** p<0.01. Risk is the square root of the ratio of variances
after and before the deal. Market adjusted variances is the ratio of the variables after and before the deal adjusted for market wide variance. The total number of observations in the following models is 224. In the Anglo-American context, we do find some empirical evidence where insider ownership has non-linear
relationship with risk taking (Wright, Kroll, Lado, & Van Ness, 2002), and also, firm value (McConnel &
Servaes, 1990). This relationship is comprehensible if one considers the fact that a professional manager’s
employment risk is non-diversifiable. However, the non-linearity observed (between risk/M&A activity and
insider ownership) in the Indian corporate risk-taking is interesting, yet puzzling. The manager in Indian companies is oftentimes an insider, that is, a promoter. Such an owner-manager, who is an
entrepreneur, doesn’t face the non-diversifiable employment risk. Note. This table presents the results of the tobit regression analysis on the risk taking behaviour of insider owners. We g
β2 Insider Ownrscrease in post vior.ion,atio of director′o use the ratio of and thesis concerning the presence of prinicpal −t different insider ownership proxies. The Model: M&A Activityi = α + β1Insider Owni + 5. Results and Discussion Although, one could argue that his wealth
might be ill-diversified since the substantial part of his wealth is invested in a single firm. However, this
argument of ‘portfolio concentration’ would hold only for the stand alone companies, i.e., the companies that are
not affiliated to any business group. Such companies form one-third of our sample. 38 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Table 4. Bidder M&A activity and insider ownership - negative binomial regression
Variable
insiderown_
proxy1
insiderown_
proxy2
insiderown_
proxy3
insiderown_
proxy4
insiderown_
proxy5
insiderown_
proxy6
insiderown
-4.383***
-3.112**
-3.842***
-7.339***
-4.944***
-1.1410
[0.003]
[0.024]
[0.000]
[0.000]
[0.010]
[0.227]
insiderown_sqr
4.142***
2.994**
3.845***
5.342***
3.694**
1.1710
[0.006]
[0.037]
[0.003]
[0.001]
[0.037]
[0.337]
Rel_FF
0.0203
0.0044
0.0162
-0.0830
-0.0281
-0.0219
[0.905]
[0.979]
[0.924]
[0.598]
[0.865]
[0.902]
Log_Assets
0.272***
0.282***
0.301***
0.314***
0.296***
0.303***
[0.000]
[0.000]
[0.000]
[0.000]
[0.000]
[0.000]
DE
0.0424
0.0342
0.1920
0.0642
-0.0033
0.0818
[0.795]
[0.832]
[0.200]
[0.686]
[0.984]
[0.580]
Post_1991
-0.1190
-0.1290
-0.0650
-0.1020
-0.0994
-0.1450
[0.582]
[0.548]
[0.764]
[0.632]
[0.647]
[0.508]
ConsMatBldg
0.411**
0.521***
0.454**
0.767***
0.488**
0.656***
[0.046]
[0.009]
[0.026]
[0.000]
[0.014]
[0.001]
ITConltServ
0.776***
0.854***
0.963***
0.640***
0.711***
0.999***
[0.003]
[0.003]
[0.001]
[0.005]
[0.003]
[0.002]
OilGasPow
0.0161
0.0080
-0.0816
-0.0133
0.0671
-0.0274
[0.952]
[0.976]
[0.747]
[0.959]
[0.792]
[0.913]
Yr._2009
0.2960
0.2740
0.1890
0.2460
0.2550
0.2130
[0.108]
[0.136]
[0.280]
[0.175]
[0.155]
[0.241]
Yr._2008
0.1670
0.1530
0.0958
0.1600
0.1580
0.1020
[0.481]
[0.521]
[0.684]
[0.488]
[0.504]
[0.668]
lnalpha
-0.819***
-0.733**
-0.858***
-0.978***
-0.864***
-0.653**
[0.006]
[0.011]
[0.006]
[0.003]
[0.005]
[0.027]
N
204
204
204
204
204
204
pseudo R-Sq
0.0930
0.0870
0.0970
0.1030
0.0940
0.0810
Chi-Sq
80.870
78.090
89.790
74.010
71.680
70.440
p
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
LL
-295.9
-297.7
-294.6
-292.7
-295.4
-299.7
Note. The overall M&A Activity is the dependent variable. This table presents negative binomial regression results for different models with
different insider ownership proxies The Model: M&A Activity = α + β Insider Own + Table 4. Bidder M&A activity and insider ownership - negative binomial regression nin post vior.ion, atio of director′o use the ratio of and thesis concerning the presence of prinicpal −teri
2Onsider rscrease β2Insider Ownin post vior.ion, atio of director′o use the ratio of and thesis concerning the presence of prinicpal −teri
2Onsider rscrease
+ β3Rel_FFi + β4 Controlsi (eg.Log Assets,DE,Post_1991, industry effects,year effects.), is estimated using negative binomial regression
analysis. P-values are in the parentheses. erall M&A Activity is the dependent variable. This table presents negative binomial regression results for different models wit 5. Results and Discussion * p<0.1, ** p<0.05, *** p<0.01. The regression is estimated with White robust standard errors. The
total number of observations in the following modes is 204. β2Insider Ownin post vior.ion, atio of director′o use the ratio of and thesis concerning the presence of prinicpal −teri
2Onsider rscrease
+ β3Rel_FFi + β4 Controlsi (eg.Log Assets,DE,Post_1991, industry effects,year effects.), is estimated using negative binomial regression
analysis. P-values are in the parentheses. * p<0.1, ** p<0.05, *** p<0.01. The regression is estimated with White robust standard errors. The
total number of observations in the following modes is 204. The two-thirds of the firms in our sample are business group affiliated firms, where the promoter-manager has
his wealth invested in other group companies as well. Although it is difficult to assess the extent of portfolio
diversification thus attained by a promoter manager, the argument of investment concentration weakens. But,
there is a possibility that a business group firm is resorting to ‘tunnelling’ (Morck & Yeung, 2003). This can be
interpreted as an indication that it is likely that the promoter managers are doing more risky projects through the
firms in which they have lower cash flow rights compared to the control exhibited. Therefore, it is probable that
through the lower layer firms the promoters are taking more risks, tunnelling profits to higher layer firms when
profits occur, but when losses are suffered, the lower layer firms absorb them. Since, higher layer firms are the
ones where promoter holds higher stake, i.e., higher cash flow rights, these are the firms where risk-aversion is
resorted to. Thus, the evidence of risk-reduction and increased diversification (& overall M&A) activity beyond
a level of insider ownership around the majority-stake level, points to the astounding fact that these
promoter-managers are pursuing goals that are different from the objectives of the minority (dispersed)
shareholders. We observe that deal size has a positive association with the risk measure, suggesting that the principal-principal
conflict is more of a concern in the smaller sized deals, but the same is well avoided in the bigger deals. We have
employed firm size measured as the log of total assets of bidder in the M&A activity model (Table 4 and 5), 39 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef since in the context of deal activity, it is a more appropriate control variable than the deal size. 5. Results and Discussion since in the context of deal activity, it is a more appropriate control variable than the deal size. Table 5. Bidder M&A activity in unrelated industries and insider ownership - negative binomial regression
Variable
insiderown_pro
xy1
insiderown_pro
xy2
insiderown_pro
xy3
insiderown_pro
xy4
insiderown_prox
y5
insiderown_prox
y6
insiderown
-4.408**
-3.037*
-5.259***
-7.361**
-4.495
-1.5040
[0.037]
[0.087]
[0.000]
[0.040]
[0.136]
[0.236]
insiderown_sqr
3.943*
2.783
4.695***
5.201*
3.0720
1.4640
[0.064]
[0.134]
[0.007]
[0.061]
[0.260]
[0.333]
Rel_FF
0.3160
0.2780
0.3050
0.2040
0.2640
0.2360
[0.177]
[0.235]
[0.178]
[0.351]
[0.241]
[0.320]
Log_Assets
0.274***
0.285***
0.313***
0.330***
0.306***
0.313***
[0.001]
[0.001]
[0.000]
[0.000]
[0.000]
[0.000]
DE
0.0796
0.0804
0.3140
0.1030
0.0236
0.1610
[0.727]
[0.720]
[0.107]
[0.639]
[0.918]
[0.438]
Post_1991
0.0902
0.0758
0.2510
0.1010
0.1080
0.0807
[0.738]
[0.781]
[0.360]
[0.702]
[0.688]
[0.773]
ConsMatBldg
0.832**
0.967***
0.755**
1.195***
0.907***
1.098***
[0.017]
[0.003]
[0.028]
[0.000]
[0.006]
[0.001]
ITConltServ
1.104***
1.209***
1.308***
0.944***
1.049***
1.384***
[0.000]
[0.000]
[0.000]
[0.003]
[0.000]
[0.000]
OilGasPow
0.2030
0.1890
0.1090
0.1350
0.2230
0.1520
[0.575]
[0.605]
[0.753]
[0.715]
[0.530]
[0.664]
Yr._2009
0.453*
0.4190
0.2570
0.3740
0.4030
0.3400
[0.086]
[0.111]
[0.216]
[0.137]
[0.119]
[0.171]
Yr._2008
0.1910
0.1810
0.1210
0.2150
0.1900
0.1510
[0.573]
[0.600]
[0.714]
[0.532]
[0.580]
[0.658]
lnalpha
-0.2370
-0.1680
-0.4780
-0.2490
-0.2510
-0.0838
[0.454]
[0.588]
[0.186]
[0.435]
[0.426]
[0.783]
N
204
204
204
204
204
204
pseudo R-Sq
0.1000
0.0950
0.1210
0.1030
0.1000
0.0920
Chi-Sq
55.290
53.360
73.130
55.310
52.620
55.690
p
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
LL
-203.7
-204.9
-199
-202.9
-203.8
-205.6
Note. The M&A Activity in unrelated industries is the dependent variable. This table presents negative binomial regression results for different Bidder M&A activity in unrelated industries and insider ownership - negative binomial regression Industry relatedness is a dummy variable employed to separate diversification deals from the deals in the related
industries. The proponents of portfolio theory under the aegis of modern financial theory have always considered
diversification as a means of reducing unsystematic risk (Wagner & Lau, 1971, Statman, 1987). However,
Lubatkin and O’Neill (1987) have argued and empirically shown that the implications of the portfolio theory fail
to hold when corporations diversify. In the words of Lubatkin and O’Neill (1987), ‘Diversification will not
reduce unsystematic risk because management actions may alter the underlying risk profiles of combining
businesses’. They argue that the success of a diversification deal depends largely on a manager’s ability to
handle the process. The M&A Activity in unrelated industries is the dependent variable. This table presents negative binomial regression results fo We observe that higher debt-equity levels lead to greater risk taking (model IV), but the group affiliation makes Note. The M&A Activity in unrelated industries is the dependent variable. This table presents negative binomial reg + β2 Insider Ownrscrease in post vior.ion, atio of director′o use the ratio of and thesis concerning the presence of prinicpal −teri
2Onsider
+ β3Reli + β4 Controlsi, is estimated using negative binomial regression. P-values are in the parentheses. * p<0.1, ** p<0.05, *** p<0.01.
The regression is estimated with White robust standard errors. The total number of observations in the following modes is 204. 5.2 Bidder Returns on M&A Announcements and the Promoter Holdings We have presented a summary of significant cumulative abnormal returns (CARs) in Table 6, classified as per
promoter holdings. When we segregate the bidder abnormal returns in three categories of promoter holdings, we
observe significant positive abnormal returns in different event windows for those bidders who have promoter
holdings above 26 per cent (ref. Table 6, significant mean values are in bold). Twenty-six per cent holding acts as
an important cut-off since a shareholder can block special resolutions with shareholdings in excess of
twenty-five per cent (as per Companies Act, 1956). Thus, for promoter holdings of twenty-six per cent or more,
the deal announcement abnormal returns are persistently positive across different event windows leading up to
the day of the announcement. Table 6. Bidder abnormal returns and promoter holdings
No. of
Obs. Day 0
Day -1
to 0
Day -3
to 0
Day -5
to 0
Day -7
to 0
Day 0
to 1
Day 0 to
7
Day -1
to 1
Day -3
to 3
Day -2
to 0
Day -2
to 1
Day -3
to 1
Day -3
to -1
Panel I: Promoter Holdings<26%
28
Mean
0.00
0.00
-0.01
-0.01
-0.01
0.01
0.02
0.01
0.01
0.00
0.00
0.00
-0.01
P-value
0.69
0.92
0.64
0.52
0.54
0.36
0.27
0.64
0.63
0.70
0.80
0.95
0.34
Panel II: Promoter holdings >= 26% but less than 50%
112
Mean
0.00
0.01
0.01
0.01
0.02
0.00
-0.01
0.01
0.01
0.01
0.01
0.01
0.01
P-value
0.14
0.04
0.03
0.04
0.07
0.65
0.06
0.20
0.43
0.08
0.28
0.11
0.10
Panel III: Promoter Holdings >= 50%
137
Mean
0.01
0.02
0.02
0.02
0.01
0.01
0.01
0.02
0.01
0.02
0.02
0.02
0.01
P-value
0.00
0.00
0.00
0.02
0.08
0.01
0.43
0.01
0.04
0.00
0.01
0.01
0.11
Note. This table presents a summary of bidder abnormal returns, i.e., cumulative abnormal returns over different event windows. For
example, event window ‘Day -1 to 0’ presents cumulative abnormal returns over two days – a day before the event and the event day. The
segregation is based on the significant ownership thresholds, beyond which a shareholder can either block special resolutions (in case of
ownership of 26 per cent or more), or has majority holdings (in case of 50 per cent or more). No. of obs. are the number of deals that satisfied
the cut-off levels of promoter holdings. 5. Results and Discussion Our results on the industry relatedness (Table 3) –show positive relationship between the
diversification deals and the risk-taking behaviour of bidders, however, the coefficient is not significant. Moreover, this co-efficient shows the negative relationship with risk measure in the M&A activity model, yet
again it is not significantly different from zero. Hence, with respect to the diversification dummy (industry
relatedness), we are unable to support either of the contradictory propositions (Wagner & Lau, 1971 versus
Lubatkin & O’Neill, 1987). Industry relatedness is a dummy variable employed to separate diversification deals from the deals in the related
industries. The proponents of portfolio theory under the aegis of modern financial theory have always considered
diversification as a means of reducing unsystematic risk (Wagner & Lau, 1971, Statman, 1987). However,
Lubatkin and O’Neill (1987) have argued and empirically shown that the implications of the portfolio theory fail
to hold when corporations diversify. In the words of Lubatkin and O’Neill (1987), ‘Diversification will not
reduce unsystematic risk because management actions may alter the underlying risk profiles of combining
businesses’. They argue that the success of a diversification deal depends largely on a manager’s ability to
handle the process. Our results on the industry relatedness (Table 3) –show positive relationship between the
diversification deals and the risk-taking behaviour of bidders, however, the coefficient is not significant. Moreover, this co-efficient shows the negative relationship with risk measure in the M&A activity model, yet
again it is not significantly different from zero. Hence, with respect to the diversification dummy (industry
relatedness), we are unable to support either of the contradictory propositions (Wagner & Lau, 1971 versus
Lubatkin & O’Neill, 1987). We observe that higher debt-equity levels lead to greater risk taking (model IV), but the group affiliation makes 40 International Journal of Economics and Finance www.ccsenet.org/ijef Vol. 8, No. 7; 2016 Vol. 8, No. 7; 2016 them risk-averse (Table 3). An interesting result to be noted with respect to the control variables is the one with
respect to the year dummy for 2009. In 2009, bidders exhibited risk aversion across all deals. them risk-averse (Table 3). An interesting result to be noted with respect to the control variables is the one with
respect to the year dummy for 2009. In 2009, bidders exhibited risk aversion across all deals. 5.2 Bidder Returns on M&A Announcements and the Promoter Holdings Mean –is the mean value of the cumulative abnormal returns over a given event window of all the
observations. Table 6. Bidder abnormal returns and promoter holdings 5. Results and Discussion Fink, Grullon, Fink, and Weston (2004) have empirically shown that younger firms are risk takers, but our
empirical analysis fails to support this view. In fact, the age of the firm has no significant effect on the risk
behaviour of its managers (except in one case, Table 3). 6. Conclusion The cash-flow
rights are much lower compared to the control held (through the pyramid) in the lower layer firms, and therefore,
a promoter manager can do risky investments, tunnel the gains out, and distance himself from the burden of
losses when suffered. The above evidence suggests that principal-principal conflicts are likely to exist in Indian firms, especially in
bidding firms with very high ownership concentration. However, on studying the abnormal returns on
deal-announcements, we observe that when the Indian bidders with high ownership concentration announce
M&A deals, they create value. Therefore, even if the deals undertaken by Indian acquirers reduce post-deal risk,
such deals do not destroy shareholder wealth. Thus, the subsequent result on positive abnormal returns on deal
announcements weakens the possibility of the presence of principal-principal conflicts that adversely affect
shareholder wealth. Acknowledgements The authors would like to thank Prof. Purusottam Sen and Prof. Manisha Chakrabarty, and the conference
participants and the discussants at the 6th IIM Ahmedabad Doctoral Colloquium 2013 and at the 51st Annual
Eastern Finance Association Meeting 2015, for their valuable suggestions, feedback and comments. 6. Conclusion In this study, we look at the agency theory relevant to emerging economies, which is called as the
principal-principal agency conflict in the popular academic literature. There is extant empirical evidence pointing
to opportunism undertaken by managers in the widely held Anglo-American companies. The primary driver for
managers to resort to risk aversion is their employment risk which is non-diversifiable. We undertake an inquiry into the risk-taking behaviour of promoter managers in an emerging economy, which
presents us with a distinctive business setting with characteristics like high ownership concentration and
complex structures -in the form of business groups with cross holdings and pyramidal arrangements. This
context posits the possibility of the existence of the principal-principal agency between the dispersed
shareholders and the majority shareholders. On conducting an analysis on the risk-taking behaviour of bidders, we observe a curvilinear relationship between
the insider ownership and the idiosyncratic risk of bidders. We observe a similar curvilinear relationship between
high ownership concentration and the diversification activity (as well as overall M&A activity) undertaken by
promoter-managers. The direct relationship between risk-taking behaviour and ownership concentration, and the
indirect relation between diversification activity and insider ownership, is consistent with the theoretical
predictions. However, the non-linearity in these relationships suggest that insider managers resort to risk
aversion beyond the majority (or the near-majority) level of ownership. The above evidence on risk-taking behaviour is quite intriguing, since the ‘non-diversification of employment
risk’ argument doesn’t hold for business-group firms which comprise two-thirds of our sample. But, the 41 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef business-group affiliated firms have a tendency to resort to tunnelling, and that could be distorting their
risk-taking behaviour. The promoter-manager could be using lower layers firms for undertaking risky projects,
and cushioning the higher level firms (where higher stakes are held) from the downsides of risks. The cash-flow
rights are much lower compared to the control held (through the pyramid) in the lower layer firms, and therefore,
a promoter manager can do risky investments, tunnel the gains out, and distance himself from the burden of
losses when suffered. business-group affiliated firms have a tendency to resort to tunnelling, and that could be distorting their
risk-taking behaviour. The promoter-manager could be using lower layers firms for undertaking risky projects,
and cushioning the higher level firms (where higher stakes are held) from the downsides of risks. References Agrawal, A., & Mandelker, G. N. (1987). Managerial incentives and corporate investment and financing
decisions. The Journal of Finance, 42(4), 823-837. http://dx.doi.org/10.1111/j.1540-6261.1987.tb03914.x Agrawal, A., & Mandelker, G. N. (1987). Managerial incentives and corporate investment and financing
decisions. The Journal of Finance, 42(4), 823-837. http://dx.doi.org/10.1111/j.1540-6261.1987.tb03914.x Amihud, Y., & Lev, B. (1981). Risk reduction as a managerial motive for conglomerate mergers. The Bell
Journal of Economics, 605-617. http://dx.doi.org/10.2307/3003575 Bertrand, M., Mehta, P., & Mullainathan, S. (2002). Ferreting out tunneling: An application to Indian business
groups. Quarterly Journal of Economics, 117, 121-48. http://dx.doi.org/10.1162/003355302753399463 Bettis, R. A. (1983). Modern financial theory, corporate strategy and public policy: Three conundrums. Academy
of Management Review, 8(3), 406-415. http://dx.doi.org/10.5465/AMR.1983.4284379 Brown, S. J., & Warner, J. B. (1985). Using daily stock returns: The case of event studies. Journal of Financial
Economics, 14(1), 3-31. http://dx.doi.org/10.1016/0304-405X(85)90042-X Caprio, L., Croci, E., & Del Giudice, A. (2011). Ownership structure, family control, and acquisition decisions. Journal of Corporate Finance, 17(5), 1636-1657. http://dx.doi.org/10.1016/j.jcorpfin.2011.09.008 Chen, Y. Y., & Young, M. N. (2010). Cross-border mergers and acquisitions by Chinese listed companies: A
principal–principal
perspective. Asia
Pacific
Journal
of
Management,
27(3),
523-539. http://dx.doi.org/10.1007/s10490-009-9150-7 Cornett, M. M., Hovakimian, G., Palia, D., & Tehranian, H. (2003). The impact of the manager–shareholder
conflict
on
acquiring
bank
returns. Journal
of
Banking
&
Finance,
27(1),
103-131. http://dx.doi.org/10.1016/S0378-4266(01)00210-2 Dharwadkar, B., George, G., & Brandes, P. (2000). Privatization in emerging economies: An agency theory
perspective. Academy
of
Management
Review,
25(3),
650-669. http://dx.doi.org/10.5465/AMR.2000.3363533 Fink, J., Grullon, G., Fink, K., & Weston, J. (2004). Firm age and fluctuations in idiosyncratic risk. Available at
SSRN 891173. Frye, M. B. (2004). Equity‐based compensation for employees: Firm performance and determinants. Journal of
Financial Research, 27(1), 31-54. http://dx.doi.org/10.1111/j.1475-6803.2004.00076.x Guay, W. R. (1999). The sensitivity of CEO wealth to equity risk: An analysis of the magnitude and determinants. Journal of Financial Economics, 53(1), 43-71. http://dx.doi.org/10.1016/S0304-405X(99)00016-1 Huchet, J., & Ruet, J. (2006). Globalisation and Opening Markets in Developing Countries and Impact on
National Firms and Public Governance: The Case of India. Project Report, Project co-finance by the
European Union under the EU-India Small Projects Facility Programme. Jensen, M. C. (1986). Agency cost of free cash flow, corporate finance, and takeovers. American Economic
Review, 76(2), 323-329. 42 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Jensen, M. C. (1993). The modern industrial revolution, exit, and the failure of internal control systems. Journal
of Finance, 48(3), 831-880. http://dx.doi.org/10.1111/j.1540-6261.1993.tb04022.x Jensen, M. References C., & Meckling, W. H. (1976). Theory of the firm: Managerial behavior, agency costs and ownership
structure. Journal
of
Financial
Economics,
3(4),
305-360. http://dx.doi.org/10.1016/0304-405X(76)90026-X Khanna, T., & Palepu, K. (2000a). Emerging market business groups, foreign intermediaries, and corporate
governance. In Morck, R. (Ed.), Concentrated Corporate Ownership (pp. 265-92). Chicago, IL: University
of Chicago Press. Khanna, T., & Palepu, K. (2000b). The future of business groups in emerging markets: Long-run evidence from
Chile. Academy of Management journal, 43(3), 268-285. http://dx.doi.org/10.2307/1556395 Khanna, T., & Rivkin, J. W. (2001). Estimating the performance effects of business groups in emerging markets. Strategic
Management
Journal,
22(1),
45-74. http://dx.doi.org/10.1002/1097-0266(200101)22:1<45::AID-SMJ147>3.0.CO;2-F Laeven, L., & Levine, R. (2007). Is there a diversification discount in financial conglomerates? Journal of
Financial Economics, 85(2), 331-367. http://dx.doi.org/10.1016/j.jfineco.2005.06.001 Lane, P. J., Cannella, A. A., & Lubatkin, M. H. (1998). Agency problems as antecedents to unrelated mergers and
diversification: Amihud and Lev reconsidered. Strategic Management Journal, 19(6), 555-578. http://dx.doi.org/10.1002/(SICI)1097-0266(199806)19:6<555::AID-SMJ955>3.0.CO;2-Y Lewellen, W., Loderer, C., & Rosenfeld, A. (1985). Merger decisions and executive stock ownership in acquiring
firms. Journal
of
Accounting
and
Economics,
7(1),
209-231. http://dx.doi.org/10.1016/0165-4101(85)90038-2 Lewellen, W., Loderer, C., & Rosenfeld, A. (1989). Mergers, executive risk reduction, and stockholder wealth. Journal of Financial and Quantitative Analysis, 24(4), 459-472. http://dx.doi.org/10.2307/2330979 Lloyd, W. P., Modani, N. K., & Hand, J. H. (1987). The effect of the degree of ownership control on firm
diversification, market value, and merger activity. Journal of Business Research, 15(4), 303-312. http://dx.doi.org/10.1016/0148-2963(87)90002-6 López de Silanes, F., La Porta, R., Shleifer, A., & Vishny, R. (1998). Law and finance. Journal of Political
Economy, 106, 1113-1155. http://dx.doi.org/10.3386/w5661 Lubatkin, M., & O'Neill, H. M. (1987). Merger strategies and capital market risk. Academy of Management
Journal, 30(4), 665-684. http://dx.doi.org/10.2307/256154 MacKinlay, A. C. (1997). Event studies in economics and finance. Journal of Economic Literature, 35 Martin, J. D., & Sayrak, A. (2003). Corporate diversification and shareholder value: A survey of recent literature. Journal of Corporate Finance, 9(1), 37-57. http://dx.doi.org/10.1016/S0929-1199(01)00053-0 McConnell, J. J., & Servaes, H. (1990). Additional evidence on equity ownership and corporate value. Journal of
Financial Economics, 27(2), 595-612. http://dx.doi.org/10.1016/0304-405X(90)90069-C Minnick, K., Unal, H., & Yang, L. (2011). Pay for performance? CEO compensation and acquirer returns in
BHCs. Review of Financial Studies, 24(2), 439-472. http://dx.doi.org/10.1093/rfs/hhq107 Morck, R., & Yeung, B. (2003). Agency problems in large family business groups. Entrepreneurship Theory and
Practice, 27(4), 367-382. http://dx.doi.org/10.1111/1540-8520.t01-1-00015 Morck, R., Shleifer, A., & Vishny, R. W. (1990). Do managerial objectives drive bad acquisitions? References The Journal
of Finance, 45(1), 31-48. http://dx.doi.org/10.1111/j.1540-6261.1990.tb05079.x Morck, R., Wolfenzon, D., & Yeung, B. (2005). Corporate Governance, Economic Entrenchment, and Growth. Journal of Economic Literature, 63, 655-720. http://dx.doi.org/10.3386/w10692 Porta, R., Lopez‐de‐Silanes, F., & Shleifer, A. (1999). Corporate ownership around the world. The Journal of
Finance, 54(2), 471-517. http://dx.doi.org/10.1111/0022-1082.00115 Rajan, R., Servaes, H., & Zingales, L. (2000). The cost of diversity: The diversification discount and inefficient
investment. The Journal of Finance, 55(1), 35-80. http://dx.doi.org/10.1111/0022-1082.00200 Roll, R. (1986). The hubris hypothesis of corporate takeovers. Journal of Business, 59(2), 197-216. http://dx.doi.org/10.1086/296325 43 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Rose, N. L., & Shepard, A. (1997). Firm Diversification and CEO Compensation: Managerial Ability or
Executive
Entrenchment? The
Rand
Journal
of
Economics,
28(3),
489-514. http://dx.doi.org/10.3386/w4723 Saunders, A., Strock, E., & Travlos, N. G. (1990). Ownership structure, deregulation, and bank risk taking. the
Journal of Finance, 45(2), 643-654. http://dx.doi.org/10.1111/j.1540-6261.1990.tb03709.x Sesil, J. C., Kroumova, M. K., Kruse, D. L., & Blasi, J. R. (2007). Broad-based employee stock options in the
US-company performance and characteristics. Management Revue, 5-22. Shekhar, C., & Torbey, V. (2005). Takeovers, Ownership, and Shareholder Wealth-The Australian Evidence. Review of Accounting and Finance, 4(3), 101-120. http://dx.doi.org/10.1108/eb043433 Shleifer, A., & Vishny, R. W. (1989). Management entrenchment: The case of manager-specific investments. Journal of Financial Economics, 25(1), 123-139. http://dx.doi.org/10.1016/0304-405X(89)90099-8 Shleifer, A., & Vishny, R. W. (1997). A survey of corporate governance. The Journal of Finance, 52(2), 737-783. http://dx.doi.org/10.1111/j.1540-6261.1997.tb04820.x Statman, M. (1987). How many stocks make a diversified portfolio? Journal of Financial and Quantitative
Analysis, 22(3), 353-363. http://dx.doi.org/10.2307/2330969 Villalonga, B. (2004). Diversification discount or premium? New evidence from the business information
tracking
series. The
Journal
of
Finance,
59(2),
479-506. http://dx.doi.org/10.1111/j.1540-6261.2004.00640.x Wagner, W. H., & Lau, S. C. (1971). The effect of diversification on risk. Financial Analysts Journal, 27(6),
48-53. http://dx.doi.org/10.2469/faj.v27.n6.48 Williams, M. A., & Rao, R. P. (2006). CEO stock options and equity risk incentives. Journal of Business Finance
& Accounting, 33(1-2), 26-44. http://dx.doi.org/10.1111/j.1468-5957.2006.01357.x Wright, P., Kroll, M., Lado, A., & Van Ness, B. (2002). The structure of ownership and corporate acquisition
strategies. Strategic Management Journal, 23(1), 41-53. http://dx.doi.org/10.1002/smj.208 Young, M. N., Peng, M. W., Ahlstrom, D., Bruton, G. D., & Jiang, Y. (2008). Corporate governance in emerging
economies: A review of the principal–principal perspective. Journal of Management Studies, 45(1), 196-220. http://dx.doi.org/10.1111/j.1467-6486.2007.00752.x Appendix Appendix
Appendix A. Variable definitions
Acq_percent
The percentage of stake acquired in a deal
BG
A dummy variable to identify business group affiliated bidders; it assumes value 1 if an acquirer is a business
group affiliated firm, otherwise it takes value 0
Cross Border
A dummy variable, which assumes value 1 if a deal is a cross border deal, otherwise it takes value 0. ConsMatBldg
A dummy variable, which assumes value 1 if an acquirer's industry is construction material,
building/construction and engineering
DE
The debt-equity ratio of an acquirer
Debt Cost
The cost of debt is measured as the ratio of interest expense and the average borrowings in the quarter before
deal announcement. Debt Cost Dummy
A dummy variable, which assumes value 1 if the acquirer's cost of debt before the deal announcement is more
than the median cost of debt, 0 otherwise. The cost of debt is measured as the ratio of interest expense and the
average borrowings in the quarter before deal announcement. FIN
The method of financing for a deal, defined as a binary variable, assuming the value 1 if it is a stock offer, 0 if
it is a cash offer
Insider Own or insiderown
The proxy for promoter holdings expressed as percentage of equity holdings by promoters. Insiderown_sqr
The square of promoter holdings. If the proxy used for insider ownership is ‘Insiderown_proxy1’, then this
term is denoted as ‘insiderown_proxy1_sqr’. Insiderown_Proxy1
The total promoter holdings, including holdings by the persons acting in concert
Insiderown_Proxy2
The sum of holdings by all the Promoters, Indian as well as foreign
Insiderown_Proxy3
The total of Indian Promoters and the persons acting in concert
Insiderown_Proxy4
The holdings by promoters as well as non-promoter institutions like mutual funds, UTI (Unit Trust of India),
insurance companies, etc. Insiderown_Proxy5
The sum of the holdings of Promoters and non-promoter FIIs
Insiderown_Proxy6
The sum of holdings by Indian promoters
ITConltSftw
A dummy variable, which assumes value 1 if an acquirer's industry is IT consulting and services, and software
Log_Assets
The log of bidder's total assets
Log Deal Size
The log of the transaction value
Market Adjusted Risk or
Mkt. Adj. Var Ratio
The market adjusted standard deviation of stock returns are used to calculate this measure. This measure is a
ratio of the post deal market adjusted standard deviation of returns over the pre-deal market adjusted standard
deviation of returns. Notes Note 1. Pyramidal structure enables greater control in the hands of the insiders, over and above their cash flow
rights (Porta et al., 1998). Note 2. Promoter(s) (and the people acting in concert, i.e., friends, relatives, etc.) is a business promoter(s) and a
shareholder(s) with substantial shareholding, and is more than likely the founder(s) of the enterprise. She has
significant control over the affairs of the firm and therefore, she could be called the insider-manager or
promoter-manager. Note 3. For more details on this statistical method please refer: Soderbom, Mans and Teal, Francis. 2008. “Corner
solutions,
Censoring
and
Truncation.”
Available
on:
http://www.economics.ox.ac.uk/Intra/Grad/MSc/2007-08/QuantMethods/Lecture%20Notes_FJT/HT_Lectures_h
andouts/lec3ht_08_censoring.pdf. Accessed on 17th October, 2012. Note 3. For more details on this statistical method please refer: Soderbom, Mans and Teal, Francis. 2008. “Corner
solutions,
Censoring
and
Truncation.”
Available
on:
http://www.economics.ox.ac.uk/Intra/Grad/MSc/2007-08/QuantMethods/Lecture%20Notes_FJT/HT_Lectures_h
andouts/lec3ht_08_censoring.pdf. Accessed on 17th October, 2012. Note 4. Source: Prowess, CMIE. http://prowess.cmie.com/, accessed on 17th October, 2012. Note 5. CMIE is Centre for Monitoring Indian Economy. It provides company financial performance data for
Indian companies through the Prowess Database. Note 5. CMIE is Centre for Monitoring Indian Economy. It provides company financial performance data for
Indian companies through the Prowess Database. Note 5. CMIE is Centre for Monitoring Indian Economy. It provides company financial performance data for
Indian companies through the Prowess Database. Note 6. Since in this sample the turning point is close to the majority-holding threshold of 50 per cent, we can
safely interpret this turning point to be at the majority threshold. Note 6. Since in this sample the turning point is close to the majority-holding threshold of 50 per cent, we can
safely interpret this turning point to be at the majority threshold. 44 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Appendix This variable is defined in section 3. Merger
A dummy variable, which takes value 1 if the form of a deal is merger, otherwise it takes value 0
Non-Prom Hold
Percentage of outstanding shares held by non-promoters in a bidding company
OilGasPow
A dummy variable, which assumes value 1 if an acquirer's industry is oil and gas, petrochemicals, power, and
other energy
Percent Acq26
A dummy variable based on the percentage of stake acquired in a deal. It assumes value 1 if the per cent
acquired exceeds 26 per cent, otherwise it takes value zero
Percent Owned
The percentage of the target's outstanding shares held by an acquirer after the bid
Premium
The ratio of the offer price to the target's share price (four weeks prior to the deal announcement). Prom Hold
Promoter holdings of an acquirer before deal announcement, expressed as a percentage of total outstanding
shares. Prom Hold Acq50
The percentage of promoter holdings for a deal if the percentage of stake acquired is 50 per cent or more. This
variable assumes value 0 for the observations where the percentage of stake acquired is less than 50. Post 1991
Companies that were established post 1991. This measure is provided by the CMIE's Prowess Database. Recession Yr. Dummy
A dummy variable to identify recession years -2007, 2008 and 2009
Rel_FF
The industry relatedness dummy variable for a deal, assuming value 0 if the acquirer and the target are in the
same industry, 1 otherwise. For determining whether a merger is happening in the same industry we have
considered the 49 industry classification provided by Fama-French. Rel Size
The relative size of a transaction, measured as the ratio of the value of the transaction over the market value of
its acquirer. Risk
The raw standard deviation of stock returns are used to calculate this measure. This measure is the ratio of the
post deal standard deviation of returns over the pre-deal standard deviation of returns. Sqrt DE
The square root of the acquirer's debt-equity ratio before deal announcement
Var Ratio
Post-deal risk over pre-deal risk as defined in section 3. The variance in this ratio is not market-adjusted. Yr_2008
A dummy variable that assumes value 1 if the deal was announced in 2008
Yr_2009
A dummy variable that assumes value 1 if the deal was announced in 2009 Appendix A. Appendix Variable definitions A dummy variable, which assumes value 1 if an acquirer's industry is oil and gas, petrochemicals, power, and
other energy The percentage of the target's outstanding shares held by an acquirer after the bid The ratio of the offer price to the target's share price (four weeks prior to the deal announcement). Promoter holdings of an acquirer before deal announcement, expressed as a percentage of total outstanding
shares. The percentage of promoter holdings for a deal if the percentage of stake acquired is 50 per cent or more. This
variable assumes value 0 for the observations where the percentage of stake acquired is less than 50. mpanies that were established post 1991. This measure is provided by the CMIE's Prowess Database. Companies that were established post 1991. This measure is provided by the CMIE's Prowess Database. A dummy variable to identify recession years -2007, 2008 and 2009 The industry relatedness dummy variable for a deal, assuming value 0 if the acquirer and the target are in the
same industry, 1 otherwise. For determining whether a merger is happening in the same industry we have
considered the 49 industry classification provided by Fama-French. The relative size of a transaction, measured as the ratio of the value of the transaction over the market value of
its acquirer. The raw standard deviation of stock returns are used to calculate this measure. This measure is the ratio of the
post deal standard deviation of returns over the pre-deal standard deviation of returns. 45 International Journal of Economics and Finance Vol. 8, No. 7; 2016 www.ccsenet.org/ijef Copyrights Copyright for this article is retained by the author(s), with first publication rights granted to the journal. Copyright for this article is retained by the author(s), with first publication rights granted to the journal. This is an open-access article distributed under the terms and conditions of the Creative Commons Attribution Copyright for this article is retained by the author(s), with first publication rights granted to the journal. This is an open-access article distributed under the terms and conditions of the Creative Commons Attribution
license (http://creativecommons.org/licenses/by/3.0/). This is an open-access article distributed under the terms and conditions of the Creative Commons Attribution
license (http://creativecommons.org/licenses/by/3.0/). 46 46
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Still Wrestling with Monsters: A Response to Pat Norman
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CHAPTER 15 C. Grice (*)
University of Sydney, Sydney, NSW, Australia
e-mail: christine.grice@sydney.edu.au © The Author(s) 2024
R. Y. S. Low et al. (eds.), Using Social Theory in Higher Education,
https://doi.org/10.1007/978-3-031-39817-9_15 Christine Grice Christine Grice ‘Interesting’ is a word replete with connotations, used by the polite to
indicate a pretence of agreement alongside hidden respectful disagree
ment. Something can taste ‘interesting’, which does not mean delicious,
look ‘interesting’, which does not mean attractive, or sound ‘interesting’,
which does not mean tuneful. Žižek (2012) connects ‘interesting’ with
crisis, where our ‘interesting’ irrational, fast, and often contradictory solu
tions are, as Norman notes, potentially destroying the planet. Is the role
of curriculum to envisage the Anthropocene as the end? How can educa
tors grapple with truth and crisis and reclaim genuinely interesting and
creative solutions to global problems, as Norman suggests, with hope and
possibility in a world of inequity and degradation? We teach and lead education and pedagogy in interesting times. Most
recently, interesting times in education might be considered as contradic
tory, such as opening up physical classroom walls alongside the boundary
ing and boxing of online learning or providing the necessary focus on
wellbeing following COVID isolation, but narrowing being well to 185 © The Author(s) 2024
R. Y. S. Low et al. (eds.), Using Social Theory in Higher Education,
https://doi.org/10.1007/978-3-031-39817-9_15 185 C. GRICE 186 bandaid solutions that increase workload for educators and thus risk their
wellbeing. Žižek (2012) invites us to slow down from all of this exhaus
tion. The crises of wellbeing, education, and the planet invite us to care
fully consider philosophical solutions in practice, by reconsidering the
civic purpose of education beyond citizenship. The role of education as an
act of citizenship is important for stretching beyond the human endeavour
of ourselves and our own academic performance, but citizenship curricu
lum could be a historic alternative to a contemporary problem. As global
citizens, we have a civil responsibility to humanity—beyond our civic
responsibility to our nation and other people groups and their biases that
divide—towards each other. What this means as we wrestle with pedagogy
is paramount. Education is ultimately about conscience and that comes from our
assumptions. It is important that I declare mine. I am an educator who has
taught in Australia and overseas in government and non-government
schools in the wealthiest and poorest of contexts. Throughout my career I
have held leadership positions in curriculum, pastoral, and school manage
ment. I now research in the field of educational leadership, which often
involves system-level leadership research. Christine Grice My pedagogy and research stem
from dialogic theories that come from my views that we learn by thinking,
talking, and listening made from our experiences, practices, and beliefs. Assumptions form our perspectives about self and society and cannot be
separated, or we lose our own narratives, which form the paradoxes Žižek
invites us to critique. Systems and ecologies are social logics we use for
dealing with problems in interesting times, as Žižek writes, and these are
understood through our assumptions and experiences. Systems are after
all made up of individuals, and individuals are replete with paradoxes. At best, educational leaders solve problems of practice that transform
understanding and possibilities for education, but as Moller (2022) sug
gests, leaders today are often doing ‘the splits’ as they navigate compliance
while attempting to imagine new possibilities for their students. This is an
‘interesting’ predicament that calls into question whether principals are
leaders at all. They do not write curriculum or policy and lead with others
by navigating choices about its enactment. In terms of curriculum, former
Australian Deputy Prime Minister John Anderson lamented that in
Australia today “education only covers what we did wrong” (2022). As
‘The Apology’ by then Prime Minister Kevin Rudd (2008) indicates,
Australia has whitewashed education for a long time. The purpose of 15 STILL WRESTLING WITH MONSTERS: A RESPONSE TO PAT NORMAN 187 education is to uncover uncomfortable truths as it both celebrates success
and humbles us in failure, and these truths should lead to action. As we wrestle with the monsters of capitalism and neoliberalism, of
wellbeing, vanity, and of ourselves we also wrestle with conscience and the
other. The juxtaposition of individualism and universalism is an interesting
conundrum for school leaders as they encourage individuals to be their
best, alongside civic and civil responsibilities. Civic society is the realm of
the state, and civil society is the realm of the citizen. Both are about the
individual and the collective, but civil society supports and creates the
conditions for the realisation of human rights. Ivan Illich led a civil-minded
life following his study of history, crystallography, theology, and philoso
phy in Europe. In 1950 he came to New York and worked as a parish
priest. In 1960 Illich moved to Mexico and learned that financial freedom
and freedom of choice are less accessible to the poor. Christine Grice Illich began to
understand that the citizen was more important than the state in building
community and social equity. Žižek understands that democracy holds
both promise and contradiction as it struggles with individualism and uni
versalism concurrently where power-over is an inevitable part of structure
and social relationships even as citizens. Illich (1971) argues that power
relations pervade schooling and impose institutionalisation, limiting genu
ine relationships: School prepares for the alienating institutionalisation of life, by teaching the
need to be taught. Once this lesson is learned, people lose their incentive to
grow in independence, they no longer find relatedness attractive, and close
themselves off to the surprises which life offers when it is not predetermined
by institutional definition. (p. 22) Illich’s radical image of societal learning from civil freedom through
interwebs—where the village is the place of learning, open with commu
nity—is a creative solution beyond the current limitations of school struc
tures and systems that intend to build community, but concurrently limit
its possibilities. Ž Žižek (2012) invites us to think, and Arendt (1985) agrees that think
ing brings hope. Where Žižek (2012) is about refining our thinking,
Arendt is about nascent action, for action is where hope exists. We have to
think in order to know how to act, and this involves challenging taken-for-
granted logics. Norman suggests student voice as a solution to climate
change, where we can find teachable moments and act. However, voice is C. GRICE 188 not enough. At the heart of education is pedagogy: How we think deter
mines what we think. We need to get better at open-minded debate and
grow through alternate perspectives. Rather than declaring victory, we
need more inquiry, discovery, and shared understanding. Good pedagogy
should discombobulate us and provide us with more questions than
answers. Arendt, who famously wrote about totalitarianism given she sur
vived the Holocaust, chose to dine with those she disagreed with, and of
course with those with whom she loved, so that she could understand
herself. This in itself is a pedagogical act. Arendt lamented that she was too
busy being with students to waste time on coursework design. Pedagogy
is relational and involves two-way dialogue, as Norman agrees. The ques
tion that lingers today is whether education helps us to think, and peda
gogy provides us with answers. The loss of thinking time is a legitimate
concern. Christine Grice The increased self-service labour of tertiary work affords less
time for philosophy. It’s hard to do philosophy when you spend more time
on administrative tasks than on the core purpose of your work, as Shahjahan
(2014) also writes. Our philosophy group helped us to carve out the nec
essary time to grow and think. Not all of our work has a price tag, and yet
neither can we hide from the contradictory fact that we work for an insti
tution of privilege. Bono, lead singer of U2 (2022), in his autobiography,
like Žižek, grapples with paradox and asks if it is the role of the artist to
uncover paradox and wonders whether to resolve every contradiction is
too much to ask of any human. What do we do with such educational privilege as we work in the acad
emy? Bono acknowledges his rock star privilege and the opportunities he
has taken from fame to be a modern philosopher and activist. Unable to
provide a solution to rebooting capitalism (p. 478), whilst acutely aware of
his earning capacity alongside a lifetime of global charity work and aware
ness raising of global inequity, Bono concludes that the answers to chang
ing the world do rest in what we seek to change through our work, through
action and advocacy that he refers to as ‘actualism’ (p. 482), where prag
matism and idealism connect. Bono knows this is the outworking of some
thing spiritual. Changing the world starts with surrendering our ego to the
Big Other, an idea that stretches beyond the super ego of Freud (1978) or
Lacan’s Big Other of language and ego as object whilst knowing the para
doxical limitations, even of self-work. Lacan (1955) sees the mirror as an
object that alienates us from how we see ourselves, towards how others
perceive us, helping us to develop own alter-ego of empathy, a nod to
Žižek’s other: the mirror. Bono’s Big Other is his own encounter with God. 189 15 STILL WRESTLING WITH MONSTERS: A RESPONSE TO PAT NORMAN As we look into the mirror, Žižek invites us to ask what masks we wear
and to consider our own integrity as Norman also suggests. Civil society
invites relational authenticity where civic society invites masks wrought by
structure and titles. In my first week as an academic I interviewed a school
Deputy Head and Principal. Christine Grice “The key to actual freedom rather resides in the ‘apolitical’ network of
social relations” (Žižek, 2012, p. 37). Žižek invites us to imagine a new
universal ‘we’ of the human species (Žižek, 2011, p. 332) in order to get
beyond ourselves. Norman grapples with this by acknowledging that
unsustainable consumption actually consumes us. It divides us as social
beings. He proposes that we recognise climate change as a universal strug
gle that transcends ideological lines. Žižek suggests this vast problem is a
collective responsibility, a “universal project shared by all” (Žižek, 2012,
p. 39) beyond the individual. The importance of collective responsibility
has been shown during COVID through mandated mask wearing to pro
tect others, and the loss of collective responsibility when governments no
longer mandated masks as they were forced to decide whether zero cases
of COVID and fewer deaths were more or less important than mental
health and wellbeing. These political decisions were seen as economic
necessity as Žižek reminds us, and yet the heart of the problem was our
loss of relationship, and this was particularly felt by educators because
pedagogy is relationship. There is increased global dissatisfaction and mistrust in government
that is impacting government education, which is in turn disrupting com
munity. O’Neill (2002), a British philosopher and a crossbench member
of the House of Lords, writes in the BBC Reith lectures about how loss of
trust and increased suspicion comes from deception. Parents understand
the capitalist machine and are asserting their control through school
choice, even in the poorest of countries. What should our expectations of
government be for education? Does government regulation of education
bring equity or mere curriculum compliance? With increased numbers of
home schooling, further exacerbated by COVID, what is the role of par
ent and community in education? If democracy is about independent
choice and freedom, does this come at the cost of equity? These are inter
esting times where civil and civic society have crossed lines in education. If
“School is the advertising agency which makes you believe that you need
the society as it is” (Illich, 1971), it is no longer working for us and the
ways we imagine education need to change, both from within and from
outside. Christine Grice Prior to the interview recording, the Deputy
Head asked me about my background in education. I explained that I had
started my career as a primary teacher, and then had moved into school
leadership, and as a PhD candidate had worked in the tertiary sector
alongside a school middle leadership role. He quickly quipped that pri
mary teachers are all about the children, secondary teachers are all about
the curriculum, and academics are all about themselves. We laughed, and
my role in establishing a warm interview rapport was achieved. But those
words never left me. What is my academic identity? Was I to be entering
the academy to be all about myself? Does the intellectual work of the acad
emy have any practical use? Our inaction is the opposite of praxis, of mor
ally formed action. And yet rearticulating problems to transform
understandings and possibilities is essential to moral formation. Thinking
and action are connected. Whilst we navigate these interesting contradic
tions as academics, we wear masks. Our social media and published identi
ties cultivate and collate what we choose to share of ourselves. Masks
reveal more than they obscure about our desires as Žižek (2012) claims.i How do we use our educational privilege for the benefit of others? We
assume that we will promote social equity. Illich smashed this assumption
decades ago arguing that worshipping universal education makes false
promises to the poor. Illich (1971) argues that our attempts to do school
ing are futile in their current state, unless we recreate education through
community: Universal education through schooling is not feasible. It would be no more
feasible if it were attempted by means of alternative institutions built on the
style of present schools. The current search for new educational funnels
must be reversed into the search for their institutional inverse: educational
webs which heighten the opportunity for each one to transform each moment
of his living into one of learning, sharing, and caring. We hope to contribute
concepts needed by those who conduct such counterfoil research on educa
tion and also to those who seek alternatives. (p. 2) Illich captures the tensions between democracy, capitalism, and social
equity that Žižek (2012) is questioning. Norman invites relational, 190 C. GRICE dialogical, and emancipatory solutions that White et al. (2022) invite us to
reimagine. The answers are in relationships, as Žižek and Illich concur. Christine Grice Illich chose to live frugally and, despite feeling crippled by over
thinking, opened his doors to collaborators and drop-ins with generosity,
running non-stop educational learning which was celebratory, spiritual,
open-ended, and egalitarian. This is hope in action that comes from 15 STILL WRESTLING WITH MONSTERS: A RESPONSE TO PAT NORMAN 191 choosing relationships and humanity first for a higher purpose, choosing
pedagogy as embodied diplomacy (Sarson et al., 2019). We too have a
choice between settling for good manners in interesting times in our
schools and classrooms or to think more carefully about the value of diplo
macy as “the art of restraining power” as Kissinger (1995) advised and
redistributing it. Language matters. At its heart, education is the hope of regeneration. Pedagogy enables
that power through shared voice, dialogue, listening, wisdom, and deep
respect for humanity through relationship. Only when we are humble
enough to suspect that we can be wrong can we accept that embodied
diplomacy learned through pedagogy can invite peace. Žižek invites us to
reimagine, and the academy invites us to disrupt, and this is our privilege,
enabled through our global networks that we must harness wisely to
unearth possibilities for new relationships and discover unheard voices
that create new art and new songs. Acknowledgements I would like to thank Pat Norman, Amani Bell, and friends
for the philosophical conversations and correspondence that led to the develop
ment of this piece, that I have dearly enjoyed. References Anderson, J (2022). Good schools: global lessons for high caliber, low cost educa
tion. https://johnanderson.net.au/conversations-james-tooley/ Anderson, J (2022). Good schools: global lessons for high caliber, low cost educa
tion. https://johnanderson.net.au/conversations-james-tooley/ Anderson, J (2022). Good schools: global lessons for high caliber, low cost educa
tion. https://johnanderson.net.au/conversations-james-tooley/ Arendt, H. (1985). The human condition. The University of Chicago Press. Bono. (2022). Surrender: 40 songs, one story. Hutchinson Heinemann. Arendt, H. (1985). The human condition. The University of Chicago Press. Bono. (2022). Surrender: 40 songs, one story. Hutchinson Heinemann. ,
(
)
y
g
Bono. (2022). Surrender: 40 songs, one story. Hutchinson Heinemann. Freud, S. (1978). The Standard Edition of the Complete Psychological Works of
Sigmund Freud. Volume XIX (1923–26). In The Ego and the Id and Other
Works. Strachey, James., Freud, Anna, 1895–1982, Rothgeb, Carrie Lee, Richards,
Angela., Scientific Literature Corporation. Hogarth Press. Illich, I (1971). Deschooling Society. h
Illich_Ivan_Deschooling_Society.pdf Illich, I (1971). Deschooling Society. https://monoskop.org/images/1/17/
Illich_Ivan_Deschooling_Society.pdf Kissinger, H. (1995). Diplomacy. US: Touchstone. Lacan, J. (1955). The Seminar. Book III. The Psychoses, 1955–1956, translated by
Russell Grigg New York: W. W. Norton & Company, 1997.l Moller, V. (2022). Leading practices of Steiner school principals: a reflective prac
tice perspective. Journal of Educational Administration and History, 55(1),
39–53. https://doi.org/10.1080/00220620.2022.2125937 O’Neill, O. (2002). A question of trust: the BBC Reith Lectures. Cambridge, England. 192 C. GRICE Rudd, K. (2008). Apology to Australia’s Indigenous Peoples. https://parlinfo. aph.gov.au/parlInfo/genpdf/chamber/hansardr/2008-02-13/0003/han
sard_frag.pdf;fileType=application%2Fpdf Sarson, L., Muzik, V., Ray, B., Gambrell, G., Yona, L., & Comeau, R. (2019). The
Model Arctic Council: Simulated Negotiations as Pedagogy and Embodied
Diplomacy. American Review of Canadian Studies, 49(1), 105–122. https://
doi.org/10.1080/02722011.2019.1570955 Shahjahan, R. A. (2014). Being ‘Lazy’ and Slowing Down: Toward decolonizing
time, our body, and pedagogy. Educational Philosophy and Theory, 47(5),
488–501. https://doi.org/10.1080/00131857.2014.880645 White, P. J., Ferguson, J. P., Smith, N. O. C., & Carre, H. O. S. (2022). School
strikers enacting politics for climate justice: Daring to think differently about
education. Australian Journal of Environmental Education, 38(1), 26–39. Žižek, S. (2011). Living in the End Times. Verso. Ž Žižek, S. (2012). Living in the Time of Monsters. Counterpoints, 422, 32–44. References http://www.jstor.org/stable/42981752 Open Access This chapter is licensed under the terms of the Creative Commons
Attribution 4.0 International License (http://creativecommons.org/licenses/
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Critical Role of O-Linked β-N-Acetylglucosamine Transferase in Prostate Cancer Invasion, Angiogenesis, and Metastasis
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Journal of biological chemistry/The Journal of biological chemistry
| 2,012
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cc-by
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Critical Role of O-Linked -N-Acetylglucosamine Transferase
in Prostate Cancer Invasion, Angiogenesis, and Metastasis*□
S Received for publication,September 8, 2011, and in revised form, January 11, 2012 Published, JBC Papers in Press,January 24, 2012, DOI 10.1074/jbc.M111.302547
Thomas P. Lynch, Christina M. Ferrer, S. RaElle Jackson, Kristina S. Shahriari, Keith Vosseller, and Mauricio J. Reginato1
FromtheDepartmentofBiochemistryandMolecularBiology,DrexelUniversityCollegeofMedicine,Philadelphia, Pennsylvania 19102 Background: Cancer cells display altered metabolism and expression of the nutrient sensor O-linked -N-acetylglucosa-
mine transferase (OGT). mine transferase (OGT). Results: Through regulation of FoxM1, OGT contributes to increased invasion, angiogenesis, and metastasis of prostate cancer
cells. Conclusion: OGT plays a critical role in prostate cancer. Results: Through regulation of FoxM1, OGT contributes to increased invasion, angiogenesis, and metastasis of prostate cancer
cells. Conclusion: OGT plays a critical role in prostate cancer. Significance: OGT may provide a novel therapeutic target for treating prostate cancer. Cancer cells universally increase glucose and glutamine con-
sumption,leadingtothealteredmetabolicstateknownastheWar-
burg effect; one metabolic pathway, highly dependent on glucose
and glutamine, is the hexosamine biosynthetic pathway. Increased
flux through the hexosamine biosynthetic pathway leads to
increasesinthepost-translationaladditionofO-linked-N-acetyl-
glucosamine(O-GlcNAc)tovariousnuclearandcytosolicproteins. A number of these target proteins are implicated in cancer, and
recently, O-GlcNAcylation was shown to play a role in breast can-
cer; however, O-GlcNAcylation in other cancers remains poorly
defined. Here, we show that O-GlcNAc transferase (OGT) is over-
expressed in prostate cancer compared with normal prostate epi-
thelium and that OGT protein and O-GlcNAc levels are elevated
in prostate carcinoma cell lines. Reducing O-GlcNAcylation in
PC3-ML cells was associated with reduced expression of matrix
metalloproteinase(MMP)-2,MMP-9,andVEGF,resultingininhi-
bition of invasion and angiogenesis. OGT-mediated regulation of
invasion and angiogenesis was dependent upon regulation of the
oncogenic transcription factor FoxM1, a key regulator of invasion
and angiogenesis, as reducing OGT expression led to increased
FoxM1 protein degradation. Conversely, overexpression of a deg-
radation-resistantFoxM1mutantabrogatedOGTRNAi-mediated
effects on invasion, MMP levels, angiogenesis, and VEGF expres-
sion. Using a mouse model of metastasis, we found that reduction
ofOGTexpressionblockedbonemetastasis.Altogether,thesedata
suggest that as prostate cancer cells alter glucose and glutamine
levels, O-GlcNAc modifications and OGT levels become elevated
and are required for regulation of malignant properties, implicat-
ing OGT as a novel therapeutic target in the treatment of cancer. in a phenomenon known as the Warburg effect (2). Cancer cells
have increased utilization rates of glucose and glutamine, which
are established hallmarks of tumor metabolism (3, 4). As gly-
colysis is much less efficient in generating ATP than is oxidative
phosphorylation, increased glucose flux must occur to com-
pensate. 2 The abbreviations used are: HBP, hexosamine biosynthetic pathway;
O-GlcNAc, O-linked -N-acetylglucosamine; OGT, O-GlcNAc transfer-
ase; MMP, matrix metalloproteinase; HUVEC, human umbilical vein
endothelial cell; qRT-PCR, quantitative RT-PCR; APC/C, anaphase-pro-
moting complex/cyclosome. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 14, pp. 11070–11081, March 30, 2012
© 2012 by The American Society for Biochemistry and Molecular Biology, Inc.
Published in the U.S.A. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 14, pp. 11070–11081, March 30, 2012
© 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 14, pp. 11070–11081, March 30, 2012
© 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 14, pp. 11070–11081, March 30, 2012
© 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Critical Role of O-Linked -N-Acetylglucosamine Transferase
in Prostate Cancer Invasion, Angiogenesis, and Metastasis*□
S
Received for publication,September 8, 2011, and in revised form, January 11, 2012 Published, JBC Papers in Press,January 24, 2012, DOI 10.1074/jbc.M111.302547
Thomas P. Lynch, Christina M. Ferrer, S. RaElle Jackson, Kristina S. Shahriari, Keith Vosseller, and Mauricio J. Reginato1
FromtheDepartmentofBiochemistryandMolecularBiology,DrexelUniversityCollegeofMedicine,Philadelphia, Pennsylvania 19102
Background: Cancer cells display altered metabolism and expression of the nutrient sensor O-linked -N-acetylglucosa-
mine transferase (OGT). Results: Through regulation of FoxM1, OGT contributes to increased invasion, angiogenesis, and metastasis of prostate cancer
cells. Conclusion: OGT plays a critical role in prostate cancer. Significance: OGT may provide a novel therapeutic target for treating prostate cancer. * Thisworkwassupported,inwholeorinpart,byNationalInstitutesofHealth
Grant R01 CA155413 (to M. J. R.). This work was also supported by Drexel
University College of Medicine CURE grants.
□
S This article contains supplemental Figs. 1–7 and additional references.
1 To whom correspondence should be addressed: Dept. of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 245 N. 15th St.,
Philadelphia, PA 19102. Tel.: 215-762-3554; Fax: 215-762-4452; E-mail:
mauricio.reginato@drexelmed.edu. * Thisworkwassupported,inwholeorinpart,byNationalInstitutesofHealth
Grant R01 CA155413 (to M. J. R.). This work was also supported by Drexel
University College of Medicine CURE grants.
□ pp
g
1 To whom correspondence should be addressed: Dept. of Biochemistry and
Molecular Biology, Drexel University College of Medicine, 245 N. 15th St.,
Philadelphia, PA 19102. Tel.: 215-762-3554; Fax: 215-762-4452; E-mail:
mauricio.reginato@drexelmed.edu. y
g
g
□
S This article contains supplemental Figs. 1–7 and additional references. OGT Regulation of Prostate Cancer Recently, we and others found that OGT and O-
GlcNAcylation are elevated in breast cancer cells and that
reducing OGT levels blocks breast cancer growth in vitro and in
vivo (16) and reduces metastasis in mouse breast cancer cells
(17). Metabolic alterations in breast cancer cells also increase
O-GlcNAc cycling, and this has profound effects on cancer
phenotypes, including growth and invasion; however, reducing
OGT and O-GlcNAc levels has minimal effects on growth and
differentiation of immortalized mammary epithelial cells
(16). OGT regulation of breast cancer growth is dependent
on regulation of the oncogenic transcription factor FoxM1,
as reducing O-GlcNAc levels increases degradation of
FoxM1. Because altered metabolism is a general hallmark of
many cancers and because FoxM1 is frequently overex-
pressed in a number of human malignancies, including pan-
creatic (18), lung (19), liver (20), and prostate (21) cancer, we
examined whether elevation of O-GlcNAc and OGT occurs
in other epithelial cancers. Cell Culture—RWPE-1, NPTX-1532, PC3, PC3-ML, and
DU145 cell lines were kindly provided by M. Stearns (Depart-
ment of Pathology, Drexel University College of Medicine). RWPE-1 and NPTX-1532 cells were routinely cultured in Kera-
tinocyte-SFM (Invitrogen) supplemented with bovine pituitary
extract, 10 ng/ml EGF, and 1% penicillin/streptomycin. PC3,
PC3-ML, and DU145 cells were cultured in DMEM (Mediat-
ech, Manassas, VA) supplemented with 10% fetal bovine serum,
1%
L-glutamine, and 1% penicillin/streptomycin. Human
umbilical vein endothelial cells (HUVECs) were a kind gift of P. Lelkes (School of Biomedical Engineering, Science, and Health
Systems, Drexel University) and were routinely cultured in
Clonetics complete endothelial cell growth medium. The deg-
radation-resistant FoxM1 mutant pBabe-FLAG-FoxM1-N/
KEN was described previously (16). Retroviruses were pack-
aged and used to stably transduce PC3-ML cells with pBabe or
pBabe-FLAG-FoxM1-N/KEN virus as described previously
(16, 17, 23, 24). Bioluminescent PC3-ML cells were generated
by stable transfection with firefly luciferase in a pWZL-Hygro
vector (kindly provided by M. Murphy, Fox Chase Cancer
Center). p
Here, through examination of OncomineTM microarray
databases, we have found that OGT is overexpressed in prostate
cancer tissue compared with normal prostate epithelium and
that elevated OGT levels are associated with poor clinical out-
come. Moreover, we provide the first evidence that the expres-
sion of OGT and the levels of O-GlcNAc modifications are
elevated in prostate cancer cell lines compared with non-trans-
formed prostate cells. OGT Regulation of Prostate Cancer Using RNAi targeting OGT expression in
the metastatic prostate cancer cell line PC3-ML, we inhibited
growth, which was associated with decreased FoxM1 levels and
increased expression of the cyclin-dependent kinase inhibitor
p27Kip1. In addition, we observed a reduction in invasive phe-
notypes by reducing O-GlcNAcylation in PC3-ML cells, as well
as a reduction in matrix metalloproteinase (MMP)-2 and
MMP-9 expression. We show for the first time that reducing
OGT levels inhibits angiogenic potential and VEGF expression
in PC3-ML cells, which is dependent on FoxM1. Finally, reduc-
ing OGT expression in human prostate cancer cells inhibits
metastasis to bone. Thus, by regulating the growth, invasion,
angiogenesis, and metastasis of prostate cancer cells, OGT is
positioned as a novel target for therapeutic intervention in the
treatment of human prostate cancer. Immunoblotting—Cell lysates from 1–5 106 cells were pre-
pared in radioimmune precipitation assay lysis buffer (150 mM
NaCl, 1% Nonidet P-40, 0.5% deoxycholate, 50 mM Tris-HCl
(pH 8), 0.1% SDS, 10% glycerol, 5 mM EDTA, 20 mM NaF, and 1
mM Na3VO4) supplemented with 1 g/ml pepstatin, 1 g/ml
leupeptin, 1 g/ml aprotinin, and 200 g/ml PMSF. Lysates
were cleared by centrifugation at 16,000 g for 20 min at 4 °C
and analyzed by SDS-PAGE and autoradiography. Proteins
were analyzed by immunoblotting using primary antibodies as
indicated above. Three-dimensional Morphogenesis Assays—Assays were
performed as described previously (16). Briefly, RWPE-1 or
PC3-ML cells were seeded at a concentration of 1.25 104/well
in 8-well chamber slides (BD FalconTM) that had been previ-
ously coated with 50 l of growth factor-reduced Matrigel. Cells were then overlaid with the respective growth medium
supplemented with 2% growth factor-reduced Matrigel. Cells
were harvested and counted at the indicated times. Immuno-
fluorescence of three-dimensional structures was performed as
described (16). Critical Role of O-Linked -N-Acetylglucosamine Transferase
in Prostate Cancer Invasion, Angiogenesis, and Metastasis*□
S To serve the less efficient energy-producing glycolytic
route, tumor cells increase glucose uptake; clinical tumors gen-
erally show an order of magnitude increase in uptake (5). Changes in tumor cell glucose uptake and metabolism may also
alter distinct nutrient signaling pathways, including the mTOR
(mammalian target of rapamycin) pathway, the AMP-activated
protein kinase pathway, and the hexosamine biosynthetic path-
way (HBP)2 (6). The HBP is highly dependent on glucose and glutamine and
functions as a minor branch of the glycolytic pathway, as
3–5% of total glucose enters this pathway (7). The rate-limit-
ing enzyme glutamine:fructose-6-phosphate amidotransferase
uses glutamine to convert fructose 6-phosphate into glucosa-
mine 6-phosphate, which is then utilized further to synthesize
the end product, UDP-GlcNAc (7). UDP-GlcNAc is required
for the biosynthesis of many classes of extracellular glyco-
polymers, including N- and O-glycans (8). UDP-GlcNAc is the
obligatory
substrate
for
O-linked
-N-acetylglucosamine
(O-GlcNAc) transferase (OGT). This enzyme adds the
O-GlcNAc moiety to the free hydroxyl of select serine and
threonine residues on a diverse population of nuclear and
cytosolic proteins (9). Increased O-GlcNAc cycling has been
suggested to play a key role in insulin resistance, as many key
substrates involved in the insulin signaling pathway are
modified by O-GlcNAc (10), and OGT overexpression in
liver promotes insulin resistance in mice (11). Moreover, a
number of cancer-associated proteins, including p53 (12),
IB kinase (13), c-Myc (14), and Snail (15), are regulated by
O-GlcNAcylation, yet the role of O-GlcNAc in cancer biol-
ogy is just now being defined. Cancer cells characteristically display altered metabolism,
producing ATP independent of the oxygen concentration (1), 11070
JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 287•NUMBER 14•MARCH 30, 2012 RESULTS OGT Levels Are Elevated in Prostate Cancer—We and others
have recently demonstrated that OGT and O-GlcNAc modifi-
cations are overexpressed in breast cancer (16, 17). To deter-
mine whether OGT is overexpressed in other tumor types, we
examined OGT expression using the OncomineTM Database. We found four independent microarray gene expression stud-
ies showing elevated OGT mRNA expression patterns in
human prostate carcinoma compared with normal adjacent tis-
sue samples (supplemental Fig. 1). A survey of the National
Center for Biotechnology Information Gene Expression Omni-
bus (25, 26) indicated a positive correlation (r2 0.996)
between high OGT expression and metastatic progression in
normal, primary tumor, and metastatic prostate tumor tissues
(Fig. 1A). Furthermore, an additional study (27) of 94 patient
tumor samples, when stratified by the level of OGT expression,
indicated that disease-free survival 5 years post-treatment for
prostate cancer was higher (75% probability of survival) in
patients with a low OGT expression profile compared with
patients with increased OGT expression (25% probability of
survival) (Fig. 1B). Endothelial Tube Formation Assay—Endothelial tube for-
mation assays were performed as described (18) with the fol-
lowing modifications. Antibiotic-selected PC3-ML cells stably
expressing control or OGT shRNA were used to condition
RPMI 1640 medium (Invitrogen) for 24 h and passed through
0.45-m syringe filters. Tube length was quantified using
iVision-Mac (version 4.0.14) software (BioVision Technolo-
gies, Exton, PA) from digital images taken using an inverted
microscope In Vivo Bioluminescent Xenograft Model of Metastasis—Male
severe combined immunodeficient mice (5–6 weeks old) were
anesthetized with ketamine (100 mg/kg) and xylazine (20
mg/kg) and inoculated in the left cardiac ventricle with 5 105
PC3-ML cells stably expressing luciferase containing either
OGT or control shRNA in 100 l of serum-free DMEM/F-12
(Invitrogen) using a 30-gauge needle. Mice were injected intra-
peritoneally with 200 l of D-luciferin solution (9 mg/ml; Cali-
per Life Sciences, Hopkinton, MA), and bioluminescence imag-
ing was done 30 min after the intracardiac injection to detect
the distribution of prostate cancer cells; mice were imaged
weekly. Images were acquired with an IVIS 200 imaging system,
and results were analyzed using Living Image software (Caliper
Life Sciences). Metastatic lesions were counted for each mouse
at week 5 and averaged for both groups. All protocols involving
the use of animals were approved by the Institutional Animal
Care and Use Committee at the Fox Chase Cancer Center. OGT Regulation of Prostate Cancer (Hs00173626_m1). Expression levels were normalized to
cyclophilin A. (Hs00173626_m1). Expression levels were normalized to
cyclophilin A. Histological Analysis of Mouse Tissues—To confirm the pres-
ence of PC3-ML cells in the bone metastatic regions, tissues
were excised from the mice at necropsy. Tissue was prepared
and analyzed by the Pathology Diagnostic Laboratory at Drexel
University College of Medicine. Briefly, tissues were fixed in 4%
formaldehyde, cut at the midpoint, and embedded in paraffin
blocks. Serial paraffin longitudinal sections were stained with
hematoxylin/eosin. Soft Agar Colony Formation Assays—Base layers consisting
of growth medium containing a 1% low melting point agarose
(ICS BioExpress, Kaysville, UT) made in 10 mM HEPES (pH 7.5)
were poured onto 6-well plates and allowed to solidify. Cells
(1 104/well) were plated in triplicate on top layers consisting
of growth medium containing 0.3% agarose and 5 mM HEPES. The top layer was also allowed to set and then further overlaid
with 1 ml of medium. Colonies were stained after 14 days with
500 l of 0.05% p-iodonitrotetrazolium violet overnight, and
colonies measuring 50 m were counted manually. Data Mining—OGT gene expression data from four inde-
pendent prostate cancer studies were obtained using the
OncomineTM Database. In the four studies retrieved, we com-
pared samples of normal prostate tissue and prostate carci-
noma. These data were regraphed using GraphPad Prism soft-
ware (GraphPad Software, La Jolla, CA) and are presented as
scatter plots, including the mean S.E. Survivorship data were
additionally acquired through the OncomineTM Database;
OGT expression data were stratified as either being high (above
the dataset mean) or low (below the dataset mean) and
regraphed to represent probability of survival at the indicated
time point. Tissue-specific OGT expression data were acquired
through the National Center for Biotechnology Information
Gene Expression Omnibus and graphed to depict average OGT
expression for the indicated tissue type. Flow Cytometry—At 48 h post-infection with control or OGT
shRNA lentivirus, cells were harvested and washed with PBS. Pellets were fixed in cold 70% ethanol and maintained at
20 °C for at least 2 h. Propidium iodide (Sigma) in a solution of
Triton X-100 (Sigma) and DNase-free RNase A (Fisher) was
used for cell cycle distribution staining, and an FITC mouse
anti-human Ki-67 kit (BD Pharmingen) was used according to
the manufacturer’s protocol for Ki-67 staining. EXPERIMENTAL PROCEDURES shRNA Infections—RWPE-1 and PC3-ML cells were infected
with control (scrambled sequence), OGT-1, and OGT-2
shRNA construct-containing lentiviruses and stably selected as
described previously (16). Materials—Growth factor-reduced Matrigel was purchased
from BD Biosciences. The O-GlcNAcase inhibitor 9D was a
kind gift from D. Vocadlo (Department of Biochemistry, Simon
Fraser University). The OGT inhibitor ST060266 was pur-
chased from TimTec (Newark, DE). Lactacystin was purchased
from Sigma. The antibodies used were anti-actin and anti-
FoxM1 from Santa Cruz Biotechnology (Santa Cruz, CA); anti-
MGEA5 (O-GlcNAcase) from Abcam (Cambridge, MA);
anti-MMP-2 and anti-MMP-9 from Cell Signaling (Danvers,
MA); anti-OGT from Sigma; anti-p27, anti-integrin 5, and
anti-integrin 6 from BD Biosciences; and anti-VEGF from
NeoMarkers (Fremont, CA). The anti-O-GlcNAc antibody
(CTD110.6) has been described previously (22), and the anti-
Sp1 antibody was a kind gift provided by J. Clifford-Azizkhan
(Department of Biochemistry and Molecular Biology, Drexel
University College of Medicine). Quantitative RT-PCR (qRT-PCR)—Total RNA was isolated
using an RNeasy mini kit (Qiagen) according to the manufac-
turer’s protocol for monolayer animal cell RNA extraction. The
levels of OGT, MMP-2, MMP-9, VEGF, and cyclophilin A were
determined using a Stratagene Mx3000P QPCR device with a
Brilliant II QRT-PCR Master Mix kit (Stratagene) according
to the manufacturer’s protocol. Data analysis was performed
with the MxPro software package (Stratagene). TaqMan
gene expression assay primers/probes were purchased from
Applied Biosystems (Foster City, CA) for cyclophilin A
(Hs99999904_m1),
OGT
(Hs00914634_g1),
MMP-2
(Hs00234472_m1), MMP-9 (Hs00234579_m1), and VEGF MARCH 30, 2012•VOLUME 287•NUMBER 14 MARCH 30, 2012•VOLUME 287•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 11071 OGT Regulation of Prostate Cancer All data were
collected and analyzed using a Guava EasyCyte Plus system and
CytoSoft (version 5.3) software (Millipore). Ki-67 data are pre-
sented as the mean fluorescence intensity of gated cells, nor-
malized to the isotype control, and are expressed as intensity
relative to the appropriate control shRNA. Statistical Analysis—All results are from at least three inde-
pendent experiments. Statistical significance was ascertained
with Student’s t test, with a p value threshold of 0.05. Transwell Invasion Assays—Invasion assays were performed
using BD BioCoat growth factor-reduced Matrigel invasion
chambers (BD Biosciences) following the manufacturer’s pro-
tocol, utilizing serum-free medium in the upper chamber and
complete medium in the lower chamber over a 12-h incubation
period. Invasive cells were visualized with DAPI (5 g/ml; Sig-
ma); cells in four fields were counted for each chamber. RESULTS A, OGT expression data from normal prostate tissue (n 17), normal prostate tissue adjacent to
tumor (n 64), primary prostate cancer tumor tissue (n 65), and metastatic prostate cancer tumor tissue (n 25) available through the National Center for
Biotechnology Information Gene Expression Omnibus (NCBI GEO accession number GDS2545) graphed as average expression (error bars indicate S.E.) for the
indicated tissue type, with the best fit line fitted to a plot (r2 0.99627). B, OGT expression data mined from the OncomineTM Database (27), segregated into
high or low expression profiles and correlated with follow-up patient survival data. Prostate cancer patients having a low OGT expression profile (OGT less than
the average of sample population) associate with high disease-free prognosis up to 5 years post-therapy, whereas patients having a high OGT expression
profile (OGT more than the average of sample population) associate with persistence of disease post-therapy. C, normal prostate cell lines RWPE-1 and
NPTX-1532 and prostate cancer cell lines PC3, PC3-ML, and DU145 were lysed and subjected to immunoblotting with the indicated antibodies. OGA,
O-GlcNAcase. D, total RNA was collected from RWPE-1 and PC3-ML cells and then subjected to qRT-PCR for OGT expression. Error bars indicate S.E. for n 3. *,
p 0.01. A.U., arbitrary units. Targeting OGT Decreases Prostate Cancer Growth—A lenti-
viral delivery system was used to stably introduce either control
(scrambled sequence) or two different OGT (OGT-1 or
OGT-2) shRNA constructs into PC3-ML cells. The level of
OGT knockdown and decrease in O-GlcNAcylation was con-
firmed by immunoblotting for OGT and global O-GlcNAc lev-
els (Fig. 2A). These cells were subsequently cultured in soft agar
for 16 days, and the resulting colonies were stained and count-
ed; there was an 80% reduction in the anchorage-indepen-
dent growth of OGT shRNA-expressing cells compared with
control PC3-ML cells (supplemental Fig. 2). The ability of
PC3-ML cells expressing OGT shRNA to grow in three-dimen-
sional culture was also significantly impaired by 65% com-
pared with control cells (Fig. 2B); however, non-transformed
RWPE-1 cells expressing OGT shRNA, which contained
decreased O-GlcNAc levels (supplemental Fig. 3B), did not
demonstrate significant changes in growth during three-di-
mensional culture (supplemental Fig. 3C). (28) formed highly disorganized structures, which displayed
features of invasive phenotypes and loss of integrin 6 basal
localization (supplemental Fig. 3A). RESULTS To examine whether prostate cancer cells contain elevated
OGT expression levels, we compared the expression of OGT
and total O-GlcNAc modifications among a panel of normal
and prostate carcinoma cell lines. In three-dimensional culture,
the non-transformed immortalized prostate RWPE-1 cells
formed organized prostate duct-like acinar structures, which
closely resembled their native architecture in vivo, as evidenced
by acinus-like architecture, including the basal localization of
integrin 6 and the formation of hollowed lumens (supplemen-
tal Fig. 3A). In contrast, the prostate cancer cell line PC3-ML VOLUME 287•NUMBER 14•MARCH 30, 2012 11072
JOURNAL OF BIOLOGICAL CHEMISTRY OGT Regulation of Prostate Cancer FIGURE 1. OGT is overexpressed in prostate carcinoma. A, OGT expression data from normal prostate tissue (n 17), normal prostate tissue adjacent to
tumor (n 64), primary prostate cancer tumor tissue (n 65), and metastatic prostate cancer tumor tissue (n 25) available through the National Center for
Biotechnology Information Gene Expression Omnibus (NCBI GEO accession number GDS2545) graphed as average expression (error bars indicate S.E.) for the
indicated tissue type, with the best fit line fitted to a plot (r2 0.99627). B, OGT expression data mined from the OncomineTM Database (27), segregated into
high or low expression profiles and correlated with follow-up patient survival data. Prostate cancer patients having a low OGT expression profile (OGT less than
the average of sample population) associate with high disease-free prognosis up to 5 years post-therapy, whereas patients having a high OGT expression
profile (OGT more than the average of sample population) associate with persistence of disease post-therapy. C, normal prostate cell lines RWPE-1 and
NPTX-1532 and prostate cancer cell lines PC3, PC3-ML, and DU145 were lysed and subjected to immunoblotting with the indicated antibodies. OGA,
O-GlcNAcase. D, total RNA was collected from RWPE-1 and PC3-ML cells and then subjected to qRT-PCR for OGT expression. Error bars indicate S.E. for n 3. *,
p 0.01. A.U., arbitrary units. OGT Regulation of Prostate Cancer FIGURE 1 OGT i
d i
t t
i
A OGT
i
d t f FIGURE 1. OGT is overexpressed in prostate carcinoma. RESULTS Data are expressed as
average cells/well; error bars indicate S.E. for n 3. *, p 0.05. C, PC3-ML cells described in A were stained with propidium iodide for cell cycle analysis. Data are
presented as percentage of the gated population in the indicated phase; error bars indicate S.E. for n 3. *, p 0.05. D, PC3-ML cells stably expressing control,
OGT-1, or OGT-2 shRNA were incubated with FITC-conjugated antibodies against Ki-67 or an isotype control and analyzed by flow cytometry. Data are
presented as percentage of the gated population positive for Ki-67; error bars indicate S.E. for n 3. *, 0.01. creased the expression of FoxM1, and increased the expression
of p27Kip1 (supplemental Fig. 7). To further examine the growth inhibitory effect of OGT
knockdown in prostate cancer cells, we examined the possible
effects on cell cycle progression using propidium iodide stain-
ing, followed by flow cytometry. OGT knockdown in PC3-ML
cells induced a statistically significant (p 0.05) accumulation
of cells in G1 phase and a slight decrease in S phase (Fig. 2C). There was also a concomitant reduction in the proliferation
marker Ki-67 in PC3-ML cells expressing OGT shRNA con-
structs compared with those expressing control shRNA (Fig. 2D). Consistent with cell cycle arrest, we observed a decrease in
expression of the cell cycle- and proliferation-associated tran-
scription factor FoxM1 and an increase in the cyclin-dependent
kinase inhibitor p27Kip1 (Fig. 2A). Interestingly, we did not
detect an increase in G1 arrest (supplemental Fig. 4B) or a
decrease in Ki-67 positivity (supplemental Fig. 4C) in the non-
transformed RWPE-1 cells expressing OGT shRNA (supple-
mental Fig. 4A). The effects on PC3-ML growth and signaling
by targeting OGT with RNAi are dependent upon the catalytic
activity of OGT, as treatment of PC3-ML cells with a previously
characterized OGT inhibitor (16) reduced O-GlcNAcylation,
reduced growth in three-dimensional morphogenesis, de- Targeting OGT Reduces Invasion of PC3-ML Cells and Is
Associated with Decreased MMP-2 and MMP-9 Expression—
When placed in three-dimensional basement membrane cul-
ture, PC3-ML cells exhibited a morphological phenotype that is
consistent with invasive potential (supplemental Fig. 2); how-
ever, when cultured under three-dimensional conditions,
PC3-ML cells expressing OGT shRNA exhibited reduced inva-
sive protrusions compared with control shRNA-expressing
cells (Fig. 3A). RESULTS The RWPE-1 cells, as well
as the normal prostate epithelial cell line NPTX-1532 (29),
exhibited lower levels of both O-GlcNAc and OGT compared
with the prostate carcinoma cell lines PC3, PC3-ML, and
DU145 (Fig. 1C). Furthermore, PC3-ML cells contained
2-fold more OGT mRNA compared with RWPE-1 cells as
quantified by qRT-PCR (Fig. 1D). In addition to global
O-GlcNAcylation and OGT expression being elevated in pros-
tate
carcinoma
cell
lines,
we
also
observe
decreased
O-GlcNAcase protein levels in prostate carcinoma cell lines
compared with normal prostate epithelial cells (Fig. 1C). Thus,
these results show that prostate cancer cell lines and tissue con-
tain elevated levels of OGT RNA and protein, as well as
increased total O-GlcNAcylation, and that the elevation of
OGT levels in prostate cancer may be associated with poor
clinical prognosis. MARCH 30, 2012•VOLUME 287•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 11073 OGICAL CHEMISTRY 11073 JOURNAL OF BIOLOGICAL CHEMISTRY 11073 MARCH 30, 2012•VOLUME 287•NUMBER 14 OGT Regulation of Prostate Cancer FIGURE 2. Targeting OGT decreases malignant growth and proliferation in vitro. A, PC3-ML cells stably expressing control, OGT-1, or OGT-2 shRNA were
lysed and immunoblotted with the indicated antibodies. B, PC3-ML cells stably expressing control or OGT shRNA were seeded on a bed of Matrigel, overlaid
with dilute Matrigel in three-dimension culture medium, and assayed for proliferation as measured by cells/well (depicted graphically). Data are expressed as
average cells/well; error bars indicate S.E. for n 3. *, p 0.05. C, PC3-ML cells described in A were stained with propidium iodide for cell cycle analysis. Data are
presented as percentage of the gated population in the indicated phase; error bars indicate S.E. for n 3. *, p 0.05. D, PC3-ML cells stably expressing control,
OGT-1, or OGT-2 shRNA were incubated with FITC-conjugated antibodies against Ki-67 or an isotype control and analyzed by flow cytometry. Data are
presented as percentage of the gated population positive for Ki-67; error bars indicate S.E. for n 3. *, 0.01. FIGURE 2. Targeting OGT decreases malignant growth and proliferation in vitro. A, PC3-ML cells stably expressing control, OGT-1, or OGT-2 shRNA were
lysed and immunoblotted with the indicated antibodies. B, PC3-ML cells stably expressing control or OGT shRNA were seeded on a bed of Matrigel, overlaid
with dilute Matrigel in three-dimension culture medium, and assayed for proliferation as measured by cells/well (depicted graphically). RESULTS for n 3. *, 0.05. D, PC3-ML cells described in B were lysed and immunoblotted
with the indicated antibodies. an 50% reduction in MMP-9 mRNA levels by qRT-PCR (Fig. 3C) in PC3-ML cells with reduced OGT expression compared
with control cells. Additionally, MMP-2 and MMP-9 protein
levels were decreased upon knockdown of OGT (Fig. 3D). tate cancer cells. We first determined if reducing levels of
OGT in PC3-ML cells alters endothelial tube formation, an
indirect measure of angiogenesis (18). After 24 h of stably
expressing control or OGT shRNA in PC3-ML cells, we col-
lected the conditioned medium. This conditioned medium
was then used to stimulate HUVECs in an endothelial tube
formation assay; HUVECs were seeded onto a bed of Matri-
gel
and
then
overlaid
with
PC3-ML
cell-conditioned
medium. After 6 h, the HUVECs were imaged, and tube
length was quantified using iVision-Mac software. As shown
in Fig. 4A, there was a statistically significant (p 0.05)
reduction in the ability of the conditioned medium from
PC3-ML cells expressing OGT shRNA to stimulate tube for-
mation in HUVECs compared with the medium from control
shRNA-expressing cells. RNA was harvested from the same
PC3-ML cells used to condition the media, and the levels of
VEGF RNA were determined. As expected, the levels of OGT
RNA were decreased in cells expressing OGT shRNA; how-
ever, VEGF RNA levels were also significantly (p 0.05)
decreased, by 50% (Fig. 4B), consistent with the decreased
ability of OGT knockdown cells to stimulate endothelial
tube formation (Fig. 4A). Because FoxM1 had not been pre-
viously shown to induce VEGF expression in prostate cancer
cells, we examined VEGF levels in PC3-ML cells in which we
knocked down FoxM1 levels with RNAi. PC3-ML cells stably
expressing FoxM1 shRNA compared with control cells con- It has been previously shown that targeting OGT in breast
cancer results in a reduction of the oncogenic transcription
factor FoxM1 (16), and it has also been previously estab-
lished that FoxM1 regulates expression of MMP-2 in breast
cancer cells (32); however, the role of FoxM1 in prostate
cancer invasion and MMP-2 regulation had not been exam-
ined. Thus, we examined whether FoxM1 can also regulate
expression of MMP-2 and regulate invasion in prostate can-
cer cells. Knockdown of FoxM1 in PC3-ML cells with stably
expressed shRNA constructs resulted in a reduction of
MMP-2 protein expression (supplemental Fig. RESULTS This reduction in invasive morphology upon
decreased OGT expression led us to assay the invasive potential
of PC3-ML cells in Transwell invasion chamber inserts. As
shown in Fig. 3B, there was an 60% reduction in the ability of
PC3-ML cells to invade through the Matrigel coating of the
Transwell membrane inserts with decreased OGT expression
compared with control cells. Because it has previously been
established that MMP-2 and MMP-9 are associated with pros-
tate cancer progression and metastasis (30, 31), we examined
the expression of MMP-2 and MMP-9 in the context of OGT
knockdown. We observed an 70% reduction in MMP-2 and VOLUME 287•NUMBER 14•MARCH 30, 2012 11074
JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 287•NUMBER 14•MARCH 30, 2012 OGT Regulation of Prostate Cancer FIGURE 3. Targeting OGT decreases invasive phenotypes in vitro. A, bright-field (upper panels) and confocal (lower panels) micrographs comparing control,
OGT-1, and OGT-2 shRNA-expressing PC3-ML cells maintained in three-dimensional culture systems over 12 days. Actin, integrin 6, and DAPI are shown in the
confocal images. B, PC3-ML cells expressing control, OGT-1, or OGT-2 shRNA were assayed for ability to invade through Matrigel-coated Transwell membranes. Data are presented as relative invasion compared with control shRNA; error bars indicate S.E. for n 3. *, 0.05. C, total RNA was collected from PC3-ML cells
expressing control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for MMP-2, MMP-9, and OGT. Data were normalized to cyclophilin A and are presented
as relative expression compared with control shRNA; error bars indicate S.E. for n 3. *, 0.05. D, PC3-ML cells described in B were lysed and immunoblotted
with the indicated antibodies. g FIGURE 3. Targeting OGT decreases invasive phenotypes in vitro. A, bright-field (upper panels) and confocal (lower panels) micrographs comparing control,
OGT-1, and OGT-2 shRNA-expressing PC3-ML cells maintained in three-dimensional culture systems over 12 days. Actin, integrin 6, and DAPI are shown in the
confocal images. B, PC3-ML cells expressing control, OGT-1, or OGT-2 shRNA were assayed for ability to invade through Matrigel-coated Transwell membranes. Data are presented as relative invasion compared with control shRNA; error bars indicate S.E. for n 3. *, 0.05. C, total RNA was collected from PC3-ML cells
expressing control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for MMP-2, MMP-9, and OGT. Data were normalized to cyclophilin A and are presented
as relative expression compared with control shRNA; error bars indicate S.E. RESULTS Thus,
reducing OGT inhibits angiogenic potential and VEGF levels
in prostate cancer cells. altered by OGT knockdown compared with control RNAi (Fig. 5B). To test whether FoxM1 regulation by OGT is required for
alterations of PC3-ML angiogenic and invasive potential, we
examined whether the non-degradable FoxM1 mutant could
reverse the phenotypes of PC3-ML cells caused by down-
regulating OGT. PC3-ML cells overexpressing non-degrad-
able mutant FoxM1 (Fig. 5B) were able to fully overcome the
inhibition of angiogenesis mediated by OGT silencing (Fig. 5D), as well as the reverse inhibition of VEGF expression
(Fig. 5C). altered by OGT knockdown compared with control RNAi (Fig. 5B). To test whether FoxM1 regulation by OGT is required for
alterations of PC3-ML angiogenic and invasive potential, we
examined whether the non-degradable FoxM1 mutant could
reverse the phenotypes of PC3-ML cells caused by down-
regulating OGT. PC3-ML cells overexpressing non-degrad-
able mutant FoxM1 (Fig. 5B) were able to fully overcome the
inhibition of angiogenesis mediated by OGT silencing (Fig. 5D), as well as the reverse inhibition of VEGF expression
(Fig. 5C). p
Degradation-resistant FoxM1 Mutant Rescues Angiogenic
Potential and Invasive Capacity of OGT Knockdown Cells—To
investigate the O-GlcNAcylation status of FoxM1 in PC3-ML
cells, we immunoprecipitated endogenous FoxM1 without and
with 9D treatment to enhance total cellular O-GlcNAcylation
and subjected the resulting proteins to immunoblotting with
anti-O-GlcNAc antibody. As shown in supplemental Fig. 6,
FoxM1 protein did not appear O-GlcNAcylated, unlike the well
known O-GlcNAcylated transcription factor Sp1 (34). Previous
work in breast cancer cells has indicated that the N terminus of
FoxM1, which contains degron destruction D-box and KEN-
box sequences (35), is essential for regulation by OGT (16, 17,
23, 24) and suggests that OGT regulates FoxM1 via protea-
some-mediated degradation. Because decreasing OGT expres-
sion also decreased FoxM1 protein levels in PC3-ML cells (Fig. 2A), we tested directly whether OGT regulates FoxM1 via the
proteasome. Treatment of PC3-ML cells with the proteasome
inhibitor lactacystin for 6 h reversed FoxM1 inhibition in OGT
knockdown cells (Fig. 5A), suggesting that OGT regulation of
FoxM1 protein levels is a proteasome-mediated process. RESULTS 5A), invasive
structures in three-dimensional culture (supplemental Fig. 5B), and inhibition of invasion through Matrigel-coated
Transwell invasion chambers (supplemental Fig. 5C). Con-
sistent with these data, we observed a marked reduction in
FoxM1 protein levels in PC3-ML cells stably expressing
OGT shRNA (Fig. 2A). Targeting OGT Reduces Angiogenic Potential and VEGF
Expression in PC3-ML Cells—FoxM1 has been to shown to
regulate VEGF expression in breast (32), pancreatic (18), and
gastric (33) cancer, suggesting that decreasing OGT may also
inhibit angiogenic potential and VEGF expression in pros- MARCH 30, 2012•VOLUME 287•NUMBER 14 MARCH 30, 2012•VOLUME 287•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 11075 11075 OGT Regulation of Prostate Cancer OGT Regulation of Prostate Cancer FIGURE 4. Targeting OGT decreases angiogenic potential in vitro. A, conditioned RPMI 1640 medium from control, OGT-1, or OGT-2 shRNA-expressing
PC3-ML cells was used to overlay HUVECs seeded on a bed of Matrigel for 6 h in endothelial cell tube formation assays. Relative tube length to control shRNA
was calculated; error bars indicate S.E. for n 3. *, p 0.05. Representative images are depicted above. B, total RNA was collected from PC3-ML cells expressing
control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for VEGF and OGT. Data were normalized to cyclophilin A and are presented as relative expression
compared with control shRNA; error bars indicate S.E. for n 3. *, 0.05. A.U., arbitrary units. C, PC3-ML cells described in B were lysed and immunoblotted with
the indicated antibodies. OGT Regulation of Prostate Cancer FIGURE 4. Targeting OGT decreases angiogenic potential in vitro. A, conditioned RPMI 1640 medium from control, OGT-1, or OGT-2 shRNA-expressing
PC3-ML cells was used to overlay HUVECs seeded on a bed of Matrigel for 6 h in endothelial cell tube formation assays. Relative tube length to control shRNA
was calculated; error bars indicate S.E. for n 3. *, p 0.05. Representative images are depicted above. B, total RNA was collected from PC3-ML cells expressing
control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for VEGF and OGT. Data were normalized to cyclophilin A and are presented as relative expression
compared with control shRNA; error bars indicate S.E. for n 3. *, 0.05. A.U., arbitrary units. C, PC3-ML cells described in B were lysed and immunoblotted with
the indicated antibodies. tained reduced levels of VEGF (supplemental Fig. 5A). RESULTS Con-
sistent with these data, the levels of a non-degradable FoxM1
mutant lacking the N terminus, which contains D-box and
KEN-box motifs, overexpressed in PC3-ML cells were not Expression of the non-degradable FoxM1 mutant in PC3-ML
cells coexpressing OGT shRNA was also able reverse inhibition
of invasive protrusions in cells cultured in three-dimensional
basement membranes (Fig. 6A) and nearly completely restored
invasion through Transwell invasion inserts to control levels
(Fig. 6B). Furthermore, expression of MMP-2 RNA was
restored to near control levels, and expression of MMP-9 RNA
was partially restored (Fig. 6C). Thus, we have demonstrated
that the decrease in PC3-ML angiogenic potential and invasive
capacity upon decreased OGT expression is at least partially
dependent upon FoxM1 function. Reducing OGT Levels Inhibits Prostate Cancer Metastasis to
Bone—Depletion of OGT in prostate cancer cells leads to
decreased invasion and angiogenesis, suggesting that OGT may
also regulate prostate cancer metastasis. To test directly
whether OGT signaling is functionally important for human VOLUME 287•NUMBER 14•MARCH 30, 2012 11076
JOURNAL OF BIOLOGICAL CHEMISTRY 11076
JOURNAL OF BIOLOGICAL CHEMISTRY The
progression of bone metastasis after left ventricle intracardiac
injection of tumor cells was monitored by bioluminescence
imaging using a stably expressed firefly luciferase reporter. After 5 weeks, 56% animals injected with control shRNA-
expressing PC3-ML cells developed metastatic foci to bone,
whereas 13% animals injected with OGT shRNA-expressing
PC3-ML cells developed metastatic foci in either the mandi-
bles or hind limbs (Fig. 7B). Animals injected with OGT
knockdown PC3-ML cells had 4.7-fold less bone metastases
to mandibles and hind limbs (Fig. 7C). Histological analysis
of mandibles and hind limbs from injected mice confirmed
that the luciferase signal corresponded with the presence of
metastatic PC3-ML cells within bone lesions in mice prostate cancer metastasis, we injected the highly bone meta-
static PC3-ML cells stably overexpressing control or OGT
RNAi intracardially into immunocompromised mice. We
found that OGT shRNA-expressing PC3-ML cells showed a
reduction in OGT expression of 60% compared with control
PC3-ML cells as analyzed by Western blotting (Fig. 7A). The
progression of bone metastasis after left ventricle intracardiac
injection of tumor cells was monitored by bioluminescence
imaging using a stably expressed firefly luciferase reporter. After 5 weeks, 56% animals injected with control shRNA-
expressing PC3-ML cells developed metastatic foci to bone,
whereas 13% animals injected with OGT shRNA-expressing
PC3-ML cells developed metastatic foci in either the mandi-
bles or hind limbs (Fig. 7B). Animals injected with OGT
knockdown PC3-ML cells had 4.7-fold less bone metastases
to mandibles and hind limbs (Fig. 7C). Histological analysis
of mandibles and hind limbs from injected mice confirmed
that the luciferase signal corresponded with the presence of
metastatic PC3-ML cells within bone lesions in mice Overall, we have shown that OGT and O-GlcNAcylation are
elevated in prostate cancer cells and are required for growth,
invasion, angiogenesis, and metastasis and that this pheno-
type requires, in part, regulation of FoxM1, as a degradation-
resistant mutant was able to rescue invasion and angiogene-
sis defects. Thus, OGT may serve as a novel therapeutic
target for treatment of primary and metastatic prostate
cancers. 11076
JOURNAL OF BIOLOGICAL CHEMISTRY C, conditioned RPMI 1640 medium from control, OGT-1, or OGT-2 shRNA-expressing PC3-ML-pBabe or PC3-ML-pBabe-FoxM1-N/KEN cells was used to
overlay HUVECs seeded on a bed of Matrigel as described in the legend to Fig. 4A. Relative tube length to control shRNA was calculated; error bars indicate S.E. for n 3. *, 0.05. Representative images are depicted above. D, total RNA was collected from PC3-ML-pBabe and PC3-ML-pBabe-FoxM1-N/KEN cells
expressing control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for VEGF and OGT. Data were normalized to cyclophilin A and are presented as relative
expression compared with the respective control shRNA; error bars indicate S.E. for n 3. *, 0.05. FIGURE 5. Expression of non-degradable FoxM1 mutant (FoxM1-N/KEN) partially rescues angiogenic potential of OGT shRNA-expressing PC3-ML
cells. A, PC3-ML cells stably expressing control or OGT shRNA were treated with lactacystin (100 M) for 6 h. Lysates were collected and analyzed by immuno-
blotting with the indicated antibodies. B, OGT was targeted in PC3-ML cells stably expressing a vector control (pBabe) or a FoxM1 mutant (pBabe-FoxM1-N/
KEN), and cells were subsequently lysed and immunoblotted with the indicated antibodies. Endogenous FoxM1 (*) and mutant FoxM1 (**) are indicated. C, conditioned RPMI 1640 medium from control, OGT-1, or OGT-2 shRNA-expressing PC3-ML-pBabe or PC3-ML-pBabe-FoxM1-N/KEN cells was used to
overlay HUVECs seeded on a bed of Matrigel as described in the legend to Fig. 4A. Relative tube length to control shRNA was calculated; error bars indicate S.E. for n 3. *, 0.05. Representative images are depicted above. D, total RNA was collected from PC3-ML-pBabe and PC3-ML-pBabe-FoxM1-N/KEN cells
expressing control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for VEGF and OGT. Data were normalized to cyclophilin A and are presented as relative
expression compared with the respective control shRNA; error bars indicate S.E. for n 3. *, 0.05. FIGURE 5. Expression of non-degradable FoxM1 mutant (FoxM1-N/KEN) pa injected with control cells but not cells depleted of OGT (Fig. 7D). These results support the functional role for OGT in
prostate bone metastasis. prostate cancer metastasis, we injected the highly bone meta-
static PC3-ML cells stably overexpressing control or OGT
RNAi intracardially into immunocompromised mice. We
found that OGT shRNA-expressing PC3-ML cells showed a
reduction in OGT expression of 60% compared with control
PC3-ML cells as analyzed by Western blotting (Fig. 7A). 11076
JOURNAL OF BIOLOGICAL CHEMISTRY OGT Regulation of Prostate Cancer FIGURE 5. Expression of non-degradable FoxM1 mutant (FoxM1-N/KEN) partially rescues angiogenic potential of OGT shRNA-expressing PC3-ML
cells. A, PC3-ML cells stably expressing control or OGT shRNA were treated with lactacystin (100 M) for 6 h. Lysates were collected and analyzed by immuno-
blotting with the indicated antibodies. B, OGT was targeted in PC3-ML cells stably expressing a vector control (pBabe) or a FoxM1 mutant (pBabe-FoxM1-N/
KEN), and cells were subsequently lysed and immunoblotted with the indicated antibodies. Endogenous FoxM1 (*) and mutant FoxM1 (**) are indicated. C, conditioned RPMI 1640 medium from control, OGT-1, or OGT-2 shRNA-expressing PC3-ML-pBabe or PC3-ML-pBabe-FoxM1-N/KEN cells was used to
overlay HUVECs seeded on a bed of Matrigel as described in the legend to Fig. 4A. Relative tube length to control shRNA was calculated; error bars indicate S.E. for n 3. *, 0.05. Representative images are depicted above. D, total RNA was collected from PC3-ML-pBabe and PC3-ML-pBabe-FoxM1-N/KEN cells
expressing control, OGT-1, or OGT-2 shRNA and subjected to qRT-PCR for VEGF and OGT. Data were normalized to cyclophilin A and are presented as relative
expression compared with the respective control shRNA; error bars indicate S.E. for n 3. *, 0.05. g FIGURE 5. Expression of non-degradable FoxM1 mutant (FoxM1-N/KEN) partially rescues angiogenic potential of OGT shRNA-expressing PC3-ML
cells. A, PC3-ML cells stably expressing control or OGT shRNA were treated with lactacystin (100 M) for 6 h. Lysates were collected and analyzed by immuno-
blotting with the indicated antibodies. B, OGT was targeted in PC3-ML cells stably expressing a vector control (pBabe) or a FoxM1 mutant (pBabe-FoxM1-N/
KEN), and cells were subsequently lysed and immunoblotted with the indicated antibodies. Endogenous FoxM1 (*) and mutant FoxM1 (**) are indicated. C, conditioned RPMI 1640 medium from control, OGT-1, or OGT-2 shRNA-expressing PC3-ML-pBabe or PC3-ML-pBabe-FoxM1-N/KEN cells was used to FIGURE 5. Expression of non-degradable FoxM1 mutant (FoxM1-N/KEN) partially rescues angiogenic potential of OGT shRNA-expressing PC3-ML
cells. A, PC3-ML cells stably expressing control or OGT shRNA were treated with lactacystin (100 M) for 6 h. Lysates were collected and analyzed by immuno-
blotting with the indicated antibodies. B, OGT was targeted in PC3-ML cells stably expressing a vector control (pBabe) or a FoxM1 mutant (pBabe-FoxM1-N/
KEN), and cells were subsequently lysed and immunoblotted with the indicated antibodies. Endogenous FoxM1 (*) and mutant FoxM1 (**) are indicated. OGT Regulation of Prostate Cancer Recent studies have implicated flux through
the HBP as playing a key role in coordinating glucose and glu-
tamine metabolism by regulating the surface expression of
growth factor receptors via N-linked glycosylation (41). Whether cancer cells have increased flux through the HBP has
not been directly examined; future studies will be aimed at elu-
cidating the origins of elevated O-GlcNAcylation in cancer
cells. FIGURE 6. Expression of non-degradable FoxM1 mutant (FoxM1-N/
KEN) partially rescues invasive capacity of OGT shRNA-expressing
PC3-ML cells. A, representative bright-field micrographs comparing day 12
control, OGT-1, or OGT-2 shRNA-expressing PC3-ML-pBabe or PC3-ML-
pBabe-FoxM1-N/KEN cells maintained in three-dimensional culture sys-
tems. B, PC3-ML cells as described in A were subjected to Transwell inva-
sion assays. Error bars indicate S.E. for n 3. *, 0.05. C, PC3-ML cells as
described in A were subjected qRT-PCR for MMP-2, MMP-9, and OGT and
normalized to the respective control. Error bars indicate S.E. for n 3. n.s.,
not significant. In addition to blocking invasion, angiogenesis, and metas-
tasis, targeting OGT blocked the growth and proliferation of
prostate cancer cells. The growth inhibition seen in PC3-ML
cells expressing OGT RNAi suggests that targeting OGT
blocks not only the ability of PC3-ML cells to metastasize but
also the ability of primary tumors to expand and secondary
metastases to establish at distant sites. It is possible that
reducing OGT in prostate cancer cells induced defects in
growth, invasion, and angiogenesis, all contributing to inhi-
bition of bone metastasis. OGT silencing in the mouse breast
cancer cell line 4T1 inhibits metastatic nodules to lungs but
does not inhibit primary tumor growth (17). The effects of
reducing OGT and O-GlcNAc via RNAi are dependent on
OGT catalytic activity, as chemical inhibitors of OGT have
similar effects on oncogenic phenotypes in vitro. Thus, tar-
geting OGT therapeutically may impair growth at the pri-
mary tumor site, the ability of cancer cells to escape primary to invade through a reconstituted extracellular matrix-coated
membrane. Furthermore, targeting OGT decreased VEGF
expression and the ability of PC3-ML cells to stimulate endo-
thelial tube formation, suggesting that targeting OGT may
block angiogenesis in prostate cancer cells. Taken together,
these data suggest that OGT plays a role in the metastatic
potential of human prostate cancer, and indeed, we observed a
decrease in the ability of PC3-ML cells to establish metastases
in an intracardiac injection mouse model system. OGT Regulation of Prostate Cancer association between OGT expression and metastasis in breast
cancer (17). FIGURE 6. Expression of non-degradable FoxM1 mutant (FoxM1-N/
KEN) partially rescues invasive capacity of OGT shRNA-expressing
PC3-ML cells. A, representative bright-field micrographs comparing day 12
control, OGT-1, or OGT-2 shRNA-expressing PC3-ML-pBabe or PC3-ML-
pBabe-FoxM1-N/KEN cells maintained in three-dimensional culture sys-
tems. B, PC3-ML cells as described in A were subjected to Transwell inva-
sion assays. Error bars indicate S.E. for n 3. *, 0.05. C, PC3-ML cells as
described in A were subjected qRT-PCR for MMP-2, MMP-9, and OGT and
normalized to the respective control. Error bars indicate S.E. for n 3. n.s.,
not significant. Increasing evidence suggests that OGT plays a critical role
during oncogenesis and tumor progression in numerous can-
cers; indeed, several reports have implicated OGT overexpres-
sion and elevated O-GlcNAcylation in cancers ranging from
solid tumors (including breast (16, 18), lung (23), colon (23),
liver (36), and now prostate)) to chronic myeloid leukemia (16,
17, 23, 24). More recently, expression of the enzyme that
removes O-GlcNAcylation, O-GlcNAcase, has been found to
be reduced in breast (37) and liver (36) cancer. Knockdown
of O-GlcNAcase in liver cancer cells increases total O-
GlcNAcylation levels and increases the migration and invasion
of these cells. In addition, the O-GlcNAcase gene is localized in
frequently altered chromosomal regions, critical in the patho-
genesis of breast and ovarian cancer (38). Thus, increased OGT
and decreased O-GlcNAcase levels in cancers may lead to a
general increase in O-GlcNAc cycling that has diverse tumor-
promoting functions. Despite emerging evidence for the role of O-GlcNAc in var-
ious cancers, it is not immediately clear as to how OGT expres-
sion is regulated in cancer. Here, we have shown that both OGT
protein (Fig. 1C) and RNA (Fig. 1D) are up-regulated in prostate
cancer, but the exact mechanism by which cancer cells up-reg-
ulate OGT and O-GlcNAcylation is currently not clear. It is
known, however, that cancer cells up-regulate the flux of glu-
cose and glutamine, both substrates of the HBP (39). The HBP
generates the activated substrate UDP-GlcNAc for OGT and,
in this manner, may serve as a potential mechanism by which
global O-GlcNAcylation occurs in cancer cells. The UDP-
GlcNAc generated by HBP can also be used as a substrate for
N-glycan blanching, which has also been found to be elevated in
cancer cells (40). DISCUSSION The data presented here describe a critical role for the ele-
vated expression of OGT and O-GlcNAcylation observed in
prostate cancer in the invasion, angiogenesis, and metastasis of
such cancer cells. Reducing the expression of OGT via RNAi
attenuated not only the invasive phenotype of PC3-ML cells in
three-dimensional culture but also the ability of PC3-ML cells MARCH 30, 2012•VOLUME 287•NUMBER 14 11077 JOURNAL OF BIOLOGICAL CHEMISTRY 11077 MARCH 30, 2012•VOLUME 287•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 11077 OGT Regulation of Prostate Cancer These obser-
vations concur with and expand upon a previously reported 11078
JOURNAL OF BIOLOGICAL CHEMISTRY OGT Regulation of Prostate Cancer OGT Regulation of Prost IGURE 7. OGT depletion inhibits prostate cancer bone metastasis. A, PC3-ML cells stably expressing either control or OGT-2 shRNA were lysed and FIGURE 7. OGT depletion inhibits prostate cancer bone metastasis. A, PC3-ML cells stably expressing either control or OGT-2 shRNA were lysed and
immunoblotted with the indicated antibodies prior to being injected intracardially into 6-week-old male severe combined immunodeficient mice.B, reduction
of OGT inhibits prostate cancer metastatic lesions to mandibles and limbs. Animals were imaged using the IVIS Lumina system at 5 weeks post-injection with
control and OGT-2 shRNA-expressing PC3-ML cells. The red arrows indicates metastatic foci to mandibles or limbs. Metastatic foci were counted for control (n
9)andOGT-2(n8)shRNAmiceandgraphed.ErrorbarsindicateS.E.*,0.05(right).C,representativeimages(magnification4)fromimmunohistochemistry
analysis (hematoxylin/eosin) of mandibles (upper panels) and limbs (lower panels) from mice injected with control or OGT RNAi-expressing PC3-ML cells. T,
tumor; I, incisor; DP, dental pulp; B, bone; BM, bone marrow; M, muscle. tumors, and the ability of cancer cells to establish and colo-
nize secondary sites. cancer cells. Reducing FoxM1 expression in multiple cancer
cells led to a marked reduction in invasive potential (18, 21, 32),
consistent with the OGT-mediated reduction in FoxM1
expression observed here. For example, FoxM1 was shown to
stimulate invasion and angiogenesis in pancreatic cancer cells
through induction of MMP-2, MMP-9, and VEGF (18). Our
studies here are the first to show that FoxM1 is required for
prostate cancer invasion and regulation of MMP-2 and VEGF. Moreover, our data are consistent with studies showing that
FoxM1 overexpression coincides with metastasis of prostate
cancer (25). In total, our data point to a mechanism of OGT-
mediated invasion, angiogenesis, and metastasis regulation that
is due, in part, to stabilization of FoxM1 expression in prostate
cancer. The effects of targeting OGT seem to be partly dependent
upon proteasomal regulation of the oncogenic transcription
factor FoxM1, as inhibition of the proteasome reversed loss
of FoxM1 expression in OGT knockdown cells. Moreover,
expression of a non-degradable mutant version of FoxM1 res-
cued OGT depletion-mediated phenotypes; however, it is not
clear how OGT regulates FoxM1 degradation. FoxM1 is poly-
ubiquitinated by the anaphase-promoting complex/cyclosome
(APC/C)-Cdh1 for degradation by the proteasome (35). APC/C
is a critical regulator of cell cycle progression by controlling the
ubiquitination-mediated proteolysis of cell cycle regulators and
is thought to be active from mitosis to late G1 phase (42). 11078
JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 287•NUMBER 14•MARCH 30, 2012 pletion inhibits prostate cancer bone metastasis. A, PC3-ML cells stably expressing either control or OGT-2 shRNA were lysed and
h the indicated antibodies prior to being injected intracardially into 6-week-old male severe combined immunodeficient mice.B, reduction
state cancer metastatic lesions to mandibles and limbs. Animals were imaged using the IVIS Lumina system at 5 weeks post-injection with
hRNA-expressing PC3-ML cells. The red arrows indicates metastatic foci to mandibles or limbs. Metastatic foci were counted for control (n
)shRNAmiceandgraphed.ErrorbarsindicateS.E.*,0.05(right).C,representativeimages(magnification4)fromimmunohistochemistry
lin/eosin) of mandibles (upper panels) and limbs (lower panels) from mice injected with control or OGT RNAi-expressing PC3-ML cells. T,
, dental pulp; B, bone; BM, bone marrow; M, muscle. OGT Regulation of Prostate Cancer OGT Regulation of P OGT Regulation of Prostate Cancer OGT Regulation of Prostate Cancer 2831–2842 drug design of novel OGT inhibitors will be greatly facili-
tated. These data suggest OGT as a novel target in the treat-
ment of prostate cancer progression and metastasis. 17. Gu, Y., Mi, W., Ge, Y., Liu, H., Fan, Q., Han, C., Yang, J., Han, F., Lu, X., and
Yu, W. (2010) GlcNAcylation plays an essential role in breast cancer me-
tastasis. Cancer Res. 70, 6344–6351 18. Wang, Z., Banerjee, S., Kong, D., Li, Y., and Sarkar, F. H. (2007) Down-
regulation of Forkhead Box M1 transcription factor leads to the inhibition
of invasion and angiogenesis of pancreatic cancer cells. Cancer Res. 67,
8293–8300 Acknowledgments—We thank M. Murphy for kindly providing the
pWZL-Hygro-luciferase plasmid, H. Hensley (Fox Chase Cancer Cen-
ter) for technical assistance using the IVIS 200 imaging system, M. Stearns for kindly providing prostate cancer cell lines, D. Vocadlo for
providing the 9D O-GlcNAcase inhibitor, P. Lelkes for kindly provid-
ing the HUVECs, and J. Clifford-Azizkhan for the anti-Sp1 antibody. We also thank F. Garcia (Department of Pathology, Drexel University
College of Medicine) for assisting in histological analysis and A. Fata-
tis (Department of Pharmacology and Physiology, Drexel University
College of Medicine) for technical assistance with intracardiac
injections. Acknowledgments—We thank M. Murphy for kindly providing the
pWZL-Hygro-luciferase plasmid, H. Hensley (Fox Chase Cancer Cen-
ter) for technical assistance using the IVIS 200 imaging system, M. Stearns for kindly providing prostate cancer cell lines, D. Vocadlo for
providing the 9D O-GlcNAcase inhibitor, P. Lelkes for kindly provid-
ing the HUVECs, and J. Clifford-Azizkhan for the anti-Sp1 antibody. We also thank F. Garcia (Department of Pathology, Drexel University
College of Medicine) for assisting in histological analysis and A. Fata-
tis (Department of Pharmacology and Physiology, Drexel University
College of Medicine) for technical assistance with intracardiac
injections. 19. Yang, D. K., Son, C. H., Lee, S. K., Choi, P. J., Lee, K. E., and Roh, M. S. (2009) Forkhead box M1 expression in pulmonary squamous cell carci-
noma: correlation with clinicopathologic features and its prognostic sig-
nificance. Hum. Pathol. 40, 464–470 20. Kalinichenko, V. V., Major, M. L., Wang, X., Petrovic, V., Kuechle, J.,
Yoder, H. M., Dennewitz, M. B., Shin, B., Datta, A., Raychaudhuri, P., and
Costa, R. H. (2004) FoxM1b transcription factor is essential for develop-
ment of hepatocellular carcinomas and is negatively regulated by the
p19ARF tumor suppressor. Genes Dev. 18, 830–850 21. Kalin, T. REFERENCES Cell 139, 1229–1241 27. Holzbeierlein, J., Lal, P., LaTulippe, E., Smith, A., Satagopan, J., Zhang, L.,
Ryan, C., Smith, S., Scher, H., Scardino, P., Reuter, V., and Gerald, W. L. (2004) Gene expression analysis of human prostate carcinoma during hor-
monal therapy identifies androgen-responsive genes and mechanisms of
therapy resistance. Am. J. Pathol. 164, 217–227 9. Hart, G. W., Housley, M. P., and Slawson, C. (2007) Cycling of O-linked
-N-acetylglucosamine on nucleocytoplasmic proteins. Nature 446,
1017–1022 10. Wells, L., Vosseller, K., and Hart, G. W. (2003) A role for N-acetylgluco-
samine as a nutrient sensor and mediator of insulin resistance. Cell. Mol. Life Sci. 60, 222–228 28. Wang, M., and Stearns, M. E. (1991) Isolation and characterization of PC3
human prostatic tumor sublines which preferentially metastasize to select
organs in S.C.I.D. mice. Differentiation 48, 115–125 11. McClain, D. A., Lubas, W. A., Cooksey, R. C., Hazel, M., Parker, G. J., Love,
D. C., and Hanover, J. A. (2002) Altered glycan-dependent signaling in-
duces insulin resistance and hyperleptinemia. Proc. Natl. Acad. Sci. U.S.A. 99, 10695–10699 29. Bright, R. K., Vocke, C. D., Emmert-Buck, M. R., Duray, P. H., Solomon, D.,
Fetsch, P., Rhim, J. S., Linehan, W. M., and Topalian, S. L. (1997) Gener-
ation and genetic characterization of immortal human prostate epithelial
cell lines derived from primary cancer specimens. Cancer Res. 57,
995–1002 12. Yang, W. H., Kim, J. E., Nam, H. W., Ju, J. W., Kim, H. S., Kim, Y. S., and
Cho, J. W. (2006) Modification of p53 with O-linked N-acetylglucosamine
regulates p53 activity and stability. Nat. Cell Biol. 8, 1074–1083 30. Sauer, C. G., Kappeler, A., Späth, M., Kaden, J. J., Michel, M. S., Mayer, D.,
Bleyl, U., and Grobholz, R. (2004) Expression and activity of matrix met-
alloproteinase-2 and -9 in serum, core needle biopsies, and tissue speci-
mens of prostate cancer patients. Virchows Arch. 444, 518–526 13. Kawauchi, K., Araki, K., Tobiume, K., and Tanaka, N. (2009) Loss of p53
enhances catalytic activity of IKK through O-linked -N-acetylgluco-
samine modification. Proc. Natl. Acad. Sci. U.S.A. 106, 3431–3436 14. Chou, T. Y., Dang, C. V., and Hart, G. W. (1995) Glycosylation of the
c-Myc transactivation domain. Proc. Natl. Acad. Sci. U.S.A. 92,
4417–4421 31. Zhang, L., Shi, J., Feng, J., Klocker, H., Lee, C., and Zhang, J. (2004) Type IV
collagenase (matrix metalloproteinase-2 and -9) in prostate cancer. Pros-
tate Cancer Prostatic Dis. 7, 327–332 15. REFERENCES 1. Dang, C. V., and Semenza, G. L. (1999) Oncogenic alterations of metabo-
lism. Trends Biochem. Sci. 24, 68–72 22. Comer, F. I., Vosseller, K., Wells, L., Accavitti, M. A., and Hart, G. W. (2001) Characterization of a mouse monoclonal antibody specific for O-
linked N-acetylglucosamine. Anal. Biochem. 293, 169–177 2. Warburg, O. (1956) On the origin of cancer cells. Science 123, 309–314 3. Deberardinis, R. J., Sayed, N., Ditsworth, D., and Thompson, C. B. (2008)
Brick by brick: metabolism and tumor cell growth. Curr. Opin. Genet. Dev. 18, 54–61 23. Mi, W., Gu, Y., Han, C., Liu, H., Fan, Q., Zhang, X., Cong, Q., and Yu, W. (2011) O-GlcNAcylation is a novel regulator of lung and colon cancer
malignancy. Biochim. Biophys. Acta 1812, 514–519 4. Kim, J. W., and Dang, C. V. (2006) Cancer’s molecular sweet tooth and the
Warburg effect. Cancer Res. 66, 8927–8930 24. Shi, Y., Tomic, J., Wen, F., Shaha, S., Bahlo, A., Harrison, R., Dennis, J. W.,
Williams, R., Gross, B. J., Walker, S., Zuccolo, J., Deans, J. P., Hart, G. W.,
and Spaner, D. E. (2010) Aberrant O-GlcNAcylation characterizes
chronic lymphocytic leukemia. Leukemia 24, 1588–1598 5. Gatenby, R. A. (1995) Models of tumor-host interaction as competing
populations: implications for tumor biology and treatment. J. Theor. Biol. 176, 447–455 6. Marshall, S. (2006) Role of insulin, adipocyte hormones, and nutrient-
sensing pathways in regulating fuel metabolism and energy homeostasis: a
nutritional perspective of diabetes, obesity, and cancer. Sci. STKE 2006,
re7 25. Chandran, U. R., Ma, C., Dhir, R., Bisceglia, M., Lyons-Weiler, M., Liang,
W., Michalopoulos, G., Becich, M., and Monzon, F. A. (2007) Gene ex-
pression profiles of prostate cancer reveal involvement of multiple molec-
ular pathways in the metastatic process. BMC Cancer 7, 64 7. Marshall, S., Bacote, V., and Traxinger, R. R. (1991) Discovery of a meta-
bolic pathway mediating glucose-induced desensitization of the glucose
transport system. Role of hexosamine biosynthesis in the induction of
insulin resistance. J. Biol. Chem. 266, 4706–4712 26. Yu, Y. P., Landsittel, D., Jing, L., Nelson, J., Ren, B., Liu, L., McDonald, C.,
Thomas, R., Dhir, R., Finkelstein, S., Michalopoulos, G., Becich, M., and
Luo, J. H. (2004) Gene expression alterations in prostate cancer predicting
tumor aggression and preceding development of malignancy. J. Clin. On-
col. 22, 2790–2799 8. Dennis, J. W., Nabi, I. R., and Demetriou, M. (2009) Metabolism, cell
surface organization, and disease. OGT Regulation of Prostate Cancer Inter-
estingly, APC/C-Cdh1 substrates are often overexpressed in
human cancers, including FoxM1, Skp2, PLK1, cyclin A, and
Aurora A, and are associated with poor clinical outcome (43). Recent studies have suggested that Cdh1 may be a haploinsuf-
ficient tumor suppressor, as Cdh1 heterozygosity in mice
results in tumor development (44). Because OGT does not
O-GlcNAcylate FoxM1 directly (supplemental Fig. 6), it is likely
that OGT regulates the activity of APC/C-Cdh1 by a yet unde-
fined mechanism. In summary, we have described a novel role for the meta-
bolic sensor OGT in the growth, invasion, angiogenesis, and
metastasis of human prostate cancer cells through, in part,
the regulation of FoxM1 via modulation of downstream
effectors, such as MMP-2, MMP-9, and VEGF. This apparent
global increase in OGT expression and O-GlcNAcylated
proteins seems to be a common feature of cancer cells and
presents a novel therapeutic target (45). Indeed, we have
shown that a first generation small molecule inhibitor of
OGT activity blocks prostate and breast cancer (16) growth
and invasion in vitro. With the recent resolution of a crystal
structure for OGT bound to a peptide substrate (46), rational The reduction in invasion and angiogenesis effectors
(MMP-2, MMP-9, and VEGF) was at least partially restored by
expression of the FoxM1 mutant in OGT-depleted prostate MARCH 30, 2012•VOLUME 287•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 11079 11079 11079 MARCH 30, 2012•VOLUME 287•NUMBER 14 OGT Regulation of Prostate Cancer V., Wang, I. C., Ackerson, T. J., Major, M. L., Detrisac, C. J.,
Kalinichenko, V. V., Lyubimov, A., and Costa, R. H. (2006) Increased levels
of the FoxM1 transcription factor accelerate development and progres-
sion of prostate carcinomas in both TRAMP and LADY transgenic mice. Cancer Res. 66, 1712–1720 11080
JOURNAL OF BIOLOGICAL CHEMISTRY OGT Regulation of Prostate Cancer human gastric cancer angiogenesis and progression. Cancer Res. 69,
3501–3509 39. Slawson, C., Copeland, R. J., and Hart, G. W. (2010) O-GlcNAc signaling:
a metabolic link between diabetes and cancer? Trends Biochem. Sci. 35,
547–555 34. Jackson, S. P., and Tjian, R. (1988) O-Glycosylation of eukaryotic tran-
scription factors: implications for mechanisms of transcriptional regula-
tion. Cell 55, 125–133 40. Lau, K. S., and Dennis, J. W. (2008) N-Glycans in cancer progression. Glycobiology 18, 750–760 35. Laoukili, J., Alvarez-Fernandez, M., Stahl, M., and Medema, R. H. (2008)
FoxM1 is degraded at mitotic exit in a Cdh1-dependent manner. Cell
Cycle 7, 2720–2726 41. Wellen, K. E., Lu, C., Mancuso, A., Lemons, J. M., Ryczko, M., Dennis,
J. W., Rabinowitz, J. D., Coller, H. A., and Thompson, C. B. (2010) The
hexosamine biosynthetic pathway couples growth factor-induced gluta-
mine uptake to glucose metabolism. Genes Dev. 24, 2784–2799 36. Zhu, Q., Zhou, L., Yang, Z., Lai, M., Xie, H., Wu, L., Xing, C., Zhang, F., and
Zheng, S. (2011) O-GlcNAcylation plays a role in tumor recurrence of
hepatocellular carcinoma following liver transplantation. Med. Oncol. 10.1007/s12032-011-9912-1 mine uptake to glucose metabolism. Genes Dev. 24, 2784–2 42. Peters, J. M. (2006) The anaphase-promoting complex/cyclosome: a ma-
chine designed to destroy. Nat. Rev. Mol. Cell Biol. 7, 644–656 43. Carter, S. L., Eklund, A. C., Kohane, I. S., Harris, L. N., and Szallasi, Z. (2006) A signature of chromosomal instability inferred from gene expres-
sion profiles predicts clinical outcome in multiple human cancers. Nat. Genet. 38, 1043–1048 37. Krzeslak, A., Forma, E., Bernaciak, M., Romanowicz, H., and Brys, M. (2011) Gene expression of O-GlcNAc cycling enzymes in human breast
cancers. Clin. Exp. Med. 10.1007/s10238-011-0138-5 p
38. Dahl, E., Sadr-Nabavi, A., Klopocki, E., Betz, B., Grube, S., Kreutzfeld, R.,
Himmelfarb, M., An, H. X., Gelling, S., Klaman, I., Hinzmann, B., Kristian-
sen, G., Grützmann, R., Kuner, R., Petschke, B., Rhiem, K., Wiechen, K.,
Sers, C., Wiestler, O., Schneider, A., Höfler, H., Nährig, J., Dietel, M.,
Schäfer, R., Rosenthal, A., Schmutzler, R., Dürst, M., Meindl, A., and Nie-
deracher, D. (2005) Systematic identification and molecular characteriza-
tion of genes differentially expressed in breast and ovarian cancer. J. Pathol. 205, 21–28 44. García-Higuera, I., Manchado, E., Dubus, P., Cañamero, M., Méndez, J.,
Moreno, S., and Malumbres, M. (2008) Genomic stability and tumor sup-
pression by the APC/C cofactor Cdh1. Nat. Cell Biol. 10, 802–811 45. Lynch, T. REFERENCES Park, S. Y., Kim, H. S., Kim, N. H., Ji, S., Cha, S. Y., Kang, J. G., Ota, I.,
Shimada, K., Konishi, N., Nam, H. W., Hong, S. W., Yang, W. H., Roth, J.,
Yook, J. I., and Cho, J. W. (2010) Snail1 is stabilized by O-GlcNAc modi-
fication in hyperglycemic condition. EMBO J. 29, 3787–3796 32. Ahmad, A., Wang, Z., Kong, D., Ali, S., Li, Y., Banerjee, S., Ali, R., and
Sarkar, F. H. (2010) FoxM1 down-regulation leads to inhibition of prolif-
eration, migration, and invasion of breast cancer cells through the modu-
lation of extracellular matrix-degrading factors. Breast Cancer Res. Treat. 122, 337–346 16. Caldwell, S. A., Jackson, S. R., Shahriari, K. S., Lynch, T. P., Sethi, G.,
Walker, S., Vosseller, K., and Reginato, M. J. (2010) Nutrient sensor
O-GlcNAc transferase regulates breast cancer tumorigenesis through tar-
geting of the oncogenic transcription factor FoxM1. Oncogene 29, 33. Li, Q., Zhang, N., Jia, Z., Le, X., Dai, B., Wei, D., Huang, S., Tan, D., and Xie,
K. (2009) Critical role and regulation of transcription factor FoxM1 in 11080
JOURNAL OF BIOLOGICAL CHEMISTRY 11080 VOLUME 287•NUMBER 14•MARCH 30, 2012 VOLUME 287•NUMBER 14•MARCH 30, 2012 OGT Regulation of Prostate Cancer P., and Reginato, M. J. (2011) O-GlcNAc transferase: a sweet
new cancer target. Cell Cycle 10, 1712–1713 46. Lazarus, M. B., Nam, Y., Jiang, J., Sliz, P., and Walker, S. (2011) Structure of
human O-GlcNAc transferase and its complex with a peptide substrate. Nature 469, 564–567 MARCH 30, 2012•VOLUME 287•NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 11081 MARCH 30, 2012•VOLUME 287•NUMBER 14
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Water Addition Prolonged the Length of the Growing Season of the Desert Shrub Nitraria tangutorum in a Temperate Desert
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Frontiers in plant science
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cc-by
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Water Addition Prolonged the Length
of the Growing Season of the Desert
Shrub Nitraria tangutorum in a
Temperate Desert Fang Bao 1,2, Minghu Liu 3, Yanli Cao 1, Jiazhu Li 1, Bin Yao 1, Zhiming Xin 3,4, Qi Lu 1,3
and Bo Wu 1,2* 1 Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China, 2 Key Laboratory for Desert Ecosystem
and Global Change, Chinese Academy of Forestry, Beijing, China, 3 Experimental Center of Desert Forestry, Chinese
Academy of Forestry, Dengkou, China, 4 Inner Mongolia Dengkou Desert Ecosystem National Observation Research Station,
Dengkou, China Climate models often predict that more extreme precipitation events will occur in arid and
semiarid regions, where plant phenology is particularly sensitive to precipitation changes. To understand how increases in precipitation affect plant phenology, this study conducted
a manipulative field experiment in a desert ecosystem of northwest China. In this study, a
long-term in situ water addition experiment was conducted in a temperate desert in
northwestern China. The following five treatments were used: natural rain plus an
additional 0, 25, 50, 75, and 100% of the local mean annual precipitation. A series of
phenological events, including leaf unfolding (onset, 30%, 50%, and end of leaf unfolding),
cessation of new branch elongation (30, 50, and 90%), and leaf coloration (80% of leaves
turned yellow), of the locally dominant shrub Nitraria tangutorum were observed from
2012 to 2018. The results showed that on average, over the seven-year-study and in all
treatments water addition treatments advanced the spring phenology (30% of leaf
unfolding) by 1.29–3.00 days, but delayed the autumn phenology (80% of leaves
turned yellow) by 1.18–11.82 days. Therefore, the length of the growing season was
prolonged by 2.11–13.68 days, and autumn phenology contributed more than spring
phenology. In addition, water addition treatments delayed the cessation of new branch
elongation (90%) by 5.82–12.61 days, and nonlinear relationships were found between
the leaves yellowing (80% of leaves) and the amount of watering. Linear relationships were
found between the cessation of new branch elongation (90%), the length of the growing
season, and amount of water addition. The two response patterns to water increase
indicated that predictions of phenological events in the future should not be based on one
trend only. ORIGINAL RESEARCH
published: 21 July 2020
doi: 10.3389/fpls.2020.01099 Edited by: Edited by:
Yongshuo Fu,
Beijing Normal University, China Reviewed by:
Xuancheng Zhou,
Beijing Normal University, China
Bao Yang,
Chinese Academy of Sciences, China Reviewed by:
Xuancheng Zhou,
Beijing Normal University, China
Bao Yang,
Chinese Academy of Sciences, China
*Correspondence:
Bo Wu
wubo@caf.ac.cn *Correspondence:
Bo Wu
wubo@caf.ac.cn Specialty section:
This article was submitted to
Functional Plant Ecology,
a section of the journal
Frontiers in Plant Science Specialty section:
This article was submitted to
Functional Plant Ecology,
a section of the journal
Frontiers in Plant Science Specialty section:
This article was submitted to
Functional Plant Ecology,
a section of the journal
Frontiers in Plant Science
Received: 25 February 2020
Accepted: 03 July 2020
Published: 21 July 2020 Received: 25 February 2020
Accepted: 03 July 2020
Published: 21 July 2020 Keywords: desert species, growing season, foliar phenology, branch phenology, water addition Edited by:
Yongshuo Fu,
Beijing Normal University, China
Reviewed by:
Xuancheng Zhou,
Beijing Normal University, China
Bao Yang,
Chinese Academy of Sciences, China
*Correspondence:
Bo Wu
wubo@caf.ac.cn INTRODUCTION This is true for ecosystems without
chronic seasonal water stress; however, the effects of temperature
on vegetation phenology may be critically modulated in arid and
semiarid ecosystems by soil water availability (Moore et al.,
2015). Many studies have investigated how precipitation
regulates plant phenology in seasonally dry tropical forests
(Hayden et al., 2010) and other water-limited ecosystems
(Patrick et al., 2009; Lesica and Kittelson, 2010; Liu et al., 2015;
Zhou and Jia, 2016). For example, in a water-limited ecosystem
in California, the rainfall volume and timing during winter
jointly influenced the timing of vegetative bud break, where
high rainfall in December and March delayed bud break, while
high rainfall in February advanced bud break (Mazer et al.,
2015). The degree of budburst and leaf extension was shows to be
a function of irrigation intensity at the Estacion Biologia de
Chamela in western Mexico (Hayden et al., 2010). Based on
remote sensing data, preseason precipitation (i.e., precipitation
before the growing season) was found to exert a stronger
influence on the starting date of the vegetation growing season
(SOS) of grasslands in drier areas than in wetter areas of the
Qinghai–Tibetan Plateau (Shen et al., 2011; Shen et al., 2015). Moreover, the effect of total preseason precipitation on the end
date of the growing season (EOS) in dry grasslands is greater
than that of temperature for Inner Mongolia, China (Liu et al.,
2015; Zhou and Jia, 2016). Similar results were also reported for
arid and semiarid regions of Africa (Zhang et al., 2005; Gaughan
et al., 2012). Shoot elongation during the growing season is an
integral component of the annual sequence of developmental
events in plants (Codesido and López, 2003). Shoot elongation
rates were found to be related to rainfall in the two evergreen,
woody, Brazilian Cerrado species Leandra lacunose and Miconia
albicans (Damascos et al., 2005). Th
h
l
l
f
l
d Deserts across northwestern China cover an area of
approximately 1.3 million km2 and are constantly expanding
into neighboring ecosystems because of climatic changes and
human activities (Huang et al., 2015a; Huang et al., 2015b). Future climate scenarios predict that the precipitation regimes in
the desert regions of northwestern China will likely change,
following an increasing trend (Gao et al., 2012; Chen, 2013;
IPCC, 2014; Li et al., 2016; Wang et al., 2017). INTRODUCTION Sakkir et al., 2014; Yan et al., 2016; Huang et al., 2018). Desert
ecosystems cover approximately 30% of the land surface and are
strongly controlled by water availability (Patrick et al., 2009). Precipitation and water availability likely affect desert plant
phenology stronger and more directly than the phenology of
ecosystems with greater precipitation (Ghazahfar, 1997; Yan
et al., 2016). Several studies have explored the responses of
desert plant phenology to precipitation variation in their
natural conditions. For example, the onset and duration of
growth in chamaephytes and therophytes are highly correlated
with both the timing and abundance of precipitation, whereas
phanerophytes are least affected in the gravel desert of northern
Oman (Ghazahfar, 1997) and in eastern United Arab Emirates
(Sakkir et al., 2014). At the regional scale, spatial shifts in the
onset of the vegetation growing season are controlled by summer
rainfall in the southern Sahara Desert (Yan et al., 2016). Winter
precipitation explained 14.2% of the inter-annual variations of
spring phenology in the desert ecosystem of northwestern China
(Wu and Liu, 2013). Plant phenology, i.e., the timing of seasonal life cycle events, such
as leafing out and flowering, plays a fundamental role in the
function of terrestrial ecosystems (Fu et al., 2014a; Fu et al., 2015;
Browning et al., 2019). The timing of phenological events is
strongly controlled by the prevailing climate and has long been
regarded as one of the most sensitive and accurate bio-indicators
to track climate change (Badeck et al., 2004; Bertin, 2008; Gordo
and Sanz, 2010). Advancing the understanding of the
phenological response to climate change is therefore important
for forecasts of the impact of future climate change on terrestrial
ecosystems (Cleland et al., 2007; Nord and Lynch, 2009). With
the climate change observed over recent years, advances of spring
phenology and delays of autumn phenology have been reported
worldwide such as in Europe (Menzel and Fabian, 1999; Menzel
et al., 2001; Fu et al., 2014a), North America (Schwartz and
Reiter, 2000; Jeong et al., 2011; Fridley, 2012), the Southern
Hemisphere (Chambers et al., 2013; Ma et al., 2013), and China
(Ge et al., 2014; Ge et al., 2015; Zheng et al., 2016). This variation
was attributed to prevailing climate warming trends (Cleland
et al., 2007; Bertin, 2008). Citation: Bao F, Liu M, Cao Y, Li J, Yao B, Xin Z,
Lu Q and Wu B (2020) Water Addition
Prolonged the Length of the Growing
Season of the Desert Shrub Nitraria
tangutorum in a Temperate Desert. Front. Plant Sci. 11:1099. doi: 10.3389/fpls.2020.01099 July 2020 | Volume 11 | Article 1099 1 Frontiers in Plant Science | www.frontiersin.org Water Addition Prolonged Growing Season Bao et al. Frontiers in Plant Science | www.frontiersin.org INTRODUCTION For example,
based on the RCP8.5 scenario, increases in annual precipitation of
25%, 50% (Gao et al., 2012), and greater than 100% (Wang et al.,
2017) of mean annual precipitation are expected in specific desert
regions at the middle and end of the 21st Century compared with
the end of the 20th Century (Song et al., 2020). Most of the
biological processes in desert ecosystems are controlled by soil
water availability, which is generally controled by rainfall events
(Song et al., 2020). Precipitation increases likely impose substantial
impacts on plant phenology in these deserts in response to climate
change. Few studies examined the effects of water addition on
reproductive phenology of six annuals on the southern fringe of
the Gurbantunggut Desert in northwestern China and the results
were only based on a short-time manipulative experiment (Huang
et al., 2018). The results showed that water addition consistently
advanced both the flowering and fruiting time of four spring
ephemerals; however, their effects on two spring–summer annuals
were inconsistent, where advances were found in one species, while
delays were found in another (Huang et al., 2018). Since this study
only focused on ephemerals, it remains unknown how the desert
plant phenology of dominant perennials responds to an increase in
precipitation, especially long-term precipitation increases. To address this question, this study conducted a long-term in
situ water addition experiment in a temperate desert of
northwestern China, which is dominated by the shrub species
Nitraria tangutorum. Five simulated future precipitation regimes
(natural rain and natural rain plus an additional 25, 50, 75, and
100% of local long-term mean annual precipitation (145 mm))
were studied during the growing seasons from 2008 to 2018. A
series of phenological events, including leaf unfolding (onset, The phenological responses of plants in desert ecosystems in
particular are causing increasing concern (Ghazahfar, 1997; Ogle
and Reynolds, 2004; Leeuwen et al., 2010; Kigel et al., 2013; July 2020 | Volume 11 | Article 1099 2 Water Addition Prolonged Growing Season Bao et al. approximately 145 mm, 95% of which falls from May to
September. The mean annual temperature is 7.6°C, and the
mean annual potential evaporation is 2,381 mm. The
vegetation is dominated by the shrub species N. tangutorum. Other species, such as Artemisia ordosica, Psammochloa villosa,
Agriophyllum squarrosum, and Corispermummon golicum, can
also be found occasionally. N. tangutorum has a high tolerance to
drought, wind erosion, and sand burial. INTRODUCTION It is a pioneer species
that is widely distributed throughout the northwestern regions of
China and plays an important ecological role in the fixing of sand
dunes because of its exceptional capabilities to form so-called
nebkha dunes, or nebkhas (Zhang et al., 2015). Nebkhas are
phytogenic mounds composed of wind-borne sediments within
or around shrub canopies (Li et al., 2013). The experiment was
performed in a patchy landscape with N. tangutorum nebkhas
(Figure 1) interspersed on hard clay deposited by the Yellow
River. The plant cover on these nebkhas was approximately 45–
75%. The soil types were sandy soil and gray-brown desert soil
(Zhang et al., 2015). The underground water at the experimental
site was at a depth below 5 m, which does not affect plant growth. The soil chemical properties at the 0–10 cm depth are shown in
Table 1. 30%, 50%, and end of leaf unfolding), cessation of new branch
elongation (30, 50, 90%), and leaf coloration (80% of leaves
turned yellow) of N. tangutorum were assessed from 2012–2018. This in situ long-term water addition experiment provides
accurate phenological information at the species level. The
specific aims of this study were to: (i) clarify how increased
water availability will affect phenological events (specifically,
whether these will be advanced or delayed); (ii) identify how
water increases affect the length of the growing season
(specifically, whether it will be prolonged or shortened); (iii)
determine how phenological events and the duration of the
growing season respond to water addition (specifically,
whether these responses will be linear or nonlinear). Experimental Design of Water
Addition Treatments Leaf
unfolding
Onset of leaf unfolding
30% of leaves
unfolded
50% of leaves
unfolded
End of leaf unfolding
Cessation
of new
branch
elongation
30% of new branches
ceased elongating
50% of new branches
ceased elongating
90% of new branches
ceased elongating
Leaf
coloration
80% of leaves turned
yellow Leaf
unfolding
Onset of leaf unfolding
At least one bud in each nebkha has at
least one leaf completely out of the bud,
first leaves visible, but not yet at full size. 30% of leaves
unfolded
30% of buds in each nebkha have their
leaves out, fully expanded. 50% of leaves
unfolded
50% of buds in each nebkha have their
leaves out, fully expanded. End of leaf unfolding
More than 90% of buds in each nebkha
have their leaves out, fully expanded. Cessation
of new
branch
elongation
30% of new branches
ceased elongating
30% of new branches in each nebkha have
their terminal withered and cease
elongating
50% of new branches
ceased elongating
50% of the new branches in each nebkha
have their terminal withered and cease
elongating
90% of new branches
ceased elongating
Over 90% of the new branches in each
nebkha have their terminal end withered
and ceased elongating
Leaf
coloration
80% of leaves turned
yellow
Over 80% of the leaves in each nebkha
show yellow color. Leaf
unfolding
Onset of leaf unfolding A completely random design was used with five water addition
treatments: natural rain plus an additional 0% (Control), 25%
(+25%), 50% (+50%), 75% (+75%), and 100% (+100%) of local
long-term mean annual precipitation (145 mm). Furthermore,
four replicates for each treatment were established since 2008
(113 m2 per plot, 20 plots in total, Figure 1B). The water
addition treatments were applied equally every month from
May to September, and the additional water amounts were 0,
7.3, 14.5, 21.8, and 29.0 mm each time for the five water addition
treatments, respectively. The water was pumped from a well near
the plots into a water tank with water meters and then
transported to each sprinkler (Figure 1C). The sprinklers were
installed on the top of each nebkha (plot) via an irrigation system
(Figure 1B). The sprinklers had two automatically rotating
spraying arms (6 m in length) that could uniformly sprinkle
water over the treatment area. More detailed information on the
experimental design and the irrigation system can be found in
our previous publication (He et al., 2019). TABLE 2 | Phenological events recorded in this study. All shrubs in each
treatment plot (nebkha) were considered and counted. TABLE 2 | Phenological events recorded in this study. All shrubs in each
treatment plot (nebkha) were considered and counted. Statistical Analysis Simple linear regression analysis was used to determine the inter-
annual trends of meteorological factors and phenological events. Pearson correlation was used to analyze the relationships
between phenological events and meteorological factors. Linear
mixed models were used to examine the effects of water addition
treatments, year, and their interactions on phenological events
over the seven years (2012–2018). Water and year were used as
fixed factors, while plot was used as a random factor. The
dependent factor was the timing of different phenological
events (Type I Sum of Squares was used). Duncan post hoc
tests were used to determine pairwise differences for significant
effects. Regression analyses were used to determine the
relationships between changes in phenological events and
water addition amounts or soil water content. Repeated
Measurement ANOVA (RMANOVA) analysis was used to test
the effects of water addition treatments, time of treatment
application, and their interactions on soil water content. One- Phenology Recording p
y
y
A series of phenological events, including leaf unfolding
(onset, 30%, 50%, and end of leaf unfolding), cessation of new
branch elongation (30, 50, 90%), and leaf coloration (80% of
leaves turned yellow) were recorded (Table 2). Precipitation, air
temperature, relative humidity, and evaporation data were
recorded by a standard meteorological station near the
experimental plots. The soil gravimetric water content (SWC)
of the 0–20 cm soil layer was measured using the oven-drying
method. SWC measurements were conducted on the day before
water-addition treatments and every two days after in May, July,
and September in 2012, but only one day each month in 2017
(see details in Figure 3). Experimental Design of Water
Addition Treatments No chemical
components were added to the water, and thus, the water used
here could be used to simulate natural rainfall (Song et al., 2020). Leaf
unfolding
Onset of leaf unfolding At least one bud in each nebkha has at
least one leaf completely out of the bud,
first leaves visible, but not yet at full size. 30% of buds in each nebkha have their
leaves out, fully expanded. 50% of buds in each nebkha have their
leaves out, fully expanded. More than 90% of buds in each nebkha
have their leaves out, fully expanded. 30% of new branches in each nebkha have
their terminal withered and cease
elongating
50% of the new branches in each nebkha
have their terminal withered and cease
elongating
Over 90% of the new branches in each
nebkha have their terminal end withered
and ceased elongating
Over 80% of the leaves in each nebkha
show yellow color. where daytreat represents the day for a given event or the length of
the growing season under water addition plots, dayCtrl represents
the corresponding day in control plots, and n represents the
number of experimental years. Then, Ddays <0 indicates that
phenological events (growing season length) were advanced
(shortened) under water addition, while Ddays >0 indicates
that phenological events (growing season length) were delayed
(prolonged) under water addition. Phenology Recording The phenology observations were conducted from 2012 to 2018
following the standard protocols of Phenological Observation
Methodology in China (Wan and Liu, 1979) with minor
modifications. Phenology recording was conducted by the same
observer from March 2012 to May 2014 and from March 2015 to
November 2018, while from May 2014 to November 2014 the
recordings were conducted by another observer who had been
trained for one month by the first observer. Phenological events for
all shrubs in each plot (each nebkha) were recorded every other day. A series of phenological events, including leaf unfolding
(onset, 30%, 50%, and end of leaf unfolding), cessation of new
branch elongation (30, 50, 90%), and leaf coloration (80% of
leaves turned yellow) were recorded (Table 2). Precipitation, air
temperature, relative humidity, and evaporation data were
recorded by a standard meteorological station near the
experimental plots. The soil gravimetric water content (SWC)
of the 0–20 cm soil layer was measured using the oven-drying
method. SWC measurements were conducted on the day before
water-addition treatments and every two days after in May, July,
and September in 2012, but only one day each month in 2017
(see details in Figure 3). The phenology observations were conducted from 2012 to 2018
following the standard protocols of Phenological Observation
Methodology in China (Wan and Liu, 1979) with minor
modifications. Phenology recording was conducted by the same
observer from March 2012 to May 2014 and from March 2015 to
November 2018, while from May 2014 to November 2014 the
recordings were conducted by another observer who had been
trained for one month by the first observer. Phenological events for
all shrubs in each plot (each nebkha) were recorded every other day. This study investigated whether the heat requirement (often
expressed as growing degree days, GDD) and chilling day (CD)
affected the inter-annual variation of the onset of leaf unfolding
in the natural condition. GDD was calculated as the sum of the
daily mean temperature exceeding 5°C and below 30°C from Jan
1st to the day before the onset of leaf unfolding (Fu et al., 2013;
Anandhi, 2016). CD is the number of days with a daily mean
temperature below 0°C from Nov 1st the previous year to the
onset of leaf unfolding. Cessation
of new
branch
elongation Site Description This study was conducted at the Desert Ecosystem Water
Addition Platform (106°43'E, 40°24'N, 1,050 m above sea level
(a.s.l.)) which was set up in Dengkou County, Inner Mongolia,
China, in 2008. The long-term mean annual precipitation is FIGURE 1 | Illustrations of Nitraria tangutorum nebkhas above-ground and below-ground structures, cited from Zhang et al., 2015 (A); distribution of the 20 plots
and the water addition system (B); sprinkler on nebkhas (C). FIGURE 1 | Illustrations of Nitraria tangutorum nebkhas above-ground and below-ground structures, cited from Zhang et al., 2015 (A); distribution of the 20 plots
and the water addition system (B); sprinkler on nebkhas (C). TABLE 1 | Mean ( ± SE) values of soil chemical properties in 0–10 cm deep soil at the end of the 2010 growing season (n = 4). Treatment
SOC (%)
Soil N (%)
Soil C/N
Soil pH
Ctrl
0.13 ± 0.01(abc)
0.018 ± 0.001(b)
7.80 ± 0.48(a)
8.90 ± 0.11(a)
+25%
0.12 ± 0.01(bc)
0.021 ± 0.002(ab)
5.71 ± 0.71(bc)
9.02 ± 0.12(a)
+50%
0.11 ± 0.01(c)
0.024 ± 0.001(a)
4.57 ± 0.34(c)
8.92 ± 0.11(a)
+75%
0.16 ± 0.01(a)
0.026 ± 0.002(a)
5.94 ± 0.32(bc)
8.66 ± 0.07(a)
+100%
0.15 ± 0.01(ab)
0.024 ± 0.002(a)
6.48 ± 0.62(ab)
8.87 ± 0.06(a)
SOC, soil organic carbon. The same letters in parentheses within each soil property indicate no significant differences between water addition treatments, while different letters denote
significant differences (P < 0.05). TABLE 1 | Mean ( ± SE) values of soil chemical properties in 0–10 cm deep soil at the end of the 2010 growing season (n = 4). July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 3 Water Addition Prolonged Growing Season Water Addition Prolonged Growing Season Bao et al. Meteorological Factors Temporal variations in annual mean relative humidity, air
temperature, evaporation, and annual precipitation at the study
site from 1983 to 2018 are shown in Figure SI1. Relative
humidity followed a significant increasing trend since 1983
(Figure SI1A). No significant temporal trends were found for
air temperature (Figure SI1B) and evaporation (Figure SI1C). Annual precipitation followed increasing trends from 1983 to
1998 and from 1999 to 2018 (Figure SI1D). Data Processing The observed dates of phenological events were first transformed
to the day-of-year format. The length of the growing season was
calculated as the difference between the days when 80% of the
leaves had turned yellow and the onset of leaf unfolding. The
relative change of the days (Ddays) was used to test the effects of
water addition treatments on each event. D days = 1
no
n
i=0
(daytreat −dayCtrl)
(1) (1) July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org Water Addition Prolonged Growing Season Bao et al. summer rainfall exceeded 35 mm in all seven years (2012–2018),
with the highest value in 2012 (178.5 mm) and the lowest value
in 2014 (38.5 mm) (Figure 2H). There was a large variation in
autumn rainfall (2012–2018), with the highest value in 2015
(65.6 mm) and the lowest value in 2013 (7.6 mm) (Figure 2I). Annual precipitation in 2012, 2013, 2014, 2015, 2016, 2017, and
2018 was 213.3 mm, 59.1 mm, 95.2 mm, 147 mm, 189.2 mm,
86.0 mm, and 59.1 mm, respectively (Figure 2J). Based on the
deviation from the long-term mean, 2012 and 2016 were “above-
average” (i.e., wet) years, 2013 was an “ultra below-average” (i.e.,
extremely dry) year, while 2014, 2017, and 2018 were “below-
average” (i.e., dry) years, and 2015 was an “average” year. way ANOVA analyses were used to test the effects of water
addition treatments on the timing of different phenological
events, separately for each year. Homogeneity of variances was
tested by Levene's tests. One-sample Kolmogorov-Smirnov tests
were used to validate normality of the data distribution. All these
above-mentioned procedures were performed in SPSS (SPSS for
Windows, version 20.0, Chicago, IL, USA). Changes in Soil Water Content g
RMANOVA analysis showed that both the amount of added
water and time had significant effects on soil water content
(SWC) (P <0.01), and their interaction was also significant
(P <0.01). The SWC significantly changed after water addition
treatments each month (Figures 3A, B). The change in
magnitude depended on the amount and time of water added. Larger water addition resulted in a larger response magnitude
(Figures 3A, B). The relative changes of soil water contents after
water addition treatments were highest in spring, followed by
autumn, and were lowest in summer (Figures 3A, B). A
B
D
E
F
G
I
H
J
C
FIGURE 2 | Variations in air temperature (A–E) and precipitation (F–J) over
the period of 2012–2018. Variation Trends of Phenological Events
for 2012-2018 The dates of phenological events (in days of the year) under
different water addition treatments are shown in Table SI1. No
significant advancing or delaying trends were found for almost
all phenological events under all treatments for 2012–2018 (all
P >0.05) with only one exception (the onset of leaf unfolding)
(Table SI2). The onset of leaf unfolding dates showed
significantly earlier trends for 2012–2018 for all treatments (all
P <0.05, Figure SI2). Among all meteorological factors, only
relative humidity (RH) was significantly negatively correlated
with the dates of onset of leaf unfolding under all treatments (all
P <0.05, Table SI3). Almost no significant relationships were
found between all other phenological events and meteorological
factors (Table SI3). No significant effects of temperature (winter,
spring, summer, autumn, and annual) were detected for any of
the phenological events in this study (all P >0.05, Table SI3). Seasonal variations in precipitation and air temperature are
shown in Figure 2. Mean air temperatures in winter, spring,
summer, and autumn were −7.34°C, 11.39°C, 23.9 8°C, and
9.09°C, respectively. The mean annual temperature was 9.60°C
for 2012–2018, and no significant increasing or decreasing trends
were found (Figures 2A–E). Winter precipitation only occurred
in three of the years from 2012–2018 and the amounts were very
low, with less than 1 mm in 2014 and 2016, and less than 5 mm
in 2018 (Figure 2F). Spring rainfall varied over 2012–2018, with
the highest value in 2015 (38.6 mm, including one large rain
event with 36.5 mm) and zero in 2016 (Figure 2G). Accumulated Changes in Autumn Phenology Linear Mixed Model analysis showed that water addition
treatments had significant effects on the cessation of new
branch elongation (90%) and 80% of leaves turned yellow (all
P <0.05, Table 3), while the effect on the cessation of new branch
elongation (30%) was marginally significant (P = 0.07, Table 3). Year affected all events significantly (all P <0.05, Table 3). No
interaction was found between water addition treatments and
year (all P >0.05, Table 2). The cessation of new branch elongation (90%) was delayed in all
four water addition treatments and all seven years (2012–2018) with
one exception in 2012 (Figure 5A). On average over the seven years
(2012–2018), the cessation of new branch elongation (90%) in +50,
+75, and +100% treatments were delayed by 5.82, 12.11, and 12.61 d,
respectively. Significant differences from control occurred in +75 and
+100% treatments (all P <0.05, Figure 5C). On average in six years of
the study (2012–2018, excluding 2014), the cessation of new branch
elongation (90%) in +50, +75, and +100% treatments were delayed by
6.79, 12.79, and 13.63 d, respectively. Significant differences from the
control occurred in +100% treatment (P <0.05, Figure 5E). FIGURE 3 | Relative changes of 0–20 cm soil water content (SWC)
compared with control (Ctrl) in +25, +50, +75, and +100% water addition
treatment plots in spring (May), summer (July), and autumn (September) in
2012 (A). Variation in 0–20 cm SWC during the growing season (May to
September) of 2017 (B). SWCCtrl represents SWC in control plots. SWCtreat
represents the SWC in water addition treatment plots. Arrows in (A) represent
the water addition treatment application time. TABLE 3 | Results (P-values) of Linear Mixed Model (MIXMOD) analysis on the
fixed effects of water addition treatments (water), year, and their interactions on
the phenological events and the length of the growing season from 2012–2018. TABLE 3 | Results (P-values) of Linear Mixed Model (MIXMOD) analysis on the
fixed effects of water addition treatments (water), year, and their interactions on
the phenological events and the length of the growing season from 2012–2018. The dates when 80% of leaves turned yellow were delayed in
all four water addition treatments and in all seven years in almost
all cases except for 2012 and 2014 (Figure 5B). Changes in Autumn Phenology On average over
the seven years (2012–2018), the occurrence of 80% of leaves
turning yellow was delayed in +25, +50, +75, and 100%
treatments by 1.18, 5.00, 7.07, and 11.82 d, respectively. A
significant difference from the control occurred in the +100%
treatment (Figure 5D). On average over six years of the study
(2012–2018, excluding 2014), the occurrence of 80% of leaves
turned yellow was delayed in +25, +50, +75, and 100%
treatments by 2.71, 6.92, 9.50, and 14.71 d, respectively. A
significant difference from the control occurred in the +100%
treatment (P <0.05, Figure 5F). Phenological events
Water
Year
Water ×
Year
Leaf unfolding
Onset of leaf unfolding
0.16
<0.01
0.20
30% of leaves unfolded
0.03
<0.01
0.65
50% of leaves unfolded
0.08
<0.01
0.73
End of leaf unfolding
<0.01
<0.01
0.32
Cessation of new
branch elongation
30% of new branches
ceased elongating
0.07
<0.01
0.24
50% of new branches
ceased elongating
0.85
<0.01
0.80
90% of new branches
ceased elongating
0.01
<0.01
0.53
Leaf coloration
80% of leaves turned
yellow
0.02
<0.01
0.41
The length of the growing season
0.01
<0.01
0.53 Changes in Spring Phenology Linear Mixed Model analysis showed that water addition treatments
had significant effects on the occurrence of 30% of leaves unfolded
and the end of leaf unfolding (all P <0.05, Table 3), and had
marginally significant effects on the occurrence of 50% of leaves
unfolded (P = 0.08, Table 3). Year affected all events significantly (all
P <0.05, Table 2). There was no interaction between water addition
treatment and year (all P >0.05, Table 3). Two of the four spring events (leaf unfolding), 30% of leaves
unfolded (Figure 4A) and the end of leaf unfolding (Figure 4B),
showed consistent directional shifts (both advanced) in all four
water addition treatment plots in all seven years except for 2014
(Figure 4). On average over the seven years (2012–2018), the
occurrence of 30% of leaves unfolded events in +25, +50, +75, and July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 5 Water Addition Prolonged Growing Season Bao et al. A
B
FIGURE 3 | Relative changes of 0–20 cm soil water content (SWC)
compared with control (Ctrl) in +25, +50, +75, and +100% water addition
treatment plots in spring (May), summer (July), and autumn (September) in
2012 (A). Variation in 0–20 cm SWC during the growing season (May to
September) of 2017 (B). SWCCtrl represents SWC in control plots. SWCtreat
represents the SWC in water addition treatment plots. Arrows in (A) represent
the water addition treatment application time. +100% treatments (all P <0.05, Figure 4E). On average over all
seven years (2012–2018), the occurrences of the end of leaf
unfolding event in +25, +50, +75, and +100% treatments were
advanced by 4.00, 7.00, 6.71, and 6.29 d, respectively, and
significant differences from the control occurred in +50, +75,
and +100% treatments (all P <0.05, Figure 4D). On average in six
years of the study (2012–2018, excluding 2014), the occurrences of
the end of leaf unfolding event in +25, +50, +75, and +100%
treatments were advanced by 4.83, 8.92, 8.75, and 6.83 d,
respectively. Significant differences from the control occurred in
+25, +50, +75, and +100% treatments (all P <0.05, Figure 4F). A
B B Changes in the Length of the
Growing Season Linear Mixed Model analysis showed that both water addition
treatments and year had significant effects on the length of the
growing season (P <0.05, Table 3), and there was no interaction
between them. +100% treatments were advanced by 1.29, 3.43, 2.64, and 3.00 d,
respectively, which was significantly different from control in the
+50% treatment (P <0.05, Figure 4C). On average in six years of
the study (2012–2018, excluding 2014), the occurrence of 30% of
leaves unfolded events in +25, +50, +75, and +100% treatments
were advanced by 1.58, 4.33, 4.08, and 3.00 d, respectively. Significant differences from the control occurred in +75 and The growing season was prolonged in all four water addition
treatments and in all seven years (2012–2018) in all cases except
for 2012 and 2014 (Figure 6A). On average over the seven years
(2012–2018), the growing season was prolonged in +25, +50, July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 6 Water Addition Prolonged Growing Season Bao et al. A
B
D
E
F
C
FIGURE 4 | Relative changes (△days; mean ± SE) of the two spring events of N. tangutorum after water addition treatments (+25% to +100%) compared with the
control (Ctrl). Positive and negative values represent delayed and advanced days, respectively. A, C, E represent the 30% of leaves unfolded event. B, D, F
represent the End of leaf unfolding event. * indicates significant differences at the P <0.05 level compared with values in control plots. FIGURE 4 | Relative changes (△days; mean ± SE) of the two spring events of N. tangutorum after water addition treatments (+25% to +100%) compared with the
control (Ctrl). Positive and negative values represent delayed and advanced days, respectively. A, C, E represent the 30% of leaves unfolded event. B, D, F
represent the End of leaf unfolding event. * indicates significant differences at the P <0.05 level compared with values in control plots. A
B
D
E
F
C
FIGURE 5 | Relative changes (△days; mean ± SE) of the two autumn events of N. tangutorum after water addition treatments (+25% to +100%) compared with
the control (Ctrl). Positive and negative values represent delayed and advanced days, respectively. A, C, and E represent the cessation of new branch elongation. B, D, and F represent 80% of leaves turned yellow. Relationships Between Phenological
Events and Water Addition Amounts Autumn phenology. Significant positive linear relationships were
found between the timing of cessation of new branch elongation
(90%) and amount of water addition on average from 2012–2018
(all P <0.05, Figure 7A). Among the seven years, significant or
marginally significant relationships were determined in five years
including 2012 (P = 0.07), 2013 (P <0.01), 2016 (P = 0.02), 2017 (P =
0.08), and 2018 (P = 0.03) (Figure 7D). However, a significantly
increased quadratic relationship between 80% of leaves turned
yellow and water addition amount was determined on average
over the period of 2012–2018 without an apparent threshold (all
P <0.05, Figure 7B). Among the seven years, significant
relationships were found in four years, such as linear relationships
in 2012 (P <0.01) and 2016 (P = 0.04), and increasing quadratic
relationships in 2017 (P <0.01) and 2018 (P = 0.09) (Figure 7E). Gebauer and Ehleringer (2000) irrigated five dominant cold
desert shrub species in southern Utah during different seasons. Based on stable isotope data, they found that all species derived less
than 10% of the irrigation water in spring (May) and used most of
the water in autumn (September). This result implies that shrubs
mainly use soil water in early spring (Golluscio et al., 1998). Compared to control plots, the additionally added water could
help to recharge spring soil in water addition treatment plots, and if
more water was added, the deeper soil could also be recharged (Ogle
and Reynolds, 2004). As a result, in the present study, it is reasonable
to attribute the advanced spring phenology to the increased
antecedent soil moisture condition caused by the long-term water
addition treatment even though the data are not available. Growing season length. Significant positive linear relationships
were found between the growing season length and amount of water
addition on average from 2012–2018 (all P <0.05, Figure 7C). Among the seven years, significant relationships were found in four
years, such as linear relationships in 2012 (P <0.01), 2014 (P = 0.06),
and 2017 (P = 0.01), and an increasing quadratic relationship in
2016 (P = 0.08) (Figure 7F). Impact of Water Addition Treatment on
Autumn Phenology Autumn phenology regulates multiple aspects of ecosystem
function (e.g., altering carbon/nitrogen cycling and biotic
interactions), along with associated feedback to the climate
system (Keenan and Richardson, 2015; Xie et al., 2018). Delayed autumn phenology lengthened the duration of the
growing season of N. tangutorum. According to the growing
season length calculation formula (time of 80% of leaves turned
yellow minus time of onset of leaf unfolding), it is reasonable to
conclude that autumn events contributed more to the lengthening
of the growing season than the early spring event in this study. The lengthened growing season possibly implies a longer carbon Relationships Between Phenological
Events and Water Addition Amounts water addition treatment did not affect the timing of the green-up
of dominant species but delayed the senescence time of selected
species by 1.93–9.57 days in one year (Han et al., 2015). In the
present study, the water addition treatment advanced spring
phenology (30% of leaves unfolded, end of leaf unfolding) and
delayed the autumn phenology (80% of leaves turned yellow) in the
desert shrub N. tangutorum. This is partly consistent with the
results reported by Han et al., 2015. In general, in the present study,
increasing the water addition amount only affected the variation
magnitudes of phenological events but not their shifting direction. p
g
Events and Water Addition Amounts
Spring phenology. Significant decreases were observed in quadratic
relationships between the timing of the onset of leaf unfolding and
soil water content in 2012 and 2017 (all P <0.05, Figure SI3A), and
between the timing of 30% of leaves unfolding (P <0.05, Figure
SI3B), 50% of leaves unfolding (P <0.05, Figure SI3C), and end of
leaf unfolding (P <0.05, Figure SI3D) and soil water content in 2017. Autumn phenology. Significant positive linear relationships were
found between the timing of cessation of new branch elongation
(90%) and amount of water addition on average from 2012–2018
(all P <0.05, Figure 7A). Among the seven years, significant or
marginally significant relationships were determined in five years
including 2012 (P = 0.07), 2013 (P <0.01), 2016 (P = 0.02), 2017 (P =
0.08), and 2018 (P = 0.03) (Figure 7D). However, a significantly
increased quadratic relationship between 80% of leaves turned
yellow and water addition amount was determined on average
over the period of 2012–2018 without an apparent threshold (all
P <0.05, Figure 7B). Among the seven years, significant
relationships were found in four years, such as linear relationships
in 2012 (P <0.01) and 2016 (P = 0.04), and increasing quadratic
relationships in 2017 (P <0.01) and 2018 (P = 0.09) (Figure 7E). Spring phenology. Significant decreases were observed in quadratic
relationships between the timing of the onset of leaf unfolding and
soil water content in 2012 and 2017 (all P <0.05, Figure SI3A), and
between the timing of 30% of leaves unfolding (P <0.05, Figure
SI3B), 50% of leaves unfolding (P <0.05, Figure SI3C), and end of
leaf unfolding (P <0.05, Figure SI3D) and soil water content in 2017. leaf unfolding (P <0.05, Figure SI3D) and soil water content in 2017. Changes in the Length of the
Growing Season * indicates significant differences at the P <0.05 level compared with values in control plots. FIGURE 5 | Relative changes (△days; mean ± SE) of the two autumn events of N. tangutorum after water addition treatments (+25% to +100%) compared with
the control (Ctrl). Positive and negative values represent delayed and advanced days, respectively. A, C, and E represent the cessation of new branch elongation. B, D, and F represent 80% of leaves turned yellow. * indicates significant differences at the P <0.05 level compared with values in control plots. +75, and 100% treatments by 2.11, 7.64, 8.00, and 13.68 d,
respectively, and a significant difference from control occurred
in the +100% treatment (P <0.05, Figure 6B). On average in six
years of the study (2012–2018, excluding 2014), the growing season was prolonged in +25, +50, +75, and 100% treatments by
4.04, 10.50, 12.08, and 16.46 d, respectively, and significant
differences from the control occurred in +75 and +100%
treatments (all P <0.05, Figure 6C). July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 7 Bao et al. Water Addition Prolonged Growing Season A
B
C
FIGURE 6 | Relative changes (△days; mean ± SE) in the growing season length of N. tangutorum after water addition treatments (+25% to +100%) compared with
the control (Ctrl). Positive and negative values represent prolonged and shortened days, respectively. A–C represent the length of the growing season. * indicates
significant differences at the P <0.05 level compared with values in control plots. FIGURE 6 | Relative changes (△days; mean ± SE) in the growing season length of N. tangutorum after water addition treatments (+25% to +100%) compared with
the control (Ctrl). Positive and negative values represent prolonged and shortened days, respectively. A–C represent the length of the growing season. * indicates
significant differences at the P <0.05 level compared with values in control plots. Relationships Between Phenological
Events and Water Addition Amounts Impact of Water Addition Treatment on
Spring Phenology Han et al. (2015) conducted a two-year water addition experiment
in a temperate desert steppe of northwestern China, and found that July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 8 Water Addition Prolonged Growing Season Bao et al. A
B
D
E
F
C
FIGURE 7 | Correlations between the amount of water addition (Ctrl), +25, +50, and +100%) and the changes (△days) of the phenological events of N. tangutorum. The solid lines indicate P ≤0.05, and the dashed lines indicate 0.05< P <0.1. A, D represent cessation of new branch elongation. B, E represent 80% of
the leaves turned yellow. C, F represent the length of the growing season. E FIGURE 7 | Correlations between the amount of water addition (Ctrl), +25, +50, and +100%) and the changes (△days) of the phenological events of N. tangutorum. The solid lines indicate P ≤0.05, and the dashed lines indicate 0.05< P <0.1. A, D represent cessation of new branch elongation. B, E represent 80%
the leaves turned yellow. C, F represent the length of the growing season. water addition treatment enhanced the activities of photosynthetic-
related enzymes of N. tangutorum (Bao et al., 2017; He et al., 2019)
and slowed the speed of chlorophyll degradation during leaf
senescence (Fracheboud et al., 2009). uptake period and increased accumulation of photosynthates
(Zhang et al., 2012). This might outweigh the potential risk of
frost damage because of cold spells caused by the earlier leaf
unfolding of N. tangutorum in spring. The delayed cessation of
branch elongation in the present study further confirmed this
conclusion. The prolonged branch elongation stage may improve
carbohydrate allocation to root production, which, in turn, would
enhance water and nutrient utilization in N. tangutorum. Frontiers in Plant Science | www.frontiersin.org Effects of Year on Plant Phenology The shifting directions under water addition treatments were
consistent for almost all events except for several exceptions,
such as 30% of leaves unfolded in 2014 and 2018, the end of
leaf unfolding in 2014, and autumn phenology in both 2012 and
2014. GDD, CD, precipitation, and insolation have complex
interactions in their effects on spring vegetation green-up
phenology (Fu et al., 2012; Fu et al., 2014a; Fu et al., 2015). In
2012, 2013, 2014, 2015, 2016, 2017, and 2018 in control plots,
GDD was 429.9 heat unit (HU), 392.4 HU, 303.85 HU, 269.00
HU, 195.40 HU, 241.30 HU, and 279.45 HU, respectively. In 2012,
2012, 2013, 2014, 2015, 2016, 2017, and 2018 in control plots, CD
was 112, 111, 112, 107, 108, 99, and 106 d, respectively. GDD and
CD in 2012 and 2014 were neither too high nor too low from 2012
cessation 2018, suggesting that heat and chilling requirements The start of autumn phenology is a highly regulated process that
involves the sequential degradation of macromolecules and the
extensive salvage of nutrients (Fracheboud et al., 2009). Environmental factors, such as temperature and photoperiod
(Fracheboud et al., 2009), precipitation (Zhou and Jia, 2016),
frost and moisture condition (rainfall patterns) (Xie et al., 2015),
heat and drought stress (Xie et al., 2018), as well as spring
phenology (Fu et al., 2014b; Keenan and Richardson, 2015), were
found to significantly affect inter-annual variation in autumn
phenology. No significant correlations were found between
spring and autumn phenology in the present study. The delayed
autumn phenology found in this study may be partly because the July 2020 | Volume 11 | Article 1099 9 Water Addition Prolonged Growing Season Bao et al. were sufficiently met to break dormancy in the two years and
should not be related to the exceptions. In addition to
temperature, the antecedent soil moisture plays an important
role in regulating the effects of water addition on plant phenology
as it may either diminish or amplify the effects of water increase
on plant growth and photosynthesis (Reynolds et al., 2004). The
soil water condition in the early springs of 2014 and 2018 might be
dry because the soil water could not have been well recharged by
the low autumn rainfalls of the previous years (Mazer et al., 2015;
Moore et al., 2015; Cleverly et al., 2016) of only 7.6 mm in 2013
and 22.2 mm in 2017. AUTHOR CONTRIBUTIONS FB contributed to manuscript writing, data analysis, and data
collecting. ML, YC, ZX, JL, and BY contributed to the data
collecting. QL and BW contributed to manuscript writing and
data collecting. CONCLUSION The findings of the present study suggest that the phenological
pattern of the desert shrub species N. tugutorum was significantly
influenced by increased precipitation and soil water availability. This offers insight on the effects of other environmental factors
(in addition to temperature) on phenology. However, the soil
water content during non-growing seasons (late autumn, winter,
and early spring) was not monitored. Given the important role of
the early spring water availability, which affects early spring
phenological events, the soil water content should be monitored
in all seasons in the future. Since different species have different
phenological responses to climate change (Xie et al., 2018), more
desert species should be studied in future experiments. DATA AVAILABILITY STATEMENT All datasets generated for this study are included in the article/
Supplementary Material. ACKNOWLEDGMENTS We thank Zhiqiang Wang and Chun Wang for collecting
phenology data in the field. FUNDING Many studies have shown that water plays an important role in
driving plant phenology, such as budburst (Hayden et al., 2010),
green-up (Zhang et al., 2005; Liu et al., 2013), flowering
(Crimmins et al., 2010; Lesica and Kittelson, 2010; Crimmins
et al., 2011; Crimmins et al., 2013; Kigel et al., 2013; Sakkir et al.,
2014; Huang et al., 2018), and fruiting (Lotfiand Mohamed,
2006; Galindo et al., 2014), in water-limited ecosystems. However, most of these studies are focused on natural
conditions, while the relationship between water increase and
phenological events based on water addition experiments has not
been explored, nor has the effects of water addition on branch
phenology of desert plants. The magnitude of spring phenology
advance under water addition treatments might be limited by the
acquisition of nutrients by roots, while root growth will be limited
by the availability of photosynthates from leaves (Linares et al.,
2012). In addition, leaf lifespan (autumn phenology) is associated
with nutrient remobilization (especially nitrogen) and storage of
photosynthates (Kozlowski and Pallardy, 1997). There are trade-
offs between leaf unfolding and carbohydrate allocation to roots, as
well as between leaf coloration and nutrient remobilization. That This research was supported by Funds of the National Key Research
and Development Project (Grant Nos. 2016YFC0500806 and
2016YFC0501004), the National Natural Science Foundation of
China (Grant No. 31400421), and the Surplus Funds of Institute of
Desertification Studies, CAF (Grant Nos. IDS2008JY-3 and
IDS2018JY-9). This research was supported by Funds of the National Key Research
and Development Project (Grant Nos. 2016YFC0500806 and
2016YFC0501004), the National Natural Science Foundation of
China (Grant No. 31400421), and the Surplus Funds of Institute of
Desertification Studies, CAF (Grant Nos. IDS2008JY-3 and
IDS2018JY-9). Effects of Year on Plant Phenology Moreover, the low spring rainfall in both
years (2014, 12.1 mm; 2018, 1.7 mm) further aggravated the
situation. Lower water addition treatments (+25, +50, and +75%)
were insufficient for the alleviation of natural drought. As a result,
the delay of the spring events in +25, +50, and +75% water
addition treatment plots in 2014 and 2018 can mainly be
attributed to variations in the antecedent soil water availability
(Ogle and Reynolds, 2004; Reynolds et al., 2004) and the
complicated interactions with environmental factors (Xie et al.,
2015). The advanced autumn phenology in 2012 might be related
to the water stress caused by several large rainfall events during
that year (Xie et al., 2015). However, the advanced autumn
phenology in 2014 might be related to an extremely dry
summer which resulted in heat and drought stress on plant
phenology even in the water addition treatment plots (Xie et al.,
2015; Xie et al., 2018). Alternatively, it might be affected by the
change of the phenology observer (Figures 4–7, these observations
have not affected the conclusion of this manuscript; therefore, the
data from 2014 were included). It is reasonable to speculate that
climate change projections of an earlier and longer growing season
in response to the increasing precipitation in desert ecosystems
remains elusive for years when plants face consecutively extreme
drought and water-logging stress (Adams et al., 2015). may be why non-linear patterns were found between phenology
and water availability. The present study captured the nonlinear
nature of plant responses to increased water availability (Ogle and
Reynolds, 2004), suggesting that predictions of phenological
events in the future should not be based only on linear trends. Frontiers in Plant Science | www.frontiersin.org REFERENCES multiscale observations. Glob. Ecol. Biogeogr. 23, 1255–1263. doi: 10.1111/
geb.12210 multiscale observations. Glob. Ecol. Biogeogr. 23, 1255–1263. doi: 10.1111/
geb.12210 Adams, H. D., Collins, A. D., Briggs, S. P., Vennetier, M., Dickman, L. T., Sevanto,
S. A., et al. (2015). Experimental drought and heat can delay phenological
development and reduce foliar and shoot growth in semiarid trees. Glob. Change Biol. 21 (11), 4210–4220. doi: 10.1111/gcb.13030 Fu, Y. S. H., Campioli, M., Vitasse, Y., De Boeck, H. J., Van den Berge, J., AbdElgawad, H.,
et al. (2014b). Variation in leaf flushing date influences autumnal senescence and
next year's flushing date in two temperate tree species. Proc. Natl. Acad. Sci. U.S.A. 111, 7355–7360. doi: 10.1073/pnas.1321727111 Anandhi, A. (2016). Growing degree days-Ecosystem indicator for changing
diurnal temperatures and their impact on corn growth stages in Kansas. Ecol. Indic. 61, 149–158. doi: 10.1016/j.ecolind.2015.08.023 Fu, Y. S. H., Piao, S. L., Vitasse, Y., Zhao, H. F., Boeck, H. J., Liu, Q., et al. (2015). Increased heat requirement for leaf flushing in temperate woody species over
1980-2012: effects of chilling, precipitation and insolation. Glob. Change Biol. 21, 2687–2697. doi: 10.1111/gcb.12863 Badeck, F. W., Bondeau, A., Bottcher, K., Doktor, D., Lucht, W., Schaber, J., et al. (2004). Responses of spring phenology to climate change. New Phytolog. 162
(2), 295–309. doi: 10.1111/j.1469-8137.2004.01059.x Galindo, A., Rodrı́guez, P., Collado-González, J., Cruz, Z. N., Torrecillas, E.,
Ondoño, S., et al. (2014). Rainfall intensifies fruit peel cracking in water
stressed pomegranate trees. Agric. For. Meteorol. 194, 29–35. doi: 10.1016/
j.agrformet.2014.03.015 Bao, F., He, J., Cao, Y. L., Liu, M. H., Xin, Z. M., and Wu, B. (2017). Response and
acclimation of photosynthesis in Nitraria tangutorum to rain addition
treatments in temperate desert in Northwest China. J. Univ. Chin. Acad. Sci. 34 (4), 508–514. doi: 10.7523/j.issn.2095-6134.2017.04.018 Gao, X. J., Shi, Y., Zhang, D. F., and Giorgi, F. (2012). Climate change in China in
the 21st centuryas simulated by a high-resolution regional climate model. Chin. Sci. Bull. 57, 1188–1195. doi: 10.1007/s11434-011-4935-8 Sci. Bull. 57, 1188–1195. doi: 10.1007/s11434-011-4935-8 Bao, F., Liu, M., Cao, Y. L., Li, J., Yao, B., Xin, Z., et al. Water Addition Prolonged
the Length of the Growing Season of the Desert Shrub Nitraria tangutorum in a
Temperate Desert. Frontiers in Plant Science, section Functional Plant Ecology. doi: 10.3389/fpls.2020.01099 Gaughan, A. E., Stevens, F. R., Gibbes, C., Southworth, J., and Binford, M. (2012). REFERENCES Linking vegetation response to seasonal precipitation in the Okavango-
Kwando-Zambezi catchment of southern Africa. Int. J. Remote Sens. 33 (21),
6783–6804. doi: 10.1080/01431161.2012.692831 Bertin, R. I. (2008). Plant phenology and distribution in relation to recent climate
change. J. Torrey Bot. Soc 135 (1), 126–146. doi: 10.3159/07-RP-035R.1 Ge, Q. S., Wang, H. J., Zheng, J. Y., This, R., and Dai, J. H. (2014). A 170year spring
phenology index of plants in eastern China. J. Geophys. Res. Biogeosci. 119,
301–311. doi: 10.1002/2013JG002565 Browning, D. M., Snyder, K. A., and Herrick, J. E. (2019). Plant Phenology: Taking
the Pulse of Rangelands. Rangelands 41 (3), 129–134. doi: 10.1016/
j.rala.2019.02.001 Ge, Q. S., Wang, H. J., Rutishauser, T., and Dai, J. H. (2015). Phenological response
to climate change in China: a meta-analysis. Glob. Change Biol. 21 (1), 265–
274. doi: 10.1111/gcb.12648 Chambers, L. E., Altwegg, R., Barbraud, C., Barnard, P., Beaumont, L. J., Crawford,
R. J., et al. (2013). Phenological changes in the southern hemisphere. PloS One
8 (10), e75514. doi: 10.1371/journal.pone.0075514 Gebauer, R. L. E., and Ehleringer, J. R. (2000). Water and nitrogen uptake patterns
following moisture pulses in a cold desert community. Ecology 81, 1415–1424. doi: 10.1890/0012-9658(2000)081[1415:WANUPF]2.0.CO;2 Chen, H. (2013). Projected change in extreme rainfall events in China by the end
of the21st century using CMIP5 models. Chin. Sci. Bull. 58, 1462–1472. doi:
10.1007/s11434-012-5612-2 Ghazahfar, S. A. (1997). The phenology of desert plants: A 3-year study in a gravel
desert wadi in northern Oman. J. Arid Environ. 35, 407–417. doi: 10.1006/
jare.1996.0190 Cleland, E. E., Chuine, I., Menzel, A., Mooney, H. A., and Schwartz, M. D. (2007). Shifting plant phenology in response to global change. Trends Ecol. Evol. 22 (7),
357–365. doi: 10.1016/j.tree.2007.04.003 Golluscio, R. A., Sala, O. E., and Lauenroth, W. K. (1998). Differential use of large
summer rainfall events by shrubs and grasses: a manipulative experiment in the
Patagonian steppe. Oecologia 115, 17–25. doi: 10.1007/s004420050486 Golluscio, R. A., Sala, O. E., and Lauenroth, W. K. (1998). Differential use of large
summer rainfall events by shrubs and grasses: a manipulative experiment in the Cleverly, J., Eamus, D., Restrepo, C. N., Chen, C., Maes, W., Li, L., et al. (2016). Soil
moisture controls on 3 phenology and productivity in a semi-arid critical zone. Sci. Total Environ. 568, 1227–1237. doi: 10.1016/j.scitotenv.2016.05.142 summer rainfall events by shrubs and grasses: a manipulative experiment in the
Patagonian steppe. Oecologia 115, 17–25. REFERENCES doi: 10.1007/s004420050486 Gordo, O., and Sanz, J. J. (2010). Impact of climate change on plant phenology in
Mediterranean ecosystems. Glob. Change Biol. 16 (3), 1082–1106. doi: 10.1111/
j.1365-2486.2009.02084.x Codesido, V., and López, J. F. (2003).Shoot phenology studies to determine growth
cycles in two Pinus radiata D. Don progeny tests in northern Spain, in:
Conference: Silviculture and the conservation of genetic resources for sustainable
forest. Han, J., Chen, J., Xia, J., and Li, L. (2015). Grazing and watering alter plant
phenological processes in a desert steppe community. Plant Ecol. 216 (4), 599–
613. doi: 10.1007/s11258-015-0462-z Crimmins, T. M., Crimmins, M. A., and Bertelsen, D. C. (2010). Complex
responses to climate drivers in onset of spring flowering across a semi-arid
elevation gradient. J.Ecol 98 (5), 1042–1051. doi: 10.1111/j.1365-
2745.2010.01696.x Hayden, B., Greene, D. F., and Quesada, M. (2010). A field experiment to
determine the effect of dry-season precipitation on annual ring formation
and leaf phenology in a seasonally dry tropical forest. J. Trop. Ecol. 26 (02),
237–242. doi: 10.1017/S0266467409990563 Crimmins, T. M., Michael, A., Crimmins,, and Bertelsen, C. D. (2011). Onset of
summer flowering in a ‘Sky Island' is driven by monsoon moisture. New Phytol. 191 (2), 468–479. doi: 10.1111/j.1469-8137.2011.03705.x He, J., Bao, F., Wu, B., Zhang, J. H., and Jia, Z. Y. (2019). Photosynthetic acclimation
of a desert species Nitraria tangutorum to long term rain addition in north-
western china. Intl. J. Agric. Biol. 22, 1050–1058. doi: 10.17957/IJAB/15.1168 Crimmins, T. M., Crimmins, M. A., and Bertelsen, C. D. (2013). Spring and
summer patterns in flowering onset, duration, and constancy across a water-
limited gradient. Am. J. Bot. 100 (6), 1137–1147. doi: 10.3732/ajb.1200633 Huang, J. P., Ji, M. X., Xie, Y. K., Wang, S. S., He, Y. L., and Ran, J. L. (2015a). Global semi-arid climate change over last 60 years. Clim. Dynam. 46 (3-4),
1131–1150. doi: 10.1007/s00382-015-2636-8 Damascos, M. A., Prado, C. H., and Ronquim, C. C. (2005). Bud composition,
branching patterns and leaf phenology in Cerrado Woody Species. Ann. Bot. 96, 1075–1084. doi: 10.1093/aob/mci258 Huang, J. P., Yu, H. P., Guan, X. D., Wang, G. Y., and Guo, R. X. (2015b). Accelerated dryland expansion under climate change. Nat. Clim. Change. 6,
166–172. doi: 10.1038/nclimate2837 Fracheboud, Y., Luquez, V., BjÖrken, L., SjÖdin, A., Tuominen, H., and Jansson, S. (2009). The control of autumn senescence in European aspen. Plant Physiol. 149, 1982–1991. doi: 10.1104/pp.108.133249 Huang, G., Li, C. H., and Li, Y. SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online
at: https://www.frontiersin.org/articles/10.3389/fpls.2020.01099/
full#supplementary-material July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 10 Water Addition Prolonged Growing Season Bao et al. REFERENCES X., Gu, L. H., Bao, F., Cao, Y. L., Hao, Y. G., He, J., et al. (2015). Nitrogen control
of d13C enrichment in heterotrophic organs relative to leaves in a landscape-building
desert plant species. Biogeosciences 12 (1), 15–27. doi: 10.5194/bg-12-15-2015 Menzel, A., Estrella, N., and Fabian, P. (2001). Spatial and temporal variability of
the phenological seasons in Germany from 1951 to 1996. Glob. Change Biol. 7,
657–666. doi: 10.1046/j.1365-2486.2001.00430.x Zheng, Z., Zhu, W., Chen, G., Jiang, N., Fan, D., and Zhang, D. (2016). Continuous
but diverse advancement of spring-summer phenology in response to climate
warming across the Qinghai-Tibetan Plateau. Agric. For. Meterol. 223, 194–
202. doi: 10.1016/j.agrformet.2016.04.012 Moore, L. M., Lauenroth, W. K., Bell, D. M., and Schlaepfer, D. R. (2015). Soil
Water and Temperature Explain Canopy Phenology and Onset of Spring in
a Semiarid Steppe. Great Plains Res. 25, 121–138. doi: 10.1353/
gpr.2015.0027 Zhou, Y. Z., and Jia, G. S. (2016). Precipitation as a control of vegetation
phenology for temperate steppes in China. Atmos. Oceanic Sci. Lett. 9 (3),
162–168. doi: 10.1080/16742834.2016.1165594 Nord, E. A., and Lynch, J. P. (2009). Plant phenology: a critical controller of soil
resource acquisition. J. Exp. Bot. 60 (7), 1927–1937. doi: 10.1093/jxb/erp018 Ogle, K., and Reynolds, J. F. (2004). Plant responses to precipitation in desert
ecosystems: integrating functional types, pulses, thresholds, and delays. Oecologia 141 (2), 282–294. doi: 10.1007/s00442-004-1507-5 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Patrick, L. D., Ogle, K., Bell, C. W., Zak, J., and Tissue, D. (2009). Physiological
responses of two contrasting desert plant species to precipitation variability are
differentially regulated by soil moisture and nitrogen dynamics. Glob. Change
Biol. 15 (5), 1214–1229. doi: 10.1111/j.1365-2486.2008.01750.x Copyright © 2020 Bao, Liu, Cao, Li, Yao, Xin, Lu and Wu. This is an open-access
article distributed under the terms of the Creative Commons Attribution License
(CC BY). The use, distribution or reproduction in other forums is permitted, provided
the original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms. Reynolds, J. F., Kemp, P. R., and Ogle, K. (2004). REFERENCES H., Chen, J., Zhu, X. L., and Zheng, Y. H. (2011). Influences
of temperature and precipitation before the growing season on spring
phenology in grasslands of the central and eastern Qinghai-Tibetan Plateau. Agric. For. Meterol. 151, 1711–1722. doi: 10.1016/j.agrformet.2011.07.003 Leeuwen, W. J. D., van,, Davison, J. E., Casady, G. M., and Marsh, S. E. (2010). Phenological Characterization of Desert Sky Island Vegetation Communities
with Remotely Sensed and Climate Time Series Data. Remote Sens. 2 (2), 388–
415. doi: 10.3390/rs2020388 Agric. For. Meterol. 151, 1711–1722. doi: 10.1016/j.agrformet.2011.07.003 Lesica, P., and Kittelson, P. M. (2010). Precipitation and temperature are associated
with advanced flowering phenology in a semi-arid grassland. J. Arid Environ. 74 (9),
1013–1017. doi: 10.1016/j.jaridenv.2010.02.002 Shen, M. G., Piao, S. L., Cong, N., Zhang, G. X., and Jassens, I. A. (2015). Precipitation impacts on vegetation spring phenology on the Tibetan Plateau. Shen, M. G., Piao, S. L., Cong, N., Zhang, G. X., and Jassens, I. A. (2015). Precipitation impacts on vegetation spring phenology on the Tibetan Plateau. Glob. Change Biol. 21 (10), 467–3656. doi: 10.1111/gcb.12961 Glob. Change Biol. 21 (10), 467–3656. doi: 10.1111/gcb.12961 Li, B. F., Chen, Y. N., Chen, Z. S., Xiong, H. G., and Lian, L. S. (2016). Why does
precipitation in northwest China show a significant increasing trend from 1960
to 2010? Atmos. Res. 167, 275–284. doi: 10.1016/j.atmosres.2015.08.017 Song, W. M., Chen, S. P., Zhou, Y. D., and Lin, G. H. (2020). Rainfall amount and
timing jointly regulate the responses of soil nitrogen transformation processes
to rainfall increase in an arid desert ecosystem. Geoderma 364, 11497. doi: 10.1016/j.geoderma.2020.114197 Li, Q., Xu, J., Li, H., Wang, S., Yan, X., and Xin, Z. (2013). Effects of Aspect on
Clonal Reproduction and Biomass Allocation of Layering Modules of Nitraria
tangutorum in Nebkha Dunes. PLoS ONE 8 (10), e79927. doi: 10.1371/
journal.pone.0079927 Wan, M. W., and Liu, X. (1979). Phenology observation methodology in China
(Beijing: Science Press). Wang, Y., Zhou, B., Qin, D., Wu, J., Gao, R., and Song, L. (2017). Changes in mean
and extreme temperature and precipitation over the arid region of
northwestern China: observation and projection. Adv. Atmos. Sci. 34 (3),
289–305. doi: 10.1007/s00376-016-6160-5 Linares, J. C., Covelo, F., Carreira, J. A., and Merino, J. A. (2012). Phenological and
water-use patterns underlying maximum growing season length at the highest
elevations: implications under climate change. Tree Physiol. 32, 161–170. doi: 10.1093/treephys/tps003 Wu, X. C., and Liu, H. Y. (2013). REFERENCES Consistent shifts in spring vegetation green-up
date across temperate biomes in China 1982-2006. Glob Chang Biol. 19, 870–
880. doi: 10.1111/gcb.12086 Liu, H., Tian, F., Hu, H. C., Hu, H. P., and Sivapalan, M. (2013). Soil moisture controls
on patterns of grass green-up in Inner Mongolia: an index-based approach. Hydrol. Earth Syst. Sci. 17 (2), 805–815. doi: 10.5194/hess-17-805-2013 Xie, Y. Y., Wang, X. J., and Silander, J. A. Jr. (2015). Deciduous forest responses to
temperature, precipitation, and drought imply complex climate change impacts. Proc. Natl. Acad. Sci. U. S. A. 112 (44), 13585–13590. doi: 10.1073/pnas.1509991112 Liu, Q., Fu, Y. H., Zeng, Z. Z., Huang, M. R., Li, X. R., and Piao, S. L. (2015). Temperature, precipitation, and insolation effects on autumn vegetation
phenology in temperate China. Glob. Change Biol. 22, 1–11. doi: 10.1111/
gcb.13081 Xie, Y. Y., Wang, X. J., Wilsonb, A. M., and Silander, J. A. Jr. (2018). Predicting
autumn phenology: how deciduous tree species respond to weather stressors. Agric. For. Meterol. 250-251, 127–137. doi: 10.1016/j.agrformet.2017.12.259 Lotfi, A., and Mohamed, C. (2006). Water status and growth phenology of a
Saharan shrub in north Africa. Afri. J. Ecol. 45, 80–85. doi: 10.1111/j.1365-
2028.2006.00683.x Yan, D., Zhang, X. Y., Yu, Y. Y., Guo, W., and Hanan, N. P. (2016). Characterizing land
surface phenology and responses to rainfall in the Sahara Desert. J. Geophys. Res. Biogeosci. 121, 2243–2260. doi: 10.1002/2016JG003441 Ma, X. L., Huete, A., Yu, Q., Coupe, N. R., Davies, K., Broich, M., et al. (2013). Spatial patterns and temporal dynamics in savanna vegetation phenology
across the North Australian Tropical Transect. Remote Sens. Environ. 139,
97–115. doi: 10.1016/j.rse.2013.07.030 Zhang, X. Y., Friedl, M. A., Schaaf, C. B., Strahler, A. H., and Liu, Z. (2005). Monitoring the response of vegetation phenology to precipitation in Africa by
coupling MODIS and TRMM instruments. J. Geophys. Res. 110, D12103. doi: 10.1029/2004JD005263 Mazer, S. J., Gerst, K. L., Matthews, E. R., and Evenden, A. (2015). Species-specific
phenological responses to winter temperature and precipitation in a water-
limited ecosystem. Ecosphere 6 (6), 98. doi: 10.1890/ES14-00433.1 Zhang, B. C., Cao, J. J., Bai, Y. F., Zhou, X. H., Ning, Z. G., Yang, S. J., et al. (2012). Effects of rainfall amount and frequency on vegetation growth in a Tibetan alpine
meadow. Clim. Change 118 (2), 197–212. doi: 10.1007/s10584-012-0622-2 Menzel, A., and Fabian, P. (1999). Growing season extended in Europe. Nature
397, 659. doi: 10.1038/17709 Zhang, J. REFERENCES (2018). Phenological responses to nitrogen and
water addition are linked to plant growth patterns in a desert herbaceous
community. Ecol. Evol. 8 (10), 5139–5152. doi: 10.1002/ece3.4001 Fridley, J. D. (2012). Extended leaf phenology and the autumn niche in deciduous
forest invasions. Nature 485 (7398), 359–362. doi: 10.1038/nature11056 IPCC (2014). Climate Change 2014: Synthesis Report. Contribution of Working
Groups I, II and III to the Fifth Assessment Report of the Intergovernmental
Panel on Climate Change. Eds. R. K. Pachaur and L. A. Meyer (Geneva: IPCC). Fu, Y. S. H., Campioli, M., Deckmyn, G., and Janssens, I. A. (2012). The impact of
winter and spring temperatures on temperate tree budburst dates: results from
an experimental climate manipulation. PloS One 7 (10), e47324. doi: 10.1371/
journal.pone.0047324 Jeong, S. J., Ho, C. H., Gim, H. J., and Brown, M. E. (2011). Phenology shifts at
start vs. end of growing season in temperate vegetation over the Northern
Hemisphere for the period 1982-2008. Glob. Change Biol. 17 (7), 2385–2399. doi: 10.1111/j.1365-2486.2011.02397.x Fu, Y. S. H., Campioli, M., Deckmyn, G., and Janssens, I. A. (2013). Sensitivity of
leaf unfolding to experimental warming in three temperate tree species. Agr. For. Meteorol. 181, 125–132. doi: 10.1016/j.agrformet.2013.07.016 doi: 10.1111/j.1365-2486.2011.02397.x Keenan, T. F., and Richardson, A. D. (2015). The timing of autumn senescence is
affected by the timing of spring phenology: implications for predictive models. Glob. Change Biol. 21, 2634–2641. doi: 10.1111/gcb.12890 Fu, Y. S. H., Piao, S. L., Op de Beeck, M., Cong, N., Zhao, H. F., Zhang, Y., et al. (2014a). Recent spring phenology shifts in western Central Europe based on July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 11 Water Addition Prolonged Growing Season Bao et al. Kigel, J., Konsens, I., Rosen, N., Rotem, G., Kon, A., and Fragman-Sapir, O. (2013). Relationships Between Flowering Time and Rainfall Gradients Across
Mediterranean-Desert Transects. Isr. J. Ecol. Evol. 57 (1-2), 91–109. doi:
10.1560/IJEE.57.1-2.91 Sakkir, S., Shah, J. N., Cheruth, A. J., and Kabshawi, M. (2014). Phenology of desert
plants from an arid gravel plain in eastern United Arab Emirates. J. Arid Land. 7 (1), 54–62. doi: 10.1007/s40333-014-0036-2 Schwartz, M. D., and Reiter, B. E. (2000). Changes in North American spring. Int. J. Climatol. 20 (8), 929–932. doi: 10.1002/1097-0088(20000630)20:8<929::AID-
JOC557>3.0.CO;2-5 Kozlowski, T. T., and Pallardy, S. G. (1997). Physiology of woody plants (New York:
Academic Press), 454. Shen, M. G., Tang, Y. REFERENCES Modifying the ‘pulse–
reserve' paradigm for deserts of North America: precipitation pulses, soil
water, and plant responses. Oecologia 141, 194–210. doi: 10.1007/s00442-
004-1524-4 July 2020 | Volume 11 | Article 1099 Frontiers in Plant Science | www.frontiersin.org 12
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Genetic engineering to enhance microalgal-based produced water treatment with emphasis on CRISPR/Cas9: A review
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Frontiers in bioengineering and biotechnology
| 2,023
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cc-by
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OPEN ACCESS Alaa Hassanien1, Imen Saadaoui1,2, Kira Schipper1, Sara Al-Marri3,
Tasneem Dalgamouni1, Mustapha Aouida4, Suhur Saeed3 and
Hareb M. Al-Jabri1,2* Alaa Hassanien1, Imen Saadaoui1,2, Kira Schipper1, Sara Al-Marri3,
Tasneem Dalgamouni1, Mustapha Aouida4, Suhur Saeed3 and
Hareb M. Al-Jabri1,2* 1Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar
University, Doha, Qatar, 2Biological and environmental Sciences Department, College of Arts and Sciences,
Qatar University, Doha, Qatar, 3ExxonMobil Research Qatar (EMRQ), Doha, Qatar, 4Division of Biological and
Biomedical Sciences, Qatar Foundation, College of Health and Life Sciences, Education City, Hamad Bin
Khalifa University, Doha, Qatar In recent years, the increased demand for and regional variability of available water
resources, along with sustainable water supply planning, have driven interest in the
reuse of produced water. Reusing produced water can provide important economic,
social, and environmental benefits, particularly in water-scarce regions. Therefore,
efficient wastewater treatment is a crucial step prior to reuse to meet the
requirements for use within the oil and gas industry or by external users. Bioremediation using microalgae has received increased interest as a method for
produced water treatment for removing not only major contaminants such as
nitrogen and phosphorus, but also heavy metals and hydrocarbons. Some
research publications reported nearly 100% removal of total hydrocarbons, total
nitrogen, ammonium nitrogen, and iron when using microalgae to treat produced
water. Enhancing microalgal removal efficiency as well as growth rate, in the
presence of such relevant contaminants is of great interest to many industries to
further optimize the process. One novel approach to further enhancing algal
capabilities and phytoremediation of wastewater is genetic modification. A
comprehensive
description
of
using
genetically
engineered
microalgae
for
wastewater bioremediation is discussed in this review. This article also reviews
random and targeted mutations as a method to alter microalgal traits to produce
strains capable of tolerating various stressors related to wastewater. Other methods
of genetic engineering are discussed, with sympathy for CRISPR/Cas9 technology. This is accompanied by the opportunities, as well as the challenges of using
genetically engineered microalgae for this purpose. Hassanien A, Saadaoui I, Schipper K,
Al-Marri S, Dalgamouni T, Aouida M,
Saeed S and Al-Jabri HM (2023), Genetic
engineering to enhance microalgal-based
produced water treatment with emphasis
on CRISPR/Cas9: A review. Front. Bioeng. Biotechnol. 10:1104914. doi: 10.3389/fbioe.2022.1104914 COPYRIGHT
© 2023 Hassanien, Saadaoui, Schipper, Al-
Marri, Dalgamouni, Aouida, Saeed and Al-
Jabri. Abbreviations: CCU, carbon capture and utilization; Cd, Cadmium; CO2, carbon dioxide; CoCl2, Cobalt (II)
chloride; COD, chemical oxygen demand; CRISPR, clustered regularly interspaced short palindromic
repeats; CuSO4, Copper (II) sulfate; EPS, extracellular polysaccharides; GMO, genetically modified
organism; INDELs, insertions or deletions; NORM, naturally occurring radioactive material; PW, Produced
water; RNPs, ribonucleoproteins; TALEN, Transcription activator-like effector nuclease; TDS, total dissolved
solids; TN, Total Nitrogen; TOC, Total Organic Carbon; UV, ultraviolet; ZFN, Zinc finger nuclease. TYPE Review
PUBLISHED 13 January 2023
DOI 10.3389/fbioe.2022.1104914 TYPE Review
PUBLISHED 13 January 2023
DOI 10.3389/fbioe.2022.1104914 TYPE Review
PUBLISHED 13 January 2023
DOI 10.3389/fbioe.2022.1104914 Frontiers in Bioengineering and Biotechnology bioremediation, CRISPR/cas9, genetic engineering, microalgae, produced wastewater KEYWORDS
bioremediation, CRISPR/cas9, genetic engineering, microalgae, produced wastewater Genetic engineering to enhance
microalgal-based produced water
treatment with emphasis on
CRISPR/Cas9: A review OPEN ACCESS
EDITED BY
Jixiang Yang,
University of Chinese Academy of
Sciences, China
REVIEWED BY
Dipanwita Deb,
KIIT University, India
Badr A. Mohamed,
Cairo University, Egypt
*CORRESPONDENCE
Hareb M. Al-Jabri,
h.aljabri@qu.edu.qa
SPECIALTY SECTION
This article was submitted to
Industrial Biotechnology,
a section of the journal
Frontiers in Bioengineering and
Biotechnology
RECEIVED 22 November 2022
ACCEPTED 30 December 2022
PUBLISHED 13 January 2023 KEYWORDS 2 Microalgae: Promising alternative for
produced water bioremediation Produced water (PW) is the highest volume of liquid waste
generated and discharged during the production of oil and gas. The
worldwide
volume
of
produced
water
generated
is
approximately 1.3 times that of hydrocarbon production (Gray,
2020). PW varies in composition and volume from one formation
to another, and predominant constituents include total dissolved
solids (TDS), such as natural salts and minerals, as well as
dissolved and volatile organic compounds, oil and grease, heavy
metals, dissolved gases, bacteria, naturally occurring radioactive
materials (NORM, radionuclides such as radium), and the additives
used in hydrocarbon production (Al-Ghouti et al., 2019). In recent
years, the increased demand for and regional variability of available
water resources, along with sustainable water supply planning, have
driven interest in the reuse of produced water. As freshwater supplies
become scarcer, produced water can be a crucial source of water after
suitable treatment. There has been an increased focus on reclaiming,
reusing, and recycling water that is usually wasted to meet the
communities’ needs for freshwater sources (Gray, 2020). In recent times, a greater focus has appeared on using biological
systems, including microalgae, for treating produced wastewater
effluents (Graham et al., 2017; Rahman et al., 2020; Alsarayreh
et al., 2022). Application of microalgae in wastewater treatment
even shows competitive advantages over other treatment methods
to improve water quality, due to its high treatment efficiency as well as
carbon capture and biomass valorization opportunities (Molazadeh
et al., 2019; Leng et al., 2020; Alsarayreh et al., 2022). Various methods can be applied to enhance the bioremediation
efficiencies of microalgae, including advanced cultivation systems,
consortiums,
and
genetic
modification. Microalgal
cells
are
transformable; their genomes can be redesigned to include a
desired feature by employing the proper delivery system to
introduce
DNA
for
transformation
(Gimpel
et
al.,
2015). Transformation of different microalgal species using multiple
genetic engineering tools has been successfully applied to enhance
metabolite production for biofuels (Radakovits et al., 2010) as well as
for other products (Ibuot et al., 2017; Rahman et al., 2020). Genetic
engineering is a powerful tool to enhance the ability of many
microorganisms’ to bioremediate wastewater. For example (Huang
et
al.,
2015),
inserted
the
arsenite
S-adenosylmethionine
methyltransferase
gene
obtained
from
the
red
microalgae
Cyanidioschyzon merolae into Bacillus subtilis. The transformed
Bacillus was able to methylate the inorganic arsenic. Such studies
provide proof for concept of using transformed microbes for treating
different kinds of contaminants. 1 Introduction overview and explore about the importance of genetic engineering in
enhancing algae phytoremediation efficiency. Combining the two
topics allows us a forward look at genetic engineering strategies to
enhance microalgal efficiency in phytoremediation of produced
wastewater. Microalgae are photosynthetic microscopic organisms, either
prokaryotic or eukaryotic that could live in all bodies of water and
utilize sunlight and carbon dioxide (CO2) as their sole energy and
carbon sources to produce organic compounds via photosynthesis
(Zhu et al., 2016; Deviram et al., 2020). This, together with their fast
growth rates, and ability to produce high value metabolites of interest
for many industrial applications, make microalgae an attractive
subject for researchers in the field of sustainable production
(Saadaoui et al., 2019; Arias et al., 2020; Rasheed et al., 2020;
Saadaoui et al., 2019; Veiga et al., 2020; Saadaoui et al., 2019;
Varaprasad et al., 2021; Bounnit et al., 2022; Bello et al., 2022). Furthermore, microalgae have also been found to be able to
efficiently remove contaminants from various types of wastewater
effluents, including pharmaceutical (Singh et al., 2020), agricultural
(Leite et al., 2019), and industrial (Al-Jabri et al., 2021). In the tertiary
treatment stage, they can eliminate macro-nutrients from the water
mainly nitrogen and phosphorus, as well as heavy metals (Molazadeh
et al., 2019). Even in particularly contaminated wastewaters, such as
produced water from the oil and gas industry, microalgae have
demonstrated the ability to degrade specific components as a
treatment step toward clean water (Graham et al., 2017; Rahman
et al., 2020; Alsarayreh et al., 2022). Overall, cultivation of microalgae
on different types of wastewaters is considered a sustainable
technology for bioremediation due to its capacity to thrive by
consuming present contaminants (Mehariya et al., 2021). Non-
etheless, due to immature technologies, instabilities of wastewater
components,
and
required
improvements
of
bioremediation
efficiencies, microalgae are not yet widely applied for wastewater
treatment (Feng et al., 2020; Li et al., 2022). OPEN ACCESS This is an open-access article
distributed under the terms of the Creative
Commons Attribution License (CC BY). The use, distribution or reproduction in
other forums is permitted, provided the
original author(s) and the copyright
owner(s) are credited and that the original
publication in this journal is cited, in
accordance with accepted academic
practice. No use, distribution or
reproduction is permitted which does not
comply with these terms. 01 Frontiers in Bioengineering and Biotechnology frontiersin.org Hassanien et al. Hassanien et al. 10.3389/fbioe.2022.1104914 10.3389/fbioe.2022.1104914 Frontiers in Bioengineering and Biotechnology 2 Microalgae: Promising alternative for
produced water bioremediation It is not surprising that algae have a high potential for PW
treatment. For decades, researchers have studied their general
wastewater
treatment
capabilities,
optimizing
their
treatment
efficiencies and growth on different types of wastewaters. Salgueiro
et al. (2016) for example demonstrated that Chlorella vulgaris was able
to remove 99.2% of phosphorus from artificial wastewater containing
glucose, ammonium chloride, urea, monopotassium phosphate and
reduce the chemical oxygen demand (COD) by 71.1%. Likewise (El-
Kassas and Mohamed, 2014), showed that Chlorella vulgaris was able
to treat textile wastewater, with COD and color removal percentages of
69.9% and 76.32%, respectively. Furthermore (Wang et al., 2019),
investigated the use of the marine diatom Phaeodactylum tricornutum
to treat municipal wastewater mixed with seawater. The results
revealed that the diatom was able to remove up to 89.9% of COD,
86.7% of Total Nitrogen (TN), 84.2% of ammonium, and 97.0% of
total phosphorus. Moreover, the strains were able to produce a high
amount of lipids, which could potentially be applied for biodiesel
production (Jayakumar et al., 2021). Produced water, on the other
hand, can be more challenging, due to potential toxicity and the
presence of heavy metals, hydrocarbons, surfactants, and anti-
corrosives. Non-etheless,
various
studies
have
shown
that
bioremediation
of
PW
using
microalgae
has
shown
a
high
potential. For example (Das et al., 2019), demonstrated the ability This
review
provides
the
status
of
microalgal-based
bioremediation of produced water, as well as the most recent
microalgal
applicable
genetic
engineering
tools:
zinc
finger
nucleases (ZFNs), Transcription activator-like effector nucleases
(TALENs), and clustered regularly interspaced short palindromic
repeats
(CRISPR/Cas9). Previous
reviews
of
this
field
have
particularly focused on multiple wastewater treatment such as
agricultural or municipal, or on genetic engineering as a tool to
enhance efficiency the efficiency of microalgae to serve different
purposes. This review is the first of its kind to develop a critical 02 frontiersin.org 10.3389/fbioe.2022.1104914 Hassanien et al. of Chlorella sp. (QUCCCM10) to bioremediate pretreated PW, after
pH adjustment and removal of suspended matter. The microalga was
found to be able to reduce the concentration of various elements, such
as arsenic, cadmium, iron, nickel, and potassium, as well as remove
92% and 94.2% of TN and Total Organic Carbon (TOC), respectively. 2 Microalgae: Promising alternative for
produced water bioremediation DDVG strain in municipal wastewater under
mixotrophic condition to test the strain availability to survive and
remove major contaminants form the water. The results showed that
Scenedesmus efficiently removed ≈75% of COD and ≈100% of total
nitrogen with a biomass of nearly 3.4 gL−1 after 10 days of cultivation. 2 Microalgae: Promising alternative for
produced water bioremediation In a more recent study (Rahman et al., 2021), showed that Galdieria
sulphuraria was able to grow in PW concentrations of up to 50%, with
biomass productivities of up to .72 g L−1·d−1, and 99.6% and 74.2%
nitrogen and phosphorus removal rates, respectively, without the
addition of extra micronutrients. Similarly (Ammar et al., 2018),
inoculated two marine microalgae species, Nannochloropsis oculata
and Isochrysis galbana, with different concentrations of PW obtained
from an oil field located in Iraq. Although higher PW loadings were
found to have a negative impact on biomass productivities; successive
adaptation biomass yields of .31 g L−1 were still achieved for both
strains at 50% PW loading. Optimal contaminant removal however
occurred at lower PW loadings of 10% and 25%, at which
Nannochloropsis oculata was able to remove up to 89% and 81%
oil content and 90% and 72% COD, respectively. these and other recent studies investigating algal-mediated PW
treatment,
including
the
different
strains,
experimental
and
cultivation conditions applied. To summarize, utilizing microalgae for PW bioremediation can be
advantageous and efficient owing to i) its capability of removing heavy
metals, hydrocarbons, and other pollutants, ii) its ability to produce
high-value bioproducts such as biofuels (Cho et al., 2011), iii) its ability
to reduce the need for fresh water and nutrients for algae cultivation
(Rahman et al., 2020; Ahmad et al., 2021) and iv) its potential for
carbon capture and utilization (CCU) from industrial point-sources
(Kalra et al., 2021). Non-etheless, some obstacles and complications
still arise when applying this technology, which will need to be
mitigated for it to be applied on a large scale. Such concerns
include the requirement for long residence times for efficient
contaminant removal, the risk of contamination, the existence of
contaminants that may inhibit the algae growth, and the cost of
nutrients added and for biomass harvesting (Ahmad et al., 2021;
Watanabe and Isdepsky, 2021). The ability of microalgae to remove pollutants from wastewater is
due to different mechanisms they can perform. First, microalgae have
the ability to take advantage of mixotrophic modes of nutrition. Which
means it can switch their metabolism from using only CO2 as a carbon
source to using organic matter based on its availability in the growth
medium (Alalawy et al., 2019). (Devi et al., 2022) cultivated
Scenedesmus sp. 3 Genetic engineering as promising tool
to enhance bioremediation efficiencies A possible option to improve the application of algae in industrial
processes, such as PW treatment, could be strain improvement
through genetic engineering (Ahmad et al., 2022). Even though
advanced tools for genetic engineering have emerged at a great
pace, they remain underutilized for microalgae as compared to
other microorganisms. This is despite the demonstrated benefits of
improving yields and overcoming challenges of high production costs
(Bajhaiya et al., 2017; Kumar et al., 2020). In this section, we go over
the different types of genetic modification which can be applied to
algae, as well as how they can be used to improve PW bioremediation
efforts. Microalgal removal of organic compounds from the wastewater
can be credited to biodegradation and biosorption processes. Biodegradation is known to be the most effective method by which
microalgae use different enzymes to eliminate organic micropollutants
from the aqueous environment (Nguyen et al., 2021). Biosorption is
defined as the physical-chemical process in which substances are
removed from solution using biological matter. Due to the negative
charge of the cell wall in microalgae, cationic pollutants can efficiently
adhere to the surface. However, it is less efficient in term of pollutants
removal
compared
to
biodegradation
(Nguyen
et
al.,
2021). Biodegradation and biosorption of different contaminants including
organic compounds are extensively studied by Pathak et al. (2018). Frontiers in Bioengineering and Biotechnology 3.1 Random mutagenesis One of the powerful trait alteration tools for microalgae is random
mutagenesis (Manandhar-Shrestha and Hildebrand, 2013; Arora et al.,
2020). Obtaining
mutants
through
random
mutagenesis
is
accomplished through various methods, ranging from chemical,
nuclear irradiation, plasmas, and ultraviolet (UV) mutagenesis. This, combined with a strong selective selection pressure, has
proven to be a reliable strategy for producing strains with
improved stress tolerances, resistance to contaminants, increased
productivities (Cabanelas et al., 2016), but also higher metabolite
production rates (Lai et al., 2004; Cordero et al., 2011; Doan and
Obbard, 2012). Recently (Qi et al., 2018), developed a mutant of
Scenedesmus obliquus for the purpose of increasing the CO2 bio-
fixation and enhancing biomass production under elevated CO2 levels. The mutants with genetic stability as well as potential for increased
CO2 tolerance were found through UV mutagenesis, as well as
applying a low pH as a selective pressure. The authors found that
the mutant strain was able to achieve higher biomass productivities
and light conversion efficiencies under elevated CO2 concentrations
compared to the parent strains, as well as contain 37% and 25% higher
carbohydrate and lipid contents, respectively. Applying radon
mutagenesis to algae strains such as those investigated by (Ammar Microalgae have enormous potential not only for bioremediation
of produced water, but also for biomass reutilization in a variety of
applications. Algae cultivated in wastewater are rich source of primary
and secondary metabolites that could benefit in producing many
valuable bioproducts such as biofuels, biofertilizers, and feed
supplements
(Shahid
et
al.,
2020). Combining
algae-based
wastewater treatment with producing high-value compounds will
greatly reduce the economic cost of the process. For instance
(Japar et al., 2021), successfully increased the biomass production
and lipid content of Chlorella vulgaris and Chlorella sorokiniana
UKM3 grown in industrial wastewater by acclimatization process. . Since wastewater can be used as a sustainable growth medium, a
variety of wastewater types have been proposed to increase algal
biomass (Srimongkol et al., 2022). In this
context,
biomass
generated from produced water treatment can be a promising
source
for
valuable
metabolite
production
for
numerous
applications. In Table 1, more detailed information is shown on 03 frontiersin.org Hassanien et al. 10.3389/fbioe.2022.1104914 TABLE 1 Selected recent literature on algal bioremediation of PW. 3.1 Random mutagenesis Strain
Wastewater type
Cultivation conditions
Highest
biomass
yield (g·L−1)
Pollutants
removed
Highest
removal
efficiency (%)
Reference
1
Chlorella sp
produced water from a Qatari
local petroleum company
In a temperature-controlled room,
a glass bottle was agitated with
compressed air and illuminated
with an light intensity of 600 µmol
photons·m−2·s−1
1.72
TOC
73
Das et al. (2019)
total Nitrogen
92
2
Chlorella vulgaris
Produced water from an oil
and gas facility in
United States. Tissue Culture Roller Drum
Apparatus inside an incubator with
a constant level of CO2 of 2%–3%
(v/v), a temperature of 28°C with
16:8 h light:dark cycle and an
illumination of ~4000 lux
3.1 ± 0.5
total Nitrogen
100
Rahman et al. (2021)
phosphorus
≈74.2
3
Chlorella vulgaris
PW from dumping site
generated by oil wells in
Colombia
fluorescent light at an irradiance of
36.8 ± 4.2 μmol photons m−2 s−1 at
the surface of the culture medium,
temperature at 20 °C and
permanent aeration supplied by a
blower
—
Total
hydrocarbons
≈100
Calderón-delgado
et al. (2019)
4
Chlorella
pyrenoidosa
PW from oilfield in Algeria
outdoor, under sunlight radiation,
using an open system sited in the
desert area in the winter season. The temperatures fluctuated from
26 to 31°C during the day
1.15
COD
89.67%
Rahmani et al. (2022)
Ammonium
nitrogen
100%
total Nitrogen
57.14%,
total
Phosphorus
75.51%
Copper
73.39
Lead
72.80
Cadmium
48.42
5
Nannochloropsis
oculata
Produced water from oil field
in Iraq
Florescence light (2000 lux) at and
a light photoperiod of 18:6 h light:
dark, 25°C±1°C, continuous filtered
air at a constant flow rate via two
aquarium air pumps
1.13
Oil
66.5
Ammar et al. (2018)
COD
54
6
Nannochloropsis
oculata
Produced water from a
TOTAL operating site in
France
14/10 h light/dark periods, by LED
lamps, temperature at (21 ± 1°C),
autotrophic conditions with air. CO2 was added in pulse, 5 s each
20–40 min and pH between
7.5 and 9
—
Ammonium
nitrogen
≈100
Parsy et al. (2020)
COD
70
Iron
100
7
Nannochloropsis
oculata
Produced water from an oil
field in Brazil
Aerated photobioreactors (3 L
min−1), cold white LED lamps with
light intensity of 57 μmol m−2·s−1,
photoperiod of 12:12 h. Temperature controlled at
21°C±.9°C. The pH was fixed at 7
—
PAHs
94
Marques et al. (Continued on following page) 3.1 Random mutagenesis (2021)
NAP
96
APT
95
FLU
91
PHE
83
BbF
95
DA
90
BaP
95
Iron
96.80
8
Galdieria
sulphuraria
Produced water from an oil
and gas facility in
United States. Tissue Culture Roller Drum
Apparatus inside an incubator CO2
level was kept constant at 2%–3%
(v/v), temperature 42°C with 24 h
of continuous illumination
(~4000 lux)
5.12 ± .28
total Nitrogen
≈100
Rahman et al. (2021)
(Continued on following page) TABLE 1 Selected recent literature on algal bioremediation of PW. 04 Frontiers in Bioengineering and Biotechnology Frontiers in Bioengineering and Biotechnology frontiersin.org Hassanien et al. 10.3389/fbioe.2022.1104914 TABLE 1 (Continued) Selected recent literature on algal bioremediation of PW. Strain
Wastewater type
Cultivation conditions
Highest
biomass
yield (gL−1)
Pollutants
removed
Highest
removal
efficiency (%)
Reference
9
Isochrysis galbana
Produced water from oil field
in Iraq
Florescence light (2000 lux), and a
photoperiod of 18:6 h light: dark,
25°C±1°C, continuous filtered air at
a constant flow rate via two
aquarium air pumps
1.01
Oil
68
Ammar et al. (2018)
COD
56
10
Dunaliella
tertiolecta
Produced water from an oil
production facility in the
Permian Basin of southeast
New Mexico
Temperature controlled at 24°C in
a growth chamber with fluorescent
illumination of 100 μmol photons
m−2 s−1. agitation was set at at
140 rpm with a 16-h light/8-h dark
cycle
≈0.3
nitrate
≈99.6
Hopkins et al. (2019)
Phosphate
≈99.6
PAHs, polycyclic aromatic hydrocarbons; NAP, naphthalene; AP, acenaphthylene; FLU, fluorene; PHE, phenanthrene; BbF, benzo(b)fluoranthene; DA, dibenzo (a, h) anthracene; BaP, benzo(a)
pyrene. TABLE 1 (Continued) Selected recent literature on algal bioremediation of PW. et al., 2018), followed by exposure to high PW loadings, could
potentially result in strains’ abilities to bioremediate PW without
dilution, increasing its industrial and economic feasibility as a
treatment option. Nevertheless, although interesting, the technology
also exhibits some weaknesses, such as the fact that mutants may lose
the mutation of interest within a number of generations, thus losing
their enhanced trait, as well as the fact that experiments can have a
long time span (Arora and Philippidis, 2021), making their application
cumbersome. et al., 2013). The ZFNs were created to target the COP3 gene using
paromomycin-resistance as a marker activity. Furthermore, this work
proves that transient ZFN expression is not toxic for the cells as it
results in stable transformed colonies. 3.2 Targeted genetic engineering Besides random mutagenesis, using targeted genetic modification
methods for heterologous expression of foreign genes is very
promising for enhancing specific algae traits. Recently, genetic
engineering has gained momentum because new and strong genetic
tools are progressively offered and redesigning and improving
metabolic pathways reveal new opportunities for the industrial
development of microalgae (Ng et al., 2017). In the past decade,
gene-editing
tools
such
as
(TALEN),
(ZFN)
(CRISPR/Cas9)
technologies have emerged as the most popular recombinant DNA
technologies that have been applied on a variety of different
microorganisms, including microalgae (Fajardo et al., 2020; Kumar
et al., 2020). 3.1 Random mutagenesis Similarly (Greiner et al., 2017),
used ZFNs to reliably edit genes by homologous recombination in
multiple strains of Chlamydomonas, including the wild type. This
work also reported that promising results were achieved when the ZFN
protocol was changed to replace glass beads with electroporation. Regardless of the numerous benefits of editing DNA with ZFNs, some
issues may arise when it is applied. For example, there are limited sites
to be targeted for nuclease selection. Also, there is a potential that
double strand breaks may occur at an off-target site (Gupta and
Musunuru, 2014). A simplified workflow of ZFN process is illustrated
in (Figure 1). Frontiers in Bioengineering and Biotechnology 3.2.2 Transcription activator-like effector nucleases
(TALEN) Transcription activator-like effector nucleases (TALEN) are one of
the first developed molecular editing tools (Zhang et al., 2016). TALEs
are proteins that exist in nature in Xanthomonas bacteria (Malzahn
et al., 2017), and are distinguished by their ability to recognize and
bind to single base pairs of a DNA sequence (Gaj et al., 2013). When
TALE proteins fuse with FokI nuclease, a double strand break is
induced in the DNA, which enables knocking out genes or introducing
mutations (Jeon et al., 2017) (Figure 1B). TALEN has many
advantages, most importantly: i) it can be engineered to target a
specific site in the genome; ii) it is much easier to design compared to
ZFNs; iii) it is available commercially, as well as a TALEN-based
library has been constructed; iv) it is not limited by the length of
sequence it can bind to; v) fewer obstacles appear when selecting the
binding site (Gupta and Musunuru, 2014). On the other hand, some
constraints must be taken into consideration when applying TALEN. As such, compared to ZFNs, it appears to be much larger in size,
knowing that the large size makes it less specific. Also, the larger the
TALENs, the harder it becomes to deliver them to cells. Moreover, the
host plasmid vector of the TALEN sequence tends to rearrange after
transduction (Kumar et al., 2020). Several studies have reported the
modification of the genomes of different microalgae. TALENs were
used to enhance lipid metabolic pathways in the genome of the diatom
Phaeodactylum tricornutum, according to (Daboussi et al., 2014) and 3.2.1 Zinc-finger nucleases (ZFN) (Nain et al., 2010) describe zinc-finger nucleases (ZFNs) as a
powerful tool that reshapes the boundaries of biological research. It is
composed of programmable modules that bind to a specific DNA
sequence. Excitingly,
ZFN
enables
a
wide
range
of
genetic
modifications
by
allowing
DNA
double-strand
breaks
that
stimulate error repairs at specific genomic sites (Jabalameli et al.,
2015; Kanchiswamy et al., 2015). The specificity of ZFNs arises from
their versatility and ability to recognize a customized DNA binding
location (Gaj et al., 2013) (Figure 2C). ZFNs have been used multiple
times for chosen modifications of microalgal genomic DNA. It works
by creating a cleavage site where insertions or deletions (INDELs) can
take place (Jeon et al., 2017). ZFN technology was successfully applied
to the model microalga Chlamydomonas reinhardtii in 2013 (Sizova 05 frontiersin.org Hassanien et al. 10.3389/fbioe.2022.1104914 FIGURE 1
Simplified workflow for ZFN, TALEN and CRISPR/Cas9 mediated microalgae genome editing. (A) ZFN, (B) TALEN and (C) CRISPR/Cas9. The 3 tools have
4 steps (1) using bioinformatic tools to identify the targeted sequence and design accordingly, (2) construct the delivery method by choosing the vector, (3)
select the delivery method to insert the plasmid into the microalgae cell, (4) subculture the microalgae on a selective medium and determine the efficiency of
gene editing. FIGURE 1
Simplified workflow for ZFN, TALEN and CRISPR/Cas9 mediated microalgae genome editing. (A) ZFN, (B) TALEN and (C) CRISPR/Cas9. The 3 tools have
4 steps (1) using bioinformatic tools to identify the targeted sequence and design accordingly, (2) construct the delivery method by choosing the vector, (3)
select the delivery method to insert the plasmid into the microalgae cell, (4) subculture the microalgae on a selective medium and determine the efficiency of
gene editing. Slattery et al., 2018). ((Nymark et al., 2016; Slattery et al., 2018). The
mechanism of designing the CRISPR/Cas9 system to manipulate
microalgae genome is expressed in (Figure 1) while its structure is
shown in (Figure 2A) (Hao et al., 2018). Likewise (Takahashi et al., 2018), enhanced the lipid
content in the green microalga Coccomyxa sp. Another example of
successful utilization of the platinum TALENs is efficiently mutating
the nitrate reductase and acyltransferase genes in Nannochloropsis
oceanica (Kurita et al., 2020). The process of applying TALEN in
microalgae is shown in (Figure 1). 3.2.1 Zinc-finger nucleases (ZFN) The first successful application of CRISPR/Cas9 in microalgae was
demonstrated in 2014, by (Jiang et al., 2014) on Chlamydomonas
reinhardtii, although improvements were needed to reduce the
cytotoxic effect of Cas9 on the algae strain (Baek et al., 2016; Shin
et al., 2016). Since then, Chlamydomonas transformation using
CRISPR
system
was
accomplished
multiple
times,
e.g.,
for
increasing
lipids
and
pigments
content
(Song
et
al.,
2022),
increasing triacylglycerol productivity (Lee et al., 2022); lipid
accumulation (Nguyen T. H. T. et al., 2020); and for understanding
CO2 sequestration mechanism (Asadian et al., 2022). Frontiers in Bioengineering and Biotechnology frontiersin.org 3.2.3 CRISPR/Cas9 FIGURE 2
Genetic engineering tools-induced genome editing in Microalgae. The double-stranded breaks (DSBs) introduced at the target site by CRISPR/Cas or
TALEN or ZFN complexes stimulates the endogenous DNA repair machineries, non-homologous end joining (NHEJ) in the absence of the donor template or
the homology-directed repair (HDR) in presence of the donor template. The NHEJ is generally associated with the introduction of insertions and/or deletions
(indels) of varying lengths at the DSB site, often leading to the disruption of the reading frame of the target gene. The HDR pathway results in a precise
insertion or deletion at the DSB site by homologous recombination. The preferred tool is the CRISPR/Cas9 which is highlighted in red as it is very accurate,
easy, and fast. major differences between these technologies stating the advantages
and disadvantages of each individually (Jeon et al., 2017; Liu et al.,
2022). These new approaches are of great interest to optimize specific
traits of microalgae to boost their effectiveness in phytoremediation. degradation could induce increased lipid yields in different microalgal
species (Nguyen A. D. et al., 2020; Chang et al., 2020). Several other
studies were also successful in implementing CRISPR/Cas9 to increase
the production of different carotenoids in Dunaliella salina (Hu et al.,
2021); and in Chlamydomonas reinhardtii (Baek et al., 2016), to
improve the thermal tolerance of Tetraselmis suecica (Xu J. et al.,
2020), and to investigate gene function in Phaeodactylum tricornutum
(Hao et al., 2022; Llavero-Pasquina et al., 2022). Overall, CRISPR/
Cas9 has been successfully applied on many other algae species to
improve their biomass productivities, tolerances to abiotic stressors, or
increase lipid content, or that of other biomolecules and value-added
products (Kumar et al., 2020; Jeon et al., 2021; Wang et al., 2021). Frontiers in Bioengineering and Biotechnology 3.2.3 CRISPR/Cas9 Due to its simplicity and versatility, CRISPR/cas9-mediated
genome-editing is one of the most promising novel techniques for
gene editing and has been shown to be successful in a variety of living
organisms (Bortesi and Fischer, 2015; Xu M. et al., 2020). It offers an
excellent time and labor efficient system (Doudna and Charpentier,
2014; Zhang et al., 2020) and multiple mitigation strategies succeeded
in significantly reducing off-target effects (Han et al., 2020). Moreover,
implementing a plasmid-free CRISPR-Cas9 system has resulted in
very stable ribonucleoproteins (RNPs) in the studied cells (Song et al.,
2019). To use genetically manipulated algae on an industrial scale,
transformed cells need to demonstrate a stable gene expression on
long term. Therefore, large scale algal cultivation require fully
integrated gene cassettes within the genome the transformed strain
(Patel et al., 2019). Many cases of CRISPR/Cas9 genetically
manipulated microalgae have reported stable mutants, which may
alleviate the problem of unsettled mutations (Nymark et al., 2016; Due to its role in biofuel production; several studies have been
conducted on algal cells for increasing lipid content through CRISPR/
Cas9 genetic modification (D’Alessandro and Antoniosi Filho, 2016;
Shokravi et al., 2020). For instance, a recent study by (Lin and Ng,
2020) investigated the improvement of the lipid content of Chlorella
vulgaris, through targeted editing of the omega-3 fatty acid desaturase
gene (fad3). Results showed that the genetically modified strain was
able to reach up to 46% higher lipid content and 20% higher biomass
concentrations, as compared to the wild type of strain. Other studies
suggested that knocking out genes involved in the process of fatty acid 06 frontiersin.org 10.3389/fbioe.2022.1104914 Hassanien et al. FIGURE 2
Genetic engineering tools-induced genome editing in Microalgae. The double-stranded breaks (DSBs) introduced at the target site by CRISPR/Cas or
TALEN or ZFN complexes stimulates the endogenous DNA repair machineries, non-homologous end joining (NHEJ) in the absence of the donor template or
the homology-directed repair (HDR) in presence of the donor template. The NHEJ is generally associated with the introduction of insertions and/or deletions
(indels) of varying lengths at the DSB site, often leading to the disruption of the reading frame of the target gene. The HDR pathway results in a precise
insertion or deletion at the DSB site by homologous recombination. The preferred tool is the CRISPR/Cas9 which is highlighted in red as it is very accurate,
easy, and fast. 3.3.1 Tolerance and accumulation of heavy metals 2015), constructed the pCom8 vector to express alkane hydroxylase in
Escherichia. coli (E. coli) DH5α, after which it was inoculated in diesel
containing media to induce gene expression and perform biodegradation
assays. Furthermore, applying a consortium of Acinetobacter and the
transgenic E. coli strain improved diesel biodegradation by up to 49%
compared to the control. Another study conducted by (Kang et al., 2017)
cloned a two-component flavin-diffusible monooxygenase gene (cph)
from Arthrobacter chlorophenolicus for enzyme overexpression. This
enzyme is responsible for the degradation and removal of 4-
chlorophenol (4-CP) and transformed strains could remove up to
82.7% of 4-CP from the media. Various wastewaters contain hazardous and toxic pollutants that pose
a significant environmental risk, including heavy metals (Gray, 1998). Furthermore, the removal of heavy metals from wastewater is a serious
issue and can be challenging in many cases (Kaur and Roy, 2021). However, numerous algal strains have been found to be capable of
sequestering metals through the use of extracellular polysaccharides
(EPS) and intracellular polyphosphates, which chelate metal ions
(Opeolu et al., 2010). Additionally, the potential use of genetically
engineered microalgae for metal bioremediation is paving the way for
more evaluations and selections of novel genes that are involved in metal
accumulation (Cheng et al., 2019). Besides the introduction of genes involved in hydrocarbon
degradation, increasing biosurfactant production to aid degradation
can be of great interest (Ochsner et al., 1994). Several microalgae and
cyanobacteria were tested for their capability of producing biosurfactant. Dunaliella salina and Porphyridium cruentum, two marine microalgal
species that produce extracellular polymeric substances that can be used as
emulsifiers to metabolize oil hydrocarbons (Sukla et al., 2019). Also
(Radmann et al., 2015), stated that Arthrospira sp. and other
cyanobacteria and microalgae can produce biosurfactant as a by-
product in the presence of certain organic carbon. In this context,
genetic engineering can be helpful to increase the potential of
microalgae to secrete biosurfactant. Numerous research efforts were
made to understand their production on the molecular level, and the
different genes involved in enhancing it were discovered. For instance, the
Emt1, Mmc1, Mac1, Mac2 genes in Ustilago maydis were studied for their
association with the expression of Mannosylerythritol Lipids (MELs),
which are class of biosurfactant (Markande et al., 2021). These lipids are
also expressed in different microalgae (Luca et al., 2021). 3.3.1 Tolerance and accumulation of heavy metals Moreover, using
wastewater as a substrate for Pseudozyma tsukubaensis made it possible to
successfully increase the production of MELs (Andrade et al., 2017).An
overview of these and other reported genes that influence heavy metal and
hydrocarbon degradation is given in Table 2. Using gene-editing
technologies like CRISPR to apply such genes to microalgae could
potentially increase the feasibility of using it for produced water treatment. The most common genetic manipulation techniques for algal-based
metal recovery are overexpression of genes and introducing exogenous
DNA by constructing transgenic algal strains (Cheng et al., 2019). Interestingly, it is worth mentioning that numerous authors have
discussed and studied the introduction of foreign DNA fragments to
different organisms for the purpose of increasing their heavy metal
tolerance, such as plants and bacteria; only few have highlighted this
genetic manipulation strategy for microalgae. One such example in
bacteria comes from (Sriprang et al., 2003), who introduced genes for
phytochelating synthase (PCSAt) in Mesorhizobium huakuiiwhich. PCSAt is a protease-like enzyme that catalyzes the synthesis of
peptides, which in turn chelate metals (Rigouin et al., 2013). It was
reported that the transformation resulted in a transgenic strain that
accumulated Cd+2 9–19-fold more than the strain that did not contain
the PCSAt. In another study, ACC deaminase and iaaM genes were
introduced into the Petunia hybrida Vilm plant via agrobacterium-
mediated transformation, and the transgenic plants were continuously
treated with Copper (II) sulfate CuSO4 and Cobalt (II) chloride CoCl2 to
test for heavy metal tolerance (Zhang et al., 2008). The authors planted
the transgenic Petunia in heavily heavy metal contaminated soil and
found that the mutant plant had double the growth of the wild-type
plant. Also, they grew bigger, healthier, and faster in the heavy metal
contaminated soil, most likely related to the increased tolerance to cobalt
that resulted from the co-expression of both introduced genes. Other
genes that could potentially improve heavy metal tolerance and
accumulation were identified by (Peng et al., 2020) in the plant
Kandelia obovate. This study showed that KoCBF1 and KoCBF3
genes were highly expressed in the presence of lead (Pb (NO3)2),
implying that they are involved in growth and heavy metal
accumulation. One
of
the
few
examples
found
in
literature
demonstrated that wild-type C. 3.3.1 Tolerance and accumulation of heavy metals reinhardtii could not survive in the
presence of Cadmium (Cd) in the cultivation media, whereas a
transgenic strain with high expression level of the CrMTP4 gene was
able to grow well under the metal stress (Ibuot et al., 2017). In
summation,
microalgae
can
ideally
contribute
to
the
bioremediation of heavily contaminated water with heavy metals or
organic pollutants. Owing to its fast adaptability to use these
contaminants
to
thrive. Additionally,
the
role
of
genetic
engineering to develop and understand the mechanism in which
microalgae consume such pollutants cannot be ignored. Thus, to
overcome the growing environmental threat of produced water on
the sustainable development; an increased focused research is acquired
to strengthen the large-scale use of genetically engineered microalgae
and to fill the knowledge gap in this field. 3.3 Applying CRISPR/Cas9 for improving PW
treatment: Target genes Although the application of CRISPR/Cas9 to enhance many microalgal
traits, productivities, and production of primary metabolites has been
increasing, there are very few studies that report the use of CRISPR/Cas9 to
enhance microalgal applications in wastewater treatment (Patel et al., 2019;
Feng et al., 2020). In general, there are a plethora of candidate genes that
can alter metabolic pathways in favor of bioremediation of wastewaters,
with the potential to improve bioremediation and biomass production
(Balzano et al., 2020). To enhance microalgal PW treatment through
genetic engineering, two strategies can be applied: (a) improving strain
tolerance and degradability of certain pollutants, such as hydrocarbons or
heavy metals, or (b) expressing and producing of degradation aiding
molecules, such as surfactants or antifouling ingredients (Feng et al.,
2020). In both cases, the first step is the identification of target genes
for transformation into selected microalgae strains. In summary, microalgae are emerging and thriving as sustainable
base for biotechnology in general and produced wastewater treatment. Yet, it is not currently viable on the industrial scale due to many obstacles. Therefore, it is considered practical to use genetic engineering to enable
the use of microalgae on a bigger scale. Furthermore, genome editing
techniques may be used to further our understanding of the mechanisms
behind the genes that enable microalgae to survive in such harmful
environments. ZFNs, TALENs, and CRISPR/Cas9 were successfully
implemented
in
enhancing
various
applications
of
microalgae
including production of pharmaceutical products lipid, carotenoids,
and protein (Grama et al., 2022). Several reviews summarized the 07 frontiersin.org Hassanien et al. Hassanien et al. 10.3389/fbioe.2022.1104914 10.3389/fbioe.2022.1104914 Frontiers in Bioengineering and Biotechnology 3.3.2 Hydrocarbon degradation It is well known that the composition of wastewater, including
PW, varies greatly based on its origin, also applying to the level of
TOC, including hydrocarbons. As an example, TOC in PW collected
from a petroleum industrial site in Qatar was found to be 720.33 mg
L−1 (Das et al., 2019), however, values of up to 2430 mg L−1 have also
been reported (Shaikh et al., 2020). Many water treatment methods depend on using microbes that
degrade pollutants. Recently, there has been a great focus on
genetically modifying such microorganisms to augment their
ability for bioremediation. Nevertheless, there are limitations and
challenges linked to redesign microorganisms’ DNA related to gene
expression efficiency and the stability of introduced genes according
to (Fajardo et al., 2020) and (Tran and Kaldenhoff, 2020); the success
of genetic transformation is highly dependent on the species Microbial degradation of hydrocarbons is a common phenomenon,
although its applications in bioremediation are still limited (Ławniczak
et al., 2020). These microorganisms can however be the source of relevant
genes that are in control of hydrocarbon degradation and organic carbon
digestion which could be applied in microalgae. For example (Luo et al., 08 frontiersin.org Hassanien et al. 10.3389/fbioe.2022.1104914 TABLE 2 Candidate genes for heavy metal tolerance and accumulation and hydrocarbon degradation. Gene
Plasmid
Promotor
Application
Reference
PCSAt
pBBR1MCS-2 pMP220
nifH
Accumulation of Cd+2
Sriprang et al. (2003)
KoCBF3
Accumulation of Pb
Peng et al. (2020)
ACC deaminase
pBI-iaaM/ACC
CaMV 35S
Accumulation of copper and cobalt
Zhang et al. (2008)
iaaM
pBI-iaaM
GRP
Accumulation of copper and cobalt
Zhang et al. (2008)
CrMTP4
CrMTP4gDNA-pH2GW7
Not mentioned
Increase Mn and Cd content in the cell
Ibuot et al. (2017)
alkane hydroxylase (alkB)
pCom8
Not mentioned
Degrading diesel oil
Luo et al. (2015)
cph
pET-24a
Not mentioned
Removal of 4-chlorophenol
Kang et al. (2017)
mat1
pET15b
—
Biosurfactant
Hewald et al. (2006) TABLE 2 Candidate genes for heavy metal tolerance and accumulation and hydrocarbon degradation. selection. Some diatoms and microalgal species are known for their
low stability after nuclear transformation such as Thalassiosira
weissflogii, Ulva lactuca, and Gracilaria changii (Fajardo et al.,
2020). Another major concern is the presence of off-target effects
of CRISPR/Cas9(Zhang et al., 2015). Additionally, genome-editing
techniques can be very expensive and involve complex procedures
with some technical challenges, such as TALEN (Khan, 2019). Funding This work was supported by ExxonMobil funding (QUEX-CAS-
EMRQ-20/21). The findings herein reflect the work and are solely the
responsibility of the authors. Author contributions AH: Writing-original draft preparation, writing- reviewing and
editing. IS: Supervision, conceptualization, writing-reviewing and
editing; KS: Writing- reviewing and editing, project administration;
SA-M and TD: Writing- reviewing and editing. MA and SS:
Conceptualization
and
writing-
reviewing
and
editing. HA-J:
Conceptualization, writing- reviewing and editing, and funding
acquisition. Thus, even though this technology has the potential for future
use, its sustainability and large-scale use are still in question. Optimization for a more sustainable use on a large scale should
be considered. Finally, microalgae have great potential for many
biotechnological applications, but to date, the development and
improvement of industrial production using CRISPR/Cas9 or
other biotechnologies has yet to be conducted and tested for
feasible and satisfying outcomes. Frontiers in Bioengineering and Biotechnology 3.3.2 Hydrocarbon degradation Furthermore, in order to manipulate the genome of microalgae to
improve its removal of a specific contaminant, such as heavy metals,
a complete understanding of the cells’ metabolism and structure
during metal stress is required to ensure the maximum effectiveness
of those engineered cells for bioremediation (Ranjbar and Malcata,
2022). the genome of microalgae. It is believed that they have a great
opportunity to improve the tolerance of microalgae to toxic
mediums like the produced water. As well as to enhance its ability
to remove existing contaminants. Deeper investigation of these
technologies is crucial the potential genes and understand their
mechanism and function for bioremediation. However, CRISPR/
Cas9, the latest and most promising tool for genome modification
is
believed
to
hold
applicational
advantages
over
the
other
technologies as it offers more stability to the introduced gene; and
it consumes less time and effort with fewer technical issues. Therefore, it is highly recommended to extend the research on
CRISPR/Cas9 application to serve the purpose of bioremediation of
produced water using microalgae given that they are efficient and
economically feasible candidate to make the PW reusable and lower its
negative impact on the environment. Finally, more research effort is
required to overcome the problems that arise when CRISPR/Cas9 is
being applied such as the off-target effects. Other limitations of using genetically enhanced microalgae on a
large-scale, include environmental concerns and issues related to
public health (Janssen and Stucki, 2020; Kumar et al., 2020). Thus,
the environmental impact assessments and other assessments that
comprise biosafety must be performed prior to using a genetically
modified organism (GMO) (Sayler and Ripp, 2000). Nevertheless,
several successful studies were conducted about releasing transgenic
organisms into the environment. For instance, the field trials of
genetically engineered mosquitos in North America (Neuhaus,
2018), and the release of Pseudomonas fluorescens HK44 in a
controlled field in the US (Ripp et al., 2000). Also (De Leij et al.,
1995), spread transgenic Pseudomonas fluorescens in a wheat field in
1995. Using GMOs in bioremediation poses a risk of horizontal gene
transfer as well as regulatory and ecological complications (Singh et al.,
2011). 4 Conclusion and recommendations The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be
construed as a potential conflict of interest. This review discussed the potential of using the genetic
engineering tools ZFNs, TALENs, and CRISPR/Cas9 to manipulate 09 frontiersin.org frontiersin.org Hassanien et al. Hassanien et al. 10.3389/fbioe.2022.1104914 References doi:10.1038/nbt1295-1488 Alsarayreh, M., Almomani, F., Khraisheh, M., Nasser, M. S., and Soliman, Y. (2022). Biological-based produced water treatment using microalgae: Challenges and efficiency. Sustainability 14 (1), 499. doi:10.3390/su14010499 Devi, N. D., Sun, X., Ding, L., Goud, V. V., and Hu, B. (2022). Mixotrophic growth
regime of novel strain Scenedesmus sp. DDVG I in municipal wastewater for concomitant
bioremediation and valorization of biomass. J. Clean. Prod. 365, 132834. doi:10.1016/j. jclepro.2022.132834 Ammar, S. H., Khadim, H. J., and Isam, A. (2018). Cultivation of Nannochloropsis oculata
and Isochrysis galbana microalgae in produced water for bioremediation and biomass
production. Environ. Technol. Innovation 10, 132–142. doi:10.1016/j.eti.2018.02.002 Deviram, G., Mathimani, T., Anto, S., Shan, T., Arul, D., and Pugazhendhi, A. (2020). Applications of microalgal and cyanobacterial biomass on a way to safe, cleaner and a
sustainable environment. J. Clean. Prod. 253, 119770. doi:10.1016/j.jclepro.2019.119770 Andrade, C. J., de, B, L. M. de A., Rocco, S. A., Sforça, M. L., Pastore, G. M., and Jauregi,
P. (2017). A novel approach for the production and purification of mannosylerythritol
lipids (MEL) by Pseudozyma tsukubaensis using cassava wastewater as substrate. Sep. Purif. Technol. 180, 157–167. doi:10.1016/j.seppur.2017.02.045 Doan, T. T. Y., and Obbard, J. P. (2012). Enhanced intracellular lipid in
Nannochloropsis sp. via random mutagenesis and flow cytometric cell sorting. Algal
Res. 1, 17–21. doi:10.1016/j.algal.2012.03.001 Arias, D. M., Uggetti, E., and García, J. (2020). Assessing the potential of soil
cyanobacteria for simultaneous
wastewater treatment and carbohydrate-enriched
biomass production. Algal Res. 51, 102042. doi:10.1016/j.algal.2020.102042 Doudna, J. A., and Charpentier, E. (2014). Genome editing. The new frontier of genome
engineering with CRISPR-Cas9. Science 346, 1258096. doi:10.1126/science.1258096 Arora, N., and Philippidis, G. P. (2021). Microalgae strain improvement strategies:
Random mutagenesis and adaptive laboratory evolution. Trends Plant Sci. 26, 1199–1200. doi:10.1016/j.tplants.2021.06.005 El-Kassas, H. Y., and Mohamed, L. A. (2014). Bioremediation of the textile waste effluent
by Chlorella vulgaris. Egypt. J. Aquatic Res. 40, 301–308. doi:10.1016/j.ejar.2014.08.003 Fajardo, C., De Donato, M., Carrasco, R., Martínez-Rodríguez, G., Mancera, J. M., and
Fernández-Acero, F. J. (2020). Advances and challenges in genetic engineering of
microalgae. Rev. Aquac. 12, 365–381. doi:10.1111/raq.12322 Arora, N., Yen, H.-W., and Philippidis, G. P. (2020). Harnessing the power of
mutagenesis and adaptive laboratory evolution for high lipid production by oleaginous
microalgae and yeasts. Sustainability 12, 5125. doi:10.3390/su12125125 Feng, S., Hu, L., Zhang, Q., Zhang, F., Du, J., Liang, G., et al. (2020). CRISPR/Cas
technology promotes the various application of Dunaliella salina system. Appl. Microbiol. Biotechnol. 104, 8621–8630. References Ahmad, A., Banat, F., Alsafar, H., and Hasan, S. W. (2022). Algae biotechnology for
industrial wastewater treatment, bioenergy production, and high-value bioproducts. Sci. Total Environ. 806, 150585. doi:10.1016/j.scitotenv.2021.150585 Cho, S., Luong, T. T., Lee, D., Oh, Y. K., and Lee, T. (2011). Reuse of effluent water from a
municipal wastewater treatment plant in microalgae cultivation for biofuel production. Bioresour. Technol. 102, 8639–8645. doi:10.1016/j.biortech.2011.03.037 Ahmad, A., Banat, F., Alsafar, H., and Hasan, S. W. (2022). Algae biotechnology for
industrial wastewater treatment, bioenergy production, and high-value bioproducts. Sci. Total Environ. 806, 150585. doi:10.1016/j.scitotenv.2021.150585 Cordero, B. F., Obraztsova, I., Couso, I., Leon, R., Vargas, M. A., and Rodriguez, H. (2011). Enhancement of lutein production in Chlorella sorokiniana (chorophyta) by
improvement of culture conditions and random mutagenesis. Mar. Drugs 9, 1607–1624. doi:10.3390/md9091607 Ahmad, I., Abdullah, N., Koji, I., Yuzir, A., and Mohamad, S. E. (2021). Potential of
microalgae in bioremediation of wastewater. Bull. Chem. React. Eng. 16, 413–429. doi:10. 9767/bcrec.16.2.10616.413-429 Ahmad, I., Abdullah, N., Koji, I., Yuzir, A., and Mohamad, S. E. (2021). Potential of
microalgae in bioremediation of wastewater. Bull. Chem. React. Eng. Catal. 16, 413–429. doi:10.9767/bcrec.16.2.10616.413-429 Daboussi, F., Leduc, S., Maréchal, A., Dubois, G., Guyot, V., Perez-Michaut, C., et al. (2014). Genome engineering empowers the diatom Phaeodactylum tricornutum for
biotechnology. Nat. Commun. 5, 3831–3837. doi:10.1038/ncomms4831 Al-Ghouti, M. A., Al-Kaabi, M. A., Ashfaq, M. Y., and Da’na, D. A. (2019). Produced
water characteristics, treatment and reuse: A review. J. Water Process Eng. 28, 222–239. doi:10.1016/j.jwpe.2019.02.001 D’Alessandro, E. B., and Antoniosi Filho, N. R. (2016). Concepts and studies on lipid
and pigments of microalgae: A review. Renew. Sustain. Energy Rev. 58, 832–841. doi:10. 1016/j.rser.2015.12.162 Al-Jabri, H., Das, P., Khan, S., Thaher, M., and Abdulquadir, M. (2021). Treatment of
wastewaters by microalgae and the potential applications of the produced biomass—A
review. WaterSwitzerl. 13, 27. doi:10.3390/w13010027 Das, P., AbdulQuadir, M., Thaher, M., Khan, S., Chaudhary, A. K., Alghasal, G., et al. (2019). Microalgal bioremediation of petroleum-derived low salinity and low pH produced
water. J. Appl. Phycol. 31, 435–444. doi:10.1007/s10811-018-1571-6 Alalawy, A. I. A., Sh Alabdraba, W. M., and Omer, E. A. (2019). Nutrients and organic
matters removal of ospitals wastewater by microalgae. J. Phys. Conf. Ser. 1294, 072002. doi:10.1088/1742-6596/1294/7/072002 De Leij, F. A. A. M., Sutton, E. J., Whipps, J. M., Fenlon, J. S., and Lynch, J. M. (1995). Field release of a genetically modified Pseudomonas fluorescens on wheat: Establishment,
survival and dissemination. Bio/Technology 13, 1488–1492. Publisher’s note organizations, or those of the publisher, the editors and the
reviewers. Any product that may be evaluated in this article, or
claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. organizations, or those of the publisher, the editors and the
reviewers. Any product that may be evaluated in this article, or
claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. All claims expressed in this article are solely those of the authors
and
do
not
necessarily
represent
those
of
their
affiliated References doi:10.1007/s00253-020-10892-6 Asadian, M., Saadati, M., Bajestani, F. B., Beardall, J., Abdolahadi, F., and Mahdinezhad,
N. (2022). Knockout of Cia5 gene using CRISPR/Cas9 technique in Chlamydomonas
reinhardtii and evaluating CO2 sequestration in control and mutant isolates. J. Genet. 101,
6. doi:10.1007/s12041-021-01350-x Gaj, T., Gersbach, C. A., and Barbas, C. F. (2013). ZFN, TALEN, and CRISPR/Cas-based
methods for genome engineering. Trends Biotechnol. 31, 397–405. doi:10.1016/j.tibtech. 2013.04.004 Baek, K., Kim, D. H., Jeong, J., Sim, S. J., Melis, A., Kim, J.-S., et al. (2016). DNA-free two-
gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins. Sci. Rep. 6, 30620. doi:10.1038/srep30620 Gimpel, J. A., Henríquez, V., and Mayfield, S. P. (2015). In metabolic engineering of
eukaryotic microalgae: Potential and challenges come with great diversity. Front. Microbiol. 6, 1376. doi:10.3389/fmicb.2015.01376 Bajhaiya, A. K., Ziehe Moreira, J., and Pittman, J. K. (2017). Transcriptional engineering
of microalgae: Prospects for high-value chemicals. Trends Biotechnol. 35, 95–99. doi:10. 1016/j.tibtech.2016.06.001 Grama, S. B., Liu, Z., and Li, J. (2022). Emerging trends in genetic engineering of
microalgae for commercial applications. Mar. Drugs 20, 285. doi:10.3390/md20050285 Balzano, S., Sardo, A., Blasio, M., Chahine, T. B., Dell’Anno, F., Sansone, C., et al. (2020). Microalgal metallothioneins and phytochelatins and their potential use in bioremediation. Front. Microbiol. 11, 517. doi:10.3389/fmicb.2020.00517 Gray, M. (2020). “Reuse of produced water in the oil and gas industry,” in SPE
International
Conference
and
Exhibition
on
Health,
Safety,
Environment
and
Sustainability SPE-199498-MSy, England, July 20 2020. Bortesi, L., and Fischer, R. (2015). The CRISPR/Cas9 system for plant genome editing
and beyond. Biotechnol. Adv. 33, 41–52. doi:10.1016/j.biotechadv.2014.12.006 Gray, S. N. (1998). Fungi as potential bioremediation agents in soil contaminated with
heavy or radioactive metals. Biochem. Soc. Trans. 26, 666–670. doi:10.1042/bst0260666 Cabanelas, I. T. D., van der Zwart, M., Kleinegris, D. M. M., Wijffels, R. H., and Barbosa,
M. J. (2016). Sorting cells of the microalga Chlorococcum littorale with increased
triacylglycerol productivity. Biotechnol. Biofuels 9, 183. doi:10.1186/s13068-016-0595-x Greiner, A., Kelterborn, S., Evers, H., Kreimer, G., Sizova, I., and Hegemann, P. (2017). Targeting of photoreceptor genes in Chlamydomonas reinhardtii via zinc-finger nucleases
and CRISPR/Cas9. Plant Cell 29, 2498–2518. doi:10.1105/tpc.17.00659 Calderón-delgado, I. C., Mora-solarte, D. A., and Velasco-Santamaría, Y. M. (2019). Physiological and enzymatic responses of Chlorella vulgaris exposed to produced water
and its potential for bioremediation. Environ. Monit. Assess. 191, 399. doi:10.1007/s10661-
019-7519-8 Gupta, R. M., and Musunuru, K. (2014). Expanding the genetic editing tool kit: ZFNs,
TALENs, and CRISPR-cas9. J. Clin. Investigation 124, 4154–4161. Frontiers in Bioengineering and Biotechnology References doi:10.1111/nph.18296 Hu, L., Feng, S., Liang, G., Du, J., Li, A., and Niu, C. (2021). CRISPR/Cas9-induced β-
carotene hydroxylase mutation in Dunaliella salina CCAP19/18. Amb. Express 11, 83. doi:10.1186/s13568-021-01242-4 Luca, M. D., Pappalardo, I., Limongi, A. R., Viviano, E., Radice, R. P., Todisco, S., et al. (2021). Lipids from microalgae for cosmetic applications. Cosmetics 8, 52. doi:10.3390/
cosmetics8020052 Huang, K., Chen, C., Shen, Q., Rosen, B. P., and Zhao, F.-J. (2015). Genetically
engineering Bacillus subtilis with a heat-resistant arsenite methyltransferase for
bioremediation of arsenic-contaminated organic waste. Appl. Environ. Microbiol. 81,
6718–6724. doi:10.1128/AEM.01535-15 Luo, Q., He, Y., Hou, D. Y., Zhang, J. G., and Shen, X. R. (2015). GPo1 <italic>
alkB</italic> gene expression for improvement of the degradation of diesel oil by a
bacterial
consortium. Braz. J. Microbiol. 46,
649–657. doi:10.1590/S1517-
838246320120226 Ibuot, A., Dean, A. P., McIntosh, O. A., and Pittman, J. K. (2017). Metal bioremediation
by CrMTP4 over-expressing Chlamydomonas reinhardtii in comparison to natural
wastewater-tolerant microalgae strains. Algal Res. 24, 89–96. doi:10.1016/j.algal.2017. 03.002 Malzahn, A., Lowder, L., and Qi, Y. (2017). Plant genome editing with TALEN and
CRISPR. Cell & Biosci. 7, 21. doi:10.1186/s13578-017-0148-4 Jabalameli, H. R., Zahednasab, H., Karimi-Moghaddam, A., and Jabalameli, M. R. (2015). Zinc finger nuclease technology: Advances and obstacles in modelling and treating
genetic disorders. Gene 558, 1–5. doi:10.1016/j.gene.2014.12.044 Manandhar-Shrestha, K., and Hildebrand, M. (2013). Development of flow cytometric
procedures for the efficient isolation of improved lipid accumulation mutants in a
Chlorella sp. microalga. J. Appl. Phycol. 25, 1643–1651. doi:10.1007/s10811-013-0021-8 Janssen, D. B., and Stucki, G. (2020). Perspectives of genetically engineered microbes for
groundwater bioremediation. Environ. Sci. Process. Impacts 22, 487–499. doi:10.1039/c9em00601j Markande, A. R., Patel, D., and Varjani, S. (2021). A review on biosurfactants:
Properties, applications and current developments. Bioresour. Technol. 330, 124963. doi:10.1016/j.biortech.2021.124963 Japar, A. S., Takriff, M. S., and Mohd Yasin, N. H. (2021). Microalgae acclimatization in
industrial wastewater and its effect on growth and primary metabolite composition. Algal
Res. 53, 102163. doi:10.1016/j.algal.2020.102163 Marques, I. M., Oliveira, A. C. V., de Oliveira, O. M. C., Sales, E. A., and Moreira, Í. T. A. (2021). A photobioreactor using Nannochloropsis oculata marine microalgae for removal
of polycyclic aromatic hydrocarbons and sorption of metals in produced water. Chemosphere 281, 130775. doi:10.1016/j.chemosphere.2021.130775 Jayakumar, S., Bhuyar, P., Pugazhendhi, A., Rahim, M. H. A., Maniam, G. P., and
Govindan, N. (2021). Effects of light intensity and nutrients on the lipid content of marine
microalga (diatom) Amphiprora sp. References doi:10.1172/JCI72992 Han, H. A., Pang, J. K. S., and Soh, B. S. (2020). Mitigating off-target effects in CRISPR/
Cas9-mediated in vivo gene editing. J. Mol. Med. 98, 615–632. doi:10.1007/s00109-020-
01893-z Chang, K. S., Kim, J., Park, H., Hong, S. J., Lee, C. G., and Jin, E. S. (2020). Enhanced lipid
productivity in AGP knockout marine microalga Tetraselmis sp. using a DNA-free CRISPR-
Cas9 RNP method. Bioresour. Technol. 303, 122932. doi:10.1016/j.biortech.2020.122932 Hao, X., Chen, W., Amato, A., Jouhet, J., Maréchal, E., Moog, D., et al. (2022). Multiplexed CRISPR/Cas9 editing of the long-chain acyl-CoA synthetase family in the
diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the
synthesis of storage lipids. New Phytol. 233, 1797–1812. doi:10.1111/nph.17911 Cheng, S. Y., Show, P., Lau, F., Chang, J., and Ling, T. C. (2019). New prospects for
modified algae in heavy metal adsorption. Trends Biotechnol. 37, 1255–1268. doi:10.1016/j. tibtech.2019.04.007 10 frontiersin.org Hassanien et al. Hassanien et al. 10.3389/fbioe.2022.1104914 10.3389/fbioe.2022.1104914 Li, M., Zamyadi, A., Zhang, W., Dumée, L. F., and Gao, L. (2022). Algae-based water
treatment: A promising and sustainable approach. J. Water Process Eng. 46, 102630. doi:10. 1016/j.jwpe.2022.102630 Hao, X., Luo, L., Jouhet, J., Rébeillé, F., Maréchal, E., Hu, H., et al. (2018). Enhanced
triacylglycerol production in the diatom Phaeodactylum tricornutum by inactivation of a
Hotdog-fold thioesterase gene using TALEN-based targeted mutagenesis. Biotechnol. Biofuels 11, 312–319. doi:10.1186/s13068-018-1309-3 Lin, W. R., and Ng, I. S. (2020). Development of CRISPR/Cas9 system in Chlorella
vulgaris FSP-E to enhance lipid accumulation. Enzyme Microb. Technol. 133, 109458. doi:10.1016/j.enzmictec.2019.109458 Hewald, S., Linne, U., Scherer, M., Marahiel, M. A., Bo, M., and Bo€lker, M. (2006). Identification of a gene cluster for biosynthesis of mannosylerythritol lipids in the
basidiomycetous fungus Ustilago maydis. Appl. Environ. Microbiol. 72, 5469–5477. doi:10.1128/AEM.00506-06 Liu, K., Chen, R., Yang, R., Chen, Y., Zhu, C., Tang, Y., et al. (2022). “Genome editing
approaches applied to microalgae-based fuels,” in 3rd generation biofuels (Netherlands:
Elsevier), 47–64. doi:10.1016/B978-0-323-90971-6.00013-9 Hopkins, T. C., Graham, E. J. S., and Schuler, A. J. (2019). Biomass and lipid productivity
of Dunaliella tertiolecta in a produced water-based medium over a range of salinities. J. Appl. Phycol. 31, 3349–3358. doi:10.1007/s10811-019-01836-3 Llavero-Pasquina, M., Geisler, K., Holzer, A., Mehrshahi, P., Mendoza-Ochoa, G. I.,
Newsad, S. A., et al. (2022). Thiamine metabolism genes in diatoms are not regulated by
thiamine despite the presence of predicted riboswitches. New Phytol. 235, 1853–1867. References for promising biodiesel production. Sci. Total
Environ. 768, 145471. doi:10.1016/j.scitotenv.2021.145471 Mehariya, S., Goswami, R. K., Verma, P., Lavecchia, R., and Zuorro, A. (2021). Integrated approach for wastewater treatment and biofuel production in microalgae
biorefineries. Energies 14, 2282. doi:10.3390/en14082282 Jeon, M. S., Han, S.-I., Jeon, M., and Choi, Y.-E. (2021). Enhancement of phycoerythrin
productivity in Porphyridium purpureum using the clustered regularly interspaced short
palindromic repeats/CRISPR-associated protein 9 ribonucleoprotein system. Bioresour. Technol. 330, 124974. doi:10.1016/j.biortech.2021.124974 Molazadeh, M., Ahmadzadeh, H., Pourianfar, H. R., Lyon, S., and Rampelotto, P. H. (2019). The use of microalgae for coupling wastewater treatment with CO2 biofixation. Front. Bioeng. Biotechnol. 7, 42. doi:10.3389/fbioe.2019.00042 Jeon, S., Lim, J. M., Lee, H. G., Shin, S. E., Kang, N. K., Park, Y. Il, et al. (2017). Current
status and perspectives of genome editing technology for microalgae. Biotechnol. Biofuels
10, 267. doi:10.1186/s13068-017-0957-z Nagamangala Kanchiswamy, C., Sargent, D. J., Velasco, R., Maffei, M. E., and Malnoy,
M. (2015). Looking forward to genetically edited fruit crops. Trends Biotechnol. 33, 62–64. doi:10.1016/j.tibtech.2014.07.003 Jiang, W., Brueggeman, A. J., Horken, K. M., Plucinak, T. M., and Weeks, D. P. (2014). Successful transient expression of Cas9 and single guide RNA genes in Chlamydomonas
reinhardtii. Eukaryot. Cell 13, 1465–1469. doi:10.1128/EC.00213-14 Nain, V., Sahi, S., and Verma, A. (2010). CPP-ZFN: A potential DNA-targeting anti-
malarial drug. Malar. J. 9, 258. doi:10.1186/1475-2875-9-258 Neuhaus, C. P. (2018). Community engagement and field trials of genetically modified
insects and animals. Hastings Cent. Rep. 48, 25–36. doi:10.1002/hast.808 Kalra, R., Gaur, S., and Goel, M. (2021). Microalgae bioremediation: A perspective
towards wastewater treatment along with industrial carotenoids production. J. Water
Process Eng. 40, 101794. doi:10.1016/j.jwpe.2020.101794 Ng, I., Tan, S., Kao, P., Chang, Y., and Chang, J. (2017). Recent developments on genetic
engineering of microalgae for biofuels and bio-based chemicals. biotechnology 12, 1600644. doi:10.1002/biot.201600644 Kang, C., Yang, J. W., Cho, W., Kwak, S., Park, S., Lim, Y., et al. (2017). Oxidative
biodegradation of 4-chlorophenol by using recombinant monooxygenase cloned and
overexpressed from Arthrobacter chlorophenolicus A6. Bioresour. Technol. 240, 123–129. doi:10.1016/j.biortech.2017.03.078 Nguyen, A. D., Kim, D., and Lee, E. Y. (2020a). Unlocking the biosynthesis of
sesquiterpenoids from methane via the methylerythritol phosphate pathway in
methanotrophic bacteria, using α-humulene as a model compound. Metab. Eng. 61,
69–78. doi:10.1016/j.ymben.2020.04.011 Kaur, S., and Roy, A. (2021). Bioremediation of heavy metals from wastewater using
nanomaterials. Environ. Dev. Sustain. 23, 9617–9640. doi:10.1007/s10668-020-01078-1 Nguyen, H. T., Yoon, Y., Ngo, H. H., and Jang, A. (2021). References The application of microalgae
in removing organic micropollutants in wastewater. Crit. Rev. Environ. Sci. Technol. 51,
1187–1220. doi:10.1080/10643389.2020.1753633 Khan, S. H. (2019). Genome-editing technologies: Concept, pros, and cons of various
genome-editing techniques and bioethical concerns for clinical application. Mol. Ther. -
Nucleic Acids 16, 326–334. doi:10.1016/j.omtn.2019.02.027 Nguyen, T. H. T., Park, S., Jeong, J., Shin, Y. S., Sim, S. J., and Jin, E. (2020b). Enhancing
lipid productivity by modulating lipid catabolism using the CRISPR-Cas9 system in
Chlamydomonas. J. Appl. Phycol. 32, 2829–2840. doi:10.1007/s10811-020-02172-7 Kumar, G., Shekh, A., Jakhu, S., Sharma, Y., and Kapoor, R. (2020). Bioengineering of
microalgae: Recent advances, perspectives, and regulatory challenges for industrial
application. Front. Bioeng. Biotechnol. 8, 914. doi:10.3389/fbioe.2020.00914 Nymark, M., Sharma, A. K., Sparstad, T., Bones, A. M., and Winge, P. (2016). A CRISPR/
Cas9 system adapted for gene editing in marine algae. Sci. Rep. 6, 24951. doi:10.1038/
srep24951 Kurita, T., Moroi, K., Iwai, M., Okazaki, K., Shimizu, S., Nomura, S., et al. (2020). Efficient
and multiplexable genome editing using Platinum TALENs in oleaginous microalga,
Nannochloropsis oceanica NIES-2145. Genes Cells 25, 695–702. doi:10.1111/gtc.12805 Ochsner, U., Koch, A., Fiechter, A., and Reiser, J. (1994). Isolation and characterization
of a regulatory gene affecting rhamnolipid biosurfactant synthesis in Pseudomonas
aeruginosa. J. Bacteriol. 176, 2044–2054. doi:10.1128/jb.176.7.2044-2054.1994 Lai, Y.-P., Huang, J., Wang, L.-F., Jun Li, Z.-R. W., and Wu, Z. R. (2004). A new approach to
random mutagenesis in vitro. Biotechnol. Bioeng. 86, 622–627. doi:10.1002/bit.20066 Ławniczak, Ł., Woźniak-Karczewska, M., Loibner, A. P., Heipieper, H. J., and
Chrzanowski, Ł. (2020). Microbial degradation of hydrocarbons—basic principles for
bioremediation: A review. Molecules 25 (4), 856. doi:10.3390/molecules25040856 Opeolu, B. O., Bamgbose, O., Arowolo, T. A., and Adetunji, M. T. (2010). Utilization of
biomaterials as adsorbents for heavy metals removal from aqueous matrices. Sci. Res. Essays 5, 1780–1787. doi:10.5897/SRE.9000983 Lee, Y., Rudolph, P., Miller, S. M., and Li, Y. (2022). Genetic compensation of
triacylglycerol biosynthesis in the green microalga Chlamydomonas reinhardtii. Plant J. 111, 1069–1080. doi:10.1111/tpj.15874 Parsy, A., Sambusiti, C., Baldoni-andrey, P., Elan, T., and Périé, F. (2020). Cultivation of
Nannochloropsis oculata in saline oil & gas wastewater supplemented with anaerobic
digestion effluent as nutrient source. Algal Res. 50, 101966. doi:10.1016/j.algal.2020.101966 Leite, L. de S., Hoffmann, M. T., and Daniel, L. A. (2019). Microalgae cultivation for
municipal and piggery wastewater treatment in Brazil. J. Water Process Eng. 31,
100821–100827. doi:10.1016/j.jwpe.2019.100821 Patel, V. K., Soni, N., Prasad, V., Sapre, A., Dasgupta, S., and Bhadra, B. (2019). Frontiers in Bioengineering and Biotechnology References A review of
algae-based produced water treatment for biomass and biofuel production. WaterSwitzerl. 12 (9), 2351. doi:10.3390/W12092351 Sukla, L. B., Subudhi, E., and Pradhan, D. (2019). The role of microalgae in wastewater
treatment. Germany: Springer. Rahman, A., Pan, S., Houston, C., and Selvaratnam, T. (2021). Evaluation of galdieria
sulphuraria
and
chlorella
vulgaris
for
the
bioremediation
of
produced
water. WaterSwitzerl. 13 (9), 1183. doi:10.3390/w13091183 Sullivan Graham, E. J., Dean, C. A., Yoshida, T. M., Twary, S. N., Teshima, M., Alvarez,
M. A., et al. (2017). Oil and gas produced water as a growth medium for microalgae
cultivation: A review and feasibility analysis. Algal Res. 24, 492–504. doi:10.1016/j.algal. 2017.01.009 Rahmani, A., Zerrouki, D., Tabchouche, A., and Djafer, L. (2022). Oilfield - produced
water as a medium for the growth of Chlorella pyrenoidosa outdoor in an arid region. Environ. Sci. Pollut. Res. 29, 87509–87518. doi:10.1007/s11356-022-21916-1 Takahashi, K., Ide, Y., Hayakawa, J., Yoshimitsu, Y., Fukuhara, I., Abe, J., et al. (2018). Lipid productivity in TALEN-induced starchless mutants of the unicellular green alga
Coccomyxa sp. strain Obi. Algal Res. 32, 300–307. doi:10.1016/j.algal.2018.04.020 Ranjbar, S., and Malcata, F. X. (2022). Is genetic engineering a route to enhance
microalgae-mediated bioremediation of heavy metal-containing effluents? Molecules 27,
1473. doi:10.3390/molecules27051473 Tran, N. T., and Kaldenhoff, R. (2020). Achievements and challenges of genetic
engineering of the model green alga Chlamydomonas reinhardtii. Algal Res. 50,
101986. doi:10.1016/j.algal.2020.101986 Rigouin, C., Nylin, E., Cogswell, A. A., Schaumlöffel, D., Dobritzsch, D., and Williams, D. L. (2013). Towards an understanding of the function of the phytochelatin synthase of
schistosoma mansoni. PLoS Neglected Trop. Dis. 7, e2037. doi:10.1371/journal.pntd.0002037 Varaprasad, D., Narasimham, D., Paramesh, K., Sudha, N. R., Himabindu, Y., Keerthi
Kumari, M., et al. (2021). Improvement of ethanol production using green alga
Chlorococcum minutum. Environ. Technol. 42, 1383–1391. doi:10.1080/09593330.2019. 1669719 Ripp, S., Nivens, D. E., Ahn, Y., Werner, C., Jarrell, J., Easter, J. P., et al. (2000). Controlled field release of a bioluminescent genetically engineered microorganism for
bioremediation process monitoring and control. Environ. Sci. Technol. 34, 846–853. doi:10.1021/es9908319 Veiga, M. C., Fontoura, M. M., de Oliveira, M. G., Costa, J. A. V., and Santos, L. O. (2020). Magnetic fields: Biomass potential of spirulina sp. for food supplement. Bioprocess
Biosyst. Eng. 43, 1231–1240. doi:10.1007/s00449-020-02318-4 Saadaoui, I., Sedky, R., Rasheed, R., Bounnit, T., Almahmoud, A., Elshekh, A., et al. (2019). Assessment of the algae-based biofertilizer influence on date palm (Phoenix
dactylifera L.) cultivation. J. Appl. Phycol. 31, 457–463. References CRISPR–Cas9 system for genome engineering of photosynthetic microalgae. Mol. Biotechnol. 61, 541–561. doi:10.1007/s12033-019-00185-3 Leng, L., Wei, L., Xiong, Q., Xu, S., Li, W., Lv, S., et al. (2020). Use of microalgae based
technology for the removal of antibiotics from wastewater: A review. Chemosphere 238,
124680. doi:10.1016/j.chemosphere.2019.124680 Pathak, B., Gupta, S., and Verma, R. (2018). “Biosorption and biodegradation of
polycyclic aromatic hydrocarbons (PAHs) by microalgae,” in Green Adsorbents for
pollutant removal environmental chemistry for a sustainable world. Editors G. Crini 11 Frontiers in Bioengineering and Biotechnology frontiersin.org Hassanien et al. 10.3389/fbioe.2022.1104914 and E. Lichtfouse (Cham: Springer International Publishing), 215–247. doi:10.1007/978-3-
319-92111-2_7 maintenance of synthetic pathways in Phaeodactylum tricornutum. ACS Synth. Biol. 7,
328–338. doi:10.1021/acssynbio.7b00191 Peng, Y. L., Wang, Y. S., Fei, J., and Sun, C. C. (2020). Isolation and expression analysis of
two novel C-repeat binding factor (CBF) genes involved in plant growth and abiotic stress
response in mangrove Kandelia obovata. Ecotoxicol. Lond. Engl. 29, 718–725. doi:10.1007/
s10646-020-02219-y Song, I., Kim, S., Kim, J., Oh, H., Jang, J., Jeong, S. J., et al. (2022). Macular pigment-
enriched oil production from genome-edited microalgae. Microb. Cell Fact. 21, 27. doi:10. 1186/s12934-021-01736-7 Song, R., Zhai, Q., Sun, L., Huang, E., Zhang, Y., Zhu, Y., et al. (2019). CRISPR/
Cas9 genome editing technology in filamentous fungi: Progress and perspective. Appl. Microbiol. Biotechnol. 103, 6919–6932. doi:10.1007/s00253-019-10007-w Qi, F., Wu, D., Mu, R., Zhang, S., and Xu, X. (2018). Characterization of a microalgal UV
mutant for CO 2 biofixation and biomass production. BioMed Res. Int. 2018, 1–8. doi:10. 1155/2018/4375170 Srimongkol, P., Sangtanoo, P., Songserm, P., Watsuntorn, W., and Karnchanatat, A. (2022). Microalgae-based
wastewater
treatment
for
developing
economic
and
environmental sustainability: Current status and future prospects. Front. Bioeng. Biotechnol. 10, 904046. doi:10.3389/fbioe.2022.904046 Radakovits, R., Jinkerson, R. E., Darzins, A., and Posewitz, M. C. (2010). Genetic
engineering of algae for enhanced biofuel production. Eukaryot. Cell 9, 486–501. doi:10. 1128/EC.00364-09 Radmann, E. M., Morais, E. G. De, Oliveira, C. F., Jorge, A. V. C., Alberto, J., and Costa,
V. (2015). Microalgae cultivation for biosurfactant production. Afr. J. Microbiol. Res. 9,
2283–2289. doi:10.5897/AJMR2015.7634 Sriprang, R., Hayashi, M., Ono, H., Takagi, M., Hirata, K., and Murooka, Y. (2003). Enhanced accumulation of Cd2+ by a Mesorhizobium sp. transformed with a gene from
Arabidopsis thaliana coding for phytochelatin synthase. Appl. Environ. Microbiol. 69,
1791–1796. doi:10.1128/AEM.69.3.1791-1796.2003 Rahman, A., Agrawal, S., Nawaz, T., Pan, S., and Selvaratnam, T. (2020). References doi:10.1007/s10811-018-1539-6 Wang, Q., Gong, Y., He, Y., Xin, Y., Lv, N., Du, X., et al. (2021). Genome engineering of
Nannochloropsis with hundred-kilobase fragment deletions by Cas9 cleavages. Plant J. 106,
1148–1162. doi:10.1111/tpj.15227 Salgueiro, J. L., Pérez, L., Maceiras, R., Sánchez, A., and Cancela, A. (2016). Bioremediation of wastewater using chlorella vulgaris microalgae: Phosphorus and
organic matter. Int. J. Environ. Res. 10, 465–470. doi:10.22059/ijer.2016.58766 Wang, X.-W., Huang, L., Ji, P.-Y., Chen, C.-P., Li, X.-S., Gao, Y.-H., et al. (2019). Using a
mixture of wastewater and seawater as the growth medium for wastewater treatment and
lipid production by the marine diatom Phaeodactylum tricornutum. Bioresour. Technol. 289, 121681. doi:10.1016/j.biortech.2019.121681 Sayler, G. S., and Ripp, S. (2000). Field applications of genetically engineered
microorganisms for bioremediation processes. Curr. Opin. Biotechnol. 11, 286–289. doi:10.1016/S0958-1669(00)00097-5 Watanabe, M. M., and Isdepsky, A. (2021). Biocrude oil production by integrating
microalgae polyculture and wastewater treatment: Novel proposal on the use of deep
water-depth polyculture of mixotrophic microalgae. Energies 14, 6992. doi:10.3390/
en14216992 Shahid, A., Malik, S., Zhu, H., Xu, J., Nawaz, M. Z., Nawaz, S., et al. (2020). Cultivating
microalgae in wastewater for biomass production, pollutant removal, and atmospheric carbon
mitigation; a review. Sci. Total Environ. 704, 135303. doi:10.1016/j.scitotenv.2019.135303 Xu, J., Soni, V., Chopra, M., and Chan, O. (2020a). Genetic modification of the
HSP90 gene using CRISPR-cas9 to enhance thermotolerance in T. Suecica. Undergrad. Res. Nat. Clin. Sci. Technol. (URNCST) J. 4, 1–6. doi:10.26685/urncst.178 Shaikh, S. S., Abu-Dieyeh, M. H., Al Naemi, F. A., Ahmed, T., and Al-Ghouti, M. A. (2020). Environmental impact of utilization of “produced water” from oil and gas operations in
turfgrass systems. Sci. Rep. 10 (1), 15051. doi:10.1038/s41598-020-72069-5 Xu, M., Weng, Q., and Ji, J. (2020b). Applications and advances of CRISPR/Cas9 in
animal cancer model. Briefings Funct. Genomics 19, 235–241. doi:10.1093/bfgp/elaa002 Shin, S.-E., Lim, J.-M., Koh, H. G., Kim, E. K., Kang, N. K., Jeon, S., et al. (2016). CRISPR/
Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii. Sci. Rep. 6, 27810. doi:10.1038/srep27810 Zhang, S., Guo, F., Yan, W., Dai, Z., Dong, W., Zhou, J., et al. (2020). Recent advances of
CRISPR/Cas9-Based genetic engineering and transcriptional regulation in industrial
biology. Front. Bioeng. Biotechnol. 7, 459. doi:10.3389/fbioe.2019.00459 Shokravi, Z., Shokravi, H., Chyuan, O. H., Lau, W. J., Koloor, S. S. R., Petrů, M., et al. (2020). Improving ‘lipid productivity’ in microalgae by bilateral enhancement of biomass
and lipid contents: A review. Sustain. Switz. 12 (21), 9083. References doi:10.3390/su12219083 Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., and Yang, S.-H. (2015). Off-target
effects in CRISPR/Cas9-mediated genome engineering. Mol. Ther. Nucleic Acids 4, e264. doi:10.1038/mtna.2015.37 Singh, A., Ummalyma, S. B., and Sahoo, D. (2020). Bioremediation and biomass
production of microalgae cultivation in river water contaminated with pharmaceutical
effluent. Bioresour. Technol. 307, 123233. doi:10.1016/j.biortech.2020.123233 Zhang, Y., Huang, H., Zhang, B., and Lin, S. (2016). TALEN- and CRISPR-enhanced
DNA homologous recombination for gene editing in zebrafish. Methods Cell Biol. 135,
107–120. doi:10.1016/bs.mcb.2016.03.005 Singh, J. S., Abhilash, P. C., Singh, H. B., Singh, R. P., and Singh, D. P. (2011). Genetically
engineered bacteria: An emerging tool for environmental remediation and future research
perspectives. Gene 480, 1–9. doi:10.1016/j.gene.2011.03.001 Zhang, Y., Zhao, L., Wang, Y., Yang, B., and Chen, S. (2008). Enhancement of heavy
metal accumulation by tissue specific co-expression of iaaM and ACC deaminase genes in
plants. Chemosphere 72, 564–571. doi:10.1016/j.chemosphere.2008.03.043 Sizova, I., Greiner, A., Awasthi, M., Kateriya, S., and Hegemann, P. (2013). Nuclear gene
targeting in Chlamydomonas using engineered zinc-finger nucleases. Plant J. 73, 873–882. doi:10.1111/tpj.12066 Zhu, L. D., Li, Z. H., and Hiltunen, E. (2016). Strategies for lipid production
improvement in microalgae as a biodiesel feedstock. BioMed Res. Int. 2016, 1–8. doi:10.1155/2016/8792548 Slattery, S. S., Diamond, A., Wang, H., Therrien, J. A., Lant, J. T., Jazey, T., et al. (2018). An expanded plasmid-based genetic toolbox enables Cas9 genome editing and stable 12 frontiersin.org Frontiers in Bioengineering and Biotechnology
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MATLAB - A Ubiquitous Tool for the Practical Engineer
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MATLAB
– A UBIQUITOUS TOOL FOR
THE PRACTICAL ENGINEER Edited by Clara M. Ionescu MATLAB – A Ubiquitous Tool for the Practical Engineer
Edited by Clara M. Ionescu Published by InTech
Janeza Trdine 9, 51000 Rijeka, Croatia y
Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech py g
All chapters are Open Access distributed under the Creative Commons Attribution 3.0
license, which permits to copy, distribute, transmit, and adapt the work in any medium,
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g
Technical Editor Teodora Smiljanic Technical Editor Teodora Smiljanic Cover Designer Jan Hyrat Notice Statements and opinions expressed in the chapters are these of the individual contributors
and not necessarily those of the editors or publisher. No responsibility is accepted for the
accuracy of information contained in the published chapters. The publisher assumes no
responsibility for any damage or injury to persons or property arising out of the use of any
materials, instructions, methods or ideas contained in the book. Publishing Process Manager Davor Vidic
Technical Editor Teodora Smiljanic
Cover Designer Jan Hyrat
Image Copyright thrashem, 2011. Used under license from Shutterstock.com
MATLAB® (Matlab logo and Simulink) is a registered trademark of The MathWorks, Inc. Publishing Process Manager Davor Vidic Publishing Process Manager Davor Vidic g
g
Technical Editor Teodora Smiljanic
Cover Designer Jan Hyrat
Image Copyright thrashem, 2011. Used under license from Shutterstock.com
MATLAB® (Matlab logo and Simulink) is a registered trademark of The MathWorks, Inc. Cover Designer Jan Hyrat Image Copyright thrashem, 2011. Used under license from Shutterstock.com
MATLAB® (Matlab logo and Simulink) is a registered trademark of The MathWorks, Inc. First published October, 2011
Printed in Croatia A free online edition of this book is available at www.intechopen.com A free online edition of this book is available at www.intechopen.com
Additional hard copies can be obtained from orders@intechweb.org Additional hard copies can be obtained from orders@intechweb.org MATLAB – A Ubiquitous Tool for the Practical Engineer, Edited by Clara M. Ionescu
p. cm. ISBN 978-953-307-907-3 MATLAB – A Ubiquitous Tool for the Practical Engineer, Edited by Clara M. Ionescu
p. cm. ISBN 978-953-307-907-3 free online editions of InTech
Books and Journals can be found at
www.intechopen.com Contents Preface IX
Part 1
Applied Mathematics 1
Chapter 1
Effect of the Guess Function
& Continuation Method on
the Run Time of MATLAB BVP Solvers 3
Fikri Serdar Gökhan
Chapter 2
Revisiting the Ceschino Interpolation Method 23
Alain Hébert
Chapter 3
Matrix Based Operatorial Approach
to Differential and Integral Problems 37
Damian Trif
Chapter 4
Comparison of Methodologies
for Analysis of Longitudinal Data Using MATLAB 63
João Eduardo da Silva Pereira, Janete Pereira Amador
and Angela Pellegrin Ansuj
Chapter 5
Educational Simulator for Particle
Swarm Optimization and
Economic Dispatch Applications 81
Woo Nam Lee and Jong Bae Park
Chapter 6
Decomposition Approach
for Inverse Matrix Calculation 111
Krasimira Stoilova and Todor Stoilov
Part 2
Database Development 135
Chapter 7
A Cluster-Based Method for Evaluation
of Truck's Weighing Control Stations 137
Abbas Mahmoudabadi and Arezoo Abolghasem VI
Contents VI
Contents
Chapter 8
The Impact of the Data Archiving File Format
on Scientific Computing and Performance of Image
Processing Algorithms in MATLAB Using Large HDF5 and
XML Multimodal and Hyperspectral Data Sets 145
Kelly Bennett and James Robertson
Chapter 9
Energy Management in Buildings Using MATLAB 165
Shahram Javadi
Part 3
Control Applications 177
Chapter 10
Synchronous Generator
Advanced Control Strategies Simulation 179
Damir Sumina, Neven Bulić, Marija Mirošević and Mato Mišković
Chapter 11
Design of PSO-Based Optimal/Tunable
PID Fuzzy Logic Controller Using FPGA 197
Zeyad Assi Obaid, Saad Abd Almageed Salman, Hazem I. Ali, Nasri
Sulaiman, M. H. Marhaban and M. N. Hamidon
Chapter 12
Cascaded NPC/H-Bridge Inverter with Simplified Control
Strategy and Superior Harmonic Suppression 233
Tom Wanjekeche, Dan V. Nicolae and Adisa A. Jimoh
Chapter 13
MATLAB: A Systems Tool for Design
of Fuzzy LMI Controller in DC-DC Converters 259
Carlos Andrés Torres-Pinzón and Ramon Leyva
Chapter 14
MATLAB as Interface
for Intelligent Digital Control of Dynamic Systems 277
João Viana da Fonseca Neto and Gustavo Araújo de Andrade
Chapter 15
A Fuzzy Finite Element Method Programmed in MATLAB for
the Analysis of Uncertain Control Systems of Structures 291
Angel L. Morales, Jem A. Rongong and Neil D. Sims
Part 4
Modelling, Identification and Simulation 305
Chapter 16
Visual and Thermal Image Fusion
for UAV Based Target Tracking 307
K. Senthil Kumar, G. Kavitha, R. Subramanian and G. Contents Ramesh
Chapter 17
Research of Fuzzy-Systems of Automatic Frequency
and Phase Control on Basis of MATLAB 327
Vladimir Gostev
Chapter 18
Automotive Sketch Processing in C++
with MATLAB Graphic Library 371
Qiang Li Chapter 8 Contents VII Contents VII Contents VII
Chapter 19
Simulation of Rough Surfaces
and Analysis of Roughness by MATLAB 391
F. Gascón and F. Salazar
Chapter 20
MATLAB in Biomodeling 421
Cristina-Maria Dabu
Chapter 21
Non Linear Algorithm for Automatic
Image Processing Applications in FPGAs 437
Emerson Carlos Pedrino, Valentin Obac Roda and Jose Hiroki Saito
Chapter 22
Using MATLAB to Compute Heat Transfer
in Free Form Extrusion 453
Sidonie Costa, Fernando Duarte and José A. Covas
Part 5
Image Processing 475
Chapter 23
MATLAB as a Tool
in Nuclear Medicine Image Processing 477
Maria Lyra, Agapi Ploussi and Antonios Georgantzoglou
Chapter 24
Selected Methods of Image Analysis
in Optical Coherence Tomography 501
Robert Koprowski and Zygmunt Wróbel
Chapter 25
Image Processing for Optical Metrology 523
Miguel Mora-González, Jesús Muñoz-Maciel,
Francisco J. Casillas, Francisco G. Peña-Lecona,
Roger Chiu-Zarate and Héctor Pérez Ladrón de Guevara Preface A well-known statement says that the PID controller is the “bread and butter” of the
control engineer. This is indeed true, from a scientific standpoint. However,
nowadays, in the era of computer science, when the paper and pencil have been
replaced by the keyboard and the display of computers, one may equally say that
MATLAB is the “bread” in the above statement. MATLAB has became a de facto tool
for the modern system engineer. The present book is written for both engineering
students, as well as for practicing engineers. The wide range of applications in which
MATLAB is the working framework, shows that it is a powerful, comprehensive and
easy-to-use environment for performing technical computations. The book includes various excellent applications in which MATLAB is employed. Most of the authors are well skilled in working with MATLAB for their educational,
scientific or engineering purposes, as in: -
applied mathematics, -
data acquisition and communication issues for real-life experiments and
hardware-in-the-loop connections, -
communication protocols with MATLAB (Serial Interface, OPC, Ethernet
functions, Real Time Workshop) -
embedded systems (C++, S-functions) , -
image processing and data archiving -
control systems and algorithms. This book is in fact a collection of results from a wide range of users, including
engineers, scientists, computer experts and applied mathematicians. The diversity of
results and applications suggests that a wide range of readers will benefit from its
content. It is clear that MATLAB has opened a fascinating new world of possibilities. The
contributions presented in this book serve as a proof that MATLAB is a useful tool to
address many challenging problems. I would also like to add a few personal words on the concept of open access
publishing. Although not yet fully matured and not yet fully accepted by the scientific
community, the open access database offered by InTech is a great opportunity for X
Preface Preface X researchers to communicate their work in a rapid and broadly accessible manner. I do
believe that an open access to science and technology is the key of staying alert in this
continuously changing scientific environment and keep the pace with the progress
available all over the world. researchers to communicate their work in a rapid and broadly accessible manner. Preface I do
believe that an open access to science and technology is the key of staying alert in this
continuously changing scientific environment and keep the pace with the progress
available all over the world. Finally, I would like to thank the publishing department of InTech for the excellent
support and guidance in the development of this book, which is in fact a collection of
contributions bearing MATLAB as the interwoven feature. Dr. ir. Clara M. Ionescu
Faculty of Engineering and Architecture
Ghent University,
Belgium 1. Introduction The MATLAB computing environment is a package used extensively throughout industry,
research and education by users of a complete range in proficiency. MATLAB provides then
an ideal platform to introduce such an item of Boundary Value Problem (BVP) software and
indeed, Kierzenka and Shampine (Kierzenka & Shampine, 2001) developed the core BVP
Ordinary Differential Equation (ODE) software bvp4c to solve a large class of two-point
boundary value problems of the form; ( )
( , ( ), )
y x
f x y x
p
′
=
(1)
(
,
, (
), (
), )
0
L
R
L
R
g x
x
y x
y x
p =
(2) (1) (
,
, (
), (
), )
0
L
R
L
R
g x
x
y x
y x
p =
(2) (
,
, (
), (
), )
0
L
R
L
R
g x
x
y x
y x
p = (2) where f is continuous and Lipschitz function in y and p is a vector of unknown parameters. Their view was that a user solving a BVP of form (1) in MATLAB would be most interested
in the graphical representation of a solution, and as such a solver with a MIRK4-based
Simpson Method would be appropriate for graphical accuracy. where f is continuous and Lipschitz function in y and p is a vector of unknown parameters. Their view was that a user solving a BVP of form (1) in MATLAB would be most interested
in the graphical representation of a solution, and as such a solver with a MIRK4-based
Simpson Method would be appropriate for graphical accuracy. If information is specified at more than one point the problem (1) becomes a Boundary
Value Problem. The most common types of BVP are those for which information given at
precisely two points. These are known as two-point boundary value problems. The MATLAB BVP solver of bvp4c is introduced as a Residual control based, adaptive mesh
solver. An adaptive mesh solver is an alternative approach to that of a uniform mesh, which
would specify a uniform grid of data points xi over the interval [xi, xi+1] and solve
accordingly. The adaptive solver will adjust the mesh points at each stage in the iterative
procedure, distributing them to points where they are most needed. Part 1
Applied Mathematics 1 Effect of the Guess Function &
Continuation Method on the Run Time of
MATLAB BVP Solvers Fikri Serdar Gökhan
Gazikent University, Faculty of Engineering and Architecture,
Department of Electrical and Electronic Engineering, Gaziantep
Turkey Fikri Serdar Gökhan
Gazikent University, Faculty of Engineering and Architecture,
Department of Electrical and Electronic Engineering, Gaziantep
Turkey 1. Introduction This can lead to obvious
advantages in terms of computational and storage costs as well as allowing control over the
grid resolution. The concept of a residual is the cornerstone of the bvp4c framework; being
responsible for both errors control and mesh selection (Hale, 2006). The most difficult part for the solution of BVPs is to provide an initial estimation to the
solution. In order to direct the solver for the solution of interest, it is necessary to assist the
solver by informing it with a guess. Not only for the computation of the solution of interest MATLAB – A Ubiquitous Tool for the Practical Engineer 4 but also whether any solution is achieved or not depends strongly on the initial guess. Therefore, depending of the guess function, BVPs may have no solution or a single solution,
or multiple solutions. Moreover, the quality of the initial guess can be critical to the solver
performance, which reduces or augments the run time. However, coming up with a
sufficiently good guess can be the most challenging part of solving a BVP. Certainly, the
user should apply the knowledge of the problem's physical origin (MATLAB
Documentation). but also whether any solution is achieved or not depends strongly on the initial guess. Therefore, depending of the guess function, BVPs may have no solution or a single solution,
or multiple solutions. Moreover, the quality of the initial guess can be critical to the solver
performance, which reduces or augments the run time. However, coming up with a
sufficiently good guess can be the most challenging part of solving a BVP. Certainly, the
user should apply the knowledge of the problem's physical origin (MATLAB
Documentation). )
In MATLAB, when solving BVPs the user must provide a guess to assist the solver in
computing the desired solution (Kierzenka & Shampine, 2001). MATLAB BVP solvers call
for users to provide guesses for the mesh and solution. Although MATLAB BVP solvers take
an unusual approach to the control of error in case of having poor guesses for the mesh and
solution, especially for the nonlinear BVP, a good guess is necessary to obtain convergence
(Shampine et al., 2003). (
p
)
Whatever intuitive guess values/functions are imposed, eventually the BVP solver fails for
some parameters or for some lengths. If any guess values works for the range of length, the
rest of the length may be extended using continuation. 1. Introduction The method of continuation exploits
the fact that the solution obtained for one input will serve as the initial guess for the next
value tried. In case of any difficulty in finding a guess for the interval of interest, generally it
will be easier to solve the problem on a shorter interval. Then the solution of the sequence of
BVPs on the shorter interval will be used as a guess for the next section. With modest
increases in the interval, this will continue until the interval of interest is spanned
(Shampine et al., 2003). The cost of the continuation method is the increased run time. How the guess value good is,
the less computation time it takes with the continuation method. This is due the fact that, the
remaining length depends of the convergence length (based on the guess value) which its
higher value reduces the computation time. 2. Initial setup The first step in solving a problem is defining it in a way the software can understand. The
bvp4c framework uses a number of subfunctions which make it as simple as possible for the
user to enter the ODE function, initial data and parameters for a given problem. By way of
the following example we see exactly how a problem is supplied and solved by bvp4c. For
the evaluation of the guess value /function, the steady-state Brillouin equation is exploited. The coupled ODEs for the evolution of the intensities of pump Ip and Stokes Is can be written
as (Agrawal, 2001), B
P
S
p
dIp
g I I
I
dz
α
= −
−
(3)
B
P
S
S
dIs
g I I
I
dz
α
= −
+
(4) (3) B
P
S
S
dIs
g I I
I
dz
α
= −
+
(4) (4) where 0 ≤ z ≤ L is the propagation distance along the optical fiber of the total length L, α is
the fiber loss coefficient, gB is the Brillouin gain coefficient, respectively. Here, it is assumed
that, Stokes wave is launched from the rear end of the fiber. Then the known values of the
input pump power Ip(0) and the Stokes wave power Is (L) are referred as the boundary
values. where 0 ≤ z ≤ L is the propagation distance along the optical fiber of the total length L, α is
the fiber loss coefficient, gB is the Brillouin gain coefficient, respectively. Here, it is assumed
that, Stokes wave is launched from the rear end of the fiber. Then the known values of the
input pump power Ip(0) and the Stokes wave power Is (L) are referred as the boundary
values. fect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 5 The first task is to define the ODEs in MATLAB as a function to return these equations. Similarly the user then rewrites the boundary conditions to correspond to this form of the
problem. function v = guess(x) 2. Initial setup We may code the ODEs for scalar evaluation and boundary conditions,
respectively as, function dydx = bvpode(x,y)
global alpha_s gb K dydx = [ -gb *y(1)*y(2)-alpha_s*y(1)
-gb *y(1)*y(2)+alpha_s*y(2) ]; function res = bvpbc(ya,yb)
global Ip0 IsL function res bvpbc(ya,yb)
global Ip0 IsL
res = [ya(1)- Ip0
yb(2)- IsL ]; res = [ya(1)- Ip0
yb(2)- IsL ]; res = [ya(1)- Ip0
yb(2)- IsL ]; The next step is to create an initial guess for the form of the solution using a specific
MATLAB subroutine called bvpinit . The user passes a vector x and an initial guess on this
mesh in the form bvpinit (x, Yinit), which is then converted into a structure useable by
bvp4c. Aside from a sensible guess being necessary for a convergent solution the mesh
vector passed to bvpinit will also define the boundary points of the problem, i.e. xL = x[1]
and xR = x[end]. The initial guess for the solution may take one of two forms. One option is a vector where
Yinit(i) is a constant guess for the i-th component y(i,:) of the solution at all the mesh points
in x. The other is as a function of a scalar x, for example bvpinit(x,@yfun) where for any x in
[a, b], yfun(x) returns a guess for the solution y(x). It must be pointed out that even when a
function is supplied that approximates the solution everywhere in the interval; the solver
uses its values only on the initial mesh. The guess can be coded as a function of a scalar x as, global alpha_s L gb k Pp0 PsL Aeff
a=alpha_s*L;
k=gb/Aeff*Pp0*L;
epsilon=PsL/Pp0;
kappa=-log(gb/Aeff*PsL*L);
T=log(kappa*(1-kappa/k));
c0=-(PsL + PsL*k - 1)/((PsL*k^2)/2 + 1);
A=c0./(1-(1-c0).*exp(-c0*k.*x));
B=c0*(1-c0)./(exp(c0*k.*x)-1+c0);
w=(A.^(exp(-a))).*exp(-a.*x);
u=(B.*exp(a.*(x-1)));
v=[w*Pp0; u*Pp0]; global alpha_s L gb k Pp0 PsL Aeff
a=alpha_s*L;
k=gb/Aeff*Pp0*L;
epsilon=PsL/Pp0;
kappa=-log(gb/Aeff*PsL*L);
T=log(kappa*(1-kappa/k));
c0=-(PsL + PsL*k - 1)/((PsL*k^2)/2 + 1);
A=c0./(1-(1-c0).*exp(-c0*k.*x));
B=c0*(1-c0)./(exp(c0*k.*x)-1+c0);
w=(A.^(exp(-a))).*exp(-a.*x);
u=(B.*exp(a.*(x-1))); v=[w*Pp0; u*Pp0]; The next subroutine to look at is bvpset, that specifies which options bvp4c should be use in
solving it. The function is called options = bvpset(’name1’,value1,...) and since MATLAB MATLAB – A Ubiquitous Tool for the Practical Engineer 6 documentation gives an in depth account of each of the options only a brief outline of those
notable is given here (Hale, 2006). documentation gives an in depth account of each of the options only a brief outline of those
notable is given here (Hale, 2006). 2. Initial setup options = []; % default
%options = bvpset('Stats','on','RelTol',1e-5,'abstol',1e-4);
%options = bvpset(options,’Vectorized’,’on’);
%options = bvpset(options,’FJacobian’,@odeJac);
%options = bvpset(options,’BCJacobian’,@bcJac); RelTol - Relative tolerance for the residual [ positive scalar 1e-3 ]
The computed solution S(x) is the exact solution of S’(x) = F(x, S(x)) + res(x). On each
subinterval of the mesh, component i of the residual must satisfy norm ( )
Re
max(
( ( )),
( ) / Re
)
⎛
⎞≤
⎜
⎟
⎝
⎠
res i
norm
lTol
abs F i
AbsTol i
lTol AbsTol - Absolute tolerance for the residual [positive scalar or vector 1e-6]
Elements of a vector of tolerances apply to corresponding components of the residual
vector. AbsTol defaults to 1e-6. FJacobian \ BCJacobian - Analytical partial derivatives of ODEFUN \ BCFUN FJacobian \ BCJacobian Analytical partial derivatives of ODEFUN \ BCFUN
Computation of the Jacobian matrix at each mesh point can be a very expensive process. By
passing an analytic derivative of the ODE and BC functions the user can greatly reduce
computational time. For example when solving y’ = f(x, y), setting FJacobian to @FJAC
where ∂f/∂y = FJAC(x, y) evaluates the Jacobian of f with respect to y. Stats - Display computational cost statistics [ on — off ] Vectorized - Vectorized ODE function [ on — off ] As will be discussed in section 6, bvp4c is able to accept a vectorised function which can
markedly increase the efficiency of calculating local Jacobians over using finite differences
with the odenumjac subroutine. Hence in the following programs, we will define options = bvpset('Stats','on','RelTol',1e-5,'abstol',1e-4) solinit = bvpinit(linspace(0,L,2), @guess); And call the bvp4c routine with: And call the bvp4c routine with: p
l = bvp4c(@ode,@bc,solinit,optio sol = bvp4c(@ode,@bc,solinit,options); The above essentially ends the user input in solving the BVP system and the rest is left to
bvp4c. Within the framework there are several notable steps which should be expounded. 3. Derivation of the guess In this chapter, four guess functions are derived for the assistance of the MATLAB BVP
solvers with the help of MATLAB symbolic toolbox. 3.1 1st Guess If the constant guess is used as the initial values i.e., for the pump “Ip0” and for the Stokes
“IsL” and L = 10000; Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 7 solinit = bvpinit(linspace(0,L,2),@guess);
options = bvpset('Stats','on','RelTol',1e-5);
function v = guess(x)
global Ip0 IsL
v=[Ip0 ; IsL]; solinit = bvpinit(linspace(0,L,2),@guess);
options = bvpset('Stats','on','RelTol',1e-5);
function v = guess(x)
global Ip0 IsL
v=[Ip0 ; IsL]; It prompts as, “Unable to solve the collocation equations -- a singular Jacobian
encountered”. However, if the computation length is decreased as, L = 1000,the solver is
able to solve coupled equations with these poor guesses v=[Ip0 ; IsL]. Therefore, with these
guess values the convergence length (the maximum length which the solver is able to
converge) is 1000 meter. The evolution of the guess values (estimate) with the real solution
is shown in Fig. 1 g. 1. Evolution of the guess values and real solution according to 1st guess
a
b a b Fig. 1. Evolution of the guess values and real solution according to 1st guess MATLAB – A Ubiquitous Tool for the Practical Engineer 8 3.2 2nd Guess
If we guess that Ip and Is is linearly changing as, 3.2 2nd Guess 3.2 2nd Guess
If we guess that Ip and Is is linearly changing as, 3
Guess
If we guess that Ip and Is is linearly changing as, If we guess that Ip and Is is linearly changing as, Ip ~ Ip0+A*z ;
Is ~ Is0+B*z ; xploiting with the MATLAB Symbolic Toolbox using the following script, Exploiting with the MATLAB Symbolic Toolbox using the following script, syms Is Ip Is0 Ip0 IsL gb L alpha A B z syms Is Ip Is0 Ip0 IsL gb L alpha A B z eqn1 = collect(diff(Ip,'z') + (gb)*Ip*Is+alpha*Ip);
eqn2 = collect(diff(Is,'z') + (gb)*Ip*Is-alpha*Is); eqn1 = collect(diff(Ip,'z') + (gb)*Ip*Is+alpha*Ip);
eqn2 = collect(diff(Is,'z') + (gb)*Ip*Is-alpha*Is); The below output is produced; eqn3 = A + Ip0*alpha + (Ip0*Is0*gb)
eqn4 = B - Is0*alpha - L*(B*alpha - (gb*(A*Is0 + B*Ip0))) +
(Ip0*Is0*gb) + (A*B*L^2*gb) eqn3 = A + Ip0*alpha + (Ip0*Is0*gb)
eqn4 = B - Is0*alpha - L*(B*alpha - (gb*(A*Is0 + B*Ip0))) +
(Ip0*Is0*gb) + (A*B*L^2*gb) Is0=IsL-B*L; Here, there are two equations and two unknowns A and B. With the substitution of Is0, It
can be solved simultaneously by the below script, Here, there are two equations and two unknowns A and B. With the substitution of Is0, It
can be solved simultaneously by the below script,
eqn= solve(A + Ip0*alpha + (Ip0*(IsL-B*L)*gb),... B - (IsL-B*L)*alpha - L*(B*alpha - (gb*(A*(IsL-B*L) + B*Ip0)))+
(Ip0*(IsL-B*L)*gb) + (A*B*L^2*gb),... 'A','B') solve(A + Ip0*alpha + (Ip0*(IsL-B*L)*gb),... B - (IsL-B*L)*alpha - L*(B*alpha - (gb*(A*(IsL-B*L) + B*Ip0)))+
(Ip0*(IsL-B*L)*gb) + (A*B*L^2*gb),... 'A','B') eqn = eqn = A: [1x1 sym]
B: [1x1 sym] Here A and B can be obtained as, Here A and B can be obtained as, Here A and B can be obtained as, A=-(Ip0*alpha_s + Ip0^2*IsL*L*gb^2 + Ip0*IsL*gb –
Ip0*IsL*L*alpha_s*gb)/(Ip0*IsL*L^2*gb^2); B=(IsL*alpha_s + Ip0*IsL^2*L*gb^2 - Ip0*IsL*gb +
Ip0*IsL*L*alpha_s*gb)/(Ip0*IsL*L^2*gb^2) Ip ~ Ip0+A.*x ; fect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 9 Is ~ (IsL-B.*L)+B.*x ;
The evolution of the 2nd guess values with the real solution is shown in Fig. 2
Fig. 2. Evolution of the guess values and real solution according to 2nd guess
a
b Is ~ (IsL-B.*L)+B.*x ; Is ~ (IsL-B.*L)+B.*x ; The evolution of the 2nd guess values with the real solution is shown in Fig. 2 The evolution of the 2nd guess values with the real solution is shown in Fig. 2 The evolution of the 2nd guess values with the real solution is shown in Fig. 2 a b Fig. 2. Evolution of the guess values and real solution according to 2nd guess MATLAB – A Ubiquitous Tool for the Practical Engineer 10 3.3 3rd Guess If it is guessed that Ip and Is is exponentially changing as, Ip ~ Ip0*exp(gamma1*z) ;
Is ~ Is0*exp(kappa1*z) ;
with using the following script,
syms Ip Is Is0 Ip0 gb z L IsL alpha gamma1 kappa1 Ip ~ Ip0*exp(gamma1*z) ;
Is ~ Is0*exp(kappa1*z) ;
with using the following script,
syms Ip Is Is0 Ip0 gb z L IsL alpha gamma1 kappa1
Ip = Ip0*exp(gamma1*z) ;
Is = Is0*exp(kappa1*z) ;
eqn1 = collect(diff(Ip,'z') + (gb)*Ip*Is+alpha*Ip);
eqn2 = collect(diff(Is,'z') + (gb)*Ip*Is-alpha*Is);
eqn3=taylor(eqn1,1,0)
eqn4=taylor(eqn2,1,L) g
g
p
syms Ip Is Is0 Ip0 gb z L IsL alpha gamma1 kappa1 g
g
p
syms Ip Is Is0 Ip0 gb z L IsL alpha gamma1 kappa1 Ip = Ip0*exp(gamma1*z) ;
Is = Is0*exp(kappa1*z) ;
eqn1 = collect(diff(Ip,'z') + (gb)*Ip*Is+alpha*Ip);
eqn2 = collect(diff(Is,'z') + (gb)*Ip*Is-alpha*Is);
eqn3=taylor(eqn1,1,0)
eqn4=taylor(eqn2,1,L) The below output is produced; eqn3 =Ip0*alpha + Ip0*gamma1 + (Ip0*Is0*gb)
eqn4 =Is0*kappa1*exp(L*kappa1) - Is0*alpha*exp(L*kappa1) +
(Ip0*Is0*gb*exp(L*gamma1)*exp(L*kappa1)) eqn3 =Ip0*alpha + Ip0*gamma1 + (Ip0*Is0*gb)
eqn4 =Is0*kappa1*exp(L*kappa1) - Is0*alpha*exp(L*kappa1) +
(Ip0*Is0*gb*exp(L*gamma1)*exp(L*kappa1)) gamma1 and kappa1 can be obtained as;
eqn5=solve(Ip0*alpha + Ip0*gamma1 + (Ip0*Is0*gb),'gamma1')
gamma1= -(alpha + Is0*gb)
using the same way;
kappa1 = (alpha - Ip0*gb*exp(L*gamma1)); Therefore, Is ~ IsL/exp(kappa1*L)*exp(kappa1*z) ; The evolution of the 3rd guess values with the real solution is shown in Fig. 3 The evolution of the 3rd guess values with the real solution is shown in Fig. 3 the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 11 Fig. 3. Evolution of the guess values and real solution according to 3rd guess
a
b a Fig. 3. Evolution of the guess values and real solution according to 3rd guess 3.4 4th Guess Highly intuitive guess function may be derived the using the solution of lossless system, i.e.,
with eliminating the α coefficient in the Eq (3) and Eq. (4), B
P
S
dIp
g I I
dz = −
(5)
B
P
S
dIs
g I I
dz = −
(6) B
P
S
dIp
g I I
dz = −
(5)
B
P
S
dIs
g I I
dz = −
(6) B
P
S
dIp
g I I
dz = −
(5) (5) B
P
S
dIs
g I I
dz = −
(6) (6) With neglecting the attenuation coefficient, the solution of the Eq.(5) and Eq.( 6) is found as
(Kobyakov et al., 2006), With neglecting the attenuation coefficient, the solution of the Eq.(5) and Eq.( 6) is found as
(Kobyakov et al., 2006), 1
0
0
0
( )
[1
(1
)exp(
)]
(0)
P
A
c
c
c k
P
ζ
ζ
−
=
−
−
−
(7) 1
0
0
0
( )
[1
(1
)exp(
)]
(0)
P
A
c
c
c k
P
ζ
ζ
−
=
−
−
−
(7)
1
0
0
0
0
( )
(1
)[exp(
)
1
]
(0)
P
B
c
c
c k
c
P
ζ
ζ
−
=
−
−+
(8) (7) 1
0
0
0
0
( )
(1
)[exp(
)
1
]
(0)
P
B
c
c
c k
c
P
ζ
ζ
−
=
−
−+
(8) (8) MATLAB – A Ubiquitous Tool for the Practical Engineer 12 where, where, where, 0
1
ln
(1
)
c
k
k
⎧
⎫
Λ
⎡
⎤
≈
Λ +
Λ
−
⎨
⎬
⎢
⎥
⎣
⎦
⎩
⎭
,
(0)
B
P
eff
g
k
P
L
A
=
,
z
L
ζ =
(9) (9) where, 0
ln(
)
ln[
]
SL
B
SL
p
eff
P
g
k
P L
P
A
Λ = −
= −
,
0
1
SL
p
P
k
P
(10) (10) Exploiting the solution of Eq.( 7) and Eq. 3.4 4th Guess (8), general expression of Pp(z) and PS(z) can be
derived as, 2
( )
( ) [1
(
)]
=
⋅
−
⋅
⋅
+
⋅
P
P z
A z
a
A x
B x
(11) 2
( )
( ) [1
(
)]
=
⋅
−
⋅
⋅
+
⋅
P
P z
A z
a
A x
B x
(11)
2
( )
( ) [1
(
)]
=
⋅
−
⋅
⋅
+
⋅
SP z
B z
a
C x
D x
(12) (11) (12) If a→0, then
( )
( )
P
P z
A z
=
and
( )
( )
SP z
B z
= If a→0, then
( )
( )
P
P z
A z
=
and
( )
( )
SP z
B z
= If a→0, then
( )
( )
P
P z
A z
=
and
( )
( )
SP z
B z
= A B C D a AA BB c0 x eqn2 =
… + ((2*D*a*c0*(c0 - 1))/(c0 + exp(c0*k*z) - 1) - (C*a^2*c0*(c0 -
1))/(c0 + exp(c0*k*z) - 1) + (c0^2*k*(A*a + C*a)*(c0 - 1))/(((c0 -
1)/exp(c0*k*z) + 1)*(c0 + exp(c0*k*z) - 1)) -
(C*a*c0^2*k*exp(c0*k*z)*(c0 - 1))/(c0 + exp(c0*k*z) - 1)^2)*x …
+ (a*c0*(c0 - 1))/(c0 + exp(c0*k*z) - 1) + (C*a*c0*(c0 - 1))/(c0 +
exp(c0*k*z) - 1) - (c0^2*k*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0
+ exp(c0*k*z) - 1)) + (c0^2*k*exp(c0*k*z)*(c0 - 1))/(c0 +
exp(c0*k*z) - 1)^2 syms z k A B C D a AA BB c0 x syms z k A B C D a AA BB c0 x syms z k A B C D a AA BB c0 x AA=c0/(1-(1-c0)*exp(-c0*k*z));
BB=c0*(1-c0)/(exp(c0*k*z)-1+c0);
w=(AA*(1-a*(A*x+B*x^2)));
u=(BB*(1-a*(C*x+D*x^2)));
eqn1 = collect(diff(w,1,'z') + (k*u*w)+a*w)
eqn2 = collect(diff(u,1,'z') + (k*u*w)-a*u)
The output produces, eqn1 =
…+ ((c0^2*k*(A*a + C*a)*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0 +
exp(c0*k*z) - 1)) - (A*a^2*c0)/((c0 - 1)/exp(c0*k*z) + 1) -
(2*B*a*c0)/((c0 - 1)/exp(c0*k*z) + 1) - (A*a*c0^2*k*(c0 -
1))/(exp(c0*k*z)*((c0 - 1)/exp(c0*k*z) + 1)^2))*x …
+ (a*c0)/((c0 - 1)/exp(c0*k*z) + 1) - (A*a*c0)/((c0 - 1)/exp(c0*k*z)
+ 1) + (c0^2*k*(c0 - 1))/(exp(c0*k*z)*((c0 - 1)/exp(c0*k*z) + 1)^2)
- (c0^2*k*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0 + exp(c0*k*z) -
1)) eqn1 =
…+ ((c0^2*k*(A*a + C*a)*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0 +
exp(c0*k*z) - 1)) - (A*a^2*c0)/((c0 - 1)/exp(c0*k*z) + 1) -
(2*B*a*c0)/((c0 - 1)/exp(c0*k*z) + 1) - (A*a*c0^2*k*(c0 -
1))/(exp(c0*k*z)*((c0 - 1)/exp(c0*k*z) + 1)^2))*x …
+ (a*c0)/((c0 - 1)/exp(c0*k*z) + 1) - (A*a*c0)/((c0 - 1)/exp(c0*k*z)
+ 1) + (c0^2*k*(c0 - 1))/(exp(c0*k*z)*((c0 - 1)/exp(c0*k*z) + 1)^2)
- (c0^2*k*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0 + exp(c0*k*z) -
1)) ))/(
p(
) ((
)/
p(
)
)
))
+ (a*c0)/((c0 - 1)/exp(c0*k*z) + 1) - (A*a*c0)/((c0 - 1)/exp(c0*k*z)
+ 1) + (c0^2*k*(c0 - 1))/(exp(c0*k*z)*((c0 - 1)/exp(c0*k*z) + 1)^2)
- (c0^2*k*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0 + exp(c0*k*z) -
1)) + 1) + (c0^2*k*(c0 - 1))/(exp(c0*k*z)*((c0 - 1)/exp(c0*k*z) + 1)^2)
- (c0^2*k*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0 + exp(c0*k*z) -
1)) eqn2 =
… + ((2*D*a*c0*(c0 - 1))/(c0 + exp(c0*k*z) - 1) - (C*a^2*c0*(c0 -
1))/(c0 + exp(c0*k*z) - 1) + (c0^2*k*(A*a + C*a)*(c0 - 1))/(((c0 -
1)/exp(c0*k*z) + 1)*(c0 + exp(c0*k*z) - 1)) -
(C*a*c0^2*k*exp(c0*k*z)*(c0 - 1))/(c0 + exp(c0*k*z) - 1)^2)*x …
+ (a*c0*(c0 - 1))/(c0 + exp(c0*k*z) - 1) + (C*a*c0*(c0 - 1))/(c0 +
exp(c0*k*z) - 1) - (c0^2*k*(c0 - 1))/(((c0 - 1)/exp(c0*k*z) + 1)*(c0
+ exp(c0*k*z) - 1)) + (c0^2*k*exp(c0*k*z)*(c0 - 1))/(c0 +
exp(c0*k*z) - 1)^2 13 Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers We are interested in the behavior as z → 0 and so, the higher the power of x, the less effect it
has in these expansions. Our goal is to satisfy the equations as well as possible, so we want
to choose coefficients that make as many successive terms zero as possible, starting with the
lowest power. syms z k A B C D a AA BB c0 x To eliminate the constant terms, we see from the expansions that we must
take A= 1; C=-1;
B= -(a - a/exp(c0*k*z) + (a*c0)/exp(c0*k*z) - (c0*k)/exp(c0*k*z) +
(c0^2*k)/exp(c0*k*z))/((2*c0)/exp(c0*k*z) - 2/exp(c0*k*z) + 2)
D= (a - a/exp(c0*k*z) + (a*c0)/exp(c0*k*z) - (c0*k)/exp(c0*k*z) +
(c0^2*k)/exp(c0*k*z))/((2*c0)/exp(c0*k*z) - 2/exp(c0*k*z) + 2) A= 1; C=-1;
B= -(a - a/exp(c0*k*z) + (a*c0)/exp(c0*k*z) - (c0*k)/exp(c0*k*z) +
(c0^2*k)/exp(c0*k*z))/((2*c0)/exp(c0*k*z) - 2/exp(c0*k*z) + 2)
D= (a - a/exp(c0*k*z) + (a*c0)/exp(c0*k*z) - (c0*k)/exp(c0*k*z) +
(c0^2*k)/exp(c0*k*z))/((2*c0)/exp(c0*k*z) - 2/exp(c0*k*z) + 2) The evolution of the 4rd guess values with the real solution is shown in Fig. 4 The evolution of the 4rd guess values with the real solution is shown in Fig. 4 The evolution of the 4rd guess values with the real solution is shown in Fig. 4 The evolution of the 4rd guess values with the real solution is shown in Fig. 4
Fig. 4. Evolution of the guess values and real solution according to 4th guess
b
a a b Fig. 4. Evolution of the guess values and real solution according to 4th guess MATLAB – A Ubiquitous Tool for the Practical Engineer 14 Guess
Length(mt)
/mesh
Convergence
length/mesh
Computation Time
(with bvp4c) at
8000 meter
1st Guess - values (Ip0,IsL)
8000/ 40
8000/40
~1.18 sec
2nd Guess - functions (linear)
8000/ 40
9000/453
~1.13 sec
3rd Guess -functions
(exponential)
8000/ 40
15000/56
~1.13 sec
4th Guess functions (modified
exponential)
8000/ 35
30000/61
~1.0 sec
Table 1. Guess values/functions versus convergence length/mesh and run time. Table 1. Guess values/functions versus convergence length/mesh and run time. As can be seen from Table 1 and Fig.4 the best estimation is the 4th guess. Because its’
convergence length (30000) is more than the others (15000, 9000, 8000, respectively). The
performance of the 2nd guess is approximately same as the first one. Because it hardly
converge the solution using 453 points at 9000 meter. However, its performance is same as
the first one with 40 points at 8000 meter. 4. Continuation The method of continuation exploits the fact that generally the solution of one BVP is a good
guess for the solution of another with slightly different parameters. If you have difficulty in
finding a guess for the solution that is good enough to achieve convergence for the interval
of interest, it is frequently the case that the problem is easier to solve on a shorter interval. The idea is then to solve a sequence of BVPs with the solution on one interval being used as
a guess for the problem posed on a longer interval. Of course, this technique cannot be used
to extend the interval ad infinitum; no matter how good the guess is, eventually the solver
will not be able to distinguish the different kinds of solutions (Shampine et al., 2003). For the range of interested lengths bigger than the convergence lengths, the continuation
process can be applied. Some types of snippets of continuation are illustrated below, =================#1#=========================
options = bvpset('FJacobian',@sampleJac,... 'BCJacobian',@sampleBCJac,... 'Vectorized','on');
sol = bvpinit([-1 -0.5 0 0.5 1],[1 0]); solinit = bvpinit(linspace(0,infinity,5),[0 0 1]);
sol = bvp4c(@fsode,@fsbc,solinit); solinit = bvpinit(linspace(0,infinity,5),[0 0 1]);
sol = bvp4c(@fsode,@fsbc,solinit); Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 15 Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers
1
eta = sol.x;
f = sol.y;
for Bnew = infinity+1:maxinfinity
solinit = bvpinit(sol,[0 Bnew]); % Extend solution to Bnew. sol = bvp4c(@fsode,@fsbc,solinit);
eta = sol.x;
f = sol.y;
=================#3#======================
L=30000;
for i = 1:1000:L
D = 5*i/1000; d = 1/D;
if i == 1
solinit = bvpinit(linspace(1,i,10),@guess);
else
solinit = bvpinit(sol,[d,D]);
end
sol = bvp4c(@odes,@bcs,solinit);
end
=================#4#======================
function Boundary_value_increment
global a b
a= XL; %[a
b= XR; % b]
sol = bvpinit(linspace(0,L,2),[Boundary values for each pump and
signal power]); sol = bvp4c(@odes,@bcs,solinit);
end
=================#4#======================
function Boundary_value_increment
global a b
a= XL; %[a
b= XR; % b]
sol = bvpinit(linspace(0,L,2),[Boundary values for each pump and
signal power]); options = bvpset('Stats','on','RelTol',1e-5); sol = bvp4c(@bvpode,@bvpbc,sol,options);
d If the interested length is bigger than the convergence length then continuation can be
applied with the bvpxtend function. In the recent version of MATLAB, bvpinit function is
simplified to a new function bvpxtend. Besides offering new possibilities, this function
permits extension of length of interval to only one end point at a time (Kierzenka &
Shampine, 2008). 4. Continuation Briefly, solinit = bvpxtend(sol,xnew,ynew) uses solution sol computed on [a,b] to form a
solution guess for the interval extended to xnew. The extension point xnew must be outside
the interval [a,b], but on either side. The vector ynew provides an initial guess for the
solution at xnew. For example, if it is assumed that the convergence and interested lengths are 15 and 30
km, respectively, the continuation can be applied via the below codes (Gokhan & Yilmaz,
2011a), )
=================#5#====================== )
=================#5#====================== MATLAB – A Ubiquitous Tool for the Practical Engineer 16 L= 15000;
Interested=30000;
solinit = bvpinit(linspace(0,L,2),[Guess expression running with 15
km]);
sol = bvp4c(@bvpode,@bvpbc,solinit,options);
. for Bnew=L:2000:Interested
solinit=bvpxtend(sol,Bnew);
sol = bvp4c(@bvpode,@bvpbc,solinit,options);
end L= 15000;
Interested=30000;
solinit = bvpinit(linspace(0,L,2),[Guess expression running with 15
km]);
sol = bvp4c(@bvpode,@bvpbc,solinit,options); sol = bvp4c(@bvpode,@bvpbc,solinit,options); In the above codes, 2000 is the step size which is the modest increment range. In case of
bigger step size, the solver may fail but the computation time reduces. On the other hand, if
this increment is kept little, it takes more time to reach the end of the computation. Therefore, selecting the step size is important factor for the efficiency of the computation for
continuation. One advantage of using bvpxtend function is the reduced computation time. Because, bvp solvers try to use mesh points as few as possible, the step size is incremented
automatically depending on the previous mesh points. In bvpxtend, after obtaining
convergence for the mesh, the codes adapt the mesh so as to obtain an accurate numerical
solution with a modest number of mesh points. Here it must be emphasized that, for BVPs
the most difficult part is providing an initial approximation to the solution. In the above codes, 2000 is the step size which is the modest increment range. In case of
bigger step size, the solver may fail but the computation time reduces. On the other hand, if
this increment is kept little, it takes more time to reach the end of the computation. Therefore, selecting the step size is important factor for the efficiency of the computation for
continuation. One advantage of using bvpxtend function is the reduced computation time. Because, bvp solvers try to use mesh points as few as possible, the step size is incremented
automatically depending on the previous mesh points. Table 2. The performance of continuation method versus step size 4. Continuation In bvpxtend, after obtaining
convergence for the mesh, the codes adapt the mesh so as to obtain an accurate numerical
solution with a modest number of mesh points. Here it must be emphasized that, for BVPs
the most difficult part is providing an initial approximation to the solution. If the step size is increased over the 600 meter, the computation fails with the below warning
message; g
Warning: Unable to meet the tolerance without using more than 5000
mesh points. If the step size is increased over the 600 meter, the computation fails with the below warning
message;
Warning: Unable to meet the tolerance without using more than 5000
mesh points. 5. Effect of the step size on the run time Using the snippets 5 and the 1st Guess of Table 1, the performance of the continuation over
step size is illustrated in Table 2. Using the snippets 5 and the 1st Guess of Table 1, the performance of the continuation over
step size is illustrated in Table 2. Convergence
Length (km)
Computation
Length
(km)
Linspace
(0,L,N)
Optimal
N
Step Size
(mt.)
Computation
Time at
Convergence
Length
(with bvp4c)
Total
Computation
time
Mesh
number
(between)
(with
bvp4c)
40
50
10
50
~3.2 sec
~110.0 sec
482-541
40
50
10
100
~3.2 sec
~60.0 sec
482-541
40
50
10
200
~3.2 sec
~32.8 sec
482-553
40
50
10
300
~3.2 sec
~25.3 sec
482-560
40
50
10
400
~3.2 sec
~23.6 sec
482-663
40
50
10
500
~3.2 sec
~44.5 sec
482-1984
40
50
10
600
Computation fails. Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 17 Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers The last mesh of 4106 points and the solution are available in the
output argument. The maximum residual is 0.00018931, while requested accuracy is 1e-
005. As can be seen on Table 2, for some step size over the modest increment, computation blows
up (i.e. 600 m). When the step size is between 50 and 400, the number of used mesh is
slightly different from each other. However, when it is 500 m, abruptly increase in the
number of used mesh is a sign of lack of confidence. In Fig.5, it can be seen that the distance between some mesh points, especially near the
boundaries are denser than the others. This is because the solver tries to control the residual
of the interpolating polynomial: r(x) = S’(x) – f(x,S(x)). The behavior of this residual
depends on the behavior of some high derivatives of the solution (that the solver does not
have access to). In the solver, the residual is estimated at each mesh subinterval, and
additional mesh points are introduced if the estimate is bigger than the tolerance. The mesh selection algorithm is ‘localized’, which means that if the residual is just above the
tolerance, the interval will be divided into two (and likely on each of those subintervals, the
residual will be much smaller than the tolerance). Also, the algorithm for removing mesh
points is quite conservative, so there could be regions where the residual will be quite a bit
smaller that the tolerance (i.e., the mesh could be quite a bit denser than necessary)(
Kierzenka & Shampine, 2001). Fig. 5. Evolution of mesh density along the computation Fig. 5. Evolution of mesh density along the computation MATLAB – A Ubiquitous Tool for the Practical Engineer 18 5.1 Effect of the constructing an initial guess with bvpinit function on the run time 5.1 Effect of the constructing an initial guess with bvpinit function on the run time
A
b
f
T bl
3
h
i
i i i l
i As
can
be
seen
from
Table
3,
when
constructing
an
initial
guess
using
bvpinit(linspace(0,L,N), starting with a mesh of 5-10 points could often result in a
more efficient run. It must be pointed out that with adaptive collocation solvers, using that
many points (N=50,100) with a poor guess could often be counterproductive. Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers In the case of
N=100, the solver still achieved the sufficient accuracy as it is between 2 and 10. Linspace
(0,L,N)
Optimal N
Computation Time
(with bvp4c)
Mesh number
(with bvp4c)
Maximum Residual
2-4
Singular Jacobian
encountered
5
~3.20 sec
498
9.791e-006
6
~2.85 sec
475
9.967e-006
7
~3.10 sec
483
9.983e-006
8
~2.75 sec
487
9.913e-006
9
~2.87 sec
464
9.848e-006
10
~2.68 sec
469
9.817e-006
50
~2.81 sec
478
9.938e-006
100
~3.10 sec
485
9.959e-006
Table 3. Performance of equally spaced N points for the mesh of a guess Table 3. Performance of equally spaced N points for the mesh of a guess Table 3. Performance of equally spaced N points for the mesh of a guess 6. Speeding up the run time of BVP solvers The first technique which is used to reduce run time is vectorizing the evaluation of the
differential equations. Vectorization is a valuable tool for speeding up MATLAB programs
and this greatly reduces the run time (Shampine et al., 2003). By vectorization, the function
f(x,y) is coded so that when given a vector x=[x1,x2,...] and a corresponding array of column
vectors y=[y1,y2,...], it returns an array of column vectors [f(x1,y1),f(x2,y2),...]). By default,
bvp4c and bvp4c approximate a Jacobian using finite differences. The evaluation of the
ODEs is vectorized by changing the vectors to arrays and changing the multiplication to an
array multiplication. It can be coded by changing scalar quantities like y(1) into arrays like
y(1,:) and changing from scalar operations to array operations by replacing * and ˆ with .*
and .ˆ, respectively. When vectorizing the ODEs, the solver must be informed about the
presence of vectorization by means of the option 'Vectorized','on'. options = bvpset('Stats','on','RelTol',1e-3,'Vectorized','on'); The second technique is that of supplying analytical partial derivatives or to supply a
function for evaluating the Jacobian matrix. This is because, in general, BVPs are solved
much faster with analytical partial derivatives. However, this is not an easy task since it is
too much trouble and inconvenient, although MATLAB Symbolic Toolbox can be exploited
when obtaining analytical Jacobians. The third technique is to supply analytical partial
derivatives for the boundary conditions. However, it has less effect on the computation time
compared with supplying analytical Jacobians and vectorization. The solver permits the
user to supply as much information as possible. It must be emphasized that supplying more Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 19 information for the solvers results in a shorter computation run time (Gokhan & Yilmaz,
2011b). information for the solvers results in a shorter computation run time (Gokhan & Yilmaz,
2011b). The set of equations (3) and (4) is vectorized by changing the vectors to arrays and changing
the multiplication to an array multiplication as seen below, function dydx = bvpodevectorized(x,y)
global alpha_s gb K function dydx = bvpodevectorized(x,y)
global alpha_s gb K function dydx = bvpodevectorized(x,y)
global alpha_s gb K dydx = [ -gb *y(1,:).*y(2,:)-alpha_s*y(1,:)
-gb *y(1,:).*y(2,:)+alpha_s*y(2,:) ]; dydx = [ -gb *y(1,:).*y(2,:)-alpha_s*y(1,:)
-gb *y(1,:).*y(2,:)+alpha_s*y(2,:) ]; Using vectorized ODEs with N=8, the performance of the vectorization is illustrated in
Table 4. Using vectorized ODEs with N=8, the performance of the vectorization is illustrated in
Table 4. vectorized ODEs with N=8, the performance of the vectorization is illustrated in Length
(mt)
Computation Time with
scalar evaluation
(with bvp4c)
Computation Time with
vectorization
(with bvp4c)
5000
~1.83 sec
~1.79 sec
10000
~2.26 sec
~2.15 sec
20000
~2.60 sec
~2.45 sec
30000
~2.70 sec
~2.58 sec
40000
~3.00 sec
~2.85 sec
Table 4 Comparison of the computation time with scalar evaluation and with vectoriza Table 4. Comparison of the computation time with scalar evaluation and with vectorization able 4. Comparison of the computation time with scalar evaluation and with vectorizat The code bvp4c permits you to supply analytical partial derivatives for either the ODEs or
the boundary conditions or both. It is far more important to provide partial derivatives for
the ODEs than the boundary conditions. options = bvpset('Stats','on','RelTol',1e-3,'Vectorized','on'); The solver is informed that a function is written for
evaluating ∂f/∂y by providing its handle as the value of the FJacobian option. Similarly, the
solver can be informed of a function for evaluating analytical partial derivatives of the
boundary conditions with the option BCJacobian (Shampine et al., 2003). FJacobian and
BCJacobian can be introduced as with the below codes, %options = bvpset(options,’FJacobian’,@odeJac);
%options = bvpset(options,’BCJacobian’,@bcJac); The MATLAB Symbolic Toolbox has a function jacobian that can be very helpful when
working out partial derivatives for complicated functions. Its use is illustrated with a script
for the partial derivatives of the ODEs of this example. syms res y1 y2 y1 y2 alpha_s gb
res = [ -gb*y1*y2 – alpha_s*y1
-gb*y1*y2 + alpha_s*y2];
dFdy = jacobian(res,[y1; y2])
dFdy = syms res y1 y2 y1 y2 alpha_s gb
res = [ -gb*y1*y2 – alpha_s*y1
-gb*y1*y2 + alpha_s*y2];
dFdy = jacobian(res,[y1; y2])
dFdy = res = [ -gb*y1*y2 – alpha_s*y1
-gb*y1*y2 + alpha_s*y2]; dFdy = jacobian(res,[y1; y2])
dFdy = dFdy = jacobian(res,[y1; y2]) MATLAB – A Ubiquitous Tool for the Practical Engineer 20 [ - alpha_s - gb*y2, -gb*y1]
[ -gb*y2, alpha_s - gb*y1] The performance of the insertion of analytical partial derivatives and vectorization, and both
are compared in Table 5. As can be seen from Table 5, with vectorization and analytical partial
derivatives, the computation time is reduced approximately 15 %. The calculations are
simulated using the MATLAB 7.9 (R2009b) on an Intel Core i5 2.53 GHz laptop computer. Length
(mt)
Computation
Time with
scalar
evaluation
(with bvp4c)
Computation
Time with only
vectorization
(with bvp4c)
Computation Time
with only
analytical partial
derivatives
(with bvp4c)
Computation
Time with both
vectorization &
analytical partial
derivatives
(with bvp4c)
5000
~1.83 sec
~1.79 sec
~1.69 sec
~1.59 sec
10000
~2.26 sec
~2.15 sec
~2.05 sec
~1.80 sec
20000
~2.60 sec
~2.45 sec
~2.26sec
~1.96sec
30000
~2.70 sec
~2.58 sec
~2.40 sec
~2.04 sec
40000
~3.00 sec
~2.85 sec
~2.60 sec
~2.18 sec
Table 5. Comparison of the computation time of bvp4c with vectorization, with analytical
partial derivatives and with both Table 5. Comparison of the computation time of bvp4c with vectorization, with analytical
partial derivatives and with both In Table 6, the performance of the bvp5c is illustrated. In terms of scalar evaluation, the
performance of bvp5c solver is better than bvpc4 and it is evident as the length is increased. 7. Conclusion Within the chapter, in order to analyze the effect of guess functions on the computation
time, four guess functions are derived. For better understanding, while exploiting physical
origin, guess functions are derived with the help of MATLAB Symbolic toolbox. Continuation method with functional snippets is presented to cope with poor guesses. Effect
of the step size and bvpinit function on the computation time is analyzed. Speeding up the
run time with vectorization and analytical partial derivatives are discussed and the
comparison between bvp4c and bvp5c has been made. p
p
p
As a conclusion, it is illustrated that, intuitive guess values/functions improves the
convergence length, leads the computation with fewer mesh points and consequently
lessens the computation time. On the other hand, regarding with the continuation, adjusting
the step size is important for the reduction of run time. It is illustrated that, over the modest
step size, the solver fails and below the optimum step size, the computation time is
increased. Moreover, it is showed that when constructing an initial guess using
bvpinit(linspace(0,L,N), starting with a mesh of 5-10 points could often result in a more
efficient run. Another outcome of the chapter is the illustration of the efficiency of the
vectorization and analytical partial derivatives. It is showed specifically with an example
and with bvp4c that, with the application of vectorization and analytical partial derivatives,
the computation time is reduced approximately 15 %. The performance of the bvp4c and
bvp5c is also compared. In terms of scalar evaluation, the performance of bvp5c solver is
better than bvpc4 and it is evident as the computation length is increased. Compared with
the scalar evaluation, for the bvp5c, only with vectorization and only with analytical partial
derivatives this improvement is 8% and 13 % respectively. If both is used this improvement
is about 24 %. options = bvpset('Stats','on','RelTol',1e-3,'Vectorized','on'); This improvement is about 47 % at 40 km. As in the case of bvp4c, the performance can be
increased with vectorization and analytical partial derivatives or with both. Compared with
the scalar evaluation, only with vectorization and only with analytical partial derivatives this
improvement is 8% and 13 %, respectively. If both is used this improvement is about 24 %. Length
(mt)
Computation
Time with
scalar
evaluation
(with bvp5c)
Computation
Time with only
vectorization
(with bvp5c)
Computation
Time with only
analytical
partial
derivatives
(with bvp5c)
Computation Time with
both vectorization &
analytical partial
derivatives
(with bvp5c)
5000
~1.32 sec
~1.32 sec
~1.30 sec
~1.23 sec
10000
~1.38 sec
~1.38 sec
~1.35 sec
~1.27 sec
20000
~1.44 sec
~1.42 sec
~1.38sec
~1.30sec
30000
~1.55 sec
~1.50 sec
~1.43 sec
~1.34 sec
40000
~1.60 sec
~1.52 sec
~1.47 sec
~1.36 sec
Table 6. Comparison of the computation time of bvp5c with vectorization, with analytical
partial derivatives and with both Table 6. Comparison of the computation time of bvp5c with vectorization, with analytical
partial derivatives and with both If the comparison among two solvers has made, it could be expressed that bvp5c “looks”
exactly like bvp4c. However, bvp5c controls scaled residual and true error but bvp4c
controls residual in a different norm. And, bvp5c is more efficient at stringent tolerances. Effect of the Guess Function & Continuation Method on the Run Time of MATLAB BVP Solvers 21 Also, bvp5c solves singular BVPs, but not multipoint BVPs. Moreover, bvp5c handles
unknown parameters in a different way. And also, bvp5c was added to MATLAB at R2007b
(Shampine, 2008) 8. Acknowledgments The author gratefully acknowledges the financial support from the head of scientific
research projects commission of Gazikent University. Kierzenka J. & Shampine Lawrence F. (2001), A BVP Solver Based on Residual Control and the
MATLAB PSE, ACM TOMS, vol. 27, No. 3, pp. 299-316.
Hale N.P., (2006), A Sixth-Order Extension to the MATLAB bvp4c Software of J. Kierzenka and L.
Shampine, Msc Thesis. Accessed 06.04.2011, Available from:
< http://people.maths.ox.ac.uk/hale/files/hale_mastersthesis.pdf >
MATLAB Documentation, Continuation, Accessed 06 April 2011, Available from:
< http://www.mathworks.com/help/techdoc/math/f1-713877.html>
Shampine, L.F., Gladwell, I. & Thompson, S. (2003), Solving ODEs with MATLAB, 1st ed.,
Cambridge University Press, ISBN, 978-0-521-82404-4, New York
Agrawal G. P. (2001), Nonlinear Fiber Optics, 3rd ed. Academic, Chap. 9. Kierzenka J. & Shampine Lawrence F. (2001), A BVP Solver Based on Residual Control and the
MATLAB PSE, ACM TOMS, vol. 27, No. 3, pp. 299-316. 1. Introduction The Ceschino polynomial expansion method is a generalization of the Taylor polynomial
expansion method where higher derivatives of a function are predicted in addition to the
value of the function itself. This technique was first introduced by (Ceschino, 1956), but was
largly forgotten afterward. An unsuccessfull atempt was tried in 1975 to apply the Ceschino
coupling relations to the solution of an elliptic space–dependent differential equation, but the
resulting spatial discretization was found to be less accurate than competing finite-element
approaches, as presented by (Pageau, 1975). No further published work was reported after
the Pageau thesis. g
Here, we propose to apply the Ceschino coupling relations to the basic interpolation problem,
as an alternative to existing univariate interpolation schemes, such as the cubic spline
approach. The interpolation problem consists to evaluate a functional I{ f (x); ξ} of a
continuous function (or dependent variable) f (x) at a specific point ξ in the case where
function f (x) is only known at tabulated abscissa (or independent variables) {xm+1/2 ; m =
0, M}. We also introduce the concept of interpolation factors (a. k. a. , terp factors) that
are useful for interpolating large databases with respect to a small number of independent
variables, as presented by (MacFarlane, 1984). The Ceschino polynomial expansion method
is the core component of the multiparameter reactor database system used in the reactor
physics code DRAGON for performing cross section interpolation (Hébert, 2009). We will
show that Ceschino polynomial expansion theory is an attractive choice for computing such
interpolation factors and propose sample Matlab scripts for performing this task. Revisiting the Ceschino Interpolation Method Alain Hébert
École Polytechnique de Montréal
Canada 9. References grawal G. P. (2001), Nonlinear Fiber Optics, 3rd ed. Academic, Chap. 9. 22 MATLAB – A Ubiquitous Tool for the Practical Engineer Kobyakov A., Darmanyan S., Sauer M. & Chowdhury D (2006), High-gain Brillouin
amplification: an analytical Approach, Opt.Lett. 31 1960 Kierzenka, J. & Shampine, L.F. (2008), BVP solver that controls residual and error, Journal of
Numerical Analysis, Industrial and Applied Mathematics (JNAIAM), Vol. 3 Nos
1/2, pp. 27-41, available at: www.jnaiam.org/downloads.php?did=44
(Accessed 06 April 2011). Gokhan F. S., & Yilmaz G, (2011a), Solution of Raman fiber amplifier equations using MATLAB
BVP solvers, COMPEL: The International Journal for Computation and
Mathematics in Electrical and Electronic Engineering, Vol. 30 Iss: 2, pp.398 – 411 Gokhan F. S., & Yilmaz G, (2011b), Novel Guess Functions for Efficient Analysis of Raman Fiber
Amplifiers, COMPEL: The International Journal for Computation and Mathematics
in Electrical and Electronic Engineering, accepted in 2010 g
g
p
Shampine L.F, (2008). Control of Residual and Error, In: CAIMS-Canadian Mathematical
Society, Accessed 06 April 2011,
Available from: < http://faculty.smu.edu/shampine/Montreal.pdf> 02 2. Ceschino polynomial expansion theory The polynomial expansion theory is first applied over the one-dimensional domain depicted
in Fig. 1. A continuous function f (x) is defined over this domain and is known at specific
abscissa points xm+1/2. A (J + 1)–th order Taylor series expansion of f (x) around x = xm−1/2
is written
J fm+1/2 =
J
∑
j=0
(Δxm)j M(j)
m−1/2 + O(Δxm)J+1
(1) (1) where the mesh width is equal to Δxm = xm+1/2 −xm−1/2
(2) Δxm = xm+1/2 −xm−1/2 (2) 224 MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer m
m+1
xm-1/2
xm+1/2
xm+3/2
∆xm
∆xm+1
X
region
region
Fig. 1. Definition of the 1D domain. m
m+1
xm-1/2
xm+1/2
xm+3/2
∆xm
∆xm+1
X
region
region
Fig. 1. Definition of the 1D domain. m+1
region xm m
Fig. 1. Definition of the 1D domain. and where and where fm+1/2 ≡f (xm+1/2) ≡M(0)
m+1/2 and
M(j)
m−1/2 ≡1
j! dj f
dxj
xm−1/2
. (3) (3) A Ceschino expansion is nothing but the Taylor’s expansion for the derivatives f (k)(x) of
function f (x). It is written A Ceschino expansion is nothing but the Taylor’s expansion for the derivatives f (k)(x) of
function f (x). It is written M(k)
m+1/2 =
J
∑
j=k
(Δxm)j−k j
k
M(j)
m−1/2 + O(Δxm)J−k+1
(4) (4) where the binomial coefficients are defined as where the binomial coefficients are defined as j
k
≡
j! (j −k)! k! . (5) (5) Our interpolation strategy is based on two– and three–point coupling relations obtained
directly from the Ceschino polynomial expansion (4). Two points relations are used at
the extremities of the domain and three–point relations are used inside. Cubic Hermite
polynomials will also be introduced to perform the interpolation operation. Our interpolation strategy is based on two– and three–point coupling relations obtained
directly from the Ceschino polynomial expansion (4). Two points relations are used at
the extremities of the domain and three–point relations are used inside. Cubic Hermite
polynomials will also be introduced to perform the interpolation operation. 2.1 Two–points Ceschino coupling relations Our relations are coupling the first N derivatives of f (x), with N = 1 leading to a cubic
interpolation strategy. We set J = 2N in Eq. (4), leading to a truncation error of order 2N + 1 if
(k) Our relations are coupling the first N derivatives of f (x), with N = 1 leading to a cubic
interpolation strategy. We set J = 2N in Eq. (4), leading to a truncation error of order 2N + 1 if
k = 0. We next perform a linear combination of the first N components M(k)
m+1/2, introducing
coefficients θk. The linear combination permits to maintain the order of the truncation error to
2N + 1. We write k = 0. We next perform a linear combination of the first N components M(k)
m+1/2, introducing
coefficients θk. The linear combination permits to maintain the order of the truncation error to
2N + 1. We write 2N + 1. We write N
∑
k=0
θk M(k)
m+1/2 =
N
∑
k=0
2N
∑
j=k
θk (Δxm)j−k j
k
M(j)
m−1/2 + O(Δxm)2N+1 . (6) (6) After permutation of the two summations with the corresponding indices j and k in the
right-hand-side, we get After permutation of the two summations with the corresponding indices j and k in the
right-hand-side, we get N
∑
k=0
θk M(k)
m+1/2 =
N
∑
k=0
k
∑
j=0
θj (Δxm)k−j k
j
M(k)
m−1/2
+
2N
∑
k=N+1
N
∑
j=0
θj (Δxm)k−j k
j
M(k)
m−1/2 + O(Δxm)2N+1 . (7) (7) Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method 3
25 We choose coefficients θj in such a way that We choose coefficients θj in such a way that We choose coefficients θj in such a way that N
∑
j=0
θj (Δxm)k−j k
j
= 0 ; k = N + 1, 2N
(8) (8) and we define coefficients ¯θk as and we define coefficients ¯θk as and we define coefficients ¯θk as ¯θk = −
k
∑
j=0
θj (Δxm)k−j k
j
; k = 0, N . (9) (9) We have obtained our (2N + 1)–th order two–points Ceschino coupling relations as N
∑
k=0
¯θk M(k)
m−1/2 + θk M(k)
m+1/2
= 0 . (10) (10) where the O(Δxm)2N+1 error term is not given. 2.1 Two–points Ceschino coupling relations We need to determine a set of 2(N + 1) coefficients θk and ¯θk. Equations (8) and (9) permit
to determine 2N + 1 of them, leaving θ0 to be fixed. However, all values of θ0 leads to valid
solutions, making this choice arbitrary. We have chosen θ0 = 1/(Δxm)2 in order to simplify
the resulting mathematical formalism. g
In the specific case of cubic Ceschino interpolation, we set N = 1, so that Eqs. (8) and (9)
reduce to 2Δxm θ1 = −(Δxm)2 θ0
¯θ0 = −θ0
and ¯θ1 = −Δxm θ0 −θ1
(11) (11) so that our coefficients are ¯θ0 = −
1
(Δxm)2 ,
θ0 =
1
(Δxm)2
¯θ1 = −
1
2Δxm
and θ1 = −
1
2Δxm
. (12) (12) 2.2 Three–points Ceschino coupling relations 2.2 Three–points Ceschino coupling relations The three–points Ceschino coupling relations span two consecutive regions along the X axis,
as depicted in Fig. 1. We set J = 3N in Eq. (4), leading to a truncation error of order 3N + 1 if
k = 0. The Ceschino expansion are written M(k)
m−1/2 =
3N
∑
j=k
(−Δxm)j−k j
k
M(j)
m+1/2 + O(Δxm)3N−k+1
M(k)
m+3/2 =
3N
∑
j=k
(Δxm+1)j−k j
k
M(j)
m+1/2 + O(Δxm+1)3N−k+1
(13) M(k)
m+3/2 =
3N
∑
j=k
(Δxm+1)j−k j
k
M(j)
m+1/2 + O(Δxm+1)3N−k+1
(13) (13) e the mesh widths are equal to where the mesh widths are equal to where the mesh widths are equal to Δxm = xm+1/2 −xm−1/2
and
Δxm+1 = xm+3/2 −xm+1/2 . (14) (14) 426 MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer We next perform a linear combination of the first N components M(k)
m−1/2 and M(k)
m+3/2,
introducing coefficients ˘βk and βk. The linear combination permits to maintain the order of
the truncation error to 3N + 1. We write N
∑
k=0
˘βk M(k)
m−1/2 + βk M(k)
m+3/2
=
N
∑
k=0
3N
∑
j=k
˘βk (−Δxm)j−k + βk (Δxm+1)j−k j
k
M(j)
m+1/2
(15) N
∑
k=0
˘βk M(k)
m−1/2 + βk M(k)
m+3/2 =
N
∑
k=0
3N
∑
j=k
˘βk (−Δxm)j−k + βk (Δxm+1)j−k j
k
M(j)
m+1/2
(15) (15) where the truncation error is a linear combination of O(Δxm)3N+1 and O(Δxm+1)3N+1. After permutation of the two summations with the corresponding indices j and k in the
right-hand-side, we get (
m)
(
m+1)
After permutation of the two summations with the corresponding indices j and k in the
right-hand-side, we get N
∑
k=0
˘βk M(k)
m−1/2 + βk M(k)
m+3/2
=
N
∑
k=0
k
∑
j=0
˘βj (−Δxm)k−j + βj (Δxm+1)k−j k
j
M(k)
m+1/2
+
3N
∑
k=N+1
N
∑
j=0
˘βj (−Δxm)k−j + βj (Δxm+1)k−j k
j
M(k)
m+1/2 . (16) N
∑
k=0
˘βk M(k)
m−1/2 + βk M(k)
m+3/2 +
3N
∑
k=N+1
N
∑
j=0
˘βj (−Δxm)k−j + βj (Δxm+1)k−j k
j
M(k)
m+1/2 . 2.2 Three–points Ceschino coupling relations (17) and (18)
reduce to −2Δxm ˘β1 + 2Δxm+1 β1 = −(Δxm)2 ˘β0 −(Δxm+1)2 β0
3(Δxm)2 ˘β1 + 3(Δxm+1)2 β1 = (Δxm)3 ˘β0 −(Δxm+1)3 β0
¯β0 = −( ˘β0 + β0)
and
¯β1 = Δxm ˘β0 −Δxm+1 β0 −( ˘β1 + β1)
(20) −2Δxm ˘β1 + 2Δxm+1 β1 = −(Δxm)2 ˘β0 −(Δxm+1)2 β0
3(Δxm)2 ˘β1 + 3(Δxm+1)2 β1 = (Δxm)3 ˘β0 −(Δxm+1)3 β0
¯β0 = −( ˘β0 + β0) (20) and
¯β1 = Δxm ˘β0 −Δxm+1 β0 −( ˘β1 + β1)
(20) Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method 5
27 so that our two independent sets of coefficients are so that our two independent sets of coefficients are so that our two independent sets of coefficients are so that our two independent sets of coefficients are
˘β0 = −
1
(Δxm)2 ,
¯β0 =
1
(Δxm)2 −
1
(Δxm+1)2 , β0 =
1
(Δxm+1)2 ,
˘β1 = −
1
3Δxm
,
¯β1 = −2
3
1
Δxm +
1
Δxm+1
, β1 = −
1
3Δxm+1
(21)
and
˘β0 =
1
(Δxm)3 ,
¯β0 = −
1
(Δxm)3 −
1
(Δxm+1)3 , β0 =
1
(Δxm+1)3 ,
˘β1 =
1
2(Δxm)2 ,
¯β1 = 1
2
1
(Δxm)2 −
1
(Δxm+1)2
, β1 = −
1
2(Δxm+1)2 . (22) ˘β0 = −
1
(Δxm)2 ,
¯β0 =
1
(Δxm)2 −
1
(Δxm+1)2 , β0 =
1
(Δxm+1)2 ,
˘β1 = −
1
3Δxm
,
¯β1 = −2
3
1
Δxm +
1
Δxm+1
, β1 = −
1
3Δxm+1
(21)
and
˘β0 =
1
(Δxm)3 ,
¯β0 = −
1
(Δxm)3 −
1
(Δxm+1)3 , β0 =
1
(Δxm+1)3 ,
˘β1 =
1
2(Δxm)2 ,
¯β1 = 1
2
1
(Δxm)2 −
1
(Δxm+1)2
, β1 = −
1
2(Δxm+1)2 . (22) ˘β0 = −
1
(Δxm)2 ,
¯β0 =
1
(Δxm)2 −
1
(Δxm+1)2 , β0 =
1
(Δxm+1)2 ,
˘β1 = −
1
3Δxm
,
¯β1 = −2
3
1
Δxm +
1
Δxm+1
, β1 = −
1
3Δxm+1
(21)
and
˘β0 =
1
(Δxm)3 ,
¯β0 = −
1
(Δxm)3 −
1
(Δxm+1)3 , β0 =
1
(Δxm+1)3 ,
˘β1 =
1
2(Δxm)2 ,
¯β1 = 1
2
1
(Δxm)2 −
1
(Δxm+1)2
, β1 = −
1
2(Δxm+1)2 . (22) (21) and (22) 2.3 Interpolation with cubic Hermite polynomials 2.2 Three–points Ceschino coupling relations (16) (16) We choose coefficients ˘βj and βj in such a way that N
∑
j=0
˘βj (−Δxm)k−j + βj (Δxm+1)k−j k
j
= 0 ; k = N + 1, 3N
(17) (17) and we define coefficients ¯βk as ¯βk = −
k
∑
j=0
˘βj (−Δxm)k−j + βj (Δxm+1)k−j k
j
; k = 0, N . (18) (18) We have obtained our (3N + 1)–th order three–points Ceschino coupling relations as N
∑
k=0
˘βk M(k)
m−1/2 + ¯βk M(k)
m+1/2 + βk M(k)
m+3/2
= 0 . (19) (19) We need to determine a set of 3(N + 1) coefficients ˘βk, ¯βk and βk. Equations (18) and (19)
permit to determine 3N + 1 of them, leaving ˘β0 and β0 to be fixed. A first set of coefficients
can be obtained by setting ˘β0 = −1/(Δxm)2 and β0 = 1/(Δxm+1)2. A second independent
set can be obtained by setting ˘β′
0 = 1/(Δxm)3 and β′
0 = 1/(Δxm+1)3. Any other consistent set
is a linear combination of these two. In the specific case of cubic Ceschino interpolation, we set N = 1, so that Eqs. 2.3 Interpolation with cubic Hermite polynomials
( ) Knowledge of M(0)
m+1/2 and the capability to easily obtain M(1)
m+1/2 on each tabulated point
xm+1/2 makes possible the interpolation of function f (x) at each values of the independent
variable x with a cubic Hermite polynomial in x. Such polynomial guarantee that the
interpolated value and first derivative of the dependent variable remains continuous in x over
the complete domain. As pointed out by (Rozon et al., 1981), this continuity property of the
first derivative is often required in numerical applications such as those based on perturbation
theory. y
The first operation consists to solve a tridiagonal linear matrix system for obtaining the
unknown vector M(1) = col{M(1)
m+1/2 ; m = 0, M} over a M–region domain, considering the
known values M(0)
m+1/2 of f (x) at tabulation points xm+1/2. The linear matrix system is made
with the first independent set of coefficients from Eq. (21) for linking the unknowns inside the
domain. We have selected the first set in order to obtain a symmetric C matrix with minimum
powers of Δxm as coefficients. The first and last line coefficients are obtained from Eq. (12). Using coefficients from Eq. (12) with those from Eq. (22) leads to a singular C matrix. This last
observation gives an additional clue for selecting three-point coefficients from Eq. (21). The linear system is written C M(1) = S(0)
(23) (23) where the symmetric tridiagonal matrix is written where the symmetric tridiagonal matrix is written where the symmetric tridiagonal matrix is written where the symmetric tridiagonal matrix is written C =
⎡
⎢⎢⎢⎢⎢⎢⎢⎢⎢⎣
1
Δx1
1
Δx1
0
. . . 0
1
Δx1 2
1
Δx1 +
1
Δx2
1
Δx2
. . . 0
0
1
Δx2
2
1
Δx2 +
1
Δx3
. . . 0
... ... ... ... ... 0
0
0
. . . 2.3 Interpolation with cubic Hermite polynomials
( ) 1
ΔxM
⎤
⎥⎥⎥⎥⎥⎥⎥⎥⎥⎦
(24) (24) MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer 628 and where the source term is written and where the source term is written and where the source term is written and where the source term is written S(0) =
⎡
⎢⎢⎢⎢⎢⎢⎢⎢⎢⎢⎢⎣
2
(Δx1)2
M(0)
3/2 −M(0)
1/2
3
(Δx1)2
M(0)
3/2 −M(0)
1/2
+
3
(Δx2)2
M(0)
5/2 −M(0)
3/2
3
(Δx2)2
M(0)
5/2 −M(0)
3/2
+
3
(Δx3)2
M(0)
7/2 −M(0)
5/2
... 2
(ΔxM)2
M(0)
M+1/2 −M(0)
M−1/2
⎤
⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎦
. (25) (25) The solution of the linear system in Eq. (23) can be performed without pivoting, as matrix C
is diagonally dominant. We next introduce the cubic Hermite polynomials defined over a reference region −1/2 ≤
u ≤1/2. They are The solution of the linear system in Eq. (23) can be performed without pivoting, as matrix C
is diagonally dominant. W
t i t
d
th
bi H
it
l
i l d fi
d
f
i
1/2 ≤ The solution of the linear system in Eq. (23) can be performed without pivoting, as matrix C
is diagonally dominant. We next introduce the cubic Hermite polynomials defined over a reference region −1/2 ≤
u ≤1/2. They are H1(u) = 3
1
2 −u
2
−2
1
2 −u
3
H2(u) =
1
2 −u
2
−
1
2 −u
3
H3(u) = 3
1
2 + u
2
−2
1
2 + u
3
H4(u) =
1
2 + u
2
+
1
2 + u
3
(26) H4(u) =
1
2 + u
2
+
1
2 + u
3
(26) (26) so that a function f (u) defined over this domain can be expressed as so that a function f (u) defined over this domain can be expressed as f (u) ≃f (−1/2) H1(u) + f ′(−1/2) H2(u) + f (1/2) H3(u) + f ′(1/2) H4(u)
(27)
where −1/2 ≤u ≤1/2. (27) where −1/2 ≤u ≤1/2. The above relation can be generalized to the interpolation of function f (x) at ξ over region m. 2.3 Interpolation with cubic Hermite polynomials
( ) We first perform the change of variable u =
1
Δxm
ξ −1
2 (xm−1/2 + xm+1/2)
(28) (28) so that so that I{ f (x); ξ} = M(0)
m−1/2 H1(u) + Δxm M(1)
m−1/2 H2(u) + M(0)
m+1/2 H3(u)
+ Δxm M(1)
m+1/2 H4(u)
(29) (29) where xm−1/2 ≤ξ ≤xm+1/2. where xm−1/2 ≤ξ ≤xm+1/2. 7
29 Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method 2.4 Introduction of interpolation factors Interpolation factors are useful to interpolate a large number of dependent variables at a
unique value ξ of the independent variable. The interpolation factors are function only of
the tabulated abscissas {xm+1/2 ; m = 0, M} and on the interpolation abscissa x. Using
interpolation factors {tm+1/2(ξ) ; m = 0, M}, an interpolated dependent variable I{ f (x); ξ}
of f (ξ) is obtained from I{ f (x); ξ} =
M
∑
m=0
tm+1/2(ξ) f (xm+1/2)
(30) (30) where where M
∑
m=0
tm+1/2(ξ) = 1 . (31) (31) Interpolation factors can be obtained if the interpolation operation is distributive, that is, if it
can be distributed to the sum of two functions f (x) and g(h) according to Interpolation factors can be obtained if the interpolation operation is distributive, that is, if it
can be distributed to the sum of two functions f (x) and g(h) according to I{ f (x) + g(x); ξ} =
M
∑
m=0
tm+1/2(ξ) [ f (xm+1/2) + g(xm+1/2)]
= I{ f (x); ξ} + I{g(x); ξ} . (32) (32) The simplest form of interpolation factors are those corresponding to linear Lagrange
interpolation. In this case, the interpolated value of f (x), with xm−1/2 ≤ξ ≤xm+1/2, is
given by Eq. (30) with The simplest form of interpolation factors are those corresponding to linear Lagrange
interpolation. In this case, the interpolated value of f (x), with xm−1/2 ≤ξ ≤xm+1/2, is
given by Eq. (30) with tα(ξ) =
⎧
⎪
⎨
⎪
⎩
1
2 −u,
if α = m −1/2 ;
1
2 + u,
if α = m + 1/2 ;
0,
otherwise. (33) (33) Similar interpolation factors exist for cubic Ceschino interpolation and can be obtained with
the following procedure. The source term defined in Eq. (25) can be written in matrix form as Similar interpolation factors exist for cubic Ceschino interpolation and can be obtained with
the following procedure. The source term defined in Eq. (25) can be written in matrix form as S(0) = S M(0)
(34) S(0) = S M(0)
(34)
where
S =
⎡
⎢⎢⎢⎢⎢⎢⎢⎢⎢⎢⎢⎣
−
2
(Δx1)2
2
(Δx1)2
0
. . . 0
−
3
(Δx1)2
3
(Δx1)2 −
3
(Δx2)2
3
(Δx2)2
. . . 0
0
−
3
(Δx2)2
3
(Δx2)2 −
3
(Δx3)2 . . . 0
... ... ... ... ... 0
0
0
. . . 2
(ΔxM)2
⎤
⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎦
. 2.4 Introduction of interpolation factors (35)
The interpolated value of f (ξ), with xm−1/2 ≤ξ ≤xm+1/2, is therefore given by the relation
I{ f (x); ξ} =
H1(ξ)⊤+ H2(ξ)⊤C−1 S
M(0)
(36) (34) where 0
. . . 0
3
(Δx2)2
. . . 0
3
(Δx2)2 −
3
(Δx3)2 . . . 0
... ... ... 0
. . . 2
(ΔxM)2
⎤
⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎦
. (35) 0
. . . 0
3
(Δx2)2
. . . 0
3
(Δx2)2 −
3
(Δx3)2 . . . 0
... ... ... 0
. . . 2
(ΔxM)2
⎤
⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎥⎦
. (35) (35) The interpolated value of f (ξ), with xm−1/2 ≤ξ ≤xm+1/2, is therefore given by the relation
I{ f (x); ξ} =
H1(ξ)⊤+ H2(ξ)⊤C−1 S
M(0)
(36) (36) MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer 830 where H1(ξ) = {H1,m+1/2(ξ) ; m = 0, M} with where H1(ξ) = {H1,m+1/2(ξ) ; m = 0, M} with where H1(ξ) = {H1,m+1/2(ξ) ; m = 0, M} with H1,α(ξ) =
⎧
⎪
⎪
⎪
⎨
⎪
⎪
⎪
⎩
3
1
2 −u
2
−2
1
2 −u
3
,
if α = m −1/2 ;
3
1
2 + u
2
−2
1
2 + u
3
,
if α = m + 1/2 ;
0,
otherwise
(37) (37) otherwise otherwise and H2(ξ) = {H2,m+1/2(ξ) ; m = 0, M} with and H2(ξ) = {H2,m+1/2(ξ) ; m = 0, M} with and H2(ξ) = {H2,m+1/2(ξ) ; m = 0, M} with and H2(ξ) = {H2,m+1/2(ξ) ; m = 0, M} with H2,α(ξ) =
⎧
⎪
⎪
⎪
⎨
⎪
⎪
⎪
⎩
1
2 −u
2
−
1
2 −u
3
,
if α = m −1/2 ;
1
2 + u
2
+
1
2 + u
3
,
if α = m + 1/2 ;
0,
otherwise. (38) (38) The vector T(ξ) = {tm+1/2(ξ) ; m =
0, M} of interpolation factors is obtained after
transposition of Eq. (36), leading to I{ f (x); ξ} = M(0)⊤
H1(ξ) + S⊤C−1 H2(ξ)
(39) (39) so that T(ξ) = H1(ξ) + S⊤C−1 H2(ξ) . (40) (40) 3. Matlab scripts and numerical examples Derivation example. Fig. 3. Derivation example. 3. Matlab scripts and numerical examples Two Matlab scripts are proposed in Appendices A and B as prototypes of the cubic
Ceschino interpolation method. The first script, alterp() is used to obtain the terp factors
corresponding to an interpolation (if lderiv=false) or to a derivation (if lderiv=true). The second script, alteri() is used to obtain the terp factors corresponding to the definite
integration of f (x). The following Matlab session is an example of interpolation similar to the
spline Matlab tutorial. x=0:10;
y=sin(x); xx=0:.25:10; yy=zeros(1,size(xx,2)); for i=1:size(xx,2) yy(i)=y*alterp(x,xx(i),false); plot(x,y,’o’,xx,yy) Execution of the above script leads to Fig. 2. Similarly, the first derivative of f (x) = sin(x) can
be computed by setting lderiv = true, as described in the following Matlab session. yy=zeros(1,size(xx,2)); for i=1:size(xx,2) yy(i)=y*alterp(x,xx(i),true); plot(x,cos(x),’o’,xx,yy) plot(x,cos(x),’o’,xx,yy) Execution of the above script leads to Fig. 3. We observe that the order of the numerical
derivation approximation is less than the order of the interpolation, as expected. The
higher derivation errors are observed at extremities of the domain, where two-point Ceschino
coupling relation are used. Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method 9
31 0
1
2
3
4
5
6
7
8
9
10
−1
−0.8
−0.6
−0.4
−0.2
0
0.2
0.4
0.6
0.8
1
Fig. 2. Interpolation example. 0
1
2
3
4
5
6
7
8
9
10
−1.5
−1
−0.5
0
0.5
1
1.5
Fig. 3. Derivation example. 4. Conclusion
We have presented a straightforward numerical technique based on Ceschino polynomial
expansion. Three applications of this approach permit to perform interpolation, derivation
and definite integration of tabulated data. Equation (36) is efficient to interpolate few
dependent variables over a large number of points ξ. Equation (39) introduces the concept
of interpolation factors and is efficient to interpolate a large number of dependent variables
over a few number of points ξ. Matlab scripts are provided as basic implementation of the 0
1
2
3
4
5
6
7
8
9
10
−1
−0.8
−0.6
−0.4
−0.2
0
0.2
0.4
0.6
0.8
1
Fig. 2. Interpolation example. 0
1
2
3
4
5
6
7
8
9
10
−1
−0.8
−0.6
−0.4
−0.2
0
0.2
0.4
0.6
0.8
1 Fig. 2. Interpolation example. 0
1
2
3
4
5
6
7
8
9
10
−1.5
−1
−0.5
0
0.5
1
1.5 0
1
2
3
4
5
6
7
8
9
10
−1.5
−1
−0.5
0
0.5
1
1.5
Fig. 3. 4. Conclusion We have presented a straightforward numerical technique based on Ceschino polynomial
expansion. Three applications of this approach permit to perform interpolation, derivation
and definite integration of tabulated data. Equation (36) is efficient to interpolate few
dependent variables over a large number of points ξ. Equation (39) introduces the concept
of interpolation factors and is efficient to interpolate a large number of dependent variables
over a few number of points ξ. Matlab scripts are provided as basic implementation of the
Ceschino interpolating method. We have presented a straightforward numerical technique based on Ceschino polynomial
expansion. Three applications of this approach permit to perform interpolation, derivation
and definite integration of tabulated data. Equation (36) is efficient to interpolate few
dependent variables over a large number of points ξ. Equation (39) introduces the concept
of interpolation factors and is efficient to interpolate a large number of dependent variables
over a few number of points ξ. Matlab scripts are provided as basic implementation of the
Ceschino interpolating method. We have presented a straightforward numerical technique based on Ceschino polynomial
expansion. Three applications of this approach permit to perform interpolation, derivation
and definite integration of tabulated data. Equation (36) is efficient to interpolate few
dependent variables over a large number of points ξ. Equation (39) introduces the concept
of interpolation factors and is efficient to interpolate a large number of dependent variables
over a few number of points ξ. Matlab scripts are provided as basic implementation of the
Ceschino interpolating method. 1032 MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer The Ceschino interpolation technique is an alternative to the cubic spline approach based on
different mathematical bases. In fact, the interpolating function obtained by this method is a
piecewise polynomial function of degree 3 which is only a C1 function compared to the cubic
spline which is a C2 function. It would be important to obtain error estimates to compare
both approaches. However, the Ceschino interpolation technique is currently implemented in
legacy applications and its behavior is already found acceptable. Appendix A The first Matlab script is used to compute interpolation/derivation factors (a. k. a., terp
factors) using Eq. (40). The user must provide the tabulated abscissa defined as {xm+1/2 ; m =
0, M} and one interpolation point ξ. A logical variable, lderiv, select interpolation or
derivation mode. The script returns a column vector containing the corresponding terp factors
{tm+1/2(ξ) ; m = 0, M}. function terp=alterp(x,val,lderiv) % determination of the terp interpolation/derivation factors using % determination of the terp interpolation/derivation factor % the order 4 Ceschino method with cubic Hermite polynomials. % function terp=alterp(x,val,lderiv) % x
abscissas (row vector)
% val
abscissa of the interpolated point. % x
abscissas (row vector)
% val
abscissa of the interpolated point. % val
abscissa of the interpolated point. % lderiv
set to true to compute the first derivative with respect to x. %
set to false to interpolate. % lderiv
set to true to compute the first derivative with respect to x
%
set to false to interpolate % lderiv
set to true to compute the first derivative
%
set to false to interpolate. % lderiv
set to true to compute the first derivative with respect to x. %
set to false to interpolate. % lderiv
set to true to compute the fi
%
set to false to interpolate. set to false to interpolate. % output parameters: % terp
interpolation factors (column vector) error(’invalid number of points’ error(’invalid number of points’) terp=zeros(n,1) ; if n == 2 if lderiv
terp(1)=-1.0/(x(2)-x(1)) ;
terp(2)=1.0/(x(2)-x(1)) ; else
terp(1)=(x(2)-val)/(x(2)-x(1)) ;
terp(2)=1.0-terp(1) ; else wk=zeros(3,n) ; %
interval identification. temp1=find(val>=x(1:end-1)) ; temp2=find(val<=x(2:end)) ; if (size(temp1,2) == 0) | (size(temp2,2) == 0) |
error(’unable to interpolate’) end i0=temp1(end) ; dx=x(i0+1)-x(i0) ; u=(val-0.5*(x(i0)+x(i0+1)))/dx ; Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method 11
33 Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method if lderiv
h1=(-6.0*(0.5-u)+6.0*(0.5-u)^2)/dx ;
h2=(-2.0*(0.5-u)+3.0*(0.5-u)^2)/dx ;
h3=(6.0*(0.5+u)-6.0*(0.5+u)^2)/dx ;
h4=(-2.0*(0.5+u)+3.0*(0.5+u)^2)/dx ;
test=0.0 ; h4=(-2.0*(0.5+u)+3.0*(0.5+u)^2)/dx ;
test=0.0 ; else h1=3.0*(0.5-u)^2-2.0*(0.5-u)^3 ; h1=3.0*(0.5-u)^2-2.0*(0.5-u)^3 ;
h2=(0.5-u)^2-(0.5-u)^3 ; h2=(0.5-u)^2-(0.5-u)^3 ; h3=3.0*(0.5+u)^2-2.0*(0.5+u)^3 ; h4=-(0.5+u)^2+(0.5+u)^3 ; test=1.0 ; end terp(i0)=h1 ; terp(i0+1)=h3 ; wk(3,i0)=h2*dx ; wk(3,i0+1)=h4*dx ; %
%
compute the coefficient matrix. %---- hp=1.0/(x(2)-x(1)) ; wk(1,1)=hp ; wk(2,1)=hp ; for i=2:n-1 hm=hp ; hp=1.0/(x(i+1)-x(i)) ; wk(1,i)=2.0*(hm+hp) ; wk(2,i)=hp ; end wk(1,n)=hp ; wk(2,n)=hp ; %----
%
forward elimination. %---- %
forward elimination. pmx=wk(1,1) ; wk(3,1)=wk(3,1)/pmx ; for i=2:n
gar=wk(2,i-1) ;
wk(2,i-1)=wk(2,i-1)/pmx ;
pmx=wk(1 i) gar*wk(2 i 1) pmx=wk(1,i)-gar*wk(2,i-1) ; wk(3,i)=(wk(3,i)-gar*wk(3,i-1))/pmx ; end %
back substitution. for i=n-1:-1:1 for i=n-1:-1:1
wk(3,i)=wk(3,i)-wk(2,i)*wk(3,i+1) ; end %
compute the interpolation factors. %---- gar=zeros(1,n+2) ; gar(2:n+1)=wk(3,:) ; wk=zeros(3,n) ; hp2=1.0/(x(2)-x(1)) ; 1234 MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer wk(2,1)=-2.0*hp2*hp2 ;
wk(1,2)=2.0*hp2*hp2 ;
for i=2:n-1
hp1=hp2 ;
hp2=1.0/(x(i+1)-x(i)) ;
wk(3,i-1)=-3.0*hp1*hp1 ;
wk(2,i)=3.0*hp1*hp1-3.0*hp2*hp2 ;
wk(1,i+1)=3.0*hp2*hp2 ;
end
wk(3,n-1)=-2.0*hp2*hp2 ;
wk(2,n)=2.0*hp2*hp2 ;
for j=1:n
terp(j)=terp(j)+gar(j:j+2)*wk(:,j) ;
test=test-terp(j) ;
end
if abs(test) > 1.0e-5
error(’wrong terp factors’)
end
terp(find(abs(terp) <= 1.0e-7))=0.0 ;
end wk(2,i)=3.0*hp1*hp1-3.0*hp2*hp2 ; wk(3,n-1)=-2.0*hp2*hp2 ; wk(2,n)=2.0*hp2*hp2 ; if abs(test) > 1.0e-5 error(’wrong terp factors’) error(’wrong terp factors’)
end terp(find(abs(terp) <= 1.0e-7))=0.0 ;
end end Appendix B The second Matlab script is used to compute integration factors permitting to evaluate a
definite integral. The user must provide the tabulated abscissa {xm+1/2 ; m = 0, M} and
the integration limits. The script returns a column vector containing the corresponding terp
factors. function terp=alteri(x,val0,val1) determination of the terp integrati % determination of the terp integration factors using the order 4 % Ceschino method with cubic Hermite polynomials. Ceschino method with cubic Hermite p % function terp=alteri(x,val0,val1) % input parameters: % x
abscissas (row vector) % val0
left integration limit. % val1
right integration limit. % output parameters: % terp
integration factors (column vector) % (c) 2007 Alain Hebert, Ecole Polytechnique de Montreal
n=size(x,2) ;
if n <= 1
error(’invalid number of points’)
elseif val1 <= val0
error(’invalid limits’)
elseif (val0 < x(1)) | (val1 > x(n))
error(’unable to integrate’)
end
terp=zeros(n,1) ;
if n == 2
terp(1)=(x(2)-0.5*(val0+val1))*(val1-val0)/(x(2)-x(1)) ;
terp(2)=(0.5*(val0+val1)-x(1))*(val1-val0)/(x(2)-x(1)) ;
else
wk=zeros(3,n) ;
%---- error(’invalid number of points’) elseif (val0 < x(1)) | (val1 > x(n)) error(’unable to integrate’) terp=zeros(n,1) ; terp(1)=(x(2)-0.5*(val0+val1))*(val1-val0)/(x(2)-x(1)) ;
terp(2) (0 5*(val0+val1) x(1))*(val1 val0)/(x(2) x(1)) terp(2)=(0.5*(val0+val1)-x(1))*(val1-val0)/(x(2)-x(1)) ;
else wk=zeros(3,n) ; 13
35 Revisiting the Ceschino Interpolation Method
Revisiting the Ceschino Interpolation Method terp(find(abs(terp) <= 1.0e-7))=0.0 ; terp(find(abs(terp) <= 1.0e-7))=0.0 ; end %
interval identification. %
interval identification. %---- %
interval identification. %----
for i0=1:n-1
if (val0 < x(i0+1)) & (val1 > x(i0))
a=max(val0,x(i0)) ;
b=min(val1,x(i0+1)) ;
cc=0.5*(b-a) ;
dx=x(i0+1)-x(i0) ;
u1=(a-0.5*(x(i0)+x(i0+1)))/dx ;
u2=(b-0.5*(x(i0)+x(i0+1)))/dx ;
uu(1)=0.5*(-(u2-u1)/sqrt(3.0)+u1+u2) ;
uu(2)=0.5*((u2-u1)/sqrt(3.0)+u1+u2) ;
for js=1:2
h1=(3.0*(0.5-uu(js))^2-2.0*(0.5-uu(js))^3)*cc ;
h2=((0.5-uu(js))^2-(0.5-uu(js))^3)*cc ;
h3=(3.0*(0.5+uu(js))^2-2.0*(0.5+uu(js))^3)*cc ;
h4=(-(0.5+uu(js))^2+(0.5+uu(js))^3)*cc ;
terp(i0)=terp(i0)+h1 ;
terp(i0+1)=terp(i0+1)+h3 ;
wk(3,i0)=wk(3,i0)+h2*dx ;
wk(3,i0+1)=wk(3,i0+1)+h4*dx ;
end
end
end
%----
%
compute the coefficient matrix. %----
hp=1.0/(x(2)-x(1)) ;
wk(1,1)=hp ;
wk(2,1)=hp ;
for i=2:n-1
hm=hp ;
hp=1.0/(x(i+1)-x(i)) ;
wk(1,i)=2.0*(hm+hp) ;
wk(2,i)=hp ;
end
wk(1,n)=hp ;
wk(2,n)=hp ;
%----
%
forward elimination. %----
pmx=wk(1,1) ;
wk(3,1)=wk(3,1)/pmx ;
for i=2:n
gar=wk(2,i-1) ;
wk(2,i-1)=wk(2,i-1)/pmx ;
pmx=wk(1,i)-gar*wk(2,i-1) ;
wk(3,i)=(wk(3,i)-gar*wk(3,i-1))/pmx ;
end
%----
%
back substitution. %----
for i=n-1:-1:1
wk(3,i)=wk(3,i)-wk(2,i)*wk(3,i+1) ;
end u1=(a-0.5*(x(i0)+x(i0+1)))/dx ; uu(1)=0.5*(-(u2-u1)/sqrt(3.0)+u1+u2) ; (2)=0.5*((u2-u1)/sqrt(3.0)+u1+u2) ; j
h1=(3.0*(0.5-uu(js))^2-2.0*(0.5-uu(js))^3)*cc ; h2=((0.5-uu(js))^2-(0.5-uu(js))^3)*cc ; h3=(3.0*(0.5+uu(js))^2-2.0*(0.5+uu(js))^3)*cc ; h4=(-(0.5+uu(js))^2+(0.5+uu(js))^3)*cc ; wk(3,i0)=wk(3,i0)+h2*dx ; wk(3,i0+1)=wk(3,i0+1)+h4*dx ; %
compute the coefficient matrix. %---- hp=1.0/(x(2)-x(1)) ; wk(1,1)=hp ; wk(2,1)=hp ; wk(2,i)=hp ; end wk(1,n)=hp ; wk(2,n)=hp ; %
forward elimination. pmx=wk(1,1) ; wk(3,1)=wk(3,1)/pmx ; back substitution. for i=n-1:-1:1 end MATLAB
MATLAB – A Ubiquitous Tool for the Practical Engineer 1436 %----
%
compute the integration factors.
%---- %----
%
compute the integration factors. %---- wk(2,i)=3.0*hp1*hp1-3.0*hp2*hp2 ; wk(1,i+1)=3.0*hp2*hp2 ; wk(3,n-1)=-2.0*hp2*hp2 ; wk(3,n-1)=-2.0*hp2*hp2 ; wk(2,n)=2.0*hp2*hp2 ; for j=1:n
terp(j)=terp(j)+gar(j:j+2)*wk(:,j) ; test=test-terp(j)/(val1-val0) ; if abs(test) > 1.0e-5
error(’wrong terp factors’) if abs(test) > 1.0e-5 error(’wrong terp factors’) error(’wrong terp factors’) 1. Introduction Many problems of the real life lead us to linear differential equations of the form m
∑
k=0
Pk(x) dky
dxk = f (x),
x ∈[a, b]
(1) (1) (1) with the general conditions with the general conditions m
∑
j=1
α(1)
ij y(j−1)(x(1)
ij ) + · · · +
m
∑
j=1
α(m)
ij
y(j−1)(x(m)
ij
) = βi,
i = 1, ..., m
(2) (2) where x(k)
ij
∈[a, b], ∀i, j, k = 1, ..., m. These multipoint conditions include (for m = 2, for
example) where x(k)
ij
∈[a, b], ∀i, j, k = 1, ..., m. These multipoint conditions include (for m = 2, for
example) p )
- initial value conditions, y(a) = β1, y′(a) = β2, , y( )
β1, y ( )
β2,
- boundary value conditions α11y(a) + α12y′(a) = β1, α21y(b) + α22y′(b) = β2,
- periodic conditions y(a) −y(b) = 0, y′(a) −y′(b) = 0. p
y( )
y( )
y ( )
y ( )
Eigenvalue problems for linear differential operators p
y
y
y
y
Eigenvalue problems for linear differential operators m
∑
k=1
Pk(x) dky
dxk + (P0(x) −λw(x)) y = 0,
x ∈[a, b]
m
∑
j=1
α(1)
ij y(j−1)(x(1)
ij ) + · · · +
m
∑
j=1
α(m)
ij
y(j−1)(x(m)
ij
) = 0,
i = 1, ..., m m
∑
k=1
Pk(x) dky
dxk + (P0(x) −λw(x)) y = 0,
x ∈[a, b] m
∑
j=1
α(1)
ij y(j−1)(x(1)
ij ) + · · · +
m
∑
j=1
α(m)
ij
y(j−1)(x(m)
ij
) = 0,
i = 1, ..., m are also included in this general form. Moreover, nonlinear problems where the r.h.s. f (x)
is replaced by f (x, y(x), y′(x), ..., y(m−1)(x)) can be solved using Newton’s method in the
functional space Cm [a, b] by solving a sequence of linear problems (1)+(2). are also included in this general form. Moreover, nonlinear problems where the r.h.s. f (x)
is replaced by f (x, y(x), y′(x), ..., y(m−1)(x)) can be solved using Newton’s method in the
functional space Cm [a, b] by solving a sequence of linear problems (1)+(2). p
[
]
y
g
q
p
MATLAB
uses
different
methods
to
solve
initial
condition
problems
(ode
family)
or
boundary
value
problems
(bvp4c
or
bvp5c)
based
on
Runge-Kutta,
Adams-Bashforth-Moulton, BDF algorithms, etc. Matrix Based Operatorial Approach to Differential
and Integral Problems Damian Trif
Babes-Bolyai University of Cluj-Napoca
Romania Damian Trif
Babes-Bolyai University of Cluj-Napoca
Romania 5. References Ceschino, F. (1956). L’intégration approchée des équations différentielles, Compte Rendu de
l’Académie des Sciences, Paris, 243, pp. 1478 – 1479. Hébert, A. (2009). Applied Reactor Physics, Presses Internationales Polytechnique, ISBN
978-2-553-01436-9, 424 p., Montréal. MacFarlane, R. E. (1984). TRANSX-CTR: A code for Interfacing MATXS Cross-Section Libraries
to Nuclear Transport Codes for Fusion Systems Analysis, LA-9863-MS, Los Alamos
Scientific Laboratory, New Mexico. y
Pageau, R. (1975). Application des méthodes TCNR et des séries de Fourier aux Problèmes statique
bi-dimensionnels en physique des réacteurs, Master Thesis, École Polytechnique de
Montréal. Rozon, D.; Hébert, A.; McNabb, D. (1981). The Application of Generalized Perturbation Theory and
Mathematical Programming to Equilibrium Refueling Studies of a CANDU Reactor, Nucl. Sci. Eng., 78, pp. 211 – 226. 03 1. Introduction We give here a comparison between DMS, Chebfun and
our proposed package Chebpack (based on the tau spectral method) for an eigenvalue problem
suggested by Solomonoff and Turkel. Let us consider the evolution problem and the conditions (2) are enclosed in the matrix A and in the vector F. The numerical solution
of the differential problem is now Y = A−1F. We note that MATLAB capabilities of working
with matrices make it an ideal tool for matrix based operatorial approach. and the conditions (2) are enclosed in the matrix A and in the vector F. The numerical solution
of the differential problem is now Y = A−1F. We note that MATLAB capabilities of working
with matrices make it an ideal tool for matrix based operatorial approach. There is a price to pay for using pseudospectral methods: the differentiation matrix D is full
(while for finite differences or finite element methods it is sparse) and, more importantly, D
is very sensitive to rounding errors. We give here a comparison between DMS, Chebfun and
our proposed package Chebpack (based on the tau spectral method) for an eigenvalue problem
suggested by Solomonoff and Turkel. Let us consider the evolution problem ut = −xux, u(x, 0) = f (x), x ∈[−1, 1] , with the exact solution u(x, t) = f (xe−t). Here x = ±1 are outflow boundaries so that
no boundary conditions are required. Using a Chebyshev spectral method to discretize the
spatial part of the equation, the stability of time integration depends on the eigenvalues of
that spatial part −xux = λu, x ∈[−1, 1] . (4) −xux = λu, x ∈[−1, 1] . (4) ct (polynomial) eigenvectors are the monomials xn and the corresponding eigenvalues
= −n, n = 0, 1, ... . n
,
, ,
The commands for the DMS package The commands for the DMS package [x,D]=chebdif(64,1);L=eig(-diag(x)*D); 1. Introduction One of the most effective methods for solving (1)+(2) is to shift the problem to the interval
[−1, 1] and then to use the Chebyshev spectral methods, i.e. to approximate the solution y by a
finite sum of the Chebyshev series y(x) = 1
2c0T0(x) + c1T1(x) + c2T2(x).... (3) (3) 238 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Here Tk(x) = cos(k cos−1(x)), k = 0, 1, ... are the Chebyshev polynomials of the first kind and
the coefficients ck, k = 0, 1, ...are unknown. A spectral method is characterized by a specific
way to determine these coefficients. The Chebyshev spectral methods could be implemented
as Here Tk(x) = cos(k cos−1(x)), k = 0, 1, ... are the Chebyshev polynomials of the first kind and
the coefficients ck, k = 0, 1, ...are unknown. A spectral method is characterized by a specific
way to determine these coefficients. The Chebyshev spectral methods could be implemented
as - Galerkin and tau methods, where we work in the spectral space of the coefficients c = c0, c1,
c2, ... of y or as c2, ... of y or as - spectral collocation (or pseudospectral) methods, where we work in the physical space of
the values of y at a specific grid x = x1, x2, ... ∈[−1, 1]. The well known MATLAB packages which use spectral methods, MATLAB Differentiation
Matrix Suite (DMS) (Weideman & Reddy, 2000) and Chebfun (Trefethen et al., 2011), are based
on the pseudospectral methods. Usually, these methods are implemented in an operatorial
form: a differentiation matrix D (or linear operator) is generated so that Y′ = DY where the
vector Y′ contains the values of the derivative y′ at the specific grid while Y contains the
values of y at the same grid. The equation (1) becomes
m
∑
k=0
diag(Pk(x))Dk
Y = f (x) i.e. AY = F and the conditions (2) are enclosed in the matrix A and in the vector F. The numerical solution
of the differential problem is now Y = A−1F. We note that MATLAB capabilities of working
with matrices make it an ideal tool for matrix based operatorial approach. There is a price to pay for using pseudospectral methods: the differentiation matrix D is full
(while for finite differences or finite element methods it is sparse) and, more importantly, D
is very sensitive to rounding errors. Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems Fig. 1. Eigenvalues for the problem (4) Fig. 1. Eigenvalues for the problem (4) Fig. 1. Eigenvalues for the problem (4) give the 64 approximated eigenvalues successively in the vector L and they are represented in
Fig. 1. We see that DMS and Chebfun calculate accurately only a small number of eigenvalues,
while Chebpack gives exactly all 64 eigenvalues. The proposed package Chebpack, which is described in this chapter, is based on the
representation (3) of the unknown functions and uses the tau method for linear operators
(such as differentiation, integration, product with the independent variable,...)
and the
pseudospectral method for nonlinear operators – nonlinear part of the equations. The tau method was invented by Lanczos (1938, 1956) and later developed in an operatorial
approach by Ortiz and Samara (Ortiz & Samara, 1981). In the past years considerable work
has been done both in the theoretical analysis and numerical applications. y
pp
Chebpack is freely accessible at https://sites.google.com/site/dvtrif/ and at (Trif,
2011). All the running times in this chapter are the elapsed times for a 1.73GHz laptop and for
MATLAB 2010b under Windows XP. for Chebfun N=chebop(@(x,u) -x.*diff(u),[-1,1]);L=eigs(N(66),64,’LR’);
and for Chebpack N=chebop(@(x,u) -x.*diff(u),[-1,1]);L=eigs(N(66),64,’LR’); and for Chebpack X=mult(64,[-1,1]);D=deriv(64,[-1,1]);L=eig(full(-X*D)); X=mult(64,[-1,1]);D=deriv(64,[-1,1]);L=eig(full(-X*D)); 3
39 2. Chebpack, basic module The package contains, at the basic module – level0, the tools which will be used in the next
modules. Let us start with the Chebyshev series expansion of a given function y (Boyd, 2000):
THEOREM 1. If y is Lipschitz continuous on [-1, 1], it has a unique representation as an absolutely
and uniformly convergent series y(x) = c0
2 T0(x) + c1T1(x) + c2T2(x) + ..., Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 440 and the coefficients are given by the formula and the coefficients are given by the formula and the coefficients are given by the formula ck = 2
π
1
−1
y(x)Tk(x)
√
1 −x2 dx, k = 0, 1, 2, .... he truncation of the above Chebyshev series Let yN−1 be the truncation of the above Chebyshev series Let yN−1 be the truncation of the above Chebyshev series yN−1(x) = c0
2 T0(x) + c1T1(x) + c2T2(x) + · · · + cN−1TN−1(x)
(5) (5) and dom = [−1, 1] be the working interval. Any interval [a, b] can be shifted and scaled to
[−1, 1] by using the shifted Chebyshev polynomials and dom = [−1, 1] be the working interval. Any interval [a, b] can be shifted and scaled to
[−1, 1] by using the shifted Chebyshev polynomials T∗
k (x) = Tk(αx + β), α =
2
b −a, β = −b + a
b −a, x ∈[a, b] . First of all, we need a set of N collocation points x1, ..., xN
∈dom in order to find a
good transformation between the above spectral approximation (5) of y and its physical
representation y(x1), y(x2), ..., y(xN). Let First of all, we need a set of N collocation points x1, ..., xN
∈dom in order to find a
good transformation between the above spectral approximation (5) of y and its physical
representation y(x1), y(x2), ..., y(xN). Let pN−1(x) = a0
2 T0(x) + a1T1(x) + ... + aN−1TN−1(x)
(6) (6) be the unique polynomial obtained by interpolating y(x) through the points x1, ..., xN, see
(Trefethen, 2000) for more details on the coefficients ak versus ck. The next theorem of (Boyd,
2000) estimates the error: at least N derivatives on dom. Then THEOREM 2. Let y have at least N derivatives on dom. Then THEOREM 2. Let y have at least N derivatives on dom. 2. Chebpack, basic module Then y(x) −pN−1(x) = 1
N! y(N) (ξ)
N
∏
k=1
(x −xk) for some ξ on the interval spanned by x and the interpolation points. The point ξ depends on the
function y, upon N, upon x and upon the location of the interpolation points. for some ξ on the interval spanned by x and the interpolation points. The point ξ depends on the
function y, upon N, upon x and upon the location of the interpolation points. for some ξ on the interval spanned by x and the interpolation points. The point ξ depends on the
function y, upon N, upon x and upon the location of the interpolation points. Consequently, the optimal interpolation points are the roots of the Chebyshev polynomial
( ) for some ξ on the interval spanned by x and the interpolation points. The point ξ depends on the
function y, upon N, upon x and upon the location of the interpolation points. Consequently, the optimal interpolation points are the roots of the Chebyshev polynomial
TN(x), (Chebyshev points of the first kind) f
y
p
p
p
f
p
p
Consequently, the optimal interpolation points are the roots of the Chebyshev polynomial
TN(x), (Chebyshev points of the first kind) xk = −cos (2k −1)π
2N
, k = 1, ..., N. (7) (7) For these points x, the polynomials {pN−1} are generally nearly as good approximations to y
as the polynomials {yN−1} and if y is analytic on dom, then both ∥y −yN−1∥and ∥y −pN−1∥
decrease geometrically as N →∞. This is the spectral convergence property, i.e. the convergence
of ∥y −yN−1∥and ∥y −pN−1∥towards zero is faster than any power of 1
N as N →∞. Numerical integration and Lagrangian interpolation are very closely related. The standard
formulas for a continuous function f on [−1, 1] are of the type For these points x, the polynomials {pN−1} are generally nearly as good approximations to y
as the polynomials {yN−1} and if y is analytic on dom, then both ∥y −yN−1∥and ∥y −pN−1∥
decrease geometrically as N →∞. This is the spectral convergence property, i.e. the convergence
of ∥y −yN−1∥and ∥y −pN−1∥towards zero is faster than any power of 1
N as N →∞. ∥y
yN
1∥
∥y
pN
1∥
y p
N
Numerical integration and Lagrangian interpolation are very closely related. 2. Chebpack, basic module The standard
formulas for a continuous function f on [−1, 1] are of the type 1
−1 f (x)dx ≈
N
∑
k=1
wk f (xk),
(8) (8) where wk are the quadrature weights where wk are the quadrature weights wk =
1
−1
N
∏
j=1,j̸=k
x −xj
xk −xj
dx, k = 1, 2, ..., N. 5
41 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems The Gauss quadrature formulas are based on the optimal Legendre points xk, k = 1, ..., N and
these formulas are exact for polynomials f up to degree 2N −1. The idea of Clenshaw-Curtis
quadrature is to use Chebyshev points x instead of the above optimal nodes. By using the
Chebyshev points of the first kind (7) one obtains the “classical” Clenshaw-Curtis formula
while by using the zeros of the first derivative of a Chebyshev polynomial plus the endpoints
±1, i.e. the Chebyshev extrema xk = −cos (k −1)π
N −1 , k = 1, ..., N
(9) (9) in [−1, 1] (the so called Chebyshev points of the second kind) one obtains the “practical”
Clenshaw-Curtis formula. Both formulas have all the good properties of the Gaussian
quadrature, see (Trefethen, 2008) for more details. Consequently, we may use Chebyshev points of the first kind or of the second kind both for
quadrature formulas and for physical representation of a function y on [−1, 1]. Any interval
[a, b] may be scaled to [−1, 1] and we obtain the corresponding formulas. Moreover, by using
the mapping x = cos θ and Tk(x) = cos kθ we see that the following two series y(x) = c0
2 T0(x) + c1T1(x) + c2T2(x) + ... y(cos θ) = c0
2 + c1 cos θ + c2 cos 2θ + ... are equivalent. A Chebyshev series is in fact a Fourier cosine series so that the FFT and iFFT
may be used to transform the spectral representation of y into the physical one and conversely,
the physical representation into the spectral representation. The quadrature weights w could
also be calculated by a fast algorithm given in (Waldvogel, 2006). are equivalent. [int,gridpts] = quadcheb(myfun,n,dom,kind,tol,gridpts,I) in the folder Chebpack\examples\ex_level0 which uses pd into a recursive procedure. Precisely, starting from the initial interval dom = [a, b], pd is used with n points in [a, b] and
on two subintervals [a, c] and [c, b] where c = (a + b)/2 . If the results differe by more than a
tolerance ε, the interval [a, b] is divided to that subintervals . Now quadcheb is called again
for each subinterval and at each step we sum the results. For N = 128 we obtain
Elapsed time = 0.013672 seconds. err = 4.907093620332148e-010 Of course, this non-optimized quadrature calculation is only a collateral facility in Chebpack
and it does not work better than the basic quadrature command quadgk from MATLAB,
which is designated for highly oscillatory integrals. The next codes of level0 v = t2x(c,kind) and c = x2t(v,kind) are inspired by chebpolyval.m and chebpoly.m from chebfun (Trefethen et al., 2011). These
codes perform the correspondence between the spectral representation c of a function f and
its physical representation v = f (x) on Chebyshev points of the first or second kind. It is
important to remark that linear operators are better represented in the spectral space, while
the nonlinear operators are easily handled in the physical space. are inspired by chebpolyval.m and chebpoly.m from chebfun (Trefethen et al., 2011). These
codes perform the correspondence between the spectral representation c of a function f and
its physical representation v = f (x) on Chebyshev points of the first or second kind. It is
important to remark that linear operators are better represented in the spectral space, while
the nonlinear operators are easily handled in the physical space. p
y
p y
p
In t2x and x2t, c and v are matrices of the same dimension, each column represents the
coefficients or the values for some other function, the number of rows is the above dimension
N, while kind specifies the type of Chebyshev points used in v. For example, the code dom=[0,1];kind=2;x=pd(n,dom,kind); vs=sin(x);vc=cos(x);ve=exp(x);c=x2t([vs,vc,ve],kind); gives in the columns of c the coefficients of the Chebyshev series (6) of sin(x), cos(x) and
exp(x) calculated by using the values of these functions on Chebyshev points of the second
kind on [0, 1]. We remark here that, taking into account the term c0T0/2, the coefficient c0 is
doubled. Another code from level0, inspired from bary.m of chebfun (Trefethen et al., 2011) and useful
for graphical representation of the functions is fxn = barycheb(xn,fk,xk,kind) 2. Chebpack, basic module A Chebyshev series is in fact a Fourier cosine series so that the FFT and iFFT
may be used to transform the spectral representation of y into the physical one and conversely,
the physical representation into the spectral representation. The quadrature weights w could
also be calculated by a fast algorithm given in (Waldvogel, 2006). The first code of level0, inspired from chebpts.m of chebfun (Trefethen et al., 2011) is y
g
g
g
code of level0, inspired from chebpts.m of chebfun (Trefethen et al., 2011) is [x,w] = pd(N,dom,kind) (pd means “physical domain”). It calculates the grid x = [x1, ..., xN]T (column vector) and the
quadrature weights w = [w1, ..., wN] (row vector) for the quadrature formula b
a f (x)dx ≈
N
∑
j=1
wj f (xj) ≡w · f (x). The input parameters are N – the dimension of the vectors x and w, dom – the computational
domain [a, b] and kind which can be 1 or 2 in order to calculate x as the Chebyshev points of
the first or of the second kind. The input parameters are N – the dimension of the vectors x and w, dom – the computational
domain [a, b] and kind which can be 1 or 2 in order to calculate x as the Chebyshev points of
the first or of the second kind. Some short tests show the performances of this code. Let us approximate 1
0 x sin 1
x dx = cos(1) + sin(1) + Si(1)
2
−π
4 ≈0.37853001712416130988... for N
=
10, 102, ..., 106. Here we use Chebyshev points of the first kind and hence
we have no problems with the singularity at the origin. We have instead problems
with the highly oscillatory behavior of the integrand near the origin. The code is
Chebpack\examples\ex_level0\quad_ex1.m and the result for N = 106 is
Elapsed time = 0.938258074699438 seconds
err = 1.9568e-11. A more efficient code is 642 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer [int,gridpts] = quadcheb(myfun,n,dom,kind,tol,gridpts,I) [int,gridpts] = quadcheb(myfun,n,dom,kind,tol,gridpts,I) fxn = barycheb(xn,fk,xk,kind) It interpolates the values fk of a function f at the Chebyshev nodes xk of the first or second
kind in dom by calculating the values fxn at the new (arbitrary) nodes xn in dom. The
barycentric weights are calculated depending on kind. It interpolates the values fk of a function f at the Chebyshev nodes xk of the first or second
kind in dom by calculating the values fxn at the new (arbitrary) nodes xn in dom. The
barycentric weights are calculated depending on kind. y
g
p
g
Precisely, cf. (Berrut & Trefethen, 2004), the barycentric formula is f (x) =
∑N
k=1
wk
x−xk fk
∑N
k=1
wk
x−xk
, wk =
1
∏
j̸=k
(xk −xj), k = 1, ..., N. For Chebyshev points one can give explicit formula for barycentric weights w. For the
Chebyshev points of the first kind we have For Chebyshev points one can give explicit formula for barycentric weights w. For the
Chebyshev points of the first kind we have xk = −cos (2k −1)π
2N
, wk = (−1)k sin (2k −1) π
2N
, k = 1, ..., N 7
43 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems the Chebyshev points of the second kind we have and for the Chebyshev points of the second kind we have xk = −cos (k −1)π
N −1 , wk = (−1)kδk, δk =
1
2, k = 1, N
1, otherwise , k = 1, ..., N. We remark that for a general interval dom = [a, b] and if the sign changes for all xk and wk the
weights must be multiplicated by ±2N−1(b −a)1−N. This factor cancels out in the barycentric
formula so that it is no need to include it. We remark that for a general interval dom = [a, b] and if the sign changes for all xk and wk the
weights must be multiplicated by ±2N−1(b −a)1−N. This factor cancels out in the barycentric
formula so that it is no need to include it. Let us calculate now the differentiation matrix D such that if f is the column of the Chebyshev
coefficients of a function f, then Df is the column of the Chebyshev coefficients of the
derivative function d f
dx . fxn = barycheb(xn,fk,xk,kind) On [−1, 1] the derivatives of Ti satisfy T0 = T′
1, T1 = T′
2
4 , ..., Ti =
T′
i+1
2(i + 1) −
T′
i−1
2(i −1),
i ≥2 from where T′
0
2 = 0, T′
i = 2i (Ti−1 + Ti−3 + ... + T1) ,
i even
T′
i = 2i (Ti−1 + Ti−3 + ... + 0.5T0) ,
i odd. Consequently, D is a sparse upper triangular matrix with Dii = 0, Dij = 0 for (j −i) even and Dij = 2j otherwise. Of course, the differentiation could be iterated, i.e. the coefficients of f (p) are Dpf. The
corresponding code from level0 is Of course, the differentiation could be iterated, i.e. the coefficients of f (p) are Dpf. The
corresponding code from level0 is D=deriv(n,dom) where n is the dimension of the matrix D. For dom = [a, b] the above matrix D is multiplied
by 2/(b −a). Similarly, the code [J,J0]=prim(n,dom) calculates the sparse integration matrix J such that the coefficients of x f (t)dt are Jf. Here the
first coefficient of the result Jf may be changed in order to obtain the coefficients for a specific primitive
of f. For example, the coefficients of the primitive which vanishes at a = dom(1) are obtained
by using J0f. The basic formulas for dom = [−1, 1] are ic formulas for dom = [−1, 1] are
T0
2 dx = T1
2 ,
T1dx = T0/2
2
+ T2
4 ,
Tkdx = 1
2
Tk+1
k + 1 −Tk−1
k −1
, k ≥2 T0
2 dx = T1
2 ,
T1dx = T0/2
2
+ T2
4 ,
Tkdx = 1
2
Tk+1
k + 1 −Tk−1
k −1
, k ≥2 from where from where Jk,k = 0, J0,1 = 1
2, Jk,k−1 = 1
2k = −Jk,k+1, k = 1, 2, .... Jk,k = 0, J0,1 = 1
2, Jk,k−1 = 1
2k = −Jk,k+1, k = 1, 2, .... For a general dom = [a, b] the above matrix J is multiplied by (b −a)/2. For a general dom = [a, b] the above matrix J is multiplied by (b −a)/2. fxn = barycheb(xn,fk,xk,kind) 844 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer As an important example, let us calculate the coeficients of a specific primitive F(x) of the
function f (x). We must then solve the initial-value problem As an important example, let us calculate the coeficients of a specific primitive F(x) of the
function f (x). We must then solve the initial-value problem dF
dx = f (x), y(−1) = α, x ∈[−1, 1]. If c are the Chebyshev coefficients of F and f are the coefficients of f, the equation is discretized
in spectral space as Dc = f. In order to implement the initial condition, we remark that If c are the Chebyshev coefficients of F and f are the coefficients of f, the equation is discretized
in spectral space as Dc = f. In order to implement the initial condition, we remark that y(−1) = c0
T0
2 + c1T1(−1) + c2T2(−1) + ... + cN−1TN−1(−1) = α can be written as Tc = α where T =
T0
2 , T1(−1), T2(−1), ..., TN−1(−1)
. This means that we can replace the last row of D by T and the last entry of f by α, thus
obtaining a new matrix D and a new vector f. Finally, c = D−1 f are the coefficients of the
specific primitive. p
p
The following code from level0 T=cpv(n,xc,dom) (chebyshev polynomial values) implements such conditions. Here xc is an arbitrary vector in
dom = [a, b] and cpv calculates the values of the Chebyshev polynomials Tk, k = 0, 1, .., n −1
at the column of nodes ξ (chebyshev polynomial values) implements such conditions. Here xc is an arbitrary vector in
dom = [a, b] and cpv calculates the values of the Chebyshev polynomials Tk, k = 0, 1, .., n −1
at the column of nodes ξ T = [T0/2, T1(ξ), T2(ξ), ..., TN−1(ξ)], ξ =
2xc
b −a −b + a
b −a, 1 ≤ξ ≤1. The code is based on the recurrence formulas of Chebyshev polynomials on [−1, 1] T0(x) = 1, T1(x) = x, Tk(x) = 2xTk−1(x) −Tk−2(x), k ≥2. The test code Chebpack\examples\ex_level0\quad_ex3 performs these calculations
for the special case y′ = cos x, y(0) = 0, with the solution y = sin(x). fxn = barycheb(xn,fk,xk,kind) The coefficients c are
obtained by using the differentiation matrix, cc are the coefficients of the exact solution, ccc
are obtained by using the integration matrix J and cccc are obtained by using the integration
matrix J0. The test code Chebpack\examples\ex_level0\quad_ex3 performs these calculations
for the special case y′ = cos x, y(0) = 0, with the solution y = sin(x). The coefficients c are
obtained by using the differentiation matrix, cc are the coefficients of the exact solution, ccc
are obtained by using the integration matrix J and cccc are obtained by using the integration
matrix J0. We also remark that if T=cpv(n,x,dom), f (x) = 0.5c0T∗
0 (x) + c1T∗
1 (x) + ... + cN−1T∗
N−1(x)
(10) (10) and c = (c0, ..., cN−1)T, we have f (x) = Tc, for x ∈[a, b]. The code cpv could be
used to transform between the spectral representation f of the function f and the physical
representation v = f (x) of values at the Chebyshev grid x, v = Tf, f = T−1v. v = Tf, f = T−1v. These transforms are performed by FFT in the codes x2t and t2x, but for a small dimension
N we may use this direct matrix multiplication. p
y
N we may use this direct matrix multiplication. 9
45 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems As another example, let us calculate the values at the grid points x of the specific primitive
which vanishes at a = dom(1) F(xi) =
xi
a
f (t)dt, i = 1, ..., n Starting with the values f = f (x) we have the Chebyshev coefficients T−1f , then J0T−1f are
the Chebyshev coefficients of the specific primitive on [a, b] and finally, F(x) = TJ0T−1f. (11) (11) Another code from level0 Another code from level0 X=mult(n,dom) X=mult(n,dom) calculates the sparse multiplication matrix X such that if f is the column vector of the
Chebyshev coefficients of a function f (x), then Xf is the column vector of the coefficients
of the function x f (x). The code is based on the formulas xT0 = T1, xT1(x) = T0
2 + T2
2 , ..., xTk(x) = Tk−1(x)
2
+ Tk+1(x)
2
, k ≥2 for x ∈[−1, 1]. Consequently, for x ∈[−1, 1]. from level0. The test code Chebpack\examples\ex_level0\fact_ex1.m calculates cosh(X) using
fact and funm from Matlab. We remark that X is a sparse matrix, so that funm must be
applied to full(X). 3. Chebpack, linear module At the first level – level1, the package contains subroutines to solve p
g
- initial and boundary value problems for high order linear differential equations - initial and boundary value problems for high order linear differential equations - initial and boundary value problems for high order linear differ y
p
g
- initial value problems for first order linear differential systems y
g
- initial value problems for first order linear differential systems
- linear integral equations - eigenvalues and eigenfunctions for differential problems. - discretization using the differentiation matrix D - discretization using the integration matrix J - splitting the interval dom = [d1, d2, ..., dp]. - splitting the interval dom = [d1, d2, ..., dp]. A=fact(a,m) A=fact(a,m) from level0. 3.1 Discretization using the differentiation matrix D g
The corresponding code is Chebpack\level1\ibvp_ode.m The corresponding code is Chebpack\level1\ibvp_ode.m [x,solnum]=ibvp_ode(n,dom,kind) fxn = barycheb(xn,fk,xk,kind) Consequently, Xk,k = 0, Xk,k−1 = Xk,k+1 = 1
2, k = 2, 3, ..., N −1,
X1,1 = 0, X1,2 = 1, XN,N−1 = 1
2. Then, in general, the coefficients of xp f (x) are given by Xpf and the coefficients of a(x) f (x)
are given by a(X)f for analytical functions a(x), where a(X) is the matricial version of the
function a. Moreover, if f (x)
xp
has no singularity at the origin, then its coefficients are X−pf. Of course, X is a tri-diagonal matrix, X2 is a penta-diagonal matrix and so on but, generally,
the matrix version funm(full(X))of the scalar function a(x) or X−p = [inv(X)]p are not
sparse matrices. For a general interval dom = [a, b], X is replaced by b−a
2 X + b+a
2 IN where IN
is the sparse unit matrix speye(N). p
Another method to calculate a(X) is to pass from the values a(x) at the Chebyshev grid x to
the Chebyshev coefficients a using x2t and to approximate a(x) ≈. a0
2 +
m−1
∑
k=1
akTk(x). (12) (12) Here m must be chosen sufficiently large, but m ≤N so that the known function a(x) is
correctly represented by a0, a1, ..., am−1. Here m must be chosen sufficiently large, but m ≤N so that the known function a(x) is
correctly represented by a0, a1, ..., am−1. y
p
y
0
1
m
1
der to calculate the coefficients of the product y
p
y
In order to calculate the coefficients of the product a(x) f (x) =
a0
2 +
m−1
∑
k=1
akTk(x)
⎛
⎝f0
2 +
n−1
∑
j=1
fjTj(x)
⎞
⎠ we may use the formula we may use the formula 1046 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Tj(x)Tk(x) =
Tj+k(x) + T|j−k|(x)
2
, ∀j, k. he needed coefficients are given by Af where the matrix A ≈a(X) is given by the code The needed coefficients are given by Af where the matrix A ≈a(X) is given by the code
A f
t(
) Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems A(n-1,:)=T(1,:)*D;b(n-1)=1;A(n,:)=T(2,:);b(n)=0;end
The program is called by p
g
y
[x,solnum]=ibvp_ode_test(32,[0 1],2);
\ p
g
y
[x,solnum]=ibvp_ode_test(32,[0 1],2); p
g
y
[x,solnum]=ibvp_ode_test(32,[0 1],2);
Other examples are coded in Chebpack\examples\ex_level1\ibvp_ode_ex*.m p
g
y
[x,solnum]=ibvp_ode_test(32,[0 1],2);
O h
l
d d
\
\
\ r examples are coded in Chebpack\examples\ex_level1\ibvp_ode_ex*.m
l f
f
l/b
d
l
bl
f
h
h
d
l
d ff Other examples are coded in Chebpack\examples\ex_level1\ibvp_ode_ex*.m
The general form for initial/boundary value problems for high order linear differential
equations is (1) and its discrete form is Ac ≡
m
∑
k=0
Pk(X)Dk
c = b where the unknown y is represented in the spectral space by its Chebyshev coefficients c,
while b are the Chebyshev coefficients of the r.h.s. f (x). where the unknown y is represented in the spectral space by its Chebyshev coefficients c,
while b are the Chebyshev coefficients of the r.h.s. f (x). e
e
e C e ys e
coe
c e
s o
e
s f ( )
We remark that the coefficients Pk(X) of the equation can y
f ( )
We remark that the coefficients Pk(X) of the equation can be defined in myDE - directly, for example Pk(x) = −x gives Pk(X) = −X
- using f unm, for example Pk(x) = sin x gives Pk(X) = f unm( f ull(X), @sin), i.e. using the
Taylor series of sin X - directly, for example Pk(x) = −x gives Pk(X) = −X
- using f unm, for example Pk(x) = sin x gives Pk(X) = f unm( f ull(X), @sin), i.e. using the
Taylor series of sin X y
- using f act, for example Pk(x) = cos x gives Pk(X) = f act(x2t(cos(x), kind), m), i.e. using the
Chebyshev series of cos X y
- using f act, for example Pk(x) = cos x gives Pk(X) = f act(x2t(cos(x), kind), m), i.e. using the
Chebyshev series of cos X y
- if Pk(x) is a constant, say Pk, then Pk(X) = Pk · speye(N). y
- if Pk(x) is a constant, say Pk, then Pk(X) = Pk · speye(N). y
The boundary conditions of the general type (2) are implemented using cpv. For example, for
y(x1c) −y′(x2c) + 2y′′(x3c) = yc we calculate T=cpv(N,[x1c,x2c,x3c],dom). One of the
last rows of A is replaced by T(1,:)-T(2,:)*D+2*T(3,:)* D^2 and the corresponding
entry of the vector b is replaced by yc. [x,solnum]=ibvp_ode(n,dom,kind) where n, dom, kind have the same significance as above, x is the Chebyshev grid and solnum
is the numerical solution in the physical space calculated at the grid x. The structure of ivp ode is function [x,solnum]=ibvp_ode(n,dom,kind) x=pd(n,dom,kind);X=mult(n,dom);D=deriv(n,dom); myDE;myBC;sol=A\b;solnum = t2x(sol,kind);myOUT;
end where myDE, myBC and myOUT must be written by the user and describe the differential
equation, the boundary conditions and the output of the program. For example, for the problem y′′′ −xy = (x3 −2x2 −5x −3)ex, x ∈[0, 1]
y(0) = 0, y′(0) = 1, y(1) = 0 we have
function myDE
A=D^3-X;b=x2t((x.^3-2*x.^2-5*x-3).*exp(x),kind);end
function myBC
T=cpv(n,dom,dom);A(n-2,:)=T(1,:);b(n-2)=0; we have
function myDE
A=D^3-X;b=x2t((x.^3-2*x.^2-5*x-3).*exp(x),kind);end
function myBC
T=cpv(n,dom,dom);A(n-2,:)=T(1,:);b(n-2)=0; 11
47 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems 3.2 Discretization using the integration matrix J The corresponding code is Chebpack\level1\ibvp_ode_int.m [x,solnum]=ibvp_ode_int(n,dom,kind) [x,solnum]=ibvp_ode_int(n,dom,kind) [x,solnum]=ibvp_ode_int(n,dom,kind) We remark that the discretization using the differentiation matrix D does not work well for
large N. For example, this type of discretization for the problem εy′′ + xy′ = −επ2cos(πx) −π x sin(πx), x ∈[−1, 1] , ε = 10−5,
(13)
y(−1) = −2, y(1) = 0 (13) with N = 2048 and an error about 5.46 × 10−11 leads us to a sparse system Ac = b but
with a sparsity factor about 25% that increases the computational time to 6.4 sec, see the
example ibvp_ode_ex.m in the folder Chebpack\examples\ex_level1. A better idea
is to integrate two times the above equation using the much more sparse integration matrix J. This integration make the coefficients c0 and c1 arbitrary and we may fix their values by using
the boundary conditions, this time at the first two rows of A and b. P
i
l
h fi
d h
d i
i
f h
i
(13)
i Precisely, the first and the second integration of the equation (13) gives εy′ + xy −
x
y =
x
−επ2cos(πx) −π x sin(πx)
εy +
x
xy −
x x
y =
x x
−επ2cos(πx) −π x sin(πx)
. The discrete form is
εIN + JX −J2
c
=
J2f where c are the Chebyshev coefficients
of the solution y and f are the Chebyshev coefficients of the r.h.s. The new code 1248 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer ibvp_ode_int_ex.m in the same folder as above gives the same accuracy for the same
N = 2048, but needing only 0.12 sec. The new matrix A has now a sparsity factor of about
0.2439% for the dimension 2048. This higher sparsity qualifies the integration method to be used for splitting the interval
dom = [a, b] into dom = [a, d1] ∪[d1, d2] ∪... ∪[dm−1, b] as well as for differential systems,
where the dimension N of matrices is multiplied by the number of subintervals or by the
number of differential equations in the system. We give the formulas for first order equations and a general formula. 3.2 Discretization using the integration matrix J For the first order we
have in myDE P1(x)y′ + P0(x)y = F =⇒P1(x)y −
P′
1(x)y +
P0(x)y =
F,
Ac ≡
P1(X) + J
P0(X) −P′
1(X)
c = Jf ≡b. Generally, if we denote the differentiation operator on functions P by dP, the identity operator
by I and the formal k power of the operator I −Jd by [ ](k), we obtain, after m integrations,
Ac = b where Generally, if we denote the differentiation operator on functions P by dP, the identity operator
by I and the formal k power of the operator I −Jd by [ ](k), we obtain, after m integrations,
Ac = b where y
Ac = b where A =
m
∑
k=0
Jm−k [I −Jd](k) Pk(X), b = Jmf. (14) (14) For example, for m = 3 we have
P0(x)y(x) →J3P0(X)c,
P1(x)y′(x) →J2
P1(X) −JP′
1 (X)
c,
P2(x)y′′(x) →J
P2(X) −2JP′
2 (X) + J2P′′(X)
c,
P3(x)y′′′(x) →
P3(X) −3JP′
3(X) + 3J2P′′
3 (X) −J3P′′′
3 (X)
c. It is important to remark that the absolute value of the Chebyshev coefficients gives us
some information about the necessary dimension N of the discretized problem in order
to capture the correct behavior of the solution. For example, let us consider the problem
ibvp_ode_int_ex2.m in the folder Chebpack\examples\ex_level1 εy′′ + (x2 −w2)y = 0, y(−1) = 1, y(1) = 2, x ∈[−1, 1] for w = 0.5, ε = 1.e −6. The command for w = 0.5, ε = 1.e −6. The command for w = 0.5, ε = 1.e −6. The command [x,solnum]=ibvp_ode_int_ex2(1024,[-1 1],2); gives the results in Fig. 2. We see that up to a dimension about N = 400, the algorithm cannot
resolve y accurately, due to its highly oscillatory behavior. After that, the Chebyshev series
begins to converge rapidly. For N = 1024 the elapsed time is about 0.05 sec. 3.3 Discretization using the integration matrix J and splitting the interval
The corresponding code is Chebpack\level1\ibvp_ode_split.m 1450 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer The boundary conditions are now the given boundary conditions say at d1 and d4
supplemented by smoothness conditions at d2, d3 y(1) (d2 −0) = y(2) (d2 + 0) , dy(1)
dx
(d2 −0) = dy(2)
dx
(d2 + 0) ,
(15)
y(2) (d3 −0) = y(3) (d3 + 0) , dy(2)
dx
(d3 −0) = dy(3)
dx
(d3 + 0) . (15) Of course, for a higher order equation (say m) we have coincidence conditions (15) until the
derivatives of order m −1. The given boundary conditions are implemented in the first m
rows of the first block-row of the matrix A and in the first entries of the first block of the
vector b, while the coincidence conditions are implemented in the first m rows of each of the
following block-rows of A and in the first m entries of each following block of b. The sparsity
structure of A with 4 subintervals is given in Fig. 3. Here we have 16 blocks of size 64 × 64, the Of course, for a higher order equation (say m) we have coincidence conditions (15) until the
derivatives of order m −1. The given boundary conditions are implemented in the first m
rows of the first block-row of the matrix A and in the first entries of the first block of the
vector b, while the coincidence conditions are implemented in the first m rows of each of the
following block-rows of A and in the first m entries of each following block of b. The sparsity
structure of A with 4 subintervals is given in Fig. 3. Here we have 16 blocks of size 64 × 64, the Fig. 3. The sparsity structure of the matrix A with boundary conditions implemented for 4
subintervals Fig. 3. The sparsity structure of the matrix A with boundary conditions implemented for 4
subintervals 4 diagonal segments come from the matrices A(i), i = 1, 2, 3, 4, the first horizontal segments
come from the given boundary conditions while the next 3 pairs of horizontal segments come
from connectivity conditions. Each block acts on the corresponding block coefficients c(i),
i = 1, 2, 3, 4. 3.3 Discretization using the integration matrix J and splitting the interval
The corresponding code is Chebpack\level1\ibvp_ode_split.m 3.3 Discretization using the integration matrix J and splitting the interval
The corresponding code is Chebpack\level1\ibvp_ode_split.m [x,solnum]=ibvp_ode_split(n,dom,kind) Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems 13
49 Fig. 2. The Chebyshev coefficients and the numerical solution for ex2 Fig. 2. The Chebyshev coefficients and the numerical solution for ex2 Sometimes, the solution of a differential problem has a different behavior in different
subintervals. For example, for small ε the solution of the problem (13) has a shock near the
origin and we need a very large N in order to capture its correct behavior. In these cases it is
better to split the working interval dom[a, b] into disjoint subintervals [d1, d2] ∪[d2, d3] ∪... ∪
[dp−1, dp] = [a, b] adapted to the behavior of the solution. The great advantage is to use a
small N for each subinterval. The partial solutions on each subinterval are connected by some
level of smoothness. Precisely, let us consider for example a second order differential problem on [a, b] and let
us split the interval as [a, b] = [d1, d2] ∪[d2, d3] ∪[d3, d4]. This splitting is given by dom =
[d1, d2, d3, d4] on input. If we calculate the basic ingredients xs, Xs, Ds, Js for the standard
interval [−1, 1], then for each subinterval [di, di+1], i = 1, 2, 3 the corresponding ingredients
become x = len ∗xs + med, X = len ∗Xs + med ∗IN, D = Ds
len, J = len ∗Js where len = di+1−di
2
, med = di+1+di
2
. 2
2
Using the matrix J for the discretization we obtain on each subinterval i
= 1, 2, 3 the
discretized form A(i)c(i) = b(i) where the matrix A(i) and the vector b(i) are given by (14)
as above, while c(i) are the Chebyshev coefficients of the solution y(i) on that subinterval i. Now, using the Kronecker product and the reshape command of Matlab, we build a large
(but very sparse) system Ac = b ⎛
⎝
A(1)
O
O
O
A(2)
O
O
O
A(3)
⎞
⎠
⎛
⎝
c(1)
c(2)
c(3)
⎞
⎠=
⎛
⎝
b(1)
b(2)
b(3)
⎞
⎠. 3.4 Linear first-order systems y
Let us consider a first order linear differential system for x ∈[a, b] Let us consider a first order linear differe P1(x)y′
1 + P11(x)y1 + ... + P1m(x)ym = f1(x), y1(a) = y1a,
P2(x)y′
2 + P21(x)y1 + ... + P2m(x)ym = f2(x) , y2(a) = y2a, ........................................... Pm(x)y′
m + Pm1(x)y1 + ... + Pmm(x)ym = fm(x), ym(a) = yma. If we denote by c = (c(1), ..., c(m))T the Chebyshev coefficients of y1(x), ..., ym(x) and by
f(1), ..., f(m) the coefficients of f1, ..., fm then the discretized version of the system is Ac = b
where A =
⎛
⎜
⎝
P1(X)D + P11(X) · · ·
P1m(X)
... ... ... Pm1(X)
· · · Pm(X)D + Pmm(X)
⎞
⎟
⎠, b =
⎛
⎜
⎜
⎝
f(1)
... f(m)
⎞
⎟
⎟
⎠. The initial conditions are implemented like in (15): the last row of each block in the above
matrix is replaced by T or zeros for the corresponding columns and the last entry of each block
in the r.h.s. is replaced by yka such that [O, ..., T, ..., O]c = yka for each k. The corresponding
code from level1 is [x,solnum]=ibvp_sys(n,dom,kind,y0) where y0 is the column vector of the initial values [y1a, ..., yma]T. Of course, we may use the
integration matrix J instead of D for discretization, obtaining again a system Ac = b where A =
⎛
⎜
⎝
P1(X) −JP′
1(X) + JP11(X) · · ·
JP1m(X)
... ... ... JPm1(X)
· · · Pm(X) −JP′m(X) + JPmm(X)
⎞
⎟
⎠, b =
⎛
⎜
⎜
⎝
Jf(1)
... Jf(m)
⎞
⎟
⎟
⎠ with the implementation of the initial conditions on the first row of each block,
see
ibvp_sys_ex3_int.m,
or
we
may
consider
systems
of
higher
order,
see
ibvp_sys_ex2x2.m from the folder Chebpack\examples\ex_level1. with the implementation of the initial conditions on the first row of each block,
see
ibvp_sys_ex3_int.m,
or
we
may
consider
systems
of
higher
order,
see
ibvp_sys_ex2x2.m from the folder Chebpack\examples\ex_level1. 3.3 Discretization using the integration matrix J and splitting the interval
The corresponding code is Chebpack\level1\ibvp_ode_split.m 4 diagonal segments come from the matrices A(i), i = 1, 2, 3, 4, the first horizontal segments
come from the given boundary conditions while the next 3 pairs of horizontal segments come
from connectivity conditions. Each block acts on the corresponding block coefficients c(i),
i = 1, 2, 3, 4. Using this technique for the problem (13) for example, the command from the folder Chebpack\examples\ex_level1 gives the numerical solution with an
accuracy of about 6 × 10−15 with four subintervals with N = 64 in only 0.014 sec. The new
matrix A has now a sparsity factor of about 3.2257% and the dimension 256. 15
51 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems 3.4 Linear first-order systems 3.4 Linear first-order systems [x,solnum]=volt_eq(n,dom,kind) from the folder Chebpack\level1. The folder Chebpack\examples\ex_level1
contains some examples in the files fred_eq_ex* and volt_eq_ex*. Of course, these codes work well only if the kernel K(x, t) is sufficiently smooth such that it
can be spectrally represented by an acceptable number of Chebyshev polynomials. from the folder Chebpack\level1. The folder Chebpack\examples\ex_level1
contains some examples in the files fred_eq_ex* and volt_eq_ex*. Of course, these codes work well only if the kernel K(x, t) is sufficiently smooth such that it
can be spectrally represented by an acceptable number of Chebyshev polynomials. 3.6 Eigenvalues/eigenfunctions for Sturm-Liouville problems
Let us consider now the second order spectral problem p
The corresponding model code from Chebpack is p
The corresponding model code from Chebpack is [x,solnum]=volt_eq(n,dom,kind) 3.5 Linear integral equations 3.5 Linear integral equations
Let us consider a Fredholm integral equation g
q
Let us consider a Fredholm integral equation Let us consider a Fredholm integral equation y(x) =
b
a K(x, t)y(t)dt + f (x) ≡A(y)(x) + f (x), x ∈[a, b]. (16) (16) The Fredholm integral operator A(y) becomes after discretization with shifted Chebyshev
polynomials A(y)(x) =
b
a K(x, t)
N−1
∑
k=0
ckT∗
k (t)dt =
N−1
∑
k=0
ck
b
a K(x, t)T∗
k (t)dt =
N−1
∑
k=0
ck · Ik(x) =
N−1
∑
k=0
ck
N−1
∑
j=0
kjkT∗
j (x) =
N−1
∑
j=0
N−1
∑
k=0
kjkck
T∗
j (x). 1652 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Consequently, if c = (c0, ..., cN−1)T are the coefficients of y, then Kc are the coefficients of
A(y), given by the matrix K = (kjk)j,k=0,...,N−1. Th
i K
b
l
l
d
i
f
h
h
i
l
l (y) g
y
( j )j,
, ,
The matrix K can be calculated starting from the physical values Ik(xs) =
b
a K(xs, t)T∗
k (t)dt =
N−1
∑
i=0
wiK (xs, xi) T∗
k (xi), s, k = 0, ..., N −1. In matrix form, this means In matrix form, this means (Ik(xs))k,s=0,...,N−1 = (K (xs, xi))s,i=0,...,N−1 · diag((wi)i=0,...,N−1) · T where T=cpv(n,x,dom) and then we apply x2t, see also (Driscoll, 2010). The Fredholm integral equation (16) becomes (IN −K)c = f where f are the Chebyshev
coefficients of f and we obtain the solution by solving this linear system. The corresponding
model code from the folder Chebpack\level1 is [x,solnum]=fred_eq(n,dom,kind) Similarly, for a Volterra integral equation Similarly, for a Volterra integral equation y(x) =
x
a K(x, t)y(t)dt + f (x) ≡A(y)(x) + f (x), x ∈[a, b] we obtain, using (11), for the Volterra integral operator A(y)(x) =
x
a K(x, t)y(t)dt =
TJ0T−1. ∗K(xi, xj)
y, where y are the values of y(x) at the grid points x. Consequently, the physical representation
of the Volterra integral operator is the matrix Vphys = TJ0T−1. ∗K(xi, xj), see again (Driscoll,
2010) while its spectral representation is Vspec = T−1VphysT. The Volterra integral equation
becomes in physical representation (IN −K)y = f where f are now the values of f at the grid
points x. 3.6 Eigenvalues/eigenfunctions for Sturm-Liouville problems
Let us consider now the second order spectral problem P2(x)y′′ + P1(x)y′ + P0(x)y = λR(x)y with homogeneous boundary value conditions as above. Using tau method, we get the
following N – dimensional matrix eigenproblem with homogeneous boundary value conditions as above. Using tau method, we get the
following N – dimensional matrix eigenproblem (P2(X)D2 + P1(X)D + P0(X))c = λR(X)c 17
53 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems of the form Ac = λBc. The conditions give Tc = 0 and combining these equations we derive
the generalized eigenproblem T
A
c = λ
1
λ∗T
B
c i.e. Ac = λ Bc where we retain only the first N rows of the matrices to obtain A and B. Here λ∗is chosen by
the user as a large and known value. We remark that for λ ̸= λ∗we get Tc = 0 as above but
now the matrix B behaves well. Consequently, the eigenproblem has instead of two infinite
eigenvalues two known λ∗eigenvalues that can be eliminated. The same procedure is applied
for higher order problems. g
p
The corresponding model code from the folder Chebpack\level1 is [lam,phi,x]=eig_ode2(n,dom,kind,numeigval) [lam,phi,x]=eig_ode2(n,dom,kind,numeigval) The folder Chebpack\examples\ex_level1 contains some other examples in the files
eig_ode2_ex*, eig_ode3_ex and eig_ode4_ex. An older package LiScEig is also freely
accessible at (Trif, 2005). 4. Chebpack, nonlinear module At the second level – level2, we have subroutines to solve - initial and boundary value problems for nonlinear differential equations
- nonlinear integral equations. - initial and boundary value problems for nonlinear differential equations
- nonlinear integral equations. g
q
Here the codes of the first level are used at each step of the Newton method applied in the
functional space. Another method could be the successive iteration method. 4.1 Successive iteration method Let us consider, as an example, the nonlinear Emden boundary value problem xy′′ + 2y′ = −xy5, y′(0) = 0, y(1) =
√
3
2 , x ∈[0, 1] . If the starting spectral approximation of y is, for example, Y0 = 1 then the discretization of the
problem is AY = F. Here A = XD2 + 2D and F = F(x, Y0) are the coefficients of the r.h.s. modified by using the boundary value conditions. We apply successively If the starting spectral approximation of y is, for example, Y0 = 1 then the discretization of the
problem is AY = F. Here A = XD2 + 2D and F = F(x, Y0) are the coefficients of the r.h.s. modified by using the boundary value conditions. We apply successively Yn+1 = A−1F(x, Yn), n = 0, 1, 2, ..., nmax. If Yn converges, then it converges to a solution of the bvp. If Yn converges, then it converges to a solution of the bvp. If Yn converges, then it converges to a solution of the bvp. The Matlab codes are ibvp_ode_succapprox.m from the folder Chebpack\level2 or
ibvp_ode_ex1.m from the folder Chebpack\examples\ex_level2. Of course, the discretization could be performed using the integration matrix J instead of D. Let us consider, for example, the Lotka-Volterra system If Yn converges, then it converges to a solution of the bvp. The Matlab codes are ibvp_ode_succapprox.m from the folder Chebpack\level2 or
ibvp_ode_ex1.m from the folder Chebpack\examples\ex_level2. Of course, the discretization could be performed using the integration matrix J instead of D. g
g
p
The Matlab codes are ibvp_ode_succapprox.m from the folder Chebpack\level2 or
ibvp_ode_ex1.m from the folder Chebpack\examples\ex_level2. ibvp_ode_ex1.m from the folder Chebpack\examples\ex_level2. Of course, the discretization could be performed using the integration matrix J instead of D. Let us consider, for example, the Lotka-Volterra system Of course, the discretization could be performed using the integration matrix J instead of D. Let us consider, for example, the Lotka-Volterra system y′
1 −Ay1 = −By1y2, y′
2 + Cy2 = By1y2, t ∈[0, 100]
y1(0) = y2 (0) = 0.5, A = 0.1, B = 0.2, C = 0.05. Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 1854 We transform this system to integral form We transform this system to integral form y1 −A
y1dt = −B
y1y2dt, y2 + C
y2dt = B
y1y2dt and the discretized form in spectral representation is In −AJ
0
0
In + CJ
Ynew
1
Ynew
2
=
−BJF
BJF
where F is the column vector of the coefficients of yold
1 (t)yold
2 (t) obtained by using t2x.m and
x2t.m. In this discretized form we implement the initial conditions as usually and we must
solve this system which has a sparsity factor of about 6% for n = 32 and about 3% for n = 64. For a long interval dom given as dom = [d0, d1, ..., dm], we apply the successive approximations
method at each subinterval. The initial approximation for the following subinterval is given
by the final values of the solution for the current subinterval. To test the numerical solution,
we remark that the Lotka-Volterra system has as invariant Λ = By1 + By2 −C log y1 −
A log y2. If Yn converges, then it converges to a solution of the bvp. The code is used by the command y
num]=ibvp_sys_succapprox(32,[0:10:100],2,[0.5,0.5]); g y
y
[x,solnum]=ibvp_sys_succapprox(32,[0:10:100],2,[0.5,0.5]);
and the result is given in Fig 4 with the value of the invariant Λ
0 303972077083 [x,solnum]=ibvp_sys_succapprox(32,[0:10:100],2,[0.5,0.5]);
and the result is given in Fig. 4, with the value of the invariant Λ = 0.3039720770839. [x,solnum] ibvp_sys_succapprox(32,[0:10:100],2,[0.5,0.5]);
and the result is given in Fig. 4, with the value of the invariant Λ = 0.3039720770839. Fig. 4. The solution of the Lotka-Volterra problem
In the case of nonlinear integral equations, for example
y(x) = f (x) +
b
K(x t y(t))dt Fig. 4. The solution of the Lotka-Volterra problem Fig. 4. The solution of the Lotka-Volterra problem
In the case of nonlinear integral equations, for example y(x) = f (x) +
b
0 K(x, t, y(t))dt, we perform successive iterations (if this method works) we perform successive iterations (if this method works) ynew(x) = f (x) +
b
0 K(x, t, yold(t))dt 19
55 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems starting with a suitable yold. For each x = xs in the grid and at each iteration, the integral is
evaluated as
b
n b
0 K(xs, t, yold(t))dt ≈
n
∑
k=1
wkK(xs, tk, yold(tk)), b
0 K(xs, t, yold(t))dt ≈
n
∑
k=1
wkK(xs, tk, yold(tk)), where {tk, k = 1, ..., n} is the Chebyshev grid on [0, b] and {wk, k = 1, ..., n} are the
corresponding weights. Consequently, we obtain where {tk, k = 1, ..., n} is the Chebyshev grid on [0, b] and {wk, k = 1, ..., n} are the
corresponding weights. Consequently, we obtain ynew(xs) =
n
∑
k=1
wkK(xs, tk, yold(tk)), s = 1, ..., n. Taking into account the nonlinearities, all the calculations are performed into the physical
space. Next, yold
←−
ynew until
ynew −yold
<
ε. The corresponding code is
ibvp_int_succapprox.m from the folder Chebpack\level2. Taking into account the nonlinearities, all the calculations are performed into the physical
space. Next, yold
←−
ynew until
ynew −yold
<
ε. The corresponding code is
ibvp_int_succapprox.m from the folder Chebpack\level2. which becomes in the discrete form We solve this equation in spectral form as in the previous section and the corrected value of y
is y0 + z. We repeat this step until convergence, i.e. until ∥z∥< ε. There are many examples
in the folder Chebpack\examples\level2. We solve this equation in spectral form as in the previous section and the corrected value of y
is y0 + z. We repeat this step until convergence, i.e. until ∥z∥< ε. There are many examples
in the folder Chebpack\examples\level2. which becomes in the discrete form [In + J (A(X) −JacF(X, Yn))] Z = −[Yn + JA(x)]Yn + JF(x, Yn). i.e AZ = B. In the l.h.s the matrix J (A(X) −JacF(X, Yn)) is calculated using the code fact.m. This code uses the physical values of A(x) −JacF(x, Yn) and converts them into spectral
coefficients. In the r.h.s the code also starts with the physical values and converts them into
their spectral coefficients. The initial conditions are implemented now in the rows 1, n + 1, .... Of course, this code ibvp_sys_newton.m from the folder Chebpack\level2 can be used
in a long-term integration algorithm that starts with the initial values ya1, yb1, calculates the
solution on [a, b], extracts the final values yb1, yb2 which become initial values for the same
code on a new interval [b, c] and so on. A short comparison between the successive approximations method (SA) and the Newton
method (N) for the example from ibvp_sys_newton_ex1 shows that, for the same n = 64,
dom = [0, 1, 2 : 2 : 200] and M = 8, [
]
SA: 2910 iterations, 3.4 sec elapsed time, 12940 Chebyshev coefficients calculated
N
490 i
i
6
l
d i
6475 Ch b
h
ffii
l
l
d [
]
- SA: 2910 iterations, 3.4 sec elapsed time, 12940 Chebyshev coefficients calculated
- N : 490 iterations, 6 sec elapsed time, 6475 Chebyshev coefficients calculated. - SA: 2910 iterations, 3.4 sec elapsed time, 12940 Chebyshev coefficients calculated
- N : 490 iterations, 6 sec elapsed time, 6475 Chebyshev coefficients calculated. In the case of a nonlinear integral equation (of Fredholm or Volterra) type SA: 2910 iterations, 3.4 sec elapsed time, 12940 Chebyshev coefficients calculated
N : 490 iterations, 6 sec elapsed time, 6475 Chebyshev coefficients calculated. 490 iterations, 6 sec elapsed time, 6475 Chebyshev coefficients calculated. p
y
In the case of a nonlinear integral equation (of Fredholm or Volterra) type P(y) ≡y(x) −
a K(x, t, y(t))dt −f (x) = 0, we start with an initial approximation y0 (in physical space) and at each Newton step we
obtain the linear equation for the correction z we start with an initial approximation y0 (in physical space) and at each Newton step we
obtain the linear equation for the correction z z(x) −
a
∂K
∂y (x, t, y0(t))z(t)dt = −y0(x) +
a K(x, t, y0(t))dt + f (x). 4.2 Newton method As above, Yn+1 = Yn + Z until ∥Z∥< ε. We remark that in the linear step we use the integration Z +
[A(x) −JacF(x, Yn)] Z = −
Y′
n + AYn −F(x, Yn)
4.2 Newton method Let us consider again a nonlinear differential problem of the form Ly(x) = f (x, y(x)), x ∈[a, b] where L is a linear differential operator, such as Ly(x) = xy′′(x) + 2y′(x) and f is the nonlinear
part. We have also the boundary or initial conditions BC/IC. If we denote by where L is a linear differential operator, such as Ly(x) = xy′′(x) + 2y′(x) and f is the nonlinear
part. We have also the boundary or initial conditions BC/IC. If we denote by P(y)(x) = Ly(x) −f (x, y(x)), BC/IC P(y)(x) = Ly(x) −f (x, y(x)), BC/IC the problem is of the form P(y)(x) = 0 where P is the operator of the problem and y is the
unknown. the problem is of the form P(y)(x) = 0 where P is the operator of the problem and y is the
unknown. The Newton method works as follows. Starting with an initial approximation y0(x) verifying
the initial or boundary conditions, we must solve at each step n the linear problem P′(yn)(yn+1 −yn)(x) = −P(yn)(x), for yn+1 −yn, with the corresponding homogeneous IC/BC. Next, yn+1 = yn + (yn+1 −yn)
and we perform these iterations until ∥yn+1 −yn∥< ε. For our problem, the linear step is for yn+1 −yn, with the corresponding homogeneous IC/BC. Next, yn+1 = yn + (yn+1 −yn)
and we perform these iterations until ∥yn+1 −yn∥< ε. For our problem, the linear step is L −∂f (x, yn(x))
∂y
(yn+1 −yn)(x) = −[Lyn(x) −f (x, yn(x))] . The corresponding code is ibvp_ode_newton.m from the folder Chebpack \level2. It
starts with y0(x) verifying or not the IC/BC and solves at each step the above linear problem
for yn+1 with the nonhomogeneous IC/BC. A nonlinear system (of order 2 for example) y′
1 + a11y1 + a12y2 = f1(x, y1, y2), x ∈[a, b]
y′
2 + a21y1 + a22y2 = f2(x, y1, y2), y1(a) = y1a, y2(a) = y2a is in matrix form Y′(x) + A(x)Y(x) = F(x, Y). At the linear step it becomes [Z′ + [A(x) −JacF(x, Yn)] Z = −
Y′
n + AYn −F(x, Yn)
Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 2056 where Z = Yn+1 −Yn is the correction, Yn ≡Y(xn) and JacF(x, Yn) =
∂f1(x,y1n,y2n)
∂y1
∂f1(x,y1n,y2n)
∂y2
∂f2(x,y1n,y2n)
∂y1
∂f2(x,y1n,y2n)
∂y2
. As above, Yn+1 = Yn + Z until ∥Z∥< ε. 5.1 Partial differential evolution equations ut = uxx, x ∈[−4, 2], t > 0
u(x, 0) = u(0)(x) ≡max(0, 1 −abs(x)),
u(−4, t) = 1, u(2, t) = 2. ut = uxx, x ∈[−4, 2], t > 0
u(x, 0) = u(0)(x) ≡max(0, 1 −abs(x)),
u(−4, t) = 1, u(2, t) = 2. First, we discretize in time by a backward finite difference on the grid 0 = t0 < t1 < ... < tK
starting with u(0)(x)
(k
)
(k) First, we discretize in time by a backward finite difference on the grid 0 = t0 < t1 < ... < tK
starting with u(0)(x) u(k+1)(x) −u(k)(x)
dt
= u(k+1)
xx
(x), where u(k)(x) = u(x, tk), u(k)
xx (x) = uxx(x, tk). We obtain the second order boundary value
problems in x where u(k)(x) = u(x, tk), u(k)
xx (x) = uxx(x, tk). We obtain the second order boundary value
problems in x
I −dt ∂2
∂x2
u(k+1)(x) = u(k)(x), u(k+1)(−4) = 1, u(k+1)(2) = 2. These problems, for each k = 1, 2, ..., K, are also discretized by the spectral Chebyshev method
with some N, dom = [−4, 2], kind as These problems, for each k = 1, 2, ..., K, are also discretized by the spectral Chebyshev method
with some N, dom = [−4, 2], kind as In −dtD2
c(k+1) = c(k), u(k+1)(−4) = 1, u(k+1)(2) = 2. Here c(k) are the Chebyshev spectral coefficients
c(k)
0 , c(k)
1 , ..., c(k)
N−1
of u(k) (x) corresponding
to the grid x1, ..., xN in dom. This way we may obtain the solution u(xj,tk) on the
computational grid
xj, tk
k=1,...,K
j=1,...,N. The corresponding code is pde_lin.m from the folder
Chebpack\level3. \
Similarly, for nonlinear equations of the form ut = Lu + Nu where L is a linear operator and
N a nonlinear one, for example for the Burgers equation ut = νuxx −
u2
2
x
, x ∈[−1, 1] , t > 0, ν = 0.01
π ,
u(x, 0) = sin πx, u(0, t) = u(1, t) = 0, u(x, 0) = sin πx, u(0, t) = u(1, t) = 0, we may take the backward Euler finite difference for the linear part while the forward Euler
finite difference for the nonlinear part. 5. Chebpack, experimental module Finally, the package contains an experimental level – level3, in progress, for
- partial differential equations of evolution type p
q
yp
- fractional differential equations (i.e. differential equations of non-integer order). 21
57 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems 5.1 Partial differential evolution equations
Let us consider, as a simple example, a problem from (Trefethen et al., 2011) 5.1 Partial differential evolution equations
Let us consider, as a simple example, a problem from (Trefethen et al., 2011) 5.1 Partial differential evolution equations we may take the backward Euler finite difference for the linear part while the forward Euler
finite difference for the nonlinear part. u(k+1)(x) −u(k)(x)
dt
= Lu(k+1)(x) + Nu(k)(x), We obtain We obtain (I −dt L) u(k+1)(x) = u(k)(x) + dt Nu(k)(x), u(k+1)(0) = u(k+1)(1) = 0 which is implemented in pde_nonlin.m. Of course, we may take the approximating solution in the physical representation on the grid
x1, ..., xn and the semidiscrete problem becomes u′(x, t) = Du(x, t) where D = TD2T−1 is
the physical second order derivative. The boundary value condition imposes u(x1, t) = α, 2258 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer u(xn, t) = β and therefore at these points we don’t need to satisfy the equation. Consequently,
if D = D (2 : n −1, 2 : n −1) is obtained by eliminating the first and last rows and columns
from D, the problem becomes u(xn, t) = β and therefore at these points we don’t need to satisfy the equation. Consequently,
if D = D (2 : n −1, 2 : n −1) is obtained by eliminating the first and last rows and columns
from D, the problem becomes u′(t) = D ∗ u(t) + D(2 : n −1, [1, n]) ∗BC, u(0) = u(0),
where BC = (α, β)T, i.e. u′(t) = D ∗ u(t) + b, u(0) = u(0) with the solution
u(t) = expm(t D) · u(0) + D−1 ·
expm(t D) −In−2
· b. u(t) = expm(t D) · u(0) + D−1 ·
expm(t D) −In−2
· b. Here expm(A) is the matricial exponential function of A. The code pde_lin_matr.m uses
this procedure Here expm(A) is the matricial exponential function of A. The code pde_lin_matr.m uses
this procedure. p
The same thing may be performed in spectral space. The problem u′ = L · u, u(0) = u0, BC = T · u u′ = L · u, u(0) = u0, BC = T · u (where L is a linear differential operator with constant coefficients and T is given by cpv from
level0) may be expanded as (where L is a linear differential operator with constant coefficients and T is given by cpv from
level0) may be expanded as u′
BC
=
L L
T T
·
u
u
. We obtain Therefore, successively, Therefore, successively, Therefore, successively, u′ = L u + L u, BC = T u + T u, u = T
−1
BC − T u
,
(17)
u′ =
L − L T
−1 T
u + L T
−1
BC, u′ = L · u + L · BC. (17) The exact solution of the last equation is given by The exact solution of the last equation is given by u (t) = et L · u0 + et L −I
L
L · BC and, using (17), u = ( u, u)T. This
procedure
is
coded
in
pde_lin_ex2.m
from
the
folder
Chebpack\examples\ex_level3. In the case of a nonlinear problem and, using (17), u
(u, u) . This
procedure
is
coded
in
pde_lin_ex2.m
from
the
folder
Chebpack\examples\ex_level3. In the case of a nonlinear problem and, using (17), u
(u, u) . This
procedure
is
coded
in
pde_lin_ex2.m
from
the
folder
Chebpack\examples\ex_level3. In the case of a nonlinear problem ,
g (
),
( , )
This
procedure
is
coded
in
pde_lin_ex2.m
from
the
folder
Chebpack\examples\ex_level3. I
th
f
li
bl In the case of a nonlinear problem u′ = L · u + Nu, u(0) = u0, BC = T · u the same procedure leads to the same procedure leads to u (t) = et L · u0 + et L −I
L
L · BC +
Nu and to the same u given by (17). This fixed point equation must now be solved using
successive iterations method (for t sufficiently small) or using Newton method. It is coded in and to the same u given by (17). This fixed point equation must now be solved using
successive iterations method (for t sufficiently small) or using Newton method. It is coded in 23
59 Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems pde_nonlin_ex4.m in the folder Chebpack\examples\ex_level3 for the Korteweg-de
Vries problem pde_nonlin_ex4.m in the folder Chebpack\examples\ex_level3 for the Korteweg-de
Vries problem ut + 6u ux + uxxx = 0, x ∈[−20, 20] , t ∈[0, 4]
u(x, 0) = 2sech(x)2, u(−20, t) = u(20, t) = ux(20, t) = 0. applied in a symmetric form applied in a symmetric form c = eLdt/2c(k) + eLdt/2 −I
L
N(c), c(k+1) = eLdt/2c + eLdt/2 −I
L
N(c). Here, the first fixed point problem is solved using successive iterations starting with c(k),
where c(k) are the Chebyshev coefficients of the numerical solution at the time level k. Here, the first fixed point problem is solved using successive iterations starting with c(k),
where c(k) are the Chebyshev coefficients of the numerical solution at the time level k. We obtain This problem of the form ut = Lu + N(u) is numerically solved in spectral space c′(t) =
Lc(t) + N(c(t)) by using the so called implicit exponential time differencing Euler method c(k+1) = eLdtc(k) + eLdt −I
L
N(c(k+1)), 5.2 Fractional differential equations Dphys times the vector of physical values of f gives the vector of physical values of Dq
∗f. For the spectral form,
1 Dspec =
1
Γ(1 −q) · T−1 · I · D, Dspec =
1
Γ(1 −q) · T−1 · I · D, i.e. Dspec times the vector T−1 f (x) of the coefficients of f gives the vector of the coefficients of
Dq
∗f. If q > 1 then let ex be [q] and q will be replaced by q −[q]. In this case, the differentiation
matrix will be
D
1
T−1
I D(ex+1) i.e. Dspec times the vector T−1 f (x) of the coefficients of f gives the vector of the coefficients of
Dq
∗f. If q > 1 then let ex be [q] and q will be replaced by q −[q]. In this case, the differentiation
matrix will be
1
1
(ex+1) Dspec =
1
Γ(1 −q) · T−1 · I · D(ex+1). In order to avoid the singularity of the fractional derivative Dq f if f (0) ̸= 0, we suppose that
f(0) = 0. The problem of computing the integrals In order to avoid the singularity of the fractional derivative Dq f if f (0) ̸= 0, we suppose that
f(0) = 0. The problem of computing the integrals Ik(x) =
x
0
Tk(αx −1)
(x −t)q
dt Ik(x) =
x
0
Tk(αx −1)
(x −t)q
dt for each x of the grid may be solved iteratively, see (Piessens & Branders, 1976). Indeed, we
have, by direct calculation, using the recurrence formula for Chebyshev polynomials, as well
as for the derivatives of the Chebyshev polynomials, for k = 3, 4, .. Ik(x) ·
1 + 1 −q
k
= 2 (αx −1) · Ik−1(x) +
1 −q
k −2 −1
· Ik−2(x) −2 (−1)k
k(k −2) x1−q and I0(x) = x1−q
1 −q /2, I1(x) =
αx2−q
(2 −q)(1 −q) −x1−q
1 −q,
I2(x) =
4α2x3−q
(3 −q)(2 −q)(1 −q) −
4αx2−q
(2 −q)(1 −q) + x1−q
1 −q. This recurrence is as stable as the recurrence which calculates the Chebyshev polynomials. The calculation of the fractional derivative matrix Dspec is coded in deriv_frac.m from the
folder Chebpack\level3. Next, if needed, Dphys =
1
Γ(1−q) · I · D(ex+1) · T−1 = T · Dspec · T−1. 5.2 Fractional differential equations The fractional derivative Dq f (x) with 0 < q < 1, 0 < x ≤b, in the Riemann-Liouville version,
is defined by (Podlubny, 1999) Dq f (x) =
1
Γ(1 −q)
d
dx
x
0
f (t)(x −t)−qdt while the Caputo fractional derivative is while the Caputo fractional derivative is Dq
∗f (x) =
1
Γ(1 −q)
x
0
f ′(t)(x −t)−qdt and we have and we have and we have
Dq f (x) = f (0)x−q
Γ(1 −q) + Dq
∗f (x). Dq f (x) = f (0)x−q
Γ(1 −q) + Dq
∗f (x). Let us consider a function f : [0, b] →IR, with the spectral representation
n−1
2 Let us consider a function f : [0, b] →IR, with the spectral representation f (x) =
n−1
∑
k=0
ckTk(αx + β), α = 2
b , β = −1 Using the spectral derivative matrix D, we have Using the spectral derivative matrix D, we have f ′(x) =
n−1
∑
k=0
(Dc)k Tk(αx + β) and using the linearity of the fractional derivative of order q ∈(0, 1), we obtain and using the linearity of the fractional derivative of order q ∈(0, 1), we obtain Dq
∗f (x) =
1
Γ(1 −q)
x
0
f ′(t)dt
(x −t)q =
1
Γ(1 −q)
n−1
∑
k=0
(Dc)k
x
0
Tk(αx + β)
(x −t)q
dt. 2460 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer By calculating the physical values of the above integrals in the columns k of a matrix I, each
row corresponding to a sample of x from the Chebyshev grid, the formula for the fractional
derivative is
1 By calculating the physical values of the above integrals in the columns k of a matrix I, each
row corresponding to a sample of x from the Chebyshev grid, the formula for the fractional
derivative is Dq
∗f (x) =
1
Γ(1 −q) · I · D · T−1 f (x) where T is the matrix given by cpv.m. This means that the Caputo fractional differentiation
matrix D in physical form is given by Dphys =
1
Γ(1 −q) · I · D · T−1 Dphys =
1
Γ(1 −q) · I · D · T−1 i.e. Dphys times the vector of physical values of f gives the vector of physical values of Dq
∗f. For the spectral form, i.e. 5.2 Fractional differential equations Using an idea of Sugiura & Hasegawa (Sugiura & Hasegawa, 2009), let J(s; f ) be This recurrence is as stable as the recurrence which calculates the Chebyshev polynomials. The calculation of the fractional derivative matrix Dspec is coded in deriv_frac.m from the
folder Chebpack\level3. Next, if needed, Dphys =
1
Γ(1−q) · I · D(ex+1) · T−1 = T · Dspec · T−1. Using an idea of Sugiura & Hasegawa (Sugiura & Hasegawa, 2009), let J(s; f ) be J(s; f ) =
s
0 f ′(t)(s −t)−qdt Matrix Based Operatorial Approach to Differential and Integral Problems
Matrix Based Operatorial Approach to Differential and Integral Problems 25
61 and, approximating f (t) by a combination pn(t) of Chebyshev polynomials on (0, 1) we have
the approximations |J(s; f ) −J(s; pn)| ∼O(nρ−n), for some ρ > 1. and, approximating f (t) by a combination pn(t) of Chebyshev polynomials on (0, 1) we have
the approximations |J(s; f ) −J(s; pn)| ∼O(nρ−n), for some ρ > 1. Of
thi
th d i
t
it bl
f
th
f
ti
ith
i
l
it
i
[0 1] and, approximating f (t) by a combination pn(t) of Chebyshev polynomials on (0, 1) we have
the approximations |J(s; f ) −J(s; pn)| ∼O(nρ−n), for some ρ > 1. Of course, this method is not suitable for the functions with a singularity in [0, 1] or
singularities of lower-order derivatives, like x0.1 for example. In this case, n must be
excessively large. pp
|J( ; f )
J( ; pn)|
( ρ
),
ρ
Of course, this method is not suitable for the functions with a singularity in [0, 1] or
singularities of lower-order derivatives, like x0.1 for example. In this case, n must be
excessively large. Of course, this method is not suitable for the functions with a singularity in [0, 1] or
singularities of lower-order derivatives, like x0.1 for example. In this case, n must be
excessively large. y
g
he initial value problems for fractional differential equations, let us consider the proble Dq
∗y(x) = x2 +
2
Γ(3 −q) x2−q −y(x), y(0) = 0, q = 0.5, x ∈[0, 1] . 5.2 Fractional differential equations The physical discretization is The physical discretization is Ay = b, A = T · DF · T−1 + IN, b = x2 + 2/Γ(3 −q) · x2−q where, in order to implement the initial condition, the first row of A is replaced by [1, 0, ..., 0]
and b(1) is replaced by 0. The solution is now y(x) = A−1B. The example is coded in
deriv_frac_ex1.m from the folder Chebpack\examples\ex_level3. If we use the spectral representation, for example for the problem Dqy(x) + y(x) = 1, y(0) = 0, y′(0) = 0, q = 1.8, x ∈[0, 5],
with the exact solution yex = xqEq,q+1(−xq), the spectral discretized form becomes
Ay ≡(Dq + In) y = T−1 · 1 = B,
A(
1 )
T(1 ) B(
1)
0 A(
)
T(1 )
D B( )
0 Dqy(x) + y(x) = 1, y(0) = 0, y′(0) = 0, q = 1.8, x ∈[0, 5], q+1(−xq), the spectral discretized form becomes Ay ≡(Dq + In) y = T−1 · 1 = B, Ay ≡(Dq + In) y = T
· 1 = B,
A(n −1, :) = T(1, :), B(n −1) = 0, A(n, :) = T(1, :) ∗D, B(n) = 0, A(n −1, :) = T(1, :), B(n −1) = 0, A(n, :) = T(1, :) ∗D, B(n) = 0, see deriv_frac_ex2.m For nonhomogeneous initial conditions like y(0) = c0, y′(0) = c1, we perform a function
change y(x) = c0 + c1x + z(x) where z verifies the same equation but with homogeneous
initial conditins (c0 + c1x disappears by differentiation), see deriv_frac_ex3.m. Examples
for discontinuous data, boundary value problems or eigenproblems are also given. 6. Conclusion The new package Chebpack (Trif, 2011) is a large and powerful extension of LiScEig (Trif, 2005). It is based on the Chebyshev tau spectral method and it is applied to linear and nonlinear
differential or integral problems, including eigenvalue problems. An experimental module
contains applications to linear or nonlinear partial differential problems and to fractional
differential problems. Each module is illustrated by many examples. A future version will
handle also piecewise functions as well as functions with singularities. p
g
owing comparisons with MATLAB codes bvp4c, bvp5c as well as with DMS or Chebfun
he efficiency of Chebpack. The elapsed time was evaluated after three code executions. The following comparisons with MATLAB codes bvp4c, bvp5c as well as with DMS or Chebfun
prove the efficiency of Chebpack. The elapsed time was evaluated after three code executions. The first test problem (test1.m in the folder Chebpack\tutorial) is p
y
p
p
The first test problem (test1.m in the folder Chebpack\tutorial) is −u′′ −1
6x u′ + 1
x2 u = 19
6 x1/2, u(0) = u(1) = 0, x ∈[0, 1] with the exact solution uex(x) = x3/2 −x5/2. The elapsed time and the errors are presented in
Table 1. Here Chebpack uses the differentiation matrix. The second test problem (test2.m in the folder Chebpack\tutorial) is (13) with ε = 10−4. The elapsed time and the errors are presented in Table 2. Here Chebpack uses the integration
matrix. The second test problem (test2.m in the folder Chebpack\tutorial) is (13) with ε = 10−4. The elapsed time and the errors are presented in Table 2. Here Chebpack uses the integration
matrix 2662 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer bvp4c
bvp5c
dms
Chebfun Chebpack
RelTol=1.e-5 RelTol=1.e-4 N=64 N=98
N=80
elapsed time (sec) 0.737
0.744
0.004 0.192
0.005
errors
3.2e-7
9.2e-8
2.3e-7 1.8e-7
4.6e-7
Table 1. Test 1
bvp4c
bvp5c
dms
Chebfun
Chebpack
default default N=1024 N=[13,114,109,14] N=1024
elapsed time (sec) 0.131
0.244
3.471
1.053
0.041
errors
8.6e-5
6.6e-6
8.4e-13 1.0e-12
1.e-14
Table 2. Test 2 Comparison of Methodologies for Analysis of
Longitudinal Data Using MATLAB
João Eduardo da Silva Pereira, Janete Pereira Amador
and Angela Pellegrin Ansuj
Federal University of Santa Maria
Brazil João Eduardo da Silva Pereira, Janete Pereira Amador
and Angela Pellegrin Ansuj
Federal University of Santa Maria
Brazil 7. References Berrut, J. P. & Trefethen, L. N. (2004). Barycentric Lagrange interpolation, SIAM Review
Vol.46(No.3): 501–517. (
)
Boyd, J. P. (2000). Chebyshev and Fourier Spectral Methods, Dover Publications, Inc. Canuto, C., Hussaini, M. Y., Quarteroni, A. & Zang, T. A. (1988). Spectral Methods in Fluid
Dynamics, Springer-Verlag, Berlin. y
p
g
g
Driscoll, T. A. (2010). Automatic spectral collocation for integral, integro-differential, and
integrally reformulated differential equations, J. Comp. Phys. Vol.229: 5980–5998. Mason, J. & Handscomb, D. (2003). Chebyshev Polynomials, Chapman & Hall/CRC Ortiz, E. L. & Samara, H. (1981). An operational approach to the tau method for the numerical
solution of non-linear differential equations, Computing Vol.27: 15–25. Piessens, R. & Branders, M. (1976). Numerical solution of integral equations of mathematical
physics, using Chebyshev polynomials, J. Comp. Phys. (1976) Vol.21: 178–196. p y
g
y
p
y
p
y
Podlubny, I. (1999). Fractional Differential Equations, Academic Press. Sugiura, H. & Hasegawa, T. (2009). Quadrature rule for Abel’s equations:
Uniformly
approximating fractional derivatives, J. Comp. Appl. Math. Vol.223: 459–468. Trefethen, L. N. (2000). Spectral Methods in MATLAB, SIAM, Philadelphia. Trefethen, L. N. (2000). Spectral Methods in MATLAB, SIAM, Philadelphia. Trefethen, L. N. (2008). Is Gauss quadrature better than Clenshaw–Curtis?, SIAM Review
Vol.50(No.1): 67–87. (
)
Trefethen, L. N. et al. (2011). Chebfun Version 4.0, The Chebfun Development Team. URL: http://www.maths.ox.ac.uk/chebfun/ Trif, D. (2005). LiScEig, MATLAB Central. URL: http://www.mathworks.com/matlabcentral/fileexchange/8689-lisceig Trif, D. (2011). Chebpack, MATLAB Central. URL: http://www.mathworks.com/matlabcentral/fileexchange/32227-chebpack p
fi
g
p
Waldvogel, J. (2006). Fast construction of the Fejér and Clenshaw–Curtis quadrature rules,
BIT Numerical Mathematics Vol.46: 195–202. p
fi
g
p
Waldvogel, J. (2006). Fast construction of the Fejér and Clenshaw–Curtis quadra
BIT Numerical Mathematics Vol.46: 195–202. Weideman, J. A. C. & Reddy, S. C. (2000). A MATLAB differentiation matrix su
URL: http://www.mathworks.com/matlabcentral/fileexchange/29-dmsuite Weideman, J. A. C. & Reddy, S. C. (2000). A MATLAB differentiation matrix suite
URL: http://www.mathworks.com/matlabcentral/fileexchange/29-dmsuite 4 1. Introduction In this context this work proposes to develop a single and easy computational
implementation to solve a great number of practical problems of analysis of longitudinal MATLAB – A Ubiquitous Tool for the Practical Engineer 64 data, through the decomposition of the sum of squares error of the polynomial models of
regression. In light of the above, not independents the computational support MatLab looks likes an
ideal tool for the implementation and dissemination of this kind of statistical analysis
methods, and linear models, first because its matrix structure fits perfectly well for linear
models which facilitates the construction of models for univariate and multivariate analysis,
and second because being a large diffusion tool of, it allows for that the models to be
implemented, modified and reused in several uses in different situations by several users
who have access to a MatLab community on the internet. This avoids the need for the
acquisition of expensive software with black box structure. 1. Introduction In several areas of scientific knowledge there is a need for studying the behavior
of one or more variables using data generated by repeated measurements of the same unit of
observations along time or spatial region. Due to this, many experiments are constructed in
which various treatments are applied on the same plot at different times, or only one
treatment is applied to an experimental unit and it is made a measurement of a
characteristic or a set of features in more than one occasion [Khattree & Naik, 2000]. Castro
and Riboldi [Castro & Riboldi, 2005] define data collected under these kinds of experimental
setups as repeated measures. More specifically, he asserts that “repeated measures is
understood as the data generated by repeatedly observing a number of investigation units
under different conditions of evaluation, assuming that the units of investigation are a
random sample of a population of interest”. In order to analyze repeated measures data it is
necessary to take a care about not independency between observations. This is so because it
is expected a high degree of correlation between data collected on the same observation unit
over time, and there is usually more variability in the measurements between the subjects
than within a given subject. A very common type of repeated measures is longitudinal data,
i.e., repeated measures where the observations within units of investigation were not or can
not have been randomly assigned to different conditions of evaluation, usually time or
position in space. There are basically two paths to be taken in the analysis of longitudinal data; univariate
analysis, which requires as a precondition a rigid structure of covariances, or multivariate
analysis, which, despite being more flexible, is less efficient in detecting significant
differences than the univariate methodology. In Advances in Longitudinal Data Analysis [Fitzmaurice et al., 2009], Fitzmaurice comments
that despite the advances made in statistical methodology in the last 30 years there has been
a lag between recent developments and their widespread application to substantive
problems, and adds that part of the problem why the advances have been somewhat slow to
move into the mainstream is due to their limited implementation in widely available
standard computer software. 2. Review As far as the analysis of experiments using longitudinal data is concerned the methods
traditionally used are: univariate analyis or Univariate Profile Model whereby longitudinal
data is considered as if it were observations done in subdivisions of the slots, usually
requiring that the variance of the response be constant in the occasions of evaluation and
that the covariance between responses in different occasions be equal; multivariate analysis
or Multivariate Profile Model whereby it is admitted that these variances and covariances be
distinct. Despite its apparent versatility, as far as the dimension of the matrix of variances
and covariances, the multivariate model becomes less attractive, because its results are hard
to interpret, and its estimates are not consistent. The univariate profile model gives
consistent estimates and should be used every time when its presuppositions are met. Otherwise, the multivariate profile model is a viable alternative [Castro & Riboldi, 2005;
Johnson & Wichern, 1998]. Using the univariate analysis in split-plot designs, regarding time as a sub-plot may cause
problems because, as it is known, this design presupposes that the covariance matrix meets
the condition of sphericity which does not always happen. What is found in the literature is
that repeated measures in one same experimental unit along time are in general correlated,
and that these correlations are greater for closer times [Malheiros, 1999]. Xavier [Xavier, 2000] asserts that a sufficient condition for the F test of the analysis of
variance of the sub-plots for the time factor and the interaction time*treatments, be valid, is
that the covariance matrix has a so called composite symmetry shape. The composite
symmetry occurs when the variance and covariance matrix may be expressed as: 2
2
2
2
2
(σ
σ )
σ
σ
σ
1
1
1
1
2
2
2
2
2
σ
(σ
σ )
σ
σ
1
1
1
1
2
2
2
2
2
σ
σ
(σ
σ )
σ
1
1
1
1
2
2
2
2
2
σ
σ
σ
(σ
σ )
1
1
1
1
(1)
where: (1) where: 2
σ
: is the variance of the sub-plot (within-subjects);
2
1
σ : is the variance of the plot (among-subjects). 2. Review 2
σ
: is the variance of the sub-plot (within-subjects); 2
σ
: is the variance of the sub-plot (within-subjects); 2
1
σ : is the variance of the plot (among-subjects). 2
1
σ : is the variance of the plot (among-subjects). The composite symmetry condition implies that the random variable be equally correlated
and has equal variances considering the different occasions. A more general condition of the The composite symmetry condition implies that the random variable be equally correlated
and has equal variances considering the different occasions. A more general condition of the 65 Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB is described by Huynh and Feldt [Huynh & Feldt, 1970]. This condition, called HUYNH-
FELDT (H-F) or sphericity condition (circularity), specifies that the elements of the
matrix be expressed for one λ
0,
as: is described by Huynh and Feldt [Huynh & Feldt, 1970]. This condition, called HUYNH-
FELDT (H-F) or sphericity condition (circularity), specifies that the elements of the
matrix be expressed for one λ
0,
as: 2
2
2
2
2
2
(σ
σ )
(σ
σ )
(σ
σ )
2
1
3
1
2
1
4
σ
λ
λ
λ
1
2
2
2
2
2
2
2
2
2
(σ
σ )
(σ
σ )
(σ
σ )
2
2
3
1
2
2
4
λ
σ
λ
λ
2
2
2
2
2
2
2
2
2
2
(σ
σ )
(σ
σ )
(σ
σ )
2
3
1
3
2
3
4
λ
λ
σ
λ
3
2
2
2
2
2
2
2
2
2
(σ
σ )
(σ
σ )
(σ
σ )
2
4
3
4
1
4
2
λ
λ
λ
σ4
2
2
2
(2) (2) where λ is the difference between the means of the variances and the means of the
covariances. The H-F condition is necessary and sufficient for the F test in the usual analysis of variance
in split-plot in time to be valid. 2. Review This condition is equivalent to specifying that the variances
of the difference between pairs of errors are equal, and if the variances are all equal then the
condition is equivalent to compound symmetry [Xavier, 2000]. To check the condition of circularity Mauchly [Mauchly, 1940] presents the test of sphericity. This test uses H-F condition for the covariance matrix of (t-1) normalized orthogonal
contrasts for repeated measures not correlated with equal variances. Vonesh and Chinchilli
[Vonesh & Chinchilli, 1997] state that the sphericity test is not very powerful for small
samples and is not robust when there is violation of the normality assumption. According to Box; Greenhouse & Geisser; and Huynh & Feldt [Box, 1954; Greenhouse &
Geisser, 1959; Huynh & Feldt, 1976], although the matrix may not satisfy the condition
of sphericity, the central F distribution may be used, in an approximate form, if a correction
in the degrees of freedom associated with the causes of variation involving the time factor is
made. The degrees of freedom correction in these sources of variation is done by
multiplying the original degrees by a factor . When is uniform, the value of =1. According to Freitas [Freitas, 2007] the correction of the number of degrees of freedom
should be made only in statistics that involve comparisons within subjects (time factor and
interaction time*treatments). The statistics involving comparisons between subjects do not
need corrections in the degrees of freedom because there is always an exact central F
distribution. When the pattern of the matrix is not satisfied, not even close, the multivariate
techniques are used since this type of solution is applicable to any matrix. The only
requirement of the multivariate procedure is that the matrix should be common to all
treatments. Due to the essentially multivariate nature of the response vectors, in studies involving
longitudinal data, the multivariate analysis technique also known as multivariate profile
analysis is a natural alternative to the problem at hand [Wald, 2000]. The multivariate
profile analysis is well discussed in the literature by authors such as [Lima, 1996; Morrison,
1990; Singer, 1986]. 66 MATLAB – A Ubiquitous Tool for the Practical Engineer The multivariate profile analysis is one of the statistics technique used to analyze
observations derived from experiments that use longitudinal data. This technique bases
itself both in the number of experimental units and the sample size [Castro, 1997]. 2. Review The multivariate profile analysis is one of the statistics technique used to analyze
observations derived from experiments that use longitudinal data. This technique bases
itself both in the number of experimental units and the sample size [Castro, 1997]. Unlike the univariate profile analysis model, the multivariate profile analysis model does
not require that the variance of the repeated measures or that the correlation between pairs
of repeated measures remain constant along time. Nevertheless, both models require that
the variances and the correlations be homogeneous in each moment in time [Vieira, 2006]. g
The routine techniques for analysis of variance impose the condition of independence of
observations. However, this restriction generally does not apply to longitudinal data where
the observations in the same individual are usually correlated. In such case, the adequate
manner for treating the observations would be the multivariate form [Vonesh & Chinchilli,
1997]. ]
Cole & Grizzle [Cole & Grizzle, 1966] use the multivariate analysis of variance according to
the Smith et al. [Smith et al., 1962] formulation and comment on its versatility in the
construction of specific hypothesis testing that may be obtained as particular cases of the
general linear multivariate hypothesis test procedure. They assert that such hypothesis may
be tested by three alternative criterions, all of which dependent on characteristic roots of
matrix functions due to the hypothesis and of the matrix due to the error: criterion of the
maximum characteristic root, criterion of the product of the roots (criterion of the
verosimilarity ratio) and criterion of the sum of the roots. The authors illustrate the
application of the multivariate analysis of variance and demonstrate that the information
requested from these experiments may be formulated in terms of the following null
hypotheses: yp
i. there are no principal effects of “measured conditions” (occasions); yp
i. there are no principal effects of “measured conditions” (occasions); ii. there are no effects of treatments; iii. there is no interaction of treatment and occasions. The multivariate analysis of variance is a powerful instrument to analyze longitudinal data
but if the uniformity hypothesis of the variance and covariance matrix is not rejected the
univariate analysis should be employed. Nonetheless, if the variance and covariance matrix The multivariate analysis of variance is a powerful instrument to analyze longitudinal data
but if the uniformity hypothesis of the variance and covariance matrix is not rejected the
univariate analysis should be employed. 2. Review Nonetheless, if the variance and covariance matrix of repeated measures has the serial correlation structure one should use an analysis method
that takes into account the structure of this matrix in order that one might have an
increment in the testing power. In this way the multivariate analysis of variance becomes
the most convenient one if not the only appropriate one among the available procedures
[Cole & Grizzle, 1966; Smith et al., 1962]. Lima [Lima, 1996] asserts that the multivariate profile analysis possesses as its main
advantage the fact that is allows for the adoption of a very general model to represent the
structure of covariances admitting that the variances of responses in each time and the
covariances of responses between distinct times be different. p
In studying longitudinal data investigation methods, Greenhouse & Geisser [Greenhouse &
Geisser, 1959] observed that the ratios between the mean squares obtained in the analysis of
variance for the mixed univariate model will only have exact distribution of probability F if
the observations in time be normally distributed with equal variances and be mutually
independent or equally correlated. Because these presuppositions are strict, the authors
prefer considering the observations in time as a vector of samples of a normal multivariate
distribution with an arbitrary variance and covariance matrix. Being so, the multivariate
perspective presented by Morrison [Morrison, 1990] allows for the adoption of a general
model to represent the covariance structure of the observations. In this case, the covariance 67 Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB matrix is known as being non structured where all variances and covariances might be
different and, as pointed out by Andreoni [Andreoni, 1989], it is only applicable when: p
y
[
]
y pp
there be no theoretical or empirical basis to establish any pattern for this matrix; p
y
y pp
-
there be no theoretical or empirical basis to establish any pattern for this matrix;
-
there be no need to extrapolate the model beyond the occasions of the considered
observations. The quantity of parameters associated with the non structured matrix that need to be
estimated is proportional to the number of conditions of evaluation. 3.1 Data In order to conduct the study it was created a data matrix with the following structure:
ijk
Y
y
, where
ijk
y
is the observation j belonged the period i of the treatment k. To simulate
growth curves composed of two treatments, seven observations over time and five
repetitions, each observation of Y matrix was defined as
ijk
y
=
i
ijr
f
with a fixed part
if ,
with i = 1,2, and where
2
1
46
88
57
f
X
X
and
2
2
42
88
53
f
X
X
and a variable
portion
ijk
randomly generated with normal distribution with zero mean and variance
proportional to E(
if ) in which the variation coefficient remains constant in 0,05, under
these conditions is imposed on the model
1f a linear growth higher than compared to the
2f model and both with the same regression model. 2. Review In situations where the
number is large, when the number of experimental units is small in relation to the number
of evaluation events or when there is the presence of many incomplete observations the
efficiency of the estimators might be affected. In some cases it may be impossible to estimate
the parameters of this covariance matrix [Wald, 2000]. Meredith & Stehman [Meredith & Stehman, 1991] state that the disadvantage of the
multivariate analysis is the lack of power to estimate the parameters of the covariance
matrix in case when t (number of measurement events or times) is large and n is small. multivariate analysis is the lack of power to estimate the parameters of the covariance
matrix in case when t (number of measurement events or times) is large and n is small. Stuker [Stuker, 1986] comments on the restriction of the multivariate analysis of covariance
in which the number of experimental units minus the number of treatments should be
greater than the number of observations taken in each experimental unit otherwise the
required matrix due to error for these tests is singular. Stuker [Stuker, 1986] comments on the restriction of the multivariate analysis of covariance
in which the number of experimental units minus the number of treatments should be
greater than the number of observations taken in each experimental unit otherwise the
required matrix due to error for these tests is singular. Timm [Timm, 1980] claims that the restrictions to the application of the multivariate profile
analysis occur due to the need for complete individual response profiles and to the low
power of these hypothesis tests due to excessive parametering. On the other hand, except for
these restrictions, the majority of the cases in longitudinal data studies, the analysis
procedure of multivariate analysis of variance is the most convenient if not the only
appropriate one among the available techniques. 3.1.1 Data base structure To analyze the longitudinal data, the data base was structured in the following way; the
first column refers to the independent variable X
[x ]i
or to periods with i
1...p
, the
second column the response variable Y
[y
]
ijk
, in which
ijk
y
, refers to the observation
referring to the repetition j of the period i of treatment k, with j
1...r
., and the third
column refers to the control variable F
[f ]
k
or treatments, with
1... j
t
. MATLAB – A Ubiquitous Tool for the Practical Engineer 68 File.txt=
1
y
1
111
. y
. 121
. . . . . . p
y
t
prt
(3) File.txt=
1
y
1
111
. y
. 121
. . . . . . p
y
t
prt
(3) File.txt=
1
y
1
111
. y
. 121
. . . . . . p
y
t
prt
(3) (3) The following Matlab commands upload and dimension the file in addition to determining
the index of the column of each variable. [n,c]=size(M); a=input('column of the independent variable X =');
b=input('column of the dependent variable Y =');
aa=input('initial column of the control variable curve =');
nc=input('number of curves to be compared =');
npc=input('number of points per curve ='); b=input('column of the dependent variable Y ='); aa=input('initial column of the control variable curve ='); p
(
nc=input('number of curves to be compared ='); 3.2 Data analysis y
Once the data base is correctly structured the first step is to adjust the best polynomial model
that explains the variation of Y in function of the X periods. Towards this, the parameters of
the polynomial of adjustment will be estimated by the matrix expression below. ˆY
BX
(4)
β
[bo
b
.... b ]
g
1
(5)
nomial
g
2 ˆY
BX
(4)
β
[bo
b
.... b ]
g
1
(5) (4) ˆY
BX
(5) in which g is a degree of the polynomial in which g is a degree of the polynomial g
2
X
[1
x
x . . . x ]
i
i
i
(6)
1
ˆ g
2
X
[1
x
x . . . x ]
i
i
i
(6)
1
ˆβ
(X'X)
(X'Y)
(7) (6) 1
ˆβ
(X'X)
(X'Y)
(7) (7) To determine what is the best degree of the polynomial for the data under analysis it was
used a scatterplot. The following commands prepare the data for visualization. M(
(b 1)) To determine what is the best degree of the polynomial for the data un
used a scatterplot. The following commands prepare the data for visualiz
x=M(:,a:(b-1));
Y=M(:,b:(aa-1));
Trat=M(:,aa);
M=[x Y Trat];
[tmp,idx]=sort(M(:,aa));
M=M(idx,:),
set(plot(x,Y,'o'))
From the scatterplot, choose the degree of polynomial to be adjusted. g=input('choose the degree of polynomial Degree =');
The following procedures were used to estimate ˆ
[n,r]=size(M);
X=ones(n,npc); Y=M(:,b:(aa-1)); Trat=M(:,aa); M=[x Y Trat]; [tmp,idx]=sort(M(:,aa)); M=M(idx,:), set(plot(x,Y,'o')) From the scatterplot, choose the degree of polynomial to be adjusted
g=input('choose the degree of polynomial Degree ='); The following procedures were used to estimate ˆ The following procedures were used to estimate ˆ
[n,r]=size(M); [n,r]=size(M); X=ones(n,npc); Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB 69 X X(:,1:(d+1));
BT=(inv((X'*X)))*(X'*(M(:,b:aa-1)));
T t
t th h
th
i
0
H
i
t
0
H
th F t
t i
l
d ( , (
));
inv((X'*X)))*(X'*(M(:,b:aa-1))); ( , (
));
BT=(inv((X'*X)))*(X'*(M(:,b:aa-1))); (
(
))
BT=(inv((X'*X)))*(X'*(M(:,b:aa-1))); To test the hypothesis:
0 :
0
H
against
1 :
0
H
, the F test is employed. To test the hypothesis:
0 :
0
H
against
1 :
0
H
, the F test is employed. 3.2 Data analysis QMr
F
QMε
(8) QMr
F
QMε
(8) QMr
F
QMε
(8) that have the Snedecor F distribution with (g-1) and (n-g) degrees of freedom. at have the Snedecor F distribution with (g-1) and (n-g) degrees of freedom. 1
2
QMr
β(X'Y)
nY
(g
1)
(9) (9) 1
QMε
[(Y'Y)
β(X'Y)]
(n
g)
=
1
(n
g)
ˆ
ˆ
(Y
Y)'(Y
Y)
(10) (10) And to measure the degree of explanation of the variability of Y according to the polynomial
model it is used the coefficient of determination. And to measure the degree of explanation of the variability of Y according to the polynomial
model it is used the coefficient of determination. SQr
2
R
SQT
(11)
2
SQr
β(X'Y)
nY
(12)
2
SQT
(Y'Y)
nY
(13) SQr
2
R
SQT
(11)
2
SQr
β(X'Y)
nY
(12)
2
SQT
(Y'Y)
nY
(13) SQr
2
R
SQT
(11) (11) 2
SQr
β(X'Y)
nY
(12)
2
SQT
(Y'Y)
nY
(13) (12) 2
SQT
(Y'Y)
nY
(13) (13) And to measure the degree of explanation of the Y variability in function of the polynomial
model it is employed the determination coefficient. And to measure the degree of explanation of the Y variability in function of the polynomial
model it is employed the determination coefficient. SQr
2
R
SQT
(14) SQr
2
R
SQT
(14)
in which SQr
2
R
SQT
(14) in which in which 2
SQr
β(X'Y)
nY
(15) 2
SQr
β(X'Y)
nY
(15)
and (15) and and 2
SQT
(Y'Y)
nY
(16) 2
SQT
(Y'Y)
nY
(16) After the adjustment of the polynomial model for the data set, the next step is to adjust the
same model for each of the k treatments separately, so MATLAB – A Ubiquitous Tool for the Practical Engineer 70 1
ˆY
(X'X)
(X'Y )
k
k
(17) 1
ˆY
(X'X)
(X'Y )
k
k
(17) Where 1
ˆb
(X'X)
(X'Yk)
k
(18) (18) The test for comparing the curves is based on the decomposition of SQε in one part
explained by the variation between the curves and the other by the variation within the
curves. 3.2 Data analysis The test for comparing the curves is based on the decomposition of SQε in one part
explained by the variation between the curves and the other by the variation within the
curves. SQε =
t
ˆ
ˆ
ˆ
ˆ
(Y
Yk)'(Y
Yk)
k
1
+
t
ˆ
ˆ
(Yk
Yk)'(Yk
Yk)
. k
1
(19) (19) in which
t
K 1
ˆ
ˆ
ˆ
ˆ
(Y
Yk)'(Y
Yk)
is the variation explained by the treatments, and
1
t
K
ˆ
ˆ
(
)'(
)
. Yk
Yk
Yk
Yk
is the variation within each treatment. And the
t
ˆ
ˆ
ˆ
((Y
Yk)'(Y
Yk))(n
t)(p
1)
k 1
F
t
ˆ
ˆ
((Y
Yk)'(Y
Yk))(p
1)(t
1)
K 1
(20) (20) has a Snedecor F distribution with (
1)(
1)
p
t
and (n
t)(p
1)
degrees of freedom. And the reason
t
ˆ
ˆ
ˆ
((Y
Yk)'(Y
Yk))(n
t)(p
1)
k 1
F
t
ˆ
ˆ
((Y
Yk)'(Y
Yk))(p
1)(t
1)
K 1
(21) (21) Has a Snedecor F distribution with (p
1)(t
1)
and (n
t)(p
1)
degrees of freedom. Has a Snedecor F distribution with (p
1)(t
1)
and (n
t)(p
1)
degrees of freedom. The following commands calculate the regression parameters for the individual curves. [c,r]=size(M1); The following commands calculate the regression parameters for the individual curves. [c,r]=size(M1); [c,r]=size(M1);
Yobs(:,i)=M1(:,b)
X=ones(c,npc);
y1=ones(c,1);
for j=2:npc
X(:,j)=M1(:,a).*y1;
y1=X(:,j);
end
Y=M1(:,b);
X=X(:,1:(d+1));
B(:,i)=(inv((X'*X)))*(X'*Y);
Y1est(:,i)=X*BT;
end 71 Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB The following commands print the graph with the curves estimated. Yest=X*B;
y=[Y1est Yest];
x=X(:,b);
plot(x,y)
The following commands execute analysis of variance. [n,c]=size(M)
SQmodelo=sum(sum((Y1est-Yest).*(Y1est-Yest)))
SQerro=sum(sum((Yest-Yobs).*(Yest-Yobs)))
SQtotal=sum(sum((Y1est-Yobs).*(Y1est-Yobs)))
glmodelo=(npc-1)*(nc-1)
gltotal=(n-nc)
glerro=gltotal-glmode
R=(SQmodelo/SQtotal)
F=(SQmodelo/glmodelo)/(SQerro/glerro)
p=fpdf(F,glmodelo,glerro)
The following commands format the ANOVA Table printout. Table=zeros(3,5);
Table(:,1)=[ RSS SSE TSS]';
Table(:,2)=[df1 df2 df3]';
Table(:,3)=[ RSS/df1 SSE/df2 Inf ]';
Table(:,4)=[ F Inf Inf ]';
Table(:,5)=[ p Inf Inf ]';
colheads = ['Source ';' SS ';' df ';... 3.2 Data analysis ' MS ';' F ';' Prob>F '];
atab = num2cell(Table);
for i=1:size(atab,1)
for j=1:size(atab,2)
if (isinf(atab{i,j}))
atab{i,j} = [];
end
end
end
if (nargout > 1)
anovatab = atab
end
The following commands prepare the file for the multivariate analysis. M=[X Yobs];
nt=M(:,2);
x=nt(1); The following commands print the graph with the curves estimated. Yest=X*B; The following commands print the graph with the curves estimated. [
' MS ';' F ';' Prob>F ']; atab = num2cell(Table); if (nargout > 1) anovatab = atab end The following commands prepare the file for the multivariate analysis. M [X Y b ] M=[X Yobs];
nt=M(:,2);
x=nt(1);
n=1;
idx=1;
for i=2:length(nt)
if nt(i)==x(idx)
n(idx)=n(idx)+1;
else M=[X Yobs];
nt=M(:,2);
x=nt(1);
n=1;
idx=1;
for i=2:length(nt)
if nt(i)==x(idx)
n(idx)=n(idx)+1;
else (
)
x=nt(1); n=1; idx=1; else MATLAB – A Ubiquitous Tool for the Practical Engineer 72 idx=idx+1;
x(idx)=nt(i);
n(idx)=1;
end
n=cumsum(n);
B=ones(d+1,nc);
for i=1:length(n)
idx=find(M(:,aa)==M(n(i),aa));
M2=M(idx,:);
end For the multivariate analysis it was employed a new structure of the data file. File2.txt=
1
[
. . . ]
jk
jk
pjk
x
y
y
File2.txt=[X Y] In which, the first column has the values for the j repetitions for each of the k treatments,
each one of the following i columns contains the values of Y for the j repetitions of the k
treatments. As seen in the structure below. x
y
. . . . . y
11
111
711
x
y
. . . . . y
21
121
721
x
y
. . . . . y
31
131
731
x
y
. . . . . y
41
141
741
x
y
. . . . . y
51
151
751
File2.txt
x
y
. . . . . y
12
112
712
x
y
. . . . . y
22
122
722
x
y
. . . . . y
32
132
732
x
y
. . . . . y
42
142
742
x
y
. . . . . y
52
152
752
(22) (22) The following commands change the structure of the file. 3.2 Data analysis g
g
M=Mtemp;
[n,c]=size(M);
nt=M(:,1);
z=nt(1);
n=1;
idx=1;
for i=2:length(nt);
if nt(i)==z(idx)
n(idx)=n(idx)+1;
else
idx=idx+1;
z(idx)=nt(i);
n(idx)=1;
end M=Mtemp;
[n,c]=size(M);
nt=M(:,1);
z=nt(1);
n=1;
idx=1;
for i=2:length(nt);
if nt(i)==z(idx)
n(idx)=n(idx)+1;
else
idx=idx+1;
z(idx)=nt(i);
n(idx)=1;
end M=Mtemp;
[n,c]=size(M);
nt=M(:,1);
z=nt(1);
n=1;
idx=1;
for i=2:length(nt);
if nt(i)==z(idx)
n(idx)=n(idx)+1;
else
idx=idx+1;
z(idx)=nt(i);
n(idx)=1;
end Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB 73 end end n=cumsum(n); for i=1:npc M1=M(idx,:); trat=M1(:,aa); M1=M1(:,b); (
)
Ymult(:,i)=M1; (
)
Ymult(:,i)=M1; end Y=[trat Ymult]; Y=[trat Ymult]; [
]
For the multivariate data analysis the employed procedure was proposed by Johnson and
Wishern [Johnson and Wishern, 1998] in which the standardized variable employed for the
comparison of the curves is W
Wp
(23) (23) in which W
(X'
- X'
)' * (X'
- X'
)
T
T
(24) in which W
(X'
- X'
)' * (X'
- X'
)
T
T
(24) in which W
(X'
- X'
)' * (X'
- X'
)
T
T
(24) (24) 10
20
11
21
12
22
b
b
b
b
bdk
b
b
(25) (25) where bdk
is the polynomial coefficient of d order of the k treatment. 3.2 Data analysis 1
1
1
(
'
)
(
'
)
X S
X
X S
Y
(26)
1 (
)'(
)
(
)
S
Y
Y
Y
Y
rt
(27)
W
(Y - X' T)' * (Y - X' T)
p
(28)
1
1
1
(
'
)
(
'
)
T
X S
X
X S
Y
p
p
(29)
1
2
(
1)
(
)
1
t
S
n
S
p
k
k
n
t K
(30) 1
1
1
(
'
)
(
'
)
X S
X
X S
Y
(26)
1 (
)'(
)
(
)
S
Y
Y
Y
Y
rt
(27) (26) (27) W
(Y - X' T)' * (Y - X' T)
p
(28)
1
1
1
(
'
)
(
'
)
T
X S
X
X S
Y
p
p
(29)
1
2
(
1)
(
)
1
t
S
n
S
p
k
k
n
t K
(30) (28) (29) (30) Where
2
. .cov
. . . . S
matrix of
ariance of the treatment k
k
In order to test if there is a difference between curves the standardized variable is employed Where
2
. .cov
. . . . S
matrix of
ariance of the treatment k
k
In order to test if there is a difference between curves the standardized variable is employed Where k
In order to test if there is a difference between curves the standardized variable is employed In order to test if there is a difference between curves the standardized variable is employed 2
1
ln
2
N
p
d
t
(31) (31) MATLAB – A Ubiquitous Tool for the Practical Engineer 74 74 has a chi square distribution with (p-q-1) degrees of freedom. The following commands run the multivariate analysis. temp=M(:,b:c); Y1obs=temp'; V=cov(temp); S=inv(V); temp=(sum(temp))./n; Y=temp; [n,c]=size(V); X=ones(n,c); y1=X(:,i); end d=input('choose the polynomial degree ='); X=X(:,1:(d+1)); BT=(inv(X'*S*X))*(X'*S*Y'); (
(
Y1est=X*BT; Y1est=temp; 75 Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB 4. Results The following parameters must be furnished when running the program: The following parameters must be furnished when running the program:
independent variable column X =1
dependent variable column Y =2
initial column of the control variable curve =3
number of curves to be compared =2
number of points per curve =7 The following parameters must be furnished when running the program:
independent variable column X =1
dependent variable column Y =2
initial column of the control variable curve =3
number of curves to be compared =2
number of points per curve =7 MATLAB – A Ubiquitous Tool for the Practical Engineer 76 The following graph is generated in order to choose the degree of the polynomial to be
adjusted. The following graph is generated in order to choose the degree of the polynomial to be
adjusted. Fig. 1. Scatterplot of the data. Fig. 1. Scatterplot of the data. A second degree polynomial was chosen to model the data according to the scatterplot
above. The estimated coefficients for the second order polynomial were: The estimated coefficients for the second order polynomial were: 2
ˆ
48.464
81965
56.806
T
Y
X
X
] with (P<0000,1) with (P<0000,1) 2
0.3405
R 2
0.3405
R he analysis of variance of the complete polynomial model is presented in table 1. The analysis of variance of the complete polynomial model is presented in table 1. Causes of variation
DF
SS
SQ
F
P
Polynomial
2
5.2799E+007
2.6384E+007
3.8235E+003
1.2054E-072
Error
68
4.6924E+005
6.9006E+003
Total
69
5.3238E+007 Table 1. ANOVA for polynomial model Table 1. ANOVA for polynomial model The output of the program has the following format
anovatab1 = The output of the program has the following format
anovatab1 = Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB MATLAB – A Ubiquitous Tool for the Practical Engineer 78 The output of the program has the following format: The output of the program has the following format: p
p
g
g
B = 50.3069 46.9023
89.0928 76.8230
57.0744 56.5484 After the choice of the polynomial model and its test of significance, the same model was
applied on each one of the treatments separately, the results are as follows:
anovatab = anovatab
[1.5976e+005] [ 6] [2.6626e+004] [5.4202] [2.5262e-004]
[3.0948e+005] [63] [4.9124e+003] [] []
[4.6924e+005] [69] [] [] [] anovatab
[1.5976e+005] [ 6] [2.6626e+004] [5.4202] [2.5262e-004]
[3.0948e+005] [63] [4.9124e+003] [] []
[4.6924e+005] [69] [] [] [] anovatab
[1.5976e+005] [ 6] [2.6626e+004] [5.4202] [2.5262e-004]
[3.0948e+005] [63] [4.9124e+003] [] []
[4.6924e+005] [69] [] [] [] The graph below presents a central line resulting from the estimated polynomial for the
whole data set and the external lines are one for each treatment. For the multivariate test it was calculated the standardized variable The graph below presents a central line resulting from the estimated polynomial for the
whole data set and the external lines are one for each treatment. whole data set and the external lines are one for each treatment. For the multivariate test it was calculated the standardized variable For the multivariate test it was calculated the standardized variable 2
1
ln
2
N
p
d
t
= 192.0591 with (P<0,001). The program outputs were as follows. 5. Conclusion Given its matrix structure, Matlab presented itself as an efficient tool for linear models. The
programs and the methodology presented were efficient to the comparing of polynomial
growth curves. The modular sequence in which the programs were developed allows the
user to implement new routines as well as new methodology proposals for the solution of
the proposed problem. The solutions presented for the problem of comparison of
polynomial growth curves may be used in part or in conjunction for the solution of other
linear models problems. S. M. J. (1997). A metodologia de análise de dados longitudinais. Thesis (BS. in
Statistics), Federal University of Rio Grande do Sul, Porto Alegre, Brazil. Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB 77 [5.2769e+007] [ 2] [2.6384e+007] [3.8235e+003] [1.2054e-072]
[4.6924e+005] [68] [6.9006e+003] [] []
[5.3238e+007] [69] [] [] []
After the choice of the polynomial model and its test of significance, the same model was
applied on each one of the treatments separately, the results are as follows: [5.2769e+007] [ 2] [2.6384e+007] [3.8235e+003] [1.2054e-072]
[4.6924e+005] [68] [6.9006e+003] [] []
[5.3238e+007] [69] [] [] []
After the choice of the polynomial model and its test of significance, the same model was
applied on each one of the treatments separately, the results are as follows: After the choice of the polynomial model and its test of significance, the same model was
applied on each one of the treatments separately, the results are as follows: 2
ˆY
50.31
89.10X
57.10X
1
2
2ˆ
46.90
76.82
56.55
Y
X
X
2
ˆY
50.31
89.10X
57.10X
1
2
ˆY
50.31
89.10X
57.10X
1
2
2ˆ
46.90
76.82
56.55
Y
X
X
2
0.3405
R The analysis of variance for decomposition of error was employed to test the difference
between the curves and is presented in table 2. Causes of variation
DF
SS
SQ
F
P
Polynomial
6
1.5976E+005
2.6626E+004
5.4202
2.52652E-004
Error
63
3.0948E+005
4.912E+003
Total
69
4.6924E+005 Table 2. Analysis of variance to compare the curves. Table 2. Analysis of variance to compare the curves. e 2. Analysis of variance to compare the curves. Fig. 2. Central line resulting from the estimated polynomial for the entire data set and the
external lines, one for each treatment. Fig. 2. Central line resulting from the estimated polynomial for the entire data set and the
external lines, one for each treatment. 6. References Andrade, D. F. & Singer, J. M. (1986). Análise de dados longitudinais. Proceedings of VII
Simpósio Nacional de Probabilidade e Estatística, pp. 19-26, Campinas, SP, Brazil, 1986. Andreoni, S. (1989). Modelos de efeitos aleatórios para a análise de dados longitudinais não
balanceados em relação ao tempo. Dissertation (MS. in Statistics) Institute of
Mathematics, São Paulo University, São Paulo, Brazil, 1989. Box, G. E. P. (1954). Some Theorems on Quadratic Forms Applied in the Study of Analysis of
Variance Problems, I. Effect of Inequality of Variance in the One-Way
Classification. Annals of Mathematical Statistics, Vol.25, No. 2, 1954, DOI: 10.1214, pp. 290-302. Box, G. E. P. (1954). Some Theorems on Quadratic Forms Applied in the Study of Analysis of
Variance Problems, I. Effect of Inequality of Variance in the One-Way
Classification. Annals of Mathematical Statistics, Vol.25, No. 2, 1954, DOI: 10.1214, pp. 290-302. Castro, S. M. J. (1997). A metodologia de análise de dados longitudinais. Thesis (BS. in
Statistics), Federal University of Rio Grande do Sul, Porto Alegre, Brazil. Comparison of Methodologies for Analysis of Longitudinal Data Using MATLAB 79 Castro, S. M. J. & Riboldi, J. (2005). A construção do modelo em dados longitudinais: escolha
dos efeitos fixos e aleatórios, modelagem das estruturas de covariância. Proceedings
of the Annual Meeting of the Brazilian Region of the International Biometrics Society, and
of the Simpósio de Estatística Aplicada a Experimentação Agronômica, pp. 157-158,
Londrina, Paraná, Brazil, 2005. Cole, J. W. L. & Grizzle, J. E. (1966). Applications of Multivariate Analysis of Variance to
Repeated Measurements Experiments. Biometrics, Vol. 22, 1966, ISSN 0006341x, pp. 810 – 828. Fitzmaurice, G. et al. Ed(s).). (2009). Longitudinal Data Analysis. Chapman & Hall/CRC
Taylor & Francis Group, ISBN 978-1-58488-658-7, Boca Raton, Florida. Freitas, G. E. (2007). Análise de dados longitudinais em experimentos com cana-de-açúcar. Dissertation (MS. in Agronomics), Escola Superior de Agricultura “Luis de
Queiroz”, São Paulo University, Piracicaba, Brazil, 2007. Q
,
y,
,
,
Greenhouse, S. W. & Geisser, S. (1959). On methods in the analysis of profile data. Psychometrika, Vol.24, No. 2, June 1959, DOI: 10.1007, pp.95-112. Huynh, H. & Feldt, L.S. (1970) Condition under which mean square ratios in repeated
measurements designs have exact F-distributions. J. Am. Stat. Assoc., Vol.72, 1970,
ISSN 0162-1459, pp.320-340. pp
Huynh, H. & Feldt, L. S. (1976). Estimation of the box correction for degrees of freedom from
sample data in randomized block and split-plot designs. J. H. (1986). Análise multivariada para dados onde a característica observada é
subdividida em K classes. Dissertation (MS in Agronomics), Escola Superior de
Agricultura “Luiz de Queiroz”, São Paulo University, Piracicaba, 1986. 6. References Educational and
Behavioral Statistics, Vol.1, No.1, March 1976, DOI: 10.3102/10769986001001069,
pp.69-82. pp
Johnson, R. A. & Wichern, D. W. (1998). Applied multivariate statistical analysis, 4 ed. Prentice
Hall, ISBN 0-13-834194-x, Upper Saddle River, New Jersey. Khattree, R. & Naik, D. N. (2000). Multivariate data reduction and discrimination with SAS
software. SAS Institute Inc., ISBN 1-58025-696-1, Cary, North Carolina, USA. Lima, C. G. (1996). Análise de dados longitudinais provenientes de experimento em blocos
casualizados. Dissertation (PhD in Agronomics), Escola Superior de Agricultura
“Luiz de Queiroz”, São Paulo University, Piracicaba, Brazil, 1996. Malheiros, E.B. (1999). Precisão da análise de dados longitudinais, com diferentes estruturas
para a matriz de variâncias e covariância, quando se utiliza o esquema em parcelas
subdivididas. Revista de Matemática e Estatística UNESP, Vol.17, 1999, ISSN 0102-
0811, pp.263-273. Mauchly, J. W. (1940). Significance test for sphericity of a normal n-variate distribution. An. Math. Stat., Vol.11, No. 2, June 1940,ISSN 00034851, pp.204-209. Meredith, M.P.; Stehman, S.V. (1991). Repeated measures experiments in forestry: focus on
analysis of response curves. Canadian Journal of Forest Research, Vol.21, 1991, ISSN
0045-5067, pp.957-965. Smith, H. R. et al. (1962). Multivariate Analysis of Variance. (MANOVA). Biometrics, Vol.2,
1962, ISSN 0006-341X, pp. 61 – 67. Morrison, D. F. (1990). Multivariate Statistical Methods. 3 ed, McGraw-Hill, ISBN 0-07-043187-
6, Singapore. Stuker, H. (1986). Análise multivariada para dados onde a característica observada é
subdividida em K classes. Dissertation (MS in Agronomics), Escola Superior de
Agricultura “Luiz de Queiroz”, São Paulo University, Piracicaba, 1986. 80 MATLAB – A Ubiquitous Tool for the Practical Engineer Timm, N.H. (1980). Multivariate analysis of variance of repeated measurements. In:
Handbook of Statistics Analysis of Variance, Vol. 1, P. R. Krishnaiah (Ed), pp.41-87,
North-Holland, ISBN:0444853359, New York. Vieira, F. T. P. A. (2006). Uma Abordagem Multivariada em Experimento Silvipastoril com
Leucaena leucocephala (Lam.) de Wit. no Agreste de Pernambuco. Dissertation
(MS. in Biometrics), Rural Federal University of Pernambuco, Pernambuco, Brazil,
2006. Vonesh, F. E. & Chinchilli, V.M. (1997). Linear and nonlinear models for the analysis of repeated
measurements. Marcel Dekker, ISBN 0-8247-8248-8, New York. Wald, V. B. (2000). A metodologia de modelos mistos não lineares aplicados à análise de
dados longitudinais em plantas forrageiras. Dissertation (MS in Zootechnique),
Federal University of Rio Grande do Sul, Brazil, 2000. y
Xavier, L. H. (2000). Modelos univariado e multivariado para análise de medidas repetidas e
verificação da acurácia do modelo univariado por meio de simulação. 6. References Dissertation
(MS in Statistics and Agronomics experimentation), Escola Superior de Agricultura
“Luiz de Queiroz”, São Paulo University, Piracicaba, Brazil, 2000. 5 Educational Simulator for Particle
Swarm Optimization and Economic
Dispatch Applications Woo Nam Lee and Jong Bae Park
Konkuk University
Korea 1. Introduction Optimization problems are widely encountered in various fields in science and technology. Sometimes such problems can be very complex due to the actual and practical nature of the
objective function or the model constraints. Most of power system optimization problems
have complex and nonlinear characteristics with heavy equality and inequality constraints. Recently, as an alternative to the conventional mathematical approaches, the heuristic
optimization techniques such as genetic algorithms (GAs), Tabu search, simulated
annealing, and particle swarm optimization (PSO) are considered as realistic and powerful
solution schemes to obtain the global or quasi-global optimums (K. Y. Lee et al., 2002). In 1995, Eberhart and Kennedy suggested a PSO based on the analogy of swarm of bird and
school of fish (J. Kennedy et al., 1995). The PSO mimics the behavior of individuals in a
swarm to maximize the survival of the species. In PSO, each individual makes his decision
using his own experience together with other individuals' experiences (H. Yoshida et al.,
2000). The algorithm, which is based on a metaphor of social interaction, searches a space by
adjusting the trajectories of moving points in a multidimensional space. The individual
particles are drawn stochastically toward the present velocity of each individual, their own
previous best performance, and the best previous performance of their neighbours (M. Clerc
et al., 2002). h
l
d
h (
)
bl
h
l
d
l
f
l
ff Optimization problems are widely encountered in various fields in science and technology. Sometimes such problems can be very complex due to the actual and practical nature of the
objective function or the model constraints. Most of power system optimization problems
have complex and nonlinear characteristics with heavy equality and inequality constraints. Recently, as an alternative to the conventional mathematical approaches, the heuristic
optimization techniques such as genetic algorithms (GAs), Tabu search, simulated
annealing, and particle swarm optimization (PSO) are considered as realistic and powerful
solution schemes to obtain the global or quasi-global optimums (K. Y. Lee et al., 2002). In 1995, Eberhart and Kennedy suggested a PSO based on the analogy of swarm of bird and
school of fish (J. Kennedy et al., 1995). The PSO mimics the behavior of individuals in a
swarm to maximize the survival of the species. In PSO, each individual makes his decision
using his own experience together with other individuals' experiences (H. Yoshida et al.,
2000). 2. Overview of particle swarm optimization Kennedy and Eberhart (J. Kennedy et al., 1995) developed a PSO algorithm based on the
behavior of individuals of a swarm. Its roots are in zoologist's modeling of the movement of
individuals (e.g., fishes, birds, or insects) within a group. It has been noticed that members
within a group seem to share information among them, a fact that leads to increased
efficiency of the group (J. Kennedy et al., 2001). The PSO algorithm searches in parallel using
a group of individuals similar to other AI-based heuristic optimization techniques. In a physical n-dimensional search space, the position and velocity of individual i are
represented as the vectors
(
)
1,
,
i
i
in
X
x
x
=
"
and
(
)
1,
i
i
in
V
v
v
=
"
in the PSO algorithm. Let
(
)
1
,
,
Pbest
Pbest
i
i
in
Pbest
x
x
=
"
and
(
)
1
,
,
Gbest
Gbest
n
Gbest
x
x
=
"
be the best position of individual i (
)
1
,
,
Pbest
Pbest
i
i
in
t
x
x
=
"
and
(
)
1
,
,
Gbest
Gbest
n
Gbest
x
x
=
"
be the best position of individua and its neighbors’ best position so far, respectively. The modified velocity and position of
each individual can be calculated using the current velocity and the distance from
i
Pbest to
Gbest as follows: 1
1
1
2
2
(
)
(
)
k
k
k
k
i
i
i
i
k
k
i
V
V
c rand
Pbest
X
c rand
Gbest
X
+ = ω
+
×
−
+
×
−
(1) (1) 1
1
k
k
k
i
i
i
X
X
V
+
+
=
+
(2) 1
1
k
k
k
i
i
i
X
X
V
+
+
=
+ (2) where, k
i
V velocity of individual i at iteration k, ω weight parameter, ω weight parameter, 1
2
,
c
c acceleration coefficien 1
2
,
c
c acceleration coefficients, 1
2
,
rand
rand random numbers between 0 and 1, k
i
X position of individual i at iteration k, k
i
Pbest best position of individual i until iteration k, k
Gbest best position of the group until iteration k. 1. Introduction The algorithm, which is based on a metaphor of social interaction, searches a space by
adjusting the trajectories of moving points in a multidimensional space. The individual
particles are drawn stochastically toward the present velocity of each individual, their own
previous best performance, and the best previous performance of their neighbours (M. Clerc
et al., 2002). The practical economic dispatch (ED) problems with valve-point and multi-fuel effects are
represented as a non-smooth optimization problem with equality and inequality constraints,
and this makes the problem of finding the global optimum difficult. Over the past few
decades, in order to solve this problem, many salient methods have been proposed such as a
hierarchical numerical method (C. E. Lin et al., 1984), dynamic programming (A. J. Wood et
al., 1984), evolutionary programming (Y. M. Park et al., 1998; H. T. Yang et al., 1996; N. Sinba et al., 2003), Tabu search (W. M. Lin et al., 2002), neural network approaches (J. H. Park et al., 1993; K. Y. Lee et al., 1998), differential evolution (L. S. Coelho et al., 2006),
particle swarm optimization (J. B. Park et al., 2005; T. A. A. Victoire et al., 2004; T. A. A. Victoire et al., 2005), and genetic algorithm (D. C. Walters et al., 1993). )
g
g
(
)
This chapter would introduce an educational simulator for the PSO algorithm. The purpose
of this simulator is to provide the undergraduate students with a simple and useable tool for This chapter would introduce an educational simulator for the PSO algorithm. The purpose
of this simulator is to provide the undergraduate students with a simple and useable tool for MATLAB – A Ubiquitous Tool for the Practical Engineer 82 gaining an intuitive feel for PSO algorithm, mathematical optimization problems, and
power system optimization problems. To aid the understanding of PSO, the simulator has
been developed under the user-friendly graphic user interface (GUI) environment using
MATLAB. In this simulator, instructors and students can set parameters related to the
performance of PSO and can observe the impact of the parameters to the solution quality. This simulator also displays the movements of each particle and convergence process of a
group. In addition, the simulator can consider other mathematical or power system
optimization problems with simple additional MATLAB coding. 2. Overview of particle swarm optimization The constants
1c and
2c represent the weighting of the stochastic acceleration terms that
pull each particle toward the Pbest and Gbest positions. Suitable selection of inertia weight
provides a balance between global and local explorations, thus requiring less iteration on
average to find a sufficiently optimal solution. In general, the inertia weight ω has a linearly Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 83 decreasing dynamic parameter framework descending from
max
ω
to
min
ω
as follows (K. Y. Lee et al., 2002; H. Yoshida et al., 2000; J. B. Park et al., 2005). decreasing dynamic parameter framework descending from
max
ω
to
min
ω
as follows (K. Y. Lee et al., 2002; H. Yoshida et al., 2000; J. B. Park et al., 2005). max
min
max
max
Iter
Iter
ω
−ω
ω = ω
−
×
(3) (3) Were,
max
Iter
is maximum iteration number and Iter is current iteration number. Were,
max
Iter
is maximum iteration number and Iter is current iteration number. 3.1 Purpose and motivation of simulator p
As a result of the rapid advances in computer hardware and software, computer-based
power system educational tools have grown from very simple implementations, providing
the user with little more than a stream of numerical output, to very detailed representations
of the power system with an extensive GUI. Overbye, et al. had developed a user-friendly
simulation program, PowerWorld Simulator, for teaching power system operation and
control (T. J. Overbye et al., 2003). They applied visualization to power system information
to draw user's attention and effectively display the simulation results. Through these works,
they expected that animation, contouring, data aggregation and virtual environments would
be quite useful techniques that are able to provide efficient learning experience to users. Also they presented experimental results associated with human factors aspects of using
this visualization (D. A. Wiegmann et al., 2005; D. A. Wiegmann et al., 2006; N. Sinba et al.,
2003). Therefore, like other previous simulators, the motivation for the development of this
simulator is to provide the students with a simple and useable tool for gaining an intuitive
feel for the PSO algorithm, mathematical and power system optimization problems. 3.2 Functions of simulator The basic objectives of this simulator were to make it easy to use and to provide effective
visualization capability suitable for presentations as well as individual studies. This
educational simulator was developed by MATLAB 2009b. MATLAB is a scientific
computing language developed by The Mathworks, Inc. that is run in an interpreter mode
on a wide variety of operating systems. It is extremely powerful, simple to use, and can be
found in most research and engineering environments. The structure and data flow of the developed PSO simulator is shown in Fig. 1. The
simulator consists of 3-parts, that is, i) user setting of optimization function as well as
parameters, ii) output result, and iii) visualized output variations, as shown in Figs. 2, 3, and
4, respectively. Since the main interaction between user and the simulator is performed
through the GUI, it presents novice users with the information they need, and provides easy
access for advanced users to additional detailed information. Thus, the GUI is instrumental
in allowing users to gain an intuitive feel of the PSO algorithm, rather than just learning
how to use this simulator. In this simulator, parameters (i.e., maximum number of the iteration, maximum and
minimum number of inertia weight, acceleration factors
1c and
2
c , and number of particles)
that have the influence of PSO performance can be directly inputted by users. In addition, MATLAB – A Ubiquitous Tool for the Practical Engineer 84 Fig. 1. Structure of the developed PSO simulator Fig. 1. Structure of the developed PSO simulator Fig. 1. Structure of the developed PSO simulator Fig. 2. A window for user setting Fig. 2. A window for user setting Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 85 Fig. 3. Output result window
Fig. 4. Viewing parts of output variation Fig. 3. Output result window Fig. 3. Output result window Fig. 3. Output result window Fig. 3. Output result window Fig. 4. Viewing parts of output variation Fig. 4. Viewing parts of output variation MATLAB – A Ubiquitous Tool for the Practical Engineer 86 “Input Default Value” check-box was added for users who don’t know the proper
parameter values of the PSO. Fig. 5. Simulation for a mathematical example 3.2 Functions of simulator If the users push the “START” button finally, then the users
can observe the evolution process of the particles on contours of the objective function (in
case of a mathematical example) or the output histogram of each generator through
MATLAB animation functions and check the changes of the values of the objective function
and control variables at each iteration. The “Disable axes” check-box is used when the users
want to show only the values of the final result fast. When the check-box is checked, only
the final results (i.e., the value of the objective function and control variables) are expressed
in the “Result Output Window”. At any point in time in the simulation, the user can pause
or restart the simulation by pushing the “PAUSE” button. As shown in Figs. 5 and 6, user
can observe movements of each particle as well as the trend of the value of the objective
function. Fig. 5. Simulation for a mathematical example Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 87 Fig. 6. Simulation for an economic dispatch problem. Fig. 6. Simulation for an economic dispatch problem. 4.2 Valve-point effects The generating units with multi-valve steam turbines exhibit a greater variation in the fuel-
cost functions. Since the valve point results in ripples, a cost function contains high order
nonlinearities (H. T. Yang et al., 1996; N. Sinba et al., 2003; D. C. Walters et al. 1993). Therefore, the cost function (5) should be replaced by the following to consider the valve-
point effects: 2
min
(
)
sin(
(
))
j
j
j
j
j
j
j
j
j
j
j
F P
a
b P
c P
e
f
P
P
=
+
+
+
×
×
−
(7) (7) (7) and
j
f
are the cost coefficients of generator j reflecting valve-point effects. where
je Here, the sinusoidal functions are added to the quadratic cost functions. Here, the sinusoidal functions are added to the quadratic cost functions. Here, the sinusoidal functions are added to the quadratic cost functions. 4.1 Basic ED problem formulation The ED problem is one of the basic optimization problems for the students who meet the
power system engineering. The objective is to find the optimal combination of power
generations that minimizes the total generation cost while satisfying an equality constraint
and a set of inequality constraints. The most simplified cost function can be represented in a
quadratic form as following (A. J. Wood et al., 1984): (
)
j
j
j J
C
F P
∈
= ∑
(4) (
)
j
j
j J
C
F P
∈
= ∑ (4) 2
(
)
j
j
j
j
j
j
j
F P
a
b P
c P
=
+
+
(5) 2
(
)
j
j
j
j
j
j
j
F P
a
b P
c P
=
+
+ (5) C total generation cost; jF cost function of generator j; jF cost function of generator j; ,
,
j
j
j
a b c cost coefficients of generator j; jP electrical output of generator j; 88 MATLAB – A Ubiquitous Tool for the Practical Engineer J set for all generators. J set for all generators. While minimizing the total generation cost, the total generated power should be the same as
the total load demand plus the total line loss. However, the transmission loss is not
considered in this paper for simplicity. In addition, the generation output of each generator
should be laid between minimum and maximum limits as follows: min
max
j
j
j
P
P
P
≤
≤
(6) (6) where
min
jP
and
max
jP
are the minimum and maximum output of generator j, respectively. 5. Case studies This simulator can choose and run five different mathematical examples and two different
ED problems: (i) The Sphere function, (ii) The Rosenbrock (or banana-valley) function, (iii)
Ackley's function, (iv) The generalized Rastrigin function, (v) The generalized Griewank
function, (vi) 3-unit system with valve-point effects, and (vii) 40-unit system with valve-
point effects. In the case of each mathematical example (functions (i)-(v)), two input
variables (i.e., 2-dimensional space) have been set in order to show the movement of
particles on contour. For the case study, 30 independent trials are conducted to observe the
variation during the evolutionary processes and compare the solution quality and
convergence characteristics. To successfully implement the PSO, some parameters must be assigned in advance. The
population size NP is set to 30. Since the performance of PSO depends on its parameters
such as inertia weight ω and two acceleration coefficients (i.e.,
1c and
2c ), it is very
important to determine the suitable values of parameters. The inertia weight is varied from
0.9 (i.e.,
max
ω
) to 0.4 (i.e.,
min
ω
), as these values are accepted as typical for solving wide
varieties of problems. Two acceleration coefficients are determined through the experiments
for each problem so as to find the optimal combination. 5.1 Mathematical examples For development of user's understanding of the PSO algorithm, five non-linear
mathematical examples are used here. In each case, the maximum number of iterations (i.e.,
max
iter
) was set to 500. The acceleration coefficients (i.e.,
1c and
2c ) was equally set to 2.0 89 Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications from the experimental results for each case using the typical PSO algorithm. And all of the
global minimum value of each function is known as 0. The global minimum value was
successfully verified by the simulator. from the experimental results for each case using the typical PSO algorithm. And all of the
global minimum value of each function is known as 0. The global minimum value was
successfully verified by the simulator. 5.1.1 The sphere function 5.1.1 The sphere function p
he function and the initial position range of input variables (i.e.,
ix ) are as follows: 2
0
1
( )
n
i
i
f
x
x
=
= ∑
(8)
5 12
5 12
≤
≤ (8) 5.12
5.12
ix
−
≤
≤ 5.12
5.12
ix
−
≤
≤ Initial and final stages of the optimization process for the Sphere function are shown in
Fig. 7. (b) Final stage (a) Initial stage
(b) Final stage
Fig. 7. Optimization process for the sphere function. (a) Initial stage (a) Initial stage (b) Final stage (b) Final stage Fig. 7. Optimization process for the sphere function. Fig. 7. Optimization process for the sphere function. Fig. 7. Optimization process for the sphere function. 5.1.2 The rosenbrock (or banana-valley) function 5.1.2 The rosenbrock (or banana-valley) function
The function and the initial position range of input variables (i.e.,
ix ) are as follows: The function and the initial position range of input variables (i.e.,
ix ) are as follows: /2
2
2
2
1
2
2
1
2
1
1
( )
(100(
)
(1
) )
n
i
i
i
i
f
x
x
x
x
−
−
=
=
−
+
−
∑
(9)
2.048
2.048
ix
−
≤
≤ (9) Initial and final stages of the optimization process for the Rosenbrock function are shown in
Fig. 8. MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer 90 (a) Initial stage
b) Final stage
Fig. 8. Optimization process for the Rosenbrock function. b) Final stage (a) Initial stage b) Final stage (a) Initial stage (a) Initial stage Fig. 8. Optimization process for the Rosenbrock function. 5.1.3 The ackley’s function
The function and the initial position range of input variables (i.e.,
ix ) is as follows: 5.1.3 The ackley’s function y
The function and the initial position range of input variables (i.e.,
ix ) is as follows: 2
2
1
1
1
1
( )
20exp
0.2
exp
cos(2
)
20
n
n
i
i
i
i
f
x
x
x
e
n
n
=
=
⎛
⎞
⎛
⎞
⎜
⎟
= −
−
−
π
+
+
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
∑
∑
(10) 2
2
1
1
1
1
( )
20exp
0.2
exp
cos(2
)
20
n
n
i
i
i
i
f
x
x
x
e
n
n
=
=
⎛
⎞
⎛
⎞
⎜
⎟
= −
−
−
π
+
+
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
∑
∑
(10)
30
30
ix
−
≤
≤ (10) 30
30
ix
−
≤
≤ 30
30
ix
−
≤
≤ Initial and final stages of the optimization process for the Ackley’s function are shown in
Fig. 9. Initial and final stages of the optimization process for the Ackley’s function are shown in
Fig. 9. (a) Initial stage
(b) Final stage
Fig. 9. Optimization process for Ackley's function. (a) Initial stage
(b) Final stage
Fig. 9. Optimization process for Ackley's function. 5.1.4 The generalized rastrigin function
The function and the initial position range of input variables (i.e.,
ix ) is as follows: (a) Initial stage Fig. 9. Optimization process for Ackley's function. Fig. 9. Optimization process for Ackley's function. 5.1.4 The generalized rastrigin function
The function and the initial position range of input variables (i.e.,
ix ) is as follows: 5.1.4 The generalized rastrigin function
The function and the initial position range of input variables (i.e.,
ix ) is as follows: 5.1.4 The generalized rastrigin function
The function and the initial position range of input variables (i.e.,
ix ) is as follows: Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 91 2
3
1
( )
(
10cos(2
)
10)
n
i
i
i
f
x
x
x
=
=
−
π
+
∑
(11)
5.12
5.12
ix
−
≤
≤ 2
3
1
( )
(
10cos(2
)
10)
n
i
i
i
f
x
x
x
=
=
−
π
+
∑ (11) 5.12
5.12
ix
−
≤
≤ Initial and final stages of the optimization process for the generalized Rastrigin function are
shown in Fig. 10. (a) Initial stage
(b) Final stage
Fig. 10. 5.1.3 The ackley’s function Optimization process for Rastrigin function. (b) Final stage (a) Initial stage (a) Initial stage Fig. 10. Optimization process for Rastrigin function. Fig. 10. Optimization process for Rastrigin function. Fig. 10. Optimization process for Rastrigin function. 5.1.5 The generalized griewank function 5.1.5 The generalized griewank function
The function and the initial position range of input variables (i.e.,
ix ) is as follows: g
g
The function and the initial position range of input variables (i.e.,
ix ) is as follows: 2
4
1
1
1
( )
cos
1
4000
n
n
i
i
i
i
x
f
x
x
i
=
=
⎛
⎞
=
−
+
⎜
⎟
⎝
⎠
∑
∏
(12) (12) Initial and final stages of the optimization process for the generalized Griewank function are
shown in Fig. 11. Table 1 shows the average values of objective functions and two input variables for each
function achieved by the PSO simulator. Function Name
Objective Function Value
1
x
2
x
Sphere
0
0
0
Rosenbrock
0
1
1
Ackley
-8.8818e-16
-2.9595e-16
1.6273e-16
Rastrigin
0
9.7733e-10
-7.9493e-10
Griewank
0
100
100
Table 1. Results for Each Test Function Table 1. Results for Each Test Function MATLAB – A Ubiquitous Tool for the Practical Engineer 92 (b) Final stage (a) Initial stage
(b) Final stage
Fig. 11. Optimization process for Griewank function. (a) Initial stage (a) Initial stage (b) Final stage (b) Final stage Fig. 11. Optimization process for Griewank function. Table 3. Generation Output of Each Generator and The Corresponding Cost in 3-Unit
System 5.2 Economic dispatch(ED) problems with valve-point effects This simulator also offers examples to solve ED problem for two different power systems: a
3-unit system with valve-point effects, and a 40-unit system with valve-point effects. The
total demands of the 3-unit and the 40-unit systems are set to 850MW and 10,500MW,
respectively. All the system data and related constraints of the test systems are given in (N. Sinba et al., 2003). Because these systems have more than 3 input variables, the simulator
shows a histogram for the generation output instead of the contour and particles. Since the
global minimum for the total generation cost is unknown in the case of the 40-unit system,
the maximum number of iterations (i.e.,
max
iter
) is set to 10,000 in order to sufficiently
search for the minimum value. Table 2 shows the minimum, mean, maximum, and standard deviation for the 3-unit system
obtained from the simulator. The generation outputs and the corresponding costs of the best
solution for 3-unit system are described in Table 3. Case
Minimum Cost
($)
Average Cost
($)
Maximum
Cost ($)
Standard
Deviation
3-Unit System
8234.0717
8234.0717
8234.0717
0
* Global value of the 3-unit system was known as 8234.0717.T
Table 2. Convergence Results for 3-Unit System
Unit
Generation
Cost
1
300.2669
3087.5099
2
400.0000
3767.1246
3
149.7331
1379.4372
TP/TC
850.0000
8234.0717
*TP: total power [MW], TC: total generation cost [$]
Table 3. Generation Output of Each Generator and The Corresponding Cost in 3-Unit
System Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 93 In order to find the optimal combination of parameters (i.e.,
max
ω
,
min
ω
,
1c , and
2c B), six
cases are considered as given in Table 4. The parameters are determined through the
experiments for 40-unit system using the simulator. In Table 4, the effects of parameters are
illustrated Cases
max
ω
min
ω
c1,c2
Minimum
Cost ($)
Average
Cost ($)
Maximum
Cost ($)
Standard
Deviation
1
1.0
0.5
1
121755.49
122221.90
122624.07
156.97
2
0.9
0.4
1
121761.40
122343.32
123087.16
303.62
3
0.8
0.3
1
121949.15
122842.59
124363.11
602.06
4
1.0
0.5
2
121865.23
122285.12
122658.29
175.19
5
0.9
0.4
2
121768.69
122140.32
122608.27
187.74
6
0.8
0.3
2
121757.09
122158.00
122615.71
212.36
Table 4. Influence of Acceleration Coefficients for 40-Unit System Table 4. Influence of Acceleration Coefficients for 40-Unit System The result screens for 3-unit and 40-unit system are shown in Figs. 12 and 13, respectively. The result screens for 3-unit and 40-unit system are shown in Figs. 12 and 13, respectively.
Each histogram expresses the result of generation output for each generator. 6. Conclusion This chapter presents an educational simulator for particle swarm optimization (PSO) and
application for solving mathematical test functions as well as ED problems with non-smooth
cost functions. Using this simulator, instructors and students can select the test functions for
simulation and set the parameters that have an influence on the PSO performance. Through
visualization process of each particle and variation of the value of objective function, the
simulator is particularly effective in providing users with an intuitive feel for the PSO
algorithm. This simulator is expected to be an useful tool for students who study electrical
engineering and optimization techniques. 5.2 Economic dispatch(ED) problems with valve-point effects Each histogram expresses the result of generation output for each generator. Fig. 12. Result screen for the 3-units system. Fig. 12. Result screen for the 3-units system. MATLAB – A Ubiquitous Tool for the Practical Engineer 94 Fig. 13. Result screen for the 40-units system. Fig. 13. Result screen for the 40-units system. 7. Appendix 1: pso.m function varargout = pso(varargin)
g i Singleton
1 function varargout = pso(varargin) gui_Singleton = 1; _
gui_State = struct('gui_Name', _
gui_State = struct('gui_Name', mfilename, ... g
_
( g
_
,
,
'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @pso_OpeningFcn, ... 'gui_OutputFcn', @pso_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); 'gui_OutputFcn', @pso_OutputFcn, ... _
if nargin & isstr(varargin{1}) if nargin & isstr(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end if nargin & isstr(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end gui_State.gui_Callback = str2func(varargin{1});
d if nargout g
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else gui_mainfcn(gui_State, varargin{:}); gui_mainfcn(gui_State, varargin{:}); function pso_OpeningFcn(hObject, eventdata, handles, varargin) _
handles.output = hObject; guidata(hObject, handles); function varargout = pso_OutputFcn(hObject, eventdata, handles) function varargout = pso_Output varargout{1} = handles.output; function select_func_CreateFcn(hObject, eventdata, handles)
if ispc p
set(hObject,'BackgroundColor','white'); p
set(hObject,'BackgroundColor','white');
else set(hObject,'BackgroundColor','white');
else lse
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'
d set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end function select_func_Callback(hObject, eventdata, handles) _
_
function default_value_Callback(hObject, eventdata, handles) _
_
set(handles.default_value, 'Value', 1); set(handles.default_value, 'Value', 1); set(handles.reset, 'Value', 0); set(handles.reset, 'Value', 0); set(handles.wmax, 'String', 0.9); set(handles.wmax, 'String', 0.9); set(handles.wmin, 'String', 0.4); set(handles.X_max, 'String', 5.12); set(handles.X_max, 'String', 5.12); set(handles.X_min, 'String', -5.12); set(handles.X_min, 'String', -5.12); set(handles.c1, 'String', 2); set(handles.c1, 'String', 2); set(handles.c2, 'String', 2); set(handles.c2, 'String', 2); set(handles.N, 'String', 30); set(handles.itmax, 'String', 500); set(handles.itmax, 'String', 500); function reset_Callback(hObject, eventdata, handles) function reset_Callback(hObject, ev _
set(handles.default_value, 'Value', 0); set(handles.default_value, 'Value', 0); _
set(handles.reset, 'Value', 1); _
set(handles.reset, 'Value', 1); set(handles.wmax, 'String', 0); set(handles.wmax, 'String', 0); set(handles.wmin, 'String', 0); set(handles.wmin, 'String', 0); set(handles.X_max, 'String', 0); set(handles.X_max, 'String', 0); set(handles.X_min, 'String', 0); set(handles.X_min, 'String', 0); set(handles.c1, 'String', 0); set(handles.c1, 'String', 0); set(handles.c2, 'String', 0); set(handles.N, 'String', 0); set(handles.N, 'String', 0); set(handles.itmax, 'String', 0); set(handles.itmax, 'String', 0); function wmax_CreateFcn(hObject, eventdata, handles) function wmax_CreateFcn(hObject, e set(hObject,'BackgroundColor','white'); set(hObject,'BackgroundColor','white');
else else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor') else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end function wmax_Callback(hObject, eventdata, handles) wmax = str2double(get(hObject,'String')); if isnan(wmax) isnan(wmax)
set(hObject, 'String', 0); set(hObject, 'String', 0); errordlg('Input must be a number','Error'); errordlg('Input must be a number','Error');
end Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 95 end pso_para = getappdata(gcbf, 'metricdata'); pso_para.wmax = wmax; pso_para.wmax = wmax;
setappdata(gcbf, 'metricdata', pso_para); _
setappdata(gcbf, 'metricdata', pso_para); function wmin_CreateFcn(hObject, eventdata, handles)
if ispc set(hObject,'BackgroundColor','white');
else set(hObject,'BackgroundColor','white');
else else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end MATLAB – A Ubiquitous Tool for the Practical Engineer 96 function wmin_Callback(hObject, eventdata, handles) function wmin_Callback(hObject, eventdata, handles) wmin = str2double(get(hObject,'String')); wmin = str2double(get(hObject,'String')); if isnan(wmin)
set(hObject, 'String', 0); errordlg('Input must be a number','Error'); errordlg('Input must be a number','Error');
end pso_para = getappdata(gcbf, 'metricdata'); pso_para.wmin = wmin; setappdata(gcbf, 'metricdata', pso_para);
function c1 CreateFcn(hObject
eventdata
handles) setappdata(gcbf, 'metricdata', pso_para); function c1_CreateFcn(hObject, eventdata, handles)
if ispc p
set(hObject,'BackgroundColor','white');
l p
set(hObject,'BackgroundColor','white');
else lse
et(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor')); set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end function c1_Callback(hObject, eventdata, handles) c1 = str2double(get(hObject,'String')); c1 = str2double(get(hObject,'String')); set(hObject, 'String', 0);
errordlg('Input must be a number','Error'); errordlg('Input must be a number','Error'); pso_para = getappdata(gcbf, 'metricdata'); pso_para.c1 = c1; setappdata(gcbf, 'metricdata', pso_para); setappdata(gcbf, metricdata , pso_para);
function c2 CreateFcn(hObject, eventdata, handles) _
function c2_CreateFcn(hObject, eventdata, handles) function c2_CreateFcn(hObject, eventdata, handles)
if ispc set(hObject,'BackgroundColor','white');
l lse
et(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor')); set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end function c2_Callback(hObject, eventdata, handles) c2 = str2double(get(hObject,'String')); c2 = str2double(get(hObject,'String')); if isnan(c2)
set(hObject, 'String', 0);
errordlg('Input must be a number','Error'); pso_para = getappdata(gcbf, 'metricdata'); pso_para.c2 = c2; setappdata(gcbf, 'metricdata', pso_para); setappdata(gcbf, 'metricdata', pso_para);
function N_CreateFcn(hObject, eventdata, handles) function N_CreateFcn(hObject, eventdata, handles)
if ispc set(hObject,'BackgroundColor','white');
else lse
et(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor')); set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end function N_Callback(hObject, eventdata, handles) N = str2double(get(hObject,'String')); if isnan(N)
set(hObject, 'String', 0);
errordlg('Input must be a number','Error'); set(hObject, 'String', 0);
errordlg('Input must be a number','Error'); (
j
,
g ,
);
errordlg('Input must be a number','Error'); pso_para = getappdata(gcbf, 'metricdata'); pso_para.N = N; ata(gcbf, 'metricdata', pso_para); setappdata(gcbf, 'metricdata', pso_para);
function itmax_CreateFcn(hObject, eventdata, handles) _
j
,
,
if ispc
set(hObject,'BackgroundColor','white'); f ispc
set(hObject,'BackgroundColor','white'); p
set(hObject,'BackgroundColor','white'); Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 97 else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
function itmax_Callback(hObject, eventdata, handles)
itmax = str2double(get(hObject,'String'));
if isnan(itmax)
set(hObject, 'String', 0);
errordlg('Input must be a number','Error');
end
function start_Callback(hObject, eventdata, handles)
if get(handles.select_func,'value')>=7
eldrun
else
runpso
end
function Result_window_CreateFcn(hObject, eventdata, handles)
if ispc
set(hObject,'BackgroundColor','white');
else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
function Result_window_Callback(hObject, eventdata, handles) else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
function itmax_Callback(hObject, eventdata, handles)
itmax = str2double(get(hObject,'String'));
if isnan(itmax)
set(hObject, 'String', 0);
errordlg('Input must be a number','Error');
end
function start_Callback(hObject, eventdata, handles)
if get(handles.select_func,'value')>=7
eldrun
else
runpso
end
function Result_window_CreateFcn(hObject, eventdata, handles)
if ispc
set(hObject,'BackgroundColor','white');
else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end
function Result_window_Callback(hObject, eventdata, handles)
f
ti
C llb
k(hObj
t
td t
h
dl
) hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor')); hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor')); function Result_window_Callback(hObject, eventdata, handles) _
_
function pause_Callback(hObject, eventdata, handles) set(handles.start,'Enable','off'); set(handles.pause,'String','PAUSE') function disable_Callback(hObject, eventdata, handles)
function close Callback(hObject
eventdata
handles) function disable_Callback(hObject, eventdata, handles)
function close Callback(hObject, eventdata, handles) function disable_Callback(hObject, eventdata, handles)
function close_Callback(hObject, eventdata, handles) elete(get(0,'CurrentFigure')); function X_max_Callback(hObject, eventdata, handles) function X_max_Callback(hObject, X_max = str2double(get(hObject,'String')); if isnan(X_max)
set(hObject, 'String', 0); errordlg('Input must be a number','Error'); pso_para = getappdata(gcbf, 'metricdata'); pso_para.X_max = X_max; _
_
_
setappdata(gcbf, 'metricdata', pso_para);
function X max CreateFcn(hObject
eventdata
handles) setappdata(gcbf, 'metricdata', pso_para); function X_max_CreateFcn(hObject, eventdata, handles)
if ispc set(hObject,'BackgroundColor','white');
l else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end function X_min_Callback(hObject, eventdata, handles) X_min = str2double(get(hObject,'String')); if isnan(X_min)
set(hObject, 'String', 0); errordlg('Input must be a number','Error'); errordlg('Input must be a number','Error');
end pso_para = getappdata(gcbf, 'metricdata'); MATLAB – A Ubiquitous Tool for the Practical Engineer 98 setappdata(gcbf, 'metricdata', pso_para); _
function X_min_CreateFcn(hObject, eventdata, handles)
if ispc if ispc
set(hObject,'BackgroundColor','white'); else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor')
end else
set(hObject,'BackgroundColor',get(0,'defaultUicontrolBackgroundColor'));
end cla; ;
set(handles.start,'Enable','off'); set(handles.start,'Enable','off'); set(handles.pause,'String','PAUSE','Enable','on'); set(handles.text14,'String','Search State '); functnames = get(handles.select_func,'String'); functname = functnames{get(handles.select_func,'Value')}; wmax = str2double(get(handles.wmax, 'String')); wmin = str2double(get(handles.wmin, 'String')); X_max = str2double(get(handles.X_max, 'String')) c1 = str2double(get(handles.c1, 'String')); c2 = str2double(get(handles.c2, 'String')); N = str2double(get(handles.N, 'String')); itmax = str2double(get(handles.itmax, 'String')); pso_para = getappdata(gcbf, 'metricdata'); pso_para = getappdata(gcbf, 'me pso_para.wmax = wmax; pso_para.wmin = wmin; pso_para.X_max = X_max; pso_para.X_min = X_min; pso_para.c1 = c1; pso_para.c2 = c2; pso_para.N = N; pso_para.itmax = itmax; setappdata(gcbf, 'metricdata', pso_para); D=2; % Dimension % Weight Parameter for iter=1:pso_para.itmax W(iter)= pso_para.wmax-((pso_para.wmax- pso_para.wmin)/pso_para.itmax)*iter;
end %Initialization of positions of agents % agents are initialized between -5.12,+5.12 randomly a= X_min; %min b= X_max; %max x=a+(b-a)*rand(pso_para.N,D,1); _
%Initialization of velocities of agents %Between -5.12 , +5.12, (which can also be started from zero)
m=X_min; m=X_min; n=X_max; V=m+(n-m)*rand(pso_para.N,D,1); %Function to be minimized. %Function to be minimized. Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 99 F = feval(functname,x(:,:,1)); %Matrix composed of gbest vector Fbest(1,1,1) = feval(functname,G(1,:,1));
pbest=x; Calculating Velocity
(:,:,2) = W(1) * V(:,:,1) + pso_para.c1*rand*(pbest(:,:,1)-
(:,:,1)) + pso para.c2*rand*(G(:,:,1)-x(:,:,1)); g
y
V(:,:,2) = W(1) * V(:,:,1) + pso_para.c1*rand*(pbest(:,:,1)-
(
1))
2*
d*(G(
1)
(
1)) (:,:,2) = W(1) * V(:,:,1) + pso_para.c1*rand*(pbest(:,:,1)-
(:,:,1)) + pso_para.c2*rand*(G(:,:,1)-x(:,:,1)); x(:,:,1)) + pso_para.c2*rand*(G(:,:,1)-x(:,:,1)); x(:,:,2)=x(:,:,1) + V(:,:,2); Fb(1,1,1) = feval(functname,gbest(1,:,1)); for j=2:pso_para.itmax for j=2:pso_para.itmax for j=2:pso_para.itmax 100 MATLAB – A Ubiquitous Tool for the Practical Engineer Fbest(1,1,j) = feval(functname,G(1,:,j)); pbest(i,:,j)=x(i,:,I); V(:,:,j+1)= W(j)*V(:,:,j) + pso_para.c1*rand*(pbest(:,:,j)-
(:,:,j)) + pso_para.c2*rand*(G(:,:,j)-x(:,:,j)); x(:,:,j+1)=x(:,:,j)+V(:,:,j+1); Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 101 num2str(Fbest(1,1,1)),'
','Gbest','1','=','(',num2str(gbest(1,1,1)),',',num2str(gbest(1,2,1)
),')']}]; ResultStr(j) = [{['Fbest',num2str(j),' ','=',' ',
num2str(Fbest(1,1,end)),' ','Gbest',num2str(j),'=','(',num2str(gbest(1,1,end)),',',num2str(gbe
st(1,2,end)),')']}]; set(handles.Result_window, 'String', ResultStr);
%%%%%%%%% end of Display %%%%%%%%%%%%%%%%% set(handles.Result_window, 'String', ResultStr);
%%%%%%%%% end of Display %%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%% AXE-1 %%%%%%%%%%%%%%%%%
axes(handles.axes1);
cla;
set(gca,'xlim',[0 pso_para.itmax],'ylim',[0 Fbest(1,1,1)]),
plot(Fbest(:),'r-')
if j<=pso para itmax/2 set(gca,'xlim',[0 pso_para.itmax],'ylim',[0 Fbest(1,1,1)]),
plot(Fbest(:),'r-') if j<=pso_para.itmax/2 _
text(j,Fbest(1,1,end),['Fbest = ', text(j,Fbest(1,1,end),['Fbest = ', num2str(Fbest(1,1,end))],'HorizontalAlignment','Left','VerticalAlign
ment','bottom','EdgeColor','blue','LineWidth',3);
else text(j,Fbest(1,1,end),['Fbest = ', text(j,Fbest(1,1,end),['Fbest = ', (j,
( , ,
),[
,
num2str(Fbest(1,1,end))],'HorizontalAlignment','Right','VerticalAlig
nment','bottom','EdgeColor','blue','LineWidth',3);
end
l
d('Fb
t') (j,
( , ,
),[
,
num2str(Fbest(1,1,end))],'HorizontalAlignment','Right','VerticalAlig
nment' 'bottom' 'EdgeColor' 'blue' 'LineWidth' 3); j,
, ,
,
,
num2str(Fbest(1,1,end))],'HorizontalAlignment','Right','VerticalAlig
nment','bottom','EdgeColor','blue','LineWidth',3); num2str(Fbest(1,1,end))],'HorizontalAlignment','Right','Vert num2str(Fbest(1,1,end))], HorizontalAlignment , Right , VerticalAlig
nment','bottom','EdgeColor','blue','LineWidth',3);
end nment','bottom','EdgeColor','blue','LineWidth',3);
end legend('Fbest'); hold on %%%%%%%%%%%%%%%%% AXE-2 %%%%%%%%%%%%%%%%
axes(handles.axes2); axes(handles.axes2); axis([a b a b]) [c,h]=contour(con_m,con_n,r_save,10);
hold on plot(pbest(:,1,j),pbest(:,2,j),'r*') end end
end
if get(handles.disable,'Value')==1
ResultStr = [{['Fbest ','=',' ', num2str(Fbest(1,1,end)),'
','Gbest','=','(',num2str(gbest(1,1,end)),',',num2str(gbest(1,2,end)
),')']}];
set(handles.Result_window, 'String', ResultStr);
end
set(handles.start,'Enable','on');
set(handles.pause,'String','PAUSE','Enable','off'); end
end
if get(handles.disable,'Value')==1
ResultStr = [{['Fbest ','=',' ', num2str(Fbest(1,1,end)),'
','Gbest','=','(',num2str(gbest(1,1,end)),',',num2str(gbest(1,2,end)
),')']}];
set(handles.Result_window, 'String', ResultStr);
end
set(handles start,'Enable','on'); if get(handles.disable,'Value')==1 if get(handles.disable,'Value')==1
ResultStr = [{['Fbest ','=',' ', num2str(Fbest(1,1,end)),'
','Gbest','=','(',num2str(gbest(1,1,end)),',',num2str(gbest(1,2,end)
),')']}];
set(handles.Result window, 'String', ResultStr); if get(handles.disable, Value )
1
ResultStr = [{['Fbest ','=',' ', num2str(Fbest(1,1,end)),'
','Gbest','=','(',num2str(gbest(1,1,end)),',',num2str(gbest(1,2,end)
),')']}]; if get(handles.disable, Value )
1
ResultStr = [{['Fbest ','=',' ', num2str(Fbest(1,1,end)),'
','Gbest','=','(',num2str(gbest(1,1,end)),',',num2str(gbest(1,2,end)
),')']}]; ','Gbest','=','(',num2str(gbest(1,1,end)),',',num2str(gbest(1,2
),')']}];
set(handles.Result_window, 'String', ResultStr);
end ), ) ]}];
set(handles.Result_window, 'String', ResultStr);
end set(handles.start,'Enable','on'); set(handles.start,'Enable','on');
set(handles.pause,'String','PAUSE','Enable','off'); set(handles.pause,'String','PAUSE','Enable','off'); MATLAB – A Ubiquitous Tool for the Practical Engineer 102 9. Appendix 3: eldrun.m cla; unctnames = get(handles.select_func,'String'); unctname = functnames{get(handles.select_func,'Value')}; max = str2double(get(handles.wmax, 'String')); min = str2double(get(handles.wmin, 'String')); c1 = str2double(get(handles.c1, 'String')); c2 = str2double(get(handles.c2, 'String')); N = str2double(get(handles.N, 'String')); itmax = str2double(get(handles.itmax, 'String')); pso_para = getappdata(gcbf, 'm pso para = getappdata(gcbf, 'metricdata'); pso_para.wmax = wmax; pso_para.wmin = wmin; pso_para.c1 = c1; pso_para.c2 = c2; pso_para.N = N; pso_para.itmax = itmax; _
setappdata(gcbf, 'metricdata', pso_para); [Gen,Demand]=feval(functname); [Gen,Demand]=feval(functname); %Initialization of PSO parameters p
D=size(Gen,1); % Dimension (Number of Generator)
CR = 0.5; D=size(Gen,1); % Dimension (Number of Generator)
CR = 0 5; for iter=1:pso_para.itmax for iter=1:pso_para.itmax
W(iter)= pso_para.wmax-((pso_para.wmax- W(iter)= pso_para.wmax-((pso_para.wmax- pso_para.wmin)/pso_para.itmax)*iter; pso_para.wmin)/pso_para.itmax)*iter;
end %Initialization of positions of agents
%agents are initialized between P_min,P_ %Initialization of positions of agents
%agents are initialized between P_min,P_max randomly
for i=1:D or i 1:D
P_min(i) = Gen(i,6); % P_min
P_max(i) = Gen(i,7); % P_max % Constraints handling Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 103 end
end
L=1;
while ok==0
A(L) = Demand -(sum(A(:))-A(L)
if A(L) < P_min(p(L))
A(L) = P_min(p(L));
ok=0;
L = L+1;
if L==D+1
ok=1;
yes=1;
else
end
else
if A(L) > P_max(p(L))
A(L) = P_max(p(L));
ok=0;
L= L+1;
if L==D+1
ok=1;
yes =1;
else
end
else
ok=1;
yes=0;
end
end
end
end
for k=1:D
x(i,p(k))=A(k);
end
end
%Initialization of velocities of agents end MATLAB – A Ubiquitous Tool for the Practical Engineer 104 MATLAB – A Ubiquitous Tool for the Practical Engineer %Between V_min , V_max, (which can also be started from zero)
for i=1:pso_para.N %Between V_min , V_max, (which can also be started from zero)
for i=1:pso_para.N m(j) = Gen(j,6) - x(i,j); %V_min _
n(j) = Gen(j,7) - x(i,j); %V_max _
V(i,j) = m(j) + (n(j)-m(j)) * rand; % End of Initialization % Function to be minimized. for i=1:pso_para.N; for j 1:D;
Cost(i,j) = Gen(j,1) + Gen(j,2)*x(i,j) + Gen(j,3)*x(i,j).^2
s(Gen(j,4)*sin(Gen(j,5)*(Gen(j,6)-x(i,j)))); j
;
Cost(i,j) = Gen(j,1) + Gen(j,2)*x(i,j) + Gen(j,3)*x(i,j).^2
+ abs(Gen(j,4)*sin(Gen(j,5)*(Gen(j,6)-x(i,j))));
end F(i,1) = sum(Cost(i,:)); % Total Cost
end Gen_sum(1,1) = sum(gbest(1,:)); %Matrix composed of gbest vector Cost_Best(1,j) =
Gen(j,1)+Gen(j,2)*gbest(1,j)+Gen(j,3)*gbest(1,j).^2
+abs(Gen(j,4)*sin(Gen(j,5)*(Gen(j,6)-gbest(1,j))));
end Fbest(1,1) = sum(Cost_Best(1,:)); % Total Cost
%
i
h
dli Fbest(1,1) = sum(Cost_Best(1,:)); % Total Cost % Constraints handling % Constraints handling
for i=1:pso_para.N
yes=1;
while yes==1
p=randperm(D);
for n=1:D-1
g = p(n);
V(i,g) = W(1) * V(i,g) + c1*rand*(pbest(i,g)-x(i,g)) +
c2*rand*(gbest(1,g)-x(i,g));
x(i,g)=x(i,g) + V(i,g);
if rand<=CR
x_adj(i,g) = x(i,g);
else
x_adj(i,g) = pbest(i,g);
end
A(n) = x_adj(i,g);
if A(n) < P_min(g)
A(n) = P_min(g);
else
if A(n) > P_max(g)
A(n) = P_max(g); % Constraints handling
for i=1:pso_para.N
yes=1;
while yes==1
p=randperm(D);
for n=1:D-1
g = p(n);
V(i,g) = W(1) * V(i,g) + c1*rand*(pbest(i,g)-x(i,g)) +
c2*rand*(gbest(1,g)-x(i,g));
x(i,g)=x(i,g) + V(i,g);
if rand<=CR
x_adj(i,g) = x(i,g);
else
x_adj(i,g) = pbest(i,g);
end
A(n) = x_adj(i,g);
if A(n) < P_min(g)
A(n) = P_min(g);
else
if A(n) > P_max(g)
A(n) = P_max(g); for i=1:pso_para.N for i=1:pso_para.N
yes=1; while yes==1 A(n) = x_adj(i,g); _
if A(n) < P_min(g) _
g
A(n) = P_min(g); _
A(n) = P_max(g); Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 105 MATLAB – A Ubiquitous Tool for the Practical Engineer 106 q
end
end
end
for k=1:D
x_adj(i,p(k))=A(k);
end
end
for j=2:pso_para.itmax
% Calculation of new positions
for i=1:pso_para.N
for k=1:D
Cost(i,k) =
Gen(k,1)+Gen(k,2)*x_adj(i,k)+Gen(k,3)*x_adj(i,k).^2
+abs(Gen(k,4)*sin(Gen(k,5)*(Gen(k,6)-x_adj(i,k))));
end
F(i,j) = sum(Cost(i,:)); % Total Cost
end
for i=1:pso_para.N
[C,I]=min(F(i,:));
if F(i,j)<=C
pbest(i,:)=x_adj(i,:);
else
end
end
for i=1:pso_para.N
for k=1:D
Cost_pbest(i,k) =
Gen(k,1)+Gen(k,2)*pbest(i,k)+Gen(k,3)*pbest(i,k).^2
+abs(Gen(k,4)*sin(Gen(k,5)*(Gen(k,6)-pbest(i,k))));
end
F_pbest(i,1) = sum(Cost_pbest(i,:)); % Total Cost
end
[C,I]=min(F_pbest(:,1));
for k=1:D
gbest(1,k)=pbest(I,k);
end
Gen_sum(j,1) = sum(gbest(1,:));
Fbest(j,1) = C;
% Constraints handling
for i=1:pso_para.N
yes=1;
while yes==1
p=randperm(D);
for n=1:D-1
g = p(n); pbest(i,:)=x_adj(i,:); F_pbest(i,1) = sum(Cost_pbest(i,:)); % Total Cost
end
i
1 [C,I]=min(F_pbest(:,1)); for k=1:D Gen_sum(j,1) = sum(gbest(1,:)); Ge _su (j, )
su (gbest( ,:));
Fbest(j,1) = C;
% Constraints handling
for i=1:pso_para.N
yes=1;
while yes==1
p=randperm(D);
for n=1:D-1
g = p(n);
V(i,g) = W(j) * V(i,g) + c1*rand*(pbest(i,g)-x(i,g))
+ c2*rand*(gbest(1,g)-x(i,g));
x(i,g) = x(i,g) + V(i,g);
if rand<=CR if rand<=CR set(handles.Result_window, 'String', ResultStr);
end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
set(handles.start,'Enable','on');
set(handles.pause,'String','PAUSE','Enable','off'); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
set(handles.start,'Enable','on'); set(handles.start,'Enable','on'); set(handles.start,'Enable','on');
set(handles.pause,'String','PAUSE','Enable','off'); set(handles.pause,'String','PAUSE','Enable','off'); Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 107 x_adj(i,g) = x(i,g);
else
x_adj(i,g) = pbest(i,g);
end
A(n) = x_adj(i,g);
if A(n) < P_min(g)
A(n) = P_min(g);
else
if A(n) > P_max(g)
A(n) = P_max(g);
else
end
end
end
SUM=0;
for f=1:D-1
SUM = SUM + A(f);
end
A(D) = Demand - SUM;
g=p(D);
if A(D) < P_min(g)
A(D) = P_min(g);
ok=0;
else
if A(D) > P_max(g)
A(D) = P_max(g);
ok=0;
else
ok=1;
yes=0;
end
end
L=1;
while ok==0
A(L) = Demand -(sum(A(:))-A(L));
if A(L) < P_min(p(L))
A(L) = P_min(p(L));
ok=0;
L = L+1;
if L==D+1
ok=1;
yes=1;
else
end
else
if A(L) > P_max(p(L))
A(L) = P_max(p(L));
ok=0;
L= L+1; MATLAB – A Ubiquitous Tool for the Practical Engineer 108 if L==D+1
ok=1;
yes=1;
else
end
else
ok=1;
yes=0;
end
end
end
end
for k=1:D
x_adj(i,p(k))=A(k);
end
end if L==D+1
ok=1;
yes=1;
else
end
else
ok=1;
yes=0;
end
end
end
end
for k=1:D
x_adj(i,p(k))=A(k);
end
end if L==D+1
ok=1;
yes=1;
else
end
else
ok=1;
yes=0;
end
end
end
end
for k=1:D
x_adj(i,p(k))=A(k);
end
end end if get(handles.disable,'Value')==0
set(gcf,'Doublebuffer','on');
%%%%%%%%% Display to the ListBox%%%%%%%%%%
ResultStr(1) = [{['Total Generation Cost %%%%%%%%% Display to the ListBox%%%%%%%%%%
ResultStr(1) = [{['Total Generation Cost at Iteration
','1',' ','=',' ', num2str(Fbest(1,1))]}];
ResultStr(j) = [{['Total Generation Cost at Iteration
',num2str(j),' ','=',' ', num2str(Fbest(end,1))]}];
set(handles.Result window, 'String', ResultStr); ','1',' ','=',' ', num2str(Fbest(1,1))]}];
ResultStr(j) = [{['Total Generation Cost ResultStr(j) = [{[ Total Generation Cost at Iteration
',num2str(j),' ','=',' ', num2str(Fbest(end,1))]}];
set(handles.Result window, 'String', ResultStr); ',num2str(j),' ','=',' ', num2str(Fbest(end,1))]}];
i
i ',num2str(j),' ','=',' ', num2str(Fbest(end,1))]}];
set(handles.Result_window, 'String', ResultStr); set(handles.Result_window, 'String', ResultStr); %%%%%%%%% end of Display %%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%% AXE-1 %%%%%%%%%%%%%%%%%
axes(handles.axes1);
cla;
set(gca,'xlim',[0 pso_para.itmax],'ylim',[0 Fbest(1,1)]),
plot(Fbest(:),'r-')
if j<=pso para.itmax/2 cla;
set(gca,'xlim',[0 pso_para.itmax],'ylim',[0 Fbest(1,1)]),
plot(Fbest(:),'r-')
if j<=pso para.itmax/2 set(gca,'xlim',[0 pso_para.itmax],'ylim',[0 Fbest(1,1)]), plot(Fbest(:),'r-') if j<=pso_para.itmax/2 _
text(j,Fbest(end,1),['Fbest = ', j
Fbest(end,1))],'HorizontalAlignment','Left','VerticalAlignme
tom','EdgeColor','blue','LineWidth',3); num2str(Fbest(end,1))],'HorizontalAlignment','Left','VerticalAlignme
nt','bottom','EdgeColor','blue','LineWidth',3);
else text(j,Fbest(end,1),['Fbest = ',
num2str(Fbest(end,1))],'HorizontalAlignment','Right','VerticalAlignm
ent','bottom','EdgeColor','blue','LineWidth',3);
end ent','bottom','EdgeColor','blue','LineWidth',3);
end legend('Fbest'); hold on %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%% AXE-2 %%%%%%%%%%%%%%%% axes(handles.axes2); axis([0 D+1 0 max(Gen(:,7))+50] bar(Gen(:,7),'r') hold on bar(gbest,'w') Educational Simulator for Particle Swarm Optimization and Economic Dispatch Applications 109 drawnow
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else
end
end
if get(handles.disable,'Value')==1
cla;
ResultStr = [{['Total Generation Cost ','=',' ',
num2str(Fbest(end,1))]}];
set(handles.Result_window, 'String', ResultStr);
end
%%%%%%%%%%%%%%%%% AXE-2 %%%%%%%%%%%%%%%%
axes(handles.axes2);
axis([0 D+1 0 max(Gen(:,7))+50])
bar(Gen(:,7),'r')
hold on
bar(gbest(end,:),'w')
drawnow
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 10. References A. J. Wood and B. F. Wollenbergy (1984). Power Genration, Operation, and Control, New
York: Wiley. y
C. E. Lin and G. L. Viviani (1984). Hierarchical economic dispatch for piecewise quadratic
cost functions, IEEE Trans. Power App. System, vol. PAS-103, no. 6, pp. 1170-1175. D. A. Wiegmann, G. R. Essenberg, T. J. Overbye, and Y. Sun (2005). Human Factor Aspects
of Power System Flow Animation, IEEE Trans. Power Syst., vol. 20, no. 3, pp. 1233-
1240. D. A. Wiegmann, T. J. Overbye, S. M. Hoppe, G. R. Essenberg, and Y. Sun (2006). Human
Factors Aspects of Three-Dimensional Visualization of Power System Information,
IEEE Power Eng. Soci. Genral Meeting, pp. 7. g
g pp
D. C. Walters and G. B. Sheble (1993). Genetic algorithm solution of economic dispatch with
the valve point loading, IEEE Trans. Power Syst., vol. 8, pp. 1325-1332. H. T. Yang, P. C. Yang, and C. L. Huang (1996). Evolutionary programming based economic
dispatch for units with nonsmooth fuel cost functions, IEEE Trans. Power Syst., vol. 11, no. 1, pp. 112-118. pp
H. Yoshida, K. Kawata, Y. Fukuyama, S. Takayama, and Y. Nakanishi (2000). A particle
swarm optimization for reactive power and voltage control considering voltage
security assessment, IEEE Trans. Power System, vol. 15, pp. 1232-1239. y
y
pp
J. B. Park, K. S. Lee, J. R. Shin, and K. Y. Lee (2005). A particle swarm optimization for
economic dispatch with nonsmooth cost functions, IEEE Trans. Power Syst., vol. 20,
no. 1, pp. 34-42. J. H. Park, Y. S. Kim, I. K. Eom, and K. Y. Lee (1993). Economic load dispatch for piecewise
quadratic cost function using Hopfield neural network, IEEE Trans. Power Syst., vol. 8, pp. 1030-1038. 110 MATLAB – A Ubiquitous Tool for the Practical Engineer J. Kennedy and R. Eberhart (1995). Particle swarm optimization, Proc. IEE Int. Conf. Neural
Networks (ICNN'95), vol. IV, Perth, Australia, pp.1942-1948. pp
J. Kennedy and R. C. Eberhart (2001). Swarm Intelligence. San Francisco, CA: Morgan
Kaufmann. f
K. Y. Lee, A. Sode-Yome, and J. H. Park (1998). Adaptive Hopfield neural network for
economic load dispatch, IEEE Trans. Power Syst., vol. 13, pp. 519-526. y
K. Y. Lee and M. A. El-Sharkawi, Eds. (2002). Modern Heuristic Optimization Techniques
with Applications to Power Systems: IEEE Power Engineering Society (02TP160). L. S. Coelho and V. C. Mariani (2006). Decomposition Approach for
Inverse Matrix Calculation
Krasimira Stoilova and Todor Stoilov
Institute of Information and Communication Technologies
Academy of Sciences
Bulgaria Krasimira Stoilova and Todor Stoilov
Institute of Information and Communication Technologies
Academy of Sciences
Bulgaria 10. References Combining of chaotic differential evolution and
quadratic programming for economic dispatch optimization with valve-point
effect, IEEE Trans. Power Syst., vol. 21, No. 2. M. Clerc and J. Kennedy (2002). The particle swarm-expolsion, stability, and convergence in
a multidimensional complex space, IEEE Trans. Evol. Comput., vol. 6, no. 1, pp. 58-
73. N. Sinha, R. Chakrabarti, and P. K. Chattopadhyay (2003). Evolutionary programming
techniques for economic load dispatch, IEEE Trans. on Evolutionary Computations,
Vol. 7, No. 1, pp. 83-94. ,
, pp
T. A. A. Victoire and A. E. Jeyakumar (2004). Hybrid PSO-SQP for economic dispatch with
valve-point effect, Electric Power Syst. Research, vol. 71, pp. 51-59. Victoire and A. E. Jeyakumar (2005). Reserve constrained dynamic dispatch of units
with valve-point effects, IEEE Trans. Power Syst., vol. 20, No. 3, pp. 1273-1282. T. J. Overbye, D. A. Wiegmann, A. M. Rich, and Y. Sun (2003). Human Factor Aspects of
Power System Voltage Contour Visualizations, IEEE Trans. Power Syst., vol. 18, no. 1, pp. 76-82. W. M. Lin, F. S. Cheng, and M. T. Tasy (2002). An improved Tabu search for economic
dispatch with multiple minima, IEEE Trans. Power Syst., vol. 17, pp. 108-112. Y. M. Park, J. R. Won, and J. B. Park (1998). A new approach to economic load dispatch
based on improved evolutionary programming, Eng. Intell. Syst. Elect. Eng. Commun., vol. 6, no. 2, pp. 103-110. 6 1. Introduction Frequently, numerical algorithms are based on sequentially solution of linear set of equation
Ax=b, applying small influences of few components of matrix A, which changes to a new
one A*. Thus, new equation set is defined, with new matrix A*, which has to be solved for
the current numerical iteration. Instead of solving the new equation set, it is beneficial to
evaluate a new inverse matrix A*-1, having the evaluations for the previous inverse matrix A-
1. Many control algorithms, on-line decision making and optimization problems reside on
the prompt evaluation of the inverse matrix A-1, stated as a quadratic nonsingular, e.g. A.A-1=A-1. A=I, where I is identity matrix. Currently, for the evaluation of the inverse matrix
A-1 three general types of A factorization are applied: LU factorization, QR – decomposition
and SVD-decomposition to singular values of A. LU – factorization. It results after the application of Gauss elimination to linear set of
equations Ax=b to obtain a good computational form of A (Fausett, 1999). The factorization
of A is obtained by multiplication of two triangular matrices, upper U and lower L
triangular, related to the initial one by LU=A , or 11
11
12
13
11
12
13
21
22
22
23
21
22
23
31
32
33
33
31
32
33
0
0
0 . 0
. 0
0
l
u
u
u
a
a
a
l
l
u
u
a
a
a
l
l
l
u
a
a
a
The LU factorization can be applied for the solution of linear set of equations to evaluate the
inverse matrix of A: A-1. The evaluation of A-1 is performed on two steps, for given LU
factorization of A, A=LU (L,U - given): First: the matrix equation LY=I is solved. The first column of matrix Y is found from the
linear equation system
(:,1)
1
0
... 0
T
LY
. The next columns of Y are calculated by
solving this linear equation set with the next columns of matrix I. The solution of this set of solving this linear equation set with the next columns of matrix I. The solution of this set of
equations is found by sequential substitution from top to down, because the matrix L is a
lower triangular and there is no need to find the inverse L-1. 1. Introduction g
Second: Using the solution matrix Y* a new linear matrix equation system is solved U.X=Y*. Because U is upper triangular, each column of X is calculated with the corresponding 112 MATLAB – A Ubiquitous Tool for the Practical Engineer column of Y* by substitutions from bottom to top. Thus, no inverse matrix U –1 is calculated,
which speeds up the calculations. column of Y* by substitutions from bottom to top. Thus, no inverse matrix U –1 is calculated,
which speeds up the calculations. The solution X=A-1 is the inverse matrix of the initial one A. Thus, the inverse matrix A-1 is
found by LU factorization of A and twice solution of triangular linear matrix equation
systems, applying substitution technique. QR decomposition The QR decomposition of matrix A is defined by the equality A=Q.R,
where R is upper triangular matrix and Q is orthogonal one, Q-1=QT. Both matrices Q and R
are real ones. As the inverse A-1 is needed, A-1=R-1.Q-1. Following the orthogonal features of
Q, it is necessary to evaluate only R-1, which can be done from the linear matrix system
R.Y=I. Because R is upper triangular matrix, the columns of the inverse matrix Y=R-1 can be
evaluated with corresponding columns of the identity matrix I by merely substitutions from
bottom to down. Hence, the inverse matrix A-1 is found by QR factorization of A, sequential
evaluation of R-1 by substitutions in linear upper triangular matrix system and finally by
multiplication of R-1 and QT. SVD – decomposition to singular values This decomposition is very powerful, because it allows
to be solved system equations when A is singular, and the inverse A-1 does not exist in
explicit way (Flannery, 1997). The SVD decomposition, applied to a rectangular MxN matrix
A, represents the last like factorization of three matrices: A=U.W.VT, Instead of direct finding an
inverse matrix, it is worth to find analytical relations where lower dimensions inverse
l bl
l
l
l
f
l
l of a corresponding inverse of a modified matrix A* -1 are derived in (Strassen, 1969). The
components of the inverse matrix can be evaluated analytically. of a corresponding inverse of a modified matrix A -1 are derived in (Strassen, 1969). The
components of the inverse matrix can be evaluated analytically. Finding the inverse matrix is related with a lot of calculations. Instead of direct finding an
inverse matrix, it is worth to find analytical relations where lower dimensions inverse
matrices components are available. Here analytical relations for inverse matrix calculation
are derived and the corresponding MATLAB codes are illustrated. Finding the inverse matrix is related with a lot of calculations. Instead of direct finding an
inverse matrix, it is worth to find analytical relations where lower dimensions inverse
matrices components are available. Here analytical relations for inverse matrix calculation
are derived and the corresponding MATLAB codes are illustrated. 2. Analytical relations among the components of inverse matrix Initial optimization problem is given in the form 1
1
1
1
2
1
2
2
2
2
0
1
min
0
2
T
T
T
T
x
Q
x
x
x
x
R
R
Q
x
x
(1) (1) 1 1
2
2
1 1
1
2
2
2
a x
a x
d
b x
C
b x
C
1 1
2
2
1 1
1
2
2
2
a x
a x
d
b x
C
b x
C
where the matrices dimensions are:
1
1
1
|n x
x
;
1
1
1|n xn
Q
;
1
1
1
|n x
R
;
0
1
1|m xn
a
;
0 1
|m x
d where the matrices dimensions are:
1
1
1
|n x
x
;
1
1
1|n xn
Q
;
1
1
1
|n x
R
;
0
1
1|m xn
a
;
0 1
|m x
d where the matrices dimensions are:
1
1
1
|n x
x
;
1
1
1|n xn
Q
;
1
1
1
|n x
R
;
0
1
1|m xn
a
;
0 1
|m x
d 2
2
1
|n x
x
;
2
2
2|n xn
Q
;
2
2
1
|n x
R
;
0
2
2|m xn
a
;
1
1
1|m xn
b
;
1
1
1
|m x
C
;
2
2
2|m xn
b
;
2
2
1
|m x
C
;
1
2
0
0
Q
Q
Q
;
1
2
R
R
R
Peculiarity of problem (1) is that the connected condition
1 1
2
2
a x
a x
d
distributes a
common resource d while the subsystems work with own resources С1 and С2. A=U.W.VT, where U is MxN orthogonal matrix, W is NxN diagonal matrix with nonnegative
components (singular values) and VT is a transpose NxN orthogonal matrix V or UTU=VTV=I NxN . The SVD decomposition can always be performed, nevertheless of the singularity of the
initial matrix A. If A is a square NxN matrix, hence all the matrices U, V and W are square
with the same dimensions. Their inverse ones are easy to find because U and V are
orthogonal and their inverses are equal to the transpose ones. W is a diagonal matrix and the
corresponding inverse is also diagonal with components 1/wj , j=1,N. Hence, if matrix A is
decomposed by SVD factorization, A=U.W.VT, then the inverse one is A-1=V.[diag1/wj].UT. The problem of the evaluation of the inverse A-1 appears if a singular value wj exists, which
tends to zero value. Hence, if matrix A is a singular one, the SVD decomposition easily
estimates this case. Hence, the peculiarities of LU, QR and SVD factorizations determine the computational
efficiency of the evaluations for finding the inverse matrix A-1. Particularly, the simplest
method, from evaluation point of view, is LU factorization followed by QR decomposition
and SVD factorization. All these methods do not use peculiarities, if matrix A* slightly differs
from the initial matrix A. The inverse of A* has to be evaluated starting with its factorization
and sequentially solution of linear matrix equation systems. Hence, it is worth to find
methods for evaluation of the inverse of A*, which differs from A in few components and A-1
is available. The new matrix A* can contain several modified components aij. Hence, the
utilization of components from the inverse A-1 for the evaluation of the new inverse matrix
A*-1 can speed up considerably the numerical calculations in different control algorithms and
decreases the evaluation efforts. Relations for utilization of components of A-1 for evaluation 113 Decomposition Approach for Inverse Matrix Calculation of a corresponding inverse of a modified matrix A* -1 are derived in (Strassen, 1969). The
components of the inverse matrix can be evaluated analytically. of a corresponding inverse of a modified matrix A* -1 are derived in (Strassen, 1969). The
components of the inverse matrix can be evaluated analytically. Finding the inverse matrix is related with a lot of calculations. 2. Analytical relations among the components of inverse matrix For
simplicity of the writing it can be put 0
1
0
1
2
1
1
1
2
1
1
1 (
)
1
|
0
m xn
m
m
m
xn
m xn
m xn
a
A
b
;
0
2
0
1
2
2
1
2
2
2
2
2 (
)
2
|
0
m xn
m
m
m
xn
m xn
m xn
a
A
b
; 0
1
2
1
2 (
) 1
m
m
m
x
d
D
C
C
;
0
1
2
1
2
1
2
(
) (
)
| m
m
m
x n xn
A
A
A
. (2) ;
0
1
2
1
2
1
2
(
) (
)
| m
m
m
x n xn
A
A
A
. (2) (2) 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h (5) It is necessary to be known the matrices A1, A2, Q1, Q2, R1, R2 for evaluating the solutions (5)
Determination of
1
T
AQ
A
It is necessary to be known the matrices A1, A2, Q1, Q2, R1, R2 for evaluating the solutions (5)
Determination of
1
T
AQ
A
Determination of
1
T
AQ
A
f
Q
Applying (3) it is obtained f
3) it is obtained Applying (3) it is obtained Applying (3) it is obtained 1
1
1
1
1
1
1
2
1
1
1
2
2
2
1
2
2
0
0
T
T
T
T
T
Q
A
AQ
A
A
A
A Q
A
A Q
A
Q
A
. (6) (6) Using (2) it follows Using (2) it follows Using (2) it follows 0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
0
0
0
0
T
T
m xm
m xm
m xm
T
T
T
m xm
m xm
m xm
m xm
m xm
m xm
a Q
a
a Q b
A Q
A
b Q
a
b Q b
,
(7)
0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
2
2
2
2
2
2
1
2
2
2
1
1
2
2
2
2
2
2
0
0
0
0
0
T
T
m xm
m xm
m xm
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
a Q
a
a Q b
A Q
A
b Q
a
b Q b
. 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h 2.1 Decomposition of the initial problem by goal coordination
The initial problem (1) can be solved by two manners using hierarchical approach according
to the hierarchical multilevel systems (Mesarovich et al, 1973; Stoilov & Stoilova, 1999): by
goal coordination and by predictive one. Taking into account the substitutions 1
2
0
0
Q
Q
Q
;
1
2
R
R
R
;
1
2
A
A
A
;
1
2
x
x
x
,
(3) (3) MATLAB – A Ubiquitous Tool for the Practical Engineer 114 the solution of (1) can be found in analytical form (Stoilova, 2010) : the solution of (1) can be found in analytical form (Stoilova, 2010) : 1
1
1
1
(
) (
)
opt
T
T
x
Q
R
A
AQ
A
AQ
R
D
(4) 1
1
1
1
(
) (
)
opt
T
T
x
Q
R
A
AQ
A
AQ
R
D
(4) (4) or or
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
opt
T
T
T
x
Q R
Q
A
A Q
A
A Q
A
A Q
R
A Q
R
D
(5)
1
1
1
1
1
1
1
2
2
2
2
1
1
1
2
2
2
1
1
1
2
2
2
2
opt
T
T
T
x
Q R
Q
A
A Q
A
A Q
A
A Q R
A Q
R
D
. 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h (8) (7) (8) After substitution of (7) and (8) in (6)
1
T
AQ
A
and
1
1
(
)
T
AQ
A
can be determined 0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
2
2
2
1
1
1
1
1
1
1
1
2
2
2
2
2
2
0
0
T
T
T
T
m xm
m xm
m xm
T
T
T
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
a Q
a
a Q
a
a Q b
a Q b
AQ
A
A Q
A
A Q
A
b Q
a
b Q b
b Q
a
b Q b
(9) (9) 0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
1
2
2
2
1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
(
)
(
)
0
0
T
T
T
T
T
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
AQ
A
A Q
A
A Q
A
a Q
a
a Q
a
a Q b
a Q b
b Q
a
b Q b
b Q
a
b Q b
. (10) (10) 115 Decomposition Approach for Inverse Matrix Calculation The manner of definition of matrix
1
T
AQ
A
shows that it is a symmetric one. The manner of definition of matrix
1
T
AQ
A
shows that it is a symmetric one. 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h Determination of
1
AQ R
D
Using (2) and (3) it follows 1
1
1
1
1
2
2
2
1
1
1
1
1
1
1
2
2
2
2
a Q
R
a Q
R
d
AQ
R
D
b Q
R
C
b Q
R
C
(11) (11) Determination of
1
1
1
(
) (
)
T
AQ
A
AQ
R
D
Using (10) and (11), it is obtained Determination of
1
1
1
(
) (
)
T
AQ
A
AQ
R
D
Using (10) and (11), it is obtained Determination of
1
1
1
(
) (
)
T
AQ
A
AQ
R
D
Using (10) and (11), it is obtained 0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
(
) (
)
0
0
T
T
T
T
m xm
m xm
m xm
T
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
a Q
a
a Q
a
a Q b
a Q b
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
a
b Q b
b Q
R
C
b Q
R
C
b Q
a
b Q b
0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
11
12
13
1
1
1
2
2
2
1
1
1
1
21
22
23
1
1
1
1
1
31
32
33
2
2
2
2
(
) (
)
m xm
m xm
m xm
T
m xm
m xm
m xm
m xm
m xm
m xm
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
R
C
b Q
R
C
where 0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
(
) (
)
0
0
T
T
T
T
m xm
m xm
m xm
T
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
a Q
a
a Q
a
a Q b
a Q b
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
a
b Q b
b Q
R
C
b Q
R
C
b Q
a
b Q b
0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
(
) (
)
0
0
T
T
T
T
m xm
m xm
m xm
T
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
a Q
a
a Q
a
a Q b
a Q b
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
a
b Q b
b Q
R
C
b Q
R
C
b Q
a
b Q b
0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
(
) (
)
0
0
T
T
T
T
m xm
m xm
m xm
T
T
T
m xm
m xm
m xm
T
T
m xm
m xm
m xm
a Q
a
a Q
a
a Q b
a Q b
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
a
b Q b
b Q
R
C
b Q
R
C
b Q
a
b Q b
0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
11
12
13
1
1
1
2
2
2
1
1
1
1
21
22
23
1
1
1
1
1
31
32
33
2
2
2
2
(
) (
)
m xm
m xm
m xm
T
m xm
m xm
m xm
m xm
m xm
m xm
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
R
C
b Q
R
C
where 0
1
0
2
0
0
1
0
1
1
1
2
2
0
2
1
2
2
1
1
11
12
13
1
1
1
2
2
2
1
1
1
1
21
22
23
1
1
1
1
1
31
32
33
2
2
2
2
(
) (
)
m xm
m xm
m xm
T
m xm
m xm
m xm
m xm
m xm
m xm
a Q
R
a Q
R
d
AQ
A
AQ
R
D
b Q
R
C
b Q
R
C
where 0
1
2
0
1
2
11
12
13
1
1
21
22
23
31
32
33 (
) (
)
(
)
T
m
m
m
x m
m
m
AQ
A
(12) (12) Taking into account the structure of matrix
1
1
(
)
T
AQ
A
, then
23
32
0,
0
. 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h They are useful only if the components ij of the inverse matrix (12) are known. However, if ij are not known (the usual case) relations (15) can not be applied. Analytical relations (15) are a result of applying a goal coordination for solving the initial
problem (1). They are useful only if the components ij of the inverse matrix (12) are known. However, if ij are not known (the usual case) relations (15) can not be applied. 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h Consequently, the term
1
1
1
(
) (
)
T
AQ
A
AQ
R
D
is 1
1
1
1
11
1
1
1
2
2
2
12
1
1
1
1
13
2
2
2
2
1
1
1
1
1
1
1
21
1
1
1
2
2
2
22
1
1
1
1
23
2
2
2
2
0
1
1
1
31
1
1
1
2
2
2
32
1
1
1
1
3
0
(
)
(
)
(
)
(
)
(
)
(
)
(
)
(
)
(
)
(
)
T
a Q
R
a Q
R
d
b Q
R
C
b Q
R
C
AQ
A
AQ
R
D
a Q
R
a Q
R
d
b Q
R
C
b Q
R
C
a Q
R
a Q
R
d
b Q
R
C
0
1
2
1
1
1
1
3
2
2
2
2
(
)
m x
m x
m x
b Q
R
C
(13) (13) Determination of
1
1
1
(
) (
)
T
T
A
AQ
A
AQ
R
D
After a substitution of (2) in (13) it follows MATLAB – A Ubiquitous Tool for the Practical Engineer 116 1
0
1
0
1
2
2
0
2
1
2
2
1
1
1
1
1
2
2
0
(
) (
)
0
T
T
n xm
m xm
n xm
T
T
T
n xm
n xm
n xm
a
b
AQ
A
AQ
R
D
a
b
0
0
0
1
0
2
0
1
2
1
2
1
0
1
1
0
0
0
2
0
11
12
13
1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
1
1
1
1
1
2
2
2
2
21
22
1
1
1
11
1
1
2
2
1
1
1
2
2
2
31
1
(
)
(
)
(
)
0
(
m xm
m xm
m xm
T
T
T
T
T
T
m x
m x
m x
m xm
m xm
m xm
m xm
T
T
m x
m xm
a
b
a Q R
a Q R
d
a
b
b Q R
C
a
b
b Q R
C
a
b
a Q R
a Q R
d
0
2
0
1
1
2
1
2
2
2
13
12
1
1
2
2
1
1
1
1
2
2
2
2
2
2
33
1
1
)
(
)
(
)
0
m xm
m xm
T
T
T
T
m x
m x
m xm
m xm
a
b
b Q R
C
a
b
b Q R
C
Consequently, the term
1
1
1
(
) (
)
T
T
A
AQ
A
AQ
R
D
becomes Consequently, the term
1
1
1
(
) (
)
T
T
A
AQ
A
AQ
R
D
becomes 1
1
1
1
1
2
2
2
1
11
12
13
1
1
1
1
1
1
21
22
1
2
2
2
2
1
1
1
1
1
1
1
1
2
2
2
1
11
12
13
2
2
1
1
1
1
31
33
1
2
2
2
2
0
(
) (
)
0
T
T
T
T
T
T
a Q
R
a Q
R
d
a
b
b Q
R
C
b Q
R
C
A
AQ
A
AQ
R
D
a Q
R
a Q
R
d
a
b
b Q
R
C
b Q
R
C
(14) (14) After putting (3) and (14) in (5) the analytical solutions of the initial problem (1) are After putting (3) and (14) in (5) the analytical solutions of the initial problem (1) are 1
1
1
1
1
2
2
2
1
1
1
11
12
13
1
1
1
1
1
1
1
1
1
1
21
22
1
2
2
2
2
0
opt
T
T
a Q
R
a Q
R
d
x
Q
R
Q
a
b
b Q
R
C
b Q
R
C
(15)
1
1
1
1
1
2
2
2
1
1
1
11
12
13
2
2
2
2
2
1
1
1
1
2
31
33
1
2
2
2
2
0
opt
T
T
a Q
R
a Q
R
d
x
Q
R
Q
a
b
b Q
R
C
b Q
R
C
(15) Analytical relations (15) are a result of applying a goal coordination for solving the initial
problem (1). 2.1 Decomposition of the initial problem by goal coordination
h
l
bl
( )
b
l
d b
h The
manner of definition of the inverce matrix shows that it is a symmetric one. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d According to the hierarchical approach, the subsystems work independently. The idea of the
predictive coordination is that the coordinator influences to each subsystem by independent
impacts instead of common impact in goal coordination. For the initial problem (1) Decomposition Approach for Inverse Matrix Calculation 117 decomposition by goal coordination can not be fully accomplished because of the connected
relation
1 1
2
2
a x
a x
d
. Applying predictive coordination, the connected restriction can be
decomposed to: decomposition by goal coordination can not be fully accomplished because of the connected
relation
1 1
2
2
a x
a x
d
. Applying predictive coordination, the connected restriction can be
decomposed to: 1 1
1
a x
y
;
2
2
2
a x
y
(16) (16) observing the condition for resource limitation observing the condition for resource limitation 1
2
y
y
d
(17) 1
2
y
y
d
(17) Fig. 1. Hierarchical approach for solving (1)
Coordinator
Subsystem 1
Subsystem 2
y1
y2
x1(y1)
x2(y2) Coordinator x1(y1) Subsystem 1 Subsystem 2 Fig. 1. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d Hierarchical approach for solving (1) Applying (16), the initial optimization problem (1) is decomposed to two optimization
subproblems with lower dimensions than the initial one: 1
1 1
1
1
1
min 2
T
T
x Q x
R x
2
2
2
2
2
1
min 2
T
T
x Q x
R x
(18)
0
1
0
1
1
1
1
m xn
m x
a
x
y
0
2
0
2
2
2
1
m xn
m x
a
x
y
1
1
1
1
1
1
1
m xn
m x
b
x
C
;
2
2
2
2
2
2
1
m xn
m x
b
x
C
1
1 1
1
1
1
min 2
T
T
x Q x
R x
2
2
2
2
2
1
min 2
T
T
x Q x
R x
(18) (18) where 0
1
0
1
2
1
1
1
2
1
1
1 (
)
1
|
0
m xn
m
m
m
xn
m xn
m xn
a
A
b
;
0
2
0
1
2
2
1
2
2
2
2
2 (
)
2
|
0
m xn
m
m
m
xn
m xn
m xn
a
A
b
;
0
1
2
1
1
1
1
1
1
0
m x
m x
m x
d
y
C
;
0
1
2
1
2
1
2
2
1
0
m x
m x
m x
d
y
C
and it can be realized and it can be realized and it can be realized 1
2
y
y
D
or
1
2
y
y
d
. The analytical solution of the first subproblem (18), according to (4), is The analytical solution of the first subproblem (18), according to (4), is
1
1
1
1
1
1
1
1
1
1
1
1
1
1
(
) (
)
opt
T
T
x
Q
R
A
A Q
A
A Q
R
D
. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d However, in the solution of problem (1) takes part a sum of the matrices
1
1
(
)
T
i
i
i
A Q
A
, so that the sum matrix
1
1
(
)
T
AQ
A
has a full rank. This matrix has a high
dimension and for it can not be used the specific structure
1
T
i
i
i
A Q
A
. To use the less rank
of matrices
1
T
i
i
i
A Q
A
, the definition of subproblems (18) has to be done by rejecting the
zero rows in matrices A1 and A2 . Respectively, the subproblems are obtained of the initial problem (1) by additional
modification of the admissible areas, determined by the matrices A1 and A2 instead of
direct decomposition. In that manner the modified subproblems will present only the
corresponding meaning components as follows: 1
_
1
1
1
1
1
0
a
a
A
b
A
b
;
2
_
2
2
2
2
2
0
a
a
A
A
b
b
;
1
_
1
1
1
1
1
0
y
y
y
C
y
C
;
2
_
2
2
2
2
2
0
y
y
y
y
C
C
. The modified subproblems (19) have lower dimension in comparison with (18), obtained by
direct decomposition The modified subproblems (19) have lower dimension in comparison with (18), obtained by
direct decomposition 1
1 1
1
1
1
min 2
T
T
x Q x
R x
;
2
2
2
2
2
1
min 2
T
T
x Q x
R x
(19) (19) __
_
1
1
1
A x
y
;
_
_
2
2
2
A x
y
0
1
1
_
1
1
(
)
1
m
m
xn
a
A
b
;
0
2
2
_
2
2
(
)
2
m
m
xn
a
A
b
0
1
_
1
1
(
) 1
1
m
m
x
y
y
C
;
0
2
_
2
2
(
) 1
2
m
m
x
y
y
C
. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d 1
1
1
1
1
1
1
1
1
1
1
1
1
1
(
) (
)
opt
T
T
x
Q
R
A
A Q
A
A Q
R
D
. 1
1
1
1
1
1
1
1
1
1
1
1
1
1
(
) (
)
opt
T
T
x
Q
R
A
A Q
A
A Q
R
D
. MATLAB – A Ubiquitous Tool for the Practical Engineer 118 The analysis of matrix A1 shows that it has zero rows. Respectively, the square matrix
1
1
T
T The analysis of matrix A1 shows that it has zero rows. Respectively, the square matrix The analysis of matrix A1 shows that it has zero rows. Respectively, the square matrix 1
1
1
1
2
1
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
(
)
(
)
0
|
0
0
0
0
0
0
T
T
T
T
T
T
T
n xn
n x m l
l
m l
l
xn
a Q a
a Q b
a
A Q
A
b
Q
a
b
b Q a
b Q b
has zero rows and columns, which means that the inverse matrix
1
1
(
)
T
AQ
A
does not
exist. However, in the solution of problem (1) takes part a sum of the matrices
1
1
(
)
T
i
i
i
A Q
A
, so that the sum matrix
1
1
(
)
T
AQ
A
has a full rank. This matrix has a high
dimension and for it can not be used the specific structure
1
T
i
i
i
A Q
A
. To use the less rank
of matrices
1
T
i
i
i
A Q
A
, the definition of subproblems (18) has to be done by rejecting the
zero rows in matrices A1 and A2 . has zero rows and columns, which means that the inverse matrix
1
1
(
)
T
AQ
A
does not
exist. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d The solutions of (18), obtained in analytical forms using (4), are 1
_
_
_
_
_
1
1
1
(
) (
)
1,2
opt
T
T
i
i
i
i
i
i
i
i
i
i
i
x
Q
R
A
A Q
A
A Q
R
y
i
. fter substitution of matrices
_
i
A with the corresponding matrix components, it follows After substitution of matrices
_
i
A with the corresponding matrix components, it follows 1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
(
)
T
T
T
T
T
T
a Q
a
a Q b
a Q
R
y
x
y
Q
R
a
b
b Q b
b Q
a
b Q
R
C
. Decomposition Approach for Inverse Matrix Calculation 119 It is put It is put It is put It is put
0
0
0
1
0
0
0
1
1
0
1
1
1
0
1
1
1
1
1
1
1
1
1
1
1
11
12
1
1
21
22
1
1
1
1
1
1
T
T
m xm
m xm
m xm
m xm
T
T
m xm
m xm
m xm
m xm
a Q
a
a Q b
b Q
a
b Q b
. (20) (20) where the matrix is a symmetric one by definition. Consequently,
1
1
(
)
x
y
can be
developed to: where the matrix is a symmetric one by definition. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d If the optimal resources
1
2
,
opt
opt
y
y
are known, after their substitution in (21)-(22), the solution
of the initial problem (1) can be obtained If the optimal resources
1
2
,
opt
opt
y
y
are known, after their substitution in (21)-(22), the solution
of the initial problem (1) can be obtained If the optimal resources
1
2
,
opt
opt
y
y
are known, after their substitution in (21)-(22), the solution
of the initial problem (1) can be obtained 1
2
1
1
2
2
(
),
(
)
opt
opt
opt
opt
x
x
y
x
x
y
. The determination of the optimal resources
1
2
,
opt
opt
y
y
is done by solution of the coordination
problem. 2.2 Decomposition of the initial problem by predictive coordination
A
di
h hi
hi
l
h
h
b
k i d
d Consequently,
1
1
(
)
x
y
can be
developed to: 1
11
12
1
1
1
1
1
1
1
1
1
1
1
1
1
1
21
22
1
1
1
1
(
)
T
T
a Q
R
y
x
y
Q
R
Q
a
b
b Q
R
C
. (21) (21) 11
12
1
1
1
1
1
1
1
1
1
1
1
1
1
1
21
22
1
1
1
1
(
)
T
T
a Q
R
y
x
y
Q
R
Q
a
b
b Q
R
C
. (21)
Analogically,
2
2
(
)
x
y
is 21
22
1
1
1
1
b Q
R
C
Analogically,
2
2
(
)
x
y
is Analogically,
2
2
(
)
x
y
is 1
11
12
2
2
2
2
1
1
2
2
2
2
2
2
2
1
21
22
2
2
2
2
(
)
T
T
a Q
R
y
x
y
Q
R
Q
a
b
a Q
R
C
. (22) (22) where matrix is a symmetric one by definition,
12
21
T
where matrix is a symmetric one by definition,
12
21
T
where matrix is a symmetric one by definition,
12
21
T
where matrix is a symmetric one by definition,
12
21
T
0
0
0
2
0
0
0
2
2
0
2
2
2
0
2
2
1
1
1
2
2
2
2
2
2
11
12
1
1
21
22
2
1
2
2
2
2
T
T
m xm
m xm
m xm
m xm
T
T
m xm
m xm
m xm
m xm
a Q
a
a Q b
b Q
a
b Q b
. 2.2.1 Determination of the coordination problem Analogically, for the second subproblem is valid: 2
2
2
0
0
2
2
1
20
1
2
2
1
(
)n x
n x
n xm
m x
x
y
x
X
y
(27) (27) 2
2
2
0
0
2
2
1
20
1
2
2
1
(
)n x
n x
n xm
m x
x
y
x
X
y
2
2
2
0
0
2
2
1
20
1
2
2
1
(
)n x
n x
n xm
m x
x
y
x
X
y
2
2
2
0
0
2
2
1
20
1
2
2
1
(
)n x
n x
n xm
m x
x
y
x
X
y
where 1
11
12
2
2
2
1
1
20
2
2
2
2
2
1
21
22
2
2
2
2
T
T
a Q
R
x
Q
R
Q
a
b
b Q R
C
(28) (28)
0
0
2
0
2
2
2
0
2
0
2
2
11
1
2
2
2
2
21
m xm
T
T
n xm
n xn
m xm
n xm
n xm
X
Q
a
b
(29) (29) After substitution of (24) in w1(y1) of (23), it follows: After substitution of (24) in w1(y1) of (23), it follows: After substitution of (24) in w1(y1) of (23), it follows: 1
1
10
1
1
1
10
1
1
1
10
1
1
1
(
)
(
)
(
)
(
)
2
T
T
T
T
w
y
x
y X
Q x
X y
R
x
X y
=
=
10
1 10
10
1
1
1
1
1
1 10
1
1
1
1
1
1
10
1
1
1
1
1
1
1
2
2
2
2
T
T
T
T
T
T
T
T
x Q x
x Q X y
y X Q x
y X Q X y
R x
R X y
1
1
10
1
1
1
10
1
1
1
10
1
1
1
(
)
(
)
(
)
(
)
2
T
T
T
T
w
y
x
y X
Q x
X y
R
x
X y
= =
10
1 10
10
1
1
1
1
1
1 10
1
1
1
1
1
1
10
1
1
1
1
1
1
1
2
2
2
2
T
T
T
T
T
T
T
T
x Q x
x Q X y
y X Q x
y X Q X y
R x
R X y
The components
10
1
1
1
T
x Q X y and
1
1
1 10
T
T
y X Q x
are equal, as they are transposed of
corresponding equal relations. 2.2.1 Determination of the coordination problem As
(
)
i
i
x y
is inexplicit function, it can be approximated in Mac-Laurin series at point yi=0 As
(
)
i
i
x y
is inexplicit function, it can be approximated in Mac-Laurin series at point yi=0 1
1
1
0
0
1
1
1
10
1
1
1
1
(
)n x
n x
n xm
m x
x
y
x
X
y
(24) 1
1
1
0
0
1
1
1
10
1
1
1
1
(
)n x
n x
n xm
m x
x
y
x
X
y
(24) where 1
11
12
1
1
1
1
1
1
0
1
1
1
1
1
1
21
22
1
1
1
1
T
T
i
a Q R
x
Q
R
Q
a
b
b Q
R
C
(25) (25)
0
0
1
0
1
1
1
0
1
0
1
1
11
1
1
1
1
1
21
m xm
T
T
n xm
n xn
m xm
n xm
n xm
X
Q
a
b
(26) (26) where x10 is solution of subproblem (19) having zero resource, y1=0 . Analogically, for the second subproblem is valid: where x10 is solution of subproblem (19) having zero resource, y1=0 . 2.2.1 Determination of the coordination problem After substitution of relations
1
1
(
)
x
y
and
2
2
(
)
x
y
in the initial problem (1) and taking into
account the resource constraint (17), the coordination problem becomes 1
1
1 1
1
1
1
1
2
2
2
2
2
2
2
2
1
1
min
( )
min
(
)
(
)
(
)
(
)
(
)
(
)
2
2
y
T
T
T
T
y S w y
x
y Q x
y
R x
y
x
y
Q x
y
R x
y
1
2
y
S
y
y
d
, or 120 MATLAB – A Ubiquitous Tool for the Practical Engineer
1
1
2
2
min
( )
(
)
(
)
w y
w y
w
y
(23)
1
2
y
y
d
1
1
2
2
min
( )
(
)
(
)
w y
w y
w
y
(23)
1
2
y
y
d
1
1
2
2
min
( )
(
)
(
)
w y
w y
w
y
1
1
2
2
min
( )
(
)
(
)
w y
w y
w
y
(23) 1
2
y
y
d
1
2
y
y
d
1
2
y
y
d
1
2
y
y
d
where where where where where
1
(
)
(
)
(
)
(
)
1 2
T
T
Q
R
i 1
(
)
(
)
(
)
(
),
1,2
2
T
T
i
i
i
i
i
i
i
i
i
i
w y
x
y Q x y
R x y
i
. 1
(
)
(
)
(
)
(
),
1,2
2
T
T
i
i
i
i
i
i
i
i
i
i
w y
x
y Q x y
R x y
i
. 2.2.1 Determination of the coordination problem 2
2
2
2
T
q
X Q X
; 2
2
2
20
2
2
T
T
r
X Q x
X R
. 2
2
2
2
T
q
X Q X
; 2
2
2
20
2
2
T
T
r
X Q x
X R
. Functions wi(yi) has to be presented in terms of the initial problem (1) by the following
transformations. ment of q1 Development of q1 n q1 is presented like Relation q1 is presented like 1
11
1
11
1
1
1
1
1
1
1
11
21
1
1
1
1
1
11
21
1
1
1
1
21
1
21
T
T
T
T
T
T
T
T
T
I
a
a
q
X Q X
Q
Q Q
a
b
Q
a
b
b
b
or or 1
1
1
1
1
1
1
1
1
1
11
1
1
1
11
1
1
1
21
1
11
21
11
21
1
1
1
1
21
1
1
1
1
1
1
1
1
1
11
1
1
1
21
T
T
T
T
T
T
T
T
T
T
T
T
a Q a
a Q b
a Q a
a Q b
q
b Q a
b Q b
b Q a
b Q b
. 2.2.1 Determination of the coordination problem Consequently, the coordination problem becomes Decomposition Approach for Inverse Matrix Calculation 121 1
1
1
1
1
1
1
1
1
1 10
1
1
1
1
(
)
2
T
T
T
T
T
T
w y
y X Q X y
y X Q x
y X R
(30) 1
1
1
1
1
1
1
1
1
1 10
1
1
1
1
(
)
2
T
T
T
T
T
T
w y
y X Q X y
y X Q x
y X R
(30) 1
1
1
1
1
1
1
1
1
1 10
1
1
1
1
(
)
2
T
T
T
T
T
T
w y
y X Q X y
y X Q x
y X R
(30) or or or 1
1
1
1
1
1 1
1
(
)
2
T
T
w y
y q y
y r
where 1
1
1
1
T
q
X Q X
; 1
1
1 10
1
1
T
T
r
X Q x
X R
1
1
1
1
T
q
X Q X
; 1
1
1 10
1
1
T
T
r
X Q x
X R
Analogically, for the second subproblem, it follows: Analogically, for the second subproblem, it follows: 2
2
2
2
2
2
2
2
2
2
20
2
2
2
1
(
)
2
T
T
T
T
T
T
w
y
y X Q X y
y X Q x
y X R
(31)
or
2
2
2
2
2
2 2
1
(
)
2
T
T
w
y
y q y
y r
2
2
2
2
2
2
2
2
2
2
20
2
2
2
1
(
)
2
T
T
T
T
T
T
w
y
y X Q X y
y X Q x
y X R
(31) (31) or or 2
2
2
2
2
2 2
1
(
)
2
T
T
w
y
y q y
y r
where where 2
2
2
2
T
q
X Q X
; 2
2
2
20
2
2
T
T
r
X Q x
X R
. 2.2.1 Determination of the coordination problem Consequently, the coordination problem becomes The components
10
1
1
1
T
x Q X y and
1
1
1 10
T
T
y X Q x
are equal, as they are transposed of
corresponding equal relations. 2.2.1 Determination of the coordination problem (32) (32) According to the manner of definition of matrix from (20) the following matrix equality is
performed According to the manner of definition of matrix from (20) the following matrix equality is
performed
0
0
0
0
0
1
0
0
0
1
0
1
1
1
1
0
1
0
1
1
1
0
1
1
1
1
1
1
1
1
1
1
1
11
12
1
1
21
22
1
1
1
1
1
1
0
0
T
T
m xm
m xm
m xm
m xm
m xm
m xm
T
T
m xm
m xm
m xm
m xm
m xm
m xm
a Q
a
a Q b
I
I
b Q
a
b Q b
(33) (33) i.e. an unit matrix is obtained. Consequently, the following equations are performed 122 MATLAB – A Ubiquitous Tool for the Practical Engineer 0
0
1
1
1
1
1
11
1
1
1
21
T
T
m xm
a Q a
a Q b
I
(34)
1
0
1
1
1
1
1
11
1
1
1
21
0
T
T
m xm
b Q
a
b Q b
. 0
0
1
1
1
1
1
11
1
1
1
21
T
T
m xm
a Q a
a Q b
I
(34) 0
0
1
1
1
11
1
1
1
21
m xm
(
)
1
0
1
1
1
1
1
11
1
1
1
21
0
T
T
m xm
b Q
a
b Q b
. 1
0
1
1
1
1
1
11
1
1
1
21
0
T
T
m xm
b Q
a
b Q b
. After substitution of (34) in (32) it is obtained After substitution of (34) in (32) it is obtained as
11
is a symmetric and square or 1
11
q
. (35) 1
11
q
. (35)
Analogically,
2
11
q
(36)
D
l
t f 1
11
q
. 2.2.1 Determination of the coordination problem Analogically, (35) 2
11
q
(36) 2
11
q (36) 2
11
q p
f
i. In a similar way the relations of ri are developed to the expressions 1
1
1
1
1
1
1 10
1
11
21
1
1
1
1
1
(
)
T
T
T
a Q
R
r
X
Q x
R
b Q R
C
(37) 1
1
1
1
1
1
1 10
1
11
21
1
1
1
1
1
(
)
T
T
T
a Q
R
r
X
Q x
R
b Q R
C
(37)
1
2
2
2
2
2
2
20
2
11
21
1
2
2
2
2
(
)
T
T
T
a Q
R
r
X
Q x
R
b Q R
C
. (37) The coordination problem becomes The coordination problem becomes 1
1
2
2
1
1
1
1
1
2
2
2
2
2
1
1
min
(
)
(
)
2
2
T
T
T
T
w y
w
y
y q y
r y
y q y
r y
(38) (38) 0
0
0
0
0
0
1
2
2
m xm
m xm
m x m
y
y
d
I
I
;
1
2
;
y
y
y
1
2
0
0
q
q
q
1
2
;
r
r
r
The coordination problem (38) is a linear-quadratic one and its solution can be found in an
analytical form according to (4) or 1
1
1
1
(
) (
)
opt
T
T
I
I
I
I
y
q
r
A
A q
A
A q r
d
. 2.2.1 Determination of the coordination problem (39) (39) Relation (39) is developed additionally to the form Relation (39) is developed additionally to the form 1
1
1
1
1
1
1
1
1
1
1
2
1
1
2
2
1
(
) (
)
opt
y
q r
q
q
q
q r
q r
d
(40)
1
1
1
1
1
1
1
2
2
2
1
2
1
1
2
2
2
(
) (
)
opt
y
q r
q
q
q
q r
q
r
d
. 1
1
1
1
1
1
1
1
1
1
1
2
1
1
2
2
1
(
) (
)
opt
y
q r
q
q
q
q r
q r
d
(40) 1
1
1
1
1
1
1
1
1
1
1
2
1
1
2
2
1
(
) (
)
opt
y
q r
q
q
q
q r
q r
d
(40)
1
1
1
1
1
1
1
(
) (
)
opt
d (40) 1
1
1
1
1
1
1
2
2
2
1
2
1
1
2
2
2
(
) (
)
opt
y
q r
q
q
q
q r
q
r
d
. Decomposition Approach for Inverse Matrix Calculation 123 After additional transformations it follows To get the explicit analytical form of
relations
(
)
opt
i
i
x y
, (42) is substituted in (21) and (22) and after transformations follows 1
1
1
1
1
1
1
1
1
1
1
11
11
11
11
11
21
11
11
11 21
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
21 11
11
11
11
21
1
1
1
1
21 11
11
11
11 21
21 11
11
11
1
22
21 11
21
(
)
(
)
(
)
(
)
(
)
(
)
(
)
T
T
opt
T
T
T
T
T
x
y
Q
R
Q
a
b
(43)
1
1
1
1
1
2
2
2
1
1
1
1
1
1
2
2
2
2
*
a Q
R
a Q
R
d
b Q
R
C
b Q
R
C
1
1
1
1
1
1
1
1
1
1
1
11
11
11
11
11
21
11
11
11 21
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
21 11
11
11
11
21
1
1
1
1
21 11
11
11
11 21
21 11
11
11
1
22
21 11
21
(
)
(
)
(
)
(
)
(
)
(
)
(
)
T
T
opt
T
T
T
T
T
x
y
Q
R
Q
a
b
(43) (43) 1
1
1
1
1
1
1
1
1
1
1
11
11
11
11
11
21
11
11
11 21
1
1
1
1
1
1
1
2
2
2
2
2
2
2
21 11
11
11
11
21
1
1
1
1
1
1
1
1
1
21 11
11
11
21 11
11
11
11
21
1
22
21 11 21
(
)
(
)
(
)
(
)
*
(
)
(
)
(
)
T
T
opt
T
T
T
T
T
x
y
Q
R
Q
a
b
(44) (44) 1a Q 1
1
1
1
2
2
2
1
1
1
1
1
1
2
2
2
2
. After additional transformations it follows After additional transformations it follows 1
1
1
1
1
1
1
1
1
2
2
2
1
1
1
1
1
1
1
11
11
21
11
11
11
11
11
21
11
11
21
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
(
)
opt
T
T
T
T
T
T
a Q
R
a Q
R
a Q R
y
d
b Q
R
C
b Q R
C
b Q
R
C
(42)
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
11
11
21
11
11
11
11
11
21
11
11
21
2
1
1
1
2
2
2
2
1
1
1
1
2
2
2
2
(
)
opt
T
T
T
T
T
T
a Q R
a Q
R
a Q
R
y
d
b Q R
C
b Q
R
C
b Q R
C
. ubstitution of optimal resources
opt
iy
, i=1,2 from (42) in the expressions of
1
1
(
)
x
y After substitution of optimal resources
opt
iy
, i=1,2 from (42) in the expressions of
1
1
(
)
x
y
from (21) and
2
2
(
)
x
y
from (22) the analytical relations
1
1
(
)
opt
x
y
and
2
2
(
)
opt
x
y
, which are
solutions of the initial problem (1) are obtained. 2.2.2 Presenting the resources
opt
iy
in terms of the initial problem It is necessary the values of
opt
iy
to be presented by the matrices and vectors of the initial
problem ai , bi , Qi, Ri , Ci , , , i=1,2 . According to (35) and (36), it is performed 1
1
1
11
1
11
q
q
(41)
1
1
2
11
2
11
q
q
. 1
1
1
11
1
11
q
q
(41) (41) 1
1
2
11
2
11
q
q
. After additional transformations it follows After additional transformations it follows This allows the matrix to be determined by fewer calculations in
comparison with its direct inverse transformation because the inverse matrices and
have less dimensions. Relations (45) can be applied for calculation of the components
ij
of
the inverse matrix (with large dimension) by finding the inverse matrices and
(with fewer dimensions). The computational efficiency for evaluating the inverse matrix
with high dimension using relations (45) is preferable in comparison with its direct
calculation (Stoilova & Stoilov, 2007). After additional transformations it follows (45) Consequently, after applying the both coordination strategies towards the same initial
problem (1) analytical relations (15) and respectively (43) and (44) are obtained. This allows
to be received analytical relations among the components of the inverse matrices , and
, which were not able to be determined directly because by definition: 1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
0
0
T
T
T
T
T
T
T
T
a Q
a
a Q
a
a Q b
a Q b
b Q
a
b Q b
b Q
a
b Q b
;
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
T
T
T
T
a Q
a
a Q b
b Q
a
b Q b
1
1
1
2
2
2
2
2
2
1
1
2
2
2
2
2
2
T
T
T
T
a Q
a
a Q b
b Q
a
b Q b
. 1
1
1
1
1
1
1
1
2
2
2
1
1
1
2
2
2
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
0
0
T
T
T
T
T
T
T
T
a Q
a
a Q
a
a Q b
a Q b
b Q
a
b Q b
b Q
a
b Q b
;
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
T
T
T
T
a Q
a
a Q b
b Q
a
b Q b
1
1
1
2
2
2
2
2
2
1
1
2
2
2
2
2
2
T
T
T
T
a Q
a
a Q b
b Q
a
b Q b
. Consequently, using (45) the components of the inverse matrix can be determined when
and are given. After additional transformations it follows R
a Q
R
d
b Q
R
C
b Q
R
C
The obtained results in (43) and (44)
(
),
1,2
opt
i
i
x y
i
are after applying the predictive
coordination for solving the initial problem (1). The solutions
,
1,2
opt
ix
i
from (15) are
obtained by applying goal coordination to the same initial problem. As the solutions
(
),
1,2
opt
i
i
x y
i
and
,
1,2
opt
ix
i
are equal, after equalization of (15) with (43) and (44) 124 MATLAB – A Ubiquitous Tool for the Practical Engineer relations among the components of the inverse matrix and the components of the inverse
and are obtained. According to (15) and (43), it follows: relations among the components of the inverse matrix and the components of the inverse
and are obtained. According to (15) and (43), it follows: 1
1
1
11
11
11
(
)
;
1
1
1
1
12
11
11
11
21
(
)
T
;
1
1
1
1
13
11
11
11
21
(
)
T
1
1
1
1
21
21 11
11
11
(
)
;
1
1
1
1
1
1
22
21 11
11
11
11
21
22
21 11
21
(
)
T
T
;
1
1
1
1
1
23
21 11
11
11
11
21
(
)
T
(45)
1
1
1
1
31
21 11
11
11
(
)
;
1
1
1
1
1
32
21 11
11
11
11
21
(
)
T
;
1
1
1
1
1
1
33
21 11
11
11
11 21
22
21 11 21
(
)
T
T
. Decomposition Approach for Inverse Matrix Calculation Decomposition Approach for Inverse Matrix Calculation 125 (47) 0
1
0
2
0
3
1 1
2
2
3 3
m xn
m xn
m xn
a x
a x
a x
d
(47) 0
1
0
2
0
3
1 1
2
2
3 3
m xn
m xn
m xn
a x
a x
a x
d
1
1
2
2
3
3
1 1
1
2
2
2
3 3
3
m xn
m xn
m xn
b x
C
b x
C
b x
C
where the dimensions of the vectors and matrices are appropriately defined where the dimensions of the vectors and matrices are appropriately defined 1
1
1
n x
x
;
2
2
1
n x
x
;
3
3
1
n x
x
;
1
1
1
n x
R
;
2
2
1
n x
R
;
3
3
1
n x
R
;
0
1
1m xn
a
;
0
2
2m xn
a
;
0
3
3m xn
a
;
0 1
m x
d
; 1
1
1m xn
b
;
2
2
2m xn
b
;
3
3
3m xn
b
;
1
1
1
m x
C
;
2
2
1
m x
C
;
3
3
1
m x
C
; 0
1
2
3
1
2
3
1
2
3 (
) (
)
m
m
m
m
x n
n
n
d
C
C
C
C
;
1
2
3
0
0
0
0
0
0
Q
Q
Q
Q
;
1
2
3
R
R
R
R
;
0
1
2
3
1
2
3
1
2
3
1
2
3 (
) (
)
0
0
0
0
0
0
m
m
m
m
x n
n
n
a
a
a
b
A
b
b
. ;
1
2
3
0
0
0
0
0
0
Q
Q
Q
Q
;
1
2
3
R
R
R
R
; The peculiarity of problem (46), which formalizes the management of hierarchical system
with three subsystems, concerns the existence of local resources С1, С2, С3, which are used by
each subsystem. According to the coupling constraint (47) additional resources d are
allocated among the subsystems. 3. Predictive coordination for block-diagonal problem of quadratic
programming with three and more subsystems Analytical relations for predictive coordination strategy for the case when the subsystems in
the bi-level hierarchy are more than two are developed. The case of bi-level hierarchical
system with three subsystems is considered, figure 2 The initial optimization problem, solved by the hierarchical system is stated as 1
1
1
1
2
3
2
2
1
2
3
2
3
3
3
0
0
1
min
0
0
2
0
0
T
T
T
T
T
T
x
x
Q
x
x
x
Q
x
R
R
R
x
Q
x
x
(46) (46) Decomposition Approach for Inverse Matrix Calculation Decomposition Approach for Inverse Matrix Calculation The initial problem can be solved by four or more subsystems. Decomposition Approach for Inverse Matrix Calculation The relations between the
components of the matrix
(
)
ij
and the matrices with lower sizes
, ,
are given
below 11
12
13
1
1
1
1
11
11
1
1
1
1
1
1
1
1
1
1
1
11
11
11
11
11
21
11
11
11
21
1
11
21
21
22
23
2
1
1
1
1
21
11
11
11
1
1
1
1
21
11
11
11
1
11
21
22
21
(
)
*
(
)
(
)
(
)
*
(
)
*
(
)
*
j
T
T
T
j
T
1
1
1
1
1
1
1
1
21
11
11
11
21
11
11
11
1
1
1
11
21
11
21
11
21
31
32
33
3
1
1
1
1
1
1
1
1
21 11
11
11
21 11
11
11
1
1
1
1
21 11
11
11
1
1
11
21
11
21
22
(
)
*
(
)
*
*
*
(
)
*
(
)
*
(
)
*
*
T
T
T
j
T
T
1
1
1
1
21 11
11
11
1
1
21 11
21
11
21
1
2
3
1
1
1
1
1
1
1
1
1
1
1
1
21
11
11
11
21
11
11
11
21
11
11
11
1
1
1
1
21
11
11
11
1
1
1
11
21
11
21
11
21
(
)
*
*
(
)
*
(
)
*
(
)
*
(
)
*
*
T
T
i
i
i
ij
T
T
T
1
22
21
11
21
T
(50)
4. Decomposition Approach for Inverse Matrix Calculation Problem (46) can be presented in a general form, using the
substitutions Fig. 2. Hierarchical approach with three subsystems for solving initial problem
Coordinator
Subsystem 2
Subsystem 3
Subsystem 1
y1
y2
y3
)
(
1
1 y
x
)
(
2
2 y
x
)
(
3
3 y
x Subsystem 1 Subsystem 3 Fig. 2. Hierarchical approach with three subsystems for solving initial problem 0
1
1
1
0
1
2
3
1
2
1
3
1
1
1
1
(
)
0
0
m xn
m xn
m
m
m
m
xn
m xn
m xn
a
b
A
;
0
3
1
3
0
1
2
3
3
2
3
3
3
3
3
(
)
3
0
0
m xn
m xn
m
m
m
m
xn
m xn
m xn
a
A
b
;
0
1
2
3
1
2
(
) 1
3
m
m
m
m
x
d
C
D
C
C
(48) 0
1
1
1
0
1
2
3
1
2
1
3
1
1
1
1
(
)
0
0
m xn
m xn
m
m
m
m
xn
m xn
m xn
a
b
A
;
0
3
1
3
0
1
2
3
3
2
3
3
3
3
3
(
)
3
0
0
m xn
m xn
m
m
m
m
xn
m xn
m xn
a
A
b
;
0
1
2
3
1
2
(
) 1
3
m
m
m
m
x
d
C
D
C
C
(48) (48) 126 MATLAB – A Ubiquitous Tool for the Practical Engineer 0
1
2
3
1
2
3
1
2
3 (
) (
)
m
m
m
m
x n
n
n
A
A
A
A
. Decomposition Approach for Inverse Matrix Calculation Assessment of the calculation efficiency of the analytical results for
determination of inverse matrix components 11
12
13
1
1
11
1
1
1
1
1
1
1
1
1
1
1
11
11
11
11
11
21
11
11
11
21
1
11
21
21
22
23
2
1
1
1
1
21
11
11
11
1
1
1
1
21
11
11
11
1
11
21
22
21
(
(
)
(
)
(
)
*
(
)
*
(
)
*
j
T
T
T
j
T
1
1
1
1
1
1
21
11
11
11
21
11
11
1
1
1
11
21
11
21
11
21
31
32
33
3
1
1
1
1
1
1
1
1
21 11
11
11
21 11
11
11
1
1
1
1
21 11
11
11
1
1
11
21
11
21
22
(
)
*
(
*
*
(
)
*
(
)
*
(
)
*
*
T
T
T
j
T
T
1
1
21 11
11
1
1
21 11
21
11
21
1
2
3
1
1
1
1
1
1
1
1
1
1
21
11
11
11
21
11
11
11
21
11
11
1
1
1
1
21
11
11
11
1
1
1
11
21
11
21
11
21
(
*
(
)
*
(
)
*
(
(
)
*
*
T
T
i
i
i
ij
T
T
T
22
1
1
1
1
11
11
1
11
21
2
(
)
*
*
j
T
j
1
1
1
1
21
11
11
11
1
11
21
3
(
)
*
*
T
j
1
1
1
1
21 11
11
11
1
11
21
1
1
1
1
21
11
11
11
1
11
21
(
)
*
*
(
)
*
T
ij
T
1
22
21
11
21
T
(50) (50) 4. Decomposition Approach for Inverse Matrix Calculation Analogically to the previous case with two subsystems, analytical relations for determining
the inverse matrix components by matrices with fewer dimensions are obtained 1
1
1
1
11
11
11
11
(
)
;
1
1
1
1
1
12
11
11
11
11
21
(
)
T
(49)
1
1
1
1
1
13
11
11
11
11 21
(
)
T
;
1
1
1
1
1
14
11
11
11
11
21
(
)
T
(49) 1
1
1
1
1
21
21 11
11
11
11
(
)
;
1
1
1
1
1
1
1
22
21 11
11
11
11
11
21
22
21 11
21
(
)
T
T
21
21 11
11
11
11
(
)
;
22
21 11
11
11
11
11
21
22
21 11
21
(
)
1
1
1
1
1
1
23
21 11
11
11
11
11 21
(
)
T
;
1
1
1
1
1
1
24
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
31
21 11
11
11
11
(
)
;
1
1
1
1
1
1
32
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
1
33
21 11
11
11
11
11 21
22
21 11 21
(
)
T
T
;
1
1
1
1
1
1
34
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
41
21 11
11
11
11
(
)
;
1
1
1
1
1
1
42
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
23
21 11
11
11
11
11 21
(
)
T
;
1
1
1
1
1
1
24
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
23
21 11
11
11
11
11 21
(
)
T
;
1
1
1
1
1
1
24
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
23
21 11
11
11
11
11 21
(
)
T
;
1
1
1
1
1
1
24
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
31
21 11
11
11
11
(
)
;
1
1
1
1
1
1
32
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
1
33
21 11
11
11
11
11 21
22
21 11 21
(
)
T
T
;
1
1
1
1
1
1
34
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
31
21 11
11
11
11
(
)
;
1
1
1
1
1
1
32
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
1
33
21 11
11
11
11
11 21
22
21 11 21
(
)
T
T
;
1
1
1
1
1
1
34
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
41
21 11
11
11
11
(
)
;
1
1
1
1
1
1
42
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
1
33
21 11
11
11
11
11 21
22
21 11 21
(
)
T
T
;
1
1
1
1
1
1
34
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
1
33
21 11
11
11
11
11 21
22
21 11 21
(
)
T
T
;
1
1
1
1
1
1
34
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
(
)
1
1
1
1
1
1
(
)
T
1
1
1
1
1
41
21 11
11
11
11
(
)
;
1
1
1
1
1
1
42
21 11
11
11
11
11
21
(
)
T
1
1
1
1
1
1
43
21 11
11
11
11
11 21
(
)
T
;
1
1
1
1
1
1
1
44
21 11
11
11
11
11
21
22
21 11
(
)
T
1
1
1
1
1
1
43
21 11
11
11
11
11 21
(
)
T
;
1
1
1
1
1
1
1
44
21 11
11
11
11
11
21
22
21 11
21
(
)
T
T
. Decomposition Approach for Inverse Matrix Calculation Assessment of the calculation efficiency of the analytical results for
determination of inverse matrix components 4. Assessment of the calculation efficiency of the analytical results for
determination of inverse matrix components For simplicity of working the notations for right matrices with lower dimensions are
introduced. In the case of 2 subsystems, the matrices c and d are the corresponding right Decomposition Approach for Inverse Matrix Calculation 127 matrices of the inverse matrices and . By definition having in mind (46) c and d are
symmetric ones
0
0
0
1
0
0
0
1
1
0
1
1
1
0
1
1
1
1
1
1
1
1
1
1
11
12
1
1
21
22
1
1
1
1
1
1
T
T
m xm
m xm
m xm
m xm
T
T
m xm
m xm
m xm
m xm
a Q
a
a Q b
c
c
c
c
c
b Q
a
b Q b
; =
11
12
21
22
= c-1
0
0
0
2
0
0
0
2
2
0
2
2
2
0
2
2
1
1
2
2
2
2
2
2
11
12
1
1
21
22
2
1
2
2
2
2
T
T
m xm
m xm
m xm
m xm
T
T
m xm
m xm
m xm
m xm
a Q
a
a Q b
d
d
d
d
d
b Q
a
b Q b
=
11
12
21
22
= d-1. Analogically, for 3 subsystems the right matrix is e and the corresponding inverse matrix is
(e − ); for 4 subsystems - (f − ). Analogically, for 3 subsystems the right matrix is e and the corresponding inverse matrix is
(e − ); for 4 subsystems - (f − ). An example for computational efficiency of the proposed relations (45) /2 subsystems is
given below with a symmetric matrix AL with dimension from 17×17 to 26×26 which varies
according to variation of dimension m1 from 2 to 11, while m0 is 4 and m2 is 11. 4. Assessment of the calculation efficiency of the analytical results for
determination of inverse matrix components Matrix AL is
in the form m0=4
m1=211
m2=11
c11+d11
c12
d12
AL =
c21
c22
0
d21
0
d22 m0=4
m1=211
m2=11
c11+d11
c12
d12
AL =
c21
c22
0
d21
0
d22 The MATLAB’s codes are given below: %example of inversion of AL (dimension 26x26) when m1=11 c11=[1 2 3 1; 2 3 2 2; 3 2 4 2; 1 2 2 1]; c12=[ -2 1 0 -1 2 4 0 -1 -3 2 2; -5 0 2 1 4 6 -5
7 1 9 1; 0 7 2 1 3 -8 9 1 0 2 3; 4 2 -1 0 2 -1
2 1 3 1 1];
c21=c12'; c22=[ 1 2 1 -3 1 0 1 5 2 8 2;
2 3 -4 1 0 2 9 8 5 1 -3;
1 -4 1 -1 1 5 -6 2 1 3 1;
-3 1 -1 4 3 2 1 0 -1 -2 2;
1 0 1 3 2 1 1 5 -3 3 -1;
0 2 5 2 1 4 2 1 0 1 1;
1 9 -6 1 1 2 6 3 1 0 2;
5 8 2 0 5 1 3 5 -2 7 0;
2 5 1 -1 -3 0 1 -2 3 1 1; MATLAB – A Ubiquitous Tool for the Practical Engineer 128 8 1 3 -2 3 1 0 7 1 4 2;
2 -3 1 2 -1 1 2 0 1 2 4];
c=[c11 c12; c21 c22];
d11=[3 0 0 -2; 0 -6 2 0; 0 2 -2 -1; -2 0 -1 2];
d12=[1 0 2 1 3 -4 2 0 1 -3 1 ;
3 -1 0 2 -2 -1 0 1 1 0 2 ;
3 0 1 0 5 3 7 1 2 -2 0;
2 2 0 1 3 2 1 0 1 -1 1];
d21=d12';
d22=[ 1 3 7 2 2 1 1 0 -2 -1 1;
3 2 1 1 1 -1 -2 -3 0 1 0 ;
7 1 5 2 4 2 3 -1 -3 -2 1 ;
2 1 2 1 2 3 0 1 -2 -4 2;
2 1 4 2 1 -1 3 7 -1 2 0;
1 -1 2 3 -1 0 2 1 4 1 2;
1 -2 3 0 3 2 2 1 -3 -1 1;
0 -3 -1 1 7 1 1 0 1 2 1;
-2 0 -3 -2 -1 4 -3 1 -2 0 2;
-1 1 -2 -4 2 1 -1 2 0 1 1;
1 0 1 2 0 2 1 1 2 1 5];
d=[d11 d12; d21 d22];
%definition of AL
mm=size(c12);
m0=mm(1);
%m0=4
m1=mm(2);
%m1=11
mm=size(d12);
m2=mm(2);
%m2=11
m10=zeros(m1,m2);
m20=m10';
al=[c11+d11 c12 d12; c21 c22 m10; d21 m20 d22];
flops(0);
alpha1=inv(al);
%direct inversion of AL
fl_al=flops
%flops for direct matrix inversion
%matrix inversion by hierarchical approach
flops(0); d22=[ 1 3 7 2 2 1 1 0 -2 -1 1;
3 2 1 1 1 -1 -2 -3 0 1 0 ;
7 1 5 2 4 2 3 -1 -3 -2 1 ;
2 1 2 1 2 3 0 1 -2 -4 2;
2 1 4 2 1 -1 3 7 -1 2 0;
1 -1 2 3 -1 0 2 1 4 1 2;
1 -2 3 0 3 2 2 1 -3 -1 1;
0 -3 -1 1 7 1 1 0 1 2 1;
-2 0 -3 -2 -1 4 -3 1 -2 0 2;
-1 1 -2 -4 2 1 -1 2 0 1 1;
1 0 1 2 0 2 1 1 2 1 5]; ;
1 0 1 2 0 2 1 1 2 1 5]; d=[d11 d12; d21 d22]; d=[d11 d12; d21 d22]; %definition of AL
mm=size(c12);
m0=mm(1);
%m0=4
m1=mm(2);
%m1=11
mm=size(d12);
m2=mm(2);
%m2=11
m10=zeros(m1,m2);
m20=m10'; %definition of AL mm=size(c12);
m0=mm(1);
%m0=4
m1=mm(2);
%m1=11
mm=size(d12);
m2=mm(2);
%m2=11
m10=zeros(m1,m2);
m20=m10'; mm=size(c12);
m0=mm(1);
%m0=4
m1=mm(2);
%m1=11
mm=size(d12);
m2=mm(2);
%m2=11
m10=zeros(m1,m2);
m20=m10'; al=[c11+d11 c12 d12; c21 c22 m10; d21 m20 d22]; flops(0);
alpha1=inv(al);
%direct inversion of AL
fl_al=flops
%flops for direct matrix inversion %matrix inversion by hierarchical approach %matrix inversion by hierarchical approach beta=inv(c); gama=inv(d); invbeta11=inv(beta(1:m0,1:m0)); invgama11=inv(gama(1:m0,1:m0)); Decomposition Approach for Inverse Matrix Calculation 129 Decomposition Approach for Inverse Matrix Calculation ff=flops
flops(0);
alpha11=inv(invbeta11+invgama11);
alpha12=alpha11*invbeta11beta21T;
alpha13=alpha11*invgama11*gama(m0+1:m0+m2,1:m0)';
alpha21=alpha12';
alpha22=invbeta11beta21T'*alpha12+beta(m0+1:m0+m1,m0+1:m0+m1)-
beta(m0+1:m0+m1,1:m0)*invbeta11beta21T;
alpha23=invbeta11beta21T'*alpha13;
alpha31=alpha13';
alpha32=alpha23';
alpha33=invgama11gama21T'*alpha13+gama(m0+1:m0+m2,m0+1:m0+m2)-
gama(m0+1:m0+m2,1:m0)*invgama11gama21T;
alpha=[alpha11 alpha12 alpha13; alpha21 alpha22 alpha23; alpha3
alpha32 alpha33];
fl_nic=flops
fl_full=ff+fl_nic
%flops using noniterative coordin p
alpha11=inv(invbeta11+invgama11); p
p
alpha13=alpha11*invgama11*gama(m0+1:m0+m2,1:m0)'; p
p
;
alpha22=invbeta11beta21T'*alpha12+beta(m0+1:m0+m1,m0+1:m0+m1)- beta(m0+1:m0+m1,1:m0)*invbeta11beta21T; eta(m0+1:m0+m1,1:m0)*invbeta11beta21T; alpha23=invbeta11beta21T'*alpha13; alpha31=alpha13'; alpha32=alpha23'; p
p
alpha33=invgama11gama21T'*alpha13+gama(m0+1:m0+m2,m0+1:m0+m2)-
( 0+1
0+ 2 1
0)*i
11
21T alpha33=invgama11gama21T'*alpha13+gama(m0+1:m0+m2,m0+1:m0+m2)-
gama(m0+1:m0+m2,1:m0)*invgama11gama21T; alpha33=invgama11gama21T'*alpha13+gama(m0+1:m0+m2,m0+1:m0+m2)-
gama(m0+1:m0+m2,1:m0)*invgama11gama21T; alpha=[alpha11 alpha12 alpha13; alpha21 alpha22 alpha23; alpha31
alpha32 alpha33]; fl_nic=flops
fl_full=ff+fl_nic
%flops using noniterative coordination fl_nic=flops %flops using noniterative coordination al2=inv(alpha); This code has been used for two types of calculations: 1. Direct calculation of - inversion of matrix AL by built-in MATLAB function INV. The
amount of calculations is presented as a dashed red line in Figure 3. 1. Direct calculation of - inversion of matrix AL by built-in MATLAB function INV. The
amount of calculations is presented as a dashed red line in Figure 3. p
g
2. Evaluation of applying relations (45). The amount of calculation is presented as a
solid blue line in Figure 3. p
g
2. Evaluation of applying relations (45). The amount of calculation is presented as a
solid blue line in Figure 3. The comparison of the both manners of calculations shows that the analytical relations are
preferable when the matrix dimension increases. From experimental considerations it is
preferable to hold the relation 3m0 < m1 + m2, which gives boundaries for the decomposition
of the initial matrix AL. For the initial case of m0=4 m1=2 m2=11 these values are near to
equality of the above relation and that is why the decomposition approach does not lead to
satisfactory result. y
Second example A 29×29 symmetric block-diagonal matrix denoted by AL is considered. It
has to be inversed to the matrix by two manners: direct MATLAB’s inversion and using
relations (45) and (50). This matrix will be calculated by hierarchical approach and
decomposition with 2, 3, and 4 subsystems. Case 1. al2=inv(alpha); The right matrix AL can be inversed to by the above analytical relations applying
4 subsystems where AL is presented by the matrices c, d, e and f in the manner: m0
m1
m2
m3
m4
c11+d11+e11+f11
c12
d12
e12
f12
c21
c22
0
0
0
AL =
d21
0
d22
0
0
e21
0
0
e22
0
f21
0
0
0
f22 MATLAB – A Ubiquitous Tool for the Practical Engineer 130 AL=
m0=3
m1=6
m2=6
m3=7
m4=7
5 1 -3 -1 2 4 -1 2 1 -4 1 0 1 -3 2 0 2 1 1 -2 0 -3 1 0 3 6 -1 1 4
1 4 5 -3 1 0 5 4 -1 -2 -1 0 -2 1 4 2 4 0 -5 7 1 -4 3 2 1 -1 4 -1 -2
-3 5 -4 3 2 1 0 3 2 -2 1 0 1 -1 -2 1 -2 1 3 1 0 1 4 1 3 2 4 1 -2
-1 -3 3 3 -4 1 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 1 2 -4 1 -1 1 5 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4 0 1 1 -1 7 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 5 0 0 1 3 9 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 4 3 2 5 2 1 8 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 -1 2 1 -1 3 2 -1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-4 -2 -2 0 0 0 0 0 0 1 -1 -2 -1 -1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 -1 1 0 0 0 0 0 0 -1 -2 3 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 -2 3 -1 1 -2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 -2 1 0 0 0 0 0 0 -1 0 1 -2 -4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-3 1 1 0 0 0 0 0 0 -1 1 -2 -4 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 4 -2 0 0 0 0 0 0 1 2 4 2 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 2 1 5 1 1 -2 1 0 0 0 0 0 0 0
2 4 -2 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 4 1 3 2 0 0 0 0 0 0 0
1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 5 2 3 2 1 -1 1 0 0 0 0 0 0 0
1 -5 3 0 0 0 0 0 0 0 0 0 0 0 0 1 4 2 5 -1 3 -2 0 0 0 0 0 0 0
-2 7 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 6 1 -1 0 0 0 0 0 0 0
0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 -2 3 -1 3 1 2 1 0 0 0 0 0 0 0
-3 -4 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 -2 -1 1 3 0 0 0 0 0 0 0
1 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 3 1 2 1 4
0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 2 1 3 -2 1 0
3 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 1 -2 -1 -2 1
6 -1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 -2 1 -3 1 -2
-1 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 -2 -1 -3 2 1 -1
1 -1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 -2 1 1 3 1
4 -2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 1 -2 -1 1 1 m0=3
m1=6
2 -1 2 -1 2 4 -1 2 1
-1 1 2 -3 1 0 5 4 -1
2 2 3 3 2 1 0 3 2
-1 -3 3 3 -4 1 0 2 1
2 1 2 -4 1 -1 1 5 -1
4 0 1 1 -1 7 3 2 3
-1 5 0 0 1 3 9 1 2
2 4 3 2 5 2 1 8 -1
1 -1 2 1 -1 3 2 -1 2
d =
m0=3
m2=6
-1 -1 -1 -4 1 0 1 -3 2
-1 2 0 -2 -1 0 -2 1 4
-1 0 -2 -2 1 0 1 -1 -2
-4 -2 -2 1 -1 -2 -1 -1 1
1 -1 1 -1 -2 3 0 1 2
0 0 0 -2 3 -1 1 -2 4
1 -2 1 -1 0 1 -2 -4 2
-3 1 1 -1 1 -2 -4 1 3
2 4 -2 1 2 4 2 3 2
(51) (51) Decomposition Approach for Inverse Matrix Calculation Decomposition Approach for Inverse Matrix Calculation 131 e =
m0=3
m3=7
3 0 -2 0 2 1 1 -2 0 -3
0 -4 2 2 4 0 -5 7 1 -4
-2 2 1 1 -2 1 3 1 0 1
0 2 1 2 1 5 1 1 -2 1
2 4 -2 1 3 2 4 1 3 2
1 0 1 5 2 3 2 1 -1 1
1 -5 3 1 4 2 5 -1 3 -2
-2 7 1 1 1 1 -1 6 1 -1
0 1 0 -2 3 -1 3 1 2 1
-3 -4 1 1 2 1 -2 -1 1 3
f =
m0=3
m4=7
1 3 -2 1 0 3 6 -1 1 4
3 5 1 3 2 1 -1 4 -1 -2
-2 1 -4 4 1 3 2 4 1 -2
1 3 4 1 -1 3 1 2 1 4
0 2 1 -1 2 1 3 -2 1 0
3 1 3 3 1 1 -2 -1 -2 1
6 -1 2 1 3 -2 1 -3 1 -2
-1 4 4 2 -2 -1 -3 2 1 -1
1 -1 1 1 1 -2 1 1 3 1
4 -2 -2 4 0 1 -2 -1 1 1 Here is assessed the efficiency of usage of relations (50) for finding the inverse matrix
when the matrices with fewer dimensions c, d, e and f are given. The assessment is done by
measurement of “flops” in MATLAB environment. MATLAB – A Ubiquitous Tool for the Practical Engineer alpha41=delta(m0+1:m0+m3,1:m0)*invdelta11*alpha11;
alpha42=alpha41*invbeta11beta21T;
alpha43=alpha41*invgama11gama21T;
alpha44=alpha41*invdelta11delta21T+delta(m0+1:m0+m3,m0+1:m0+m3)-
delta(m0+1:m0+m3,1:m0)*invdelta11delta21T;
alpha=[alpha11 alpha12 alpha13 alpha14;
alpha21 alpha22 alpha23 alpha24;
alpha31 alpha32 alpha33 alpha34;
alpha41 alpha42 alpha43 alpha44];
fl_nic=flops;
fl_full=ff+fl_nic
al2=inv(alpha);%verification For direct inversion of AL the flops are 50220 and for using (50) - 16329, figure 4. Case 2. The same matrix AL is given however is determined by a different manner - by 3
subsystems: direct inversion of AL the flops are 50220 and for using (50) - 16329, figure 4. The same matrix AL is given however is determined by a different manner - by 3 c11+d11+e11
c12
d12
e12
c21
c22
0
0
AL =
d21
0
d22
0
e21
0
0
e22 where c and d are the same as in (51) , however the right matrix e is different. Decomposition Approach for Inverse Matrix Calculation A part of the MATLAB’s codes which
performs relations (50) for inverse matrix calculations and assess the computational
performance are given below al=[c11+d11+e11 c12 d12 e12 ; c21 c22 m10 m30; d21
m20 d22 m40; e21 m50 m60 e22];
flops(0);
alpha1=inv(al);
fl_al=flops
flops(0);
beta=inv(c);
gama=inv(d);
delta=inv(e);
invbeta11=inv(beta(1:m0,1:m0));
invgama11=inv(gama(1:m0,1:m0));
invdelta11=inv(delta(1:m0,1:m0));
invbeta11beta21T=invbeta11*beta(m0+1:m0+m1,1:m0)';
invgama11gama21T=invgama11*gama(m0+1:m0+m2,1:m0)';
invdelta11delta21T=invdelta11*delta(m0+1:m0+m3,1:m0)';
ff=flops
flops(0);
alpha11=inv(invbeta11+invgama11+invdelta11);
alpha12=alpha11*invbeta11beta21T;
alpha13=alpha11*invgama11*gama(m0+1:m0+m2,1:m0)';
alpha14=alpha11*invdelta11delta21T;
alpha21=alpha12';
alpha22=invbeta11beta21T'*alpha12+beta(m0+1:m0+m1,m0+1:m0+m1)-
beta(m0+1:m0+m1,1:m0)*invbeta11beta21T;
alpha23=invbeta11beta21T'*alpha13;
alpha24=alpha21*invdelta11delta21T;
alpha31=gama(m0+1:m0+m2,1:m0)*invgama11*alpha11;
alpha32=alpha31*invbeta11beta21T;
alpha33=invgama11gama21T'*alpha13+gama(m0+1:m0+m2,m0+1:m0+m2)-
gama(m0+1:m0+m2,1:m0)*invgama11gama21T;
alpha34=alpha31*invdelta11delta21T; al=[c11+d11+e11 c12 d12 e12 ; c21 c22 m10 m30; d21
m20 d22 m40; e21 m50 m60 e22];
flops(0);
alpha1=inv(al);
fl_al=flops
flops(0);
beta=inv(c);
gama=inv(d);
delta=inv(e);
invbeta11=inv(beta(1:m0,1:m0));
invgama11=inv(gama(1:m0,1:m0));
invdelta11=inv(delta(1:m0,1:m0));
invbeta11beta21T=invbeta11*beta(m0+1:m0+m1,1:m0)';
invgama11gama21T=invgama11*gama(m0+1:m0+m2,1:m0)';
invdelta11delta21T=invdelta11*delta(m0+1:m0+m3,1:m0)';
ff=flops
flops(0);
alpha11=inv(invbeta11+invgama11+invdelta11);
alpha12=alpha11*invbeta11beta21T;
alpha13=alpha11*invgama11*gama(m0+1:m0+m2,1:m0)';
alpha14=alpha11*invdelta11delta21T;
alpha21=alpha12'; invbeta11=inv(beta(1:m0,1:m0)); invgama11=inv(gama(1:m0,1:m0)); invdelta11=inv(delta(1:m0,1:m0)); invbeta11beta21T=invbeta11*beta(m0+1:m0+m1,1:m0)'; invgama11gama21T=invgama11*gama(m0+1:m0+m2,1:m0)'; invdelta11delta21T=invdelta11*delta(m0+1:m0+m3,1:m0)';
ff fl alpha11=inv(invbeta11+invgama11+invdelta11); alpha12=alpha11*invbeta11beta21T; p
p
alpha13=alpha11*invgama11*gama(m0+1:m0+m2,1:m0)'; pha13=alpha11*invgama11*gama(m0+ alpha14=alpha11*invdelta11delta21T; alpha21=alpha12'; p
p
;
alpha22=invbeta11beta21T'*alpha12+beta(m0+1:m0+m1,m0+1:m0+m1)-
b t ( 0 1
0
1 1
0)*i
b t 11b t 21T alpha22=invbeta11beta21T'*alpha12+beta(m0+1:m0+m1,m0+1:m0+m1)- beta(m0+1:m0+m1,1:m0)*invbeta11beta21T; alpha23=invbeta11beta21T'*alpha13; alpha24=alpha21*invdelta11delta21T; alpha31=gama(m0+1:m0+m2,1:m0)*invgama11*alpha11; alpha32=alpha31*invbeta11beta21T; alpha33=invgama11gama21T'*alpha13+gama(m0+1:m lpha33=invgama11gama21T'*alpha13+gama(m0+1:m0+m2,m0+1:m0+m2)- p
g
g
p
g
(
,
)
gama(m0+1:m0+m2,1:m0)*invgama11gama21T; gama(m0+1:m0+m2,1:m0)*invgama11gama21T; gama(m0+1:m0+m2,1:m0) invgama11gama2
alpha34=alpha31*invdelta11delta21T; alpha34=alpha31*invdelta11delta21T; MATLAB – A Ubiquitous Tool for the Practical Engineer 132 MATLAB – A Ubiquitous Tool for the Practical Engineer It utilizes the
previous matrices e and f : e =
m0=3
m3=14
4
3 -4
0
2
1
1
-2
0
-3
1
0
3
6
-1
1
4
3
1
3
2
4
0
-5
7
1
-4
3
2
1
-1
4
-1 -2
-4
3 -5
1 -2
1
3
1
0
1
4
1
3
2
4
1
-2
0
2
1
2
1
5
1
1
-2
1
0
0
0
0
0
0
0
2
4 -2
1
3
2
4
1
3
2
0
0
0
0
0
0
0
1
0
1
5
2
3
2
1
-1
1
0
0
0
0
0
0
0
1
-5 3
1
4
2
5
-1
3
-2
0
0
0
0
0
0
0
-2
7
1
1
1
1
-1
6
1
-1
0
0
0
0
0
0
0
0
1
0
-2 3
-1
3
1
2
1
0
0
0
0
0
0
0
-3 -4 1
1
2
1
-2 -1
1
3
0
0
0
0
0
0
0
1
3
4
0
0
0
0
0
0
0
1
-1
3
1
2
1
4
0
2
1
0
0
0
0
0
0
0
-1
2
1
3
-2
1
0
3
1
3
0
0
0
0
0
0
0
3
1
1
-2 -1 -2
1
6
-1 2
0
0
0
0
0
0
0
1
3
-2
1
-3
1
-2
-1
4
4
0
0
0
0
0
0
0
2
-2 -1 -3
2
1
-1
1
-1 1
0
0
0
0
0
0
0
1
1
-2
1
1
3
1
4
-2 -2
0
0
0
0
0
0
0
4
0
1
-2 -1
1
1 The calculations in flops for direct inversing of AL are 50220 and using (49) - 23082, figure 4
Case 3. The inverse matrix is determined by 2 subsystems and AL is in the form c11+d11
c12
d12
AL
c21
c22
0
d21
0
d22 AL Decomposition Approach for Inverse Matrix Calculation 133 where c is the same as in (51) but the right matrix d covers d, e and f from Case 1 or d and e
from Case 2. MATLAB – A Ubiquitous Tool for the Practical Engineer where c is the same as in (51) but the right matrix d covers d, e and f from Case 1 or d and e
from Case 2. The calculations for direct inversing AL are 50232 flops and for using (45) are 37271, figure 4
The results of the experiments of the second example show that if the number of the
subsystems increases, the computational efficiency increases because the matrices’
dimensions decrease. This is in harmony with the multilevel hierarchical idea for
decomposition of the initial problem leading to better efficiency of the system’s
functionality. Fig. 3. Relation flops- m1 matrix dimension
Fig. 4. Relation flops-subsystems number Fig. 3. Relation flops- m1 matrix dimension Fig. 3. Relation flops- m1 matrix dimension Fig. 4. Relation flops-subsystems number Fig. 4. Relation flops-subsystems number MATLAB – A Ubiquitous Tool for the Practical Engineer 134 5. Conclusion The inverse matrix evaluations are decomposed to a set of operations, which does not
consist of calculations of inverse high order matrix. Such decomposition benefits the inverse
calculations when the initial large scale matrix is composed of low order matrices, which
inverses are calculated with less computational efforts. The decomposition approach
benefits the case when an initial matrix is known with its inverse, but few modifications of
its components change it and new inverse has to be calculated. The decomposition approach
for the inverse calculations is assessed and increase of the computational efficiency is
illustrated. The MATLAB implementation of the presented sequence of calculations
(49)−(50) is easy to perform because it results in consequent matrix sum and multiplications,
and low order inverse matrix evaluations. 6. References Fausett, L.(1999). Applied numerical analysis. Prentice Hall, NY, 596 p. Flannery, B.(1997) Numerical recipes in C. The art of Scientific Computing. Cambridge
University press, William Press, Second edition, 965p. Mesarovich, M., D. Mako I. Takahara (1973) Theory of Hierarchical Multilevel Systems,
Moscow, Mir (in Russian) Stoilov T., K. Stoilova (1999). Noniterative coordination in multilevel systems. Kluwer Academic
Publisher, ISBN 0-7923-5879-1, Dordrecht /Boston/London. Stoilova, K. (2010). Noniterative predictive coordination. Professor M. Drinov Academic
Publisher, ISBN 978-954-322-268-1, Sofia (in Bulgarian) Stoilova, K. (2010). Noniterative predictive coordination. Profes
Publisher, ISBN 978-954-322-268-1, Sofia (in Bulgarian) Stoilova K., T. Stoilov (2007) Computational efficiency of inverse matrix evaluations. Proceedings of International Conference Computer Systems and Technologies
“CompSysTech 2007”, ISBN 978-954-9641-50-9, Russe, Bulgaria, pp.IIIA.2-1 –
IIIA.2-6. Strassen V., (1969). Numerische Mathematik, vol.13, pp.354-356. Database Development 7 1. Introduction Effective and safe road network is essential to economic growth and social welfare (Islamic
Republic of Iran Majlis, 2005). More than 550 million tons of goods are transported by road
network in Islamic Republic of Iran, which is a large amount of total cargo transportation's rate
(RMTO, 2009). Overloading of vehicles increases safety risk and pavement damages (Planning
and Management Organization, 1996), so to improve road safety and restrain pavement
damages, legislation based on maximum allowable axle and total load is applied for heavy
vehicles, which are passing on the roads (Mohammadi, 1999). Law enforcement control is
done by weighing control equipments, which have been installed near the arterial roads, and
to evaluate law enforcement, clustering method can be used as an effective technique. Clustering method is used to classify data and decision making in transportation studies. Some researchers (Ahmed and Kanhere, 2007) used clustering method for public transport
modeling in order to improve situation and possibility of changing decision in public
transportation. They showed that using a step forward algorithm for clustering the nodes in
finding routes problems while using clustering method, improves effectiveness of algorithm. Clustering has been used to classify accident types (Depaire et al. 2008). They used a model
based on clustering data, which divide accident data to 7 homogenous groups and finally
analyzed injuries in each group .Comparing results based on divided groups and total data
analysis showed that classifying data could be used for safety issues researchers with more
accuracy. Effective and safe road network is essential to economic growth and social welfare (Islamic
Republic of Iran Majlis, 2005). More than 550 million tons of goods are transported by road
network in Islamic Republic of Iran, which is a large amount of total cargo transportation's rate
(RMTO, 2009). Overloading of vehicles increases safety risk and pavement damages (Planning
and Management Organization, 1996), so to improve road safety and restrain pavement
damages, legislation based on maximum allowable axle and total load is applied for heavy
vehicles, which are passing on the roads (Mohammadi, 1999). Law enforcement control is
done by weighing control equipments, which have been installed near the arterial roads, and
to evaluate law enforcement, clustering method can be used as an effective technique. g
q
Clustering method is used to classify data and decision making in transportation studies. 1. Introduction Some researchers (Ahmed and Kanhere, 2007) used clustering method for public transport
modeling in order to improve situation and possibility of changing decision in public
transportation. They showed that using a step forward algorithm for clustering the nodes in
finding routes problems while using clustering method, improves effectiveness of algorithm. Clustering has been used to classify accident types (Depaire et al. 2008). They used a model
based on clustering data, which divide accident data to 7 homogenous groups and finally
analyzed injuries in each group .Comparing results based on divided groups and total data
analysis showed that classifying data could be used for safety issues researchers with more
accuracy. Clustering method is used to classify data and decision making in transportation studies. Some researchers (Ahmed and Kanhere, 2007) used clustering method for public transport
modeling in order to improve situation and possibility of changing decision in public
transportation. They showed that using a step forward algorithm for clustering the nodes in
finding routes problems while using clustering method, improves effectiveness of algorithm. Clustering has been used to classify accident types (Depaire et al. 2008). They used a model
based on clustering data, which divide accident data to 7 homogenous groups and finally (Fielding et. al 1985) used clustering method for analyzing transit systems equipments,
considering vehicle's size, average speed, urban transportation situation, and bus specified
routes, and have classified transit situation to 12 categories. Difference of characteristics for
all categories was identified using variance analysis, detached group and tree decision-
making method. Grouping data were made by seven main transit efficiency factors and
finally some suggestion for each group was supposed to productivity evaluation. In this paper after a brief review on methods of controlling cargo transportation and existing
regulation in rural roads network, an evaluation method of trucks weighing control is
presented using clustering analysis method. For evaluation and comparing results, available
data on trucks weighing control, which have been collected by local authorities in all over 138 MATLAB – A Ubiquitous Tool for the Practical Engineer the country, have been analyzed based on clustering and finally weighing stations have
been categorized in different groups. 2. Goods transportation controlling on road network Overloading vehicles are important from two sides of decreasing transportation safety and
fateful damages on roads surface and infrastructures. Overloaded vehicles in addition to
damage road surface, because of Pre-designing of braking system particularly at slides and
curves, endanger other vehicles. Increasing goods' transportation will lead to economical
growth from one side of the view, and the other side will increase maintenance costs and
safety risks. Studies show that the most important factor of roads destruction is heavy
vehicle's axle load. Based on researches the damage on roads surface is related to the vehicle
axle load by a non-linear acceleration rate mostly in a polynomial equation of forth degree. Because of limited budget in roads maintenance activities, it is essential to apply over
loaded vehicles limitation rules effectively. In spite of heavy maintenance costs, do not
repairing road surfaces leads to destroy vehicles and decreasing traffic speed, so pavement
management is very important issue because of overloading vehicles passage . At the present, the method of trucks weighing control in Iran is using weighing control Overloading vehicles are important from two sides of decreasing transportation safety and
fateful damages on roads surface and infrastructures. Overloaded vehicles in addition to
damage road surface, because of Pre-designing of braking system particularly at slides and
curves, endanger other vehicles. Increasing goods' transportation will lead to economical
growth from one side of the view, and the other side will increase maintenance costs and
safety risks. Studies show that the most important factor of roads destruction is heavy
vehicle's axle load. Based on researches the damage on roads surface is related to the vehicle
axle load by a non-linear acceleration rate mostly in a polynomial equation of forth degree. Because of limited budget in roads maintenance activities, it is essential to apply over
loaded vehicles limitation rules effectively. In spite of heavy maintenance costs, do not
repairing road surfaces leads to destroy vehicles and decreasing traffic speed, so pavement
management is very important issue because of overloading vehicles passage . At the present, the method of trucks weighing control in Iran is using weighing control
equipments including static, dynamic, and portable scales at weighing stations (and Weigh
in Motion System in 6 points). Maximum permitted axle load for different types of heavy
vehicles, which has been identified by laws, is under the control of weighing stations. 3. Proposed method According to importance of controlling overloaded vehicles, performance evaluation of
weighing control is inevitable. Identifying effective parameters on weighing control, data
standardizing and ranking weighing stations have done in this paper in the sequence
process using a well-known method of statistical process of clustering. 3.1 Clustering method Clustering method is a statistical method that divides observation data according to their
similarity to homogenous and detached groups (Sharma, 1996). In this method, similarity
criterion is firstly identified. The number of groups would be analyzed and recognized. Observation data in each group are similar to each other based on similarity criterion and
each group is different from the other groups. It is possible to consider more than one
variable simultaneously as similarity criterion in clustering method. However, there are
some different methods of identifying similarity criterions, but the common method for
defining similarity is known as equation number 1 while the similarity of itk and jtk
observed data of kth variable is defined by P2ij. 2
2
1
(
)
p
ij
ik
jk
k
P
x
x
=
= ∑
(1) (1) Clustering is a hierarchically process means that the nearest observations are merged
continuously to make larger groups. This process will be continued until number of groups
is reached to the proposed number of desired clusters. Merging observations is done by
different methods such as Centroid, Farthest- Neighbour, Nearest- Neighbour, Average 139 A Cluster-Based Method for Evaluation of Truck's Weighing Control Stations Linkage, and Ward method usually chosen by analysts based on acceptable frequency. Based on experience, experts’ view and comparing results of clustering Ward method is
used to merge data in this research. 3.2 Data normalization Because of existing the effective parameters in decision-making techniques, if there are
different dimensions, for variables normalization or standardizing methods are used to
assimilate (Sharma, 1996). If data can be fitted by a normal distribution function,
normalization method is used. In addition, there are different methods of output and input
data normalization, which the most regular methods convert data to, numbers between 0 to
1 and -1 to 1. Equations (2) and (3) converts data to zero to 1 numbers and are used for data
more than zero. max
old
new
X
X
X
=
(2) (2) min
max
min
old
new
X
X
X
X
X
−
=
−
(3) (3) If it is necessary to convert data in the range of -1 to 1, equation (4) is used: If it is necessary to convert data in the range of -1 to 1, equation (4) is used: max
min
0
0
old
new
old
old
new
old
X
X
X
X
X
X
X
X
⎧
⎫
=
∀
≥
⎪
⎪
⎪
⎪
⎨
⎬
⎪
⎪
=
∀
≤
⎪
⎪⎭
⎩
(4) (4) In order to standardize data assuming distribution function is normal, equation (5) is used
which Xold is preliminary amount of factor and Xnew is standardized form: In order to standardize data assuming distribution function is normal, equation (5) is used
which Xold is preliminary amount of factor and Xnew is standardized form: 2
1
(
)
1
old
new
n
i
i
X
X
X
X
X
n
=
−
=
−
−
∑
(5) (5) 3.3 Data gathering To evaluate truck's weighing control performance, number of registered overloaded
vehicles, amount of detected overload, the type of scale, average heavy vehicle's daily
traffic, and number of overloaded vehicles with more than 5 tons overload are collected
from all over the country in 6 mount period to use defined below parameters: •
Number of registered overloaded vehicles of six months period •
Detected amount of overloading of six months period •
Detected amount of overloading of six months period •
Proportion of registered overloaded vehicles of six months period to the same period in
last year y
•
Proportion of detected amount of overloading of six months period to the same period
in last year •
Proportion of detected amount of overloading of six months period to the same period
in last year y
•
Average heavy vehicles daily traffic of six months period 140 MATLAB – A Ubiquitous Tool for the Practical Engineer •
The fraction of number of overloaded vehicles with more than 5 ton overload to total
registered overloaded vehicles of six months period
Tables 1 and 2 show maximum, minimum, average, and standard deviation of collected data •
The fraction of number of overloaded vehicles with more than 5 ton overload to total
registered overloaded vehicles of six months period •
The fraction of number of overloaded vehicles with more than 5 ton overload to total
registered overloaded vehicles of six months period
Tables 1 and 2 show maximum, minimum, average, and standard deviation of collected data
before and after standardizing data respectively. As it is observed, to homogenize data,
standardization is used because of having a normal distribution function. Tables 1 and 2 show maximum, minimum, average, and standard deviation of collected data
before and after standardizing data respectively. As it is observed, to homogenize data,
standardization is used because of having a normal distribution function. standardization is used because of having a normal distribution function. 3.4 Setting number of clusters The number of clusters is specified in two ways. In the first method, analysts specify
number of clusters when the number of clusters needs to be applied to other decision-
making process, for example using clustering method to fuzzy modeling. Second method of
specifying number of clusters, is minimizing Within-Group Sum of Squares (Sharma, 1996)
while the sum of total deviation is calculated and number of clusters is identified in such a
way that inter clusters sum of squares, which is named missed sum of squares, would be
minimized. Also proportional sum of deviation squares as Between-Group Sum of Squares
is used as a criterion to specifying number of clusters. Since the number of clusters in this research work is not too important, second method
which is more scientific has been used and the number of clusters is specified in such a way
that minimizes Within-Group, deviation. Table 3 shows total deviation, Within-Group and
Between-Group deviation and proportion of Within-Group to total deviation which is
decision making parameter. According to table (3), if it is proposed that 85 percent of deviation is reserved, number of
clusters would be 16, and if it is proposed to reserve 90 percent of deviation, number of
clusters would be 22. As it is shown at table (3) rest of deviations after 22 would change
slowly means increasing the number of clusters doesn’t have significant rule in decision
process. p
Figure (1) shows changes in total deviation, Within-Group and Between-Group deviation
based on the number of clusters. As it has been shown in this figure, difference between
Total deviation and Between-Group deviation would be decreased after 16, since 16
covers 85 percent of deviations, so in this research 16 number of clusters has been
considered to evaluate weighing stations performance in controlling goods transported by
heavy vehicles. 3.3 Data gathering Experimental Data
Parameter's Name
Row
Standard
Deviation
Average
Min
Max
255
193
2
1754
Number of registered overloaded vehicles
1
655
519
2
4014
Detected amount of overloading(ton)
2
143
88
-96
615
Proportion of detected overloaded vehicles
of six months period to the same period in
last year
3
162
89
-94
718
Amount of detected overloading proportion
of six months period to the same period in
last year
4
6493
3887
103
41059
Average daily heavy vehicles traffic
5
0.09
0.07
0
0.35
Number of more than 5 ton overloaded
vehicles to number of total overload
proportion
6
Table 1. Parameters, experimental data
. Standardized Data
Parameter's Name
Row
Standard
Deviation
Average
Min
Max
1
0
-0.75
6.12
Number of detected overloaded
vehicles
1
1
0
-0.79
5.37
Detected amount of overloading(ton)
2
1
0
-1.29
3.69
Proportion of detected overloaded
vehicles of six months period to the
same period in last year
3
1
0
-1.13
3.89
Amount of detected overloading
proportion of six months period to the
same period in last year
4
1
0
-0.58
5.72
Average daily heavy vehicles traffic
5
1
0
-0.87
3.16
Number of more than 5 ton overloaded
vehicles to number of total overload
proportion
6
Table 2. Parameters, standardized data 141 A Cluster-Based Method for Evaluation of Truck's Weighing Control Stations Table 3. Deviation from average sum of square errors 3.4 Setting number of clusters Row
Number
of
Clusters
Deviation From Average Sum of Square Errors
Total
Within
Groups
Between
Groups
Proportion of
Between Groups to
Total
1
4
750
352
398
53
2
6
750
236
514
69
3
8
750
183
567
76
4
10
750
156
594
79
5
12
750
145
605
81
6
14
750
122
628
84
7
16
750
113
637
85
8
18
750
102
648
86
9
20
750
81
669
89
10
22
750
77
673
90
11
24
750
68
682
91
12
26
750
63
687
92
13
28
750
61
689
92
14
30
750
55
695
93 142 MATLAB – A Ubiquitous Tool for the Practical Engineer Fig. 1. Plot of square errors (Within, Between and Total) Fig. 1. Plot of square errors (Within, Between and Total) 4. How to use MATLAB software There is a command in MATLAB software, which has ability to cluster observations based
on many parameters. As shown in tables 1 and 2, there are six parameters for clustering. Clusterdata is a well-known command in order to cluster data. There is a matrix 126×6
contains data used in this research work. If matrix named as X figure 2 shows the format of
data. Code
X(:,1)
X(:,2)
X(:,3)
X(:,4)
X(:,5)
X(:,6)
5707
0.011113
-0.0353
-0.64109
-0.81193
-0.46864
-0.86858
5704
0.819076
0.992241
-0.65484
-0.90436
-0.36345
-0.86858
…
…
…
…
…
…
…
5108
0.611202
1.519068
-0.08919
-0.82648
0.333153
0.958812
5106
-0.68703
-0.72033
0.783371
1.209399
0.448663
-0.86858
Fig. 2. Matrix contains data with six parameters Fig. 2. Matrix contains data with six parameters When command ''clusterdata'' is typed, results, are generated and are shown in a matrix
contain two columns. The first column corresponds the row of observation and the second
corresponds assigned cluster. For example if the first row of result matrix contains, 1 and 15,
it means that station coded as 5707 in the first row of matrix X, belong to the 14th cluster. The other command in MATLAB is kmeans, which is used to calculate the distance between
observation and centre of the cluster. There is a output variable of SUMD in kmeans
command to set distances and within group sum of square errors will be calculated by sum
of the square distances of variable SUMD. Between sum of square errors will be calculated
by total sum of square errors minus within sum of square errors while total sum of square
errors is calculated as below (Sharma, 1996): When command ''clusterdata'' is typed, results, are generated and are shown in a matrix
contain two columns. The first column corresponds the row of observation and the second
corresponds assigned cluster. For example if the first row of result matrix contains, 1 and 15,
it means that station coded as 5707 in the first row of matrix X, belong to the 14th cluster. The other command in MATLAB is kmeans, which is used to calculate the distance between The other command in MATLAB is kmeans, which is used to calculate the distance between
observation and centre of the cluster. When 126 is the number of observations and 6 is the number of standardized parame 4. How to use MATLAB software There is a output variable of SUMD in kmeans
command to set distances and within group sum of square errors will be calculated by sum
of the square distances of variable SUMD. Between sum of square errors will be calculated
by total sum of square errors minus within sum of square errors while total sum of square
errors is calculated as below (Sharma, 1996): Total sum of square errors = (126-1) × 6 = 750 Total sum of square errors = (126-1) × 6 = 750 5. Results Considering the number of clusters by 16 and Ward Method to merging data, using
clustering method of well-known software of MATLAB version R2008a, weighing station
grades considering six identified variables are presented as table 4. Class
Station’s code
Number of
stations
1
1126, 3603
2
2
3607, 3601
2
3
4507, 4102, 8708, 2109
4
4
1106
1
5
1125, 1104, 5408, 8701
4
6
5409, 8705, 8706, 3202, 2110, 9101
6
7
5108, 5107, 5109, 9703, 9702
5
8
1190, 1112, 3609, 3606, 3602, 7504
6
9
1108, 3608, 3604
3
10
9748, 4502, 8709, 3203, 3303, 7702, 2107
7
11
5102, 1122, 7503, 5401, 5406, 1403, 4110, 2104, 5703, 5704
11
12
5106, 1116, 4508, 4553, 4506, 4106, 41014, 4108, 4106, 4104, 6108,
6107, 2116, 2106, 9104, 9105
14
13
2105, 6401, 5402, 5403, 5404, 9701, 9506, 9502, 2111, 2105
10
14
5104, 1103, 1114, 7502, 4503, 4501, 4504, 1405, 4117, 6110, 6105, 8702,
7701, 2108, 2101, 5701, 5702, 5707
19
15
6402, 6404, 6403, 5407, 6106, 6102, 6101, 8704, 3201, 3301, 7706, 9505,
9501, 2103, 2102, 9103, 9102
17
16
3610, 7505, 6405, 4114, 4111, 4122, 4109, 4105, 4112, 4101, 6108, 6103,
7704, 9503, 5706
15 Total sum of square errors = (126-1) × 6 = 750 n 126 is the number of observations and 6 is the number of standardized parameters. A Cluster-Based Method for Evaluation of Truck's Weighing Control Stations 143 6. Conclusion and future research In this research, number of detected overloaded vehicles, amount of overload, scale's type,
average heavy vehicle's daily traffic, and number of overloaded vehicles with more than 5
ton overload are collected from all over the country in a six month period and using
standardization method are homogenized. By using minimum deviation method of Average
within-Groups, number of clusters is calculated and considering Ward method for merging
data, and using clustering method, the performance of weighing stations have been
classified in 16 groups. Results show that this method is appropriate to use evaluation of
weighing control performance in weighing stations. Future studies, recommended using ranking method by similarity factors for traffic laws
enforcement control, and any other important factors such as vehicles speed, overtaking,
and left diversion control. Ranking enforcement stations and at a wider view ranking
provinces could provide a comprehensive and precise image for mangers about
enforcement stations performance. MATLAB – A Ubiquitous Tool for the Practical Engineer 144 7. References Ahmed, S.; Kanhere, S.S, (Oct 2007), “Cluster-based Forwarding in Delay Tolerant Public
Transport, Networks”, 32nd IEEE Conference, Pages 625-634. Bolghari, M., (2010, 1389 local calender), “Driving laws and regulations”, Second version,
Department of transportation, Tehran municipality, 2010. Depaire, B., Wets, G., Vanhoof, K., (July 2008), “Traffic accident segmentation by means of
latent class clustering”, Accident Analysis and Preventation, Vol, 40, Issue 4, Pages
1257-1266. Fielding, G.J., Brenner, M.E., Faust, K., (May 1985), “Typology for Bus Transit”,
Transportation Research, Part A, Vol 40, Issue 4, Pages 1257-1266. p
g
Islamic Republic of Iran Majlis, (2005, 1384 local calender) “Forth five-year developing plan
of Islamic republic of Iran”, available on www.majlis.ir Mohammadi Asa, A., (1999, 1378 local calender), “Laws and regulations in road transport”,
Road maintenance and transportation organization. g
Planning and management organization, (1996, 1375 local calender) “Road pavement and
asphalt manual”, Vol. 234. p
Road Maintenance and Transportation Organization, (2009, 1388 local calender) “Annual
survey of road transport in Iran”, available on www.rmto.ir Subhash Sharma, (1996), “Applied Multivariable Techniques”, University of South Carolina,
USA. 8 The Impact of the Data Archiving File Format
on Scientific Computing and Performance
of Image Processing Algorithms in MATLAB
Using Large HDF5 and XML Multimodal and
Hyperspectral Data Sets
Kelly Bennett1 and James Robertson2
1U.S. Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, MD
2Clearhaven Technologies LLC, Severna Park, MD
U.S.A Kelly Bennett1 and James Robertson2
1U.S. Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, MD
2Clearhaven Technologies LLC, Severna Park, MD
U.S.A 1. Introduction Scientists require the ability to effortlessly share and process data collected and stored on a
variety of computer platforms in specialized data storage formats. Experiments often
generate large amounts of raw and corrected data and metadata, which describes and
characterizes the raw data. Scientific teams and groups develop many formats and tools for
internal use for specialized users with particular references and backgrounds. Researchers
need a solution for querying, accessing, and analyzing large data sets of heterogeneous data,
and demand high interoperability between data and various applications (Shasharina et al.,
2007; Shishedjiev et al., 2010). j
Debate continues regarding which data format provides the greatest transparency and
produces the most reliable data exchange. Currently, Extensible Markup Language (XML)
and Hierarchical Data Format 5 (HDF5) formats are two solutions for sharing data. XML is a
simple, platform-independent, flexible markup meta-language that provides a format for
storing structured data, and is a primary format for data exchange across the Internet
(McGrath, 2003). XML data files use Document Type Definitions (DTDs) and XML Schemas
to define the data structures and definitions, including data formatting, attributes, and
descriptive information about the data. A number of applications exist that use XML-based
storage implementations for applications, including radiation and spectral measurements,
simulation data of magnetic fields in human tissues, and describing and accessing fusion
and plasma physics simulations (Shasharina et al., 2007; Shishedjiev et al., 2010). Debate continues regarding which data format provides the greatest transparency and
produces the most reliable data exchange. Currently, Extensible Markup Language (XML)
and Hierarchical Data Format 5 (HDF5) formats are two solutions for sharing data. XML is a
simple, platform-independent, flexible markup meta-language that provides a format for
storing structured data, and is a primary format for data exchange across the Internet
(McGrath, 2003). XML data files use Document Type Definitions (DTDs) and XML Schemas
to define the data structures and definitions, including data formatting, attributes, and
descriptive information about the data. A number of applications exist that use XML-based
storage implementations for applications, including radiation and spectral measurements,
simulation data of magnetic fields in human tissues, and describing and accessing fusion
and plasma physics simulations (Shasharina et al., 2007; Shishedjiev et al., 2010). HDF5 is a data model, library, and file format for storing and managing data. HDF5 is
portable and extensible, allowing applications to evolve in their use of HDF5 (HDF Group). 1. Introduction HDF5 files provide the capability for self-documenting storage of scientific data in that the
HDF5 data model provides structures that allow the file format to contain data about the file
structure and descriptive information about the data contained in the file (Barkstrom, 2001). Similar to XML, numerous applications using the HDF5 storage format exist, such as fusion HDF5 is a data model, library, and file format for storing and managing data. HDF5 is
portable and extensible, allowing applications to evolve in their use of HDF5 (HDF Group). HDF5 files provide the capability for self-documenting storage of scientific data in that the
HDF5 data model provides structures that allow the file format to contain data about the file
structure and descriptive information about the data contained in the file (Barkstrom, 2001). Similar to XML, numerous applications using the HDF5 storage format exist, such as fusion 146 MATLAB – A Ubiquitous Tool for the Practical Engineer and plasma physics, astronomy, medicine and bio-imaging (Shasharina et al., 2007;
Dougherty et al., 2009). and plasma physics, astronomy, medicine and bio-imaging (Shasharina et al., 2007;
Dougherty et al., 2009). In this chapter, we will use hyperspectral images stored in XML and HDF5 format to
compare the relative performance of the file format using computationally intensive signal
and image processing algorithms running in MATLAB on Windows® 64-bit and Linux 64-
bit workstations. Hyperspectral imaging refers to the multidimensional character of the
spectral data set, where the acquisition of images takes place over many contiguous spectral
bands throughout the visible and infrared (IR) regions (Goetz et al., 1985). Sensor fusion and
advanced image processing techniques are now possible using the information from these
different bands that allow applications in aerospace, defense, medicine, and other fields of
study. To assist researchers in exchanging the data needed to develop, test, and optimize the
techniques, selecting the best file format for computing environments (such as MATLAB)
requires additional analysis. Such analysis includes analyzing the relative performance of
the file format, including scalability, with respect to various computational tools, computer
architectures, and operating systems (Bennett & Robertson, 2010). In this chapter we provide
insights into the challenges researchers face with a growing set of data, along with
expectations for performance guidelines on workstations for processing large HDF5 and
XML hyperspectral image data. 2. Analysis of HDF5 and XML Formats The goals of this analysis are to: 1. Determine strengths and weaknesses of using HDF5 and XML formats for typical
processing techniques associated with large hyperspectral images; 1. Determine strengths and weaknesses of using HDF5 and XML formats for typical
processing techniques associated with large hyperspectral images; 2. Compare and analyze processing times on Windows and Linux 64-bit workstations for
HDF5 and XML hyperspectral images; and 2. Compare and analyze processing times on Windows and Linux 64-bit workstations for
HDF5 and XML hyperspectral images; and 3. Identify areas that require additional research to help improve efficiencies associated
with processing large HDF5 and XML files, such as hyperspectral images. 3. Identify areas that require additional research to help improve efficiencies associated
with processing large HDF5 and XML files, such as hyperspectral images. 1. Introduction Additionally, in this chapter, we provide specific results
comparing data load, process, and memory usage for the differing data formats, along with
detailed discussions and implications for researchers. ® Registered trademark of Microsoft Corporation. 3. Methodology for Analysis of HDF5 and XML Formats To address the analysis goals a set of 100 files containing multimodal hyperspectral images,
ranging in size from 57 MB to 191 MB, stored in HDF5 format provided the input for the
creation of HDF5 and XML dataset files as part of a preprocessing step for further analysis. The created HDF5 and XML dataset files provided the input to a series of analysis
techniques typically associated with image and signal processing. Two different
workstations running 64-bit Windows and Linux operating systems are used. The
workstations are equipped with MATLAB (scientific programming language). Table 1
displays the descriptions of each of the workstations. The hyperspectral images were originally stored in HDF5 format and included several
different types of metadata in the form of HDF5 Groups and Datasets. Metadata in a typical
HDF5 file includes ground truth, frequency bandwidths, raw image data, TIFF (Tagged The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 147 Image File Format)-formatted images, collection information, and other ancillary
information, allowing researchers to understand the images and their collection parameters. Descriptor
Windows 64-bit
Linux 64-bit
Operating System
Windows 7 home premium
Red Hat Enterprise Linux 5
CPU
Intel i7 920 @2.67 GHz
2 processor, quad core Xeon
2.0 GHz
Memory
6 GB
16 GB
MATLAB version
7.11.0 (R2010b)
7.11.0 (R2010b)
Table 1 Research Equipment Descriptions Descriptor
Windows 64-bit
Linux 64-bit
Operating System
Windows 7 home premium
Red Hat Enterprise Linux 5
CPU
Intel i7 920 @2.67 GHz
2 processor, quad core Xeon
2.0 GHz
Memory
6 GB
16 GB
MATLAB version
7.11.0 (R2010b)
7.11.0 (R2010b)
Table 1. Research Equipment Descriptions. Table 1. Research Equipment Descriptions. Each original HDF5 file went through a number of preprocessing steps to remove the
metadata in preparation for analysis. For analysis purposes, we needed to remove the
metadata from the original HDF5 files and create new HDF5 and XML formatted files
consisting of only raw sensor data prior to performing image processing. These steps included
loading the original HDF5 file structures, searching through the HDF5 groups to find the raw
image data, saving the new HDF5 file, creating and populating an XML document node, and
saving the XML file. Figure 1 shows the overall steps in processing the original HDF5 file,
along with some critical MATLAB code associated with each of those steps. Fig. 1. 3. Methodology for Analysis of HDF5 and XML Formats The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 149 Once stored as numeric arrays, the processing for the XML and the HDF5 files were the
same and these processing steps include image adjustment, histogram calculation, and
descriptive statistics, filtering to remove noise, edge detection and 2-D FFT threshold feature
detection. Each of these image-processing techniques includes possible techniques users
may invoke when processing hyperspectral images. Table 2 provides a brief description of
each of these techniques and an example call within MATLAB. In Table 2, “im” represents
the original image and ‘im2’ represents a processed image of ‘im’. Each row in Table 2
shows various processing operations performed on ‘im’ or ‘im2’. Figure 2 shows the flow of
the image processing techniques. Once stored as numeric arrays, the processing for the XML and the HDF5 files were the
same and these processing steps include image adjustment, histogram calculation, and
descriptive statistics, filtering to remove noise, edge detection and 2-D FFT threshold feature
detection. Each of these image-processing techniques includes possible techniques users
may invoke when processing hyperspectral images. Table 2 provides a brief description of
each of these techniques and an example call within MATLAB. In Table 2, “im” represents
the original image and ‘im2’ represents a processed image of ‘im’. Each row in Table 2
shows various processing operations performed on ‘im’ or ‘im2’. Figure 2 shows the flow of
the image processing techniques. Fig. 2. Image Processing Overview. Some of the metrics used for assessing the performance of each file format are calculation of
load times, process times, and memory usage statistics for each file format and machine. These metrics reveal the computational performance of processing large archived data files
in MATLAB using typical image processing algorithms. MATLAB’s tic and toc methods
were convenient to measure elapsed times associated with each processing step. Hyperspectral images consist of multiple segments representing different spectral bands or
narrow frequency bands, with data collected for each image segment and averaged for
reporting purposes. For example, an image with 62 segments would generate data for each
of the 62 segments and the mean of those values, with the results described in the Results
section of this paper. A typical sequence of elapsed time measurement would occur as
shown in Figure 3. 3. Methodology for Analysis of HDF5 and XML Formats Original HDF5 File Preprocessing Overview for the creation of HDF5 and XML
Dataset Files. Fig. 1. Original HDF5 File Preprocessing Overview for the creation of HDF5 and XML
Dataset Files Fig. 1. Original HDF5 File Preprocessing Overview for the creation of HDF5 and XML
Dataset Files. Fig. 1. Original HDF5 File Preprocessing Overview for the creation of HDF5 and XML
Dataset Files. 148 MATLAB – A Ubiquitous Tool for the Practical Engineer After creating the HDF5 and XML files for the raw sensor data, each file was loaded into
MATLAB, converted to an array as needed, and run through a number of image processing
steps. XML stores the array data as a large ASCII character string, which requires converting
the character array into a numeric array before beginning any processing. Unfortunately, the
arrays were too large to use MATLAB’s str2num() function, so a novel custom method was
developed to read each character and convert it into numbers before writing the numbers
into a MATLAB array. Technique
Description
Example MATLAB Call
Image
Adjustment
Maps the values in intensity to
new values such that 1% of data
saturates at low and high
intensities of the original image. im2= imadjust(im);
Histogram
Calculates a histogram where
the variable bin specifies the
number of bins used in the
histogram. [COUNTS,X] = imhist(im2,bin);
Descriptive
Statistics
Computes the mean and
standard deviations of the
image values. imagemean=mean2(im2);
imagestd=std2(im2);
Median Noise
Filter
Performs a median filtering of
the image using a 3-by-3
neighborhood. J=medfilt2(im2);
Weiner Noise
Filter
Performs a filtering of the image
using pixel-wise adaptive
Wiener filtering, using
neighborhoods of size fx-by-fy
to estimate the local image
mean and standard deviation
K = wiener2(im2,[fx fy]);
Sobel Edge
Detection
Sobel method finds edges using
the Sobel approximation to the
derivative. It returns edges at
those points where the gradient
is maximum
BW1 = edge(im2,'sobel');
Canny Edge
Detection
The Canny method finds edges
by looking for local maxima of
the gradient. The derivative of a
Gaussian filter provides the
approach for calculating the
gradient. BW2 = edge(im2,'canny');
FFT 2D
Threshold
Feature
Detection
FFT approach to template
matching and feature detection. z= im2(minx:maxx,miny:maxy);
C = real(ifft2(fft2(im2) .*
fft2(rot90(z,2),dims(1),dims(2))));
t=max(C(:)) - .05*max(C(:));
Table 2. Image Processing Technique Descriptions. Table 2. Image Processing Technique Descriptions. % Adjust the image for better display
tic;
im2= imadjust(im);
adjustIM(i,j)=toc; After loading each created dataset file, both in HDF5 and XML, measuring the memory will
determine the average memory usage. For the Windows environment, MATLAB’s memory
functions perform the process of determining the physical memory available at that point in
time. For the Linux environment, system calls to the Linux memory functions determine the
physical memory available after loading the file. MATLAB does not provide a Linux
memory function at this time. Figure 4 shows a typical Windows memory call. % Measure Windows Memory
[USERVIEW, SYSTEMVIEW] = memory;
pmem(i,j)=SYSTEMVIEW.PhysicalMemory.Available;
Fig 4 Windows Memory Measurement Example Code % Measure Windows Memory
[USERVIEW, SYSTEMVIEW] = memory;
pmem(i,j)=SYSTEMVIEW.PhysicalMemory.Available;
Fig. 4. Windows Memory Measurement Example Code. Fig. 4. Windows Memory Measurement Example Code. Test
Description
Performance Factors
LU
Perform LU of a full matrix
Floating-point, regular memory access
FFT
Perform FFT of a full vector
Floating-point, irregular memory access
ODE
Solve van der Pol equation with
ODE45
Data structures and MATLAB function
files
Sparse Solve a symmetric sparse linear system
Mixed integer and floating-point
2-D
Plot Bernstein polynomial graph
2-D line drawing graphics
3-D
Display animated L-shape membrane
logo
3-D animated OpenGL graphics
Table 3. MATLAB’s Benchmark Descriptions. Prior to running the algorithms, each computer system performed baseline benchmarks. MATLAB has a convenient built-in benchmark named “bench” that executes six different
MATLAB tasks and compares the execution speed with the speed of several other
computers. Table 3 shows the six different tasks. The LU test performs a matrix factorization, which expresses a matrix as the product of two
triangular matrices. One of the matrices is a permutation of a lower triangular matrix and
the other an upper triangular matrix. The fast Fourier transform (FFT) test performs the
discrete Fourier transform computed using an FFT algorithm The ordinary differential Prior to running the algorithms, each computer system performed baseline benchmarks. MATLAB has a convenient built-in benchmark named “bench” that executes six different
MATLAB tasks and compares the execution speed with the speed of several other
computers. Table 3 shows the six different tasks. p
The LU test performs a matrix factorization, which expresses a matrix as the product of two
triangular matrices. One of the matrices is a permutation of a lower triangular matrix and
the other an upper triangular matrix. The fast Fourier transform (FFT) test performs the
discrete Fourier transform computed using an FFT algorithm. 3. Methodology for Analysis of HDF5 and XML Formats In the Figure 3 example, all files ("i") and segments ("j") perform the
timing process for the image adjustment algorithm. Fig. 2. Image Processing Overview. Fig. 2. Image Processing Overview. Fig. 2. Image Processing Overview. Some of the metrics used for assessing the performance of each file format are calculation of
load times, process times, and memory usage statistics for each file format and machine. These metrics reveal the computational performance of processing large archived data files
in MATLAB using typical image processing algorithms. MATLAB’s tic and toc methods
were convenient to measure elapsed times associated with each processing step. Hyperspectral images consist of multiple segments representing different spectral bands or
narrow frequency bands, with data collected for each image segment and averaged for
reporting purposes. For example, an image with 62 segments would generate data for each
of the 62 segments and the mean of those values, with the results described in the Results
section of this paper. A typical sequence of elapsed time measurement would occur as
shown in Figure 3. In the Figure 3 example, all files ("i") and segments ("j") perform the
timing process for the image adjustment algorithm. Some of the metrics used for assessing the performance of each file format are calculation of
load times, process times, and memory usage statistics for each file format and machine. These metrics reveal the computational performance of processing large archived data files
in MATLAB using typical image processing algorithms. MATLAB’s tic and toc methods
were convenient to measure elapsed times associated with each processing step. Hyperspectral images consist of multiple segments representing different spectral bands or
narrow frequency bands, with data collected for each image segment and averaged for
reporting purposes. For example, an image with 62 segments would generate data for each
of the 62 segments and the mean of those values, with the results described in the Results
section of this paper. A typical sequence of elapsed time measurement would occur as
shown in Figure 3. In the Figure 3 example, all files ("i") and segments ("j") perform the
timing process for the image adjustment algorithm. 150 MATLAB – A Ubiquitous Tool for the Practical Engineer % Adjust the image for better display
tic;
im2= imadjust(im);
adjustIM(i,j)=toc; 4. Data analysis Data analysis included calculating descriptive statistics on each test to include mean,
standard deviation, variance, minimum and maximum values, and t-test analysis; to
determine relationships and differences in performance measurements comparing XML and
HDF5 formats for both computer systems. The t-test is one of the most commonly used
statistics to determine whether two datasets are significantly different from one another
(Gay & Airasian, 2003). The t-test determines if the observed variation between the two
datasets is sufficiently larger than a difference expected purely by chance. For this research,
the significance level (α) was set at 0.05. This value is commonly accepted and is the default
value for many statistical packages that include the t-test (Gay & Airasian, 2003; SAS
Institute, 2003; MathWorks, 2011). For each processing, memory, or loading algorithm, the descriptive statistics for each
hyperspectral image create relevant data for a final analysis. The information obtained from
averaging across each segment of the multiple segmented images creates the analytical data
products used in the results. In addition to the descriptive statistics for each process, graphical plots illustrate the load
times, process times, and memory usage as a function of file size for each data type and test
environment. These plots provide an ability to identify differences between the XML and
HDF5 data types and possible processing bottlenecks and limitations. % Adjust the image for better display
tic;
im2= imadjust(im);
adjustIM(i,j)=toc; The ordinary differential
equation (ODE) test solves equations using the ODE45 solver. The Sparse test converts a p
The LU test performs a matrix factorization, which expresses a matrix as the product of two
triangular matrices. One of the matrices is a permutation of a lower triangular matrix and
the other an upper triangular matrix. The fast Fourier transform (FFT) test performs the
discrete Fourier transform computed using an FFT algorithm. The ordinary differential
equation (ODE) test solves equations using the ODE45 solver. The Sparse test converts a The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 151 matrix to sparse form by removing any zero elements. Finally, the 2-D and 3-D measure 2-D
and 3-D graphics performance, including software or hardware support for OpenGL (Open
Graphics Library). matrix to sparse form by removing any zero elements. Finally, the 2-D and 3-D measure 2-D
and 3-D graphics performance, including software or hardware support for OpenGL (Open
Graphics Library). The benchmark results in a speed comparison between the current machine and industry-
available machines. 5. Results and Implications Scientists and researchers need a reliable format for exchanging large datasets for use in
computational environments (such as MATLAB). MATLAB has many advantages over
conventional languages (such as FORTRAN, and C++) for scientific data analysis, such as
ease of use, platform independence, device-independent plotting, graphical user interface,
and the MATLAB compiler (Chapman, 2008). Previous results have shown HDF5 format
provided faster load and process times than XML formats, and loads large amounts of data
without running into memory issues (Bennett & Robertson, 2010). This research supports
these findings. This section provides results and discussion of this current research. After the baseline
benchmarks provide results for each machine, the analysis will show example images and
descriptive statistics for each image-processing algorithm, along with tables, plots, and
discussion comparing HDF5 and XML formats for each task. g
Table 4 shows the average of 10 MATLAB bench time results for each of the machines for
the LU, FFT, ODE, Sparse, 2D, and 3D tests. For most tests, the Windows 64-bit machine
performed better (as indicated by smaller execution times) than the Linux 64-bit machine. One exception to this was the 2D graphics, where the Linux 64-bit machine was slightly
faster than the Windows machine. Based on these results, the Windows 64-bit machine
should perform slightly faster for the subsequent image processing tasks. MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer 152 Machine
LU
FFT
ODE
Sparse
2D
3D
Windows 64-
bit
0.0389
0.0511
0.1353
0.1789
0.4409
0.7531
Linux 64-bit
0.0872
0.1221
0.2267
0.3137
0.3301
0.8154
Table 4. MATLAB’s Bench Results. Machine
LU
FFT
ODE
Sparse
2D
3D
Windows 64-
bit
0.0389
0.0511
0.1353
0.1789
0.4409
0.7531
Linux 64-bit
0.0872
0.1221
0.2267
0.3137
0.3301
0.8154
Table 4. MATLAB’s Bench Results. Figure 5 shows a typical image used in this analysis. This image represents one specific
frequency range (spectral band) for a 460 x 256 image after adjusting of the intensity for
display. Figure 5 shows a typical image used in this analysis. This image represents one specific
frequency range (spectral band) for a 460 x 256 image after adjusting of the intensity for
display. Fig. 5. Example 460 x 256 Image. A quad chart (Figure 6) displays processed images showing some of the techniques. The
first image in Figure 6 is an image in the upper-left corner representing the image adjusted
for intensity. 5. Results and Implications The image in the upper-right corner represents the image after the Weiner
noise filter is applied. Next, the image in the lower-left corner represents the image after the
Canny edge detection is applied. Lastly, the image in the lower-right corner represents the
FFT threshold results. Recall from Figure 1, preparing the images for processing requires several steps. The first
step was to load the HDF5 structures, followed by finding and loading the HDF5 raw image
data, saving the HDF5 raw image data, populating the XML docNode, and saving the XML
raw image data. Fig. 5. Example 460 x 256 Image. A quad chart (Figure 6) displays processed images showing some of the techniques. The
first image in Figure 6 is an image in the upper-left corner representing the image adjusted
for intensity. The image in the upper-right corner represents the image after the Weiner
noise filter is applied. Next, the image in the lower-left corner represents the image after the
Canny edge detection is applied. Lastly, the image in the lower-right corner represents the
FFT threshold results. A quad chart (Figure 6) displays processed images showing some of the techniques. The
first image in Figure 6 is an image in the upper-left corner representing the image adjusted
for intensity. The image in the upper-right corner represents the image after the Weiner
noise filter is applied. Next, the image in the lower-left corner represents the image after the
Canny edge detection is applied. Lastly, the image in the lower-right corner represents the
FFT threshold results. Recall from Figure 1, preparing the images for processing requires several steps. The first
step was to load the HDF5 structures, followed by finding and loading the HDF5 raw image
data, saving the HDF5 raw image data, populating the XML docNode, and saving the XML
raw image data. The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 153 Fig. 6. Quad Image Example 460 by 256 Image. Fig. 6. Quad Image Example 460 by 256 Image. Fig. 6. Quad Image Example 460 by 256 Image. Fig. 6. Quad Image Example 460 by 256 Image. A total of 100 original HDF5 files, ranging from 57 to 191 MB in size, provide the input for
the creation of the HDF5 and XML dataset files. 5. Results and Implications Table 5 displays the original HDF5 file size
statistics for this research. The original HDF5 files contained ground truth, collection
information, processed data, and spectral content, in addition to the raw image data. The
computed image processing statistics use only the raw image data extracted from the HDF5
files and saved to HDF5 and XML formats. Descriptor
Value (MB)
Mean
116.7304
Minimum
56.9807
Maximum
191.7729
Standard Deviation
28.5472
Variance
814.9406
Table 5. Original HDF5 File Size Descriptions. Descriptor
Value (MB)
Mean
116.7304
Minimum
56.9807
Maximum
191.7729
Standard Deviation
28.5472
Variance
814.9406
Table 5. Original HDF5 File Size Descriptions. Table 5. Original HDF5 File Size Descriptions. The average times associated with each of these steps are shown in Table 6 for the Windows
64-bit and Table 7 for Linux 64-bit machine. The column labeled “Total (s)” represents the
sum of each of the processing steps for the respective machines. For the current
configuration of the Windows 64-bit machine, the mean preparation time per file was just
over 9 s, with preparation times ranging between almost 7 and approximately 16.5 s. For the
current configuration of the Linux 64-bit machine, the mean preparation time per file was
almost 11 s, with times ranging between almost 9 and approximately 19.5 s. MATLAB – A Ubiquitous Tool for the Practical Engineer 154 Statistic
Load (s)
Read (s)
HDF5 Save
(s)
docNode (s)
XML Save
(s)
Total (s)
Mean
0.3313
0.3665
0.0996
7.129
1.1577
9.0841
Minimum
0.0261
0.0097
0.0168
6.0196
0.9191
6.9913
Maximum
1.1602
0.7236
0.5047
12.2276
1.9504
16.567
Standard
Deviation
0.2269
0.1384
0.1275
1.8607
0.301
Variance
0.0515
0.0192
0.0163
3.4623
0.0906
Table 6. Windows 64-bit HDF5 Data Average Preparation Times. Table 6. Windows 64-bit HDF5 Data Average Preparation Times. Statistic
Load (s)
Read (s)
HDF5 Save
(s)
docNode (s)
XML Save
(s)
Total (s)
Mean
0.043
0.0226
0.0653
9.5711
1.0478
10.75
Minimum
0.0076
0.0107
0.044
8.146
0.7723
8.9806
Maximum
0.3131
0.1311
0.1404
16.775
2.1607
19.52
Standard
Deviation
0.0382
0.0171
0.0245
2.6023
0.3637
Variance
0.0015
0.0003
0.0006
6.7721
0.1322
Table 7. Linux 64-bit HDF5 Data Average Preparation Times. Table 7. Linux 64-bit HDF5 Data Average Preparation Times. Table 8 shows the average free physical memory for each system during the preprocessing
steps. Free physical memory can vary throughout a run based on system processing during
the run and the amount of memory allocated to MATLAB for processing the run. 5. Results and Implications For all
runs during this research, the MATLAB Java heap memory was set to its maximum possible
value to avoid any potential out-of-memory issues. In MATLAB version 2010b, selecting
File, then Preferences, then General, and then Java Heap Memory, and then using the scroll
bar to set its maximum setting changes the memory. The maximum setting for the Windows
64-bit machine was 1533 MB, while the maximum setting for the Linux 64-bit machine was
4011 MB. One trade-off with the Java heap memory being larger in Linux is that less
physical memory is available for the run. However, increasing the Java heap memory does
allow for larger possible Java objects, which is useful when dealing with large image arrays. Statistic
Windows 64-bit (GB)
Linux 64-bit (GB)
Mean
2.7223
0.2374
Minimum
2.5234
0.0791
Maximum
2.9228
1.8715
Standard Deviation
0.0738
0.3696
Variance
0.0054
0.1366
Table 8. Free Physical Memory during HDF5 Preparation Steps. Table 8. Free Physical Memory during HDF5 Preparation Steps. After the preparation steps are complete, saving the raw image data to HDF5 and XML files
is the next step. The new raw image files in HDF5 and XML contain only the image The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 155 dimension information and the raw image pixel values. Table 9 provides the file statistics of
the raw image data in both HDF5 and XML format. In all cases, the XML files are larger
compared to the HDF5 files. In most cases, the resulting XML file is between 2.5 and 3 three
times as large as the similar HDF5 file. This finding is consistent with other published
results (Bennett & Robertson, 2010). Statistic
HDF5 Raw Image Size (MB)
XML Raw Image Size (MB)
Mean
17.8374
49.3223
Minimum
13.9301
41.0791
Maximum
30.1252
86.0207
Standard Deviation
6.6819
13.7911
Variance
44.6480
190.1954
Table 9. HDF5 and XML Raw Image File Size Statistics. Table 9. HDF5 and XML Raw Image File Size Statistics. Table 9. HDF5 and XML Raw Image File Size Statistics. After saving the raw image data to HDF5 and XML files, each file was loaded and processed
according to the steps shown previously in Figure 2. These steps include loading the file,
adjusting the image, calculating image statistics, removing noise, detecting edges, and
detecting features. Table 10. Windows 64-bit HDF5 and XML Image Processing Execution Times. Some other results worth mentioning confirm the expected relative calculation times
between differing noise filters and edge detection methods. As expected, the Weiner Filter
(using adaptive techniques) took more time than the Median Filter. In addition, the more
complex Canny edge detection algorithm took more time than the Sobel edge detection
algorithm. 5. Results and Implications Algorithms include two different noise removal algorithms (Median and
Weiner Filtering) and two different edge detection algorithms (Sobel and Canny). All of
these algorithms, unmodified for this research effort, are available within the MATLAB
Image Processing toolbox. g
g
Table 10 shows the statistical results of the execution times for each of these image-
processing algorithms for HDF5 and XML formats for the Windows 64-bit. Table 11 shows
the results for the Linux 64-bit machine. HDF5
XML
Process
Mean
Min
Max
Std
Var
Mean
Min
Max
Std
Var
Load (s) 0.0258 0.0013 0.0530 0.0072 0.0001
0.7309
0.6117
1.3135
0.2059
0.0424
Adjust (s) 0.0162 0.0058 0.0778 0.0235 0.0006
0.0419
0.0055
0.2366
0.0828
0.0069
Histogram (s) 0.0128 0.0013 0.0730 0.0262 0.0007
0.0225
0.0022
0.1256
0.0447
0.0020
Mean2 (s) 0.0005 0.0001 0.0026 0.0008 0.0000
0.0007
0.0001
0.0037
0.0013
0.0000
STD2 (s) 0.0124 0.0009 0.0735 0.0261 0.0007
0.0089
0.0005
0.0489
0.0179
0.0003
Median (s) 0.0057 0.0021 0.0273 0.0081 0.0001
0.0822
0.0097
0.4280
0.1545
0.0239
Weiner (s) 0.1111 0.0098 0.6541 0.2309 0.0533
0.1307
0.0088
0.7117
0.2597
0.0674
Sobel (s) 0.0663 0.0069 0.3890 0.1347 0.0181
0.0661
0.0051
0.3542
0.1288
0.0166
Canny (s) 0.7276 0.0673 4.1964 1.4975 2.2425
0.5622
0.0532
2.9744
1.0781
1.1622
FFT
Feature (s)
0.1222 0.0124 0.6884 0.2398 0.0575
0.1461
0.0122
0.7627
0.2759
0.0761
Total (s) 1.1006 0.1079 6.2351
1.7922
0.7090
6.9594 156 MATLAB – A Ubiquitous Tool for the Practical Engineer On both the Windows and Linux machines, the total execution times for the HDF5 files were
significantly less than the total execution times for the XML files. Comparing the results for
the mean execution time for the Windows machine, HDF5 demonstrates excellent
performance (~1.1 s) compared to XML (~1.8 s). The execution times for the windows
machine ranged between ~0.1 and ~6.2 s for the HDF5 files, compared to ~0.7 – ~6.9 s for
the XML files. Similarly, comparing the results for the mean execution time for the Linux
machine, HDF5 demonstrates excellent performance (~1.5 s) compared to XML (~3.1 s). The
execution times for the Linux machine ranged between ~0.15 and ~9.2 s for the HDF5 files,
compared to ~1.3 – ~12.3 s for the XML files. On both the Windows and Linux machines, the total execution times for the HDF5 files were
significantly less than the total execution times for the XML files. Table 11. Linux 64-bit HDF5 and XML Image Processing Execution Times. 5. Results and Implications Comparing the results for
the mean execution time for the Windows machine, HDF5 demonstrates excellent
performance (~1.1 s) compared to XML (~1.8 s). The execution times for the windows
machine ranged between ~0.1 and ~6.2 s for the HDF5 files, compared to ~0.7 – ~6.9 s for
the XML files. Similarly, comparing the results for the mean execution time for the Linux
machine, HDF5 demonstrates excellent performance (~1.5 s) compared to XML (~3.1 s). The
execution times for the Linux machine ranged between ~0.15 and ~9.2 s for the HDF5 files,
compared to ~1.3 – ~12.3 s for the XML files. p
The total execution time difference for both the Windows and Linux machines is primarily
due to the “load” process. Loading XML files requires far more execution time due to the
larger file sizes of the created XML data files (~3 times larger file size when storing the raw
data in XML format). )
Additional loading difficulties with XML files include: Additional loading difficulties with XML files include: 1. Slowness of the serialization process of converting Unicode XML into binary memory
storage (McGrath, 2003). 2. MATLAB loading algorithm (‘xmlread’ method) uses the Document Object Model
(DOM) to load XML files. DOM is memory and resource intensive, and can consume as
much as 10 times the computer memory as the size of the actual XML data file (Wang et
al., 2007). 3. In general, and of particular concern for users performing 32-bit processing, processing
speeds associated with XML loading can be greatly diminished as virtual memory
becomes insufficient compared with the size of the XML file as the computer starts to
run out of memory. 5. Results and Implications HDF5
XML
Process
Mean Min
Max
Std
Var
Mean
Min
Max
Std
Var
Load (s)
0.0199 0.0021 0.0509 0.0095 0.0001 1.3520
1.2015
2.0415
0.2444
0.0597
Adjust (s) 0.0250 0.0087 0.1276 0.0371 0.0014 0.0757
0.0095
0.4293
0.1503
0.0226
Histogram (s) 0.0160 0.0017 0.0914 0.0326 0.0011 0.0290
0.0028
0.1697
0.0598
0.0036
Mean2 (s) 0.0007 0.0003 0.0036 0.0010 0.0000 0.0020
0.0004
0.0106
0.0036
0.0000
STD2 (s)
0.0216 0.0019 0.1309 0.0447 0.002
0.0136
0.0012
0.0806
0.0285
0.0008
Median (s) 0.0631 0.0074 0.3595 0.1265 0.0160 0.1135
0.0127
0.6524
0.2291
0.0525
Weiner (s) 0.1564 0.0179 0.8985 0.3137 0.0984 0.1615
0.0140
0.9496
0.3351
0.1123
Sobel (s)
0.0699 0.0090 0.4486 0.1385 0.0192 0.1221
0.0095
0.7272
0.2573
0.0662
Canny (s) 0.8779 0.0746 5.1806 1.8290 3.3453 0.9195
0.0667
5.4927
1.9447
3.7817
FFT
Feature (s)
0.2810 0.0229 1.8790 0.5845 0.3416 0.2960
0.0235
1.7437
0.6157
0.3791
Total (s)
1.5315 0.1465 9.1706
3.0850
1.3417
12.2973
Table 11. Linux 64-bit HDF5 and XML Image Processing Execution Times. Some other results worth mentioning confirm the expected relative calculation times
between differing noise filters and edge detection methods. As expected, the Weiner Filter
(using adaptive techniques) took more time than the Median Filter. In addition, the more
complex Canny edge detection algorithm took more time than the Sobel edge detection
algorithm. HDF5
XML
Process
Mean Min
Max
Std
Var
Mean
Min
Max
Std
Var
Load (s)
0.0199 0.0021 0.0509 0.0095 0.0001 1.3520
1.2015
2.0415
0.2444
0.0597
Adjust (s) 0.0250 0.0087 0.1276 0.0371 0.0014 0.0757
0.0095
0.4293
0.1503
0.0226
Histogram (s) 0.0160 0.0017 0.0914 0.0326 0.0011 0.0290
0.0028
0.1697
0.0598
0.0036
Mean2 (s) 0.0007 0.0003 0.0036 0.0010 0.0000 0.0020
0.0004
0.0106
0.0036
0.0000
STD2 (s)
0.0216 0.0019 0.1309 0.0447 0.002
0.0136
0.0012
0.0806
0.0285
0.0008
Median (s) 0.0631 0.0074 0.3595 0.1265 0.0160 0.1135
0.0127
0.6524
0.2291
0.0525
Weiner (s) 0.1564 0.0179 0.8985 0.3137 0.0984 0.1615
0.0140
0.9496
0.3351
0.1123
Sobel (s)
0.0699 0.0090 0.4486 0.1385 0.0192 0.1221
0.0095
0.7272
0.2573
0.0662
Canny (s) 0.8779 0.0746 5.1806 1.8290 3.3453 0.9195
0.0667
5.4927
1.9447
3.7817
FFT
Feature (s)
0.2810 0.0229 1.8790 0.5845 0.3416 0.2960
0.0235
1.7437
0.6157
0.3791
Total (s)
1.5315 0.1465 9.1706
3.0850
1.3417
12.2973 Some other results worth mentioning confirm the expected relative calculation times
between differing noise filters and edge detection methods. As expected, the Weiner Filter
(using adaptive techniques) took more time than the Median Filter. In addition, the more
complex Canny edge detection algorithm took more time than the Sobel edge detection
algorithm. 5. Results and Implications g
)
The load times (Figures 7 and 8) for both HDF5 and XML show similar behavior on both the
Windows and Linux machines. The cross platform behavior demonstrates the file size
dependency for XML loading performance, and the lack of file size dependency for HDF5
loading performance. As expected from the benchmark testing results, the XML loading
performance on the Windows machine is slightly faster than the Linux. An additional processing step is required to prepare the large raw data for processing. In
XML files, the raw image data is stored as ASCII characters with whitespace separators. As
the image gets larger, converting from the ASCII character data to a MATLAB array can take
considerable time. MATLAB has a num2str() function that works very nice for small arrays,
but this function would not work for these large character arrays. A novel process allows the
reading of each character, one at a time, parse on spaces, and then load into the array,
resulting in a tremendous savings (as much as two orders of magnitude) in processing time. C or other software development languages may provide other more efficient methods to
reduce this processing restriction. However, preparing the XML data for processing is a very
important process step. Additional new research and software tools may simplify and
dit th C or other software development languages may provide other more efficient methods to
reduce this processing restriction. However, preparing the XML data for processing is a very
important process step. Additional new research and software tools may simplify and
expedite the process. T-test analysis on the total image processing times confirmed that there was a significant
difference between the HDF5 and XML file processing times not attributable to random
chance. Specifically, HDF5 files took less processing time than XML files on the Windows
64-bit machine (t (198) = 2.27, ρ = .0014) and the Linux 64-bit machine (t (198) = 3.25, ρ =
.0244). The t (198), or t-value, represents the difference of the mean values for total
processing times for HDF5 and XML, respectively, divided by the standard error of the two
means. The 198 represents the degrees of freedom, or sample size minus 2 for an unpaired t-
test, which is appropriate for the independent groups in this analysis. 5. Results and Implications The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 157 The load times were larger for the XML files compared to the HDF5 files. This difference is
most likely due to the larger XML file size. Figure 7 visually displays the load times for the
XML and HDF5 files for the Linux 64-bit machine. Figure 8 shows a similar result for the
Windows 64-bit machine. The load times were larger for the XML files compared to the HDF5 files. This difference is
most likely due to the larger XML file size. Figure 7 visually displays the load times for the
XML and HDF5 files for the Linux 64-bit machine. Figure 8 shows a similar result for the
Windows 64-bit machine. XML and HDF5 files for the Linux 64 bit machine. Figure 8 shows a similar result for the
Windows 64-bit machine. Fig. 7. Linux 64-bit XML and HDF5 Load Times. Fig. 8. Windows 64-bit XML and HDF5 Load Times. 100 Fig. 7. Linux 64-bit XML and HDF5 Load Times. Fig. 7. Linux 64-bit XML and HDF5 Load Times. Fig. 7. Linux 64-bit XML and HDF5 Load Times. Fig. 7. Linux 64-bit XML and HDF5 Load Times. Fig. 8. Windows 64-bit XML and HDF5 Load Times. 100 Fig. 8. Windows 64-bit XML and HDF5 Load Times. 100 Fig. 8. Windows 64-bit XML and HDF5 Load Times. 158 MATLAB – A Ubiquitous Tool for the Practical Engineer Corresponding increases in XML file size contribute to the large jumps observed in the XML
load times around file ID 75 and 90 (Figures 7 and 8). Similar arguments made earlier in the
chapter (slowness of serialization of converting Unicode to binary storage and resource
intensive DOM loading methods) offer explanation of the larger loading process times
compared to the more efficient loading of HDF5 binary files. p
g
y
HDF5 load times do not significantly vary depending on file size. Efficient methods of
loading HDF5 binary data files, combined with excellent memory usage and use of
computing resources, into the MATLAB workspace, demonstrate the superior benefit of
archiving data in HDF5 versus XML. HDF5 provides seamless integration of data into
MATLAB without performance degradation (especially for large data sets) and is the ‘de
facto’ standard for MATLAB data files containing workspaces over 2 GB in size (Mather &
Rogers, 2007). 5. Results and Implications The important value
(ρ) represents the probability of the difference (t-value) being due to chance is .0014 for the
Windows 64-bit machine, and .0244 for the Linux 64-bit machine. Setting the significance
level to .05 indicates that in both cases, the difference in processing times between HDF5
and XML is not by chance. These results suggest a significant difference between the total
process times for HDF5 and XML files for both machines. Further t-test analysis on the
individual components contributing to the total process time indicated significant
differences in execution times for load, adjust, and mean calculations for the Linux 64-bit
machine and load, adjust, and median noise filter for the Windows 64-bit machine. It seems
reasonable the load times would be different between the XML and HDF5 formats. To
provide insight into the differences between the XML and HDF5 formats for the image The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 159 adjust, median noise filter, and image mean calculations, requires additional research and
analysis, since these routines should provide similar results because the data format should
not impact the results for these processes. Table 12 displays the t-test results for each of the components, resulting in significant
differences between the XML and HDF5 files. The t-test results for each of the other
components shows no significant difference between XML and HDF files. Test
Windows 64-bit
Linux 64-bit
Load
t (198) = 34.39, ρ < .0001
t (198) = 54.73, ρ < .0001
Image Adjust
t (198) = 2.99, ρ = .0031
t (198) = 3.29, ρ = .0012
Image Mean
t (198) = 1.55, ρ = .122 (Not
significant)
t (198) = 3.35, ρ = .0009
Median Filter
t (198) = 4.97, ρ < .0001
t (198) = 1.93, ρ = .050
(Not significant)
Table 12. T-test Process Time Components Results. Table 12. T-test Process Time Components Results. Figures 9 and 10 graphically depict these findings by displaying the total processing time for
the HDF5 and XML files for the Linux 64-bit and Windows 64-bit test systems. In both cases,
the XML process times were significantly greater than the HDF5 process times. Fig. 9. Linux 64-bit Image Processing Times- HDF5 and XML. 5. Results and Implications For each file format and test machine, the amount of calculated free physical memory usage
during the image processing stage shows definite differences between the file formats. Table
13 shows the descriptive statistics of these data. Similar to the preprocessing step, setting the
maximum Java heap memory to maximum for each run results in no out-of-memory errors. For both machines, the XML files required more physical memory than the HDF5 files, as
indicated by less free physical memory in Table 13. This result is consistent with XML
loading requiring relatively large amounts of memory compared to the XML file size (Wang
et al., 2007). 100 Fig 9 Linux 64-bit Image Processing Times- HDF5 and XML
100 Fig. 9. Linux 64-bit Image Processing Times- HDF5 and XML. For each file format and test machine, the amount of calculated free physical memory usage
during the image processing stage shows definite differences between the file formats. Table
13 shows the descriptive statistics of these data. Similar to the preprocessing step, setting the
maximum Java heap memory to maximum for each run results in no out-of-memory errors. For both machines, the XML files required more physical memory than the HDF5 files, as
indicated by less free physical memory in Table 13. This result is consistent with XML
loading requiring relatively large amounts of memory compared to the XML file size (Wang
et al., 2007). MATLAB – A Ubiquitous Tool for the Practical Engineer 160 Fig. 10. Windows 64-bit Image Processing Times- HDF5 and XML. 100 Fig. 10. Windows 64-bit Image Processing Times- HDF5 and XML. Statistic
Windows 64-bit (GB)
Linux 64-bit (GB)
HDF5
XML
HDF5
XML
Mean
3.6608
3.2726
13.6388
11.0808
Minimum
3.5995
3.0064
11.9786
11.0215
Maximum
3.6874
3.7858
14.4033
11.1872
Standard Deviation
0.0194
0.4446
0.6277
0.0924
Variance
0.0004
0.1976
0.394
0.0085
Table 13. Free Physical Memory during Image Processing Steps. Table 13. Free Physical Memory during Image Processing Steps. 6. Ethics of data sharing There is a large, complex set of concerns when openly sharing data — especially electronic
data over the Internet. From a scientific viewpoint of discovery, open sharing of scientific
data allows many researchers and scientists the ability to form a common understanding of
data, which is essential for furthering science. However, there are many ethical concerns in
the process of sharing data, particularly over the Web. For example, a given medical study
group collects sensitive, personal medical information as part of a medical case study using
public government funds. All of the data is stored (archived) on a government computer
system. Many years later, another researcher wants to use the data for another study, which
could help save the lives of many people. Should the second researcher be able to use the
archived data for a purpose other than the intent of the original study? Many arguments
come into discussion in this situation. The right to use data paid for with publically collected
funds seems reasonable; however, what about the right of human participants to privacy? What happens if a data release into the public domain harms any of the participants? Such
harm may take the form of job loss or denial of life insurance, etc. The ethics of sharing data
is complex and the ethical dilemma of sharing data is an area of study requiring much
thought and discussion. The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 161 Many of the ethical concerns stem from a balance of beneficial results from sharing data
versus ethical concerns researchers have in such sharing. Ethical data sharing and
management involves reconciliation of diverse conflicting values (Sieber, 2005). Among
these concerns are the sharing of data for the benefit of society and science, while protecting
the interest of human participants in data collections (Mauthner & Perry, 2010). For many
years, researchers took the position of protecting the interests of the human participants in
such data; however, with the advent of sharing data across the Web, the interest of human
participants is certainly less sure and threatens the overall fabric of the trust-based
relationship that exists between researcher and participant. A definite loss of data control
can exist when sharing data across the Web, possibility resulting in the loss of privacy and
protection of human participants (Mauthner & Perry, 2010). 6. Ethics of data sharing p
p
p
(
y
)
Another ethical concern is the rights of those who collect data and receive no recognition by
those who download the data through public Web interfaces for use in their research. The
process of collecting high quality data requires much time, effort, and expense; moreover,
many of the individuals who collect data (data producers) are in a positional or career
situation where they are vulnerable to receiving little recognition for their data collection
efforts by indiscriminate availability of data over the Web. Such individuals are not nearly
as protected as data users, such as algorithm designers, who can protect their interests
through intellectual property rights (Mauthner & Perry, 2010). Along with recognition of the data as a contribution deserving recognition, intellectual
property rights assigning ownership and rightful claims to the data are another ethical
concern. Reductions or even elimination of researcher’s data rights occurs when funding
agencies require a researcher to share data, especially over the Web, allowing anyone to
access the information. Certain government agencies are always balancing the public’s right
to information collected with public funds, and the right to protect both the researcher’s
intellectual property and the test participant’s privacy rights. Archiving and disseminating data over the Web creates a “data as commodity” mindset,
where the ethical concerns of both the researcher and human participant become lost in the
impersonal downloading of archived data (Mauthner & Perry, 2010). When sharing data,
regardless of the methods, confidentially of human participants is important at all times. Data providers must take great care in judging the sensitivity of the data and may find it
necessary to restrict access based on ethical, legal, or security justifications, even in the case
of publicly funded data collections. Further safeguards in data dissemination include
restricting others (end users) of disseminating data as a third party; thus, requiring an end
user to go to the original source to acquire the data (MIT Libraries, 2011). The ethics of data sharing is clearly more complex today than before the advent of the
Internet. However, many general guiding principles apply to all data sharing situations. As
a core group of guiding principles, every data collector and provider has a duty to: The ethics of data sharing is clearly more complex today than before the advent of the
Internet. However, many general guiding principles apply to all data sharing situations. 7. Conclusions This research processed 100 large hyperspectral images in both HDF5 and XML formats on
Windows 64-bit and Linux 64-bit machines. A number of image processing steps available
within MATLAB, including intensity adjustment, histogram calculation, statistical analysis,
noise removal, edge detection and feature extraction, provided the algorithms to fulfill the
goals of the research: g
1. Determine strengths and weaknesses of using HDF5 and XML formats for typical
processing techniques associated with large hyperspectral images. g
1. Determine strengths and weaknesses of using HDF5 and XML formats for typical
processing techniques associated with large hyperspectral images. p
g
q
g
yp
p
g
2. Compare and analyze processing times on Windows and Linux 64-bit machines for
HDF5 and XML hyperspectral images. g
g
y
g
2. Compare and analyze processing times on Windows and Linux 64-bit machines for
HDF5 and XML hyperspectral images. y
g
3. Identify areas that require additional research to help improve efficiencies associated
with processing large HDF5 and XML hyperspectral images. 3. Identify areas that require additional research to help improve efficiencies associated
with processing large HDF5 and XML hyperspectral images. The research identified a number of strengths and weaknesses. First, the overal
processing results show reduced processing times for images stored in HDF5 comp The research identified a number of strengths and weaknesses. First, the overall image
processing results show reduced processing times for images stored in HDF5 compared to XML format. The main contribution to this difference is the large load time and the
preprocessing step required to convert an ASCII XML character string to a numeric array in
MATLAB. The relative size of the files is the main factor in the difference in load speed with
the XML files being almost three times as large as the HDF5 files. A larger file will always
take more time to load using any application. g
preprocessing step required to convert an ASCII XML character string to a numeric array in
MATLAB. The relative size of the files is the main factor in the difference in load speed with
the XML files being almost three times as large as the HDF5 files. A larger file will always
take more time to load using any application. g
y pp
The preprocessing required to convert an ASCII XML character string to a numeric array
was very time-consuming and a potential huge process bottleneck. 6. Ethics of data sharing As
a core group of guiding principles, every data collector and provider has a duty to: 1. Protect the confidentially of human participants in data collections (UK Data Archive,
2011). 1. Protect the confidentially of human participants in data collections (UK Data Archive,
2011). 2. Avoid providing sensitive information of human test participants, which may endanger
data test participants (UK Data Archive, 2011). 2. Avoid providing sensitive information of human test participants, which may endanger
data test participants (UK Data Archive, 2011). 3. Consult with the test participants on making data publically available and be sensitive
to their wishes (UK Data Archive, 2011). 4. Inform the test participants on the use of the data, and the methods, procedures, and
intentions of archiving and disseminating the data, prior to using them as test
participants (UK Data Archive, 2011). 4. Inform the test participants on the use of the data, and the methods, procedures, and
intentions of archiving and disseminating the data, prior to using them as test
participants (UK Data Archive, 2011). 162 MATLAB – A Ubiquitous Tool for the Practical Engineer 5. Make data available to the public, which doesn’t violate ethical, legal, or security
principles (UK Data Archive, 2011). 7. Conclusions Additional considerations to protect the privacy and interests of human participants in
data collections require additional guidance when sharing data in a completely public
forum where the researcher (and organization) has no control over how the data is used. There will always exist a balance between sharing data for scientific discovery and Web. Additional considerations to protect the privacy and interests of human participants in
data collections require additional guidance when sharing data in a completely public
forum where the researcher (and organization) has no control over how the data is used. There will always exist a balance between sharing data for scientific discovery and
advancement, and ethical concerns and requirements. 7. Conclusions The processing of large
XML files requires additional tools and approaches with an easier out-of-the-box solution,
making XML processing more practical. In addition to the processing time differences,
HDF5 requires less physical memory and, hence, allows larger objects to be loaded without
out-of-memory errors. HDF5 data files are much smaller (~3 times) than the corresponding
XML versions of same data files. Binary files in general are far more efficient in storing
numerical data than XML files using Unicode. As discussed earlier, XML loading of data can
consume as much as 10 times the amount of computer memory as the size of the actual XML
file (Wang et al., 2007), and conversion of Unicode to binary storage is memory intensive
requiring much more physical memory and resources than the loading of HDF5 files of
similar data (McGrath, 2003). MATLAB can process very large arrays, but it will run out of
memory quickly when processing very large XML files. On another test machine that was
running MATLAB with only 760 MB Java heap memory, several of the larger XML datasets
would not load. HDF5 files on any machine even when experimenting with HDF5 files as
large as 800MB did not experience any problems. Clearly, for machines with less memory
available and smaller processing capability, HDF5 files are preferred. Defining upper limit
processing for both HDF5 and XML files requires additional research and analysis. The
upper limit appears to have relationships to processing speed, physical memory, and other
constraints. Exploring these limits as a function of different environmental parameters
requires recommended future research. The archiving and processing of large image data requires the use of HDF5, until additional
tools and processes are in place that allow for the quick and efficient processing of XML files
using computational tools such as MATLAB. The Impact of the Data Archiving File Format on Scientific Computing and
Performance of Image Processing Algorithms in MATLAB Using Large HDF5… 163 There are many important ethical considerations when sharing data, especially over the
Web. Additional considerations to protect the privacy and interests of human participants in
data collections require additional guidance when sharing data in a completely public
forum where the researcher (and organization) has no control over how the data is used There are many important ethical considerations when sharing data, especially over the
Web. UK
Data
Archive,
“Create
and
Manage
Data
-
Consent
and
Ethics:
Ethical/Legal/Overview”, http://www.data-archive.ac.uk (2011). MATLAB – A Ubiquitous Tool for the Practical Engineer
164
UK
Data
Archive,
“Create
and
Manage
Data
-
Consent
and
Ethics:
Ethical/Legal/Overview”, http://www.data-archive.ac.uk (2011).
Wang, F., Li, J., Homayounfar, “A Space Efficient XLM DOM Parser”, Data and Knowledge
Engineering,Volume 60, Issue 1, p. 185-207 (2007). g
p
(
)
Wang, F., Li, J., Homayounfar, “A Space Efficient XLM DOM Parser”, Data and Knowledge
Engineering,Volume 60, Issue 1, p. 185-207 (2007). Energy Management in
Buildings Using MATLAB Shahram Javadi
Islamic AZAD University, Central Tehran Branch
Iran 8. References Barkstrom, B., “Ada 95 Bindings for the NCSA Hierarchical Data Format”, proceedings of
the 2001 annual ACM SIGAda International Conference on ADA (2001). Bennett, K., Robertson, J., “The Impact of the Data Archiving Format on the Sharing of
Scientific Data for Use in Popular Computational Environments”, Proc. SPIE 7687,
Orlando Florida (April 2010). Chapman, S.J., “MATLAB Programming for Engineers; 4th edition; Thomson publishing,
Ontario, Canada, 2008. Dougherty, M., Folk, M., Zadok, E., Bernstein, H., Bernstein, F., Eliceiri, K., Benger, W., Best,
C., ”Unifying Biological Image Formats with HDF5”, communications of the ACM
(CACM), 52(10): p. 42-47 (2009). (
)
(
) p
(
)
Gay, L.R. Airasian, P. Educational Research. Prentice Hall, Columbus, Ohio, 2003. Goetz, A.F.H., Vane, G., Solomon, E., Rock, B.N., “Imaging Spectrometry for Earth Remote
Sensing”, Science, Vol. 228, p. 1147-1153 (1985). g
p
(
)
Mather, J., Rogers, A., “HDF5 in MATLAB”, Presentation at the HDF5 and HDF-EOS
Workshop X, Raytheon System Corporation, Upper Marlboro, MD (November
2007). MATLAB User’s Guide, “Statistical Toolbox, Ttest2”,
http://www.mathworks.com/help/toolbox/stats/ (April, 2011). p
p
( p
)
Mauthner, M., Perry, O., “Ethical Issues in Digital Data Archiving and Sharing”, eResearch
Ethics, http://eresearch-ethics.org (October 2010). McGrath, R., “XML and Scientific File Formats,” Report generated by National Center for
Supercomputing Applications, University of Illinois, Urbana-Champaign, in
support of work under a Cooperative Agreement with NASA under NASA grant
NAG 5-2040 and NAG NCCS-599 (August 2003). (
g
)
MIT Libraries, “Data Management and Publishing: Ethical and Legal Issues”,
http://libraries.mit.edu (November 2011). http://libraries.mit.edu (November 2011). SAS/STAT User’s Guide, “T-Test Procedure”, http://support.sas.com/documentation
(April, 2011). p
(
)
SAS/STAT User’s Guide, “T-Test Procedure”, http://support.sas.com/documentation
(April, 2011). Shasharina, S., Li, C., Nanbor, W., Pundaleeka, R., Wade-Stein, D., “Distributed
Technologies for Remote Access of HDF Data”, proceedings of the 16th IEEE
International Workshop on Enabling Technologies: Infrastructure for Collaborative
Enterprises (2007). Shishedjiev, B., Goranova M., Georgieva, J., “XML-based Language for Specific Scientific
Data Description”,proceedings of the 2010 Fifth International Conference on
Internet and Web Applications and Services (2010). pp
(
)
Sieber, J., “Ethics of Sharing Scientific and Technological Data: A Heuristic for Coping with
Complexity & Uncertainty”, Data Science Journal, Vol 4, p. 165 (December 2005). 164 g
p
(
)
Wang, F., Li, J., Homayounfar, “A Space Efficient XLM DOM Parser”, Data and Knowledge
Engineering,Volume 60, Issue 1, p. 185-207 (2007). 9 1. Introduction Some Benefits of BMS are:
Building tenant/occupants
Good control of internal comfort conditions
Possibility of individual room control
Increased staff productivity 166 MATLAB – A Ubiquitous Tool for the Practical Engineer
Effective monitoring and targeting of energy consumption
Improved plant reliability and life
Effective response to HVAC-related complaints
Save time and money during the maintenance
BEMS is used to create a central computer controlled method which has three basic
functions: controlling, monitoring and optimizing. It comprises:
Effective monitoring and targeting of energy consumption
Improved plant reliability and life
Effective response to HVAC-related complaints
Save time and money during the maintenance
BEMS is used to create a central computer controlled method which has three basic
functions: controlling, monitoring and optimizing. It comprises:
Save time and money during the maintenance BEMS is used to create a central computer controlled method which has three basic
functions: controlling, monitoring and optimizing. It comprises:
Power systems
Illumination system Electric power control system
Heating, Ventilation and Air-conditioning HVAC System Security and observation system Magnetic card and access system
Fire alarm system
Lifts, elevators etc.
Plumbing system
Burglar alarms
Other engineering systems
Trace Heating
BEMS uses a control strategy with the following objectives: gy
g
j
i. To obtain a flexible system for operator to maintain thermal, visual, security,
illumination and air quality in a building. i. To obtain a flexible system for operator to maintain thermal, visual, security,
illumination and air quality in a building. ii. To reduce the energy consumption for all loads in a building. iii. To provide a monitoring/controlling system in a building. p
g/
g y
g
The above objectives are achieved by the use of a fuzzy controller at each zone level of the
building, supervised by a suitable cost function. The detailed description of the control
strategy has been described in next parts. The above objectives are achieved by the use of a fuzzy controller at each zone level of the
building, supervised by a suitable cost function. The detailed description of the control
strategy has been described in next parts. 1. Introduction MATLAB is an applicable software in various aspects of engineering such as Electrical
engineering and its different sub majors. There are a lot of examples and demos on these
majors, although there is a few text or example on MATLAB application in energy
management. In this text, I have provided a general application of energy management in
buildings using MATLAB software. Considering limit source of fuel energy, we need to use energy and resources carefully and
it is an economical and ecological challenge as well as being one which is important for
survival and which can only be mastered by highly qualified engineers. A significant
percentage of the energy used nationally is consumed in buildings, which means there are
considerable potential for savings and a corresponding need for responsible behavior.The
building sector worldwide uses up to 40% of primary energy requirements and also a
considerable amount of overall water requirements. Building Energy Management Systems (BEMS), aims to improve environment within the
building and may control temperature, carbon dioxide levels. BEMS is not sufficient enough
due to human interference. Human is a dynamic part of the building; therefore he/she
should be taken into account in the control strategy. Latest trends in designing Intelligent
Building Energy management Systems (IBEMS) integrate a Man Machine Interface that
could store the human’s preferences and adapt the control strategy accordingly. BEMS have been developed after the Energy crisis in the late 70’s combined with the fast
development of computers science. The aims of these systems are to monitor and control the
environmental parameters of the buildings and at the same time to minimize the energy
consumption and cost. Since then, BEMS have become commercial tools and are
implemented in a wide range of applications, especially in large office buildings; thus useful
experience is available regarding their benefits and drawbacks. Systems linked to a BMS typically represent 40% of a building's energy usage; if lighting is
included, this number approaches 70%. Systems linked to a BMS typically represent 40% of a building's energy usage; if lighting is
included, this number approaches 70%. 2. Fuzzy systems Fuzzy logic originally is identified and set forth by Lotfi A. Zadeh is a form of multi-
valued logic derived from fuzzy set theory to deal with reasoning that is fluid or
approximate rather than fixed and exact. In contrast with "crisp logic", where binary
sets have two-valued logic, fuzzy logic variables may have a truth value that ranges in
degree between 0 and 1. Put more simply, fuzzy logic is a superset of conventional
(boolean) logic that has been extended to handle the concept of partial truth, where the
truth value may range between completely true and completely false. Furthermore,
when linguistic variables are used, these degrees may be managed by specific functions. As the complexity of a system increases, it becomes more difficult and eventually
impossible to make a precise statement about its behavior, eventually arriving at a point
of complexity where the fuzzy logic method born in humans is the only way to get at
the problem. Fuzzy logic is used in system control and analysis design, because it shortens the time for
engineering development and sometimes, in the case of highly complex systems, is the only
way to solve the problem. A fuzzy controller consists of the following major components depicted in figure 1: Energy Management in Buildings Using MATLAB 167 Fig. 1. Fuzzy system diagram Fig. 1. Fuzzy system diagram 3.1 Illumination system Lighting or illumination is the deliberate application of light to achieve some aesthetic or
practical effect. Lighting includes use of both artificial light sources such as lamps and
natural illumination of interiors from daylight. Daylighting (through windows, skylights,
etc.) is often used as the main source of light during daytime in buildings given its high
quality and low cost. Artificial lighting represents a major component of energy
consumption, accounting for a significant part of all energy consumed worldwide. Artificial lighting is most commonly provided today by electric lights, but gas lighting,
candles, or oil lamps were used in the past, and still are used in certain situations. Proper
lighting can enhance task performance or aesthetics, while there can be energy wastage
and adverse health effects of poorly designed lighting. Indoor lighting is a form of fixture
or furnishing, and a key part of interior design. Lighting can also be an intrinsic
component of landscaping Providing daylight in a building does not by itself lead to energy efficiency. Even a well day
building may have a high level of lighting energy use if the lighting controls are
inappropriate. However, improved control in building management and automation system
through research and development will definitely help to improve energy savings in
buildings. This part presents the development of an automated fuzzy lighting/dimming
control system. The schematic diagram of the system is shown in Fig. 1. Fuzzy logic is an
innovative technology that allows the description of desired system behavior using
everyday spoken language Fuzzy logic can be derived into three stages which are:
Fuzzification, Fuzzy Inference and Defuzzification. In a typical application, all three stages
must be employed. 3.1.1. Indoor natural lighting What we have to do is solve an equation of the type rec
E
A
168 MATLAB – A Ubiquitous Tool for the Practical Engineer Where E is the illumination level required at the work surface and A is the total area of the
plane where the work is done. The factor rec is the flux of light received on the working
surface. The average indoor illuminance Εin (lx) is calculated (DHW Li and JC Lam, 2000,
“Measurements of solar radiation and illuminance on vertical surfaces and daylighting
implications”) using the equation: (1
)
w
v
in
in
A
E
E
A
(1) (1
)
w
v
in
in
A
E
E
A
(1) where
Aw (m2) the window surface
(-) the light transmittance of the window glazing
Εv (lx) the vertical illuminance on the window
Ain (m2) the total area of all indoor surfaces
ρ (-) the area weighted mean reflectance of all indoor surfaces. The vertical illuminance on the window Εv (lx) is given by the following equation Aw (m2) the window surface (-) the light transmittance of the window glazing ρ (-) the area weighted mean reflectance of all indoor surfaces. The vertical illuminance on the window Εv (lx) is given by the following equation v
G
v
E
k G
(2) v
G
v
E
k G
(2) Where: *
AL
u
: The actuating signal of the artificial light controller, ranging from 0-1. This signal is
driven by the artificial lighting fuzzy controller. The same signal is also fed into the building
model (Archimed.bui) to drive the actuator for the artificial lights. If
*
0
AL
u
means that all
lights are off. If
*
1
AL
u
means that all lights are on at full power. 3.1.2 Artificial lighting g
g
The Equation below is used to calculate the average artificial light intensity inside the
buildings: *
(
)
2
2
(
)
AL
u
N
P V n
H
h
AL
(8) (8) with kG (lm.W-1) the luminous efficacy of global solar radiation
Gv (W.m-2) the global solar radiation on the window surface
The luminous efficacy of global solar radiation (M. Perraudeau, 1994, “Estimation of
illuminances from solar radiation data”) can be calculated by the following relation kG (lm.W-1) the luminous efficacy of global solar radiation 1
h
h
G
D
s
h
h
D
D
k
k
k
G
G
(3) (3) with
Dh (W.m-2) the diffuse horizontal solar radiation
Gh (W.m-2) the global horizontal solar radiation
kD (lm.W-1) the luminous efficacy of diffuse solar radiation
kS (lm.W-1) the luminous efficacy of beam solar radiation. The luminous efficacy of diffuse solar radiation is calculated (P. Littlefair, 1993, S. Ashton
and H. Porter, "Luminous efficacy algorithms”,) using the equation: The luminous efficacy of diffuse solar radiation is calculated (P. Littlefair, 1993, S. Ashton
and H. Porter, "Luminous efficacy algorithms”,) using the equation: 144
29
D
k
C
(4) 144
29
D
k
C
(4) 2
3
1
0.55
1.22
1.68
C
NI
NI
NI
(5) 2
3
1
0.55
1.22
1.68
C
NI
NI
NI
(5) 2
3
1
0.55
1.22
1.68
C
NI
NI
NI
(5) 0.82
1
1
0.12037sin
(
)
h
h
z
D
G
NI
(6) (6) with θz (deg) the solar zenith angle. 169 Energy Management in Buildings Using MATLAB Finally, the luminous efficacy of the beam solar radiation can be calculated (S. Aydinli
and J. Krochmann, 1983, “Data on daylight and solar radiation: Guide on Daylight”) using the
relation Finally, the luminous efficacy of the beam solar radiation can be calculated (S. Aydinli
and J. Krochmann, 1983, “Data on daylight and solar radiation: Guide on Daylight”) using the
relation kS = 17.72 + 4.4585 θz – 8.7563 10-2 (θz)2 + 7.3948 10-4
(θz)3 – 2.167 10-6 (θz)4 – 8.4132 10-10 (θz)5
(7) (7) (7) 3.1.3 Fuzzy controller for lighting All lighting control systems are based on one of the following strategies: All lighting control systems are based on one of the following strategies: ghting control systems are based on one of the following strategies:
Occupancy sensing, in which lights are turned on and off or dimmed according to
occupancy;
Scheduling, in which lights are turned off according to a schedule; Tuning, in which power to electric lights is reduced to meet current user needs;
Daylight harvesting (daylighting control), in which electric lights are dimmed or turned
off in response to the presence of daylight;
Demand response, in which power to electric lights is reduced in response to utility
curtailment signals or to reduce peak power charges at a facility;
Adaptive compensation, in which light levels are lowered at night to take
advantage of the fact that people need and prefer less light at night than they do
during the day. Daylight is a dynamic source of lighting and the variations in daylight can be quite large
depending on season, location or latitude, and cloudiness. Different skylight levels can be
found under the same sunlight conditions, and, even when the sky pattern remains the
same, the range of solar illuminances may increase as a result of a momentary turbidity
filter or scattering of particles over the sun. In consequence, any prediction system has to be
flexible to allow for the multivariate changes that characterize the combination of sunlight
and skylight. The proposed daylighting fuzzy control uses two sensing devices (an occupancy/motion
sensor and a photosensor), continuously electronic dimming ballasts for every luminaries
aiming the control of the electric lighting output, and a fuzzy controller. h
h g
g
g
p
y
A proposed algorithm is assigned to control the illumination: 170 MATLAB – A Ubiquitous Tool for the Practical Engineer if illuminance is between 500 and 550 lux and motion sensor is ON then all lamps is full powered
else use the fuzzy controller for lighting control if illuminance is between 500 and 550 lux and motion sensor is ON then all lamps is full powered
else use the fuzzy controller for lighting control The input linguistic variables of the fuzzy controller are the level of the illuminance
measured by the photosensor (A) while the output variable is the level of the DC control
signal sent to electronic ballasts in the control zone (µ1). 3.1.3 Fuzzy controller for lighting The fuzzy membership functions of
Input/Output variables are shown in figures 2 and 3: Fig. 2. Membership Function of Input A
Fig. 3. Membership Function of Output (DC Voltage Level)
A rule-based fuzzy controller is evaluated for this system as follow:
1. If A is DARK then DC-Output-Level is VERY-HIGH
2. If A is HALF-DARK then DC-Output-Level is HIGH
3. If A is MEDIUM then DC-Output-Level is MEDIUM
4. If A is HALF-LIGHT then DC-Output-Level is LOW
5. If A is LIGHT then DC-Output-Level is VERY-LOW
Control surface of this system is shown in figure 4. As it is seen, the controller is
very smooth action and it causes the ballast has a long life with a low harmonic feed into the
grid. Fig. 2. Membership Function of Input A Fig. 2. Membership Function of Input A Fig. 3. Membership Function of Output (DC Voltage Level) A rule-based fuzzy controller is evaluated for this system as follow: y
y
1. If A is DARK then DC-Output-Level is VERY-HIGH 5. If A is LIGHT then DC-Output-Level is VERY-LOW
Control surface of this system is shown in figure 4. As it is seen, the controller is
very smooth action and it causes the ballast has a long life with a low harmonic feed into the
grid. Energy Management in Buildings Using MATLAB 171 Fig. 4. Control Surface of Controller Fig. 4. Control Surface of Controller 3.2 HVAC system In this part the role of fuzzy modeling in heating, ventilating and air conditioning (HVAC)
and control models is presented. HVAC design professionals are required to evaluate
numerous design alternatives and properly justify their final conceptual selection through
modeling. This trend, coupled with the knowledge of experienced designers, increasing
complexity of the systems, unwillingness to commit additional funds to the design phase
itself, can only be satisfied by approaching the conceptual design process in more scientific,
comprehensive and rational manner as against the current empirical and often adhoc
approach. Fuzzy logic offers a promising solution to this conceptual design through fuzzy
modeling. Numerous fuzzy logic studies are available in the non- mechanical engineering
field and allied areas such as diagnostics, energy consumption analysis, maintenance,
operation and its control. Relatively little exists in using fuzzy logic based systems for
mechanical engineering and very little for HVAC conceptual design and control. Temperature and relative humidity are essential factors in meeting physiological
requirements. q
To identify the FLC’s variables, various (control or explicit) parameters may be considered
depending on the HVAC system, sensors and actuators such as:
Room Temperature as a thermal comfort index
Relative Humidity
Relative Humidity
Difference between supply and room temperatures
Indoor Air Quality (CO2 concentration)
Outdoor Temperature
HVAC system actuators (valve positions, operating modes, fan speeds, etc.)
HVAC system actuators (valve positions, operating modes, fan speeds, etc.) y
g
As man is more sensitive to temperature than to humidity, most of the comforts air-
conditioning systems are designed to provide relatively accurate temperature control and
relative humidity. Two parameters T (Temperature) and H (Humidity) are controlled by Fuzzy controller
system in order to regulate the room temperature and humidity to their desired values, Tref
and Href (Zheng Xiaoqing, 2002 , “Self-Tuning Fuzzy Controller for Air-Conditioning Systems”). The block diagram of the air-conditioning control system is a simple closed loop system as
shown in figure 5. Two parameters T (Temperature) and H (Humidity) are controlled by Fuzzy controller
system in order to regulate the room temperature and humidity to their desired values, Tref
and Href (Zheng Xiaoqing, 2002 , “Self-Tuning Fuzzy Controller for Air-Conditioning Systems”). The block diagram of the air-conditioning control system is a simple closed loop system as
shown in figure 5. MATLAB – A Ubiquitous Tool for the Practical Engineer 172 Fig. 5. 3.2 HVAC system Membership functions of outputs Rule base of this controller is defined as table 1: Rule base of this controller is defined as table 1: Rule base of this controller is defined as table 1: NL
NM
NS
Z
PS
PM
PL
NL
PL
PL
PM
PM
PS
PS
NS
NM
PL
PL
PM
PS
PS
NS
NS
NS
PM
PS
PS
PS
NS
NS
NM
Z
PM
PM
PS
Z
NS
NM
NM
PS
PM
PS
PS
NS
NS
NM
NM
PM
PS
PS
NS
NS
NM
NL
NL
PL
PS
NS
NS
NM
NM
NL
NL
Table 1. Rules of Fuzzy HVAC Table 1. Rules of Fuzzy HVAC For example:
If the room temperature error is NL and its rate of change is NL, then supply air fan
speed is PL or
If the room humidity error is NL and its rate of change is NL, then chilled water valve
opening is PL p
g
In this case we have 49 rules to have smooth control surface for HVAC control. p
g
In this case we have 49 rules to have smooth control surface for HVAC control. 3.2 HVAC system Block diagram of the air-conditioning control system As it is seen, two independent fuzzy controllers are assigned to control Temperature and
Humidity parameters. Error signal and its derivation are fed to each fuzzy controller. The
output of fuzzy controllers is assigned as inputs of air conditioner system. The output of
system is feedback to controller to make a closed-loop controller. The control strategy used can be expressed by the following linguistic rules: gy
p
y
g
g
If room temperature is higher than the set point, then increase the supply air fan spee If room humidity is higher than the set point, then increase the chilled water valve opening. Seven linguistic variables are chosen for each of Temperature and Humidity error and also
their derivations as follow: Fig. 6. Membership functions of inputs
Also seven linguistic variables are chosen for supply air fan speed and chilled water valve
opening as its outputs. It is show in figure 7. Fig. 6. Membership functions of inputs Also seven linguistic variables are chosen for supply air fan speed and chilled water valve
opening as its outputs. It is show in figure 7. Also seven linguistic variables are chosen for supply air fan speed and chilled water valve
opening as its outputs. It is show in figure 7. Energy Management in Buildings Using MATLAB 173 Fig. 7. Membership functions of outputs
Rule base of this controller is defined as table 1:
NL
NM
NS
Z
PS
PM
PL
NL
PL
PL
PM
PM
PS
PS
NS
NM
PL
PL
PM
PS
PS
NS
NS
NS
PM
PS
PS
PS
NS
NS
NM
Z
PM
PM
PS
Z
NS
NM
NM
PS
PM
PS
PS
NS
NS
NM
NM
PM
PS
PS
NS
NS
NM
NL
NL
PL
PS
NS
NS
NM
NM
NL
NL
Table 1. Rules of Fuzzy HVAC
For example:
If the room temperature error is NL and its rate of change is NL, then supply air fan
speed is PL
or
If the room humidity error is NL and its rate of change is NL, then chilled water valve
opening is PL
In this case we have 49 rules to have smooth control surface for HVAC control. Fig. 7. Membership functions of outputs
Rule base of this controller is defined as table 1: Fig. 7. Membership functions of outputs Fig. 7. 3.3 Elevator system With the advancement of intelligent computerized buildings in recent years, there have been
strong demands for intelligent elevator control with more sophistication and diverse
functions. The design criteria of an intelligent elevator control system would include
optimizing the movement of a group of elevators with respect to time, energy, load, etc. In
this paper, a new elevator group supervisory control system based on the ordinal structure
fuzzy logic algorithm is proposed. The system determines the optimum car to answer a hall
call using the knowledge and experiential rules of experts. Software has been developed to 174 MATLAB – A Ubiquitous Tool for the Practical Engineer simulate the traffic flow of three elevator cars in a 15-floor building. The software simulates
the movements of the cars as found in practical elevator systems. It can be verified through
simulation that the new system can bring about considerable improvements in the average
waiting time, riding time, etc. in comparison with conventional methods. g
g
In a conventional elevator system, the task of controlling a large number of elevators is
numerically evaluated by calculating a specified fixed-evaluation function. It has been
realized that knowledge and experiential rules of experts can be incorporated in the elevator
system to improve performance. However, such expert knowledge is fragmentary and fuzzy
which are difficult to organize. Furthermore, the choice of “good” rules and evaluation
functions are too complicated in many cases. It is difficult to adequately incorporate such
knowledge into products using conventional software and hardware technology. In order to overcome such problems as described above, a new elevator control system
using fuzzy logic algorithm is proposed based on the ordinal structure theory. This system
determines the optimum car within a group of elevators to answer a hall call using the
knowledge and experiential rules of experts. Instead of using the simple up and down hall
call buttons, destination oriented keypads at each floor is used. This system requires the
passengers to enter their desired floors on the keypad before they enter the car. The system
then assigns the passenger the respective optimal car to take through information displayed
on dot matrix displays near the keypad. This new elevator supervisory control system has
several
objectives
which
can
meet
users’
satisfaction. It
can
improve
not
only the average waiting time, but also the riding time, load, energy and so on. 3.3 Elevator system MATLAB – A Ubiquitous Tool for the Practical Engineer 176 The proposed fuzzy inference rules are shown in Table 2: The proposed fuzzy inference rules are shown in Table 2:
Rule No. Inference Rules
R1
If waiting time is Short then priority is Big. R2
If waiting time is Medium then priority is Medium
R3
If waiting time is Long then priority is Small. R4
If riding time is Short then priority is Big. R5
If riding time is Medium then priority is Medium. R6
If loading is Long then priority is Small
R7
If loading is Small then priority is Big
R8
If loading is Medium then priority is Medium
R9
If loading is Big then priority is Small
R10
If travelling distance is Close then priority is Big
R11
If travelling distance is Middle then priority is Medium
R12
If travelling distance is Far then priority is Small. R13
If hall call area weight is Close then priority is Big. R14
If hall call area weight is Middle then priority is Medium
R15
If hall call area weight is Far then priority is Small. R16
If destination area weight is Close then priority is Big. R17
If destination area weight is Middle then priority is Medium. R18
If destination area weight is Far then priority is Small. Table 2 A total of 18 fuzzy inference rules Table 2. A total of 18 fuzzy inference rules 4. Conclusion In this chapter one of the applications of MATLAB is introduced in order to apply energy
management in buildings. Three major systems were considered and a fuzzy controller was
developed for each of them. It can be open a new vision to the students to learn MATLAB
more applicable and more efficient. 3.3 Elevator system This
paper discusses the design and operations of the proposed fuzzy logic elevator control
system. y
In order to achieve good traffic performance, the elevator fuzzy control system uses six
kinds of parameters as the control inputs and one parameter for the output. These
parameters represent the criteria or objectives to be optimized in this elevator system which
are as follows:
Waiting Time: Total time an elevator needed to travel from its current position to the
new hall call.
Riding Time: Total time a passenger spent in the elevator until he reached as his
destination.
Loading: Number of passengers in an elevator.
Loading: Number of passengers in an elevator.
Travelling Distance: Distance between elevator position and new hall call in terms of
number of floors.
Hall call Area Weight: The area weight of the elevator which goes to the floor where a
new hall call is generated.
Destination Area Weight: The area weight of the elevator which goes to the floor where
the destination of the new hall call is generated.
Priority: Output of the fuzzy controller, where the elevator with highest value will be
assigned. As can be observed, it is difficult to configure six kinds of parameters at a time using the
conventional fuzzy reasoning method. Thus, the ordinal structure model of fuzzy reasoning
is used. With this model, all the fuzzy inference rules are described in one dimensional
space for each input and output. The membership function of the inputs and output
variables are shown in Figures 9 and 10. As can be observed, it is difficult to configure six kinds of parameters at a time using the
conventional fuzzy reasoning method. Thus, the ordinal structure model of fuzzy reasoning
is used. With this model, all the fuzzy inference rules are described in one dimensional
space for each input and output. The membership function of the inputs and output
variables are shown in Figures 9 and 10. 175 Energy Management in Buildings Using MATLAB Fig. 8. Membership functions of the elevator system inputs. Fig. 9. The membership function of the output of the elevator system. Fig. 8. Membership functions of the elevator system inputs. Fig. 8. Membership functions of the elevator system inputs. Fig. 9. The membership function of the output of the elevator system. 5. References A. Guillemin and N. Morel, 2001, “An innovative lighting controller integrated in a self-adaptive
building control system”, Energy and Buildings, vol. 33, no. 5, pp. 477–87. DHW Li and JC Lam, 2000, “Measurements of solar radiation and illuminance on vertical surfaces
and daylighting implications”, Renewable Energy, vol. 20, pp. 389-404 y g
g
p
gy
M. Perraudeau, 1994, “Estimation of illuminances from solar radiation data”, Joule 2 DAYLIGHT
II Program: Availability of Daylight – Design of a European Daylighting Atlas,
CSTB Nantes. P. Littlefair, 1993, S. Ashton and H. Porter, "Luminous efficacy algorithms”, Joule 1 Program –
Dynamic characteristics of daylight data and daylighting design in Buildings, Final
Report, CEC Brussels. S. Aydinli and J. Krochmann, 1983, “Data on daylight and solar radiation: Guide on Daylight”,
Draft for CIE TC 4.2. Zheng Xiaoqing, 2002 , “Self-Tuning Fuzzy Controller for Air-Conditioning Systems”, M.Sc. Thesis Synchronous Generator Advanced Control
Strategies Simulation Damir Sumina, Neven Bulić, Marija Mirošević and Mato Mišković
University of Zagreb/Faculty of Electrical Engineering and Computing,
University of Rijeka, Faculty of Engineering,
University of Dubrovnik/Department of Electrical Engineering and Computing
Croatia Part 3
Control Applications 10 Synchronous Generator Advanced Control
Strategies Simulation
Damir Sumina, Neven Bulić, Marija Mirošević and Mato Mišković
University of Zagreb/Faculty of Electrical Engineering and Computing,
University of Rijeka, Faculty of Engineering,
University of Dubrovnik/Department of Electrical Engineering and Computing
Croatia 1. Introduction During the last two decades, a number of research studies on the design of the excitation
controller of synchronous generator have been successfully carried out in order to improve
the damping characteristics of a power system over a wide range of operating points and to
enhance the dynamic stability of power systems (Kundur, 1994; Noroozi et.al., 2008;
Shahgholian, 2010). When load is changing, the operation point of a power system is varied;
especially when there is a large disturbance, such as a three-phase short circuit fault
condition, there are considerable changes in the operating conditions of the power system. Therefore, it is impossible to obtain optimal operating conditions through a fixed excitation
controller. In (Ghandra et.al., 2008; Hsu & Liu, 1987), self-tuning controllers are introduced
for improving the damping characteristics of a power system over a wide range of operating
conditions. Fuzzy logic controllers (FLCs) constitute knowledge-based systems that include
fuzzy rules and fuzzy membership functions to incorporate human knowledge into their
knowledge base. Applications in the excitation controller design using the fuzzy set theory
have been proposed in (Karnavas & Papadopoulos, 2002; Hiyama et. al., 2006; Hassan et. al.,
2001). Most knowledge-based systems rely upon algorithms that are inappropriate to
implement and require extensive computational time. Artificial neural networks (ANNs)
and their combination with fuzzy logic for excitation control have also been proposed,
(Karnavas & Pantos, 2008; Salem et. al., 2000a, Salem et. al., 2000b). A simple structure with
only one neuron for voltage control is studied in (Malik et. al., 2002; Salem et. al., 2003). The
synergetic control theory (Jiang, 2009) and other nonlinear control techniques, (Akbari &
Amooshahi, 2009; Cao et.al., 2004), are also used in the excitation control. One of the disadvantages of artificial intelligence methods and nonlinear control techniques
is the complexity of algorithms required for implementation in a digital control system. For
testing of these methods is much more convenient and easier to use software package
Matlab Simulink. So, this chapter presents and compares two methods for the excitation
control of a synchronous generator which are simulated in Matlab Simulink and compared
with conventional control structure. The first method is based on the neural network (NN)
which uses the back-propagation (BP) algorithm to update weights on-line. In addition to 180 MATLAB – A Ubiquitous Tool for the Practical Engineer the function of voltage control the proposed NN has the function of stabilizing generator
oscillations. 1. Introduction The second method proposes a fuzzy logic controller (FLC) for voltage control
and the stabilization of generator oscillations. The proposed control algorithms with neural
networks and a fuzzy controller are tested on a simulation model of synchronous generator
weakly connected through transmissions lines to an AC network. The simulations are
carried out by step changes in voltage reference. 2. Simulation models Simulation models of synchronous generator and different control structures are made in
Matlab Simulink. The generator is connected over transformer and transmission lines to the
AC network (Fig. 1). SG
Transmission
lines
X e
U
AC
network
Synchronous generator
Transformer
Fig. 1. Synchronous generator connected to AC network AC
network X e Transmission
lines Fig. 1. Synchronous generator connected to AC network Fig. 1. Synchronous generator connected to AC network 2.1 Simulation model of a synchronous generator Mathematical model of synchronous generator is represented in dq axis form. Based on that
it is necessary to perform transformation from abc coordinate system to dq coordinate
system. Assumption is that voltages are symmetrical in all phases and there is only one
harmonic of magnetic flux in air gap. Equations are represented in per-unit system and time
is absolute. The synchronous generator under consideration is assumed to have three armature
windings, one field winding, and damper windings. One damper winding is located along
the direct axis (D) and another is located along the quadrature axis (Q). 2.1 Simulation model of a synchronous generator Accordingly, the
basis for the mathematical model of the synchronous generator is a system of voltage
equations of the generator in the rotating dq coordinate system, where u, i, r, x and Ψ denote
voltage, current, resistance, reactance and flux, respectively (Kundur, 1994): 1
=
d
d
d
q
s
d
u
r i
dt
ω
ω
Ψ
−
⋅
+
⋅
+
⋅Ψ
(1) 1
=
d
d
d
q
s
d
u
r i
dt
ω
ω
Ψ
−
⋅
+
⋅
+
⋅Ψ
(1)
1
=
q
q
q
d
s
d
u
r i
dt
ω
ω
Ψ
−
⋅
+
⋅
−
⋅Ψ
(2)
1
=
f
f
f
f
s
d
u
r
i
dt
ω
Ψ
⋅
+
⋅
(3) (1) (1) 1
=
q
q
q
d
s
d
u
r i
dt
ω
ω
Ψ
−
⋅
+
⋅
−
⋅Ψ
(2) (2) 1
=
f
f
f
f
s
d
u
r
i
dt
ω
Ψ
⋅
+
⋅
(3) (3) Synchronous Generator Advanced Control Strategies Simulation Synchronous Generator Advanced Control Strategies Simulation
181 181 1
0 =
D
D
D
s
d
r
i
dt
ω
Ψ
⋅
+
⋅
(4)
1
0 =
Q
Q
Q
s
d
r
i
dt
ω
Ψ
⋅
+
⋅
(5) (4) 1
0 =
Q
Q
Q
s
d
r
i
dt
ω
Ψ
⋅
+
⋅
(5) (5) The equations defining the relations between fluxes and currents are: The equations defining the relations between fluxes and currents are: =
d
d
d
ad
f
dD
D
x
i
x
i
x
i
Ψ
⋅
+
⋅
+
⋅
(6)
=
q
q
q
qQ
Q
x
i
x
i
Ψ
⋅
+
⋅
(7)
=
f
ad
d
f
f
fD
D
x
i
x
i
x
i
Ψ
⋅
+
⋅
+
⋅
(8)
=
D
dD
d
fD
f
D
D
x
i
x
i
x
i
Ψ
⋅
+
⋅
+
⋅
(9)
=
Q
qQ
q
Q
Q
x
i
x
i
Ψ
⋅
+
⋅
(10) =
f
ad
d
f
f
fD
D
x
i
x
i
x
i
Ψ
⋅
+
⋅
+
⋅ =
D
dD
d
fD
f
D
D
x
i
x
i
x
i
Ψ
⋅
+
⋅
+
⋅ (10) =
Q
qQ
q
Q
Q
x
i
x
i
Ψ
⋅
+
⋅ The motion equations are defined as follows: The motion equations are defined as follows: (
)
=
1
s
d
dt
δ
ω
ω
−
⋅
(11)
(
)
1
= 2
m
e
d
T
T
dt
H
ω
⋅
−
(12) (11) (12) where δ is angular position of the rotor, ω is angular velocity of the rotor, ωs is synchronous
speed, H is inertia constant, Tm is mechanical torque, and Te is electromagnetic torque. 2.1 Simulation model of a synchronous generator The electromagnetic torque of the generator Te is determined by equation: =
e
q
d
d
q
T
i
i
Ψ ⋅
−Ψ ⋅
(13) (13) Connection between the synchronous generator and AC network is determined by the
following equations: Connection between the synchronous generator and AC network is determined by the
following equations: =
e
d
d
d
e
e
q
sd
s
x
di
u
i
r
x
i
u
dt
ω
ω
⋅
+
⋅
+
⋅
⋅
+
(14) =
e
d
d
d
e
e
q
sd
s
x
di
u
i
r
x
i
u
dt
ω
ω
⋅
+
⋅
+
⋅
⋅
+
(14)
=
q
e
q
q
e
e
d
sq
s
di
x
u
i
r
x
i
u
dt
ω
ω
⋅
+
⋅
−
⋅
⋅
+
(15)
(
)
=
sin
sd
m
u
U
δ
⋅−
(16)
=
cos
sq
m
u
U
δ
⋅
(17) (14) =
q
e
q
q
e
e
d
sq
s
di
x
u
i
r
x
i
u
dt
ω
ω
⋅
+
⋅
−
⋅
⋅
+
(15) (15) (
)
=
sin
sd
m
u
U
δ
⋅−
(16)
=
cos
sq
m
u
U
δ
⋅
(17) (
)
=
sin
sd
m
u
U
δ
⋅− (16) (17) =
cos
sq
m
u
U
δ
⋅ MATLAB – A Ubiquitous Tool for the Practical Engineer 182 transformer and transmission line resistance, xe is transformer and transmission line
reactance, and Um is AC network voltage. Synchronous generator nominal data and
simulation model parameters are given in Table 1. Terminal voltage
400 V
Phase current
120 A
Power
83 kVA
Frequency
50 Hz
Speed
600 r/min
Power factor
0,8
Excitation voltage
100 V
Excitation current
11.8 A
d-axis synchronous reactance Xd
0.8 p.u. q-axis synchronous reactance Xq
0.51 p.u. Inertia constant H
1.3
d-axis transient open-circuit time
constant Tdo′
0.55 s
d-axis transient reactance Xd’
0.35 p.u. d-axis subtransient reactance Xd''
0.15 p.u. q-axis subtransient reactance Xq'' 0.15 p.u. Short-circuit time constant Td''
0.054 s
Short-circuit time constant Tq''
0.054 s
Transformer and transmission
line resistance re
0.05 p.u. Transformer and transmission
line reactance xe
0.35 p.u. hronous generator nominal data and simulation model param Table 1. Synchronous generator nominal data and simulation model parameters Table 1. Synchronous generator nominal data and simulation model parameters 2.2 Conventional control structure Conventional control structure (CCS) for the voltage control of a synchronous generator is
shown in Fig. 3. The structure contains a proportional excitation current controller and,
subordinate to it, a voltage controller. Simulation model of conventional control structure is
shown in Fig. 4. 183 Synchronous Generator Advanced Control Strategies Simulation Synchronous Generator Advanced Control Strategies Simulation
1
Delta
U
I
5
Q
4
P
If
2
w
1
ws
w,Tel,delta
Tm
w
Tel
delta
psi
psid
psiq
Yq11,Yq12
Yq21,Yq22,
Ad,Bd,Cd,Aq,Bq
Yd11,Yd12,Yd13
Yd21,Yd22,Yd23
Yd31,Yd32,Yd33
xe
Xq
0.51
Xl
0.04
Xfd=f(psid)
Xd2
Xd1
0.35
Xd 1
0.35
Xd
0.8
Ud,Uq
Umd,Umq
Ud
Uq
Umd
Umq
Td01
0.55
Td2
0.054
re
R
0.04
Parameters
Xl
Xq
R
Xd1
Xd2
Xd1
Xq2
xe
re
Tf
ws
H
Tq2
Td2
Xd
K,L,M,N,I,P
Ikd,Ikq,Idv,Iqv
Idk
Iqk
Idv
Iqv
Id,Iq,ID,IQ
Id
Iq
ID
IQ
I,P,Q,S,U,If
I
P
Q
U
If
S
H
1.3
Goto1
Um
Goto
Uf
From7
[psid]
Um
3
Uf
2
Tm
1
0.15
0.05
0.35
6
7
3
100*pi
Fig. 2. Simulation model of synchronous generator
G
Uref
Voltage
controller
Excitation current
controller
If
Ifref
D
uab
ucb
Control loop
~
A B C
U
Clarke
3x400 V
Fig. 3. Conventional control structure
[U]
Synchronous
generator
Tm
Uf
Um
w
If
P
Q
I
U
Delta
[Q]
PI voltage
controller
Uref
U
Kp
Ki
Ifref
P type excitation
controller
Ifref
If
Kp
D
Mechanical torque
[Tm]
Exitation current
[If]
10
10
0.05
10
Compensation
Ug
Q
K
U
Chopper
D Uf
AC network
voltage
1
Fig. 4. Simulation model of conventional control structure Delta
U
I
5
Q
4
P
If
2
w
1
ws
w,Tel,delta
Tm
w
Tel
delta
psi
psid
psiq
Yq11,Yq12
Yq21,Yq22,
Ad,Bd,Cd,Aq,Bq
Yd11,Yd12,Yd13
Yd21,Yd22,Yd23
Yd31,Yd32,Yd33
xe
Xq
0.51
Xl
0.04
Xfd=f(psid)
Xd2
Xd1
0.35
Xd 1
0.35
Xd
0.8
Ud,Uq
Umd,Umq
Ud
Uq
Umd
Umq
Td01
0.55
Td2
0.054
re
R
0.04
Parameters
Xl
Xq
R
Xd1
Xd2
Xd1
Xq2
xe
re
Tf
ws
H
Tq2
Td2
Xd
K,L,M,N,I,P
Ikd,Ikq,Idv,Iqv
Idk
Iqk
Idv
Iqv
Id,Iq,ID,IQ
Id
Iq
ID
IQ
I,P,Q,S,U,If
I
P
Q
U
If
S
H
1.3
Goto1
Um
Goto
Uf
From7
[psid]
Um
3
Uf
2
Tm
1
0.15
0.05
0.35
6
7
3
100*pi
Fig. 2. 2.2 Conventional control structure AC/DC converter for supplying generator excitation current (a) and simulation
model (b) 2.2 Conventional control structure Simulation model of synchronous generator Delta
U
I
5
Q
4
P
If
2
w
1
ws
w,Tel,delta
Tm
w
Tel
delta
psi
psid
psiq
Yq11,Yq12
Yq21,Yq22,
Ad,Bd,Cd,Aq,Bq
Yd11,Yd12,Yd13
Yd21,Yd22,Yd23
Yd31,Yd32,Yd33
xe
Xq
0.51
Xl
0.04
Xfd=f(psid)
Xd2
Xd1
0.35
Xd 1
0.35
Xd
0.8
Ud,Uq
Umd,Umq
Ud
Uq
Umd
Umq
Td01
0.55
Td2
0.054
re
R
0.04
Parameters
Xl
Xq
R
Xd1
Xd2
Xd1
Xq2
xe
re
Tf
ws
H
Tq2
Td2
Xd
K,L,M,N,I,P
Ikd,Ikq,Idv,Iqv
Idk
Iqk
Idv
Iqv
Id,Iq,ID,IQ
Id
Iq
ID
IQ
I,P,Q,S,U,If
I
P
Q
U
If
S
H
1.3
Goto1
Um
Goto
Uf
From7
[psid]
Um
3
Uf
2
Tm
1
0.15
0.05
0.35
6
7
3
100*pi
Fig 2 Simulation model of synchronous generator Fig. 2. Simulation model of synchronous generator Fig. 2. Simulation model of synchronous generator
G
Uref
Voltage
controller
Excitation current
controller
If
Ifref
D
uab
ucb
Control loop
~
A B C
U
Clarke
3x400 V
Fig. 3. Conventional control structure G
Uref
Voltage
controller
Excitation current
controller
If
Ifref
D
uab
ucb
Control loop
~
A B C
U
Clarke
Fig. 3. Conventional control structure G~ Fig. 3. Conventional control structure Fig. 3. Conventional control structure Fig. 3. Conventional control structure Fig. 3. Conventional control structure
[U]
Synchronous
generator
Tm
Uf
Um
w
If
P
Q
I
U
Delta
[Q]
PI voltage
controller
Uref
U
Kp
Ki
Ifref
P type excitation
controller
Ifref
If
Kp
D
Mechanical torque
[Tm]
Exitation current
[If]
10
10
0.05
10
Compensation
Ug
Q
K
U
Chopper
D Uf
AC network
voltage
1
Fig. 4. Simulation model of conventional control structure Ifref Fig. 4. Simulation model of conventional control structure 184 MATLAB – A Ubiquitous Tool for the Practical Engineer For supplying the generator excitation current, an AC/DC converter is simulated. The
AC/DC converter includes a three-phase bridge rectifier, a DC link with a detection of DC
voltage, a braking resistor, and a DC chopper (Fig. 5). 3 x 400 V
C
R
PWM
V1
V3
V2
V4
G
~
V5
Uf
1
sw1
UDC
[UDC]
U=f(D)
1
0.01s+1
<
>
AND
If
[If]
-1
0.30
0.05
D
1
DC link overvoltage
protection
(a)
(b)
Fig. 5. AC/DC converter for supplying generator excitation current (a) and simulation
model (b) Uf
1
sw1
UDC
[UDC]
U=f(D)
1
0.01s+1
<
>
AND
If
[If]
-1
0.30
0.05
D
1
(b) (b) (a) Fig. 5. 2.3 Neural network based control 7. Tansig activation function and its derivation −4
−2
0
2
4
0
0.2
0.4
0.6
0.8
1
Input
Output −4
−2
0
2
4
−1
−0.5
0
0.5
1
Input
Output Fig. 7. Tansig activation function and its derivation 1
( )
1
1
cv
v
e
ψ
−
=
−
+
(18)
2
2
2
2
4
( )
(1
)
(1
)
cv
cv
e
v
c
c
e
ψ
ψ
−
−
′
=
=
⋅
−
+
(19) 1
( )
1
1
cv
v
e
ψ
−
=
−
+
(18) (18) 2
2
2
2
4
( )
(1
)
(1
)
cv
cv
e
v
c
c
e
ψ
ψ
−
−
′
=
=
⋅
−
+
(19) (19) The NN uses a simple procedure to update weights on-line and there is no need for any off-
line training. Also, there is no need for an identifier and/or a reference model. The NN is
trained directly in an on-line mode from the inputs and outputs of the generator and there is
no need to determine the states of the system. The NN uses a sampled value of the machine
quantities to compute the error using a modified error function. This error is back-
propagated through the NN to update its weights using the algorithm shown in Fig. 8. When the weights are adjusted, the output of the neural network is calculated. The NN uses a simple procedure to update weights on-line and there is no need for any off-
line training. Also, there is no need for an identifier and/or a reference model. The NN is
trained directly in an on-line mode from the inputs and outputs of the generator and there is
no need to determine the states of the system. The NN uses a sampled value of the machine
quantities to compute the error using a modified error function. This error is back-
propagated through the NN to update its weights using the algorithm shown in Fig. 8. When the weights are adjusted, the output of the neural network is calculated. 2.3 Neural network based control The structure of the proposed NN is shown in Fig. 6. The NN has three inputs, six neurons
in the hidden layer and one neuron in the output layer. The inputs in this NN are the
voltage reference Uref, the terminal voltage U and the previous output from the NN y(t-1). Bringing the previous output to the NN input is a characteristic of dynamic neural
networks. The function tansig is used as an activation function for the neurons in the hidden
layer and for the neuron in the output layer. The graphical representation of the tansig function and its derivation is shown in Fig. 7. The
numerical representation of the tansig function and its derivation are given as follows
(Haykin, 1994): +
+
+
+
+
+
+
Uref
Ug
y = y21
y(t-1)
w111
w121
w131
w112
w162
w163
w143
y11 , x21
y12 , x22
y13
y14
y15
y16
w211
w212
w213
w214
w215
w216
b1
b2
1. layer
2. layer
Inputs
x11
x12
x13
v11
v12
v13
v14
v15
v16
v21
Fig. 6. Structure of the proposed neural network 1. layer Fig. 6. Structure of the proposed neural network Synchronous Generator Advanced Control Strategies Simulation 185 −4
−2
0
2
4
−1
−0.5
0
0.5
1
Input
Output
−4
−2
0
2
4
0
0.2
0.4
0.6
0.8
1
Input
Output
Fig. 7. Tansig activation function and its derivation
1
( )
1
1
cv
v
e
ψ
−
=
−
+
(18)
2
2
2
2
4
( )
(1
)
(1
)
cv
cv
e
v
c
c
e
ψ
ψ
−
−
′
=
=
⋅
−
+
(19)
The NN uses a simple procedure to update weights on-line and there is no need for any off-
line training. Also, there is no need for an identifier and/or a reference model. The NN is
trained directly in an on-line mode from the inputs and outputs of the generator and there is
no need to determine the states of the system. The NN uses a sampled value of the machine
quantities to compute the error using a modified error function. This error is back-
propagated through the NN to update its weights using the algorithm shown in Fig 8 −4
−2
0
2
4
−1
−0.5
0
0.5
1
Input
Output
−4
−2
0
2
4
0
0.2
0.4
0.6
0.8
1
Input
Output
Fig. 2.3 Neural network based control ∑
∑
∑
Two layer feedforward
Neural network
∑
∑
∑
φ(*)
φ(*)
φ(*)
∑
φ(*)
φ´(*)
φ´(*)
v
X
X
X
∑
∑
∑
X1
X2
X
v2
o1
e1
δ(2)
Back
propagation
φ(*)
φ(*)
φ(*)
X
X
X
∑
∑
∑
δ(1)
W1,Θ1
W2,Θ2
y2
y1
p
Fig. 8. Back-propagation algorithm φ´(*) φ´(*)
φ´(*)
v
X
X
X
∑
∑
∑
e1
δ(2)
Back
propagation
X
X
X
∑
∑
∑
δ(1) φ´(*) Fig. 8. Back-propagation algorithm Fig. 8. Back-propagation algorithm 186 MATLAB – A Ubiquitous Tool for the Practical Engineer Training of the NN with the BP algorithm is described in (Haykin, 1994). Inputs and outputs
of one neuron in the NN can be determined as follows: Training of the NN with the BP algorithm is described in (Haykin, 1994). Inputs and outputs
of one neuron in the NN can be determined as follows: 1
ki
kij
kj
k
y
w
x
b
ψ ⎛
⎞
=
⋅
+
⎜
⎟
⎝
⎠
∑
(20) (20) The BP algorithm is an iterative gradient algorithm designed to minimize the mean square
error between the actual output and the NN desired output. 2.3 Neural network based control The ynchronous Generator Advanced Control Strategies Simulation 187 Synchronous Generator Advanced Control Strategies Simulation complete modified error function for the excitation control of a synchronous generator is
given as follows: (
)
1
3
2
(
)
ref
ki
dU
dP
K U
U
k
k
P
k
y
dt
dt
∂ℑ
⎡
⎤
⎡
⎤
=
−
−
−
Δ
+
⎢
⎥
⎢
⎥
∂
⎣
⎦
⎣
⎦
(29) (29) The modified error function is divided into two parts. The first part is used for voltage
control and the second part for power system stabilization. Parameters K, k1, k2 and k3 are
given in Table 2. Simulation model of NN control structure is shown in Fig. 9. The modified error function is divided into two parts. The first part is used for voltage
control and the second part for power system stabilization. Parameters K, k1, k2 and k3 are
given in Table 2. Simulation model of NN control structure is shown in Fig. 9. K
2.5
k1
0.3
k2
0.6
k3
0.25
Table 2. Parameters of neural network K
2.5
k1
0.3
k2
0.6
k3
0.25
Table 2. Parameters of neural network Table 2. Parameters of neural network [P]
[U]
Synchronous
generator
Tm
Uf
Um
w
If
P
Q
I
U
Delta
[Q]
P type excitation
controller
Ifref
If
Kp
D
Neural network
voltage
controller
Uref
U
P
Ifref
Mechanical torque
[Tm]
[If]
0.05
10
Compensation
Ug
Q
K
U
Chopper
D Uf
AC network
voltage
1
Fig. 9. Simulation model of neural network control structure
Neural network based controller is realized as S-function in Matlab and is called in every
simulation step. [P]
[U]
Tm
Uf
w
If
P
Q
I
U
[Q]
P type excitation
controller
Ifref
If
Kp
D
Neural network
voltage
controller
Uref
U
P
Ifref
Mechanical torque
[Tm]
[If]
0.05
10
Compensation
Ug
Q
K
U
Chopper
D Uf [P]
[U]
[Q]
Neural network
voltage
controller
Uref
U
P
Ifref
0.05
Compensation
Ug
Q
K
U Neural network
voltage
controller [P] P type excitation
controller Um AC network
voltage Fig. 9. Simulation model of neural network control structure
Neural network based controller is realized as S-function in Matlab and is called in every
simulation step. 2.3 Neural network based control This is a recursive algorithm
starting at the output neuron and working back to the hidden layer adjusting the weights
according to the following equations: (
1)
( )
( )
kij
kij
kij
w
t
w
t
w
t
+
=
+ Δ
(21)
( )
( )
( )
ji
j
i
w n
n
y n
η δ
Δ
=
⋅
⋅
(22)
( )
( )
(
( ))
j
j
j
j
n
e n
v n
δ
φ′
=
⋅
(23) (21) (22) ( )
( )
(
( ))
j
j
j
j
n
e n
v n
δ
φ′
=
⋅
(23) (23) The error function commonly used in the BP algorithm can be expressed as: (
)
2
1
2
ki
ki
t
y
ℑ=
−
(24) (24) If the neuron is in the output layer, the error function is: If the neuron is in the output layer, the error function is: ki
ki
ki
t
y
y
∂ℑ=
−
∂
(25) (25) If the neuron is in the hidden layer, the error function is recursively calculated as (Haykin,
1994): If the neuron is in the hidden layer, the error function is recursively calculated as (Haykin,
1994): (
1)
1,
1,1,
1
1,
n k
k
p
k
i
p
ki
k
p
w
y
y
ψ
+
+
+
=
+
∂ℑ
∂ℑ
′
=
⋅
⋅
∂
∂
∑
(26) (26) If the NN is used for the excitation control of a synchronous generator, it is required that we
not only change the weights based only on the error between the output and the desired
output but also based on the change of the error as follows: (
)
ki
ki
ki
ki
dy
t
y
y
dt
∂ℑ=
−
−
∂
(27) (27) In this way, the modified error function speeds up the BP algorithm and gives faster
convergence. Further, the algorithm becomes appropriate for the on-line learning
implementation. The error function for the NN used for voltage control is expressed as: 1
(
)
ref
ki
dU
K U
U
k
y
dt
∂ℑ=
−
−
∂
(28) (28) In order to perform the power system stabilization, the active power deviation ΔP and the
derivation of active power dP/dt are to be imported in the modified error function. 2.4 Fuzzy logic controller y
g
The detailed structure of the proposed fuzzy logic controller (FLC) is shown in Fig. 10. The
FLC has two control loops. The first one is the voltage control loop with the function of MATLAB – A Ubiquitous Tool for the Practical Engineer 188 voltage control and the second one is the damping control loop with the function of a power
system stabilizer. A fuzzy polar control scheme is applied to these two control loops. U
-
+
U ref
D
e(k)
ed(k)
Fuzzy logic
control
rules
Kiv
I
+
I fref
Fuzzy logic
control rules
ustab(k)
R
I
R
-P
+
+
R-reset filter
∆ω
0 p.u. 0
2 p.u. 2 p.u. 0
Umax v
u(k)
-Umaxs
+Umaxs
p.u. a
p.u. Fig. 10. Structure of the fuzzy logic stabilizing controller Umax v Fig. 10. Structure of the fuzzy logic stabilizing controller The PD information of the voltage error signal e (k) is utilized to get the voltage state and to
determine the reference Ifref for the proportional excitation current controller. To eliminate
the voltage error, an integral part of the controller with parameter Kiv must be added to the
output of the controller. The damping control signal ustab is derived from the generator
active power P. The signal a is a measure of generator acceleration and the signal Δω is a
measure of generator speed deviation. The signals a and Δω are derived from the generator
active power through filters and the integrator. The damping control signal ustab is added to
the input of the voltage control loop. The fuzzy logic control scheme is applied to the voltage and stabilization control loop
(Hiyama et. al., 1996). The generator operating point in the phase plane is given by p(k) for
the corresponding control loop (Fig. 11a): p(k) = (X(k), As·Y(k))
(30) (30) where X(k) is e(k) and Y(k) is ed(k) for the voltage control loop, and X(k) is Δω(k) and Y(k) is
a(k) for the stabilization control loop. Parameter As is the adjustable scaling factor for Y(k). 2.4 Fuzzy logic controller Phase plane (a) and angle membership functions (b) max
( ( ))
( ( ))
( )
( )
( ( ))
( ( ))
v
N
k
P
k
u k
G k U
N
k
P
k
Θ
−
Θ
=
⋅
⋅
Θ
+
Θ
(33) max
( ( ))
( ( ))
( )
( )
( ( ))
( ( ))
v
N
k
P
k
u k
G k U
N
k
P
k
Θ
−
Θ
=
⋅
⋅
Θ
+
Θ
(33)
stab
max
( ( ))
( ( ))
( )
( )
( ( ))
( ( ))
s
N
k
P
k
u
k
G k U
N
k
P
k
Θ
−
Θ
=
⋅
⋅
Θ
+
Θ
(34) max
( ( ))
( ( ))
( )
( )
( ( ))
( ( ))
v
N
k
P
k
u k
G k U
N
k
P
k
Θ
−
Θ
=
⋅
⋅
Θ
+
Θ
(33)
stab
max
( ( ))
( ( ))
( )
( )
( ( ))
( ( ))
s
N
k
P
k
u
k
G k U
N
k
P
k
Θ
−
Θ
=
⋅
⋅
Θ
+
Θ
(34) (33) stab
max
( ( ))
( ( ))
( )
( )
( ( ))
( ( ))
s
N
k
P
k
u
k
G k U
N
k
P
k
Θ
−
Θ
=
⋅
⋅
Θ
+
Θ
(34) (34) The radius membership function G (k) is given by: The radius membership function G (k) is given by: The radius membership function G (k) is given by: G(k) = D(k) / Dr for D(k) ≤ Dr
G(k) = 1 for D(k) > Dr(35) G(k) = D(k) / Dr for D(k) ≤ Dr
G(k) = 1 for D(k) > Dr(35) G(k) = D(k) / Dr for D(k) ≤ Dr
G(k) = 1 for D(k) > Dr(35) Simulation models of the voltage control loop, stabilization control loop and fuzzy logic
control structure are presented on the Figs. 12, 13, and 14, respectively. Parameters As, Dr
and α for the voltage control loop and the damping control loop are given in Tables 3 and 4. As
0.1
Dr
1
Kiv
10
Umaxv
2 p.u. Table 4. FLC parameters for damping control loop 2.4 Fuzzy logic controller Polar information, representing the generator operating point, is determined by the radius
D(k) and the phase angle Θ(k): 2
2
( )
( )
(
( ))
s
D k
X k
A Y k
=
+
⋅
(31)
( )
( )
(
)
( )
s
A Y k
k
arctg
X k
⋅
Θ
=
(32) (31) (32) The phase plane is divided into sectors A and B defined by using two angle membership
functions N(Θ(k)) and P(Θ(k)) (Fig. 11b). The phase plane is divided into sectors A and B defined by using two angle membership
functions N(Θ(k)) and P(Θ(k)) (Fig. 11b). The principles of the fuzzy control scheme and the selection of the membership functions
are described in (Hiyama et. al., 1996). By using the membership functions N(Θ(k)) and
P(Θ(k)) the output control signals u(k) and ustab(k) for each control loop are given as follows: Synchronous Generator Advanced Control Strategies Simulation 189 (a)
)
(Θ
P
)
(Θ
N
Θ
α
(b)
Fig. 11. Phase plane (a) and angle membership functions (b) (a)
)
(Θ
P
)
(Θ
N
Θ
α
(b)
Fig. 11. Phase plane (a) and angle membership functions (b) (a) ( )
( )
Fig. 11. Phase plane (a) and angle membership functions (b) Fig. 11. 2.4 Fuzzy logic controller α
90° As
0.1
Dr
1
Kiv
10
Umaxv
2 p.u. α
90°
Table 3. FLC parameters for voltage control loop Table 3. FLC parameters for voltage control loop Table 3. FLC parameters for voltage control loop As
0.01
Dr
0.01
Umaxs
0.1 p.u. α
90°
Table 4. FLC parameters for damping control loop As
0.01
Dr
0.01
Umaxs
0.1 p.u. α
90° MATLAB – A Ubiquitous Tool for the Practical Engineer 190 MATLAB – A Ubiquitous Tool for the Practical Engine
190
Ifref
1
atan
s
s+1
Quadrant
calculation
ed
e
theta1
theta
P(theta)
N(theta)
u2
u2
sqrt
1
s
e
ed
theta
P_theta
N_theta
theta1
Gv
Dv
180/pi
G(D)
[P_theta]
[e]
[e]
[ed]
[ed]
[ed]
[e]
[theta]
[theta1]
[Gv]
[theta]
[Dv]
2
1
2
Kiv
4
Asv
3
U
2
Uref
1
Fig. 12. Simulation model of voltage control loop
Ustab
1
atan
Quadrant
calculation
a
dw
theta1s
thetas
P(theta)1
N(theta)1
u2
u2
sqrt
P_thetas
Goto8
dw
Goto7
a
N_thetas
Gs
theta1s
thetas
Ds
180/pi
G(D)1
[theta1s]
[thetas]
[dw]
[a]
[Ds]
[P_thetas]
[Gs]
[a]
[dw]
[a]
[thetas]
[dw]
0.1
1
2
Ass
3
dw
2
a
1
Fig. 13. Simulation model of stabilization control loop Ifref
1
atan
s
s+1
Quadrant
calculation
ed
e
theta1
theta
P(theta)
N(theta)
u2
u2
sqrt
1
s
e
ed
theta
P_theta
N_theta
theta1
Gv
Dv
180/pi
G(D)
[P_theta]
[e]
[e]
[ed]
[ed]
[ed]
[e]
[theta]
[theta1]
[Gv]
[theta]
[Dv]
2
1
2
Kiv
4
Asv
3
U
2
Uref
1
Fig. 12. Simulation model of voltage control loop atan
s
s+1
Quadrant
calculation
ed
e
theta1
theta
P(theta)
N(theta)
u2
u2
sqrt
e
ed
theta
P_theta
N_theta
theta1
Gv
Dv
180/pi
G(D)
[e]
[e]
[ed]
[ed]
[ed]
[e]
[theta]
[theta1]
[theta]
[Dv]
Asv
3
U
2
Uref
1 Ifref
1
atan
s
s+1
Quadrant
calculation
ed
e
theta1
theta
P(theta)
N(theta)
u2
u2
sqrt
1
s
e
ed
theta
P_theta
N_theta
theta1
Gv
Dv
180/pi
G(D)
[P_theta]
[e]
[e]
[ed]
[ed]
[ed]
[e]
[theta]
[theta1]
[Gv]
[theta]
[Dv]
2
1
2
Kiv
4
Asv
3
U
2
Uref
1
Fig. 12. Simulation model of voltage control loop Dv Fig. 12. Simulation model of voltage control loop Fig. 12. 2.4 Fuzzy logic controller Simulation model of voltage control loop Ustab
1
atan
Quadrant
calculation
a
dw
theta1s
thetas
P(theta)1
N(theta)1
u2
u2
sqrt
P_thetas
Goto8
dw
Goto7
a
N_thetas
Gs
theta1s
thetas
Ds
180/pi
G(D)1
[theta1s]
[thetas]
[dw]
[a]
[Ds]
[P_thetas]
[Gs]
[a]
[dw]
[a]
[thetas]
[dw]
0.1
1
2
Ass
3
dw
2
a
1
Fig. 13. Simulation model of stabilization control loop [a] Fig. 13. Simulation model of stabilization control loop Synchronous Generator Advanced Control Strategies Simulation 191 [P]
[U]
Synchronous
generator
Tm
Uf
Um
w
If
P
Q
I
U
Delta
[Q]
P type excitation
controller
Ifref
If
Kp
D
Mechanical torque
[Tm]
Fuzzy voltage
controller
Uref
U
P
Asv
Ass
Ki
Ifref
[If]
10
0.05
0.01
0.1
10
Compensation
Ug
Q
K
U
Chopper
D Uf
AC network
voltage
1
Fig. 14. Simulation model of fuzzy logic control structure Mechanical torque P type excitation
controller Fig. 14. Simulation model of fuzzy logic control structure 3. Simulation results In order to verify the performance of the proposed control structures several simulations
were carried out. In these experiments, voltage reference is changed in 0.1 s from 1 p.u. to
0.9 p.u. or 1.1 p.u. and in 1 s back to 1 p.u. at a constant generator active power. g
For the quality analysis of the active power oscillations two numerical criteria are used: the
integral of absolute error (IAE) and the integral of absolute error derivative (IAED). If the
response is better, the amount of criteria is smaller. Fig. 15 presents active power responses for step changes in voltage reference from 1 p.u. to
0.9 p.u. and back to 1 p.u. at an active power of 0.5 p.u. The numerical criteria of the
responses in Fig. 15 are given in Table 5. Fig. 15. Active power responses for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at
an active power of 0.5 p.u. Fig. 15. Active power responses for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at
an active power of 0.5 p.u. MATLAB – A Ubiquitous Tool for the Practical Engineer 192 IAE
IAED
CCS
0.389
0.279
FLC
0.255
0.097
NN
0.235
0.090
Table 5. Numerical criteria for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at an
active power of 0.5 p.u. Table 5. Numerical criteria for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at an
active power of 0.5 p.u. Table 5. Numerical criteria for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at an
active power of 0.5 p.u. Fig. 16 shows active power responses for step changes in voltage reference from 1 p.u. to 1.1
p.u. and back to 1 p.u. at an active power of 0.5 p.u. The numerical criteria of the responses
in Fig. 16 are given in Table 6. Fig. 16. Active power responses for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at
an active power of 0.5 p.u. Fig. 16. Active power responses for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at
an active power of 0.5 p.u. IAE
IAED
CCS
0.264
0.196
FLC
0.202
0.092
NN
0.192
0.091
Table 6 Numerical criteria for step changes in voltage reference 1 p u 1 1 p u 1 p u at an IAE
IAED
CCS
0.264
0.196
FLC
0.202
0.092
NN
0.192
0.091 Table 6. 3. Simulation results Numerical criteria for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at an
active power of 0.5 p.u. Table 6. Numerical criteria for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at an
active power of 0.5 p.u. 193 Synchronous Generator Advanced Control Strategies Simulation Synchronous Generator Advanced Control Strategies Simulation Fig. 17 presents active power responses for step changes in voltage reference from 1 p.u. to
0.9 p.u. and back to 1 p.u. at an active power of 0.8 p.u. The numerical criteria of the
responses in Fig. 17 are given in Table 7. Fig. 17 presents active power responses for step changes in voltage reference from 1 p.u. to
0.9 p.u. and back to 1 p.u. at an active power of 0.8 p.u. The numerical criteria of the
responses in Fig. 17 are given in Table 7. Fig. 17. Active power responses for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at
an active power of 0.8 p.u. Fig. 17. Active power responses for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at
an active power of 0.8 p.u. IAE
IAED
CCS
0.52
0.373
FLC
0.248
0.114
NN
0.219
0.106
Table 7 Numerical criteria for step changes in voltage reference 1 p u -0 9 p u -1 p u at an Table 7. Numerical criteria for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at an
active power of 0.8 p.u. Table 7. Numerical criteria for step changes in voltage reference 1 p.u.-0.9 p.u.-1 p.u. at an
active power of 0.8 p.u. Fig. 18 shows active power responses for step changes in voltage reference from 1 p.u. to 1.1
p.u. and back to 1 p.u. at an active power of 0.8 p.u. The numerical criteria of the responses
in Fig. 18 are given in Table 8. MATLAB – A Ubiquitous Tool for the Practical Engineer 194 Fig. 18. Active power responses for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at
an active power of 0.8 p.u. Fig. 18. Active power responses for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at
an active power of 0.8 p.u. IAE
IAED
CCS
0.312
0.234
FLC
0.130
0.097
NN
0.119
0.090
Table 8. Numerical criteria for step changes in voltage reference 1 p.u.-1.1 p.u.-1 p.u. at an
active power of 0.8 p.u. 3. Simulation results Based on the numerical criteria it can be concluded that the neural network-based controller
with stabilization effect in the criteria function has two to three percent better damping of
oscillations than the fuzzy logic controller. 4. Conclusion Also, using the software package Matlab Simulink allows users to easily test the
proposed algorithms. 4. Conclusion Three different structures for the excitation control of a synchronous generator were
simulated in Matlab Simulink: the first structure is a conventional control structure which
includes a PI voltage controller, while the second structure includes a fuzzy logic controller,
and the third structure includes a neural network-based voltage controller. Performances of
the proposed algorithms were tested for step changes in voltage reference in the excitation
system of a synchronous generator, which was connected to an AC network through a
transformer and a transmission line. For the performance analysis of the proposed control structures two numerical criteria were
used: the integral of absolute error and the integral of absolute error derivative. In the
comparison with the PI voltage controller neural network-based controller and the fuzzy
logic controller show a significant damping of oscillations. It is important to emphasize that Synchronous Generator Advanced Control Strategies Simulation 195 the stabilizer was not used in the conventional control structure, which would definitely
reduce the difference between the conventional and the proposed control structures. the stabilizer was not used in the conventional control structure, which would definitely
reduce the difference between the conventional and the proposed control structures. The simulation results show justification for the use of the advanced control structure based
l
k
d f
l
i
i
h
i
i
l
f
h the stabilizer was not used in the conventional control structure, which would definitely
reduce the difference between the conventional and the proposed control structures. the stabilizer was not used in the conventional control structure, which would definitely
reduce the difference between the conventional and the proposed control structures. The simulation results show justification for the use of the advanced control structure based
on neural networks and fuzzy logic in the excitation control system of a synchronous
generator. Also, using the software package Matlab Simulink allows users to easily test the
proposed algorithms. p
p
The simulation results show justification for the use of the advanced control structure based
on neural networks and fuzzy logic in the excitation control system of a synchronous
generator. Also, using the software package Matlab Simulink allows users to easily test the
proposed algorithms. The simulation results show justification for the use of the advanced control structure based
on neural networks and fuzzy logic in the excitation control system of a synchronous
generator. 5. References Akbari, S., & Karim Amooshahi, M. (2009). Power System Stabilizer Design Using
Evolutionary Algorithms, International Review of Electrical Engineering, 4, 5, (October
2009), pp. 925-931. Cao, Y., Jiang, L., Cheng, S., Chen, D., Malik, O.P., & Hope, G.S. (1994). A nonlinear variable
structure stabilizer for power system stability, IEEE Transactions on Energy
Conversion, 9, 3, (1994), pp. 489-495. Ghandra, A., Malik, & O. P., Hope, G.S. (1988). A self-tuning controller for the control of
multi-machine power systems, IEEE Trans. On Power Syst., 3, 3, (August 1988), pp. 1065-1071. Hassan, M.A., Malik, O.P., & Hope, G.S. (1991). A Fuzzy Logic Based Stabilizer for a
Synchronous Machine, IEEE Trans. Energy Conversion, 6, 3, (1991), pp. 407-413. Haykin, S. (1994). Neural Networks: A Comprehensive Foundation, IEEE Press Hiyama T., Oniki S., & Nagashima H. (1996). Evaluation of advanced fuzzy logic PSS on
analog network simulator and actual installation on hydro generators, IEEE Trans. on Energy Conversion, 11, 1, (1996), pp. 125-131. Hsu, Y.Y., & Liou, K.L. (1987). Design of self-tuning PID power system stabilizers for
synchronous generators, IEEE Trans. on Energy Conversion, 2, 3, (1987), pp. 343-
348. Jiang, Z. (2009). Design of a nonlinear power system stabilizer using synergetic control
theory, Electric Power Systems Research, 79, 6, (2009), pp. 855-862. Karnavas, Y.L., & Pantos, S. (2008). Performance evaluation of neural networks for µC
based excitation control of a synchronous generator, Proceedings of 18th
International Conference on Electrical Machines ICEM 2008, Portugal, September
2008. Karnavas, Y.L., & Papadopoulos, D. P. (2002). AGC for autonomous power system using
combined intelligent techniques, Electric Power Systems Research, 62, 3, (July 2002),
pp. 225-239. Kundur, P. (1994). Power System Stability and Control, McGraw-Hill Malik, O.P., Salem, M.M., Zaki, A.M., Mahgoub, O.A., & Abu El-Zahab, E. (2002). Experimental studies with simple neuro-controller based excitation controller,
IEE Proceedings Generation, Transmission and Distribution, 149, 1, (2002), pp. 108-
113. Noroozi, N., Khaki, B., & Seifi, A. (2008). Chaotic Oscillations Damping in Power System by
Finite Time Control, International Review of Electrical Engineering, 3, 6, (December
2008), pp. 1032-1038. MATLAB – A Ubiquitous Tool for the Practical Engineer 196 Salem, M.M., Malik, O.P., Zaki, A.M., Mahgoub, O.A., & Abu El-Zahab, E. (2003). Simple neuro-controller with modified error function for a synchronous
generator, Electrical Power and Energy Systems, 25, (2003), pp. 759-771. Salem, M.M., Zaki, A.M., Mahgoub, O.A., Abu El-Zahab, E., & Malik, O.P. (2000a). 5. References Studies on Multi-Machine Power System With a Neural Network Based
Excitation Controller, Proceedings of Power Engineering Society Summer Meeting,
2000. Salem, M.M., Zaki, A.M., Mahgoub, O.A., Abu El-Zahab, E., & Malik, O.P. (2000b). Experimental Veification of Generating Unit Excitation Neuro-Controller,
Proceedings of IEEE Power Engineering Society Winter Meeting, 2000. Shahgholian, G. (2010). Development of State Space Model and Control of the
STATCOM for Improvement of Damping in a Single-Machine Infinite-Bus,
International Review of Electrical Engineering, 5, 1, (February 2010), pp. 1367-1375. 11 1. Introduction These include the restriction or limitation of the shapes 198 MATLAB – A Ubiquitous Tool for the Practical Engineer of fuzzy sets implemented in the fuzzifier block, such as those in the controllers proposed in
(Hassan et al., 2007) and (Seng et al., 1999). It is desirable to simplify the structure of the
PIDFC controller to offer higher flexibility versus low-chip resources. The majority of PID
fuzzy controller applications belong to the direct action (DA) type; here the fuzzy inference
is used to compute the PID controller actions, not to tune the PID parameters (Mann et al.,
1999). Therefore, it is necessary to design a tuning method inside the digital fuzzy chip,
especially with the DA type, in order to scale the universe of discourse for the
inputs/outputs variable in the PIDFC, and to obtain the best tuning case in the operational
range. Changing the scaling gains at the input and output of PIDFC has a significant impact
on the performance of the resulting fuzzy control system, as well as the controller’s stability
and performance (Leonid et al., 2000). Therefore, it is necessary to use an optimization
method to calculate the optimal values of these gains. In recent years, several researchers
have designed fuzzy controllers with different ranges of accuracy. Most of these controllers
have 6-8 bits of accuracy (Poorani et al., 2005), (Tipsuwanpornet al., 2004), (Hassan et al.,
2007), (Solano et al., 1997), (Gabrielli et al., 2009). This accuracy has a trade off with the
speed of the process and it may affect the process behavior inside the digital fuzzy chip
(Jantzen, 1998), (Ibrahim, 2004). Furthermore, increasing the accuracy will also increase the
hardware complexity versus low-speed performance and vice versa. However, none have
evaluated the same controller with different ranges of accuracy. Hence, it is necessary to
find the best accuracy inside the digital chip that offers low hardware complexity versus
high-speed performance. The aim of this chapter is to design a PIDFC that can efficiently
replace other fuzzy controllers realized as a computer program, that have the ability to serve
a wide range of systems with real-time operations. To achieve this aim, the following points
are addressed: Ref No. 1. Introduction Fuzzy Logic controllers have been successfully applied in a large number of control
applications, with the most commonly used controller being the PID controller. Fuzzy logic
controllers provide an alternative to PID controllers, as they are a good tool for the control
of systems that are difficult to model. The control action in fuzzy logic controllers can be
expressed with simple “if-then” rules (Poorani et al., 2005). Fuzzy controllers are more
sufficient than classical controllers as they can cover a much wider range of operating
conditions than classical Controllers. In addition, fuzzy controllers operate with noise and
disturbances of a different nature. The common method for designing a fuzzy controller is
to realize it as a computer program. Higher density programmable logic devices, such as the
FPGA, can be used to integrate large amounts of logic in a single IC. The FPGA provides
greater flexibility than ASIC, and can be used with tighter time-to-market schedules. The
term programmable highlights the customization of the IC by the user. Many researchers
have discussed the design of the hardware implementation of fuzzy logic controllers. A
number was specialized for control applications, and aimed to get better control responses. These researches have concern using new techniques in fuzzy control, in order to get higher
processing speed versus low utilization of chip resource (Jain et al., 2009 and Islam et al.,
2007) The hardware implementation of fuzzy logic controllers has many requirements, such as
high-speed performance, low complexity and high flexibility (Leonid, 1997). With this type
of application, and to provide these requirements, it is necessary to avoid various limitations
and challenges. In deriving a practical PIDFC structure, it is desirable to reduce the number
of inputs. In addition, it is difficult to formulate the fuzzy rules with the variable sum of
error (
e
∑), as its steady-state value is unknown for most control problems (Mann et al.,
1999), (Hassan et al., 2007), (Obaid et al., 2009). Hence, it is necessary to design the FPGA-
based PIDFC with fewer inputs and rules to get higher processing speed versus low
utilization of chip resources. In addition, the design of digital fuzzy controllers has
limitations concerning the structure. 1. Introduction Controller type
Optimization and
tuning method
System Type
(Li and Hu , 1996)
PID with FIS
Tuned by FIS
Process control
(Tipsuwanpornet al.,
2004)
Gain scheduling
PID FC
Gain scheduling
Tuning method
Level and temperature
(Poorani et al., 2005)
Specific FC
6-inputs, 1-output
No method
Speed control of
electric vehicle
(Alvarez et al., 2006)
Optimal FC
2-inputs, 1-output
No method
Multi phase converter
(Gonzalez-Vazquez et
al, 2006)
PD FC
No method
No system
(Khatr and Rattan,
2006)
Multi-layered
PDFC
No method
Autonomous mobile
robot
(Hassan et al., 2007)
PID FC
No method
Linear system
(Jain et al., 2009)
Optimal PID
controller
Bacterial Foraging
Optimization method
Inverted pendulum
Table 1. Summary of the Related FPGA-Based Controller in the Literature Table 1. Summary of the Related FPGA-Based Controller in the Literature 199 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 1. To design a PIDFC with improved fuzzy algorithm that offers low implementation size
versus high processing speed. 1. To design a PIDFC with improved fuzzy algorithm that offers low implementation size
versus high processing speed. 1. To design a PIDFC with improved fuzzy algorithm that offers low implementation size
versus high processing speed. g
p
g p
2. To aid the PIDFC with a tuning gains block inside the FPGA chip that makes the design
able to accept PSO-based optimal scaling gains. 2. To aid the PIDFC with a tuning gains block inside the FPGA chip that makes the design
able to accept PSO-based optimal scaling gains. p
p
g g
3. To design two versions of the proposed PIDFC. The first one is an 8-bits PIDFC, while
the second one is a 6-bits PIDFC. g g
3. To design two versions of the proposed PIDFC. The first one is an 8-bits PIDFC, while
the second one is a 6-bits PIDFC. 4. To test the proposed design with different plants models with a unity feedback control
system. 4. To test the proposed design with different plants models with a unity feedback control
system. Many researchers have discussed different approaches to the present fuzzy algorithms that
offer high-processing speed and small chip size. Many of the fuzzy controllers implemented
in the literature using FPGA, have many limitations and challenges with the structure, such
as those in the shape of fuzzy sets implemented in the Fuzzifier block. This thesis will deal
with some of these limitations. 2. PID fuzzy logic controller A PID fuzzy controller is a controller that takes error, summation of error and rate of change
of error (rate for short) as inputs. Fuzzy controller with three inputs is difficult and not easy
to implement, because it needs a large number of rules and memory (Leonid, 1997). In the
proposed design, if each input is described with eight linguistic values, then 8x8x8=512
rules will be needed. The PIDFC can be constructed as a parallel structure of a PDFC and a
PIFC, and the output of the PIDFC is formed by algebraically adding the outputs of the two
fuzzy control blocks (Leonid, 1997). In deriving a practical PIDFC structure, the following
remarks are made (Hassan et al., 2007) (Mann et al., 1999), (Leonid, 1997), (Obaid et al.,
2009): Remark 1: For any PIDFC, the error (e) is considered as the necessary input for
deriving any PID structure. Remark 2: It is difficult to formulate control rules with the input
variable sum-of-error ∑e, as its steady-state value is unknown for most control problems. To
overcome the problem stated in remark 2, a PDFC may be employed to serve as a PIFC in
incremental form, where a PD fuzzy logic controller, with summation at its output, is used
instead of the PIFC (Hassan et al., 2007), (Obaid et al., 1999). 1. Introduction Table I lists the related FPGA-based controllers in the
literature, highlighting the tuning and optimization methods used as well as the type of
application and the type of controller. 3. Particle swarm optimization PSO is an evolutionary computation technique-based developed by Eberhart and Kennedy
in 1995 (Wang et al., 2006). It was inspired by the social behavior of birds flocking or fish
schooling, more specifically, the collective behaviors of simple individuals interacting with
their environment and each other (Wang et al., 2006). PSO has been successfully applied in
many areas: function optimization, artificial neural network training, fuzzy system control,
and other areas where evolutionary computation can be applied. Similar to evolutionary
computation (EC), PSO is a population-based optimization tool (Wang et al., 2006), (Allaoua
et al., 2009). The system is initialized with a population of random solutions and searches for
optima by updating generations. All of the particles have fitness values that are evaluated
by the fitness function to be optimized, and have velocities that direct the flying of the
particles (Wang et al., 2006). In a PSO system, particles change their positions by flying
around in a multidimensional search space until computational limitations are exceeded. 200 MATLAB – A Ubiquitous Tool for the Practical Engineer The concept of the modification of a searching point by PSO is shown in Fig. 1 (Allaoua et
al., 2009). The concept of the modification of a searching point by PSO is shown in Fig. 1 (Allaoua et
al., 2009). Fig. 1. Concept of the Modification of a Searching Point by PSO (Allaoua et al., 2009). 1
+
k
i
X
i
Gbest
i
Pbest
k
iV
k
i
X
1
+
k
iV
Gbest
iV
Pbest
iV Fig. 1. Concept of the Modification of a Searching Point by PSO (Allaoua et al., 2009). In the PSO algorithm, instead of using evolutionary operators such as mutation and
crossover, to manipulate algorithms, for a d-variable optimization problem, a flock of
particles are put into the d-dimensional search space with randomly chosen velocities and
positions knowing their best values so far (Pbest) and the position in the d-dimensional
space. The velocity of each particle, adjusted according to its own flying experience and the
other particle’s flying experience. For example, the i-th particle is represented as xi = (xi, 1,
xi, 2… xi, d) in the d-dimensional space. The best previous position of the i-th particle is
recorded and represented as (Allaoua et al., 2009): Pbesti = (Pbesti, 1, Pbesti, 2 ... Pbest i, d)
(1) Pbesti = (Pbesti, 1, Pbesti, 2 ... Pbest i, d)
(1) (1) The index of best particle among all of the particles in the group is gbestd. The velocity for
particle i is represented as vi = (vi,1 ,vi,2 ,…, vi,d). The modified velocity and position of each
particle can be calculated using the current velocity and the distance from Pbesti, d to gbestd
as shown in the following formulas (Allaoua et al., 2009): (
1)
( )
( )
( )
,
,
1
,
,
2
,
. *
() * (
)
*
() * (
)
t
t
t
t
i m
i m
i m
i m
m
i m
V
W V
c
rand
Pbest
X
c
rand
gbest
X
+
=
+
−
+
−
(2)
(
1)
( )
(
1)
,
,
,
t
t
t
i m
i m
i m
X
X
V
+
+
=
+
; i= 1, 2… n; m=1, 2… d
(3) (
1)
( )
( )
( )
,
,
1
,
,
2
,
. *
() * (
)
*
() * (
)
t
t
t
t
i m
i m
i m
i m
m
i m
V
W V
c
rand
Pbest
X
c
rand
gbest
X
+
=
+
−
+
−
(2) (2) (
1)
( )
(
1)
,
,
,
t
t
t
i m
i m
i m
X
X
V
+
+
=
+
; i= 1, 2… n; m=1, 2… d (3) Where: N: Number of particles in the group, N: Number of particles in the group, p
D: dimension, D: dimension, t: Pointer of iterations (generations), ( )
,
t
i m
V
: Velocity of particle I at iteration t,
( )
min
max
,
t
d
i m
d
V
V
V
≤
≤ W: Inertia weight factor, c1, c2: Acceleration constant, rand ( ): Random number between 0 and 1 ( )
,
t
i m
X
: Current position of particle i at iterations, Pbesti: Best previous position of i-th particle, Gbest: Best particle among all the particles in the population. 201 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 5. Block diagram of the PIDFC The proposed controller accepts two signals, the first one is the plant output (
p
y ) and the
second one is the desired output (
dy ), both of them are digital signals, and deliver the
control action signal as a digital output. It also accepts four 8-bit digital signals that
represent the optimal gain parameters needed by the controller (
p
K ,
d
K ,
i
K , and
o
K ). These
parameters are used to aid the tuning block with optimal values of the scaling gains online
with the digital FPGA chip. Other two (one-bit) signals have been used to select the type of
the controller (PDFC, PIFC, or PIDFC) online with the chip. Fig. 3 shows the general block
diagram of the controller chip in a unity feedback control system. In recent years, many of
the digital fuzzy applications have different ranges of the accuracy. Most of them have 6-8
bits of accuracy (Poorani et al., 2005), (Tipsuwanpornet al., 2004), (Hassan et al., 2007),
(Solano et al., 1997), (Gabrielli et al., 2009), (Obaid et al., 2009), (Obaid et al., 1999). This
accuracy may affect the process behavior inside the digital fuzzy chip; also it has a trade off
with the speed of the process (Leonid , 1997), (Jantzen, 1998), (Ibrahim, 2004). Therefore, it is
necessary to find which range has better accuracy inside the digital chip. Two versions of
the proposed PIDFC were designed, the first one is an 8-bit which uses 8 bits for each
input/output variables. The second version is a 6-bit which uses 6 bits for each
input/output variable. To make the discussion clear and general for the proposed controller
in the following sections, symbol (q) will be used to represent the range of accuracy, (q=8) in
the proposed 8-bits design, and (q=6) in the 6-bits version of the proposed design. 4. The proposed PSO algorithm The main aim of the PSO algorithm is to tune the controller parameters [Kp, Kd, Ki, Ko], by
minimizing the cost function for minimum values in order to get the optimal gains value for
these parameters. The target cost function is the integral square error (ISE), this is simple
function and can easy represented in the fuzzy algorithm. The cost function (equation 4) is
calculated by swapping the searching results in the local position with the minimum value
of the function until reaching the best global search. In this case, the proposed PSO
algorithm is 6-dimension in the population size for PIDFC (also can do it by 4-dimenssion),
3-dimension in the case of the PIFC and PDFC. This dimension belongs to the controller
parameters, which represent the particle (X) inside the population space. These particles are
explained in equations (5, 6 and 7) with ith iteration path. Note that during the search
process the resulting gains were constrained by the interval [Xmin Xmax] to search with
these limits in order to cover the range of the operational range (universe of discourse). Fig. 2 shows the flow chart of the proposed PSO algorithm. Fig. 2. Flowchart of the Proposed PSO Algorithm Fig. 2. Flowchart of the Proposed PSO Algorithm 202 MATLAB – A Ubiquitous Tool for the Practical Engineer 2
0
( ( ))
Maxiteration
t
ISE
e t
=
= ∑
(4)
X(PIDFC)= [x(1) x(2) x(3) x(4) x(5) x(6)]=
[Kp Kd Ko + Kp Ki Ko] , Dimension = 6
(5)
X(PIFC)= [x(1) x(2) x(3)]= [Kp Ki Ko] , Dimension = 3
(6)
X(PDFC)= [x(1) x(2) x(3)]= [Kp Kd Ko] , Dimension = 3
(7) 2
0
( ( ))
Maxiteration
t
ISE
e t
=
= ∑
(4) (4) X(PIDFC)= [x(1) x(2) x(3) x(4) x(5) x(6)]=
( ) (5) (7) 6. Structure of the PIDFC design Generally, to represent PIDFC, it is required to design a fuzzy inference system with three
inputs that represent the proportional, derivative, and integral components, and each one of
them can have up to eight fuzzy sets. Therefore, the maximum number of the required fuzzy
rules is 83=512 rules. To avoid this huge number of rules, the proposed controller was
designed using two parallel PDFC to design the PIDFC as discussed earlier (Hassan et al.,
2007), (Obaid et al., 2009), (Obaid et al., 1999). The second PDFC was converted to a PIFC by
accumulating its output. Fig. 4 shows the structure of proposed PIDFC, where FIS refers to
the fuzzy inference system with its three blocks, Fuzzifier, inference engine and defuzzifier. Both controllers, PDFC and PIFC, receive the same error signal. The structure of the single
PDFC is discussed in the next sections. The main block in the PDFC is the fuzzy inference
block which has two inputs (e(n) and
( )
e n
Δ
), one output (U(n)) fuzzy system of Mamdani 203 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA type that uses singleton membership functions for the output variable. Initially, the two
input signals are multiplied by a gain coefficient (Kp and Kd or Kp and Ki) before entering the
fuzzy inference block. Similarly, the output of the fuzzy inference block is multiplied by a
gain coefficient (Ko) (Hassan et al., 2007), (Obaid et al., 2009), (Obaid et al., 1999). At the same
time, the output of the fuzzy inference block in the second PDFC is multiplied by a gain
coefficient and then accumulated to give the output of the PIFC. Subsequently, both outputs
of the PDFC and PIFC are added together to give the PIDFC output (uPID). The final design
works as a PDFC, PIFC, or PIDFC, depending on the two selection lines sw1 and sw0,, which
provide a more flexible design to cover a wide range of systems. The PIDFC is designed
using two blocks of PDFC, and the main block in the proposed design is the PDFC block. The main components inside the PDFC block are: Tuning-gain block, Fuzzifier block, inference
engine block, and Defuzzifier block. type that uses singleton membership functions for the output variable. Initially, the two
input signals are multiplied by a gain coefficient (Kp and Kd or Kp and Ki) before entering the
fuzzy inference block. 6. Structure of the PIDFC design Similarly, the output of the fuzzy inference block is multiplied by a
gain coefficient (Ko) (Hassan et al., 2007), (Obaid et al., 2009), (Obaid et al., 1999). At the same
time, the output of the fuzzy inference block in the second PDFC is multiplied by a gain
coefficient and then accumulated to give the output of the PIFC. Subsequently, both outputs
of the PDFC and PIFC are added together to give the PIDFC output (uPID). The final design
works as a PDFC, PIFC, or PIDFC, depending on the two selection lines sw1 and sw0,, which
provide a more flexible design to cover a wide range of systems. The PIDFC is designed
using two blocks of PDFC, and the main block in the proposed design is the PDFC block. The main components inside the PDFC block are: Tuning-gain block, Fuzzifier block, inference
engine block, and Defuzzifier block. Fig. 3. Block Diagram of the PIDFC in a Unity Feedback Control System. Fig. 4. Main structure of the Proposed Controller Fig. 3. Block Diagram of the PIDFC in a Unity Feedback Control System. g. 3. Block Diagram of the PIDFC in a Unity Feedback Control System. Fig. 3. Block Diagram of the PIDFC in a Unity Feedback Control System. Fig. 4. Main structure of the Proposed Controller Fig. 4. Main structure of the Proposed Controller Fig. 4. Main structure of the Proposed Controller 204 MATLAB – A Ubiquitous Tool for the Practical Engineer Tuning-Gain Block The tuning-gain block is used at each of the two inputs and also at the output of each PDFC
block. This block receives and multiplies two inputs: the variable to be scaled (input or
output) and its related gains, this implies the proposed tuning method via scaling the
universe of discourse. An eight-bit latch was used at each Tuning-gain block to store the
gain coefficient value received from one of the gain ports, depending on selection line
values. The “*” operator was used in the VHDL files of the design to express a
multiplication process just like a conventional language. This process has been designed at
the behavioral level of abstraction in VHDL code, i.e. during the design synthesis process, if
the library “IEEE.std_logic_signed” was included in the VHDL files (Hassan et al., 2007),
(Obaid et al., 2009), (Obaid et al., 1999). Fig. 5 shows the Tuning-gain block with more
details. Fig. 5. Input/Output Tuning Block
Every “*” operator is synthesized to a signed number multiplier directly (Hassan et al., 2007),
(Obaid et al., 2009), (Obaid et al., 1999). Fig. 6 shows the Tuning-gain block with more
details. The fuzzy inference block in each PDFC can handle positive values only, and the
error and its rate signals can have positive and negative values (Hassan et al., 2007), as the
shifting process has been designed to convert the input variables range from
[
1
1
2
2
1
q
q
−
−
−
→
−
] to [ 0
2
1
q
→
−
]. This process implies adding the number (
1
2
q−) to the input
variable. This addition has been designed by inverting the last bit (MSB) of the input
variable (Hassan et al., 2007), (Obaid et al., 2009), (Obaid et al., 1999). The shift process at the Fig. 5. Input/Output Tuning Block Every “*” operator is synthesized to a signed number multiplier directly (Hassan et al., 2007),
(Obaid et al., 2009), (Obaid et al., 1999). Fig. 6 shows the Tuning-gain block with more
details. Tuning-Gain Block The fuzzy inference block in each PDFC can handle positive values only, and the
error and its rate signals can have positive and negative values (Hassan et al., 2007), as the
shifting process has been designed to convert the input variables range from
[
1
1
2
2
1
q
q
−
−
−
→
−
] to [ 0
2
1
q
→
−
]. This process implies adding the number (
1
2
q−) to the input
variable. This addition has been designed by inverting the last bit (MSB) of the input
variable (Hassan et al., 2007), (Obaid et al., 2009), (Obaid et al., 1999). The shift process at the Every “*” operator is synthesized to a signed number multiplier directly (Hassan et al., 2007),
(Obaid et al., 2009), (Obaid et al., 1999). Fig. 6 shows the Tuning-gain block with more
details. The fuzzy inference block in each PDFC can handle positive values only, and the
error and its rate signals can have positive and negative values (Hassan et al., 2007), as the
shifting process has been designed to convert the input variables range from
[
1
1
2
2
1
q
q
−
−
−
→
−
] to [ 0
2
1
q
→
−
]. This process implies adding the number (
1
2
q−) to the input
variable. This addition has been designed by inverting the last bit (MSB) of the input
variable (Hassan et al., 2007), (Obaid et al., 2009), (Obaid et al., 1999). The shift process at the 205 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA output has been designed using subtraction, instead of addition, to convert the range of the
output variable from [ 0
2
1
q
→
−
] to [
1
1
2
2
1
q
q
−
−
−
→
−
]. This specification will increase the
flexibility of the proposed design. Fuzzifier Block The overlapping degree (V) in the proposed design is two, which means that at each time
instance there are two active, (have nonzero membership values), fuzzy sets for each input
variable at maximum. The proposed fuzzification process has been designed using two
fuzzifier blocks, one for each input variable. The fuzzifier block implies the fuzzification
process by taking the input and producing four output values. These values represent the
sequence numbers of the two active fuzzy sets (e1, e2 and de1, de2) and the membership
degrees of the variable for each one of them (μe1, μe2 and μde1, μde2 ). The memory base
was designed using ROM. The use of ROM is better than RAM when the programmability is
directly achieved by the implementation techniques (as in the case of FPGA) (Barriga et al.,
2006). The fuzzifier block was designed using memory based membership functions
(MBMSF) (Solano et al., 1997), (Barriga et al., 2006). This method reduces the restrictions of
the fuzzy set shapes, even it needs a smaller memory size than other method such as the
arithmetic method. The memory model has been implemented with maximum possible
membership values in the proposed design, where the maximum coded in p values is
( 2
1
p −
), where p=4 bits in the 6-bits version of the PIDFC, and p=6 bits in the 8-bits version
of the PIDFC. This dictates that the summation of membership values of two consecutive
fuzzy set is always equal to ( 2
1
p −
). Each word in the MBMSF is divided into two parts. The
first part represents the sequence number of the active fuzzy set (3-bits, in both versions). Assigning 3 bits for the sequence number of the fuzzy sets, gives the controller flexibility to
accept for each input variable for up-to 8 fuzzy sets. The second part of the memory word is
p bits data word which represents the membership value of the input in the active fuzzy set. The total memory length for each input is equal to ( 2
q ). Fig. 6. Two Inputs Fuzzifier Block. Fig. 6. Two Inputs Fuzzifier Block. 206 MATLAB – A Ubiquitous Tool for the Practical Engineer Inference Engine Block The inference engine consists of three blocks: rule selector, rule memory, and minimum circuit as
shown in Fig. 7. Different mechanisms have been used to minimize both the calculation time
and the area of the fuzzy inference system; among the most interesting methods is the active
rules selector concept (Hassan et al., 2007), (Solano et al., 1997), (Obaid et al., 2009), (Barriga
et al., 2006), (Huang and Lai, 2005), (Obaid et al., 1999). This block uses the information from
fuzzifier, which belongs to the active fuzzy sets to launch only active rules. This reduces the
number of processed rules. Furthermore, by using an active rule selector, the number of
rules to be processed will be reduced according to this equation (Hassan et al., 2007): Fig. 7. Inference Engine Block Fig. 7. Inference Engine Block Number of active rules =
m
V
(8) Number of active rules =
m
V
(8) Number of active rules =
m
V Number of active rules =
m
V (8) Where m is the number of inputs, and V is the maximum number of overlapped fuzzy sets. In the proposed design, it is assumed that m = 2 and V = 2. Hence, the number of active
rules at each time is:
2
2
4
m
V
=
=
rules. In each counter cycle, the membership degrees
delivered from the two multiplexers are combined through the minimum circuit to calculate
the applicability degree of the rule (µk), while the active fuzzy set sequence numbers are
combined directly to address a rule memory location that contains the corresponding rule
consequent (ßk). The rule memory is a (
2 3
2
q
× ×
) bits ROM, and each word in it represents the
position of the output singleton membership functions of one rule. Defuzzifier Block The defuzzification process in the defuzzifier block has been designed using the Centroid
method. The four main components that represent the proposed defuzzifier are: two
accumulators, one multiplier, and one divider. The defuzzifier block accepts the information
from the inference engine (four (µk), and four (ßk) each time), and produces an output (crisp
set) to the output –tuning gain block, as shown in Fig. 8. 207 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA Fig. 8. Defuzzifier Block. e
NB
NM
NS
NZ
PZ
PS
PM
PB
de
NB
-1
-1
-1
-0.7
-0.7
-0.4
-0.1
0.1
NM
-1
-1
-0.7
-0.7
-0.4
-0.1
0.1
0.1
NS
-1
-0.7
-0.7
-0.4
-0.1
0.1
0.1
0.4
NZ
-0.7
-0.7
-0.4
-0.1
0.1
0.1
0.4
0.7
PZ
-0.7
-0.4
-0.1
-0.1
0.1
0.4
0.7
0.7
PS
-0.4
-0.1
-0.1
0.1
0.4
0.7
0.7
1
PM
-0.1
-0.1
0.1
0.4
0.7
0.7
1
1
PB
-0.1
0.1
0.4
0.7
0.7
1
1
1
Table 2. Fuzzy Rules. The defuzzifier block was designed with two stages to reduce the memory size of the target
device. Both accumulators are reset every four clock cycles to receive the next four active
rules of the next input. Note that µk and ßk are delivered from the inference engine in series
during four consecutive clock cycles, instead of being produced in parallel in one clock Fig. 8. Defuzzifier Block. Fig. 8. Defuzzifier Block. Fig. 8. Defuzzifier Block. Fig. 8. Defuzzifier Block. e
NB
NM
NS
NZ
PZ
PS
PM
PB
de
NB
-1
-1
-1
-0.7
-0.7
-0.4
-0.1
0.1
NM
-1
-1
-0.7
-0.7
-0.4
-0.1
0.1
0.1
NS
-1
-0.7
-0.7
-0.4
-0.1
0.1
0.1
0.4
NZ
-0.7
-0.7
-0.4
-0.1
0.1
0.1
0.4
0.7
PZ
-0.7
-0.4
-0.1
-0.1
0.1
0.4
0.7
0.7
PS
-0.4
-0.1
-0.1
0.1
0.4
0.7
0.7
1
PM
-0.1
-0.1
0.1
0.4
0.7
0.7
1
1
PB
-0.1
0.1
0.4
0.7
0.7
1
1
1
Table 2. Fuzzy Rules. The defuzzifier block was designed with two stages to reduce the memory size of the target
device. Both accumulators are reset every four clock cycles to receive the next four active
rules of the next input. Note that µk and ßk are delivered from the inference engine in series
during four consecutive clock cycles, instead of being produced in parallel in one clock
cycle. Defuzzifier Block This will reduce the used area of the FPGA device, at the expense of increasing time
interval between input latching and output producing (Hassan et al., 2007). However,
during the design, whenever a trade off between area and speed is found, it is directed to
optimize (reduce) area at the expense of speed reduction, since the maximum time delay
caused by controller is still much less than the minimum sampling time in many control
systems. Even less than other controllers proposed in the literature (Poorani et al., 2005),
(Tipsuwanpornet al., 2004), (Hassan et al., 2007), (Obaid et al., 2009), (Alvarez et al., 2006),
(Lund et al., 2006), (Obaid et al., 1999). Here, the multiplication process was designed at the
behavioral level (the method used in the tuning-gain block). The only difference is that
another library called “IEEE.std_logic_unsigned” must be used instead of the library
“IEEE.std_logic_signed”, to ensure that the produced multiplier after the synthesis process is
an unsigned number multiplier (because the proposed fuzzy inference block can only
handle positive numbers only) (Hassan et al., 2007), (Obaid et al., 2009). The group involves
eight triangular membership functions for each input variable, eight singleton membership
functions for output variable, and the rule table of 64 rules has been used in the proposed 208 MATLAB – A Ubiquitous Tool for the Practical Engineer PIDFC, as shown in Fig. 9 and Table II. The use of a singleton membership function is to
increase the computation speed versus low complexity (Leonid , 1997). And also for the
majority of applications, using singleton fuzzy sets is more sufficient (Ying, 2000). PIDFC, as shown in Fig. 9 and Table II. The use of a singleton membership function is to
increase the computation speed versus low complexity (Leonid , 1997). And also for the
majority of applications, using singleton fuzzy sets is more sufficient (Ying, 2000). Fig. 9. (a) Inputs Membership Functions, (b) Output Membership Functions. Fig. 9. (a) Inputs Membership Functions, (b) Output Membership Functions. 7. FPGA design considerations The proposed device for the hardware implementation is the Virtex FPGAs family from
Xilinx Company. Vertex FPGAs family is a useful device to the proposed design, it has
internal RAM block. Virtex FPGAs consist of several large block memories. These
complement the Look Up Table (LUT). This performance is very useful because the fuzzy
system always needs large memory to store fuzzy sets information and rules table (Xilinx
Company, 2009). The final design of the PIDFC has (3*q + 36) pins, four 8-bit input ports,
two q-bits input ports and one q-bit output ports as well as 4 control signal pins, Table (III)
lists the port names, sizes, and types. Port name
Port size (bit)
Port type
Desired output
q
Input data
Plant output
q
Input data
Control action
q
Output data
Kp
8
Input data
Kd
8
Input data
Ki
8
Input data
Ko
8
Input data
sw1
1
Control signal
sw0
1
Control signal
Reset
1
Control signal
Clock
1
Control signal
Table 3. Port Names, Sizes, and Types Which Used In the Proposed Controlle Port name
Port size (bit)
Port type
Desired output
q
Input data
Plant output
q
Input data
Control action
q
Output data
Kp
8
Input data
Kd
8
Input data
Ki
8
Input data
Ko
8
Input data
sw1
1
Control signal
sw0
1
Control signal
Reset
1
Control signal
Clock
1
Control signal
Table 3. Port Names, Sizes, and Types Which Used In the Proposed Controller. Table 3. Port Names, Sizes, and Types Which Used In the Proposed Controller. Table 3. Port Names, Sizes, and Types Which Used In the Proposed Controller. 209 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA Note that the Reset signal does not change the contents of ROM or gain coefficients latches. However, the contents of ROM, as stated before can not be altered during the operation of
the controller. The clock speed has a maximum frequency of 40 MH. This is necessary to
cover a wide range of systems with a high sampling time. 8. Simulation environments The Altera Quartus II 9.0 program was used to get the compilation and timing test results as
well as the synthesized design. The ModelSim simulation program was also used for the
purpose of simulation for all tests with the proposed design. The same design was designed
in Matlab environments in order to make comparisons. The ModelSim stores the simulation
data in text files, these files are used in Matlab and convert it to decimal vectors, which are
used to plot the analog responses. Fig. 10 shows the Coding and Simulation environments
used with the proposed design. Fig. 10. Coding and Simulation Environments. Fig. 10. Coding and Simulation Environments. 9. Timing analysis The overall structure of the proposed PIDFC needs 16 clock cycles to complete one process. The input tuning-gain block needs one clock cycle. The fuzzification process needs one clock
cycle. The inference engine needs four clock cycles to generate the four active rules
consequent,
1
2
3
4
,
,
,
β
β
β
β and their corresponding applicability degrees
1
2
3
4
,
,
,
μ
μ
μ μ . Another four clock cycles are needed to calculate the terms
4
k
μ
∑
and
4
k
k
μ
β
×
∑
. Three of The overall structure of the proposed PIDFC needs 16 clock cycles to complete one process. The input tuning-gain block needs one clock cycle. The fuzzification process needs one clock
cycle. The inference engine needs four clock cycles to generate the four active rules
consequent,
1
2
3
4
,
,
,
β
β
β
β and their corresponding applicability degrees
1
2
3
4
,
,
,
μ
μ
μ μ . Another four clock cycles are needed to calculate the terms
4
1
k
k
μ
=∑
and
4
1
k
k
k
μ
β
=
×
∑
. Three of
these four clocks are parallel to the four clocks of the inference engine, because the
accumulation process starts after delivering the first rule consequent
1
β and its applicability
degree
1
μ . Subsequently, the division process starts and it takes eight clock cycles, which
are split into two four-clock stages. The last clock cycle is needed to perform the output
tuning gain block these four clocks are parallel to the four clocks of the inference engine, because the
accumulation process starts after delivering the first rule consequent
1
β and its applicability
degree
1
μ . Subsequently, the division process starts and it takes eight clock cycles, which
are split into two four-clock stages. The last clock cycle is needed to perform the output
tuning-gain block. 210 MATLAB – A Ubiquitous Tool for the Practical Engineer 10. Control surfaces test (comparison case study) This test is performed to make sure that the fuzzy inference system used inside the FPGA-
based controller (FBC) is working properly. This test involves generating the control surface
using fuzzy sets and the rule shown in Fig. 9 and Table 2. This test has been used to make a
comparison between both types of FBC with MSBC in order to evaluate the accuracy of the
digital design implemented on FPGA with respect to the Matlab design. The control surfaces
generated by MSBPD, 6FBC, MSBC and 8FBC are shown in Fig. 11 and Fig. 12. This surface
reveals the effect of rounding and approximation processes (inside the FPGA design) on the
result and also shows the accuracy of each version of the controller with respect to the
Matlab-Based design. Generally, these statistics show that the surfaces generated by the
fuzzy inference system of 8FBC are smoother than the surfaces generated by the fuzzy
inference system of 6FBC with respect to MSBC, since the 8FBC has better accuracy and is
adequate for this design. Fig. 11. (a) Control surface of MSBC (b) Control surface of 6FBC Fig. 11. (a) Control surface of MSBC (b) Control surface of 6FBC Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 211 Fig. 12. (a) Control surface of MSBC (b) Control surface of 8FBC g. 12. (a) Control surface of MSBC (b) Control surface of 8FBC 11. The proposed controller with unity feedback control system As mentioned before, the simplest and most usual way to implement a fuzzy controller is to
realize it as a computer program on general purpose computers. Therefore, a comparison
has been made between the simulation results of the two FPGA-based controller versions. The 6 bits FPGA-Based Controller (6FBC) and the 8 bits FPGA-Based Controller (8FBC), and
the simulation results of the Software Base Controller designed using Matlab (MSBC). These
comparisons are necessary to show that how FPGA-based design is close to Matlab-based
design. The first level of this comparison was made using ModelSim as the test bench
simulation before generating the results in a Text File. Subsequently, as explained before,
these files were taken to the Matlab environment to do the comparison. The controllers 212 MATLAB – A Ubiquitous Tool for the Practical Engineer (6FBC, 8FBC, and MSBC) have been used in unity feedback control systems, and subjected
to 0.5 step input. Mathematical models of five different plants have been used for this test. These consist of four case studies with linear systems and one case study with a nonlinear
system. Each one of these plants has been designed in MATLAB software (for simulation in
MATLAB), and also in non-synthesizable VHDL code (for simulation in ModelSim). Since
each controller could serve as PDFC, PIFC, or PIDFC, a test was made for each one of these
types. PSO was used to obtain the optimal values of the controller parameters that represent
the tuning gains. Where the information of the proposed PSO algorithm is listed as follows:
Population size: 100, W= [0.4 to 0.9], C1, C2=2, Iteration reached with every case is=1000
iteration path, and the particle searching range depends on the trial and is different in every
case. All X-axes represent the time. Table 4. Optimal Gains Values Used With Cs1. 11.1 First order plant (first case study) p
(
y)
Many industrial processes such as level process can be represented by a first order model
(Hu et al., 1999). Equation (9) shows the mathematical plant model (in s-plane). A discrete
transfer function of this model has been obtained using the ZOH method, and the selected
sampling period (T) is 0.1. Equation (10) shows the discrete transfer functions, (in z-plane). The searching range of the particle for this case ranges from [Xmin Xmax], and by using trial
to reach the operational range with the universe of discourse. The optimal values of Kp, Kd,
Ki, and Ko used in this test were selected using PSO; and listed in Table 4. ( )
1
1
1
CS
s
s
=
+
(9) (9) ( )
1
0.09516
0.9048
CS
z
z
=
−
, T = 0.1
(10) (10) Range of Particle X
Controller type
Gain type
Value
0.0001
5
X
≤
≤
PIDFC
Kp
4.5111
Kd
0.8751
Ki
4.6875
Ko
0.5625
0.0001
3.5
X
≤
≤
PIFC
Kp
0.6875
Ki
2.4375
Ko
1.0212
0.0001
15
X
≤
≤
PDFC
Kp
13.7501
Kd
0.6251
Ko
0.5011
Table 4. Optimal Gains Values Used With Cs1. Table 4. Optimal Gains Values Used With Cs1. Table 4. Optimal Gains Values Used With Cs1. 213 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA Fig. 13 shows the test bench simulation results using ModelSim. This test is generated using
non-synthesizable VHDL code, and the controller gives action at 0.3 µs. The 6FBC has the
same procedure except the real data which has different values. ModelSim stores the results
as digital data in a text file; this file is manipulated in Matlab environments to change the
data to decimal before using it as a comparison. The closed loop responses with 0.5 step
input are shown in Fig. 14. In Fig. 14-a, it seems that the response has a large study state
error. This is because the controller is PDFC, this controller affects the transient response
(rise time, overshoot), but has no effect on the steady state error (at most). When the PIFC is
applied on the first order system, the error disappears, and the system is first order, since
there is no overshoot in this system (Fig. 14-b). When the PIDFC is applied for this system,
as shown in Fig. 14-c, the response has a fast rising time with zero overshoot and error. 11.1 First order plant (first case study) However, although the 6FBC can sometimes give a response close to the MSBC response, at
most, the 8FBC has smoother responses to MSBC than the 6FBC. The response performance
of the proposed controllers is listed in Table 5. Controller type
Error
Over shoot
Rising time
Settling time
PDFC
0.025
0.0
0.89
0.1
PIFC
0.0
0.0
0.3
0.4
PIDFC
0.0
0.0
0.15
0.198
Table 5. Responses Performance of the Proposed 8fbc with Cs1. Table 5. Responses Performance of the Proposed 8fbc with Cs1. Fig. 13. Test Bench Results using ModelSim of the Proposed Controller (8FBC) with CS1 in
unity Feedback Control system. Fig. 13. Test Bench Results using ModelSim of the Proposed Controller (8FBC) with CS1 in
unity Feedback Control system. MATLAB – A Ubiquitous Tool for the Practical Engineer 214 (a)
(b) (a)
(b) (a) Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 215 (c)
Fig. 14. First Order Linear Plant Controlled by (a) PDFC, (b) PIFC and (c) PIDFC. (c) Fig. 14. First Order Linear Plant Controlled by (a) PDFC, (b) PIFC and (c) PIDFC. 11.2 Delayed first order plant (second case study) Table 6. Optimal Gains Values Used With CS2. l Gains Values Used With CS2. 1.2 Delayed first order plant (second case study) y
p
(
y)
The time delay occurs when a sensor or an actuator is used with a physical separation (Hu
et al., 1999). Equation (11) shows the mathematical plant model (in s-plane). The discrete
transfer functions of this model were obtained using the ZOH method, and the selected
sampling period (T) is 0.1. Equation (12) shows the discrete transfer functions, (in z-plane). The searching range of the particle for this case is [Xmin Xmax], and by using trial to reach
the operational range with the universe of discourse. The optimal values of Kp, Kd, Ki, and Ko
used in this test were selected using PSO; and listed in Table 6. Range of Particle X
Controller type
Gain type
Value
0.0001
1.9
X
≤
≤
PIDFC
Kp
1.4372
Kd
1.687
Ki
0.5625
Ko
0.437
0.0001
1.9
X
≤
≤
PIFC
Kp
0.501
Ki
1.5
Ko
0.51
0.0001
6
X
≤
≤
PDFC
Kp
5
Kd
0.125
Ko
0.375
Table 6. Optimal Gains Values Used With CS2. 216 MATLAB – A Ubiquitous Tool for the Practical Engineer ( )
( )
2
2
1
CS
z
z
CS
z
−
=
×
(11)
( )
2
2
0.09516
0.9048
CS
z
z
z
−
⎛
⎞
=
×⎜
⎟
−
⎝
⎠
, T = 0.1
(12) (11) (12) Fig. 15 shows the test bench simulation results using ModelSim. This test is generated in the
same procedure as explained before. The controller gives action at 0.3 µs (Fig. 15), the delay
with the systems affects the beginning of the real data (the response). The closed loop
responses with 0.5 step input are shown in Fig. 16. In Fig. 16-a, again the response has a
large study state error with the PDFC. When the PIFC is applied on the first order system
(see Fig. 16-b), the error disappears with 8FBC. The 6FBC has a large steady state error, as
the responses of the systems that use 8FBC are closer to the MSBC responses. When the
PIDFC is applied for this system, as shown in Fig. 16-c, the response is close to the responses
when using the PIFC. In all this, 8FBC has smoother responses to the MSBC than the 6FBC. The responses performance of the 8FBC are listed in Table 7. Fig. 15. Timing Diagram using ModelSim of the Controller (8FBC) with CS2 in unity
Feedback Control system. Fig. 15. Table 7. Responses Performance of the Proposed 8fbc with CS2. MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer (c)
Fig. 16. Delayed first order linear plant controlled by(a) PDFC, (b) PIFC and (c) PIDFC. (c) g. 16. Delayed first order linear plant controlled by(a) PDFC, (b) PIFC and (c) PIDFC. 1.2 Delayed first order plant (second case study) Timing Diagram using ModelSim of the Controller (8FBC) with CS2 in unity
Feedback Control system. Controller
type
Error
Over
shoot
Rising
time
Settling
time
PDFC
0.11
0.01
1.12
1.2
PIFC
0.01
0.0
0.8
0.9
PIDFC
0.02
0.0
0.48
0.49
Table 7. Responses Performance of the Proposed 8fbc with CS2. Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 217 (a) (a)
(b) (b) 218 11.3 Second order plant (third case study) The position control of an AC motor process or temperature control can be represented by a
second order model (Hu et al., 1999). Equation (13) shows the mathematical plant model (in
s-plane). Discrete transfer functions of this model were obtained using the ZOH method, and
the selected sampling period (T) is 0.2. Equation (14) shows the discrete transfer functions,
(in z-plane). The searching range of the particle for this case is ranging as [Xmin Xmax], and
by using trial to reach the operational range with the universe of discourse. The optimal
values of Kp, Kd, Ki, and Ko used in this test were selected using PSO; and listed in Table 8. ( )
3
2
1
4
3
CS
s
s
s
=
+
+
(13)
( )
3
2
0.01544 z+ 0.01183
1.368 z + 0.4493
CS
z
z
=
−
, T = 0.2
(14) ( )
3
2
1
4
3
CS
s
s
s
=
+
+
(13) (13) ( )
3
2
0.01544 z+ 0.01183
1.368 z + 0.4493
CS
z
z
=
−
, T = 0.2
(14) (14) Fig. 17 shows the test bench simulation results using ModelSim for 8FBC; this test is
generated using the same procedure as explained. The controller gives action at 0.3 µs (Fig. 17). This means the same action with CS1 and CS2, which represent the linear models. The
closed loop responses with 0.5 step input are shown in Fig. 17. CS3 is a second order plant,
and has a steady state error with non-controlled response. In Fig. 18-a, when PDFC is
applied the overshoot is limited by the action of this controller, but the response still has a
steady state error. When the PIFC is applied to this system (see Fig. 18-b), the error is
disappears with 8FBC, and the system still has overshoot. The 6FBC has a rough and non-
smooth response as can be seen in the control action figures where sharp spikes appear
along the steady state part, while the responses of the systems that use 8FBC are closer to
the MSBC responses. When the PIDFC is applied for this system, as shown in Fig. 18-c, the 219 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 8FBC response is close to the responses using MSBC, with zero error and little overshoot. 11.3 Second order plant (third case study) The Responses Performance of the proposed 8FBC with CS3 is listed in Table 9. The Responses Performance of the proposed 8FBC with CS3 is listed in Table 9. Range of Particle X
Controller type
Gain type
Value
0.0001
8.5
X
≤
≤
PIDFC
Kp
5.0191
Kd
7.101
Ki
1.6875
Ko
0.937
0.0001
2
X
≤
≤
PIFC
Kp
1.02
Ki
1.812
Ko
1.75
0.0001
15
X
≤
≤
PDFC
Kp
14.625
Kd
6.021
Ko
1.062
Table 8. Optimal Gains Values Used With CS3. Fig. 17. Timing Diagram using ModelSim of the Controller (8FBC) with CS3 in unity
Feedback Control system. Range of Particle X
Controller type
Gain type
Value
0.0001
8.5
X
≤
≤
PIDFC
Kp
5.0191
Kd
7.101
Ki
1.6875
Ko
0.937
0.0001
2
X
≤
≤
PIFC
Kp
1.02
Ki
1.812
Ko
1.75
0.0001
15
X
≤
≤
PDFC
Kp
14.625
Kd
6.021
Ko
1.062
Table 8. Optimal Gains Values Used With CS3. Table 8. Optimal Gains Values Used With CS3. Table 8. Optimal Gains Values Used With CS3. Table 8. Optimal Gains Values Used With CS3. Fig. 17. Timing Diagram using ModelSim of the Controller (8FBC) with CS3 in unity
Feedback Control system. Fig. 17. Timing Diagram using ModelSim of the Controller (8FBC) with CS3 in unity
Feedback Control system. MATLAB – A Ubiquitous Tool for the Practical Engineer 220 (a) (a)
(b) Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 221 (c)
Fig. 18. Second order linear plant controlled by(a) PDFC, (b) PIFC and (c) PIDFC. (c) Fig. 18. Second order linear plant controlled by(a) PDFC, (b) PIFC and (c) PIDFC. Controller
type
Error
Over
shoot
Rising
time
Settling
time
PDFC
0.02
0.02
2.1
2.3
PIFC
0.005
0.03
1.89
2
PIDFC
0.0
0.005
1.6
1.8
Table 9. Responses Performance of the Proposed 8fbc with CS3. Table 9. Responses Performance of the Proposed 8fbc with CS3. 11.4 Delayed second order plant (fourth case study) y
(
y)
The time delay occurs when a sensor or an actuator are used with a physical separation (Hu
et al., 1999). Equation (15) shows the mathematical plant model (in s-plane). Discrete transfer
function of this model was obtained using the ZOH method, and the selected sampling
period (T) is 0.2. Equation (16) shows the discrete transfer functions, (in z-plane). The
searching range of the particle for this case is ranging as [Xmin Xmax], and by using trial to
reach the operational range with the universe of discourse. The optimal values of Kp, Kd, Ki,
and Ko used in this test were selected using PSO; and listed in Table 10. ( )
2
4
3
CS
z
z
CS
−
=
×
(15) ( )
2
4
3
CS
z
z
CS
−
=
× (15) ( )
2
4
2
0.01544 z+ 0.01183
1.368 z+ 0.4493
CS
z
z
z
−
⎛
⎞
=
×⎜
⎟
−
⎝
⎠
; T = 0.2
(16) (16) 222 MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer 224 MATLAB – A Ubiquitous Tool for the Practical Engineer (c)
Fig. 20. Delayed second order linear plant controlled by (a) PDFC, (b) PIFC and (c) PIDFC. (c) g. 20. Delayed second order linear plant controlled by (a) PDFC, (b) PIFC and (c) PIDF g. 20. Delayed second order linear plant controlled by (a) PDFC, (b) PIFC and (c) PIDF Controller
type
Error
Over
shoot
Rising
time
Settling
time
PDFC
0.07
0.02
4.9
5.3
PIFC
0.0
0.0
2.3
2.4
PIDFC
0.0
0.0
2.4
2.5
Table 11. Responses Performance of the Proposed 8FBC with CS4. MATLAB – A Ubiquitous Tool for the Practical Engineer Range of Particle X Controller type Gain type
Value
0.0001
8.5
X
≤
≤
PIDFC
Kp
2.11
Kd
1.687
Ki
0.5012
Ko
0.375
0.0001
2
X
≤
≤
PIFC
Kp
0.253
Ki
1.185
Ko
1.251
0.0001
15
X
≤
≤
PDFC
Kp
7.18
Kd
8.754
Ko
0.503
Table 10. Optimal Gains Values Used with CS4. Table 10. Optimal Gains Values Used with CS4. Fig. 19 shows the test bench simulation results using ModelSim for 8FBC. This test is
generated using the same procedure as explained before. The delay with the system only
affects the value of the real data (response). The controller gives action at 0.3 µs. The closed
loop responses with 0.5 step input are shown in Fig. 20. CS4 is the same model as CS3 but
with delay. In Fig. 20-a, when the PDFC is applied, the overshoot is limited by the action of
this controller, but the response has a large steady state error. In this case the 8FBC is very
close to the MSBC while the 6FBC has a non-smooth response. When the PIFC is applied to Fig. 19. Timing Diagram using ModelSim of the Controller (8FBC) with CS4 in unity
Feedback Control system. Fig. 19. Timing Diagram using ModelSim of the Controller (8FBC) with CS4 in unity
Feedback Control system. 223 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA this system (see Fig. 20-b), the error disappears with the 8FBC with little overshoot. The
6FBC has a large steady state error while the responses of the systems that use 8FBC are
closer to the MSBC responses. When the PIDFC is applied for this system, as shown in Fig. 20-c, the 8FBC response has better overshoot to the responses using MSBC, and is very close
to the MSBC in the steady state response. The 6FBC has a long rising time with steady state
error. The Responses Performance of the proposed 8FBC with CS4 is listed in Table 11. (a)
(b) (a)
(b) (a) (b) 11.5 Non-linear plant model (fifth case study) A mathematical model of nonlinear plant (inverted pendulum) has been used to test the
PIDFC with unity feedback control system; this model is characterized by Equation (17) and
Equation (18) (Passino and Yurkovich, 1998). 2
5
2
0.25
sin( )
9.8sin( )
cos( )
1.5
4
1
0.5
cos ( )
3
3
u
y
y
y
y
CS
y
y
−−
⎡
⎤
+
⎢
⎥
⎣
⎦
=
=
⎡
⎤
−
⎢
⎥
⎣
⎦
(17) (17) 100
100
u
u
u
=−
+
(18) (18) The first order filter on u to produce ū represents an actuator. Assuming the initial
conditions y(0) = 0.1 radians (= 5.73 deg.), y˙(0) = 0, and the initial condition for the actuator
state is zero. For simulation of the fourth-order, the Runge-Kutta method was used with an
integration step size of 0.01 (Passino and Yurkovich, 1998), (Obaid et al., 1999). Again, this
plant has been designed using MATLAB software (for simulation in MATLAB), and in 225 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA VHDL code (for simulation in ModelSim). A special package was designed in VHDL code to
represent the trigonometric functions and fourth-order Runge-Kutta method, which are not
available in Quartus II (or in ISE) standard libraries (Obaid et al., 1999). The searching range
of the particle for this case is [Xmin Xmax], and by using trial to reach the proposed
algorithm, the values of Kp, Kd, Ki, and Ko used in this test were selected using PSO. These
values are listed in Table XII. VHDL code (for simulation in ModelSim). A special package was designed in VHDL code to
represent the trigonometric functions and fourth-order Runge-Kutta method, which are not
available in Quartus II (or in ISE) standard libraries (Obaid et al., 1999). The searching range
of the particle for this case is [Xmin Xmax], and by using trial to reach the proposed
algorithm, the values of Kp, Kd, Ki, and Ko used in this test were selected using PSO. These
values are listed in Table XII. Range of Particle X
Controller type
Gain type
Value
0.0001
11.5
X
≤
≤
PIDFC
Kp
1.1012
Kd
10.1103
Ki
1.5013
Ko
5.0032
ble 12. Optimal Gains Values Used With CS5. Table 12. Optimal Gains Values Used With CS5. Fig. 11.5 Non-linear plant model (fifth case study) 21 shows the test bench simulation results using ModelSim for 8FBC and the controller
gives an output at 0.7 µs after the input latching (Fig. 21). The 6FBC has the same procedure
in ModelSim and produces an output at 0.62 µs. The Responses Performance of the
proposed controller with CS5 is listed in Table 13. Where the bound of the settling time of
the pendulum to reach its initial position with the force applied to the cart is -0.02 and +0.02
with both versions. The first time of the pendulum reach s the initial position is listed as the
rising time. When using a nonlinear system for testing, both versions (6FBC and 8FBC)
provide generally good responses although there is some oscillation. One must not be
deceived by the steady state error that appears in Fig. 22, as it represents less than 1% of the
output range in the case of 6FBC and less than 0.5% of the output range, in the case of 8FBC. The absolute mean difference between the nonlinear plant response, using MSBC, and the Fig. 21. Timing Diagram using ModelSim of the Controller (8FBC) with CS5 in unity
Feedback Control system. Fig. 21. Timing Diagram using ModelSim of the Controller (8FBC) with CS5 in unity
Feedback Control system. 226 MATLAB – A Ubiquitous Tool for the Practical Engineer nonlinear plant response, using 6FBC is less than 0.017. The absolute mean difference
between the nonlinear plant response, using MSBC, and the nonlinear plant response, using
8FBC is less than 0.006 as shown in Fig. 22. The experimental result is carried out by using
the nonlinear inverted pendulum (the last case study CS5). The experimental data recorded
to the inverted pendulum has been used in this test in unity feedback control system. This
data has been recorded by Sultan (Sultan, 2006) to analyze, design & develop a control loop
for the given inverted pendulum (with servomechanism). The pendulum reaches the initial
position zero at 0.058 second with overshoot equal to 0.025 and undershoot equal to 0.02. Fig. 23 shows the experimental data simulation of the inverted pendulum with the PIDFC in
8-bit version. The controller (8FBC) provides a good control performance with respect to the
simulation results of the same case as shown in Table 13. Fig. 23. Experimental data simulation of the PIDFC with
the inverted pendulum in unity feedback control system. Fig. 23. 11.5 Non-linear plant model (fifth case study) Experimental data simulation of the PIDFC with
the inverted pendulum in unity feedback control system. Controller type
Error
Over
Peak angle (rad)
Under
Peak angle (rad)
Rising time
Settling time
6FBC
0.017
0.0
-0.01
0.13
0.1
8FBC
0.006
0.0
-0.01
0.13
0.1
6MSBC
0.0
0.018
-0.041
0.13
0.1
8MSBC
0.0
0.018
-0.041
0.13
0.1
Experimental case
0.0
0.025
0.024
0.029
0.058
Table 13. Responses Performance of the Proposed 8fbc with CS5. Table 13. Responses Performance of the Proposed 8fbc with CS5. 12. Results comparison and discussion The proposed design has been coded in Matlab environments as explained before. The aim
of this test is to find to what extent the 6FBC and 8FBC responses are close to the MSBC
responses with respect to the accuracy. In contrast to the 6FBC, the responses of the systems
that use 8FBC are smooth (as MSBC responses). When the 6FBC or 8FBC is used as PIFC or 227 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA PIDFC, the system responses will settle at a value close to the response settling value of
systems that use MSBC. The reason being the rounding error in the PI component, the
proposed PIDFC consists of a PDFC and PIFC, the PIFC is a PDFC with a summation block
at its output. This error could be positive or negative. Sometimes, during the summation
process, the rounding error cancels itself. Commonly, in CS1 and CS2, it is clear that the
responses have a steady state error with PDFC, because these systems do not have an
overshoot, only a steady state error (no need to use PDFC), and this test is used to evaluate
the multi structure in the proposed PIDFC. The absolute mean of differences between the
MSBC and 6FBC was less than 0.07 with the linear systems and less than 0.017 with the
nonlinear system, while the absolute mean of differences between MSBC and 8FBC was less
than 0.017 with the linear systems and less than 0.006 with the nonlinear system. The
proposed controller has good responses performance with respect to the classical controller
proposed in the literature, and also better responses as compared it with other type of fuzzy
PID controller. CS1, CS2 and CS3 have been used in the work proposed in (Hu et al., 1999). In this work,
Genetic algorithm (GA) based optimal fuzzy PID controller was used with new
methodology (Matlab-based). Table 14 lists the comparison of the responses performance of
this work with respect to the proposed PIDFC (8FBC) with CS1, CS2 and CS3. This
comparison consists of rising time (Tr), settling time (Ts) and overshoot (OV). The proposed
PSO-PIDFC with the linear cases CS1 and CS2 have no overshoot and a short rising and settling time with respect to other types of
controller designed in the literature with the same models. 12. Results comparison and discussion For the CS3, there is a 0.005
overshoot and short rising and settling time with respect to other types of controller
designed in the literature with the same model. The proposed PSO-PIDFC with the
nonlinear cases (CS5) have zero overshoot and 0.13, 0.1 rising and settling time respectively,
while other types of controller with the same nonlinear model have an overshoot and longer
rising and settling time. In CS5, a mathematical model of nonlinear plant (inverted
pendulum) was used to test the controller with a unity feedback control system. This case
has been used in (Jain et al., 2009), (Masmoudi et al., 1999) and (Jain et al., 1999) (Matlab-
based) with different types of controllers. In (Jain et al., 2009), Bacterial Foraging (BF)
algorithm was used for tuning the parameters of the PID controller for optimal
performance, while (Jain et al., 1999) used a comparison between Evolutionary Algorithms
namely Gas (Genetic Algorithms), and Swarm Intelligence i.e. PSO and BG. In (Jain et al.,
1999) as there was no need to know the value of rising time as they used a reference input
equal to zero. It is not considered by this author either. Therefore, a comparison is made
with the proposed 8FB (PIDFC) with those presented in (Jain et al., 2009), (Masmoudi et al.,
1999) and (Jain et al., 1999). This comparison is listed in Table 15. In the case of (Jain et al.,
1999), PSO had the best responses with respect to the other methods proposed by this
author, hence, we will compare with PSO and ISE only. Other comparison has been made to
the proposed design with respect to FPGA chip resources. This comparison involves the
utilization of the chip resources in the proposed FPGA-based PIDFC with respect to the
other FPGA-based controllers proposed in the literature. It also involves a comparison with
respect to the time required per one action with the maximum frequency. This comparison
was made after compiling the design using the ISE program provided by Xilinx Company,
because this tool provides a clear Report for the chip resources, even it was used by the
authors in the literature. This comparison is listed in Table 16. 12. Results comparison and discussion MATLAB – A Ubiquitous Tool for the Practical Engineer 228 Case
Performance
Proposed
FPGA-based PIDFC
with PSO
GA - Fuzzy PID
In (Hu et al., 1999)
GA -Optimal PID
In (Hu et al., 1999)
CS1
Tr (s)
0.19
0.16
0.2
Ts(s)
0.23
0.2
0.36
OV
0.0
0.0
0.0039
CS2
Tr (s)
0.48
0.16
0.38
Ts(s)
0.49
0.46
0.74
OV
0.0
0.0051
0.0162
CS3
Tr (s)
1.6
0.74
0.88
Ts(s)
1.8
2.34
1.34
OV
0.005
0.0622
0.0107
Table 14. Performance Comparison of the PIDFC with the Work Proposed by Hu et al. In
(Hu et al., 1999) Case
Performance
Proposed
FPGA-based PIDFC
with PSO
GA - Fuzzy PID
In (Hu et al., 1999)
GA -Optimal PID
In (Hu et al., 1999)
CS1
Tr (s)
0.19
0.16
0.2
Ts(s)
0.23
0.2
0.36
OV
0.0
0.0
0.0039
CS2
Tr (s)
0.48
0.16
0.38
Ts(s)
0.49
0.46
0.74
OV
0.0
0.0051
0.0162
CS3
Tr (s)
1.6
0.74
0.88
Ts(s)
1.8
2.34
1.34
OV
0.005
0.0622
0.0107
Table 14. Performance Comparison of the PIDFC with the Work Proposed by Hu et al. In
(Hu et al., 1999)
Performance
The proposed
Controller In
Experimental
Case with CS5
The
Proposed
FPGA-based
PIDFC
With PSO
Optimal PID
In (Jain et al.,
2009)
With BG
Fuzzy logic
controller
in
(Masmoudi
et al., 1999)
Optimal PD-PI
In (Jain et al.,
1999)
With PSO
Ts (s)
0.058
0.1
0.4
0.21
2.4
Tr(s)
0.029
0.13
0.2
0.22
---
Peak angle
(rad)
0.025
0.0
0.178
0.75
0.00127
Table 15. Performance Comparison of the PIDFC (8FBC) With Those Proposed In (Jain et al.,
2009), (Masmoudi et al., 1999) and (Jain et al., 1999) By Using CS5. Table 14. Performance Comparison of the PIDFC with the Work Proposed by Hu et al. In
(Hu et al., 1999) e 14. Performance Comparison of the PIDFC with the Work Proposed by Hu et al. In
et al., 1999) Performance
The proposed
Controller In
Experimental
Case with CS5
The
Proposed
FPGA-based
PIDFC
With PSO
Optimal PID
In (Jain et al.,
2009)
With BG
Fuzzy logic
controller
in
(Masmoudi
et al., 1999)
Optimal PD-PI
In (Jain et al.,
1999)
With PSO
Ts (s)
0.058
0.1
0.4
0.21
2.4
Tr(s)
0.029
0.13
0.2
0.22
---
Peak angle
(rad)
0.025
0.0
0.178
0.75
0.00127
Table 15. Table 16. FPGA Chip Resources Comparison between the PIDFC and Other Type of
Controllers Proposed In the Literature. 13. Conclusion From the design and simulation results of the PIDFC, it can be concluded that: Higher
execution speed versus small chip size is achieved by designing PIDFC with a simplified
fuzzy algorithm as a parallel structure of PDFC and PIFC and also by designing PIFC by
accumulating the output of the PDFC. These methods significantly reduce the number of
rules needed. It also enables the controller to work as a PIFC, PDFC or PIDFC depending on
two external signals to provide high-flexibilities with different applications. The controller
needs 16 clock cycles to generate an output with a maximum clock frequency of 40 MHz. Therefore, the proposed controller will be able to control a wide range of systems with a
high sampling rate. Higher flexibility versus good control performance is achieved by
designing tuning-gains block at each input/output stage. This block involves a tuning by
scaling the universe of discourse for the input/output variables (renormalization). This
block makes the controller chip accept the PSO-based optimal scaling gains, and also
enables the digital controller chip able to accept unsigned inputs. The PSO algorithm has
better simulation results than other intelligent optimization methods proposed in the
literature such as genetic algorithm. This block is very important and is useful for providing
a best tuning case for the universe of discourse. g
In addition, it makes the design applicable for different systems without requiring
reprogramming the controller chip. Higher execution speed and small chip size versus
acceptable accuracy is achieved by designing each one of the scaling gains as two parts:
integer and fraction, and perform all mathematical operations using integer number
algorithms, which are smaller in the implementation size than floating number algorithms,
and even faster. Sufficient design accuracy can be achieved with 8FBC in Particular. 8FBC is
superior to 6FBC since it presents higher accuracy versus moderately low target device
utilizations. 8FBC was able to produce a control action in 0.3 µs after input latching (the
computational time of the controller is 0.3 µs). The 8FBC produced responses approximately
similar or better than the MSBC compared with the 6FBC or with the results in the literature. 13. Conclusion The absolute mean of differences between the responses of the 6FBC and the MSBC, was less
than 4% of the output range, for the linear plants, and less than 0.5% of the output range for
the nonlinear plant, while the absolute mean of differences between the responses of 8FBC
and the MSBC, was less than 1% of the output range, for the linear plants, and less than 0.3%
of the output range for the nonlinear plant. Both versions showed some error at the steady
state part of the response when serving as PIFLC or PIDFLC because of the accumulation of
the rounding error at the summation block. This error depends on the rounding error;
therefore it becomes larger when using the 6FBC than when using 8FBC. As a result, the
proposed controller could be used to control many industrial applications with high
sampling time. Its small size versus high speed makes it a good choice for other
applications, such as robots. It is hoped that some future work could settle down the
feasibility of the suggestions: Increasing the number of the first part of the fuzzy set in the
MBMSF inside the fuzzifier block more than (3-bits) could make the design accept more
than 8 fuzzy sets at each input. Increasing the number of bits of the entire design may be
useful in decreasing the error in the PIFC component (in some cases) of the controller at the
expense of increasing design area and processing time. Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 229 Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 12. Results comparison and discussion Performance Comparison of the PIDFC (8FBC) With Those Proposed In (Jain et al.,
2009), (Masmoudi et al., 1999) and (Jain et al., 1999) By Using CS5. Table 15. Performance Comparison of the PIDFC (8FBC) With Those Proposed In (Jain et al.,
2009), (Masmoudi et al., 1999) and (Jain et al., 1999) By Using CS5. References
Number of
CLBs
Number of
IOBs
Frequency
Time per
action
PIDFC
494
68
40 MHz
0.3 µs
(Poorani et al.,
2005)
757
39
8 KHz
41.1 ms
(Tipsuwanpornet
al., 2004)
---
---
40.55 MHz
2.1 µs
(Hassan et al.,
2007)
1394
61
40.245 MHz
0.421 µs
(Alvarez et al.,
2006)
3492
51
100 MHz
1.4 µs
(Lund et al., 2006)
63
---
20 MHz
1 µs
Table 16. FPGA Chip Resources Comparison between the PIDFC and Other Type of
Controllers Proposed In the Literature. Table 16. FPGA Chip Resources Comparison between the PIDFC and Other Type of
Controllers Proposed In the Literature. 14. Acknowledgment The authors would firstly like to thank God, and all friends who gave us any help related to
this work. Other Appreciation goes to the Assist chancellor amend to Diyala University-Iraq 230 MATLAB – A Ubiquitous Tool for the Practical Engineer (Prof. Dr Amer Mohammed Ibrahim) and the Dean of Collage of Engineering-Diyala
University- Iraq (Assist. Prof. Dr. Adel Khaleel Mahmoud). Further appreciation goes to My
Colleagues Mr. Waleed Fawwaz and Mrs. Areej Sadiq for their wide help and support. Finally, a heartfelt thank to our families and home countries. 15. References Poorani, S., Priya, T.V.S.U., Kumar, K.U., and Renganarayanan, S., (2005) "FPGA Based Fuzzy
Logic Controller for Electric Vehicle," Journal of the Institution of Engineers,
Singapore, Vol. 45 Issue 5. g p
Jain, T., Patel, V., Nigam and M.J., "Implementation of PID Controlled SIMO Process on FPGA
Using Bacterial Foraging for Optimal Performance," International Journal of Computer
and Electrical Engineering, Vol. 1, No. 2, p: 1793-8198, June. Tipsuwanporn, V., Intajag, S. and Krongratana, V., (2004) "Fuzzy Logic PID Controller Based
on FPGA for Process Control," Proceedings of IEEE International Symposium on
Industrial Electronics, Vol. 2, May 4-7, page(s):1495-1500. y
g
Karasakal, O., Yesl, E., Guzelkaya, M. and Eksin, I., (2005) "Implementation of a New Self-
Tuning Fuzzy PID Controller on PLC," Turk J Elec Engin, Vol.13, NO.2. Hassan, M.Y., and Sharif, W.F., (2007) "Design of FPGA based PID-like Fuzzy Controller for
Industrial Applications," IAENG International Journal of Computer Science, Vol. 34
Issue 2, November. Kim, D., (2000) "An Implementation of Fuzzy Logic Controller on the Reconfigurable FPGA
System," IEEE Transactions on Industrial Electronics, Vol. 47, No. 3, p: 703- 715,
June. Solano, S.S., Barriga, A., Jimenez, C.J and Huertas, J.L., (1997) "Design and Application of
Digital Fuzzy Controllers", Proceedings of Sixth IEEE International Conference on
Fuzzy Systems (FUZZ-IEEE’97), Vol. 2, July 1-5, page(s):869-874. Islam, S., Amin, N., Bhuyan, M.S, Zaman, M., Madon, B. and Othman, M., (2007) "FPGA
Realization of Fuzzy Temperature Controller for Industrial Application", WSEAS
Transactions on Systems and Control, Volume 2, Issue 10, p: 484- 490, October. Mann, G.K.I., Hu, B.G. and Gosine, R.G., (1999) "Analysis of Direct Action Fuzzy PID
Controller Structures", IEEE Transactions on Systems, Man, and Cybernetics—Part
B: Cybernetics, Vol. 29, No. 3, p: 371 – 388, June. y
p
Seng, T.L., Khalid, M. and Yusuf, R., (1999) "Tuning of a Neuro-Fuzzy Controller by Genetic
Algorithm", IEEE Transactions on Systems, Man, and Cybernetics—Part B:
Cybernetics, Vol. 29, No. 2, P: 226- 236, April. y
Leonid, R., Ghanayem, O. and Bourmistrov, A., (2000) "PID plus fuzzy controller structures as
a design base for industrial applications", Engineering Applications of Artificial
Intelligence, Elsevier Science Ltd, 13, p: 419-430. g
p
Leonid, R. (1997). Fuzzy Controllers, first edition, Newnes. Gabrielli, Gandolfi, E. and Masetti, M., (2009) "Design of a Very High Speed Fuzzy Processor by
VHDL
Language",
Physics
Department
University
of
Bologna,
URL:http://www.bo.infn.it/dacel/papers/96_03_parigi_EDTC.pdf. Accessed on 4
October 2009. Jantzen, J., (1998) "Design of Fuzzy Controllers". 15. References Technical University of Denmark, and
Department of Automation, reports no 98-H 869 (soc), 19 Aug. him, A.M., (2004) "Fuzzy Logic for Embedded Systems Applications", USA, Elsevier Science Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA Design of PSO-Based Optimal/Tunable PID Fuzzy Logic Controller Using FPGA 231 Obaid, Z.A., Sulaiman, N. and Hamidon, M.N., (2009) “Developed Method of FPGA-based
Fuzzy Logic Controller Design with the Aid of Conventional PID Algorithm”, Australian
Journal of Basics and Applied Science, Vol. 3(3), P: 2724-2740. Ying, H., (2000) "Fuzzy Control and Modeling, Analytical Foundations and Applications",
Institute of Electrical and Electronic Engineers Inc., USA. Wang, J., Zhang, Y. and Wang, W., (2006) "Optimal design of PI/PD controller for non-minimum
phase system", Transactions of the Institute of Measurement and Control, Vol. 28 No. 1, p: 27-35. Allaoua, B., Gasbaoui, B. and Mebarki, B., (2009) "Setting Up PID DC Motor Speed Control
Alteration Parameters Using Particle Swarm Optimization Strategy", Leonardo
Electronic Journal of Practices and Technologies, Issue 14, p: 19-32, January-June
2009. Barriga, A., Sanchez-Solano, S., Brox, P., Cabrera, A., and Baturone, I., (2006) "Modeling and
implementation of Fuzzy Systems Based on VHDL", International Journal of
Approximate Reasoning, Elsevier Inc, Vol. 41, p: 164–178. Huang, S.H. and Lai, J.Y., (2005) "A High Speed Fuzzy Inference Processor with Dynamic
Analysis and Scheduling Capabilities", IEICE Transaction Information & System., Vol. E88-D, No.10 October. Alvarez, J., Lago, A. and Nogueiras, A., (2006) "FPGA Implementation of a Fuzzy Controller for
Automobile DC-DC Converters" Proceeding of IEEE International Conference on
Field Programmable Technology, December, page(s): 237-240. Lund, T., Aguirre, M. and Torralba, A., (2004) "Fuzzy Logic Control via an FPGA: A Design
using techniques from Digital Signal Processing", Proceedings of IEEE International
Symposium on Industrial Electronics, vol. 1, May 4-7, page(s): 555- 559. Sultan, KH., “Inverted Pendulum, Analysis, Design and Implementation” IIEE Visionaries
Document Version 1.0, Institute of Industrial Electronics Engineering, Karachi,
Pakistan. [Available
online
at]
Matlab
Central
File
Exchange
http://www.Mathworks.com. p
Xilinx Company. 2009. Virtex 2.5 V Field Programmable Gate Arrays, Data Sheet DS003,
URL www.xilinx.com. Accessed on 2009. Hu, B.G., Mann, G.K. and Gosine, R.G, (1999) "New Methodology for Analytical and Optimal
Design of Fuzzy PID Controllers", IEEE Transactions on Fuzzy Systems, Vol. 7, No. 5,
pp. 521-539, October. pp
Passino, K.M., and Yurkovich, S., (1998) "Fuzzy Control, Addison-Weslwey Longman Inc.,
USA. Masmoudi, N., Hachicha, M. 15. References and Kamoun, L., (1999) "Hardware Design of Programmable
Fuzzy Controller on FPGA", Proceedings of IEEE International Fuzzy Systems
Conference Proceedings, August 22-25, page(s):1675-1679. g
g
p g ( )
Jain, T. and Nigam, M.J., (2008) "Optimization of PD-PI Controller Using Swarm Intelligence",
Journal of Theoretical and Applied Information Technology, Page: 1013-1018, 2008. Obaid, Z.A., Sulaiman, N., Marhaban, M.H. and Hamidon, M.N. (2010), "Implementation of
Multistructure PID-like Fuzzy Logic Controller using Field Programmable Gate
Array” IEICE Electronics Express, Vol. 7 No. 3, P: 132-137, 10 February. y
p
y
Li J. and Hu B.S., (1996) "The Architecture of Fuzzy PID Gain Conditioner and its FPGA
Prototype Implementation", Proceedings of the Second International Conference on
ASIC, October 21-24, page(s):61-65. 232 MATLAB – A Ubiquitous Tool for the Practical Engineer Khatr, A. P., and Rattan, K.S., (2006) "Implementation of a Multi-Layered Fuzzy Controller
on an FPGA", Annual meeting of the North America, by IEEE Fuzzy Information
Processing Society, Page(s): 420- 425. J.L. Gonzalez-vazquez, O. Castillo and L.T. Aguilar-bustos, "A Generic Approach to Fuzzy
Logic Controller Synthesis on FPGA", Proceedings of IEEE international conference
on fuzzy systems, 2006, page(s): 2317 – 2322. y y
p g ( )
Gonzalez-Vazquez, J.L., Castillo, O. and Aguilar-bustos, L.T., (2006) "A Generic Approach to
Fuzzy Logic Controller Synthesis on FPGA", Proceedings of IEEE international
conference on fuzzy systems, page(s): 2317 – 2322. 12 1. Introduction In recent decades the electric power systems has suffered significant power quality
problems caused by the proliferation of non linear loads, such as arc furnace lighting loads
adjustable ac drives etc., which causes a large amount of characteristic harmonics, low
power factor and significantly deteriorates the power quality of the distribution system
(Benslimane, 2007; Franquelo et. al., 2008; Gupta et al., 2008). The increasing restrictive
regulations on power quality have significantly stimulated the development of power
quality mitigation equipments. For high power grid connected systems, the classical two
level or three level converters topology are insufficient due to the rating limitations imposed
by the power semiconductors (Holmes & McGrath, 2001; Koura et al., 2007). Hence
considerable attention has been focused on multilevel inverter topologies. This important
multilevel technology has found widespread application in medium and high voltage
electric drives, renewable energy – grid interface, power conditioning, and power quality
application (Lai & Peng, 1996; Peng et al., 1996; Rodriguez et al., 2002; Sinha & Lipo, 1996;
Tolbert et al., 1999). Multilevel converters offer several advantages compared to their conventional counterparts
(Manjrekar & Lipo, 1988, 1998, 200; Corzine & Familiant, 2002; Lund et. al., 1999; Sneineh et. al., 2006; Park et. al., 2003; Zhang et al., 2002; Ding et. al., 2004; Duarte et al., 1997; Rojas &. Ohnishi, 1997). By synthesizing the AC output terminal voltage from several voltage levels,
staircase waveforms can be produced, which in their turn approach the sinusoidal
waveform with low harmonic distortion, thus reducing filters requirements. However the
several sources on the DC side of the converter make multilevel technology difficult to
control by the need to balance the several DC voltages. For the class of multilevel inverter
called diode clamped, if a higher output voltage is required one of the viable methods is to
increase the number of inverter voltage levels. For Neutral Point Clamped (NPC) inverter
voltage can only be increased up to five level beyond which DC voltage balancing becomes
impossible. For single Phase H Bridge inverter, an increase in the number levels leads to
increase in the number of separate DC sources, thus the proposed hybrid model is
developed by combining the NPC and H- bridge topologies (Wu et al., 1999). 1. Introduction 234 MATLAB – A Ubiquitous Tool for the Practical Engineer A lot of research has been done on single phase H- Bridge inverter where each inverter level
generate three different voltage outputs, +Vdc, 0, and –Vdc by connecting the dc source to the
ac output using different combinations of the four switches of the Bridge (Peng et al., 1996). There has also been more emphasis on modeling and control of a five level NPC/H-bridge
inverter without cascading the bridge (Cheng & Wu, 2007). This fails to address the
principle of realizing a general cascaded n- level NPC/H-Bridge. It is on this need of
realizing a higher voltage output with simplified control algorithm that this book chapter
proposes a simplified control strategy for a cascaded NPC/H-bridge inverter with reduced
harmonic content. Because of the modularity of the model only two cascaded cells which
gives a 9 level cascaded NPC/H-bridge inverter is considered. The new control strategy is
achieved by decomposing the nine level output into four separate and independent three-
level NPC PWM output. By combining the three- level NPC PWM back to back using DC
sources and properly phase shifting the modulating wave and carrier a simplified control
strategy is achieved with reduced number of components. The control strategy is applied on
cascaded NPC/H-bridge inverter that combines features from NPC inverter and cascaded
H-Bridge inverter. For higher voltage applications, this structure can be easily extended to
an n- level by cascaded NPC/H-Bridge PWM inverters. y
g
The article starts by developing a control algorithm based on novel phase shifted PWM
technique on the proposed inverter model. This is done on a two cell of the cascaded model
to realize nine level voltage output. A theoretical harmonic analysis of the model with the
proposed control algorithm is carried out based on double Fourier principle. Spectral
characteristics of the output waveforms for all operating conditions are studied for a five-
level and nine- level voltage output. Theoretical results are verified using MATLAB
simulation.The results shows that the spectrum can be made to only consist of the multiples
of fourth order for a five level and with proper phase shift combination, a multiple of eighth
order is achieved for nine level voltage output. 1. Introduction The results are compared with those of a
conventional multicarrier PWM approach; it is shown that with the proposed phase shifted
PWM approach, the inverter exhibits reduced harmonic content are present. Finally the
article compares the components count of the the model with the convetional cascaded H-
bridge inverter, it is clealry shown that the proposed model requires a lesser number of
separate dc sources as compared to conventional cascaded H-bridge inverter. 2.1 Main system configuration Fig 1 shows the circuit configuration of the proposed nine- level cascaded NPC/H-Bridge
PWM inverter which consists of two legs for each cell connected to a common bus. Four
active switches, four freewheeling diodes and two diodes clamped to neutral are adopted in
each leg. The voltage stress of all the eight power switches is equal to half of DC bus voltage. The power switches in each leg are operated in high frequency using phase shifted PWM
control technique to generate the three voltage levels on the ac terminal to neutral voltage
point p
The building block of the whole topology consists of two identical NPC cascaded cells. The
inverter phase voltage Van is the sum of the two cascaded cells, i.e., 01
02
an
V
V
V
=
+
(1) (1) 01
02
an
V
V
V
=
+ Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t
d Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression 235 Cascaded NPC/H Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression . Van
Fig. 1. Schematic diagram of the proposed cascaded NPC/H-bridge inverter model Fig. 1. Schematic diagram of the proposed cascaded NPC/H-bridge inverter model Assuming that the two capacitor voltages on the DC bus voltage are equal, five different
voltage levels +2Vdc, +Vdc, 0, -Vdc and –2Vdc, are generated on the ac terminal V01 which
consist of two legs. Same applies to V02 fig. 2 shows the switching model for a nine- level
output [6]. This implies that by cascading two NPC/H-Bridge inverters (V01 and V02) and
properly phase shifting the modulating wave and carriers, a nine- level PWM output is
achieved. The number of output voltage levels is given by 4
1
m
N
=
+
(2) (2) Where N is the number of series connected NPC/H-Bridges. The topology is made up of
four three level legs and each leg has four active switches and four freewheeling diodes. 2.2 System operation y
Most of the past research on modeling of cascaded multilevel inverter has concentrated on
realizing a switching model of conventional H- bridge inverter without giving a guideline MATLAB – A Ubiquitous Tool for the Practical Engineer 236 q
g
Fig. 2. Operating modes of one cell of NPC/H-Bridge inverter
on how one can get operating modes of cascaded NPC/H-bridge inverter and hence obtain
lid
d l f
th t
l
Thi
ti
l
i ht
lid
ti
d
f
ll Bridge inverter Fig. 2. Operating modes of one cell of NPC/H-Bridge inverter on how one can get operating modes of cascaded NPC/H-bridge inverter and hence obtain
a valid model for the topology. This section analyses eight valid operating modes of one cell
of the proposed topology. The following assumptions are made in the modeling and
analysis process: Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression Cascaded NPC/H-Bridge Inverter Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression 237 •
All components (power switches and capacitors) are ideal. p
(p
p
)
•
The DC- link capacitors V1, V2, V3 and V4 have the same capacitance. •
PV cells supplies constant and equal voltages to the four DC link capacitors. •
The reference phase voltage is assumed to be a constant value during one switching
period. p
re 3 shows the operation modes for one NPC/H-bridge cell from the 9-level inverter. Figure 3 shows the operation modes for one NPC/H-bridge cell from the 9-level inverter. In mode 1 the power switches S11 & S12 and S23 & S24 are turned on to supply voltage at the
output of first NPC/H-bridge cell that is equal to V01= V1+ V2. The capacitors C1 and C2 are
discharged as they supply power to the utility as shown in figure 2 (a). The modes 2 to 8 are
as shown in figures 2 (b) to 2 (h) respectively. In mode 2 the output voltage is V01= V2, in
mode 3: V01= - (V1+ V2), in mode 4: V01= -V2, in mode 5: V01= V1, in mode 6: V01= -V1: in
mode 7: V01= 0 and in mode 8: V01= 0. Based on the analysis of the operation model, the state variable equation for the proposed
inverter can be estimated. 2.2 System operation To prevent the top and bottom power switched in each inverter
leg from conducting at the same time, the constraints of power switches can be expressed as: }
1
3
2
4
1;
1
i
i
i
i
S
S
S
S
+
=
+
=
(3) (3) Where i = 1, 2. Let’s define the switch operator as: T1 = S11 & S12 ; T2 = S13 & S13 ; T3 = S21 & S22
T4 = S23 & S24. The four valid expressions are given by: Where i = 1, 2. Let’s define the switch operator as: T1 = S11 & S12 ; T2 = S13 & S13 ; T3 = S21 & S22
T4 = S23 & S24. The four valid expressions are given by: 11
12
1
1
&
0
if both S
S
are ON
T
Otherwise
⎧
= ⎨
⎩
(4) (4) 13
14
2
1
&
0
if both S
S
are ON
T
Otherwise
⎧
= ⎨
⎩
(5) (5) 21
22
3
1
&
0
if both S
S
are ON
T
Otherwise
⎧
= ⎨
⎩
(6) (6) 23
24
4
1
&
0
if both S
S
are ON
T
Otherwise
⎧
= ⎨
⎩
(7) (7) From fig. 4 taking two legs for each cell to be a and b, the equivalent switching function are: From fig. 2.2 System operation 4 taking two legs for each cell to be a and b, the equivalent switching function are: 1
12
2
1
1
0
1
1
1
a
if T
K
if S
if T
=
⎧
⎪
= ⎨
⎪−
=
⎩
&
3
22
4
1
1
0
1
1
1
b
if T
K
if S
if T
=
⎧
⎪
= ⎨
⎪−
=
⎩
(8) (8) Using equation (3 – 7), a switching state and corresponding voltage output Vo1 can be
generated as shown in table 1 which clearly indicates that there are 8 valid switching states;
From table 1, the voltage V01 generate by the inverter can be expressed as: Using equation (3 – 7), a switching state and corresponding voltage output Vo1 can be
generated as shown in table 1 which clearly indicates that there are 8 valid switching states;
From table 1, the voltage V01 generate by the inverter can be expressed as: 01
a
b
V
V
V
=
+
(9) (9) For the control technique stated above; the voltage level for one leg of the cell is given For the control technique stated above; the voltage level for one leg of the cell is given as: he control technique stated above; the voltage level for one leg of the cell is given as: MATLAB – A Ubiquitous Tool for the Practical Engineer 238 Ka
Kb
T1
T2
S12
T3
T4
S21
Va
Vb
V01
Mode
1
-1
1
0
1
0
1
0
V1
-V2
V1+ V2
1
0
-1
0
0
1
0
1
0
0
-V2
V2
2
-1
0
0
1
0
0
0
1
0
V2
-V2
3
1
0
1
0
1
0
0
1
V1
0
V1
4
0
1
0
0
1
1
0
1
-V1
0
-V1
5
1
1
1
0
1
1
0
1
V1
V1
0
6
-1
-1
0
1
1
0
1
1
V2
V2
0
7
-1
-1
0
1
0
1
0
1
V2
V1
-V1- V2
8 Table 1. Switching States and Corresponding Voltage(s) for One Cell of NPC/H-bridge
Inverter Table 1. Table 2. Switching scheme for one phase leg of a nine level cascaded NPC/H- bridge
inverter 3. Mathematical analysis Most of the past research on modeling of cascaded multilevel inverter has concentrated on
realizing a switching model of conventional H- bridge inverter without giving a guideline
on how one can get operating modes of cascaded NPC/H-bridge inverter and hence obtain
a valid model for the topology. This section analyses eight valid operating modes of one cell
of the proposed topology and proposes an equivalent circuit for the topology. The following assumptions are made for deriving the mathematical model of the cascaded The following assumptions are made for deriving the mathematical model of the cascaded
H-bridge inverters. g
The grid is assumed to be AC current source, •
The grid is assumed to be AC current source, •
The power losses of the whole system are categorized as series loss and parallel loss. The series loss and interfacing inductor loss are represented as equivalent series
resistance (ESR). Parallel losses are represented as shunt connected resistances across
the dc-link capacitors. •
The power losses of the whole system are categorized as series loss and parallel loss. The series loss and interfacing inductor loss are represented as equivalent series
resistance (ESR). Parallel losses are represented as shunt connected resistances across
the dc-link capacitors. p
The differential equations describing the dynamics of the coupling inductor between the
NPC/H-bridge inverter and the grid of the model shown in fig. 1 can be derived as: p
The differential equations describing the dynamics of the coupling inductor between the
NPC/H-bridge inverter and the grid of the model shown in fig. 2.2 System operation Switching scheme for one phase leg of a nine level cascaded NPC/H- bridge
inverter Cascaded NPC/H-Bridge Inverter Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression
239 Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression 239 g
with Simplified Control Strategy and Superior Harmonic Suppression From equation (9), the voltage output for one cell of the model can be deduced as; From equation (9), the voltage output for one cell of the model can be deduced as; (
)
(
)
2
2
01
1
2
1
2
2
2
a
b
a
b
K
K
K
K
V
V
V
V
V
−
−
=
+
+
−
(12) (12) For the compound nine level inverter let’s assume that V1 = V2 = V3 = V4 = V, the switching
states are as shown in Table 2. For the compound nine level inverter let’s assume that V1 = V2 = V3 = V4 = V, the switching
states are as shown in Table 2. For a nine level cascaded NPC/H-bridge inverter, there are 22 valid switching states though
two of the switching states are short circuits and thus cannot compensate the DC capacitor
as current do not pass through either of the four DC- link capacitors. 2.2 System operation Switching States and Corresponding Voltage(s) for One Cell of NPC/H-bridge
Inverter 1
2
1
1
2
2
a
a
a
a
a
K
K
V
K
V
K
V
+
−
⎛
⎞
⎛
⎞
=
−
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
(10) (10) or the second leg the expression is given by (11) Similarly for the second leg the expression is given by (11) 1
2
1
1
2
2
b
b
b
b
b
K
K
V
K
V
K
V
+
−
⎛
⎞
⎛
⎞
=
−
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
(11) (11) S11
S12
S21
S22
S31
S32
S41
S42
V01
V02
Van
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
-Vdc
0
-Vdc
0
0
0
1
0
0
0
1
-Vdc
-Vdc
-2Vdc
0
0
0
1
0
0
1
1
-Vdc
-2Vdc
-3Vdc
0
0
0
1
0
1
0
0
-Vdc
Vdc
0
0
0
0
1
1
1
0
0
-Vdc
2Vdc
Vdc
0
0
1
1
0
0
0
0
-2Vdc
0
-2Vdc
0
0
1
1
0
0
0
0
-2Vdc
-Vdc
-3Vdc
0
0
1
1
0
0
1
0
-2Vdc
-2Vdc
-4Vdc
0
0
1
1
0
1
0
0
-2Vdc
Vdc
-Vdc
0
0
1
1
1
1
0
0
-2Vdc
2Vdc
0
0
1
0
0
0
0
0
0
Vdc
0
Vdc
0
1
0
0
0
0
0
1
Vdc
-Vdc
0
0
1
0
0
0
0
1
1
Vdc
-2Vdc
-Vdc
0
1
0
0
0
1
0
0
Vdc
Vdc
2Vdc
0
1
0
0
1
1
0
0
Vdc
2Vdc
3Vdc
1
1
0
0
0
0
0
0
2Vdc
0
2Vdc
1
1
0
0
0
0
0
1
2Vdc
-Vdc
Vdc
1
1
0
0
0
0
1
1
2Vdc
-2Vdc
0
1
1
0
0
0
1
0
0
2Vdc
Vdc
3Vdc
1
1
0
0
1
1
0
0
2Vdc
2Vdc
4Vdc
1
1
1
1
1
1
1
1
0
0
0
Table 2. Switching scheme for one phase leg of a nine level cascaded NPC/H- bridge
i
t Table 2. 3. Mathematical analysis 1 can be derived as: 1
1
1
1
2
2
2
2
fx
f
cx
fx
f x
x
x
sx
f
cx
sx
f
x
sx
di
L
V
i R
V
V
dt
di
L
V
i R
V
dt
δ
δ
⎧
= −
−
+
+
⎪⎪⎨
⎪
= −
−
−
⎪⎩
(13) (13) According to Kirchhoff’s law, the currents flowing into the dc link capacitors C1 and C2 can
be expressed as: According to Kirchhoff’s law, the currents flowing into the dc link capacitors C1 and C2 can
be expressed as: 1
1
2
1
1
1
2
1
2
2
2
2
1
2
1
2
3
C
x fx
C
x fx
fx
CX
f
fx
sx
fx
dV
V
V
i
C
i
dt
R
R
dV
V
V
i
C
i
dt
R
R
dV
i
C
i
i
dt
dV
dV
C
C
i
dt
dt
δ
δ
δ
⎧
=
=
+
⎪
⎪
⎪
=
= −
+
⎪⎪⎨
⎪
=
=
−
⎪
⎪
⎪
−
=
⎪⎩
(14) (14) The equations (13) and (14) can be rearranged as: 240 MATLAB – A Ubiquitous Tool for the Practical Engineer 1
1
1
2
2
1
1
1
1
1
2
2
2
1
1
1
2
1
1
1
2
2
1
2
2
2
2
1
2
3
1
2
fx
f x
cx
x
x
f
f
f
f
f
sx
cx
sx
f
f
f
x fx
x fx
f
fx
sx
f
f
fx
di
R
V
V
V
dt
L
L
L
L
R
di
V
V
dt
L
L
L
i
dV
V
V
dt
C
RC
RC
i
dV
V
V
dt
C
RC
RC
dV
i
i
dt
C
C
dV
dV
i
C
C
dt
dt
δ
δ
δ
δ
δ
⎧
=
−
+
+
⎪
⎪
⎪
⎪
=
−
−
⎪
⎪
⎪
⎛
⎞
=
−
+
⎪
⎜
⎟
⎪
⎝
⎠
⎨
⎪
⎛
⎞
=
−
+
⎪
⎜
⎟
⎝
⎠
⎪
⎪
⎪
=
−
⎪
⎪
⎪
=
−
⎪⎩
(15) 1
1
1
2
2
1
1
1
1
1
2
2
2
1
1
1
2
1
1
1
2
2
1
2
2
2
2
1
2
3
1
2
fx
f x
cx
x
x
f
f
f
f
f
sx
cx
sx
f
f
f
x fx
x fx
f
fx
sx
f
f
fx
di
R
V
V
V
dt
L
L
L
L
R
di
V
V
dt
L
L
L
i
dV
V
V
dt
C
RC
RC
i
dV
V
V
dt
C
RC
RC
dV
i
i
dt
C
C
dV
dV
i
C
C
dt
dt
δ
δ
δ
δ
δ
⎧
=
−
+
+
⎪
⎪
⎪
⎪
=
−
−
⎪
⎪
⎪
⎛
⎞
=
−
+
⎪
⎜
⎟
⎪
⎝
⎠
⎨
⎪
⎛
⎞
=
−
+
⎪
⎜
⎟
⎝
⎠
⎪
⎪
⎪
=
−
⎪
⎪
⎪
=
−
⎪⎩
(15) (15) Equation (16) can be written in the format of: Equation (16) can be written in the format of: Zx
Ax
B
=
+
(16) Zx
Ax
B
=
+
(1 (16) Capacitor current, inverter current and utility line current and DC- Link capacitors are taken
as state variables: Capacitor current, inverter current and utility line current and DC- Link capacitors are taken
as state variables: 1
2
[
]T
fx
sx
c
x
i
i
V V V
=
(17)
1
2
1
2
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
f
f
L
L
Z
C
C
C
⎡
⎤
⎢
⎥
⎢
⎥
⎢
⎥
= ⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
(18)
[0
0 0 0 ]T
s
B
V
=
−
(19) 1
2
[
]T
fx
sx
c
x
i
i
V V V
=
(17)
1
2
1
2
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
f
f
L
L
Z
C
C
C
⎡
⎤
⎢
⎥
⎢
⎥
⎢
⎥
= ⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
(18) 1
2
[
]T
fx
sx
c
x
i
i
V V V
=
(17)
1
2
1
2
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
f
f
L
L
Z
C
C
C
⎡
⎤
⎢
⎥
⎢
⎥
⎢
⎥
= ⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
(18)
[0
0 0 0 ]T
B
V
(19) (17) (18) [0
0 0 0 ]T
s
B
V
=
−
(19) [0
0 0 0 ]T
s
B
V
=
−
(19) (19) Matrix A depends on each operating mode as such Matrix A depends on each operating mode as such
•
For V01 = +V2 Matrix A depends on each operating mode as such
•
For V01 = +V2 1
2
1
1
1
1
1
0
1
0
1
0
1
0
0
0
1
1
0
0
0
0
0
1
0
0
f
f
R
R
A
R
R
R
R
−
−
−
−
−
−
⎡
⎤
⎢
⎥
−
⎢
⎥
⎢
⎥
−
= ⎢
⎥
⎢
⎥
⎢
⎥
−
⎢
⎥
⎣
⎦
(20) 1
2
1
1
1
1
1
0
1
0
1
0
1
0
0
0
1
1
0
0
0
0
0
1
0
0
f
f
R
R
A
R
R
R
R
−
−
−
−
−
−
⎡
⎤
⎢
⎥
−
⎢
⎥
⎢
⎥
−
= ⎢
⎥
⎢
⎥
⎢
⎥
−
⎢
⎥
⎣
⎦
(20)
•
For V01 = - V2
5
1
T
A
A
=
(21) (20) •
For V01 = - V2 5
1
T
A
A
=
(21) 5
1
T
A
A
= 5
1
T
A
A
= (21) Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression
241 Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t
d 241 •
For V01 = +V1
1
2
2
1
1
1
1
0
1
1
0
0
1
0
0
0
1
1
0
0
1
0
0
0
0
0
f
f
R
R
A
R
R
R
R
−
−
−
−
−
−
⎡
⎤
⎢
⎥
−
⎢
⎥
⎢
⎥
−
= ⎢
⎥
⎢
⎥
−
⎢
⎥
⎢
⎥
⎣
⎦
(22)
•
For V01 = - V1
6
2
T
A
A
=
(23)
•
For V01 = 0
1
2
4
0
1
1
1
0
1
0
0
0
1
1
0
0
0
1
0
0
0
0
1
0
0
0
f
f
R
R
A
−
−
−
⎡
⎤
−
⎢
⎥
−
⎢
⎥
⎢
⎥
=
−
⎢
⎥
⎢
⎥
−
⎢
⎥
−
⎣
⎦
(24) •
For V01 = +V1 •
For V01 = +V1 •
For V01 = +V1
1
2
2
1
1
1
1
0
1
1
0
0
1
0
0
0
1
1
0
0
1
0
0
0
0
0
f
f
R
R
A
R
R
R
R
−
−
−
−
−
−
⎡
⎤
⎢
⎥
−
⎢
⎥
⎢
⎥
−
= ⎢
⎥
⎢
⎥
−
⎢
⎥
⎢
⎥
⎣
⎦
(22) (22) •
For V01 = - V1 6
2
T
A
A
=
(23)
•
For V01 = 0
1
2
4
0
1
1
1
0
1
0
0
0
1
1
0
0
0
1
0
0
0
0
1
0
0
0
f
f
R
R
A
−
−
−
⎡
⎤
−
⎢
⎥
−
⎢
⎥
⎢
⎥
=
−
⎢
⎥
⎢
⎥
−
⎢
⎥
−
⎣
⎦
(24) 6
2
T
A
A
=
(23) (23) (24) Considering the same assumption made earlier that the dc link capacitors have the same
capacitance C1 = C2 = C which implies V1 = V2 = Vdc/2, the state space equation (17) can be
simplified to: '
'
'
Z x
A x
B
=
+
(25)
With '
'
'
Z x
A x
B
=
+
(25) '
'
'
Z x
A x
B
=
+
(25) '
'
'
Z x
A x
B
=
+
(25) With With [
/2]T
fx
sx
c
dc
x
i
i
V V
=
(26)
1
2
'
0
0
0
0
1
0
0
0
0
0
0
0
f
f
T
L
L
Z
C
C
⎡
⎤
⎢
⎥
⎢
⎥
= ⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
(27)
[0
0 0 0 ]T
s
B
V
=
(28)
1
2
'
0
0
0
1
0
0
0
0
0
f
f
R
k
k
R
k
A
k
k
−
−
⎡
⎤
⎢
⎥
−
⎢
⎥
= ⎢
⎥
−
⎢
⎥
⎢
⎥
−
⎣
⎦
(29) (26) 1
2
'
0
0
0
0
1
0
0
0
0
0
0
0
f
f
T
L
L
Z
C
C
⎡
⎤
⎢
⎥
⎢
⎥
= ⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
(27) (27) (28) (29) Where k depends on the operating mode and can take five different values: 1. •
For V01 = +V1 3.1 Harmonic analysis of a nine level cascaded NPC/H-bridge inverter Having realized a nine- level output from the a cascaded 9- level model, it is important to
theoretically investigate its harmonic structure and show how harmonic suppression is
achieved. Based on the principle of double Fourier integral (Holmes & Thomas, 2003). the
first modulation between triangular carrier vcr1, and the positive sinusoidal waveform a
naturally sampled PMW output Vp(t) of equation (30). Where M is the modulation index, Vdc
is the DC link voltage of the PWM inverter and Jn is the nth order Bessel function of the first
kind. 3. Mathematical analysis 0.5 0, -05, -1. re k depends on the operating mode and can take five different values: 1. 0.5 0, -05, -1. 242 MATLAB – A Ubiquitous Tool for the Practical Engineer For a three phase system, Vs is replaced Vs(cosωot), Vs(cosωo-2π/3) and Vs(cosωo+2π/3. similarly the Z, A and B matrices are expanded accordingly to three phase. Where Vs is the
grid voltage. For a three phase system, Vs is replaced Vs(cosωot), Vs(cosωo-2π/3) and Vs(cosωo+2π/3. similarly the Z, A and B matrices are expanded accordingly to three phase. Where Vs is the
grid voltage. 3.1 Harmonic analysis of a nine level cascaded NPC/H-bridge inverter Five- level obtained by taking the differential output between the two legs and is given by
(35). Similarly the output between the other two legs of the second cell of the hybrid model
is achieved by replacing ωs with ωs+ π and ωc with ωc + π/4 which gives another five level
inverter for equation given by equation (34) 1
1
4,8,12
1 3 5
01
8
1
2
cos(
)
( )
(
)cos(
)
2
dc
dc
s
n
m
n
c
s
V
V
t
J
m
V
t
m
M
m
t
n
t
ω
π
π
ω
ω
∞
∞
=
=± ± ±
⎧
+
⎪⎪
= ⎨
⎪
+
⎪⎩
∑
∑
(34)
4
1
1
4,8,12
1 3 5
02
8
( 1)
2
cos(
)
( )
(
)cos(
)
2
m n
dc
dc
s
n
m
n
c
s
V
V
t
J
m
V
t
m
M
m
t
n
t
ω
π
π
ω
ω
+
∞
∞
=
=± ± ±
⎧
⎪
−
−
−
⎪
= ⎨
⎪
⎪
+
⎩
∑
∑
(35) 1
1
4,8,12
1 3 5
01
8
1
2
cos(
)
( )
(
)cos(
)
2
dc
dc
s
n
m
n
c
s
V
V
t
J
m
V
t
m
M
m
t
n
t
ω
π
π
ω
ω
∞
∞
=
=± ± ±
⎧
+
⎪⎪
= ⎨
⎪
+
⎪⎩
∑
∑
(34) (34) 4
1
1
4,8,12
1 3 5
02
8
( 1)
2
cos(
)
( )
(
)cos(
)
2
m n
dc
dc
s
n
m
n
c
s
V
V
t
J
m
V
t
m
M
m
t
n
t
ω
π
π
ω
ω
+
∞
∞
=
=± ± ±
⎧
⎪
−
−
−
⎪
= ⎨
⎪
⎪
+
⎩
∑
∑
(35) (35) Equations (34) and (35) clearly show that for five- level inverter, the proposed control
strategy has achieved; Suppression of carrier harmonics to multiples of four; Elimination of
even side harmonics around multiples of four carrier harmonics of Multiples of four carrier
harmonics. Finally the output for a nine level is achieved differentiating the output voltage
between the two cells of the five level cells and this is given by equation (36). 3.1 Harmonic analysis of a nine level cascaded NPC/H-bridge inverter It can be
concluded that for a cascaded N-level inverter the carrier harmonic order is pushed up by
factor of 4N where N is the number of cascaded hybrid inverters. The output voltages and
spectral waveforms to confirm the validation of the control strategy using this approach of
double Fourier transform will be discussed later. 1
1
8,16,24
1 3 5
8
1
4
cos(
)
( )
(
)cos(
)
2
dc
dc
s
n
m
n
an
c
s
V
V
t
J
m
V
t
m
M
m
t
n
t
ω
π
π
ω
ω
∞
∞
=
=± ± ±
⎧
+
⎪⎪
= ⎨
⎪
+
⎪⎩
∑
∑
(36) (36) 3.1 Harmonic analysis of a nine level cascaded NPC/H-bridge inverter Using vcr2 which is the same carrier but displaced by minus unity, the naturally
sampled PWM output Vn is as given in equation (31) 1
1
1
0
1
1
1
0
2
1
cos
(
)
2
2
2
2
1
( )
sin
cos
2
(
)sin(
)
cos(
)
2
2
dc
dc
dc
s
m
dc
p
s
n
m
n
n
c
s
V
V
M
V
t
J
m
M
m
V
V t
m
t
J
m
m
M
m
n
n
t
n
t
π
ω
π
π
ω
π
π
π
ω
ω
∞
=
∞
∞
=
=−∞
⎧
⎪
+
+
⎪
⎪
⎪
=
+
⎨
⎪
⎪
⎪
+
+
⎪⎩
∑
∑∑
∓
(30) (30) 1
1
1
0
1
1
1
0
2
1
cos
(
)
2
2
2
2
1
( )
sin
cos
2
(
)sin(
)
cos(
)
2
2
dc
dc
dc
s
m
dc
n
s
n
m
n
n
c
s
V
V
M
V
t
J
m
M
m
V
V t
m
t
J
m
m
M
m
n
n
t
n
t
π
ω
π
π
ω
π
π
π
ω
ω
∞
=
∞
∞
=
=−∞
⎧
⎪
−
−
⎪
⎪
⎪
=
+
⎨
⎪
⎪
⎪
+
+
⎪⎩
∑
∑∑
∓
(31) (31) (
)sin(
)
cos(
)
2
2
c
s
m
M
m
n
n
t
n
t
π
π
ω
ω
⎪
+
+
⎪⎩ The output of leg ‘a’ is given by Va (t) = Vp (t) –Vn (t) which is: The output of leg ‘a’ is given by Va (t) = Vp (t) –Vn (t) which is: The output of leg ‘a’ is given by Va (t) = Vp (t) –Vn (t) which is: 1
1
2,4,6
1 3 5
4
1
cos(
)
( )
(
)cos(
)
2
dc
dc
s
n
m
n
a
c
s
V
V
t
J
m
V t
m
M
m
t
n
t
ω
π
π
ω
ω
∞
∞
=
=± ± ±
⎧
+
⎪⎪
= ⎨
⎪
+
⎪⎩
∑
∑
(32) (32) The output of leg ‘b’ is realized by replacing ωs with ωs+ π and using vcr2 which is same as
phase displacing vcr1 by minus unity which gives The output of leg ‘b’ is realized by replacing ωs with ωs+ π and using vcr2 which is same as
phase displacing vcr1 by minus unity which gives 1
1
2,4,6
1 3 5
4
( 1)
cos(
)
( )
(
)cos(
)
2
m n
dc
dc
s
n
m
n
b
c
s
V
V
t
J
m
V t
m
M
m
t
n
t
ω
π
π
ω
ω
+
∞
∞
=
=± ± ±
⎧
−
−
−
⎪⎪
= ⎨
⎪
+
⎪⎩
∑
∑
(33) (33) Cascaded NPC/H-Bridge Inverter 243 Cascaded NPC/H Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression From equations (32) and (33), it can be clearly deduced that that odd carrier harmonics and
even sideband harmonics around even carrier harmonic orders are completely eliminated. 4. Proposed hybrid control method The above section has illustrated in general the switching technque for one cell of the
cascaded NPC/H-bridge model, because of the modularity of the model, two cells will be
considered for modulatin and analysis in this section.For the two cells an improved strategy
for realizing nine level output is proposed in this book chapter. The article uses the principle
of decomposition where each leg is treated independently and gives a three level output
(Naderi &. Rahmati, 2008). Positive and negative legs are connected together back to back and they share the same
voltage source Vdc. PD modulation is used for achieving three level output (Rodriguez et al.,
2002). To achieve a five level PWM output two triangular carriers Vcr1 and Vcr2 in phase but
vertically disposed and modulating wave phase shifted by π are used. The multilevel
converter model is modulated using phase shifted PWM technique as illustrated in fig. 3 244 MATLAB – A Ubiquitous Tool for the Practical Engineer and 4 for the two NPC/H-Bridge cells. Finally a nine- level PWM output is achieved by
using the same two carriers but phase shifted by π/4 and modulating wave phase shifted by
π as shown in fig. 5. This is a simple control strategy that can be easily implemented in a
digital signal processor. The switching states for one phase leg of a nine- level NPC/H-
bridge inverter is shown in table 2, as can be seen there several redundant states which can
be utilized in DC voltage balance, this is not within the scope of this paper. The control strategy has two advantages as compared to multicarrier PWM approach
(Holmes & McGrath, 2001). First for an N-level cascaded NPC/H-bridge PWM inverter, we
can use a switching frequency of 4N times less to achieve the same spectrum as multicarrier
approach. This has an advantage of reducing the switching losses, which is an important
feature in high power application. Secondly the multicarrier PWM approach requires 8
carriers to achieve nine level output, but the proposed control strategy requires only one
carrier phase shifted by (N-1)π/4 where N is the number of series connected NPC/H-Bridge
inverter. and 4 for the two NPC/H-Bridge cells. Finally a nine- level PWM output is achieved by
using the same two carriers but phase shifted by π/4 and modulating wave phase shifted by
π as shown in fig. 5. 4. Proposed hybrid control method This is a simple control strategy that can be easily implemented in a
digital signal processor. The switching states for one phase leg of a nine- level NPC/H-
bridge inverter is shown in table 2, as can be seen there several redundant states which can
be utilized in DC voltage balance, this is not within the scope of this paper. and 4 for the two NPC/H-Bridge cells. Finally a nine- level PWM output is achieved by
using the same two carriers but phase shifted by π/4 and modulating wave phase shifted by
π as shown in fig. 5. This is a simple control strategy that can be easily implemented in a
digital signal processor. The switching states for one phase leg of a nine- level NPC/H-
bridge inverter is shown in table 2, as can be seen there several redundant states which can
be utilized in DC voltage balance, this is not within the scope of this paper. The control strategy has two advantages as compared to multicarrier PWM approach
(Holmes & McGrath, 2001). First for an N-level cascaded NPC/H-bridge PWM inverter, we
can use a switching frequency of 4N times less to achieve the same spectrum as multicarrier
approach. This has an advantage of reducing the switching losses, which is an important
feature in high power application. Secondly the multicarrier PWM approach requires 8
carriers to achieve nine level output, but the proposed control strategy requires only one
carrier phase shifted by (N-1)π/4 where N is the number of series connected NPC/H-Bridge
inverter. 0.005
0.01
0.015
0.02
0.025
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
(a)
(b)
Fig. 3. (a) PWM scheme and (b) output voltage waveform for one cell of NPC/H-Bridge
inverter
Vcr2
Vcr1 0.005
0.01
0.015
0.02
0.025
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
(a)
Vcr2
Vc (a) (b) (b) Fig. 3. (a) PWM scheme and (b) output voltage waveform for one cell of NPC/H-Bridge
inverter Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t 245 0.005
0.01
0.015
0.02
0.025
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
(a)
(b)
4. 4. Proposed hybrid control method (a) Phase shifted PWM scheme and (b) output voltage waveform for the second cell o
aded NPC/H-Bridge inverter 0.005
0.01
0.015
0.02
0.025
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
(a) 0.005
0.01
0.015
0.02
0.025
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1 Fig. 4. (a) Phase shifted PWM scheme and (b) output voltage waveform for the second cell of
cascaded NPC/H-Bridge inverter MATLAB – A Ubiquitous Tool for the Practical Engineer 246 0
0.002
0.004
0.006
0.008
0.01
0.012
0.014
0.016
0.018
0.02
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
(a)
(b)
Fig. 5. (a) PWM scheme and (b) output voltage waveform for a nine level cascaded NPC/H-
Bridge inverter 0
0.002
0.004
0.006
0.008
0.01
0.012
0.014
0.016
0.018
0.02
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
(a) (a) (b) Fig. 5. (a) PWM scheme and (b) output voltage waveform for a nine level cascaded NPC/H-
Bridge inverter 5. MATLAB simulation Part of the Matlab simulation has already been carried out in section 4 to investigate the
proposed phase shifted PWM control technique. In order verify that a nine- level output is
achieved by cascading two NPC/H-Bridge PWM inverter and properly phase shifting the
carrier and the modulating wave, a model as shown in fig. 6 was developed and simulated
in MATLAB. The control strategy to minimize harmonics was designed and developed in
MATLAB as shown in fig. 7 (wanjekeche et.al., 2009). It is assumed that the dc voltage input
for each module is E = 1OOV. The inverter operates under the condition of fm=50HZ, mf=20
for a five level output and ma=0.9. The device switching frequency is found from fsw,dev= mf/2
X fm=500HZ Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression 247 Fig. 6. Four legs of a nine-level cascaded NPC/H-bridge inverter Fig. 6. Four legs of a nine-level cascaded NPC/H-bridge inverter MATLAB – A Ubiquitous Tool for the Practical Engineer 248 Fig. 7. Control strategy for a nine-level cascaded NPC/H-bridge inverter Fig. 7. Control strategy for a nine-level cascaded NPC/H-bridge inverter 5.1 Simulation results and discussion Five- level inverter output are shown in figs.8, 9 and 10 for various switching frequency. Fig.8 shows the simulated waveform for the phase voltage V01 of the NPC/H-Bridge PWM
inverter and its harmonic content. The waveform V01 is a five voltage levels, whose
harmonics appear as sidebands centered around 2mf and its multiples such as 4mf, 6mf. This
simulation verifies analytical equation (34) which shows that the phase voltage does not
contain harmonics lower than the 31st, but has odd order harmonics (i.e. n=±1±3±5) centered
around m=4, 8, 12. Figs. 9 & 10 shows five- level NPC/H-Bridge inverter output for device
inverter switching frequency of 1000HZ and 200HZ respectively. Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression
249
(a)
(b)
Fig. 8. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase voltage
(fm=50HZ, fsw,dev=500HZ, mf=20, ma=0.9) 249 (a) (a) (a) (b)
Fig. 8. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase voltage
(fm=50HZ, fsw,dev=500HZ, mf=20, ma=0.9) (b) (b) Fig. 8. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase voltage
(fm=50HZ, fsw,dev=500HZ, mf=20, ma=0.9) MATLAB – A Ubiquitous Tool for the Practical Engineer
250
(a)
(b)
. Fig. 9. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase voltage
(fm=50HZ, fsw,dev=1000HZ, mf=40, ma=0.9) MATLAB – A Ubiquitous Tool for the Practical Engineer 250 (a) (a)
(b)
. Fig. 9. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase voltage
(fm=50HZ, fsw,dev=1000HZ, mf=40, ma=0.9) . Fig. 9. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase voltage
(fm=50HZ, fsw,dev=1000HZ, mf=40, ma=0.9) Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t 251 (a)
(b)
ig. 10. (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase
oltage (fm=50HZ, fsw,dev=2000HZ, mf=80, ma=0.9
ig. 11 shows the waveform of the phase voltage of a nine level NPC/H-Bridge PWM
nverter. It has sidebands around 4mf and its multiples, this shows further suppression in
armonic content. This topology operates under the condition of fm=50HZ, mf=40 and (b) (b) g. 10. 5.1 Simulation results and discussion (a) Waveform and (b) Spectrum for a five level NPC/H-Bridge inverter phase
oltage (fm=50HZ, fsw,dev=2000HZ, mf=80, ma=0.9 Fig. 11 shows the waveform of the phase voltage of a nine level NPC/H-Bridge PWM
inverter. It has sidebands around 4mf and its multiples, this shows further suppression in
harmonic content. This topology operates under the condition of fm=50HZ, mf=40 and
ma=0.9. The device switching frequency is found from fsw,dev= mf/4 X fm=500HZ. This
simulation verifies analytical equation (36) which shows that the phase voltage does not
contain harmonics lower than the 67th, but has odd order harmonics (i.e. n=±1±3±5) centered
around m=8, 16, 32. As can be seen from fig. 12, a switching frequency of 1KHZ which fits
most of high power switching devices has a THD of 0.18% this makes the topology a perfect
fit for most high power application such as utility interface power quality control and
Medium Voltage drives. Fig. 11 shows the waveform of the phase voltage of a nine level NPC/H-Bridge PWM
inverter. It has sidebands around 4mf and its multiples, this shows further suppression in
harmonic content. This topology operates under the condition of fm=50HZ, mf=40 and
ma=0.9. The device switching frequency is found from fsw,dev= mf/4 X fm=500HZ. This
simulation verifies analytical equation (36) which shows that the phase voltage does not
contain harmonics lower than the 67th, but has odd order harmonics (i.e. n=±1±3±5) centered
around m=8, 16, 32. As can be seen from fig. 12, a switching frequency of 1KHZ which fits
most of high power switching devices has a THD of 0.18% this makes the topology a perfect
fit for most high power application such as utility interface power quality control and
Medium Voltage drives. MATLAB – A Ubiquitous Tool for the Practical Engineer
252
(a)
(b)
Fig. 11. (a) Waveform and (b) Spectrum for a nine- level cascaded NPC/H-Bridge inverter
phase voltage (fm=50HZ, fsw,dev=500HZ, mf=40, ma=0.9) MATLAB – A Ubiquitous Tool for the Practical Engineer 252 (a) (b)
Fig. 11. (a) Waveform and (b) Spectrum for a nine- level cascaded NPC/H-Bridge inverter
phase voltage (fm=50HZ, fsw,dev=500HZ, mf=40, ma=0.9) (b) Fig. 11. (a) Waveform and (b) Spectrum for a nine- level cascaded NPC/H-Bridge inverter
phase voltage (fm=50HZ, fsw,dev=500HZ, mf=40, ma=0.9) Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression 253 (a)
(b)
Fig. 12. 5.1 Simulation results and discussion (a) Waveform and (b) Spectrum for a nine- level cascaded NPC/H-Bridge inverter
phase voltage (fm=50HZ, fsw,dev=1000HZ, mf=80, ma=0.9) (a) (b) (b) Fig. 12. (a) Waveform and (b) Spectrum for a nine- level cascaded NPC/H-Bridge inverter
phase voltage (fm=50HZ, fsw,dev=1000HZ, mf=80, ma=0.9) 6. Comparison of the proposed control technique with conventional PWM
multicarrier approach As can be seen from fig. 1, to achieve the same voltage levels N for each phase, only (N-1)/4
separate dc sources are needed for one phase leg converter of the cascaded NPC/H-bridge
model, whereas (N-1)/2 separate voltage voltages is need for cascaded H –bridge inverter. Thus for an n- cascaded NPC/H-bridge inverter, the number of separate DC sources S is
given by: As can be seen from fig. 1, to achieve the same voltage levels N for each phase, only (N-1)/4
separate dc sources are needed for one phase leg converter of the cascaded NPC/H-bridge
model, whereas (N-1)/2 separate voltage voltages is need for cascaded H –bridge inverter. model, whereas (N-1)/2 separate voltage voltages is need for cascaded H –bridge inverter. Thus for an n- cascaded NPC/H-bridge inverter, the number of separate DC sources S is
given by: 1
4
N
S
−
=
(37) (37) Table 3 shows comparison on the number of components for various multilevel inverters,
cascaded NPC/H-bridge inverter requires 16 switching devices just as the other topologies
but used only two carriers for any level of voltage output. For comparison between the two
cascaded inverters it is readily shown in table 4 that the NPC/H-bridge inverter has an
advantage of realizing the same voltage level as cascaded H-bridge inverter with a half
number of separate DC sources which is more expensive as compared to clamping diodes. MATLAB – A Ubiquitous Tool for the Practical Engineer 254 Diode
clamped
Flying
capacitor
Cascaded
H- bridge
Cascaded
NPC/H-
bridge
Switching devices
16
16
16
16
Clamping diodes
56
0
0
8
Flying capacitors
0
56
0
0
Carriers
8
8
4
2
Separate cells
0
0
4
2
Separate dc
sources
1
0
4
2
Table 3. Component comaprison for different multilevel inverters for nine level voltage
output
Topology
No. of
Components Table 3. Component comaprison for different multilevel inverters for nine level voltage
output Table 3. Component comaprison for different multilevel inverters for nine level voltage
output Cascaded
H- bridge
Cascaded
NPC/H-bridge
Switching devices
2N-1
2N-1
Clamping diodes
0
N-1
Flying capacitors
0
0
Carriers
(N-1)/2
2
Separate cells
(N-1)/2
(N-1)/4
Separate dc sources
(N-1)/2
(N-1)/4
Table 4. Component comaprison for different multilevel inverters for nine level voltage
output
Topology
No. 6. Comparison of the proposed control technique with conventional PWM
multicarrier approach of
Components Cascaded
H- bridge
Cascaded
NPC/H-bridge
Switching devices
2N-1
2N-1
Clamping diodes
0
N-1
Flying capacitors
0
0
Carriers
(N-1)/2
2
Separate cells
(N-1)/2
(N-1)/4
Separate dc sources
(N-1)/2
(N-1)/4
Table 4. Component comaprison for different multilevel inverters for nine level voltage
output
Topology
No. of
Components Table 4. Component comaprison for different multilevel inverters for nine level voltage
output Table 4. Component comaprison for different multilevel inverters for nine level voltage
output 6.1 Comparison of the MATLAB simulation results of the two PWM control methods
To clearly investigate the superiority of the model under the proposed PWM control
technique, Matlab simulation results was carried out on a cascaded NPC/H-bridge nine
level inverter model under the conditions of fm=50HZ, fc =1000Hz and ma=0.9. With the proposed Phase – shifted PWM technique, there is further harmonic suppression
as shown in fig. 13 (b), as compared to conventional PWM Phase shifted approach. This is
clearly illustrated in fig. 13 (a) where Phase Disposition and Phase shifted PWM
modulation strategy is adopted (Jinghua & Zhengxi, 2008). This is beacuse with
conventional PWM multicarrier approach, optimum harmonic cancellation is achieved by
phase shifting each carrier by (i-1)π/N (Holmes & Thomas, 2003). where i is the ith
converter, N is the number of series – connected single the multicarrier PWM approach
requires 8 carriers to achieve nine level output, but the proposed control strategy requires
only one carrier phase shifted by (N-1)π/4 as stated in section 4.1(Wanjekeche et al.,
2009). level inverter model under the conditions of fm=50HZ, fc =1000Hz and ma=0.9. With the proposed Phase – shifted PWM technique, there is further harmonic suppression
as shown in fig. 13 (b), as compared to conventional PWM Phase shifted approach. This is
clearly illustrated in fig. 13 (a) where Phase Disposition and Phase shifted PWM
modulation strategy is adopted (Jinghua & Zhengxi, 2008). This is beacuse with
conventional PWM multicarrier approach, optimum harmonic cancellation is achieved by
phase shifting each carrier by (i-1)π/N (Holmes & Thomas, 2003). where i is the ith
converter, N is the number of series – connected single the multicarrier PWM approach
requires 8 carriers to achieve nine level output, but the proposed control strategy requires
only one carrier phase shifted by (N-1)π/4 as stated in section 4.1(Wanjekeche et al.,
2009). 6. Comparison of the proposed control technique with conventional PWM
multicarrier approach Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t
d Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression scaded NPC/H-Bridge Inverter
h Simplified Control Strategy and Superior Harmonic Suppression
(a)
Module 1 output
Voltage harmonics 255 (a)
Module 1 output
Voltage harmonics Module 1 output
Voltage harmonics 256 MATLAB – A Ubiquitous Tool for the Practical Engineer (b)
Fig. 13. Spectra voltage waveforms of NPC/H-bridge topology using (a) conventional
multicarrier phase shifted PWM approach (b) proposed phase shifted PWM approach
Superposed output
Voltage harmonics (b)
Superposed output
Voltage harmonics Superposed output
Voltage harmonics (b) Fig. 13. Spectra voltage waveforms of NPC/H-bridge topology using (a) conventional
multicarrier phase shifted PWM approach (b) proposed phase shifted PWM approach 8. References Benslimane, T. (2007). Open Switch Faults Detection and Localization Algorithm for Three
Phase Shunt Active Power Filter based on Two Level Voltage Source Inverter,”
Electronics and Electrical Engineering Conference 2(74), pp. 21- 24, ISSN 1392 -1215 Franquelo, L.G.; Rodriquez, J.; Leon, J.I.; Kouro, S.; Portillo, R. & Prats, M.A.M. (2008). The
Age of Multilevel Converters Arrives, IEEE Industrial Electronics Magazine, pp. 28-
39, ISSN 1932-4529 Gupta, R.; Ghosh, A. & Joshi, A. (2008). Switching Characteristics of Cascaded Multilevel
Inverter Controlled Systems, IEEE Transactions on Industrial Electronics, vol.55, no.3,
pp. 1047- 1058, ISSN: 0278-0046 pp
Holmes, D.G. & McGrath, B.P. (2001). Opportunities for harmonic cancellation with carrier-
based PWM for two – level and multilevel cascaded inverters, IEEE Transaction on
Industrial Applications, vol. 37, no. 2, pp.547 – 582, ISSN 0093-9994, August 2002 Kouro, S.; Rebolledo J. & Rodriquez J. (2005). Reduced switching frequency modulation
algorithm for high power multilevel inverters, IEEE Transaction on Industrial
Electronics, vol.54, no.5, pp. 2894- 2901, ISBN 0-7803-9033-4, January 2006 pp
y
Lai, J. S. & Peng, F. Z. (1995). Multilevel Converters - A New Breed of Power Converters,”
IEEE Transactions on Industry Applications, vol. 32, no. 3, pp. 509-517, ISBN 0-7803-
3008-0 August 2002 Peng, F. Z.; Lai, J. S.; McKeever, J. W. & VanCoevering, J. (1996). A Multilevel Voltage-
Source Inverter with Separate DC Sources for Static Var Generation, IEEE
Transactions on Industry Applications, vol. 32, no. 5, pp. 1130-1138, Aug. 2002. ISBN:
0-7803-3008-0 Rodriguez, J.; Lai, J. S. & Peng, F. Z. (1995). Multilevel Inverters: Survey of Topologies,
Controls, and Applications, IEEE Transactions on Industry Applications, vol. 49, no. 4,
pp. 724-738, ISSN 0278-0046 pp
Sinha, G. & Lipo, T. A. (1996). A Four Level Rectifier-Inverter System for Drive Applications,
IEEE-IAS Conference Record, pp. 980-987, ISBN 0-7803-3544-9, August 2002 Tolbert, L. M.; Peng, F. Z. & Habetler, T. (1999). Multilevel Converters for Large Electric
drives, IEEE Trans. Ind. Application, vol.35, pp. 36-44, ISSN 0093-9994, August 2002 Manjrekar, M.D. & Lipo, T.A. (1988). A hybrid multilevel inverter topology for drive
applications, IEEE APEC, pp. 523-529, ISBN 0-7803-4340-9, August 2002 pp
pp
Manjrekar, M.D. & Lipo, T.A. (1998). A generalized str
Proc. IEEE PEDS, 62-67, ISBN 0-7803-4879-6 pp
pp
g
Manjrekar, M.D. & Lipo, T.A. (1998). A generalized structure of multilevel power converter,
Proc. IEEE PEDS, 62-67, ISBN 0-7803-4879-6 Manjrekar, M.D. & Lipo, T.A. (2000). 7. Conclusion In this chapter it has been demonstrates with proper modeling of the converter, the
operating characteristic and the control technique to be applied on the model can be easily
found. This can be used to develop standard model for cascaded NPC/H-bridge inverter
which is currently not available. In this chapter it has been demonstrates with proper modeling of the converter, the
operating characteristic and the control technique to be applied on the model can be easily
found. This can be used to develop standard model for cascaded NPC/H-bridge inverter
which is currently not available. y
The article has developed an improved topology that can be used to achieve a nine- level
NPC/H-Bridge PWM inverter. It has been clearly shown that five level NPC/H-Bridge
inverter that has been proposed by many researchers gives a higher THD which is not
acceptable in most high and medium power application unless a filter is used. And since
there is limited research on cascaded this important hybrid model, the chapter has
developed a novel phase shifted PWM control technique that was tested on a two cell
cascaded NPC/H-bridge model. In the proposed control technique it has been shown that
by properly phase shifting both the modulating wave and the carrier, a nine- level voltage
output can be achieved with a reduced harmonic content. With a THD of 0.18% without
a filter, this makes the control strategy for a cascaded nine level NPC/H-bridge
inverter a good option for medium and high power application such as utility
interface and medium drives. The simulation results obtained clearly verifies the analytical equations from double Fourier
transform, showing that a nine- level output has multiples of eighth- order cross modulated
harmonics. From the mathematical analysis it has been shown that cross modulated
harmonics for a generalized m- level cascaded NPC/H-Bridge inverter is a multiple of 4N
where N is the number of series connected NPC/H-Bridge inverter And finally the superiority of the proposed phase shifted PWM control technique is
validated by comparing its waveform spectra with that of the conventional phase shifted
PWM technique and it was shown the inverter exhibits reduced harmonic content Cascaded NPC/H-Bridge Inverter
with Simplified Control Strategy and Superior Harmonic Suppression Cascaded NPC/H-Bridge Inverter
ith Si
lifi d C
t
l St
t 257 8. References Hybrid multilevel power conversion system: A
competitive solution for higher power application, IEEE Transaction on Industry
Application, Vol. 36, no. 3, pp. 834-841, ISSN 0093-9994, August 2002 Corzine, K. & Familiant, Y. (2002). A new cascaded multilevel H- bridge drive, IEEE Trans on
Power Electronics, Vol. 17, no.1, pp. 125-131, ISSN 0885-8993 Lund, R. et. al., (1999). Control strategies for hybrid seven level inverter, EPE Conference
Proceedings Sneineh, A.A.; Wang, M. W. & Tian, K. (2006). A new topology for capacitor clamp cascaded
multilevel converters, IEEE –IPEMC, pp. 1-5, ISSN 1-4244-0448-7, February 2009 Park J. et. al., (2003). A new single phase 5 – level PWM inverter employing a deadbeat
control scheme, IEEE Transaction on Power Electronics, vol.18, no.3, pp. 831-843, ISSN
0885-8993 258 MATLAB – A Ubiquitous Tool for the Practical Engineer Zhang, L.; Watkins, S.J. & Shepherd, W. (2002). Analysis and control of multilevel flying
capacitor inverter, IEEE CIEP, pp. 66-71, ISBN 0-7803-7640-4, August 2003 Ding, K. et. al., (2004). A novel hybrid diode clamp cascade multilevel converter for high
power application, IEEE Transaction on Industry Application, 39th IAS Annual
Meeting, 820-827, ISBN 0-7803-8486-5 Duarte, J.L.; Jullicher, P.J.M.; Offringa L.J.J. & Groningen, W.D.H. (1997). Stability analysis of
multilevel converters with imbricated cells, EPE Conference Proceedings, pp. 168-174. Rojas, R. & Ohnishi, T. (1997). PWM control method with reduced of total capacitance
required in a three- level inverter, COBEP Conference Proceedings, pp. 103-108 Wu, C.M.; Lau W.H. & Chung, H. (1999). A five-level neutral-point-clamped H-bridge PWM
inverter with superior harmonics suppression: A theoretical analysis, ISACS ’99,
proceedings of the 1999 IEEE international symposium, vol. 5, pp.198-201 p
g
f
y p
pp
Cheng, Z. & Wu, B. (2007). A novel switching sequence design for five-Level NPC/H-Bridge
inverters with improved output voltage spectrum and minimized device switching
frequency, IEEE Transactions on Power Electronics, vol. 22 no.6, 2138 – 2145, ISSN
0885-8993 Naderi, R. & Rahmati, A. (2008). Phase shifted carrier PWM technique for general
cascade inverters, IEEE Transactions on power electronics, vol. 23, no.3, pp.1256-
1269, ISSN 0885-8993 Jinghua, Z. & Zhengxi, L. (2008). Research on hybrid modulation strategies based on general
hybrid topology of multilevel inverter, International symposium on power electronics
and electric drives, automation and motion (SPEEDAM), pp. 784 – 788, ISBN 978-1-
4244-1663-9 Holmes, D.G. & Thomas, A.L. (2003). Pulse Width Modulation for Power Converters –principles
and practices, IEEE press series, A John Wiley & Sons inc. 1. Introduction DC-DC switching converters are devices usually used to adapt primary energy sources to
the load requirements (Erickson & Macksimovic, 2001). These devices produce a regulated
output voltage despite changes in the feed voltage or in the load current. There are three
basic topologies of dc-dc converters, namely the buck, the boost and the buck-boost converter. The buck converter is used to reduce output voltage, while the boost converter increase the
output voltage. In the buck-boost converter, the output voltage can be maintained either
higher or lower than the source but in the opposite polarity. These basic converters consist of
two reactive elements; namely, an inductor and a capacitor, besides a transistor and a diode
to perform the commutation, the size of reactive elements are chosen to guarantee a low level
of ripple and hence an averaged dynamical model behavior is a good approximation of the
switched behavior. In order to maintain a regulated output and to have a damped enough response some control
loops are added to command the converter. The signal which drives the transistor used to be
a squared, constant-period and high frequency signal. The design of the control loops is commonly based on linearized dynamic models around
equilibrium point of the converter (Erickson & Macksimovic, 2001). Nevertheless, commonly
the averaged dynamical models of these plants are nonlinear and their linearization is non
minimum phase. Therefore, using linear controllers can only ensures stability and dynamic
performances around equilibrium point, and hence, instabilities or bad performances may
appear when large signal perturbations occur. This fact has prompted several authors to apply
nonlinear control methods to regulate switching converters. g
g
Some of the first researches on nonlinear controller design for dc-dc converters can be found
in the studies of (Sanders & Verghese, 1992) and (Kawasaki et al., 1995). These authors
propose non-linear strategies based on Lyapunov functions, which allows the converter to
ensure stability over a wide range of operating conditions. More recent studies are those
of (Leyva et al., 2006) and (He & Luo, 2006) which derive robust non-linear controller for
large-signal stability in dc-dc converters and present efficient implementations. g
g
y
p
p
Furthermore, robust control approaches have been applied in dc-dc converters which take
into account nonlinearities and uncertainties (Olalla et al., 2009; 2010). Another promising nonlinear technique for controlling power converters is the model-based
fuzzy control technique. 8. References publication, ISBN: 978-0-
471-20814-3, 445 Hoes Lane, Piscataway NJ 0885 y
Wanjekeche, T. Jimoh, A.A. & Nicolae, D.V. (2009). A Novel Multilevel 9- level inverter
based on 3 – level NPC/H-Bridge topology for Photovoltaic application”
international review of electrical engineering, Vol. 4, No.5, ISSN 1827- 6679 f
g
g
Wanjekeche, T. Nicolae, D.V. & Jimoh, A.A. (2009). A Cascaded NPC/H-bridge inverter
with simplified control strategy and minimum component count, IEEE – Africon,
pp. 1-6, ISBN 978-1-4244-3918-8 13 2. Modeling of DC-DC converters. A dynamical review This section presents basic PWM converters and their state-space models which are used in
the following sections. Specifically, the section describes the dynamic behavior of buck and
boost converters. 1. Introduction The first
example shows the LMI controller of a buck converter, while in the second, we obtain an LMI
Fuzzy controller for a boost converter working at different operating point. Both examples
have been simulated with Matlab and the results are in perfect agreement with the design )
Nowadays, thanks to the powerful computational tools and optimization techniques, many
robust and fuzzy control designs based on LMIs can be readily solved. Matlab is a powerful
tool in this process. The LMI Toolbox of Matlab is an efficient software tool based on
interior point methods (Gahinet et al., 1995), which it can be used to numerically solve many
LMI control problems that otherwise could not be solved since they have not an analytical
solution. The main advantage of the LMI formulations is the ability to combine various design
constraints and objectives in a numerically tractable manner. j
y
This chapter presents a synthesis of LMI fuzzy controllers for dc-dc converters. The chapter
describes in detail a compact control design methodology which takes into account constraints
such as: control effort and the decay rate of state variables. The chapter is organized as
follows: First, in section 2, we review the dynamics of a buck and a boost converter. In section
3, we introduce the T-S fuzzy representation of dc-dc converters, with their corresponding
uncertainties. Aspects of the LMI fuzzy control design are explained in section 4. In section
5, we present two design examples to illustrate the advantages of the procedure. The first
example shows the LMI controller of a buck converter, while in the second, we obtain an LMI
Fuzzy controller for a boost converter working at different operating point. Both examples
have been simulated with Matlab and the results are in perfect agreement with the design
specification. Finally, we summarize the main ideas in section 6. 1. Introduction The model-based fuzzy approaches begin by constructing the 2260 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer corresponding (T-S) Takagi−Sugeno fuzzy model representation of the nonlinear system
(Tanaka & Wang, 2001). This T-S fuzzy representation is described by fuzzy rules IF-THEN
which represent local linear input-output relations of the nonlinear plant. Once fuzzy rules
are obtained with linear submodels, the control design is based on the technique known
as Parallel Distributed Compensator (PDC), where each control rule is designed from the
corresponding rule of the T-S fuzzy model (Korba et al., 2003). The stability analysis is
carried out using Lyapunov functions on the closed-loop system. The Lyapunov functions are
formulated into linear matrix inequalities (LMIs). This approach is fundamentally different
from heuristics based fuzzy control (Tanaka & Wang, 2001) where the rules are based on
heuristic knowledge. A model-based fuzzy control for dc-dc converters have been described
in (Kuang et al., 2006), where the authors show a fuzzy law for the buck and ZVT buck
converters. Other authors who applied this technique in dc-dc converters are (Lan & Tan,
2009) )
Nowadays, thanks to the powerful computational tools and optimization techniques, many
robust and fuzzy control designs based on LMIs can be readily solved. Matlab is a powerful
tool in this process. The LMI Toolbox of Matlab is an efficient software tool based on
interior point methods (Gahinet et al., 1995), which it can be used to numerically solve many
LMI control problems that otherwise could not be solved since they have not an analytical
solution. The main advantage of the LMI formulations is the ability to combine various design
constraints and objectives in a numerically tractable manner. This chapter presents a synthesis of LMI fuzzy controllers for dc-dc converters. The chapter
describes in detail a compact control design methodology which takes into account constraints
such as: control effort and the decay rate of state variables. The chapter is organized as
follows: First, in section 2, we review the dynamics of a buck and a boost converter. In section
3, we introduce the T-S fuzzy representation of dc-dc converters, with their corresponding
uncertainties. Aspects of the LMI fuzzy control design are explained in section 4. In section
5, we present two design examples to illustrate the advantages of the procedure. Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters Tool for Design of Fuzzy LMI Controller in DC-DC Converters
Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters 3
261 Vg
R
+
−
u = 1
iL
vC
+
−
C
u = 0
L
Fig. 1. Schematic circuit of a buck converter
Vg
R
+
−
iL
vC
+
−
C
L
(a)
Vg
R
+
−
iL
vC
+
−
C
L
(b)
Fig. 2. Equivalent circuit during Ton (a) and To f f (b). Vg
R
+
−
u = 1
iL
vC
+
−
C
u = 0
L
Fig. 1. Schematic circuit of a buck converter R Fig. 1. Schematic circuit of a buck converter Fig. 1. Schematic circuit of a buck converter Fig. 1. Schematic circuit of a buck converter Vg
R
+
−
iL
vC
+
−
C
L
(a)
Vg
R
+
−
iL
vC
+
−
C
L
(b) Vg
R
+
−
iL
vC
+
−
C
L
(a)
Vg
R
+
−
iL
vC
+
−
C
L
(b) (a) Fig. 2. Equivalent circuit during Ton (a) and To f f (b). Fig. 2. Equivalent circuit during Ton (a) and To f f (b). Fig. 2. Equivalent circuit during Ton (a) and To f f (b). in state-space at each position correspond to in state-space at each position correspond to ˙x(t) = Aonx(t) + Buon
during Ton
˙x(t) = Ao f f x(t) + Buo f f during To f f
(1) (1) being Aon = Ao f f =
0 −1
L
1
C −1
RC
Buon =
⎡
⎣
Vg
L
0
⎤
⎦Buo f f =
0
0
(2)
x(t) =
iL(t) vC(t)
T Aon = Ao f f =
0 −1
L
1
C −1
RC
Buon =
⎡
⎣
Vg
L
0
⎤
⎦Buo f f =
0
0
(2) (2) and and where Vg is the feed voltage or primary source and vC is the output voltage. R models the
load, while L and C stand for inductance and capacitance values, respectively. The state vector
x(t) consists of the inductor current iL(t) and the capacitor voltage vC(t). Aon and Buon are
the transition matrix and input vector, respectively, during Ton and Ao f f and Buo f f are the
transition matrix and input vector during To f f. 2.1 Model of PWM buck converters Fig.1 shows a dc-dc step-down (buck) converter, this power electronic stage reduces and
regulates the output voltage from a primary voltage source. The converter switch alternates periodically between two positions. Fig. 2 shows the circuits
corresponding to on and o f f during intervals Ton and To f f, respectively. These positions are
driven by the binary signal u whose values are u = 1 during Ton and u = 0 during To f f. The
voltage reduction of this converter in steady state corresponds to the ratio Ton/Ts. We model
the converter dynamics at each position by using the Kirchhoff laws. Its dynamic expressions Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters Usually the bilinear model (4) is linearized around equilibrium point by considering that the
system variables consist of two components: Thus, the averaged state vector x corresponds to x =
iL, vC
T; where iL and vC are the
averaged values of inductor current and capacitor voltage during a switching period. Usually the bilinear model (4) is linearized around equilibrium point by considering that the
system variables consist of two components: Usually the bilinear model (4) is linearized around equilibrium point by considering that the
system variables consist of two components: x(t) = X + ˆx(t)
d(t) = D + ˆd(t)
(5) x(t) = X + ˆx(t)
d(t) = D + ˆd(t)
(5) (5) where X and D represent the equilibrium values and ˆx and ˆd are the perturbed values of the
state and duty cycle. Therefore, equation (4) can be written as follows where X and D represent the equilibrium values and ˆx and ˆd are the perturbed values of the
state and duty cycle. Therefore, equation (4) can be written as follows ˙ˆx =
Ao f f +
Aon −Ao f f
D
ˆx +
Bon −Bo f f
+
Aon −Ao f f
X
ˆd
(6) (6) The equilibrium state in the buck converter corresponds to The equilibrium state in the buck converter corresponds to X =
⎡
⎣
VgD
R
VgD
⎤
⎦
(7) (7) Taking into account (2), we can model the buck converter as Taking into account (2), we can model the buck converter as ˙ˆx(t) =
0 −1
L
1
C −1
RC
ˆx(t) +
Vg
L
0
ˆd(t)
(8) (8) The model can be augmented to ensure zero steady-state error of vC by introducing a new
state variable x3 corresponding to The model can be augmented to ensure zero steady-state error of vC by introducing a new
state variable x3 corresponding to x3(t) =
vC(t) −Vre f
dt
(9) (9) here Vre f is the voltage reference. where Vre f is the voltage reference. where Vre f is the voltage reference. Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters where Vg is the feed voltage or primary source and vC is the output voltage. R models the
load, while L and C stand for inductance and capacitance values, respectively. The state vector
x(t) consists of the inductor current iL(t) and the capacitor voltage vC(t). Aon and Buon are
the transition matrix and input vector, respectively, during Ton and Ao f f and Buo f f are the
transition matrix and input vector during To f f. f f
The binary signal u turn on and off the switch which is controlled by means of a pulse width
modulator (PWM), whose switching period Ts is equals to the sum of Ton and To f f. The PWM
duty cycle is noted as d. y y
The expressions (1) and (2) can be written compactly in terms of the binary signal u as follows y y
The expressions (1) and (2) can be written compactly in terms of the binary signal u as follows ˙x(t) = Ao f f x(t) + Bo f f +
Aon −Ao f f
xu +
Bon −Bo f f
u
(3) (3) The converter operates in continuous conduction mode (CCM) when the inductor current iL
is ever greater than zero. We assume this operation mode then the switched model (3) can be The converter operates in continuous conduction mode (CCM) when the inductor current iL
is ever greater than zero. We assume this operation mode then the switched model (3) can be 4262 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer approximated using state-space averaging method (Middlebrook & Cuk, 1976), replacing the
binary signal u by its respective duty cycle d and the state variables by their averaged values
during the switching period. The result of this averaging process can be written as ˙x(t) = Ao f f x(t) + Bo f f +
Aon −Ao f f
xd +
Bon −Bo f f
d
(4) (4) Thus, the averaged state vector x corresponds to x =
iL, vC
T; where iL and vC are the
averaged values of inductor current and capacitor voltage during a switching period. Thus, the averaged state vector x corresponds to x =
iL, vC
T; where iL and vC are the
averaged values of inductor current and capacitor voltage during a switching period. 2.2 Model of PWM boost converters The Fig.3 shows the well-known boost converter (Erickson & Macksimovic, 2001), which is
capable of regulating a dc output voltage when it is higher than the dc feed voltage. The dynamic behavior of boost converter during Ton and To f f shown in the Fig. 4 can be
written as
The Fig.3 shows the well-known boost converter (Erickson & Macksimovic, 2001), which is
capable of regulating a dc output voltage when it is higher than the dc feed voltage. g
g
p
g
g
g
behavior of boost converter during Ton and To f f shown in the Fig. 4 can be Aon =
0
0
0 −1
RC
Ao f f =
0 −1
L
1
C −1
RC
Buon = Buo f f =
Vg
L
0
(12) (12) x(t) =
iL(t) vC(t)
T where x(t) is the state-space vector composed of iL, which represents the inductor current,
and vC, which represents the capacitor voltage. These variables are measurable and available
for feedback purposes. Vg
R
+
−
iL
vC
+
−
C
L
(a) Vg
R
+
−
iL
vC
+
−
C
L
(a)
Vg
R
+
−
iL
vC
+
−
C
L
(b)
Fig. 4. Equivalent circuit of boost converter for Ton (a) and To f f (b). Vg
R
+
−
iL
vC
+
−
C
L
(b) (b) Fig. 4. Equivalent circuit of boost converter for Ton (a) and To f f (b). Fig. 4. Equivalent circuit of boost converter for Ton (a) and To f f (b). Fig. 4. Equivalent circuit of boost converter for Ton (a) and To f f (b). Therefore, according to (12), the equilibrium state in the boost converter corresponds to Therefore, according to (12), the equilibrium state in the boost converter corresponds to herefore, according to (12), the equilibrium state in the boost converter corresponds to X =
Vg
RD′2
Vg
D′
(13) (13) where D′ = 1 −D is the complementary steady-state duty-cycle. where D′ = 1 −D is the complementary steady-state duty-cycle. where D′ = 1 −D is the complementary steady-state duty-cycle. Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters Th
th
t d
d l
b
itt re f
g
Thus, the augmented model can be written as f
Thus, the augmented model can be written as ˙ˆx(t) = A ˆx(t) + Bu ˆd(t)
(10)
where
A =
⎡
⎢⎢⎣
0 −1
L 0
1
C −1
RC 0
0
1
0
⎤
⎥⎥⎦Bu =
⎡
⎣
Vg
L
0
0
⎤
⎦
(11) ˙ˆx(t) = A ˆx(t) + Bu ˆd(t)
(10) ˙ˆx(t) = A ˆx(t) + Bu ˆd(t) (10) where A =
⎡
⎢⎢⎣
0 −1
L 0
1
C −1
RC 0
0
1
0
⎤
⎥⎥⎦Bu =
⎡
⎣
Vg
L
0
0
⎤
⎦
(11) (11) In the next subsection, we develop the same procedure for the boost converter. In the next subsection, we develop the same procedure for the boost converter. 5
263 Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters Vg
R
+
−
u = 1
iL
vC
+
−
C
u = 0
L
Fi
3 S h
ti
i
it f
b
t
t Vg
R
+
−
u = 1
iL
vC
+
−
C
u = 0
L Fig. 3. Schematic circuit of a boost converter Fig. 3. Schematic circuit of a boost converter atic circuit of a boost converter Fig. 3. Schematic circuit of a boost converter 2.2 Model of PWM boost converters 2.2 Model of PWM boost converters 3. Takagi-Sugeno fuzzy representation of DC-DC converters There exist several approaches to fuzzy representation of dynamic systems, between them the
most common are the Mamdani fuzzy representation (Driankov et al., 1993) and the T-S fuzzy
representation (Tanaka & Wang, 2001). In the first representation, it is assumed that there is
no model of the plant, while the second representation is always based on a dynamical model
of the plant. This T-S representation describes the dynamic system by means of an interpolation of linear
submodels. The performance requirements of a linear model may be expressed by means of
LMI. B1
B2
Br
h1
h2
hr
C1
C2
Cr
h1
h2
hr
A1
A2
Ar
h1
h2
hr
x(t)
x(t)
y(t)
u(t)
Fig 5 Final structure of the Takagi Sugeno fuzzy model Fig. 5. Final structure of the Takagi-Sugeno fuzzy model Fig. 5. Final structure of the Takagi-Sugeno fuzzy model Fig. 5. Final structure of the Takagi-Sugeno fuzzy model Figure 5 shows the model of the nonlinear plant as a group of linear models, which locally
represent the relationship input-output system (Takagi & Sugeno, 1985), described of the
form: Ri : I f δ1 is Mi1 and . . . and δj is Mji then
˙xi(t) = Aix(t) + Biu(t) i = 1, 2, . . . r
(16) (16) ˙xi(t) = Aix(t) + Biu(t) i = 1, 2, . . . r Where r is the number of submodels, Ai is the system matrix of the i-th linear submodel, Bi
is the input matrix, x(t) is the global state-space vector, u(t) is the input vector, Mji are fuzzy
sets, and δj is the scheduling vector (Korba et al., 2003). Where r is the number of submodels, Ai is the system matrix of the i-th linear submodel, Bi
is the input matrix, x(t) is the global state-space vector, u(t) is the input vector, Mji are fuzzy
sets, and δj is the scheduling vector (Korba et al., 2003). j
Fuzzy sets Mji have associated membership functions η′s which characterize the degree
of membership (Takagi & Sugeno, 1985). The nonlinearities of the plant will determine
the variables of the scheduling vector δi used in the antecedent, i.e., a correct election
of scheduling variables will capture all the nonlinearities of the plant, in the case of the
dc-dc converters the scheduling variables are function of the state variables δ(t) = δ(x(t))
(Korba et al., 2003; Tanaka & Wang, 2001). 2.2 Model of PWM boost converters S
A
̸
A
h
d l
f h b
b l
h h
b p
y
y
y y
on ̸= Ao f f, the average model of the boost converter is bilinear, which can be written ˙ˆx = A ˆx + Bu( ˆx) ˆd
(14) ˙ˆx = A ˆx + Bu( ˆx) ˆd
(14) (14) A =
⎡
⎣
0 −D′
L 0
D′
C −1
RC
0
1
0
⎤
⎦Bu( ˆx) =
⎡
⎢⎣
Vg
D′L +
ˆvC(t)
L
−
Vg
(D′2R)C −
ˆiL(t)
C
0
⎤
⎥⎦
(15) (15) In next section, we describes the T-S fuzzy modeling method for the DC-DC converters. In next section, we describes the T-S fuzzy modeling method for the DC-DC converters. 6264 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 3. Takagi-Sugeno fuzzy representation of DC-DC converters The entire fuzzy model of the plant corresponds
to a fuzzy weighting of the locally valid linear submodel associated to each implications Ri
(Korba et al., 2003), i.e., ˙x(t) = ∑r
i=1 wi(δ(t)) [Aix(t) + Biu(t)]
∑r
i=1 wi(δ(t))
(17) (17) Weights wi(δ(t)) are zero or positive time-variant values and the sum of all the weights is
positive. Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters 7
265 r
∑
i=1
wi(δ(t)) > 0,
wi(δ(t)) ≥0
∀
i = 1, 2, . . . , r We use the next normalized weight function hi(δ(t)) replacing wi(δ(t)), hi(δ(t)) =
wi(δ(t))
∑r
i=1 wi(δ(t)) hi(δ(t)) =
wi(δ(t))
∑r
i=1 wi(δ(t)) hi(δ(t)) =
wi(δ(t))
∑r
i=1 wi(δ(t)) that fulfill with that fulfill with 0 ≤hi(δ(t)) ≤1,
r
∑
i=1
hi(δ(t)) = 1
(18) (18) Therefore the fuzzy model (17) can be rewritten as ˙x(t) =
r
∑
i=1
hi(δ(t)) [Aix(t) + Biu(t)]
(19) (19) The T-S fuzzy model of the buck converter is expressed by only one rule given that it is
linear. The T-S fuzzy models of other topologies require several rules given that their dynamic
behaviour is bilinear. The boost converter case is shown in the next subsection. The T-S fuzzy model of the buck converter is expressed by only one rule given that it is
linear. The T-S fuzzy models of other topologies require several rules given that their dynamic
behaviour is bilinear. The boost converter case is shown in the next subsection. 3.1 Takagi-Sugeno model of a boost converter 3.1 Takagi-Sugeno model of a boost converter
We propose the next boost converter fuzzy model consisting of the following four rules. e propose the next boost converter fuzzy model consisting of the following four rules. ropose the next boost converter fuzzy model consisting of the following four rules. 1: We p opose t e
e t boost co ve te
u
y
ode co s st
g o t e o ow
g ou
u es. •
R1: R1: If ˆiL is ismall and
ˆvC is vsmall then
˙ˆx1(t) = A1 ˆx(t) + B1 ˆd(t)
(20) (20) If ˆiL is ibig and
ˆvC is vsmall then
˙ˆx2(t) = A2 ˆx(t) + B2 ˆd(t)
(21) (21) If ˆiL is ismall and
ˆvC is vbig then
˙ˆx3(t) = A3 ˆx(t) + B3 ˆd(t)
(22) (22) If ˆiL is ibig and
ˆvC is vbig then
˙ˆx4(t) = A4 ˆx(t) + B4 ˆd(t)
(23) (23) A1 = A2 = A3 = A4 = A =
⎡
⎣
0 −D′
L 0
D′
C −1
RC
0
1
0
⎤
⎦ 8266 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer B1 =
⎡
⎢⎣
Vg
D′L + vmin
L
−
Vg
(D′2R)C −imin
C
0
⎤
⎥⎦B2 =
⎡
⎢⎣
Vg
D′L + vmin
L
−
Vg
(D′2R)C −imax
C
0
⎤
⎥⎦
B3 =
⎡
⎢⎣
Vg
D′L + vmax
L
−
Vg
(D′2R)C −imin
C
0
⎤
⎥⎦B4 =
⎡
⎢⎣
Vg
D′L + vmax
L
−
Vg
(D′2R)C −imax
C
0
⎤
⎥⎦
(24) (24) being the membership function of the fuzzy sets ismall, ibig, vsmall and vbig the following ones, ηismall(ˆiL) =
imax−ˆiL
imax−imin
ηibig(ˆiL) = 1 −ηismall(ˆiL)
ηvsmall( ˆvC) =
vmax−ˆvC
vmax−vmin ηvbig( ˆvC) = 1 −ηvsmall( ˆvC)
(25) (25) Note that (20) correspond to the dynamic behavior around (imin, vmin) values, and (21)-(23)
describe the local behavior around the other interval bounds. Thus, the normalized weight
functions are Note that (20) correspond to the dynamic behavior around (imin, vmin) values, and (21)-(23)
describe the local behavior around the other interval bounds. Q
y
Given the linear dynamic system Given the linear dynamic system ˙x(t) = Ax(t)
(29) (29) the existence of a quadratic function of the form V (x(t)) = x(t)TPx(t)
(30) (30) that satisfies ˙V (x(t)) < 0, is a necessary and sufficient condition to ensure that the system is
asymptotically stable, i.e., all trajectories converge to zero. Where P is a symmetric positive
definite matrix ∈Rn×n. Since the expression ˙V (x(t)) < 0 has form quadratic, this condition
is referred as quadratic stability, and it can be rewritten as follows that satisfies ˙V (x(t)) < 0, is a necessary and sufficient condition to ensure that the system is
asymptotically stable, i.e., all trajectories converge to zero. Where P is a symmetric positive
definite matrix ∈Rn×n. Since the expression ˙V (x(t)) < 0 has form quadratic, this condition
is referred as quadratic stability, and it can be rewritten as follows ˙V (x(t)) = x(t)T
ATP + PA
x(t)
(31) (31) Thus, the system is asymptotically stable if and only if there exist a symmetric matrix P such
that Thus, the system is asymptotically stable if and only if there exist a symmetric matrix P such
that ATP + PA < 0
(32) (32) The main interest of the quadratic stability condition is that by means of a convex envelope
and numerically simple test, it is possible to conclude about the overall stability of a dynamics
system. y
For an in-deep explanation on quadratic stability see (Boyd et al., 1994). y
For an in-deep explanation on quadratic stability see (Boyd et al., 1994). Based on the results (32), the following subsection present some basic results on the stability For an in-deep explanation on quadratic stability see (Boyd et al., 1994). Based on the results (32), the following subsection present some basic results on the stability
of fuzzy control systems. 3.1 Takagi-Sugeno model of a boost converter Thus, the normalized weight
functions are h1(ˆiL, ˆvC) = ηismall.ηvsmall
h2(ˆiL, ˆvC) = ηibig.ηvsmall
h3(ˆiL, ˆvC) = ηismall.ηvbig
h4(ˆiL, ˆvC) = ηibig.ηvbig
(26) (26) therefore the entire fuzzy converter model corresponds to ˙ˆx(t) =
r
∑
i=1
hi
ˆiL, ˆvC
Ai ˆx(t) + Bi ˆd(t)
(27) (27) since ∑r
i=0 hi = 1 and Ai = A then ˙ˆx(t) = A ˆx(t) +
r
∑
i=1
hi(ˆiL, ˆvC)Bi
ˆd(t)
(28) (28) and it is worth to remark that (28) corresponds with the bilinear model (14) inside the polytope
region
ˆimin, ˆimax
× [ ˆvmin, ˆvmax]. This operating space is depicted in Fig. (6). and it is worth to remark that (28) corresponds with the bilinear model (14) inside the polytope
region
ˆimin, ˆimax
× [ ˆvmin, ˆvmax]. This operating space is depicted in Fig. (6). ˆvmax
ˆvmin
ˆimin
ˆimin
ˆimax
R1
R2
R4
R3
X(iL, vC)
0
1
0
1
ηvsmall(δ1(ˆx1))
ηvbig(δ1(ˆx1))
ηismall(δ2(ˆx2))
ηibig(δ2(ˆx2)) ˆvmax
ˆvmin
ˆimin
ˆimin
ˆimax
R1
R2
R4
R3
X(iL, vC)
0
1
0
1
ηvsmall(δ1(ˆx1))
ηvbig(δ1(ˆx1))
ηismall(δ2(ˆx2))
ηibig(δ2(ˆx2))
Fig. 6. T-S Fuzzy representation of the boost converter consisting of the 4 rules Fig. 6. T-S Fuzzy representation of the boost converter consisting of the 4 rules 9
267 Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters The approach shown here can be easily adapted for the buck-boost converter, such as shown
in (Torres-Pinzón & Leyva, 2009). In next section, we explain a control strategy where the law consist of a normalized weight
sum of linear feedback gains at each interval limit, which takes into account constraints such
as: control effort and the decay rate of state variables. 4. LMI performance requeriments This section presents the concept and basic procedure of the parallel distributed compensation
(PDC) technique and the definitions and LMI constraints used in the synthesis of control. First,
we introduce the basic concept of Lyapunov-based stability. Then, we discuss on stability
concepts for fuzzy systems in form of LMI. These concepts will be applied in Section 5 to find
a LMI fuzzy controller for the buck and boost converters. It can be observed that since the
buck converter dynamics is linear, we obtain a linear control law for this converter that is a
fuzzy controller with only one rule. 4.2 Performance constraints In this subsection, we review in detail the Parallel Distributed Compensation (PDC) technique
(Tanaka & Wang, 2001). In such fuzzy technique, each control rule is associated with the
corresponding rule of the fuzzy model, thus the controller rules are as follows, Ri : If δ1 is Mi1 and . . . and δj is Mji Then Ri : If δ1 is Mi1 and . . . and δj is Mji Then u(t) = −Fix(t) i = 1, . . . , r
(33) u(t) = −Fix(t) i = 1, . . . , r (33) 10268 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer where Fi are lineal feedback gain vectors associate with each rule. And the overall fuzzy
controller is represented as where Fi are lineal feedback gain vectors associate with each rule. And the overall fuzzy
controller is represented as u(t) = −∑r
i=1 wiFix(t)
∑r
i=1 wi
= −
r
∑
i=1
hiFix(t)
(34) (34) Substituting the control law (34) in the fuzzy model (19), the closed loop system dynamics is
given by ˙x(t) =
r
∑
i=1
r
∑
j=1
hihj
Ai −BiFj
x(t)
(35) (35) In order to select the suitable feedback gain vectors Fi, we impose Lyapunov stability
constraints and performance constraints on decay rate and control effort in form of LMIs. Therefore, the sufficient conditions for the stability of the open-loop fuzzy system (19) and In order to select the suitable feedback gain vectors Fi, we impose Lyapunov stability
constraints and performance constraints on decay rate and control effort in form of LMIs. In order to select the suitable feedback gain vectors Fi, we impose Lyapunov stability
constraints and performance constraints on decay rate and control effort in form of LMIs. Therefore, the sufficient conditions for the stability of the open-loop fuzzy system (19) and
closed-loop one (35) are obtained using quadratic stability condition of the equation (32). These conditions, derived from (Tanaka & Wang, 2001), it can be expressed by means of the
next propositions. Therefore, the sufficient conditions for the stability of the open-loop fuzzy system (19) and
closed-loop one (35) are obtained using quadratic stability condition of the equation (32). These conditions, derived from (Tanaka & Wang, 2001), it can be expressed by means of the
next propositions. Proposition 4.1. 4.2 Performance constraints The equilibrium of the continuous fuzzy system (19) with u(t) = 0 is asymptotically
stable if there exists a common positive definite matrix P such that AT
i P + PAi < 0, i=1,. . . ,r
P > 0
(36) (36) that is, a common P has to exist for all subsystems that is, a common P has to exist for all subsystems that is, a common P has to exist for all subsystems where Ai are system matrices of the linear submodels defined in the previous section. Proposition 4.2. The equilibrium of the continuous fuzzy control system described by (35) is
asymptotically stable if there exists a common positive definite matrix P such that Ai −BiFj
T
P + P
Ai −BiFj
< 0, j > i
P > 0
(37) (37) Note that the condition (37) is not linear because involves the multiplication of the variables
P and F′
js. Thus, in order to rewrite (37) in a linear manner, we multiply the inequality (37) on
the left and right by P−1, and we define a new variable W = P−1, then proposition 4.2 can be
rewritten as follows. Proposition 4.3. The continuous fuzzy system (35) is quadratically stable for some feedback gain Fi
if there exists a common positive definite matrix W such that AiW + WAT
i −BiYi −YT
i BT
i < 0,
i = 1, . . . r
AiW + WAT
i + AjW + WAT
j −BiYj −YT
j BT
i −BjYi −YT
i BT
j ≤0, i < j ≤r
(38)
being Yi = FiW so that for W > 0, we have Fi = YiW−1 (38) being Yi = FiW so that for W > 0, we have Fi = YiW−1 11
269 Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters Using these LMI conditions, we establish the first controller design constraint, next we
describe the second design restriction. As dc-dc converter control signal corresponds to the incremental duty cycle, then the control
signal is bounded in the interval [−D, 1 −D]. In order to satisfy with this limitation, we
constrain the control signal by the next proposition. 4.2 Performance constraints The satisfaction of the next proposition will assure that control signal d(t) is inside the interval
[−D, 1 −D] from starting condition x(0) to the equilibrium point. Proposition 4.4. Assume that initial condition x(0) is known. The constraint ∥d(t)∥2≤μ is enforced
at all times t ≥0 if the LMIs (39) hold
1
x(0)T
x(0)
W
≥0,
W YT
i
Yi μ2I
≥0
(39)
where W = P−1 and Yi = FiW.
1
x(0)T
x(0)
W
≥0,
W YT
i
Yi μ2I
≥0
(39) (39) where W = P−1 and Yi = FiW. Also, it will be desirable a suitable transient performances of the closed loop system. The
entire fuzzy system transient performances depends on the localizations of the poles of its
linear systems corresponding to each rule. In our case, this poles are expressed in terms
of decay rate introduced via exponential stability, which it can be seen as a special case of
pole-placement on the closed-loop system. Consequently, we impose that this poles must be inside a predetermined region as the one
pictured in Fig. 7. Therefore, the design process will add the next proposition, adapted from
(Tanaka & Wang, 2001). α
S(α)
Fig. 7. S (α) region Fig. 7. S (α) region Fig. 7. S (α) region Proposition 4.5. The eigenvalues of
Ai −BiFj
in each linear fuzzy system are inside the region
S(α) if there exist a common positive definite matrix W such that AiW + WAT
i −BiYi −YT
i BT
i + 2αW < 0,
i = 1, . . . r
T
i + AjW + WAT
j −BiYj −YT
j BT
i −BjYi −YT
i BT
j + 4αW ≤0, i < j ≤r
(40) AiW + WAT
i −BiYi −YT
i BT
i + 2αW < 0,
i = 1, . . . r
AiW + WAT
i + AjW + WAT
j −BiYj −YT
j BT
i −BjYi −YT
i BT
j + 4αW ≤0, i < j ≤r
(40)
being Fi = YiW−1. i = 1, . . . r (40) being Fi = YiW−1. 12270 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Between all the feasible set of feedback gains, the proposed algorithm finds the largest possible
decay rate (α) of the state variables, satisfying the previous LMIs. 4.2 Performance constraints Hence, the design procedure
of the LMI Fuzzy control can be formulated by the following optimization algorithm. max
α subject to
W, Yi
i = 1, . . . , r
(39), and (40)
(41) max
α subject to
W, Yi
i = 1, . . . , r
(39), and (40)
(41) (41) The solution of this optimization program with its corresponding LMIs will provide the set of
feedback gains FLMI−Fuzzy = {F1, F2, F3, F4}. The solution of this algorithm can be carried out
by means of GEVP function in MATLAB LMI toolbox. 5. Design examples This section shows two examples of LMI-based control applied to dc-dc converters. The first
case presents the control design of a step-down converter working around equilibrium point. This example takes into account the same LMIs constraints of the algorithm (41). The second
example proposes an LMI Fuzzy control for a step-up converter, allowing working at different
operating point. Both examples are tested during a start-up and under load disturbances. 5.1 LMI control of a Buck converter In this first example, we presents an LMI control approach applied to the problem of
regulating the output voltage of the buck converter. The values of the converter parameter
set are shown in Table 1. The nominal load of the converter is equal to 10 Ω, while
supply voltage equal to 48 V. Consequently, the equilibrium point satisfying (7) is equal
to [ iL vC ] =[ 4.8 24 ]T. The simulation prototype is designed to process less than 60 W
corresponding to a load resistance R = 10 Ω. The inductance and capacitance values and
switching frequency have been selected to ensure low ripple level. In order to limit the control
signal in the range [−D, 1 −D], μ is set to 1500, since simulations show no saturation of the
duty-cycle. Vg
48V
vC(Vre f )
24V
L
200 μH
C
200 μF
R
10 Ω
D′
0.5 Ω
Ts
10 μ s
Table 1. Buck converter parameters Table 1. Buck converter parameters Once the parameters values of the converter and controller have been defined, the next step
is to obtain the feedback gain vector. Thus, solving the optimization algorithm (41) for the
system (11), by means of the LMI toolbox of MATLAB (Gahinet et al., 1995), the state-feedback
controller obtained for the buck converter is FBuck =
0.0963 0.1133 −319.8021 FBuck =
0.0963 0.1133 −319.8021 10 illustrates the system responses for step changes in the load current from 2.4 A to 4.4
A at 2ms and then returns to 2.4 A at 8ms. It can be observed that the controller regulates the
output voltage vC smoothly at 24 V after a short transient period. It can also be observed that
the duty-cycle does not exceed the limits of interval [−D, 1 −D]. In the next subsection, the Fig. 10 illustrates the system responses for step changes in the load current from 2.4 A to 4.4
A at 2ms and then returns to 2.4 A at 8ms. It can be observed that the controller regulates the
output voltage vC smoothly at 24 V after a short transient period. It can also be observed that
the duty-cycle does not exceed the limits of interval [−D, 1 −D]. In the next subsection, the 0
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6
Time (s)
iL (t)
vC (t)
(a)
0
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0.004
0.006
0.008
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0.012
9
9.5
x 10
−3
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0.004
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0.5
0
0.002
0.004
0.006
0.008
0.01
0.012
2
3
4
5
Time (s)
d (t)
x3 (t)
iR (t)
(b)
Fig. 10. Simulated response of the buck converter under a load step transient of 2 A. (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t), duty-cycle
d(t) and load current iR. 0
0.002
0.004
0.006
0.008
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0.012
9
9.5
x 10
−3
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0.012
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3
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5
Time (s)
d (t)
x3 (t)
iR (t)
(b) 0
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0.004
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0.012
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23
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25
26
0
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0.012
1
2
3
4
5
6
Time (s)
iL (t)
vC (t)
(a) (b) (a) Fig. 10. Simulated response of the buck converter under a load step transient of 2 A. (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t), duty-cycle
d(t) and load current iR. LMI Fuzzy controller design for a boost converter is described. LMI Fuzzy controller design for a boost converter is described. FBuck =
0.0963 0.1133 −319.8021 with a decay rate of α = 3254, which assures a maximum constant time of 1/3254, and
consequently a maximum settling time of 4 ∗(1/3254). In order to verify the behavior of 13
271 Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters the buck converter under the control law described above, numerical simulations have been
carried out in MATLAB/Simulink, as shown in Fig.8. Fig. 9 shows the transient simulation of the state variables and duty-cycle during start-up, in
fact, represents a large signal perturbation around the equilibrium point of the state variables. It is remark that the settling time is smaller than 1.2 ms, and agrees with the decay rate
obtained. (a)
(b)
Fig. 8. Simulink diagram of a buck converter with state-feedback regulation. (a)
Implementation diagram in MATLAB/Simulink. (b) Simulink model of the buck converter. (b) (a) (b) (a) Fig. 8. Simulink diagram of a buck converter with state-feedback regulation. (a)
Implementation diagram in MATLAB/Simulink. (b) Simulink model of the buck 0
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x 10
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0.3
0.4
0.5
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Time (s)
d (t)
x3(t)
(b)
Fig. 9. Simulated response of the dc-dc buck converter during start-up. (a) Inductor current
iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t) and duty-cycle d(t). 0
0.5
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x 10
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10
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Time (s)
iL (t)
vC (t)
(a) (b) (a) Fig. 9. Simulated response of the dc-dc buck converter during start-up. (a) Inductor current
iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t) and duty-cycle d(t). 14272 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Fig. 5.2 LMI Fuzyy control of a boost converter In this subsection, we present the results of the design of the LMI Fuzzy controller applied to
fuzzy model of the boost converter shown in subsection 3.1, whose parameter set is shown in
Table 2. Consequently, the equilibrium state is given by [ iL vC ] =[ 4.8 24 ]T. q
y
q
g
y [
C ]
[
]
The design of the control law consists of solving the optimization algori Vg
12V
vC(Vre f )
24V
L
300 μH
C
300 μF
R
10 Ω
D′
0.5 Ω
Ts
20 μ s
Table 2. Boost converter parameters Vg
12V
vC(Vre f )
24V
L
300 μH
C
300 μF
R
10 Ω
D′
0.5 Ω
Ts
20 μ s
Table 2. Boost converter parameters Table 2. Boost converter parameters Table 2. Boost converter parameters four linear submodels of the fuzzy model. This submodels correspond to the vertices of the
polytopic model of the boost converter in the region defined in Fig 6. Therefore, in order to
ensure stability within the polytopic region during a start-up transition and disturbance, the
polytopic region should be
ˆimin = 0, ˆimax = 20
× [ ˆvmin = 0, ˆvmax = 10]. To demonstrate the
advantage of this Fuzzy approach, we will compare the LMI Fuzzy control with a LMI linear
Control. As in the previous subsection, the simulation prototype is designed to process less than 60
W, as well as the inductance and capacitance values and switching frequency are selected to
ensure low ripple level. To maintain the control signal under the threshold limit value, μ is set 15
273 Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters to 350, for the two control designs. So, according to the optimization algorithm (41), the fuzzy
state-feedback gains obtained via LMI Toolbox of Matlab are given follows: to 350, for the two control designs. control on Simulink, which it is written by means of a code in the MATLAB Editor.
Fig.
12 illustrates the transient simulation of the boost converter during start-up.
The
waveforms depicted in the figure are the inductor current iL, capacitor voltage vC, steady-state
error x3 and duty-cycle d(t). The response of the LMI linear contoller corresponds to dashed
line, while the waveform of the LMI Fuzzy controller has been drawn with solid line. In
Fig. 13, the converter reacts to large load disturbances. In this simulation the load current is
initially 2.4 A. At t = 2 ms, the current changes to 6.4 A, and at t = 8 ms, it returns to its initial 5.2 LMI Fuzyy control of a boost converter So, according to the optimization algorithm (41), the fuzzy
state-feedback gains obtained via LMI Toolbox of Matlab are given follows: F1 =
0.1737 0.1019 −183.4507 F1 =
0.1737 0.1019 −183.4507
F2 =
0.2737 0.1871 −313.9974
F3 =
0.1814 0.1157 −199.8689
F4 =
0.1877 0.1149 −202.6875 F1 =
0.1737 0.1019 −183.4507
F2 =
0.2737 0.1871 −313.9974
F3 =
0.1814 0.1157 −199.8689
F4 =
0.1877 0.1149 −202.6875 F2 =
0.2737 0.1871 −313.9974 F3 =
0.1814 0.1157 −199.8689 F3 =
0.1814 0.1157 −199.8689 F4 =
0.1877 0.1149 −202.6875 The decay rate value obtained is 878, which assures a maximum settling time of 4 ∗(1/878). As mentioned above, to contrast the performance and robustness of the proposed control,
we compare the LMI Fuzzy control law with a LMI linear law, which it presents the same
optimization criteria (41). The resulting controller gain vector is FBoost =
0.0895 0.1018 −159.9759 with a decay rate of 1950, that assures a maximum settling time of 4 ∗(1/1950). It can be observed that there exist differences between the decay rate obtained above. Next, we
will show its properties during a start-up and in presence of load disturbances. Fig. 11 shows
the simulation schematic of the boost converter with the LMI Fuzzy controller implemented
in MATLAB/Simulink. Note that the MATLAB Function block is used to run the LMI Fuzzy Fig. 11. Simulink implementation diagram of a boost converter with LMI Fuzzy regulation. Fig. 11. Simulink implementation diagram of a boost converter with LMI Fuzzy regulation. control on Simulink, which it is written by means of a code in the MATLAB Editor. control on Simulink, which it is written by means of a code in the MATLAB Editor. Fig. 12 illustrates the transient simulation of the boost converter during start-up. The
waveforms depicted in the figure are the inductor current iL, capacitor voltage vC, steady-state
error x3 and duty-cycle d(t). The response of the LMI linear contoller corresponds to dashed
line, while the waveform of the LMI Fuzzy controller has been drawn with solid line. In
Fig. 13, the converter reacts to large load disturbances. In this simulation the load current is
initially 2.4 A. At t = 2 ms, the current changes to 6.4 A, and at t = 8 ms, it returns to its initial Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 16274 0
1
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4
5
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x 10
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20
30
0
1
2
3
4
5
6
7
8
x 10
−3
−5
0
5
10
15
Time (s)
iL (t)
vC (t)
(a)
0
1
2
3
4
5
6
7
8
x 10
−3
5m
10m
15m
20m
5m
0
1
2
3
4
5
6
7
8
x 10
−3
−0.5
0
0.5
Time (s)
d (t)
x3 (t)
(b)
Fig. 12. F4 =
0.1877 0.1149 −202.6875 The set of LMIs, which is solved by means of LMI Toolbox, provides the feedback gains. 0
0.002
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0.006
0.008
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iL (t)
vC (t)
(a)
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20m
25m
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0.008
0.01
0.012
2
4
6
8
Time (s)
d (t)
x3 (t)
iR (t)
(b)
Fig. 13. Simulated responses of the boost converter under a load step transient of 4 A linearly
controlled (dished) and fuzzy controlled (solid). (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t), duty-cycle
d(t) and load current iR. 0
0.002
0.004
0.006
0.008
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15m
20m
25m
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Time(s)
iL (t)
vC (t)
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0.012
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20
22
24
26
28
30
vC (t) 0
0.002
0.004
0.006
0.008
0.01
0.012
0
5
10
15
20
Time(s)
iL (t)
(a) (b) (a) Fig. 13. Simulated responses of the boost converter under a load step transient of 4 A linearly
controlled (dished) and fuzzy controlled (solid). (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t), duty-cycle
d(t) and load current iR. value. It is worth noting that state variables and duty-cycle are better with the LMI Fuzzy
controller (dashed line), since it maintains its stability properties under large disturbances,
and despite that it is slower. The main advantage of this controller, is that it ensures robust
stability in broad range of operation. value. It is worth noting that state variables and duty-cycle are better with the LMI Fuzzy
controller (dashed line), since it maintains its stability properties under large disturbances,
and despite that it is slower. The main advantage of this controller, is that it ensures robust
stability in broad range of operation. F4 =
0.1877 0.1149 −202.6875 Simulated responses of the dc-dc boost converter during start-up linearly controlled
(dished) and fuzzy controlled (solid). (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t) and duty-cycle d(t). 0
1
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30
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1
2
3
4
5
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8
x 10
−3
−5
0
5
10
15
Time (s)
iL (t)
vC (t)
(a) 0
1
2
3
4
5
6
7
8
x 10
−3
5m
10m
15m
20m
5m
0
1
2
3
4
5
6
7
8
x 10
−3
−0.5
0
0.5
Time (s)
d (t)
x3 (t)
(b) (b) (a) Fig. 12. Simulated responses of the dc-dc boost converter during start-up linearly controlled
(dished) and fuzzy controlled (solid). (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t) and duty-cycle d(t). 0
0.002
0.004
0.006
0.008
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26
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30
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20
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vC (t)
(a)
0
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0.004
0.006
0.008
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0.012
10m
15m
20m
25m
0
0.002
0.004
0.006
0.008
0.01
0.012
0.2
0.4
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0.002
0.004
0.006
0.008
0.01
0.012
2
4
6
8
Time (s)
d (t)
x3 (t)
iR (t)
(b)
Fig. 13. Simulated responses of the boost converter under a load step transient of 4 A linearly
controlled (dished) and fuzzy controlled (solid). (a) Inductor current iL(t) and capacitor voltage vC(t). (b) Steady-state error x3(t), duty-cycle
d(t) and load current iR. value. It is worth noting that state variables and duty-cycle are better with the LMI Fuzzy
controller (dashed line), since it maintains its stability properties under large disturbances,
and despite that it is slower. The main advantage of this controller, is that it ensures robust
stability in broad range of operation. 6. Conclusions
This chapter presents a LMI fuzzy controller design for dc-dc converters using MATLAB. The design methodology has been applied to a buck converter and to a boost converter
where the control optimizes the decay rate of the state variables subject to a bound in
the control effort. The methodology allows us to take into account the bilinear nature of
the boost converter dynamics. We express the control objective and the bound as LMIs. Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters Matlab: a Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters
MATLAB: A Systems Tool for Design of Fuzzy LMI Controller in DC-DC Converters The dynamical performances of LMI fuzzy controlled boost converter have been compared
those of a linear-controlled boost considering the same design constraint. We have verified
the closed-loop dynamic behavior using Simulink/MATLAB. The plots exhibit a perfect
agreement with the design specifications. This design procedure ensures the stability of the
converter in a wide region. On the contrary, a linear-controlled converter deteriorates its
performances out of the operating point. The approach can be extended to more complex
converters or other types of bilinear plants. 7. Acknowledgment This work was partially supported by the Spanish Ministerio de Educación y Ciencia under
grant DPI2010-16481 This work was partially supported by the Spanish Ministerio de Educación y Ciencia under
grant DPI2010-16481 6. Conclusions This chapter presents a LMI fuzzy controller design for dc-dc converters using MATLAB. The design methodology has been applied to a buck converter and to a boost converter
where the control optimizes the decay rate of the state variables subject to a bound in
the control effort. The methodology allows us to take into account the bilinear nature of
the boost converter dynamics. We express the control objective and the bound as LMIs. The set of LMIs, which is solved by means of LMI Toolbox, provides the feedback gains. 17
275 8. References Boyd, S.; El Ghaoui, L.; Feron, E. & Balakrishnan, V. (1994). Linear Matrix Inequalities in
Systems and Control Theory, ser. Studies in Applied and Numerical Mathematics,
Philadelphia,PA:SIAM p
Chilali, M. & Gahinet, P. (1996). H∞Design with Pole Placement Constraints: An LMI
Approach, IEEE Trans. on Autom. Control., Vol. 42, No.3, (358-367) Driankov, D.; Hellendoorn, H. & Reinfrank, M. (1993). An introduction to Fuzzy Control,
Springer-Verlag, Germanny Erickson, R.W. & Macksimovic, D. (2001). Fundamental of Power Electronics, Second ed., 920
pages, Kluwer Academic Publisher, ISBN 0-7923-7270-0, USA Gahinet, P.; Nemirovski, A.; Laub, A.J.; & Chilali, M. (1995). LMI Control Toolbox for Use With
Matlab, The MathWorks, Inc, Vol. 3, No.1, (75-85) He, Y. & Luo, F.L. (2006). Sliding-mode control for dc-dc converters with constant switching
frequency, IEE Proc.-Control Theory Appl., Vol. 153, No.1, (37-45) Kawasaki, N.; Nomura, H. & Masuhiro, M. (1995). A new control law of bilinear DC-DC
converters developed by direct application of Lyapunov, IEEE Trans. Power Electron.,
Vol. 10, No.1, (318-325) Korba, P.; Babuska, R.; Verbruggen, H.B. & Frank, P.M. (2003). Fuzzy Gain Scheduling:
Controller and Observer Design Based on Lyapunov Method and Convex
Optimization, IEEE Trans. on Fuzzy Syst., Vol. 11, No.3, (285-298) p
Kuang-Yow, L.; Jeih-Jang, L. & Chien-Yu, H. (2006). LMI-Based Integral Fuzzy Control of
DC-DC Converters, IEEE Trans. on Fuzzy Syst., Vol. 14, No.1, (71-80) Lan, H.K & Tan, S.C (2009). Stability analysis of fuzzy-model-based control systems:
application on regulation of switching dc-dc converter, IET Control Theory and Appl.,
Vol. 3, No.8, (1093-1106) Leyva, R.;Cid-Pastor, A.; Alonso, C.; Queinnec, I.; Tarbouriech, S. & Martínez-Salamero, L. (2001). Passivity-based integral control of a boost converter for large-signal stability,
IEE Proc.-Control Theory Appl., Vol. 153, No.2, (March) (139-146) y
pp
(
) (
)
Middlebrook,
R. &
Cuk,
S. (1976). A
general
unified
approach
to
modeling
switching-converter power stages, in IEEE Power Electron. Special. Conf., (June)(18-34),
Cleveland Olalla, C.;Leyva, R.; El Aroudi, A. & Queinnec, I. (2009). Robust LQR Control for PWM
Converters:
An LMI Approach, IEEE Trans. Ind. Electron., Vol. 56, No.7, (July)
(2548-2558) 18276 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Olalla, C.;Leyva, R.; El Aroudi, A.; Garcés, P. & Queinnec, I. (2009). Robust LQR Control for
PWM Converters: An LMI Approach, IET Power Electron., Vol. 3, No.1, (75-85) pp
Sanders, S.R. & Verghese G.C.(1992). Lyapunov-based control for switched power converters,
IEEE Trans. Power Electron., Vol. 7, No.3, (17-24) pp
Sanders, S.R. 8. References & Verghese G.C.(1992). Lyapunov-based control
IEEE Trans. Power Electron., Vol. 7, No.3, (17-24) Takagi, T. & Sugeno, M. (1985). Fuzzy Identification of Systems and Its Applications to
Modeling and Control, IEEE Trans. on Syst., Man, and Cyber., Vol. 15, No.1, (January)
(116-132) Tanaka, K. & Wang, H.O. (2001). Fuzzy Control Systems Design an Analysis, Jhon Wiley & Sons,
INC, New York Torres-Pinzón,
C.A. & Leyva,
R. (2009). Fuzzy Control in DC-DC Converters:
an
LMI Approach,in Proc. of the IEEE Annual Conf. on Ind. Electron., IECON’09,
(November)(510-515),Porto 0
14 1. Introduction Digital control systems have shown to the developers the features and their applications in a
wide variety of plants. Tools that help the developer to promote a design methodology that
is efficient and at the same time reliable, has gained ground in the market and attributions
of control engineers. Tasks such as data acquisition system, control design and system
implementation can become arduous if there are prerequisites for sensitivity and complexity
of the controller for these tasks take time and performance of the developer which will entail
additional costs to the final product. These tools provide the designer with the scientist and
the smooth progress of their work role has important and necessary in many areas will be
subject to this study. The integration of technologies to speed and lower costs as it relates the
design phases can be observed with a proper exploration of the work tool and how knowledge
of plant and control techniques that meet in a less costly the goal of being achieved whatever
the difficulties of the project. The choice of a tool properly can be a deciding factor in a
world where time and efficiency of processes is become extremely important because the
applications are growing in scale and more complex, Moudgalya (2007), Andrade (2010). Intelligent Systems has considerable performance in accordance with plans and small large
and its design encompasses more robustness to the system as well as ease of expansion. The
mathematical simplicity that fuzzy systems can present and adaptability of neural networks
are adopted more frequently in the academy and the industry. p
q
y
y
y
An approach of intelligent systems requires a systematic and efficient operation because one
works with a data stream that needs a consistency so that the iterations will be where made
all the decisions may have minimal accounting. A tool that can assist in the design of this
requirement is most welcome in engineering projects for control system parameter becomes
constant with time,S. Sumathi (2010). The MATLAB software designers can provide facilities for development and interface with
different technologies for data acquisition through its communication protocols such as Serial
Interface, OPC, Ethernet and others. This work is mainly focused on a methodology design
of digital control systems using as development platform and implementing in software
MATLAB. 2278 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 2. Digital control and Data Acquisition Systems The Data Acquisition System (DAS)is a key part to the project and implementation of digital
controllers for the nature of digital systems is based on sampled analog system, ie played
by the analog system a digital computer and its Since the interface Digital - Analog system
performs the control actions . The Figure 1 shows a diagram of a system digital control and
its special features such as the pool Analog - Digital and Digital - Analogue, responsible for
interfacing with the analog environment. Fig. 1. Digital Control System Diagram
A digital control system is obtained from the reconstruction of analog signal contained in
nature. This reconstruction is related mainly with the data acquisition system which is also
involved modeling digital control system. Figure 2 illustrates the design of a system basic
data acquisition of an industry. Fig. 1. Digital Control System Diagram Fig. 1. Digital Control System Diagram A digital control system is obtained from the reconstruction of analog signal contained in
nature. This reconstruction is related mainly with the data acquisition system which is also
involved modeling digital control system. Figure 2 illustrates the design of a system basic
data acquisition of an industry. Fig. 2. DAQ System Diagram
Th
d
t
l
t
li d i
th
t
i d
t
b
i t d Fig. 2. DAQ System Diagram
The modern control concepts applied in the contemporary industry may be appropriated
to the development of academic research activities. The introduction of a methodology
parameters that specify and clarify the implementation of monitoring and control of dynamic
systems. In Figures 1 and 2 are shown at different levels, primary architectures to industrial control
systems. In Figure 1 is exposed a system with minimal complexity, type SISO (Single Input
- Single Output) that can occur in n times or a more complex system can be mapped as a
black box system, where internal states of the process do not matter. In Figure 2 is noted, Fig. 2. DAQ System Diagram The modern control concepts applied in the contemporary industry may be appropriated
to the development of academic research activities. The introduction of a methodology
parameters that specify and clarify the implementation of monitoring and control of dynamic
systems. The modern control concepts applied in the contemporary industry may be appropriated
to the development of academic research activities. 2. Digital control and Data Acquisition Systems The introduction of a methodology
parameters that specify and clarify the implementation of monitoring and control of dynamic
systems. y
In Figures 1 and 2 are shown at different levels, primary architectures to industrial control
systems. In Figure 1 is exposed a system with minimal complexity, type SISO (Single Input
- Single Output) that can occur in n times or a more complex system can be mapped as a
black box system, where internal states of the process do not matter. In Figure 2 is noted, 3
279 MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems however, approach of discrete variables on the process that encompasses the entire plant
worrying about sub stages. however, approach of discrete variables on the process that encompasses the entire plant
worrying about sub stages. In this work is explored a way to conceptualize these types of sound architecture in a way
such that the system can be modeled and represented whatever its complexity, thus using a
powerful tool when it comes to development concepts and analysis. 3. Discrete models of dynamic systems To be held control of dynamic systems, it is necessary in this environment, the perception of
some step that must be met for a procedure with minimum guarantees for the project. In the
following sections will show important steps as ways to implement them by programming or
graphical interface in MATLAB, Moudgalya (2007) and Charles L. Philips (1995). 3.1 Dynamic system identification tools The main tool for modeling dynamic systems to digital control is the MATLAB Identification
Tool Box of, a feature that helps the designer to seamlessly and generates discrete polynomial
transfer functions and the user without the need of programming the algorithms used for
system identification. The IDENT from MATLAB Graphical User Interface is shown in Figures 4
and 3 and in this figure that can be seen are located to the left set of data and the right answer,
ie the model to be obtained. (c) Model- Time Response (b) Data - Time Response (a) Ident GUI
(b) Data - Time Response
(c) Model- Time Response
(d) Model -Frequency Response
Fig. 4. Results From The Identification Tool Box - MATLAB (a) Ident GUI (c) Model- Time Response (b) Data - Time Response (a) Ident GUI (d) Model -Frequency Response (d) Model -Frequency Response (d) Model -Frequency Response Fig. 4. Results From The Identification Tool Box - MATLAB Still in Figure 4 can observe that the user can define various aspects modeling systems such as
filtering of data and type of modeling, as well as the analysis of response in time and frequency
of the system model, Gene F. Franklin (1998). y
Through this tool we can get two different ID type models in the output. The model based on
parameters in the output shows a polynomial equation in discrete form p
p
p
y
q
It should be added that among the numerous tools of identification, we will use polynomial
will be the identification, because it gives us a response in discrete time, which makes this
model implementable on digital computers. With the option to generate a polynomial model
identification as described in Eq.1. G(z) = Y(z)
U(z) = b0 + b1z−1 + b2z−2 + . . . bnz−n
1 + a1z−1 + a2z−2 + . . . anz−n
(1) (1) 3.1 Dynamic system identification tools The identification of dynamic systems can be facilitated so as to make procedures the control
design more efficient from the standpoint of technical feasibility and cost. processes of various
types can be considered as chemical, mechanical or even behavior, used for macroeconomic
modeling systems. The use of tools that comply with the practicality of applying the concept and system design
digital control is very suitable as mentioned before, so we introduce a way simple to obtain
mathematical models of whatever the process, however in the case of linear or linearized
process. To initiate an identification in the MATLAB we can proceed in two ways and the
designer must choose whichever is most convenient to your time and level of knowledge that
it is your process or your plan. y
p
y
p
In Command Window use the following command to open the graphical user interface the
Identification Toolbox: >> ident >> ident will produce the screens shown in Figure 3, where you can begin the process of identification. (a) Control to start Ident
(b) Ident Main Screen
Fig. 3. Opening The Identification Tool Box - MATLAB
On these screens you can start importing the measurement data on the system or even with
knowledge in the previous system will produce the screens shown in Figure 3, where you can begin the process of identifi (a) Control to start Ident (b) Ident Main Screen Fig. 3. Opening The Identification Tool Box - MATLAB On these screens you can start importing the measurement data on the system or even with
knowledge in the previous system On these screens you can start importing the measurement data on the system or even with
knowledge in the previous system 4280 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer The main tool for modeling dynamic systems to digital control is the MATLAB Identification
Tool Box of, a feature that helps the designer to seamlessly and generates discrete polynomial
transfer functions and the user without the need of programming the algorithms used for
system identification. The IDENT from MATLAB Graphical User Interface is shown in Figures 4
and 3 and in this figure that can be seen are located to the left set of data and the right answer,
ie the model to be obtained. 3.2.1 Computational and hardware setups It is understood by Hardware setups and computational specifications of the hardware and
and design specifications that are the model order and delay. Description of procedure for
conducting the experiment are presented in next sections. 3.2 The plant modeling The estimation of parameters of the transfer function of the plant is performed with the
Toolbox Identification Systems MATLAB. Using the observations of voltage and temperature
measurements, table,we can get the parameters of a 2nd order transfer function. I
Fi
5 t
t th
ti
i t
th
l
l
t f
fi
t
l
ti
f th The estimation of parameters of the transfer function of the plant is performed with the
Toolbox Identification Systems MATLAB. Using the observations of voltage and temperature
measurements, table,we can get the parameters of a 2nd order transfer function. In Figure 5 to represent the operation points thermal plant for a first evaluation of the
algorithm, shows the temperature behavior from departure to variations in operating points. g
p
In Figure 5 to represent the operation points thermal plant for a first evaluation of the
algorithm, shows the temperature behavior from departure to variations in operating points. 5
281 MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems The bands system operation are separated for purposes of calculation of the parameters of a
model of second order. The band Operation of this plant is between 580 and 60 0 as observed
in Figure 5. 3.2.3 The transfer function and polynomial form 3.2.3 The transfer function and polynomial form
The transfer function in Z plane is given by 3.2.2 OE model Using Identification Toolbox to estimate the parameters of the discrete model OE (Output-Error)
operated in the delay is given by T(t) = B(q)
F(q) ω(t) + e(t)
(2) (2) (2) where A(q) = 1 −1.52q−1 + 0.5336q−2
B(q) = 0.7426q−1 −0.7187q−2 Considering the transfer function of the deterministic signal from the ω input we have Considering the transfer function of the deterministic signal from the ω input we have T(t)
ω(t) = B(q)
F(q)
(3) (3) 3.2.3 The transfer function and polynomial form
The transfer function in Z plane is given by Sys = OE(Data,[nb nf nk] 6282 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer where where where
D t i th
bj
t
t i i
th i f
ti
i
t
d
t
t
t where
Data is the object containing the information input and output system; the object containing the information input and output system; Data is the object containing the information input and output system; Data is the object containing the information input and outpu
nb is the order of the polynomial B(q) from Equation 1; j
g
p
p
y
e order of the polynomial B(q) from Equation 1;
( ) j
g
p
nb is the order of the polynomial B(q) from Equation 1; j
g
p
nb is the order of the polynomial B(q) from Equation 1; p
y
q
q
e order of the polynomial F(q) from Equation 1;
d l We can also order the knowledge to perform analysis in continuous time by following the
identification commands M = idproc(type,value) M = idproc(type,value) M = idproc(type,value) Thereby generating a frequency domain model type Thereby generating a frequency domain model type Thereby generating a frequency domain model type G(s) = Kp
1 + Tzs
(1 + Tp1s)(1 + Tp2s)(1 + Tp3s) e−Tds
(6) (6) Where the parameters of the function idproc are inherent in the system type, order and
constant delay. The graphs in Figure 5 are constructed in accordance with the instructions from design
requirements . The first statement stores the vector medt values of temperature around the
heat source (resistor) and the actuator speed ω. The third instruction is didactic and for
implementation is not required to be codified. Fig. 5. Continuous Process Reaction Curve. Fig. 5. Continuous Process Reaction Curve. Fig. 5. Continuous Process Reaction Curve. 3.2.3 The transfer function and polynomial form
The transfer function in Z plane is given by W(z)
Va(z) = B(z)
F(z) =
0.7426z −0.718
z2 −1.52z + 0.5336
(4) (4) The poles of the transfer function in Z, pz1 = 0.9697 and pz1 = 0.5503is the positive axis that
divides the first and fourth quadrants. The zero is given by z = 0.9678 and is on top from one
pole to the nearest two decimal places. p
p
Applying the transformation C2D command of Toolbox Control gives the model transfer
function continuously in the model time we have T(s)
Va(s) = B(s)
F(s) =
0.9852s −0.03224
s2 + 0.628s + 0.01837
(5) (5) The poles of the transfer function at s,pc1 = −0.5973and pc2 = −0.0308. The zero at zc =
0 0327
l
l th
ff
t
l The poles of the transfer function at s,pc1 = −0.5973and pc2 = −0.0308. The zero at zc =
0 0327
l
l
h
ff
l The poles of the transfer function at s,pc1 = −0.5973and pc2 = −0.0308. The zero at zc =
−0.0327 nearly cancels the effect pole pc2. −0.0327 nearly cancels the effect pole pc2. −0.0327 nearly cancels the effect pole pc2. y
p
p
The MATLAB scrip execution has to read the temperature signals and actuator to estimate
the parameters a mathematical model that represents the operating point system’s thermal
system. 3.3.1 Model discrete time The procedure for the identification of parameters of discrete time is encoded in the script,
converting (describing) the discrete models in transfer function descriptions. The Figure 5 shows the comparison of behavior temperature of the continuous model obtained
by the process reaction curve The procedure for the identification of parameters of discrete time is encoded in the script,
converting (describing) the discrete models in transfer function descriptions. The Figure 5 shows the comparison of behavior temperature of the continuous model obtained converting (describing) the discrete models in transfer function descriptions. The Figure 5 shows the comparison of behavior temperature of the continuous model obtained
by the process reaction curve The Figure 5 shows the comparison of behavior temperature of the continuous model obtained
by the process reaction curve 3.3.2 Transfer functions The purpose of the transfer functions we generate the files contains models of the objects
should be stored OE to conversion models. 3.3 Model survey 3.3 Model survey
The lifting of the method consists of parametric estimation conversion this model of transfer
function in Z. 3.3 Model survey
The lifting of the method consists of parametric estimation conversion this model of transfer
function in Z. 3.3 Model survey
The lifting of the method consists of parametric estimation conversion this model of transfer
function in Z. The lifting of the method consists of parametric estimation conversion this model of transfer
function in Z. 7
283 MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems 3.3.3 Estimating parameters scripts The establishment of a procedure for estimating parameters (connotation: scientific) or lifting
of a model (connotation: engineering) presented in this section consists of three steps. The
first step is the generation each measurement. The second step consists of estimating the
parameters of functions transfer. The third step is the analysis of the model have the impulse
response, Bode diagram and step. 3.4 A Platform to testing control systems To validate our experiment we used a platform for experiments with micro digital circuits
processed with the support of micro controllers that can be easily programmed using
knowledge of language with C and a broad support to this type of application as in Ibrahim
(2006),Lewis (2001) and Wilmshurst (2007). Using the Microchip PIC micro controller family we can turn our platform to run on following
code done in C programming language. #device adc=10
#use delay(clock=4000000)
#fuses HS,NOWDT,PUT
#use rs232(baud=9600, xmit=PIN_C6,rcv=PIN_C7)
#include <mod_lcd.c> #device adc=10
#use delay(clock=4000000)
#fuses HS,NOWDT,PUT
#use rs232(baud=9600, xmit=PIN_C6,rcv=PIN_C7)
#include <mod_lcd.c> #device adc=10
#use delay(clock=4000000)
#fuses HS,NOWDT,PUT
#use rs232(baud=9600, xmit=PIN_C6,rcv=PIN_C7)
#include <mod_lcd.c>
main()
{
long int value=0;
float temp=0;
int i=0;
lcd_ini();
setup_timer_2 (T2_DIV_BY_16, 61, 1);
setup_ADC_ports (RA0_analog);
setup_adc(ADC_CLOCK_INTERNAL );
setup_ccp1(ccp_pwm);
set_pwm1_duty ( 0 );
setup_ccp2(ccp_pwm);
set_pwm2_duty ( 0 );
set_adc_channel(0);
printf ("%%------------ DAQ - System ------------ \r\n");
printf ("%%Temperature (žC) \r\n");
while(true){ main() setup_ADC_ports (RA0_analog); setup_adc(ADC_CLOCK_INTERNAL ); while(true){ 8284 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer set_pwm1_duty(1023);
delay_ms(100);
value = read_adc();
temp = ((5*(float) value)/(1024))*16.09;
printf (" %f \r\n",temp);
printf (lcd_write,"Temp = %f ",temp);
lcd_write (’\f’); if(temp>=60){
set_pwm2_duty ( 1023 );
} if(temp<=58){
set_pwm2_duty ( 0 );
} }
delay_ms(500); The code shown above is the implementation of a system that simulates the temperature, in
the form of Hardware a thermal system with relative temperature variation in responses to
time much smaller. The code shown above is the implementation of a system that simulates the temperature, in
the form of Hardware a thermal system with relative temperature variation in responses to
time much smaller. The dynamics of this system is well demonstrated in Figure 6 Fig. 6. A Diagram to System Hardware
Where the basis for the system of change of temperature in an open environment that is cooler
acts as the system actuator. The control objective, as shown in the code is to keep a room
temperature at a desired track with minimal accuracy in the output signal. Fig. 6. A Diagram to System Hardware Where the basis for the system of change of temperature in an open environment that is cooler
acts as the system actuator. The control objective, as shown in the code is to keep a room
temperature at a desired track with minimal accuracy in the output signal. Where the basis for the system of change of temperature in an open environment that is cooler
acts as the system actuator. The control objective, as shown in the code is to keep a room
temperature at a desired track with minimal accuracy in the output signal. 9
285 MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems 4. Implementing control systems on MATLAB The MATLAB software provides support, form the implementation of acquisition system
data to design a control system, which becomes possible with methods of identification and
communication required in numerical methods implementation of a controller. This tool was
incorporated for the purpose to help engineers and scientists in projects and systems design
methods numeric, or for the resolution algorithms and systems simulation. In the following
sections will be shown tools that are part of the suite of applications such as MATLAB concepts
for implementation of digital control systems. 4.1 The serial interface For the design of systems for data acquisition in MATLAB, an important tool are the
protocols for data communications in environments that are common industries. The
serial communication is known for its simplicity of connection and implementation in
both hardware and software because there are a wide variety software and programming
languages that provide libraries for development communication in serial protocol. In
MATLAB the simplicity of applying this tool can be translated by code shown below Serial_Obj = Serial(’COM1’);
fopen(Serial_Obj);
var_read = fscanf(Serial_Obj)
fprintf(var_read,’Data Receiveve’);
fclose(Serial_Obj);
Delete(Serial_Obj); Serial_Obj = Serial(’COM1’);
fopen(Serial_Obj);
var_read = fscanf(Serial_Obj)
fprintf(var_read,’Data Receiveve’);
fclose(Serial_Obj);
Delete(Serial_Obj); Serial_Obj = Serial(’COM1’); Serial_Obj = Serial(’COM1’);
fopen(Serial_Obj);
var_read = fscanf(Serial_Obj)
fprintf(var_read,’Data Receiveve’);
fclose(Serial_Obj);
Delete(Serial_Obj); fprintf(var_read,’Data Receiveve’); fclose(Serial_Obj); Delete(Serial_Obj); With the above script you can communicate and receive data from an external device to your
computer. With communication with the external hardware can open, using the following
commands, send and receive data relevant to the control system function send_data_tohard(data_ctrl,setpoint_ctrl) fprintf(Serial_Obj,data_ctrl)); printf(Serial_Obj,data_ctrl)); fprintf(Serial_Obj,setpoint_ctrl)); fprintf(Serial_Obj,setpoint_ctrl)); Therefore the system receives the data for the implementation of intelligent digital control
system: function receiv_data_fromhard(data_ctrl,data_error) unction receiv_data_fromhard(data_ctrl,data_error) data_ctrl = fscanf(Serial_Obj,’data_ctrl’); ata_ctrl = fscanf(Serial_Obj,’data_ctrl’); ata_error = fscanf(Serial_Obj,’data_error’); data_error = fscanf(Serial_Obj,’data_error’); Always observing that the variable Dataa_crtl is used for timing and appropriateness of
real-time system. Always observing that the variable Dataa_crtl is used for timing and appropriateness of
real-time system. fopen(Serial_Obj);
if Serial_Obj.Status ==open 4.4 Implementing intelligent systems The implementation of intelligent systems through MATLAB may well become a very
profitable it facilitates the testing of new techniques that use features and tools already
implemented in this software. Techniques computational intelligence can withdraw from the
digital control system the important factor in the Ts, however the system still requires real
time control. Each execution cycle lets you have the need to perform numerical derivatives
and integrals and introducing a context of researching and mapping , which may require less
computational effort. The diagram shown in Figure 8 Fig. 8. Diagram of the General System
It´s possible conclude that with the development of both the hardware and software, these
systems are likely to become the largest presence within the control and automation Fig. 8. Diagram of the General System It´s possible conclude that with the development of both the hardware and software, these
systems are likely to become the largest presence within the control and automation It´s possible conclude that with the development of both the hardware and software, these
systems are likely to become the largest presence within the control and automation It´s possible conclude that with the development of both the hardware and software, these
systems are likely to become the largest presence within the control and automation 4.3 Real time control Digital Control Systems has its roots in the interface with the analog world and thus the delay
time this conversion to occur immediately. In real-time systems is a concern that the execution
time of a given instruction does not exceed a predetermined threshold. Converging, the
realtime systems are strictly necessary in digital control because it does necessary to guarantee
instruction execution control Uc within the limit of sampling system Ts where a failure of this
requirement may lead to instability as the plant design of discrete controllers is directly related
Ts variable. MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems set(handles.con_text,’String’,’Connected’);
end 4.2 The user interface The user interface development system shown in Figure 7 is used with supervisors and control
environment of the platform. The user interface development system shown in Figure 7 is used with supervisors and control
environment of the platform. p
Using the anointing of the environment development of GUIDE MATLAB can therefore
obtain the convenience of the project environment be the same as the deployment
environment Using the anointing of the environment development of GUIDE MATLAB can therefore
obtain the convenience of the project environment be the same as the deployment
environment In the source code below is observed in connection with the generation via the serial port
textbf GUID emph MATLAB. In the source code below is observed in connection with the generation via the serial port
textbf GUID emph MATLAB. Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 10286 Fig. 7. Graphical Interface of the Platform System Fig. 7. Graphical Interface of the Platform System function
Button_01_Callback(hObject, eventdata, handles, varargin)
Serial_Obj=serial(’COM1’,’BaudRate’,9600);
opcon2 =get(handles.menu_01,’Value’); function
Button_01_Callback(hObject, event
Serial_Obj=serial(’COM1’,’BaudRate’,9600); j
Serial_Obj=serial(’COM1’,’BaudRate’,9600); opcon2 =get(handles.menu_01,’Value’); opcon = get(handles.menu_01,’String’); switch opcon{opcon2}
case ’COM1’
Serial_Obj.Port=’COM1’;
case ’COM2’
Serial_Obj.Port=’COM2’;
case ’COM3’
Serial_Obj.Port=’COM3’;
case ’COM4’
Serial_Obj.Port=’COM4’;
case ’COM5’
Serial_Obj.Port=’COM5’;
case ’COM6’
Serial_Obj.Port=’COM6’;
case ’COM7’
Serial_Obj.Port=’COM7’;
otherwise
errordlg(’Select a Valid Serial Port’,’Error’) switch opcon{opcon2}
case ’COM1’ Serial_Obj.Port=’COM4’; Serial_Obj.Port=’COM7’; end fopen(Serial_Obj);
if Serial_Obj.Status ==open 11
287 MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems 4.4.1 A fuzzy method implementation y
p
As described in Ross (2004),S. Sumathi (2010) and Andrade (2010) the commitment of systems
based on fuzzy logic both in respect of the facility as implementation of policies that take into
account not only the performance of closed loop of industrial process control as well as the 12288 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer experience acquired human with the process that can be transferred directly to the core of the
Fuzzy Logic Controller(FLC) with its implementation process described in Figure 9 Fig. 9. Diagram of the General System
The consolidation of this type of system could provide designers with a feature not found on
controllers classical, ie the aforementioned expertise. To use the Fuzzy controller is needed for
the project prior knowledge on the implementation of systems based on fuzzy logic and can
be found in Andrade (2010) and especially in Zadeh (1965). In MATLAB the design begins
by checking the feasibility of the controller and can be done by graphical interface Fuzzy Logic
Toolbox with a significant help from MathWorks (2010). To open the FLT (Fuzzy Logic Toolbox) typed: Fig. 9. Diagram of the General System The consolidation of this type of system could provide designers with a feature not found on
controllers classical, ie the aforementioned expertise. To use the Fuzzy controller is needed for
the project prior knowledge on the implementation of systems based on fuzzy logic and can
be found in Andrade (2010) and especially in Zadeh (1965). In MATLAB the design begins
by checking the feasibility of the controller and can be done by graphical interface Fuzzy Logic
Toolbox with a significant help from MathWorks (2010). The consolidation of this type of system could provide designers with a feature not found on
controllers classical, ie the aforementioned expertise. To use the Fuzzy controller is needed for
the project prior knowledge on the implementation of systems based on fuzzy logic and can
be found in Andrade (2010) and especially in Zadeh (1965). In MATLAB the design begins
by checking the feasibility of the controller and can be done by graphical interface Fuzzy Logic
Toolbox with a significant help from MathWorks (2010). Table 1. The knowledge from the Rules of Decision System And the controller output and results in a weighted sum that depends exclusively on the
method chosen. And the controller output and results in a weighted sum that depends exclusively on the
method chosen. 4.4.1 A fuzzy method implementation To open the FLT (Fuzzy Logic Toolbox) typed: >>fuzzy and the following screen will open
However the system to be implemented with MATLAB using the serial communication is
necessary to implement the intelligent system in script and can be done as follows However the system to be implemented with MATLAB using the serial communication is
necessary to implement the intelligent system in script and can be done as follows error = data_ctrl;
NG(k) = trimf(error, [a_i b_i c_i]);
NS(k) = trimf(error, [a_i b_i c_i]);
ZR(k) = trimf(error, [a_i b_i c_i]);
PS(k) = trimf(error, [a_i b_i c_i]);
PB(k) = trimf(error, [a_i b_i c_i]);
chang_error = data_ctrl;
NL(k) = trimf(chang_error, [a_i b_i c_i]);
NS(k) = trimf(chang_error, [a_i b_i c_i]);
ZR(k) = trimf(chang_error, [a_i b_i c_i]);
PS(k) = trimf(chang_error, [a_i b_i c_i]);
PL(k) = trimf(chang_error, [a_i b_i c_i]); error = data_ctrl;
NG(k) = trimf(error, [a_i b_i c_i]);
NS(k) = trimf(error, [a_i b_i c_i]);
ZR(k) = trimf(error, [a_i b_i c_i]);
PS(k) = trimf(error, [a_i b_i c_i]);
PB(k) = trimf(error, [a_i b_i c_i]);
chang_error = data_ctrl;
NL(k) = trimf(chang_error, [a_i b_i c_i]);
NS(k) = trimf(chang_error, [a_i b_i c_i]);
ZR(k) = trimf(chang_error, [a_i b_i c_i]);
PS(k) = trimf(chang_error, [a_i b_i c_i]);
PL(k) = trimf(chang_error, [a_i b_i c_i]); 13
289 MATLAB as Interface for Intelligent Digital Control of Dynamic Systems
MATLAB as Interface for Intelligent Digital Control of Dynamic Systems Fig. 10. The FLT Main Screen Fig. 10. The FLT Main Screen Where Negative Large, Negative Small, ZeRo, Positive Small and Positive Large are linguistics
vary based on experience. The system output can be given as shown in Figure 9 with a bank
of rules based on Table 1 decision-making as an example Error \ changingError NL NS ZR PS PL
NL
PL PL PL PL NL
NS
PS PS PS PS NS
ZR
PS ZR ZR NS ZR
PS
NS NS NS NS PS
PL
NL NL NL NS PS Error \ changingError NL NS ZR PS PL
NL
PL PL PL PL NL
NS
PS PS PS PS NS
ZR
PS ZR ZR NS ZR
PS
NS NS NS NS PS
PL
NL NL NL NS PS
Table 1. The knowledge from the Rules of Decision System Table 1. The knowledge from the Rules of Decision System Table 1. The knowledge from the Rules of Decision System Table 1. The knowledge from the Rules of Decision System 5. Conclusion With the aid of this important tool can facilitate the development of applications to interface
with and control devices industries. A overview of these tools has been shown here to that
may be developed to greater diversity of applications according to the need of the designer. As an environment of the computational complex, MATLAB can provide solutions for
engineering, physics and mathematics with the use of its functions basic and therefore leaving
the search more efficient and less costly. This platform is an important and necessary tool, it
can lead a project, with integration between Software and Hardware, for a safe convergence of
results, thus integrating computational resources for simulation design and implementation
from a direct single platform. 14290 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 6. References Andrade, G.A. Neto, J. L. L. (2010). A framework for modeling, digital control design
and simulations of dynamic, Computer Modelling and Simulation (UKSim), 2010 12th
International Conference on, IEEE Computer Society Digital Library. f
p
y
g
y
Charles L. Philips, H. T. N. (1995). Digital Control Systems: Analisys and Design, third edition
edn, Prentice Hall. Gene F. Franklin, J. David Powell, M. L. W. (1998). Digital Control of Dynamic Systems, 3rd edn,
Prentice Hall. Ibrahim, D. (2006). Microcontroller Based Applied Digital Control, John Wiley and Sons Lewis, C. S. (2001). Programming Microcontrollers in C, 2nd edn, LLH Publishing. MathWorks, T. (2010). Fuzzy Logic Tool Box : User’s Guide. Moudgalya, K. (2007). Digital Control, John Wiley and Sons. Ross, T. J. (2004). Fuzzy Logic With Engineering Applications, 2nd edn, John Wiley and Sons. S. Sumathi, S. P. (2010). Computational Intelligence Paradigms: Theory and Applications Using
MATLAB, CRC Press. Wilmshurst, T. (2007). Designing Embedded Systems with PIC Microcontrollers, Newnes. Zadeh, L. A. (1965). Fuzzy sets, Information and Control Proceedings . g
g
MathWorks, T. (2010). Fuzzy Logic Tool Box : User’s Guide. MathWorks, T. (2010). Fuzzy Logic Tool Box : User’s Guide. g y
(
)
g
J
y
Ross, T. J. (2004). Fuzzy Logic With Engineering Applications, 2nd edn, John Wiley and Sons. S. Sumathi, S. P. (2010). Computational Intelligence Paradigms: Theory and Applications Using
MATLAB, CRC Press. Wilmshurst, T. (2007). Designing Embedded Systems with PIC Microcontrollers, Newnes. Zadeh, L. A. (1965). Fuzzy sets, Information and Control Proceedings . g y
(
)
g
J
y
Ross, T. J. (2004). Fuzzy Logic With Engineering Applications, 2nd edn, John Wiley and Sons. S. Sumathi, S. P. (2010). Computational Intelligence Paradigms: Theory and Applications Using
MATLAB, CRC Press. g y
g
y
Ross, T. J. (2004). Fuzzy Logic With Engineering Applications, 2nd edn, John Wiley and Sons. S. Sumathi, S. P. (2010). Computational Intelligence Paradigms: Theory and Applications Using
MATLAB, CRC Press. Wilmshurst, T. (2007). Designing Embedded Systems with PIC Microcontrollers, Newnes. S. Sumathi, S. P. (2010). Computational Intelligence Paradigms: Theory and Applications Using
MATLAB, CRC Press. Wilmshurst, T. (2007). Designing Embedded Systems with PIC Microcontrollers, Newne
Zadeh, L. A. (1965). Fuzzy sets, Information and Control Proceedings . 15 1. Introduction pp
pp
y
In order to develop this work we need to integrate two different problems: the calculation of
the dynamic response of a vibrating structure via finite element models and the study of the 2292 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer uncertainty propagation via fuzzy arithmetic. Both problems can be solved using MATLAB
code obtaining very good results in terms of accuracy and computational cost. uncertainty propagation via fuzzy arithmetic. Both problems can be solved using MATLAB
code obtaining very good results in terms of accuracy and computational cost. The motivation behind this work is threefold: firstly, it is meant to show how MATLAB
provides suitable functions and specialized toolboxes in order to study the static or dynamic
response of a controlled structure via finite elements and control theory; secondly, it
demonstrates the suitability of MATLAB to solve uncertainty propagation problems through
fuzzy arithmetic minimizing the computational cost; and thirdly, it illustrates the application
of a Fuzzy Finite Element procedure, which integrates these two tools, with a specific case
study. y
The chapter is organized in the following way: Section 1 has summarized the aims and
concerns of the chapter; Section 2 deals with dynamic analysis of structures with active
damping by means of the OpenFEM Toolbox and the Control System Toolbox of MATLAB; Section
3 discusses the different types of uncertainty and how they could be analyzed using fuzzy
arithmetic programmed in MATLAB; Section 4 describes a Fuzzy Finite Element procedure
in MATLAB in order to study the propagation of uncertain parameters in control systems of
structures; Section 5 shows a case study in which the Fuzzy Finite Element procedure is tested;
Section 6 deals with the main conclusions of this work; and finally the acknowledgements and
references included through the text are included. 1. Introduction Vibration is an important aspect of many engineering systems. In most cases, such vibration is
undesirable and requires attenuation or control, which explains the huge quantity of vibration
control techniques that can be found in the literature. Nevertheless, sometimes all this
knowledge is not enough to guarantee the success in this purpose. Model inaccuracies or
parameter uncertainty are unavoidable in all relevant practical application and not only can
they degrade the performance of an otherwise well-designed control system, but they may
also lead to instability and even structural failure. y
For these reasons, robustness is of crucial importance in control-system design. Although
always being appreciated, it was not until late 1970s when a theory capable to explicitly
handle the robustness issue in feedback design was developed: the H∞optimal control theory
(Zames, 1981; Zames & Francis, 1983). This optimization approach is well developed and we
can even find a full Robust Control Toolbox in MATLAB which, in collaboration with the Control
System Toolbox, let us identify worst-case scenarios and generate optimal controllers so that
the stability and good performance of the plant is ensured (Gu et al., 2005). Obviously, the H∞optimal control theory shows some disadvantages, like the high level of
mathematical understanding needed to apply them successfully and the fact that it sometimes
leads to potentially very conservative results (Gu et al., 2005). Indeed, even when a solution
via H∞techniques is eventually found, the process may have been too expensive in terms
of designer’s time and the sensitivity to the uncertainty sources is not analyzed. These
motivations make us think that a straightforward possibilistic methodology for simulating
and analyzing the uncertainty propagation in control system would be a very valuable,
complementary and time saving tool. This work focuses on how MATLAB can supply suitable tools in order to manage uncertainty
propagation in finite element models of structures from the point of view of fuzzy arithmetic. More specifically, we will describe a methodology fully programmed in MATLAB in order
to deal with uncertain control systems of vibrating structures and we will illustrate the
application of this approach to a case study. 2. Dynamic analysis and control of structures y
p
The study of the dynamic behaviour of a structure can be carried out by means of finite
element analysis. Among all the different possibilities to solve finite elements problems,
in this chapter we focus on the use of a specific toolbox of MATLAB: the OpenFEM Toolbox
(Balmes et al., 2009). It is an open-source toolbox for finite element analysis within the matrix computing
environment MATLAB. The software is developed in collaboration between Macs and the
SDTools Company and it is distributed under a GNU Lesser General Public License, that is, a
free software license which also allows the user to make modifications in the code. Performing
finite element analysis within a matrix computing environment is of considerable interest,
in particular as regards the ease of new developments, integration of external software,
portability, post-processing, etc. This relatively young software is already quite successful
in the finite element community as it is proven by the about 300 downloads per month
(OpenFEM, 2011). Though the toolbox architecture includes graphical user interfaces for visualization, analysis
and animation of results, the powerful of this toolbox does not lie in this fact but in the
standard and advanced methods which are implemented. Moreover, the provided functions
are open and can be easily extended to suit particular needs of the user (Balmes et al., 2009),
as it is our case. Let us consider a vibrating structure. The first step in order to carry out its finite element
analysis consists in discretizing the structure. The mesh nodes, elements which join the nodes,
material properties, element properties and any additional information such as boundary
conditions, loads, etc., are stored in a struct class variable which defines the model of the
multi degree of freedom vibrating structure which is governed by the next set of equations of
motion M ¨x + C ˙x + Kx = f
(1) (1) M ¨x + C ˙x + Kx = f A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures 3
293 where M, K and C are the mass, the stiffness and the damping matrices, respectively, x the
vector of displacements of all the degrees of freedom of the structure and f a general vector
of forces. 2. Dynamic analysis and control of structures After performing the change
of variables x = Φz, where z is the vector of modal coordinates and Φ is normalized in such
a way that the modal mass matrix is the identity matrix, the governing equations in modal
coordinates read coordinates read ¨z + 2ξΩ ˙z + Ω2z = ΦT f
(2) (2) e Ω and ξ define the diagonal matrices of natural frequencies and damping factors. l
h
f
l
id
l
d
l
d
h d fii i
f h where Ω and ξ define the diagonal matrices of natural frequencies and damping factors. Finally, the software also provides several commands related to the definition of the actuators
and sensors or, strictly speaking, the input force influence vector Lu and the sensor influence
vector Ly, both of them required for the definition of either the transfer function or the state
space matrices. where Ω and ξ define the diagonal matrices of natural frequencies and damping factors. Finally, the software also provides several commands related to the definition of the actuators
and sensors or, strictly speaking, the input force influence vector Lu and the sensor influence
vector Ly, both of them required for the definition of either the transfer function or the state
space matrices. The finite element models which are obtained with this toolbox can be used to solve both
static and dynamic problems, the results of which being ready to be plotted or post-processed
under any other MATLAB toolbox. In this work, we blended these commands which those
corresponding to the Control System Toolbox. 2. Dynamic analysis and control of structures Matrices M and K arise from the finite element analysis of the structure whereas C
is usually obtained under the hypothesis of Rayleigh damping. where M, K and C are the mass, the stiffness and the damping matrices, respectively, x the
vector of displacements of all the degrees of freedom of the structure and f a general vector
of forces. Matrices M and K arise from the finite element analysis of the structure whereas C
is usually obtained under the hypothesis of Rayleigh damping. where M, K and C are the mass, the stiffness and the damping matrices, respectively, x the
vector of displacements of all the degrees of freedom of the structure and f a general vector
of forces. Matrices M and K arise from the finite element analysis of the structure whereas C
is usually obtained under the hypothesis of Rayleigh damping. Both in the state space approach and in the transfer function approach, working with physical
coordinates is not practical because of the usually high number of degrees of freedom. Thus, a
change of variables into modal coordinates is suggested. In addition, in this way the problem
can be restricted to the bandwidth of interest, neglecting the high frequency dynamics of the
system. After the computation of modes via finite element analysis one obtains the natural
frequencies of the modes and the matrix of the mode shapes Φ. After performing the change
of variables x = Φz, where z is the vector of modal coordinates and Φ is normalized in such
a way that the modal mass matrix is the identity matrix, the governing equations in modal
coordinates read Both in the state space approach and in the transfer function approach, working with physical
coordinates is not practical because of the usually high number of degrees of freedom. Thus, a
change of variables into modal coordinates is suggested. In addition, in this way the problem
can be restricted to the bandwidth of interest, neglecting the high frequency dynamics of the
system. After the computation of modes via finite element analysis one obtains the natural
frequencies of the modes and the matrix of the mode shapes Φ. 2.2 Active damping and the Control System Toolbox As far as the Positive Position Feedback scheme is concerned, it is appropriate for a structure
equipped with strain actuators and sensors (Preumont, 2002). The objective of a Positive
Position Feedback controller is to use a second order filter to improve the roll-off of the control
system, allowing high frequency gain stabilization. The implementation of this control system
is given by the following equations s
a
g
g
,
p
y
As far as the Positive Position Feedback scheme is concerned, it is appropriate for a structure
equipped with strain actuators and sensors (Preumont, 2002). The objective of a Positive
Position Feedback controller is to use a second order filter to improve the roll-off of the control
system, allowing high frequency gain stabilization. The implementation of this control system
is given by the following equations M ¨x + C ˙x + Kx = Luu
y = LTu x
¨v + β f ˙v + Ω2
f v = y
u = −Gv
(6) (6) where u is the control force acting on the structure through the influence vector Lu, y is the
difference of slope between the ends of the sensor, G = diag(gi) is the positive gain matrix,
and v is the output of the second order filter defined by the matrices β f = diag(2ξ f ω f ) and
Ω2
f = diag(ω2
f ). Note that the fact that the same localization vector (Lu) rules the actuator and
sensors is a consequence of collocation. where u is the control force acting on the structure through the influence vector Lu, y is the
difference of slope between the ends of the sensor, G = diag(gi) is the positive gain matrix,
and v is the output of the second order filter defined by the matrices β f = diag(2ξ f ω f ) and
Ω2
f = diag(ω2
f ). Note that the fact that the same localization vector (Lu) rules the actuator and
sensors is a consequence of collocation. q
ransfer function of the controller (a second order low pass filter) can be written as follow (7) (7) gD(w) = g
ω f
ω2
f + 2jωξ f ω f −ω2
(7) This compensator has both advantages and drawbacks. 2.2 Active damping and the Control System Toolbox On the one hand, the open-loop
transfer function has a roll-off of −40dB/decade, larger in comparison to Direct Velocity
Feedback (−20dB/decade), which may decrease the risk of destabilizing high frequency
dynamics. On the other hand, there is a stability limit which is reached when the open-loop
static gain is equal to 1, this fact being independent of the damping (Preumont, 2002). This compensator has both advantages and drawbacks. On the one hand, the open-loop
transfer function has a roll-off of −40dB/decade, larger in comparison to Direct Velocity
Feedback (−20dB/decade), which may decrease the risk of destabilizing high frequency
dynamics. On the other hand, there is a stability limit which is reached when the open-loop
static gain is equal to 1, this fact being independent of the damping (Preumont, 2002). Once the open loop transfer functions of the plant and the regulator are defined, they can be
used in the Control System Toolbox as transfer function class variables. Then, the desired active
damping can be obtained by selecting the proper gain g of the regulator. In order to do this,
several techniques can be used such as Bode Diagram Design, Root Locus Design, Nichols
Plot design, etc. g
Finally, the Control System Toolbox also provides valuable functions in order to analyze the
stability and performance in terms of stability margins, time responses or the position of the
closed loop poles and zeros in the pole-zero map. They will be used in our Fuzzy Finite
Element methodology as fuzzy outputs in order to analyze the behaviour of the uncertain
control system. 2.2 Active damping and the Control System Toolbox The Control System Toolbox provides a collection of matrix-based functions, usually expressed
as M-files, for the topic of control engineering. The control systems may be modelled as
transfer functions, zero-pole-gain or even using the state space approach, which allows the
designer to apply classic techniques as well as modern techniques. However, it is not our
purpose to study thoroughly this topic, so we will concentrate on briefly reviewing, as an
example, one of the most common active control techniques of structures (Preumont, 2002):
active damping with collocated piezoelectric pairs via Positive Position Feedback, which, in
the end, will be the case study discussed in Section 5. y
The transfer function of the multi degree of freedom vibrating structure obtained via modal
expansion reads G(ω) = X(ω)
F(ω) =
∞
∑
n=1
ΦnΦTn
ω2n + 2jωξnωn −ω2
(3) (3) where Φn, ωn and ξn are the mode shape, the natural frequency and the damping ratio for
the nth mode of vibration, respectively. The same model based upon the first N modes of
vibration leads to the expression where Φn, ωn and ξn are the mode shape, the natural frequency and the damping ratio for
the nth mode of vibration, respectively. The same model based upon the first N modes of
vibration leads to the expression ˆG(ω) ≈
N
∑
n=1
ΦnΦTn
ω2n + 2jωξnωn −ω2
(4) (4) where the residual term due to the contributions of the truncated nodes has been neglected. Combining the equations for the surface-bonded actuator and sensor (Dosch et al., 1992;
Sims et al., 2005) and Equation 4 which governs the structural dynamics, we obtain the where the residual term due to the contributions of the truncated nodes has been neglected. Combining the equations for the surface-bonded actuator and sensor (Dosch et al., 1992;
Sims et al., 2005) and Equation 4 which governs the structural dynamics, we obtain the 4294 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer frequency response function between the voltage Va applied to the actuator and the voltage
Vs at the output of the charge amplifier of the sensor H(ω) = Vs(ω)
Va(ω) = kaks
N
∑
n=1
LTuΦnΦTnLy
ω2n + 2jωξnωn −ω2
(5) (5) where ks and ka are the sensor gain and the actuator gain, respectively. f
h
db
k
h
d where ks and ka are the sensor gain and the actuator gain, respectively. 3. Uncertainty and fuzzy arithmetic In the literature, the use of the term uncertainty is slightly ambiguous. In order to establish the
nomenclature for the ensuing description, the reader is referred to the terminology proposed
in (Oberkampf et al., 2004). A Fuzzy Finite Element Method Programmed A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures 5
295 On the one hand, we will use the term aleatory uncertainty to describe the inherent variation
associated with the physical system or the environment under consideration. These sources
of uncertainty can be represented as randomly distributed quantities, usually in terms
of probability distribution functions. Typical examples of this kind of uncertainty are
manufacturing tolerances, environmental effects, properties of non-uniform materials or any
other identifiable disturbances. On the other hand, epistemic uncertainty derives from some
level of ignorance of the system or the environment in any activity of the modelling process. In this case, its definition stresses the lack of knowledge as the origin of this uncertainty. Thus, unlike aleatory uncertainty, a mathematical representation of epistemic uncertainty has
proven to be much more of a challenge since it is subjective and based on some expert opinion
to a certain extent. Typical examples of epistemic uncertainties are some models for boundary
conditions, simplified models for joints, models for material damping or unpredictable model
changes due to ageing, loading, etcetera. g
g
g
g
Uncertainty propagation in dynamic systems has been a very frequent topic in the
literature, which has been tackled from two different points of view (De Gersem et al., 2005):
probabilistic and possibilistic approaches. Probabilistic approaches, such as the well-known
Monte Carlo Simulation method, investigate the influence of aleatory uncertainties, this
method being particularly suitable for finite element models with certain uncertainties. Possibilistic approaches are complementary to probabilistic approaches, since not only are
they able to describe problems of aleatory uncertainties to a certain extent, yet without
statistical interpretation, but they can also handle problems where incomplete information
(epistemic uncertainty) is available. We consider that computationally expensive "brute-force"
probabilistic methods are not worthwhile in most cases, where an intuitive worst-case
scenario provides enough information. Thus, a possibilistic method in terms of fuzzy
arithmetic will be the tool that we develop and propose in order to simulate and analyze
uncertainty propagation in control systems. 3. Uncertainty and fuzzy arithmetic A later efficient implementation
of this method was carried out in (Klimke, 2003), taking advantage of the matrix
computing environment of MATLAB and providing enhanced features such as fast
processing of discretized fuzzy numbers through multi-dimensional arrays, elimination of
recurring permutations, automatic decomposition of models, treatment of single occurrences
of variables through interval arithmetic and a monotonicity test based on automatic
differentiation. Nevertheless, we have to note that the fuzzy parameters are restricted to
convex fuzzy numbers when using the Transformation Method. y
g
Specially relevant for an efficient implementation of the Transformation Method is the
elimination of recurring permutations. The decomposition scheme of this method sometimes
produces recurring points which in the end generate recurring permutations. By removing
these recurring permutations from the evaluation procedure one could save a very valuable
computation time. Indeed, we could even try to reuse as many points for different α-cuts as
possible by selecting only inner points which have already occurred in a higher-level α-cut. For symmetric triangular membership functions, the obtained discretization is identical to the
original formulation, but for other arbitrarily shaped membership functions, the distribution
of the points is less regular, but of similar density (see Figure 1). However, for the same
number of α-cuts, the less regular distribution of the inner points results in less accurate results
compared to the original formulation. The number of permutations r by using this efficient implementation of the Transformation
Method is given by the following equation r = mn + (m + 1)n
(9) (9) where m + 1 is the number of α-cuts and n is the number of fuzzy parameters. As proven in
(Klimke, 2003), the new scheme provides a valuable improvement in terms of computational
cost unless the number of α-cuts is too large compared to the number of fuzzy inputs. If that
was the case, one could disregard the removing of recurring permutations in favour of more
accurate results. 3. Uncertainty and fuzzy arithmetic y p
p g
y
Fuzzy arithmetic has been used by various researchers as a technique for propagating
uncertainty or variability through complex engineering models. The origins of this approach
can be found in the theory of Fuzzy Sets (Zadeh, 1965). In contrast to the classical set theory,
the elements of a fuzzy set are assigned a degree of membership to the set, which is referred
to as the membership level μ. The core of the set is defined as the subset of elements for which
μ = 1, whilst the support is the subset for which μ > 0. A fuzzy number is a fuzzy set that is
convex and normal, and whose membership function is piecewise continuous. p
p
The issue of performing mathematical operations on fuzzy numbers instead of on
conventional numbers can be a challenge rather than a trivial problem. In fact, the Fuzzy
Arithmetic processes are usually performed by decomposing the fuzzy numbers into a
number of intervals given by the α-cuts at the α-levels μi, (i = 0, 1, . . . , m) with μi = i
m
(8) (8) μi = i
m Then, a interval analysis via interval arithmetic can be carried out separately to each
membership level μi. Then, a interval analysis via interval arithmetic can be carried out separately to each
membership level μi. For monotonic problems this process may be trivial, since the maxima or minima of the inputs
will lead to the maxima or minima for the output. Conversely, for non-monotonic problems
this is no longer the case (Sims et al., 2010). In addition, the Standard Fuzzy Arithmetic may
become problematic and lead to different results for the same problem depending on the form
in which the solution procedure is applied, as can be seen in the examples gathered in (Hanss,
2002). In short, the application of Standard Fuzzy Arithmetic usually leads to overestimate
results to a lesser or greater extent and alternative methods must be employed. 6296 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer The Transformation Method, introduced in (Hanss, 2002), represents a special implementation
of Fuzzy Arithmetic that avoids the undesired overestimation which usually arises when
Fuzzy Arithmetic is reduced to interval computation. 4. Fuzzy Finite Element procedure in MATLAB Scheme of the numerical procedure to perform a Fuzzy Finite Element analysis using
four α-cuts. variables. Note that if μ = 1, the interval analysis degenerates into the deterministic analysis. Finally, the membership functions of the required output variables are assembled from the
interval results at all sublevels. The Fuzzy Finite Element analysis is based on the results of a previous deterministic design
of the control system. The control engineer must set the control parameters and gains of the
regulator in order to accomplish all the features required for the active damping in terms of
both stability and performance. After this process, which is usually easier and faster than
other complex control techniques such as those derived from H∞control, the Fuzzy Finite
Element analysis will simulate the behaviour of the control system when some parameters
are considered uncertain. This method is not a robust designing technique but a possibilistic
method which tests whether the deterministic design is robust enough to keep the closed
loop behaviour of the structure inside the allowable bounds for its stability and performance
features. The set of calculations which are carried out at each permutation of input values is compound
of these steps: Step 1: Finite Element calculations via the OpenFEM Toolbox Step 2: Closed loop simulation of the control system via the Control System Toolbox Step 2: Closed loop simulation of the control system via the Control System Toolbox Step 3: Analysis of stability and performance via fuzzy variables such as stability margins or
active damping. Step 3: Analysis of stability and performance via fuzzy variables such as stability margins or
active damping. The method chosen for carrying out the interval fuzzy arithmetics was the efficient
implementation of the Transformation Method proposed in (Klimke, 2003). Nevertheless, we
have included some modifications which will be introduced in the ensuing. The first modification lies in the fact that Klimke’s MATLAB script is made under the
assumption that the fuzzy output is the result of evaluating an analytical expression. In our
case, we need to replace the evaluation of such analytical function (inline class) with a list of
MATLAB commands which develops the aforementioned steps. This also allows us to include
the possibility of achieving several fuzzy outputs instead of only one. The second modification
was not necessary but it endows the method with enhance capabilities. 4. Fuzzy Finite Element procedure in MATLAB The fuzzy theory has led to the development of Fuzzy Finite Element methods as that
described in (De Gersem et al., 2005; De Munck et al., 2008; Moens & Vandepitte, 2005) for
analyzing the propagation of uncertainties in the Frequency Response Functions of a dynamic
system. When using this methodology, the uncertainties in the model parameters can be taken
into account by fuzzy numbers with their shape obtained from experimental data or assumed
from expert knowledge. Then, the numerical procedure for the implementation of these Fuzzy
Finite Element methods consists of a sequence of Interval Finite Element procedures based on
a general strategy for computing the fuzzy result from operations on fuzzy operands, i.e. the
α-sublevel or α-cuts technique. q
Figure 1 clarifies this procedure. This technique subdivides the membership range into a
number of α-cuts. At each level, the intersection with the membership function of the input
uncertainties results in an interval. Based on these input intervals for all uncertain parameters,
an interval analysis can be performed obtaining the interval of the output variables at the
considered α-cut. Strictly speaking, the interval analysis for a specific α-cut consists in running
all the finite elements calculations corresponding to all the possible permutations among
input variables at said level and choosing the lower and upper bound of the required output A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures A Fuzzy Finite Element Method Programmed A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Unc
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Contr 7
297 Fuzzy inputs
Fuzzy outputs
α 1
α 2
α n
αN-1
α N
... ... x 1
μ( )
x 1
α 1
α 2
α n
αN-1
α N
... ... x 2
μ( )
x 2
α 1
α 2
α n
αN-1
α N
. . . . . . μ( )
y1
y1
Iterative FE calculations
Deterministic analysis at α N
Interval analysis at α N-1
Interval analysis at α n
Interval analysis at α 2
Interval analysis at α 1
... ... Fig. 1. Scheme of the numerical procedure to perform a Fuzzy Finite Element analysis using
four α-cuts. Fig. 1. 4. Fuzzy Finite Element procedure in MATLAB fzin=varargin;
n = nargin;
m = size(fzin{1},1) - 1;
indices.subs = {};
indices.type = ’()’;
fzr = cell(m+1,2);
for k = 1:2
t = (floor((m+2-k)/2)+rem(m+2-k,2))*2-2+k;
for i = 1:n
c = reshape(fzin{i}(end+1-k:-2:1,:)’,t+2-k,1);
c = c(3-k:end);
repvec = t*ones(1,n);
repvec(i) = 1;
x{i} = repmat(shiftdim(c,1-i),repvec);
end
s = k;
z_cell_matrix=gtrmrecur_external_fcn(x);
for j = m+2-k:-2:1
indices.subs(1:n) = {1:s};
w = reshape(subsref(z_cell_matrix,indices),s^n,1);
wc = zeros(size(w));
for cont=1:length(wc) wc(cont)=w{cont}{2}; end;
[none,pos_min]=min(wc); fzr{j,1} = w{pos_min};
[none,pos_max]=max(wc); fzr{j,2} = w{pos_max};
s = s + 2;
end
end
for j = m:-1:1
if fzr{j+1,1}{2}>=fzr{j,1}{2}; fzr{j,1}=fzr{j,1}; else fzr{j,1}=fzr{j+1,1}; end
if fzr{j+1,2}{2}>=fzr{j,2}{2}; fzr{j,2}=fzr{j+1,2}; else fzr{j,2}=fzr{j,2}; end
end w = reshape(subsref(z_cell_matrix,indices),s^n,1); for cont=1:length(wc) wc(cont)=w{cont}{2}; end; [none,pos_max]=max(wc); fzr{j,2} = w{pos_max}; end
for j = m:-1:1
if fzr{j+1,1}{2}>=fzr{j,1}{2}; fzr{j,1}=fzr{j,1}; else fzr{j,1}=fzr{j+1,1}; end
if fzr{j+1,2}{2}>=fzr{j,2}{2}; fzr{j,2}=fzr{j+1,2}; else fzr{j,2}=fzr{j,2}; end
end for j
m: 1:1
if fzr{j+1,1}{2}>=fzr{j,1}{2}; fzr{j,1}=fzr{j,1}; else fzr{j,1}=fzr{j+1,1}; end
if fzr{j+1,2}{2}>=fzr{j,2}{2}; fzr{j,2}=fzr{j+1,2}; else fzr{j,2}=fzr{j,2}; end
end 4. Fuzzy Finite Element procedure in MATLAB It consists on using
cell class arrays instead of double class arrays to define the fuzzy outputs, so an extra field may 8298 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer be included where information about each iteration is stored (for instance, the exact value of
the fuzzy inputs at each permutation). Figures 2 and 3 show the MATLAB implementation
of the efficient Transformation Method after modifying the Klimke’s implementation. Note
that the MATLAB implementation of the external function in Figure 3 only shows an example
corresponding to the evaluation of a test function. In our case, this function would contain all
the required commands which carry out the three foregoing calculating steps. q
y
g
g
g
p
In order to prove the validity of our modified version of the Klimke’s Transformation Method,
a comparative fuzzy analysis was run. We took as a reference one example found in (Klimke,
2003) where the test function f (x1, x2) = cos(πx1)x2 is subjected to the triangular fuzzy inputs function [fzr]=gtrmrecur_modif(varargin)
% Angel L. Morales, 2011. % FZR=GTRMRECUR_MODIF(FZ1,FZ2,...,FZN) calls the gener
% method implemented by Klimke in 2003 with extended c
% The function allows N fuzzy numbers in alpha-cut rep
% An accompanying function called GTRMRECUR_EXTERNAL_F
fzin=varargin;
n = nargin;
m = size(fzin{1},1) - 1;
indices.subs = {};
indices.type = ’()’;
fzr = cell(m+1,2);
for k = 1:2
t = (floor((m+2-k)/2)+rem(m+2-k,2))*2-2+k;
for i = 1:n
c = reshape(fzin{i}(end+1-k:-2:1,:)’,t+2-k,1);
c = c(3-k:end);
repvec = t*ones(1,n);
repvec(i) = 1;
x{i} = repmat(shiftdim(c,1-i),repvec);
end
s = k;
z_cell_matrix=gtrmrecur_external_fcn(x);
for j = m+2-k:-2:1
indices.subs(1:n) = {1:s};
w = reshape(subsref(z_cell_matrix,indices),s^n,1);
wc = zeros(size(w));
for cont=1:length(wc) wc(cont)=w{cont}{2}; end;
[none,pos_min]=min(wc); fzr{j,1} = w{pos_min};
[none,pos_max]=max(wc); fzr{j,2} = w{pos_max};
s = s + 2;
end
end
for j = m:-1:1
if fzr{j+1,1}{2}>=fzr{j,1}{2}; fzr{j,1}=fzr{j,1}; else
if fzr{j+1,2}{2}>=fzr{j,2}{2}; fzr{j,2}=fzr{j+1,2}; el
end function [fzr]=gtrmrecur_modif(varargin)
% Angel L. Morales, 2011. % FZR=GTRMRECUR_MODIF(FZ1,FZ2,...,FZN) calls the general transformation
% method implemented by Klimke in 2003 with extended capabilities. % The function allows N fuzzy numbers in alpha-cut representation. % An accompanying function called GTRMRECUR_EXTERNAL_FCN is required. A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures 9
299 ˜p1 = ⟨2.5, 2.5, 2.5⟩TFN and ˜p2 = ⟨3, 2, 2⟩TFN, in accordance to the nomenclature proposed
in (Dubois & Prade, 1980). The fuzzy output obtained with the modified version clearly
matched the results obtained with the original version. Nevertheless, an unavoidable loss
of computational efficiency arose. p
y
Our modified version results more time-consuming because of the different way in which the
simulated function is handled, as it can be seen in Table 1. In the original version, the inline
class analytical expression can be executed only once with the array containing all the required
permutations of fuzzy inputs at a time. In the modified version, the expression is evaluated
separately at each permutation as it would be the case when a control system is simulated
with several MATLAB commands. The elapsed time during these operations is called t f cn. As
far as the obtention of the fuzzy output as a cell array instead of as a double array, this fact does
not add any noticeable increase of computational cost but it does lead to heavier variables and
higher memory requirements. The elapsed time during these operations is called tmax. In all
the cases, the loss of efficiency is acceptable with regard to the benefits they provide, specially
considering that the elapsed time in any finite element simulation may be on the order of
seconds and it has much more restrictive memory requirements. able 1. Efficiency comparison between the original and the modified Klimke’s Fig. 2. MATLAB implementation of the efficient Transformation Method after modifying
Klimke’s script. function [z_cell_matrix]=gtrmrecur_external_fcn(x)
% Angel L. Morales, 2011. % Z_CELL_MATRIX=GTRMRECUR_EXTERNAL_FCN(FZ1,FZ2,...,FZN) calls the function
% which executes the commands in order to obtain the fuzzy output. % It is called during the execution of FZR=GTRMRECUR_MODIF(FZ1,FZ2,...,FZN)
func = inline(’cos(pi.*x1).*x2’);
x_vector=cell(size(x));
for cont=1:length(x)
x_vector{cont} = reshape(x{cont},numel(x{cont}),1);
end
iterations=length(x_vector{1});
z_cell=cell(1,2); z_cell_array=cell(1,iterations);
for iteration=1:iterations
x1=double(x_vector{1}(iteration));
x2=double(x_vector{2}(iteration));
z_cell{1}=[x1 x2];
z_cell{2}=feval(func,x_vector{1}(iteration),x_vector{2}(iteration));
z_cell_array{iteration}=z_cell;
end
z_cell_matrix=reshape(z_cell_array,size(x{1})); function [z_cell_matrix]=gtrmrecur_external_fcn(x)
% Angel L. Morales, 2011. % Z_CELL_MATRIX=GTRMRECUR_EXTERNAL_FCN(FZ1,FZ2,...,FZN) calls the function
% which executes the commands in order to obtain the fuzzy output. % It is called during the execution of FZR=GTRMRECUR_MODIF(FZ1,FZ2,...,FZN)
func = inline(’cos(pi.*x1).*x2’); % It is called during the execution of FZR=GTRMRECUR_MODIF(FZ1,FZ2,...,FZN)
func = inline(’cos(pi.*x1).*x2’); x_vector=cell(size(x)); for cont=1:length(x) x_vector{cont} = reshape(x{cont},numel(x{cont}),1);
end iterations=length(x_vector{1}); z_cell=cell(1,2); z_cell_array=cell(1,iterations); end
z_cell_matrix=reshape(z_cell_array,size(x{1})); Fig. 3. Example of the MATLAB function called by the modified Transformation Method
which contains the commands for the obtention of the fuzzy output A Fuzzy Finite Element Method Programmed A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures 5. A case study of uncertainty propagation Geometries and material properties of the plate. Width (mm)
40
Length (mm)
100
Thickness (mm)
0.250
d33 (m/V)
0.30·10−9
d31 (m/V)
-0.15·10−9
e31 (N/Vm)
-7.5
k33
0.7
Young’s modulus (GPa)
50
Maximum traction (MPa)
80
Maximum compression (MPa)
600
Maximum electric Field (V/mm)
2000
Density (kg/m3)
7600
Maximum strain
Brittle
Maximum temperature (C)
80°C - 150°C
Table 3. Geometries and material properties of the piezoelectric (Preumont, 2002). Width (mm)
300.00
Length (mm)
500.00
Thickness (mm)
3.00
Young’s modulus (GPa)
72.00
Poisson’s coefficient
0.30
Density (kg/m3)
2700.00
Structural damping (%)
0.60 Table 2. Geometries and material properties of the plate. p
p
p
Width (mm)
40
Length (mm)
100
Thickness (mm)
0.250
d33 (m/V)
0.30·10−9
d31 (m/V)
-0.15·10−9
e31 (N/Vm)
-7.5
k33
0.7
Young’s modulus (GPa)
50
Maximum traction (MPa)
80
Maximum compression (MPa)
600
Maximum electric Field (V/mm)
2000
Density (kg/m3)
7600
Maximum strain
Brittle
Maximum temperature (C)
80°C - 150°C
Table 3. Geometries and material properties of the piezoelectric (Preumont, 2002). able 3. Geometries and material properties of the piezoelectric (Preumont, 2002). where the non-zero values are placed in the position corresponding to the active rotational
degree of freedom of the nodes in which the piezoelectric is located. where the non-zero values are placed in the position corresponding to the active rotational
degree of freedom of the nodes in which the piezoelectric is located. As described in the Section 2.2, a Positive Position Feedback control strategy designed with
the Control System Toolbox of MATLAB is to be used. Figure 5 presents the root locus of the
control system after tuning the second order filter parameters (ξf and ωf) so that the first
flexible mode of vibration become actively damped. After the tuning process (ξf = 0.9 and
ωf = 900 rad/s), the next step consists of selecting the control gain which most approaches Mode 1
f = 64.01 Hz
1
Mode 2
f = 66.46 Hz
2
Mode 3
f = 150.29 Hz
3
Mode 4
f = 176.53 Hz
4
Mode 5
f = 183.42 Hz
5
Mode 6
f = 231.02 Hz
6
Fig. 4. Mode shapes and natural frequencies for the plate in free conditions. Mode 3
f = 150.29 Hz
3 Mode 1
f = 64.01 Hz
1 Mode 2
f = 66.46 Hz
2 Mode 6
f = 231.02 Hz
6 Mode 4
f = 176.53 Hz
4 Fig. 4. 5. A case study of uncertainty propagation Consider an aluminium plate in free conditions, the dimensions and material properties of
which are detailed in Table 2. The finite element model of this plate was carried out by
means of the OpenFEM Toolbox of MATLAB (Balmes et al., 2009). After defining the mesh,
the matrices of mass (M) and stiffness (K) which define the undamped model were obtained. The eigenvalue problem can then be solved, the natural frequencies and mode shapes being
shown in Figure 4. The damping matrix (C) is constructed considering a structural damping
of ξi = 0.6% in all the modes. The piezoelectric actuator and sensor, the properties of which are detailed in Table 3, are
collocated in the centre of the plate. As described in (Dosch et al., 1992; Sims et al., 2005),
the piezoelectric actuator and sensor may be modelled as a beam which provides bending
moments at its ends and measures a voltage proportional to the difference of slope of its ends. Due to collocation, the localization vectors of actuator (Lu) and sensor (Ly) are identical and
equal to LT
u = LT
y = (0, . . . , −1, 0, . . . , 1, 0, . . . , 0)
(10)
Original Modified
ttot (s)
0.047
0.344
ttot (%)
100.00
100.00
t f cn (s)
0.016
0.313
t f cn (%)
34.04
90.99
tmax (s)
0.000
0.000
tmax (%)
0.000
0.000
toth (s)
0.031
0.031
toth (%)
65.96
9.01
Weight (bytes)
336
8568 (10) Table 1. Efficiency comparison between the original and the modified Klimke’s
implementation. The total time (ttot), the time for evaluating the analytical expression (t f cn),
the time for calculating the maxima and minima of the output fuzzy number (tmax) and the
time for other calculations (toth) are shown. The weight means the size in bytes of the output
fuzzy variable. y
p
g
implementation. The total time (ttot), the time for evaluating the analytical expression (t f cn),
the time for calculating the maxima and minima of the output fuzzy number (tmax) and the
time for other calculations (toth) are shown. The weight means the size in bytes of the output
fuzzy variable. Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 10300 Width (mm)
300.00
Length (mm)
500.00
Thickness (mm)
3.00
Young’s modulus (GPa)
72.00
Poisson’s coefficient
0.30
Density (kg/m3)
2700.00
Structural damping (%)
0.60
Table 2. 5. A case study of uncertainty propagation Mode shapes and natural frequencies for the plate in free conditions. A Fuzzy Finite Element Method Programmed A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures 11
301 the maximum damping of the first vibration mode (ξ1,max). In this particular case, a gain of
g = 0.200 entails a selected damping coefficient of ξ1,sel = 88.30%. Figure 5 also shows the
characteristic stability limit of the Positive Position Feedback control systems and the fact that
only the first and the fifth modal shapes seem to be controllable in the view of the wide loops
going from the poles to the zeros (Preumont, 2002). 100
-900
-800
-700
-600
-500
-400
-300
-200
-100
0
Imaginary part
Real part
-100
100
300
500
700
900
1100
1300
1500
1700
1900
1
2
3
4
5
6
g = 0.200
ξ = 88.30%
1,sel
g = 0.257
Stability limit
Fig. 5. Root locus of the control system after tuning the second order filter parameters to the
first flexible mode of vibration (ξf = 0.9 and ωf = 900 rad/s). Fig. 5. Root locus of the control system after tuning the second order filter parameters to the
first flexible mode of vibration (ξf = 0.9 and ωf = 900 rad/s). In the proposed case study the collocated pair of actuator and sensor are subjected to
uncertainty. More precisely, the position of the centre of both the actuator and sensor
are considered to be uncertain parameters. Additionally, another source of uncertainty
corresponding to the structural damping of the plate is included as this is known to be
uncertain in practice. Thus, we have a total of five different fuzzy numbers: ˜xa (position
“x” of the centre of the actuator), ˜ya (position “y” of the centre of the actuator), ˜xs (position
“x” of the centre of the sensor), ˜ys (position “y” of the centre of the sensor) and ˜ξ (structural
damping). The membership functions of these fuzzy parameters, assuming that they are both
symmetric and triangular, can be seen in Figure 6. After applying the Fuzzy Finite Element algorithm described in Section 4 one can obtain
several fuzzy outputs which describe the stability and performance of the control system. Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 12302 145
147
149
151
153
155
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
x , x (mm)
a
s
μ(x ), μ(x )
a
s
245
247
249
251
253
255
μ(y ), μ(y )
a
s
y , y (mm)
a
s
(a)
(b)
(c)
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
μ(ξ)
ξ (%)
0.1
0.3
0.5
0.7
0.9
1.1
Fig. 6. Membership functions of the input fuzzy numbers: (a) coordinates of the centre of the
actuator ( ˜xa and ˜xs), (b) coordinates of the centre of the sensor ( ˜ya and ˜ys) and (c) structural
damping of the plate ( ˜ξ). 0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
245
247
249
251
253
255
μ(y ), μ(y )
a
s
y , y (mm)
a
s
(b) 145
147
149
151
153
155
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
x , x (mm)
a
s
μ(x ), μ(x )
a
s
(a) (c)
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
μ(ξ)
ξ (%)
0.1
0.3
0.5
0.7
0.9
1.1 (b) Fig. 6. Membership functions of the input fuzzy numbers: (a) coordinates of the centre of the
actuator ( ˜xa and ˜xs), (b) coordinates of the centre of the sensor ( ˜ya and ˜ys) and (c) structural
damping of the plate ( ˜ξ). damping that the control systems provides at the value of gain selected in the deterministic
case. Clearly, the gain and phase margins can be used to quantify controller stability, whilst
the damping ratios serve to quantify performance and reliability. The membership functions of these variables are shown in Figure 7. We observe that the
uncertainty considered may lead to a both better and worse behaviour of the control system
in comparison to the considered deterministic situation. p
Another possibility for obtaining a global view of the whole control system lies in plotting
its root locus for different α-sublevels or α-cuts. In particular, we show in Figure 8 the root
locus for two different values of the membership. 5. A case study of uncertainty propagation In
fact, it is possible to choose those variables which better fit the effects which one is interested
in. In this particular case, the following are calculated: ˜G Gain margin. ˜P Phase margin. ˜P Phase margin. ˜ξ1,max Maximum damping coefficient of the first mode. ˜ξ1,sel Selected damping coefficient of the first mode. ˜ξ1,sel Selected damping coefficient of the first mode. The gain margin ˜G is the increase in the system gain when the phase is −180 that will result in
a marginally stable system with intersection of the −1 + j0 point on the Nyquist diagram. The
phase margin ˜P is the amount phase shift of the system at unity magnitude that will result
in a marginally stable system with intersection of the −1 + j0 point on the Nyquist diagram. The maximum damping coefficient ˜ξ1,max is the highest damping achievable in the first mode
loop independently of the selected gain, whilst the selected damping coefficient ˜ξ1,sel is the Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer Although the fourth mode has not been 0.2565
0.2570
0.2575
0.2580
0.2585
0.2590
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
G
101.70
102.00
102.30
102.60
102.90
103.20
μ(G), μ(P)
(a)
(b)
P (deg)
86.0
86.8
87.6
88.4
89.2
90.0
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
μ(ξ )
1,sel
μ(ξ ),
1,max
ξ1,max (%), ξ1,sel (%)
Fig. 7. Membership function of the output fuzzy numbers: (a) stability indicators ( ˜G in black
color and ˜P in gray color) and (b) performance indicators ( ˜ξ1,max in black color and ˜ξ1,sel in
gray color). 0.2565
0.2570
0.2575
0.2580
0.2585
0.259
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
G
101.70
102.00
102.30
102.60
102.90
103.2
μ(G), μ(P)
(a)
P (deg) (b)
86.0
86.8
87.6
88.4
89.2
90.0
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
μ(ξ )
1,sel
μ(ξ ),
1,max
ξ1,max (%), ξ1,sel (%) Fig. 7. Membership function of the output fuzzy numbers: (a) stability indicators ( ˜G in black
color and ˜P in gray color) and (b) performance indicators ( ˜ξ1,max in black color and ˜ξ1,sel in
gray color). A Fuzzy Finite Element Method Programmed in MATLAB for the Analysis of Uncertain Control Systems of Structures
A Fuzzy Finite Element Method Programmed
in MATLAB for the Analysis of Uncertain Control Systems of Structures 13
303 specifically analyzed via fuzzy variables, we can note that its zero crosses the imaginary axis
and becomes unstable for some values of the gain. Note that zeros are essentially related to
mode shapes of the structure, which tend to be more sensitive to the parameter uncertainty
than the natural frequencies. This fact warns us that a higher gain level may lead to instability
of the fourth mode when actively damping the first, which can be detected easily by means
of including new fuzzy variables in the analysis such as the maximum real part of the closed
loop poles. -900
-800
-700
-600
-500
-400
-300
-200
-100
0
100
Real part
Imaginary part
-100
100
300
500
700
900
1100
1300
1500
1700
1900
Fig. 8. Root locus of the control system for two different α-cuts: μ = 1 (black) and μ = 0
(grey). Fig. 8. Root locus of the control system for two different α-cuts: μ = 1 (black) and μ = 0
(grey). 6. Conclusion In this chapter we have shown the suitability of the matrix computing environment MATLAB
to solve control problems of structures via finite element analysis and root locus design
and how these two issues have been blended and integrated into a Fuzzy Finite Element
methodology for the analysis and simulation of uncertain control of structures. gy
y
The Fuzzy Finite Element procedure has been described. The approach relies on the α-cut
technique which subdivides the membership range into a number of α-levels. The fuzzy
arithmetic is based upon an efficient implementation in MATLAB code for the Transformation
Method. This implementation has been modified and improved with some enhanced features. This methodology has been shown to be applicable to a realistic case study related to
structural control using a Positive Position Feedback technique and piezoelectric actuators
and sensors. In the light of the obtained results, the proposed procedure may prove useful to
other analysis involving any other control technique or uncertainty source. In addition, the
efficient implementation obtained due to MATLAB programming allows us to achieve high
accuracy results together with low computational costs. Finally, further research may be carried out in this topic. Firstly, a more efficient
implementation of the Transformation Method can be found when using cell arrays instead
of double arrays or when considering multiple fuzzy outputs. Secondly, the Transformation
Method also allows a sort of sensitivity analysis which should be included in the MATLAB
implementation in order to endow our method with extended capabilities. Thirdly, and
in-depth comparison between this possibilistic methodology and the robust H∞optimal
control theory must be carried out in order to identify more precisely the situations in which
one method stand out from the other. 14304 Will-be-set-by-IN-TECH
MATLAB – A Ubiquitous Tool for the Practical Engineer 7. Acknowledgment The authors are grateful for the support received from the “Ministerio de Educación”
of the Spanish government through the “Programa Nacional de Movilidad de Recursos
Humanos del Plan Nacional de I-D+i 2008-2011” and from the EPSRC through grant reference
EP/D078601/1. EP/D078601/1. 8. References Balmes, E., Bianchi, J.-P. & Leclére, J.-M. (2009). Structural Dynamics Toolbox for use with
MATLAB: User’s guide. De Gersem, H., Moens, D., Desmet, W. & Vandepitte, D. (2005). A fuzzy finite element
procedure for the calculation of uncertain frequency response functions of damped
structures: Part 2 - numerical case studies, Journal of Sound and Vibration 288: 463–486. De Munck, M., Moens, D., Desmet, W. & Vandepitte, D. (2008). A response surface based
optimisation algorithm for the calculation of fuzzy envelope frfs of models with
uncertain properties, Computers & Structures 86: 1080–1092. ertain properties, Computers & Structures 86 Dosch, J. J., Daniel, D. J. & Garcia, E. (1992). A self-sensing piezoelectric actuator for collocated
control, Journal of Intelligent Material Systems and Structures 3: 166–185. f
g
y
Dubois, D. & Prade, H. M. (1980). Fuzzy sets and systems : theory and applications, Mathematics
in science and engineering, Academic Press, New York. Gu, D.-W., Petkov, P. H. & Konstantinov, M. M. (2005). Robust control design with MATLAB,
S
d Dubois, D. & Prade, H. M. (1980). Fuzzy sets and systems : theory and applications, Mathematics
in science and engineering, Academic Press, New York. W., Petkov, P. H. & Konstantinov, M. M. (2005). Robust control design with MATLAB,
Springer, London. Hanss, M. (2002). The transformation method for the simulation and analysis of systems with
uncertain parameters, Fuzzy Sets and Systems 130: 277–289. Klimke, A. (2003). An efficient implementation of the transformation method of fuzzy
arithmetic, (IANS), extended preprint 2003/009, Technical report, University of
Stuttgart. g
Moens, D. & Vandepitte, D. (2005). A fuzzy finite element procedure for the calculation of
uncertain frequency-response functions of damped structures: Part 1 - procedure,
Journal of Sound and Vibration 288: 431–462. f
Oberkampf, W. L., Helton, J. C., Joslyn, C. A., Wojtkiewicz, S. F. & Ferson, S. (2004). Challenge
problems: uncertainty in system response given uncertain parameters, Reliability
Engineering & System Safety 85: 11–19. g
g
y
f y
OpenFEM (2011). URL: http://support.sdtools.com/gf/project/openfem p
pp
gf p
j
p
f
Preumont, A. (2002). Vibration control of active structures: An introduction, Kluwer Academic,
Dordrecht. Sims, N. D., Bayly, P. V. & Young, K. A. (2005). Piezoelectric sensors and actuators for milling
tool stability lobes, Journal of Sound and Vibration 281: 743–762. Sims, N. D., Manson, G. & Mann, B. (2010). Fuzzy stability analysis of regenerative chatter in
milling, Journal of Sound and Vibration 329: 1025–1041. Zadeh, L. A. 8. References (1965). Fuzzy sets, Information and Control 8: 338–353. Zames, G. (1981). Feedback and optimal sensitivity:
Model reference transformations,
multiplicative seminorms and approximate inverses, IEEE Transactions on Automatic
Control 26: 301–320. Zames, G. & Francis, B. A. (1983). Feedback, minimax sensitivity and optimal robustness,
IEEE Transactions on Automatic Control 28: 585–601. Visual and Thermal Image
Fusion for UAV Based
Target Tracking K. Senthil Kumar1, G. Kavitha2,
R. Subramanian3 and G. Ramesh4
1Division of Avionics, Department of Aerospace Engineering,
Madras Institute of Technology, Anna University,
2Department of Electronics and Communication Engineering,
Madras Institute of Technology, Anna University
3Division of Avionics, Department of Aerospace Engineering,
Madras Institute of Technology, Anna University
4National Aerospace Laboratories (NAL) Bangalore,
India Modelling, Identification and Simulation 16 2. Thermal imaging Thermography which uses black body radiation law makes it to have information gathering
without visible illumination. Thermal imaging cameras detect radiation in the infrared (IR)
range of the electromagnetic spectrum (3-6 µm and 8–14 µm). g
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)
The charge coupled device (CCD) and complementary metal oxide semiconductor (CMOS)
sensors are used for visible light cameras. These can detect only the non thermal part of the
infrared spectrum called near-infrared (NIR). On the other hand, thermal imaging cameras
make use specialized focal plane arrays (FPAs) that respond to longer wavelengths (mid-
and long-wavelength infrared). There is also a difference between how far one can see with a cooled and with an uncooled
thermal imaging camera. Cooled camera systems are more expensive, but generally have a
longer range than uncooled systems under many conditions. Extremely long range thermal
imaging applications are best served by cooled camera systems. This is particularly true in
the midwave band in humid atmospheric conditions. The heat radiation is focused onto special receptors in the camera which convert it into a
format which is displayed on a monitor in monochrome which is recognisable by the human
eye. The objects emitting the greatest intensity of heat are usually presented as the darkest
(black) in the greyscale, i.e. known as ‘black-hot’. Many cameras have a function whereby
the functionality can be switched from ‘blackhot’ to ‘white-hot’ and back again at the
operator’s wish. Probably the greatest ‘enemy’ of thermal imaging is extended rainfall since
that has the effect of cooling all inanimate objects and severely reducing contrast. g
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Thermal imaging makes it possible of real time target tracking. Detection of targets in dark
and low light conditions can be done. All weather operation and dull, dirty and dangerous
(DDD) roles are possible. Thermal imaging cameras produce a clear image in the darkest of nights, in light fog and
smoke and in the most diverse weather conditions. There has also been an increased
interest in thermal imaging for all kinds of security applications, from long-range
surveillance at border crossings, truck and shipping container inspection, to the
monitoring of high-security installations such as nuclear power stations, airports, and
dams. But thermal imaging has a lot more to offer than just a night vision solution for
security applications. Car manufacturers are integrating night vision modules for driver vision enhancement into
cars. 1. Introduction Unmanned aerial vehicles (UAVs) are aircrafts which have the capability of flight without
an onboard pilot. These vehicles are remotely controlled, semi-autonomous, autonomous, or
have a combination of these capabilities. UAV’s has its applications in a whole lot of
domains. Image processing applications with specific importance to surveillance and
reconnaissance is of immense interest. UAVs are equipped with imaging sensor platform, which operates remotely controlled,
semi-autonomously or autonomously, without a pilot sitting in the vehicle. The platform
may have a small or medium size still-video or video camera, thermal or infrared camera
systems, airborne light detection and ranging (LIDAR) system, or a combination thereof. All
these different kinds of cameras are an effective sensor tool which is portable, light weight
and airborne in a platform on the UAV. Thermal images have a valuable advantage over the visual images. Thermal images do not
depend on the illumination, the output is the projection of thermal sensors of the emissions
of heat of the objects. This unique merit gives rise for effective segmentation of objects. Ultimately, surveillance measure using an UAV gets improved. y
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With the development of new imaging sensors arises the need of a meaningful combination
of all employed imaging sources. Image fusion of visual and thermal sensing outputs adds a
new dimension in making the target tracking more reliable. Target tracking at instances of
smoke, fog, cloudy conditions gets improved. With conditions of same background colour
perception of target unnoticed getting eliminated with thermal image inclusion, image
fusion gives complementary information. A holistic system which represents the combined
fused data is perceived at the control level of the UAV’s. 308 MATLAB – A Ubiquitous Tool for the Practical Engineer 3.1 2D OTSU algorithm The two dimensional Otsu algorithm is given as follows. Suppose an image pixel size is M ×
N, gray-scale of the image ranges from 0 to L-1. The neighborhood average gray g (m, n) of
the coordinate definition (m, n) pixel point is as follows: g (m,n) =
ଵ
୩୶୩∑
∑
f(m + i, n + j)
(୩-ଵ)/ଶ
୨ୀ-(୩-ଵ)/ଶ
(୩-ଵ)/ଶ
୧ୀ-(୩-ଵ)/ଶ
(1) (1) Calculating the average neighbourhood gray of each pixel point, a gray binary group (i, j)
may form. We use Cij to represent the occurrence frequency of (i, j). Then the probability Pij
of vector (i, j) may be determined by the formula: Calculating the average neighbourhood gray of each pixel point, a gray binary group (i, j)
may form. We use Cij to represent the occurrence frequency of (i, j). Then the probability Pij
of vector (i, j) may be determined by the formula: Pij =
େ୧୨
ଡ଼
(2) (2) Here, 0 ≤ I, j < L, and ∑
∑
ܲ
ିଵ
ୀ
ିଵ
ୀ
=1. Here, 0 ≤ I, j < L, and ∑
∑
ܲ
ିଵ
ୀ
ିଵ
ୀ
=1. Assuming the existence of two classes C0 and C1 in Two dimensional form, the histogram
represents their respective goals and background, and with two different probability density
distribution function. If making use of two-dimensional histogram threshold vector (s, t) to
segment the image (of which 0 ≤ s, t <L), then the probability of two classes are respectively:
The probability of background occurrence is: ω0 = P(C0) = ∑
∑
P୧୨
௧
ୀ
௦
ୀ
= ω0 (s,t)
(3) ω0 = P(C0) = ∑
∑
P୧୨
௧
ୀ
௦
ୀ
= ω0 (s,t) (3) The probability of object occurrence is: ω1 = P(C1) = ∑
∑
P୧୨
ିଵ
ୀ௧ାଵ
ିଵ
ୀ௦ାଵ
= ω1 (s,t)
(4) (4) The definition of dispersion matrix: The definition of dispersion matrix: σB = ω0 [(µ0-µτ)( µ0-µτ)T] + ω1 [(µ1-µτ)( µ1-µτ)T]
(5) (5) When the track of the above-mentioned dispersion matrix gets the maximum, the
corresponding threshold of segmentation is the optimal threshold (S, T), namely: tr(σB (S,T)) = ݉ܽݔஸ௦,௧ழ {tr(σB (S,T))}
(6) tr(σB (S,T)) = ݉ܽݔஸ௦,௧ழ {tr(σB (S,T))} (6) We know that 2-D thermal images with noise segmented by Otsu way may get better results
compared to one dimensional threshold segmentation methods. 3. Image segmentation Segmentation is the key and the first step to automatic target recognition, which will directly
affect the accuracy of the following work. As a result, the division methods and its precision
degree are essential. Infrared heat wave image is different from the visible light images. It
reflects the distribution of the object surface temperature and latent characteristics of
material form. The infrared heat radiation, due to the imperfections of the system, will bring a variety of
noise in the imaging process. The noise of complex distribution of infrared images makes
the signal to noise ratio lower than visible light images. 2. Thermal imaging By helping drivers to see at night, accidents can be avoided. Boats and yachts are being
equipped with thermal imaging cameras for night time navigation and other maritime
applications like man overboard searches. Often the thermal imager is just a small part of the complete system as in an UAS, so it
needs to be as small, light and inexpensive as possible. Low-cost thermal imager is used as a
pilot’s night vision enhancement. It helps pilots by enhancing the ability to see terrain and
other aircraft at long ranges, even in total darkness, light fog, dust and smoke. Thermal
imaging is a technology that enables detection of people and objects in total darkness and in
very diverse weather conditions. y
A typical application for thermal imaging is border security, where most threats occur at
night. Thermal imaging allows the aircraft to fly in total darkness and detect targets through
smoke. The same aircraft can also be used to detect such things as forest fires. Areas which
are hotter than the surroundings can indicate the start of a fire and can clearly be seen on a
thermal image. 309 Visual and Thermal Image Fusion for UAV Based Target Tracking 3.1 2D OTSU algorithm Segmented Image 311 Visual and Thermal Image Fusion for UAV Based Target Tracking When u = 4, the system is the chaos state of the biggest ergodicity. Genetic algorithm is a
kind of random search algorithm drawn from natural selection and natural genetic
mechanisms of biology, which is particularly well suited to deal with the complex and
nonlinear problems that traditional search methods are difficult to resolve. When u = 4, the system is the chaos state of the biggest ergodicity. Genetic algorithm is a
kind of random search algorithm drawn from natural selection and natural genetic
mechanisms of biology, which is particularly well suited to deal with the complex and
nonlinear problems that traditional search methods are difficult to resolve. Fig. 3. Thermal Image
Fig. 4. Segmented Image
The segmentation results are shown in Fig. 1 to Fig. 4 with the segmented image of the
thermal image. Fig. 3. Thermal Image Fig. 3. Thermal Image Fig. 3. Thermal Image Fig. 3. Thermal Image Fig. 3. Thermal Image Fig. 4. Segmented Image Fig. 4. Segmented Image
The segmentation results are shown in Fig. 1 to Fig. 4 with the segmented image of the
thermal image. The segmentation results are shown in Fig. 1 to Fig. 4 with the segmented image of the
thermal image. 3.1 2D OTSU algorithm However, the computation
cost gets huge, which is because the determination of the optimal threshold need to travel
all the s and t, of which 0 ≤ s, t < L. That is to say, the more gray scale value of images is, the
longer choice time of the threshold is. 310 MATLAB – A Ubiquitous Tool for the Practical Engineer The segmentation of various thermal images is illustrated here. The segmentation results
can be made more efficient in identification of targets and optimized by a number of
methods. These segmentation results are used in fused image target tracking. One such
method will be determining optimum threshold using histogram analysis. The method of
using chaos based genetic algorithm makes the process time lower. The chaos based genetic
algorithm uses Otsu algorithm as fitness function and proceeds for segmentation. The segmentation of various thermal images is illustrated here. The segmentation results
can be made more efficient in identification of targets and optimized by a number of
methods. These segmentation results are used in fused image target tracking. One such
method will be determining optimum threshold using histogram analysis. The method of
using chaos based genetic algorithm makes the process time lower. The chaos based genetic
algorithm uses Otsu algorithm as fitness function and proceeds for segmentation. g
g
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The so-called chaos refers to the uncertainty in the system appearing in seemingly without
rules. From the mathematical sense, for determined series initial values, it is possible to
predict the long-term behaviour of the system, even know its past behaviour and state by
the power system. It is a unique phenomenon of non-linear systems. Chaos has randomicity,
ergodicity and regularity. Based on these characteristics of chaos, using chaotic variables to
optimize search is no doubt better than random search. Logistic map is the most basic
chaotic map. The chaos equation of the Logistic definition can be described as follows: (7) x(n+1) = u xn (1- xn) ; 0 < u ≤ 4
(7) x(n+1) = u xn (1- xn) ; 0 < u ≤ 4 xn lies between 0 and 1. n varies from 0,1,2, etc. xn lies between 0 and 1. n varies from 0,1,2, etc. n
, , ,
Fig. 1. Thermal Image
Fig. 2. Segmented Image Fig. 1. Thermal Image Fig. 1. Thermal Image Fig. 2. 4. Image fusion process A generic categorization of image fusion methods in the following: •
Linear Superposition, Nonlinear Methods, Expectation Maximisation, Image Pyramids,
Wavelet Transform, Generic Multiresolution Fusion Scheme, Optimization Approaches, •
Linear Superposition, Nonlinear Methods, Expectation Maximisation, Image Pyramids,
Wavelet Transform, Generic Multiresolution Fusion Scheme, Optimization Approaches,
Artificial Neural Networks, Fuzzy Techniques Artificial Neural Networks, Fuzzy Techniques
Some of the prominent applications of image fusion a ficial Neural Networks, Fuzzy Techniques Artificial Neural Networks, Fuzzy Techniques Some of the prominent applications of image fusion are: •
Concealed Weapon Detection, Night Time Surveillance, Automatic Landing System,
Digital Camera Applications, Medical Diagnosis, Defect Inspection and Remote Sensing •
Concealed Weapon Detection, Night Time Surveillance, Automatic Landing System,
Digital Camera Applications, Medical Diagnosis, Defect Inspection and Remote Sensing 4. Image fusion process Image fusion is the process by which two or more images are combined into a single image
retaining the important features from each of the original images. The fusion of images is
often required for images acquired from different instrument modalities or capture
techniques of the same scene or objects. Important applications of the fusion of images
include medical imaging, microscopic imaging, remote sensing, computer vision, and 312 MATLAB – A Ubiquitous Tool for the Practical Engineer robotics. Fusion techniques include the simplest method of pixel averaging to more
complicated methods such as principal component analysis (PCA) and wavelet transform
(WT) based fusion. Image fusion is the process of relevant information extraction from two or more images. The
resulting image will encompass more information than any of the given input images. A
multi sensor, multi temporal and multi view information techniques are required which
overcome the limitations of using single senor information. The benefits of image fusion are
extended range of operation, extended spatial and temporal resolution and coverage,
reduced uncertainty, higher accuracy, reliability and compact representation. Various kinds of image fusion for visual, Infrared and Synthetic Aperture Radar (SAR)
images exist. Some of the primitive fusion process algorithms also have disadvantages. Direct fusion method makes the image blurred. The pixel based image fusion is
computationally complex for large and high resolution images. The image averaging
method produces a reduced contrast of information. The requirement is thus a novel and
efficient information fusion process. Image fusion has a significant role of recognition of
targets and objects. Target identification, localisation, filtering and data association forms an
important application of the fusion process. Thus an effective surveillance and
reconnaissance system can be formed. There is information which is redundant and at the same time complementary too. The
following summarize several approaches to the pixel level fusion of spatially registered
input images. 4.1 Wavelet transform A signal analysis method similar to image pyramids is the discrete wavelet transform. The
main difference is that while image pyramids lead to an over complete set of transform
coefficients, the wavelet transform results in a nonredundant image representation. The
discrete two dimensional wavelet transform is computed by the recursive application of low
pass and high pass filters in each direction of the input image (i.e. rows and columns)
followed by sub sampling. These basis functions or baby wavelets are obtained from a single prototype wavelet called
the mother wavelet, by dilations or contractions (scaling) and translations (shifts). They have
advantages over traditional Fourier methods in analyzing physical situations where the
signal contains discontinuities and sharp spikes. Image fusion process is achieved by multiresolution decomposition at fourth level. The
multiwavelet decomposition coefficients of the input images are appropriately merged and
a new fixed image is obtained by reconstructing the fused multiwavelet coefficients. The
theory of multiwavelets is also based on the idea of multiresolution analysis (MRA) as
shown in Fig. 5. During a single level of decomposition using a scalar wavelet transform, the
two-dimensional (2-D) image data is replaced with four blocks corresponding to the
subbands representing either low-pass or high-pass filtering in each direction. 313 Visual and Thermal Image Fusion for UAV Based Target Tracking Fig. 5. Wavelet Multi Resolution Analysis
The Haar wavelet is a certain sequence of rescaled "square-shaped" functions which together
form a wavelet family or basis. Wavelet analysis is similar to Fourier analysis in that it
allows a target function over an interval to be represented in terms of an orthonormal
function basis. The Haar wavelet is also the simplest possible wavelet. Fig. 5. Wavelet Multi Resolution Analysis The Haar wavelet is a certain sequence of rescaled "square-shaped" functions which together
form a wavelet family or basis. Wavelet analysis is similar to Fourier analysis in that it
allows a target function over an interval to be represented in terms of an orthonormal
function basis. The Haar wavelet is also the simplest possible wavelet. The Haar wavelet is a certain sequence of rescaled "square-shaped" functions which together
form a wavelet family or basis. Wavelet analysis is similar to Fourier analysis in that it
allows a target function over an interval to be represented in terms of an orthonormal
function basis. The Haar wavelet is also the simplest possible wavelet. 4.2 FIS based image fusion Neural Network and Fuzzy Logic approach can be used for sensor fusion. Such a sensor
fusion could belong to a class of sensor fusion in which case the features could be input and
decision could be output. The system can be trained from the input data obtained from the
sensors. The basic concept is to associate the given sensory inputs with some decision outputs. The
following algorithm for pixel level image fusion using Fuzzy Logic illustrate the process of
defining membership functions and rules for the image fusion process using FIS (Fuzzy
Inference System) editor of Fuzzy Logic toolbox in MATLAB. The process flow of the
process is as follows: 1. The visual and thermal image forms the inputs for the fusion system. The inputs must
be with the same field of view. 1. The visual and thermal image forms the inputs for the fusion system. The inputs must
be with the same field of view. 2. With a gray level conversion applied, the two images are transformed to a column
form. 2. With a gray level conversion applied, the two images are transformed to a column
form. 3. The number and type of membership functions for both the input images are g 3. The number and type of membership functions for both the input images are given to
the FIS. The rule base for FIS decides how the output fused image should be. 3. The number and type of membership functions for both the input images are given t
the FIS. The rule base for FIS decides how the output fused image should be. the FIS. The rule base for FIS decides how the output fused image should be. 4. The fused image is converted back to matrix format from column form. The fuzzy system considered here is Mamdani type and its’ FIS model in MATLAB is shown
in Fig. 6. The Mamdani rule base is a crisp model of a system, i.e. it takes crisp inputs and
produces crisp outputs. It does this with the use of user-defined fuzzy rules on user-defined
fuzzy variables. MATLAB – A Ubiquitous Tool for the Practical Engineer 314 Fig. 6. FIS Model Fig. 6. FIS Model Fig. 7. FIS Membership Function Fig. 7. FIS Membership Function Visual and Thermal Image Fusion for UAV Based Target Tracking
Fig. 8. Rule Base of FIS
Fig. 9. 4.2 FIS based image fusion Surface View of FIS 315 Visual and Thermal Image Fusion for UAV Based Target Tracking Fig. 8. Rule Base of FIS Fig. 8. Rule Base of FIS Fig. 9. Surface View of FIS Fig. 9. Surface View of FIS Fig. 9. Surface View of FIS 316 MATLAB – A Ubiquitous Tool for the Practical Engineer The idea behind using a Mamdani rule base to model crisp system behavior is that the rules
for many systems can be easily described in terms of fuzzy variables. Thus we can effectively
model a complex non-linear system, with common-sense rules on fuzzy variables. The idea behind using a Mamdani rule base to model crisp system behavior is that the rules
for many systems can be easily described in terms of fuzzy variables. Thus we can effectively
model a complex non-linear system, with common-sense rules on fuzzy variables. The operation of the Mamdani rule base can be broken down into four parts: 1) mapping
each of the crisp inputs into a fuzzy variable (fuzzification), 2) determining the output of
each rule given its fuzzy antecedents, 3) determining the aggregate output of all of the fuzzy
rules; 4) mapping the fuzzy output to crisp output (defuzzification). The membership function used is Guassian as shown in Fig. 7. The rule base is formed for
the fusion process as shown in Fig. 8. The surface view of the two inputs and one output is
represented in Fig. 9. 5. Target tracking of objects Automatic detection and tracking of interested targets from a sequence of images obtained
from a reconnaissance platform is an interesting area of research for defence related
application. The video images are obtained from an unmanned aerial vehicle (UAV) with
on-board guidance and navigation system. The aircraft carries a multispectral camera which
acquires images of the territory and sends the information to a ground control station (GCS)
in real time. During flight, the pilot in the ground control station may identify a region of interest as a
target. This identification can be click and target type or an intelligent perception type. During flight, the pilot in the ground control station may identify a region of interest as a
target. This identification can be click and target type or an intelligent perception type. The target which appears on a small window could be tracked by engaging track mode. Optical flow is an approximation of the local image motion based upon local derivatives in a
given sequence of images. That is, in 2D it specifies how much each image pixel moves
between adjacent images while in 3D in specifies how much each volume voxel moves
between adjacent volumes. The 2D image sequences used are formed under perspective
projection via the relative motion of a camera and scene objects. The differential methods for determining the optical flow are Lucas-Kanade, Horn-Schunck,
Buxton-Buxton, Black-Jepson and variational methods. Lucas–Kanade method is a widely used differential method for optical flow estimation
developed by Bruce D. Lucas and Takeo Kanade. The assumption in this method is that the
flow is essentially constant in a local neighbourhood of the pixel under consideration, and
solves the basic optical flow equations for all the pixels in that neighbourhood, by the least
squares criterion. q
Horn–Schunck method of estimating optical flow is a global method which introduces a
global constraint of smoothness to solve the aperture problem. The Horn-Schunck algorithm
assumes smoothness in the flow over the whole image. Thus, it tries to minimize distortions
in flow and prefers solutions which show more smoothness. 5.1 Tracking of objects in fused images The airborne video is obtained from the UAV with
a. A visual and thermal camera onboard the UAV. b. Wireless transmission of video to ground control station. 1. The airborne video is obtained from the UAV with
a. A visual and thermal camera onboard the UAV. b. Wireless transmission of video to ground control st a. A visual and thermal camera onboard the UAV. b. Wireless transmission of video to ground control station. 2. The inputs needed are two videos (visual and thermal) which are split into images with
respect to frames. The factors to be considered are:
a. Two videos are to be of same resolution and frame rate. b
Two images are to be considered with the same field of view (FOV) 2. The inputs needed are two videos (visual and thermal) which are split into images with
respect to frames. The factors to be considered are: p
a. Two videos are to be of same resolution and frame rate. b
T
i
t
b
id
d
ith th
fi ld
f
i a. Two videos are to be of same resolution and frame rate. b. Two images are to be considered with the same field of view (FOV). 3. Segmentation process is applied to the images and the targets are segmented. 4
For the fusion process: 4. For the fusion process: a. Consider two images at a time. b. Apply wavelet based image fusion with Haar transform with four level
decomposition of the image. c. An inverse transform is applied to get back the fused image. . For tracking algorithm: a. The tracking algorithm is implemented in SIMULINK in MATLAB. The fused
images are stitched to form a video of the same frame rate. b. The fused image is applied to an optical flow technique. The optical flow technique
is based on Horn-Schunck method. c. Further segmentation accompanied with thresholding principles is applied for the
output obtained after computing optical flow. d. Blob detection principles accompany the process for spotting the targets in the
frame of concern. Thus the targets are given a rectangular boundary of
identification. d. Blob detection principles accompany the process for spotting the targets in the
frame of concern. Thus the targets are given a rectangular boundary of
identification. 5.1 Tracking of objects in fused images A brief representation of the process used is as represented in Fig. 10. The visual and
thermal video is first obtained from an airborne camera. The cameras used must be of
acceptable resolution with good preprocessing features. A high resolution, light weight,
rugged, portable, stabilized platform sensing element is required to be mounted on the
airframe. The images are preprocessed for ego-sensory motion, atmospheric disturbances
and inherent noise. Then a fusion process of thermal and visual images is adapted. The
algorithms for such a fusion process would involve processing of information separately
and then fusing the data. The other way is to fuse and process the data available. Visual and Thermal Image Fusion for UAV Based Target Tracking 317 Visual and Thermal Image Fusion for UAV Based Target Tracking
317
Fig. 10. Process Flow Fig. 10. Process Flow 318 MATLAB – A Ubiquitous Tool for the Practical Engineer The transmission of information from on board real time processing and display of all
required data are done in the ground station. The control interaction with UAV is done by
wireless communication transfer. The transmission of information from on board real time processing and display of all
required data are done in the ground station. The control interaction with UAV is done by
wireless communication transfer. The video file obtained from the camera is loaded as an avi file. It is processed in MATLAB. It aids in real time and efficient implementation of the algorithm. The video is processed for
detection of targets in a sequence of frames. The target detection and localisation process
commences from applying the frames to an optical flow pattern which generates vectors. The target detection is done with respect to feature matching and extraction from the initial
frame. The target which is the region of interest is separated out effectively. By using this
novel technique, an optimized search process for an effective segmented image with less
noise effects when compared to other algorithms is obtained. The targets are thus effectively
located and segmented. The output frames are integrated to form a video file. Then effective
tracking algorithms are applied for the process. Filtering and the required data association
for the output obtained are subsequently done. The inputs needed for processing include
that of two images (Visual and thermal) for image fusion. The steps involved are: 1. The airborne video is obtained from the UAV with 1. 6. Results Image fusion results based on wavelet transform are discussed. Two images (Visual and
thermal) are taken as shown in Fig. 11 and Fig. 12. The visual image gives a realistic human sensing view. The thermal image identifies the
target with the temperature difference coming into the picture with objects possessing
different emissivity values. 319 Visual and Thermal Image Fusion for UAV Based Target Tracking Fig. 11. Visual Image
Fig. 12. Thermal Image
The fused image is given as Fig. 13. The fusion process is applied for a concealed weapon
detection process. The results for such an application are given below in Fig. 14 to Fig. 15. The visual and thermal images are fused and the fused image gives combined information
in one representation. Fig. 11. Visual Image Fig. 11. Visual Image Fig. 11. Visual Image Fig. 12. Thermal Image Fig. 12. Thermal Image The fused image is given as Fig. 13. The fusion process is applied for a concealed weapon
detection process. The results for such an application are given below in Fig. 14 to Fig. 15. The visual and thermal images are fused and the fused image gives combined information
in one representation. The fused image is given as Fig. 13. The fusion process is applied for a concealed weapon
detection process. The results for such an application are given below in Fig. 14 to Fig. 15. The visual and thermal images are fused and the fused image gives combined information
in one representation. Fig. 13. Fused Image Fig. 13. Fused Image Fig. 13. Fused Image MATLAB – A Ubiquitous Tool for the Practical Engineer 320 Fig. 14. Thermal Image
Fig. 15. Fused Image
The thermal images clearly give the information about concealed weapons. The fused image
gives both the RGB based information present in visual image and the concealed weapon
information present in thermal image. The fused image is thus capable of giving enhanced
detection capabilities. 6.1 Target tracking results
For target tracking the database of thermal and visual images is considered The video Fig. 14. Thermal Image Fig. 14. Thermal Image Fig 15 Fused Image Fig. 15. Fused Image The thermal images clearly give the information about concealed weapons. The fused image
gives both the RGB based information present in visual image and the concealed weapon
information present in thermal image. The fused image is thus capable of giving enhanced
detection capabilities. 6.1 Target tracking results For target tracking, the database of thermal and visual images is considered. The video
obtained is converted to a series of frames. Each thermal and visual image is fused and at
the end the fused images are combined to form a video which is given for target tracking
process. One such visual and thermal image from the sequence of frames is shown in Fig. 16 and Fig. 17. The fused image obtained as a result of wavelet transform using Haar wavelet is shown
in Fig. 18. 321 Visual and Thermal Image Fusion for UAV Based Target Tracking Fig. 16. Visual Image
Fig. 17. Thermal Image
Fig. 18. Fused Image
The target tracking results including segmentation, optical flow and identification of targets
in their corresponding frame are shown in Fig. 19, Fig. 20 and Fig. 21. For the four sample frames considered, the segmentation results and tracking results are
illustrated. The segmentation shows that of humans being segmented according to the
threshold values. Fig. 16. Visual Image Fig. 16. Visual Image Fig. 16. Visual Image Fig. 17. Thermal Image Fig. 17. Thermal Image Fig. 18. Fused Image
The target tracking results including segmentation, optical flow and identification of targets
in their corresponding frame are shown in Fig. 19, Fig. 20 and Fig. 21. For the four sample frames considered, the segmentation results and tracking results are
illustrated. The segmentation shows that of humans being segmented according to the
threshold values. Fig. 18. Fused Image The target tracking results including segmentation, optical flow and identification of targets
in their corresponding frame are shown in Fig. 19, Fig. 20 and Fig. 21. For the four sample frames considered, the segmentation results and tracking results are
illustrated. The segmentation shows that of humans being segmented according to the
threshold values. MATLAB – A Ubiquitous Tool for the Practical Engineer 322 Fig. 19. Segmented Image
Fig. 20. Optical Flow Detection
The optical flow which is found out from the images gives the movement of the humans
which is being tracked and given a rectangular representation. Fig. 19. Segmented Image Fig. 19. Segmented Image Fig. 20. Optical Flow Detection
The optical flow which is found out from the images gives the movement of the humans
which is being tracked and given a rectangular representation. Fig. 20. Optical Flow Detection Fig. 20. Fig. 24. Target Detection in Aerial Image Fig. 24. Target Detection in Aerial Image 6.1 Target tracking results Optical Flow Detection The optical flow which is found out from the images gives the movement of the humans
which is being tracked and given a rectangular representation. The optical flow which is found out from the images gives the movement of the humans
which is being tracked and given a rectangular representation. The optical flow which is found out from the images gives the movement of the humans
which is being tracked and given a rectangular representation. Fig. 21. Target Detected Image Fig. 21. Target Detected Image Fig. 21. Target Detected Image 323 Visual and Thermal Image Fusion for UAV Based Target Tracking The following results correspond to taking the thermal images alone and doing target tracking. The target tracking for aerial aircrafts’ motion is shown in Fig. 22 and Fig. 23. These images
correspond to the optical flow and the target detection from a real time video sequence. The
target tracking for identification of humans is given in Fig. 24. The targets are tracked with
respect to the movement of objects identified with optical flow. In this frame, an airborne
flight is being tracked. This aids to the visual perception other than usage of RADAR. Fig. 22. Optical Flow Detection Fig. 22. Optical Flow Detection Fig. 22. Optical Flow Detection Fig. 23. Target Detected Image Fig. 23. Target Detected Image Fig. 23. Target Detected Image 324 MATLAB – A Ubiquitous Tool for the Practical Engineer Further sample results for tracking of objects in thermal video is shown in Fig. 24. This is an
airborne thermal video which is tracked for vehicles and humans if present. The ego sensory
motion is present in this kind of a dynamic moving platform. They have to be compensated
for a stabilized video and for the tracking process has to be improved for a multiple target
tracking environment. Further sample results for tracking of objects in thermal video is shown in Fig. 24. This is an
airborne thermal video which is tracked for vehicles and humans if present. The ego sensory
motion is present in this kind of a dynamic moving platform. They have to be compensated
for a stabilized video and for the tracking process has to be improved for a multiple target
tracking environment. Fig. 24. Target Detection in Aerial Image 7. Conclusion The airborne images obtained from an UAV are analysed in ground control station. By using
the thermal images, all weather and night operation are possible. Visual and thermal image
fusion is done and the fused image is given for target tracking. This system has the benefit of enhanced target tracking application wherein only visual or
thermal target tracking would not provide sufficient efficiency. Thus the image fusion
process augments information leading to an improved system as a whole. The overall
system incorporates segmentation, fusion and target tracking principles. Visual and Thermal Image Fusion for UAV Based Target Tracking 325 8. Acknowledgements The authors are grateful to The Vice Chancellor, Anna University and The Dean, Madras
Institute of Technology, Anna University for providing organizational facilities for carrying
out this research work at Madras Institute of Technology. We would like to express our
sincere thanks & gratitude to The Director NAL for providing sufficient funds for successful
completion this sponsored research work. We also express special thanks to
V.S.Chandrasekhar,
B.P.Shasidhara
and
K.V.Srinivasan,
Scientists,
Aeronautical
Development
Establishment(ADE),
DRDO,
Bangalore. for
their
inspiration
and
encouragement. We would like to convey our thanks and wishes to all the Avionics
students. Ju Han and Bir Bhanu, “Fusion of color and infrared video for moving human detection,”
ACM Portal, Pattern Recognition, pp 1771-1784. 9. References Y.Chena and C.Han, “Night-time Pedestrian Detection by Visual-Infrared Video Fusion,”
Proceedings of 7th World congress on Intelligent Control and Automation, China,
2008. Anjali Malviya and S. G. Bhirud, “Visual Infrared Video Fusion for Night Vision using
Background Estimation”, Journal of Computing, Vol.2, April 2010. Alex Leykin, Yang Ran and Riad Hammoud, “Thermal-Visible Video Fusion for Moving
Target Tracking and Pedestrian Classification”, IEEE Conference on Computer
Vision and Pattern Recognition, Minneapolis, 2007. Zhang Jin-Yu, Chen Yan and Huang Xian-Xiang, “IR Thermal Image Segmentation
Based on Enhanced Genetic Algorithms and Two-Dimensional Classes Square
Error”, Second International Conference on Information and Computing
Science, 2009. Yi Wang, Aldo Camargo, Ronald Fevig, Florent Martel and Richard.R.Schultz, “Image
Mosaicking from Uncooled Thermal IR Video Captured by a Small UAV”,
Proceedings of the IEEE Southwest Symposium on Image Analysis and
Interpretation, 2008. Daniel Olmeda, Arturo de la Escalera and Jos M Armingol, “Detection and Tracking of
Pedestrians in Infrared Images”, International Conference on Signals, Circuits and
Systems, 2009. Wai Kit Wong, Poi Ngee Tan, Chu Kiong Loo and Way Soong Lim, “An Effective
Surveillance System Using Thermal Camera”, International Conference on Signal
Acquisition and Processing, 2009. H.Wang, J.Peng and W.Wu, “Fusion algorithm for multisensory images based on discrete
multiwavelet transform”, Vision, Image and Signal Processing, Proceedings of the
IEEE, Vol.149, no.5, 2002. H.B.Mitchell, Image Fusion: Theories, Techniques and Applications, Springer, 2010. www.imagefusion.org Wai Kit Wong, Hong Liang Lim, Chu Kiong Loo and Way Soong Lim, “Home alone
faint
detection
surveillance
system
using
thermal
camera”,
Second
International Conference on Computer Research and Development, Kuala
Lumpur, 2010. MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer 326 Ju Han and Bir Bhanu, “Fusion of color and infrared video for moving human detection,”
ACM Portal, Pattern Recognition, pp 1771-1784. 17 Vladimir Gostev
State University of Information and Communication Technologies
Ukraine Vladimir Gostev
State University of Information and Communication Technologies
Ukraine 1. Introduction Systems of phase auto fine tuning (phase locked loop – PLL-system) are one of the most
widespread functional knots of various electronic systems. A phase-locked loop (PLL) is a
сlosed-loop feedback control system that generates and outputs a signal in relation to
frequency and phase of an input “reference” signal. They are used in digital networks for
synchronization of some exact setting generators on the reference generator, in frequency
synthesizers for multichannel communication systems with frequency consolidation where
the grid of carrier frequencies for division of channels is required, for example, in
broadcasting and TV, in schemes of restoration bearing and clock frequencies in
synchronous communication systems, as discriminators for demodulation is frequency - and
phase-modulated bearing, as voice-frequency decoders in telephone switchboards for
decoding of figures from accepted voice-frequency combinations. In the given chapter
fuzzy-systems of frequency and phase auto fine tuning (PLL-system with the digital fuzzy
controllers working on the basis of fuzzy logic) are investigated. Research of fuzzy-systems
PLL is spent by mathematical modeling with use of the interactive environment for scientific
and engineering calculations MATLAB and a powerful tool of modelling and research of
control systems with feedback Simulink. 2.1 Fuzzy-systems of Phase Locked Loop –PLL 2.1 Fuzzy-systems of Phase Locked Loop –PLL
Let's consider widely used system of the PLL frequency control which function diagram is
resulted on fig. 2.1. Fig. 2.1. System of the PLL frequency control. Fig. 2.1. System of the PLL frequency control. 328 MATLAB – A Ubiquitous Tool for the Practical Engineer A open-ended circuit of system is consists of serial connection of frequency discriminator
FD, an amplifier A, an engine E with a reducer R, a controlling unit CU, a voltage-controlled
oscillator VCO, a mixer M and intermediate – frequency amplifier IFA. System operation
detail is described in [1]. A frequency discriminator can be presented by the series
connection of a device of comparing, nonlinearity
( )
K ω and the low-pass filter LPF. An
elementary low-pass filter is described by transfer function
1
( )
(
1)
/(
)
F
F
F
G
s
K
T s
k
s
b
−
=
+
=
+
,
where
/
F
F
k
K
T
=
,
1 /
F
b
T
=
,
F
K - gain factor
F
T - a constant of time of the filter on the
output of discriminator. We accept
0
пр
сonst
ω
=
and
c
сonst
ω =
. Inertial properties of
intensive elements can be neglected. An engine is used as an integrating element for giving
to system astaticism the first order that allows to reduce a dynamic error. It is possible to use
the electronic integrator instead of the electromechanical engine. Therefore transfer function
of control object may be written down in a type
1
0( )
[ (
)]
G s
s s
a
α
−
=
+
, where
1 /
G
a
T
=
,
G
T -
constant of time of the generator with a controlling unit. A open-ended circuit of system is consists of serial connection of frequency discriminator
FD, an amplifier A, an engine E with a reducer R, a controlling unit CU, a voltage-controlled
oscillator VCO, a mixer M and intermediate – frequency amplifier IFA. System operation
detail is described in [1]. A frequency discriminator can be presented by the series
connection of a device of comparing, nonlinearity
( )
K ω and the low-pass filter LPF. 2.1 Fuzzy-systems of Phase Locked Loop –PLL Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 329 ( ) Fig. 2.3. A nonlinearity
( )
K ω at
e
ω ≡ Fig. 2.3. A nonlinearity
( )
K ω at
e
ω ≡ It should be emphasized, that on an output of the unit of nonlinearity on the block diagram
the mismatch error is defined as
[ ( )]
[ ( )]
K
t
K e t
ω
≡
. The mismatch error on the input a
frequency discriminator is defined as
( )
( )
t
e t
ω
≡
. At the description of the discrimination characteristic represented on fig. 2.3, usually used
approximation in a type description of the discrimination characteristic represented on fig. 2.3, usually used
mation in a type 2
( )
exp(
). d
K e
K e
ae
=
−
(2.2) (2.2) For determine the parameter a at the given half-width of the discrimination characteristic
Δ area, bounded by a branch of function (2.2), which is defined as 2
0
exp(
)
2
d
d
K
K
e
ae
de
a
∞
−
=
∫
, replace an area of a right triangle (fig. 2.3) with length of legs Δ and
d
K Δ which is defined
as
2 /2. d
K Δ replace an area of a right triangle (fig. 2.3) with length of legs Δ and
d
K Δ which is defined
as
2 /2. d
K Δ From here we have
2
1 /
a =
Δ also expression (2.2) at
e
ω ≡
it will be transformed to
expression (2.1). From here we have
2
1 /
a =
Δ also expression (2.2) at
e
ω ≡
it will be transformed to
expression (2.1). A frequency discriminator FD (see fig. 2.1 ) in a figure 2.2 is presented by the comparing
circuit from the adder and characteristic of discrimination Discrim -–
( )
K ω . A low-pass
filter LPF is described by link TransferFcn1 with transfer function
( )
F
G
s . The object of
control - an integrator and the clock oscillator with a controlling unit - with transfer function
0( )
G s is presented by links Integrator and Transfer Fcn2. The digital fuzzy controller (Fuzzy controller on fig. 2.1 Fuzzy-systems of Phase Locked Loop –PLL An
elementary low-pass filter is described by transfer function
1
( )
(
1)
/(
)
F
F
F
G
s
K
T s
k
s
b
−
=
+
=
+
,
where
/
F
F
k
K
T
=
,
1 /
F
b
T
=
,
F
K - gain factor
F
T - a constant of time of the filter on the
output of discriminator. We accept
0
пр
сonst
ω
=
and
c
сonst
ω =
. Inertial properties of
intensive elements can be neglected. An engine is used as an integrating element for giving
to system astaticism the first order that allows to reduce a dynamic error. It is possible to use
the electronic integrator instead of the electromechanical engine. Therefore transfer function
of control object may be written down in a type
1
0( )
[ (
)]
G s
s s
a
α
−
=
+
, where
1 /
G
a
T
=
,
G
T -
constant of time of the generator with a controlling unit. g
g
The block diagram of system of the PLL frequency control in interactive system MATLAB
we will present in a kind fig. 2.2. For maintenance of demanded dynamics of system it is
used Fuzzy controller or PID-controller. A curve
( )
K ω is called the static discrimination characteristic. The fluctuation component
on an output of discriminator is described by spectral density
п
S and dependence
( )
п
S ω is
called of fluctuation characteristic of discriminator. At simulation fluctuation component
can considered as voltage
( )
V t - random disturbance applied to the output of the
discriminator. A mathematical model of nonlinearity
( )
K ω we are describing expression 2
2
( )
exp{
}
d
K
K
ω
ω
ω
=
−
Δ
(2.1) (2.1) where
d
K - a conversion coefficient of the discriminator, and Δ - a half-width of the
discrimination characteristic, determines resolution capacity of the discriminator, ω
пр
ω
≡Δ
-
detuning concerning nominal intermediate frequency
0
пр
const
ω
=
. Graphically a
nonlinearity
( )
K ω at
e
ω ≡
is presented at the fig. 2.3 Fig. 2.2. The block diagram of system of the PLL frequency control. Fig. 2.2. The block diagram of system of the PLL frequency control. MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min
m
m
= −
. Then recalculation of values of signals in values of elements of universal set perform
according to the formulas 1
2
3
(
)/(2
);
(
)/(2
);
(
)/(2
). m
m
m
m
m
m
u
A
A
u
B
B
u
C
C
θ
θ
θ
∗
∗
∗
∗
∗
∗
⎫
=
+
⎪⎪
=
+
⎬
⎪
=
+
⎪⎭
. Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
m
Cm
θ
= Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy controller steal up either manually, or
automatically by the decision of the optimization task. If studying of system (see fig. 2.2) the method of mathematical simulation selection
following parameters: 1
1
1;
10
;
12 5
;
1;
alf
15;
1;
1. d
k
a
c
b
, c
c
α
Δ
K
−
−
=
=
=
=
=
=
=
= The system was studied when exposed on input an equivalent harmonic signal The system was studied when exposed on input an equivalent harmonic signal ( )
1
0,5sin2
u t
Ft
π
=
+
, ( )
1
0,5sin2
u t
Ft
π
=
+
, with carrier frequency
0,1
F
Нz
=
. with carrier frequency
0,1
F
Нz
=
. y
The adjustment of a fuzzy controller is carried out by criterion of a minimum of a dynamic
error. 2.1 Fuzzy-systems of Phase Locked Loop –PLL 2.2) is fulfilled under the block diagram
with the identical triangular membership function erected in degree and consists of the
block of the shaper of sizes A (t) and B (t), the block of comparing of sizes A and B and
calculation
c
u and the block of normalization variable [2]. The mismatch error ( )t
θ
from an
output of a low-pass filter arrives on a analog-digital converter (AD converter) (Zero-Order
Hold), included at the input of a fuzzy controller . A quantization step of AD converter h
=0,01s. At the output of a fuzzy controller is included the digital to analog converter (Zero-
Order Hold1). )
For simplification of normalization (recalculation of values of signals in values of elements
of universal set) ranges of change input and output signals (parameters of a fuzzy
controller ) we is accepting by symmetric: 330 MATLAB – A Ubiquitous Tool for the Practical Engineer Is received following optimal parameters of a fuzzy controller : max
Am
0,05;
θ
=
=
max
Bm
0,4;
θ
=
=
max
Cm
10;
θ
=
=
max
Dm
150
m
=
=
. Processes in system of the PLL frequency control (see fig. 2.2) with a fuzzy controller are
shown on fig.2.4 where
( )
u t - an input action,
( )
x t - an output a system (see fig. 2.4,a),
( )
Err
e t ≡
– a mismatch error on a discriminator input (see fig. 2.4, b),
( )
m t - an output of a
fuzzy controller (see fig. 2.4, c). y
g
The maximum dynamic error (except for initial burst at the moment of signal capture) does
not exceed 0,7 % from amplitude of a sinusoid. At the fig. 2.4, d transition is presented process of system of the PLL frequency control -
response to unit step action. The system fulfills input influence in time, not exceeding 0,16 s,
without overshoot. Thus, the digital fuzzy controller provides not only greater accuracy castings input
influence, but and high system performance by an step action. Thus, the digital fuzzy controller provides not only greater accuracy castings input
influence, but and high system performance by an step action. It should be noted that the research system with the above parameters, without the
regulator shows that the system lacks stability. ld be noted that the research system with the above parameters, without the
or shows that the system lacks stability. The system (see fig. 2.2) with a digital fuzzy controller it is researched also in the presence of
a stationary white noise (Band-Limited White Noise) on a frequency discriminator output. Implementation of a white noise
( )
v t is shown at the fig. 2.5, a. A mismatch error on an
input of the slope detector ( )
e t and an output of a fuzzy controller
( )
m t thus are casual
processes (see fig. 2.5, b and c). Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 331 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB
33
a)
b)
c)
d)
Fig. 2.4. Processes in system of PLL frequency control. а)
b)
c)
d)
Fig. 2.5. MATLAB – A Ubiquitous Tool for the Practical Engineer Processes in system in the presence of a stationary white noise a)
b) c)
d) c) Fig. 2.4. Processes in system of PLL frequency control. а)
b) b) а) b) c)
d) d) c) Fig. 2.5. Processes in system in the presence of a stationary white noise 332 MATLAB – A Ubiquitous Tool for the Practical Engineer Researches of system in the presence of a stationary white noise show that noise of such
intensity (see fig. 2.5 a,) slightly influences a system output
( )
x t (see fig. 2.5,d), however
error of system increases (we compare fig. 2.4, b and 2.5b), therefore at small input
influences (at small frequency deviations of the generator from set) noise on a frequency
detector output will make the considerable impact on a dynamic error of system. p
p
y
y
System (see fig.2.2) was also studied by using a more simple fuzzy controller. Parameter a in
the fuzzy controller is chosen to be 0.2, and ranges of variation of input and output variables
left unchanged: Am
0,05;
=
Bm
0,4;
=
Cm
10;
=
Dm
150
=
. Processes in system (see fig. 2.2) with a fuzzy controller where
( )
u t – an input , ( )
x t – an
output of system (fig.2.6,a), ( )
Err
e t ≡
– a mismatch error on a discriminator input (fig.2.6,b). ( )
x t and
( )
m t - response to a unit jump of the input signal ( )
u t respectively, at the system
output and the output of fuzzy controller ( see fig.2.6,c,d). а)
b)
c)
d)
h
f
ll а)
b) b) b) d) c) c)
d) d) c) Fig. 2.6. Processes in system with a fuzzy controller Fig. 2.6. Processes in system with a fuzzy controller The maximum dynamic error (except for initial burst at the moment of signal capture) does
not exceed 0,64 % from amplitude of a sinusoid. The system fulfills input influence in time,
not exceeding 0,13s, without overshoot. g
Of interest to examine the processes in the system (see Fig.2.2), by using instead of a fuzzy
controller of the traditional PID controller. The block diagram of digital PID controller
shown in fig.2.2. MATLAB – A Ubiquitous Tool for the Practical Engineer The transfer function of the regulator 1
2
3
1
1
( )
1
z
z
W z
G
G
G
z
z
+
−
=
+
+
−
, Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 333 where
0
1
2
3
0
, G
, G
2
i
d
K h
K
G
K
h
=
=
=
,
0
h – digitization step. As a result of tuning of PID-controller at the indicated higher parameters of the system and
input an equivalent harmonic signal
( )
1
0,5sin 2
u t
Ft
π
=
+
, with carrier frequency
0,1
F
Нz
=
, is received following optimal parameters of a PID-controller, at the
0
h =0.01s:
1
171,2;
G =
2
0,48;
G =
3
1800
G =
. As a result of tuning of PID-controller at the indicated higher parameters of the system and
input an equivalent harmonic signal
( )
1
0,5sin 2
u t
Ft
π
=
+
, with carrier frequency
0,1
F
Нz
=
, is received following optimal parameters of a PID-controller, at the
0
h =0.01s:
1
171,2;
G =
2
0,48;
G =
3
1800
G =
. 1
2
3
Processes in system (see fig. 2.2) with a PID-controller are shown at the fig. 2.7 where ( )
u t -
an input action, ( )
x t - an output a system (see fig. 2.7, a), ( )
Err
e t ≡
– a mismatch error on a
discriminator input (see fig. 2.7,b). ( )
m t - an output of a fuzzy controller (see fig. 2.7,c ). The
maximum dynamic error on system of the of the PLL frequency control with a PID-
controller (except for initial burst at the moment of signal capture) does not exceed 2,4 %
from amplitude of a sinusoid. The maximum dynamic error on system of the PLL frequency
control with a PID-controller in 3,5 times more than the maximum dynamic error in system
of the PLL frequency control with a fuzzy controller and in 3,75 times with a fuzzy
controller. а)
b)
c)
d)
ig. 2.7. Processes in system with a PID-controller
t the fig. 2.4, d transition is presented process of system with a PID-controller - response t
nit step action. MATLAB – A Ubiquitous Tool for the Practical Engineer The transitional process - the oscillating with the overshoot of more tha
0%. The system fulfills input influence in time, exceeding 0,4 s. The regulation time i
ystem of the PLL frequency control with the PID-controller approximately in 2,5 times
more than regulation time in system with a fuzzy controller and in 3 times with an simpl
uzzy controller. а)
b) b) b) c)
d) c) Fig. 2.7. Processes in system with a PID-controller At the fig. 2.4, d transition is presented process of system with a PID-controller - response to
unit step action. The transitional process - the oscillating with the overshoot of more than
20%. The system fulfills input influence in time, exceeding 0,4 s. The regulation time in
system of the PLL frequency control with the PID-controller approximately in 2,5 times is
more than regulation time in system with a fuzzy controller and in 3 times with an simple
fuzzy controller. 334 MATLAB – A Ubiquitous Tool for the Practical Engineer Thus, the fuzzy controllers provide accuracy fulfills of input influences and high-speed
performance of system of the PLL frequency control it is much better, then the PID-
controller. Thus, the fuzzy controllers provide accuracy fulfills of input influences and high-speed
performance of system of the PLL frequency control it is much better, then the PID-
controller. The system (see fig. 2.2) with a digital PID-controller it is researched also in the presence of a
stationary white noise (Band-Limited White Noise) on a frequency discriminator output. Implementation of a white noise ( )
v t is shown at the fig. 2.8,a. Researches of system in the presence of a stationary white noise show that noise of such
intensity (see fig. 2.8 a,) slightly influences a system output ( )
x t (see fig. 2.5,d) however error
of system increases (we compare fig. 2.7, b and 2.8b) therefore at small input influences (at
small frequency deviations of the generator from set) noise on a frequency detector output
will make the considerable impact on a dynamic error of system. а)
b)
c)
d)
Fig. 2.8. Processes in system in the presence of a stationary white noise а)
b) а) b) b) c)
d)
Fig 2 8 Processes in system in the presence of a stationary white noise d) c) c) Fig. 2.8. MATLAB – A Ubiquitous Tool for the Practical Engineer Processes in system in the presence of a stationary white noise Let's consider a mathematical model (block diagram) of system of the of the PLL frequency
control in interactive system MATLAB (see fig. 2.9), with the low-pass filter of the second
order which has transfer function in a numerical type 2
2
0
1
0,008
( )
1
0,008
0,18
1
k
G s
a s
a s
s
s
=
=
+
+
+
+
. A frequency discriminator FD at the fig. 2.9 is presented by the comparator circuit on the
adder and the discrimination characteristic (Discrim) 2
2
2
( )
exp{
}
exp{
}
0,64
d
e
e
K e
K e
e
=
−
=
−
Δ
, Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 335 where conversion coefficient of the discriminator
d
K =1, and the half-width of the
discrimination characteristic defining resolution capability of the discriminator, Δ =0,8. The object of control - the integrator and the without inertia clock generator - with transfer
function
0( )
/
G s
alf
s
=
,
25
alf =
, is presented by link Transfer Fcn1. Fig. 2.9. The block diagram of system of the PLL frequency control Fig. 2.9. The block diagram of system of the PLL frequency control In system is used the elementary digital fuzzy controller (Fuzzy controller at the fig. 2.9) is
fulfilled under the block diagram. The controller consists of the block of the shaper of sizes
A (t) and B (t), the block of comparing of sizes A and B and calculation
c
u and the block of
normalization output variable[2]. The mismatch error
( )t
θ
from an output of a low-pass filter arrives on a analog-digital
converter (AD converter) (Zero-Order Hold), included at the input of a fuzzy controller. A
quantization step of AD converter h =0,01s. On an output of a fuzzy controller is included
the digital/analog converter DAC (Zero-OrderHold1). g
g
For simplification of normalization (recalculation of values of signals in values of elements
of universal set) ranges of change input and output signals (parameters of a fuzzy
controller) we is accepting by symmetric: max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min
m
m
= −
. MATLAB – A Ubiquitous Tool for the Practical Engineer Then recalculation of values of signals in values of elements of universal set perform
according to the formulas 1
2
3
(
)/(2
);
(
)/(2
);
(
)/(2
). m
m
m
m
m
m
u
A
A
u
B
B
u
C
C
θ
θ
θ
∗
∗
∗
∗
∗
∗
⎫
=
+
⎪⎪
=
+
⎬
⎪
=
+
⎪⎭
. Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy controller steal up either manually, or
automatically by the decision of the optimization task. 336 MATLAB – A Ubiquitous Tool for the Practical Engineer The system was studied when exposed on input an equivalent harmonic signal The system was studied when exposed on input an equivalent harmonic signal ( )
1
0,5sin 2
u t
Ft
π
=
+
, with carrier frequency
0,1
F
Hz
=
. with carrier frequency
0,1
F
Hz
=
. with carrier frequency
0,1
F
Hz . The adjustment of a fuzzy controller is carried out by criterion of a minimum of a dynamic
error. Is received following optimal parameters of a fuzzy controller: max
Am
0,05;
θ
=
=
max
Bm
0,4;
θ
=
=
max
Cm
10;
θ
=
=
max
Dm
150
m
=
=
. Processes in system of the of the PLL frequency control (see fig. 2.9) with a fuzzy controller
are shown on fig. 2.10 where ( )
u t - an input action, ( )
x t - an output a system (see fig. 2.10
a,), ( )
Err
e t ≡
– a mismatch error on a discriminator input (see fig. 2.10,b). ( )
m t - an output
of a fuzzy controller (see fig. 2.10,c). a,), ( )
Err
e t ≡
– a mismatch error on a discriminator input (see fig. 2.10,b). ( )
m t - an outp
of a fuzzy controller (see fig. 2.10,c). а)
b)
c)
d)
e)
Fig. 2.10. MATLAB – A Ubiquitous Tool for the Practical Engineer Processes in system а)
b) b) а) c)
d) d) c)
d
e) Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 337 The maximum dynamic error (except for initial burst at the moment of signal capture) does
not exceed 0,4 % from amplitude of a sinusoid. At fig. 2.10,d,e are presented reactions to unit step of input signal
( )
u t respectively, at the
output of system ( )
x t and at the output of a fuzzy controller
( )
m t . The transition process –
the oscillation, which the overshoot of more then 20%. The system fulfills input influence in
time, not exceeding 0,25 s. g
At usage in system (fig. 2.9 see) a digital PID- controller it is received following results. Tuning of PID-controller at the indicated higher parameters of the system and input an
equivalent harmonic signal
( )
1
0,5sin2
u t
Ft
π
=
+
, with carrier frequency
0,1
F
Hz
=
, is
received following earlier optimal parameters of a PID-controller, at the
0
h =0.01s:
1
171,2;
G =
2
0,48;
G =
3
1800
G =
. Therefore processes in system (see fig. 2.9) with a digital PID-controler same what are
shown at the fig. 2.7. The maximum dynamic error in system of the of the PLL frequency control with the PID-
controller (except for initial burst at the moment of signal capture) does not exceed 2,4 %
from amplitude of a sinusoid. Transfer process - oscillatory, with overshoot more than 20 %. The system fulfills input influence for time exceeding 0,4 with. The maximum dynamic error
in system of the of the PLL frequency control (fig. 2.9) with the PID-controller in 6 times
more the maximum dynamic error in system of the of the PLL frequency control with a
fuzzy controller see, and regulation time in system of the of the PLL frequency control with
the PID- controller approximately in 1,6 times is more than regulation time in system with a
fuzzy controller. y
Thus, the fuzzy controller is provided with accuracy of working off of input influences and
high-speed performance of system of the frequency self-tuning it is much better, than the
PID-controller. 2.2 Fuzzy systems of clock synchronization Clearly that inphase
operation of the transmitter and receiver DST is inconceivable without presence synhro
information (upsetting control of system of automatic control). Clock synchro signal are
worked out by clock oscillator CO. Consequently, it is necessary to carry out generating of a
clock synchro signal on transmission and on reception that in turn causes of presence TG on
transmission and on reception. Thus, the first stage of solving the problem of clock
synchronization in practice is implemented by presence TG in a regenerator or a receiving
part of the equipment DST, and clock synchronization can be shown to synchronization CO,
i.e. process of establishment and maintenance of demanded phase relationships between
clock synchro signal two or several CO. Thus CO of transmitter is leading, he works out
setting action; and CO the receiver or a regenerator - slave, the phase of his synchro signal is
a measured variable of automatic system of PLL of a phase. This circumstance is an
important feature of the synchronization system , which becomes a telemechanical system. Setting action - a phase of a clock synhro signal of leader CO in the general case, due to
random distortions when moving the synhro signal from the transmitter to the receiver,
instability of generating of pulses by leader CO, and other is unknown function of time, i.e. ( )
var. TG t
ϕ
=
This position gives the grounds to classify system of clock synchronization as
follow-up systems of automatics, and at
( )
TG t
const
ϕ
=
− as stabilizing systems. Basic element of system of clock synchronization is the system PLL which is selected by a
dotted line for fig. 2.11 In phase-locked loop systems the coordination of phases of two oscillations is carried out -
the current phase of controlled oscillations is set up under a current phase of setting
oscillations so that ideally the phase difference of these oscillations saves constant value. As
persistence of a phase difference is possible only at equality of oscillation frequencies in PLL
systems frequency of controlled oscillations ideally is installed to equal frequency of setting
oscillations. This property of PLL systems defines their double assignment - as systems of
self-locked of frequency and as systems of self-locked of a phase. 2.2 Fuzzy systems of clock synchronization Thus, the first stage of solving the problem of clock
synchronization in practice is implemented by presence TG in a regenerator or a receiving
part of the equipment DST, and clock synchronization can be shown to synchronization CO,
i.e. process of establishment and maintenance of demanded phase relationships between
clock synchro signal two or several CO. Thus CO of transmitter is leading, he works out
setting action; and CO the receiver or a regenerator - slave, the phase of his synchro signal is
a measured variable of automatic system of PLL of a phase. This circumstance is an
important feature of the synchronization system , which becomes a telemechanical system. Setting action - a phase of a clock synhro signal of leader CO in the general case, due to
random distortions when moving the synhro signal from the transmitter to the receiver,
instability of generating of pulses by leader CO, and other is unknown function of time, i.e. ( )
var. TG t
ϕ
=
This position gives the grounds to classify system of clock synchronization as
follow-up systems of automatics, and at
( )
TG t
const
ϕ
=
− as stabilizing systems. Basic element of system of clock synchronization is the system PLL which is selected by a
d tt d li
f
fi
2 11 Clock synchronization of digital signals of telecommunication DST is a process of
establishment and maintaining the required phase relations between the significant
moments of a digital signal of telecommunication DST and a clock synchro signal. Thus, into
the decision of the task of clock synchronization include: 1) formation of the clock synchro
signal solver of the receiver or a regenerator; 2) "binding" of a phase of the specified synchro
signal to a phase of the significant moments DST, accepted from a communication line; 3)
monitoring of the given phase relationship between the timing signal accepted from a
communication line and a synchro signal submitted on solver of the receiver; 4) framing of
controlling influence in the presence of an error at violation of the specified phase
relationship; 5) base service of a phase error according to the worked out control action. The solution of these problem is possible, first of all, creation of system of automatic control
of a phase of a clock synchronize of the receiver or regenerator DST. 2.2 Fuzzy systems of clock synchronization Systems of clock synchronization CS found a wide circulation in various areas of technique,
in particular on digital networks and transmission systems of information DTSI. The
modern development of technique demands requires the CS to meet the new higher quality
of indicators. At the fig. 2.11 shows a typical function diagram of CS DTSI. Diagram includes leading and
slave clock oscillator - LCO and SCO accordingly; the input device of regenerator - IDR; the
extractor of clock synchro signal (ECS); a solver - S; a phase detector – PD; a low-pass filter
LPF; a manager -M; a communication line - a CL. Fig. 2.11. System of clock synchronization Fig. 2.11. System of clock synchronization Fig. 2.11. System of clock synchronization 338 MATLAB – A Ubiquitous Tool for the Practical Engineer Clock synchronization of digital signals of telecommunication DST is a process of
establishment and maintaining the required phase relations between the significant
moments of a digital signal of telecommunication DST and a clock synchro signal. Thus, into
the decision of the task of clock synchronization include: 1) formation of the clock synchro
signal solver of the receiver or a regenerator; 2) "binding" of a phase of the specified synchro
signal to a phase of the significant moments DST, accepted from a communication line; 3)
monitoring of the given phase relationship between the timing signal accepted from a
communication line and a synchro signal submitted on solver of the receiver; 4) framing of
controlling influence in the presence of an error at violation of the specified phase
relationship; 5) base service of a phase error according to the worked out control action. The solution of these problem is possible, first of all, creation of system of automatic control
of a phase of a clock synchronize of the receiver or regenerator DST. Clearly that inphase
operation of the transmitter and receiver DST is inconceivable without presence synhro
information (upsetting control of system of automatic control). Clock synchro signal are
worked out by clock oscillator CO. Consequently, it is necessary to carry out generating of a
clock synchro signal on transmission and on reception that in turn causes of presence TG on
transmission and on reception. 2.2 Fuzzy systems of clock synchronization q
y
y
p
In the first case the immediate aim of application of system is establishment of demanded
correspondence between frequencies of two oscillations, and in the second - establishment
of demanded correspondence between phases of two oscillations. p
p
The phase-locked systems which immediate aim is establishment of demanded
correspondence between frequencies of two oscillations, received a title of phase-locked
loop systems of frequency control (PLL frequency control). If the immediate purpose of functioning of system is the coordination of phases of two
oscillations it name the same as also all class of considered systems - the phase-locked loop
system (PLL). 339 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB Distinction of titles reflects only distinction in immediate mission and does not mean
distinctions in principles of actions. Principles of action of systems PLL OF and PLL are
identical. System PLL defines accuracy and high-speed performance of all system of clock
synchronization. Object of control in system PLL is the clock VCO which taking into its
inertial can be described transfer function 1
( )
[ (
)]
G s
s s
a
α
−
=
+ f an output variable of the generator is the phase of oscillations), or transfer function ( )
/(
)
G s
s
a
α
=
+ (If an output variable of the generator is oscillation frequency), where
/
G
K
T
α =
,
1 /
a
T
=
,
G
K
- transmission factor,
/(
)
rad
s V
⋅
, Т − time constant VCO. Assuming , that the VCO is without inertial element of system PLL, its transfer function can
be defined as ( )
/
G s
s
α
= (If an output variable of the generator is the phase of oscillations), or the transfer
function ( )
G s
α
= (If an output variable of the generator is oscillation frequency), where
G
K
α =
,
G
K
-
transmission factor VCO,
/(
)
rad
s V
⋅
. The mathematical model of the phase detector can be present series connection of the device
of comparing, non linearity
( )
K ϕ and low-pass filter LPF. 2.2 Fuzzy systems of clock synchronization d
K
K
K
K
ϕ
π
ϕ
ϕ
π
ϕ
π
ϕ
π
〈−
⎧
⎪
= −
≤
≤
⎨
⎪
〉
⎩ 0
0
at
2 ,
( )
at -2
2 ,
at 2 . d
K
K
K
K
ϕ
π
ϕ
ϕ
π
ϕ
π
ϕ
π
〈−
⎧
⎪
= −
≤
≤
⎨
⎪
〉
⎩ ( )
at -2
2 ,
d
K
K
ϕ
ϕ
π
ϕ
π
⎪
= −
≤
≤
⎨
⎪ 0 at 2 . K
ϕ
π
〉 Let’s consider a block diagram (a mathematical model) of system of the PLL presented in
interactive system MATLAB, in fig.2.12 [3,4]. To ensure the dynamics of the system using
fuzzy and PID-controllers (Fuzzy controller and PID at the fig.2.12). Let’s consider a block diagram (a mathematical model) of system of the PLL presented in
interactive system MATLAB, in fig.2.12 [3,4]. To ensure the dynamics of the system using
fuzzy and PID-controllers (Fuzzy controller and PID at the fig.2.12). Fig. 2.12. System of the PLL. Phase detector FD (see fig. 2.11) in fig.2.12 is presented by the compare circuit on the adder
and discrimination characteristic Discrim –
( )
sin
d
K
K
ϕ
ϕ
=
. The low-pas filter LPF is
described by link Transfer Fcn1 with transfer function
( )
F
G
s . The clock generator with
transfer function
( )
G s is described by links Integrator and Transfer Fcn2. The digital fuzzy controller (fuzzy controller at the fig. 2.12) is fulfilled under the block Fig. 2.12. System of the PLL. Phase detector FD (see fig. 2.11) in fig.2.12 is presented by the compare circuit on the adder
and discrimination characteristic Discrim –
( )
sin
d
K
K
ϕ
ϕ
=
. The low-pas filter LPF is
described by link Transfer Fcn1 with transfer function
( )
F
G
s . The clock generator with
transfer function
( )
G s is described by links Integrator and Transfer Fcn2. Phase detector FD (see fig. 2.11) in fig.2.12 is presented by the compare circuit on the adder
and discrimination characteristic Discrim –
( )
sin
d
K
K
ϕ
ϕ
=
. The low-pas filter LPF is
described by link Transfer Fcn1 with transfer function
( )
F
G
s . 2.2 Fuzzy systems of clock synchronization The simplest LPF is described by
the transfer function ( )
/(
1)
/(
)
F
F
F
G
s
К
T s
k
s
b
=
+
=
+
, ( )
/(
1)
/(
)
F
F
F
G
s
К
T s
k
s
b
=
+
=
+
, where
/
F
F
k
К
T
=
,
1/
F
b
T
=
,
F
К −an amplification factor,
F
T – the constant of the filter
phase detector. where
/
F
F
k
К
T
=
,
1/
F
b
T
=
,
F
К −an amplification factor,
F
T – the constant of the filter
phase detector. Curve
( )
K ϕ is called the static discrimination characteristic. Mathematical model of the
nonlinearity of the type “discrimination feature” can be described by ( )
sin
d
K
K
ϕ
ϕ
=
, ( )
sin
d
K
K
ϕ
ϕ
=
, where
d
K - gain of phase detector,
( )
( )
t
e t
ϕ
≡
- a mismatch error on an input of phase
detector, or expression at the “linear discrimination characteristic at -
,
( )
0 at
. d
K
K
ϕ
ϕ
ϕ
ϕ
Δ ≤
≤Δ
⎧
= ⎨
〉Δ
⎩ at -
,
( )
0 at
. d
K
K
ϕ
ϕ
ϕ
ϕ
Δ ≤
≤Δ
⎧
= ⎨
〉Δ
⎩ Usually the half-width Δ “linear” discrimination characteristic of phase detector is equal
/2,
π
π or 2 . π
Di
i
i
ti
h
t
i ti
f
h
f
d t
t
b d
ib d b
th
i Usually the half-width Δ “linear” discrimination characteristic of phase detector is equal
/2,
π
π or 2 . π /
Discrimination characteristic of phase-frequency detector can be described by the exp Discrimination characteristic of phase-frequency detector can be described by the expression 340 MATLAB – A Ubiquitous Tool for the Practical Engineer 0
0
at
2 ,
( )
at -2
2 ,
at 2 . d
K
K
K
K
ϕ
π
ϕ
ϕ
π
ϕ
π
ϕ
π
〈−
⎧
⎪
= −
≤
≤
⎨
⎪
〉
⎩ 0
0
at
2 ,
( )
at -2
2 ,
at 2 . Values
of
ranges Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
Cm
θ
=
=
Let's notice that mathematical models of systems at the fig. 2.12 and fig. 2.2 differ only
discrimination characteristics, therefore at identical parameters of other elements it is
necessary to expect identical or close results at research of these systems. If studying of
system (see fig. 2.12) the method of mathematical simulation selection following
parameters:
1
1
1;
10
;
12 5
;
1;
alf
15. k
a
c
b
, c
c
α
−
−
=
=
=
=
=
=
The system was studied when
exposed on input an equivalent harmonic signal
( )
1
0,5sin2
u t
Ft
π
=
+
with carrier
frequency
0,1
F
Hz
=
. The adjustment of a fuzzy controller is carried out by criterion of a minimum of a dynamic
error. Is received following optimal parameters of a fuzzy controller: Am
0,05;
=
Bm
0,4;
=
Cm
10;
=
Dm
150
=
. Processes in system (see fig. 2.12) are shown at the fig. 2.13 where
( )
u t - an input action,
( )
x t - an output a system (see fig. 2.13,a), ( )
Err
e t ≡
– a mismatch error on a discriminator
input (see fig. 2.13). ( )
m t - an output of a fuzzy controller (see fig. 2.13c,). The maximum
dynamic error (except for initial burst at the moment of signal capture) does not exceed 0,7
% from amplitude of a sinusoid. At the fig. 2.13,d transition is presented process of system -
response to unit step action. The system fulfills input influence in time, not exceeding 0,22s,
with overshoot not more than 10%. Thus, the fuzzy controllers provide accuracy fulfills of input influences, but and high-speed
performance of system at the jump action. It should be noted that the study of the system
without the controller shows, that the system does not have the stability. The system (see fig. 2.12) with a fuzzy controller it is researched also in the presence of a
stationary white noise (Band-Limited White Noise) on an output of frequency discriminator
[5]. Implementation of a white noise ( )
v t is shown at the fig. 2.14,a. 2.2 Fuzzy systems of clock synchronization The clock generator with
transfer function
( )
G s is described by links Integrator and Transfer Fcn2. Phase detector FD (see fig. 2.11) in fig.2.12 is presented by the compare circuit on the adder
and discrimination characteristic Discrim –
( )
sin
d
K
K
ϕ
ϕ
=
. The low-pas filter LPF is
described by link Transfer Fcn1 with transfer function
( )
F
G
s . The clock generator with
transfer function
( )
G s is described by links Integrator and Transfer Fcn2. The digital fuzzy controller (fuzzy controller at the fig. 2.12) is fulfilled under the block
diagram, with the identical triangular membership function erected in degree and consists
of the block of the shaper of sizes A (t) and B (t), the block of comparing of sizes A and B and
calculation
c
u and the block of normalization output variable[2]. The mismatch error
( )t
θ
from an output of a low-pass filter arrives on a analog-digital converter (AD converter)
(Zero-Order Hold), included at the input of a fuzzy controller . A quantization step of AD
converter h =0,01s. On an output of a fuzzy controller is included the digital/analog
converter (Zero-Order Hold1). (
)
For simplification of normalization (recalculation of values of signals in values of elements
of universal set) ranges of change input and output signals (parameters of a fuzzy
controller ) we is accepting by symmetric: max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min
m
m
= −
. Then recalculation of values of signals in values of elements of universal set perform
according to the formulas Then recalculation of values of signals in values of elements of universal set perform
according to the formulas Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 341 1
2
3
(
)/(2
);
(
)/(2
);
(
)/(2
). m
m
m
m
m
m
u
A
A
u
B
B
u
C
C
θ
θ
θ
∗
∗
∗
∗
∗
∗
⎫
=
+
⎪⎪
=
+
⎬
⎪
=
+
⎪⎭
. 2.2 Fuzzy systems of clock synchronization Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy controller steal up either manually, or
automatically by the decision of the optimization task. Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy controller steal up either manually, or
automatically by the decision of the optimization task. Values
of
ranges A mismatch error on an
input of the slope detector ( )
e t and an output of a fuzzy controller
( )
m t thus are casual
processes (see fig. 2.14, b and c ). Researches of system in the presence of a stationary white
noise show that noise of such intensity slightly influences a system output ( )
x t ( see fig. 2.14
d) however error of system increases (we compare fig. 2.4b and 2.5b) therefore at small
input influences (at small frequency deviations of the generator from set) noise on a detector
output will make the considerable impact on a dynamic error of system. p
p
y
y
It is of interest to consider the processes in the system of PLL (see fig.2.12)if using instead of
the fuzzy controller the PID-controller [6]. The transfer function of the digital PID (PID on
fig.2.12) controller 1
2
3
1
1
( )
1
z
z
W z
G
G
G
z
z
+
−
=
+
+
−
, MATLAB – A Ubiquitous Tool for the Practical Engine
342
а)
b)
c)
d)
Fig. 2.13. Processes in system
а)
b)
c)
d)
Fig. 2.14. Processes in system with a fuzzy controller in the presence of a stationary white nois MATLAB – A Ubiquitous Tool for the Practical Engineer 342 а)
b) b) а) c)
d) c) Fig. 2.13. Processes in system Fig. 2.13. Processes in system
а)
b) b) а) b) а) c)
d) Fig. 2.14. Processes in system with a fuzzy controller in the presence of a stationary white noise Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 343 where
0
1
2
3
0
, G
, G
2
i
d
K h
K
G
K
h
=
=
=
,
0
h – a digitization step. As a result of tuning a controller at the indicated higher parameters of the system and input
an equivalent harmonic signal is received following optimal parameters of a PID –
controller, at the
0
h =0.01с:
1
130;
G =
2
0,48;
G =
3
2000
G =
. Processes in system (see fig. 2.12) with a PID-controller are shown on fig. 2.15 where
( )
u t - an input action,
( )
x t - an
output a system (see fig. Values
of
ranges 2.15,a), ( )
Err
e t ≡
– a mismatch error on a discriminator input (see
fig. 2.15,b). ( )
m t - an output of a fuzzy controller (see fig. 2.15,c ). As a result of tuning a controller at the indicated higher parameters of the system and input
an equivalent harmonic signal is received following optimal parameters of a PID –
controller, at the
0
h =0.01с:
1
130;
G =
2
0,48;
G =
3
2000
G =
. Processes in system (see fig. 2.12) with a PID-controller are shown on fig. 2.15 where
( )
u t - an input action,
( )
x t - an
output a system (see fig. 2.15,a), ( )
Err
e t ≡
– a mismatch error on a discriminator input (see
fig. 2.15,b). ( )
m t - an output of a fuzzy controller (see fig. 2.15,c ). а)
b)
c)
d)
Fig. 2.15. Processes in system with a PID-controller
The maximum dynamic error in system of PLL with a PID – controller (except for initia
burst at the moment of signal capture) attains of 2,8% from amplitude of a sinusoid. The
maximum dynamic error in system of PLL with a PID–controller in 4 times more than the
maximum dynamic error in system of PLL with a fuzzy controller. On fig. 2.15,d transition is presented process of system with a PID-controller - response to
unit step action. The transitional process - the oscillating with the overshoot of more than
20%. The system fulfills input influence in time, exceeding 0,31 s. The overshoot in system o
PLL with the PID-controller in 2 times, and the regulation time in 1,4 times more than the
appropriate parameters in system of PLL with a fuzzy controller. When reducing the dynamic error in the PLL with PID–controller increases the overshoo
and control time, and decrease in these parameters of the transition process increases а)
b)
c)
d)
Fig. 2.15. Processes in system with a PID-controller
The maximum dynamic error in system of PLL with a PID
controller (except for initia а)
b) а) b) b) а) c)
d)
Fig. 2.15. Processes in system with a PID-controller d) c) Fig. 2.15. Values
of
ranges Processes in system with a PID-controller The maximum dynamic error in system of PLL with a PID – controller (except for initial
burst at the moment of signal capture) attains of 2,8% from amplitude of a sinusoid. The
maximum dynamic error in system of PLL with a PID–controller in 4 times more than the
maximum dynamic error in system of PLL with a fuzzy controller. The maximum dynamic error in system of PLL with a PID – controller (except for initial
burst at the moment of signal capture) attains of 2,8% from amplitude of a sinusoid. The
maximum dynamic error in system of PLL with a PID–controller in 4 times more than the
maximum dynamic error in system of PLL with a fuzzy controller. On fig. 2.15,d transition is presented process of system with a PID-controller - response to
unit step action. The transitional process - the oscillating with the overshoot of more than
20%. The system fulfills input influence in time, exceeding 0,31 s. The overshoot in system of
PLL with the PID-controller in 2 times, and the regulation time in 1,4 times more than the
appropriate parameters in system of PLL with a fuzzy controller. When reducing the dynamic error in the PLL with PID–controller increases the overshoot
and control time, and decrease in these parameters of the transition process increases
dynamic error. y
Thus, the fuzzy controllers provide accuracy fulfills of input influences, and high-speed
performance of system PLL much better, then PID–controller. MATLAB – A Ubiquitous Tool for the Practical Engineer 344 The system (see fig. 2.12) with a PID-controller it is researched also in the presence of a
stationary white noise (Band-Limited White Noise) on an output of discriminator. Implementation of a white noise
( )
v t is shown at the fig. 2.16,a. A mismatch error on an
input of the detector ( )
e t and an output of a fuzzy controller
( )
m t thus are casual processes
(see fig. 2.16,b and c ). Researches of system in the presence of a stationary white noise show
that noise of such intensity slightly influences a system output ( )
x t (see fig. 2.16,d) however
error of system increases (we compare fig. Values
of
ranges 2.15,b and 2.16,c) therefore at small input
influences (at small frequency deviations of the generator from set) noise on a frequency
detector output will make the considerable impact on a dynamic error of system. The system (see fig. 2.12) with a PID-controller it is researched also in the presence of a
stationary white noise (Band-Limited White Noise) on an output of discriminator. Implementation of a white noise
( )
v t is shown at the fig. 2.16,a. A mismatch error on an
input of the detector ( )
e t and an output of a fuzzy controller
( )
m t thus are casual processes
(see fig. 2.16,b and c ). Researches of system in the presence of a stationary white noise show
that noise of such intensity slightly influences a system output ( )
x t (see fig. 2.16,d) however
error of system increases (we compare fig. 2.15,b and 2.16,c) therefore at small input
influences (at small frequency deviations of the generator from set) noise on a frequency
detector output will make the considerable impact on a dynamic error of system. а)
b)
c)
d)
Fig. 2.16. Processes in system in the presence of a stationary white noise а) b) d) Fig. 2.16. Processes in system in the presence of a stationary white noise Let’s consider the system of the PLL of oscillator with a digital fuzzy controller. One of the
main elements of the PLL oscillator is an analog phase detector, the static discrimination
characteristic which can be written down in a kind Let’s consider the system of the PLL of oscillator with a digital fuzzy controller. One of the
main elements of the PLL oscillator is an analog phase detector, the static discrimination
characteristic which can be written down in a kind cos
FD
FD
U
К
ϕ
=
(2.3) (2.3) where
FD
К
- the constant coefficient equal to the maximum value of voltage on an output of
the detector, ϕ - difference in phase fluctuation (one of which is the reference) of the same
frequency, field by to the first and second inputs of the detector (when equality the
frequencies of two oscillation, the phase difference of these oscillations is constant). Values
of
ranges When you change the frequency of input signal, the phase difference become a function of
time: where
FD
К
- the constant coefficient equal to the maximum value of voltage on an output of
the detector, ϕ - difference in phase fluctuation (one of which is the reference) of the same
frequency, field by to the first and second inputs of the detector (when equality the
frequencies of two oscillation, the phase difference of these oscillations is constant). Wh
h
th
f
f i
t i
l th
h
diff
b
f
ti
f When you change the frequency of input signal, the phase difference become a function of
time: ( )
2
( )
n
t
f t dt
ϕ
ϕ
π
=
+
Δ∫
(2.4) (2.4) 345 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB where
n
ϕ - starting value of phase difference at the moment
0
t =
, when
1
2
0
f
f
f
Δ =
−
=
. Taking into account expressions (2.3) and (2.4) block diagram of a phase detector with
variable frequency
1f and
2f input signal will have the form shown at the fig.2.17 [7]. Taking into account expressions (2.3) and (2.4) block diagram of a phase detector with
variable frequency
1f and
2f input signal will have the form shown at the fig.2.17 [7]. Fig. 2.17. Block diagram of a phase detector Based on the structural scheme of the phase detector, taking into account the inertia of the
filter at the output of the detector and the control element at the input of the oscillator (the
filter at the output of the detector and the control element is usually described aperiodic
links) can make a mathematical model of system of the PLL frequency control. The mathematical model system of PLL with a digital fuzzy controller, compiled using the
interactive system MATLAB, presented at the fig.2.18. Filter at the output of the digital
phase detector and an controlling element of the generator describe the transfer functions: 1( )
/(
)
10 /(
12,5)
G s
k
s
b
s
=
+
=
+
,
2( )
/(
)
3 /(
20)
G
s
alf
s
a
s
=
+
=
+
. The digital fuzzy controller (Fuzzy controller at the fig. 2.18) is fulfilled under the block
diagram, with the identical triangular membership function erected in degree and consists
of the block of the shaper of sizes A (t) and B (t) (block 1 collected by the diagram), the block
of comparing of sizes A and B and calculation
c
u (block 2 collected by the diagram) and the
block of normalization output variable (block 3 collected by the diagram)[2]. The digital fuzzy controller (Fuzzy controller at the fig. 2.18) is fulfilled under the block
diagram, with the identical triangular membership function erected in degree and consists
of the block of the shaper of sizes A (t) and B (t) (block 1 collected by the diagram), the block
of comparing of sizes A and B and calculation
c
u (block 2 collected by the diagram) and the
block of normalization output variable (block 3 collected by the diagram)[2]. Fig. 2.18. System of the PLL frequency control. Fig. 2.18. System of the PLL frequency control. 346 MATLAB – A Ubiquitous Tool for the Practical Engineer The
digitization
step
is
chosen
0,001s. Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy
controller steal up either manually, or automatically by the decision of the optimization task. Fig. 2.17. Block diagram of a phase detector At research of the system we will accept, that the difference of frequencies of two
fluctuations changes under the sinusoidal law:
0,2sin(
/5)
f
π
Δ =
or
0,2sin(
/10)
f
π
Δ =
(i.e. The
digitization
step
is
chosen
0,001s. Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy
controller steal up either manually, or automatically by the decision of the optimization task. At research of the system we will accept, that the difference of frequencies of two
fluctuations changes under the sinusoidal law:
0,2sin(
/5)
f
π
Δ =
or
0,2sin(
/10)
f
π
Δ =
(i.e. the maximum deviation of frequency of the generator operated pressure, from the set
reaches 20%
±
). System of PLL should compensate a deviation of frequency of the generator,
therefore an fuzzy controller it is necessary to adjust on the minimum current error of a
mismatch in system. As a result of adjustment it is received following optimum parameters
of an fuzzy controller: the maximum deviation of frequency of the generator operated pressure, from the set
reaches 20%
±
). System of PLL should compensate a deviation of frequency of the generator,
therefore an fuzzy controller it is necessary to adjust on the minimum current error of a
mismatch in system. As a result of adjustment it is received following optimum parameters
of an fuzzy controller: Am=0,03; Bm=0.5; Cm=10; Dm=20; c=1. Processes in system (see fig.2.18) at setting action 0,2sin(
/5)
π
are presented at the fig.2.19,
at setting action 0,2sin(
/10)
π
at the fig. 2.20. In figure ( )
e t - the error of a mismatch on
frequency on an input of the phase detector, ( )t
θ
− the error of a mismatch on frequency on
an output of the phase detector ,
( )
m t - operating pressure on an output of an fuzzy
controller, ( )
u t and ( )
x t - an input and output of the system accordingly. Independently of the frequency of input signal the transition process in the system finished
for 3 s. Maximum dynamic mismatch error of frequency at the input of the phase detector at
the input action 0,2sin(
/5)
π
does not exceed
3
2,8 10−
⋅
(1,4% of the amplitude of the input
action), and for input action 0,2sin(
/10)
π
is approximately
3
1,4 10−
⋅
(0,7% of the
amplitude of the input). а)
b)
c)
d)
Fig. 2.19. Processes in system at setting action 0,2sin(
/5)
π а)
b) )
)
c)
d) Fig. 2.19. Processes in system at setting action 0,2sin(
/5)
π Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 347 y
y
q
y
а)
b)
c)
d)
Fig. 2.20. Processes in system at setting action 0,2sin(
/10)
π а)
b) b) а) c)
d)
Fig. 2.20. Processes in system at setting action 0,2sin(
/10)
π Fig. 2.20. Processes in system at setting action 0,2sin(
/10)
π As show researches of system (see fig. 2.18), a fuzzy controller allows to increase the
accuracy of system PLL practically by two order in comparison with system without a
controller. Research of system PLL, accuracy of tracking which defines a synthesized fuzzy controller,
on the basis of a mathematical apparatus of interactive system MATLAB allows to define
simply enough one of system key parameters - a strip of dynamic tracking. y
g
y
y
y
g
The strip of dynamic tracing of system PLL is the greatest offset of frequency of an entry
basic signal concerning nominal frequency of oscillations of the voltage-controlled oscillator
VCO. In this strip slave devise of synchronization should remain in a mode of tracing
irrespective of speed of change of entry frequency in all range of frequencies. Am=0,03; Bm=0.5; Cm=10; Dm=20; c=1. In other
words, in a strip of dynamic tracing system PLL can track arbitrarily fast changes of the
input frequency, including spasmodic changes of frequency at the input of system. The strip of dynamic tracing of system PLL at research of mathematical model of system
PLL in interactive system MATLAB is defined simply enough, namely, submitting step
signals on input of system PLL it is necessary to find the value of jump of an input signal at
which there is a tracing failure (i.e. at which the system ceases to fulfil jump of an input
signal). For researched system transients action (responses to jumps of an input signal) are
shown at the fig. 2.21. Disruption of tracking occurs when the amplitude of jump А=0,67. This value also defines a strip of dynamic tracking. It is necessary to mark that at sinusoidal input action (at the set speed of change of input
frequency) tracing failure occurs at certain amplitude of the sinusoidal effect, and the
amplitude at which there is a tracing failure in this case will be more than at spasmodic
change of an input signal. For researched system processes (responses to input action 348 MATLAB – A Ubiquitous Tool for the Practical Engineer sin(
/10)
A
π
at various amplitudes A an input signal) are shown at the fig. 2.22. Disruption
of tracking occurs when the amplitude А=0,78. g
p
,
а)
b)
c)
d)
Fig. 2.21. Disruption of tracking occurs when the amplitude of jump А=0,67. а)
b)
c)
d)
Fig. 2.22. Responses to input action
sin(
/10)
A
π
at various amplitudes A an input signal. а)
b)
c)
d)
Fig. 2.21. Disruption of tracking occurs when the amplitude of jump А=0,67. Fig. 2.21. Disruption of tracking occurs when the amplitude of jump А=0,67. а)
b)
c)
d)
Fig. 2.22. Responses to input action
sin(
/10)
A
π
at various amplitudes A an input signal. b)
d) Fig. 2.22. Responses to input action
sin(
/10)
A
π
at various amplitudes A an input signal. Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 349 ϕ corresponds to a time shift
2
o
t
T
ϕ
π
Δ =
. Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB Disruption of tracking occurs when the amplitude А=0,78. Consider the fuzzy system PLL generator with a digital phase detector [8]. Version
execution a diagram of a phase detector is shown in fig.2.23 a. а)
b)
Fig. 2.23. Execution a diagram and principle of operation of a phase detector
RC
DR а)
RC
DR а) b) Fig. 2.23. Execution a diagram and principle of operation of a phase detector The principle of operation of digital phase detector can be explained as follows [7]. At the
input of detector come the reference
o
u and u input signals, that are previously
transformed into meander shape (see. Fig .2.23,b). The positive half-cycle - logical unit,
negative - logical zero. We suppose that the periods of both signals are identical and equal
o
T , and the phase difference is equal ϕ . The counting pulses
GCP
u
from the generator
counting pulses arrive on an input of 1 reverse counter RС only at coincidence in time of
input reference signal and for an input 2 in the presence of reference and absence input
signals. At the end of each period, the next number at the output of down reversible counter
is equal to the difference between the numbers
1
q and
2
q (see fig.2.23,b) is remembered and
the reverse counter is nullified by the device of reset DR. 2
o
FD
c
T
К
T
=
-a constant rate, is equal to the maximum number on the output of the reversible counter of digital phase detector,
o
T - period of reference signal,
c
T - period of counting
pulses, ϕ - difference in phase fluctuation (one of which is the reference) of the same
frequency, field by to the first and second inputs of the detector (when equality the
frequencies of two oscillation, the phase difference of these oscillations is constant). Sampling interval at phase sample and hold devise is defined as
2
c
o
T
T
δϕ
π
=
. A phase shift Sampling interval at phase sample and hold devise is defined as
2
c
o
T
T
δϕ
π
=
. A phase shift ϕ corresponds to a time shift
2
o
t
T
ϕ
π
Δ =
. Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB G s
k
s
b
=
+ At the output of clamp can be activated a filter for smooth the pulsations, for example, a
simple analog filter with a transfer function of an aperiodic link
1( )
/(
). G s
k
s
b
=
+ On the basis of the block diagram of the numeral phase detector taking into account
inertance of the filter on the output of a detector and a controlling unit on the input of
oscillator (a controlling unit is usually also described as an aperiodic link) can be make a
mathematical model of system of the PLL frequency control. The mathematical model of system of PLL with the digital fuzzy controller and digital phase
detector, compiled using of interactive system MATLAB, is presented on fig. 2.25. Fig. 2.25. The mathematical model of system of PLL with the digital fuzzy controller and
digital phase detector Fig. 2.25. The mathematical model of system of PLL with the digital fuzzy controller and
digital phase detector Filter at the output of the digital phase detector and an controlling element of the generator
describe the transfer function: 1( )
/(
)
10 /(
12,5)
G s
k
s
b
s
=
+
=
+
,
2( )
/(
)
3 /(
20)
G
s
alf
s
a
s
=
+
=
+
. The digital fuzzy controller (Fuzzy controller at the fig. 2.25) is fulfilled under the block
diagram, with the identical triangular membership function erected in degree and consists
of the block of the shaper of sizes A (t) and B (t), the block of comparing of sizes A and B and
calculation uc and the block of normalization output variable[2]. The digitization step is
chosen 0,001s. Values of ranges
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
at adjustment of a fuzzy controller steal up either manually, or
automatically by the decision of the optimization task. At research of the system we will accept, that the difference of frequencies of two
fluctuations changes under the sinusoidal law:
0,2sin(
/5)
f
π
Δ =
(i.e. the maximum
deviation of frequency of the generator from the set reaches 20%
±
). Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 350 MATLAB – A Ubiquitous Tool for the Practical Engineer The static discrimination characteristic of the digital phase detector ( see fig. 2.24,а) can be
represented as the shaper of function, give at on specific intervals The static discrimination characteristic of the digital phase detector ( see fig. 2.24,а) can be
represented as the shaper of function, give at on specific intervals 2
(
) at 0
;
2
( )
2
3
(
) at
2 ,
2
FD
FD
FD
К
Q
К
π
ϕ
ϕ
π
π
ϕ
π
ϕ
π
ϕ
π
π
⎧
−
≤
≤
⎪⎪
= ⎨
⎪
−
≤
≤
⎪⎩
(2.5) (2.5) And continued periodically on intervals 2
2(
1) ,
1,2,3... k
k
k
π
ϕ
π
≤
≤
+
=
, and device of
sampling-storage DSS (clamp). And continued periodically on intervals 2
2(
1) ,
1,2,3... k
k
k
π
ϕ
π
≤
≤
+
=
, and device of
sampling-storage DSS (clamp). a)
b)
Fig. 2.24. The static discrimination characteristic and block diagram of the digital phase
detector b) Fig. 2.24. The static discrimination characteristic and block diagram of the digital phase
detector Using the Fourier series expansion
is extended periodically at the intervals
2
2(
1) ,
1,2,3... k
k
k
π
ϕ
π
≤
≤
+
=
, of the functions
( )
FD
Q
ϕ we obtain expression in the form 2
8
cos3
cos5
cos7
( )
[cos
...]
9
25
49
FD
FD
Q
K
ϕ
ϕ
ϕ
ϕ
ϕ
π
=
+
+
+
+
. (2.6) (2.6) As practice shows, for determination of a mathematical model of the static discrimination
characteristic of the digital phase detector is sufficient to the first three terms of Fourier
series. When you change the frequencies of input signals, the phase difference becomes a function
of time (see the formula (2.4)). Taking into account expressions (2.4), (2.6) and the clamp the
block diagram of a digital phase detector under varying frequencies
1f i
2f of input signals
will have the form, shown at the fig. 2.24,b. 351 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB At the output of clamp can be activated a filter for smooth the pulsations, for example, a
simple analog filter with a transfer function of an aperiodic link
1( )
/(
). Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB System of PLL should
compensate a deviation of frequency of the generator, therefore a fuzzy controller it is
necessary to adjust on the minimum current error of a mismatch in system. As a result of
adjustment it is received following optimum parameters of a fuzzy controller, c=1: Am=0,08;
Bm=2.5; Cm=50; Dm=100. 352 MATLAB – A Ubiquitous Tool for the Practical Engineer Processes in system (see fig.2.25) at setting action 0,2sin(
/5)
π
are presented at the fig.2.26. Processes in system (see fig.2.25) at setting action 0,2sin(
/5)
π
are presented at the fig.2.26. Processes in system (see fig.2.25) at setting action 0,2sin(
/5)
π
are presented at the fig.2.26. In the figures ( )
e t - a mismatch error in frequency at the input of digital phase detector (а) Processes in system (see fig.2.25) at setting action 0,2sin(
/5)
π
are presented at the fig.2.26. In the figures ( )
e t - a mismatch error in frequency at the input of digital phase detector (а)
and its steady form in the dynamic mode (b),
( )t
θ
- error at the output of phase detector–
input of fuzzy controller (c) and its steady form in the dynamic mode (d),
( )
m t - an In the figures ( )
e t - a mismatch error in frequency at the input of digital phase detector (а)
and its steady form in the dynamic mode (b),
( )t
θ
- error at the output of phase detector–
input of fuzzy controller (c) and its steady form in the dynamic mode (d),
( )
m t - an
operating pressure on an output of an fuzzy controller,(e),
( )
u t and
( )
x t - an input and
output of the system (see fig.2.26) accordingly (f). p
y
(
g
)
g y ( )
Transition process in the system ends in a time not exceeding 0.6sec.The maximum dynamic
error of a mismatch on frequency on an input of the phase detector on setting action
0,2sin(
/5)
π
does not exceed
3
4 10−
⋅
. Research shows the system (see fig.2.25), the fuzzy
controller can increase the accuracy of the PLL system is almost two orders of magnitude
compared to the system without controller. а)
b)
c)
d)
e)
f)
Fig. 2.26. Processes in system at setting action 0,2sin(
/5)
π Fig. 2.26. 2.3 Combined fuzzy-system of PLL The mathematical model of combined system of PLL with the digital fuzzy controller, made
with use of interactive system MATLAB, is presented on fig.2.27. Fig. 2.27. The mathematical model of combined system of PLL with the digital fuzzy
controller Fig. 2.27. The mathematical model of combined system of PLL with the digital fuzzy
controller Automatic control system name combined (or system with the combined control) when in
the law of control except an error, derivatives and integrals from an error, additional
communications on setting action or/and on revolting action are entered. The basic system in detail considered earlier [fig. 2.18], consists of the phase detector which
block diagram is resulted on fig. 2.17 and is presented by the comparison device, an
integrating link with factor 2π (Transfer Fcn), the discrimination characteristic cosφ
(Discrim) and the low-pass filter on an output of the detector with transfer function
1( )
/(
)
G s
k
s
b
=
+
(Transfer Fcn1), an fuzzy controller (Fuzzy controller), the generator
operated pressure, with transfer function
2( )
/(
)
G
s
alf
s
a
=
+
(Transfer Fcn2), and an
individual negative feedback. Filter at the output of the detector and an operating element of the generator have the
transfer
functions
in
a
numerical
kind:
1( )
/(
)
10 /(
12,5)
G s
k
s
b
s
=
+
=
+
;
2( )
/(
)
3 /(
20)
G
s
alf
s
a
s
=
+
=
+
. Filter at the output of the detector and an operating element of the generator have the
transfer
functions
in
a
numerical
kind:
1( )
/(
)
10 /(
12,5)
G s
k
s
b
s
=
+
=
+
;
2( )
/(
)
3 /(
20)
G
s
alf
s
a
s
=
+
=
+
. The digital fuzzy controller with the identical triangular membership functions erected in
degree (Fuzzy controller at the fig.2.27) is executed under the basic scheme. The fuzzy
controller consists of the block of the shaper of sizes A (t)and B (t), the block of comparison
of sizes A (t)and B (t) and calculation
c
u and the block of normalization output variable[2]
The
digitization
step
is
chosen
0,001s. Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB Processes in system at setting action 0,2sin(
/5)
π 353 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB Application of fuzzy controllers in PLL appropriate. Since the fuzzy controller is a digital
correction device, it can be successfully applied in the digital PLL. Application of fuzzy controllers in PLL appropriate. Since the fuzzy controller is a digital
correction device, it can be successfully applied in the digital PLL. 2.3 Combined fuzzy-system of PLL Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
)
get
out
at
controller
adjustment. Additional coupling on setting action includes following elements: the
frequency discriminator with the discrimination characteristic (Discrim1) 354 MATLAB – A Ubiquitous Tool for the Practical Engineer 2
2
( )
exp{
}
d
e
K e
K e
=
−
Δ
, where
1
d
К =
and
1,
Δ =
and the filter of the bottom frequencies with transfer function
3( )
/(
)
G s
k
s
b
=
+
(Transfer Fcn3), and the amplifier (Gain) with changeable factor of
strengthening. where
1
d
К =
and
1,
Δ =
and the filter of the bottom frequencies with transfer function
3( )
/(
)
G s
k
s
b
=
+
(Transfer Fcn3), and the amplifier (Gain) with changeable factor of
strengthening. From consideration of mathematical model of combined system of PLL with a digital fuzzy
controller it is visible, that it is impossible to carry out the transfer function of additional
coupling equal to return transfer function of generator
2
1 /
( )
(
) /
(
20) /3
G
s
s
a
alf
s
=
+
=
+
,
i.e. it is impossible to carry out absolute invariancy of system from setting action, but it is
possible to reduce a dynamic error of system by selection of transmission factor of amplifier
Gain (to reach ε -invariancy). (
y)
а)
b)
c)
d)
Fig. 2.28. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
(at the disconnected
coupling on setting action) Fig. 2.28. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
(at the disconnected
coupling on setting action) At research of the combined system we will accept, that the difference of frequencies of two
fluctuations changes under the sinusoidal law:
0,2[1
sin(
/5)]
f
π
Δ =
+
(i.e. the maximum
deviation of frequency of the generator operated pressure, from the set reaches 40% ). System of PLL should compensate a deviation of frequency of the generator, therefore an
fuzzy controller it is necessary to adjust on the minimum current error of a mismatch in
system. Am=0,03; Bm=0.5; Cm=10; Dm=20; c=1.
Optimum factor of strengthening of amplifier Gain K=7,3. 2.3 Combined fuzzy-system of PLL 356 MATLAB – A Ubiquitous Tool for the Practical Engineer Ever more reduce the steady dynamic error can be achieved if in additional coupling on
setting action to enter ideal forcing link with transfer function
(
1 )
G Ts +
, where
1 /
T
a
=
,
аnd in the factor G should enter k factor and additional adjusting factor K . The combined system of PLL with the digital fuzzy controller and forcing link shown in
Fig.2.30. Ever more reduce the steady dynamic error can be achieved if in additional coupling on
setting action to enter ideal forcing link with transfer function
(
1 )
G Ts +
, where
1 /
T
a
=
,
аnd in the factor G should enter k factor and additional adjusting factor K . h
b
d
f
h h
d
l f
ll
d f
l
k
h j
g
The combined system of PLL with the digital fuzzy controller and forcing link shown in
Fig.2.30. Fig. 2.30. The combined system of PLL with the digital fuzzy controller and forcing link
In this system a digital ideal forcing link (controller _fr) realizes expression (using the first
difference from a signal arriving on its input): Fig. 2.30. The combined system of PLL with the digital fuzzy controller and forcing link
In this system a digital ideal forcing link (controller _fr) realizes expression (using the first
difference from a signal arriving on its input): Fig. 2.30. The combined system of PLL with the digital fuzzy controller and forcing link
In this system a digital ideal forcing link (controller _fr) realizes expression (using the first
difference from a signal arriving on its input): ( )
{
( )
[
( )
(
1)]/ }
out
in
in
in
U
n
k U
n
T U
n
U
n
h
=
+
−
−
. The scheme of a digital ideal forcing link is resulted on fig. 2.31 (only this link the system on
fig. 2.30 differs from the system shown on fig. 2.27). At research of the combined system we
will accept, that the difference of frequencies of two fluctuations changes under the
sinusoidal law:
0,2[1
sin(
/5)]
f
π
Δ =
+
(i.e. the maximum deviation of frequency of the
generator, from the set reaches 40% ). Fig. 2.31. The scheme of a digital ideal forcing link Fig. 2.31. 2.3 Combined fuzzy-system of PLL As a result of adjustment it is received following optimum parameters of fuzzy
controller: Am=0,03; Bm=0.5; Cm=10; Dm=20; c=1. Optimum factor of strengthening of amplifier Gain K=7,3. 355 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB Processes in system (see fig.2.27) at setting action 0,2[1
sin(
/5)]
π
+
are presented at the
fig.2.28 (at the disconnected coupling on setting action) and at the fig. 2.29 (at the included
coupling on setting action). In drawings: a) and b) ( )
e t - a dynamic error of a mismatch on
frequency on an input of the phase detector in the transitive and established modes, c)
( )
m t
- operating pressure on an output of an fuzzy controller, d)
( )
u t and
( )
x t - an input and
output of the system accordingly. The maximum dynamic error of a mismatch on frequency on an input of the phase detector
in system of PLL at the disconnected coupling on setting action 0,2[1
sin(
/5)]
π
+
in the
established dynamic mode makes size
4
9,8 10−
⋅
, and the maximum dynamic error of a
mismatch on frequency on an input of the phase detector in system of PLL at the included
coupling on setting action 0,2[1
sin(
/5)]
π
+
in the established dynamic mode makes size
4
3,6 10−
⋅
. Transient time (time of capture of an input signal) in system at the disconnected
coupling on setting action makes 4,3 seconds, and in system at the included coupling on
setting action 2,5 seconds а)
b)
c)
d)
Fig. 2.29. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
( at the included coupling
on setting action) а)
b) c)
d) d) Fig. 2.29. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
( at the included coupling
on setting action) Research combined (with additional coupling on setting action) system of PLL with a digital
fuzzy controller by method of mathematical modeling has shown, that additional coupling
on setting action reduces the established dynamic error in 2,7 times, and time of capture of
an input signal in 1,7 times, in comparison with these indicators in system without coupling
on setting action. 2.3 Combined fuzzy-system of PLL The scheme of a digital ideal forcing link 357 Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB System of PLL should compensate a deviation of frequency of the generator, therefore a
fuzzy controller it is necessary to adjust on the minimum current error of a mismatch in
system. As a result of adjustment it is received the same optimum parameters of an fuzzy
controller, as in the system shown on fig.2.27: Am=0,03; Bm=0.5; Cm=10; Dm=20; c=1. But
the optimum amplification factor of amplifier Gain will be another: К=0,82. Processes in system (see fig.2.30) at setting action 0,2[1
sin(
/5)]
π
+
are presented on fig.2.32
(at the disconnected coupling on setting action) and on fig. 2.33 (at the included coupling on
setting action). In drawings: a) and b) ( )
e t - a dynamic error of a mismatch on frequency on
an input of the phase detector in the transitive and established modes, c)
( )
m t - operating
pressure on an output of an fuzzy controller, d) ( )
u t and ( )
x t - an input and output of the
system accordingly. The maximum dynamic error of a mismatch on frequency on an input of the phase detector
in system of PLL at the disconnected coupling on setting action 0,2[1
sin(
/5)]
π
+
in the
established dynamic mode makes size
4
9,8 10−
⋅
, and the maximum dynamic error of a
mismatch on frequency on an input of the phase detector in system of PLL at the included
coupling on setting action 0,2[1
sin(
/5)]
π
+
in the established dynamic mode makes size
4
2,5 10−
⋅
. а)
b)
c)
d)
. 2.32. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
(at the disconnected
upling on setting action) а)
b) b) а) c)
d) Fig. 2.32. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
(at the disconnected
coupling on setting action) MATLAB – A Ubiquitous Tool for the Practical Engineer 358 a)
b)
c)
d)
Fig. 2.33. Processes in system at setting action 0,2[1
sin(
/5)]
π
+
(at the included coupling on
setting action) Fig. 2.33. 2.3 Combined fuzzy-system of PLL Processes in system at setting action 0,2[1
sin(
/5)]
π
+
(at the included coupling on
setting action) Transient time (time of capture of an input signal) in system at the disconnected coupling on
setting action makes 4,3 seconds, and in system at the included coupling on setting action
2,4 seconds. Thus, in system of PLL with the digital fuzzy controller and a digital ideal forcing link
additional communication on setting action reduces the established dynamic error in 3,9
times, and time of capture of an input signal in 1,79 times, in comparison with these
indicators in system without communication on setting influence. 2.4 System of PLL with the phase-frequency discriminators Operating principle of phase-frequency discriminator 360 MATLAB – A Ubiquitous Tool for the Practical Engineer at
2 ,
( )
at -2
2 ,
2
at
2 . o
o
o
U
U
K
U
ϕ
π
ϕ
φ
π
ϕ
π
π
ϕ
π
−
< −
⎧
⎪⎪
=
≤
≤
⎨
⎪
>
⎪⎩ In an interactive system MATLAB the diagram of discriminator with the characteristic
presented on fig 2.34,b can present only a block saturation (Saturation). In an interactive system MATLAB the diagram of discriminator with the characteristic
presented on fig 2.34,b can present only a block saturation (Saturation). Phase-frequency discriminator with a characteristic shown in fig.2.34, b, is a machine that
has five states (-2, -1, 0, +1, +2), and switchable on a leading edge of the reference signal and
feedback signal. Reference signal adds to the state machine unit and the feedback signal on
the contrary, subtracts. Operating principle of phase-frequency discriminator is shown at
the fig.2.36 (darkened color is shown zero state machine). At fig.2.37 shows the model on which to explore the two systems having the same phase-
frequency discriminator (Discrim1), made under the scheme fig.2.35, and the same voltage-
controlled oscillator (TransferFcn1), with a transfer function
( )
/ . G s
alf
s
=
Transfer
coefficient VCO
104
G
alf
K
=
=
rad / ( s V
⋅
). Fig. 2.37. System of PLL with phase-frequency discriminator Fig. 2.37. System of PLL with phase-frequency discriminator With the closure of a switch ManualSwitch1 in the down position simulated the system of
PLL. The block diagram of this system, except for blocks Discrim1 and Transfer Fcn1 (is
simulating the discriminator and VCO), have two additional blocks: Gain (transfer factor of
detector
Fd
K
=3,7/(4π ) V/rad) and block Correction circuit (an active filter with an
operational amplifier). The transfer function of filter 2
1
3
1
( )
(
1)
s
F s
s
s
τ
τ
τ
+
≅
=
+
3330(
4,55). (
100)
s
s s
+
+ System with active filter on the operational amplifier was studied when exposed to on input
of an equivalent harmonic signal ( )
10
5sin2
u t
Ft
π
=
+
with carrier frequency
0,1
F
Hz
=
. 2.4 System of PLL with the phase-frequency discriminators 2.4 System of PLL with the phase frequency discriminators
The phase-frequency discriminator has the specific characteristic which can be presented a
non-linear element of type "saturation" (see fig. 2.34, a,b) that allows to work in broad range
of frequencies. а)
b)
Fig. 2.34. The characteristic of the phase-frequency discriminator Fig. 2.34. The characteristic of the phase-frequency discriminator Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 359 Discrimination characteristic phase-frequency discriminator (see Fig.2.34, a) can be
described by Discrimination characteristic phase-frequency discriminator (see Fig.2.34, a) can be
described by 2
at
2 ,
( )
at -2
2 ,
2
at
2 . d
d
d
K
K
K
K
π
ϕ
π
ϕ
ϕ
π
ϕ
π
π
ϕ
π
< −
⎧
⎪
= −
≤
≤
⎨
⎪−
>
⎩ In interactive system MATLAB the diagram of discriminator with the characteristic
presented at the fig. 2.34,a it is possible to present as the connections of three block (see fig. 2.35): the switch (Switch), the inverter (Gain) and the saturation block (Saturation). At the
positive signal of an error on a discriminator input (in block Switch parameter Threshold
=0.000001) closed a upper contact of switch and the is formed a plot of characteristic
0
ϕ ≥
,
at the negative signal of an error on input discriminator is closed bottom contact and formed
a plot of characteristic
0
ϕ ≤
. Levels of restrictions in a block of saturation (Saturation) are
2
d
К
π
±
. Fig. 2.35. Diagram of discriminator with the characteristic presented at the fig. 2.34,a
Discrimination characteristic phase-frequency discriminator (see fig.2.34, b) can be described by
Fig. 2.36. Operating principle of phase-frequency discriminator Fig. 2.35. Diagram of discriminator with the characteristic presented at the fig. 2.34,a
Discrimination characteristic phase-frequency discriminator (see fig.2.34, b) can be described by Fig. 2.35. Diagram of discriminator with the characteristic presented at the fig. 2.34,a
Discrimination characteristic phase-frequency discriminator (see fig.2.34, b) can be described by Fig. 2.35. Diagram of discriminator with the characteristic presented at the fig. 2.34,a
Discrimination characteristic phase-frequency discriminator (see fig.2.34, b) can be descr Fig. 2.35. Diagram of discriminator with the characteristic presented at the fig. 2.34,a
Discrimination characteristic phase-frequency discriminator (see fig.2.34, b) can be described by Fig. 2.36. 2.4 System of PLL with the phase-frequency discriminators The mismatch error
( )t
θ
from an output of a low-pass filter arrives on a analog-digital
converter (AD converter) (Zero-Order Hold), included at the input of a fuzzy controller . A
quantization step of AD converter h =0,01s. On an output of a fuzzy controller is included
the digital/analog converter (Zero-OrderHold1). For simplification of normalization (recalculation of values of signals in values of elements
of universal set) ranges of change input and output signals (parameters of a fuzzy
controller ) we is accepting by symmetric: max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min ;
θ
θ
= −
max
min
m
m
= −
. Then recalculation of values of signals in values of elements of universal set perform
according to the formulas [2] 1
2
3
(
)/(2
);
(
)/(2
);
(
)/(2
). m
m
m
m
m
m
u
A
A
u
B
B
u
C
C
θ
θ
θ
∗
∗
∗
∗
∗
∗
⎫
=
+
⎪⎪
=
+
⎬
⎪
=
+
⎪⎭
. of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
Values
of
ranges
(
max
min
Am
;
θ
θ
=
= −
max
min
Bm
;
θ
θ
=
= −
max
min
Cm
;
θ
θ
=
= −
max
min
Dm
m
m
=
= −
) at adjustment of a fuzzy controller steal up either manually, or
automatically by the decision of the optimization task. The system of PLL with a low pass
filter LPF and a digital fuzzy controller was investigated when exposed at input an
equivalent harmonic signal ( )
10
5sin2
u t
Ft
π
=
+
with carrier frequency
0,1
F
Hz
=
. The adjustment of a fuzzy controller is carried out by criterion of a minimum of a dynamic
error Is received following optimal parameters of fuzzy controller : q
g
( )
q
y
The adjustment of a fuzzy controller is carried out by criterion of a minimum of a dynamic
error. Is received following optimal parameters of fuzzy controller : Am
0,0174;
=
Bm
0,2458;
=
Cm
4,6607;
=
Dm
249,89. 2.4 System of PLL with the phase-frequency discriminators System with active filter on the operational amplifier was studied when exposed to on input
of an equivalent harmonic signal ( )
10
5sin2
u t
Ft
π
=
+
with carrier frequency
0,1
F
Hz
=
. esearch of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 361 The processes in the system of the PLL frequency control with active filter Correction
circuit(see fig.2.37) are shown in fig.2.38 where
( )
u t – an input action,
( )
x t –an output
system (see fig.2.38,a), ( )
Err
e t ≡
– a mismatch error on the input of the discriminator (see
fig.2.38, b). ( )
m t - a filter output (see fig.2.38,c). At fig.2.38, shows reaction system on step
input ( )
10
u t =
. The results show that the system of the PLL frequency control with active filter Correction
circuit has a very high exactness working off entrance influence: a dynamic mismatch error
for a given harmonic signal is
4
4,2 10−
⋅
or 0.082% of the amplitude of input sine impact. System performance is also very high. Settling time is approximately equal to 0.06, but the
transient process is oscillatory, with overshoot almost 60% . а)
b)
c)
d)
Fig. 2.38. The processes in the system of the PLL frequency control with active filter Fig. 2.38. The processes in the system of the PLL frequency control with active filter With the closure of a switch ManualSwitch1 in the upper position simulated the system of
PLL with a low -pass filter LPF pass second and digital fuzzy controller (Fuzzy controller at
the fig.2.37) which is executed by the block diagram. The controller consists of the block of
the shaper of sizes A (t) and B (t), the block of comparing of sizes A and B and calculation uc
and the block of normalization output variable (block 3 collected by the diagram)[2]. The
filter has the transfer function 2
2
0
1
0,002
( )
1
0,008
0,18
1
k
F s
a s
a s
s
s
=
=
+
+
+
+
, which can also be written as 362 MATLAB – A Ubiquitous Tool for the Practical Engineer 2
0,25
0,25
( )
(
10)(
12,5)
22,5
125
F s
s
s
s
s
=
=
+
+
+
+
. 2.4 System of PLL with the phase-frequency discriminators = When setting up a fuzzy controller in an interactive system MATLAB we using a block NCD
(Nonlinear Control Design), which implements the method of dynamic optimization for the
design of control systems. This tool is designed for use with Simulink, automatically adjusts
a system parameters (in the system fig.2.37 adjusted parameters of the fuzzy controller, Am,
Bm, Cm, Dm,), based on certain constraints on the temporal characteristics (time of
regulating and overshoot for reaction to a step action and limits for the dynamic mismatch
error). The processes in the system of the PLL frequency control with low pass filter LPF and the
digital fuzzy controller (see fig.2.37) are shown in Fig.2.39 where ( )
u t - a input action, ( )
x t –
a system output (see fig.2.39, a) ( )
Err
e t ≡
–a mismatch error at the input of the discriminator
(see fig.2.39, b),
( )
m t - an output of fuzzy controller (see fig.2.39, c). The maximum dynamic error (except for initial burst at the moment of signal capture) does
not exceed
3
4,2 10−
⋅
or 0,82% from amplitude of a sinusoid. At fig.2.39, d shows the system response to a step action ( )
10
u t =
on the output of system
( )
x t and the output a fuzzy controller
( )
m t . Transient process have overshoot 3,4%. The
system fulfills input action in a time not exceeding 0,16 sec. Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 363 а)
b)
c)
d)
Fig. 2.39. The processes in the system of the PLL frequency control with low pass filter LPF
and the fuzzy controller Fig. 2.39. The processes in the system of the PLL frequency control with low pass filter LPF
and the fuzzy controller We remark that the PLL with a low pass filter LPF, but without the digital fuzzy controller,
has no stability. We remark that the PLL with a low pass filter LPF, but without the digital fuzzy controller,
has no stability. Thus, can conclude that the PLL with a low pass filter LPF and the digital fuzzy controller
has a bad quality indicators than the PLL with an active filter on the operational amplifier,
but has transient process (overshoot). p
(
)
Now consider the operation of these systems in the presence of internal noise. 2.4 System of PLL with the phase-frequency discriminators In this case,
the switch Manual Switch on Fig.2.37 is closed in the upper position, which corresponds to
the filing of the noise signal - a stationary white noise (Band-Limited White Noise) on the
output phase-frequency detector (Discrim1). Noise signal n (t) represented on Fig.2.40. Amplitude of the noise emissions of approximately 1% of the input signal. Fig. 2.40. Noise signal on the output phase-frequency detector Fig. 2.40. Noise signal on the output phase-frequency detector MATLAB – A Ubiquitous Tool for the Practical Engineer 364 а) а)
b)
Fig. 2.41. Mismatch errors on the input of phase-frequency discriminator b) Fig. 2.41. Mismatch errors on the input of phase-frequency discriminator At fig.2.41 are presented mismatch errors on the input of phase-frequency discriminator at
the presence of stationary white noise at the output of the discriminator in the system of a
phase-frequency locked loop with low pass filter LPF and the digital fuzzy controller Fuzzy
controller (see fig.2.41 a) and in the system of the PLL frequency control with active filter
Correction circuit (see Fig.2.41, b). As seen from the oscillograms the system of system of the PLL frequency control with a low
pass filter LPF and a digital fuzzy controller Fuzzy controller has less mismatch error at the
input phase-frequency discriminator in the presence of stationary white noise than the
system phase-frequency locked loop with active filter Correction circuit. 2.5 Servomechanism of synchronous and in-phase rotation shaft part of drive from
the alternating reference voltage
The mathematical model of servomechanism in an interactive system MATLAB is presented he mathematical model of servomechanism in an interactive system MATLAB is prese
fig.2.42. The mathematical model of the phase detector is represented serial connection of
comparison device, the nonlinearity (Discrim)
( )
sin
d
K
K
ϕ
ϕ
=
, where
d
K - coefficient of
conversion of the phase detector, and
( )
( )
t
e t
ϕ
≡
- a mismatch error on a phase detector
input, and the low-pass filter LPF (Transfer Fcn). p
p
(
)
Transfer function of a low-pass filter LPF (Transfer Fcn)[2] is 1
12,5
( )
, a
1/ ,
0,08 s. 12,5
а
G s
RC
s
а
s
τ
τ
=
=
=
=
=
+
+ Transfer function of the amplifier of power-modulator P-M (Transfer Fcn1)[2] Transfer function of the amplifier of power-modulator P-M (Transfer Fcn1)[2] 2
1
500
( )
100
K
G s
s
a
s
=
=
+
+
,
1
,
1 /
0,01 s. y
y
a
T
T
=
= Transfer function of engine EE (Zero-Pole)[2] Transfer function of engine EE (Zero-Pole)[2] Transfer function of engine EE (Zero-Pole)[2] 3
90
( )
(
)
(
10)
G s
s s
b
s s
α
=
=
+
+
, where
1 /
;
0,1 ;
/
;
9
/(
)
db
db
db
b
T
T
c
Kdb
T
Kdb
rad
V s
α
=
=
=
=
⋅ where
1 /
;
0,1 ;
/
;
9
/(
)
db
db
db
b
T
T
c
Kdb
T
Kdb
rad
V s
α
=
=
=
=
⋅ where
1 /
;
0,1 ;
/
;
9
/(
)
db
db
db
b
T
T
c
Kdb
T
Kdb
rad
V s
α
=
=
=
=
⋅ Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 365 Fig. 2.42. The mathematical model of servomechanism
Transfer function of the tacho-generator (Gane + Derivation)[2]
4( )
G
s
ks
=
,
0,03
/
. k
V s
rad
=
⋅ Fig. 2.42. The mathematical model of servomechanism Fig. 2.42. The mathematical model of servomechanism Transfer function of the tacho-generator (Gane + Derivation)[2] ansfer function of the tacho-generator (Gane + Derivation)[2] 4( )
G
s
ks
=
,
0,03
/
. 2.5 Servomechanism of synchronous and in-phase rotation shaft part of drive from
the alternating reference voltage
The mathematical model of servomechanism in an interactive system MATLAB is presented k
V s
rad
=
⋅ At adjustment of a fuzzy controller in interactive system MATLAB we use unit NCD
(Nonlinear Control Design) which implements a method of dynamic optimization for
designing of management systems. The system is researched at typical influences on an input: input: 1.single jump, 2.the
equivalent of a harmonic signal ( )
0,5sin 2
u t
Ft
π
=
with carrying frequency
0,1
F
Hz
=
and 3. a linear signal Ramp ( )
u t
t
= . Adjustment of a fuzzy controller is carried out by criterion of a minimum of a dynamic error
at the equivalent harmonic signal without influence of noise on a phase detector output
(contacts of switch are closed in the lower position). Receive the following optimal
parameters of fuzzy controller: Am=0,072; Bm=0,168; Cm=1,579; Dm=61,798. Processes in servomechanism (fig. 2.42 see) with a fuzzy controller without influence of
noise on a phase detector output (contacts of switch Manual Switch are closed in the lower
position) are shown on fig. 2.43 at an single jump of an input signal, on fig. 2.44 at influence
of the equivalent harmonic signal ( )
0,5sin 2
u t
F
π
=
, with carrying frequency
0,1
F
Hz
=
and
on fig. 2.45 at of the linear signal ( )
u t
t
= . In pictures ( )
u t – input influence, ( )
x t – a system
output, ( )
Err
e t ≡
– a mismatch error on a discriminator input,
( )
m t - a signal on an engine
input. At an single jump of an input signal transient phenomenon has overshoot of 13 % and ends
at time 2,8 (see fig. 2.43). The installed dynamic error is equal to zero. At action of a
harmonic signal the maximum dynamic error (except for the release initial at the moment of 366 MATLAB – A Ubiquitous Tool for the Practical Engineer signal capture) does not exceed 0,5% from amplitude of a sinusoid (see fig. 2.44). At action
of the linear signal ( )
u t
t
= transient phenomenon comes to an end in time, not exceeding 2c,
and the installed dynamic error is close to zero (approximately
4
2 10−
⋅
). Therefore the signal
output practically repeats input action (fig. 2.45 see). а)
а)
b)
b)
c)
c)
2.43. 2.5 Servomechanism of synchronous and in-phase rotation shaft part of drive from
the alternating reference voltage
The mathematical model of servomechanism in an interactive system MATLAB is presented Processes in servomechanis at an
le jump
Fig. 2.44. Processes in servomechanism at
the equivalent harmonic signal а)
а) а) b)
b) b) c)
c) Fig. 2.44. Processes in servomechanism at
the equivalent harmonic signal Fig. 2.43. Processes in servomechanis at an
single jump Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 367 а)
b)
c)
d)
Fig. 2.45. Processes in servomechanism at the linear action b)
d) b) а)
c) а) c) Fig. 2.45. Processes in servomechanism at the linear action Adjustment of a fuzzy controller by criterion of a minimum of a dynamic error at action of
noise on a phase detector output (contacts of switch Manual Switch are closed in the upper
position) is enough difficult. The noise signal n (t) - a stationary white noise (Band-Limited
White Noise) on a phase detector output (Discrim) is presented on fig. 2.46,a. Current value
of a root from root-mean-square of a noise signal (root mean squared value) calculated in
unit CRMS is shown at the fig. 2.46b Instead of fuzzy controller FC (Fuzzy Controller), is executed under the basic scheme, with
identical triangular functions of an accessory in the presence of a noise signal on an output
of the phase detector for obtaining of a smaller dynamic error in system it is expedient to
use fuzzy controller (Fuzzy Controller), fulfilled on the schematic circuit with identical
exponential membership functions. For the purpose of an exception (or the considerable
decrease) a dynamic error at tracking controlling action, on an output of a fuzzy controller
two integrators for giving to a closed circuit of follow-up system astaticism the second order
are included. At system adjustment, except selection of values of ranges Am, Bm, Cm, Dm and parameter
c of exponential membership functions in a fuzzy controller, it was required to optimize
coefficient k of the tacho-generator of an alternating current. At adjustment of a fuzzy
controller in interactive system MATLAB is used unit NCD (Nonlinear Control Design) and
received the following optimal parameters of system: MATLAB – A Ubiquitous Tool for the Practical Engineer 368 а)
b)
Fig. 2.46. Noise signal
а)
а)
b)
b)
c)
c)
Fig. 2.47. Processes in system at the unit step
Fig. 2.48. Processes in system at the
equivalent harmonic signal а)
b) Fig. 2.46. Noise signal а) а)
b) а)
b) b) c) c) )
Fig. 2.48. Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB The signal output practically
repeats input action (fig. 2.49 see). At action of the linear signal ( )
u t
t
= transient phenomenon ends at time, not exceeding 1,2
s, and the installed dynamic error does not exceed
3
8 10−
⋅
. The signal output practically
repeats input action (fig. 2.49 see). а)
b)
c)
Fig. 2.49. Processes in system at the linear action
3. References
[1] Klepper Dzh., Frenk Dzh. A phase-and frequency-locked frequency. - M.: Energiya, 1977. - 440 s. b) а)
b) b) а)
c) Fig. 2.49. Processes in system at the linear action Research of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB esearch of Fuzzy-Systems of Automatic Frequency and Phase Control on Basis of MATLAB 369 h=0,01; Am=3,9822; Bm=8,6779; Cm=86,357; Dm=116.,64; c=0,19476; m=3,9822; Bm=8,6779; Cm=86,357; Dm=116.,64; c=0,19476; a=12,5;a1=100;K=500; alf=90;b=10;k=1,2865. a=12,5;a1=100;K=500; alf=90;b=10;k=1,2865. Processes in servomechanism (fig. 2.42 see) with a fuzzy controller at influence of noise on a
phase detector output (contacts of switch Manual Switch are closed in the upper position)
are shown on fig. 2.47 at an unit step of an input signal, on fig. 2.48 at action of the
equivalent harmonic signal ( )
0,5sin 2
u t
F
π
=
, with carrying frequency
0,1
F
Hz
=
and on fig. 2.49 at action of the linear signal
( )
u t
t
= . In figure
( )
u t – an input action, ( )
x t – a system
output, ( )
Err
e t ≡
– a mismatch error on input of a discriminator,
( )
m t - a signal on an input
of engine. At an single jump of an input signal transient phenomenon has overshoot of 16% and comes
to an end during 0,93 s (fig. 2.47 see). The installed dynamic error is equal to zero. At action
of a harmonic signal the maximum dynamic error (except for initial burst at the moment of
signal capture) does not exceed 1,5% from amplitude of a sinusoid (fig. 2.48 see). At action of the linear signal ( )
u t
t
= transient phenomenon ends at time, not exceeding 1,2
s, and the installed dynamic error does not exceed
3
8 10−
⋅
. The signal output practically
repeats input action (fig. 2.49 see). At an single jump of an input signal transient phenomenon has overshoot of 16% and comes
to an end during 0,93 s (fig. 2.47 see). The installed dynamic error is equal to zero. At action
of a harmonic signal the maximum dynamic error (except for initial burst at the moment of
signal capture) does not exceed 1,5% from amplitude of a sinusoid (fig. 2.48 see). of a harmonic signal the maximum dynamic error (except for initial burst at the moment of
signal capture) does not exceed 1,5% from amplitude of a sinusoid (fig. 2.48 see). At action of the linear signal ( )
u t
t
= transient phenomenon ends at time, not exceeding 1,2
s, and the installed dynamic error does not exceed
3
8 10−
⋅
. 2.5 Servomechanism of synchronous and in-phase rotation shaft part of drive from
the alternating reference voltage
The mathematical model of servomechanism in an interactive system MATLAB is presented Processes in system at the
equivalent harmonic signal )
Fig. 2.47. Processes in system at the unit step )
Fig. 2.47. Processes in system at the unit step 3. References [1] Klepper Dzh., Frenk Dzh. A phase-and frequency-locked frequency. - M.: Energiya, 1977. - 440 s. [1] Klepper Dzh., Frenk Dzh. A phase-and frequency-locked frequency. - M.: Energiya, 1977. - 440 s. [1] Klepper Dzh., Frenk Dzh. A phase-and frequency-locked frequency. - M.: Energiya, 1977. - 440 s. 370 MATLAB – A Ubiquitous Tool for the Practical Engineer [2] Gostev V.I., Skurtov S.N. Fuzzy systems frequency and phase auto-tuning: monograph. -
Nezhin: OOO "Vidavnictvo -Aspekt-Poligraf", 2010. 388 p. g
[3] Gostev V.I. Fuzzy-system phase-locked loop oscillator // Zviyazok. - 2008. - № 4. [ ]
h k
h
l
k
h
d
l f [4] Gostev V.I., Baranov A.A. Storchak K.P. The system clock with a digital fuzzy controller
// Zviyazok. - 2007. - № 3 (71). - S.51-54. [5] Gostev V.I., Kunah N.I., Drobik A.V., Nevol'ko V.A. Investigation of processes in the
systems and phase locked loop in the presence of internal noise // Naukovi zapiski
Ukrains'kogo naukovo-doslidnogo institutu zvyazku. Naukovo-virobnichii zbirnik. - 2008. - №6(8). p. 51-54 [6] Gostev V.I., Krihoveckii G.Ya., Storchak K.P. The system clock with a digital PID
controller with random phase changes of the input // Visnik Derzhavnogo
universitetu Informacyino-komunikacyinih tehnologyi. - 2007.- Spec. vip., p. 72-75 y
y
gy
p
p p
[7] Vagapov V.B., Burlyai I.Yu., Ryumshin N.A. Theory of electronic tracking systems. - K.:
Tehnika, 2002. - 284 p. [8] Gostev V.I. Fuzzy-system phase-locked loop oscillator with a digital phase detector //
Zviyazok. - 2008. - № 5-6 (81-82). - p. 68-72. 18 Automotive Sketch Processing in C++
with MATLAB Graphic Library Qiang Li
Jilin University
P. R. China 1. Introduction The purpose of automotive sketch processing is to separate the sketch into patches and
extract the useful information and apply it to assist 2D to 3D transformation. How to extract
the useful information depends on what the resources are, what kinds of information are
needed, and what methods are applied. In sketches, the information may be extracted from
features such as the geometry features, shading, colours and lighting. Geometry features are
the most important because they contain the information to identify and distinguish
between forms. For example, edges can be used to determine the shapes, and areas can be
used to match the size. This chapter introduces a way to make the automotive sketches ready for 2D to 3D
transformation. Three aspects of problems are discussed including the pre-processing of
sketches outside computer, the processing of pre-processed sketches inside computer, and
the extraction of features. Some of sketch processing algorithms are implemented in C++
using the MATLAB image processing toolbox, Graphic Library and Math Library. Some
have been developed from scratch. The work describe in this chapter is concerned with the
production of a feasible routine, from the point of view of application, which is capable of
dealing with the real world characteristics of automotive sketches. There is no established
method which provides a suitable starting point for the transformation of real automotive
sketches. The combined algorithms, which are discussed in this chapter, have been found to
be useful. 2.2 Multiple working modes The system needs to deal with 2D sketches and 3D surface models, and
transformationfrom 2D to 3D as well. Therefore, the working modes should be easily
exchanged between 2D and 3D. In the system, the multiple working modes have been
implemented for 2D and 3D manipulations. It is easy to switch the modes, see Fig. 1. 2D
sketch is considered as the background in 3D space. Therefore, the 2D working mode is
that the background plane containing the sketch is displayed without the 3D models, see
Fig. 1a; the 3D working mode is that the 3D models are displayed without the
background, see Fig. 1b; and the mixed working mode is that both the 3D models and the
2D background are displayed at the same time, see Fig. 1c. The 2D sketch background is
not affected by any 3D manipulations. c. 23D mode a. 2D mode b. 3D mode c. 23D mode
Fig. 1. Three working modes b. 3D mode c. 23D mode Fig. 1. Three working modes Fig. 1. Three working modes 2.1 The development environment 2.1 The development environment
The main development language is Microsoft Visual C++® (Ladd, 1996; Seed, 1996; Smith,
1997; Schildt, 1998) with OpenGL® (Kilgard, 1996; Wright & Sweet, 1996; Fosner, 1997;
Silverio et al., 1997; Chin et al., 1998; Segal & Akeley, 2001), MATLAB® C/C++ Math and
Graphics Libraries (MathWorks, 2001). The basic functions and some algorithms are
implemented based on the Open Geometry (Glaeser & Stachel, 1999), MATLAB
optimisation toolbox (MathWorks, 2000), spline toolbox, and image processing toolbox
(MathWorks, 2001), Image Analysis Pro (IaePro) (Matthews, 2002) and Microsoft VisSDK
(The Vision Technology Group, 2000). 2. A glimpse of the 23D system A brief set of requirements, from a usability point of view, for 2D to 3D tool can be
summaried as follow: •
Can deal with 2D sketches and 3D models. •
Can deal with 2D sketches and 3D models. •
Intuitive, simplified and robust. •
Flexible and expandable. mpatible with other CAD and CAM systems •
Compatible with other CAD and CAM systems. •
Compatible with other CAD and CAM systems. Co
pat b e
t
ot e C
a d C M syste
s. Following the above requirements, a prototype of 2D to 3D system, called “23D”, has been
implemented to support the novel method of transforming 2D automotive sketches quickly
into 3D surface models. p
y
Following the above requirements, a prototype of 2D to 3D system, called “23D”, has been
implemented to support the novel method of transforming 2D automotive sketches quickly
into 3D surface models. MATLAB – A Ubiquitous Tool for the Practical Engineer 372 3. The pre-processing of a sketch The sketches are not realistic images. The forms and shadings may contain many
inconsistencies compared with a true projection of a possible real object. In addition, the
reverse transformations from 2D to 3D are rather complicated and contain possible
ambiguities, in that a 2D shape may represent many possible shapes in 3D. Therefore, some
assumptions have to be made in order to simplify the problem. The fundamental
assumptions made here include: p
•
The scanned sketches will be pre-processed to reduce the inconsistencies in them. The
end result of the pre-processing will be that boundaries are complete and are all closed
contours or silhouettes. Any key lines will be clear and without ambiguities so as to
give enough information for further processing. With these conditions satisfied, the
sketch can be separated into patches which can be represented by parametric models. 373 Automotive Sketch Processing in C++ with MATLAB Graphic Library •
Shadings of sketches may be ignored initially, since many techniques of the
representations in sketches are not realistic and exact. To derive meaning from them
requires psychological interpretation of the intention of the designer, which is beyond
the scope of this project. •
Shadings of sketches may be ignored initially, since many techniques of the
representations in sketches are not realistic and exact. To derive meaning from them
requires psychological interpretation of the intention of the designer, which is beyond
the scope of this project. •
Any side, front, rear or top view of automotive model in the sketches is considered to be
orthographic projection, others such as front or rear ¾ perspective views are considered
to be perspective projection. •
Any side, front, rear or top view of automotive model in the sketches is considered to be
orthographic projection, others such as front or rear ¾ perspective views are considered
to be perspective projection. •
Minor details are ignored and allowing concentration on the major ones which establish
the essential 3D geometry. It is possible that these could be restored after the basic form
has been determined, perhaps using parts from a parts library. •
Minor details are ignored and allowing concentration on the major ones which establish
the essential 3D geometry. It is possible that these could be restored after the basic form
has been determined, perhaps using parts from a parts library. 3. The pre-processing of a sketch •
There is a limit to the exaggeration of forms in a sketch that can be used. Designers
often do use exaggerated geometry to achieve a desired mood. If translated into 3-D,
the resultant model will also contain exaggerated geometry. •
No attempt is made to correct ambiguities of the reverse transformation automatically. These functions are best left for user intervention. The user is likely to be the stylist,
who is in a good position to judge which of a number of possibilities best represents the
intended vehicle. As known, not all the sketches are suitable for 3D modelling by the 23D system, but many
do contain the required characteristics. There are many different styles in automotive
sketching, according to the stylist’s personal practice. The information contained varies at
the different conceptual design stages, and is not exactly correct in geometry shape and
projection, because the sketches are not real-world images. Humans can easily interpret the
shape through adding additional information, in the form of prior knowledge of automotive
forms to the sketches and ignoring the faults according to this knowledge. However, the
computer is not as agile as the human. It must have available enough information to create
the shape, which can come from various sources. One approach is to establish a powerful
knowledge database to support the object recognition; another approach is to add the
information before image processing. The former needs larger investment and longer time
to train the computer, and the later needs less investment and is easy to realize. Two
examples of the use of an original sketch as a basis for two well established edge detection
algorithms are shown in Fig. 2c and 2d. The results show that they are difficult to be
interpreted, even by a human. If the results are to be interpretable by a computer program,
significantly more sophisticated processing will be required. Therefore, it is necessary and
feasible to establish some input requirements for the sketches that will be used for 3D
modelling by the method proposed in 23D system, and will form the requirements for the
pre-processing stage. The requirements are relative. The more powerful the pre-processing
method is, the lower the requirements for the interpretive program are. The original
sketches are drawn by stylist, as shown in Fig. 2a and 2e. The results after pre-processing are
shown in Fig. 2b and 2f. 3. The pre-processing of a sketch The aim of the pre-processing of sketches is to allow the requirements for the interpretive
program to be met by a greater variety of original sketches. Essentially, the pre-processing
emphasises useful features in the sketches and eliminates useless ones. According to the
analysis of Tingyong Pan (Pan, 2002), the form-lines and form-shadings should be enhanced
and kept, and the non-form-lines and non-form-shadings should be ignored. The vehicle
components should be simplified in details and ambiguities removed. One of the important 374 MATLAB – A Ubiquitous Tool for the Practical Engineer requirements is that the input sketches should have completed and closed contours or
silhouettes. Any key form-lines should be clear to give enough information to the further
processing. For example, the original sketches (Fig. 2a and 2e) leave some missing and
unclear contours or silhouettes to give an imaginary space. These should be redrawn by
stylists, see the sketches in Fig. 2b and 2f. All the silhouettes are closed and clear. Some
details are ignored such as small lights, highlights, and shadings. The shading information
can be separated from the contour or silhouette information. If the shading information is
important and near realistic, and is within the closed contours, it can be kept. Otherwise, it
should be ignored or further processed to a suitable form. The shadows of the vehicles are
deleted, and the completed silhouettes of wheels are added, which are very important for
the determination of the 3D coordinates. Side elevations, front and rear ¾ perspective views
are the best starting point for system processing. a. The original sketch b. The pre-processed sketch
(Both sketches by courtesy of Tingyong Pan)
c. Canny method d. Sobel method
e. Canny method f. Sobel method
(Both sketches by courtesy of Tingyong Pan)
Fig. 2. The pre-processing of the sketch a. The original sketch b. The pre-processed sketch
(Both sketches by courtesy of Tingyong Pan) a. The original sketch b. The pre-processed sketch
(Both sketches by courtesy of Tingyong Pan) b. The pre-processed sketch b. The pre-processed sketch a. The original sketch (Both sketches by courtesy of Tingyong Pan) (Both sketches by courtesy of Tingyong Pan) (
y
y
gy
g
)
c. Canny method d. Sobel method d. Sobel method d. Sobel method c. Canny method e. Canny method f. Sobel method
(Both sketches by courtesy of Tingyong Pan) f. Sobel method e. Canny method
(Both ske Fig. 2. 3. The pre-processing of a sketch The pre-processing of the sketch Fig. 2. The pre-processing of the sketch Fig. 2. The pre-processing of the sketch 375 Automotive Sketch Processing in C++ with MATLAB Graphic Library It is also important to produce pre-processed sketches with simple patches, which can be
represented using existing parametric models. It is also important to produce pre-processed sketches with simple patches, which can be
represented using existing parametric models. Because the features extracted from sketches are currently pixel-based in order to keep the
balance between the speed of processing and the precision of calculation, the suitable size of It is also important to produce pre-processed sketches with simple patches, which can be
represented using existing parametric models. Because the features extracted from sketches are currently pixel-based in order to keep the
balance between the speed of processing and the precision of calculation, the suitable size of
input sketches should be carefully considered. 4. Sketch processing Even though the sketches have been pre-processed before scanning, they also need to be
subject to further image processing before transforming them into 3D. Some basic functions
- such as the adjustment of lightness, hue, and saturation, the exchange from colour to grey
scale and B&W, the erasure of unnecessary areas in the sketch, the separation of form from
non-form line and shading - are used before edge detection and segmentation. To decrease
the size of the dataset and smooth the boundaries, B-spline or NURBS curve fitting to the
outlines are applied. These form-lines are disassembled into spline segments and are used to
build up the patches, which represent the whole surface model. The original sketches (if applicable) or pre-processed sketches still need to be processed
further in order to obtain a sketch with single pixel edges and closed boundaries, and this
sketch is separated into patches for the downstream processes. Therefore, it is necessary to
investigate a set of efficient image processing algorithms for this application. 4.1 Image mode selection There are many modes for the different purposes of raster image processing including
colour and non-colour ones. Some typical colour modes such as RGB (red, green and blue),
HSV (hue, saturation and value), HLS (hue, lightness and saturation), and CYMK (cyan,
yellow, magenta and black) have been described in the books (Foley et al., 1996; Salomon,
1999). The Adobe Photoshop 6.0 supports colour modes such as RGB, CYMK, Lab (lightness,
green-red axis and blue-yellow axis), Indexed Colour, and HSB (hue, saturation and
brightness), and non-colour modes such as Greyscale, Multi-channel, Bitmap and Duotone. There are four modes for image displaying and processing supported by the 23D system:
RGB colour, 256 greyscale, 16 greyscale, and black and white (B&W). The internal format is
RGBA colour; therefore the modes can be changed reversibly. The algorithms of greyscale
are different. For example, the Image Analysis Explorer Pro (IaePro) supports three methods
to obtain a greyscale as follows. 0.2125
0.7154
0.0721
Greyscale BT709
0.299
0.587
0.114
Greyscale Y
0.5
0.419
0.081
Greyscale RMY
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
R
G
B
A
R
G
B
R
G
B
⎧
+
+
⎪⎪
=
+
+
⎨
⎪
+
+
⎪⎩
(1) (1) However, for simplification, the transformation from RGB to 256 greyscale used here is an
average algorithm of the colour RGB values (Jain, 1995, pp. 281). 0,
,
_
1
0,
,
_
1
1
1
(
)
3
i
BmpBgr
w
ij
ij
ij
ij
j
BmpBgr
h
A
R
G
B
=
−
=
−
=
+
+
"
"
(2) (2) 376 MATLAB – A Ubiquitous Tool for the Practical Engineer Where
1ij
A
is the greyscale value of a point in image including three components
ij
R ,
ij
G
and
ij
B ; BmpBgr_w and BmpBgr_h are the width and the height of sketch in pixels,
respectively. In B&W mode, the two levels are obtained from a point between 0 and 255
to bisect the whole range. A similar function is used in Adobe Photoshop 6.0 (Adobe,
2000). 4.1 Image mode selection 0,
,
_
1
0,
,
_
1
0
1
0
0
2
1
255
1
255
ij
L
i
BmpBgr
w
ij
L
ij
j
BmpBgr
h
A
D
A
D
A
=
−
=
−
≤
<
⎡⎤
⎡
⎤
=
=
⎢⎥
⎢
⎥
≤
≤
⎣⎦
⎣
⎦
"
"
(3) (3) Where
2ij
A
is determined by
1ij
A
, and
L
D is a threshold to determine a dividing level. The
default of
L
D is 192, and can be adjusted. The change from 256 greyscale to 16 greyscale is
obtained according to the average rule. A coding scheme proposed in 23D system is that the
values of 16 intervals are increased through adding the value 17 for smoothness and
keeping it spanning to the two ends (0 and 255). p
g
p
g
(
)
n example is shown in Fig. 3 for the four modes of processing allowed by the system. a. RGB colour
b. 256 greyscale
c. 16 greyscale d. B&W with a threshold of 192
(Colour sketch by courtesy of geocities.com)
Fig. 3. The four display modes of the system a. RGB colour
b. 256 greyscale a. RGB colour a. RGB colour b. 256 greyscale b. 256 greyscale b. 256 greyscale a. RGB colour c. 16 greyscale d. B&W with a threshold of 192
(Colour sketch by courtesy of geocities.com)
Fig 3 The four display modes of the system c. 16 greyscale d. B&W with a threshold of 192 (Colour sketch by courtesy of geocities.com) (Colour sketch by courtesy of geocities.com) Fig. 3. The four display modes of the system Fig. 3. 4.1 Image mode selection The four display modes of the system Automotive Sketch Processing in C++ with MATLAB Graphic Library 377 0,
,
_
1
0,
,
_
1
0
0
1
17
2
34
3
51
4
68
5
85
6
102
7
119
3
8
136
9
153
10
170
11
187
12
204
13
221
14
238
15
255
i
BmpBgr
w
ij
j
BmpBgr
h
A
=
−
=
−
⎡
⎤
⎡
⎤
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
=
=
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎢
⎥
⎢
⎢
⎥
⎢
⎢
⎥
⎢
⎢
⎥
⎢
⎣
⎦
⎣
⎦
"
"
0
1
16
16
1
32
32
1
48
48
1
64
64
1
80
80
1
96
96
1
112
112
1
128
128
1
144
144
1
160
160
1
176
176
1
192
192
1
208
208
1
224
224
1
240
240
1
255
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
ij
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
≤
<
⎥
⎥
≤
<
⎥
⎥
≤
<
⎥
≤
≤
(4) (4) 4.2 Brightness and contrast adjustment 4.2 Brightness and contrast adjustment
h
d
f b
h
d 4.2 Brightness and contrast adjustment 0
1
1
1
0
0
0
2
1
0
0
2
2
2
0
0
0.5
/
[
(
/
)(100
)]
255;
0.5(
),
0.5(
)
where
0.5
/
(255
)
0;
c
h
x
dy
k
y
t
k
tg arctg dy
dx
f
h
t
y
y
t
x
h
l y
t
b
l
x
dy
k
y
b
y
y
k
x
l
b
y
y
b
y
y
kx
=
+
≥
=
+
⎧
⎧
⎪
⎪
=
=
<
=
+
=
+
⎪
⎪
⎨
⎨
=
−
≤
=
+
−
⎪
⎪
⎪
⎪
=
=
>
=
−
⎩
⎩
(8) 0
1
1
1
0
0
0
2
1
0
0
2
2
2
0
0
0.5
/
[
(
/
)(100
)]
255;
0.5(
),
0.5(
)
where
0.5
/
(255
)
0;
c
h
x
dy
k
y
t
k
tg arctg dy
dx
f
h
t
y
y
t
x
h
l y
t
b
l
x
dy
k
y
b
y
y
k
x
l
b
y
y
b
y
y
kx
=
+
≥
=
+
⎧
⎧
⎪
⎪
=
=
<
=
+
=
+
⎪
⎪
⎨
⎨
=
−
≤
=
+
−
⎪
⎪
⎪
⎪
=
=
>
=
−
⎩
⎩
(8) (8) The Gamma value fγ is adjusted according to the original value
0
fγ as follow. The Gamma value fγ is adjusted according to the original value
0
fγ as follow. (
)
1.2
0 /5
[1,10]
f
f
f
γ
γ
γ
=
∈
(9) (
)
1.2
0 /5
[1,10]
f
f
f
γ
γ
γ
=
∈
(9) (9) Therefore, the RGB values of each pixel can be calculated as follow. Therefore, the RGB values of each pixel can be calculated as follow. 4.2 Brightness and contrast adjustment (
)
(
)
(
)
(
)/(
)
(
)/(
)
(
)/(
)
(
)
0,
,
_
1
(
)
0,
,
_
1
(
)
ij
ij
ij
R
l
h l
ij
G
l
h l
ij
B
l
h l
ij
b
t
b C
R
i
BmpBgr
w
G
b
t
b C
j
BmpBgr
h
B
b
t
b C
γ
γ
γ
−
−
−
−
−
−
⎡
⎤
+
−
⎡
⎤
⎢
⎥
⎢
⎥
=
−
⎢
⎥
=
+
−
⎢
⎥
⎢
⎥
=
−
⎢
⎥
⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
+
−
⎣
⎦
"
"
(10) (10) The dialog window and examples are shown in Fig. 4. The range of the sliders is 100
±
. 4.2 Brightness and contrast adjustment The adjustments of brightness and contrast supply the basic means of image enhancement,
which compensate for the losses caused by imperfect scanning methods. The algorithm from
MATLAB (MathWorks, 2001) imadjust function was used to control the values of RGB
components directly. The brightness
bf can be adjusted as follows. }
}
0
0
0
0
0
0
(255
) /100
0
(255
)/100
[0,255]
/100
0
/100
b
b
b
b
b
b
b
b
f
b
t
b
f
f
t
t
b
f
f
f t
t
b
f
f b
t
b
−
≥
⎧
≥
⎪
−
<
⎪
=
∈
⎨
≥
⎪
<
⎪
<
⎩
(5) (5) Where
0
bf
is the original value of brightness; t and b are the top and the bottom values of
brightness. They are adjusted by
bf ,
b
t
t
f
=
+
and
b
b
b
f
=
+
; h and l are the highest and the
lowest values among the values of RGB. The differences are defined as dx
h
l
=
−, dy
t
b
=
−
. They are limited within 0~255. Where
0
bf
is the original value of brightness; t and b are the top and the bottom values of
brightness. They are adjusted by
bf ,
b
t
t
f
=
+
and
b
b
b
f
=
+
; h and l are the highest and the
lowest values among the values of RGB. The differences are defined as dx
h
l
=
−, dy
t
b
=
−
. They are limited within 0~255. 4.2 Brightness and contrast adjustment (255
)
/
,
255
255
/
,
0
0
/
,
0
0
(
255)
/
,
255
255
h
l
b dx
dy t
t
h
l
bdx
dy t
t
l
h
tdx
dy b
b
l
h
t
dx
dy b
b
= +
−
=
>
⎧
⎪
= −
=
<
⎪⎨=
−
=
<
⎪
⎪=
−
−
=
>
⎩
(6) (6) If the original value
0
0
cf
≥
, the contrast
cf can be adjusted as If the original value
0
0
cf
≥
, the contrast
cf can be adjusted as the original value
0
0
cf
≥
, the contrast
cf can be adjusted as MATLAB – A Ubiquitous Tool for the Practical Engineer 378 MATLAB – A Ubiquitous Tool for the Practical Engineer 0
/200
[0,255]
c
c
c
f
f dx
f
=
∈
(7) (7) Then h and l should be adjusted as
c
h
h
f
=
−
and
c
l
l
f
= +
. Otherwise, the image is not
enhanced. The boundaries should be adjusted again. 4.3 Edge detection Many algorithms for edge detection have been developed for different image resources. Because the sketches are not the real-world images and can be pre-processed before
imported into the system, the edge detection is just a simple routine to quickly find the
necessary points for the further processing. Therefore some basic and common algorithms
are implemented into the system including Sobel, Prewitt, Roberts, Canny, Zerocross, Direct
and Sobel+. The system was built using the MATLAB C++ Math Library and the Graphics
Library (MathWorks, 2000). The dialog window is shown in Fig.5, which is similar to the
MATLAB find edges function. Some examples are shown in Fig. 6 and Fig. 7. In most cases, the algorithms from the
MATLAB edge functions can give good results for original sketches, shown in Fig. 6. However, they give poor results on pre-processed sketches, shown in Fig. 7b and Fig. 7d. The pre-processed sketches are composed of sets of dense and thick strokes coming from a
quick expression of the edges according to the original sketches. Therefore, a hybrid
algorithm, Direct, is proposed to deal with such styled sketches. The idea comes from a demo – Region Labelling of Steel Grains – in the MATLAB image
processing toolbox. Two binary images are obtained from pre-processed sketches by using
low and high thresholds. The edge points from low threshold image are used to delete the
same points from high threshold image. The left edge points from the high threshold image
are considered as the edges. In this way minor regions caused by strokes are deleted. The
result is shown in Fig. 7c produce from a thick edge image. Automotive Sketch Processing in C++ with MATLAB Graphic Library 379 a. Original Sketch b. fb = -33%
c. fc = 45%
d. fb = 34%, fc = -50%
e. fγ = 25%
f. The dialog window designed
Fig. 4. The samples of the brightness and contrast adjustment a. Original Sketch b. fb = -33% a. Original Sketch b. fb = -33% d. fb = 34%, fc = -50% c. fc = 45% d. fb = 34%, fc = -50% c. fc = 45% e. fγ = 25%
f. The dialog window designed
Fig. 4. The samples of the brightness and contrast adjustment f. The dialog window designed e. fγ = 25% e. fγ = 25% f. The dialog window designed Fig. 4. 4.3 Edge detection The samples of the brightness and contrast adjustment Fig. 5. The dialog window of Find Edges function Fig. 5. The dialog window of Find Edges function MATLAB – A Ubiquitous Tool for the Practical Engineer 380 MATLAB A Ubiquitous Tool for the Practical Engineer
380
a. Original sketch b. Sobel algorithm, threshold = 0.13
c. Canny algorithm, threshold = 0.15-1.0 d. LoG algorithm, threshold = 0.007
(Original sketch by courtesy of Cor Steenstra, Foresee Car Design)
Fig. 6. Edge detection of the original colour sketch with the different algorithms
a. Pre-processing sketch b. Roberts algorithm, threshold = 0.1
c. Hybrid algorithm d. Sobel+ algorithm
Fig. 7. Edge detection of the pre-processed sketch a. Original sketch b. Sobel algorithm, threshold = 0.13
c. Canny algorithm, threshold = 0.15-1.0 d. LoG algorithm, threshold = 0.007
(Original sketch by courtesy of Cor Steenstra, Foresee Car Design)
Fig. 6. Edge detection of the original colour sketch with the different algorithms b. Sobel algorithm, threshold = 0.13 c. Canny algorithm, threshold = 0.15-1.0 d. LoG algorithm, threshold = 0.007
(Original sketch by courtesy of Cor Steenstra, Foresee Car Design)
Fig. 6. Edge detection of the original colour sketch with the different algorithms ny algorithm, threshold = 0.15-1.0 d. LoG algorithm, threshold = 0.007
(Original sketch by courtesy of Cor Steenstra, Foresee Car Design)
e detection of the original colour sketch with the different algorithms c. Canny algorithm, threshold = 0.15-1.0 y
g
,
g
,
(Original sketch by courtesy of Cor Steenstra, Foresee Car Design)
dge detection of the original colour sketch with the different algorithms (Original sketch by courtesy of Cor Steenstra, Foresee Car Design) (Original sketch by courtesy of Cor Steenstra, Foresee Car Design)
Fig. 6. Edge detection of the original colour sketch with the different algorithms (
g
y
y
g )
Fig. 6. Edge detection of the original colour sketch with the different algorithms a. Pre-processing sketch b. Roberts algorithm, threshold = 0.1
c. Hybrid algorithm d. Sobel+ algorithm
Fig. 7. Edge detection of the pre-processed sketch a. Pre-processing sketch b. Roberts algorithm, threshold = 0.1 a. Pre-processing sketch b. Roberts algorithm, threshold = 0.1 c. Hybrid algorithm d. Sobel+ algorithm
Fig. 7. Edge detection of the pre-processed sketch c. Hybrid algorithm d. Sobel+ algorithm Fig. 7. Edge detection of the pre-processed sketch Fig. 7. 4.4 Edge morphing Edge morphing can further refine the image obtained from edge detection. This function is
implemented using the MATLAB bwmorph function including the method Bothat, Bridge,
Clean, Close, Diag, Dilate, Erode, Fill, Hbreak, Majority, Open, Remove, Shrink, Skel, Spur,
Thicken, Thin and Tophat, as shown in Fig. 8. It can apply specific morphological operations
to the binary image. Repeated application of these operations may be necessary. Infinite
means that Times are determined by the methods automatically. Fig. 8. The dialog window of Edge Morphing function Fig. 8. The dialog window of Edge Morphing function
a. Thin operation (Times = 7)
b. Debubble algorithm
Fig. 9. Edge thins and debubbles (Please refer to Fig. 7c)
When the edges are not single pixels such as the ones shown in Fig. 7c, edge morphing
should be applied. The result after the seven applications of the thin operation is shown in
Fig. 9a. The edges become the single pixels, but with some small holes and spurs. This is stil
not a satisfactory starting point for the transformation. The bubbles and spurs must be
eliminated. Fig. 8. The dialog window of Edge Morphing function a. Thin operation (Times = 7)
b. Debubble algorithm
Fig. 9. Edge thins and debubbles (Please refer to Fig. 7c) a. Thin operation (Times = 7) b. Debubble algorithm a. Thin operation (Times = 7) a. Thin operation (Times = 7) b. Debubble algorithm Fig. 9. Edge thins and debubbles (Please refer to Fig. 7c) Fig. 9. Edge thins and debubbles (Please refer to Fig. 7c) When the edges are not single pixels such as the ones shown in Fig. 7c, edge morphing
should be applied. The result after the seven applications of the thin operation is shown in
Fig. 9a. The edges become the single pixels, but with some small holes and spurs. This is still
not a satisfactory starting point for the transformation. The bubbles and spurs must be
eliminated. When the edges are not single pixels such as the ones shown in Fig. 7c, edge morphing
should be applied. The result after the seven applications of the thin operation is shown in
Fig. 9a. The edges become the single pixels, but with some small holes and spurs. This is still
not a satisfactory starting point for the transformation. The bubbles and spurs must be
eliminated. 4.3 Edge detection Edge detection of the pre-processed sketch 381 Automotive Sketch Processing in C++ with MATLAB Graphic Library To obtain a satisfactory result, it is crucial to select a suitable threshold for edge detection. However, some problems are still left such as thick edges, double edges and broken edges
which cause unclosed boundaries, and small ‘spurs’ or ‘prickles’. Therefore, further
processing is needed to eliminate these problems. 4.5 Debubble – a hybrid algorithm It has not proved to be possible to obtain the required result using a single method. Different hybrid methods have been applied to achieve a good result. Here is a hybrid
algorithm proposed in this research to perform an operation of deleting the small holes and
spurs, such as shown in Fig. 9a. The algorithm entitled Debubble, shown in Fig. 10, applies 382 MATLAB – A Ubiquitous Tool for the Practical Engineer firstly the Bwlabel algorithm in MATLAB to find the small bubbles (holes), which are
determined by the bubble size parameter. Once the small bubbles are found, they are filled
into solid areas. Then the Skel and Spur algorithms are applied to obtain the single pixel
edges. The actual bubble size is the percentage of the maximum size in pixels, which is
compared with the image size in pixels. For example, to obtain the result in Fig. 9b, the
actual bubble size is 165, and the image size is 524288 (1024×512). This is just 0.0315% of the
image size – very small bubbles! In this case, all the bubbles those are smaller than 165 are
deleted. The result shown in Fig. 9b is quite acceptable. Using the Direct, Thin, and Debubble
algorithms for the pre-processed sketches can give a good result. Fig. 10. The dialog window of Debubble function Fig. 10. The dialog window of Debubble function 4.6 Edge refinement Once satisfactory edges are obtained, the image is ready for segmentation. However, there
are still anomalies that must be handled. For example, see the case in Fig. 11a, the crossing
point of the three patches is not unique. This produces three crossing points. In order to
delete this small error, the edge points must be checked and refined. a. Crossing points are not unique
b. Unique crossing point
Fi
11 C
i
i t
hi An algorithm is proposed here to perform this operation. It is described as follow: •
Every point is checked in the whole image. •
If it is an edge point, a counter is set with initial value of zero. The point is the current
point. •
The eight neighbours of the current point are checked one by one from 0 to 7, see Fig. 12a •
If it is an edge point, a counter is set with initial value of zero. The point is the current
point. •
The eight neighbours of the current point are checked one by one from 0 to 7, see Fig. 12a. e eight neighbours of the current point are checked one by one from 0 to 7, see Fig. . •
Once a neighbour point is edge point, the counter is increased by one. •
The current neighbour point is anomaly point, once the counter reaches three within the
eight neighbours. Automotive Sketch Processing in C++ with MATLAB Graphic Library 383 •
The last current neighbour is deleted. 3
2
1
5
1
4
4
●
0
a
2
●
0
b
5
6
7
6
3
7
Fig. 12. Eight-neighbour graph •
The last current neighbour is deleted. •
The last current neighbour is deleted. 3
2
1
5
1
4
4
●
0
a
2
●
0
b
5
6
7
6
3
7
Fig. 12. Eight-neighbour graph •
The last current neighbour is deleted. Fig. 12. Eight-neighbour graph The result is shown in Fig. 11b. Now the three patches share the same single pixel
boundaries and have a unique crossing point. 4.8 Curve fitting After the segmentation, the sketch is separated into small patches with zigzag boundaries. In most cases, the shape does not vary largely compared with the original sketch. However,
at some corners which contain crossing points, the shape may look strange. The use of spline
curve fitting can smooth the zigzag boundaries and provide modification of the shapes if
necessary. The patches are selected by the user, shown in Fig. 15b, for performing the curve fitting. The
basic functions are implemented from the MATLAB Splinetool function in the spline toolbox
[THEM01c]. The similar dialog window, as shown in Fig. 16, was designed. An example is
given to demonstrate the curve fitting process, shown in Fig. 15 (refer to the area in Fig. 7c). Comparing the areas from Fig. 15a and Fig. 15d, the boundary of the light is smooth and its
shape has been improved. a. The original boundary of the patch 16 b. Select the points around the boundary
c. Curve fitting using the points d. The closed spline
Fig. 15. The curve-fitting and shape modification
5. Feature extraction
The features include the point, curve and patch features extracted from the sketch, which
are put into a data structure. b. Select the points around the boundary a. The original boundary of the patch 16 a. The original boundary of the patch 16 b. Select the points around the boundary d. The closed spline c. Curve fitting using the points d. The closed spline
Fig. 15. The curve-fitting and shape modification c. Curve fitting using the points c. Curve fitting using the points d. The closed spline Fig. 15. The curve-fitting and shape modification Fig. 15. The curve-fitting and shape modification 4.7 Patch segmentation with colours It is easy to separate an image with closed boundaries into patches by applying the
MATLAB Bwlabel function, and it can then be displayed with the different colour maps. The
Pseudo Colormap includes Autumn, Bone, Colorcube, Cool, Copper, Flag, Gray, Hot, HSV, Jet,
Lines, Pink, Prism, Spring, Summer, White and Winter, as shown in Fig. 13. The label 0 is
assigned to the boundaries between the patches. Label 1 is assigned to the background and
used as the silhouette of the whole vehicle. From label 2 onwards, they are assigned to the
patches which form the surfaces of the vehicle. After labelling, a pseudo colour map is
added for separating the patches. The labelled image is shown in Fig. 14. Fig. 13. The dialog window of Patch Segmentation function Fig. 13. The dialog window of Patch Segmentation function Fig. 13. The dialog window of Patch Segmentation function
a. Labelled sketch
b. Multiple Selection of patches
Fig. 14. The sketch after segmentation Fig. 13. The dialog window of Patch Segmentation function a. Labelled sketch
b. Multiple Selection of patches
Fig. 14. The sketch after segmentation b. Multiple Selection of patches Fig. 14. The sketch after segmentation Fig. 14. The sketch after segmentation 384 MATLAB – A Ubiquitous Tool for the Practical Engineer As well as the labelling and colour mapping, some other tasks are performed at the same
time, such as finding out the start points of each patch on the boundary and the maximum
rectangles containing each patch, initialising the boundary node data and searching all the
sequential nodes and the crossing points on the boundary of each patch, and calculating the
areas and centres of patches. As well as the labelling and colour mapping, some other tasks are performed at the same
time, such as finding out the start points of each patch on the boundary and the maximum
rectangles containing each patch, initialising the boundary node data and searching all the
sequential nodes and the crossing points on the boundary of each patch, and calculating the
areas and centres of patches. 5.1 Data structure for sketch The points after labelling contain a lot of information for further processing and analysis. Therefore, it is important to establish an efficient data management system. A proposed
sketch structure is shown in Fig. 17. The basic unit is a single point, a set of points presents a
curve, a close curve or several curves stands for a patch, all the patches make a vehicle. Fig. 17. Sketch data structure
5.2 Point features
After labelling, the sketch becomes a two-dimensional integer array. Zero stands for
boundaries as known, but it is necessary to find out which patch it belongs to. They are just
the separate edge points with the value of zero at the moment, nothing else. They should be
reorganised to useful data. As the basic unit from data structure, 2D point contains three basic features – the
coordinates {x, y}, attributes (crosspoint, selected, breakpoint), and links (previous point,
next point). Sketch
Patch
Patch
Patch
Point
Point
Point
Curve
Curve
Curve
Curve
Curve
Curve Fig. 17. Sketch data structure
Sketch
Patch
Patch
Patch
Point
Point
Point
Curve
Curve
Curve
Curve
Curve
Curve Fig. 17. Sketch data structure 5. Feature extraction The features include the point, curve and patch features extracted from the sketch, which
are put into a data structure. The features include the point, curve and patch features extracted from the sketch, which
are put into a data structure. Automotive Sketch Processing in C++ with MATLAB Graphic Library 385 Fig. 16. The dialog window of Curve Fitting function Fig. 16. The dialog window of Curve Fitting function 5.2 Point features 5.2 Point features
After labelling, the sketch becomes a two-dimensional integer array. Zero stands for
boundaries as known, but it is necessary to find out which patch it belongs to. They are just
the separate edge points with the value of zero at the moment, nothing else. They should be
reorganised to useful data. As the basic unit from data structure, 2D point contains three basic features – the After labelling, the sketch becomes a two-dimensional integer array. Zero stands for
boundaries as known, but it is necessary to find out which patch it belongs to. They are just
the separate edge points with the value of zero at the moment, nothing else. They should be
reorganised to useful data. After labelling, the sketch becomes a two-dimensional integer array. Zero stands for
boundaries as known, but it is necessary to find out which patch it belongs to. They are just
the separate edge points with the value of zero at the moment, nothing else. They should be
reorganised to useful data. g
As the basic unit from data structure, 2D point contains three basic features – the
coordinates {x, y}, attributes (crosspoint, selected, breakpoint), and links (previous point,
next point). As the basic unit from data structure, 2D point contains three basic features – the
coordinates {x, y}, attributes (crosspoint, selected, breakpoint), and links (previous point,
next point). 386 MATLAB – A Ubiquitous Tool for the Practical Engineer After labelling, each boundary point has at least two different neighbours. If more than two,
the point is a crosspoint. If the point is selected for spline fitting, the selected attribute is
true. If the point is used for breaking whole boundary into pieces, the breakpoint attribute is
true. The links like a chain join the separated points into a sequential structure. The
extraction of point features follows the other feature calculations. A simple algorithm searching related neighbours is developed as follows A simple algorithm searching related neighbours is developed as follows •
Assume that the current point is an edge point. The eight neighbours of the current
point are checked one by one from 0 to 7, see Fig. 12a. •
Once a neighbour is not an edge point, the first related neighbour is found and s •
Carry on searching, any different neighbour will be saved until all neighbours are
checked. 5.2 Point features Return the number of related neighbours and an array containing the different
neighbours. •
If the number of related neighbours is greater than two, the current point is a
breakpoint. •
If the number of related neighbours is greater than two, the current point is a
breakpoint. 5.3 Curve features A set of edge points around a patch make a closed curve. Each closed boundary may have
more than one curve segments, i.e., each segment has its own point set. The point sets may
be sparse for curve fitting in order to reduce the size of data and obtain a precise
representation of the sketch. The following features need to be extracted in a curve: •
Number of points, and the coordinates of each point (values) •
Number of points, and the coordinates of each point (values) •
Number of breakpoints if a closed boundary is broken down to several segment •
Number of breakpoints if a closed boundary is broken down to several segments. •
The first point and the last point, if the last point is equal to the first point, it is a closed
boundary. •
Curve type, either the outer silhouette curve or the internal curve
If using spline fitting to present a curve, the following features need to be extracte •
Number of selected points for curve fitting •
Number of selected points for curve fitting •
Fitting method selected. •
End conditions. If the point doesn’t belong to the original boundary point, a changed tag is given. If displaying a spline, a view tag is given. •
If displaying marks on each node, a mark tag is given. •
If displaying marks on each node, a mark tag is given. A searching algorithm of boundary curve point setting is based on single pixel has been
developed as follows. •
If a point is an edge point and one of its neighbours is the patch, the edge point belongs
to the patch. •
The first edge point is the start point of boundary curve, and it becomes the current
point, previous point 1 and previous point 2. •
Check the eight neighbours of the current point using the graph in Fig. 12b •
Once a neighbour point is the edge point and it belongs to the patch, and it is not the
previous point 1 and 2, it is a new edge point. Add it to the curve. •
The new edge point becomes the current point. Repeat the same procedure from
beginning, until the point is equal to the first point. g
g
p
q
p
In the algorithm, two previous points are used to determine the direction of processing. 5.5 Sketch features When a sketch is separated into patches, the features such as the number of patches and
each patch features will be obtained. The neighbourhood will be established. Each patch has
the number of neighbours, the shared boundaries with the neighbours. A boundary with
one neighbour is the outer silhouette, with two is the inter boundary. The features directly
derived from the sketch are shown in Fig. 18. Fig. 18. Features in sketch
Currently, the features directly used for the 2D to 3D transformation are the area and centre
of patch. However, more features can be extracted from the points and basic features for
further application. It is easy for humans to distinguish where the patch belongs to, what
size it is, and where the characteristic points are located. The use of human recognition of
patches can help provide a direct and interactive transformation from 2D to 3D, without the
need for sophisticated recognition methods. For example, the features such as the position of
patch, size and curvature can be used to determine which part of surface it belongs to; the
features such as the principal axis of ellipse, size and position can be used for determine the
position and tangent points of wheels for coordinate system determination; and features
such as symmetric points from breakpoints and the curve between the them, and shading
features can be used to determine the curvature of surface, the difference of the areas of 2D
patch and its corresponding 3D surface can be used for the adjustment of coordinates. This
Minimum rectangle of patch
Minimum rectangle of whole vehicle
Internal boundary
Crossing point
Start and end points of boundary curve
Centre
Area
Inner Patch
Outer Patch
Outer Silhouette Minimum rectangle of patch
Minimum rectangle of whole vehicle
Internal boundary
Crossing point
Start and end points of boundary curve
Centre
Area
Inner Patch
Outer Patch
Outer Silhouette Fig. 18. Features in sketch Fig. 18. Features in sketch Currently, the features directly used for the 2D to 3D transformation are the area and centre
of patch. However, more features can be extracted from the points and basic features for
further application. It is easy for humans to distinguish where the patch belongs to, what
size it is, and where the characteristic points are located. 5.3 Curve features Using the neighbour graph in Fig. 12b will obtain slightly smoother curves than using the
one in Fig. 12a. Automotive Sketch Processing in C++ with MATLAB Graphic Library 387 5.4 Patch features Several curve segments are joined together into a closed curve to form a patch. The
following features can be extracted. •
The patch serial number, i.e. the label number •
The patch serial number, i.e. the label number
•
The colour and the title of patch
•
If selected for display or processing, a selected tag is given
•
The minimum rectangle containing the patch
•
The area and centre of the area of patch, the area value is the number of points within
the patch. The centre is the sum of coordinates divided by the area. •
If selected for display or processing, a selected tag is given •
The minimum rectangle containing the patch •
The area and centre of the area of patch, the area value is the number of points within
the patch. The centre is the sum of coordinates divided by the area. 7. Conclusion The approach here has been to reduce the problem of pre-processing of the sketch into a
number of separate stages, each of which refines or extracts a particular piece of information
embodied in the sketch. Some conclusions are summarized below: •
The pre-processing of sketches plays an important role for the input sketches. The more
precise the sketches are, the easier the sketch processing is. Pre-processing can be used
to translate ‘imprecise’ sketches to more ‘precise’ ones, providing a better starting point
for the transformation process. This approach allows the system to deal with sketches
that have roughly closed boundaries, in turn allowing easier separation into patches. g
y
g
•
For the pre-processed sketches, the related processing algorithms have been
investigated in order to obtain the separated patches with single-pixel and closed
boundary, which are ready for the 2D to 3D transformation. Facing the specific
sketches, some existing or new algorithms and new hybrid algorithms have been
proposed. •
Some basic features are extracted from the patches to present points, curves and
patches. They are listed below. •
Some basic features are extracted from the patches to present points, curves and
patches. They are listed below. •
The boundary points •
The relationships of the patches •
The minimum rectangle containing the patches •
The start and end points for each boundary •
The areas and geometric centres of the patches •
The attributes of the points whether they are the selected, break or crossing points
Related searching and calculating algorithms have been also developed. Some features are
discussed and may be applied in further research. •
The attributes of the points whether they are the selected, break or crossing points
Related searching and calculating algorithms have been also developed. Some features are
discussed and may be applied in further research. •
The sketch processing and feature extraction depend on the raster data. Therefore, the
method is device dependent. The inherent error is one pixel. Increasing the sketch size
can reduce error. But the important issue is the quality of the input sketch. A good
sketch will produce significantly better results. •
Curve fitting supplies an additional way to improve the patches. Through the selection
and modification of the edge points, the shapes of the patches can be smoothed or even •
Curve fitting supplies an additional way to improve the patches. 5.5 Sketch features The use of human recognition of
patches can help provide a direct and interactive transformation from 2D to 3D, without the
need for sophisticated recognition methods. For example, the features such as the position of
patch, size and curvature can be used to determine which part of surface it belongs to; the
features such as the principal axis of ellipse, size and position can be used for determine the
position and tangent points of wheels for coordinate system determination; and features
such as symmetric points from breakpoints and the curve between the them, and shading
features can be used to determine the curvature of surface, the difference of the areas of 2D
patch and its corresponding 3D surface can be used for the adjustment of coordinates. This Currently, the features directly used for the 2D to 3D transformation are the area and centre
of patch. However, more features can be extracted from the points and basic features for
further application. It is easy for humans to distinguish where the patch belongs to, what
size it is, and where the characteristic points are located. The use of human recognition of
patches can help provide a direct and interactive transformation from 2D to 3D, without the
need for sophisticated recognition methods. For example, the features such as the position of
patch, size and curvature can be used to determine which part of surface it belongs to; the
features such as the principal axis of ellipse, size and position can be used for determine the
position and tangent points of wheels for coordinate system determination; and features
such as symmetric points from breakpoints and the curve between the them, and shading
features can be used to determine the curvature of surface, the difference of the areas of 2D
patch and its corresponding 3D surface can be used for the adjustment of coordinates. This 388 MATLAB – A Ubiquitous Tool for the Practical Engineer can all be done in a straightforward manner so long as the patch is correctly identified,
which is most readily done by human intervention (although an automated, possibly
artificial intelligence based method for this may be feasible, but is outside the scope of this
research). 6. Implementation of MATLAB functions As mentioned above, the 23D system has been implemented the MATLAB functions. Differing from the proposed method of MATLAB implementation, our method was to apply
directly the kernel part of their functions. At first, the MATLAB *.m files were converted
into *h and *.cpp files of C++. Then, it was to extract the kernel part of the function, and to
add them into the 23D system. It was necessary to implement all the related functions. Therefore, no *.dll or *.lib files of MATLAB were used. This method is quite simple and easy
to change or enhance the implemented functions. 7. Conclusion Through the selection
and modification of the edge points, the shapes of the patches can be smoothed or even 389 Automotive Sketch Processing in C++ with MATLAB Graphic Library be changed in some places. This process allows resolution of a further set of
imperfections in the original sketch. be changed in some places. This process allows resolution of a further set of
imperfections in the original sketch. •
Direct implementation of MATLAB functions is a feasible way to enhance 23D system
functions. 8. Acknowledgment I would like to take this opportunity to express my special thanks to my supervisor, Dr. R. M. Newman, for his invaluable guidance, supports and helps in the research project. Many
thanks also go to the other members of the research group, Prof. M. Tovey, C. S. Porter and
J. Tabor, for their ideas, supports and helps in the research project, and T. Y. Pan for his
exchanging the information, ideas and supports with me. I am grateful to a number of staffs and students in the MIS, especial in the CTAC, who have
discussed with me on my project and have given me lots of support and help, especially to
Prof. Keith. J. Burnham, Mrs. A. Todman, and Miss Y. Xie. 9. References Adobe System Incorporated. (2000). Adobe® Photoshop® 6.0 user guide for Windows® and
Macintosh, Adobe System Incorporated, 90024592 Chin, N.; Frazier, C. & Ho, P. (1998). The OpenGL® Graphics System Utility Library. version
1.3, ed. Leech, J. Foley, J. D.; van Dam, A. & Feiner, S. K. (1996), Computer graphics: principles and practice,
2nd ed. in C, Addison-Wesley Publishing Company, Inc. ISBN 0-201-84840-6 Fosner, R. (1997). OpenGLTM Programming for Windows® 95 and Windows NTTM. Addison-Wesley, ISBN 0-201-40709-4 y
Glaeser, G. & Stachel, H. (1999). Open Geometry: OpenGL® + Advanced Geometry. Springer-Verlag New York, Inc., ISBN 0-387-98599-9 Kilgard, M. J. (1996). The OpenGL Utility Toolkit (GLUT) Programming Interface. API
version 3, Silicon Graphics, Inc. Ladd, S. R. (1996). C++ Templates and Tools. 2nd ed., M&T Books, ISBN 1-55851-465- Matthews, J. (2002). Image Analysis Explorer Pro. version 1.01, http://www.gener-
ation5.org/iae.shtml g
Pan, T. Y. (2002). Identification of 3D Information from 2D Sketches in Automotive Design,
MPhil paper, School of Art and Design, Coventry University p p
g
y
y
Salomon, D. (1999), Computer graphics and geometric modelling, Springer-Verlag New
York, Inc. ISBN 0-387-98682-0 Schildt, H. (1998). C++ from the Ground up. 2nd ed., Osborne/McGraw-Hill, ISBN 0-07-
882405-2 Seed, G. H. (1996). An Introduction to Object-oriented Programming in C++: With
Applications in Computer Graphics. Springe-Verlag London Ltd., ISBN 3-540-
76042-3 Segal, M. & Akeley, K. (2001). The OpenGL® Graphics System: A Specification. version 1.3,
ed. Leech, J. Silverio, C. J.; Fryer, B. & Hartman, J. (1997). OpenGL® Porting Guide. rev. Kempf, R. ed. Cary, C., Silicon Graphics, Inc. 390 MATLAB – A Ubiquitous Tool for the Practical Engineer Smith, J. T. (1997). C++ Toolkit for Scientists and Engineers. International Thomson
Computer Press, ISBN 1-85032-889-7 The MathWorks, Inc. (2000). MATLAB® C/C++ Graphics Library – The Language of
Technical Computing - User’s Guide, version 2 The MathWorks, Inc. (2000). MATLAB® C Math Library – The Language of Technical
Computing - User’s Guide, version 2 p
g
The MathWorks, Inc. 2000, “MATLAB® C++ Math Library – The Language of Technical
Computing - User’s Guide”, version 2, The MathWorks, Inc. The MathWorks, Inc. 2001, “MATLAB® Compiler – The Language of Technical Computing -
User’s Guide”, version 2, The MathWorks, Inc. The MathWorks Inc. (2001). MATLAB® The Image Processing Toolbox User's Guide,
version 3 The MathWorks, Inc. (2001). Spline Toolbox for Use with MATLAB® - User’s Guide, version
3. The Vision Technology Group, Microsoft Research. (2000). Simulation of Rough Surfaces and
Analysis of Roughness by MATLAB
F. Gascón1 and F. Salazar2
1Departamento de Física Aplicada II. ETS Arquitectura (US).
Avda. Reina Mercedes 2, 41012 Sevilla
2Departamento de Física Aplicada. ETSI Minas (UPM).
C/Ríos Rosas 21, 28003 Madrid
Spain F. Gascón1 and F. Salazar2
epartamento de Física Aplicada II. ETS Arquitectura (US). Avda. Reina Mercedes 2, 41012 Sevilla
2Departamento de Física Aplicada. ETSI Minas (UPM). C/Ríos Rosas 21, 28003 Madrid
Spain 9. References The Microsoft Vision SDK. version 1.2, VisSDK@microsoft.com. Wright, R. S. & Sweet M. (1996). OpenGL Superbible: The Complete Guide to OpenGL
Programming for Windows NT and Windows 95. The Waite Group, Inc. 19 Simulation of Rough Surfaces and
Analysis of Roughness by MATLAB
F. Gascón1 and F. Salazar2
1Departamento de Física Aplicada II. ETS Arquitectura (US). Avda. Reina Mercedes 2, 41012 Sevilla
2Departamento de Física Aplicada. ETSI Minas (UPM). C/Ríos Rosas 21, 28003 Madrid
Spain 1. Introduction 392 MATLAB – A Ubiquitous Tool for the Practical Engineer The surface analysis of materials is of great importance, since many technological problems
require, previously, the study of the surface state. One of the parameters of any material that
changes easily with time is the roughness. Indeed, in many sectors, as civil engineering,
architecture, mechanical engineering, etc. materials of different forms and properties are
commonly employed, which must meet certain requirements to ensure their use. For this
reason, the measurement of some surface parameters, as roughness, must be taking into
consideration. The surface analysis of materials is of great importance, since many technological problems
require, previously, the study of the surface state. One of the parameters of any material that
changes easily with time is the roughness. Indeed, in many sectors, as civil engineering,
architecture, mechanical engineering, etc. materials of different forms and properties are
commonly employed, which must meet certain requirements to ensure their use. For this
reason, the measurement of some surface parameters, as roughness, must be taking into
consideration. There are different methods for determining roughness. One of the most employed is the
profilometer (see next section). However, this paper deals with an optical method based on
the speckle interferometry which has some advantages. The methodology is fast, accurate,
and does not contact the specimen. Above all this we will talk in the next sections 1. Introduction The simulation of physical phenomena in science and engineering has become an important
tool because it allows studying a wide range of real problems. On the other hand, it allows
resolving problems that, because of its difficulty, it would be not possible to solve by
analytical methods. Moreover, simulation is fast and versatile since it permits to vary
parameters of the problem easily, allowing analyzing the effect of the modification of them
in the response of the system examined. p
y
Simulation requires programming, for which there are many different languages. Each of
them has a particular internal structure that distinguishes it from others. Therefore,
depending on the problem to be study, it may be advisable to use a specific programming
language. In the scientific-technical context MATLAB has been increasingly used by the great
advantages that it offers. For example, the instructions are interpreted and not compiled, the
user to enter commands interactively. The data processing is flexible. They can be read and
stored in two different formats, ASCII and MATLAB format. ASCII has the advantage that
the data and results may be used for other programs. However, MATLAB format may be
faster. On the other hand, many functions and libraries of MATLAB are written MATLAB
language, enabling the user access to the source files. It is possible to execute instructions of
the operating system without exiting the program. Moreover, this language is portable in
platforms as Windows or Apple, commonly employed by the researcher. From the point of
view of numerical calculation, the use of matrices as basic elements makes it efficient and
easy to employ, being also possible to perform graphics of curves and surfaces. Finally, the
operations can be performed with simple and intuitive expressions similar to those used in
science and engineering. g
g
MATLAB has been used for many applications in general physics, mathematics, optics,
electronics, chemistry, biology, medicine, and artificial intelligence, among others. Now we
want to employ MATLAB to simulate an optical procedure to measure surface roughness. Thus, the aim of this paper is the determination of the roughness of a surface from the
analysis of the speckle pattern obtained in the far field, when the object is illuminated with a
monochromatic beam perpendicularly to its surface. 2. Discretization of the problem. Roughness The distance u between two points may be likened to the ball diameter
bd of the profilometer. h(x)
O
X
Fig. 2. Rough surface represented by z=h(x). If the sampling period is chosen small, the
discrete function h(xp) is very similar to the actual surface. h(x)
O
X Fig. 2. Rough surface represented by z=h(x). If the sampling period is chosen small, th
discrete function h(xp) is very similar to the actual surface. If N samples are taken, they form a string of N integers for which a value zp =h(xp) is given. This set of numbers is collecting in a matrix IF of dimension N 1. The range of variation of
the index p is 1, 2, 3,..., N, and it represents the element p of the string. Therefore this index p
is related with the sampling period as follows: x = 0, u, 2u, 3u, ..., (p-1)u. Two neighboring
elements of the IF matrix contain the values of the surface heights of the grooves of two
points on the reference plane separated u meters. As it will see, when studying the phenomenon of diffraction in the far field, the Fourier
transformation must be applied. Therefore, we need to study also the sampling in the
frequency domain. When calculating the finite discrete Fourier transform (DFT) of the IF matrix of N elements,
a new set of N numbers is obtained which is grouped in another matrix FO of dimension
N1. Due to the Fourier transform is performed from the discrete values of IF, the result is
also discrete. As a result the distance between two points of the transformed numbers in
frequency domain is also quantified. Denoting by ν (1,2,…N) the index for the matrix FO,
the row index represents the harmonic components whose frequencies are α= 0, 1 / (Nu), 2
/ (Nu), ..., (ν-1) / (Nu). The sampling frequency is defined as fs ≡ 1/u, measured in m-1, and
represents the number of measures per unit length. By using this expression, spatial
frequency components may also be written in the form α = 0, fs / N, 2 fs / N, ..., (ν-1) fs/N . In general, the matrix element ν of FO represents the harmonic
in the space of
frequencies
1
Nu
. (1)
1
Nu
. 2. Discretization of the problem. Roughness A classic device for measuring surface roughness is the mechanical profilometer which is
formed by a tiny stylus (with a small ball), and a displacement sensor. The typ moves along
a straight line parallel to the surface plane and records the displacements in the
perpendicular direction, tracing out the outline of the surface. If the ball has a diameter bd it
can not be inserted between two grooves whose distance is less than bd, being only possible
to detect the topographic level with a distance between grooves greater than bd. z=h(x,y)
X
bd
Fig. 1. Classical device for measuring roughness. Observe that when the diameter of the end
needle bd is greater than the groove, the transducer can not reproduce the high frequencies
of the surface outline. bd Fig. 1. Classical device for measuring roughness. Observe that when the diameter of the end
needle bd is greater than the groove, the transducer can not reproduce the high frequencies
of the surface outline. In this article we are interested in using a speckle technique to measure the roughness of a
surface. From a didactic viewpoint, the explained idea of the profilometer may be employed
to understand the sampling, when a rough surface is simulated by MATLAB. In this article we are interested in using a speckle technique to measure the roughness of a
surface. From a didactic viewpoint, the explained idea of the profilometer may be employed
to understand the sampling, when a rough surface is simulated by MATLAB. p
g
g
y
To start let us suppose a one-dimensional rough surface, and then we extend the results to
the case of two variables. The height of the rough surface can also be measured by sampling. With this aim let us
consider a curve z=h(x) as shown in Fig. (2), aligned on the OX axis. For sampling the Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 393 function h(x) the X co-ordinate axis is divided into intervals of length u measured with
respect the origin O resulting in a system of aligned points of co-ordinates 0, u, 2u, 3u,… The
distance u between two neighbor points, i.e. the sample interval, is called the sampling
period and its value is chosen depending of the function to be investigated (in our case the
form of the surface). 2. Discretization of the problem. Roughness (1) Thus there is a correspondence between the index ν = 1, 2, 3, ..., N, and the spatial frequency
by means of the factor (fs/N). Obviously, the sampling process implies that some
information about the sampled function is loosed, because no value between two
neighboring points is known. However, depending on the physical problem studied, using
the Shannon theorem, the sample interval can be modified so that the data be enough for
numerical calculus. Taking into account that the expression obtained for representing a point on the OX-axis has
the form (p-1)u, it seems to be appropriate to change to non-dimensional variables. To do so 394 MATLAB – A Ubiquitous Tool for the Practical Engineer we divide x for u resulting (x/u)=(p-1), p being 1,2,…,N. This new variable represents the
distance from the origin O to an arbitrary point on OX (Fig.3), measured in units of the
sampling period u, and the elements of the matrix IF the surface heights at each point. The
same idea applies to frequency domain. q=y/u+1
p=x/u+1
N
1
2
3
N
1
2
3
Fig. 3. Reference system without dimensions. The numbers represent the co-ordinates of the
matrix elements. At each point (p,q) we assign the corresponding value of the surface height. Fig. 3. Reference system without dimensions. The numbers represent the co-ordinates of the
matrix elements. At each point (p,q) we assign the corresponding value of the surface height. Fig. 3. Reference system without dimensions. The numbers represent the co-ordinates of the
matrix elements. At each point (p,q) we assign the corresponding value of the surface height. 1 2
3
1
2
3
u
u)+1
N
N
Fig. 4. Space of non-dimensional frequencies. Observe that this grid is initially determined
by the matrix IF, then it also has NxN elements u)+1 Fig. 4. Space of non-dimensional frequencies. Observe that this grid is initially determined
by the matrix IF, then it also has NxN elements Fig. 4. Space of non-dimensional frequencies. Observe that this grid is initially determined
by the matrix IF, then it also has NxN elements 395 Simulation of Rough Surfaces and Analysis of Roughness by MATLAB By setting (Nu)= /(1/Nu) =(ν-1) the spatial frequency is converted in a dimensionless
number representing the basic unities of measurement in this space. 2. Discretization of the problem. Roughness Furthermore, /(1/Nu)
is directly the frequency measured in unities of (1/Nu) corresponding to the element ν of the
matrix FO (Fig.4). When generating a rough surface the components of IF are real numbers (Fig.3). However,
as we will see, the diffraction of a light beam by a surface can introduce phase factors
resulting in complex numbers in the elements of matrix IF. In any case the resulting N1
string of IF and its fast Fourier transform (FFT), are calculated without difficulty with
MATLAB. One advantage of the aforementioned procedure is that the sampling distance u
between two points of IF is not directly involved in the numerical calculation, and then it
may be considered as a parameter. For this reason the DFT and the FFT of IF, i.e. FO, is
universal respect to the parameter u, because the components of FO depend only of the non-
dimensional elements of the matrix IF. Although with the change of variables introduced the components of IF and FO are
dimensionless, they have physical meaning. In the present study the p element of IF is a
measure of the height of the point at position x = (p-1) u. FO may be interpreted in the same
way. So setting any number to the sampling period u the values obtained for FO show the
harmonic amplitudes. For example, giving u the arbitrary value 10-4 m, and choosing N = 64,
we have for the first non-zero frequency components, =156.2, 312.5, 468.8,… m-1. The above is easily applied to a two-dimensional simulation. For this let us consider two
coordinates (x,y) of the system OXY (Figs.3,4). For each point of this reference plane is
assigned a value which corresponds to the surface height at this point. The data are placed
in a two-dimensional array IF. If the sampling is done with the same number of samples, say
N, the dimension of the matrix IF is NN (Fig. 3). Two points of coordinates (xi, yj) and (xk,
yl) respectively are separated in the matrix IF a distance ((i-j)2+ (k-l)2)1/2 u, and in
dimensionless co-ordinates ((i-j)2+(k-l)2)1/2. In relation to FO similar expressions may be
obtained, but in frequency space. So the spatial frequencies between two points whose
coordinates are
,
h
k
and
,
l
m
is ((h-k)2+ (l-m)2)1/2 (1/Nu) in m-1, and without
dimensions ((h-k)2+ (l-m)2)1/2. 3. Fraunhofer diffraction with MATLAB In this section we are interested in the phenomenon of diffraction of light, given the
importance to understand the speckle patterns. With this objective let us use the
experimental lay-out depicted in Fig.(5). A collimated monochromatic laser beam LB of
wavelength is directed to a beam splitter BS, which projects the light perpendicularly on
a diffracting rough sample S located on the OXY plane. The surface has, in principle, a
variable reflectance R(x,y). This means the different scatters that form the surface may have
distinct reflection properties. The shape of the radiation beam used determines the geometry
and the intensity inside of the illuminated area. If we suppose a beam of homogeneous
intensity, its geometry can be expressed easily (in view of the simulation) as an opaque
mask M placed on the surface, which has the function to define the illuminated area (Fig. 6). Taking into consideration the most cases studied in optics, we will choose a circular mask of
diameter D. An observation screen is placed parallel to the diffracting surface at a distance
of z from its plane. The points on the observation plane are specified by means of its x’, y’
coordinates, with respect to an O’X’Y’ coordinate system (on the CCD camera). MATLAB – A Ubiquitous Tool for the Practical Engineer 396 L
BS
CCD
S
LB
Fig. 5. Experimental set-up. L, laser; LB, laser beam; S, rough sample; BS, beam splitter; CCD
camera. S BS Fig. 5. Experimental set-up. L, laser; LB, laser beam; S, rough sample; BS, beam splitter; CCD
camera Fig. 5. Experimental set-up. L, laser; LB, laser beam; S, rough sample; BS, beam splitter; CCD
camera. M
LS
OS
RS
FFT
X
Y
z
BS
X'
Y'
Fig. 6. Steps employed for simulating the rough surface, the aperture, and the speckle
pattern. RS, rough surface; M, mask; BS, beam splitter; FO, matrix which elements represent
the Fourier transform of the reflectance R(x,y) on the OX’Y’ reference system. The intensity
2
OS
FO
can be interpreted also as an angular spectrum
,
. BS X OS Fig. 6. Steps employed for simulating the rough surface, the aperture, and the speckle
pattern. RS, rough surface; M, mask; BS, beam splitter; FO, matrix which elements represent
the Fourier transform of the reflectance R(x,y) on the OX’Y’ reference system. 3. Fraunhofer diffraction with MATLAB The intensity
2
OS
FO
can be interpreted also as an angular spectrum
,
. Supposing that the scalar diffraction theory applies, the Fresnel-Kirchhoff integral and the
theories of Rayleigh-Sommerfeld can be used. However, the calculation of the diffraction
pattern through these theories is not always easy to carry out. Sometimes the procedure may
be simplified under certain conditions of the problem. So if the linear dimensions of the
aperture (mask in our case) is much greater than the wavelength, i.e. D>>, and the distance
z between the surface and the observation plane is great enough, the paraxial theories apply. In this case, the mathematical expression for the diffracted field depends on the specific Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 397 dependence between D and z. When expanding the phase term in the Fresnell-Kirchhoff
integral is not possible to neglect the quadratic terms that appear we speaks of Fresnel
diffraction. On the contrary, if these terms can not be tacked into consideration we have
Fraunhofer diffraction. These approximations are the most important cases in the field of the
classical optics. A possible quantitative criterion to be employed in order to use the Fraunhofer
approximation, or that of Fresnel, is based on taking a circle of diameter D, which only
includes the regions of interest (in the present case the hole of the mask). Let r be the
distance from a point on the diffracting surface to the observation point. Let be the
distance from the centre of the circle to a point inside its circle. If 2r/ varies linearly with
, the diffraction is called Fraunhofer diffraction; if the variation has non-linear terms of
magnitude comparable with /2, the diffraction is said Fresnel diffraction. Therefore, for
Fraunhofer diffraction we obtain zD2/(4). In short, the diffracting area must be greater
than and the observation of the intensity pattern must be carried out from a large distance
with respect to the scatter surface. In other circumstances, i.e. if the distance z does not fulfil
the conditions needed, non-paraxial terms of the phase must be included in the integrand of
the Fresnell-Kirchhoff integral (higher expansion coefficients). Fraunhofer diffraction is related with the Fourier transform which takes an angular
spectrum of the reflectance (or transmittance) to be considered. 3. Fraunhofer diffraction with MATLAB From a physical point of
view it is equivalent to observe the phenomenon in the far field (another possibility is to
employ a lens and locate the observation plane on its back focal plane). This angular
spectrum means that the Fraunhofer diffraction gives the behaviour of the field amplitude
for the directions in space. If we use two variables, the amplitude of the diffracted field done
through the Fourier transform depends on andwhich are related with the directions
,
x
y
through the following expressions cos
x
,
cos
y
. (2) (2) As we will see in the following section, the proposed method for measuring roughness is
developed under the supposition that the conditions of the Fraunhofer diffraction apply. Therefore, this case must be translated to the context of MATLAB. As we will see in the following section, the proposed method for measuring roughness is
developed under the supposition that the conditions of the Fraunhofer diffraction apply. Therefore, this case must be translated to the context of MATLAB. With this aim, the basic results of the preceding section should used. The elements foij of the
matrix FO belonging to a row or column represent the complex amplitude of two harmonics
separated 1/(Nu). Therefore the first angular direction is
1
1
cos
1
2
x
sf
N
, which corresponds to the frequency
0
and the direction for the least coefficient of FO is
x = cos-1[(N-1)fs/N] corresponding to the higher frequency = (N-1) fs/N. In the case of non-
dimensional variables we can use for the two axes Nu cos x/and Nu
cos
y
/respectively. If the diffraction pattern is observed on a plane screen a distance z
from the diffusing surface, the spatial frequencies may be related with points on that plane. 4. Speckle pattern generation When a laser beam illuminates a rough surface at scale of the wavelength, the diffraction
pattern consists of a random distribution of intensity called speckle. The apparition of
speckle may be understood by the fact that the coherent waves falling on the rough surface
travel a different optical path from the diffusing surface to the observation point. When the
object is rough, the reflectance is a random function on the aperture, and then the
corresponding optical paths for the different scatters vary rapidly. As a result, the intensity
on the observation screen (or space) also varies very quickly from one point to another of its
surroundings, giving brilliant and dark spots irregular in shape. A model of diffusing and non-absorbent surface is proposed, in which the height of the
scatters with respect to a reference plane are supposed as a random variable, and with a
gaussian probability density function. A surface of these characteristics is, for example, a
metal which is not well polished. We suppose that the rough surface is illuminated by a
collimated light beam perpendicularly to its plane resulting in a speckle pattern which is
calculated by means of the FFT (Fig. 7). Due to that optical path followed by the different points of the wavefront is not the same,
consequently, neither is the phase 2. As we have to count the return path, the path
length and height h(x,y) of the surface referred to the plane z=0 are related by the expression
4
( , )
h x y
. Thus, the reflectance will be proportional to the exponential of this phase
factor, adopting the form
0
4
,
,
exp
( , )
i
R x y
R
x y
h x y
,
(4) (4) where R0(x,y) is the reflection coefficient of the surface, and
4
( , )
ih x y
is the phase. In
the simulation presented in this paper we choose R0(x,y)=1. where R0(x,y) is the reflection coefficient of the surface, and
4
( , )
ih x y
is the phase. In
the simulation presented in this paper we choose R0(x,y)=1. By measuring the random height h(x,y) of the sampled points (Fig.8), it would be possible to
construct the reflectance matrix of NN elements. 3. Fraunhofer diffraction with MATLAB For small angles it can be written: cos
'
x
x
z
,
(3) cos
'
x
x
z
, (3) MATLAB – A Ubiquitous Tool for the Practical Engineer 398 and cos
'
y
y
z
. Due to the properties of the Fourier transform, the FFT of the reflectance will contain N/2 of
positive frequencies, and N/2 negative, whose zero spatial frequency occurs at =1. In the
FFT, the independent variable is the frequency, and in the representation with positive and
negative frequencies its maximum value will be fs/2. Based on a reflectance matrix of NxN
elements located at the XOY axes associated, practically centred in the middle, we calculate
FO by means of the FFT, obtaining another matrix from the centre of which the amplitude of
the null frequency harmonic component is indicated. The intensity registered over a direction
,
is found by computing the square modulus
of the Fourier transform (FT) of the scattering surface delimited by the mask M, after
centring the FFT by means of the command C(i,j)=(-1)(i+j). 4. Speckle pattern generation Following the nomenclature of the Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 399 Fig. 7. Three dimensional representation of the intensity of a speckle pattern captured by a
CCD camera in the laboratory. The values of the intensity over the OZ axis are in the
interval [0,255]. Fig. 7. Three dimensional representation of the intensity of a speckle pattern captured by a
CCD camera in the laboratory. The values of the intensity over the OZ axis are in the
interval [0,255]. Fig. 8. Rough surface generated by MATLAB. The plane of the figure (OXY) depicts a plot of
the surface contour. Fig. 8. Rough surface generated by MATLAB. The plane of the figure (OXY) depicts a plot of
the surface contour. 400 MATLAB – A Ubiquitous Tool for the Practical Engineer preceding section we call this array the IF matrix (Fig.9). The elements of IF contain the
complex reflectance R(x,y) corresponding to each point of the surface, which are separated
from their neighbors a distance equal to the sampling period u. The area of the delimiting
mask will be represented by points outside a circle with zero reflectance. Fig. 9. View of the grid chosen on the OXY reference plane for N=64. The colours represent
the surface heights at each point (pixel). Fig. 9. View of the grid chosen on the OXY reference plane for N=64. The colours represent
the surface heights at each point (pixel). Following the same way as in preceding paragraphs, we employ the ratio has a non-
dimensional variable, which will be very useful when changing the wavelength. In the
model this variable is equal to a constant multiplied by a random number, which will
provide information on the roughness in the simulation. We will call in the program this
constant RU and it represents a roughness modulating factor. Random numbers with
Gaussian distribution are generated in MATLAB by the command randn. The mathematical
expression for reflectance is
0
4
,
,
exp
i
R x y
R
x y
RU rndn N
,
(5) (5) where
h
RU
randn N
,
(6) (6) and the phase and the phase
4
RU
randn N
. (7) (7) 401 Simulation of Rough Surfaces and Analysis of Roughness by MATLAB Thus, an element of RUrandn is a number equal to an optical path measured in wavelengths. For example, an RU=1 and a randn=2 give rise max(RUrandn)=2, which indicates a
maximum path difference of 2, that is to say, a groove on the reflecting surface with depth
equal to However with the same randn, but with the modulating factor equal to 0.1, the
roughness would be a tenth part. Hence the RU factor represents the roughness measured in
wavelengths. To account the transversal geometry of the incident laser beam on the surface, the rough
surface is delimited by means of a round mask of diameter D (geometry could be different;
see section 7.2). The diameter D must be greater than the wavelength and the sampling
period u. On the other hand it is supposed that the number of sampled points inside the
diameter D is large enough, in order be sure that the statistics applies. Once that the characteristics of the surface and beam are defined, the diffraction pattern is
obtained by means of the FFT of the reflectance matrix IF. The registered intensity of the
diffracted light by the rough surface is proportional to the square modulus of the diffracted
amplitude, e.g. 2
FO
. 5. Definitions of roughness
BD
q
h x y
R
BD
,
(11) (11) and its non-dimensional value and its non-dimensional value 2
2
( , )
4
(
)
2
q
BD
BD
h x y
randn N
R
RU
BD
BD
. (12) (12) 5. Definitions of roughness In this section we try to adapt some definitions of roughness to our specific problem. We
start the quantitative definition of the average roughness Ra from the mean surface level, as
the average absolute value of the height, for all the points along a straight line (remember
the profilometer). Then in a circular matrix of diameter D inside the IF, corresponds
2 4
BD
elements. Therefore, the roughness of the sample may be expressed by the
following formulae 4
( , )
BD
a
h x y
R
BD
,
(8) (8) where the sum is extended to the sampled points within the circle of diameter BD. As
previously, if we transform this Eq.(8) to non-dimensional variables, we get where the sum is extended to the sampled points within the circle of diameter BD. As
previously, if we transform this Eq.(8) to non-dimensional variables, we get ( , )
4
4
(
)
a
BD
BD
h x y
R
RU
randn N
BD
BD
. (9) (9) The number of elements G within the beam of diameter D (BD) is less than the NN
elements of IF. Say L the length of the square side where the surface is defined. In any
case BD
L
, being a constant
1
, then it holds The number of elements G within the beam of diameter D (BD) is less than the NN
elements of IF. Say L the length of the square side where the surface is defined. In any
case BD
L
, being a constant
1
, then it holds
2
1
4
G
N
N
,
(10) (10) whose maximum value is 0.8, approximately (
1)
. If N and BD are large enough, and
surface heights are randomly distributed, the G values are representative and Ra can be
calculated using G elements. 402 MATLAB – A Ubiquitous Tool for the Practical Engineer Similarly, the roughness Rq (root mean square) could be expressed as function of BD. In fact,
considering the usual definition of this parameter, the following formulae may be written 2
( , )
2. 7.1 Circular beam Figures 10 shows the results of numerical calculations performed with a PC. In order to the
numerical calculations are easy to obtain the data were N = 64, BD = 6, RU = 0, 0.1, 0.2, 0.3
0.4 0.5. The successive rows of the figure refer to these values of roughness, respectively. The first column of the figure corresponds to the surface height along the diameter of the
illuminated area. The second column represents the intensity of the diffraction pattern, FIDI,
and the third one shows the autoconvolution, CO. For beginning a surface without roughness was chosen. The first row shows the area under
study for a perfect mirror, illuminated by a circular beam of diameter BD = 6. The calculated
diffraction pattern shows the classical Airy disc corresponding to diffraction by a hole. With
the proposed values N = 64 and BD = 6 is N/BD = 64/6, and as D = BDu, gives Nu = 64D/6. The analysis of Figure 4 shows that the first minimum of the Airy disc in the frequency
space is 24, approximately. From Fig 1 it follows
1
12
1
cos
11
1
0.17
64
64
Nu
u
u
u
. On the other hand, the first minimum given in the theory of diffraction by a circular hole is On the other hand, the first minimum given in the theory of diffraction by a circular hole is cos
1
1
1
1.22
1.22
0.20
6
Du
u
u
. Both results agree and differ in a small amount. The difference can be attributed to the small
number of values chosen. The second row refers to the same mirror, but not completely polished, and with a
coefficient RU = 0.1. The profile shows small heights and valleys. The Airy disk is a little
blurred, and not as clear as in the previous case. In the third row RU = 0.2 the central disk
appears deformed and a speckleled. In the fourth and fifth rows the figure is quit different
with respect to the first one, and the speckles are on all the pattern. In the last row only
speckle may be seen, and no traces of the Airy disk are present. 11. The autoconvolution CO of FIDI, and its maximum COV is computed. p
12. In order to manipulate the data more easily, the logarithm of COV is given (log(C
The detailed program may be found in appendix A 6. Programming using MATLAB We will see that the simulated specklegram corresponding to the diffraction of a
monochromatic radiation by a rough surface is altered by the roughness of the object within
a certain range, which depends on the wavelength of the beam used. Therefore, by
analyzing some characteristics of the intensity pattern it would be possible to measure
roughness. To understand the idea let us suppose a flat surface, well polished, delimited by an aperture
(mask). If a beam strikes on the surface, the delimiting aperture diffracts it resulting in an
intensity pattern that depends on the geometry of the obstacle. Now if the surface is
scratched, the intensity registered changes, although the aperture maintains its geometry. In
both cases the autoconvolution of the intensity is different, which means that the roughness
produced on the surface is the cause of the change. Therefore, the convolution of the
diffraction pattern could be indicative of the degree of surface polish. p
g
p
To test the hypothesis, first we constructed a computer model of a rough surface, and
second we simulate the diffraction of a collimated monochromatic beam by this surface. The
resulting random intensity, that is, the speckle, is stored in a matrix (FO) and its
autoconvolution (CO) is performed. Once all data of CO are obtained, the functional
relationship of the maximum value of the autoconvolution and its relation with the
roughness is analyzed. g
y
The program consists of the following steps: The program consists of the following steps: 1. Begin by setting the number of samples N along each axis. 2. The matrix IF is constructed by using the command RAN = randn (N). 3. The diameter of the laser beam BD is specified, measured in number of array elements. 4. A value to the RU is assigned. g
5. The BS array is constructed. The mask is 0 outside the circle and 1 inside. The matrix RURAN = RU * RAN is introduced, representing the surface heights f
each pixel on the area NxN. The matrix hs is defined as hs = RURAN.*BS. It represents the height of the points insid
the circle (mask M). 8. The reflectance matrix is obtained. Its expression is ts = exp (4πi RURAN). 9. The array FO is calculated, which is the FFT of ts. 10. The intensity of the diffraction pattern is determined ,
2
FIDI
FO
. 6. Programming using MATLAB 403 Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 11. The autoconvolution CO of FIDI, and its maximum COV is computed. 12. In order to manipulate the data more easily, the logarithm of COV is given (log(COV)). The detailed program may be found in appendix A 7.1 Circular beam When the roughness is RU =
0.5 (bottom row) yields a rough surface with high grooves. The intensity is formed by
irregular random spots being unknown directly the form of the mask, e.g. the symmetrical
intensity circle of the Airy function. In summary, diffraction by a specular surface delimited
by an aperture produces an intensity pattern concentrated around the direction of the
reflected beam, but if the roughness is increasing, the light is diffracted producing speckle
which structure is random. The third figure of each row (third column) corresponds to autoconvolución (CO), which
has a maximum at the center (COV). In effect, the values for the logarithm of COV are,
respectively: logCOV(RU=0.0) = 7.78, logCOV(RU=0.1) = 7.10, logCOV(RU=0.2) = 6.86,
logCOV(RU=0.3)=6.90, logCOV(RU=0.4)= 6.88, and logCOV(RU=0.5)=6.91. In this calculus
the logarithm of the autoconvolution hass been used because the maximum value of CO is
very large. Employing log(COV), the data are easier to manipulate. MATLAB – A Ubiquitous Tool for the Practical Engineer 404 0
20
40
60
80
-1
0
1
10
20
30
40
50
60
20
40
60
20
40
60
80
100
120
20
40
60
80
100
120
0
20
40
60
80
-0.1
0
0.1
10
20
30
40
50
60
20
40
60
20
40
60
80
100
120
20
40
60
80
100
120
0
20
40
60
80
-0.2
0
0.2
10
20
30
40
50
60
20
40
60
20
40
60
80
100
120
20
40
60
80
100
120
0
20
40
60
80
-0.5
0
0.5
10
20
30
40
50
60
20
40
60
20
40
60
80
100
120
20
40
60
80
100
120
0
20
40
60
80
-0.5
0
0.5
10
20
30
40
50
60
20
40
60
20
40
60
80
100
120
20
40
60
80
100
120
0
20
40
60
80
-0.5
0
0.5
10
20
30
40
50
60
20
40
60
20
40
60
80
100
120
20
40
60
80
100
120
ig. 10. Computer results for N = 64, BD = 6, RU = 0, 0.1, 0.2, 0.3 0.4 0.5. The first column
hows the roughness along the illuminated area. The second represents the intensity of th
diffraction pattern, FIDI, and the third column is the autoconvolution, CO. The rows
orrespond to the different values of RU. 7.1 Circular beam 0
20
40
60
80
-1
0
1 10
20
30
40
50
60
20
40
60 0
20
40
60
80
-0.1
0
0.1 10
20
30
40
50
60
20
40
60 80 0
20
40
60
80
-0.2
0
0.2 20
40
60
80
100
120
20
40
60
80
100
120 10
20
30
40
50
60
20
40
60 20
40
60
80
100
120 0
20
40
60
80
-0.5
0
0.5 20
40
60
80
100
120
20
40
60
80
100
120 10
20
30
40
50
60
20
40
60 60 0
20
40
60
80
0
20
40
60
80
-0.5
0
0.5
0
20
40
60
80
-0.5
0
0.5 0
20
40
60
80
-0.5
0
0.5 20
40
60
80
100
120
20
40
60
80
100
120 10
20
30
40
50
60
20
40
60 0
20
40
60
80
-0.5
0
0.5 20
40
60
80
100
120
20
40
60
80
100
120 10
20
30
40
50
60
20
40
60 Fig. 10. Computer results for N = 64, BD = 6, RU = 0, 0.1, 0.2, 0.3 0.4 0.5. The first column
shows the roughness along the illuminated area. The second represents the intensity of the
diffraction pattern, FIDI, and the third column is the autoconvolution, CO. The rows
correspond to the different values of RU. 405 Simulation of Rough Surfaces and Analysis of Roughness by MATLAB These results show that the values of their maxima are not the same. On the contrary, the
maximum value for each one depends on the surface roughness. For this reason it seems
suitable to employ the maximum value of the autoconvolution of the speckle pattern, as a
possible procedure for measuring the roughness of a surface, if the roughness is smaller
than the wavelength of light used in the experiment. At the same time, COV depends on the diameter of the beam used (BD) also. To see the
effect in the autoconvolution when the wide of the laser is changed, we computed logCOV
with N and D for two different number of data and diameters. 7.1 Circular beam For example if N= 64, and BD
= 32, it yields logCOV = 12.0, 11.7, 10.7, 9.8, 9.7, 9.7,
whereas with N = 128 and BD = 32 whereas with N = 128 and BD = 32 logCOV = 12.6, 12.3, 11.3, 10.4, 10.3, 10.3 . logCOV = 12.6, 12.3, 11.3, 10.4, 10.3, 10.3 . Therefore the maximum reached by the autoconvolution depends on the number of samples
N and the beam diameter BD. This result is reasonable if we bear in mind the definition of autoconvolution. In fact,
convolution may be regarded as the overlapping area between two functions (in this case
the same function) when one is reversed and moves on the other. The result depends on the
wide and height of the functions involved. Therefore, if the diameter of the beam changes
the autoconvolution modifies its value too. With the aim to apply this result to laboratory experiments, it seems necessary to have more
values of the autoconvolution in other circumstances. In he same way as explained, the
following table provide useful data of the logCOV, for N=512 when the diameter D ranges
from 23 to 23+m (m=1,2,…5). The detailed results for this calculation can be seen in the
appendix B. D\RU
0.0
0.1
0.2
0.3
0.4
0.5
8
10.233
9.231
9.148
9.185
9.078
9.128
18
12.036
10.867
10.35
10.351
10.348
10.368
32
13.810
12.558
11.536
11.546
11.548
11.542
64
15.607
14.294
12.734
12.736
12.740
12.742
128
17.412
16.037
13.945
13.938
13.941
13.937
256
19.216
17.838
15.149
15.141
15.145
15.142
512
21.257
19.881
16.428
16.347
16.347
16.349
T bl 1 V l
f th
t
l ti
l
(COV) f
diff
t di
t
d
h Table 1. Values of the autoconvolution log(COV) for different diameters and roughness
parameters. The results in yellow do not give information since they are very similar. From these results may be inferred that if the area of the illuminated surface is known,
measuring experimentally the autoconvolution of the speckle pattern, it would be possible
measuring the roughness of this surface. To conduct laboratory experiments would be
necessary to build larger tables with more values, for different incident beam intensities. This property will be important for ulterior calculations. This property will be important for ulterior calculations. 7.1 Circular beam By examining the calculations it also follows that for values of RU close to zero, the
difference between logCOV, corresponding to a BD, and a diameter corresponding to half
l
i
i
t l
t
t
d
l t 2 i y
g
By examining the calculations it also follows that for values of RU close to zero, the
difference between logCOV, corresponding to a BD, and a diameter corresponding to half
value, is approximately constant and equal to 2, i.e. 406 MATLAB – A Ubiquitous Tool for the Practical Engineer logCOV’- logCOV=2
=> COV’/COV=102, logCOV’- logCOV=2 and, in general, and, in general, '
(
')
10
(
)
N
N
COV N
COV N
. (13) (13) This property will be important for ulterior calculations. 7.2 Square mask In the preceding developing calculations, a circular geometry for the beam was supposed. However, other possibilities may occur. For instance, when a laser ray is directed onto a sample under an angle of incidence, the effective area intersected by the beam has a quasi-
elliptical form. Although an elliptical mask is easy to simulate with MATLAB, this
paragraph deals with the study of the effect of employing a square aperture. This
approximation simplifies the program, since there is no need the beam diameter datum. Moreover, from the point of view of the results, it has little influence in the final values
when comparing these values with those obtained for an elliptical mask. p
g
p
The simulation gives the results of log(COV) for RU = 0.0, 0.1, ... 0.5, and N = 16, 32, 64, 128,
256, 512, that appear in the following table: N\RU
0.0
0.1
0.2
0.3
0.4
0.5
16
9.63
9.24
8.08
7.52
7.59
7.57
32
12.04
11.72
10.73
9.49
9.33
9.34
64
14.45
14.10
13.05
11.47
11.14
11.14
128
16.86
16.51
15.48
13.81
12.95
12.95
256
19.27
18.92
17.89
16.19
14.80
14.75
512
21.67
21.33
20.30
18.57
16.68
16.56
Table 2. Values of the autoconvolution log(COV) for different data and roughness parameter
RU. The results in green do not give information. Table 2. Values of the autoconvolution log(COV) for different data and roughness parameter
RU. The results in green do not give information. Figure 11 represents the values of the attached table II. These curves show the dependence
of log(COV) with the roughness for different values of N, provide that the roughness is less
than 0.4. Therefore, the trend is maintained even if the aperture is different. From the figure
it follows that, except for values marked in green on the table, the dependence of logCOV
with roughness is approximately parabolic, and can be approximated by the equation 2
logCOV
a
b
RU
. (14) (14) As in section 7.1., the difference of the log(COV) for consecutive values of RU, follows
certain regularity. In fact, if the values of log(COV) for RU=0 are examined (see figure 11),
we observe that for adjacent values of this variable, the differences between two consecutive
points (corresponding to double N) are: 2.41, 2.41,2.41, 2.41, 2.40. 7.2 Square mask Taking into consideration
these differences, the following mathematical relationship is verified: Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 407 Fig. 11. Values of log(COV) for roughness RU = 0.0, 0.1, ... 0.5. 2.41
8
'
log
' log
2.41
10
257
2
'/
2
COV
COV
COV
N
N
COV
. (15) (15) Table 3 below relates the difference of logarithms with the ratio N’/N. N’/N
1
2
4
8
….. 2n
logCOV’-logCOV
0
2.41
2×2.41
3×2.41
….. n×2.41
Table 3. Logarithmic difference for RU=0 N’/N
1
2
4
8
….. 2n
logCOV’-logCOV
0
2.41
2×2.41
3×2.41
….. n×2.41
Table 3. Logarithmic difference for RU=0 N’/N
1
2
4
8
….. 2n
logCOV’-logCOV
0
2.41
2×2.41
3×2.41
….. n×2.41
Table 3. Logarithmic difference for RU=0 From these values it yields, log(
'/
)
'
2
log 2
n
N
N
N
n
N
,
(16) (16) log(
/
)
2
log 2
n
N
N
N
n
N
,
(16)
therefore, therefore, 2.41/log 2
7.999
8
2.41/log 2
2.41/log 2
8
2.41/log 2
2.41/log 2
log(
'/
)
'
log
' log
2.41
log
log 2
log(
'/
)
log(
'/
)
log(
'/
)
'
'
(
'/
)
'
N
N
COV
COV
COV
COV
N
N
N
N
N
N
COV
COV
COV
N
N
k
COV
kN
kN
COV
N
N
, log(
'/
)
'
log
' log
2.41
log
log 2
N
N
COV
COV
COV
COV
where k is a constant. From the definition of k it follows that where k is a constant. From the definition of k it follows that where k is a constant. From the definition of k it follows that 2.41
log
log
log
log 2
k
COV
N
. (17) (17) Applying this formula for N = 64 we have ng this formula for N = 64 we have 408 MATLAB – A Ubiquitous Tool for the Practical Engineer 2.41
log
14.45
log64
0.01000
0.9772
log 2
k
k
,
(18) (18) therefore, therefore, 2.41
log
0.01
log
0.01
8.006log
log 2
COV
N
N
. 7.2 Square mask (19) (19) Using this result to the values of N: 32, 64, 256, 512 (RU=0), we btain for log(COV): 12.04,
14.45, 16.86, 19.27, and 21.68, respectively. These results agree with those of the table II. A more general fit for log(COV) considering and RU can be found, provided that RU ≤ 0.4: 2
log
0.01000
8.006log
COV
N
b
RU
. (20) (20) o determine the value of b, we choose, for example, N=128 and RU=0.2, which yields To determine the value of b, we choose, for example, N=128 and RU=0.2, which yields To determine the value of b, we choose, for example, N=128 and RU=0.2, which yields alue of b, we choose, for example, N=128 and RU=0.2, which yields 2
15.48
0.01000
8.006log128
0.2
34.50
b
b
(21) (21) 2
2
log
0.01000
8.006log
34.50
8.006log
34.50
COV
N
RU
N
RU
. Solving the unknown in Eq. (20) we have 2
2
log
0.01000
8.006log
34.50
8.006log
34.50
COV
N
RU
N
RU
. Solving the unknown in Eq. (20) we have 2
2
log
0.01000
8.006log
34.50
8.006log
34.50
COV
N
RU
N
RU
. Solving the unknown in Eq. (20) we have Solving the unknown in Eq. (20) we have 8
1 log
34.5
N
RU
COV
. (22) (22) The advantage of this formula is that it allows calculating the value of the roughness for
each N and D. The advantage of this formula is that it allows calculating the value of the roughness for
each N and D. To verify the accuracy of these results, we introduce some values of roughness and number The advantage of this formula is that it allows calculating the value of the roughness for
each N and D. To verify the accuracy of these results, we introduce some values of roughness and number
of samples in Eq.(20). For RU=0.1, N=32: The advantage of this formula is that it allows calculating the value of the roughness for
each N and D. To verify the accuracy of these results, we introduce some values of roughness and number
of samples in Eq.(20). 7.2 Square mask To verify the accuracy of these results, we introduce some values of roughness and number
of samples in Eq.(20). For RU=0.1, N=32: 2
log
8.006log 32
34.50
0.1
11.70
COV
. For RU =0.1, N =512: 2
log
8.006log 512
34.50
0.1
21.35
COV
. For RU =0.3, N =32: 2
log
8.006log 32
34.50
0.3
8.95
COV
. For RU =0.3, N =512: For RU =0.3, N =512: 2
log
8.006log 512
34.50
0.3
18.59
COV
. It may be seen that the differences between these values calculated with the formula (20)
and those displayed in table II are equal to or less than 0.02, except for the case N = 32, RU =
0.3, which is 0.15. But as in this case the value of the table does not correspond to the
difference of logarithms (marked in green), it follows that the equation obtained is suitable
for the specified intervals. Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 409 Fig. 12. Values of RU (from 0.0 to 0.5) as a function of N and COV (Eq.(22)). Fig. 13. Thissurface represents the function log(COV) for differerent values of N and RU (Eq.(21)). Fig. 12. Values of RU (from 0.0 to 0.5) as a function of N and COV (Eq.(22)). Fig. 12. Values of RU (from 0.0 to 0.5) as a function of N and COV (Eq.(22)). Fig. 13. Thissurface represents the function log(COV) for differerent values of N and RU (Eq.(21)). Fig. 13. Thissurface represents the function log(COV) for differerent values of N and RU (Eq.(21 13. Thissurface represents the function log(COV) for differerent values of N and RU (Eq.(21 8. Apendix A
L=…….? BD=…..? RAN=randn(L);
colormap(gray)
RU1=0
RU2=0.1
RU3=0.2
RU4=0.3
RU5=0.4
RU6=0.5
for i=1:L
for j=1:L
if (BD/2)^2<=((i-.5-L/2)^2+(j-.5-L/2)^2) 8. Apendix A 8. Apendix A
L=…….? BD=…..? RAN=randn(L);
colormap(gray)
RU1=0
RU2=0.1
RU3=0.2
RU4=0.3
RU5=0.4
RU6=0.5
for i=1:L
for j=1:L
if (BD/2)^2<=((i-.5-L/2)^2+(j-.5-L/2)^2) MATLAB – A Ubiquitous Tool for the Practical Engineer 410 g
(
)
RURAN3=RU3*RAN; h3=RURAN3.*BS; C3=h3(L/2,:); RURAN4=RU4*RAN; 411 Simulation of Rough Surfaces and Analysis of Roughness by MATLAB RURAN6=RU6*RAN;
h6=RURAN6.*BS;
C6=h6(L/2,:);
ts6=BS.*exp(4i*pi*RURAN6);
FO6=fft2(ts6);
FIDI6=(abs(FO6)).*(abs(FO6));
CO6=conv2(FIDI6,fliplr(flipud(FIDI6)));
COV6=conv2(FIDI6,fliplr(flipud(FIDI6)),'va
LCOV6=log10(COV6) MATLAB – A Ubiquitous Tool for the Practical Engineer 412 Apendix B
0
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g. 14. N=500; D=8; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. ffraction pattern. (c) Autoconvolution. 9. Apendix B 9. Apendix B 9. Apendix B 100
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100
200
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500 Fig. 14. N=500; D=8; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b)
Diffraction pattern. (c) Autoconvolution. Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 413 0
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g. 15. N=500; D=16; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter
eckle pattern. (c) Autoconvolution. 200400600 8001000 200400600 8001000 Fig. 15. N=500; D=16; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b)
Speckle pattern. (c) Autoconvolution. 9. Apendix B MATLAB – A Ubiquitous Tool for the Practical Engineer 414 0
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g. 16. N=500; D=32; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b)
peckle pattern. (c) Autoconvolution. Fig. 16. N=500; D=32; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b)
Speckle pattern. (c) Autoconvolution. Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 415 0
100
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300
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600
-1
0
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g. 17. N=500; D=64; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (
eckle pattern. (c) Autoconvolution. 9. Apendix B 0
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1 100
200
300
400
500
100
200
300
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500 200
400
600
800
1000
200
400
600
800
1000 Fig. 17. N=500; D=64; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b)
Speckle pattern. (c) Autoconvolution. MATLAB – A Ubiquitous Tool for the Practical Engineer 416 0
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g. 18. N=500; D=128; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. ) Speckle pattern. (c) Autoconvolution. 0
500
1000
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500 0
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2 Fig. 18. N=500; D=128; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b) Speckle pattern. 10. References Born, M; Wolf, E; (1999) Principles Optics, Cambridge University Press. pp. 412-484. Etter, D.M.; (1997) Engineering problem solving with MATLAB. Prentice-Hall. Gascón, F.; Salazar, F.; (2006) A simple method to simulate diffraction and speckle patterns
with a PC, Optik, Vol. 117, pp. 49-57. Gascón, F.; Salazar, F.; (2008) Numerical computation of in-plane displacements and their
detection in the near field by double-exposure objective speckle photography, Opt. Commun., Vol. 281, pp- 6097-6106. pp
Glio, M.; Musazzi, S.; Perini, U.; Surface measurement by means of speckle wavelength
decorrelation”, Opt. Commun. Vol. 28, 1979, pp. 166-170. p
pp
Goodman, J.W.; (1975) Dependence of image speckle contrast on surface roughness. Opt. Commun, Vol. 14, pp. 324-327. Huntley, J.M.; (1989) Speckle photography fringe analysis: assessment of current algorithms,
Appl. Opt. Vol. 28, pp. 4316-4322. (See references therein). Kreis, T.; (2005) Handbook of Holographic Interferometry. Wiley-VCH, Weinheim, Ch.1, 2. Lehmann, P.; Patzelt, S.; Schöne, A.; (1997) Surface roughness measurement by means of
polychromatic speckle elongation. Appl. Opt. Vol. 36, pp. 2188-2197. Leonhardt, K.; Tiziani, H.J.; (1982) Removing ambiguities in surface roughness
measurement. Optica Acta, Vol. 29, pp. 493-499 Lipson, S.G.; Lipson, H.; (1995) Tannhauser: Optical Physics. Cambridge University Press,
Cambridge, p.162. Patzelt, S.; Horn, F; Goch, (2006) G; Fast integral optical roughness measurement of specular
reflecting surfaces in the nanometer range. XVIII Imeko World Congress, Rio de
Janeiro, Brazil. Persson, U.; (2006) Surface roughness measurement on machined surfaces using angular
speckle correlation. J. Mater. Process. Tech., Vol. 180, pp. 233-238. p
pp
Pearson, U.; (1993) Measurement of surface roughness on rough machined surfaces using
spectral speckle correlation and image analysis. Wear, Vol. 160, pp. 221-225. Pérez Quintián, F., Rebollo, M.A; Nogert, E.N.; Landau M. R.; Gaggioli, N.G.; (1996)
Relationship between speckle correlation and refraction index variations:
applications for roughness measurements”, Opt. Eng. Vol 35, , pp. 1175-1178. Ruffing, B.; (1986) Application of speckle-correlation methods to surface-roughness
measurement: a theoretical study, J. Opt. Soc. Am. A, vol. 3, pp. 1297-1304. Ruffing, B.; (1987) Non-contacting roughness measurement of technical surfaces by speckle-
correlation method. Doctoral Thesis. University of Karlsruhe. (In german) Spagnolo, G.S.; Paoletti, D.; (1996) Digital speckle correlation for on-line real-time
measurement. Opt. Commun. Vol. 132, pp. 24-28. p
pp
Stratton, J.A.: (1961) Théorie de l´électromagnétisme, Dunod, Paris. p. 531 (
)
g
p
Tay, C. J.; Toh, S. L.; Shang, H. M.; Zhang, J.; (1995) Whole-field determination of surface
roughness by speckle correlation. Appl. Opt, vol. 9. Apendix B (c) Autoconvolution. Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 417 0
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Fig. 19. N=500; D=256; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b) Speckle pattern. (c) Autoconvolution. Fig. 19. N=500; D=256; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b) Speckle pattern. (c) Autoconvolution. MATLAB – A Ubiquitous Tool for the Practical Engineer 418 0
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20. N=500; D=500; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diamete
Speckle pattern. (c) Autoconvolution. 00
100200300400500
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1000 Fig. 20. N=500; D=500; RU= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5. (a) Surface height along the diameter. (b) Speckle pattern. (c) Autoconvolution. Simulation of Rough Surfaces and Analysis of Roughness by MATLAB 419 Yoshimura, T.; Kato, K.; Nakagawa, K.; (1990) Surface-roughness dependence of the
intensity correlation function under speckle-pattern illumination, J. Opt. Soc. Am. A,
Vol. 7, pp. 2254-2259. 1. Introduction Mathematical modeling and computer simulations are widespread instruments used for
biological systems study. Matlab and Simulink are powerful, high-level programming language which offer the
opportunity to apply the principles of linear systems theory in the analysis of biological
systems; the opportunity to develop adequate computer simulation techniques and
algorithms in order to model dynamic responses of physiological systems, and to collect and
analyze data and to visualize the results information for the simulation processes MATLAB in Biomodeling Cristina-Maria Dabu
CRIFST – Romanian Academy
Romania 10. References 34, pp. 2324-2335. Xiaomei, Xu.; (2009) Non-contact Surface Roughness Measurement Based on Laser
Technology and Neural Network. Proc. IEEE, International Conference on
Mechatronics and Automation. Changchun, China. g
Yamaguchi, I.; Kobayashi, K.; Yaroslavsky, L.; (2004) Measurement of surface roughness by
speckle correlation. Opt. Eng., Vol. 43, pp. 2753-2761. MATLAB – A Ubiquitous Tool for the Practical Engineer 420 Yoshimura, T.; Kato, K.; Nakagawa, K.; (1990) Surface-roughness dependence of the
intensity correlation function under speckle-pattern illumination, J. Opt. Soc. Am. A,
Vol. 7, pp. 2254-2259. Zhao, Gao; Xuezeng, Zhao; (2008) On-Line Surface Roughness Measurement Based on
Specular Intensity Component of Speckle Patterns. Proc. IEEE 2008, International
Conference on Information and Automation. Zhangjiajie, China. 20
MATLAB in Biomodeling
Cristina-Maria Dabu
CRIFST – Romanian Academy
Romania 20 2. Systemic modeling in biosciences The algorithm for developing systemic and mathematical models in neurobiology
Biological systems are adaptive systems, stable, equipped with control mechanism
(feedback) extremely fine (Heinrich, 1996). In fig.2 we have considered a model rule to
regulate processes within the neuron, a model that, in various forms, otherwise we will find
all subprocesses in regulating cell. In the neuronal cell, extracellular and intracellular stimuli are captured and measured by
specialized receptor structures located in the cytoplasm and in the cell membrane. Stimul
are represented by various substances that circulate in the body (hormones, oxygen ions
different protein structures), environmental factors (radiation, temperature variations, etc. and electrical impulses from adjacent cells. Based on these stimuli, and coded programs to
DNA, control mechanisms (feedback) provides nerve cell adaptation to environmenta
conditions. They aim to develop cell responses to stimuli coming from the externa
environment and internal, depending on the deviation e(t) measured between the mode
output (encoded at the genetic level) yM(t) and output biosystem (neuronal cell) y(t). ( )
M
ε t = y (t) - y(t)
(1.1
Under ideal operating conditions for the neuronal cell (t)
0
ε
→
Where:
u(t) = input size
r(t) = size reference
y(t) = output size
p(t) = disturbance g. 1. The algorithm for developing systemic and mathematical models in neurobiology Biological systems are adaptive systems, stable, equipped with control mechanisms
(feedback) extremely fine (Heinrich, 1996). In fig.2 we have considered a model rule to
regulate processes within the neuron, a model that, in various forms, otherwise we will find
all subprocesses in regulating cell. g
g
In the neuronal cell, extracellular and intracellular stimuli are captured and measured by
specialized receptor structures located in the cytoplasm and in the cell membrane. Stimuli
are represented by various substances that circulate in the body (hormones, oxygen ions,
different protein structures), environmental factors (radiation, temperature variations, etc.)
and electrical impulses from adjacent cells. Based on these stimuli, and coded programs to
DNA, control mechanisms (feedback) provides nerve cell adaptation to environmental
conditions. They aim to develop cell responses to stimuli coming from the external
environment and internal, depending on the deviation e(t) measured between the model
output (encoded at the genetic level) yM(t) and output biosystem (neuronal cell) y(t). 2. Systemic modeling in biosciences Models are extremely useful in understanding how the neuronal cell stores, computes,
integrates and transmit the information necessary for the survival of the organism. Computer assisted models permit also to create a variety of test scenarios that would be too
difficult, expensive or dangerous to allow to happen in reality. The main goal in modeling and simulation in the area of Biosciences is to develop
integrative models and simulation which allow the dynamic representation of signaling and
metabolic networks in the neuronal cell as open systems with distinct input and output
ports and specific response mechanisms. The systemic approach in the actual researches in
the field of biomodeling aim to fit together the different level at which complex biological
systems are working, from genes through cells, organs to the whole organism (Noble, 2002). The majority of biological and physiological control systems are nonlinear and the control is
often accomplished parametrically. p
p
y
Biological systems are hierarchical systems, characterized by: y
Biological systems are hierarchical systems, characterized by: 1. Each level has unique language, concepts or principles; g
g
2. Each level is an integration of items from a lower level; discoveries or descriptions at
i-th tlevel aid understanding of phenomena at i+1 level; 2. Each level is an integration of items from a lower level; discoveries or descriptions at
i-th tlevel aid understanding of phenomena at i+1 level; 2. Each level is an integration of items from a lower level
i-th tlevel aid understanding of phenomena at i+1 level; 3. Relationship between levels is not symmetrical; p
y
In fig.1. is presented the algorithm used for developing biological systemic and
mathematical models. Control systems theory, applied in the neuronal modeling, is used to
analyze the dynamic properties of the neuronal metabolic and signaling pathways and to
understand the role of feedback loops in the reaction networks. The essence of this approach
lies in the dynamics of the system and cannot be described merely by enumerating the
components of the system. In the systemic approach, the neuronal cell is considered an open
system with distinct input and output ports and specific response mechanisms. MATLAB – A Ubiquitous Tool for the Practical Engineer 422 Fig. 1. The algorithm for developing systemic and mathematical models in neurobiology Fig. 1. MATLAB in Biomodeling Models about the mechanisms of neuron refers to adaptive changes in cell metabolism,
compared with the extracellular environment. In the presence of enzymes, synthesized as a
result of chemical reactions, substances taken from the cell improper turns feeding their cell
substance. Exchange with the outside is permanent and will work antientropic cell, because
it will prevent their growth through disruption of entropy. Fig. 2. The systemic model for the regulation processes in the neuronal cell Fig. 2. The systemic model for the regulation processes in the neuronal cell 2. Systemic modeling in biosciences (1.1) ( )
M
ε t = y (t) - y(t) Under ideal operating conditions for the neuronal cell (t)
0
ε
→ Under ideal operating conditions for the neuronal cell (t)
0
ε
→ Under ideal operating conditions for the neuronal cell (t)
0
ε
→
Where: u(t) = input size
r(t) = size reference
y(t) = output size
p(t) = disturbance 423 MATLAB in Biomodeling 3. Neuronal cell processes modeling 3.1 The systemic and mathematical models of protein synthesis in the neuronal cell
From the systems theory viewpoint, the neuronal cell is an open system with distinct input
and output ports and specific response mechanisms. Signaling action through the pathways
result in different categories of cellular responses like ionic channel opening or closing,
neuronal differentiation or neuronal cell death. The dynamical models of signaling pathways
are nonlinear and the analysis of their behavior in challenging request specific algorithms. In a first approximation, the protein synthesis process at neuronal level may be modeled like
a open three-compartmental system (fig.3.) y
g
g
g
In a first approximation, the protein synthesis process at neuronal level may be modeled like
a open three-compartmental system (fig.3.) Fig. 3. The three-compartmental model for the protein synthesis process Fig. 3. 3. Neuronal cell processes modeling The three-compartmental model for the protein synthesis process MATLAB – A Ubiquitous Tool for the Practical Engineer 424 The equilibrium equations which are describing the system are: The equilibrium equations which are describing the system are: The equilibrium equations which are describing the system are: NR
N
NC
CN
C
R
d q (t) = (-k
+ k
)q
- k
q
dt
(2.1.1)
C
NC
CN
N
CR
R
d q (t) = (k
- k
)q
- k
q
+ i(t)
dt
(2.1.2)
R
NR
N
CR
C
e
f
d q (t) = k
q
- k
q
- k P (t)
dt
(2.1.3) C
NC
CN
N
CR
R
d q (t) = (k
- k
)q
- k
q
+ i(t)
dt
(2.1.2) R
NR
N
CR
C
e
f
d q (t) = k
q
- k
q
- k P (t)
dt
(2.1.3) Passing in the matrix form, we have: Passing in the matrix form, we have: dq = Aq
dt
(2.1.8) dq = Aq
dt
(2.1.8)
N
N
C
C
R
R
e f
0
q
(t)
q
(t)
d
dq
q (t)
= q
q (t)
=
I(t)
=
dt
dt
q (t)
q (t)
-k P (t)
b
⎛
⎞
⎛
⎞
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
⎝
⎠
(2.1.5) dq = Aq
dt
(2.1.8)
N
N
C
C
R
R
e f
0
q
(t)
q
(t)
d
dq
q (t)
= q
q (t)
=
I(t)
=
dt
dt
q (t)
q (t)
-k P (t)
b
⎛
⎞
⎛
⎞
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
⎝
⎠
(2.1.5)
NC
CN
NR
CN
CR
NC
NR
CR
0
(-k
+ k
)
-k
-(-k
+ k
)
0
-k
= A
k
k
0
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
(2.1.6) (2.1.8) N
N
C
C
R
R
e f
0
q
(t)
q
(t)
d
dq
q (t)
= q
q (t)
=
I(t)
=
dt
dt
q (t)
q (t)
-k P (t)
b
⎛
⎞
⎛
⎞
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
⎝
⎠
⎝
⎠
(2.1.5) NC
CN
NR
CN
CR
NC
NR
CR
0
(-k
+ k
)
-k
-(-k
+ k
)
0
-k
= A
k
k
0
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
(2.1.6) (2.1.6) (2.1.6) Using the substitutions (2.5) and (2.6) we get the next afine equation: dq
= Aq + b
dt
(2.1.7) (2.1.7) With the initial condition:
0
0
q(t ) = q With the initial condition:
0
0
q(t ) = q In order to solving this equation, we have firste to determinate the solution of the
homogenous equation: dq = Aq
dt
(2.1.8) dq = Aq
dt (2.1.8) The General solution of such an equation is: The General solution of such an equation is: 0
3,3
A(t-t )
q(t) = Ce
,A
M
(R)
∈
(2.1.9)
0
0
n 0
n
A (t - t )
A(t-t )
e
=
n! 3. Neuronal cell processes modeling ≥∑
(2.1.10) 0
3,3
A(t-t )
q(t) = Ce
,A
M
(R)
∈
(2.1.9) (2.1.9) where: 0
0
n 0
n
A (t - t )
A(t-t )
e
=
n! ≥∑
(2.1.10) (2.1.10) 425 MATLAB in Biomodeling MATLAB in Biomodeling The proper values of matrix A, used in the study of the protein synthesis process stability
are: 1
2
CR
CN
NR
3
CR
CN
NR
λ = 0
2
2
2
λ = i k
+ k
+ k
2
2
2
λ = i k
+ k
+ k
(2.1.11) The main biochemical process in the protein synthesis is the formation of the peptide bound. The necessary information for the synthesis of a protein is stored at the specific structural
gene level coded as purines and pyrimidine bases of DNA molecule structure. To each
amino acid is corresponding a characteristic group of three bases, called codon, the total
number of specific combinations being 64. Through a process of transcription, the code is
transferred in the form of an mRNA molecule, synthesized in the nucleus and then
transferred into the cytoplasm. The RNA molecule acts on the ribosomes, in the initiation
stage of synthesis process. During the transcription process, each sequence of DNA is copied
into a corresponding sequence on the mRNA. p
g
q
The RNA synthesized in the neuronal cell nucleus is transferred through the nuclear pores
in the cytoplasm in two forms: mRNA and tRNA, each of the two macromolecular structures
fulfilling specific roles in the synthesis the proteins. Also, in the cytoplasm of amino acid
activation occurs in the presence of ATP, under the influence of specific amino-synthase,
resulting in an amino-AMP synthetase complex. In this specific tRNA, also synthesized by the
DNA transcription synthase is released, forming amino acid-activated tRNA complex. acids activated and coupled with tRNA, reach the ribosomes structures where protein
is takes place in three phases: •
termination phase In the protein synthesis process are implied: Messenger RNA, formed the nucleus (mRNA) Cytoplasmic transfer RNA (tRNA) •
Enzyme activation of amino acids (amino tRNA-synthase) •
Initiation Factors •
Transfer Factors •
Termination factors The initiation phase The protein synthesis process is triggered under the influence of initiation factors existing in
the cytoplasm, and, especially, the mRNA, which contains an initiation codon Uracil-
Guanine-Adenine (UGA), which is fixed on the 40S ribosomal subunit. On the initiation
codon is fixing the initiation tRNA, which is containing the initiation anticodons (sequence
complementary codon UGA) and carries the emtionina. The tRNA initiation is carried at the
P-site P-peptidyl from the 60S subunit (Haulica, 1997). MATLAB – A Ubiquitous Tool for the Practical Engineer 426 The elongation phase On the codone that follows the initaiting one, is fixing itself the corresponding tRNA which is
bringing the first aminoacid from the proteic sequence, and positioning itself on an second
site (A) from the 60S subunit. When two tRNA molecules are fixed on the ribosome, is acting a
ribosomal transpeptidase which is transferring the formilmetioninic residue from the P site
tRNA on the A site tRNA, forming a dipeptidil-tRNA is. Then, through a phenomenon of
translocation, during which the ribosome dipeptidil-tRNA is and moving in opposite
directions on the distance of a codon, dipeptidil reach the site of P-tRNA, and the site of,
remained open, it's loaded with fixed tRNA the second amino acid sequence. By repeating the
process, to add new amino acids, in accordance with the code sent. The process described is
carried out based on energy supplied by ATP and GTP, and elongation of existing factors in
the cytoplasm (Haulica, 1997). The terminal phase Based on bio-physiological processes described above, we have developed the following
model for the systemic process of protein synthesis in the neuronal cell (fig.4), where: DNA = deoxyribonucleic acid y
A = messenger ribonucleic acid mRNA = messenger ribonucleic acid tRNA = transfer ribonucleic acid tRNA = transfer ribonucleic acid rRNA = ribosomal ribonucleic acid In the cytoplasm, the conservation equations for tRNA and mRNA mass will be: t
AMP
P
L
D
RNA
RNA
RNA
RNA
RNA
t
t
t
t
dM
= Q
+ Q
- Q
- Q
dt
(2.1.12)
m
m
m
m
P
L
D
R
RNA
RNA
RNA
RNA
RNA
m
dM
= Q
+ Q
- Q
- Q
dt
(2.1.13) Where: MRNAm, MRNAt = mass of mRNA, respectively mass of tRNA; MRNAm, MRNAt = mass of mRNA, respectively mass of tRNA; QRNAmP, QRNAtP = mRNA flows, respectively tRNA flows, coming from the nucleus i
cytoplasm through nuclear pores; QRNAmP, QRNAtP = mRNA flows, respectively tRNA flows, coming from the nucleus into the
cytoplasm through nuclear pores; y
p
g
p
QRNAmL, QRNAtL = mRNA flows, and that tRNA, which are in free state in the cytoplasm RNAmD, QRNAtD = mRNA flows, and that tRNA, degraded citosolic nuclease; QRNAmD, QRNAtD = mRNA flows, and that tRNA, degraded citosolic nuclease; QRNAmR = flow mRNA, ribosomal binding sites linked in tRNA; QRNAmR = flow mRNA, ribosomal binding sites linked in tRNA; QRNAtAMP = = flow, which combined with amino-AMP-synthetase complex, forming a
complex amino acid-activated tRNA (Dabu, 2001) When the cell is in rest, we have: RNAm
dM
= 0
dt
(2.1.14) RNAm
dM
= 0
dt (2.1.14) dt MATLAB in Biomodeling
427 MATLAB in Biomodeling 427 P
L
D
R
RNA
RNA
RNA
RNA
m
m
m
m
0 = Q
+Q
- Q
- Q
(2.1.15) P
L
D
R
RNA
RNA
RNA
RNA
m
m
m
m
0 = Q
+Q
- Q
- Q
(2.1.15)
RNAt
dM
= 0
dt
(2.1.16)
P
L
D
RNA
RNA
RNA
ARN
t
t
t
AMP
0 = Q
+ Q
- Q
- Q
t
(2.1.17) P
L
D
R
RNA
RNA
RNA
RNA
m
m
m
m
0 = Q
+Q
- Q
- Q
(2.1.15)
RNAt
dM
= 0
dt
(2.1.16) RNAt
dM
= 0
dt
(2.1.16) dt P
L
D
RNA
RNA
RNA
ARN
t
t
t
AMP
0 = Q
+ Q
- Q
- Q
t
(2.1.17) P
L
D
RNA
RNA
RNA
ARN
t
t
t
AMP
0 = Q
+ Q
- Q
- Q
t
(2.1.17) Fig. The terminal phase Is triggered by mRNA termination codon (UGA or UAA), reached the site of the codon A. tRNA is not fixed, but protein termination. At this point, unlink transpeptidase peptide chain
composed of the last tRNA. Peptide passes into the cytoplasm, being separated into ribosomal
subunits (Haulica, 1997). 3.2 Modeling the behavior of Ca2+ ions as second messengers The dynamical model for the Ca2+ regulation is nonlinear and the analysis of this process
behavior request specific algorithms and tools. MatLab and Simulink offer adequate tools
and algorithms for modeling these kind of processes. g
g
p
In a neuronal cell in resting state, Ca2+ concentration is maintained at values below 10-7
mol/l, because the existing balance between influx and efflux of Ca2+. Ca2+ influxes that may
come from outside the cell by IL-type channels, the ISA, the messengers I, or G protein
receptor complex or other messengers (cAMP, cGMP, IP4). Another source is the influx of
Ca2+ stores in cell Ca2+ bound in the mitochondria or reticulum endo (sarco) plasma. Increasing concentrations of free cytoplasmic Ca2+ is compensated (in the idle state of the
cell) by effluxes equivalent achievement either to exter (pump ATPase Ca2+ receptor-
operated and how other messengers II system and antiport third Na+/Ca2+) or to deposits
(by the Ca2+ ATPase) (Haulica 1997). ( y
) (
)
Cell activation through the occurrence of an action potential (AP) or through the coupling
action of a messenger I with specific receptors, stimulates the Ca2+ influx and mobilization of
deposits. When the concentration of cytoplasmic free Ca2+ exceeds the threshold value of
10-5 mol/l, cell response is triggered by Ca2+ as second messenger. Depending on the
receptors involved in the process and the path followed, cell responses may get different
aspects: the degradation of cAMP and cGMP, the formation of cGMP and cAMP,
glycogenolysis, the release of synaptic neuromediators, protein synthesis, etc. g y
g
y
y
p
p
y
The effects of activation of other second messengers, Ca2+-CaM complex, modulatory
activated creates the possibility of two or more lines of receptor-activated intracellular
signaling a significant effect on the final pool of the cell response (Rousset et al. 2003) The terminal phase 4. The multi-compartmental model of protein synthesis process in the neuronal cell g. 4. The multi-compartmental model of protein synthesis process in the neuronal cell MATLAB – A Ubiquitous Tool for the Practical Engineer 428 Fig. 5. Chart status for tRNA and mRNA in the neuronal cell Fig. 5. Chart status for tRNA and mRNA in the neuronal cell 3.2 Modeling the behavior of Ca2+ ions as second messengers 3.2.1 Modeling the behavior of neuronal Ca2+ when cell is in rest 3
ode
g t e be a
o o
eu o a Ca
e
ce
s
est
When the cell is at rest, free cytoplasmic Ca2+ concentration is maintained at values below
10-7 mol/l, and the system is described by the following equation (Dabu, 2001): 429 MATLAB in Biomodeling L
SA
I
L
2+
2+
2+
2+
2+
2+
Ca
I
Ca
I
Ca
Msg
Ca
G
Ca
Mit
Ca
RE
2+
2+
Ca
EATP
Ca
LATP
2+
d[Ca
] = Q
+ Q
+ Q
+ Q
+ Q
+ Q
-
dt
-Q
- Q
⎧
⎪⎪⎨
⎪
⎪⎩
(2.2.1) (2.2.1) Where:
[Ca2+L] = concentration of free Ca2+ in nerve cell cytoplasm in a state of rest;
QCa2+IL = influx of extracellular Ca2+ ion channels IL;
QCa2+ISA = influx of extracellular free Ca2+ ion channels ISA;
QCa2+ MsgI = free extracellular Ca2+ influx through messengers I. QCa2+G = free extracellular Ca2+ influx through G protein;
QCa2+Mit = flow freely from the mitochondrial Ca2+ deposits
QCa2+RE = free flow of Ca2+ from the endoplasmic reticulum;
QCa2+EATP = efflux by intracellular free Ca2+ ATPase pump;
QCa2+LATP = intracellular free Ca2+ flux through the ATPase of caught
and stored Ca2+ in mitochondria Where:
[Ca2+L] = concentration of free Ca2+ in nerve cell cytoplasm in a state of rest;
QCa2+IL = influx of extracellular Ca2+ ion channels IL;
QCa2+ISA = influx of extracellular free Ca2+ ion channels ISA;
QCa2+ MsgI = free extracellular Ca2+ influx through messengers I. QCa2+G = free extracellular Ca2+ influx through G protein;
QCa2+Mit = flow freely from the mitochondrial Ca2+ deposits
QCa2+RE = free flow of Ca2+ from the endoplasmic reticulum;
QCa2+EATP = efflux by intracellular free Ca2+ ATPase pump;
QCa2+LATP = intracellular free Ca2+ flux through the ATPase of caught
and stored Ca2+ in mitochondria Fig. 6. The states chart for Ca2+ inside the neuronal cell in rest state Fig. 6. The states chart for Ca2+ inside the neuronal cell in rest state 3.2.2 The cellular response modeling Ca2+ acts as a messenger II in activating the cellular response when the neuronal cell is
activated either by the occurrence of an action potentialor after coupling a messenger I with
a specific receptor and the concentration of Ca2+ free in the cytoplasm exceeds the threshold 430 MATLAB – A Ubiquitous Tool for the Practical Engineer value of about 10-5 mol/l. At the occurrence of an action potential in the neuronal cell as
result of releasing the synaptic mediator in the synaptic space, the membrane depolarization
at terminal button level stopes the penetration of Na+ from outside the cell and generate the
increasing of Ca2 + influx inside the cell. value of about 10-5 mol/l. At the occurrence of an action potential in the neuronal cell as
result of releasing the synaptic mediator in the synaptic space, the membrane depolarization
at terminal button level stopes the penetration of Na+ from outside the cell and generate the
increasing of Ca2 + influx inside the cell. The ions penetrate from the extracellular environment through two kinds of channels:
1. voltage-dependent Na+ channels opened by action potential g
y
2. voltage-dependent ionic channels, which are opened with a certain delay. Fig. 7. States diagram for the free Ca2+ as cell reponse initiator in the activated neuronal cell
t
l Fig. 7. States diagram for the free Ca2+ as cell reponse initiator in the activated neuronal cell
cytoplasm Fig. 7. States diagram for the free Ca2+ as cell reponse initiator in the activated neuronal cell
cytoplasm 2+
Ca
G
2+
L
2+
2+
2+
2+
2+
Ca
I
Ca
I
Ca
Msg
Ca
Mit
Ca
RE
L
SA
I
2+
+
2+
2+
2+
2+
Ca
Na
Ca
EATP
Ca
LATP
Ca
Cmd
Ca
TnC
2+
-5
L
d[Ca
] = Q
+ Q
+ Q
+ Q
+ Q
+ Q
+
dt
+Q
- Q
- Q
- Q
- Q
d[Ca
0,99 * 10
dt
⎧
⎪
⎪
⎪⎨
⎪
⎪
≥
⎪⎩
(2.2.2) (2.2.2) [Ca2+L] = free concentration of the nerve cell cytoplasm in rest state; = free concentration of the nerve cell cytoplasm in rest state; [Ca2+L] = free concentration of the nerve cell cytoplasm in rest state;
QCa2+IL = influx of extracellular Ca2+ ion channels IL;
QCa2+ISA = influx of extracellular free Ca2+ ion channels ISA;
QCa2+Msgl = free extracellular Ca2+ influx through Messengers I channels. 3.2.2 The cellular response modeling q
g
y
The models were developed with MATLAB 4.2 for Windows and SIMULINK 1.3. development, the following were considered: 1. Intracellular Ca2+ is one of the most important messengers II, having a decisive role in
secretion, motility, intermediary metabolism, cellular division, and cell death; 2. Intracellular Ca2+ concentration is very important in information processing at n
level; The mechanisms for regulation of Ca2+ distribution within a neuronal cell includ
mainly non-linear processes, whose kinetics depends both on time and space 4. Not all the sub-systems that contribute to the regulation of intracellular Ca2+
concentration operate at the same rate. Some are rapid systems, while others are slow
systems, with delays and idle periods; 5. Research demonstrated the existence of more Ca2+ transport sub-systems at neuronal
level: mitochondrial sub-system, endo(sarco)plasmatic reticulum sub-system, ionic
channels transportation, Ca2+ ATPases transportation and transport through Na+/Ca2+
ion exchangers 6. Laboratory tests carried out on mouse hippocampus cells demonstrated that, following
and action potential, intracellular Ca2+ concentration could reach the value of 1mM, while,
at rest, intracellular Ca2+ concentration is about 0.1 mM. Laboratory tests analysis,
performed with the FURA-2 system have shown that the induction of an intracellular
depolarization, following 10-20 action potentials, increases the level of intracellular Ca2+
concentration within soma and proximal apical dendrites from 0.02-0.05 mM to 0.1-0.2
mM. The time required for the concentration level to come back to the initial value was
about 100 ns. Other similar Laboratory tests analyzes have shown that the level of
intracellular Ca2+ concentration could increase by 400-500% as a response to an electric
pulse applied for 500 ms, with a comeback to the initial value period of 5 s. p
pp
p
7. Fluctuation of the Ca2+ concentration at cell level depends on:
•
the volume of the substance where the process takes place;
•
local diffusion coefficient 7. Fluctuation of the Ca2+ concentration at cell level depends on:
•
the volume of the substance where the process takes place; •
geometry of the elements and structures analyzed (Dabu,2008)
I
fi
8
d 11
t d th
Si
li k
d l f
th
l ti •
geometry of the elements and structures analyzed (Dabu,2008)
In figures 8 and 11 are presented the Simulink models for the regulation of the Ca2+ in the
neuronal cell in rest state and activated state of the cell. 3.2.2 The cellular response modeling QCa2+G = free extracellular Ca2+ influx through G protein channels;
QCa2+Mit = flow freely from the mitochondrial Ca2+ deposits
QCa2+RE = free flow of Ca2+ from the endoplasmic reticulum;
QCa2+EATP = efflux by intracellular free Ca2+ ATPase pump;
QCa2+LATP = intracellular free Ca2+ flux through the Ca2+ ATPase of captured
and stored in mitochondria Ca2+;
QCa2+Na+ = Ca2+ influx through voltage-dependent Na+ channels opened by action potential
QCa2+Cmd = free flow of cytoplasmic Ca2 + which combines with Calmodulin QCa2+IL = influx of extracellular Ca2+ ion channels IL; gl = free extracellular Ca2+ influx through Messengers I channels. = free extracellular Ca2+ influx through G protein channels; QCa2+Na+ = Ca2+ influx through voltage-dependent Na+ channels opened by action potential
QCa2+Cmd = free flow of cytoplasmic Ca2 + which combines with Calmodulin QCa2+Na+ = Ca2+ influx through voltage-dependent Na+ channels opened by action potential
QCa2+Cmd = free flow of cytoplasmic Ca2 + which combines with Calmodulin 431 MATLAB in Biomodeling QCa2+TnC = free flow of cytoplasmic Ca2+, which combine with TnC QCa2+TnC = free flow of cytoplasmic Ca2+, which combine with TnC
In order to developing the model in SIMULINK, in order to describe the behavior of
intracellular Ca2+ as messenger II, the following things were considered: -
description of the biological process -
description of the biological process
-
analysis of a great number of lab tests regarding the behavior of Ca2+ , including: g
analysis of a great number of lab tests regarding the behavior of Ca2+ , including: The models that were built are characterized by the fact that, for input data that is similar
(from the point of view of equivalence with the real world) to measurable input data for the
real system in laboratory conditions, the output data, from point of view of values and
l
i
i
i
l
h
i
l d
b
i
d f
h l b y
y
p
p
evolution in time, was very close to the experimental data obtained from the lab tests lso, the obtained models have been verified, to establish their validity and adjustm
ere made where it was required, for a higher fidelity of the models. Also, the obtained models have been verified, to establish their validity and adju
were made where it was required, for a higher fidelity of the models. 3.2.2 The cellular response modeling The input ports are the input ionic
channels and receptor sites from the neuronal membrane where signaling molecules initiate
coupled sets of chemical reactions within the cellular space The output ports are the output
ionic channels and the specific binding sites from the neuronal membrane where the
signaling molecules are binding and initiate bio-chemical reactions outside the cell. MATLAB – A Ubiquitous Tool for the Practical Engineer 432 Fig. 8. The Simulink model for the regulation of the Ca2+ in the rest state of the neuronal cell
The results of the simulations are Presented in figures 9 and 10 Fig. 8. The Simulink model for the regulation of the Ca2+ in the rest state of the neuronal cell
The results of the simulations are Presented in figures 9 and 10 Fig. 9. Simulation results with low variation of Ca2+ concentration Fig. 9. Simulation results with low variation of Ca2+ concentration
Fig. 10. Simulation results with higher variation of Ca2+ concentration Fig. 9. Simulation results with low variation of Ca2+ concentration Fig. 10. Simulation results with higher variation of Ca2+ concentration Fig. 10. Simulation results with higher variation of Ca2+ concentration 433 MATLAB in Biomodeling Fig. 11.The Simulink model for the regulation of the Ca2+ in the activate state of the cell g. 11.The Simulink model for the regulation of the Ca2+ in the activate state of the cell Fig. 12. Simulation for the activate neuronal cell
4. Matlab and simulink in computer assisted modeling and systemic
approach for aerobic bioremediation
The aerobic bioremediation treatment process technology use special bacteria blends
engineered in order to biodegrade the organic contamination (fig. 13) into harmless carbon
dioxide and water, to derive energy, with no potential environmental impacts, as compared
to conventional burning methods. Some of the carbon is used by bacteria as ”food” to derive
new carbohydrates, proteins and nucleic acids for growth. One bacteria category is
initializing the process, and other bacteria families are continuing the process (figure 2). The
absence of one bacteria species from the bacteria blend is diminishing the purifying capacity
f h
h l Fig. 12. Simulation for the activate neuronal cell Fig. 12. Simulation for the activate neuronal cell 4. Matlab and simulink in computer assisted modeling and systemic
approach for aerobic bioremediation The aerobic bioremediation treatment process technology use special bacteria blends
engineered in order to biodegrade the organic contamination (fig. 13) into harmless carbon
dioxide and water, to derive energy, with no potential environmental impacts, as compared
to conventional burning methods. Some of the carbon is used by bacteria as ”food” to derive
new carbohydrates, proteins and nucleic acids for growth. One bacteria category is
initializing the process, and other bacteria families are continuing the process (figure 2). The
absence of one bacteria species from the bacteria blend is diminishing the purifying capacity
of the whole system . MATLAB – A Ubiquitous Tool for the Practical Engineer 434 Fig. 13. The systemic model for aerobic bioremediation Fig. 13. The systemic model for aerobic bioremediation For bioremediation to be effective, microorganisms must enzymatically attack the pollutants
and convert them to harmless products. As bioremediation can be effective only where
environmental conditions permit microbial growth and activity, its application often
involves the manipulation of environmental parameters to allow microbial growth and
degradation to proceed at a faster rate. The most used procedures for environmental
parameters manipulation are: biosparging, bioventing, the use of oxygen releasing
compounds; pure oxygen injection, hydrogen peroxide infiltration, ozone injection. All these
procedure add in the contaminated area supplemental supply of oxygen which becomes
available
to
aerobic,
hydrocarbon-degrading
bacteria. Like
other
technologies,
bioremediation has its limitations. Some contaminants, such as chlorinated organic or high
aromatic hydrocarbons, are resistant to microbial attack. They are degraded either slowly or
not at all, hence it is not easy to predict the rates of clean-up for a bioremediation exercise. There are no rules to predict if a contaminant can be degraded (Rockne et al., 2000). Fig. 14. The compartmental systemic model for aerobic bioremediation
Microbial growth and activity are readily affected by pH, temperature, and moisture. Temperature affects biochemical reactions rates, and the rates of many of them double for
each 10°C rise in temperature. Above a certain temperature, however, the cells die. Available water is essential for all the living organisms, and irrigation is needed to achieve
the optimal moisture level. The amount of available oxygen will determine whether the
system is aerobic or anaerobic (fig.14) h
l
d l f
b
b
d Fig. 14. The compartmental systemic model for aerobic bioremediation Microbial growth and activity are readily affected by pH, temperature, and moisture. 4. Matlab and simulink in computer assisted modeling and systemic
approach for aerobic bioremediation Temperature affects biochemical reactions rates, and the rates of many of them double for
each 10°C rise in temperature. Above a certain temperature, however, the cells die. Available water is essential for all the living organisms, and irrigation is needed to achieve
the optimal moisture level. The amount of available oxygen will determine whether the
system is aerobic or anaerobic (fig.14) 435 MATLAB in Biomodeling Biomodeling using Simulink and Matlab can provide important answers regarding the
mechanisms of biodegradation reactions and the evolution of degenerative capabilities in
bacteria/microorganisms. They are usefully to predict the outcome of the bioprocesses and
to evaluate the time and the costs of the intervention, it is necessary to create and use
systemic and computer assisted mathematical models to describe the bioremediation
processes (Dabu 2004). p
(
)
For developing such models, it is necessary to look down the following steps: 1. Establishing the scope of the required treatment; 2. Identifying the inputs and outputs of the system; 3. Identifying the environmental parameters which affect the process and the
corresponding sub-processes (bioavailability, penetration or uptake of the compounds
trough the cell envelope, flow and transport, biochemical reactions, release of products); corresponding sub processes (bioavailability, penetration or uptake of the compounds
trough the cell envelope, flow and transport, biochemical reactions, release of products);
4. Identifying the inhibitory and activator effects of different compounds or
microorganism classes; g
p ,
p
,
,
p
);
4. Identifying the inhibitory and activator effects of different compounds or
microorganism classes; g
5. Identifying the compartmental systemic model of the process. y
g
p
y
p
6. Identifying the transfer functions which are describing every compartment of the model
and the transfer function for the entire model (Dabu & Nicu 1998, Dabu 2004). 6. Identifying the transfer functions which are describing every compartment of the model
and the transfer function for the entire model (Dabu & Nicu 1998, Dabu 2004). Fig. 15. The Simulink model for an anaerobic bioremediation process
Fig. 16. The simulation output Fig. 15. The Simulink model for an anaerobic bioremediation process Fig. 15. The Simulink model for an anaerobic bioremediation process Fig. 16. The simulation output Fig. 16. The simulation output MATLAB – A Ubiquitous Tool for the Practical Engineer 436 1. Introduction Mathematical morphology supplies powerful tools for low-level image analysis. The design
of morphological operators for a given application is not a trivial one. For some problems in
low level image processing the best result is achieved applying to the image an ordered
sequence of morphological operators, that can be done manually, but is not easy and not
always leads to the best solution. Genetic programming (GP) is a branch of evolutionary
computing, and it is consolidating as a promising method for applications of digital image
processing. The main objective of genetic programming is to discover how computers can
learn to solve problems without being programmed for that. In the search for a practical
automatic solution for low level image processing using mathematical morphology and
genetic programming we present in this chapter a Matlab algorithm used for this purpose. Two sample images feed the Matlab application, the first one the original image with all
defects, the second one the goal image where the defects of the original image were
corrected. If we want to find the mathematical morphology operators that implement a
certain filter that removes specific noise from the image, we supply a noisy image and an
image were the noise was removed. The second image can be obtained from the noisy image
applying an image manipulation program. After the parameters are supplied to the Matlab
algorithm, the developed program starts to search for the sequence of morphological
operators that leads to the best solution. The program works iteratively, and at each
iteration compares the result of the morphological operations applied to the image set with
the previous ones. To quantify how good is the solution at each iteration the resulting image
is compared with the reference image using the mean absolute error (MAE) of the pixels. The best solution of the process is the image from a certain set whose error is less than a
reference error indicated to the function. Using this methodology it was possible to solve a
number of low level image processing problems, including edge detection, noise removal,
separation of text from figures, with an error less than 0.5%, most of the time. Examples are
presented along the text to clarify the use of the proposed algorithm. Non Linear Algorithm for Automatic Image
Processing Applications in FPGAs
Emerson Carlos Pedrino1, Valentin Obac Roda2 and Jose Hiroki Saito1,3
1Federal University of Sao Carlos, Department of Computer Science
2Federal University of Rio Grande do Norte, Department of Electrical Engineering
3Faculty of Campo Limpo Paulista
Brazil Emerson Carlos Pedrino1, Valentin Obac Roda2 and Jose Hiroki Saito1,3
1Federal University of Sao Carlos, Department of Computer Science
2Federal University of Rio Grande do Norte, Department of Electrical Engineering
3Faculty of Campo Limpo Paulista
Brazil 5. References B. N. Anderson & R. D. B. N. Anderson & R. D. Henkler. (2000). Monitoring and Control of
Field Bioremediation. Biotechnology 2000:Proceedings of the 11th International
Biotechnology Symposium & 18th DECHEMA Annual Meeting on Biotechnology,
Berlin. Section VI, Environmental Biotechnology, pp. 403-407 gy pp
Cristina – Maria Dabu, M. D. Nicu, “Environmental Biotechnologies and their Implications
in Ecological Problems”, Modern Biotechnologies and the Environment Protection,
1998, 130-135; Dabu C.M. Contributions about mathematical and computer aided modeling of neuronal
structures applied in radiobiology, “Politehnica” University of Bucharest, 2001, pp
5-15 Dr. Cristina –Maria Dabu,. Environmental Biotechnologies and the environment quality
A.G.I.R. Bulletin, no. 4, 2004, 85-88; Dabu C.M. Computational Models end e-Science, Dr. Eng. Cristina – Maria Dabu,
E_COMM_LINE 2005 Volume, 2005, pp351-355 pp
Jiri Dambrosky, Computer modelling of microbial hydrolytic dehalogenation, Pure &Appl. Chem., vol.70, No.7, 1998, 1375-1383; Gonzalez Perez P.P, Modelling intracellular signalling networks using behaviour-based
systems and the blackboard architecture, Universidad Nacional Autónoma de
México, pp.1 pp
Haulica, I., Fiziologie umama, Editia a II -a, Ed. Medicala , Bucuresti, 1997, pp 45-99 Heinrich, R. & Schuster, S. 1996 The regulation of cellular systems. New York: Chapman &
Hall Rockne, K. J., J. C. Chee-Sanford, R. A. Sanford, B. Hedlund, J. T. Staley, S. E. Strand (2000)
Anaerobic naphthalene degradation by microbial pure cultures under nitrate-
reducing conditions. Applied Environmental Microbiology. 66 (4), 1595-1601. Matthieu Rousset, Thierry Cens, Sophie Gavarini, Andreas Jeromin, Pierre Charnet, Down-
regulation of Voltage-gated Ca2_ Channels by Neuronal Calcium Sensor-1 Is _
Subunit-specific, The Journal of Biological Chemistry, Vol. 278, No. 9, Issue of
February 28, pp. 7019–7026, 2003 y
pp
Noble, D. 2002 Modeling the heart—from genes to cells to the whole organ. Science 295,
1678–1682. (doi:10.1126/science.1069881) (
)
Shreedhar Maskey, Andreja Jonoski, Dimitri P. Solomatine, Groundwater Remediation
Strategy Using Global Optimization Algorithms, Jourmal of Water Resources
Planning and Management, 2002, 431-440; M. Vidali, Bioremediation. An overview, IUPAC, Pure and Applied Chemistry 73, 2001,
1163–1172 21 Non Linear Algorithm for Automatic Image
Processing Applications in FPGAs
Emerson Carlos Pedrino1, Valentin Obac Roda2 and Jose Hiroki Saito1,3
1Federal University of Sao Carlos, Department of Computer Science
2Federal University of Rio Grande do Norte, Department of Electrical Engineering
3Faculty of Campo Limpo Paulista
Brazil 2.1 Mathematical morphology Morphological image processing is a nonlinear branch in image processing developed by
Matheron and Serra in the 1960´s, based on geometry, and on the mathematical theory of
order (Dougherty, 1992; Serra, 1982; Weeks, 1996; Soille, 1999; Sonka et al., 1993; Facon,
1996). Morphological image processing has proved to be a powerful tool for binary and
grayscale image computer vision processing tasks, such as edge detection, noise
suppression, skeletonization, segmentation, pattern recognition, and enhancement. Initial
applications of morphological processing were biomedical and geological image analysis
problems. In the 1980´s, extensions of classical mathematical morphology and connections to
other fields were developed by several research groups worldwide along various directions,
including: computer vision problems, multi scale image processing, statistical analysis, and
optimal design of morphological filters, to name just a few (Pedrino et al., 2010). The basic
operations in mathematical morphology are the dilation and the erosion, and these
operations can be described by logical and arithmetic operators. Dilation and erosion
morphological operators can be represented respectively by the sum and subtraction of
Minkowski sets (Dougherty, 1992): A⊕B=⋃{B+a|a ∈ A}
(1)
A⊝-B=∩{A+b|b ∈ B}
(2) (1) (2) In Equation (1), A is the original binary image, B is the structuring element of the
morphological operation, and B+a is the B displacement by a. Therefore, the dilation
operation is obtained by the union of all B displacements in relation to the valid A elements. In Equation (2), -B is the 180o rotation of B in relation to its origin. Therefore, the erosion
operation corresponds to intersection of the A displacements by the valid points of -B. According to Equation (1), the dilation operation will expand an image, and the erosion
operation will shrink it. These operations are fundamental to morphological processing, and
many of the existing morphological algorithms are based on these two primitives
operations. These ideas can be extended to gray level image processing using maximum and
minimum operators, too (Gonzalez & Woods, 2008). Many applications examples can be
found in that text. In addition, color is known to play a significant role in human visual
perception. The application of mathematical morphology to color images is difficult due to
the vector nature of the color data. Mathematical Morphology is based on the application of
lattice theory to spatial structures (Angulo & Serra, 2005). The definition of morphological
operators needs a totally ordered complete lattice structure. 1. Introduction In addition, the
sequence of operators obtained by the Matlab procedure was used to reconfigure an
hardware architecture implemented in FPGAs to process images with the generated
instructions in real time. 438 MATLAB – A Ubiquitous Tool for the Practical Engineer 2. Theoretical background In this section it will be presented a brief review of the theoretical background needed to
understand the concepts used in the development of the current work. Firstly, it will be
presented the theoretical basis of mathematical morphology followed by the fundamentals
ideas of the genetic programming approach. 2.2 Genetic programming Genetic programming (GP) is a technique for automatic programming nowadays and may
provide a better context for the automatic generation of morphological procedures. GP is a
branch of evolutionary computation and artificial intelligence, based on concepts of genetics
and Darwin’s principle of natural selection to genetically breed and evolve computer
programs to solve problems (Koza, 1992). Genetic Programming is the extension of the
genetic algorithms (Holland, 1975) into the space of programs. That is, the objects that
constitute the population are not fixed-length character strings that encode possible
solutions to a certain problem. They are programs (expressed as parse trees) that are the
candidate solutions to the problem. There are few applications of GP for the automatic
construction of morphological operators. According to Koza, in GP, populations of many
computer programs are genetically bred by means of the Darwinian principle of survival
and reproduction of the fittest individual in a population. In this approach, GP starts with
an initial population of computer programs generated randomly, in which each program is
represented by functions and terminals (operands) appropriate to a certain problem domain. Each chromosome (computer program) in the population is measured in terms of its fitness
measure. This measure indicates how well a particular individual performs in a particular
problem environment. The nature of the fitness depends on the problem at hand. A new
offspring population of chromosomes is generated based on the current population using
the Darwinian principle of reproduction and survival of the fittest, as seen before. In
addition, the genetic crossover operator is used, too. The reproduction operator can copy, in
proportion to a fitness, a chromosome (computer program) from current population into the
new population. The crossover operator can produce new offspring computer programs
from two parental chromosomes based on their fitness. Typically, the programs are of
different sizes and shapes. After these process, a new population of individuals is generated
and the old one is deleted. This process is repeated for many generations until a desired
result can be obtained. 2.1 Mathematical morphology A lattice is a partially ordered
set in which any two elements have at least an upper bound (supremum) and a greatest
lower bound (infimum). The supremum and the infimum are represented by the symbols
and , respectively. Thus, a lattice is complete if every subset of the lattice has a single
supremum and a single infimum. The application of mathematical morphology to color
images is difficult due to the vector nature of the color data. The extension of concepts from
grayscale morphology to color morphology must first choose an appropriate color ordering, In Equation (1), A is the original binary image, B is the structuring element of the
morphological operation, and B+a is the B displacement by a. Therefore, the dilation
operation is obtained by the union of all B displacements in relation to the valid A elements. In Equation (2), -B is the 180o rotation of B in relation to its origin. Therefore, the erosion
operation corresponds to intersection of the A displacements by the valid points of -B. According to Equation (1), the dilation operation will expand an image, and the erosion
operation will shrink it. These operations are fundamental to morphological processing, and
many of the existing morphological algorithms are based on these two primitives
operations. These ideas can be extended to gray level image processing using maximum and
minimum operators, too (Gonzalez & Woods, 2008). Many applications examples can be
found in that text. In addition, color is known to play a significant role in human visual
perception. The application of mathematical morphology to color images is difficult due to
the vector nature of the color data. Mathematical Morphology is based on the application of
lattice theory to spatial structures (Angulo & Serra, 2005). The definition of morphological
operators needs a totally ordered complete lattice structure. A lattice is a partially ordered
set in which any two elements have at least an upper bound (supremum) and a greatest
lower bound (infimum). The supremum and the infimum are represented by the symbols
and , respectively. Thus, a lattice is complete if every subset of the lattice has a single
supremum and a single infimum. The application of mathematical morphology to color
images is difficult due to the vector nature of the color data. 2.1 Mathematical morphology The extension of concepts from
grayscale morphology to color morphology must first choose an appropriate color ordering, 439 Non Linear Algorithm for Automatic Image Processing Applications in FPGAs a color space that determines the way in which colors are represented, and an infimum, and
a supremum operator in the selected color space should also be defined. There are several
techniques for ordering vectors. The two main approaches are marginal ordering and vector
ordering. In the marginal ordering, each component P of a pixel is ordered independently,
and the operations are applied to each channel; unfortunately, this procedure has some
drawbacks, e.g., producing new colors that are not contained in the original image and may
be unacceptable in applications that use color for object recognition. The vector ordering
method for morphological processing is more advisable. Only one processing over the three
dimensional data is performed using this method. There are several ways of establishing the
order, e.g., ordering by one component, canonical ordering, ordering by distance and
lexicographical ordering (Chanussot & Lambert, 1998). Once these orders are defined, then
the morphological operators are defined in the classical way (Pedrino, 2010). 3. Developed system The developed system for automatic construction of morphological operators uses a genetic
programming algorithm that operates with two images from a certain image set, an input
image, and an image containing only features of interest which should be extracted from the
input image. The genetic procedure looks in the space of mathematical morphology
operators for sequences that allow extracting the features of interest from the original image. The operators are predefined procedures from a database that work with any kind of 440 MATLAB – A Ubiquitous Tool for the Practical Engineer structuring elements having different shapes and sizes. It is also possible to include new
operators in the database when necessary. The program output is a tree based structure
containing the best individual of the final population. The genetic algorithm parameters are
supplied by the user using a text user interface. The main parameters are: tree depth,
number of chromosomes, number of generations, crossover rate, mutation rate, and certain
kinds of operators suited to a particular problem. The mean absolute error (MAE) was used
as a fitness measure. The cost function using the MAE was calculated as follows: d(a,b)=∑i∑j |(a(i,j)-b(i,j)|/XY
(3) (3) d(a,b)=∑i∑j |(a(i,j)-b(i,j)|/XY In Equation (3), 'a' is the resulting image evaluated by a particular chromosome (program),
and 'b' is the goal image with the same size as 'a', and '(i,j)' is the pixel coordinate. The
programs are encoded as tree structure chromosome. The main steps of the proposed
algorithm are illustrated in Figure 1. In the Figure, the index 'i' refers to an individual in the
population. The reprodution rate is 'pr', the crossover rate is 'pc', and the mutation rate is 'pm'. The goal image can be created using an editor program. As Figure 1 shows, initially the genetic
parameters are selected by the user, along with a couple of sample images that represent the
problem to be solved. Then, the genetic procedure generates a random population of computer
programs (chromosomes), according to the user specifications. A fitness value is assigned to
each program, after the operations of reproduction, crossover and mutation, a new population
of individuals is generated. The described evolutionary process is repeated by many
generations and can be stopped according to a stop condition. 3. Developed system The mutation operator, that was
not previously discussed, simply generates an individual belonging to the space of solutions of
the problem and connects it to a random point of a particular randomly chosen chromosome. Such operation is performed with a given probability. Fig. 1. Flowchart of developed system Fig. 1. Flowchart of developed system 441 Non Linear Algorithm for Automatic Image Processing Applications in FPGAs The process of evaluating a given depth four chromosome of the population of individuals
is shown in Figure 2. 'Img_in' corresponds to the input image, 'ero' and 'dil' instructions
corresponds to the erosion and dilation operations respectively. The argument 'end_n'
matches an address of a table containing all combinations of structuring element for a
given problem. Both the instructions, and the arguments are found in an intelligent manner
when a pair of input images are presented to the genetic procedure. It can be seen in Figure
2 that initially the input image is eroded, followed by two dilations and the resulting image
is eroded again. All the morphological operators in the example use the same structuring
element pointed by 'end_n'. Fig. 2. Example of a chromosome representing a morphological filter and its arguments Fig. 2. Example of a chromosome representing a morphological filter and its arguments Fig. 2. Example of a chromosome representing a morphological filter and its argumen The tournament selection method was the one chosen to be used in this work (Koza, 1992). The training set, used to extract the pair of images used in the presented method, was
obtained using samples of synthetic images of various resolutions. For each resolution the
maximum depth size for each chromosome tree and the error calculation functions were
changed. The training will be further detailed in Section 3.1. As follows, the Matlab
developed algorithm is presented along with some examples. In all the examples binary
images were used, however, the method can be extended to handle any type of image. 3.1 Matlab algorithm The Matlab algorithm for binary images mathematical morphology automatic processing
developed in this work is presented as follows. The Matlab algorithm for binary images mathematical morphology automatic processing
developed in this work is presented as follows. % - Developed Algorithm % - pop: Initial Population % - nc: number of chromosomes % - cr: randomly generated chromosome % - cr_col: columns of cr _
% - num_instr: number of instructions _
% - profd: maximum tree depth % - arg: pointer to the table of arguments pop=pop_init(nc,cr,cr_col,num_instr,profd,arg); % - ger: generations % - ger: generations % - ng: number of generations % - ct aux: auxiliary cost ger=0; ct_aux=inf; while (ger<=ng) 442 MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer % - ct_gn: costs from generation 'n'
% - img_org: input image
% - img_obj: goal image
% - instr: instruction table
ct_gn=cost(nc,pop,img_org,img_obj,instr,profd);
% - elt: best program of generation 'n'
% - ct_min: cost of best program
[elt,ct_min]=elit_indv(pop,ct_gn);
% - Elitism
% - sol: best program found
if (ct_min < ct_aux)
ct_aux=ct_min;
sol=elt;
end
% err: tolerated error
if (ct_aux<=err)
break;
end
% - Crossover
% - pop_g: new population
% - tx_cs: crossover rate
tx_cs_conv=(-10*tx_cs/100)+10; % - ct_gn: costs from generation 'n' _
% - img_org: input image % - img_obj: goal image % - instr: instruction table ct_gn=cost(nc,pop,img_org,img_obj,instr,profd); % - elt: best program of generation 'n' % - ct min: cost of best program _
[elt,ct_min]=elit_indv(pop,ct_gn % - sol: best program found if (ct_min < ct_aux) ct_aux=ct_min; % - pop_g: new population % - tx_cs: crossover rate tx cs conv=(-10*tx cs/100)+10; pop_g=crossover(tx_cs_conv,pop,nc,img_org,img_obj,instr
,profd,sol);
% - Mutation
tx_mt_conv=(-10*tx_mt/100)+10;
pop=mutation(pop_g,num_instr,profd,nc,tx_mt_conv,arg);
ger=ger+1;
end end According to the previous code, the function pop_init is responsible for generating
randomly, using user provided parameters, the initial population of individuals. The
parameters are described as follows. -
nc: number of chromosomes (programs); -
nc: number of chromosomes (programs); -
nc: number of chromosomes (programs);
-
cr: initial chromosome user created;
-
cr_col: number of columns of cr;
-
num_instr: instruction number;
-
profd: maximum depth tree tolerated;
-
arg: pointers vector for the arguments table; -
cr: initial chromosome user created; -
cr_col: number of columns of cr; -
num_instr: instruction number; -
profd: maximum depth tree tolerated; -
arg: pointers vector for the arguments table; -
arg: pointers vector for the arguments table; The implementation of the algorithm pop_init function is shown as follows. This function
uses another function called ger_cr to generate chromosomes randomly. function p_i=pop_init(nc,cr,cr_col,num_instr,profd,arg)
% Initial Population of Individuals
pop(1,1:cr_col)=cr;
for i=2:nc
cr=gera_cr(num_instr,profd,arg);
pop(i,:)=cr;
end
p_i=pop; function p_i=pop_init(nc,cr,cr_col,num_instr,profd,arg % Initial Population of Individuals pop(1,1:cr_col)=cr; for i=2:nc end 443 Non Linear Algorithm for Automatic Image Processing Applications in FPGAs Non Linear Algorithm for Automatic Image Processing Applications in FPGAs function cr=ger_cr(num_instr,profd,arg)
cr=zeros(1,profd*4);
[~,num_arg]=size(arg);
for i=1:4:profd*4
aleat=round(rand*(num_instr-1));
cr(i)=aleat;
aleat=round(rand*(num_arg-1))+1;
cr(i+1)=aleat;
aleat=round(rand*(num_arg-1))+1;
cr(i+2)=aleat;
aleat=round(rand*(num_arg-1))+1;
cr(i+3)=aleat;
end function cr=ger_cr(num_instr,profd,arg)
cr=zeros(1,profd*4); _
cr=zeros(1,profd*4); [~,num_arg]=size(arg); [ ,
_
g]
(
g);
for i=1:4:profd*4
aleat=round(rand*(num_instr-1));
cr(i)=aleat;
aleat=round(rand*(num_arg-1))+1;
cr(i+1)=aleat;
aleat=round(rand*(num_arg-1))+1;
cr(i+2)=aleat;
aleat=round(rand*(num_arg-1))+1;
cr(i+3)=aleat;
end cr(i+3)=aleat; end The cost function is responsible for calculating the cost of each chromosome in current
population of individuals. Internally, it uses two other functions, build_op and comp, the first
one is responsible for building the program, according to the tree structure shown
previously, and the second is responsible for calculating the fitness of chromosomes. Below,
the code part related to the cost and build_op functions is presented. Following, the function
comp is presented, too. The main parameters used for each function are the following. -
nc: number of chromosomes; -
pop: current population; -
img_org: input image; -
img_obj: goal image; -
instr: instructions vector; -
profd: maximum depth allowed to each chromosome. -
profd: maximum depth allowed to each chromosome. The build_op function is responsible for the construction of each individual, using functions
and arguments provided by the user through the instructions vector and by the table of
arguments. The input image is applied to each program generated automatically and the
comp function tests whether the object pixels and the image background pixels correspond to
the pixels of the object and background of the goal image, thereby creating a vector
containing all the costs associated to each program obtained in the present generation. Non Linear Algorithm for Automatic Image Processing Applications in FPGAs function c=cost(nc,pop,img_org,img_obj,instr,profd)
% - It Evaluates the Cost of Each Individual from the Current
Population
c=ones(1,nc);
for i=1:nc
sample=build_op(instr,pop(i,:),profd,img_org);
c(i)=comp(amostra_c,img_obj);
end function c=cost(nc,pop,img_org,img_obj,instr,profd) % - It Evaluates the Cost of Each Individual from the Current
Population c=ones(1,nc); for i=1:nc sample=build_op(instr,pop(i,:),profd,img_org); function op = build_op(instr,cr,profd,img)
% - It Builds a Program
% to be Applied to the
% Input Image
op=eval([char(instr(cr(1)+1)),'(','img',',',num2str(cr(2)),',
',num2str(cr(3)),',',num2str(cr(4)),')']); function op = build_op(instr,cr,profd,img) % - It Builds a Program % to be Applied to the % Input Image p
g
op=eval([char(instr(cr(1)+1)),'(','img',',',num2str(cr(2)),',
',num2str(cr(3)),',',num2str(cr(4)),')']); MATLAB – A Ubiquitous Tool for the Practical Engineer 444 aux_op=op;
% - Building
for i=5:4:profd*4
op=eval([char(instr(cr(i)+1)),'(','aux_op',',',num2str(
cr(i+1)),',' ,num2str(cr(i+2)),',',num2str(cr(i+3)),')']);
aux_op=op;
end
function comp_ab = comp(a,b)
% - It Compares two images (a and b)
TP=0.005;
FN=0.005;
TN=0.005;
FP=0.005;
[lin,col]=size(a);
for i=1:lin
for j=1:col
if b(i,j) && a(i,j)
TP=TP+1;
else
if b(i,j) && ~a(i,j)
FP=FP+1;
else if ~b(i,j) && ~a(i,j)
TN=TN+1;
else
if ~b(i,j) && a(i,j)
FN=FN+1;
end
end
end
end
end
end
SV=TP/(TP+FN);
SP=TN/(TN+FP);
comp_ab=1-(sqrt((1-SP)^2+(1-SV)^2))/sqrt(2);
comp_ab=1-comp_ab; aux_op=op;
% - Building
for i=5:4:profd*4
op=eval([char(instr(cr(i)+1)),'(','aux_op',',',num2str(
cr(i+1)),',' ,num2str(cr(i+2)),',',num2str(cr(i+3)),')']);
aux_op=op;
end end The elit_indv function returns the best current generation chromosome, the elite, and their
associated cost; its parameters are the following. -
pop: current population; -
ct_gn: vector cost for the current population; -
ct_gn: vector cost for the current population; The implementation of the elit_indv function is shown as follows. The implementation of the elit_indv function is shown as follows function [elt,ct_min]=elite_indv(pop,ct) function [elt,ct_min]=elite_indv _
% Best Individual [ct_min,ind]= min(ct); elt=pop(ind,:); The next function implemented was the genetic crossing (crossover), which can be seen
below. Its main parameters are: The next function implemented was the genetic crossing (crossover), which can be seen
below. Its main parameters are: 445 Non Linear Algorithm for Automatic Image Processing Applications in FPGAs -
tx_cs: crossing rate, between 0 and 1 (0 - 100%);
-
pop: current population;
-
nc: number of chromosomes;
-
img_org: input image;
-
img_obj: goal image;
-
instr: instructions vector;
-
profd: maximum depth allowed for each chromosome;
-
sol: best chromosome (program) found so far. The crossing is performed between two trees in the population of individuals, selected
according to a given probability, user specified. Non Linear Algorithm for Automatic Image Processing Applications in FPGAs The crossing method used is similar to the
i
l
t d b
K
(K
1992) -
tx_cs: crossing rate, between 0 and 1 (0 - 100%); -
pop: current population; -
nc: number of chromosomes; -
img_org: input image; -
img_obj: goal image; -
instr: instructions vector; -
profd: maximum depth allowed for each chromosome; -
profd: maximum depth allowed for each chromosome; -
sol: best chromosome (program) found so far. The crossing is performed between two trees in the population of individuals, selected
according to a given probability, user specified. The crossing method used is similar to the
one implemented by Koza (Koza, 1992). function
pop_g=crossover(tx_cs,pop,nc,img_org,img_obj,instr,profd,sol)
% - Crossover. pop_g=pop;
pop_g(1,:)=sol;
pop_indv_at=2;
while (pop_indv_at<=nc)
rd_c=round(rand*nc+.5);
p1=pop(rd_c,:);
rd_c=round(rand*nc+.5);
p2=pop(rd_c,:);
rd_c=round(rand*nc+.5);
p3=pop(rd_c,:);
px=[p1;p2;p3];
% - Tournament selection. ct_gn=custo(3,px,img_org,img_obj,instr,profd);
[elt,~]=elite_indv(px,ct_gn);
% father
p=elt;
[~,ind_p2]=sort(ct_gn);
% mother
m=px(ind_p2(2),:);
rd_num=rand*10;
if (rd num>tx cs) pop_g=pop; pop_g(1,:)=sol; pop_indv_at=2; rd_c=round(rand*nc+.5); p3=pop(rd_c,:); px=[p1;p2;p3]; % - Tournament selection. ct_gn=custo(3,px,img_org,img_obj,instr,profd); _gn=custo(3,px,img_org,img_obj,i [~,ind_p2]=sort(ct_gn); if (rd_num>tx_cs)
ind_imp=1:4:profd*4;
[~,c_ind_imp]=size(ind_imp);
ind_p=ind_imp(round(rand*(c_ind_imp)+0.5));
ind_m=ind_imp(round(rand*(c_ind_imp)+0.5));
gen_p=p(ind_p);
gen_m=m(ind_m);
p(ind_p)=gen_m;
m(ind_m)=gen_p;
aux=round(rand*(3)+0.5);
crt_p=ind_p+aux;
crt_m=ind_m+aux;
gen_p=p(crt_p:ind_p+3);
gen_m=m(crt_m:ind_m+3);
p(crt_p:ind_p+3)=gen_m; if (rd_num>tx_cs)
ind_imp=1:4:profd*4;
[~,c_ind_imp]=size(ind_imp);
ind_p=ind_imp(round(rand*(c_ind_imp)+0.5));
ind_m=ind_imp(round(rand*(c_ind_imp)+0.5));
gen_p=p(ind_p);
gen_m=m(ind_m);
p(ind_p)=gen_m;
m(ind_m)=gen_p;
aux=round(rand*(3)+0.5);
crt_p=ind_p+aux;
crt_m=ind_m+aux;
gen_p=p(crt_p:ind_p+3);
gen_m=m(crt_m:ind_m+3);
p(crt_p:ind_p+3)=gen_m; crt_m=ind_m+aux; p(crt_p:ind_p+3)=gen_m; MATLAB – A Ubiquitous Tool for the Practical Engineer 446 m(crt_m:ind_m+3)=gen_p;
pop_g(pop_indv_at,:)=p;
pop_indv_at=pop_indv_at+1;
if (~rem(nc,2))
pop_g(pop_indv_at,:)=m;
pop_indv_at=pop_indv_at+1;
end
else
pop_g(pop_indv_at,:)=p;
pop_indv_at=pop_indv_at+1;
if (~rem(nc,2))
pop_g(pop_indv_at,:)=m;
pop_indv_at=pop_indv_at+1;
end
end
end -
The mutation function swaps parts of the selected programs, according to a given
probability, with parts of programs belonging to the space of solutions of a given
problem; its parameters are shown as follows. -
The mutation function swaps parts of the selected programs, according to a given
probability, with parts of programs belonging to the space of solutions of a given
problem; its parameters are shown as follows. -
pop: current population; -
profd: maximum depth allowed for each chromosome;
-
nc: number of chromosomes; -
profd: maximum depth allowed for each chromosome; -
tx_mt: mutation rate, between 0 and 1 (0 - 100%); -
arg: pointers vector for the argument table. function pop_g=mutation(pop,num_instr,profd,nc,tx_mt,arg)
% Mutation. [~,num_arg]=size(arg);
pop_g=pop;
for i=1:nc
for j=1:4:profd*4
rd_num=rand*10;
if (rd_num>tx_mt)
rd=round(rand*(num_instr-1));
pop_g(i,j)=rd;
end
rd_num=rand*10;
if (rd_num>tx_mt)
rd=round(rand*(num_arg-1))+1;
pop_g(i,j+1)=rd;
end
rd_num=rand*10;
if (rd_num>tx_mt)
rd=round(rand*(num_arg-1))+1;
pop_g(i,j+2)=rd;
end
rd_num=rand*10;
if (rd_num>tx_mt)
rd=round(rand*(num_arg-1))+1; function pop_g=mutation(pop,num_instr,profd,nc,tx_mt,arg)
% Mutation. function pop_g=mutation(pop,num_instr,profd,nc,tx_mt,arg)
% Mutation. rd_num=rand*10; rd_num=rand*10; rd_num=rand*10; rd_num=rand*10; if (rd_num>tx_mt) Non Linear Algorithm for Automatic Image Processing Applications in FPGAs 447 pop_g(i,j+3)=rd;
d pop_g(i,j+3)=rd;
d p
end
end
end 3.2 Application examples pp
p
In this subsection some application examples, using the algorithm described in the previous
subsection, are presented. All examples are for binary images and use equations 1 and 2
shown in subsection 2.1. A synthetic image containing four objects with different shapes
was generated for implementation of the examples. The training set consisted of three
samples with different resolutions for each picture object. In addition, they were used three
different maximum allowed sizes for each tree size, representing the chromosomes. Also,
in each case the algorithm was run three times. In the first example, it was tried to find a
combination of morphological filters and logical operators to recognize the star present in
the input image (Figure 3). In this figure it is possible to see the desired image and the
training process. The error found for this example was zero. Other training pairs were used
through the training set also resulting in errors very close to zero. For this example the
following genetic parameters and arguments were used. 50 g
nc=500, tx_cs=90%, tx_mt=10%, arg=[1 2 3 4 5 6 7 8], g
tb_arg=[0 0 0;0 0 1;0 1 0;0 1 1;1 0 0;1 0 1;1 1 0; 1 1 1]. tb_arg=[0 0 0;0 0 1;0 1 0;0 1 1;1 0 0;1 0 1;1 1 0; 1 1 1]. The 'arg' vector pointers to 'tb_arg' that corresponds to the table of structuring elements
used in the morphological operations. The instructions vector used in this example was the
following: instr={'nop' 'dil' 'ero' 'or1' 'and1' 'sto1' 'cpl'}, were: nop means no operation; dil corresponds to a dilation through the structuring elements contained in tb_arg;
ero corresponds to an erosion through the structuring elements contained in tb arg; dil corresponds to a dilation through the structuring elements contained in tb_arg;
ero corresponds to an erosion through the structuring elements contained in tb_arg;
1 i
i
l
t t
l
i
l OR
ti sto1 corresponds to a storage operator of the current results in a temporary memory
variable; "5 4 2 4 2 7 5 2 3 5 3 6 3 2 2 8 4 4 5 6 6 6 7
2 1 2 4 5 2 4 4 4 6 6 3 7 4 6 3 6 2 7 5 7 4 4 7
7 3 7 3 2 4 6 7 3 5 2 4 5 2 2 3 6 4 5 7 2 4 7 5
1 3 2 7 3 5 5 5 7 6 6 6 1 1 2 8 8 2 5 7 6 6 5 5
8 0 6 6 5 1 6 5 2 6 1 2 2 6 4 3 3 1 5 2 7 2 7 2
4 6 6 2 3 4 5 1 2" "5 4 2 4 2 7 5 2 3 5 3 6 3 2 2 8 4 4 5 6 6 6 7
2 1 2 4 5 2 4 4 4 6 6 3 7 4 6 3 6 2 7 5 7 4 4 7
7 3 7 3 2 4 6 7 3 5 2 4 5 2 2 3 6 4 5 7 2 4 7 5
1 3 2 7 3 5 5 5 7 6 6 6 1 1 2 8 8 2 5 7 6 6 5 5
8 0 6 6 5 1 6 5 2 6 1 2 2 6 4 3 3 1 5 2 7 2 7 2
4 6 6 2 3 4 5 1 2" Figure 4 shows the algorithm generated to recognize the star presented in the input image. The arguments are pointers to the arguments table containing the structuring elements 448 MATLAB – A Ubiquitous Tool for the Practical Engineer for the morphological operators. The generated machine code, in decimal, for the given
example considering the architecture cited in this work can be seen as follows. were: The above code is transferred to a FPGA dedicated processor architecture. The FPGA
processor processes in real time the images from a video camera with the objective of
determining the shapes intended, according to the training algorithm. The addresses for the
arguments table containing the structuring elements are shown in bold characters, thus
the three arguments will point to three rows of the table forming a structuring element of
size 3x3, equivalent to the size used in implementing each stage of the above architecture. Using this approach it is possible to build 512 different shapes structuring elements. The
numbers representing the functions are pointers to the instruction vector 'instr', whose
index starts at zero, and are not represented in bold characters. Thus, for example, code 1 6 5
2 corresponds to the instruction dil (img, [1 0 1, 1 0 0, 0 0 1]), which is a dilation of 'img'
by the structuring element shown as argument. The image 'img' is obtained from the result
of the previous instruction by a pipeline process, and so on. Fig. 3. Example of an automatic filter construction for recognizing the star present in the
input image Fig. 3. Example of an automatic filter construction for recognizing the star present in the
input image Another application example obtained by the developed system, was the decomposition of
an any shape structuring element in smaller size 3x3 structuring elements. For this example
we used the same parameters of the previous example. The training process for the
evolutionary system of the given problem is illustrated in Figure 5. A binary 17x17 size
object, not decomposed by the algorithm proposed by Park and Chin (Park & Chin, 1995),
could be decomposed by the proposed methodology. The process converged after iteration
300, and the error obtained was zero. The following opcode was generated for the addressed
problem. "0 7 2 5 0 1 2 4 0 5 1 2", Non Linear Algorithm for Automatic Image Processing Applications in FPGAs 449 where the zeros correspond to successive dilations of the input image by the following
structuring elements. where the zeros correspond to successive dilations of the input image by the following
structuring elements. [1 1 0;0 0 1;1 0 0], [0 0 0;0 0 1;0 1 1], e [1 0 0;0 0 0;0 0 1] [1 1 0;0 0 1;1 0 0], [0 0 0;0 0 1;0 1 1], e [1 0 0;0 0 0;0 0 1] After successive dilations of a central point by the above structuring elements, it was
possible to find the object shown in Figure 5. Fig. 4. Algorithm generated for the automatic pattern recognition filter construction problem
shown in Figure 3 Fig. 4. Algorithm generated for the automatic pattern recognition filter construction problem
shown in Figure 3 MATLAB – A Ubiquitous Tool for the Practical Engineer 450 Fig. 5. Example of decomposition of a 17x17 structuring element Fig. 5. Example of decomposition of a 17x17 structuring element Fig. 5. Example of decomposition of a 17x17 structuring element As mentioned earlier in this chapter, the results obtained by the aforesaid system were used
to set up a FPGA implemented architecture, whose block diagram is shown in Figure 6. The
architecture has several reconfigurable pipeline stages that can deal with 3x3 structuring
elements. The concatenation of several stages allows operations with larger size structuring
elements, whose shape can also be flexible. Fig. 6. Architecture used to process the programs generated by the proposed system
(Pedrino et al., 2010) Fig. 6. Architecture used to process the programs generated by the proposed system
(Pedrino et al., 2010) 4. Conclusion The construction of a Matlab algorithm using a methodology for automatic construction of
morphological and logical operators by the use of genetic programming was presented in
this chapter. When presenting pairs of images to the system from a training set, a set of Non Linear Algorithm for Automatic Image Processing Applications in FPGAs 451 instructions and arguments for a given problem and appropriate genetic parameters, an
evolutionary process builds a sequence of nonlinear image operators that given an input
image produces an output image as close as possible to the goal image provided. The
algorithm generated in this work was also used to configure a pipeline processing
architecture in FPGA, capable of processing images in real time, with the images provided
by a CCD video camera. Examples were shown in the text in order to demonstrate the
feasibility of the developed methodology for automatic construction of image processing
algorithms. The task of designing an imaging processing sequence of operators is not so
trivial, so the proposed methodology might be very helpful as an aid for the expert in this
situation. 5. Acknowledgments Emerson C. Pedrino is grateful to the "Fundação de Amparo a Pesquisa do Estado de São
Paulo" for the financial support of this work, thoughout the project, proc. 2009/17736-4. The
authors are also grateful to the Departament of Computer Science/University Federal de
São Carlos, Faculty of Campo Limpo Paulista, and to the Department of Electrical
Engineering/UFRN. Holland, J. (1975). Adaptation in Natural and Artificial Systems, MIT Press, Cambridge, Mass,
USA Park, H. & Chin, R. T. Decomposition of arbitrarily shaped morphological structuring
elements, IEEE Trans. Pattern Anal. Mach. Intell., Vol.17, No1, pp. 2-15 MATLAB – A Ubiquitous Tool for the Practical Engineer Holland, J. (1975). Adaptation in Natural and Artificial Systems, MIT Press, Cambridge, Mass,
USA
Park, H. & Chin, R. T. Decomposition of arbitrarily shaped morphological structuring MATLAB – A Ubiquitous Tool for the Practical Engineer
452
Holland, J. (1975). Adaptation in Natural and Artificial Systems, MIT Press, Cambridge, Mass,
USA
Park, H. & Chin, R. T. Decomposition of arbitrarily shaped morphological structuring
elements, IEEE Trans. Pattern Anal. Mach. Intell., Vol.17, No1, pp. 2-15 Using MATLAB to Compute Heat
Transfer in Free Form Extrusion Sidonie Costa, Fernando Duarte and José A. Covas
University of Minho
Portugal 6. References Dougherty, E. R. (1992). An Introduction to Morphological Image Processing, SPIE, Bellingham,
Wash, USA Serra, J. (1982). Image Analysis and Mathematical Morphology, Academic Press, San Diego,
Calif, USA Serra, J. (1982). Image Analysis and Mathematical Morphology, Academic Press, San Diego,
Calif, USA
Weeks Jr., A. R. (1996). Fundamentals of Electronic Image Processing, SPIE, Bellingham, Wash, Weeks Jr., A. R. (1996). Fundamentals of Electronic Image Processing, SPIE, Bellingham
USA Weeks Jr., A. R. (1996). Fundamentals of Electronic Image Processing, SPIE, Bellingham, Wash,
USA
Soille, P. (1999). Morphological Image Analysis, Principles and Applications, Springer, Berlin, Soille, P. (1999). Morphological Image Analysis, Principles and Applications, Springer,
Germany Soille, P. (1999). Morphological Image Analysis, Principles and Applications, Springer, Berlin,
Germany
Sonka, M., Hlavac, V. & Boyle, R. (1993). Image Processing, Analysis and Machine Vision, ,
(
)
p
g
g
y
,
p
pp
,
p
g
,
,
Germany
Sonka, M., Hlavac, V. & Boyle, R. (1993). Image Processing, Analysis and Machine Vision,
Chapman & Hall, Boca Raton, Fla, USA Germany
Sonka, M., Hlavac, V. & Boyle, R. (1993). Image Processing, Analysis and Machine Vision,
Chapman & Hall, Boca Raton, Fla, USA p
Facon, J. (1996). Morfologia Matemática: Teoria e Exemplos, Editora Universitária da Pontifícia
Universidade Católica do Paraná, Prado Velho, Brazil (In portuguese) Pedrino, E. C., Roda, V. O. & Saito, J. H. (2010). A Genetic Programming Approach to
Reconfigure a Morphological Image Processing Architecture. International Journal of
Reconfigurable Computing, Vol.2011, pp. 712494-712503 f g
p
g
pp
Gonzalez, R. C. & Woods, R. E. (2008). Digital Image Processing. Prentice Hall, Upper Saddle
River, NJ Angulo, J. & Serra, J. (2005). Morphological Coding of Color Images by Vector Connected
Filters, In: Centre de Morphologie Mathématique, Ecole des Mines de Paris, Paris,
France Chanussot, J. & Lambert, P. (1998). Total ordering based on space filling curves for
multivalued morphology, In: Proceedings of the 4th International Symposium on
Mathematical Morphology and Its Applications, 51–58 Koza, J. (1992). Genetic Programming, MIT Press, Cambridge, Mass, USA MATLAB – A Ubiquitous Tool for the Practical Engineer 452 22 1. Introduction Rapid Prototyping (RP) is a group of techniques used to quickly fabricate a scale model of a
part or assembly using three-dimensional computer aided design (CAD) data (Marsan,
Dutta, 2000). A large number of RP technologies have been developed to manufacture
polymer, metal, or ceramic parts, without any mould, namely Stereolithography (SL),
Laminated Object Manufacturing (LOM), Selected Laser Sintering (SLS), Ink-jet Printing
(3DP) and Fused Deposition Modeling (FDM). (
)
p
g (
)
In Fused Deposition Modelling (developed by Stratasys Inc in U.S.A.), a plastic or wax
filament is fed through a nozzle and deposited onto the support (Pérez, 2002; Ahn, 2002;
Ziemian & Crawn, 2001) as a series of 2D slices of a 3D part. The nozzle moves in the X–Y
plane to create one slice of the part. Then, the support moves vertically (Z direction) so that
the nozzle deposits a new layer on top of the previous one. Since the filament is extruded as
a melt, the newly deposited material fuses with the last deposited material. y
p
p
Free Form Extrusion (FFE) is a variant of FDM (Figure 1), where the material is melted and
deposited by an extruder & die (Agarwala, Jamalabad, Langrana, Safari, Whalen &
Danthord, 1996; Bellini, Shor & Guceri, 2005). FFE enables the use of a wide variety of
polymer systems (e.g., filled compounds, polymer blends, composites, nanocomposites,
foams), thus yielding parts with superior performance. Moreover, the adoption of co-
extrusion or sequential extrusion techniques confers the possibility to combine different
materials for specific properties, such as soft/hard zones or transparent/opaque effects. Fig. 1. Free Form Extrusion (FFE). Fig. 1. Free Form Extrusion (FFE). 454 MATLAB – A Ubiquitous Tool for the Practical Engineer Due to their characteristics - layer by layer construction using melted materials - FDM and
FFE may originate parts with two defects: i) excessive filament deformation upon cooling
can jeopardize the final dimensional accuracy, ii) poor bonding between adjacent filaments
reduces the mechanical resistance. Deformation and bonding are mainly controlled by the
heat transfer, i. e., adequate bonding requires that the filaments remain sufficiently hot
during enough time to ensure adhesion and, simultaneously, to cool down fast enough to
avoid excessive deformation due to gravity (and weight of the filaments above them). 1. Introduction Therefore, it is important to know the evolution in time of the filaments temperature and to
understand how it is affected by the major process variables. Rodriguez (Rodriguez, 1999)
studied the cooling of five elliptical filaments stacked vertically using via finite element
methods and later found a 2D analytical solution for rectangular cross-sections (Thomas &
Rodriguez, 2000). Yardimci and Guceri (Yardimci & S.I. Guceri, 1996) developed a more
general 2D heat transfer analysis, also using finite element methods. Li and co-workers (Li,
Sun, Bellehumeur & Gu, 2003; Sun, Rizvi, Bellehumeur & Gu, 2004) developed an analytical
1D transient heat transfer model for a single filament, using the Lumped Capacity method. Although good agreement with experimental results was reported, the model cannot be
used for a sequence of filaments, as thermal contacts are ignored. q
g
The present work expands the above efforts, by proposing a transient heat transfer analysis
of filament deposition that includes the physical contacts between any filament and its
neighbours or supporting table. The analytical analysis for one filament is first discussed,
yielding an expression for the evolution of temperature with deposition time. Then, a
MatLab code is developed to compute the temperature evolution for the various filaments
required to build one part. The usefulness of the results is illustrated with two case studies. 2. Heat transfer modelling During the construction of a part by FDM or FFE, all the filaments are subjected to the same
heat transfer mechanism but with different boundary conditions, depending on the part
geometry and deposition sequence (Figure 2). Fig. 2. Example of a sequence of filaments deposition. Consider that N is the total number of deposited filaments and that Tr(x,t) is the temperature
at length x of the r-th filament (r Є {1,…,N}) at instant t. The energy balance for an element
dx of the r-th filament writes as: Fig. 2. Example of a sequence of filaments deposition. Fig. 2. Example of a sequence of filaments deposition. Consider that N is the total number of deposited filaments and that Tr(x,t) is the temperature
at length x of the r-th filament (r Є {1,…,N}) at instant t. The energy balance for an element
dx of the r-th filament writes as: sup
in int
Energy in at one face
Heat loss by convection with surroundings
Heat loss by conduction with adjacent filaments or with
port
Change
ernal energy
Energy out at opposite face
⎧
−
⎪
=
⎨−
⎪⎩
=
+ sup
Energy in at one face
Heat loss by convection with surroundings
Heat loss by conduction with adjacent filaments or with
port
⎧
−
⎪
=
⎨−
⎪⎩ in int
Change
ernal energy
Energy out at opposite face
=
+ 455 Using MATLAB to Compute Heat Transfer in Free Form Extrusion This can be expressed as a differential equation. After some assumptions and simplifications
(Costa, Duarte & Covas, 2008): This can be expressed as a differential equation. 2. Heat transfer modelling After some assumptions and simplifications
(Costa, Duarte & Covas, 2008): (
)
(
)
1
1
1
i
i
i
n
n
r
conv
r
i
r
E
i r
i
r
r
i
i
T
P
h
a
T
T
h a
T
T
t
CA
=
=
⎛
⎞
⎛
⎞
∂
= −
−
λ
−
+
λ
−
⎜
⎟
⎜
⎟
⎜
⎟
∂
ρ
⎝
⎠
⎝
⎠
∑
∑
(1) (1) (1) where P is filament perimeter, ρ is density, C is heat capacity, A is area of the filament cross-
section, hconv is heat transfer coefficient, n is number of contacts with adjacent filaments or
with the support, λi is fraction of P that in contact with an adjacent filament, TE is
environment temperature, hi is thermal contact conductance for contact i (
{1,..., }
i
n
∈
) and
ir
T is temperature of the adjacent filament or support at contact i (
{1,...,
1}
ir
N
∈
+
,
ir
r
≠
,
T1,…, TN are temperatures of filaments, TN+1 is support temperature). In this expression,
variables
ira are defined as (see Figure 3): 1
,
{1,..., },
{1,...,
}
0
ir
if the r
th filament has the i
th contact
a
i
n
r
N
otherwise
−
−
⎧
=
∀∈
∀∈
⎨
⎩
(2) 1
,
{1,..., },
{1,...,
}
0
ir
if the r
th filament has the i
th contact
a
i
n
r
N
otherwise
−
−
⎧
=
∀∈
∀∈
⎨
⎩
(2) 1
,
{1,..., },
{1,...,
}
0
ir
if the r
th filament has the i
th contact
a
i
n
r
N
otherwise
−
−
⎧
=
∀∈
∀∈
⎨
⎩
(2) ,
{1,..., },
{1,...,
}
ct
i
n
r
N
∀∈
∀∈ (2) Fig. 3. Contact areas of a filament (n = 5). 2. Heat transfer modelling Considering that:
(
)
(
)
(
)
1
1
1
1
1
1
1
,...,
1
1
,...,
,...,
n
i
i
i
i
i
n
n
n
n
r
r
conv
r
i
r
i
i
i
i
n
n
conv
r
i
E
r
i
i r
i
i
r
r
r
r
b a
a
h
a
a h
h
a
T
a h
T
Q a
a
b a
a
=
=
=
=
⎧
⎛
⎞
=
−
λ
+
λ
⎪
⎜
⎟
⎪
⎝
⎠
⎪
⎛
⎞
⎨
−
λ
+
λ
⎜
⎟
⎪
⎝
⎠
⎪
=
⎪⎩
∑
∑
∑
∑
(3)
equation (1) can be re-written as: Fig. 3. Contact areas of a filament (n = 5). Fig. 3. Contact areas of a filament (n = 5). Fig. 3. Contact areas of a filament (n = 5). Fig. 3. Contact areas of a filament (n = 5). 2. Heat transfer modelling (5) becomes: When Bi is lower than 0.1, the filaments are thermally thin, i.e., thermal gradients
throughout the cross section can be neglected. In this case, Eq. (5) becomes: (
)
(
)
(
)(
)
(
)
1
1
1
,...,
0
0.1
( )
,...,
,...,
r
rn
r
n
n
PL b a
a
t t
VC
r
r
r
r
r
r
Bi
T t
T
Q a
a
e
Q a
a
−
−
ρ
≤
⇒
=
−
+
(7) (7) 3. Computer modelling Equations (5) and (7) quantify the temperature of a single filament fragment along the
deposition time. In practice, consecutive filament fragments are deposited during the
manufacture of a part. Thus, it is convenient to generalize the computations to obtain the
temperature evolution of each filament fragment at any point x of the part, for different
deposition techniques and 3D configuration structures. 2. Heat transfer modelling (
)
(
)
(
)
1
1
1
1
1
1
1
,...,
1
1
,...,
,...,
n
i
i
i
i
i
n
n
n
n
r
r
conv
r
i
r
i
i
i
i
n
n
conv
r
i
E
r
i
i r
i
i
r
r
r
r
b a
a
h
a
a h
h
a
T
a h
T
Q a
a
b a
a
=
=
=
=
⎧
⎛
⎞
=
−
λ
+
λ
⎪
⎜
⎟
⎪
⎝
⎠
⎪
⎛
⎞
⎨
−
λ
+
λ
⎜
⎟
⎪
⎝
⎠
⎪
=
⎪⎩
∑
∑
∑
∑ (3) equation (1) can be re-written as: equation (1) can be re-written as: MATLAB – A Ubiquitous Tool for the Practical Engineer 456 (
)
(
)
1
1
( )
( )
,...,
,...,
n
n
r
r
r
r
r
r
T t
VC
T t
Q a
a
t
PL b a
a
∂
ρ
+
=
∂
(4) (
)
(
)
1
1
( )
( )
,...,
,...,
n
n
r
r
r
r
r
r
T t
VC
T t
Q a
a
t
PL b a
a
∂
ρ
+
=
∂
(4) (4) Since the coefficients are constants, the characteristic polynomial method can be used to
yield the solution: (
)
(
)
(
)(
)
(
)
1
1
1
,...,
0
( )
,...,
,...,
r
rn
r
n
n
PL b a
a
t t
VC
r
r
r
r
r
r
T t
T
Q a
a
e
Q a
a
−
−
ρ
=
−
+
(5) (5) In this expression, tr is the instant at which the r-th filament starts to cool down or contact
with another filament and
0
( )
r
r
r
T
T t
=
is the temperature of the filament at instant tr. Taking
k as thermal conductivity, the Biot number can be defined (Bejan, 1993): (
)
1 ,...,
n
r
r
b a
a
A
Bi
P
k
=
(6) (6) When Bi is lower than 0.1, the filaments are thermally thin, i.e., thermal gradients
throughout the cross section can be neglected. In this case, Eq. 3.2 Computing the temperatures The computational flowchart is presented in Figure 5 and a MatLab code was generated. In
order to visualize the results using another software (Excel, Tecplot...), a document in txt
format is generated after the computations, that includes all the temperature results along
deposition time. 3.1 Generalizing the heat transfer computations Up-dating the thermal conditions: The boundary conditions must be up-dated as the
deposition develops. The code activates the physical contacts and redefines the boundary
conditions for a specific filament position, time and deposition sequence. For all the
filaments, three variables need to be up-dated: -
time tr (TCV-1): instant at which the r-th filament starts cooling down, or enters in
contact with another filament; -
time tr (TCV-1): instant at which the r-th filament starts cooling down, or enters in
contact with another filament; -
temperature Tr0 (TCV-2): temperature at tr; p
(
)
p
-
-vector ari (TCV-3): in Eq. (3), sets in the contacts for the r-th filament (i∈{1,...,n}, where
n is the number of contacts). -
-vector ari (TCV-3): in Eq. (3), sets in the contacts for the r-th filament (i∈{1,...,n}, where
n is the number of contacts). Simultaneous computation of the filaments temperature: During deposition, some filaments are
reheated when new contacts with hotter filaments arise; simultaneously, the latter cool
down due to the same contacts. This implies the simultaneous computation of the filaments
temperature via an iterative procedure. The convergence error was set at ε = 10-3, as a good
compromise between accuracy and the computation time. Simultaneous computation of the filaments temperature: During deposition, some filaments are
reheated when new contacts with hotter filaments arise; simultaneously, the latter cool
down due to the same contacts. This implies the simultaneous computation of the filaments
temperature via an iterative procedure. The convergence error was set at ε = 10-3, as a good
compromise between accuracy and the computation time. 457 Using MATLAB to Compute Heat Transfer in Free Form Extrusion Deposition sequence: The deposition sequence defines the thermal conditions TCV-1, TCV-2
and TCV-3. Three possibilities were taken in: unidirectional and aligned filaments,
unidirectional and skewed filaments, perpendicular filaments (see Figure 4). In all cases, the
filaments are deposited continuously under constant speed (no interruptions occur between
successive layers). Some parts with some geometrical features may require the use of a support material, to be
removed after manufacture. This possibility is considered in the algorithm for unidirectional
and aligned filaments. a)
b) c)
Fig. 4. Deposition sequences: a) unidirectional and aligned filaments; b) unidirectional and
skewed filaments; c) perpendicular filaments. c) c) b) a) Fig. 4. Deposition sequences: a) unidirectional and aligned filaments; b) unidirectional and
skewed filaments; c) perpendicular filaments. 4. MatLab code for one filament layer In order to illustrate how the MatLab code “FFE.m” was implemented, the segment dealing
with the temperature along the deposition time for the first layer of filaments, using one or
two distinct materials, is presented here. The code has the same logic and structure for the
remaining layers. 4.1 Input variables p
Two arguments need to be introduced in this MatLab function: p
Two arguments need to be introduced in this MatLab function: -
A matrix representing the deposition sequence, containing m rows and n columns, for
the number of layers and maximum number of filaments in a layer, respectively. Each
cell is attributed a value of 0, 1, or 2 for the absence of a filament, the presence of a
filament of material A or of a filament of material B, respectively. An example is given
in Figure 6. g
-
The vertical cross section of the part (along the filament length) where the user wishes
to know the temperature evolution with time. The code includes one initial section where all the variables are defined (Figure 7), namely
environment and extrusion temperatures, material properties, process conditions, etc. The
dimensions of all matrixes used are also defined. MATLAB – A Ubiquitous Tool for the Practical Engineer 458 Fig. 5. General procedure to compute all the temperatures. Fig. 5. General procedure to compute all the temperatures. Using MATLAB to Compute Heat Transfer in Free Form Extrusion 459 Fig. 6. Example of deposition sequence and corresponding input matrix. Fig. 6. Example of deposition sequence and corresponding input matrix. function FFE(matrix,x)
%____________________________________ STEP 1 ____________________________________
%Definition of the vector that contains the number of total filaments in each layer
matrix_lin = size(matrix,1);
matrix_col = size(matrix,2);
vector = zeros(matrix_lin,2);
contar = 0;
for i = matrix_lin:-1:1
contar = contar + 1;
for j = 1:matrix_col
if matrix(i,j) ~= 0
vector(contar,1) = vector(contar,1) + 1;
end
end
end
%Number of layers
m = length(vector(:,1));
%Number of filaments
n = 0;
for j = 1:m
if m == 1
n = vector(1,1);
else
if vector(j,2) <= 1
n = n + vector(j,1);
end
end
end
%____________________________________ STEP 2 ____________________________________
%Computation variables
passo = 0.05;
%Step time
temp_mais = 15;
%Additional time computation after construction of the part
erro = 0.001;
%Convergence error 460 MATLAB – A Ubiquitous Tool for the Practical Engineer %____________________________________ STEP 3 ____________________________________
%Definition of the size of the variables
h = zeros(1,5); lambda = zeros(1,5); a = zeros(n,5); T = zeros (n,5);
vec_b = zeros(n,5); vec_Q = zeros(n,5); b = zeros(1,n); Q = zeros(1,n);
T_begin = zeros(1,n); dif = zeros(1,n); Biot = zeros(1,n); save_T = zeros(1,n);
old_T = zeros(1,n); save_lim = zeros(1,n); viz = zeros(11,n); old_T = zeros(1,n); save_lim = zeros(1,n); viz = zeros(11,n);
%____________________________________ STEP 4 ____________________________________
%Process Variables
T_L = 270;
%Extrusion temperature (ºC)
T_E = 70;
%Temperature of the envelope (ºC)
v = 0.02;
%Velocity of the extrusion head (m/sec)
for lin = 1:n
%Temperature of support (ºC)
T(lin,1) = T_E;
end
%Filament dimensions
w = 0.0003;
%Layer Thickness (meters)
L = 0.02;
%Length of the filament (meters)
area = pi * (w/2)^2; %Area of the cross section of filament (meters^2)
per = pi * w;
%Perimeter of the cross section of filament (meters)
vol = area*L;
%Volume of the filament
A_p = per*L;
%Superficial area of the filament
% Material Properties
%Thermal conductivity (W/m.K)
conductivity(1) = 0.1768; % material A
conductivity(2) = 0.5;
% material B
%Density (kg/m^3)
ro(1) = 1050;
% material A
ro(2) = 1500;
% material B
%Specific heat (J/kg.K)
C(1) = 2019.7;
% material A
C(2) = 2500.7;
% material B
%____________________________________ STEP 5 ____________________________________
% Heat transfer coefficient (lost of heat by natural convection)
h_conv = 45;
%Thermal contact conductances between
h(1,1) = 200;
% filament and left adjacent filament
h(1,2) = 200;
% filament and down adjacent filament
h(1,3) = 200;
% filament and right adjacent filament
h(1,4) = 200;
% filament and top adjacent filament
h(1,5) = 10;
% filament and support
%Fraction of perimeter contact between
lambda(1,1) = 0.2;
% filament and left adjacent filament
lambda(1,2) = 0.25;
% filament and down adjacent filament
lambda(1,3) = 0.2;
% filament and right adjacent filament
lambda(1,4) = 0.25;
% filament and top adjacent filament
lambda(1,5) = 0.25;
% filament and support
Fig. %____________________________________ STEP 8 _______________________
%Definition of the periods of time between two successive contacts
for i = 1:(n+2)
if i
dd(i)
1 Fig. 8. Definition of the parameters to be used for the computation of temperatures and time
between two consecutive contacts. Fig. 8. Definition of the parameters to be used for the computation of temperatures and time
between two consecutive contacts. 2 Computation of the temperatures for the first filament of the first layer 7. Definition of the variables. Fig. 7. Definition of the variables. Fig. 7. Definition of the variables. The parameters used in Equation (5) and those necessary to compute variables b and Q
(in Eq. (3)) must also be defined. Finally, the time increment between two consecutive
contacts is calculated taking into consideration the type of deposition sequence
(Figure 8). Using MATLAB to Compute Heat Transfer in Free Form Extrusion 461 %____________________________________ STEP 6 ____________________________________
%Definition of the parameters influenced by the contacts
for col = 1:5
for lin = 1:n
vec_b(lin,col) = h(1,col)*lambda(1,col);
vec_Q(lin,col) = vec_b(lin,col)*T(lin,col);
end
end
%____________________________________ STEP 7 ____________________________________
%Definition of the parameters influenced by the material properties
contar = 0;
number_filament = 0;
for i = matrix_lin:-1:1
contar = contar + 1;
if isodd(contar) == 1
for j = 1:matrix_col
if matrix(i,j) ~= 0
number_filament = number_filament + 1;
escalar(number_filament) = -per/(ro(matrix(i,j))*area*C(matrix(i,j)));
esc(number_filament) = h_conv/(ro(matrix(i,j))*L*C(matrix(i,j)));
kt(number_filament) = conductivity(matrix(i,j));
end
end
else
for j = matrix_col:-1:1
if matrix(i,j) ~= 0
number_filament = number_filament + 1;
escalar(number_filament) = -per/(ro(matrix(i,j))*area*C(matrix(i,j)));
esc(number_filament) = h_conv/(ro(matrix(i,j))*L*C(matrix(i,j)));
kt(number_filament) = conductivity(matrix(i,j));
end
end
end
end
%____________________________________ STEP 8 ____________________________________
%Definition of the periods of time between two successive contacts
for i = 1:(n+2)
if isodd(i) == 1
limite(i,1) = (i*L-x)/v;
limite(i,2) = (i*L+x)/v;
else
limite(i,1) = limite(i-1,2);
limite(i,2) = ((i+1)*L-x)/v;
end
end
for road = 1:n
linha = 0;
for i = 0:passo:limite(n,2)
linha = linha + 1;
temp(linha,road) = T_L;
end
end
Fig. 8. Definition of the parameters to be used for the computation of temperatures and t
between two consecutive contacts. 4.2 Computation of the temperatures for the first filament of the first layer
Computation of the temperatures starts with the activation of the contact between the
filament and the support. Parameters b and Q (equation (3)) are calculated (Figure 9). %___________________________________
%Definition of the parameters influe
for col = 1:5
for lin = 1:n
vec_b(lin,col) = h(1,col)*lamb
vec_Q(lin,col) = vec_b(lin,col
end
end
%___________________________________
%Definition of the parameters influe
contar = 0;
number_filament = 0;
for i = matrix_lin:-1:1
contar = contar + 1;
if isodd(contar) == 1
for j = 1:matrix_col
if matrix(i,j) ~= 0
number_filament = number
escalar(number_filament)
esc(number_filament) = h
kt(number_filament) = c
end
end
else
for j = matrix_col:-1:1
if matrix(i,j) ~= 0
number_filament = number
escalar(number_filament)
esc(number_filament) = h
kt(number_filament) = c
end
end
end
end
%___________________________________
%Definition of the periods of time b
for i = 1:(n+2)
if isodd(i) == 1
limite(i,1) = (i*L-x)/v;
limite(i,2) = (i*L+x)/v;
else
limite(i,1) = limite(i-1,2);
limite(i,2) = ((i+1)*L-x)/v;
end
end
for road = 1:n
linha = 0;
for i = 0:passo:limite(n,2)
linha = linha + 1;
temp(linha,road) = T_L;
end
end
Fig. 8. Definition of the parameters to b
between two consecutive contacts. 4.2 Computation of the temperatures
Computation of the temperatures start
filament and the support. Parameters b ____________________________________
____________________________________
%Definition of the parameters influenced by the material properties
contar = 0;
number_filament = 0;
for i = matrix_lin:-1:1
contar = contar + 1;
if isodd(contar) == 1
for j = 1:matrix_col
if matrix(i,j) ~= 0
number_filament = number_filament + 1;
escalar(number_filament) = -per/(ro(matrix(i,j))*area*C(matrix(i,j)));
esc(number_filament) = h_conv/(ro(matrix(i,j))*L*C(matrix(i,j)));
kt(number_filament) = conductivity(matrix(i,j)); end
else
for j = matrix_col:-1:1
if matrix(i,j) ~= 0
number_filament = number_filament + 1;
escalar(number_filament) = -per/(ro(matrix(i,j))*area*C(matrix(i,j)));
esc(number_filament) = h_conv/(ro(matrix(i,j))*L*C(matrix(i,j)));
kt(number_filament) = conductivity(matrix(i,j)); for j = matrix_col:-1:1 4.2 Computation of the temperatures for the first filament of the first layer p
p
y
Computation of the temperatures starts with the activation of the contact between the first
filament and the support. Parameters b and Q (equation (3)) are calculated (Figure 9). MATLAB – A Ubiquitous Tool for the Practical Engineer
462
The temperatures are computed at each time increment; confirmation of the value of Biot
number (Eq. (6)) is also made: if greater than 0.1, the code devolves a warning message
(Figure 10). for layer = 1:m
if layer == 1
for num = 1:vector(layer,1)
if num == 1
%____________________________________ STEP 9 ____________________________________
a(num,5) = 1;
%Activation of the contact with support
%____________________________________ STEP 10 ____________________________________
%Definition of the variables b and Q defined in equation Eq. 7
b(num) = h_conv*(1-lambda*a(num,:)') + vec_b(num,:)*a(num,:)';
Q(num) = (h_conv*(1-lambda*a(num,:)')*T_E +
vec_Q(num,:)*a(num,:)')/b(num);
Fig. 9. Activation of the contacts and computation of b and Q for the first filament. %____________________________________ STEP 11 ____________________________________
p = 0;
for t = 0:passo:limite(num,1)
p = p+1; abcissa(p) = t;
end
%____________________________________ STEP 12 ____________________________________
%Computation of the temperatures of the first filament
for t = (limite(num,1)+passo):passo:limite_final
p = p+1; abcissa(p) = t;
temp(p,num)=(T_L-Q(num))*exp(escalar(num)*b(num)*(t-limite(num,1)))
+Q(num);
end
%Saving the last temperature of the period time of cooling down
T_begin(num) = temp(p,num);
%____________________________________ STEP 13 ____________________________________
%Verification of the value of Biot Number
Biot(num) = (vol/A_p)*(b(num)/kt(num));
if Biot(num)>=0.1
'WARNING! We cannot use a Lumped System'
End
Fig. 10. Computation of the temperatures for the first filament and verification of the value
of the Biot number. 4 3 C
t ti
f th
t
t
f
th
i i
fil
t
f th
fi
t l 462 MATLAB – A Ubiquitous Tool for the Practical Engineer The temperatures are computed at each time increment; confirmation of the value of Biot
number (Eq. (6)) is also made: if greater than 0.1, the code devolves a warning message
(Figure 10). for layer = 1:m
if layer == 1
for num = 1:vector(layer,1)
if num == 1
%____________________________________ STEP 9 ____________________________________
a(num,5) = 1;
%Activation of the contact with support
%____________________________________ STEP 10 ____________________________________
%Definition of the variables b and Q defined in equation Eq. 7
b(num) = h_conv*(1-lambda*a(num,:)') + vec_b(num,:)*a(num,:)';
Q(num) = (h_conv*(1-lambda*a(num,:)')*T_E +
vec_Q(num,:)*a(num,:)')/b(num);
F
9 A
f h
d
f b
d Q f
h f
f l Fig. 9. Activation of the contacts and computation of b and Q for the first filament. 4.2 Computation of the temperatures for the first filament of the first layer Activation of the contacts for the current and previous filaments and up-dating of
variable b. %____________________________________ STEP 16 ____________________________________
if m == 1
if num == vector(layer,1)
limite_final = limite(num,2) + temp_mais;
else
limite_final = limite(num,2);
end
else
limite_final = limite(num,2);
end %____________________________________ STEP 16 ____________________________________
if m == 1
if num == vector(layer,1)
limite_final = limite(num,2) + temp_mais;
else
limite_final = limite(num,2);
end
else
limite_final = limite(num,2);
end Fig. 12. Definition of an additional time for the last filament. 4.2 Computation of the temperatures for the first filament of the first layer %____________________________________ STEP 11 ____________________________________
p = 0;
for t = 0:passo:limite(num,1)
p = p+1; abcissa(p) = t;
end
%____________________________________ STEP 12 ____________________________________
%Computation of the temperatures of the first filament
for t = (limite(num,1)+passo):passo:limite_final
p = p+1; abcissa(p) = t;
temp(p,num)=(T_L-Q(num))*exp(escalar(num)*b(num)*(t-limite(num,1)))
+Q(num);
end
%Saving the last temperature of the period time of cooling down
T_begin(num) = temp(p,num);
%____________________________________ STEP 13 ____________________________________
%Verification of the value of Biot Number
Biot(num) = (vol/A_p)*(b(num)/kt(num));
if Biot(num)>=0.1
'WARNING! We cannot use a Lumped System'
End
Fig. 10. Computation of the temperatures for the first filament and verification of the value
f th Bi t
b g. 9. Activation of the contacts and computation of b and Q for the first filament. Fig. 10. Computation of the temperatures for the first filament and verification of the value
of the Biot number. 4.3 Computation of the temperatures for the remaining filaments of the first layer
Before proceeding to the remaining filaments of the first layer, the lateral and support
contacts for each filament being deposited must be defined, as well as for the previous one. Consequently, the variable b in expression Eq. (3) is up-dated (Figure 11). At this point, only the lateral and support contacts must be defined, since only the first layer
is being computed. For the remaining layers, other contacts (such as the vertical ones) must
be considered. Once each filament is deposited, the code checks whether the part has been
completed. If so, it remains in the same conditions during a pre-defined time, in order to
reach the equilibrium temperature (Figure 12). Using MATLAB to Compute Heat Transfer in Free Form Extrusion 463 %____________________________________ STEP 14 ____________________________________
else
%Activation of the contacts
a(num-1,3) = 1; a(num,1) = 1; a(num,5) = 1;
%____________________________________ STEP 15 ____________________________________
%Up-dating of the variable b
for j = 1:num
b(j) = h_conv*(1-lambda*a(j,:)') + vec_b(j,:)*a(j,:)';
end
Fig. 11. Activation of the contacts for the current and previous filaments and up-dating of %____________________________________ STEP 14 ____________________________________
else
%Activation of the contacts
a(num-1,3) = 1; a(num,1) = 1; a(num,5) = 1;
%____________________________________ STEP 15 ____________________________________
%Up-dating of the variable b
for j = 1:num
b(j) = h_conv*(1-lambda*a(j,:)') + vec_b(j,:)*a(j,:)';
end
Fig. 11. Activation of the contacts for the current and previous filaments and up-dating of
variable b. Fig. 11. Activation of the contacts for the current and previous filaments and up-dating of
variable b Fig. 11. Fig. 12. Definition of an additional time for the last filament. Finally, the temperatures of the remaining filaments are computed. At each time increment,
the temperatures of the adjacent filaments are saved and parameter Q (Eq. (3) is up-dated. The value of the Biot number is checked before the deposition of a new filament (Figure 13). for t = (limite(num,1)+passo):passo:limite_final
p = p+1; abcissa(p) = t;
last = p-1;
for j = 1:num
save_T(j) = temp(last,j);
end
%____________________________________ STEP 17 ____________________________________
%Iterative process
for q = 1:100000
%Saving contacts and temperatures of adjacent filaments
for j = 1:num
if j == 1
T(j,3) = save_T(j+1);
viz(3,j) = j+1;
end
if j > 1 & j < num
T(j,1) = save_T(j-1);
viz(1,j) = j-1;
T(j,3) = save_T(j+1);
viz(3,j) = j+1;
end
if j == num
T(j,1) = save_T(j-1);
viz(1,j) = j-1;
end
for k = 1:5
if T(j,k) ~= 0 & k ~= 5 MATLAB – A Ubiquitous Tool for the Practical Engineer 464 vec_Q(j,k) = vec_b(j,k)*T(j,k);
end
end
%Up-dating of the variable Q
Q(j) = (h_conv*(1-lambda*a(j,:)')*T_E +
vec_Q(j,:)*a(j,:)')/b(j);
old_T(j) = save_T(j);
end
%Computation of the temperatures
if num == 2
save_T(1) = (T_begin(1)-Q(1))*exp(escalar(1)*b(1)*
(t-limite(1,1)))+Q(1);
save_T(2) = (T_L-Q(2))*exp(escalar(2)*b(2)*(t-
limite(1,1)))+Q(2);
save_lim(1,1) = limite(num,1);
save_lim(1,2) = limite(num,1);
else
for j=1:num-2
save_T(j) = (T_begin(j)-Q(1))*exp(escalar(j)*b(j)*
(t-save_limite(1,j)))+Q(j);
end
save_T(num-1) = (T_begin(num-1)-Q(num-1))*
exp(escalar(num-1)*b(num-1)*(t-limite(num,1)))+Q(num-
1);
save_T(num) = (T_L-Q(num))*
exp(escalar(num)*b(num)*(t-limite(num,1)))+ Q(num);
save_lim(1,num-1) = limite(num,1);
save_lim(1,num) = limite(num,1);
end
for j = 1:num
dif(j) = abs(save_T(j)-old_T(j));
end
try = 1;
stop = 0;
for j = 1:num
if dif(try) < erro
try = try+1;
end
if try == num+1;
stop = 1;
end
end
if stop == 1
for j = 1:num
temp(p,j) = save_T(j);
end
break;
end
end
end
T_begin(num) = temp(p,num);
%End of iterative process
%____________________________________ STEP 18 ____________________________________
%Verification of the Biot Number
for j=1:num
Biot(j) = (vol/A_p)*(b(j)/kt(j));
if Biot(j)>=0.1
'WARNING! 5. Results In order to demonstrate the usefulness of the code developed, two case studies will be
discussed. The first deals with a part constructed with two distinct materials, while the
second illustrates the role of the deposition sequence. Fig. 12. Definition of an additional time for the last filament. We can not use a Lumped System'
j
Biot(j)
end
end
end
end vec_Q(j,k) = vec_b(j,k)*T(j,k);
end
end
%Up-dating of the variable Q
Q(j) = (h_conv*(1-lambda*a(j,:)')*T_E +
vec_Q(j,:)*a(j,:)')/b(j);
old_T(j) = save_T(j);
end
%Computation of the temperatures
if num == 2
save_T(1) = (T_begin(1)-Q(1))*exp(escalar(1)*b(1)*
(t-limite(1,1)))+Q(1);
save_T(2) = (T_L-Q(2))*exp(escalar(2)*b(2)*(t-
limite(1,1)))+Q(2);
save_lim(1,1) = limite(num,1);
save_lim(1,2) = limite(num,1);
else
for j=1:num-2
save_T(j) = (T_begin(j)-Q(1))*exp(escalar(j)*b(j)*
(t-save_limite(1,j)))+Q(j);
end
save_T(num-1) = (T_begin(num-1)-Q(num-1))*
exp(escalar(num-1)*b(num-1)*(t-limite(num,1)))+Q(num-
1);
save_T(num) = (T_L-Q(num))*
exp(escalar(num)*b(num)*(t-limite(num,1)))+ Q(num);
save_lim(1,num-1) = limite(num,1);
save_lim(1,num) = limite(num,1);
end
for j = 1:num
dif(j) = abs(save_T(j)-old_T(j));
end
try = 1;
stop = 0;
for j = 1:num
if dif(try) < erro
try = try+1;
end
if try == num+1;
stop = 1;
end
end
if stop == 1
for j = 1:num
temp(p,j) = save_T(j);
end
break;
end
end
end
T_begin(num) = temp(p,num);
%End of iterative process
%____________________________________ STEP 18 ____________________________________
%Verification of the Biot Number
for j=1:num
Biot(j) = (vol/A_p)*(b(j)/kt(j));
if Biot(j)>=0.1
'WARNING! We can not use a Lumped System'
j
Biot(j)
end
end
end
end vec_Q(j,k) = vec_b(j,k)*T(j,k); _
save_lim(1,2) = limite(num,1); else
for j=1:num-2
save_T(j) = (T_begin(j)-Q(1))*exp(escalar(j)*b(j)*
(t-save_limite(1,j)))+Q(j); _
end
save_T(num-1) = (T_begin(num-1)-Q(num-1))*
exp(escalar(num-1)*b(num-1)*(t-limite(num,1)))+Q(num- 1); _ (
)
( _
Q(
))
exp(escalar(num)*b(num)*(t-limite(num,1)))+ Q(num); _
exp(escalar(num)*b(num)*(t-limit save_lim(1,num) = limite(num,1); 465 Using MATLAB to Compute Heat Transfer in Free Form Extrusion end
end
Fig. 13. Computation of the temperature of the filaments of the first layer and verification of
the Biot number. Fig. 13. Computation of the temperature of the filaments of the first layer and verification of
the Biot number. Fig. 13. Computation of the temperature of the filaments of the first layer and verification of
the Biot number. 5.1 Case study 1 Consider the small part with the geometry presented in Figure 14, to be manufactured
under the processing conditions summarized in Table 1. Fig. 14. Geometry of the part. Fig. 14. Geometry of the part. 14. Geometry of the part. Property
Value
Extrusion temperature (ºC)
270
Environment temperature (ºC)
70
Extrusion velocity (m/s)
0.025
Filament length (m)
0.02
Cross section x (m)
0.01
Geometric form of cross section
circle
Cross section diameter (m)
0.00035
Contact ratio
88%
Heat transfer coefficient (convection) (W/m2ºC)
60
Thermal contact conductance with filaments (W/m2ºC)
180
Thermal contact conductance with support (W/m2ºC)
10
Thermal conductivity ( W/mºC) materials A / B
0.1768 / 0.5
Specific heat (J/kgºC) materials A / B
2019.7 / 2500.7
Density materials A / B
1.05 / 1.5
Table 1. Processing conditions Property
Value
Extrusion temperature (ºC)
270
Environment temperature (ºC)
70
Extrusion velocity (m/s)
0.025
Filament length (m)
0.02
Cross section x (m)
0.01
Geometric form of cross section
circle
Cross section diameter (m)
0.00035
Contact ratio
88%
Heat transfer coefficient (convection) (W/m2ºC)
60
Thermal contact conductance with filaments (W/m2ºC)
180
Thermal contact conductance with support (W/m2ºC)
10
Thermal conductivity ( W/mºC) materials A / B
0.1768 / 0.5
Specific heat (J/kgºC) materials A / B
2019.7 / 2500.7
Density materials A / B
1.05 / 1.5
Table 1. Processing conditions Property
Value
Extrusion temperature (ºC)
270
Environment temperature (ºC)
70
Extrusion velocity (m/s)
0.025
Filament length (m)
0.02
Cross section x (m)
0.01
Geometric form of cross section
circle
Cross section diameter (m)
0.00035
Contact ratio
88%
Heat transfer coefficient (convection) (W/m2ºC)
60
Thermal contact conductance with filaments (W/m2ºC)
180
Thermal contact conductance with support (W/m2ºC)
10
Thermal conductivity ( W/mºC) materials A / B
0.1768 / 0.5
Specific heat (J/kgºC) materials A / B
2019.7 / 2500.7
Density materials A / B
1.05 / 1.5
Table 1. Processing conditions 466 MATLAB – A Ubiquitous Tool for the Practical Engineer The production of this part requires the use of a support material. Figure 15 shows the
deposition sequence and corresponding material matrix, while Figure 16 presents the
evolution of temperature of every filament with deposition time. As expected, once a new
filament is deposited, the temperature of the preceding adjacent filaments increases and
their rate of cooling decreases. Fig. 15. Filaments deposition sequence and corresponding material matrix. Fig. 16. 5.1 Case study 1 Temperature evolution with time (at x = 0.01 m), for the deposition sequence
illustrated in Figure 15. Fig. 15. Filaments deposition sequence and corresponding material matrix. Fig. 15. Filaments deposition sequence and corresponding material matrix. Fig. 15. Filaments deposition sequence and corresponding material matrix. Fig. 15. Filaments deposition sequence and corresponding material matrix. Fig. 16. Temperature evolution with time (at x = 0.01 m), for the deposition sequence
illustrated in Figure 15. Fig. 16. Temperature evolution with time (at x = 0.01 m), for the deposition sequence
illustrated in Figure 15. 5.2 Case study 2
Consider now the parallelepipedic part depicted in Figure 17, to be built using
unidirectional and aligned and perpendicular sequences, respectively, under the processing
conditions summarized in Table 2. 5.2 Case study 2 5.2 Case study 2
Consider now the parallelepipedic part depicted in Figure 17, to be built using
unidirectional and aligned and perpendicular sequences, respectively, under the processing
conditions summarized in Table 2. Figures 18 and 19 depict the deposition sequence and corresponding temperatures (this
required an additional part of the code together with the use of the Tecplot software). At Figures 18 and 19 depict the deposition sequence and corresponding temperatures (this
required an additional part of the code together with the use of the Tecplot software). At
each time increment, a 1 mm or a 0.35 mm filament portion was deposited, for 467 Using MATLAB to Compute Heat Transfer in Free Form Extrusion unidirectional and aligned and perpendicular filaments, respectively. This lower value is
related with the lower contact area arising from this deposition mode. Consequently, the
total computation time was circa 7 minutes for unidirectional and aligned deposition and
more than two and a half hours for perpendicular filaments for a conventional portable PC. As the manufacture is completed (t = 14.4 sec), the average part temperature is
approximately 120 ºC or 90 ºC depending on the deposition mode. This information is
relevant for practical purposes, such as evaluating the quality of the adhesion between
adjacent filaments, or the extent of deformation. Fig. 17. Geometry of the part and corresponding deposition sequence: top: unidirectional
and aligned; bottom: perpendicular. f h
d
d
d
d Fig. 17. Geometry of the part and corresponding deposition sequence: top: unidirectional
and aligned; bottom: perpendicular. MATLAB – A Ubiquitous Tool for the Practical Engineer 468 q
g
Property
Value
Extrusion temperature (ºC)
270
Environment temperature (ºC)
70
Extrusion velocity (m/s)
0.025
Filament length (m)
0.02
Geometric form of cross section
circle
Cross section diameter (m)
0.00035
Contact ratio
88%
Heat transfer coefficient (convection) (W/m2ºC)
70
Thermal contact conductance with filaments (W/m2ºC)
200
Thermal contact conductance with support (W/m2ºC)
15
Thermal conductivity ( W/mºC)
0.1768
Specific heat (J/kgºC)
2019.7
Density
1.05
Table 2. 5.2 Case study 2 Processing conditions
t = 0 sec
t = 0.8 sec
t = 1.6 sec
t = 2.4 sec
t = 3.2 sec
t = 4 sec Property
Value
Extrusion temperature (ºC)
270
Environment temperature (ºC)
70
Extrusion velocity (m/s)
0.025
Filament length (m)
0.02
Geometric form of cross section
circle
Cross section diameter (m)
0.00035
Contact ratio
88%
Heat transfer coefficient (convection) (W/m2ºC)
70
Thermal contact conductance with filaments (W/m2ºC)
200
Thermal contact conductance with support (W/m2ºC)
15
Thermal conductivity ( W/mºC)
0.1768
Specific heat (J/kgºC)
2019.7
Density
1.05
Table 2. Processing conditions t = 0 sec
t = 0.8 sec
t = 1.6 sec
t = 2.4 sec
t = 3.2 sec
t = 4 sec t = 0 sec
t = 0.8 sec
t = 1.6 sec
t = 2.4 sec
t = 3.2 sec
t = 4 sec t = 4 sec t = 3.2 sec Using MATLAB to Compute Heat Transfer in Free Form Extrusion 469 t = 4.8 sec
t = 5.6 sec
t = 6.4 sec
t = 7.2 sec
t = 8 sec
t = 8.8 sec
t = 9.6 sec
t = 10.4 sec t = 5.6 sec t = 7.2 sec t = 8 sec
t = 8.8 sec
t = 9.6 sec
t = 10.4 sec t = 10.4 sec t = 9.6 sec MATLAB – A Ubiquitous Tool for the Practical Engineer 470 t = 11.2 sec
t = 12 sec
t = 12.8 sec
t = 13.6 sec
t = 14.4 sec
t = 16.9 sec
t = 19.4 sec
g. 18. Deposition sequence of the part of Figure 17 (unidirectional and aligned filam t = 13.6 sec t = 14.4 sec
t = 16.9 sec
t = 19.4 sec t = 19.4 sec Fig. 18. Deposition sequence of the part of Figure 17 (unidirectional and aligned filaments). 5.2 Case study 2 Using MATLAB to Compute Heat Transfer in Free Form Extrusion 471 t = 0 sec
t = 0.8 sec
t = 1.6 sec
t = 2.4 sec t = 0.8 sec t = 0 sec
t = 0.8 sec
t = 1.6 sec
t = 2.4 sec
t = 3.2 sec
t = 4 sec
t = 4.8 sec
t = 7.4 sec t = 2.4 sec t = 1.6 sec t = 3.2 sec
t = 4 sec
t = 4.8 sec
t = 7.4 sec t = 4 sec t = 7.4 sec MATLAB – A Ubiquitous Tool for the Practical Engineer 472 t = 9.6 sec
t = 9.9 sec
t = 10.7 sec
t = 11.5 sec t = 9.6 sec
t = 9.9 sec
t = 10.7 sec
t = 11.5 sec
t = 12.3 sec
t = 13.1 sec
t = 13.6 sec
t = 14.4 sec t = 9.6 sec
t = 9.9 sec t = 10.7 sec
t = 11.5 sec t = 10.7 sec t = 11.5 sec t = 10.7 sec t = 12.3 sec
t = 13.1 sec
t = 13.6 sec
t = 14.4 sec t = 12.3 sec
t = 13.1 sec t = 13.1 sec t = 13.1 sec t = 13.1 sec t = 13.6 sec
t = 14.4 sec t = 14.4 sec t = 13.6 sec Using MATLAB to Compute Heat Transfer in Free Form Extrusion 473 t = 16.9 sec
t = 19.4 sec
Fig. 19. Deposition sequence of the part of Figure 17 (perpendicular filaments). t = 19.4 sec t = 16.9 sec Fig. 19. Deposition sequence of the part of Figure 17 (perpendicular filaments). 6. Conclusion In Free Form Extrusion, FFE, a molten filament is deposited sequentially to produce a 3D
part without a mould. This layer by layer construction technique may create problems of
adhesion between adjacent filaments, or create dimensional accuracy problems due to
excessive deformation of the filaments, if the processing conditions are not adequately set. This chapter presented a MatLab code for modelling the heat transfer in FFE, aiming at
determining the temperature evolution of each filament during the deposition stage. Two
case studies illustrated the use of the programme. p
g
q
y
This chapter presented a MatLab code for modelling the heat transfer in FFE, aiming at
determining the temperature evolution of each filament during the deposition stage. Two
case studies illustrated the use of the programme. Agarwala, M. K.; Jamalabad, V. R.; Langrana, N. A.; Safari, A.; Whalen, P. J. & Danthord, S.
C. (1996). Structural quality of parts processed by fused deposition, Rapid Prototyping
Journal, Vol.2, No.4, pp. 4-19, ISSN 1355-2546. Bellini, A.; Shor, L. & Guceri, S. (2005). New developments in fused deposition modeling of
ceramics, Rapid Prototyping Journal, Vol.11, No.4, pp. 214-220, ISSN 1355-25. MATLAB – A Ubiquitous Tool for the Practical Engineer MATLAB – A Ubiquitous Tool for the Practical Engineer
474
Agarwala, M. K.; Jamalabad, V. R.; Langrana, N. A.; Safari, A.; Whalen, P. J. & Danthord, S.
C. (1996). Structural quality of parts processed by fused deposition, Rapid Prototyping
Journal, Vol.2, No.4, pp. 4-19, ISSN 1355-2546.
Bellini, A.; Shor, L. & Guceri, S. (2005). New developments in fused deposition modeling of
ceramics, Rapid Prototyping Journal, Vol.11, No.4, pp. 214-220, ISSN 1355-25. 7. References Rodriguez, J. F. (1999). Modelling the mechanical behaviour of fused deposition acrylonitrile-
butadiene-styrene polymer components, Ph.D. Dissertation, Department of Aeorospace
and Mechanical Engineering, University of Notre Dame, Notre Dame, USA g
g
y
Thomas, J. P. & Rodríguez, J. F. (2000). Modeling the fracture strength between fused deposition
extruded roads, Solid Freeform Fabrication Symposium Proceeding, Austin. y
g
Yardimci, M. A. & Guceri, S. I. (1996). Conceptual framework for the thermal process modelling of
fused deposition, Rapid Prototyping Journal, 2, 26-31. f
p
p
yp
g
Li, L.; Sun, Q.; Bellehumeur, C. & Gu, P. (2003). Modeling of bond formation in FDM process,
Trans. NAMRI/SME, 8, 613-620. Sun, Q.; Rizvi, G.C.; Bellehumeur, C. & Gu, T. P. (2004). Experimental study and modeling of
bond formation between ABS filaments in the FDM process, Proc. SPE ANTEC'2004. f
f
p
Costa, S.; Duarte, F. & Covas, J. A. (2008). Towards modelling of Free Form Extrusion: analytical
solution of transient heat transfer, Esaform 2008, Lyon, France. f
f
y
Bejan, A. (1993). Heat Transfer, John Wiley & Sons, Inc., New York. Marsan, A.; Dutta, D. (2000). A review of process planning techniques in layered manufacturing,
Rapid Prototyping Journal, Vol.6, No.1, pp. 18-35, ISSN 1355-2546. Pérez, C. J. L. (2002). Analysis of the surface roughness and dimensional accuracy capability of fused
deposition modelling processes, International Journal of Production Research, Vol.40,
Issue 12, pp. 2865 – 2881, ISSN 1366-588X. pp
Ahn, S. H. (2002). Anisotropic material properties of fused deposition modeling ABS, Rapid
Prototyping Journal, Vol.8, No.4, pp. 248–257, ISSN 1355-2546. Ziemian, C. W. & Crawn, P. M. (2001). Computer aided decision support for fused deposition
modeling, Rapid Prototyping Journal, Vol.7, No.3, pp. 138-147, ISSN 1355-2546. MATLAB – A Ubiquitous Tool for the Practical Engineer 474 Bellini, A.; Shor, L. & Guceri, S. (2005). New developments in fused deposition modeling of
ceramics, Rapid Prototyping Journal, Vol.11, No.4, pp. 214-220, ISSN 1355-25. MATLAB as a Tool in Nuclear Medicine
Image Processing Maria Lyra, Agapi Ploussi and Antonios Georgantzoglou
Radiation Physics Unit, A’ Radiology Department, University of Athens
Greece Maria Lyra, Agapi Ploussi and Antonios Georgantzoglou
Radiation Physics Unit, A’ Radiology Department, University of Athens
Greece Image Processing 23 2. Nuclear medicine imaging Nuclear
Medicine
is
the
section
of
science
that
utilises
the
properties
of
radiopharmaceuticals in order to derive clinical information of the human physiology and
biochemistry. According to the examination needed for each patient, a radionuclide is
attached to a pharmaceutical (tracer) and the whole complex is then delivered to the patient
intravenously or by swallowing or even by inhalation. The radiopharmaceutical follows its
physiological pathway and it is concentrated on specific organs and tissues for short periods
of time. Then, the patient is positioned under a nuclear medicine equipment which can
detect the radiation emitted by the human body resulting in images of the biodistribution of
the radiopharmaceutical. p
In Nuclear Medicine, there are two main methods of patient imaging, the imaging with
Planar Imaging, Dynamic Imaging or SPECT and the PET. During the last decade, hybrid
systems have been developed integrating the CT technique with either SPECT or PET
resulting in SPECT/CT and PET/CT respectively. This chapter will concentrate on the
implementation of MatLab code in gamma camera planar imaging, SPECT and SPECT/CT
methods. The gamma camera is composed of a collimator, a scintillator crystal usually made of NaI
(or CsI), the photomultiplier tubes, the electronic circuits and a computer equipped with the
suitable software to depict the nuclear medicine examinations. In planar imaging, the
patient, having being delivered with the suitable radiopharmaceutical, is sited under the
gamma camera head. The gamma camera head remains stable at a fixed position over the
patient for a certain period of time, acquiring counts (disintegrations). These will constitute
the radiopharmaceutical distribution image. The counts measured in a specific planar
projection originate from the whole thickness of patient (Wernick & Aarsvold, 2004). p
j
g
p
(
)
In SPECT, the gamma camera head rotates around the patient remaining at well defined
angles and acquiring counts for specific periods of time per angle. What makes SPECT a
valuable tool in nuclear medicine is the fact that information in the three dimensions of the
patient can be collected in a number of slices with a finite known volume (in voxels). Thus,
SPECT technique is used to display the radiopharmaceutical distribution in a single slice
removing the contribution from the overlying and underlying tissues. 1. Introduction Advanced techniques of image processing and analysis find widespread use in medicine. In
medical applications, image data are used to gather details regarding the process of patient
imaging whether it is a disease process or a physiological process. Information provided by
medical images has become a vital part of today’s patient care. The images generated in medical applications are complex and vary notably from
application to application. Nuclear medicine images show characteristic information about
the physiological properties of the structures-organs. In order to have high quality medical
images for reliable diagnosis, the processing of image is necessary. The scope of image
processing and analysis applied to medical applications is to improve the quality of the
acquired image and extract quantitative information from medical image data in an efficient
and accurate way. MatLab (Matrix Laboratory) is a high performance interactive software package for
scientific and engineering computation developed by MathWorks (Mathworks Inc., 2009). MatLab allows matrix computation, implementation of algorithms, simulation, plotting of
functions and data, signal and image processing by the Image Processing Toolbox. It enables
quantitative analysis and visualisation of nuclear medical images of several modalities, such
as Single Photon Emission Computed Tomography (SPECT), Positron Emission
Tomography (PET) or a hybrid system (SPECT/CT) where a Computed Tomography
system (CT) is incorporated to the SPECT system. The Image Processing Toolbox
(Mathworks Inc., 2009) is a comprehensive set of reference-standard algorithms and
graphical tools for image processing, analysis, visualisation and algorithm development. It
offers the possibility to restore noisy or degraded images, enhance images for improved
intelligibility, extract features, analyse shapes and textures, and register two images. Thus, it
includes all the functions that MatLab utilises in order to perform any sophisticated analysis
needed after the acquisition of an image. Most toolbox functions are written in open MatLab
language offering the opportunity to the user to inspect the algorithms, to modify the source
code and create custom functions (Wilson et al., 2003, Perutka, 2010). (
)
This chapter emphasises on the utility of MatLab in nuclear medicine images’ processing. It
includes theoretical background as well as examples. After an introduction to the imaging
techniques in nuclear medicine and the quality of nuclear medicine images, this chapter
proceeds to a study about image processing in nuclear medicine through MatLab. 1. Introduction Image
processing techniques presented in this chapter include organ contouring, interpolation, 478 MATLAB – A Ubiquitous Tool for the Practical Engineer filtering,
segmentation,
background
activity
removal,
registration
and
volume
quantification. A section about DICOM image data processing using MatLab is also
presented as this type of image is widely used in nuclear medicine. 2. Nuclear medicine imaging g
y
g
y
g
In order to obtain the most accurate quantitative data from SPECT images, two issues that
have to be resolved are the attenuation correction and the Compton scattering that the
photons are undergone until reach and interact with the slice of interest tissues. As an
examining organ has certain dimensions, each slice along the axis of the gamma camera has
different distance from the detector. Thus, each photon experiences different attenuation. These two phenomena usually lead to distortion of the measured activity concentration
(Wernick & Aarsvold, 2004). The acquired data are processed in order to correct and
compensate the undesired effect of these physical phenomena. The projection data of each
slice constitute the sinogram. As a result, a series of sinograms is the files acquired. However, this kind of files needs reconstruction in order to get an image with diagnostic
value. The most known reconstruction methods are the Filtered Back-Projection (FBP) and
the Iterative methods. 479 MATLAB as a Tool in Nuclear Medicine Image Processing Attenuation correction is resolved by using the constant linear attenuation coefficient (μ)
method or using the transmission source method. In the first one, the distance that each
photon has travelled is calculated based on the patient geometry and the exponential
reduction of their intensity. Then, considering the human body as a uniform object, an
attenuation map is implemented in the reconstructed image. The latter method utilises a
transmission source which scans the patient. This depicts each pixel or voxel of the patient
with a specific μ producing an attenuation coefficient map. Finally, the attenuation map is
implemented on the image resulting in a more accurate diagnosis. The second issue of scatter correction can be resolved by the electronics of the gamma
camera and the filtering process during reconstruction. When a photon undergoes
scattering, its energy reduces. So, a well defined function can accept for imaging photons
with energy at a certain narrow energy window around the central photopeak of the γ-
emission. A hybrid SPECT/CT scanner is capable of implementing both a CT scan and a SPECT scan
or it can be used for each of these scans separately. Using the CT scan, the anatomy of a
specific patient area can be imaged while the SPECT scan can depict the physiology of this
area. Then, the registration of the two images drives at an image of advanced diagnostic
value. 2. Nuclear medicine imaging Moreover, the CT data is used for the implementation of attenuation correction. (Delbeke et al., 2006) The range of nuclear medicine examinations is fairly wide. It includes, among others,
patients’ studies, as myocardium perfusion by 99mTc-Tetrofosmin or 99mTc-Sestamibi,
striatum imaging in brain by 123I-Ioflupane (DaTSCAN), renal parenchyma imaging by
99mTc-De-Methylo-Sulfo-Acid (DMSA) and 99mTc-Methylo-Di-Phosphonate (MDP) for bone
scintigraphy. Fundamental image analysis methods of myocardium, brain, kidneys, thyroid,
lungs and oncological (e.g. neuroblastoma) nuclear medicine studies include regions’
properties, boundary analysis, curvature analysis or line and circle detection. Image processing serves in reconstruction of images acquired using SPECT techniques, in
improvement of the quality of images for viewing and in preparation of images for
quantitative results. Data of the mentioned examinations are used in the following applications of MatLab
algorithms to make the image processing and analysis in nuclear medicine clear and show
the MatLab utility for these studies. 2.1 Image quality in nuclear medicine Image quality plays an important role in nuclear medicine imaging as the goal is a reliable
image of the projected organ to be provided, for accurate diagnosis or therapy. The physical
characteristics that are used to describe image quality are (1) contrast, (2) spatial resolution
and (3) noise. Image contrast is the difference in intensity corresponding to different concentration of
activity in the patient. For high diagnostic accuracy, nuclear medicine images must be of
high contrast. The image contrast is principally affected by the radiopharmaceutical that is
used for imaging and the scattered radiation. In general, it is desirable to use a
radiopharmaceutical which has a high uptake within the target organ. Spatial resolution is defined as the ability of the imaging modality to reproduce the details
of a nonuniform radioactive distribution. The spatial resolution is separated into intrinsic
resolution (scintillator, photomultiplier tubes and electronic circuit) and system resolution 480 MATLAB – A Ubiquitous Tool for the Practical Engineer (collimator, scintillator, photomultiplier tubes and electronic circuit). The intrinsic resolution
depends on the thickness of scintillation crystal while the system resolution depends mainly
on the distance from the emitting source to collimator. The resolution of a gamma camera is
limited by several factors. Some of these are the patient motion, the statistical fluctuation in
the distribution of visible photons detected and the collimators geometry (Wernick &
Aarsvold, 2004). (collimator, scintillator, photomultiplier tubes and electronic circuit). The intrinsic resolution
depends on the thickness of scintillation crystal while the system resolution depends mainly
on the distance from the emitting source to collimator. The resolution of a gamma camera is
limited by several factors. Some of these are the patient motion, the statistical fluctuation in
the distribution of visible photons detected and the collimators geometry (Wernick &
Aarsvold, 2004). Noise refers to any unwanted information that prevents the accurate imaging of an object. Noise is the major factor in the degradation of image quality. Image noise may be divided
into random and structured noise. Random noise (also referred as statistical noise) is the
result of statistical variations in the counts being detected. The image noise is proportional
to N1/2 where N is the number of detected photons per pixel. Therefore, as the number of
counts increases the noise level reduces. Image noise is usually analysed in terms of
signal-to-noise-ratio (SNR). SNR is equal to N/ N1/2. 2.2 Complex topics In the previous section, several issues arising from the need of achieving the best image
quality have to be resolved. Sometimes, the whole procedure becomes really hard to be
completed. Some concepts in image processing and analysis are theory-intensive and may
be difficult for medical professionals to comprehend. Apart from that, each manufacturer uses different software environment for the application
of reconstruction and presentation of the images. This drives at a lack of a standard pattern
based on which a physician can compare or parallel two images acquired and reconstructed
by nuclear imaging systems of different vendors. This is a node on which MatLab can meet
a wide acceptance and utilisation. These complex topics can be analysed and resolved using MatLab algorithms to turn up the
most effective techniques to emerge information through medical imaging. 2.1 Image quality in nuclear medicine If the SNR is high, the diagnostic
information of an image is appreciated regardless of the noise level. Structured noise is
derived from non-uniformities in the scintillation camera and overlying structures in
patient body. 3. Image analysis and processing in nuclear medicine In the last several decades, medical imaging systems have advanced in a dynamic progress. There have been substantial improvements in characteristics such as sensitivity, resolution,
and acquisition speed. New techniques have been introduced and, more specifically,
analogue images have been substituted by digital ones. As a result, issues related to the
digital images’ quality have emerged. The quality of acquired images is degraded by both physical factors, such as Compton
scattering and photon attenuation, and system parameters, such as intrinsic and extrinsic
spatial resolution of the gamma camera system. These factors result in blurred and noisy
images. Most times, the blurred images present artefacts that may lead to a fault diagnosis. In order the images to gain a diagnostic value for the physician, it is compulsory to follow a
specific series of processing. Image processing is a set of techniques in which the data from an image are analysed and
processed using algorithms and tools to enhance certain image information that is more
useful to human interpretation (Nailon, 2010). The processing of an image permits the 481 MATLAB as a Tool in Nuclear Medicine Image Processing extraction of useful parameters and increases the possibility of detection of small lesions
more accurately. extraction of useful parameters and increases the possibility of detection of small lesions
more accurately. Image processing in nuclear medicine serves three major purposes: a) the reconstruction of
the images acquired with tomographic (SPECT) techniques, b) the quality improvement of
the image for viewing in terms of contrast, uniformity and spatial resolution and, c) the
preparation of the image in order to extract useful diagnostic qualitative and quantitative
information. 3.2 Types of digital images – MatLab The colour of each image pixel is
determined by using the corresponding value of matrix as an index into map. The greyscale image is the most convenient and preferable type utilised in nuclear medicine
image processing. When colouring depiction is needed, the RGB one should be used and
processed. The indexed type images should be converted to any of the two other types in
order to be processed. The functions used for image type conversion are: rgb2gray,
ind2rgb, ind2gray and reversely. Any image can be also transformed to binary one using
the command: im2bw. Moreover, in any image, the function impixelinfo can be used in
order to detect any pixel value. The user can move the mouse cursor inside the image and
the down left corner appears the pixel identity (x, y) as well as the (RGB) values. The pixel
range of the image can be displayed by the command imdisplayrange. 3.1 Digital images In all modern nuclear medicine imaging systems, the images are displayed as an array of
discrete picture elements (pixels) in two dimensions (2D) and are referred as digital images. Each pixel in a digital image has an intensity value and a location address (Fig. 1). In a
nuclear medicine image the pixel value shows the number of counts recorded in it. The
benefit of a digital image compared to the analogue one is that data from a digital image are
available for further computer processing. Fig. 1. A digital image is a 2D array of pixels. Each pixel is characterised by its (x, y)
coordinates and its value. Fig. 1. A digital image is a 2D array of pixels. Each pixel is characterised by its (x, y)
coordinates and its value. Digital images are characterised by matrix size, pixel depth and resolution. The matrix size
is determined from the number of the columns (m) and the number of rows (n) of the image
matrix (m×n). The size of a matrix is selected by the operator. Generally, as the matrix
dimension increases the resolution is getting better (Gonzalez et al., 2009). Nuclear medicine
images matrices are, nowadays, ranged from 64×64 to 1024×1024 pixels. g
y
g
Pixel or bit depth refers to the number of bits per pixel that represent the colour levels of
each pixel in an image. Each pixel can take 2k different values, where k is the bit depth of the
image. This means that for an 8-bit image, each pixel can have from 1 to 28 (=256) different
colour levels (grey-scale levels). Nuclear medicine images are frequently represented as 8- or
16- bit images. The term resolution of the image refers to the number of pixels per unit length of the image. In digital images the spatial resolution depends on pixel size. The pixel size is calculated by
the Field of View (FoV) divided by the number of pixels across the matrix. For a standard
FoV, an increase of the matrix size decreases the pixel size and the ability to see details is
improved. 482 MATLAB – A Ubiquitous Tool for the Practical Engineer 3.2 Types of digital images – MatLab MatLab offers simple functions that can read images of many file formats and supports a
number of colour maps. Depending on file type and colour space, the returned matrix is
either a 2D matrix of intensity values (greyscale images) or a 3D matrix of RGB values. Nuclear medicine images are grey scale or true colour images (RGB that is Red, Green and
Blue). )
The image types supported from the Image Processing Toolbox are listed below: •
Binary Images. In these, pixels can only take 0 or 1 value, black or white. •
Greyscale or intensity images. The image data in a greyscale image represent intensity
or brightness. The integers’ value is within the range of [0… 2k-1], where k is the bit
depth of the image. For a typical greyscale image each pixel can represented by 8 bits
and intensity values are in the range of [0…255], where 0 corresponds to black and 255
to white. •
True color or RGB. In these, an image can be displayed using three matrices, each one
corresponding to each of red-green-blue colour. If in an RGB image each component
uses 8 bits, then the total number of bits required for each pixel is 3×8=24 and the range
of each individual colour component is [0…255]. •
True color or RGB. In these, an image can be displayed using three matrices, each one
corresponding to each of red-green-blue colour. If in an RGB image each component
uses 8 bits, then the total number of bits required for each pixel is 3×8=24 and the range
of each individual colour component is [0…255]. •
Indexed images. Indexed images consist of a 2D matrix together with an m×3 colour
map (m= the number of the columns in image matrix). Each row of map specifies the
red, green, and blue components of a single colour. An indexed image uses direct
mapping of pixel values to colour map values. The colour of each image pixel is
determined by using the corresponding value of matrix as an index into map. •
Indexed images. Indexed images consist of a 2D matrix together with an m×3 colour
map (m= the number of the columns in image matrix). Each row of map specifies the
red, green, and blue components of a single colour. An indexed image uses direct
mapping of pixel values to colour map values. 3.3 MatLab image tool The Image Tool is a simple and user-friendly toolkit which can contribute to a quick image
processing and analysis without writing a code and use MatLab language. These properties
makes it a very useful tool when deep analysis is not the ultimate goal but quick processing
for better view is desirable. The Image Tool opens by simply writing the command imtool in the main function
window. Then a new window opens and the next step is loading an image. In the menu,
there are many functions already installed in order to use it as simple image processing
software. The tools include image information appearance, image zooming in and out,
panning, adjustment of the window level and width, adjustment of contrast, cropping,
distance measurement, conversion of the image to a pixel matrix and colour map choices
(grey scale, bone colour, hot regions among others). These are the most common functions
likely to be performed in the initial processing approach. Moreover, the user can make some
further manipulations such as 3D rotation to respective 3D images and plotting of pixel
data. 483 MATLAB as a Tool in Nuclear Medicine Image Processing 3.4 Image processing techniques - MatLab Image processing techniques include all the possible tools used to change or analyse an
image according to individuals’ needs. This subchapter presents the most widely performed
image processing techniques that are applicable to nuclear medicine images. The examples
used are mostly come from nuclear medicine renal studies, as kidneys’ planar images and
SPECT slices are simple objects to show the application of image processing MatLab tools. 3.4.1 Contrast enhancement One of the very first image processing issues is the contrast enhancement. The acquired
image does not usually present the desired object contrast. The improvement of contrast is
absolutely needed as the organ shape, boundaries and internal functionality can be better
depicted. In addition, organ delineation can be achieved in many cases without removing
the background activity. The command that implements contrast processing is the imadjust. Using this, the
contrast in an image can be enhanced or degraded if needed. Moreover, a very useful result
can be the inversion of colours, especially in greyscale images, where an object of interest
can be efficiently outlined. The general function that implements contrast enhancement is
the following: J = imadjust(I,[low_in high_in],[low_out high_out],gamma); while the function for colour inversion is the following: while the function for colour inversion is the following: J = imadjust(I,[0 1],[1 0],gamma); or J = imcomplement(I); J = imadjust(I,[0 1],[1 0],gamma); or J = imcomplement(I); suppose that J, is the new image, I, is the initial image and gamma factor depicts the shape
of the curve that describes the relationship between the values of I and J. If the gamma factor
is omitted, it is considered to be 1. J = imresize(I, 0.5, ‘bilinear’); J = imresize(I, 0.5, ‘bilinear’); J = imresize(I, 0.5, ‘bilinear’); This way of image resizing contributes to the conversion of image information during any
such process, a fact that is valuable in the precision of a measurement. Bilinear interpolation
is often used to zoom into a 2D image or for rendering, for display purposes. Apart from the
previous methods, the cubic convolution method can be applied to 3D images. 3.4.2 Organ contour In many nuclear medicine images, the organs’ boundaries are presented unclear due to low
resolution or presence of high percentage of noise. In order to draw the contour of an organ in a nuclear medicine image, the command
imcontour is used. In addition, a variable n defines the number of equally spaced contours
required. This variable is strongly related with the intensity of counts. For higher n values,
the lines are drawn with smaller spaces in between and depict different streaks of intensity. The type of line contouring can be specified as well. For example, when a contour of 5 level
contours, drawn with solid line, is the desirable outcome, the whole function is: Example 1I = imread(‘kindeys.jpg’); Example 1I = imread(‘kindeys.jpg’); Example 1I = imread(‘kindeys.jpg’);
figure, imshow(I) figure, imshow(I) J = imcontour(I,5,’-‘);
Figure, imshow(J) J = imcontour(I,5,’-‘); J = imcontour(I,5,’-‘); Figure, imshow(J) where J and I stands for the final and the initial image respectively and the symbol (’-‘)
stands for the solid line drawing. An example of the initial image, the contour with n=15
and n=5 respectively, follows. MATLAB – A Ubiquitous Tool for the Practical Engineer 484 Fig. 2. (a) Original image depicting kidneys, (b) organs contoured with n = 15, (c) organs
contoured with n = 5. Fig. 2. (a) Original image depicting kidneys, (b) organs contoured with n = 15, (c) org
contoured with n = 5. 3.4.3 Image interpolation Interpolation is a topic that has been widely used in image processing. It constitutes of the
most common procedure in order to resample an image, to generate a new image based on
the pattern of an existing one. Moreover, re-sampling is usually required in medical image
processing in order to enhance the image quality or to retrieve lost information after
compression of an image (Lehmann et al., 1999). p
g (
)
Interpreting the interpolation process, the user is provided with several options. These
options include the resizing of an image according to a defined scaling factor, the choice of
the interpolation type and the choice of low-pass filter. The general command that performs image resizing is imresize. However, the way that
the whole function has to be written depends heavily on the characteristics of the new
image. The size of the image can be defined as a scaling factor of the existing image or by
exact number of pixels in rows and columns. Concerning the interpolation types usually
used in nuclear medicine, these are the following: a) nearest-neighbour interpolation
(‘nearest’), where the output pixel obtains the value of the pixel that the point falls
within, without considering other pixels, b) bilinear interpolation (‘bilinear’), where the
output pixel obtains a weighted average value of the nearest 2x2 pixels, c) cubic
interpolation (‘bicubic’), where the output pixel obtains a weighted average value of the
nearest 4x4 pixels (Lehmann et al., 1999). When an image has to resize in a new one, with specified scaling factor and method, then
the function Implementing that, is the following: NewImage = imresize(Image, scale, method); For example, for a given image I, the new image J shrunk twice of the initial one, using the
bilinear interpolation method, the function will be: For example, for a given image I, the new image J shrunk twice of the initial one, using the
bilinear interpolation method, the function will be: 3.4.4 Image filtering The factors that degrade the quality of nuclear medicine images result in blurred and noisy
images with poor resolution. One of the most important factors that greatly affect the MATLAB as a Tool in Nuclear Medicine Image Processing 485 quality of clinical nuclear medicine images is image filtering. Image filtering is a
mathematical processing for noise removal and resolution recovery. The goal of the filtering
is to compensate for loss of detail in an image while reducing noise. Filters suppressed noise
as well as deblurred and sharpened the image. In this way, filters can greatly improve the
image resolution and limit the degradation of the image. quality of clinical nuclear medicine images is image filtering. Image filtering is a
mathematical processing for noise removal and resolution recovery. The goal of the filtering
is to compensate for loss of detail in an image while reducing noise. Filters suppressed noise
as well as deblurred and sharpened the image. In this way, filters can greatly improve the
image resolution and limit the degradation of the image. An image can be filtered either in the frequency or in the spatial domain. In the first case the
initial data is Fourier transformed, multiplied with the appropriate filter and then taking the
inverse Fourier transform, re-transformed into the spatial domain. The basics steps of
filtering in the frequency domain are illustrated in Fig. 3. An image can be filtered either in the frequency or in the spatial domain. In the first case the
initial data is Fourier transformed, multiplied with the appropriate filter and then taking the
inverse Fourier transform, re-transformed into the spatial domain. The basics steps of
filtering in the frequency domain are illustrated in Fig. 3. Fig. 3. Basics steps of frequency domain filtering. Fig. 3. Basics steps of frequency domain filtering. The filtering in the spatial domain demands a filter mask (it is also referred as kernel or
convolution filter). The filter mask is a matrix of odd usually size which is applied directly
on the original data of the image. The mask is centred on each pixel of the initial image. For each position of the mask the pixel values of the image is multiplied by the
corresponding values of the mask. The products of these multiplications are then added
and the value of the central pixel of the original image is replaced by the sum. 3.4.4.1 Mean filter Mean filter is the simplest low pass linear filter. It is implemented by replacing each pixel
value with the average value of its neighbourhood. Mean filter can be considered as a
convolution filter. The smoothing effect depends on the kernel size. As the kernel size
increases, the smoothing effect increases too. Usually a 3×3 (or larger) kernel filter is used. An example of a single 3×3 kernel is shown in the Fig. 5. Fig. 5. Filtering approach of mean filter. Fig. 5. Filtering approach of mean filter. The Fig.5 depicts that by using the mean filter, the central pixel value would be changed
from “e” to ‘’ (a+b+c+d+e+f+g+h+i) 1/9’’. 3.4.4 Image filtering This must
be repeated for every pixel in the image. The procedure is described schematically in
Fig. 4. If the filter, by which the new pixel value was calculated, is a linear function of the entire
pixel values in the filter mask (e.g. the sum of products), then the filter is called linear. If the
output pixel is not a linear weighted combination of the input pixel of the image then the
filtered is called non-linear. According to the range of frequencies they allow to pass through filters can be classified as
low pass or high pass. Low pass filters allow the low frequencies to be retained unaltered
and block the high frequencies. Low pass filtering removes noise and smooth the image but
at the same time blur the image as it does not preserve the edges. High pass filters sharpness
the edges of the image (areas in an image where the signal changes rapidly) and enhance
object edge information. A severe disadvantage of high pass filtering is the amplification of
statistical noise present in the measured counts. The next section is referred to three of the most common filters used by MatLab: the mean,
median and Gaussian filter. MATLAB – A Ubiquitous Tool for the Practical Engineer 486 Fig. 4. Illustration of filtering process in spatial domain. Fig. 4. Illustration of filtering process in spatial domain. 3.4.4.2 Median filter Median filter is a non linear filter. Median filtering is done by replacing the central pixel
with the median of all the pixels value in the current neighbourhood. A median filter is a useful tool for impulse noise reduction (Toprak & Göller, 2006). The
impulse noise (it is also known as salt and paper noise) appears as black or (/and) white 487 MATLAB as a Tool in Nuclear Medicine Image Processing pixels randomly distributed all over the image. In other words, impulse noise corresponds
to pixels with extremely high or low values. Median filters have the advantage to preserve
edges without blurring the image in contrast to smoothing filters. Fig. 6. Filtering approach of Median Filter. Fig. 6. Filtering approach of Median Filter. Fig. 6. Filtering approach of Median Filter. Example 2 The following example describes the commands’ package that can be used for the
application of the mean (average) filter in a SPECT slice for different convolution kernel
sizes (for 3×3, 9×9, 25×25 average filter). h=fspecial('average', [3 3]); b=imfilter(a,h); figure, imshow(b); i=fspecial('average', [9 9]); c=imfilter(b,h); figure, imshow(c); j=fspecial('average', [25 25]); d=imfilter(c,h); figure, imshow(d); Figure 8 presents different implementations of the mean filter on a kidneys image with
filters 3x3, 9x9, 15x15, 20x20 and 25x25. As it can be easily noticed, the mean filter balances and smoothes the image, flattening the
differences. The filtered images do not present edges at the same extent as in the original
one. For larger kernel size, the blurring of the image is more intense. Image smoothening
can be used in several areas of nuclear medicine and can serve in different points of view of
the examined organ. 3.4.4.3 Gaussian filter Gaussian filter is a linear low pass filter. A Gaussian filter mask has the form of a bell-
shaped curve with a high point in the centre and symmetrically tapering sections to either
side (Fig.7). Application of the Gaussian filter produces, for each pixel in the image, a
weighted average such that central pixel contributes more significantly to the result than
pixels at the mask edges (O’Gorman et al., 2008). The weights are computed according to the
Gaussian function (Eq.1): 2
2
1
(
) /(2
)
( )
2
x
f x
e
μ
σ
σ
π
−
−
=
(1) (1) where μ, is the mean and σ, the standard deviation. where μ, is the mean and σ, the standard deviation. Fig. 7. A 2D Gaussian function. The degree of smoothing depends on the standard deviation. The larger the standard
deviation, the smoother the image is depicted. The Gaussian filter is very effective in the
reduction of impulse and Gaussian noise. Gaussian noise is caused by random variations in
the intensity and has a distribution that follows the Gaussian curve. Fig. 7. A 2D Gaussian function. The degree of smoothing depends on the standard deviation. The larger the standard
deviation, the smoother the image is depicted. The Gaussian filter is very effective in the
reduction of impulse and Gaussian noise. Gaussian noise is caused by random variations in
the intensity and has a distribution that follows the Gaussian curve. The degree of smoothing depends on the standard deviation. The larger the standard
deviation, the smoother the image is depicted. The Gaussian filter is very effective in the
reduction of impulse and Gaussian noise. Gaussian noise is caused by random variations in
the intensity and has a distribution that follows the Gaussian curve. 488 MATLAB – A Ubiquitous Tool for the Practical Engineer 3.5 Filtering in MatLab g
In MatLab, using Image Processing Toolbox we can design and implemented filters for
image data. For linear filtering, MatLab provides the fspecial command to generate some
predefined common 2D filters. h=fspecial(filtername, parameters) B = imfilter(A,h) This function filters the multidimensional array A with the multidimensional filter h. imfilter function is more general than filter2 function. For nonlinear filtering in
MatLab the function nlfilter is applied, requiring three arguments: the input image, the
size of the filter and the function to be used. B = nlfilter(A, [m n], fun) Example 2 Y = filter2(h,X) The function filter2 filters the data in matrix X with the filter h. For multidimensional
images the function imfilter is used. B = imfilter(A,h) h=fspecial(filtername, parameters) The filtername is one of the average, disk, gaussian, laplacian, log, motion, prewitt, sobel
and unsharp filters; that is the parameters related to the specific filters that are used each
time. Filters are applied to 2D images using the function filter2 with the syntax: Y = filter2(h,X) Example 3 In this example we will try to remove impulse noise from a SPECT slice, for example in a
renal study. For this reason we mix the image with impulse noise (salt and pepper). The
image has a 512×512 matrix size and grey levels between 0 and 255. The most suitable filter 489 MATLAB as a Tool in Nuclear Medicine Image Processing for removing impulse noise is the median filter. Because it is a nonlinear filter, the command
nlfilter is now used. for removing impulse noise is the median filter. Because it is a nonlinear filter, the command
nlfilter is now used. Fig. 8. Mean filter applied on kidneys image (a) Original image, (b) average filter 3x3, (c)
average filter 9x9, (d) average filter 15x15, (e) average filter 20x20 and, (f) average filter
25x25 [(a) to (f) from left to right]. for removing impulse noise is the median filter. Because it is a nonlinear filter, the command
nlfilter is now used. Fig. 8. Mean filter applied on kidneys image (a) Original image, (b) average filter 3x3, (c)
average filter 9x9, (d) average filter 15x15, (e) average filter 20x20 and, (f) average filter
25x25 [(a) to (f) from left to right]. I = imread('kidneys.tif'); J = imnoise(I,'salt & pepper',0.05); figure, imshow(J); fun = @(x) median(x(:)); K = nlfilter(J,[3 3],fun); figure, imshow(K); Fig. 9. Impulse noise elimination by median filter. (a) Original image (b) the image with
impulse noise (c) the image on which the noise is suppressed with the median filter. [(a) to
(c) from left to right] Fig. 9. Impulse noise elimination by median filter. (a) Original image (b) the image with
impulse noise (c) the image on which the noise is suppressed with the median filter. [(a) to
(c) from left to right] 490 MATLAB – A Ubiquitous Tool for the Practical Engineer Example 3 can be very useful in the nuclear medicine examinations of parenchymatous
organs (liver, lungs, thyroid or kidneys) as it consists of a simple enough method for the
reduction of noise which interferes in the image due to the construction of electronic circuits. 3.6 Image segmentation The image segmentation describes the process through which an image is divided into
constituent parts, regions or objects in order to isolate and study separately areas of special
interest. This process assists in detecting critical parts of a nuclear medicine image that are
not easily displayed in the original image. The process of segmentation has been developed based on lots of intentions such as
delineating an object in a gradient image, defining the region of interest or separating
convex components in distance-transformed images. Attention should be spent in order to
avoid ‘over-segmentation’ or ‘under-segmentation’. In nuclear medicine, segmentation
techniques are used to detect the extent of a tissue, an organ, a tumour inside an image, the
boundaries of structures in cases that these are ambiguous and the areas that
radiopharmaceutical concentrate in a greater extent. Thus, the segmentation process serves
in assisting the implementation of other procedures; in other words, it constitutes the
fundamental step of some basic medical image processing (Behnaz et al., 2010). p
g p
g (
)
There are two ways of image segmentation: a) based on the discontinuities and, b) based on
the similarities of structures inside an image. In nuclear medicine images, the discontinuity
segmentation type finds more applications. This type depends on the detection of
discontinuities or else, edges, inside the image using a threshold. The implementation of
threshold helps in two main issues: i) the removal of unnecessary information from the
image (background activity) and, ii) the appearance of details not easily detected. g (
g
y)
)
pp
y
The edge detection uses the command edge. In addition, a threshold is applied in order to
detect edges above defined grey-scale intensity. Also, different methods of edge detection
can be applied according to the filter each of them utilises. The most useful methods in
nuclear medicine are the ‘Sobel’, ‘Prewitt’, ‘Roberts’, ‘Canny’ as well as ‘Laplacian of
Gaussian'. It is noted that the image is immediately transformed into a binary image and
edges are detected. The general function used for the edge detection is the following: [BW] = edge (image, ‘method’, threshold) Example 5 I = imread('kidneys.jpg');
Figure, imshow(I)
hy = fspecial('sobel');
hx = hy';
Iy = imfilter(double(I), hy, 'replicate');
Ix = imfilter(double(I), hx, 'replicate');
gradmag = sqrt(Ix.^2 + Iy.^2);
figure, imshow(gradmag,[])
se = strel('disk', 20);
K = imopen(I, se);
figure, imshow(K) I = imread('kidneys.jpg'); Figure, imshow(I) hy = fspecial('sobel'); Iy = imfilter(double(I), hy, 'replicate'); Ix = imfilter(double(I), hx, 'replicate'); gradmag = sqrt(Ix.^2 + Iy.^2); figure, imshow(gradmag,[]) se = strel('disk', 20); K = imopen(I, se); figure, imshow(K) Fig. 11. Gradient Magnitude process: (a) Original image, (b) image after implementation of
filter and gradient magnitude, (c) image after masking of foreground objects [(a) to (c) from
left to right] Fig. 11. Gradient Magnitude process: (a) Original image, (b) image after implementation of
filter and gradient magnitude, (c) image after masking of foreground objects [(a) to (c) from
left to right] In the final image, the outline of the organs is depicted. The area inside the kidney has been
separated into larger parts with grey-scale intensity weighted and decided from the closest
20 pixels in a circular region. In the areas of kidney that have higher activity concentrated,
more than one layer of circular regions have been added presenting a final lighter region. In the final image, the outline of the organs is depicted. The area inside the kidney has been
separated into larger parts with grey-scale intensity weighted and decided from the closest
20 pixels in a circular region. In the areas of kidney that have higher activity concentrated,
more than one layer of circular regions have been added presenting a final lighter region. [BW] = edge (image, ‘method’, threshold) [BW] = edge (image, ‘method’, threshold) [BW] = edge (image, ‘method’, threshold) Where [BW] is the new binary image produced, image is the initial one; ‘method’ refers to
the method of edge detection and ‘threshold’ to the threshold applied. In nuclear medicine,
the methods that find wide application are the sorbel, prewitt and canny. In the following
example, the canny method is applied in order to detect edges in an image. Example 4 I = imread(‘kidneys.jpg’);
figure, imshow(I)
J = edge(I,'canny', 0.048)
figure, imshow(J) I = imread(‘kidneys.jpg’);
figure, imshow(I)
J = edge(I,'canny', 0.048);
figure, imshow(J) I = imread(‘kidneys.jpg’); figure, imshow(I) J = edge(I,'canny', 0.048); figure, imshow(J) Another application of segmentation in nuclear medicine is the use of gradient magnitude. The original image is loaded. Then, the edge detection method of sobel is applied in
accordance with a gradient magnitude which gives higher regions with higher grey-scale
intensity. Finally, the foreground details are highlighted and segmented image of the
kidneys is produced. The whole code for that procedure is described below. MATLAB as a Tool in Nuclear Medicine Image Processing 491 Fig. 10. Edge detection (a) Original kidneys image, (b) edge detection with canny method
and threshold 0.2667, (c) edge detection with prewitt method and threshold 0.038. [(a) to (c)
from left to right] Fig. 10. Edge detection (a) Original kidneys image, (b) edge detection with canny method
and threshold 0.2667, (c) edge detection with prewitt method and threshold 0.038. [(a) to (c)
from left to right] Example 5 3.7 Background activity removal g
y
One of the first steps to be completed in the medical image processing is removing the
background activity. This procedure is based on image segmentation as in order to achieve
the background activity removal, the organs’ boundaries are first defined. The steps in this
procedure are the following: i) the image is read, ii) the image is appeared, iii) a grey level
threshold is decided by MatLab, iv) the image is transformed into binary image in order to
isolate the two kidneys, v) the binary image is multiplied by the initial one, vi) the final 492 MATLAB – A Ubiquitous Tool for the Practical Engineer image is appeared, vii) the colour can change (or not) according to individuals’ needs. The
following example of kidneys image describes the process. image is appeared, vii) the colour can change (or not) according to individuals’ needs. The
following example of kidneys image describes the process. Example 6 p
I = imread(‘kidneys.jpg’);
figure, imshow(I)
(fig.12a)
graythresh(I) and the value of the threshold is calculated: ans = 0.2667
I2 = im2bw(I, 0.2667)
(fig.12b)
I3 = immultiply(I2, I)
imshow(I3)
(fig.12c)
colormap(hot)
(fig.12d)
Fig. 12. Background subtraction: (a) Original image, (b) segmented binary image after
thresholding depicting only sharp organ boundaries, (c) image after background removal,
(d) change of colour to nuclear medicine pattern. [(a) to (d) from left to right] I = imread(‘kidneys.jpg’); figure, imshow(I) graythresh(I) and the value of the threshold is calculated: a I2 = im2bw(I, 0.2667) I3 = immultiply(I2, I) Fig. 12. Background subtraction: (a) Original image, (b) segmented binary image after
thresholding depicting only sharp organ boundaries, (c) image after background removal,
(d) change of colour to nuclear medicine pattern. [(a) to (d) from left to right] 3.8 Image registration Image registration is used for aligning two images of the same object into a common
coordinate system presenting the fused image. The one image is usually referred as
reference and the other as sensed (or referred). Image registration is a spatial transform. The
images can be acquired from different angles, at different times, by different or same
modalities. A typical example of the use of image registration from different modalities in
nuclear medicine is the combination of SPECT and CT images (SPECT/CT) or PET and CT
(PET/CT). Image registration is used mainly for two reasons: i) to obtain enhanced
information and details from the image for more accurate diagnosis or therapy (Li & Miller,
2010) and, ii) to compare patient’s data (Zitova & Flusser, 2003). MatLab can be used in
order to perform such a process. The whole procedure shall follow a specific order. 493 MATLAB as a Tool in Nuclear Medicine Image Processing The first step of the procedure includes the image acquisition. After that, each image is
reconstructed separately. Any filters needed are applied as well as enhancements in
brightness and contrast. The process of filter application has been described in a previous
section. The next step includes the foundation of a spatial transformation between the two
images, the one of SPECT and the other of CT. The key figure in this step concerns about the
alignment of the two images. A spatial transformation modifies the spatial relationship
between the pixels of an image relocating them to new positions in a new image. There are
several types of spatial transformation including the affine, the projective the box and the
composite (Delbeke et al., 2006). The final step in image registration is the overlapping of the
two images allowing a suitable level of transparency. A new image is created containing
information from both pictures from which, the first has been produced. The whole
procedure can be described with a set of commands which is user customised as different
registration function packages can be constructed for different uses. 3.9 Intensity volume and 3-D visualisation Volume visualisation in nuclear medicine consists of a method for extracting information
from volumetric data utilising and processing a nuclear medicine image (Lyra et al., 2010b). In MatLab, this can be achieved by constructing a 3D surface plot which uses the pixel
identities for (x, y) axes and the pixel value is transformed into surface plot height and,
consequently, colour. Apart from that, 3D voxel images can be constructed; SPECT
projections are acquired, iso-contours are depicted on them including a number of voxels
and, finally all of them can be added in order to create the desirable volume image. (Lyra et
al., 2010a). Volume rendering - very often used in 3D SPECT images - is an example of efficient coding
in MatLab. Inputs to the function are the original 3D array, the position angle, zoom or focus
of the acquired projections. The volume rendering used in 3D myocardium, kidneys,
thyroid, lungs and liver studies, took zoom and angles of 5.6 degrees, a focal length in pixels
depending of the organs’ size. The size of the re-projection is the same as the main size of
input image (e.g. 128x128 for the 128x128x256 input image). The volume rendering by
MatLab is slow enough but similar to other codes’ volume rendering. An example image of
myocardial 3-D voxel visualisation follows (Fig. 13): Fig. 13. 3D myocardial voxel visualisation; the image does not depicts the real volume but
the voxelised one (Lyra et al 2010a). Fig. 13. 3D myocardial voxel visualisation; the image does not depicts the real volume but
the voxelised one (Lyra et al 2010a). MATLAB – A Ubiquitous Tool for the Practical Engineer 494 4. MatLab mesh plot MatLab is unique in data analysis in neurological imaging. We used MatLab and the
functions of Image Processing Toolbox, to extract 3D basal ganglia activity measurements in
dopamine transporters DaTSCAN scintigraphy. It can be easily run in an ordinary computer
with Windows software, provides reproducible - user independent - results allowing better
follow-up control comparing to the semi-quantitative evaluation of tracer uptake in basal
ganglia. The surface plot or the mesh plot can be used in order to extract information about the
consistency of an organ or the loss of functionality. In order to construct a surface plot from
a striatum image, the series of images that include the highest level of information was
selected (Lyra et al 2010b) (Fig. 14): Fig. 14. A Series of central 123I-DaTSCAN SPECT imaging slices of I-123/Ioflupane; uptake
is highest in middle 4 slices, and these were summarized for region of interest analysis (Lyra
et al 2010b). Fig. 14. A Series of central 123I-DaTSCAN SPECT imaging slices of I-123/Ioflupane; uptake
is highest in middle 4 slices, and these were summarized for region of interest analysis (Lyra
et al 2010b). After the selection, ROI analysis was performed in order to concentrate on the area of
interest which is the middle site of the image. The area of interest was selected and a
package of functions was implemented. Example 7 Example 7 I = imread(‘striatum.jpg’);
figure, imshow(I)
[x,y] = size(I);
X = 1:x;
Y = 1:y;
[xx,yy] = meshgrid(Y,x);
J = im2double(I);
figure, surf(xx,yy,J);
shading interp
view(-40,60) I = imread(‘striatum.jpg’);
figure, imshow(I)
[x,y] = size(I);
X = 1:x;
Y = 1:y;
[xx,yy] = meshgrid(Y,x);
J = im2double(I);
figure, surf(xx,yy,J);
shading interp
view(-40,60) I = imread(‘striatum.jpg’); figure, imshow(I) [x,y] = size(I); figure, surf(xx,yy,J); shading interp view(-40,60) The whole procedure was, finally, resulted in the surface plot that is presented in the
Fig. 15. A point of interest could be that although the images that were used to construct the
surface plot were small and blurred, the final plot is clear and gives a lot of
information regarding the activity concentration in these two lobes. The angle of view can MATLAB as a Tool in Nuclear Medicine Image Processing 495 MATLAB as a Tool in Nuclear Medicine Image Processing be defined by the user giving the opportunity to inspect the whole plot from any point of
view. Fig. 15. Surface Plot of pixel intensity; x and y axes represent the pixels identities while the z
axis represents the pixel intensity. 5. DICOM image processing using MatLab The digital medical image processing started with the development of a standard for
transferring digital images in order to enable users to retrieve images and related
information from different modalities with a standardised way that is identical for all
imaging modalities. In 1993, a new image format was established by National Electrical
Manufacturers Association (NEMA). The Digital Imaging and Communication in Medicine
(DICOM) standard allows the communication between equipment from different modalities
and vendors facilitating the management of digital images. The DICOM standard defines a
set of common rules for the exchange, storage and transmission of digital medical images
with their accompanying information (Bidgood & Horii, 1992). y
g
g
A DICOM file consists of the data header (so called metadata) and the DICOM image data
set. The header includes image related information such as image type, study, modality, 496 MATLAB – A Ubiquitous Tool for the Practical Engineer matrix dimensions, number of stored bits, patient’s name. The image data follow the header
and contains 3D information of the geometry (Bankman, 2000). The DICOM files have a
.dcm extension. Fig. 16. Posterior image of kidneys in a DICOM format. Fig. 16. Posterior image of kidneys in a DICOM format. Fig. 16. Posterior image of kidneys in a DICOM format. In nuclear medicine, the most common and supported format for storing 3D data using
DICOM is to partition the volume (as myocardium or kidneys) into slices and to save each
slice as a simple DICOM image. The slices can be distinguished either by a number coding
in the file name or by specific DICOM tags. MatLab supports DICOM files and is a very useful tool in the processing of DICOM images. An example of reading and writing metadata and image data of a DICOM file using MatLab
is given in the next section. Let us consider a planar projection from a kidneys scan study for
a 10-month-old boy as the DICOM image (Fig. 16). y
g (
g
)
The specific DICOM image is a greyscale image. Assuming “kidneys” is the name of the
DICOM image we want to read, in order to read the image data from the DICOM file use
the command dicomread in the following function. I = dicomread('kidneys.dcm'); To read metadata from a DICOM file, use the dicominfo command. 5. DICOM image processing using MatLab The latter returns the
information in a MatLab structure where every field contains a specific piece of DICOM
metadata. For the same DICOM image as previously, info = dicominfo('kidneys.dcm') info = dicominfo('kidneys.dcm') info = dicominfo('kidneys.dcm') info = dicominfo('kidneys.dcm') A package of information appears in the command window including all the details that
accompany a DICOM image. This is a great advantage of this image format in comparison
to jpeg or tiff formats as the images retain all the information whereas the jpeg or tiff ones
lose a great majority of it. For the specific image, the following information appears: Filename: 'kidneys.dcm' FileModDate: '17-Feb-2011 14:04:18' FileSize: 128000 Format: 'DICOM' FormatVersion: 3 Width: 256 Height: 256 BitDepth: 16 dicomwrite(I, .dcm'), dicomwrite(K, .dcm') MATLAB as a Tool in Nuclear Medicine Image Processing 497 ColorType: 'grayscale' ColorType: 'grayscale' FileMetaInformationGroupLength: 212 FileMetaInformationVersion: [2x1 uint8] MediaStorageSOPClassUID: '1.2.840.10008.5.1.4.1.1.7' MediaStorageSOPInstanceUID: [1x57 char] TransferSyntaxUID: '1.2.840.10008.1.2.1' y
ImplementationClassUID: '1.2.840.113619.6.184' ImplementationVersionName: 'Xeleris 2.1220' SourceApplicationEntityTitle: 'XELERIS-6400'. The rest of the information has been omitted as there is a huge amount of details. To view
the image data imported from a DICOM file, use one of the toolbox image display functions
imshow or imtool. imshow(I,'DisplayRange',[]); imshow(K,'DisplayRange',[]); 7. Acknowledgment The authors would like to acknowledge Ms Maria Gavrilelli, Medical Physicist, MSc from
“Medical Imaging’’ Athens Paediatric Nuclear Medicine Center, Athens, Greece, for her
medical images contribution. imshow(I,'DisplayRange',[]); Similarly, an anterior planar image of thyroid gland can be imported and displayed in a
DICOM format by using the toolbox image display function imshow(K,'DisplayRange',[]); imshow(K,'DisplayRange',[]); Fig. 17. Anterior planar image of thyroid gland in a DICOM format. The image loaded can be now modified and processed in any desirable way. Many times,
words or letters that describe the slice or projection appear within the image. These can be
deleted and a new image without letters is created. To modify or write image data or
metadata to a file in DICOM format, use the dicomwrite function. The following
commands write the images I or K to the DICOM file kidneys_file.dcm and the
DICOM file thyroid_file.dcm Fig. 17. Anterior planar image of thyroid gland in a DICOM format. The image loaded can be now modified and processed in any desirable way. Many times,
words or letters that describe the slice or projection appear within the image. These can be
deleted and a new image without letters is created. To modify or write image data or
metadata to a file in DICOM format, use the dicomwrite function. The following
commands write the images I or K to the DICOM file kidneys_file.dcm and the
DICOM file thyroid_file.dcm Fig. 17. Anterior planar image of thyroid gland in a DICOM format. Fig. 17. Anterior planar image of thyroid gland in a DICOM format. The image loaded can be now modified and processed in any desirable way. Many times,
words or letters that describe the slice or projection appear within the image. These can be
deleted and a new image without letters is created. To modify or write image data or
metadata to a file in DICOM format, use the dicomwrite function. The following
commands write the images I or K to the DICOM file kidneys_file.dcm and the
DICOM file thyroid_file.dcm dicomwrite(I, .dcm'), dicomwrite(K, .dcm') dicomwrite(I, .dcm'), dicomwrite(K, .dcm') 498 MATLAB – A Ubiquitous Tool for the Practical Engineer On a DICOM format image any filtering, segmentation and background removing can be
applied to get the final image and extract the most possible information useful in Diagnosis. In Fig.18 a DICOM format planar image of thyroid gland is imported and displayed (a) and
further processed (b) by Gaussian filter and background removing. Fig. 18. (a) Thyroid gland DICOM image and (b) Gaussian filter and background removing
are applied on the same image Fig. 18. 6. Conclusion Image processing and analysis applied to nuclear medicine images for diagnosis, improve
the acquired image qualitatively as well as offer quantitative information data useful in
patient’s therapy and care. Advanced techniques of image processing and analysis find
widespread use in nuclear medicine. MatLab and Image Processing Toolbox enable both
quantitative analysis and visualization of Nuclear Medicine images acquired as planar or
angle projected images to reconstruct tomographic (SPECT, PET) slices and 3D volume
surface rendering images. imshow(I,'DisplayRange',[]); (a) Thyroid gland DICOM image and (b) Gaussian filter and background removing
are applied on the same image The dicomwrite function is very useful too, in the case that we have to partition a volume
into slices and to storage each slice as a simple DICOM image for further processing and
analysis. Bankman, I. (2000). Handbook of Medical Imaging, Academic Press, ISSN 0-12-077790-8, United
States of America Wilson, H.B.; Turcotte, L.H. & Halpern, D. (2003). Advanced Mathematics and Mechanics
Applications Using MATLAB (third edition), Chapman & Hall/CRC, ISBN 1-58488-
262-X, United States of America Wernick, M. & Aarsvold, J. (2004). Emission Tomography: The Fundamentals of PET and SPECT,
Elsevier Academic Press, ISBN 0-12-744482-3, China Zitova, B. & Flusser J. (2003). Image Registration methods: a survey. Image and Vision
Computing. Vol 21, (June 2003), pp. (977-1000) MATLAB – A Ubiquitous Tool for the Practical Engineer Wernick, M. & Aarsvold, J. (2004). Emission Tomography: The Fundamentals of PET and SPECT,
Elsevier Academic Press, ISBN 0-12-744482-3, China
Wilson, H.B.; Turcotte, L.H. & Halpern, D. (2003). Advanced Mathematics and Mechanics
Applications Using MATLAB (third edition), Chapman & Hall/CRC, ISBN 1-58488-
262-X, United States of America 8. References MATLAB as a Tool in Nuclear Medicine Image Processing 499 Bidgood, D. & Horii, S. (1992). Introduction to the ACR-NEMA DICOM standard. RadioGraphics, Vol. 12, (May 1992), pp. (345-355) Delbeke, D.; Coleman, R.E.; Guiberteau M.J.; Brown, M.L.; Royal, H.D.; Siegel, B.A.;
Townsend, D.W.; Berland, L.L.; Parker, J.A.; Zubal, G. & Cronin, V. (2006). Procedure Guideline for SPECT/CT Imaging 1.0. The Journal of Nuclear Medicine,
Vol. 47, No. 7, (July 2006), pp. (1227-1234). Gonzalez, R.; Woods, R., & Eddins, S. (2009) Digital Image Processing using MATLAB,
(second edition), Gatesmark Publishing, ISBN 9780982085400, United States of
America Lehmann, T.M.; Gönner, C. & Spitzer, K. (1999). Survey: Interpolation Methods in Medical
Image Processing. IEEE Transactions on Medical Imaging, Vol.18, No.11, (November
1999), pp. (1049-1075), ISSN S0278-0062(99)10280-5 Lyra, M.; Sotiropoulos, M.; Lagopati, N. & Gavrilleli, M. (2010a). Quantification
of Myocardial Perfusion in 3D SPECT images – Stress/Rest volume
differences, Imaging Systems and Techniques (IST), 2010 IEEE International
Conference
on
1-2
July
2010,
pp
31
–
35,
Thessaloniki,
DOI:
10.1109/IST.2010.5548486 Lyra, M.; Striligas, J.; Gavrilleli, M. & Lagopati, N. (2010b). Volume Quantification of I-123
DaTSCAN Imaging by MatLab for the Differentiation and Grading of Parkinsonism
and Essential Tremor, International Conference on Science and Social Research, Kuala
Lumpur, Malaysia, December 5-7, 2010. http://edas.info/p8295 Li, G. & Miller, R.W. (2010). Volumetric Image Registration of Multi-modality Images of CT,
MRI and PET, Biomedical Imaging, Youxin Mao (Ed.), ISBN: 978-953-307-071-1,
InTech, Available from:
http://www.intechopen.com/articles/show/title/volumetric-image-registration-
of-multi-modality-images-of-ct-mri-and-pet O’ Gorman, L.; Sammon, M. & Seul M. (2008). Practicals Algorithms for image analysis,
(second edition), Cambridge University Press, 978-0-521-88411-2, United States
of America Nailon,
W.H. (2010). Texture
Analysis
Methods
for
Medical
Image
Characterisation, Biomedical Imaging, Youxin Mao (Ed.), ISBN: 978-953-307-
071-1, InTech, Available from:
http://www.intechopen.com/articles/show/title/texture-analysis-methods-
for-medical-image-characterisation g
MathWorks Inc. (2009) MATLAB User’s Guide. The MathWorks Inc., United States of
America Perutka K. (2010). Tips and Tricks for Programming in Matlab, Matlab - Modelling,
Programming and Simulations, Emilson Pereira Leite (Ed.), ISBN: 978-953-307-125-
1, InTech, Available from: http://www.intechopen.com/articles/show/title/tips-
and-tricks-for-programming-in-matlab Toprak, A. & Guler, I. (2006). Suppression of Impulse Noise in Medical Images with the Use
of Fuzzy Adaptive Median Filter. Journal of Medical Systems, Vol. 30, (November
2006), pp. (465-471) MATLAB – A Ubiquitous Tool for the Practical Engineer 500 Wernick, M. & Aarsvold, J. (2004). Emission Tomography: The Fundamentals of PET and SPECT,
Elsevier Academic Press, ISBN 0-12-744482-3, China Wilson, H.B.; Turcotte, L.H. & Halpern, D. (2003). Selected Methods of Image Analysis in
Optical Coherence Tomography Selected Methods of Image Analysis in
Optical Coherence Tomography
Robert Koprowski and Zygmunt Wróbel
University of Silesia, Faculty of Computer Science and Materials Science
Institute of Computer Science, Department of Biomedical Computer Systems
Poland Robert Koprowski and Zygmunt Wróbel
University of Silesia, Faculty of Computer Science and Materials Science
Institute of Computer Science, Department of Biomedical Computer Systems
Poland 8. References Advanced Mathematics and Mechanics
Applications Using MATLAB (third edition), Chapman & Hall/CRC, ISBN 1-58488-
262-X, United States of America Zitova, B. & Flusser J. (2003). Image Registration methods: a survey. Image and Vision
Computing. Vol 21, (June 2003), pp. (977-1000) 24 1. Introduction OCT is a new technique of picturing that uses uninvasional and contactless optical method
based on interferometry of partially compact light for receiving sections images of human
eyes in vivo. It allows picturing structural changes caused by eyes diseases, mapping
thickness of retina and analyses shield of optical nerve and coats of nerve fibers. OCT has
been developed since 1995 when it was initiated by measurement of intraocular distance by
A.F. Frechera (Fercher el at., 1995) in years 2002-2004 the quick growth of quality and speed
of eye picturing acquisition was observed but particularly in 2003 linear picturing and 2004
fast picturing with high resolution –Fig. 1. (Leitgeb el at., 2004; Ozcan el at., 2007; Bauma B. E. & Tearney, 2002). 50 images
m. n
k
Fig. 1. The comparison of normal optic nerve head images with differential optical
coherence tomography (OCT) technologies M×N×K=740×800×50 50 images
m Fig. 1. The comparison of normal optic nerve head images with differential optical
coherence tomography (OCT) technologies M×N×K=740×800×50 In work have been won input images LGRAY in number near 1000 from optical tomograph
SOCT Copernicus in the following parameters: wave length of light source: 840nm, width of
spectrum: 50nm, pivotal resolution width (longitudinal): 6μm, traverse resolution: 12-18 μm
of tomograph window: 2mm, speed of measurement: 25 000 scans in k pivot per second,
maximum width of scanning: 10mm, maximum number of punctual scans in k pivot falling
to n pivot: 10 500, become write down in gray levels about resolution M×N×K=740×800×50
where for each pixel falls to 8 bits. The next part of considerations will be concerned with methods of analysis and processing
of images automatically appointing layers borders visible on fig. 2 like: RPE – Retinal MATLAB – A Ubiquitous Tool for the Practical Engineer 502 Pigment Epithelium, OPL – Outer plexiform layer, IS/OS – Boundary between the inner and
outer segments of the photoreceptors. Pigment Epithelium, OPL – Outer plexiform layer, IS/OS – Boundary between the in
outer segments of the photoreceptors. 0.3mm
NFL - Nerve Fiber Layer
IPL - Inner Plexiform Layer
OPL - Outer Pelxiform Layer
RPE - Retinal Pigment Epithelium
GCL - Ganglion Cell Layer
INL - Inner Nuclear Layer
IS/OS - boundary between
the Inner and Outer Segments
of photoreceptors
ELM - External Limiting Membrane
OPL - Outer Plexiform Layer
Fig. 2. 1. Introduction Section scheme of individual layers along with marked characteristic gauged areas –
image taken from SOCT Copernicus. Fig. 2. Section scheme of individual layers along with marked characteristic gauged areas –
image taken from SOCT Copernicus. These considerations will be concerned with analysis of images sequences that have been
already archived. Therefore, the possibilities of interference with the OCT device’s
apparatus will not be considered for increasing range of brightness level. Data from images
sequence will not be taken into account, either - each image is analyzed independently. The
source of acquiring given images assigned for analyses described by algorithms is free, i.e. any OCT device which allows to receive 2D image about minimum resolution 300×400
pixels. p
The need of thickness analysis of individual layers RPE, IS/OS, NFL or OPL results from
necessity of quantitative assessment but not qualitative, e.g. disease progression or
efficiency of therapy, e.g. diabetes or Birdshot Chorioretinopathy. y
py
g
p
y
methods of individual visible layers analyses will be discussed on Fig. 2 namely: Four methods of individual visible layers analyses will be discussed on Fig. 2 nam •
Method of modified active contour – ACM. This method is based on basic information
acquired from image like for example: the lightest RPE layer which will be identified in
first period and on its base the remaining layers analysis will be carried out as OPL or
IS/OS method of modified active contour for implemented line. •
The
wandering
small
part
method
in
discovering
Canny
edge
-
CCA. This method relies on preliminary edge detection using Canny detector and next
continuity of lines correction on ends and conducting their connection with remaining
ones (Canny, 1986; Koprowski & Wróbel, 2008). •
Random method of contour analysis – RAC. Points that start marking the edges are
chosen at random during the preliminary image period, next the correction of their
numbers is carried out in order for the remaining numbers, that come up to certain
expectations, to become the first points of the lines appointed with the wandering small
part method (Koprowski & Wróbel, 2009). p
(
p
)
•
Method based on hierarchic approach - HAC . There is preliminary identification of
main layers like OPL or RPE on the smallest resolution and then the remaining layers
are identified like IS/OS and the layers reconnaissance accuracy is gradually improved
OPL and RPE (Koprowski & Wróbel, 2009). 1. Introduction p
(
p
)
•
Method based on hierarchic approach - HAC . There is preliminary identification of
main layers like OPL or RPE on the smallest resolution and then the remaining layers
are identified like IS/OS and the layers reconnaissance accuracy is gradually improved
OPL and RPE (Koprowski & Wróbel, 2009). 2.1 Results acquired for algorithms processed by authors not bringing desired results
for OCT images g
Among these results there have been methods which have not given satisfactory resu 1. Method using Hough transform (Gonzalez & Woods, 1992). This method in this case
did not give satisfactory results because the wanted layers on OCT image can change
thickness and in general case can not be continuous. Additionally, the radius of
curvature describing border of layers can be changed in wide ranges (Koprowski &
Wróbel, 2009). It happens for example in shield of optical nerve (Costa el at., 2006)
where individual OPL layers , RPE or IS/OS they are much worse visible (Klinder el at.,
2009). Certain improvement of this method would be area analysis in which individual
areas (with given width) would be brought closer by the lines. However, in this case
emerges their mutual connections problem and problem of computational complexity. 1. Method using Hough transform (Gonzalez & Woods, 1992). This method in this case
did not give satisfactory results because the wanted layers on OCT image can change
thickness and in general case can not be continuous. Additionally, the radius of
curvature describing border of layers can be changed in wide ranges (Koprowski &
Wróbel, 2009). It happens for example in shield of optical nerve (Costa el at., 2006)
where individual OPL layers , RPE or IS/OS they are much worse visible (Klinder el at.,
2009). Certain improvement of this method would be area analysis in which individual
areas (with given width) would be brought closer by the lines. However, in this case
emerges their mutual connections problem and problem of computational complexity. g
p
p
p
p
y
2. Method of active contour in its typical version also does not produce desired results
(Liang el at., 2006). At automatic selection of starting points using for example, method
of Canny contour discovering or Gabor’s filters (Gonzalez & Woods, 1992) only borders
between the layers with the greatest contrast are discovered – RPE. In other cases, for
the others layers, the method does not produce the expected results unless it is applied
interactively with the user. Because the considerations in this work are applied only to
fully automatic methods, the above method cannot be taken into account because of the
mentioned interaction with the user. The method after the modifications introduced by
the authors will be presented later in the algorithm ACM and CCA. 3. Method of texture analysis. Selected Methods of Image Analysis in Optical Coherence Tomography Selected Methods of Image Analysis in Optical Coherence Tomography •
Acquired by other authors •
Acquired by authors of this work which have not brought satisfactory results in this
application. •
Acquired by authors of this work which have not brought satisfactory results in this
application. 2.1 Results acquired for algorithms processed by authors not bringing desired results
for OCT images In this case individual OPL layers, RPE or IS/OS are similar
in case of texture which almost by definition disqualifies the described method. Despite
this fact, the methods of texture analysis can be successfully used for emitting the
wanted object from background (vitreous body). For example, for other type of images
the methods have been successfully used in segmentation (Farsiu el at., 2008). 3. Method of texture analysis. In this case individual OPL layers, RPE or IS/OS are similar
in case of texture which almost by definition disqualifies the described method. Despite
this fact, the methods of texture analysis can be successfully used for emitting the
wanted object from background (vitreous body). For example, for other type of images
the methods have been successfully used in segmentation (Farsiu el at., 2008). 4. Also, methods of extended objects analyses (Koprowski el at., 2005) do not find
application here because of the possibility of great size change in both the very object
and its thickness and also the possibility of the object’s division into two or more parts. 4. Also, methods of extended objects analyses (Koprowski el at., 2005) do not find
application here because of the possibility of great size change in both the very object
and its thickness and also the possibility of the object’s division into two or more parts. y
Methods suggested below in the work and processed by the authors (Koprowski el at., 2005,
2008, 2009) are a modification of the already mentioned known methods of analyses and
processing of images and they are also new algorithms protected by copyright. 2. Present state of knowledge - results acquired with known algorithms Among results acquired with known algorithms there is in this chapter the description of
the results: 503 2.2 Results acquired by other authors According to the best of author’s knowledge there are no known algorithms analyses of eyes
retina taking into account discovering the mentioned borders OPL, RPE or IS/OS including
shield of optical nerve. Approaches suggested and introduced in (Chinn el at., 1997) or
(Drexler el at., 2003) work only for typical cases in which the degree of pathology is
insignificantly small. Applications used and enclosed for OCT device for example
Copernicus also do not work successfully. In case of greater pathology, layers identified
automatically are not continuous or they are not identified in a correct manner. The
erroneus action that occurs often is incorrect connection of the identified layers and 504 MATLAB – A Ubiquitous Tool for the Practical Engineer erroneous identifying of optical nerve shield. Additionally, the realized applications added
to such a device like Copernicus or Stratus they are protected by copyright and rigorous
form of algorithm is not rendered accessible outside. It results in the inability to estimate
quantitatively the results and their accuracy in comparison with the author approaches
suggested in this work. erroneous identifying of optical nerve shield. Additionally, the realized applications added
to such a device like Copernicus or Stratus they are protected by copyright and rigorous
form of algorithm is not rendered accessible outside. It results in the inability to estimate
quantitatively the results and their accuracy in comparison with the author approaches
suggested in this work. gg
Despite it, there is a whole big group of methods working correctly for simple cases where
in OCT images there are well identified (with sufficient contrast) individual layers. They are
the methods processed in LabVieW or in C++ (for example Bauma B. E. & Tearney, 2002) the
processed results were also published in user manual Copernicus (Optopol) or in one of the
chapters (Barry, 205). In this last position of literature (Farsiu el at., 2008) one of the few
applications that analize individually further discussed OPL or RPE layers completely
automatically is presented. It seems that OCT image analysis of eye is similar to the analysis
of skin, or even coat material of a tennis ball (Thrane, 2001) however, the specificity of
approach lies in variability in thickness of layers, individual variability of individual cases. In such cases of thickness changes of individual RPE, IS/OS, NFL or OPL layers, their
mutual positions can be so big that typical algorithms work incorrectly. 2.2 Results acquired by other authors Obviously, there is
coordinately a whole remaining group of methods interacting with user in which the user
indicates representative or marks of segmentation area, giving off of layer and the
implemented algorithm using, for example, the method of area expansion segmentates the
marked area (Klinder el at., 2009), or fractal analisys. Algorithms for which correct results
were acquired even for images of big radius of pathology distortion that work fully
automatically are presented in next chapters in the form of block schemes. Detailed
description of individual steps of discussed algorithms and their property like for example
sensitivity to parameters change is discussed in given publications (Koprowski el at., 2005,
2008, 2009). On this basis, taking into account also medical premises and taken attempts introduced
below, four algorithms of analyses and processing of images of eye retina layers OCT were
suggested. 3. The description of the suggested and compared algorithms The algorithms presented below are both, known from the literature and modified by the
authors and also new ones. Individual layers are marked in Cartesian coordinate match like
RPE-yRPE, IS/OS – yIS/OS layer. To avoid the conflict in designation, in chosen cases overhead
index indicating algorithm type (ACM, CCA, RAC or HAC) – for example yRPE (CCA) was
added. 3.1 Preliminary processing of image
l
f Preliminary processing of image is common for all discussed methods ACM (Koprowski &
Wróbel, 2009), CCA -(Koprowski & Wróbel, 2008), RAC (Koprowski el at., 2005) or HAC
(Koprowski & Wróbel, 2009). Preliminary algorithms of processing of images include
filtration with median filter of square mask sized about 21×21 for elimination of hum and
slight artefacts introduced by measuring match in the course of acquisition of image. Selection of size of mask has been carried arbitrarily on base of image resolution
M×N=740×800 and width of interests layers(OPL, RPE or IS/OS). Obviously, it must be
mentioned here that there are many others methods belonging to filtration in preliminary Selected Methods of Image Analysis in Optical Coherence Tomography 505 processing of image like for example adaptation filters, spatially adaptive wavelet filter
(Adler et al., 2004; Gnanadurai & Sadasivam, 2005) or fuzzy-based wavelet. processing of image like for example adaptation filters, spatially adaptive wavelet filter
(Adler et al., 2004; Gnanadurai & Sadasivam, 2005) or fuzzy-based wavelet. The second element of processing of preliminary image was normalization from minimum-
maximum partition of image pixels brightness for full partition from 0 for 1. This procedure
is aimed at the expansion of pixel brightness range for image on which the quality of visible
object is degraded for different reasons. j
g
So transformed images LMED (after filtration of median filter and normalization) were
subjected to analysis with available algorithms and algorithms suggested by authors (ACM,
CCA, RAC, HAC). 3.2 Description of ACM algorithm The ACM method - active modified contour, it is based on basic information acquired from
image like for example the plainest RPE layer which will be identified in the first period and
on its base the analysis of the remaining layers like OPL or IS/OS will be carried out (Akiba
et al., 2003; Choma el at., 2003). The picture 3 presents structure of unit algorithm (block
scheme) in which chosen blocks (layer analysis OPL, IS/OS, ELM ) can work independently. Area of analysis
Determination of layer RPE
Determination of layer OPL, IS/OS
Determination of layer ELM
Position correction of layers RPE, OPL, IS/OS,ELM
Preprocessing
sing Position correction of layers RPE, OPL, IS/OS,ELM Fig. 3. Block scheme of algorithm Fig. 3. Block scheme of algorithm The block scheme introduced in picture 3 divides the work of the whole ACM algorithm
into four phases:: The block scheme introduced in picture 3 divides the work of the whole ACM algorithm
into four phases:: The block scheme introduced in picture 3 divides the work of the whole ACM algorithm
into four phases:: •
Preliminary processing – filtration with median filter and normalization were described
in the former subchapter. •
Appointing of RPE layer site and next using modified active contour method assigning
remaining OPL or IS/OS layers. g
y
•
Appointment of external border of ELM retina site. •
Correction of the received layers in relation to the area of analysis - taking into account
quality of areas of introduced objects. After preliminary process of image processing (filtration and normalization receiving LMED)
LGRAY image analysis was started by analyzing the place of maximum for next columns of
images matrixes. If we mark lines and columns of the image matrixes by m and n new
LBIN(ACM) image includes value “1” in places where pixels are brighter in given column by 506 MATLAB – A Ubiquitous Tool for the Practical Engineer 90% for this column maximum taking a stand brightness. In the remaining places there is
value “0”. On this base calculating of the center sites of longest section for each image
column LBIN(ACM) receiving course yR was carried out (Fig. 2). Fig. 4. The sum of LBIN(ACM) image in 50% weight and 50% LMED and drawn yR course (yRS), Fig. 4. The sum of LBIN(ACM) image in 50% weight and 50% LMED and drawn yR course (yRS), Fig. 5. Functions of 3th row yRS (k1,k2) for any possible couples of concentrations
Course of yR function is further subjected to the operation of concentrations analyses by k-
means method acquiring yRS(k) for each k-concentration. Next the operation of
approxymation through polynomial of 3 row (yRS(k1,k2)) of each couple yRS(k1) and yRS(k2) for
k1≠k2 is performed. All polynomial functions yRS(k1,k2) received for all possible pairs of
concentration (k1, k2) are shown in Fig. 2-3. For each function yR a number of points is
appointed contained in partition ±15 pixels. Next the pair (k1,k2) is appointed for which
number of point contained in partition ±15 pixels is maximum at chosen yRS(k1*,k2*) in
simplification further called yRPE function. Result is shown in Fig. Fig. 3. Block scheme of algorithm 2-3 by white line (course
of yRPE(ACM)). ELM and IS/OS borders were appointed on the basis of course yRPE(ACM). Fi
5 F
ti
f 3th
(k k ) f
ibl
l
f Fig. 5. Functions of 3th row yRS (k1,k2) for any possible couples of concentrations Course of yR function is further subjected to the operation of concentrations analyses by k-
means method acquiring yRS(k) for each k-concentration. Next the operation of
approxymation through polynomial of 3 row (yRS(k1,k2)) of each couple yRS(k1) and yRS(k2) for
k1≠k2 is performed. All polynomial functions yRS(k1,k2) received for all possible pairs of
concentration (k1, k2) are shown in Fig. 2-3. For each function yR a number of points is
appointed contained in partition ±15 pixels. Next the pair (k1,k2) is appointed for which
number of point contained in partition ±15 pixels is maximum at chosen yRS(k1*,k2*) in
simplification further called yRPE function. Result is shown in Fig. 2-3 by white line (course
of yRPE(ACM)). ELM and IS/OS borders were appointed on the basis of course yRPE(ACM). 507 Selected Methods of Image Analysis in Optical Coherence Tomography Algorithms in both cases were very approximated for each other and they concerned in
biggest fragment method of modified active contour (exact differences between suggested
method and classic method of active contour is shown in Gonzalez & Woods 1992). According to the introduced visual scheme in Fig. 5 values of medians in areas over and
below of analysis pixel in blocks about sizes pyu×(pxl+pxp+1) for method of active contour
are appointed. Fig. 3. Block scheme of algorithm Next the value of their remainder is calculated and written down in matrix ΔS in following
form: ,4,1
,4,2
,4,3
,4,4
,3,1
,3,2
,3,3
,3,4
,2,1
,2,2
,2,3
,2,4
,1,1
,1,2
,1,3
,1,4
,0,1
,0,2
,0,3
,0,4
, 1,1
, 1,2
, 1,3
, 1,4
, 2,1
, 2,2
, 2,3
, 2,4
,
4
3
2
1
0
1
2
3
4
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
−
−
−
−
−
−
−
−
−
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
Δ
=
−
Δ
Δ
Δ
Δ
−
Δ
Δ
Δ
Δ
−
Δ
−
"
"
"
"
3,1
, 3,2
, 3,3
, 3,4
, 4,1
, 4,2
, 4,3
, 4,4
S
S
S
S
S
S
S
−
−
−
−
−
−
−
⎧
⎪
⎪
⎪
⎪
⎪
⎪
⎪⎪⎨
⎪
⎪
⎪
⎪
Δ
Δ
Δ
⎪
⎪Δ
Δ
Δ
Δ
⎪
⎪⎩
"
(1) (1) Where ΔS=med(Lu)-med(Ld) for Lu and Ld that are areas of the size properly
pyu×(pxl+pxp+1) and pyd×(pxl+pxp+1) and Where ΔS=med(Lu)-med(Ld) for Lu and Ld that are areas of the size properly
pyu×(pxl+pxp+1) and pyd×(pxl+pxp+1) and
pyu -
value of Lu line,
pyd -
value of Ld line,
pu -
partition of relocation pixel and areas Lu i Ld for top,
pd -
partition of relocation pixel and areas Lu i Ld to bottom,
pxl -
number of column on the left of the analyzed pixel,
pxp -
number of column on the right of the analyzed pixel,
ply -
distance in pivot oy respect yRPE(ACM)
pxud -
distance between neighbor pixels in pivot oy,
med –
medians. After creating ΔS matrix about size (pu+pd+1)×N sorting is performed for next columns
begining from biggest values of remainders between Lu and Ld areas. Next the analysis of
individual values for the following columns so that the pxud remainder does not surpass
the assumed level is performed. For 1000 pieces of test images this value was established at
the level of 2. The remaining parameters like pyu and pyd influence the sensitivity of the
method and pu and pd are the range of searching possible pixels sites. g
(
g
)
yIS/OS
yRPE
Fig. 7. Accommodation of function course yIS/OS(ACM) and yRPE(ACM).
3.3 Description of CCA algorithm
Method of small part wandering about in discovering Canny edge – CCA relies on
preliminary detection of edge using Canny detector and next corrections of lines continuity
on ends and performing the connection with the remaining ones– Fig. 8. g
(
g
)
yIS/OS
yRPE
Fig. 7. Accommodation of function course yIS/OS(ACM) and yRPE(ACM). 3.3 Description of CCA algorithm
Method of small part wandering about in discovering Canny edge – CCA relies on
preliminary detection of edge using Canny detector and next corrections of lines continuity
on ends and performing the connection with the remaining ones– Fig. 8. yIS/OS
yRPE
Fig. 7. Accommodation of function course yIS/OS(ACM) and yRPE(ACM). Fig. 7. Accommodation of function course yIS/OS(ACM) and yRPE(ACM). Fig. 3. Block scheme of algorithm By increasing pyu and
pyd values, time of calculations is increased. Searching for the new values of sites points of
yIS/OS(ACM) layer is started from course yRPE(ACM). Points of initial yIS/OS(ACM) layer emerge
from slip by pIy in attitude of yRPE(ACM) course. New sites are appointed in partition from yIS/OS(ACM)-pyu to yIS/OS(ACM)+pyd. The received yIS/OS(ACM), yRPE(ACM), yELM(ACM) course (layers) must additionally grant the
following conditions from premises subsequent of eye structure (these conditions will be
served in Cartesian coordinate match) (Hausler & Lindner, 1998): partition of relocation pixel and areas Lu i Ld to bottom, p
y
p
pxp -
number of column on the right of the analyzed pixel, p y
p
y
p
y
pxud -
distance between neighbor pixels in pivot oy, After creating ΔS matrix about size (pu+pd+1)×N sorting is performed for next columns
begining from biggest values of remainders between Lu and Ld areas. Next the analysis of
individual values for the following columns so that the pxud remainder does not surpass
the assumed level is performed. For 1000 pieces of test images this value was established at
the level of 2. The remaining parameters like pyu and pyd influence the sensitivity of the
method and pu and pd are the range of searching possible pixels sites. By increasing pyu and
pyd values, time of calculations is increased. Searching for the new values of sites points of
yIS/OS(ACM) layer is started from course yRPE(ACM). Points of initial yIS/OS(ACM) layer emerge
from slip by pIy in attitude of yRPE(ACM) course. p
y p y
y
New sites are appointed in partition from yIS/OS(ACM)-pyu to yIS/OS(ACM)+pyd. Fig. 3. Block scheme of algorithm The received yIS/OS(ACM), yRPE(ACM), yELM(ACM) course (layers) must additionally grant the
following conditions from premises subsequent of eye structure (these conditions will be
served in Cartesian coordinate match) (Hausler & Lindner, 1998): The received yIS/OS(ACM), yRPE(ACM), yELM(ACM) course (layers) must additionally grant the
following conditions from premises subsequent of eye structure (these conditions will be
served in Cartesian coordinate match) (Hausler & Lindner, 1998): MATLAB – A Ubiquitous Tool for the Practical Engineer 508 •
yRPE(ACM)<yIS/OS(ACM)<yELM(ACM) for each x, •
yRPE(ACM)<yIS/OS(ACM)<yELM(ACM) for each x, •
yRPE(ACM)<yIS/OS(ACM)<yELM(ACM) for each x, •
yELM(ACM) – yRPE(ACM)≈0.1 mm –being the initial value starting work of active contour
method (Ko el at., 2005), •
yELM(ACM) – yRPE(ACM)≈0.1 mm –being the initial value starting work of active contour
method (Ko el at., 2005),
(ACM)
(ACM)
d 0 d 1
f
diff
t
(Y
l t 2004) (
)
yELM(ACM) – yIS/OS(ACM) ≈ od 0 do 1 mm for different x (Yun el at., 2004). Lu
Ld
pu
pd
pxl
pyu
pyd
y
pIy
xi
pxp
9
pxud
yRPE
yRPE
(ACM)
(ACM)
(ACM)
Fig. 6. Scheme of visual values scaling difference of brightness method
Appling this restriction, correct results for automatic achieved RPE, IS/OS or ELM layer
finding has been achieved (Fig. 7). Fig. 6. Scheme of visual values scaling difference of brightness method Appling this restriction, correct results for automatic achieved RPE, IS/OS or ELM layer
finding has been achieved (Fig. 7). Appling this restriction, correct results for automatic achieved RPE, IS/OS or ELM layer
finding has been achieved (Fig. 7). Appling this restriction, correct results for automatic achieved RPE, IS/OS or ELM layer
finding has been achieved (Fig. 7). 3.3 Description of CCA algorithm p
g
Method of small part wandering about in discovering Canny edge – CCA relies on
preliminary detection of edge using Canny detector and next corrections of lines continuity
on ends and performing the connection with the remaining ones– Fig. 8. p
g
Method of small part wandering about in discovering Canny edge – CCA relies on
preliminary detection of edge using Canny detector and next corrections of lines continuity
on ends and performing the connection with the remaining ones– Fig. 8. 509 Selected Methods of Image Analysis in Optical Coherence Tomography Preprocessing
sing
Canny dge
e
detection
sing
Labeling lines
sing
Modified active contour
sing
Connecting line to detect layers
Fig. 8. Block scheme of CCA algorithm
The first period of the used CCA method is discovering edge with assistance of Canny
method (Canny, 1986) on LMED image. For so emerged binary LBIN(CCA) the operation of
labeling was conducted where each concentration (about value “1”) owns label et=1,2,...,Et-
1,Et. Next, for each label et labeling is conducted giving each concentration (line) label. Received image LIND(CCA) is shown in pseudocolors on Fig. 7. Fig. 8. Block scheme of CCA algorithm The first period of the used CCA method is discovering edge with assistance of Canny
method (Canny, 1986) on LMED image. For so emerged binary LBIN(CCA) the operation of
labeling was conducted where each concentration (about value “1”) owns label et=1,2,...,Et-
1,Et. Next, for each label et labeling is conducted giving each concentration (line) label. Received image LIND(CCA) is shown in pseudocolors on Fig. 7. The first period of the used CCA method is discovering edge with assistance of Canny
method (Canny, 1986) on LMED image. For so emerged binary LBIN(CCA) the operation of
labeling was conducted where each concentration (about value “1”) owns label et=1,2,...,Et-
1,Et. Next, for each label et labeling is conducted giving each concentration (line) label. Received image LIND(CCA) is shown in pseudocolors on Fig. 7. Fig. 9. LIND(CCA) Image in pseudocolors (label Et=131) Fig. 9. LIND(CCA) Image in pseudocolors (label Et=131) 510 MATLAB – A Ubiquitous Tool for the Practical Engineer Fig. 9 shows values of labels for the next line of LIND(CCA) image. Each continuous line of
edge visible on LIND(CCA) image (Fig. 9) for labels et=1,2,...,Et-1,Et has been transformed for
form k=1,2,3,…,K-1,K points (xet,k yet,k) in Cartesian match of coordinates. 3.3 Description of CCA algorithm The parameters of this algorithm are as follows: α -
Angle in which range the best adjusting for the given criterion is searched, Δα -
Accuracy with which we search for the best adjusting, the distance between the present and the next searched point of active contour
(
) (
)
d Δxy -
the distance between the present and the next searched point of active contour
(x1,K+1,y1,K+1), (x1,K+2,y1,K+2) and so on, Me -
Height of analyzed Lu and Ld area Ne -
Width of analyzed Lu and Ld area On the base of the above-mentioned findings and realized measurements (Koprowski &
Wróbel, 2009) values of parameters of active contour on α=45, Δα=1, Δxy=1, Me=11, Ne=11
were established. Iterations for individual et edges of active contour method have been
interrupted, then if one of the following situations happened: On the base of the above-mentioned findings and realized measurements (Koprowski &
Wróbel, 2009) values of parameters of active contour on α=45, Δα=1, Δxy=1, Me=11, Ne=11
were established. Iterations for individual et edges of active contour method have been
interrupted, then if one of the following situations happened: The possible number of iterations has been surpassed - established arbitrary for 1000,
For this point the condition of remainder in average values between areas Lu and Ld has n
been granted The possible number of iterations has been surpassed - established arbitrary for 1000,
For this point the condition of remainder in average values between areas Lu and Ld has not
been granted g
ast two points own the same coordinates - it precludes to looping of algorithm. g
At least two points own the same coordinates - it precludes to looping of algorithm. At least two points own the same coordinates - it precludes to looping of algorithm. For parameters established this way, the results have been acquired that are presented
below Fig. 10, Fig. 11). p
p
p
g
g
For parameters established this way, the results have been acquired that are presented
below Fig. 10, Fig. 11). Fig. 12. Operation of modified active contour on real image for α=40, Δα=1, Δxy=Ne=11,
Me =10. The green line marks the contour acquired with Canny method, the red line marks
next points of active contour method. Fig. 12. Operation of modified active contour on real image for α=40, Δα=1, Δxy=Ne=11,
Me =10. 3.3 Description of CCA algorithm Method of
modified active contour has been employed for each “stretch” of edge in both directions. For
this purpose for two first pairs of coordinates of first edge (x1,1,y1,1) and (x1,2,y1,2) and two
last ones (x1,K-1,y1,K-1) and (x1,K,y1,K) a straight line has been appointed going through these
points, that is according to visual drawing below (Fig. 10): Fig. 10. Graphic interpretation of modified active contour method for appointment of next
point beginning from points positions (x1,K-1,y1,K-1) and (x1,K,y1,K) for establishing new point
(pixel) (x1,K+1,y1,K+1). For simplification angle of depression of final points of edges was
established at β=0o. Fig. 10. Graphic interpretation of modified active contour method for appointment of next
point beginning from points positions (x1,K-1,y1,K-1) and (x1,K,y1,K) for establishing new point
(pixel) (x1,K+1,y1,K+1). For simplification angle of depression of final points of edges was
established at β=0o. M =1
e
M =19
e
M =20
e
Fig. 11. Artificial image and fragment of modified active contour operation for α=40, Δα=1,
Δxy=Ne=4, Me changed in range (1,20) Fig. 11. Artificial image and fragment of modified active contour operation for α=40, Δα=1,
Δxy=Ne=4, Me changed in range (1,20) 511 Selected Methods of Image Analysis in Optical Coherence Tomography Fig. 11 presents the ideas of method of active contour where beginning from points
position (x1,K-1,y1,K-1) and (x1,K,y1,K) straight line going through them is established with an
angle of depression β1 and in distance Δxy appointing of the position of new point
(x1,K+1,y1,K+1) for different potential positions (in angle partition β1(1)±α through Δα). The
choice of proper position of contour point acquired through adding next points for
existing edge is acquired on base of analyses of average values from areas Lu and Ld
about size Me×Ne (Fig. 3-8). α angle for which the best adjustment for the analyzed point
(x1,K+1,y1,K+1) exists is the one for which the remainder in average values between areas Lu
and Ld is the biggest. gg
As it happens, the suggested method of modified active contour has very curious properties. 3.4 Random method of contour analysis – RAC Points starting the operation of the algorithm – RAC are chosen at random in the
preliminary period (Koprowski & Wróbel, 2009). Next, the correction of their number is
performed, so that the remaining ones, granting proper conditions become the first points
for the appointed RPE, IS/OS, NFL or OPL layers. This line become stretched further by
method of modified active contour introduced in description of CCA algorithm (Fig. 14). Preprocessing
sing
Random points
sing
Adjustment of the number of points
Modified active contour
sing
Fig. 14. Block scheme of RAC algorithm
It has already been mentioned that preliminary position of starting points was chosen at
random. random values from monotonous partition were acquired (0,1) for each of new
points of image matrixes - Lo (about resolution of LMED image there is.: M×N). For Lo image
pixels created this way (random) binarization with threshold pr is carried out . Each new
pixel with value “1” will be further starting point o*i,j (where index “i” means next starting
point however, “j” means next points created on its base). This way, by selecting value of
threshold pr in range (0.1) we influence the number of starting points. In the next period, the
position of starting points is modified in the assigned H area of the sizes MH×NH. The Preprocessing
sing
Random points
sing
Adjustment of the number of points
Modified active contour
sing
Fig. 14. Block scheme of RAC algorithm Fig. 14. Block scheme of RAC algorithm It has already been mentioned that preliminary position of starting points was chosen at
random. random values from monotonous partition were acquired (0,1) for each of new
points of image matrixes - Lo (about resolution of LMED image there is.: M×N). For Lo image
pixels created this way (random) binarization with threshold pr is carried out . Each new
pixel with value “1” will be further starting point o*i,j (where index “i” means next starting
point however, “j” means next points created on its base). This way, by selecting value of
threshold pr in range (0.1) we influence the number of starting points. In the next period, the
position of starting points is modified in the assigned H area of the sizes MH×NH. The It has already been mentioned that preliminary position of starting points was chosen at
random. 3.3 Description of CCA algorithm The green line marks the contour acquired with Canny method, the red line marks
next points of active contour method. 512 MATLAB – A Ubiquitous Tool for the Practical Engineer Fig. 13. Operation of modified active contour after the described correction on real image for
α=40, Δα=1, Δxy=Ne=11, Me =11 Fig. 13. Operation of modified active contour after the described correction on real image for
α=40, Δα=1, Δxy=Ne=11, Me =11 As shown on drawings above (Fig. 10, Fig. 11) the suggested method discovers correctly
individual layers on OCT image of an eye. 3.4 Random method of contour analysis – RAC random values from monotonous partition were acquired (0,1) for each of new
points of image matrixes - Lo (about resolution of LMED image there is.: M×N). For Lo image
pixels created this way (random) binarization with threshold pr is carried out . Each new
pixel with value “1” will be further starting point o*i,j (where index “i” means next starting
point however, “j” means next points created on its base). This way, by selecting value of
threshold pr in range (0.1) we influence the number of starting points. In the next period, the
position of starting points is modified in the assigned H area of the sizes MH×NH. The 513 Selected Methods of Image Analysis in Optical Coherence Tomography modification relies on correction of point position o*i,1 with coordinates (x*i,1, y*i,1) to new
coordinates (xi,1, yi,1) where possibly relocation is in range xi,1= x*i,1±(NH)/2 and yi,1=
y*i,1±(MH)/2. Change of coordinates follows in area ±(MH)/2 and ±(NH)/2 in which the
biggest value is achieved in remainder between pixels in eight- neighbor match. Next the
correction of repeating points is performed- this which have the same coordinates are
deleted. For assigning layers on OCT image the component of contour were later indicated in
meaning of his fragments subjected later to modification and processing in the following
manner. For each o*i,1 point chosen at random with coordinates (x*i,1, y*i,1) iteration process
is performed relying on searching of next oi,2, oi,3, oi,4, oi,5 points and so on, according to
dependence described in CCA algorithm (Fig. 8). In the described case of iteration appointment contour component becomes essential
introduction of limitation range (next parameters) which includes: •
jMAX - maximum number of iterations - limitation whose purpose is to eliminate
algorithm looping if every time, points oi,j will be appointed with different locations
and contour will have for example spiral form. •
jMAX - maximum number of iterations - limitation whose purpose is to eliminate
algorithm looping if every time, points oi,j will be appointed with different locations
and contour will have for example spiral form. •
Stopping the iteration process if it will be discovered that xi,j=xi,j+1 and yi,j=yi,j+1. This
situation happens most often if Lu and Ld areas are of a similar size as area H or are
bigger (about sizes MH×NH). 3.4 Random method of contour analysis – RAC 514 MATLAB – A Ubiquitous Tool for the Practical Engineer In a general case, it can happen that despite relatively small values of the accepted pr
threshold, the randomly chosen oi,1 starting point is placed beyond the edge of object. Then,
the next iterations can join it with the remaining part. In such a case the deletion process of
outstanding branch is performed – alike for lopping off of branch in frameworking
(Gonzalez & Woods, 1992). In a general case, it can happen that despite relatively small values of the accepted pr
threshold, the randomly chosen oi,1 starting point is placed beyond the edge of object. Then,
the next iterations can join it with the remaining part. In such a case the deletion process of
outstanding branch is performed – alike for lopping off of branch in frameworking
(Gonzalez & Woods, 1992). (
)
Exemplary results showed on Fig. 15 are acquired for real OCT image for pr=0.02, Δα=80o,
MH×NH=35×35. Fig. 15. Exemplary results acquired for real image OCT for pr=0.02, Δα=80o, MH×NH=35×35. Fig. 15. Exemplary results acquired for real image OCT for pr=0.02, Δα=80o, MH×NH=35×35. Fig. 15. Exemplary results acquired for real image OCT for pr=0.02, Δα=80o, MH×NH=35×35. Fig. 1 - correctly indicated contour components are visible and other fragments of contour
which from the point of view of limitation are not deleted. However, on the other hand
number of available parameters and its form allow enough liberty in their selection in order
to get desired results. In majority of cases, obtaining the intentional form of contour is
possible for one established MH×NH value. However, it can turn out that the use of
hierarchic approach is required for which MH×NH size will be decreased, thanks to which
greater accuracy of the suggested method will be acquired and it will introduce weight
(hierarchies) of importance of individual contours. 3.4 Random method of contour analysis – RAC As for the random choosing and correcting starting points,
here might also appear the situation that after the correction there will be xi,j=xi,j+1 and
yi,j=yi,j+1 y ,j y ,j
•
Stopping the iteration process if yi,j>MM or xi,j>NM or in cases where the indicated oi,j
point will be outside the picture. •
Stopping the iteration process if yi,j>MM or xi,j>NM or in cases where the indicated oi,j
point will be outside the picture. •
Stopping the iteration process if still better matching point in respect does not grant
condition admissible Δα (allowable curvature contour). At this stage, components of the outline for the given parameters are obtained. These
parameters include: hx and hy mask is strictly related to resolution of image and size of identified area
d for MM×NM = 864×1024 on MH×NH=23×23 Size of hx and hy mask is strictly related to resolution of image and size of identified area
accepted for MM×NM = 864×1024 on MH×NH=23×23
pr –
threshold responsible for the number of starting points - changed practically in pr –
threshold responsible for the number of starting points - changed practically in
range 0-0.1, g
jMAX -
maximum admissible number of iterations - established arbitrarily at 100, Δα -
partition of angle established in partition 10-70o, Δα -
partition of angle established in partition 10-70o, -size of correction area, square area, converted in range MH×NH=5×5 to
=25×25 admissible maximum change of angle between the folowing points of contour
hed in partition 10-70o. The analyzing the acquired values it must be noticed that stopping the iteration process
happens only when xi,j=xi,j+1 and yi,j=yi,j+1 (as it was said earlier). Or then only if points oi,j
and oi,j+1 have the same position. This condition does not concern oi,j points which have the
same coordinates but for different “i”, that is the ones that emerged in definite point of
iterations from different initial points. Easing of this condition leads to generation overlap
on the elements of contour which must be analyzed. As it has been presented above, the performed iteration process can cause overlapping of oi,j
points with the same coordinates (xi,j, yi,j) emerged from different initial oi,1points. This
property is used for ultimate appointment of contour layers on OCT image. 3.5 Method based on hierarchic approach – HAC
h
h d b
d
h
h
h The method based on hierarchic approach – HAC (Koprowski & Wróbel, 2009).The main
NFL or RPE layers are initially identified on image of the smallest resolutions and next
remaining layers are identified like for example IS/OS and accuracy reconnaissance of NFL
and RPE layers (Fig. 3-2) is gradually increased. From foundation, described algorithm should give satisfactory results mainly from part of
criterion operation speed. The described methods (algorithms) are characterized by big
accuracy of account, however, they are not sufficiently fast (it is hard to get analysis speed of
single 2D image in time not surpassing 10ms or 50 ms on processor PII 1.33 GHz). Thus,
decrease of LMED image resolution was suggested about near 50% for such value of pixels
number in rows and columns (with M×N=740×800) which is power of value “2” there is
M×N=256×512 (LMED2) applying further decomposition for LD16 image (where symbol “D” –
means decomposition and symbol “16” means block size for which it has been received). Any exit (output) image pixel after decomposition has value equal median from area (block)
of 16×16 size entrance (input) image according to Fig. 17. Selected Methods of Image Analysis in Optical Coherence Tomography
515
Preprocessing
sing
Downscaling
sing
Recognition layer RPE, NFL
sing
Increase the resolution
sing
P
RPE, NFL
osition correction
sing
Fig. 16. Block scheme of HAC algorithm
Fig. 17. Location of blocks na obrazie LMED2
Fig. 18. Image before and after decomposition – LMED2 i LD16
Exemplary LD16 result and input LMED2 image are shown on Fig. 18. LD16 Image will be
subjected to the operation of appointment of pixel positions with maximum value for each
column. Applying this thresholding method by maximum value in rows, in 99% of cases
only one maximum value in column is received. 515 Selected Methods of Image Analysis in Optical Coherence Tomography Preprocessing
sing
Downscaling
sing
Recognition layer RPE, NFL
sing
Increase the resolution
sing
P
RPE, NFL
osition correction
sing
Fig. 16. Block scheme of HAC algorithm Fig. 16. Block scheme of HAC algorithm Fig. 17. Location of blocks na obrazie LMED2 Fig. 17. Location of blocks na obrazie LMED2 Fig. 17. Location of blocks na obrazie LMED2 Fig. 18. Image before and after decomposition – LMED2 i LD16 Fig. 18. Image before and after decomposition – LMED2 i LD16
Exemplary LD16 result and input LMED2 image are shown on Fig. 18. Fig. 19. Exemplary LDB16 image In order to appoint position of NFL and RPE borders precisely, the use one more LDB16
image was essential. This image is a binary image with white pixels placed in places for
which remainder between neighbor pixels in vertical tis greater than assigned pr threshold –
accepted in range (0, 0.2). In result, the cooridnates of points border locations yNFL(HAC) and
yRPE(HAC) are received as locations of values “1” in LDB16 image for which
yNFL(HAC)(x)≤yRPE(HAC)(x). This relative simple approach gives unbelieveably satisfactory
results. This method for selection of pr threshold on level 0.01 gives satisfactory results in
nearly 70% of images in not compound cases (that is, the ones which are not images with
visible pathology or shield of optical nerve). Unfortunately, for the remaining 30% of cases,
selection of pr threshold in accepted borders does not decrease the emerging errors (Fig. 19). The correction of erroneous reconnaissance of yNFL(HAC) and yRPE(HAC) layers is important
because for this approach these errors will be copied (In presented further hierarchic
approach) for next exact approximations. After correction taking into consideration number
of white pixels for individual LDM16 image columns, and mutual situating taking into
consideration NFL and RPE layers position, presented correction gives for above-mentioned
images class efficiency at the level of 99% of cases. Despite the accepted limitations, this
method brings erroneous results for initial columns of image (with hierarchic approach
definition) unfortunately, these errors are copied further. )
y
p
The cause of erroneous reconnaissance of layers locations is the difficulty in distinguishing
proper layers in case of discovering three “line”, three points in given column in which
position is changed in admissible range for individual x. 3.5 Method based on hierarchic approach – HAC
h
h d b
d
h
h
h LD16 Image will be
subjected to the operation of appointment of pixel positions with maximum value for each
column. Applying this thresholding method by maximum value in rows, in 99% of cases
only one maximum value in column is received. 516 MATLAB – A Ubiquitous Tool for the Practical Engineer 3.6 Decrease of decomposition area Relatively simple period of processing of tomographyc image with particular consideration
of speed of operation is escalation of accuracy and the same decrease of Am,n area’s size (Fig. 17) – block on LMED image. It was assumed that Am,n areas will be decreased in sequence to
1×1 size by a half in each iteration. Decrease of Am,n area is equivalent with next period
execution of NFL and RPE line position approximation. p
pp
Increase of accuracy (precision) position of NFL and RPE lines indicated in former iteration
is tied with two periods: •
Coordinate condensing (x,y) in meaning of indirect appointment (in center of point (x,y)
put exactly) using method of linear interpolation. •
Coordinate condensing (x,y) in meaning of indirect appointment (in center of point (x,y)
put exactly) using method of linear interpolation. •
Change of position of the condensed points so that they bring closer the wanted borders
in a better way. Selected Methods of Image Analysis in Optical Coherence Tomography 517 If first part is intuitive and it leads to resampling process, the second requires exact
explanations.The second period relies on adjusting individual point to wanted layer. Because in ox axis the image is from definition already decomposed and pixel brightness in
the analyzed image is similar to median value of the primary image, properly in window A
(Fig.17) modification of RPE and NFL point position follows in vertical axis only. Analysis
of individual RPE and NFL points is independent in meaning of addiction from the position
of point in line. Fig. 20. Results of the processes of adjusting for two iterations. White color marks input RPE
points and red and green color mark next approximations. Fig. 20. Results of the processes of adjusting for two iterations. White color marks input RPE
points and red and green color mark next approximations. Each RPE point remaining from the previous iteration and new arising from the interpolation,
are in various stages of the algorithm matched to RPE layer with ever greater precision. Change of the position of yRPE(HAC) point (x) is in the range ±pu where range of variation is not
dependent on the scale of considerations (size of A area) and follows closely the distance
between the NFL and RPE. For blocks A of size 16 × 16 to 1 × 1 pu is constant and is 2. 3.6 Decrease of decomposition area This
value was adopted on the basis of the typical average for examined hundreds of LGRAY images
the distance between the NFL and RPE of about 32 pixels which means that the decomposition
into A blocks of size 16×16 are two pixels so pu=2. In this regard, ± 2 is looking for maximum
LDM image and it adopts a new position of RPE NFL point. This way the process of RPE or
NFL is more similar to the actual conduct of the analyzed layer. Results obtained from the fit
shown in Fig. 3-6. The white color shows the input RPE values as input data for this stage of
the algorithm and the decomposition on A blocks of size 16 x 16 (LDM16 and LD16 images), red
matching results for A blocks of size 8 x 8 (LDM8 and LD8 images) and green match results for A
blocks of size 4 x 4 (LDM4 and LD4 images). As shown in Fig. 3-6 further decomposition and the
next smaller and smaller A areas and hence higher resolution, image is obtained with greater
accuracy at the expense of time (Indeed, increasing the number of analyzed yRPE(HAC)(x),
yNFL(HAC)(x) points and their neighborhoods ±pu). This method for A size 16 × 16 has large enough properties of the Global Approach to the
brightness of pixels that there is no need to introduce at this stage the additional treatment
to distinguish between closely spaced layers (that were not previously visible because of
image resolutions). By contrast, with the A areas of sizes 4 x 4 other layers are already 518 MATLAB – A Ubiquitous Tool for the Practical Engineer visible, which should be further analyzed correctly. Increasing accuracy makes IS/OS layer
visible which is located near the RPE layer (Fig. 20). Thus, in a circled area there is high
fluctuation of position in oy axis of RPE layer. Therefore, a next algorithm step was
developed taking into account the partition on RPE and IS/OS layers for appropriate high-
resolution. As shown in Fig. 21. presented method copes perfectly with detection of NFL,
RPE and IS/OS layers marked appropriately by colors red, blue and green. Fig. 21. Fragments of LMED images with drawn NFL course– red, RPE – blue and IS/OS –
green Fig. 21. Fragments of LMED images with drawn NFL course– red, RPE – blue and IS/OS –
green 4. Summary Presented methods ACM, CCA, RAC or HAC give correct results at detection (identifying)
RPE, IS/OS, NFL or OPL layers on tomographyc image of eye. Differences in suggested
methods are visible only at their comparison of efficiencie for analysis of some hundreds
mentioned tomographyc images. Comparing the mentioned methods we must bear in mind
accuracy of reconnaissance of layer, reactions of algorithms on pathologies, shields of optical
nerves and speed of operation in this case for computer (P4 CPU 3GHz, 2GB RAM). The following table Tab 1 shows composite comparison of the suggested algorithms and
Tab. 2. comparison of result acquired with assistance of the discussed algorithm taking into
consideration typical and critical fragments of operations of individual algorithms. Algorithm/Feature
ACM
CCA
RAC
HAC
Total error in the diagnosis of layers
5%
4%
7%
2%
The rate of detection layer RPE - MATLAB
15 s
5s
10s
1s
The rate of detection layer RPE - C++
0.85 s
0.27s
1.2s
50ms
Table 1. Composite comparison of the suggested algorithms Table 1. Composite comparison of the suggested algorithms Random. Described method gives correct results at appointment of contour (separation of
layers) equal on OCT images and for other images for which classic methods of
appointment of contour they not bring results or results do not supply continuous contour. Big influence of hum on the acquired results is one of the algorithm’s defects. It results from 519 Selected Methods of Image Analysis in Optical Coherence Tomography fact that number of pixels with big value that is the disturbance increases the possibility of
choosing at random the starting point in this place and in consequence element contour. Time of account is the second defect which is greater if the number of chosen points is
greater /or cause for which next oi,j+1 points search has been detained. Method A case of wrong diagnosis - due to the
nature of the method
Sample reconstruction of 3D NFL layers -
blue, RPE - red and IS / OS – green
ACM
CCA
RAC
Table 2. 4. Summary Comparison of the results obtained by the described algorithms Method A case of wrong diagnosis - due to the
nature of the method Sample reconstruction of 3D NFL layers -
blue, RPE - red and IS / OS – green Sample reconstruction of 3D NFL layers -
blue, RPE - red and IS / OS – green blue, RPE - red and IS / OS – green Table 2. Comparison of the results obtained by the described algorithms 520 MATLAB – A Ubiquitous Tool for the Practical Engineer Hierarhic. Presented algorithm discovers NFL, RPE and IS/OS layers in time for 50ms on
computer with processor 2.5GHz Intel Core 2 Quad. Performed measurement of time was
measured as value of average analysis 700 images dividing individual images on A blocks
(Fig. 3-3) about sizes 16×16, 8×8, 4×4, 2×2. It is possible to decrease this time by modifying
number of approximation blocks and simultaneously boosting identification error of
position of layer - results shown in a table below. Summary of the various stages of analysis time algorithm presented in the table above
clearly indicates that the first phase of the longest pre – stage processing image where the
dominant importance (in terms of execution time) has a filtration of median filter and the
final stage of determining the exact location of the RPE and IS/OS layers. The exact
breakdown of RPE and IS / OS, in fact involves an analysis of and the correction of the
position of credits primarily RPE and IS / OS in all columns for the most accurate image
zoom (due to the small distance between the RPE and IS / OS is not possible to carry out
this division in the previous approximations). The reduction in computation time can
therefore occur only by increasing the layer thickness of measurement error. And so, for
example, for analysis in the first approximation for a size 32 × 32 and then 16 × 16 thick
errors arising in the first stage and reproduced in subsequent. For the approximations for A
of size 16 × 16 and then 8×8, 4×4, 2×2 and 1×1 the highest accuracy is achieved but the
calculation time increases approximately twice. A key element that crowns the results obtained from the proposed algorithm is a 3D
reconstruction based on the sequence of LM(i) images. 4. Summary The sequence of images and more
precisely the location sequence of NFL(i)(n), RPE(i)(n) and IS/OS(i)(n) layers based 3D
reconstruction tompgraphyc image. For example a sequence of 50 images and the
resolution of one LM(i) image on level M×N=256×512 is obtained through the 3D image
composed of three layers of the NFL, RPE and IS/OS of size 50 × 512. The results shown
in (Koprowski & Wróbel, 2008),for example the reconstruction of the original image
(without the treatment described above) based on the pixel brightness - reconstruction
performed using the algorithm described above based on the NFL(i)(n), RPE(i)(n) and
IS/OS(i)(n) information. ,
Fig. 22. Spatial location layers RPE Fig. 22. Spatial location layers RPE Selected Methods of Image Analysis in Optical Coherence Tomography 521 Fig. 23. Layer thickness IS/OS-RPE
It is clearly apparent from the layers of the ability to automatically determine locations of
thickest positions or the thinnest between any points Fig. 23. Layer thickness IS/OS-RPE Fig. 23. Layer thickness IS/OS-RPE Fig. 23. Layer thickness IS/OS-RPE It is clearly apparent from the layers of the ability to automatically determine locations of
thickest positions or the thinnest between any points. It is clearly apparent from the layers of the ability to automatically determine loca
thickest positions or the thinnest between any points. It is clearly apparent from the layers of the ability to automatically determine locations of
thickest positions or the thinnest between any points. 5. References Adler D. C., Ko T. H., & Fujimoto J. G., “Speckle reduction in optical coherence tomography
images by use of a spatially adaptive wavelet filter,” Opt. Lett. 29, 2878–2880 (2004). Akiba, M., Chan, K. P. & Tanno, N., Full-field optical coherence tomography by
twodimensional heterodyne detection with a pair of CCD cameras. Optics Letters,
2003. 28(10): p. 816-18. Barry C.: Optical Ccoherence tomography for retinal imaging dissertation, De promotor:
Prof. Dr. T.G. van Leeuwen, De copromotor: Prof. Dr. J.F. de Boer 2005 Bauma B. E. & Tearney G. J.: Handbook of Opticall Coherence Thomography, MarcelDekker
2002 Canny J.: A Computational Approach to Edge Detection, IEEE Transactions on Pattern
Analysis and Machine Intelligence, Vol. 8, No. 6, Nov. 1986. Chinn, S. R. & Swanson, E. A. e Fujimoto, J. G., Optical coherence tomography using a
frequency-tunable optical source. Optics Letters, 1997. 22(5): p. 340-342. y
Choma MA, Sarunic MV, Yang C & Izatt JA. Sensitivity advantage of swept source and
Fourier domain optical coherence tomography. Opt Express 2003 11:2183–9. Costa, R. A., Skaf, M., et al., Retinal assessment using optical coherence tomography. Progress in Retinal and Eye Research, 2006. 25(3): p. 325-353. Drexler W, Sattmann H, Hermann B, et al. Enhanced visualization of macular pathology
with the use of ultrahigh-resolution optical coherence tomography. Arch
Ophthalmol 2003;121:695–706. [PubMed: 12742848] p
Farsiu S, Chiu SJ, Izatt JA. & Toth CA. Fast detection and segmentation of drusen in retinal
optical coherence tomography images. Proceedings of Photonics West, San Jose,
CA, February 2008; 68440D1-12 and Proc. SPIE, Vol. 6844, 68440D (2008); y
(
)
Fercher AF, Hitzenberger CK, Kamp G. & Elzaiat SY. Measurement of intraocular distances
by backscattering spectral interferometry. Opt Commun 1995;117:43–8. 522 MATLAB – A Ubiquitous Tool for the Practical Engineer Gnanadurai D. & Sadasivam V., “Undecimated wavelet based speckle reduction for SAR
images,” Pattern Recognition Letters, 26, 793-800 (2005). g
g
Gonzalez R. & Woods R.: Digital Image Processing, Addison-Wesley Publishing Company,
1992, Chap. 4. p
Hausler G. & Lindner MW. Coherence radar and spectral radar-new tools for
dermatological diagnosis. J Biomed Opt 1998;3:21–31. Klinder T., Ostermann J., Ehm M., Franz A., Kneser R. & Lorenz C., Automated model-
based vertebra detection, identification, and segmentation, Medical Image Analysis
13 (2009) 471–482 Ko, T. H., Fujimoto, J. G., et al., Comparison of ultrahigh- and standard-resolution optical
coherence tomography for imaging macular pathology. Ophthalmology, 2005. 112(11): p. 1922-1935. 1. Introduction Optical measurements offer the desirable characteristics of being noninvasive and
nondestructive techniques that are able to analyze in real time objects and phenomena in a
remote sense. Science areas that involve optical characterization include physics, biology,
chemistry and varied fields of engineering. The use of digital cameras to record objects or a
specific phenomenon permits the exploitation of the potential of that the associated images
can be processed to determine one or several parameter or characteristics of what is being
recorded. These images need to be processed and securely there will be a model associated
with the optical metrology that will provide an insight or a comprehensive understanding of
the image being analyzed. Matlab® is the suitable platform to implement image processing
algorithms due to its ability to perform the whole processing techniques and procedures to
analyze and image. At the same time it provides a flexible and a fast programming
language for user constructing algorithms. In the present chapter we provide some
fundamentals about image acquisition, filtering and processing, and some applications. Some applications are well-know techniques while others offer the state of the art in the
field under study. All authors agree that Matlab® is a powerful tool for image processing
and optical metrology. All algorithms and/or sentences used in this chapter are made in such manner so that they
work in the Matlab® R2007b platform or superior. Matlab® is a trade mark of Mathworks
Inc., from here on we will refer it as Matlab only. Also the Matlab functions and parameters
used along the chapter are typed in italics and in apostrophes, respectively. Algorithms in present chapter are presented in two formats depending on the algorithm
extension: 1) Image titles and/or figure captions for low algorithms extension; 2) Subsection
ends for larger algorithms. 2. Image processing and acquisition In the present section, image and processing acquisition principles in Matlab are established. 5. References (
) p
Koprowski R., Izdebska-Straszak G., Wróbel Z. & Adamek B. The cell structures
segmentation with using of decision trees. Pattern Recognition and Image Analysis,
Vol. 15, No. 3, 2005, Koprowski R. & Wróbel Z.: Hierarchic Approach in the Analysis of Tomographic Eye
ImageAdvances in Soft Computing, Springer Berlin / Heidelberg Volume 57, 2009,
p 463-470 Koprowski R. & Wróbel Z.: Identyfication of layers in a tomographic image of an eye based
on the Canny edge detection, Conference on Information Technologies in
Biomedicine, 2008 Koprowski R. & Wróbel Z.: Layers Recognition in Tomographic Eye Image Based on
Random Contour Analysis Advances in Soft Computing, Springer Berlin /
Heidelberg Volume 57, 2009, p 471-478 g
Koprowski R., Wróbel Z.: Determining correspondence in stereovision images of patients
with faulty posture Congress on Image and Signal Processing, 2008 Leitgeb, R. A., Drexler, W., et al., Ultrahigh resolution Fourier domain optical coherence
tomography. Optics Express, 2004. 12(10): p. 2156-2165. g
p y
p
p
(
) p
Liang J, McInerney T. & Terzopoulos D.:United Snakes, Medical Image Analysis, Volume 10,
Issue 2, April 2006, Pages 215-233 Ozcan A., Bilenca A., Desjardins A. E., B. E. Bouma B. E., & Tearney G. J., “Speckle reduction
in optical coherence tomography images using digital filtering,” J. Opt. Soc. Am. A. 24, 1901-1910 (2007). Thrane L.: Optical Coherence Tomography: Modeling and Applications, Risø National
Laboratory, Roskilde, Denmark, May 2001 25 2.1.2 Image discretization Image discretization is the process of converting an analogical image to a digital image; this
process depends on the sampling and quantization stages. Image discretization is the process of converting an analogical image to a digital image; this
process depends on the sampling and quantization stages. Correspondence between analogical and digital images is given by the number of pixels
used. If the number of pixels is enough to satisfy the Nyquist criteria (Oppenheim et al.,
1997), the acquired image is a satisfactory representation of the real object observed. Quantization is the process of assigning a color or gray discrete level to each sample. g
g
g
y
Therefore, image discretization quality depends on frequency sampling as in quantization
levels used. It must be noted that Matlab only reads digital images. Acquisition process can
be done with scanners, CCD cameras, etc. 2.1 Image acquisition g
q
Image acquisition is the initial stage in every vision system for human or artificial image
data interpretation. Image acquisition is the recording process of a real object, this implies 524 MATLAB – A Ubiquitous Tool for the Practical Engineer that the vision process totally depends on quality acquisition; this could be an analogical or
digital. The analogical acquisition process is a representation of the object with several
techniques like designing, painting, photography, and video. In a similar way, digital
imaging acquisition is able to represent a real object, however object properties are
presented in a discrete form. Every object characteristics are mapped from a real plane to a
digital plane where a group of discrete values (i.e 1, 2, 3, …,) represent position, form, color
and texture. 2.1.1 Acquisition and digital image representation Image acquisition process in Matlab can be done by the use of either imread or getsnapshot
functions for stored images or video, respectively. Each function stores the object
representation in a discrete lxmxn array, where l can be related to color data; m and n
indexes represent the image spatial coordinates. An example of a real image is shown in Figure 1a, and in Figure 1b, the representation in a
matrix array of the selected area from the image. Digital images are described as a bi-
dimensional f(x,y) function, where x and y represent the spatial coordinates. The f value at
the (x,y) position point is proportional to the intensity or gray scale of the image. In Matlab, a digital image satisfies following conditions: first, spatial and gray scale values ( y) p
p
p
p
y
g
y
g
In Matlab, a digital image satisfies following conditions: first, spatial and gray scale values
must be discrete; and second, intensities are sampling at 8 bits (255 values). Fig. 1. a) real color image, and b) matrix of the green color component of the selected area. Fig. 1. a) real color image, and b) matrix of the green color component of the selected area. 2.2.1 Histogram Histogram is the graphical representation of pixels gray values distribution. Images can be
classified according to its histogram as high, medium or low contrast images. A low contrast
image has a histogram with a low fraction of all possible gray values, around less than 40%
of the whole scale. A high contrast image has more than 90% of the gray values. Color images can also be classified in accordance with its histogram by considering human
ocular sensitivity to primary colors. This is given by the first component of the YIQ matrix: 0.299
0.587
0.114 ,
Y
R
G
B
=
+
+
(1) 0.299
0.587
0.114 ,
Y
R
G
B
=
+
+ (1) Where Y and RGB are the lumma components used in color television systems NTSC (that
represents a gray scale in the YIQ space) and the primary components, red, green and blue,
respectively. The histogram transformation for a color image is given by the following pixel
to pixel operation: (
)
,
gsl
k
k
T
r
s
=
(2) (2) where rk and sk are the original pixel intensities in color and gray scale levels (gsl)
respectively. In figure 2 is shown the image obtained by the use of equation (2) and its
corresponding histogram, these operations can be done by using the Matlab functions
rgb2gray and imhist. Fig. 2. a) gsl photography, b) histogram. 2.2.2 Histogram equalization
Histogram equalization is the transformation of the intensity values of an image that is
typically applied to enhance the contrast of the image. As an example, the contrast of the Fig. 2. a) gsl photography, b) histogram. Fig. 2. a) gsl photography, b) histogram. Fig. 2. a) gsl photography, b) histogram. 2.2 Thresholding and high contrast image Frequently, acquired images under real conditions present a background problem. When
relevant foreground elements are mixed with low interest background ones. Another Image Processing for Optical Metrology 525 problem that hides the desired information is a low contrast image. Therefore, the use of
algorithms that deals with can be implemented in order to enhance the images. Equalization, binarization and thresholding algorithm are alternatives that have proved to
be successful. problem that hides the desired information is a low contrast image. Therefore, the use of
algorithms that deals with can be implemented in order to enhance the images. Equalization, binarization and thresholding algorithm are alternatives that have proved to
be successful. In the following subsection, a method for the conversion of color images into gray levels is
presented. Next, by using histogram equalization, a high contrast image from the gray scale
levels is obtained. Finally, binarization process by establishing a thresholding is described in
order to get a two color image (black (0) and white (255)) from a gray level scale (Poon &
Banerjee, 2001). 2.2.3 Thresholding by histogram Thresholding is a non-linear operation for image segmentation that consists in the
conversion of a gsl image into a binary image according to a threshold value. This operation
is used to separate some regions of the foreground of an image from its background. Thresholding operation can be done by using the Matlab function graythresh. Binarization
may be considered as an especial case of thresholding as shown in figure 4. The Matlab
function that binaries an image is im2bw. Fig. 4. Image binarization by thresholding. Fig. 4. Image binarization by thresholding. Fig. 4. Image binarization by thresholding. 2.2.2 Histogram equalization 2.2.2 Histogram equalization
Histogram equalization is the transformation of the intensity values of an image that is
typically applied to enhance the contrast of the image. As an example, the contrast of the Histogram equalization is the transformation of the intensity values of an image that is
typically applied to enhance the contrast of the image. As an example, the contrast of the 526 MATLAB – A Ubiquitous Tool for the Practical Engineer image of the figure 2a, can be handled by applying histogram equalization and it is shown
in figure 3 with its respective histogram, this operation can be done by using the Matlab
function histeq. Fig. 3. a) Photography equalization, b) histogram. Fig. 3. a) Photography equalization, b) histogram. Fig. 3. a) Photography equalization, b) histogram. In order to get the discrete values in a gsl, the following equation is used 0
(
)
(
1),
k
j
eq
k
j
n
T
s
L
n
=
=
−
∑
(3) (3) where k = 0,1,2,…, (L-1), L represents the gray level numbers into an image (255 as an
example), nj is the frequency of appearance of an specific j-th gray level and n is the total
number of pixels of the image. where k = 0,1,2,…, (L-1), L represents the gray level numbers into an image (255 as an
example), nj is the frequency of appearance of an specific j-th gray level and n is the total
number of pixels of the image. 2.3 Spatial filtering In order to reduce noise or enhance some specific characteristics of an image some filters like
high-pass, low-pass, band-pass or band-stop are used. These filters can be applied in the 527 Image Processing for Optical Metrology frequency domain (section 2.4) or in the spatial domain. Spatial domain filtering is described
in this section. Filtering operations are directly applied to the image (pixel to pixel). The
mathematical functions applied in the spatial domain are well known as convolution, and
are described by (Mora-González et al., 2008) frequency domain (section 2.4) or in the spatial domain. Spatial domain filtering is described
in this section. Filtering operations are directly applied to the image (pixel to pixel). The
mathematical functions applied in the spatial domain are well known as convolution, and
are described by (Mora-González et al., 2008) 1
1
2
2
1
1
2
2
( , ) * ( , )
(
, ) (
,
),
M
N
M
N
m
n
f x y
g x y
f m n g x
m y
n
+
+
+
+
=−
=−
=
−
−
∑
∑
(4) (4) where f, g,(x,y), (m,n) and MxN are the original image, the convolution mask or matrix, the
original image coordinates, the coordinates where the convolution is performed, and the
size of convolution mask, respectively. Equation (4) is applied by doing a homogeneous
scanning with the convolution mask versus the whole image to be convolved. These filters
are also known as Finite Impulse Response (FIR) filters because they are applied to a finite
section of the spatial domain (In this case the finite section is the image). Equation (4) can be
implemented in Matlab by using nested for loops, also conv2, fspecial or imfilter functions can
be used too. These kinds of filters are dependent of the convolution mask form as is
explained in the following two subsections. 2.3.1 Low-pass filters p
Low-pass filters applied to images have the purpose of image smoothing, by blurring the
edges into the image and lowering the contrast. The main characteristic of a low-pass
convolution mask is that all of its elements have positive values. Some commonly used low-
pass filters are: averaging, gaussian, quadratic, triangular and trigonometric. These mask are
presented in a matrix form like 1,1
1,2
1,
2,1
2,2
2,
,
,1
,2
,
1
1
1
(
, )
,
N
N
M
N
m n
M
M
M N
m
n
w
w
w
w
w
w
g m n
w
w
w
w
=
=
⎡
⎤
⎢
⎥
⎢
⎥
=
⎢
⎥
⎢
⎥
⎢
⎥
⎣
⎦
∑∑
…
…
#
#
%
#
…
(5) (5) with with (
)
(
)
(
)
(
)
(
)
(
)
2
2
1
1
2
2
2
2
1
1
2
2
1
1
2
4
2
4
2
exp
,
1
,
,
cos
cos
,
,
M
N
M
N
M
N
A
A
A
A
B
m
n
gaussian
A
B m
B n
cuadratic
w
B m
B n
trigonometric
A
average
+
+
+
+
+
+
⎧
⎫
⎛
⎞
⎡
⎤
−
−
+
−
⎜
⎟
⎪
⎪
⎢
⎥
⎣
⎦
⎝
⎠
⎪
⎪
⎪
⎪
⎡
⎤
⎪
⎪
−
−
−
−
=
⎢
⎥
⎨
⎬
⎣
⎦
⎪
⎪
⎡
⎤
⎡
⎤
+
−
+
−
⎪
⎪
⎣
⎦
⎣
⎦
⎪
⎪
⎪
⎪
⎩
⎭
(6) (6) where A, B and w are the amplitude, the width function factor and the weight function of
the spatial filter, respectively. In order to determine the effectiveness of the masks of the
equations (5) and (6), Magnitude Spectra (MS) are obtained to analyze the low frequencies
allowed to pass by the filter and high frequencies attenuation. This is expressed as {
}
( )
20log
(
, ) ,
MS
g m n
ω =
ℑ
(7) {
}
( )
20log
(
, ) ,
MS
g m n
ω =
ℑ (7) (7) 528 MATLAB – A Ubiquitous Tool for the Practical Engineer where ω and ℑ are the MS frequency component and the Fourier transform operator,
respectively. 2.3.1 Low-pass filters In figure 5, the MS of the convolution mask from equations (5) and (6) are shown. Spatial
gaussian filter behavior is more stable because allows low frequencies to pass and also
attenuate middle and high frequencies faster than other filters, as can be observed. The mask
for nine elements is shown in table 1. It must be mentioned that the processing time slow
down conforming the convolution mask increases. Spatial filtering also has a problem in the
image edges, because they cannot be convolved and there are (M-1)/2 and (N-1)/2 lost
information elements in x and y axes, respectively. By using the fspecial function, low-pass
masks can be generated by applying the ‘gaussian’ or ‘average’ Matlab parameters. Another mask types designed for signal processing can be implemented on image
processing by a two dimensional extension. In figure 6 it is shown three different low-pass
filters applied in the test image. Fig. 5. MS of equations (5) and (6) masks, with A=1, B=1 and w=1. Matlab code
representation of equation (7) is: MS=20*log10(abs(fft(g))). Fig. 5. MS of equations (5) and (6) masks, with A=1, B=1 and w=1. Matlab code
representation of equation (7) is: MS=20*log10(abs(fft(g))). Gaussian
Quadratic
Trigonometric
Average
.0449
.1221
.0449
.1221
.3319
.1221
.0449
.1221
.0449
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
0
.1667
0
.1667
.3333
.1667
0
.1667
0
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
.1011
.1161
.1011
.1161
.1312
.1161
.1011
.1161
.1011
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
1
1
1
1 1
1
1
9 1
1
1
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
Table 1. 3x3 convolution masks g for low-pass filters of equations (5) and (6), with A=1, B=1
and w=1. Fig. 6. Low-pass 3x3 filters examples applied to figure 1a. Matlab parameters used: a)
average, b) gaussian and c) disk. Fig. 6. Low-pass 3x3 filters examples applied to figure 1a. Matlab parameters used: a)
average, b) gaussian and c) disk. Image Processing for Optical Metrology 529 2.3.2 High-pass filters 2
f
w
w
w
w
w
w
y
κ
κ
κ
∂
⎡
⎤
=
+
⋅
+
−
+
⋅
+
⎣
⎦
∂
+
(12) (12) Other used filters based on gradients are the Sobel, Prewitt and Canny. The Sobel spatial
filter uses the central weight constant k=2 (Pratt, 2001). Meanwhile the Pewwit space filter
uses k=1. The Canny space filter uses two different thresholds for weak and strong edges
detection (Canny, 1986). Table 2 shows the nine elements masks of the most utilized high-
pass filters. Figure 7 shows six examples of the application of these functions as high-pass
filters to figure 1a. It is observed that the Canny filter is the most powerful edge detector
filter. Other used filters based on gradients are the Sobel, Prewitt and Canny. The Sobel spatial
filter uses the central weight constant k=2 (Pratt, 2001). Meanwhile the Pewwit space filter
uses k=1. The Canny space filter uses two different thresholds for weak and strong edges
detection (Canny, 1986). Table 2 shows the nine elements masks of the most utilized high-
pass filters. Figure 7 shows six examples of the application of these functions as high-pass
filters to figure 1a. It is observed that the Canny filter is the most powerful edge detector
filter. 2.3.2 High-pass filters High frequency components are mostly located in image borders, like fast tone changes and
marked details. The main purpose of a high-pass filter is to highlight the image details for
skeletonizing, geometrical orientation, contrast enhancement, and revealing hidden
characteristics, among many others. One of the most common high-pass spatial filters is the
high-boost that consists in an interactive subtraction process between the original image and
low-pass filters. The weighting function for a 3x3 matrix is obtained by 1
9
1
9
9
,
2,
2 . ,
2,
2
C
m
n
w
m
n
⎧
−
=
=
⎪
= ⎨−
≠
≠
⎪⎩
(8) (8) The differential filters are another kind of high-pass filters that get its weighting function
based on the partial derivates applied to the image. The most usual differential filters are the
gradient and laplacian, based on the following equations 2
2
( ( , ))
,
,
f
f
f
f
f x y
gradient magnitude
x
y
x
y
⎛
⎞
∂
∂
∂
∂
⎛
⎞
∇
=
+
≈
+
⎜
⎟
⎜
⎟
∂
∂
∂
∂
⎝
⎠
⎝
⎠
(9) (9) and and 2
2
2
2
2
( ( , ))
,
,
f
f
f x y
laplacian
x
y
∂
∂
∇
=
+
∂
∂
(10) (10) if the magnitude of the partial derivatives work with a 3x3 mask, then 1,3
2,3
3,3
1,1
2,1
3,1
1
(
)
(
)
2
f
w
w
w
w
w
w
x
κ
κ
κ
∂
⎡
⎤
=
+
⋅
+
−
+
⋅
+
⎣
⎦
∂
+
(11)
and
1,1
1,2
1,3
3,1
3,2
3,3
1
(
)
(
) . 2
f
w
w
w
w
w
w
y
κ
κ
κ
∂
⎡
⎤
=
+
⋅
+
−
+
⋅
+
⎣
⎦
∂
+
(12) 1,3
2,3
3,3
1,1
2,1
3,1
1
(
)
(
)
2
f
w
w
w
w
w
w
x
κ
κ
κ
∂
⎡
⎤
=
+
⋅
+
−
+
⋅
+
⎣
⎦
∂
+
(11) (11) and and 1,1
1,2
1,3
3,1
3,2
3,3
1
(
)
(
) . 2.4 Mathematical discrete transforms Discrete transform analysis has played an important role in digital image processing. Several transform types are applicable to digital image processing, but due to their optical
metrology potential applications, Fourier and Radon transforms are presented in this
chapter section. 530 MATLAB – A Ubiquitous Tool for the Practical Engineer 2.4.1 Fourier transform 2.4.1 Fourier transform Discrete Fourier Transform (DFT) represents the change from spatial to frequency domain. In convergent optical systems this transform represents the propagated optical perturbation
from exit pupil to the focal point in a single lens arrangement. Equations (13) and (14)
represent the DFT pair for the mathematical two dimensional (2D) model (Gonzalez, 2002) {
}
(
)
1
1
1
( , )
( , )
( , )exp
2
,
M
N
vy
ux
M
N
x
y
f x y
F u v
f x y
i
MN
π
=
=
⎡
⎤
ℑ
=
=
−
+
⎢
⎥
⎣
⎦
∑∑
(13) (13) Sobel
Prewitt
Gradient
Laplacian
f
x
∂
∂
=
1
0
1
2
0
2
1
0
1
−
−
−
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
f
y
∂
∂
=
1
2
1
0
0
0
1
2
1
−
−
−
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
f
x
∂
∂
=
1
0
1
1
0
1
1
0
1
−
−
−
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
f
y
∂
∂
=
1
1
1
0
0
0
1
1
1
−
−
−
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
f
x
∂
∂
=
1
1
1
1
2
1
1
1
1
−
−
−
−
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
f
y
∂
∂
=
1
1
1
1
2
1
1
1
1
⎛
⎞
⎜
⎟
−
⎜
⎟
⎜
⎟
−
−
−
⎝
⎠
0
1
0
1
4
1
0
1
0
−
⎛
⎞
⎜
⎟
⎜
⎟
⎜
⎟
⎝
⎠
Table 2. Some 3x3 convolution masks g for high-pass differential filters (Bow, 2002). Fig. 7. High-pass 3x3 filters examples applied to figure 1a. Matlab parameters and functions
used: a) ‘canny’, b) ‘sobel’, c) ‘prewitt’, d) laplacian with ‘log’, e) gradient and f) high-boost
filter. Fig. 7. High-pass 3x3 filters examples applied to figure 1a. Matlab parameters and functions
used: a) ‘canny’, b) ‘sobel’, c) ‘prewitt’, d) laplacian with ‘log’, e) gradient and f) high-boost
filter. 2.4.1 Fourier transform and and {
}
(
)
1
1
1
( , )
( , )
( , )exp
2
,
M
N
vy
ux
M
N
u
v
F u v
f x y
F u v
i π
−
=
=
⎡
⎤
ℑ
=
=
+
⎢
⎥
⎣
⎦
∑∑
(14) (14) Image Processing for Optical Metrology 531 where (u,v), MxN and ℑ-1 are the Fourier space coordinates, the image size, the inverse
Fourier transform operator, respectively. Matlab has fft2 and ifft2 special functions for
equations (13) and (14), respectively, where FFT is the acronyms of Fast Fourier Transform. Other functions of Fourier transforms are fft, ifft for one dimension, and fftshift for the
shifting of the zero-frequency component to spectra center. An important characteristic
obtained from the Fourier transform is that it gives the frequencies content of the image. Due to this property, frequency filter design is a very straight forward task. Low frequencies
are located into the matrix around the central coordinates, while frequencies gradually
increase as are spread out from its center in a radial form. This characteristic is ideal for
frequency filtering (low-pass, high-pass, band-pass, and band-stop). The frequency filtering
process consists in the multiplication between image Fourier transform with a binary
circular mask. Figure 8 shows the filtered Fourier spectra and the resulting filtered images
for a high-pass, low-pass, band-pass and band-stop. Fig. 8. Fourier filtering applied to figure 1a. a) high-pass, b) low-pass, c) band-pass and d)
band-stop. Where, circle and ring are masks of 30 and 60 pixels radii. Fig. 8. Fourier filtering applied to figure 1a. a) high-pass, b) low-pass, c) band-pass and d)
band-stop. Where, circle and ring are masks of 30 and 60 pixels radii. 2.4.2 Radon transform Radon transform applied in pattern recognition or digital image processing may be
considered as the image’s gsl projection over a given angle with respect to x axis. The
mathematical model of the Radon transform is (Bracewell, 1995) {
}
(
)
( , )
( , )
cos
sin
,
f x y
f x y
R
x
y
dxdt
δ
θ
θ
∞∞
−∞−∞
ℜ
=
−
−
∫∫
(15) (15) where ℜ, δ, R and θ are the Radon transform operator, the Dirac delta function, the distance
from the origin to the profile line and the angle of direction of the same line, respectively. Each of these parameters can be observed in figure 9, Q is the origin of the profile line to be
obtained (thick blue bold line). Equation (15) is implemented in Matlab with the special
function radon. MATLAB – A Ubiquitous Tool for the Practical Engineer 532 Fig. 9. Radon transform parameters.+ Fig. 9. Radon transform parameters.+ Fig. 9. Radon transform parameters.+ 3. Optical metrology fundamentals Optical metrology is a field of physics that include theoretical and experimental methods to
estimate physical parameters using the light wavelength as fundamental scale. 3.1 Optical interferometry Optical interferometry is based in the light interference phenomenon to determine different
physical variables. A typical application is in nondestructive optical testing that requires high
accuracy. The interferometer is the optical system used by this technique, which allows by
interfering fringes the estimation of deformation components, shapes, strains or vibrations in
objects with polished or rough surfaces. According to users’ requirements, different
configurations of interferometers can be selected to measure displacements components. 3.1.1 Interference Figure 10 shows the schematic of a common optical arrangement used in interferometry
well known as Michelson interferometer. The beam splitter (BS) splits the incident
collimated laser light in two wavefronts that propagate in different directions and are
reflected by the plane mirrors M1 and M2 respectively, and then they are combined with the
same BS to form an interference pattern that can be observed directly on the screen. Fig. 10. Michelson interferometer. The superposition of the two wavefrons at a position (x,y) is expressed by the complex sum: Fig. 10. Michelson interferometer. The superposition of the two wavefrons at a position (x,y) is expressed by the comple The superposition of the two wavefrons at a position (x,y) is expressed by the complex sum: Image Processing for Optical Metrology 533 (16) 1
1
2
2
( , )
( , )exp[
( , )]
( , )exp[
( , )],
=
+
U x y
a x y
i
x y
a
x y
i
x y
φ
φ
(16) where a1(x,y) and a2(x,y) are the amplitudes and its respective phases φ1(x,y) y φ2(x,y). The
intensity at a point in the interference pattern is determined with the product of
perturbation U multiplied by its complex conjugated U*, this is *
( , )
( , )
( , ),
I x y
U x y
U
x y
=
⋅
(17) (17) then, the resulting intensity is given by then, the resulting intensity is given by 1
2
1
2
( , )
( , )
( , )
2
( , )
( , ) cos[ ( , )],
=
+
+
I x y
I
x y
I
x y
I
x y I
x y
x y
φ
(18) (18) where I1(x,y)=a12(x,y) and I2(x,y)=a12(x,y) are the intensities for each wavefront and φ(x,y) is
the phase difference between them, since these propagate along to different paths before the
interference. Due to cosine of equation (18), I(x,y) reaches its maxima when φ(x,y) corresponds to even
multiples of π (constructive interference) and its minima for odd multiples of π (destructive
interference) (Gasvik, 2002). In general, optical interferometry is applied to estimate this
phase difference, which can arise due to geometrical variations or deformations in a testing
object. 3.1.1 Interference In figure 11 are shown two synthetic interference patterns when is replaced a mirror:
a) with tilt in y and defocus and b) with defocus and coma in the interferometer of figure 10. The phase difference involving the geometrical variations of the mirrors is given by
φ(x,y)=4πΔz/λ, where λ is the wavelength of the illumination source and Δz is the shape
phase difference introduced by the mirrors. Fig. 11. Fringe patterns of mirrors with: a) tilt in y and defocus, YD; and b) defocus and
coma, DC. These wavefronts were generated using nested for loops. For these cases N=128
pixels; C1=0.01 and C2= 0.00001 are the numerical parameter of each aberration. Fig. 11. Fringe patterns of mirrors with: a) tilt in y and defocus, YD; and b) defocus and
coma, DC. These wavefronts were generated using nested for loops. For these cases N=128
pixels; C1=0.01 and C2= 0.00001 are the numerical parameter of each aberration. Fig. 11. Fringe patterns of mirrors with: a) tilt in y and defocus, YD; and b) defocus and
coma, DC. These wavefronts were generated using nested for loops. For these cases N=128
pixels; C1=0.01 and C2= 0.00001 are the numerical parameter of each aberration. Another way to generate fringe patterns is by replacing a mirror of the interferometer for a
testing object with an optically rough surface that experiments a deformation. In this case,
the interference fringe pattern is not observed directly on the screen as in the previous
described case. The superposition of a wavefront reflected by a rough surface (object beam)
with a regular wavefront (reference beam) as the reflected by a plane mirror in the
Michelson interferometer causes that I1, I2 and φ of equation (18) vary fast and randomly,
normally obtaining a speckle pattern. In speckle pattern interferometry the fringe patterns
are obtained by the correlation of two speckle patterns recorded using a CCD camera placed
at the screen position of the interferometer for the object before and after a deformation
Δφ(x,y). 3.1.2 Phase shifting In order to determine the phase φ(x,y) from fringe patterns, is applied a procedure well-
known as phase shifting. For this procedure can be registered several images introducing a
phase difference which experimentally is achieved with a piezoelectric (PZ) that modifies
the optical path length of one of the beams. A widely used algorithm to calculate the phase
employs four consecutive images shifted by π/2 (Huntley, 2001) 1
( , )
( , )
( , )
tan
,
( , )
( , )
−⎡
⎤
−
=
⎢
⎥
−
⎣
⎦
d
b
a
c
I
x y
I
x y
x y
I
x y
I x y
φ
(20) (20) where Ia(x,y), Ib(x,y), Ic(x,y) and Id(x,y) are the intensities of the shifted images. Due to the
inverse tangent, in this pattern arise an effect of wrapping in a 2π module; moreover can be
affected by noise of high frequency in the case of speckle interferograms. If the interest of
the user is to explore the reduction of speckle noise and phase unwrapping techniques can
consults references (Sirohi, 1993) and (Ghiglia, 1998). In figure 12 are shown the wrapped phases calculated with equation (20) using the fringe
patterns presented in the section. 3.1.1 Interference Assuming Ii(x,y), If(x,y) are the intensities of the speckle patterns for the initial no- 534 MATLAB – A Ubiquitous Tool for the Practical Engineer deformed state and the final deformed state respectively, the fringe patter can be calculated
by (Lehmann, 2001) deformed state and the final deformed state respectively, the fringe patter can be calculated
by (Lehmann, 2001) ( , )
( , ) ,
f
i
I
x y
I x y
−
(19) (19) and the phase difference involving the deformation of the object is given by Δφ(x,y)=4πz’/λ,
where z’ is the displacement of the object in z direction (Waldner, 2000). 3.2.1 Binary grating A binary grating can be mathematically represented by a Fourier series expansion of a step
function (fstep) bounded in the [0,T] interval, see figure 14a. The function is defined by: 2
2
,
0
( , )
,
0,
T
step
T
a
y
f
x y
y
T
⎧
<
<
⎪
= ⎨
≤
≤
⎪⎩
(22) (22) and its Fourier series expansion is given by (Tolstov, 1962) and its Fourier series expansion is given by (Tolstov, 1962) 0
2
,
[( 1)
1]
( , )
exp[
(
)],
(2 )
n
bin
m n
a
r
x y
i
mx
ny
mn
ω
π
∞
=−∞
−
−
=
+
∑
(23) (23) where T and a are the grating period and the amplitude, respectively. Then the intensity
profile at the focal plane is calculated from equations (17) and (21), with r(x,y) as vertical
binary grating of equation (23), giving (Mora-González et al., 2009) (
)
(
)
0
2
2
2
0
2
sin
( , )
,
,
k
bin
K
k
k
I
u v
h
Ku K v
k
π
ω
π
δ
∞
=−∞
⎛
⎞
⎡
⎤
⎜
⎟
=
⋅
−
⎢
⎥
⎣
⎦
⎜
⎟
⎝
⎠
∑
(24) (24) here
2
2
0
Aa
f
h
π
λ
=
is the zero diffraction order amplitude,
2
f
K
π
λ
=
is the scale factor at the focal
plane and
2
0
T
π
ω =
is the angular frequency. The binary grating intensity profile presents an
infinite number of diffraction orders (harmonics) modulated by a sinc function (see figure
14b). 3.2 Image diffraction The mathematical representation for a collimated wavefront passing through a convergent
optical system until the focal point is given by the Fourier transform, as is observed in figure
13. By setting a diffraction grating in the entrance pupil of a convergent lens, a Fraunhofer
diffraction pattern is obtained in the focal point (Goodman, 2005), given by (
)
(
)
2
2
2
exp
( , )
( , ) exp
,
f
o
f
A
j
u
v
U u v
r x y
j
xu
yv
dxdy
j f
π
λ
π
λ
λ
∞
−∞
⎡
⎤
⋅
+
⎣
⎦
⎡
⎤
=
⋅
−
+
⎣
⎦
∫∫
(21) (21) Fig. 12. Calculated wrapped phases for: a) tilt in y and defocus, wpYD; and b) defocus and
coma, wpDC. Image Processing for Optical Metrology 535 where Uo(u, v), r(x, y), A and λ are the complex amplitude distribution of the field in the
back focal plane of the lens, the grating function, the amplitude of the monochromatic plane
wave and the illumination wavelength, respectively. The result of equation (21) varies
depending on the function of the grating. For our purposes, those functions are binary and
sinusoidal. where Uo(u, v), r(x, y), A and λ are the complex amplitude distribution of the field in the
back focal plane of the lens, the grating function, the amplitude of the monochromatic plane
wave and the illumination wavelength, respectively. The result of equation (21) varies
depending on the function of the grating. For our purposes, those functions are binary and
sinusoidal. Fig. 13. Diagram for performing the Fourier transform of a grating with a positive lens. g. 13. Diagram for performing the Fourier transform of a grating with a positive lens. 3.2.2 Sinusoidal grating In order to observe the sinusoidal grating profile, it must be above x axis because negative
gsl cannot be observed. The equation proposed for the vertical sinusoidal grating is given by
(see figure 14c) 536 MATLAB – A Ubiquitous Tool for the Practical Engineer (
)
1
1
sin
0
2
2
( , )
sin
. r
x y
a
y
ω
⎡
⎤
=
+
⎣
⎦
(25) (25) The intensity profile at the focal plane from equation (21) with r(x,y) as vertical sinusoidal
grating of equation (25), giving (Mora-González et al., 2009) The intensity profile at the focal plane from equation (21) with r(x,y) as vertical sinusoidal
grating of equation (25), giving (Mora-González et al., 2009) (
)
[
]
(
)
0
0
2
2
2
sin
1
0
1
( , )
,
,
,
,
K
K
I
u v
h
Ku K v
h
Ku Kv
h
Ku K v
ω
ω
δ
δ
δ
⎡
⎤
⎡
⎤
=
+
+
+
−
⎢
⎥
⎢
⎥
⎣
⎦
⎣
⎦
(26) (26) where
2
1
Aa
f
h
π
λ
=
is the ±1 sinusoidal diffraction orders amplitude. The sinusoidal grating
intensity profile only presents three diffraction orders (see figure 14d), those harmonics are
characteristic of the Fourier transform of sinusoidal functions. where
2
1
Aa
f
h
π
λ
=
is the ±1 sinusoidal diffraction orders amplitude. The sinusoidal grating
intensity profile only presents three diffraction orders (see figure 14d), those harmonics are
characteristic of the Fourier transform of sinusoidal functions. Fig. 14. Functions of a) binary and c) sinusoidal gratings. Fourier spectra of b) binary and d)
sinusoidal gratings. Fig. 14. Functions of a) binary and c) sinusoidal gratings. Fourier spectra of b) binary and d)
sinusoidal gratings. 4. Aplications As shown in previous sections, Digital Image Processing is a useful tool to obtain improved
results in Optical Metrology. Applications details are presented in following subsections. 4.1 Fringe analysis g
y
Fringe analysis refers to the process of finding the phase associated to physical variables that
are being estimated. A typical case consists in the interpretation of the fringe patterns that
can be achieved with phase shifting techniques, when the object under study remains static
while three or more frames are acquired when the experiment conditions are free of
environmental perturbations. Another case is when the environmental conditions are not
met, and then the analysis of a single interferogram is more convenient. In both cases a
wrapped phase is obtained before the related continuous phase is assessed. Phase unwrapping is a numerical technique for retrieving a continuous phase from the
calculated phase by using the arctangent (atan2) of the sine and cosine functions of the
phase. In its simplest form, phase unwrapping consists in the addition or subtraction of a 2π
multiple when a discontinuity bigger than π is found between adjacent pixels (Robinson,
1993). This approach however is very sensitive to noise, and is said to be path dependent. It
means that any error may propagate along the path followed to phase unwrapping. In this
study we will review the least square method (Ghiglia, 1998). Basically, it consists in the
integration of the phase gradient by solving a linear equation system employing a numerical
technique. Lets assume φx(x,y) and φy(x,y) as the phase differences in the horizontal and
vertical directions, respectively. 4.1 Fringe analysis These phases are calculated from the wrapped phase φw(x,y)
as follows: Image Processing for Optical Metrology 537 1
sin
( , )
(
1, )
( , )
tan
( , ) (
1, ),
cos
( , )
(
1, )
−⎧
⎫
⎡
⎤
−
−
⎪
⎪
⎣
⎦
=
−
⎨
⎬
⎡
⎤
−
−
⎪
⎪
⎣
⎦
⎩
⎭
w
w
x
w
w
x y
x
y
x y
p x y p x
y
x y
x
y
φ
φ
φ
φ
φ
(27) (27) and and 1
sin
( , )
( ,
1)
( , )
tan
( , ) ( ,
1),
cos
( , )
( ,
1)
−⎧
⎫
⎡
⎤
−
−
⎪
⎪
⎣
⎦
=
−
⎨
⎬
⎡
⎤
−
−
⎪
⎪
⎣
⎦
⎩
⎭
w
w
y
w
w
x y
x y
x y
p x y p x y
x y
x y
φ
φ
φ
φ
φ
(28) (28) In the above equations p(x,y) is a pupil function equal to one inside of an interferogram field
and zero otherwise. A discretized Laplacian equation is then obtained from the phase
differences: ( , )
(
1, )
( , )
( ,
1)
( , )
4 ( , )
(
1, )
(
1, )
( ,
1)
( ,
1)
=
+
−
+
+
−
= −
+
+
+
−
+
+
+
−
y
y
x
x
L x y
x
y
x y
x y
x y
x y
x
y
x
y
x y
x y
φ
φ
φ
φ
φ
φ
φ
φ
φ
. (29) (29) This equation represents a linear equations system that can be solved with iterative
algorithms. In particular, is employed an overrelaxation method (SOR) due to it may be
easily programmed. 4.1 Fringe analysis The following equation is then iterated until the solution converges: 1( , )
( , )
( , )
(
1, )
(
1, )
( ,
1)
( ,
1)
( , )
,
+
=
+
⎡
⎤
−
+
−
−
−
+
−
−
+
⎣
⎦
+
k
k
k
x y
x y
d
x y
x
y
x
y
x y
x y
L x y
r
d
φ
φ
φ
φ
φ
φ
φ
(30) 1( , )
( , )
+
=
+
k
k
x y
x y
φ
φ (30) where, d=p(x+1,y)+p(x-1,y)+p(x,y+1)+p(x,y-1), and r is a parameter of the SOR method that
must be set between the [1,2] range. Figure 15 shows the wrapped phase φw obtained from
the sine and cosine of the phase and the unwrapped phase φ. A simple iterative algorithm
that unwraps the phase from the discretized Laplacian is given as: where, d=p(x+1,y)+p(x-1,y)+p(x,y+1)+p(x,y-1), and r is a parameter of the SOR method that
must be set between the [1,2] range. Figure 15 shows the wrapped phase φw obtained from
the sine and cosine of the phase and the unwrapped phase φ. A simple iterative algorithm
that unwraps the phase from the discretized Laplacian is given as: Algoritm 1. % Unwraps phase. g
p p
while (q<max)%q is the number of iterations (500 for this case) (q
q=q+1; q q
for i=1:n
for j=1:m
if p(i,j)==1
t=p(i+1,j)+p(i-1,j)+p(i,j+1)+p(i,j-1);
( )
( ) ((
( )
(
)
(
)
(
)
(
)
( ))
/ ) %
d for i=1:n for j=1:m if p(i,j)==1
t=p(i+1,j)+p(i-1,j)+p(i,j+1)+p(i,j-1); t=p(i+1,j)+p(i-1,j)+p(i,j+1)+p(i,j-1); p(
j) p(
j) p( j
) p( j
)
g(i,j)=g(i,j)-((t*g(i,j)-g(i+1,j)-g(i-1,j)-g(i,j+1)-g(i,j-1)+L(i,j))*1.95/t);%iterated equation
else
g(i,j)=0;
end,end,end,end p(
j) p(
j) p( j
) p( j
)
g(i,j)=g(i,j)-((t*g(i,j)-g(i+1,j)-g(i-1,j)-g(i,j+1)-g(i,j-1)+L(i,j))*1.95/t);%iterated equation
else
g(i j)=0; else g(i,j)=0; end,end,end,end A single interferogram with open fringes may also be analyzed for phase recovering (Creath
& Wyant, 1992). Experimentally an open fringe interferogram can be achieved if a tilt term is
added to the phase, usually by tilting the reference beam in an interferometer. Equation (18)
can be modified in order to include a tilt term in the x direction, this is as follows: 538 MATLAB – A Ubiquitous Tool for the Practical Engineer Fig. 15. a) wrapped and b) unwrapped phase. Fig. 15. a) wrapped and b) unwrapped phase. Fig. 15. a) wrapped and b) unwrapped phase. Fig. 15. a) wrapped and b) unwrapped phase. [
]
( , )
( , )
( , )cos
( , )
2
=
+
+
I x y
a x y
b x y
x y
tx
φ
π
(31) (31) where a(x,y)=I1(x,y)+I2(x,y) is known as the background intensity and b(x,y)=2[I1(x,y)I2(x,y)]½
is the modulation or visibility term. The Fourier transform of the expression below can be
written as: where a(x,y)=I1(x,y)+I2(x,y) is known as the background intensity and b(x,y)=2[I1(x,y)I2(x,y)]½
is the modulation or visibility term. The Fourier transform of the expression below can be
written as: (32) ( , )
( , )
(
, )
* (
, ). ( j)
p(
((
)
y
))
G(i,j)=1-exp(-1000*(x^2+y^2));%High pass filter ( j)
p(
((
)
y
))
G(i,j)=1-exp(-1000*(x^2+y^2));%High pass filter G(i,j)=1-exp(-1000*(x^2+y^2));%High pass filter
end,end IF=fftshift(fft2(I));%Fourier transform of the interferogram IF=fftshift(fft2(I));%Fourier transform of the interferogram IFH=IF.*H.*G; %Filtered Fourier transform Ih=ifft2(fftshift(IFH)); %Inverse Filtered Fourier transform
fw=atan2(imag(Ih),real(Ih)).*pupil;%Wrapped phase with tilt Ih=ifft2(fftshift(IFH)); %Inverse Filtered Fourier transform
fw=atan2(imag(Ih),real(Ih)).*pupil;%Wrapped phase with tilt
fw1=atan2(sin(fw-g),cos(fw-g)).*pupil; %Wrapped phase without tilt
phase1=(phase-g).*pupil; %Unwrapped phase fw atan2(imag(Ih),real(Ih)). pupil;%Wrapped phase with tilt
fw1=atan2(sin(fw-g),cos(fw-g)).*pupil; %Wrapped phase without tilt
phase1=(phase-g).*pupil; %Unwrapped phase (
g(
)
(
)) p p
pp
p
fw1=atan2(sin(fw-g),cos(fw-g)).*pupil; %Wrapped phase without tilt (
g(
)
(
)) p p
pp
p
fw1=atan2(sin(fw-g),cos(fw-g)).*pupil; %Wrapped phase without tilt
phase1=(phase g) *pupil %Unwrapped phase Algoritm 1. % Unwraps phase. I u v
a u v
C u
t v
C
u
t v
=
+
+
+
−
(32) Then the Fourier spectra of an open fringe interferogram contains three terms, ã(u,v) is a
narrow peak at the center of the Fourier spectra and C(u+t,v) and C*(u-t,v) are shifted
complex conjugate intensities symmetrically located respect to the origin of the Fourier Then the Fourier spectra of an open fringe interferogram contains three terms, ã(u,v) is a
narrow peak at the center of the Fourier spectra and C(u+t,v) and C*(u-t,v) are shifted
complex conjugate intensities symmetrically located respect to the origin of the Fourier Fig. 16. Process of phase recovery from a single interferogram with closed fringes, as shown
in algorithm 2. a) Interferogram, b) Fourier spectrum, c) filtered Fourier spectrum,
d) wrapped phase with tilt, e) wrapped phase without tilt, and f) unwrapped continuous
phase. Fig. 16. Process of phase recovery from a single interferogram with closed fringes, as shown
in algorithm 2. a) Interferogram, b) Fourier spectrum, c) filtered Fourier spectrum,
d) wrapped phase with tilt, e) wrapped phase without tilt, and f) unwrapped continuous
phase. Image Processing for Optical Metrology 539 domain (Takeda, 1982). The Fourier procedure to recover the phase consist in isolating
either C(u,v) or C*(u,v). Then the inverse transform is taken in order to retrieve the wrapped
phase from the imaginary and real parts of the filtered spectra. The last step, as done with
phase shifting procedures, is to apply a phase unwrapping procedure to recover the
continuous phase. The complete process of phase recovery from an open fringe
interferogram is observed in figure 16. domain (Takeda, 1982). The Fourier procedure to recover the phase consist in isolating
either C(u,v) or C*(u,v). Then the inverse transform is taken in order to retrieve the wrapped
phase from the imaginary and real parts of the filtered spectra. The last step, as done with
phase shifting procedures, is to apply a phase unwrapping procedure to recover the
continuous phase. The complete process of phase recovery from an open fringe
interferogram is observed in figure 16. Algoritm 2. % Phase recovery from a single interferogram Algoritm 2. 4.2 Wavefront deformation analysis Optical metrology applied for the determination of different physical variables has greatly
contributed with the constant advance of technology at a point that it is becoming a
powerful measurement alternative for the solution of problems in engineering and sciences. Algoritm 1. % Unwraps phase. % Phase recovery from a single interferogram
for i=1:256
for j=1:256
if sqrt((i-128)^2+(j-128)^2)<126 %creates a function pupil
pupil(i,j)=1;
else
pupil(i,j)=0;
end
x=(i-128)/128;
y=(j-128)/128;
phase(i,j)=2*pi*(4*(x^2+y^2)+16*x);
g(i,j)=2*pi*16*x;
back(i,j)=128*exp(-1*(x^2+y^2));
mod(i,j)=127*exp(-1*(x^2+y^2));
I(i,j)=(back(i,j)+mod(i,j)*cos(phase(i,j)))*pupil(i,j); % Interferogram with closed fringes
H(i,j)=exp(-180*((x-0.25)^2+y^2));%Band-Pass filter
G(i j)=1 exp( 1000*(x^2+y^2));%High pass filter Algoritm 2. % Phase recovery from a single interferogram
for i=1:256 ( j)
p(
(
y
))
I(i,j)=(back(i,j)+mod(i,j)*cos(phase(i,j)))*pupil(i,j); % In I(i,j)=(back(i,j)+mod(i,j)*cos(phase(i,j)))*pupil(i,j); % Interferogram with closed fring ( j) (
( j)
( j)
(p
( j))) p p ( j)
H(i,j)=exp(-180*((x-0.25)^2+y^2));%Band-Pass filter ( j) (
( j)
( j)
(p
( j))) p p ( j)
H(i,j)=exp(-180*((x-0.25)^2+y^2));%Band-Pass filter ( j) (
( j)
( j)
(p
( j))) p p ( j)
g
g
H(i,j)=exp(-180*((x-0.25)^2+y^2));%Band-Pass filter ( j)
p(
((
)
y
))
G(i,j)=1-exp(-1000*(x^2+y^2));%High pass filter 4.2.1 Deformation analysis using speckle interferometry In this section, is presented a deformation analysis for the estimation of out-of-plane
displacement components in a simulated model of a cantilever made of aluminum with a
load applied at its free end. The example corresponds to a typical problem in structural
mechanics where the Young´s modulus can be determined from the displacement of the
loaded bar made of an isotropic material. The suggested arrangement for the testing in
electronic speckle pattern interferometry (ESPI) is shown in figure 17. The laser light beam is
divided by the beam splitter BS1. One beam is reflected by a mirror attached to a
piezoelectric PZ (PC controlled), and then is expanded to uniformly illuminate at a small 540 MATLAB – A Ubiquitous Tool for the Practical Engineer angle respect to the normal of the object surface, and the other beam is coupled into an
optical fiber to obtain the reference illumination. The light reflected by the object and the
reference beam introduced with BS2 interfere on the CCD. Fig. 17. Electronic speckle pattern interferometer. The object was simulated by considering the following dimensions: 15 cm length and 3 cm
height with a thickness of 0.5 cm. Using the two intensities Ii(x,y), If(x,y) of the speckle
patterns generated by ESPI arrangement seen in the CCD image plane before and after
applying a force of 0.1 N, the correlation fringes using equation (19) is shown in figure 18a
and in figure 18b is shown the wrapped phase calculated by equation (20). In figure 18c is
shown the filtered and unwrapped phase using a conventional spatial average filter of 3 x 3
pixels and an iterative least-squares algorithm. Fig. 17. Electronic speckle pattern interferometer. Fig. 17. Electronic speckle pattern interferometer. The object was simulated by considering the following dimensions: 15 cm length and 3 cm
height with a thickness of 0.5 cm. Using the two intensities Ii(x,y), If(x,y) of the speckle
patterns generated by ESPI arrangement seen in the CCD image plane before and after
applying a force of 0.1 N, the correlation fringes using equation (19) is shown in figure 18a
and in figure 18b is shown the wrapped phase calculated by equation (20). In figure 18c is
shown the filtered and unwrapped phase using a conventional spatial average filter of 3 x 3
pixels and an iterative least-squares algorithm. Fig. 18. Deformation analysis of a cantilever with ESPI. 4.2.1 Deformation analysis using speckle interferometry a) interference fringe pattern; b)
wrapped phase and c) unwrapped phase. Fig. 18. Deformation analysis of a cantilever with ESPI. a) interference fringe pattern; b)
wrapped phase and c) unwrapped phase. 4.3 Wavefront detection Optical testing using diffraction gratings as wavefront modulators is another alternative to
detect wavefront aberrations. 4.3.1 Grating diffraction g
Diffraction gratings are optical devices commonly used on physics. There are several
gratings types, but as shown in 3.2 section, sinusoidal gratings only diffracts three harmonic Image Processing for Optical Metrology 541 modes, due to this property, sinusoidal gratings have been developed by different
techniques. According to the method reported by (Mora-González et al., 2009), is possible to
generate these gratings by laser printing on acetates. In figure 19, are shown different
increment sizes (Δy) of three sine profiles and the corresponding spectra of equations (25)
and (26), respectively. It must be pointed that for larger Δy values, the resolution diminishes
and more diffraction orders emerge. Fig. 19. Sinusoidal gratings generated in Matlab. With a) grating rsin=255*[.5+.5*sin(y)] and
b) Fourier spectra Isin=fftshift(fft2(rsin)). Fig. 19. Sinusoidal gratings generated in Matlab. With a) grating rsin=255*[.5+.5*sin(y)] and
b) Fourier spectra Isin=fftshift(fft2(rsin)). 4.4 Bio-metrology
I
h
b gy
In the present subsection several functions of Matlab and their applications as blood flow
measurement and pattern recognition in fingerprint are shown. In the present subsection several functions of Matlab and their applications as blood flow
measurement and pattern recognition in fingerprint are shown. 4.3.2 Ronchi test The Ronchi test is one of the most non invasive optical tests used in optical workshops, due
to the simplicity for observing aberrations over the optical surface. The test only needs to
propagate a convergent aberrated wavefront through a diffraction grating to obtain a
modulated fringe pattern (ronchigram) (Mora-González et al., 2001, 2003, 2011). In figure 20
is shown the typical diagram of the Ronchi test using a collimated illumination system. In figure 21 are shown the ronchigram before and after circular low-pass filtering and their
corresponding wrapped phase calculated with equation (20). Fig. 20. Collimated light Ronchi test diagram. Where f is the focus of lenses and r is the
distance between lens under test and Ronchi grating. Fig. 20. Collimated light Ronchi test diagram. Where f is the focus of lenses and r is the
distance between lens under test and Ronchi grating. MATLAB – A Ubiquitous Tool for the Practical Engineer 542 Fig. 21. Ronchi test results. a) ronchigram a: ra(x,y); b) frequency filtered ronchigram a and
applied pupil: raf(x,y); and c) wrapped phase of ronchigrams a, b, c and d: wp(x,y). Fig. 21. Ronchi test results. a) ronchigram a: ra(x,y); b) frequency filtered ronchigram
applied pupil: raf(x,y); and c) wrapped phase of ronchigrams a, b, c and d: wp(x,y). 4.4.1 Blood flow measurement Laser speckle effect is an interference phenomena that is produced when an optical rough
surface is illuminated by a laser source that can be observed directly or imaged by using an
optical system. The resulting intensity well known as speckle pattern is the result of
multiple interferences produced by the roughness of the object under test. The speckle
pattern consists in a distribution of brilliant points and dark points. By assuming ideal conditions like high coherent light source, unique frequency and perfect
diffusing surface. It can be proved that the standard deviation of the intensity fluctuations
from a speckle pattern is equal to the same that the average of the intensity. Speckle pattern
contrast is defined by the relationship between standard deviation (σ) and the averaged
intensity (I) (Goodman, 2005): . specklecontrast
I
σ
=
(33) (33) If the illuminated surface is static, the contrast observed in the speckle pattern is maximum,
however, if the surface is moving, the speckle patterns changes completely. This
phenomenon is known as “decorrelation” and can be observed when light is dispersed by a
great number of moving dispersers, i. e. moving particles into a fluid. The decorrelation is
used for fluid velocity quantification considering that a speckle pattern photography taken
at a finite time is blurred (contrast losing) in flowing areas. Contrast changes depend on
fluid velocity and photography exposure time (T). By assuming a Lorentzian velocity
distribution, speckle contrast (σ/<I>) is defined as correlation and exposure time function
(τc/T). If the illuminated surface is static, the contrast observed in the speckle pattern is maximum,
however, if the surface is moving, the speckle patterns changes completely. This
phenomenon is known as “decorrelation” and can be observed when light is dispersed by a
great number of moving dispersers, i. e. moving particles into a fluid. The decorrelation is
used for fluid velocity quantification considering that a speckle pattern photography taken
at a finite time is blurred (contrast losing) in flowing areas. Contrast changes depend on
fluid velocity and photography exposure time (T). By assuming a Lorentzian velocity
distribution, speckle contrast (σ/<I>) is defined as correlation and exposure time function
(τc/T). 1
2
2
1
exp
. 4.4.1 Blood flow measurement 2
c
c
T
I
T
τ
σ
τ
⎫
⎧
⎡
⎤
⎛
⎞
⎪
⎪
=
−
−
⎢
⎥
⎜
⎟
⎨
⎬
⎢
⎥
⎝
⎠
⎪
⎪
⎣
⎦
⎩
⎭
(34) (34) Correlation time τc is inversely proportional to local velocity of the dispersing particles. The
following code calculates a contrast image from a speckle image. Local blood flow velocity Correlation time τc is inversely proportional to local velocity of the dispersing particles. The
following code calculates a contrast image from a speckle image. Local blood flow velocity Image Processing for Optical Metrology 543 can be found from image contrast information and equation (34). Figure 22 shown speckle
images before and after processing. can be found from image contrast information and equation (34). Figure 22 shown speckle
images before and after processing. Algoritm 3. % Calculation of speckle contrast. Im2 = imread('speckle_img.bmp'); % load the bmp image file into the memory. Im2 = im2double(Im2); windowSize = 5; %define the window size for the filter. avgFilter = fspecial('average',windowSize); % generate an averaging filter. stdSpeckle = stdfilt(I,ones(windowSize)); %caculates the local standar deviation of image. avgSpeckle = imfilter(I,avgFilter,'symmetric'); %calculates the average of each pixel
ctrSpeckle = stdSpeckle./avgSpeckle; %caculates the speckle contrast image Fig. 22. Blood flow measurement results. a) speckle image of a rat cortex. b) speckle image of
contrast after processing with the code of algoritm 3. Fig. 22. Blood flow measurement results. a) speckle image of a rat cortex. b) speckle image of
contrast after processing with the code of algoritm 3. 5. Conclusion Mathematical fundamentals for Digital Image Processing and their implementation by
means of algorithms and Matlab commands were established. It has been demonstrated
according to some Optical Metrology applications, the Matlab algorithms efficiency. This
confirms that Matlab is a computational powerful tool. However, optical metrology
applications are not only limited to the discussed examples in the present chapter. Applications of all the proposed algorithms can be extended without any problem from
deformation analysis by another interferometric techniques (Speckle photography, Moiré,
etc.) or optical tests (Hartmann, Foucault, etc.), until analysis and pattern recognition in
medicine (X-Ray images, tomography, etc.), among other branches of science and
engineering. 4.4.2 Fingerprint measurement Several applications in pattern recognition are also utilized in optical metrology, finger print
parameters measurements is an example. The present subsection shows a new form for
fingerprint core determination based in the Radon transform of a fingerprint image, applied
in x and y axes directions. The core is located by the interception of the extremes (local
minimum and maximum) of the Radon transforms (Mora-González et al., 2010). Fig. 23. Images for fingerprint core point detection. a) original fingerprint im(x,y), b)
gradient of original fingerprint im_gradient(x,y), and c) binarized gradient im_binary(x,y)
and its 0° - 90° Radon transforms. Fig. 23. Images for fingerprint core point detection. a) original fingerprint im(x,y), b)
gradient of original fingerprint im_gradient(x,y), and c) binarized gradient im_binary(x,y)
and its 0° - 90° Radon transforms. Fig. 23. Images for fingerprint core point detection. a) original fingerprint im(x,y), b)
gradient of original fingerprint im_gradient(x,y), and c) binarized gradient im_binary(x,y)
and its 0° - 90° Radon transforms. 544 MATLAB – A Ubiquitous Tool for the Practical Engineer The process for core finding is very simple. First, a high-pass filter with a gradient type
convolution mask is applied to a fingerprint image in order to enhance the contrast. Next
the image is skeletonized, and the Radon Transform (RT) is applied in the x and y directions
to obtain RT90 and RT0 profiles, respectively. Finally, the noise produced from ridges and
rows in the fingerprint is minimized by a least-squares algorithm. The whole process is
illustrated in figure 23 by using the following algorithm: Algoritm 4. % Fingerprint analysis. [im,map]=imread(FileName); %read fingerprint im=double(im); %change image format im=double(im); %change image format [Nx,Ny]=size(im); %image size im_gradient=gradient(im); %gradient spatial filter level = graythresh(im_gradient); %finding the threshold of gradient
for x=1:Nx for y=1:Ny if (im_gradient(x,y)>15*level) %fingerprint skeletonization if (im_gradient(x,y)>15*level) %fingerprint skeletonization im_binary(x,y)=1; else [RT,xp] = radon(bg,[0 90]); %Radon transform [
p]
( g [
])
leastsq_0=polyfit(xp,RT(:,1),21); %21° polynomial adjustment for 0° Radon transform
leastsq_90=polyfit(xp,RT(:,2),21); %21° polynomial adjustment for 90° Radon transform
y_leastsq0=polyval(leastsq_0,xp); %least square approximation of 0° Radon transform
y_leastsq90=polyval(leastsq_90,xp); %least square approximation of 90° Radon transform y
y
y_leastsq90=polyval(leastsq_90,xp); %least square approximation of 90° Radon transf 7. References Bow, S.T. (2002). Pattern Recognition and Image Preprocesing (2nd Ed.), Marcel Dekker, Inc.,
ISBN 0-8247-0659-5, New York, USA. Bracewell, R.N. (1995). Two-Dimensional Imaging, Prentice Hall, ISBN 0-13-062621-X, New
Jersey, USA. Canny, J. (1986). A Computational Approach to Edge Detection, IEEE Trans. on Pattern
Analysis and Machine Intelligence, Vol.PAMI-8, No.6, (November 1986), pp. 679-698,
ISSN 0162-8828. Creath, K.; Schmit, J. and Wyant, J.C. (2007), Optical Metrology of Diffuse Surfaces, In:
Optical Shop Testing, 3th ed., Malacara, D., pp. 756-807, John Wiley & Sons, Inc.,
ISBN 978-0-471-48404-2, Hoboken, New Jersey, USA. y
Gasvik, K.J. (2002). Optical Metrology, John Wiley & Sons, Ltd., ISBN 0-470-84300-4,
Chichester, West Sussex, England. Ghiglia, D.C., Pritt, M.D. (1998), Two-Dimensional Phase Unwrapping: Theory Algorithms and
Software, Wiley-Interscience, ISBN 0-471-24935-1, New York, USA. f
y
Gonzalez, R.C. & Woods, R.E. (2002). Digital Image Procesing (2nd Ed.), Prentice Hall, ISBN 0-
201-18075-8, New Jersey, USA. Goodman, J.W. (2005). Introduction to Fourier Optics (3rd Ed.), Roberts and Company
Publishers, ISBN 0-9747077-2-4, Englewood, USA. Huntley, J. M. (2001), Automated analysis of speckle interferograms, In: Digital Speckle Patter
Interferometry and Related Techniques, Rastogi, P. K., pp. 59-140, John Wiley & Sons,
Ltd., ISBN 0-471-49052-0, Chichester, West Sussex, England. Lehmann, M. (2001). Speckle Statistics in the Context of Digital Speckle Interferometry, In:
Digital Speckle Patter Interferometry and Related Techniques, Rastogi, P. K.¸ pp. 1-58,
John Wiley & Sons, Ltd., ISBN 0-471-49052-0, Chichester, West Sussex, England. y
g
Mora González, M. & Alcalá Ochoa, N. (2001). The Ronchi test with an LCD grating, Opt. Comm., Vol.191, No.4-6, (May 2001), pp. 203-207, ISSN 0030-4018. (
y
) pp
Mora-González, M. & Alcalá Ochoa, N. (2003). Sinusoidal liquid crystal display grating in
the Ronchi test, Opt. Eng., Vol.42, No.6, (June 2003), pp. 1725-1729, ISSN 0091-3286. Mora-González, M.; Casillas-Rodríguez, F.J.; Muñoz-Maciel, J.; Martínez-Romo, J.C.; Luna-
Rosas, F.J.; de Luna-Ortega, C.A.; Gómez-Rosas, G. & Peña-Lecona, F.G. (2008). Reducción de ruido digital en señales ECG utilizando filtraje por convolución,
Investigación y Ciencia, Vol.16, No.040, (September 2008), pp. 26-32, ISSN 1665-4412. Mora-González, M.; Pérez Ladrón de Guevara, H.; Muñoz-Maciel, J.; Chiu-Zarate, R.;
Casillas, F.J.; Gómez-Rosas, G.; Peña-Lecona, F.G. & Vázquez-Flores, Z.M. (2009). Discretization of quasi-sinusoidal diffraction gratings printed on acetates,
Proceedings of SPIE 7th Symposium Optics in Industry, Vol.7499, 74990C, ISBN 978-0-
8194-8067-5, Guadalajara, México, September 2009. Mora-González, M.; Martínez-Romo, J.C.; Muñoz-Maciel, J.; Sánchez-Díaz, G.; Salinas-Luna,
J.; Piza-Dávila, H.I.; Luna-Rosas, F.J. & de Luna-Ortega, C.A. (2010). 6. Acknowledgment The authors wish to express their gratitude for financial support of this project to
Departamento de Ciencias Exactas y Tecnología, of Centro Universitario de los Lagos, Universidad
de Guadalajara. The image of figure 22 courtesy of Julio Cesar Ramirez San-Juan, Ph.D
(Instituto Nacional de Astrofísica Óptica y Electrónica). 545 Image Processing for Optical Metrology 7. References Radon
Transform Algorithm for Fingerprint Core Point Detection. Lecture Notes in
Computer Science, Vol.6256, No.1, (September 2010), pp. 134-143, ISSN 0302-9743. Mora-González, M.; Casillas, F.J.; Muñoz-Maciel, J.; Chiu-Zarate, R. & Peña-Lecona, F.G. (2011). The Ronchi test using a liquid crystal display as a phase grating, Proceedings
of SPIE Optical Measurement Systems for Industrial Inspection VII, Vol.8082 part two,
80823G, ISBN 978-0-8194-8678-3, Münich, Germany, May 2011. 546 MATLAB – A Ubiquitous Tool for the Practical Engineer Oppenheim, A.V.; Willsky, A.S. & Nawab, S.H. (1997). Signasl and Systems, 2nd ed., Prentice
Hall, Inc., ISBN 0-13-814757-4, New Jersey, USA. Pratt, W.K. (2001). Digital Image Processing (3th Ed.), John Wiley & Sons, Inc., ISBN 0-471-
22132-5, New York, USA. Robinson, D.W. (1993). Phase unwrapping methods, In: Interferogram Analysis, Robinson,
D.W. and Reid, G.T., pp. 195-229, IOP Publishing, ISBN 0-750-30197-X, Bristol,
England. g
Sirohi R. S. (1993), Speckle Metrology, Marcel Dekker, Inc., ISBN 0-8247-8932-6, New York,
USA. Takeda, M.; Ina, H. & Kobayashi, S. (1982). Fourier-transform method of fringe-pattern
analysis for computer-based topography and interferometry, J. Opt. Soc. Am.,
Vol.72, No.1, (January 1982), pp. 156-160, ISSN 0030-3941. (
y
) pp
Tolstov, G.P. (1962). Fourier Series, Dover Publications, Inc., ISBN 0-486-63317-9, New York,
USA. Waldner, S. P. (2000). Quantitative Strain Analysis with Image Shearing Speckle Pattern
Interferometry
(Shearography),
Doctoral
Thesis,
Swiss
Federal
Institute
of
Technology, Zurich, Swiss.
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0055817&type=printable
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English
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Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea
|
PloS one
| 2,013
|
cc-by
| 13,066
|
Gregor Gorkiewicz1*., Gerhard G. Thallinger2., Slave Trajanoski3, Stefan Lackner1,3, Gernot Stocker2,
Thomas Hinterleitner4, Christian Gu¨ lly3, Christoph Ho¨ genauer4* 1 Institute of Pathology, Medical University of Graz, Graz, Austria, 2 Institute for Genomics and Bioinformatics, University of Technology, Graz, Austria, 3 Center for Medical
Research, Medical University of Graz, Graz, Austria, 4 Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz,
Austria Abstract Funding: GGT and GS were supported by the Austrian Ministry of Science and Research, GEN AU Bioinformatics Integration Network; http://www.gen-au.at/
index.jsp?lang = en. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. * E-mail: gregor.gorkiewicz@medunigraz.at (GG); christoph.hoegenauer@medunigraz.at (CH) Competing Interests: The authors have declared that no competing interests exist. * E-mail: gregor.gorkiewicz@medunigraz.at (GG); christoph.hoegenauer@medunigraz.at (CH) * E-mail: gregor.gorkiewicz@medunigraz.at (GG); christoph.hoegenauer@medunigraz.at (CH) . These authors contributed equally to this work. . These authors contributed equally to this work. Abstract Background & Aims: Diseases of the human gastrointestinal (GI) tract are often accompanied by diarrhea with profound
alterations in the GI microbiota termed dysbiosis. Whether dysbiosis is due to the disease itself or to the accompanying
diarrhea remains elusive. With this study we characterized the net effects of osmotic diarrhea on the composition of the GI
microbiota in the absence of disease. Methods: We induced osmotic diarrhea in four healthy adults by oral administration of polyethylene glycol 4000 (PEG). Stool as well as mucosa specimens were collected before, during and after diarrhea and 16S rDNA-based microbial
community profiling was used to assess the microbial community structure. Results: Stool and mucosal microbiotas were strikingly different, with Firmicutes dominating the mucosa and Bacteroidetes
the stools. Osmotic diarrhea decreased phylotype richness and showed a strong tendency to equalize the otherwise
individualized microbiotas on the mucosa. Moreover, diarrhea led to significant relative shifts in the phyla Bacteroidetes and
Firmicutes and to a relative increase in the abundance of Proteobacteria on the mucosa, a phenomenon also noted in several
inflammatory and diarrheal GI diseases. Conclusions: Changes in microbial community structure induced by osmotic diarrhea are profound and show similarities to
changes observed in other GI diseases including IBD. These effects so must be considered when specimens from diarrheal
diseases (i.e. obtained by stratification of samples according to diarrheal status) or conditions wherein bowel preparations
like PEG (i.e. specimens obtained during endoscopy) are used. Citation: Gorkiewicz G, Thallinger GG, Trajanoski S, Lackner S, Stocker G, et al. (2013) Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea. PLoS
ONE 8(2): e55817. doi:10.1371/journal.pone.0055817 itor: Jacques Ravel, Institute for Genome Sciences, University of Maryland School of Medicine, United States of America Editor: Jacques Ravel, Institute for Genome Sciences, University of Maryland School of Medicine, United States of Americ Received August 25, 2012; Accepted January 2, 2013; Published February 8, 2013 Received August 25, 2012; Accepted January 2, 2013; Published February 8, 2013 Copyright: 2013 Gorkiewicz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: 2013 Gorkiewicz et al. This is an open-access article distributed under the terms of the Creative Commons Attribut
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. February 2013 | Volume 8 | Issue 2 | e55817 Alterations in the Colonic Microbiota in Response to
Osmotic Diarrhea Gregor Gorkiewicz1*., Gerhard G. Thallinger2., Slave Trajanoski3, Stefan Lackner1,3, Gernot Stocker2,
Thomas Hinterleitner4, Christian Gu¨ lly3, Christoph Ho¨ genauer4* Colonic Microbiota Changes Induced by Diarrhea obtained at four different time points. Two baseline samples were
taken before induction of diarrhea, sample 1 on a free diet at the
beginning of the study (time-point 1, pretreatment period, day 27)
and sample 2 seven days later on the second day of the diet (time-
point 2, diet period, day 0). Sample 3 was taken from the first stool
on the third day of PEG intake while subjects were on the standard
diet (time-point 3, diarrhea period, day 3). Sample 4 was taken 7
days after withdrawal of PEG and the standard diet (time-point 4,
posttreatment period, day 10). Colonic biopsy samples were
obtained from three of the four subjects (subjects B, C, D) at two
different time points, sample 1 on the second day of the standard
diet before diarrhea was induced (time-point 2, diet period, day 0)
and sample 2 on the third day of PEG administration (time-point
3, diarrhea period, day 3). Biopsies were taken from the sigmoid
colon 25 cm proximal to the anal canal by flexible sigmoidoscopy
without bowel preparation. The mucosa of the area was flushed
gently three times with 20 ml of physiological saline solution
before two biopsies were taken. Stool samples (abbreviated in
figures and tables as F) and mucosa samples (abbreviated in figures
and tables as M) were immediately frozen and stored at –20uC. living state will be subjected to wash-out and negatively selected
against microbes that adhere to the mucosa or are replicating fast
[17]. This principle shows that variation in just one parameter of
GI physiology, like increased transit or increased amounts of fluid
in the lumen, might have a profound influence on the microbial
composition of our gut. Thus, deduction of relevant microbial
community alterations in the light of a specific disease must take
these accompanying effects into account. To understand the effects of diarrhea on the composition of the
GI microbiota we performed a longitudinal study wherein we
induced
osmotic
diarrhea
in
four
healthy
adults
by
oral
administration of polyethylene glycol 4000 (PEG). PEG is a
polymer that is not reabsorbed or metabolized by intestinal
bacteria. It is a pure osmotic agent that binds water in the
intestinal lumen and so leads to diarrhea when administered in
higher doses [18]. It is used to treat constipation and to cleanse the
bowel prior to endoscopy. Materials and Methods The study was approved by the institutional review board of the
Medical University of Graz (protocol no. 20-090 ex 08/09) and
written informed consent was obtained from all subjects. Colonic Microbiota Changes Induced by Diarrhea Stool as well as mucosa samples were
collected before, during and after induction of diarrhea and
subjected to culture-independent 16S rDNA-based microbiota
profiling using barcoded pyrosequencing. Study Protocol y
Four healthy adult Caucasian males (subjects A, B, C, D)
participated in this study (age range 36–47 years, BMI range 24–
26.6). The subjects had had neither antibiotic therapy nor episodes
of diarrhea for at least 1 year prior to the study. Stool frequency
and consistency were recorded daily during the study and assessed
according the Bristol stool chart [19]. After 6 days on a free diet
without interventions (pre-treatment period) the subjects were
placed on a standard diet (85 g protein, 77 g fat, 250 g
carbohydrates, 25 g fiber, total calorie count 2150 kcal/d) for
five days. Oral water intake was not restricted. On the third day of
the
diet
diarrhea
was
induced
with
the
osmotic
laxative
polyethylene glycol 4000 (ForlaxH, Merck, Vienna, Austria) in a
dose of 50 g tid (150 g per day). PEG was administered in addition
to the standard diet for three days (diarrhea period). Thereafter the
subjects again noted their stool behavior without any interventions
on a free diet for seven days (post-treatment period) (Fig. 1). The
first day of PEG administration and the first day after PEG
administration were considered equilibration days and were not
included in the analysis of bowel habits. Stool samples were Introduction whether dysbiosis itself causes these diseases or is just an
epiphenomenon due to a microbial habitat altered by other
pathophysiological factors [11,12]. The human GI tract is populated by a complex community of
microorganisms that play a pivotal role in the maintenance of
health and the development of disease [1,2]. Current knowledge
indicates a crucial role for the GI microbiota in extracting
nutrients from the diet, thereby influencing host metabolism, body
growth and weight [3]. Moreover, it is a barrier against
colonization with pathogens and is essential for mucosal homeo-
stasis and for the maturation and correct function of the GI
immune system [4]. Because our GI tract and its microbiota are
interdependent, disease will affect both. A variety GI diseases
including chronic inflammatory bowel disease (IBD), irritable
bowel syndrome (IBS) and antibiotic-associated diarrhea (AAD)
show specific alterations of the microbial community, called
dysbiosis, and these diseases are supposed to be driven at least in
part by these alterations [5–12]. Nevertheless, it is questionable A hallmark of many GI diseases is diarrhea, which often
correlates with the severity of disease. Diarrhea is characterized by
increased
stool
frequency,
decreased
stool
consistency
and
increased stool weight. Pathophysiologic mechanisms leading to
diarrhea include increased amounts of fluid in the intestinal lumen
due to osmotically active substances (osmotic diarrhea), impaired
absorption or increased secretion of water and electrolytes
(secretory diarrhea) and accelerated intestinal transit [13,14]. Diarrhea is often caused by a combination of these mechanisms,
which furthermore leads to intestinal malabsorption of nutrients
such as fat or bile acids, altering the milieu within the gut [15,16]. Basically, acceleration of the luminal content influences the
composition of the microbial community. Microbes that are
replicating slowly or experiencing a particle-associated or free- February 2013 | Volume 8 | Issue 2 | e55817 1 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org Colonic Microbiota Changes Induced by Diarrhea DNA Isolation and PCR Amplification DNA was extracted from stools with the QIAamp DNA Stool
Mini kit and from biopsies with the QIAamp DNA Mini Kit
(Qiagen, Hilden, Germany) according to the recommended
protocol. The stool homogenate was incubated in a boiling water
bath for 5 min prior to DNA extraction to increase bacterial DNA
yield as recommended. The variable V1–V2 region of the
bacterial 16S rRNA gene was amplified with PCR using
oligonucleotide primers BSF8 and BSR357 as described previously
[20]. This 16S rDNA region was chosen since it gives robust
taxonomic classification and has been shown to be suitable for
community clustering [21]. We included a sample specific six-
nucleotide barcode sequence on primer BSF8 to allow for a
simultaneous analysis of multiple samples per pyrosequencing run
[22]. Oligonucleotide sequences are given in table S1. PCR
conditions were as follows: 100 ng DNA from stool samples or
10 ng from biopsy samples were subjected to PCR amplification in Figure 1. Study design. Subjects were on a free diet from day –7 to day –2 and from day 4 to day 10. From day 21 to day 0 a standardized diet was
ingested. Diarrhea was induced by PEG for 3 days (day 1 to day 3). One stool sample was obtained one week before induction of diarrhea. Before the
first dose of PEG a second stool sample and a mucosa sample were collected. A third stool and a second mucosa sample were taken at day three of
PEG administration when diarrhea was maximally pronounced. A fourth stool sample was taken one week after withdrawal of PEG. doi:10.1371/journal.pone.0055817.g001 Figure 1. Study design. Subjects were on a free diet from day –7 to day –2 and from day 4 to day 10. From day 21 to day 0 a standardized diet was
ingested. Diarrhea was induced by PEG for 3 days (day 1 to day 3). One stool sample was obtained one week before induction of diarrhea. Before the
first dose of PEG a second stool sample and a mucosa sample were collected. A third stool and a second mucosa sample were taken at day three of
PEG administration when diarrhea was maximally pronounced. A fourth stool sample was taken one week after withdrawal of PEG. DNA Isolation and PCR Amplification doi:10.1371/journal.pone.0055817.g001 February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org 2 Colonic Microbiota Changes Induced by Diarrhea a total volume of 50 ml with 16HotStar Master Mix (Qiagen) and
20 mM of each primer. For stool samples the following PCR
l
d
I i i l d
i
95uC f
12
i
followed by 22 cycles of 95uC for 30 sec, 56uC
72uC for 1 min and a final step of 72uC for 7
l
h f ll
i
PCR
l
d I i
Figure 2. Different community structure and richness in stool and mucosa specimens. (A) Relative phylum distribution i
A, B, C, D) and mucosa specimens (individual B, C, D) from pooled data from each individual. ‘‘Unclassified’’ denotes phylotype
assigned to the bacterial domain by using the 80% identity threshold for RDP classifications. ‘‘Other’’ denotes phyla prevale
Rarefaction analysis of averaged mucosa (green) and stool (red) samples (OTU distance = 0.03). The dotted line indicates 6 SEM. doi:10.1371/journal.pone.0055817.g002 Figure 2. Different community structure and richness in stool and mucosa specimens. (A) Relative phylum distribution in stool (individual
A, B, C, D) and mucosa specimens (individual B, C, D) from pooled data from each individual. ‘‘Unclassified’’ denotes phylotypes that were only
assigned to the bacterial domain by using the 80% identity threshold for RDP classifications. ‘‘Other’’ denotes phyla prevalent below 2%. (B)
Rarefaction analysis of averaged mucosa (green) and stool (red) samples (OTU distance = 0.03). The dotted line indicates 6 SEM. doi:10.1371/journal.pone.0055817.g002 followed by 22 cycles of 95uC for 30 sec, 56uC for 30 sec, and
72uC for 1 min and a final step of 72uC for 7 min. For biopsy
samples the following PCR protocol was used: Initial denaturation a total volume of 50 ml with 16HotStar Master Mix (Qiagen) and
20 mM of each primer. For stool samples the following PCR
protocol was used: Initial denaturation at 95uC for 12 min February 2013 | Volume 8 | Issue 2 | e55817 3 Colonic Microbiota Changes Induced by Diarrhea Figure 3. Stool microbiotas are highly individualized and mucosal microbiotas assimilate due to osmotic diarrhea. (A) PCA of stool
samples according to individuals and treatment periods shows individual specific clustering of stool samples. The principal components 1 & 2
accounting for up to 26.18% variability are shown including 87% confidence ellipses. DNA Isolation and PCR Amplification The inset panels identify the respective samples (A, B, C, D
denote subjects; F denotes stool sample; M denotes mucosa sample; time-points: 1, 2 pre-diarrhea, 3 diarrhea, 4 post-diarrhea). (B) PCA of stool and
the corresponding mucosa samples before and during diarrhea. The principal components 1 & 2 accounting for up to 41.67% variability are shown. Stool and mucosal communities are significantly different (P = 0.0002, Student’s t-test) and are clearly separated from each other. Mucosal
communities obtained before (time-point 2) and during diarrhea (time-point 3) are significantly different (P = 0.0044, Student’s t-test) and cluster
independent of the individual, indicating a convergence of the individualized microbiotas. doi:10.1371/journal.pone.0055817.g003 Figure 3. Stool microbiotas are highly individualized and mucosal microbiotas assimilate due to osmotic diarrhea. (A) PCA of stool
samples according to individuals and treatment periods shows individual specific clustering of stool samples. The principal components 1 & 2
accounting for up to 26.18% variability are shown including 87% confidence ellipses. The inset panels identify the respective samples (A, B, C, D
denote subjects; F denotes stool sample; M denotes mucosa sample; time-points: 1, 2 pre-diarrhea, 3 diarrhea, 4 post-diarrhea). (B) PCA of stool and
the corresponding mucosa samples before and during diarrhea. The principal components 1 & 2 accounting for up to 41.67% variability are shown. Stool and mucosal communities are significantly different (P = 0.0002, Student’s t-test) and are clearly separated from each other. Mucosal
communities obtained before (time-point 2) and during diarrhea (time-point 3) are significantly different (P = 0.0044, Student’s t-test) and cluster
independent of the individual, indicating a convergence of the individualized microbiotas. doi:10.1371/journal.pone.0055817.g003 at 95uC for 12 min followed by 35 cycles of 95uC for 30 sec, 56uC
for 30 sec, and 72uC for 1 min and a final step of 72uC for 7 min. PCR products were separated on 1% 1xTAE agarose gel and
specific bands (,300 bp) were excised and gel extracted using the
Qiagen gel extraction kit (Qiagen). Each sample was amplified and
extracted three times independently and subsequently pooled. Purified PCR products were assessed on BioAnalyzer 2100 DNA
1000 chips (Agilent Technologies, Vienna, Austria) for size and
integrity. DNA concentration was determined fluorometrically
using the QuantiDect reagent (Invitrogen, Carlsbad, CA). An
amplicon library was prepared using aequimolar amounts of PCR
products derived from the individual samples and bound to the
sequencing beads at a one molecule per bead ratio. DNA Isolation and PCR Amplification Long Read
Amplicon Sequencing using 70675 PicoTiter Plates (Roche
Diagnostics, Vienna, Austria) was done on a Genome Sequencer
FLX system (Roche Diagnostics) according to the manufacturer’s
instruction. was integrated in the phylotyping pipeline SnoWMAn (http://
SnoWMAn.genome.tugraz.at) [28]. Briefly, all sequences were
pooled and aligned with Infernal (V1.0) using a 16S rRNA
secondary structure based model for accurate position alignment
of sequences [29]. The aligned sequences were clustered by
complete linkage to form OTUs with sequence distances ranging
from 0% to 5%. For each OTU a representative sequence was
extracted and a taxonomic classification was assigned to it using
the RDP Bayesian classifier 2.0.1 [30]. Finally, the pooled
sequences were again separated according to their sample
affiliation. Taxonomic classification and biostatistical analyses
reported in this paper were performed on the clustering results for
3% distance. Statistical Analysis and Visualization The analyses were conducted using the statistical environment
R (V2.12.1) [31]. Species richness was estimated with the Chao1
estimator [32]. The abundance-based coverage estimator (ACE),
diversity and evenness were calculated using the R package
‘‘BiodiversityR’’ (V1.5) [33]. Sequence abundance in each sample
was normalized to the sample with the maximum number of
sequences. Normalization factors ranged between 1.06 and 2.69. Additionally, abundance data were log-2 transformed after adding
a value uniformly distributed between 0.75 and 1.25 to down-
weight OTUs with high abundance and to resemble the normal
Gaussian distribution more closely. Principal component analysis
(PCA) on the normalized, log-2 transformed data was performed
with the prcomp function of R. OTUs significantly changing
between time points were assessed either with Metastats using
default settings [34] or the R package ‘‘edgeR’’ (V2.14.7) using a
linear model accounting for the paired nature of the data [35]. To Data Availability Sequence data generated for this work can be accessed via the
EBI short read archive (EBI SRA) under the accession number
ERP002098. Phylogenetic Analysis As the initial step the data set was de-noised using the method
described by Quince et al. [23,24] to avoid OTU inflation due to
sequencing errors. All sequences shorter than 150 bp containing
any ambiguous characters or not matching to the forward primer
(distance.2) were discarded [25]. Subsequently, the chimeric
sequences were identified with Uchime [26] and removed together
with contaminant (human) sequences. The remaining sequences
were assigned to their respective samples by using the sample-
specific 6 bp barcode preceding the primer. In order to perform
sample- and time-point-wide comparisons, operational taxonomic
units (OTUs) were generated with an extended Ribosomal
Database Project (RDP)-Pyrosequencing approach [27], which February 2013 | Volume 8 | Issue 2 | e55817 February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org 4 Colonic Microbiota Changes Induced by Diarrhea Figure 4. The number of shared phylotypes between individuals increases due to osmotic diarrhea. The number of shared phylotypes
(OTU distance = 0.03) between individuals increases during diarrhea in stools (left) but more pronouncedly in mucosa (right) samples (8.7–10.4% vs. 13.8–25.7%). The figure indicates the relative (%) phylotype (upper number) and sequence overlap (lower number) of stool (F) and mucosa (M)
samples of individuals B, C and D at time-point 2 (top) and time-point 3 (bottom). doi:10.1371/journal.pone.0055817.g004 Figure 4. The number of shared phylotypes between individuals increases due to osmotic diarrhea. The number of shared phylotypes
(OTU distance = 0.03) between individuals increases during diarrhea in stools (left) but more pronouncedly in mucosa (right) samples (8.7–10.4% vs. 13.8–25.7%). The figure indicates the relative (%) phylotype (upper number) and sequence overlap (lower number) of stool (F) and mucosa (M)
samples of individuals B, C and D at time-point 2 (top) and time-point 3 (bottom). doi:10.1371/journal.pone.0055817.g004 samples, which were only represented by pre-diarrhea (time-point
2) and diarrhea (time-point 3) states, three 2-point profiles were
generated in a similar fashion. Finally, OTUs were assigned to
their respective reaction pattern and these associations were
visualized with Cytoscape [37]. account for multiple comparisons, p-values were adjusted by the
method proposed by Benjamini and Hochberg [36]. Adjusted p-
values less than 0.05 were considered statistically significant. Changes between time points on the level of taxonomic ranks were
investigated using a paired t-test or a ratio paired t-test. The latter
tests the ratio of the relative abundances (time-point 3: time point
2) against 1. Scoring Approach and Visualization of OTUs According
to their Change in Abundance To visualize the change in OTUs’ abundance in relation to
diarrhea we used a scoring system in which we assigned each
OTU to a respective increasing/decreasing pattern. In this way,
we calculated the mean relative abundance between the pre-
diarrhea states (time-point 1 and time-point 2) of each OTU. Together with the corresponding relative abundance values for
diarrhea (time-point 3) and post-diarrhea (time-point 4), a three
point profile (pre-diarrhea – diarrhea – post-diarrhea) of each
OTU could be drawn. Only OTUs experiencing an abundance
change of at least 0.05% in relation to the respective sample were
included. Subsequently, a scoring system was introduced that
assigned values of 21 (decreasing abundance value between two
states), +1 (increasing abundance value) or 0 (relative abundance
change,60.05%) to the (two) slopes of this profile. The score for
the first slope was multiplied by 3 and added to the score of the
second slope, yielding a specific overall score for each OTU that
related to one of the nine possible profile patterns. For mucosa A Highly Individualized Colonic Microbiota with Different
Community Structures in Stools and on the Mucosa After denoising and filtering the data set for chimeras and
contaminant (human) sequences, 452,363 high-quality 16S rDNA
sequences with an average length of 246 bp (range 230–277 bp)
remained, yielding an average of 20,562 sequences per sample
(Table. S2). The RDP classifier (80% bootstrap cutoff) assigned 10
phyla, but only 7 phyla were represented by more than 20
sequences. Most sequences were related to the phyla Bacteroidetes
(52.6%), Firmicutes (43.1%), Proteobacteria (4%) and Actinobacteria
(0.2%) [38]. We noted a strikingly different phylum distribution between
stool and mucosa samples. In stools Bacteroidetes dominated
(69.565.8%) followed by Firmicutes (22.164.7%), whereas on the PLOS ONE | www.plosone.org February 2013 | Volume 8 | Issue 2 | e55817 5 February 2013 | Volume 8 | Issue 2 | e55817 Colonic Microbiota Changes Induced by Diarrhea Figure 5. Osmotic diarrhea leads to decreased phylotype richness. (A) Rarefaction analysis of averaged stool samp
red) and during diarrhea (time-point 3, green) shows significantly decreased richness (richness time-point 2 vs. time point
test). (B) Rarefaction analysis of averaged mucosa samples before (time-point 2, red) and during diarrhea (time-point 3, green
but non-significant decrease in richness (richness time-point 2 vs. time point 3: P = 0.08 Student’s t-test). The dotted line
distance = 0.03. doi:10.1371/journal.pone.0055817.g005 Figure 5. Osmotic diarrhea leads to decreased phylotype richness. (A) Rarefaction analysis of averaged stool sample
red) and during diarrhea (time-point 3, green) shows significantly decreased richness (richness time-point 2 vs. time point 3
test). (B) Rarefaction analysis of averaged mucosa samples before (time-point 2, red) and during diarrhea (time-point 3, green
but non-significant decrease in richness (richness time-point 2 vs. time point 3: P = 0.08 Student’s t-test). The dotted line
distance = 0.03. doi:10.1371/journal.pone.0055817.g005 Figure 5. Osmotic diarrhea leads to decreased phylotype richness. (A) Rarefaction analysis of averaged stool samples before (time-point
red) and during diarrhea (time-point 3, green) shows significantly decreased richness (richness time-point 2 vs. time point 3: P = 0.029, Student’s
test) (B) Rarefaction analysis of averaged mucosa samples before (time point 2 red) and during diarrhea (time point 3 green) shows a trend towa Figure 5. Osmotic diarrhea leads to decreased phylotype richness. (A) Rarefaction analysis of averaged stool samples before (time-point 2,
red) and during diarrhea (time-point 3, green) shows significantly decreased richness (richness time-point 2 vs. time point 3: P = 0.029, Student’s t-
test). Consequences of Osmotic Diarrhea: Reduction of
Microbial Richness and Convergence of Individualized
Microbiotas on the Mucosa The administration of PEG increased stool frequency (6.061.5
vs. 1.260.6 bowel movements/day) and decreased stool consistency
(stool type: 6.760.6 vs. 3.060.9) in all 4 individuals (Table. S6). The
effect of diarrhea on the individual microbiotas was readily
identifiable in the PCA, wherein community variation at time-
point 3 exceeded intrapersonal variation between time-points 1 and
2 (Fig. 3). Diarrhea also led to a significant decrease in phylotype
richness in stools (P = 0.0295, paired t-test), further evidenced by
decreased Chao1 and abundance-based coverage (ACE) richness
estimators comparing time-point 2 with time-point 3 (P = 0.017 and
P = 0.0218, respectively; Table. S3). Although overall decreased
richness due to diarrhea was evident in the rarefaction analysis of
mucosa specimens (Fig. 5), this difference did not reach statistical
significance (P = 0.0801). Phylotype diversity and evenness showed
no significant difference between pre-diarrhea and diarrhea
samples, either in stools or on the mucosa (Table. S3). PCA clearly
separated mucosa from stool samples, reflecting the different niches,
and also separated pre-diarrhea mucosa samples by individual. It
was noteworthy that diarrhea led to a prominent shift of the mucosal
communities, which
significantly
differed
from
pre-diarrheal
mucosal communities in the PCA (P = 0.0044, Student’s t-test). Diarrhea-state mucosal communities clustered together in the PCA,
indicating an equalization of the otherwise individualized microbi-
otas (Fig. 3B). Diarrhea also led to an increase in the number of
shared phylotypes between individuals that was most pronounced in
the mucosa samples at time-point 3 (Fig. 4). Figure 6. Consistency of measures. Congruence of Metastats, edgeR
and Viz (denoted ‘‘Profile’’; in at least two individuals simultaneously) for
identification of significantly changing OTUs (diversity = 0.03) in stool
samples (A) and mucosa samples (B). doi:10.1371/journal.pone.0055817.g006 mucosa Firmicutes (75.2613.7%) were more abundant than
Bacteroidetes (17.8612.7%) (Fig. 2A). Proteobacteria were also more
abundant on the mucosa than in the stools (5.5611.1% vs. 2.161.2%). When the representation of phyla was compared
between matched stool and mucosa samples (i.e. from the same
individual at the same time point) and p-values were corrected for
multiple comparisons, Firmicutes (adjusted P = 0.001), Proteobacteria
(adusted P = 0.027), Actinobacteria (adjusted P,0.001) and Cyano-
bacteria (adjusted P,0.001) were more abundant on the mucosa
and Bacteriodes more abundant in stools (adjusted P = 0.016). Although we noted a trend towards increased microbial richness
on the mucosa compared to stools as indicated by the rarefaction
analysis (Fig. Colonic Microbiota Changes Induced by Diarrhea Figure 6. Consistency of measures. Congruence of Metastats, edgeR
and Viz (denoted ‘‘Profile’’; in at least two individuals simultaneously) for
identification of significantly changing OTUs (diversity = 0.03) in stool
samples (A) and mucosa samples (B). doi:10.1371/journal.pone.0055817.g006 during diarrhea (13.8% vs. 8.7% at time-point 2 and 25.7% vs. 10.4% at time-point 3; Fig. 4). The most abundant phylotypes across all stool specimens were
dominated by Bacteroidetes. In three individuals these were represented
by Bacteroides (individuals B, C and D) resembling the recently published
enterotype 1, in one (individual A) by Prevotella resembling enterotype 2
[39,40]. Often the most abundant stool phylotypes were more
individual specific and were rarely detected or absent in stool
specimens from other individuals (Table. S4). The most abundant
phylotypes in mucosa specimens were dominated by lactobacilli
(Weisella, Leuconostoc, Lactococcus), which were rarely detected or
completely absent in stool specimens from the same person,
underscoring the difference in microbial habitat composition (Table. S5). Interestingly, the two most abundant mucosal phylotypes matched
to the exopolysaccharide producers Weisella confusa and Weisella cibaria
(OTU_61 and OTU_24; BLAST: 100% homology either). Both were
also considered stable phylotypes (i.e. no significant relative abundance
change in respect to diarrhea; see below). Consequences of Osmotic Diarrhea: Reduction of
Microbial Richness and Convergence of Individualized
Microbiotas on the Mucosa 2B), richness was not statistically significant different
between the two habitats (P = 0.1913 and P = 0.989 at time-points
2 and time-points 3, respectively). Microbial diversity and
evenness, both measures of the uniformity of the phylotype
assembly, also showed no statistical difference between matched
stool and mucosa samples (Table. S3). The capacity of stool microbiotas to reconstitute was assessed by
comparing samples from diarrhea (time-point 3) and post-diarrhea
(time-point 4). Although species richness increased significantly
towards time-point 4 in stools (P = 0.042) an overall reduced
species richness persisted during the one week interval after PEG
administration (Fig. S1; Table. S3). Stool microbiotas were highly individualized; interpersonal
variation significantly exceeded intrapersonal variation irrespec-
tive of diarrhea (P#0.0077, Student’s t-test) as shown by the
principal component analysis (PCA; Fig. 3A). Stool and mucosa
samples represented significantly different microbial communities
(P = 0.0002, Student’s t-test) if matched stool and mucosa samples
were analyzed by PCA, which clearly separated the two habitats
irrespective of the origin from different individuals (Fig. 3B). Mucosa samples also showed more shared phylotypes between
individuals than stool samples and this proportion increased Unaltered Community Members in Response to Osmotic
Diarrhea A Highly Individualized Colonic Microbiota with Different
Community Structures in Stools and on the Mucosa (B) Rarefaction analysis of averaged mucosa samples before (time-point 2, red) and during diarrhea (time-point 3, green) shows a trend toward
but non-significant decrease in richness (richness time-point 2 vs. time point 3: P = 0.08 Student’s t-test). The dotted line indicates 6 SEM; OTU
distance = 0.03. doi:10.1371/journal.pone.0055817.g005 February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org 6 Colonic Microbiota Changes Induced by Diarrhea Unaltered Community Members in Response to Osmotic
Diarrhea To understand the community changes induced by PEG admin-
istration in more detail we assessed the relative abundance change of
phylotypes during the course of the study. Depending on the stressor
acting on the microbial community (i.e. wash-out due to osmotic
diarrhea) and the life-style of the respective microbes (adherent vs. living in suspension), certain phylotypes should experience a more February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org 7 Colonic Microbiota Changes Induced by Diarrhea Figure 7. Changing stool OTUs visualized with an association network (Viz). OTUs (distance = 0.03) are shown with their respective
progression patterns during the study (i.e. abundance change; boxes in the center). The inset exemplifies one possible abundance progression
showing an increasing-decreasing pattern. Only OTUs are displayed that were assigned to a respective reaction pattern in at least two individuals
(corresponding to thin lines connecting OTUs with their pattern). The width of lines correlates with the number of individuals in whom an OTU was
assigned to a specific pattern. Size of nodes correlates with the sum of changes during the study period (mean relative abundance change comparing
pre-diarrhea to diarrhea and diarrhea to post-diarrhea samples). OTUs are colored according to their phylum membership and named according to
the taxonomic rank conferred by the RDP classifier (80% identity threshold). M denotes significantly changed according to Metastats analysis
(P,0.05); E denotes significantly changed according to edgeR analysis (P,0.05). OTUs identified by both biostatistical methods are highlighted with a
bold outline. Note the increase of Faecalibacterium due to diarrhea (upper left) and the skew of edgeR-identified phylotypes towards decreasing
patterns (bottom). doi:10.1371/journal.pone.0055817.g007 Figure 7. Changing stool OTUs visualized with an association network (Viz). OTUs (distance = 0.03) are shown with their respective
progression patterns during the study (i.e. abundance change; boxes in the center). The inset exemplifies one possible abundance progression
showing an increasing-decreasing pattern. Only OTUs are displayed that were assigned to a respective reaction pattern in at least two individuals
(corresponding to thin lines connecting OTUs with their pattern). The width of lines correlates with the number of individuals in whom an OTU was
assigned to a specific pattern. Size of nodes correlates with the sum of changes during the study period (mean relative abundance change comparing
pre-diarrhea to diarrhea and diarrhea to post-diarrhea samples). Unaltered Community Members in Response to Osmotic
Diarrhea OTUs are colored according to their phylum membership and named according to
the taxonomic rank conferred by the RDP classifier (80% identity threshold). M denotes significantly changed according to Metastats analysis
(P,0.05); E denotes significantly changed according to edgeR analysis (P,0.05). OTUs identified by both biostatistical methods are highlighted with a
bold outline. Note the increase of Faecalibacterium due to diarrhea (upper left) and the skew of edgeR-identified phylotypes towards decreasing
patterns (bottom). d i 10 1371/j
l
0055817 007 doi:10.1371/journal.pone.0055817.g007 represented by Weisella confusa and Weisella cibaria (OTU_61 and
OTU_24, respectively; BLAST homology 100%), which also repre-
sented top abundant phylotypes on the mucosa as mentioned above
(Table. S5). Several low-abundant phylotypes were also considered
stable (Table. S7). In general, Firmicutes were overrepresented in both
mucosa and stool samples as stable phylotypes (Table. S7). The finding
that the number of stable phylotypes differed greatly between
individuals highlights the high degree of individualization of the GI
microbiota. Moreover, stable behavior seems to be related to the
individual and/or the microbial community itself and not to the
phylotype per-se. pronounced abundance change compared to others. Thus we assessed
the coefficient of variation (CV) of the relative abundances of
phylotypes between time-point 2 and time-point 3 samples. A CV of
#10% was chosen as threshold and only phylotypes prevalent with at
least 10 reads per individual were considered. This analysis revealed
that only a small fraction of phylotypes exhibited stable behavior and
the proportion of these so-called ‘‘stable’’ phylotypes differed greatly
between subjects (Table. S7). The majority of stable phylotypes were
specific to the individuals, meaning that a phylotype showing stable
behavior in one individual showed non-stable behavior in the other
individuals according to our definition. In stools only one stable
phylotype was found in two individuals simultaneously (OTU_1199;
Lachnospiriaceae), while there was none in the mucosa samples. In stool
samples the stable phylotype with the highest abundance was
represented by Bacteroides vulgatus (OTU_33; BLAST homology
100%), but only in one individual (Table. S4, Table. S7). In the
mucosa samples stable phylotypes with the highest abundance were pronounced abundance change compared to others. Thus we assessed
the coefficient of variation (CV) of the relative abundances of
phylotypes between time-point 2 and time-point 3 samples. A CV of
#10% was chosen as threshold and only phylotypes prevalent with at
least 10 reads per individual were considered. Unaltered Community Members in Response to Osmotic
Diarrhea This analysis revealed
that only a small fraction of phylotypes exhibited stable behavior and
the proportion of these so-called ‘‘stable’’ phylotypes differed greatly
between subjects (Table. S7). The majority of stable phylotypes were
specific to the individuals, meaning that a phylotype showing stable
behavior in one individual showed non-stable behavior in the other
individuals according to our definition. In stools only one stable
phylotype was found in two individuals simultaneously (OTU_1199;
Lachnospiriaceae), while there was none in the mucosa samples. In stool
samples the stable phylotype with the highest abundance was
represented by Bacteroides vulgatus (OTU_33; BLAST homology
100%), but only in one individual (Table. S4, Table. S7). In the
mucosa samples stable phylotypes with the highest abundance were Altered Community Members in Response to Osmotic
Diarrhea Interestingly, we
noted a relative increase of the proteobacterial taxon Acinetobacter
(genus level; P = 0.038) on the mucosa during diarrhea. In
the
mucosa
sample
data
set,
Metastats
identified
87
significantly changing OTUs and edgeR 79 OTUs (Table. S14,
S15). Viz identified 232 OTUs correlated with a respective
reaction pattern (abundance change threshold.60.05%), repre-
senting a fraction of 7.59% of OTUs found in mucosa specimens. If Viz analysis was narrowed down to phylotypes showing a
respective association pattern in at least in 2 individuals, 64
phylotypes were represented (Table. S16). Given these definitions,
all three methods together identified 183 significantly changing
OTUs (Table. 1, Fig. 6B). Only one OTU, a Pseudomonas sp. (OTU_1341; Pseudomonas putida, BLAST identity 100%), was
detected by all three methods simultaneously; 46 OTUs were
identified at least by two methods simultaneously (Table. 3). Community variation was readily captured by Viz; 36 out of 64
Viz-identified phylotypes (56.3%) were reconfirmed by Metastats
and/or edgeR (Fig. 8, Fig. S3). Interestingly, several Proteobacteria
experienced a relative increase in response to diarrhea revealed by
Viz and confirmed mainly by Metastats, as did several lactic acid
bacteria. From the 46 OTUs identified by at least 2 methods
simultaneously, 13 OTUs (28.3%) represented Proteobacteria (Table. 3),
among
them
several
opportunistic
pathogens
including
pseudomonads (e.g. OTU_1341, Pseudomonas putida, BLAST
identity 100%) or the e-proteobacterial taxon Arcobacter (e.g. OTU_596). There was a significant association of Proteobacteria
with the increasing abundance pattern in Viz (P = 0.000371,
Fisher’s exact test) and a significant association of Bacteroidetes with
the decreasing pattern (P = 0.000216, Fisher’s exact test). As
mentioned above several OTUs matching to Faecalibacterium (g
)
g
This approach revealed only a few significantly changing taxa. It is now evident that the human GI microbiota is highly
individualized [2]. Levels of inter-individual variation might
therefore exceed community variation induced by diarrhea. Moreover, our pilot study encompassed a relatively small sample
size (n = 22), which hampers stringent statistical assessment. Consequently, both preconditions may have obscured patterns
in the microbial community driven by osmotic diarrhea. We thus
employed an alternative strategy and assessed abundance changes
on the level of individual OTUs with three different measures. Two
biostatistical
tools
well
established
for
assessment
of
abundance data were employed, Metastats and edgeR. A not too
stringent significance threshold was used in these analyses
(P,0.05) to account for the relatively small sample size. Altered Community Members in Response to Osmotic
Diarrhea We next looked for phylotypes showing a significant relative
abundance change in response to diarrhea by comparing time- February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org 8 Colonic Microbiota Changes Induced by Diarrhea Table 1. Performance comparisons of methods used for finding changing phylotypes. Number of OTUs
Method
P-value ,0.01
P-value ,0.05
Association in at least 2
individuals
Association in at least 1
individual
Stool specimens
Metastats
25
72
n.a. n.a. EdgeR
2
20
n.a. n.a. Viz
n.a. n.a. 61
299
Mucosa specimens
Metastats
18
87
n.a. n.a. EdgeR
28
79
n.a. n.a. Viz
n.a. n.a. 64
232
n.a., not applicable. doi:10.1371/journal.pone.0055817.t001 pattern (in at least 2 individuals) in relation to diarrhea (Table. 1,
Fig. 6A) Out of them, 39 OTUs were at least identified by two
methods simultaneously (Table. 2). Community variation was
readily presented by Viz; 37 out of 61 Viz-identified phylotypes
(60.7%) were reconfirmed by Metastats and/or edgeR (Fig. 7, Fig. S2). In general, Bacteroidetes were associated with an increase and
decrease pattern in response to diarrhea but often approached
baseline values within the 1 week posttreatment interval. Firmicutes
were also associated with either an increase pattern and thereafter
approached baseline or decreased due to diarrhea and remained
so. Interestingly, several OTUs matching to the genus Faecalibac-
terium including F. prausnitzii (e.g. OTU_206; BLAST identity 97%)
experienced a relative increase in abundance due to diarrhea,
which was mirrored by a simultaneous decrease of these taxa in
the mucosa specimens. point 2 with time-point 3 samples. In stools we also assessed
significantly changing phylotypes involved in reconstitution by
comparing time-point 3 with time-point 4 samples. We initially
performed this analysis at the levels of phylogenetic ranks from
phylum down to genus. After testing for multiple comparisons only
Rikenellaceae (family level; adjusted P = 0.000), Alistipes and Holde-
mania (genus level; adjusted P = 0.000 and P = 0.032, respectively)
showed a significant relative decrease in response to diarrhea in
stools (Table. S8). No significantly changing taxon during the
reconstitution phase (comparing time-point 3 with time-point 4)
could be identified in stools (Table. S9). In the mucosa samples
Rikenellaceae (family level; adjusted P = 0.000) and Alistipes (genus
level; adjusted P = 0.000) also showed a significant relative
decrease in response to diarrhea (Table. S10). Altered Community Members in Response to Osmotic
Diarrhea The
third approach involved a scoring system with graphical data
visualization (denoted Viz), wherein the abundance change of
phylotypes (increasing and decreasing in response to diarrhea) was
scored and presented within association networks created with
Cytoscape. In stool samples Metastats identified 72 significantly changing
OTUs and edgeR 20 OTUs (Table. S11, S12). Viz identified 299
OTUs correlated with a respective reaction pattern (abundance
change threshold $60.05%) representing 9.78% of OTUs found
in stool specimens. If Viz analysis was narrowed down to
phylotypes showing a respective association pattern in at least 2
individuals, 61 phylotypes were evident (Table. S13). Discussion We used 16S rDNA-based community profiling to assess the
influence of osmotic diarrhea on the composition of the human
colonic microbiota. Our longitudinal study with simultaneously
sampled stool and mucosa specimens enabled us to compare
microbiota changes within and between individuals. We noted
strikingly different community structures between stool and
mucosa
samples
wherein
Bacteroidetes
dominated
stools
and
Firmicutes the mucosa. The dominance of Firmicutes on the mucosa
is in accordance with several earlier reports [41,42]. Bacteria
display different life styles: either they are particle associated or
they experience a free-living (‘‘planctonic’’) life style [17,43,44]. Both life styles can be found in stools as well as on the mucosa,
although in the latter the polysaccharide-rich mucus overlying the
gut epithelium constitutes a biofilm-like community, which might
favor a particle-associated life-style [45]. Niche colonization is
determined by both partners of the mutualistic human/microbe
relationship and is dependent on factors like the availability of
nutrients or the capability to adhere [17]. Recent investigations
comparing liquid phase and particle-associated communities have
also revealed that Firmicutes are dominant in the latter [46]. Interestingly, the two top-abundant phylotypes on the mucosa,
which have also been found unaltered (‘‘stable’’) in response to
diarrhea, matched to Weisella confusa and Weisella cibaria (OTU_61
and OTU_24). Both taxons are exopolysaccharide (dextran)
producers and show a strong adhesion capacity, e.g. to Caco-2
cells, which might explain their preferential colonization of the
mucosal habitat and their investigation regarding their potential as
probiotics [47,48]. We also recorded a trend toward higher
richness on the mucosa compared to stools, which is in accordance
with earlier reports [42]. Since the mucosal surface represents the
interface of host/microbe interactions, a higher phylotype richness
(‘‘biodiversity’’), which enhances the robustness and stability of an
ecosystem, might be an intrinsic safeguard against perturbations
like invasion of pathogens [49,50]. Understanding the spatial
organization of host-associated microbial communities thus poses
an important challenge for future microbiota studies of the GI
tract [21,51]. The human GI microbiota shows a high degree of inter-
individual variation at higher phylogenetic levels despite a uniform
community structure at lower levels where the phyla Firmicutes and
Bacteroidetes dominate [2,38]. This phenomenon was most prom-
inent in stools, wherein inter-individual differences exceeded any
intra-individual variation. In the mucosa samples the degree of
inter-individual variation was generally lower, despite a trend
towards higher richness. For instance, in mucosa specimens more
phylotypes were shared between individuals than in stools. including F. prausnitzii (e.g. OTU_206) experienced a relative
abundance decrease in mucosal specimens (Fig. 8, Table. 3). OTU
Score#
Method*
Mean %
time-
point 2
±SD
Mean %
time-
point 3
±SD
Taxonomic classification+
1861
2
MV
0.412
0.379
0.028
0.044
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
1959
2
ME
0.019
0.016
0.000
0.000
Bacteria1.0Firmicutes0.95Clostridia0.95Clostridiales0.95Ruminococcaceae0.5Faecalibacterium0.23
1983
2
EV
0.127
0.170
0.000
0.000
Bacteria1.0Firmicutes0.84Clostridia0.83Clostridiales0.83Ruminococcaceae0.72Faecalibacterium0.44
2034
2
EV
0.081
0.097
0.000
0.000
Bacteria1.0Firmicutes0.68Clostridia0.66Clostridiales0.63Ruminococcaceae0.54Faecalibacterium0.38
3402
2
MV
0.071
0.071
0.001
0.002
Bacteria1.0Firmicutes0.61Clostridia0.6Clostridiales0.6Peptococcaceae0.51Peptococcus0.51
#Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods. *(M) Metastats, (E) edgeR, (V) scoring & visualization. +Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score. doi:10.1371/journal.pone.0055817.t002 Altered Community Members in Response to Osmotic
Diarrhea To that end,
all
three
methods
together
identified
100
OTUs
showing
significant relative abundance variation or a respective abundance February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org 9 Colonic Microbiota Changes Induced by Diarrhea g g
p
OTU
Score#
Method*
Mean %
time-
point 2
±SD
Mean %
time-
point 3
±SD
Taxonomic classification+
32
3
MEV
0.049
0.030
0.000
0.000
Bacteria1.0Firmicutes0.66Clostridia0.64Clostridiales0.64Ruminococcaceae0.48Faecalibacterium0.44
89
3
MEV
3.635
2.869
0.056
0.097
Bacteria1.0Firmicutes0.98Clostridia0.98Clostridiales0.98Lachnospiraceae0.9Pseudobutyrivibrio0.36
95
3
MEV
0.086
0.055
0.000
0.000
Bacteria1.0Firmicutes0.99Clostridia0.99Clostridiales0.99Lachnospiraceae0.97Dorea0.54
144
3
MEV
0.148
0.163
0.000
0.000
Bacteria1.0Firmicutes0.99Clostridia0.99Clostridiales0.99Lachnospiraceae0.99Lachnospira0.79
194
3
MEV
2.529
1.296
0.080
0.100
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
246
3
MEV
0.056
0.021
0.001
0.002
Bacteria1.0Firmicutes0.56Clostridia0.52Clostridiales0.33Lachnospiraceae0.16Sporobacterium0.02
338
3
MEV
0.065
0.069
0.000
0.000
Bacteria1.0Firmicutes0.98Clostridia0.98Clostridiales0.98Lachnospiraceae0.98Roseburia0.95
466
3
MEV
0.135
0.131
0.002
0.004
Bacteria1.0Firmicutes0.75Clostridia0.69Clostridiales0.66Ruminococcaceae0.47Ethanoligenens0.37
783
3
MEV
0.074
0.065
0.000
0.000
Bacteria1.0Firmicutes0.84Clostridia0.83Clostridiales0.83Ruminococcaceae0.52Sporobacter0.17
1005
3
MEV
0.217
0.158
0.002
0.004
Bacteria0.99Bacteroidetes0.97Bacteroidetes0.67Bacteroidales0.67Rikenellaceae0.67Alistipes0.67
1171
3
MEV
0.372
0.235
0.007
0.010
Bacteria1.0Proteobacteria0.52Alphaproteobacteria0.3Sphingomonadales0.14Sphingomonadaceae0.14Sphingosinicella0.12
1660
3
MEV
0.068
0.060
0.000
0.000
Bacteria0.99Bacteroidetes0.97Bacteroidetes0.49Bacteroidales0.49Bacteroidaceae0.31Bacteroides0.31
2361
3
MEV
0.118
0.121
0.000
0.000
Bacteria1.0Firmicutes0.74Clostridia0.74Clostridiales0.74Ruminococcaceae0.58Faecalibacterium0.41
1472
2
MV
0.139
0.092
0.034
0.068
Bacteria1.0Firmicutes0.66Clostridia0.64Clostridiales0.64Ruminococcaceae0.42Faecalibacterium0.38
9
2
MV
0.012
0.019
0.210
0.174
Bacteria1.0Firmicutes1.0Clostridia1.0Clostridiales1.0Ruminococcaceae1.0Faecalibacterium1.0
13
2
MV
4.401
3.270
16.617
12.017
Bacteria1.0Bacteroidetes1.0Bacteroidetes0.99Bacteroidales0.99Bacteroidaceae0.99Bacteroides0.99
16
2
ME
0.000
0.000
0.021
0.011
Bacteria1.0Firmicutes1.0Bacilli1.0Lactobacillales1.0Leuconostocaceae0.91Weissella0.9
21
2
MV
0.018
0.007
0.073
0.034
Bacteria1.0Firmicutes0.87Clostridia0.86Clostridiales0.86Lachnospiraceae0.86Roseburia0.78
41
2
MV
0.123
0.110
0.891
0.449
Bacteria1.0Firmicutes1.0Clostridia1.0Clostridiales1.0Ruminococcaceae1.0Faecalibacterium1.0
66
2
MV
0.052
0.027
0.531
0.263
Bacteria1.0Firmicutes0.98Clostridia0.98Clostridiales0.98Lachnospiraceae0.98Roseburia0.38
74
2
MV
0.093
0.118
0.322
0.127
Bacteria1.0Firmicutes0.92Erysipelotrichi0.89Erysipelotrichales0.89Erysipelotrichaceae0.89Coprobacillus0.78
92
2
EV
0.613
1.203
0.000
0.000
Bacteria0.99Firmicutes0.54Clostridia0.49Clostridiales0.48Incertae Sedis XV0.24Aminobacterium0.22
108
2
MV
0.019
0.020
0.113
0.050
Bacteria1.0Firmicutes0.97Clostridia0.97Clostridiales0.96Lachnospiraceae0.9Roseburia0.57
206
2
MV
0.178
0.148
0.773
0.383
Bacteria1.0Firmicutes0.97Clostridia0.97Clostridiales0.97Ruminococcaceae0.97Faecalibacterium0.96
215
2
MV
0.110
0.094
0.595
0.314
Bacteria1.0Firmicutes0.99Clostridia0.99Clostridiales0.99Lachnospiraceae0.94Lachnospiraceae Incertae Sedis0.35
222
2
MV
0.386
0.153
0.024
0.028
Bacteria0.99Bacteroidetes0.95Bacteroidetes0.56Bacteroidales0.56Bacteroidaceae0.38Bacteroides0.38
343
2
MV
0.049
0.049
0.002
0.004
Bacteria1.0Firmicutes0.99Clostridia0.97Clostridiales0.97Ruminococcaceae0.94Ruminococcus0.93
479
2
MV
0.154
0.144
0.004
0.004
Bacteria1.0Bacteroidetes0.97Flavobacteria0.65Flavobacteriales0.65Cryomorphaceae0.27Fluviicola0.22
501
2
MV
0.091
0.105
0.347
0.206
Bacteria0.98Firmicutes0.84Clostridia0.84Clostridiales0.84Lachnospiraceae0.76Syntrophococcus0.64
534
2
MV
0.309
0.499
1.402
0.483
Bacteria1.0Firmicutes0.96Clostridia0.95Clostridiales0.95Lachnospiraceae0.93Lachnobacterium0.29
561
2
MV
0.380
0.205
0.073
0.078
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
654
2
MV
0.077
0.076
0.004
0.009
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
1156
2
ME
0.072
0.071
0.000
0.000
Bacteria1.0Firmicutes1.0Clostridia1.0Clostridiales1.0Ruminococcaceae1.0Acetanaerobacterium0.66
1732
2
ME
0.045
0.031
0.000
0.000
Bacteria1.0Firmicutes0.76Clostridia0.72Clostridiales0.71Incertae Sedis XIII0.29Anaerovorax0.29 10 Colonic Microbiota Changes Induced by Diarrhea Colonic Microbiota Changes Induced by Diarrhea TU
Score#
Method*
time-
point 2
±SD
time-
point 3
±SD
Taxonomic classification+
61
2
MV
0.412
0.379
0.028
0.044
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
59
2
ME
0.019
0.016
0.000
0.000
Bacteria1.0Firmicutes0.95Clostridia0.95Clostridiales0.95Ruminococcaceae0.5Faecalibacterium0.23
83
2
EV
0.127
0.170
0.000
0.000
Bacteria1.0Firmicutes0.84Clostridia0.83Clostridiales0.83Ruminococcaceae0.72Faecalibacterium0.44
34
2
EV
0.081
0.097
0.000
0.000
Bacteria1.0Firmicutes0.68Clostridia0.66Clostridiales0.63Ruminococcaceae0.54Faecalibacterium0.38
02
2
MV
0.071
0.071
0.001
0.002
Bacteria1.0Firmicutes0.61Clostridia0.6Clostridiales0.6Peptococcaceae0.51Peptococcus0.51 re#
Method*
Mean %
time-
point 2
±SD
Mean %
time-
point 3
±SD
Taxonomic classification+
MV
0.412
0.379
0.028
0.044
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
ME
0.019
0.016
0.000
0.000
Bacteria1.0Firmicutes0.95Clostridia0.95Clostridiales0.95Ruminococcaceae0.5Faecalibacterium0.23
EV
0.127
0.170
0.000
0.000
Bacteria1.0Firmicutes0.84Clostridia0.83Clostridiales0.83Ruminococcaceae0.72Faecalibacterium0.44
EV
0.081
0.097
0.000
0.000
Bacteria1.0Firmicutes0.68Clostridia0.66Clostridiales0.63Ruminococcaceae0.54Faecalibacterium0.38
MV
0.071
0.071
0.001
0.002
Bacteria1.0Firmicutes0.61Clostridia0.6Clostridiales0.6Peptococcaceae0.51Peptococcus0.51 including F. prausnitzii (e.g. OTU_206) experienced a relative
abundance decrease in mucosal specimens (Fig. 8, Table. 3). Discussion The width of lines correlates with the number of individuals in
whom an OTU was assigned to a specific pattern. Size of nodes correlates with the mean relative abundance change comparing pre-diarrhea to
diarrhea samples. OTUs are colored according to their phylum membership and named according to the taxonomic rank conferred by the RDP
classifier (80% identity threshold). M denotes significantly changed according to Metastats analysis (P,0.05); E denotes significantly changed
according to edgeR analysis (P,0.05). OTUs identified by both biostatistical methods are highlighted with a bold outline. Note the increase of various
Proteobacteria, including opportunistic pathogens (e.g. Pseudomonas, Acinetobacter, Arcobacter), and also an increase of Firmicutes due to diarrhea
(right); Bacteroidetes generally occurred together with Faecalibacterium, which was mirrored by an increase in stools. Note the skew of edgeR-
identified OTUs towards the decreasing pattern (left) and of Metastats identified OTUs towards the increasing pattern (right). doi:10.1371/journal.pone.0055817.g008 method. It is important to note that all three methods identified
several low abundant significantly changing taxa (i.e. OTUs with
about 10 reads representing just about 0.05% of the whole
community, given that about 20,000 reads were generated per
sample). But reliable detection of these low abundant taxa is highly
dependent on the sampling effort (sequencing depth), which can
hardly reach completeness given the large number of microbes
(about 1013–1014) colonizing our gut [38]. Thus some of the
identified low-abundant OTUs might represent artifacts because
of sampling bias. Removal of these low abundant OTUs (e.g. with
#10 reads) prior to statistical assessment would be a reasonable
strategy that might increase accuracy of analysis but could also
lead to loss of relevant information [57–61]. wherein certain groups of bacteria are specifically depleted [55]. Our study indicates that reduced richness per se does not
necessarily reflect or lead to pathology but is in turn a consequence
of the diarrhea prevalent in many GI diseases. Microbial communities are complex adaptive systems, in which
patterns at higher levels emerge from localized interactions and
selection processes acting at lower levels [56]. To understand the
basic reaction patterns induced by osmotic diarrhea, we assessed
the relative abundance change of individual phylotypes. To
account for the high level of inter-individual variation of the GI
microbiota with our relatively small sample size, we vigorously
tested our data set with different approaches. Discussion Importantly, diarrhea led to an equalization of the mucosal
microbiotas, which clustered together in the PCA and showed an
increased phylotype overlap at time-point 3. We induced diarrhea
with PEG, a mixture of non-absorbable, non-metabolizable
polymers acting as a pure osmotic agent ‘‘binding’’ water in the
gut lumen [52]. This led to ‘‘wash-out’’ and decreased phylotype
richness in both habitats as described by others [53,54]. In various
inflammatory and diarrheal GI diseases, reduced phylotype
richness has been reported, including AAD, C. difficile colitis, viral
enterocolitis, IBD and IBS [5,7–10,20,55]. Reduced richness can
be subverted by (opportunistic) pathogens that colonize niches
otherwise occupied by the endogenous microbiota [50]. In that
regard antibiotic treatment represents a paradigm condition PLOS ONE | www.plosone.org February 2013 | Volume 8 | Issue 2 | e55817 February 2013 | Volume 8 | Issue 2 | e55817 11 Colonic Microbiota Changes Induced by Diarrhea Figure 8. Changing mucosal OTUs visualized with an association network (Viz). OTUs (distance = 0.03) are shown with their respective
abundance change comparing pre-diarrhea (time-point 2) with diarrhea (time-point 3) samples. Only OTUs are displayed that were assigned to a
respective reaction pattern in at least two individuals (corresponding to thin lines). The width of lines correlates with the number of individuals in
whom an OTU was assigned to a specific pattern. Size of nodes correlates with the mean relative abundance change comparing pre-diarrhea to
diarrhea samples. OTUs are colored according to their phylum membership and named according to the taxonomic rank conferred by the RDP
classifier (80% identity threshold). M denotes significantly changed according to Metastats analysis (P,0.05); E denotes significantly changed
according to edgeR analysis (P,0.05). OTUs identified by both biostatistical methods are highlighted with a bold outline. Note the increase of various
Proteobacteria, including opportunistic pathogens (e.g. Pseudomonas, Acinetobacter, Arcobacter), and also an increase of Firmicutes due to diarrhea
(right); Bacteroidetes generally occurred together with Faecalibacterium, which was mirrored by an increase in stools. Note the skew of edgeR-
identified OTUs towards the decreasing pattern (left) and of Metastats identified OTUs towards the increasing pattern (right). doi:10.1371/journal.pone.0055817.g008 Figure 8. Changing mucosal OTUs visualized with an association network (Viz). OTUs (distance = 0.03) are shown with their respective
abundance change comparing pre-diarrhea (time-point 2) with diarrhea (time-point 3) samples. Only OTUs are displayed that were assigned to a
respective reaction pattern in at least two individuals (corresponding to thin lines). Discussion These measures
included two established biostatistical tools (Metastats and edgeR)
and a scoring system with graphical representation of the results
(Viz). These analyses revealed several significantly changing
phylotypes but showed reduced congruence between methods. Interestingly, the majority of phylotypes detected with Viz (in at
least two individuals simultaneously) were confirmed by at least
one biostatistical method showing the usefulness of the scoring To overcome the incongruence of the applied methods, we
narrowed the findings down to phylotypes that were detected by at
least two different methods simultaneously. In this way, we
identified several Bacteroidetes and Firmicutes experiencing a relative
increase or decrease in stools in response to diarrhea. Colonic Microbiota Changes Induced by Diarrhea OTU
Score#
Method*
Mean % time-
point 2
±SD
Mean % time-
point 3
±SD
Taxonomic classification+
1391
2
ME
0.006
0.004
0.000
0.000
Bacteria1.0Firmicutes0.99Bacilli0.99Lactobacillales0.99Leuconostocaceae0.93Weissella0.93
1477
2
MV
0.030
0.025
0.080
0.013
Bacteria1.0Firmicutes0.98Bacilli0.97Lactobacillales0.97Leuconostocaceae0.82Weissella0.81
1497
2
MV
0.020
0.019
0.080
0.033
Bacteria1.0Proteobacteria1.0Gammaproteobacteria1.0Pseudomonadales0.9Moraxellaceae0.9Acinetobacter0.9
1690
2
MV
0.034
0.043
0.120
0.057
Bacteria1.0Proteobacteria1.0Gammaproteobacteria1.0Enterobacteriales1.0Enterobacteriaceae1.0Raoultella0.28
1834
2
MV
0.084
0.066
0.247
0.119
Bacteria1.0TM70.53TM7_genera_incertae_sedis0.53
1993
2
MV
0.033
0.038
0.109
0.041
Bacteria1.0Bacteroidetes1.0Flavobacteria1.0Flavobacteriales1.0Flavobacteriaceae1.0Chryseobacterium0.79
2062
2
ME
0.008
0.006
0.000
0.000
Bacteria1.0Bacteroidetes0.97Bacteroidetes0.94Bacteroidales0.94Bacteroidaceae0.93Bacteroides0.93
2156
2
ME
0.022
0.006
0.001
0.002
Bacteria1.0Bacteroidetes0.99Bacteroidetes0.98Bacteroidales0.98Bacteroidaceae0.97Bacteroides0.97
2229
2
MV
0.025
0.021
0.087
0.018
Bacteria1.0Firmicutes0.98Bacilli0.97Lactobacillales0.97Leuconostocaceae0.94Weissella0.94
6041
2
ME
0.008
0.004
0.000
0.000
Bacteria1.0Proteobacteria0.98Betaproteobacteria0.97Burkholderiales0.9Incertae sedis 50.48Leptothrix0.26 ing relative abundance. It is noteworthy that we observed a
significantly increased fraction of Proteobacteria experiencing a rise
in relative abundance in the mucosa specimens due to diarrhea. Among them were several opportunistic pathogens including
pseudomonads like Pseudomonas and Acinetobacter (e.g. OTU_1341,
OTU_101) as well as the e-proteobacterial taxon Arcobacter (e.g. OTU_596). Several lactic-acid bacteria (e.g. Lactococcus) also
increased on the mucosa during diarrhea, and may therefore
represent interesting candidates for probiotics in the setting of
diarrheal disease [62]. Interestingly, we also observed a relative
increase in taxa matching to Faecalibacterium including F. prausnitzii
(e.g. OTU_206) in stools, which was mirrored by a simultaneous
decrease in the mucosa specimens. This observation warrants
further investigation since this anti-inflammatory GI bacterium is
reported to be decreased in IBD [63,64]. #Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods. *(M) Metastats, (E) edgeR, (V) scoring & visualization. +Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score. doi:10.1371/journal.pone.0055817.t003 The finding that Proteobacteria increase in response to diarrhea
has been reported in several diarrheal and inflammatory GI
diseases including IBD [8,11,12,65–68]. Proteobacteria are usually
considered to be generalists able to colonize various habitats with
diverse resources. For example we found that OTU_1341
matching to Pseudomonas putida significantly increased due to
diarrhea; this pathogen shows genomic adaptation to diverse
environments but can also cause severe diseases in humans [69–
72]. Since diarrhea decreases richness, as was reflected by a
significant drop in several Bacteroidetes and Firmicutes in our study, it
is reasonable to speculate that Proteobacteria can occupy and
repopulate these depleted niches more efficiently. It so seems that
diarrhea per se, irrespective of its etiology, can select for this special
community type with increased Proteobacteria. Discussion On the
mucosa Bacteroidetes showed a significant association with decreas- February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org February 2013 | Volume 8 | Issue 2 | e55817 12 Colonic Microbiota Changes Induced by Diarrhea OTU
Score#
Method*
point 2
±SD
point 3
±SD
Taxonomic classification+
1341
3
MEV
0.000
0.000
0.062
0.035
Bacteria1.0Proteobacteria1.0Gammaproteobacteria1.0Pseudomonadales0.99Pseudomonadaceae0.99Pseudomonas0.67
11
2
MV
2.292
1.527
4.509
0.841
Bacteria1.0Firmicutes0.99Bacilli0.99Lactobacillales0.99Streptococcaceae0.98Lactococcus0.9
13
2
EV
7.117
10.403
0.214
0.319
Bacteria1.0Bacteroidetes1.0Bacteroidetes0.99Bacteroidales0.99Bacteroidaceae0.99Bacteroides0.99
25
2
ME
0.034
0.023
0.000
0.000
Bacteria1.0Firmicutes0.98Clostridia0.98Clostridiales0.98Lachnospiraceae0.96Dorea0.26
27
2
EV
1.720
2.409
0.039
0.061
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Bacteroidaceae1.0Bacteroides1.0
42
2
EV
0.347
0.472
0.019
0.033
Bacteria1.0Firmicutes1.0Clostridia1.0Clostridiales1.0Ruminococcaceae1.0Faecalibacterium1.0
44
2
MV
0.187
0.112
1.069
0.706
Bacteria1.0Proteobacteria1.0Gammaproteobacteria1.0Pseudomonadales0.93Moraxellaceae0.75Acinetobacter0.73
48
2
MV
0.169
0.084
0.051
0.058
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Bacteroidaceae1.0Bacteroides1.0
51
2
MV
0.076
0.043
0.147
0.020
Bacteria1.0Firmicutes0.98Bacilli0.98Lactobacillales0.98Leuconostocaceae0.97Weissella0.97
85
2
EV
0.129
0.116
0.000
0.000
Bacteria1.0Bacteroidetes0.97Bacteroidetes0.97Bacteroidales0.97Bacteroidaceae0.95Bacteroides0.95
89
2
EV
0.243
0.258
0.000
0.000
Bacteria1.0Firmicutes0.98Clostridia0.98Clostridiales0.98Lachnospiraceae0.9Pseudobutyrivibrio0.36
94
2
EV
1.489
1.443
0.040
0.069
Bacteria1.0Bacteroidetes0.99Bacteroidetes0.99Bacteroidales0.99Bacteroidaceae0.99Bacteroides0.99
101
2
MV
0.023
0.030
0.090
0.018
Bacteria1.0Proteobacteria1.0Gammaproteobacteria.0Pseudomonadales0.93Moraxellaceae0.9Acinetobacter0.9
115
2
MV
0.857
0.548
1.711
0.161
Bacteria1.0Firmicutes0.99Bacilli0.99Lactobacillales0.99Streptococcaceae0.98Lactococcus0.98
145
2
EV
1.222
2.022
0.004
0.006
Bacteria1.0Bacteroidetes0.97Bacteroidetes0.97Bacteroidales0.97Bacteroidaceae0.97Bacteroides0.97
150
2
EV
0.385
0.348
0.000
0.000
Bacteria1.0Bacteroidetes0.99Bacteroidetes0.98Bacteroidales0.98Bacteroidaceae0.95Bacteroides0.95
158
2
MV
0.131
0.105
0.354
0.168
Bacteria1.0Proteobacteria1.0Betaproteobacteria1.0Burkholderiales1.0Comamonadaceae0.99Acidovorax0.88
177
2
EV
1.876
2.951
0.000
0.000
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Porphyromonadaceae1.0Parabacteroides1.0
194
2
EV
0.225
0.276
0.000
0.000
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Rikenellaceae1.0Alistipes1.0
212
2
MV
0.717
0.490
1.415
0.189
Bacteria1.0Firmicutes1.0Bacilli1.0Lactobacillales1.0Streptococcaceae1.0Streptococcus1.0
243
2
EV
0.101
0.097
0.000
0.000
Bacteria1.0Firmicutes0.7Clostridia0.68Clostridiales0.67Ruminococcaceae0.28Faecalibacterium0.23
284
2
MV
0.025
0.011
0.098
0.016
Bacteria1.0Proteobacteria1.0Gammaproteobacteria0.98Pseudomonadales0.9Moraxellaceae0.66Acinetobacter0.65
596
2
ME
0.000
0.000
0.022
0.019
Bacteria1.0Proteobacteria1.0Epsilonproteobacteria1.0Campylobacterales1.0Campylobacteraceae1.0Arcobacter1.0
666
2
EV
0.090
0.084
0.000
0.000
Bacteria1.0Firmicutes0.97Clostridia0.96Clostridiales0.96Lachnospiraceae0.94Dorea0.35
681
2
MV
0.094
0.044
0.163
0.025
Bacteria1.0Firmicutes0.98Bacilli0.98Lactobacillales0.97Streptococcaceae0.97Lactococcus0.92
693
2
MV
0.052
0.060
0.184
0.020
Bacteria1.0Proteobacteria1.0Epsilonproteobacteria1.0Campylobacterales0.96Campylobacteraceae0.94Sulfurospirillum0.91
791
2
MV
0.027
0.014
0.082
0.031
Bacteria1.0Firmicutes0.98Bacilli0.97Lactobacillales0.97Streptococcaceae0.97Lactococcus0.97
828
2
MV
0.052
0.033
0.120
0.009
Bacteria1.0Firmicutes0.97Bacilli0.96Lactobacillales0.96Streptococcaceae0.94Lactococcus0.94
901
2
ME
0.018
0.012
0.000
0.000
Bacteria1.0Proteobacteria0.95Betaproteobacteria0.86Burkholderiales0.65Oxalobacteraceae0.4Naxibacter0.34
902
2
ME
0.014
0.006
0.000
0.000
Bacteria1.0Proteobacteria1.0Betaproteobacteria1.0Burkholderiales1.0Incertae sedis 50.87Pelomonas0.82
911
2
ME
0.029
0.014
0.000
0.000
Bacteria1.0Bacteroidetes1.0Bacteroidetes1.0Bacteroidales1.0Bacteroidaceae1.0Bacteroides1.0
953
2
MV
0.038
0.023
0.118
0.066
Bacteria1.0Proteobacteria1.0Betaproteobacteria1.0Burkholderiales1.0Comamonadaceae1.0Acidovorax0.82
987
2
ME
0.014
0.010
0.000
0.000
Bacteria1.0Firmicutes1.0Clostridia1.0Clostridiales1.0Ruminococcaceae1.0Faecalibacterium1.0
1057
2
EV
0.064
0.064
0.000
0.000
Bacteria1.0Bacteroidetes0.98Bacteroidetes0.98Bacteroidales0.98Bacteroidaceae0.98Bacteroides0.98
1257
2
EV
0.128
0.163
0.000
0.000
Bacteria1.0Firmicutes0.93Clostridia0.93Clostridiales0.93Ruminococcaceae0.91Subdoligranulum0.61 February 2013 | Volume 8 | Issue 2 | e55817 13 Colonic Microbiota Changes Induced by Diarrhea Colonic Microbiota Changes Induced by Diarrhea It is therefore
important to note that these changes may not be specific for
diseases like IBD but may represent an epiphenomenon of the
wash-out effect due to diarrhea. Moreover, the efficient coloniza-
tion capacity of Proteobacteria might explain the effectiveness of
strains like E. coli Nissle 1917 used for the therapy of IBD [73]. It is
important to note that we assessed the relative abundances of taxa
within samples and their relative abundance changes comparing
different samples, which does not necessarily translate into
absolute changes of taxa, which would require further assessment
of specimens (e.g. by means of qPCR). #Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods. *(M) Metastats, (E) edgeR, (V) scoring & visualization. +Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score. doi:10.1371/journal.pone.0055817.t003 Capturing the true microbial representation within a sample by
cultivation-independent
techniques
is
hampered
by
various
technical challenges. Specimen handling, DNA extraction, PCR
amplification and sequencing altogether are causes of bias
[57,59,74–77]. For instance, we compared stool and biopsy
samples, which display considerable differences in their composi-
tion requiring individual protocols for efficient cell lysis and DNA
release
from
samples. To
account
for
the
‘‘rich’’
matrix
composition of stools, we utilized a recommended boiling step
prior to DNA extraction from feces, which was not used for
biopsies. Several reports emphasized the influence of DNA
extraction methods on the outcome of PCR-based microbial
community surveys [74–77]. Thus we cannot exclude that the
different extraction protocols used in our study influenced our
findings. In addition to specimen work-up, template concentra-
tion, primer sequences and PCR conditions including PCR cycle
numbers
also
influence
the
assessed
community
structure
[57,59,75,78]. The different sample types (i.e. stools and biopsies)
in our study displayed different loads of 16S-targets requiring
sample-type specific adjustment of PCR cycle numbers (22 and 35
cycles for stool and mucosa samples, respectively) to prevent PCR
substrate exhaustion and to approach a similar end-point of PCR
within the linear range of amplification. Increased PCR cycles are
reported to skew diversity measures leading to an underestimation
of diversity present in the sample [79]. Since we noted a trend PLOS ONE | www.plosone.org February 2013 | Volume 8 | Issue 2 | e55817 14 Colonic Microbiota Changes Induced by Diarrhea Table S1
Oligonucleotide primers used in this study. Table S16
Changing mucosal phylotypes identified by
Viz. (XLSX) Colonic Microbiota Changes Induced by Diarrhea (XLS) Table S7
Stable phylotypes. (XLS) Table
S8
Significantly
changing
taxa
between
pre-
diarrhea and diarrhea stool samples. (DOCX) Table S9
Significantly changing taxa between diarrhea
and post-diarrhea stool samples. (DOCX) Table S10
Significantly changing taxa between pre-
diarrhea and diarrhea mucosa samples. (DOCX) Table S11
Significantly changing stool phylotypes iden-
tified by Metastats. (XLSX) Table S12
Significantly changing stool phylotypes iden-
tified by edgeR. (XLS) Table S13
Changing stool phylotypes identified by Viz. (XLSX) In
summary,
our
study
is
proof
of
the
principle
that
manipulation of basic functions of the human GI tract enables
the detection of relevant microbial community changes and
highlights the importance of such studies investigating basic
(patho-)physiological effects on the GI microbiota. Table S14
Significantly changing mucosal phylotypes
identified by Metastats. (XLSX) Table S15
Significantly changing mucosal phylotypes
identified by edgeR. (XLS) Acknowledgments Figure S2
Significantly changing stool phylotypes visu-
alized with an association network. This supplemental
figure corresponds to Fig. 7 in the main text. The respective OUT
numbers are indicated. (PNG) We thank Bettina Halwachs and Johann Ho¨ftberger for chimera removal
and denoising of the sequences respectively. We are grateful to Eugenia
Lamont, B.A., for editorial assistance and to Andrea Mahlknecht for help
with the diet protocol. We thank Bettina Halwachs and Johann Ho¨ftberger for chimera removal
and denoising of the sequences respectively. We are grateful to Eugenia
Lamont, B.A., for editorial assistance and to Andrea Mahlknecht for help
with the diet protocol. Colonic Microbiota Changes Induced by Diarrhea (DOCX) towards an increased richness in the mucosa samples compared to
stools, albeit not statistically significant, we speculate that the PCR
cycle trade-off in our study might have led to underestimation of
richness in the mucosa samples. The challenge to optimize the
technological accuracy of human microbiome studies poses a
major challenge. Inconsistencies may remain even if up-to-date
technology with high accuracy combined with a stringent data
analysis as in our study are used [57,80]. Table S2
Read and OTU numbers. (XLSX) Table S3
Richness, diversity and evenness. (XLS) Table S4
Most abundant stool phylotypes. (DOCX) Our longitudinal study has revealed several important findings
regarding the human GI microbiota and its response to diarrhea. (I) We found that stools and the mucosa represent strikingly
different habitats with a different community structure and a
different response to stressors like diarrhea. For this reason, studies
investigating changes in the GI microbiota in association with
specific diseases need to consider that the fecal microbiota does not
readily reflect the mucosal community. (II) The finding that
Proteobacteria relatively increase in response to diarrhea on the
mucosa is suggestive of a basic principle of the community in this
niche regardless of the cause of diarrhea. When the mucosa is
severely affected as in IBD, nutrients like iron derived from blood
are available in excess for these efficient colonizers [81]. In turn
these bacteria can utilize these resources, i.e. they have developed
siderophore
uptake
systems
for iron
capture,
and so can
experience a growth advantage [12,67,82]. This phenomenon
might then lead to the persistent community change (dysbiosis)
noted in IBD, which in turn perpetuates chronic inflammation due
to the pro-inflammatory behavior of these bacteria. (III) Our
findings show definite changes of the GI microbiota in response to
PEG treatment, which is used for bowel cleansing prior to
endoscopy. Studies using colonoscopy samples for microbiota
analysis need to bear this in mind. (IV) We have shown the
usefulness of small-scale longitudinal clinical studies to find
relevant microbial community patterns of variation, if data are
assessed stringently. In this regard our newly described scoring
approach with visualization (Viz) is a valuable tool; since it readily
illustrates the reaction of the microbiota as a whole, patterns can
be caught visually by the investigator. Table S5
Most abundant mucosal phylotypes. (DOCX) Table S6
Effect of PEG on stool frequency and stool
consistency in study subjects. (DOCX) Table S7
Stable phylotypes. Supporting Information Figure S1
Rarefaction analysis of pooled stools samples
from all 4 time-points. A reduced richness is seen during
diarrhea (T3) and a sustained reduced diversity is evident one
week after diarrhea (T4). The dotted line indicates 6 SEM. (PNG) References Genome Res 13: 2498–2504. y
g
8. Spiller R, Garsed K (2009) Postinfectious Irritable Bowel Syndrome. Gastroenterology 136: 1979–1988. 38. Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and
evolutionary perspective on human-microbe mutualism and disease. Nature
449: 811–818. gy
9. Young VB, Schmidt TM (2004) Antibiotic-associated diarrhea accompanied by
large-scale alterations in the composition of the fecal microbiota. J Clin
Microbiol 42: 1203–1206. 39. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, et al. (2011)
Enterotypes of the human gut microbiome. Nature 474: 174–180. 10. Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, et al. (2008)
Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-
associated diarrhea. J Infect Dis 197: 435–438. 40. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, et al. (2011) Linking
Long-Term Dietary Patterns with Gut Microbial Enterotypes. Science 333: 105–
108. 11. Cremon C, Carini G, De Giorgio R, Stanghellini V, Corinaldesi R, et al. (2010)
Intestinal dysbiosis in irritable bowel syndrome: etiological factor or epiphe-
nomenon? Expert Rev Mol Diagn 10: 389–393. 41. Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, et al. (2004) Reduction
in diversity of the colonic mucosa associated bacterial microflora in patients with
active inflammatory bowel disease. Gut 53: 685–693. 12. Packey CD, Sartor RB (2009) Commensal bacteria, traditional and opportu-
nistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis 22: 292–301. 42. Durban A, Abellan JJ, Jimenez-Hernandez N, Ponce M, Ponce J, et al. (2011)
Assessing Gut Microbial Diversity from Feces and Rectal Mucosa. Microb Ecol
61: 123–133. p
. Read NW (1986) Diarrhee Motrice. Clin Gastroenterol 15: 657–68
G i l
C S
A
CA P
i l 13. Read NW (1986) Diarrhee Motrice. Clin Gastroenterol 15: 657–686. 43. Macfarlane S (2008) Microbial biofilm communities in the gastrointestinal tract. J Clin Gastroenterol 42 Suppl 3 Pt 1: S142–3. 14. Guirl MJ, Ho¨genauer C, Santa Ana CA, Porter JL, Little KH, et al. (2003)
Rapid intestinal transit as a primary cause of severe chronic diarrhea in patients
with amyloidosis. Am J Gastroenterol 98: 2219–2225. 44. Macfarlane S, Dillon JF (2007) Microbial biofilms in the human gastrointestinal
tract. J Appl Microbiol 102: 1187–96. 15. Schiller LR, Hogan RB, Morawski SG, Santa Ana CA, Bern MJ, et al. References 1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007)
The Human Microbiome Project. Nature 449: 804–810. 31. R Development Core Team (2011) R: A language and environment for
statistical computing. Vienna, Austria: R Foundation for Statistical Computing. j
2. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, et al. (2009)
Bacterial Community Variation in Human Body Habitats Across Space and
Time. Science 326: 1694–1697. 32. Chao A (1984) Nonparametric-Estimation of the Number of Classes in A
Population. Scand J Stat 11: 265–270. 33. Kindt R, Coe R (2005) Tree diversity analysis. A manual and software for
common statistical methods for ecological and biodiversity studies. Nairobi,
Kenya: World Agroforestry Centre. 3. Turnbaugh PJ, Gordon JI (2009) The core gut microbiome, energy balance and
obesity. J Physiol (Lond) 587: 4153–4158. y J
y
(
)
4. Chow J, Lee SM, Shen Y, Khosravi A, Mazmanian SK (2010) Host-Bacterial
Symbiosis in Health and Disease. Adv Immunol 107: 243–274. y
g
y
34. White JR, Nagarajan N, Pop M (2009) Statistical Methods for Detecting
Differentially Abundant Features in Clinical Metagenomic Samples. PLoS
Comput Biol 5: e1000352. 5. Frank DN, Amand ALS, Feldman RA, Boedeker EC, Harpaz N, et al. (2007)
Molecular-phylogenetic characterization of microbial community imbalances in 5. Frank DN, Amand ALS, Feldman RA, Boedeker EC, Harpaz N, et al. (2007)
Molecular-phylogenetic characterization of microbial community imbalances in
human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104: 13780–
13785. 35. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor
package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140. p y g
y
human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104: 13780–
13785. 6. Peterson DA, Frank DN, Pace NR, Gordon JI (2008) Metagenomic approaches
for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe
3: 417–427. 36. Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate - A
Practical and Powerful Approach to Multiple Testing. J R Stat Soc Series B Stat
Methodol 57: 289–300. 7. Codling C, O’Mahony L, Shanahan F, Quigley EMM, Marchesi JR (2010) A
Molecular Analysis of Fecal and Mucosal Bacterial Communities in Irritable
Bowel Syndrome. Dig Dis Sci 55: 392–397. 37. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A
software environment for integrated models of biomolecular interaction
networks. References (1987)
Studies of the prevalence and significance of radiolabeled bile acid malabsorp-
tion in a group of patients with idiopathic chronic diarrhea. Gastroenterology
92: 151–160. 45. Johansson MEV, Larsson JMH, Hansson GC (2011) The two mucus layers of
colon are organized by the MUC2 mucin, whereas the outer layer is a legislator
of host-microbial interactions. Proc Natl Acad Sci U S A 108: 4659–4665. 46. Walker AW, Duncan SH, Harmsen HJM, Holtrop G, Welling GW, et al. (2008)
The species composition of the human intestinal microbiota differs between
particle-associated and liquid phase communities. Environ Microbiol 10: 3275–
3283. 16. Fine KD, Fordtran JS (1992) The Effect of Diarrhea on Fecal Fat Excretion. Gastroenterology 102: 1936–1939. gy
17. Sonnenburg JL, Angenent LT, Gordon JI (2004) Getting a grip on things: how
do communities of bacterial symbionts become established in our intestine? Nature Immunol 5: 569–573. 47. Lee KW, Park JY, Jeong HR, Heo HJ, Han NS, et al. (2012) Probiotic
properties of Weissella strains isolated from human faeces. Anaerobe 18: 96–
102. 18. Hammer HF, Santaana CA, Schiller LR, Fordtran JS (1989) Studies of Osmotic
Diarrhea Induced in Normal Subjects by Ingestion of Polyethylene-Glycol and
Lactulose. J Clin Invest 84: 1056–1062. 48. Bounaix MS, Robert H, Gabriel V, Morel S, Remaud-Simeon M, et al. (2010)
Characterization of dextran-producing Weissella strains isolated from sour-
doughs and evidence of constitutive dextransucrase expression. FEMS Microbiol
Lett 311: 18–26. 19. Lewis SJ, Heaton KW (1997) Stool form scale as a useful guide to intestinal
transit time. Scand J Gastroenterol 32: 920–924. 20. McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, et al. (2008) The
macaque gut microbiome in health, lentiviral infection, and chronic enteroco-
litis. PLoS Pathog 4: e20. 49. Kennedy TA, Naeem S, Howe KM, Knops JMH, Tilman D, et al. (2002)
Biodiversity as a barrier to ecological invasion. Nature 417: 636–638. 50. Britton RA, Young VB (2012) Interaction between the intestinal microbiota and
host in Clostridium difficile colonization resistance. Trends Microbiol 20: 313–9. 21. Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H (2005) Spatial
organization and composition of the mucosal flora in patients with inflammatory
bowel disease. J Clin Microbiol 43: 3380–3389. 51. Nava GM, Friedrichsen HJ, Stappenbeck TS (2011) Spatial organization of
intestinal microbiota in the mouse ascending colon. ISME J 5: 627–638. 22. References Liu ZZ, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short
pyrosequencing reads suffice for accurate microbial community analysis. Nucleic
Acids Res 35: e120. 52. Mai V, Greenwald B, Morris JG, Raufman JP, Stine OC (2006) Effect of bowel
preparation and colonoscopy on post-procedure intestinal microbiota compo-
sition. Gut 55: 1822–1823. 23. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate
determination of microbial diversity from 454 pyrosequencing data. Nat
Methods 6: 639–641. 53. Bouhnik Y, Neut C, Raskine L, Michel C, Riottot M, et al. (2004) Prospective,
randomized, parallel-group trial to evaluate the effects of lactulose and
polyethylene glycol-4000 on colonic flora in chronic idiopathic constipation. Aliment Pharmacol Ther 19: 889–899. 24. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing Noise
From Pyrosequenced Amplicons. BMC Bioinformatics 12: 38. 54. Harrell L, Wang Y, Antonopoulos D, Young V, Lichtenstein L, et al. (2012)
Standard colonic lavage alters the natural state of mucosal-associated microbiota
in the human colon. PLoS One 7: e32545. y
q
p
25. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and
quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143. 26. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME
improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194–
2200. 55. Dethlefsen L, Relman DA (2011) Incomplete recovery and individualized
responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 108: 4554–4561. 27. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal
Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141–D145. 56. Levin SA (1998) Ecosystems and the Biosphere as Complex Adaptive Systems. Ecosystems 1: 431–436. 57. Schloss PD, Gevers D, Westcott SL (2011) Reducing the Effects of PCR
Amplification and Sequencing Artifacts on 16S rRNA-Based Studies. PLoS
ONE 6: e27310. 28. Stocker G, Snajder R, Rainer J, Trajanoski S, Gorkiewicz G et al. (2010)
SnoWMAn: High-throughput phylotyping, analysis and comparison of micro-
bial communities. Proceedings of the 110th ASM General Meeting 23-5-2010. 58. Bakker MG, Tu ZJ, Bradeen JM, Kinkel LL (2012) Implications of
Pyrosequencing Error Correction for Biological Data Interpretation. PLoS
ONE 7: e44357. g
g
29. Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA
alignments. Bioinformatics 25: 1335–1337. 30. Author Contributions Figure S3
Significantly changing mucosa phylotypes
visualized with an association network. This supplemental
figure corresponds to Fig. 8 in the main text. The respective OUT
numbers are indicated. (PNG) Conceived and designed the experiments: GG TH CH. Performed the
experiments: GG TH CH CG ST. Analyzed the data: GGT GG GS SL. Contributed reagents/materials/analysis tools: GG GGT CH CG ST. Wrote the paper: GG GGT CH. Conceived and designed the experiments: GG TH CH. Performed the
experiments: GG TH CH CG ST. Analyzed the data: GGT GG GS SL. Contributed reagents/materials/analysis tools: GG GGT CH CG ST. Wrote the paper: GG GGT CH. PLOS ONE | www.plosone.org February 2013 | Volume 8 | Issue 2 | e55817 15 Colonic Microbiota Changes Induced by Diarrhea Colonic Microbiota Changes Induced by Diarrhea Colonic Microbiota Changes Induced by Diarrhea 60. Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, et al. (2011) Reproducibility and
quantitation of amplicon sequencing-based detection. ISME J 5: 1303–13. 72. Wu XA, Monchy S, Taghavi S, Zhu W, Ramos J, et al. (2011) Comparative
genomics and functional analysis of niche-specific adaptation in Pseudomonas
putida. FEMS Microbiol Rev 35: 299–323. 61. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, et al. (2012)
Composition of the adult digestive tract bacterial microbiome based on seven
mouth surfaces, tonsils, throat and stool samples. Genome Biol 3: R42. p
73. Kruis W, Fric P, Pokrotnieks J, Lukas M, Fixa B, et al. (2004) Maintaining
remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as
effective as with standard mesalazine. Gut 53: 1617–1623. p
62. Sartor RB (2004) Therapeutic manipulation of the enteric microflora in
inflammatory bowel diseases: Antibiotics, probiotics, and prebiotics. Gastroen-
terology 126: 1620–1633. 74. Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ (2012) Evaluation of Methods
for the Extraction and Purification of DNA from the Human Microbiome. PLoS
ONE 7: e33865. 63. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, et al. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal
bacterium identified by gut microbiota analysis of Crohn disease patients. Proc
Natl Acad Sci U S A 105: 16731–16736. 75. Sergeant MJ, Constantinidou C, Cogan T, Penn CW, Pallen MJ (2012) High-
Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction
Procedure, Primer Length and Annealing Temperature. PLoS ONE 7: e38094. ´ 64. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier L, et al. (2009) Low
Counts of Faecalibacterium prausnitzii in Colitis Microbiota. Inflamm Bowel
Dis 15: 1183–1189. 76. O´ Cuı´v P, Aguirre de Ca´rcer D, Jones M, Klaassens ES, Worthley DL, et al. (2011) The effects from DNA extraction methods on the evaluation of microbial
diversity associated with human colonic tissue. Microb Ecol 61: 353–62. 65. Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A, et al. (2010)
Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce
Spontaneous and Maternally Transmitted Colitis. Cell Host Microbe 8: 292–
300. 77. Salonen A, Nikkila¨ J, Jalanka-Tuovinen J, Immonen O, Rajilic´-Stojanovic´ M, et
al. (2010) Comparative analysis of fecal DNA extraction methods with
phylogenetic microarray: effective recovery of bacterial and archaeal DNA
using mechanical cell lysis. J Microbiol Methods 81: 127–34. 66. References Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for
rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl
Environ Microbiol 73: 5261–5267. 59. Pinto AJ, Raskin L (2012) PCR Biases Distort Bacterial and Archaeal
Community Structure in Pyrosequencing Datasets. PLoS ONE 7: e43093. February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org 16 Colonic Microbiota Changes Induced by Diarrhea Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, et al. (2010) A
Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles
Vary With Inflammatory Bowel Disease Phenotypes. Gastroenterology 139:
1844–1854. 78. Gonzalez JM, Portillo MC, Belda-Ferre P, Mira A (2012) Amplification by PCR
Artificially Reduces the Proportion of the Rare Biosphere in Microbial
Communities. PLoS ONE 7: e29973. 79. Wu JY, Jiang XT, Jiang YX, Lu SY, Zou F, et al. (2010) Effects of polymerase,
template dilution and cycle number on PCR based 16 S rRNA diversity analysis
using the deep sequencing method BMC Microbiol 10: 255. 67. Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, et al. (2007)
Host-mediated inflammation disrupts the intestinal microbiota and promotes the
overgrowth of Enterobacteriaceae. Cell Host Microbe 2: 204. overgrowth of Enterobacteriaceae. Cell Host Microbe 2: 204. 80. Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, et al. (2012)
Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors
in Community Structure Estimates from PCR Amplicon Pyrosequencing. PLoS
ONE 7: e44224. 68. Papa E, Docktor M, Smillie C, Weber S, Preheim SP, et al. (2012) Non-Invasive
Mapping of the Gastrointestinal Microbiota Identifies Children with Inflamma-
tory Bowel Disease. PLoS One 7: e39242. y
69. Yang CH, Young TG, Peng MY, Weng MC (1996) Clinical spectrum of
Pseudomonas putida infection. J Formos Med Assoc 95: 754–761. 81. Foell D, Wittkowski H, Roth J (2009) Monitoring disease activity by stool
analyses: from occult blood to molecular markers of intestinal inflammation and
damage Gut 58: 859–68. 70. Yoshino Y, Kitazawa T, Kamimura M, Tatsuno K, Ota Y, et al. (2011)
Pseudomonas putida bacteremia in adult patients: five case reports and a review
of the literature. J Infect Chemother 17: 278–282. 82. Watts RE, Totsika M, Challinor VL, Mabbett AN, Ulett GC, et al. (2012)
Contribution of siderophore systems to growth and urinary tract colonization of
asymptomatic bacteriuria Escherichia coli. Infect Immun 80: 333–44. 71. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, et al. (2002) Complete
genome sequence and comparative analysis of the metabolically versatile
Pseudomonas putida KT2440. Environ Microbiol 4: 799–808. February 2013 | Volume 8 | Issue 2 | e55817 PLOS ONE | www.plosone.org PLOS ONE | www.plosone.org 17
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1 Effect of wind turbine response time on optimal
dynamic induction control of wind farms Wim Munters, Johan Meyers
Department of Mechanical Engineering, KU Leuven, Celestijnenlaan 300A, B3001 Leuven,
Belgium
E-mail: wim.munters@kuleuven.be, johan.meyers@kuleuven.be Wim Munters, Johan Meyers
Department of Mechanical Engineering, KU Leuven, Celestijnenlaan 300A, B3001 Leuven,
Belgium E-mail: wim.munters@kuleuven.be, johan.meyers@kuleuven.be Abstract. In this work, we extend recent research efforts on induction-based optimal control
in large-eddy simulations of wind farms in the turbulent atmospheric boundary layer. More
precisely, we investigate the effect of wind turbine response time to requested power setpoints on
achievable power gains. We do this by including a time-filtering of the thrust coefficient setpoints
in the optimal control framework. We consider simulation cases restricted to underinduction
compared to the Betz limit, as well as cases that also allow overinduction. Optimization results
show that, except for the most restrictive underinductive slow-response case, all cases still yield
increases in energy extraction in the order of 10% and more. 2. Methodology Simulations are performed using the OSP-Wind optimization platform, which has been
developed at KU Leuven over recent years [3, 5, 6]. We maximize wind farm-aggregated energy
extraction by minimizing the cost functional J in the following PDE-constrained optimization
problem: min
˜u,C′
T
J (˜u, C′
T ) =
Z T
0
Z
Ω
Nt
X
i=1
−f i · ˜u dx dt min
˜u,C′
T
J (˜u, C′
T ) =
Z T
0
Z
Ω
Nt
X
i=1
−f i · ˜u dx dt
N s.t. ∂˜u
∂t + ∇· (˜u˜u) = −∇(p∞+ ˜p) −∇· τ sgs +
Nt
X
i=1
f i + λ(˜up −˜u) s.t. ∂˜u
∂t + ∇· (˜u˜u) = −∇(p∞+ ˜p) −∇· τ sgs +
Nt
X
i=1
f i + λ(˜up −˜u)
in Ω× (0, T],
∇· ˜u = 0
in Ω× (0, T],
τ
d bC′
T,i
dt
= C′
T,i −bC′
T,i
for i = 1 . . . Nt in (0, T],
0 ≤C′
T,i ≤C
′max
T
for i = 1 . . . Nt. (1) ∇· ˜u = 0 in Ω× (0, T], for i = 1 . . . Nt in (0, T], for i = 1 . . . Nt. (1) ( )
The set of constraints for the optimization problem in (1) consists of the filtered Navier-Stokes
momentum and continuity equation (i.e. the state equations), a time-filter equation on the
control inputs C′
T,i, and associated bound constraints on the latter. The set of constraints for the optimization problem in (1) consists of the filtered Navier-Stokes
momentum and continuity equation (i.e. the state equations), a time-filter equation on the
control inputs C′
T,i, and associated bound constraints on the latter. T,i
The optimal control problem is solved in a reduced formulation, i.e. instead of treating
the Navier-Stokes state equations as a constraint, they are satisfied explicitly throughout the
optimization process by means of large-eddy simulations (LES). In these equations, the system
state variables ˜u and ˜p denote the filtered velocity and pressure field in the ABL. Furthermore,
∇p∞is the driving background pressure gradient, f i are the forces enacted on the flow by the Nt
wind turbines, and τ sgs is the subgrid-scale stress, for which a Smagorinsky model is employed. The Science of Making Torque from Wind (TORQUE 2016)
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Journal of Physics: Conference Series 753 (2016) 052007
doi:10.1088/1742-6596/753/5/052007 The Science of Making Torque from Wind (TORQUE 2016)
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doi:10.1088/1742-6596/753/5/052007 g
doi:10.1088/1742-6596/753/5/052007 doi:10.1088/1742-6596/753/5/052007 significant gains in energy extraction can still be obtained for smoothed time variations in wind
turbine dynamics. Moreover, in addition to reducing temporal fluctuations in turbine thrust
forces, we also study the effect of reducing their amplitudes by limiting the maximal thrust
coefficient. This work hence contributes towards actual implementation of cooperative wind-
farm controllers by quantifying the effects of adding increasingly more practical constraints to
the optimal control framework. The paper is structured as follows: Section 2 elaborates on the applied methodology for
optimal control of wind-farm boundary layers. Section 3 subsequently describes the cases
considered and their numerical setup. Section 4 discusses optimization results and their
dependence on wind turbine response time and maximal thrust coefficient. Section 5 finally
summarizes the main contributions of this work and provides suggestions for future research. 1. Introduction In large-scale wind farms, turbulent wake interactions between turbines can dramatically reduce
power extraction efficiencies in downstream rows. More specifically, in currently operational
wind farms, in which turbines individually aim to maximize their power extraction, deficits of
up to 40% have been reported. Previous efforts to alleviate wake effects and mitigate downstream
power deficits by static downrating of upstream rows have often been unsuccessful, i.e. losses
in upstream rows are not fully compensated in downstream rows (see, e.g., Refs [1, 2]). On the
other hand, recent studies on dynamic induction control of wind turbines, taking into account
their unsteady interaction with the atmospheric boundary layer (ABL), have shown gains of 16%
and 7% in aggregate power extraction for fully-developed and spatially-developing aligned wind
farms respectively. [3, 4] The latter studies investigate axial induction-based power-maximizing
optimal control of wind-farm boundary layers, considering the individual wind turbines as flow
actuators. By dynamically controlling the turbines in a coordinated manner, their energy
extraction can be regulated with the aim of optimally influencing the turbulent ABL flow for
increased global farm power extraction, e.g. through enhanced wake mixing and kinetic energy
transport. A key feature of the induction factors obtained by dynamic optimal control is the presence
of strong temporal variability in response to the unsteady turbulent flow dynamics of the ABL. Although technically feasible, such variable induction factors tend to promote power and thrust
variability on short timescales as shown in [3, 4], and hence contribute significantly to increased
fatigue loading of the wind turbines. In this work, we investigate the effect of wind turbine
response time on optimal dynamic induction control of wind farms. We do this by time-filtering
the setpoints dictated by the optimal control framework, which allows us to assess whether 1 2. Methodology The state equations are discretized using a fourth order energy-conservative finite-difference
scheme in the vertical direction, combined with a Fourier pseudo-spectral discretization in the
horizontal directions (see, e.g. Refs. [6, 7] for a detailed description of the solver). The latter
choice of discretization entails doubly periodic boundary conditions in the lateral directions,
while the top and bottom domain boundaries are treated with a free slip and wall stress boundary
condition respectively. Time integration is performed using a fourth order accurate explicit
Runge–Kutta scheme. Turbulent inflow conditions are generated by running a separate precursor
simulation in which shifted periodic boundary conditions are applied to alleviate spanwise locking
of turbulent structures and hence accelerate statistical convergence of time-averaged simulation
results [8]. Near the domain outlet, the flow field is nudged towards the generated inflow 2 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 doi:10.1088/1742-6596/753/5/052007 conditions ˜up through the addition of forcing terms with a smooth masking function λ in a
so-called fringe region [9]. conditions ˜up through the addition of forcing terms with a smooth masking function λ in a
so-called fringe region [9]. [ ]
The turbine thrust forces are calculated using a classical actuator disk model (ADM) as
f i = −1
2 bC′
T,iV 2
i Ri(x) e⊥for each of the Nt wind turbines, where Vi is the disk-averaged
velocity, Ri(x) is the geometric rotor footprint on the LES grid, and e⊥denotes the unit
vector perpendicular to the rotor plane. The disk-based thrust coefficients C′
T,i serve as the
control variables. The time-filter equation in (1) applies a one-sided exponential time filter with
a time constant τ to the control variables, resulting in an ordinary differential equation that
is discretized using a backward Euler scheme. By varying τ we can hence control the turbine
response time to variations in the requested thrust setpoints. In this way, we can assess how
much power can still be gained from optimal control while limiting potentially harmful effects
due to increased structural loading variability. Note that, instead of simply time-filtering the
optimal controls a posteriori, which would lead to sub-optimal results, the time-filtering is taken
into account explicitly during the optimization process. 2. Methodology The optimization problem is solved using the quasi-Newton L-BFGS-B algorithm of Byrd
et al. [10], which has been shown to outperform the nonlinear conjugate-gradient algorithms
that is traditionally used for PDE-constrained optimization problems [11]. Note that, due to
the high control space dimensionality (C′
T ∈Rm, with m = Nt × N∆t ≈104 −105) computing
the cost functional gradient with respect to the control variables using classical finite differences
is computationally prohibitive. Instead, the gradient is identified using the continuous adjoint
method. In this method, an additional set of partial differential equations is solved, in such a
way that the calculation of the cost functional gradient becomes tractable. More specifically, by
satisfying the following adjoint system, −∂ξ
∂t + (∇˜u)T ξ −(˜u · ∇)ξ = −∇π −∇· τ ∗
sgs +
Nt
X
i=1
f ∗
i −λξ
in Ω× (0, T]
∇· ξ = 0
in Ω× (0, T]
−τ dσi
dt = −σi + 1
2V 2
i
Z
Ω
Ri(x)(˜u −ξ) · e⊥dx
for i = 1 . . . Nt in (0, T],
(2) in Ω× (0, T] (2)
the gradient of the cost functional with respect to the control parameters ∇C′
T J can be
evaluated as (3) ∇C′
T J = −σ. (3) The adjoint equations are formulated by postulating vanishing derivatives of the Lagrangian
of (1) with respect to the state variables. The adjoint variables (ξ, π, σ) are hence the
Lagrange multipliers associated with the momentum, continuity, and time-filter equations in
(1) respectively. The resulting derivation is straightforward, although lengthy. Therefore, the
reader is referred to [12, 13] for the derivation of the adjoint formulations of the standard
transport terms in the state equations on the one hand, and to [3, 4] for the case-specific terms
regarding the ADM forces f ∗
i , subgrid-scale stress τ ∗
sgs, and fringe forcing λξ on the other. The
continuous adjoint equations are discretized with the same numerical schemes as used for the
forward state equations. The optimal wind-farm control is realized using a receding-horizon model predictive control
framework as illustrated in Figure 1: at t = 0 s, wind-farm operation is optimized over a time
window T, yielding a set of optimal controls C′∗
T . These controls are subsequently employed in a
flow advancement simulation over a time horizon TA. 2. Methodology The latter is chosen as a compromise
between mitigation of finite-horizon end effects on the one hand (favoring TA ≪T) and
computational cost (favoring TA = T) on the other. The resulting flow field at t = TA is then 3 The Science of Making Torque from Wind (TORQUE 2016)
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Journal of Physics: Conference Series 753 (2016) 052007
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Journal of Physics: Conference Series 753 (2016) 052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 g
doi:10.1088/1742-6596/753/5/052007 Flow simulation
Adjoint simulation
(gradient calculation)
Flow advancement
t = 0
t = T
TA
2TA
3TA
t = T+TA
t = T+2TA
Figure 1. Receding horizon model-predictive control strategy for optimal wind-farm control
employed in this paper. Flow simulation Adjoint simulation
(gradient calculation) t = T+TA TA Flow advancement t = T+2TA Figure 1. Receding horizon model-predictive control strategy for optimal wind-farm control
employed in this paper. used as the initial condition for a new optimization window and the procedure begins anew. The global time horizon Ttot over which the optimal control is considered is then constructed
by stringing the mentioned windows together. The specific parameters used in this work are
described in the following section. 3. Case description and numerical setup Simulation and
optimization parameters are summarized in Table 1. We consider a reference case (R) in which turbines greedily maximize individual power by
setting their thrust coefficients to the Betz-optimal value C′
T = 2. Using momentum theory, the
relationship CP = 64C′
T /(C′
T +4)3 can be derived, which has 2 solutions for every desired power
coefficient CP < 16/27 (i.e. the Betz limit) : an underinductive (C′
T < 2), and an overinductive
(C′
T > 2) thrust coefficient. We define a set of optimally controlled cases, differentiated by
whether or not overinduction is allowed, i.e. with C′max
T
= 3 and 2 respectively, and by the
turbine response time τ of 0, 5, or 30 s. This leads to a total of 6 optimal control cases, as
summarized in Table 1. Optimized cases are denoted by C<X>t<Y>, where <X> and <Y>
represent C′max
T
and τ respectively, e.g. C3t30 for the case with C′max
T
= 3 and τ = 30 s. Note that, although the optimal control problem in (1) is a general nonlinear program for which
a multitude of local minima can exist, the application of global optimization methods is well
outside the range of present-day computational resources. Tests with varying starting points
however indicate that, even though the algorithm converges to a different set of (locally) optimal
controls, the overall cost functional decrease does not differ significantly. Therefore, throughout
the current work, we limit ourselves to a single starting point with a steady C′
T = 2 for all
turbines in all optimal control cases. Simulations are initialized as follows:
firstly, a fully-developed high-Reynolds number
turbulent boundary layer is generated by simulating a perturbed logarithmic flow over a physical
timespan of approximately 36 hours. Subsequently, wind turbines are inserted in the simulation,
and the flow field is advanced in time until the effects of any wind-farm start-up transients have
subsided in the main domain. This wind-farm boundary layer in statistically stationary state is
used as initial condition for all simulation cases, and the corresponding time is set as t = 0 s in
the remainder of the manuscript. 0
2
4
6
8
10
x [km]
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
y [km]
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10 R11 R12
ux [m/s]
0.0
1.5
3.0
4.5
6.0
7.5
9.0
10.5
12.0
Figure 2. 3. Case description and numerical setup We consider an aligned wind farm consisting of 12 × 6 wind turbines, spaced apart by 6
rotor diameters in both axial and transversal directions. The simulation domain consists of
a rectangular box of 10 × 3.6 × 1 km3, in which the final 10% of the domain is reserved for
the aforementioned fringe region. The governing equations are solved on a simulation grid of
384×256×144 grid points. Time advancement is performed using a constant timestep ∆t = 0.75
s, for which a Courant–Friedrichs–Lewy number of around 0.4 is attained. The flow is forced
through the domain using a driving pressure gradient of ∂xp∞= 2.5 × 10−4 m s−2, resulting
in an upstream velocity of approximately 8.5 m s−1 at hub height. A typical snapshot of the
LES velocity field is shown in Figure 2, illustrating the complex and unsteady nature of the
interaction between the turbulent ABL and wind turbine wakes throughout the wind farm. The optimization is performed using the aforementioned L-BFGS-B method, where we retain
5 correction pairs to approximate the inverse Hessian required by the quasi-Newton algorithm. We limit the optimization procedure to 60 iterations, leading to approximately 120 PDE
evaluations (LES or adjoint), with a total simulation walltime of about 24 hours per window on
320 Ivy Bridge processor cores. The total amount of PDE evaluations depends on whether the
Newton step, initially proposed by the L-BFGS-B algorithm, satisfies the strong Wolfe conditions
(see, e.g., [14]). If not, a line search algorithm will require additional PDE evaluations until these
conditions are fulfilled. In practice however, we find that a line search is only rarely necessary. The controls are optimized over a prediction horizon of T = 240 s, after which they are applied
in a flow advancement simulation of TA = 120 s. In total, we optimize wind-farm operation over 4 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 g
doi:10.1088/1742-6596/753/5/052007 15 time windows, resulting in a total time horizon Ttot = 1800 s, or 30 minutes. Simulation and
optimization parameters are summarized in Table 1. 15 time windows, resulting in a total time horizon Ttot = 1800 s, or 30 minutes. 3. Case description and numerical setup Simulation domain for the 12 × 6 aligned wind farm. Turbines are represented as
black lines. The dashed line indicates the start of the fringe region. Figure 2. Simulation domain for the 12 × 6 aligned wind farm. Turbines are represented as
black lines. The dashed line indicates the start of the fringe region. 4. Optimization results and discussion 4. Optimization results and discussion
In this section, we discuss the results of the optimal control cases in comparison to the greedy
reference case, with special attention towards the effect of wind turbine response time τ and
maximal thrust coefficient C′max
T
. Firstly, wind farm power extraction and turbine thrust forces
are investigated. Afterwards, a concise discussion of flow features is presented. In this section, we discuss the results of the optimal control cases in comparison to the greedy
reference case, with special attention towards the effect of wind turbine response time τ and
maximal thrust coefficient C′max
T
. Firstly, wind farm power extraction and turbine thrust forces
are investigated. Afterwards, a concise discussion of flow features is presented. Figure 3 illustrates energy extraction over the entire operation time of 30 minutes, normalized
by the values in the reference case R. Figure 3a shows that power gains range between 2 and Figure 3 illustrates energy extraction over the entire operation time of 30 minutes, normalized
by the values in the reference case R. Figure 3a shows that power gains range between 2 and 5 The Science of Making Torque from Wind (TORQUE 2016)
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Journal of Physics: Conference Series 753 (2016) 052007
doi:10.1088/1742-6596/753/5/052007 The Science of Making Torque from Wind (TORQUE 2016)
IOP Publishing
Journal of Physics: Conference Series 753 (2016) 052007
doi:10.1088/1742-6596/753/5/052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 Table 1. 4. Optimization results and discussion Setup parameters
Simulation parameters
Domain size
Lx × Ly × H = (9+1) × 3.6 × 1 km3
Driving pressure gradient
∂xp∞= 2.5 × 10−4 m s−2
Turbine dimensions
D = 0.1H = 100 m,
zh = 0.1H = 100 m
Turbine spacing
Sx = 6D,
Sy = 6D
Windfarm layout
Nt = 72 turbines = 12 rows × 6 columns
Surface roughness
z0 = 10−4H = 0.1m
Grid size
Nx × Ny × Nz = 384 × 256 × 144
Cell size
∆x × ∆y × ∆z = 26 × 14 × 6.9 m3
Time step
∆t = 0.75 s
Optimization parameters
Optimization method
L-BFGS-B
Hessian correction pairs
m = 5
BFGS iterations
Nit = 60 (≈120 PDE)
Optimization time window
T = 240 s
Flow advancement time window
TA = 120 s
Total operation time
Ttot = 1800 s (15 windows)
Simulation cases
R
C′
T = 2
C3t0
0 ≤C′
T ≤3
τ = 0 s (overinductive)
C3t5
0 ≤C′
T ≤3
τ = 5 s (overinductive)
C3t30
0 ≤C′
T ≤3
τ = 30 s (overinductive)
C2t0
0 ≤C′
T ≤2
τ = 0 s (underinductive)
C2t5
0 ≤C′
T ≤2
τ = 5 s (underinductive)
C2t30
0 ≤C′
T ≤2
τ = 30 s (underinductive) Table 1. Setup parameters It can be seen 6 6 The Science of Making Torque from Wind (TORQUE 2016)
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Journal of Physics: Conference Series 753 (2016) 052007
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doi:10.1088/1742-6596/753/5/052007 IOP Publishing doi:10.1088/1742-6596/753/5/052007 C3t0
C3t5 C3t30 C2t0
C2t5 C2t30
1.00
1.05
1.10
1.15
1.20
E/ER
a)
1
2
3
4
5
6
7
8
9
10 11 12
Row
0.4
0.5
0.6
0.7
0.8
0.9
1.0
Ei/E1, R
b)
0.95
0.96
0.97
0.98
0.99
1.00
1.01
Figure 3. Energy extraction of optimally controlled wind farms normalized by greedy reference
case R. a) Total energy extraction. b) Energy extraction per row, normalized by first row of
reference case. (Legend: R: —–
—–, C3t0: —–
—–, C3t5: —–
—–, C3t30: —–
—–, C2t0: - - -
- - -, C2t5: - - -
- - -,
C2t30: - - -
- - -) 1
2
3
4
5
6
7
8
9
10 11 12
Row
0.4
0.5
0.6
0.7
0.8
0.9
1.0
Ei/E1, R
b)
0.95
0.96
0.97
0.98
0.99
1.00
1.01 Figure 3. Energy extraction of optimally controlled wind farms normalized by greedy reference
case R. a) Total energy extraction. b) Energy extraction per row, normalized by first row of
reference case. (Legend: R: —–
—–, C3t0: —–
—–, C3t5: —–
—–, C3t30: —–
—–, C2t0: - - -
- - -, C2t5: - - -
- - -,
C2t30: - - -
- - -) from these figures that C′
T varies wildly between its upper and lower bound in response to
the turbulent dynamics of the boundary layer, and that time-filtering greatly reduces temporal
variability in bC′
T . Figures 4b and 4d show the total power extraction compared to the reference
power. We see for all cases that optimal control leads to an increase in temporal variations
of extracted power, and that time-filtering significantly reduces potentially harmful variability
on shorter timescales. The periodic variations on longer timescales that can be observed for
all cases except C2t30 are caused by finite-horizon optimization effects. We note that C2t30
hardly differs from the reference case R, with bC′
T ≈2 for virtually all turbines throughout the
entire time horizon. This indicates that, for underinductive control of the considered wind-
farm setup, variations on shorter timescales are essential for significant power increase through
optimal control. Table 1. Setup parameters Table 1. Setup parameters Lx × Ly × H = (9+1) × 3.6 × 1 km3
∂xp∞= 2.5 × 10−4 m s−2
D = 0.1H = 100 m,
zh = 0.1H = 100 m
Sx = 6D,
Sy = 6D
Nt = 72 turbines = 12 rows × 6 columns
z0 = 10−4H = 0.1m
Nx × Ny × Nz = 384 × 256 × 144
∆x × ∆y × ∆z = 26 × 14 × 6.9 m3
∆t = 0.75 s 20%. The overall higher yield of all cases except C2t30, as compared to the 7% obtained in
Goit, Munters and Meyers [4] is mainly attributed to a better convergence through the use
of a better optimization method with more iterations. As expected, reducing C′max
T
and/or
increasing response time τ reduces the potential for power gains through dynamic induction
control. Interestingly, the overinductive and slow response case C3t30 shows power gains similar
to the underinductive but fast response cases C2t0 and C2t5. This shows that, for the considered
wind farm, power can be increased significantly in the range of 10% without introducing either
short-timescale variability or large amplitude thrust forces. However, C2t30 shows that this is
not possible when trying to avoid both. Figure 3b shows the energy extraction per row, normalized by the first row of the reference
case. It can be seen that the largest gains are generally achieved in rows 2 and 3, at the cost of
slightly downrating the first row. Contrastingly, C3t30 shows a minor increase in first row power. Aside from the first row of turbines, the last row extracts the most energy in all controlled cases,
since its turbines should not take into account downstream neighbors and hence maximize their
own power. Figure 4 illustrates the dynamic behavior for all cases over 30 minutes of operation time. Figures 4a and 4c depict a front-row turbine thrust coefficient setpoint C′
T and its time-filtered
counterpart bC′
T for the overinductive and underinductive cases respectively. Table 1. Setup parameters Further analysis of the optimized controls and the physical mechanisms behind
increasing power extraction is beyond the scope of this work and is subject of current research. g p
y
p
j
Figure 5 shows the dynamic behavior of the thrust force ft for a turbine in row 6 of the
wind farm, where turbulence levels at hub height approach a fully-developed state. Figure 5a
illustrates the time series of ft, normalized by the time-averaged values of the same turbine in
the reference case. It can be seen that case C3t0 exhibits high frequency force variations and
peak forces regularly exceeding values twice as large as the time average reference ft,R. Cases
C3t5 and C3t30 show that increasing response time τ not only filters out high frequency force
fluctuations, but also leads to a reduction of the largest force amplitudes for this wind turbine. A further decrease in amplitudes is achieved by reducing C′max
T
to 2. Figure 5b shows the power
spectra of the time series illustrated in 5a. Low frequency behavior (≤10−2 Hz) is similar for
all cases and tends to a –1 slope, indicating that the slowest force variations are governed by
the background atmospheric dynamics. Around 10−2 Hz, a small –5/3 range is observed. At
higher frequencies, a slope between –3 and –4 characterizes the controlled cases, while the static
reference case decays much more quickly. In this range, the turbine reponse time to variations
in control setpoint directly translates to the frequency content of the thrust force enacted by
the turbine. It is important to note that, not only should fatigue be taken into account when
considering additional cyclic turbine loading due to dynamic wind farm control, also natural
frequencies of relevant deformation modes should be avoided at all cost. For example, the
natural frequency associated with the tower fore-aft deformation mode of the NREL 5 MW
turbine is approximately 0.3 Hz [15]. Table 1. Setup parameters It can be seen from Figure 5 that cases C3t0 and C2t0 7 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 g
doi:10.1088/1742-6596/753/5/052007 0
3
0
3
0
3
C ′
T,
C′
T
a) C ′
T
max = 3
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
P/PR
b) C ′
T
max = 3
0
300
600
900
1200
1500
1800
Time [s]
0
2
0
2
0
2
C ′
T,
C′
T
c) C ′
T
max = 2
0
300
600
900
1200
1500
1800
Time [s]
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
P/PR
d) C ′
T
max = 2
Figure 4. Temporal behavior of optimally controlled wind farms. Left (a,c):
Thrust coefficient of a first row wind turbine. Colors: setpoint coefficient C′
T ,
Grey: time-filtered coefficient bC′
T . Right (b,d):
Aggregate power extraction normalized by
time average of reference power extraction. Top (a,b):
C′max
T
= 3. Bottom (c,d):
C′max
T
= 2. (Legend: R: —–
—–, τ = 0 s: —–
—–, τ = 5 s: —–
—–, τ = 30 s: —–
—–) 0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
P/PR
b) C ′
T
max = 3
0
300
600
900
1200
1500
1800
Time [s]
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
0.8
1.0
1.2
1.4
P/PR
d) C ′
T
max = 2 Figure 4. Temporal behavior of optimally controlled wind farms. Figure 4. Temporal behavior of optimally controlled wind farms. Left (a,c):
Thrust coefficient of a first row wind turbine. Colors: setpoint coefficient C′
T ,
Grey: time-filtered coefficient bC′
T . Right (b,d):
Aggregate power extraction normalized by
time average of reference power extraction. Top (a,b):
C′max
T
= 3. Bottom (c,d):
C′max
T
= 2. (Legend: R: —–
—–, τ = 0 s: —–
—–, τ = 5 s: —–
—–, τ = 30 s: —–
—–) show significant spectral energy in this range. These results indicate that a detailed analysis of
turbine structural loading, through the addition of a multi-physics aero-elastic turbine model
in the governing equations is an essential step towards actual rollout of fast-response dynamic
wind farm controllers. This is subject of ongoing work. Table 1. Setup parameters To conclude the discussion on the results of the optimal control simulations, we provide a
qualitative view of the boundary layer flow through the wind farm in Figure 6. Figures 6a and
6b illustrate the time-averaged streamwise velocity through the rotor centerline as a function
of streamwise distance, averaged over all 6 columns. It is shown that all cases exhibit higher
velocities at the turbine disks starting from row 2, which directly leads to the observed increase
in energy extraction discussed above. The difference in disk velocity for row 1 is very small,
corresponding with the minor differences in first row power shown previously in Figure 3. In
addition, overinductive cases with C′max
T
= 3 generate deeper near-wakes behind the first row
and rows 8 to 12, while this is not the case for underinductive cases with C′max
T
= 2, where
velocities are higher over the entire streamwise extent of the domain. Overall, the figure shows
that, for the overinductive case, trough-to-peak recovery between near and far wake is enhanced
significantly, while for underinductive cases wake recovery remains roughly constant. This observation is also supported by the turbulence kinetic energy (TKE) levels at hub
height throughout the wind farm, as illustrated in Figures 6c and 6d. For C′max
T
= 3, higher
turbulence energy is observed between every row of turbines, consistent with an increase in
turbulent mixing leading to better wake recovery. Interestingly, even the slow response case
C3t30 shows a significant increase in TKE compared to the reference case, even though turbine
thrust forces and power extraction vary smoothly in time. For C′max
T
= 2, TKE levels are very
similar to the static reference case. 8 0
300
600
900
1200
1500
1800
Time [s]
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
ft/ft, R
a)
10-2
10-1
Frequency [Hz]
10-14
10-12
10-10
10-8
10-6
10-4
10-2
100
102
104
106
Φf
-5/3
-1
-4
b)
Figure 5. Dynamic behavior of thrust force ft for a 6th row turbine. a) Time series of thrust
force, normalized by time-averaged reference thrust. b) Power spectra Φf of normalized thrust
force, averaged over columns. Table 1. Setup parameters (Legend:
R: —–
—–, τ = 0 s: —–
—–, τ = 5 s: —–
—–, τ = 30 s: —–
—–)
The Science of Making Torque from Wind (TORQUE 2016)
IOP Publishing
Journal of Physics: Conference Series 753 (2016) 052007
doi:10.1088/1742-6596/753/5/052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 g
doi:10.1088/1742-6596/753/5/052007 0
300
600
900
1200
1500
1800
Time [s]
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
ft/ft, R
a) 10-2
10-1
Frequency [Hz]
10-14
10-12
10-10
10-8
10-6
10-4
10-2
100
102
104
106
Φf
-5/3
-1
-4
b) Figure 5. Dynamic behavior of thrust force ft for a 6th row turbine. a) Time series of thrust
force, normalized by time-averaged reference thrust. b) Power spectra Φf of normalized thrust
force, averaged over columns. (Legend: R: —–
—–, C3t0: —–
—–, C3t5: —–
—–, C3t30: —–
—–, C2t0: - - -
- - -,
C2t5: - - -
- - -, C2t30: - - -
- - -) ,
)
a) C ′
T
max = 3
1
2
3
4
5
6
7
8
9
˜u1 [m/s]
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10
R11
R12
b) C ′
T
max = 2
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10
R11
R12
c) C ′
T
max = 3
1
2
3
4
5
6
7
8
x [km]
0.5
1.0
1.5
2.0
2.5
3.0
3.5
(˜u′
i ˜u′
i)/2 [m2/s2]
d) C ′
T
max = 2
1
2
3
4
5
6
7
8
x [km]
Figure 6. Time-averaged streamwise velocity ˜u1 (Top (a,b)) and turbulence kinetic energy
(˜u′
i˜u′
i)/2 (Bottom (c,d)) through rotor centerlines (z = zh, y = yh) as a function of streamwise
distance along turbine column. Results are averaged over all turbine columns. Vertical dashed
gray lines indicate turbine locations. Left (a,c): C′max
T
= 3. Right (b,d): C′max
T
= 2. Table 1. Setup parameters (Legend: R: —–
—–, C3t0: —–
—–, C3t5: —–
—–, C3t30: —–
—–, C2t0: - - -
- - -,
C2t5: - - -
- - -, C2t30: - - -
- - -)
The Science of Making Torque from Wind (TORQUE 2016)
IOP Publishing
Journal of Physics: Conference Series 753 (2016) 052007
doi:10.1088/1742-6596/753/5/052007 The Science of Making Torque from Wind (TORQUE 2016)
IOP Publishing
Journal of Physics: Conference Series 753 (2016) 052007
doi:10.1088/1742-6596/753/5/052007 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 0
300
600
900
1200
1500
1800
Time [s]
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
ft/ft, R
a)
10-2
10-1
Frequency [Hz]
10-14
10-12
10-10
10-8
10-6
10-4
10-2
100
102
104
106
Φf
-5/3
-1
-4
b)
Figure 5. Dynamic behavior of thrust force ft for a 6th row turbine. a) Time series of thrust
force, normalized by time-averaged reference thrust. b) Power spectra Φf of normalized thrust
force, averaged over columns. (Legend: R: —–
—–, C3t0: —–
—–, C3t5: —–
—–, C3t30: —–
—–, C2t0: - - -
- - -,
C2t5: - - -
- - -, C2t30: - - -
- - -)
a) C ′
T
max = 3
1
2
3
4
5
6
7
8
9
˜u1 [m/s]
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10
R11
R12
b) C ′
T
max = 2
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10
R11
R12
c) C ′
T
max = 3
1
2
3
4
5
6
7
8
x [km]
0.5
1.0
1.5
2.0
2.5
3.0
3.5
(˜u′
i ˜u′
i)/2 [m2/s2]
d) C ′
T
max = 2
1
2
3
4
5
6
7
8
x [km]
Figure 6. Time-averaged streamwise velocity ˜u1 (Top (a,b)) and turbulence kinetic energy
(˜u′
i˜u′
i)/2 (Bottom (c,d)) through rotor centerlines (z = zh, y = yh) as a function of streamwise
distance along turbine column. Results are averaged over all turbine columns. Vertical dashed
gray lines indicate turbine locations. Left (a,c): C′max
T
= 3. Right (b,d): C′max
T
= 2. Table 1. Setup parameters (Legend:
R: —–
—–, τ = 0 s: —–
—–, τ = 5 s: —–
—–, τ = 30 s: —–
—–) a) C ′
T
max = 3
1
2
3
4
5
6
7
8
9
˜u1 [m/s]
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10
R11
R12
b) C ′
T
max = 2
R1
R2
R3
R4
R5
R6
R7
R8
R9
R10
R11
R12
c) C ′
T
max = 3
1
2
3
4
5
6
7
8
x [km]
0.5
1.0
1.5
2.0
2.5
3.0
3.5
(˜u′
i ˜u′
i)/2 [m2/s2]
d) C ′
T
max = 2
1
2
3
4
5
6
7
8
x [km] Figure 6. Time-averaged streamwise velocity ˜u1 (Top (a,b)) and turbulence kinetic energy
(˜u′
i˜u′
i)/2 (Bottom (c,d)) through rotor centerlines (z = zh, y = yh) as a function of streamwise
distance along turbine column. Results are averaged over all turbine columns. Vertical dashed
gray lines indicate turbine locations. Left (a,c): C′max
T
= 3. Right (b,d): C′max
T
= 2. (Legend:
R: —–
—–, τ = 0 s: —–
—–, τ = 5 s: —–
—–, τ = 30 s: —–
—–) 5. Conclusions 5. Conclusions
In this work we continue the application of optimal dynamic induction control for power
maximization in LES of aligned wind farms started in earlier work [3, 4]. More specifically,
we discuss the sensitivity of achievable gains in energy extraction with respect to wind turbine
response times, with the aim of reducing detrimental effects associated with fast-varying
optimized thrust coefficients obtained by the latter studies. We consider simulation cases
restricted to underinduction, as well as cases that also allow overinduction. In summary, the
results obtained in this work show that cooperative wind farm control still yields significant 9 The Science of Making Torque from Wind (TORQUE 2016)
Journal of Physics: Conference Series 753 (2016) 052007 IOP Publishing
doi:10.1088/1742-6596/753/5/052007 doi:10.1088/1742-6596/753/5/052007 power gains after eliminating potentially structurally harmful characteristics of the dynamic
control schemes, i.e. strong temporal variations and large thrust forces. For instance, cases
C3t30 and C2t5 show increases in energy extraction compared to greedy control strategies of
8 and 10% respectively, which would still involve very significant economic profits. Spectral
analysis of thrust forces on a wind turbine indicate the need for multi-physics optimization to
accurately model additional fatigue loading and avoid the resonance excitation of deformation
modes. Near-future work will focus on identifying the main mechanisms behind the observed
increases in energy extraction, and translating the computationally expensive optimal controller
to practical suboptimal control schemes. Acknowledgements The authors acknowledge support by the European Research Council (ActiveWindFarms, grant
no: 306471). The computational resources and services used in this work were provided by the
VSC (Flemish Supercomputer Center), funded by the Research Foundation - Flanders (FWO)
and the Flemish Government department EWI. References [1] Nilsson K, Ivanell S, Hansen K S, Mikkelsen R, Sørensen J N, Breton S P and Henningson D 2015 Large-eddy
simulations of the Lillgrund wind farm. Wind Energy 18 449–467 [1] Nilsson K, Ivanell S, Hansen K S, Mikkelsen R, Sørensen J N, Breton S P and Henningson D 2015 Large-eddy
simulations of the Lillgrund wind farm. Wind Energy 18 449–467 [2] Annoni J, Gebraad P M O, Scholbrock A K, Fleming P A and Wingerden J W v 2016 Analysis of axial-
induction-based wind plant control using an engineering and a high-order wind plant model. Wind Energy
19 1135–1150 [2] Annoni J, Gebraad P M O, Scholbrock A K, Fleming P A and Wingerden J W v 2016 Analysis of axial-
induction-based wind plant control using an engineering and a high-order wind plant model. Wind Energy
19 1135–1150 [3] Goit J P and Meyers J 2015 Optimal control of energy extraction in wind-farm boundary layers. J Fluid
Mech 768 5–50 [3] Goit J P and Meyers J 2015 Optimal control of energy extraction in wind-farm boundary layers. J Fluid
Mech 768 5–50 [4] Goit J P, Munters W and Meyers J 2016 Optimal C
Wind Farm with Entrance Effects. Energies 9 29 [4] Goit J P, Munters W and Meyers J 2016 Optimal Coordinated Control of Power Extraction in LES of a
Wind Farm with Entrance Effects. Energies 9 29 [4] Goit J P, Munters W and Meyers J 2016 Optimal Coordinated Control of Power Extraction in LES of a
Wind Farm with Entrance Effects. Energies 9 29 ort S, Baelmans M and Meyers J 2009 Constrained optimization of turbulent mixing-layer evolution. ournal of Turbulence N18 [6] Meyers J and Meneveau C 2010 Large eddy simulations of large wind-turbine arrays in the atmospheric
boundary layer. AIAA Paper 827 2010 [7] Calaf M, Meneveau C and Meyers J 2010 Large eddy simulation study of fully developed wind-turbine array
boundary layers. Phys Fluids 22 015110 [8] Munters W, Meneveau C and Meyers J 2016 Shifted periodic boundary conditions for simulations of wall-
bounded turbulent flows. Phys Fluids 28 025112 y
[9] Munters W, Meneveau C and Meyers J 2016 Turbulent Inflow Precursor Method with Time-Varying D
for Large-Eddy Simulations and Applications to Wind Farms. Boundary-Layer Meteorol 159 30 [10] Byrd R H, Lu P, Nocedal J and Zhu C 1995 A limited memory algorithm for bound constrained optimization. References SIAM Journal on Scientific Computing 16 1190–1208 fi
p
g
[11] Nita C, Vandewalle S and Meyers J 2016 On the efficiency of gradient based optimization algorithms for
DNS-based optimal control in a turbulent channel flow. Computers & Fluids 125 11–24 [12] Choi H, Hinze M and Kunisch K 1999 Instantaneous control of backward-facing step flows. Applied Numerical
Mathematics 31 133–158 [13] Bewley T R, Moin P and Temam R 2001 DNS-based predictive control of turbulence: an optimal benchmark
for feedback algorithms. Journal of Fluid Mechanics 447 179–225 [14] Nocedal J and Wright S 2006 Numerical Optimization. Springer Science & Business Media [15] Jonkman J, Butterfield S, Musial W and Scott G 2009 Definition of a 5-MW reference wind turbine for
offshore system development. Tech. Rep. Technical Report NREL/TP-500-38060 National Renewable
Energy Laboratory, Golden, CO, USA 10
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English
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Optimal control of fluctuations applied to the suppression of noise-induced failures of chaos stabilization
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Izvestiâ vysših učebnyh zavedenij. Prikladnaâ nelinejnaâ dinamika
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Izv. VUZ «AND», vol. 11,
№ 3,2003 Izv. VUZ «AND», vol. 11,
№ 3,2003 Izv. VUZ «AND», vol. 11,
№ 3,2003 Izv. VUZ «AND», vol. 11,
№ 3,2003 OPTIMAL CONTROL OF FLUCTUATIONS APPLIED TO THE SUPPRESSION
OF NOISE-INDUCED FAILURES OF CHAOS STABILIZATION LA. Khovanov, №А. Khovanova апа P.V.E. McClintock Double strategy of chaos and fluctuation controls is developed. Noise-induced failures
in the stabilization of ап unstable orbit in the one-dimensional logistic тар are considered а5
large fluctuations from a stable state. The properties of the large fluctuations are examined by
determination
and
analysis
of
the
optimal
path
and
the
optimal
fluctuational
force
corresponding 10 the stabilization failure. The problem of controlling noise-induced large
fluctuations is discussed, and methods of control have been developed. Deterministic
chaos For simplicity we will stabilize ап unstable fixed point
х” оё the logistic map: For simplicity we will stabilize ап unstable fixed point
х” оё the logistic map: X, =rx(1-x,),
(1) (1) where x, is а coordinate, п 15 discrete time and r is the control parameter that determines
different regimes оЁ the map's behavior (1). The coordinate оё фе fixed point x"
is
defined by е condition: x,,,=x,, and consequently its location depends оп the parameter r:
л1
© =1-Ш. @) where x, is а coordinate, п 15 discrete time and r is the control parameter that determines
different regimes оЁ the map's behavior (1). The coordinate оё фе fixed point x"
is
defined by е condition: x,,,=x,, and consequently its location depends оп the parameter r:
л1
© =1-Ш. @) © =1-Ш. @) @) We set the parameter r=3.8, a value for which an aperiodic (chaotic) regime is observed
in (1), апа the point.x" 15 embedded in е chaotic attractor. From the range оЁ existing stabilization methods, we chose 10 work with just two: From the range оЁ existing stabilization methods, we chose 10 work with just two:
the OGY and ADP methods mentioned above. To stabilize а fixed point by the OGY method, perturbations Аг are applied 10 the To stabilize а fixed point by the OGY method, perturbations Аг are applied 10 the
parameter r, leading to the map being modified (1) in the following manner: ха = (r+ar)x, (1-x,),
Ar, = r(2¢-1)(x-x")/[x"(1-x")]. (3) (3) To stabilize а fixed point by the ADP method, perturbations Ax are applied to фе
map's coordinate, The value of the perturbation Ax is defined by the distance between the
current system coordinate and the coordinate of the stabilized state:
лаа = РД1-ж) + Ак
A%, = (5,0,
@) лаа = РД1-ж) + Ак
A%, = (5,0,
@) @) We
consider
local
stabilization
procedure. During
local
stabilization,
the
perturbations Ar and Ах @ег from zero only if the following condition 15 satisfied: ке < . (5) (5) ке < . Here
е
15
а small value: ме fixed £=0.01. 1Ё @е condition (5)
15 not satisfied then
stabilization is absent, i.e. Ar=0 or Ax=0. So, stabilization involve modifications of the initial map (1), and thus we use So, stabilization involve modifications of the initial map (1), and thus we use
another тар in the form (3) ог (4). The fixed point х* is ап attractor оё the new map. Introduction The control of chaos represents а very real апа important problem in а wide variety
оё applications, ranging from neuron assemblies 10 lasers and hydrodynamic systems [1]. The procedure used consists of stabilizing an unstable periodic orbit by the application of
precisely designed small perturbations to a parameter and/or a trajectory of the chaotic
system. Different methods of chaos control have been suggested and applied in many
different physical contexts, as well as numerically to model systems [1]. For practical
applications of these control methods, it is important to understand how noise influences
the stabilization process, because fluctuations
are inherent and inevitably present
in
dissipative systems. The problem has not been well studied. Typically,
a method
is
developed
for
stabilization
оЁ
the
orbit
without
initially
taking
any
account
оЁ
fluctuations. Only
then
the authors do check
the robustness
of
their method
by
introducing weak noise into е system [1). Thus, in е celebrated pioneering work оЁ
Ott, Grebogi and York, «Controlling chaos» [2], the authors just noted that noise can
induce failures of stabilization. In this work we consider noise-induced failures in the stabilization of an unstable In this work we consider noise-induced failures in the stabilization of an unstable
orbit and the problem of controlling these failures. The method of Ott, Grebogi and Yorke
(ОСУ) [2] and а modification оё фе adaptive method (ADP) [1] are used to stabilize ап
unstable point of the logistic map. We consider the small noise limit where stabilization
failures
аге
very
гаге and
therefore
they
can
be considered
ав
large
fluctuations
(deviations)
from
a
stable
state. We
study
the properties
of large
deviations
by
determining the optimal paths and the optimal fluctuational forces corresponding to the
failures. We employ two methods to determine the optimal paths and forces. The first of
these builds and analyzes the prehistory probability distribution to determine the optimal
ра апа optimal force [3]. The second method considers ап extended тар (relative 10 фе 46 initial one) which defines fluctuational paths and forces in е zero-noise limit [4,5]. Furthermore we use the optimal paths and forces to develop methods of controlling the
large deviations, i.e. the noise-induced failures оЁ stabilization. In the literature, methods
for stabilization are often referred to as a control methods too. To differentiate controlling
large fluctuations from controlling chaos, we therefore use the term «stabilization» to
indicate the control of chaos. Introduction In section 1 we describe the procedures for stabilization of an unstable orbit of the In section 1 we describe the procedures for stabilization of an unstable orbit of the
logistic map. The general approach to the control of a large deviation is presented in
section 2. Noise-induced failures of stabilization are considered in section 3. The results
obtained are discussed in the conclusion. 2. Control of large fluctuations Large fluctuations manifest themselves as large deviations from the stable state of
the system under the action оё fluctuational forces, Large fluctuations play а key role in
many phenomena, ranging from mutations in DNA to failures of electrical devices. In
recent years significant progress has been achieved both in understanding the physical
nature of large fluctuations and in developing approaches for describing them. The latter
are based on the concept of optimal paths
- the paths along which the system moves
during large fluctuations. Large fluctuations are very rare events during which the system
moves from
the vicinity
of
a stable
state
to
a state remote from
it,
at
a distance
significantly larger than the amplitude of the noise. Such deviations can correspond to a
transition of the system to another state, or to an excursion along some trajectory away
from the stable state and then back again. During such deviations the system is moved
with overwhelming probability along the optimal path under е action оЁ а specific
(optimal) fluctuational force. The probability of motion along any other (non-optimal)
path is exponentially smaller. In practice, therefore large fluctuations must оЁ necessity
оссиг along deterministic trajectories. The problem of controlling large fluctuations can
thus be reduced
to the
task of controlling motion along
a deterministic trajectory. Consequently, the control problem can be solved through application оё the control
methods developed for deterministic systems [6]. Let us consider the-control problem. We will follow the work [7] and consider the Let us consider the-control problem. We will follow the work [7] and consider the
control оЁ large fluctuations by а weak additive deterministic control force. Weakness
means
here аг
the спегву
оЁЁ
the
control
force
is
comparable
with е
energy
(dispersion) оё the fluctuations (see [8] for details). In this case, the extremal value оЁ the
functional R for optimal control, which moves the system from ап initial state х'
ю
а
target state х /, takes the form [7]: Ваа(х^Е) = SO() £45,
AS= (QFYA[E,0y, (&P,
®) ®) where E°7 is the optimal fluctuational force фаг induces the transition from х
to x/ in
the absence of the control force; S
15 ап energy оЁ the transition, N, апа N, are the times
аг which the fluctuational force £ starts and stops, and F 15 а parameter defining е
energy of the control force. For simplicity we will stabilize ап unstable fixed point
х” оё the logistic map: After the stabilization is switched on, а trajectory оё the тар tends 10 the fixed point х”,
and subsequently remains there. In the presence of noise the trajectory fluctuates in the vicinity of the stabilized In the presence of noise the trajectory fluctuates in the vicinity of the stabilized
state, i.e. noise-induced dynamics appears. In addition, noise can induce stabilization
failures, i.e. breakdown in the condition (5). Our aim
is
to study these noise-induced stabilization failures and analyze the Our aim
is
to study these noise-induced stabilization failures and analyze the
problem of how to suppress them. We therefore consider the maps (3) and (4) in the
presence of additive Gaussian fluctuations: 47 X, = НАк (1-х,) + О
Ar,=r(2x"-1)(x,-x")/[x"(1-x")],
(6)
ха =rx(lx)+Ax +DE,
А = (x -x"). (7) (6) (7) Here D is the noise intensity; §, 15 а Gaussian random process with zero-average (Е)=0, 5-
correlation function (§ &, ,)=8(k) апа dispersion (§%)=1. 2. Control of large fluctuations The optimal control force « * for the given functional (8) is defined [7] by: The optimal control force « * for the given functional (8) is defined [7] by: P = F(2F)2
(S,
(&
Y 8,
OR),
©)
optimal fluctuational path in the absence of the control force. The ©) where x (% 15 the optimal fluctuational path in the absence of the control force. The
minus sign т the expression (9) decreases the probability оё а transition to the state x/,
and the plus sign increases the probability. It can be seen аг the optimal control force
и
15 completely defined by
the optimal fluctuational force £, and
the optimal
fluctuational path x (%%, corresponds 10 the large fluctuation. Therefore to solve the
control problem it is necessary, first, to determine е optimal path х 09® leading from
the state х to the state х / under the action of the optimal fluctuational force &° Thus, а
solution of the control problem depends on the existence of an optimal path: it is obvious 48 that the approach described should be straightforward to apply, provided that the optimal
path exists and is unique. that the approach described should be straightforward to apply, provided that the optimal
path exists and is unique. We consider below ап application оЁ the approach described 10 suppress large
fluctuations
ш
фе one-dimensional
map. The
large
fluctuations
in
question
are
considered here 10 correspond to failures in е stabilization оё ап unstable orbit. The control procedure depends on the determination of the optimal path and The control procedure depends on the determination of the optimal path and
optimal fluctuational force and, to define them, we will use two different methods. The
first method is based on an analysis of the prehistory probability distribution (PPD) and
the second one consists of solving
a boundary problem for an extended map which
defines fluctuational trajectories. The PPD was introduced in [3] to analyze optimal paths experimentally in flow The PPD was introduced in [3] to analyze optimal paths experimentally in flow
systems. We will use the distribution 10 analyze fluctuational paths in maps. Note, that т
[9,10] it was shown that analysis of the PPD allows one ю determine both фе optimal
path and the optimal fluctuational force. 2. Control of large fluctuations The essence of this first method consists of a
determination of the fluctuational trajectories corresponding to large fluctuations for
extremely small (but finite) noise intensity, followed by
a statistical analysis of the
trajectories. In this experimental method the behaviour of the dynamical variables x, and
of the random force
§, are tracked continuously until the system makes its transition "from
ап initial state х
° Ю
а small vicinity of the target state х /. Escape trajectories x,°
reaching this state, and the corresponding noise realizations € °° оЁ the same duration, are
then stored. The system is then reset to the initial state ¥/ and the procedure is repeated. Thus, ап ensemble оё trajectories
is collected and then the fluctuational PPD p "
is
constructed for the time interval during which the system is monitored. This distribution
contains all information about the temporal evolution of the system immediately before
the trajectory arrives аё the final state х /. The existence оё ап optimal escape path is
diagnosed by the form оё the PPD p /: if there 15 ап optimal escape trajectory, еп the
distribution p " аса given time л has а sharp peak at optimal trajectory х° Therefore, (0
find ап optimal path it is necessary to build the PPD and, for each moment оё time л, 10
check for the presence of a distinct narrow peak in the PPD. The width of the peak
defines the dispersion o," оё the distribution and it has 10 be оё the order of the mean-
square noise amplitude b [3]. The optimal fluctuational force that moves the system
trajectory along the optimal path can be estimated by averaging the corresponding noise
realizations & &* over the ensemble. Note, that investigation оЁ the fluctuational prehistory
also allows us to determine the range of system parameters for which optimal paths exist. To determine the optimal path and force by means of the second method we
analyze extended maps [4,5] using the principle оё least action [5]. Such extended maps
are analogous to е Hamilton-Jacobi equation in the theory оё large fluctuations for flow
systems. For the one-dimensional тар x, ,,=f(x,)+DE,, the corresponding extended тар
in the zero-noise limit takes the form: ха =flx,) +7,/8(x,),
Y = /Е(
(10)
&) = 9f (x,)/ox, . 2. Control of large fluctuations (10) The тар 15 area-preserving, апа it defines the dynamics оё the noise-free тар х„ =f(x, ),
if y,=0. If y#0 then the coordinate x, corresponds ю
а fluctuational path, ала the
coordinate , to а fluctuational force. Stable and unstable states of the initial map become
saddle states of the extended map. So, the fixed point
x* оё the ADP (7) апа OGY (6)
maps
becomes
а
saddle
point
оЁ
the corresponding extended
map. Fluctuational
trajectories (including the optimal one) starting from х° belong 10 unstable manifolds оЁ
the fixed point (x",0) оЁ the extended map. 49 The procedure for determination of the optimal paths consists of solving the
boundary problem for the extended map (10): хх , Y=
(11)
х„
=xf,
y
=0,
(12) (11)
(12) х„
=xf,
y
=0,
(12) (12) where л" 15 the initial state апа х / 15 а target state. To solve the boundary problem different To solve the boundary problem different methods сап be used. For the one-
dimensional maps under consideration, a simple shooting method is enough [11]. We
choose an initial perturbation / along the linearized unstable manifolds in a vicinity of the
point (x,0) оё the тар (10). The procedure 10 determine а solution can be аз follows:
looking over all possible values
/, we determine a trajectory which tends to the point
(x7,0). Note а!, because these maps are irreversible there exits, in general, ап infinite
number of solutions of the boundary problem. The optimal trajectory (path) has minimal
action (energy) S=2,;y”1; here y,
is calculated along the trajectory, corresponding а
solution of the boundary task. 3. Noise-induced failures in stabilization A breakdown of the condition (5) corresponds to а failure оё stabilization, i.. 10
the noise-induced escape оЁ the trajectory from ап e-vicinity оё е fixed point x*. The
target state х / corresponds to the boundaries оЁ the stabilization region: x/=x"+e. Instead о analyzing the maps (6) апа (7) in the e-vicinity оЁ the fixed point х° ме Instead о analyzing the maps (6) апа (7) in the e-vicinity оЁ the fixed point х° ме
can investigate linearized maps of the following form: (path) has minimal ха = ax, + DE,,
(13) (13) ха = ax, + DE,, here а is а value of derivative df{x )/dx, т the fixed point л'. For the тар (6) the
derivative is equal 10 zero a,,=0, and for the тар (7) а op=-0.8. Let us investigate stabilization failure by considering the most probable (optimal) here а is а value of derivative df{x )/dx, т the fixed point л'. For the тар (6) the
derivative is equal 10 zero a,,=0, and for the тар (7) а op=-0.8. Let us investigate stabilization failure by considering the most probable (optimal) Let us investigate stabilization failure by considering the most probable (optimal)
fluctuational paths, which lead from е point х* to boundaries x"+e. For linearized maps
(13) the extended map (10) can be reduced to the form: X, =ах, + y,/a,
(14)
Эн = )/а (14) Эн = )/а with the initial condition (x,=x", y;=0) апа фе final condition х /=х"+в. It can be seen
that а solution of the тар (14) increases proportionally 10 y,=const/a” [12]. This means
that, for the ADP тар (7), the amplitude оё the fluctuational force increases slowly but
that, for the OGY тар (6), the failure arises аз the result оё only one fluctuation
(iteration). Because equation (14)
is linear, the boundary problem will have а unique
solution [11]. Thus, analysis of the linearized extended map (14) shows that there is an
optimal path, апа it gives а qualitative picture оё exit through the boundary x"+e. Let
us check
the existence
of the optimal
paths through
an analysis
of the with the initial condition (x,=x", y;=0) апа фе final condition х /=х"+в. It can be seen
that а solution of the тар (14) increases proportionally 10 y,=const/a” [12]. 3. Noise-induced failures in stabilization This means
that, for the ADP тар (7), the amplitude оё the fluctuational force increases slowly but
that, for the OGY тар (6), the failure arises аз the result оё only one fluctuation
(iteration). Because equation (14)
is linear, the boundary problem will have а unique
solution [11]. Thus, analysis of the linearized extended map (14) shows that there is an
optimal path, апа it gives а qualitative picture оё exit through the boundary x"+e. Let
us check
the existence
of the optimal
paths through
an analysis
of the Let
us check
the existence
of the optimal
paths through
an analysis
of the
prehistory of fluctuations. To obtain exit trajectories and noise realizations we use the
following procedure. At the initial moment of time, a trajectory of the map is located at
point x". The subsequent behaviour оё the trajectory
18 monitored until the moment аг
which
it exits from е e-region of the point x*. The relevant parts of the trajectory, just
before and after its exit, are stored. The time at which the exit occurs is set to zero. Thus
ensembles of exit trajectories and оё е corresponding noise realizations are collected
and PPDs are built. 50 Fig. 1. PPDs p," оё the exit trajectories (a) апа noise realizations (b) о! ADP тар for the boundary @"-e). The thick dashed lines indicate e-region of stabilization. The thin dashed lines connect maxima оё PPDs. The noise indensity is D=0.0011
To start with, we will discuss these ideas in the context of the ADP map. Fig. 1,а Fig. 1. PPDs p," оё the exit trajectories (a) апа noise realizations (b) о! ADP тар for the boundary @"-e). The thick dashed lines indicate e-region of stabilization. The thin dashed lines connect maxima оё PPDs. The noise indensity is D=0.0011
h, we will discuss these ideas in the context of the ADP map. Fig. 1,а Fig. 1. PPDs p," оё the exit trajectories (a) апа noise realizations (b) о! ADP тар for the boundary @"-e). The thick dashed lines indicate e-region of stabilization. The thin dashed lines connect maxima оё PPDs. The noise indensity is D=0.0011
start with, we will discuss these ideas in the context of the ADP map. Fig. 1,а To start with, we will discuss these ideas in the context of the ADP map. Fig. 3. Noise-induced failures in stabilization The optimal paths and
forces used in е control procedure аге marked by arrows 51 checked this prediction and found Фаг the optimal force induces the exit from ап e-region
оё the point х we selected ал initial condition а! the point x* апа included фе optimal
fluctuational force additively;
аз а result ме observed the stabilization failure. If we
decrease the amplitude оё е force by 5-10%, then the failure does not оссиг. It appears,
therefore, the deduced force allows us to induce the stabilization failure with minimal
energy (see [10] for details). Using the optimal ра and the force we can solve the opposite task [7,8]
- 10 Using the optimal ра and the force we can solve the opposite task [7,8]
- 10
decrease the probability of the stabilization failures. Indeed, if during the motion along
the optimal path we will apply a control force with the same amplitude but with the
opposite sign а5 the optimal fluctuationai force has, then, obviously, the failure will not
occur. Because we know the optimal force then, in accordance with the algorithm [7]
described above, it is necessary to determine the time moment when system
is moving
along е optimal path. For the ADP method the optimal path 15 long enough to identify
that а trajectory 15 moving along the optimal path, ап then to apply а control force. In the presence of control the map (7) is modified: In the presence of control the map (7) is modified: In the presence of control the map (7) is modified: X, = 1%,(1-x,) + Ах, + DE +u,,
(15)
Ax, = (x,-x"), (15) here u_ is the deterministic control force. We use the following scheme 10 We use the following scheme 10 suppress the stabilization failures. Initially the
control
force
is equal
to zero (u,=0) and е тар
is located
т
the point х*; ме
continuously monitor a trajectory of
the map (15) and define the time moment when the
system starts motion along the optimal path (x ). We assume (аг е system moves along
the optimal path (x,) if it passes within а small vicinity of the coordinate (x ,) апа then
within а small vicinity оЁ (x „) (see arrows in Fig. 2, а). Then оп the following iteration
we ада the control force u,=-sign(g,)(g,), n=-1 (see Fig. 2, b). In Fig. 3. Noise-induced failures in stabilization 1,а
shows PPDs of the escape trajectories of the ADP map, and the corresponding noise
realizations for the exit through the boundary (x"-¢) are shown 1 Fig. 1, b. The picture of
exit through the other boundary (x'+¢)
is symmetrical, so we present results for one
boundary only. It is evident (Fig. 1) Фаг there is the only one exit path. Note, that е
path to the boundary (х" - е) is approximately 2.8 more probable than the path to the
boundary (x"+¢). This difference arises from ап asymmetry of the map in respect оЁ the
boundaries. ry there is the only one exit path, the optimal path апа the Because for each boundary there is the only one exit path, the optimal path апа the
optimal fluctuational force can be determined by simple averaging of escape trajectories
and noise realizations respectively. In Fig. 2 the optimal exit paths and the optimal
fluctuational forces are shown for the boundaries (х*-е) and (x*+¢). The paths and the
forces coincide with а solution оё the boundary problem (circles in the Fig. 2) оЁ the
extended linear тар (14). As сап be seen the optimal ра is long, and the amplitude of the
fluctuational force increases slowly, in agreement with analysis оё the linearized тар (14). optimal fluctuational force obtained (Fig. 2, b) must correspond [10] ю the fluctuational
The optimal fluctuational force obtained (Fig. 2, b) must correspond [10] ю the
energy-optimal
deterministic
Фогсе
that induced е
stabilization
failure. We
have <„
[
0.04 [На
0.0
№
Fig. 2. The optimal paths (@) and the optimal forces (b) ог exit through the boundary @&-е) (solid line)
and the boundary (r'+&) (dashed line) for ADP map. Circles indicate е optimal paths and forces
obtained by solving the boundary problem for the lincarized extended тар (14). The optimal paths and
forces used in е control procedure аге marked by arrows <„
[
0.04 [На
0.0
№ Fig. 2. The optimal paths (@) and the optimal forces (b) ог exit through the boundary @&-е) (solid line)
and the boundary (r'+&) (dashed line) for ADP map. Circles indicate е optimal paths and forces
obtained by solving the boundary problem for the lincarized extended тар (14). 3. Noise-induced failures in stabilization 3, а dependences of the mean time ( т) between the failures оп фе noise In Fig. 3, а dependences of the mean time ( т) between the failures оп фе noise
intensity D are plotted in the absence, and in the presence, of the control procedure. It is
clear that the mean time (t) is substantially increased by е addition оё фе control, i.e. stability in the face of fluctuations is significantly improved by the addition of the control
scheme. The efficiency of the control procedure depends exponentially [7] оп the amplitude
оё the control force (Fig. 3, b), and there is ап optimal value оё е control force, which 15
very close 10 the value (arrow in Fig. 3, b) оё the optimal fluctuational force. o
>
ЕЕЕ
560850500
—-
104
:
18
2403
— 00
2.0
40°
и„*103
b
Fig. 3. (а) The dependences оё mean time
(т between stabilization failures оп noise intensityD 10 the
absence (circles) and in the presence (crosses) оЁ the control. The size of Ше stabilization region
15
е=0.01. (b) The dependence of the mean time (t) оп the amplitude of the control force и
15 presented for
the ADP method. The value of (х) corresponding to the optimal fluctuational force is marked by the arrow o
—-
18
2403 >
ЕЕЕ
560850500
104
:
— 00
2.0
40°
и„*103
b Fig. 3. (а) The dependences оё mean time
(т between stabilization failures оп noise intensityD 10 the
absence (circles) and in the presence (crosses) оЁ the control. The size of Ше stabilization region
15
е=0.01. (b) The dependence of the mean time (t) оп the amplitude of the control force и
15 presented for
the ADP method. The value of (х) corresponding to the optimal fluctuational force is marked by the arrow 52 <х>
0.75
0.0
$5
et еНе
-В
-8
-4
а
b
Fig. 4. For фе OGY map, the optimal ра (a) and the optimal force () are shown for exit through фе
boundary (x"-e) (crosses) апа the boundary (х`+е) (circles)
Now consider noise-induced stabilization failures for OGY map (6). An analysis of а Fig. 4. For фе OGY map, the optimal ра (a) and the optimal force () are shown for exit through фе
boundary (x"-e) (crosses) апа the boundary (х`+е) (circles)
Now consider noise-induced stabilization failures for OGY map (6). 3. Noise-induced failures in stabilization An analysis of Now consider noise-induced stabilization failures for OGY map (6). An analysis of
the linearized map has shown that the failure occurs as the result of a single fluctuation. We have checked the conclusion by an analysis of the fluctuational trajectories of the
map (6), much as we did for the ADP map. The optimal path and optimal force are shown
in Fig. 4 for both boundaries, (х*+е) апа (х*-е). An exit occurs during one iteration and
there
is no
a prehistory before this iteration. It means that we cannot determine the
moment at which the large fluctuation starts and, consequently, Фаг we cannot control the
stabilization failures. The existence оЁ а long prehistory is thus а key requirement т the
control the large fluctuations. Conclusion We have considered noise-induced failures in the stabilization of ап unstable orbit,
and the problem of how to control such failures. In our investigations, they correspond to
large deviations from stable points. We have shown that noise-induced failures can be
analyzed effectively in terms of linearized noisy maps. Large noise-induced deviations from the fixed point in one-dimensional maps have Large noise-induced deviations from the fixed point in one-dimensional maps have
been analyzed within the framework of the theory of large fluctuations. The key point of
our consideration is that the dynamics оЁ the optimal path, and the optimal fluctuational
force, correspond directly to stabilization failures. We have applied two approaches
-
experimental analysis of the prehistory probability distribution and the solution of the
boundary problem for extended maps
- to determine the optimal path and the optimal
fluctuational force, and we have compared their results. The two approaches give the
same results. A procedure for the control of large fluctuations in one-dimensional maps has been A procedure for the control of large fluctuations in one-dimensional maps has been
demonstrated. It is based on the control concept developed in [7] for continuous systems. We have introduced ап additional control scheme which significantly improves the
stabilization of an unstable orbit in the presence of noise. It was successful for the ADP
method of stabilization, and problematic for the OGY method. We have shown that the
control procedure has limitations connected with the presence of long time prehistory of
large fluctuation. Our consideration of фе control problem is relevant 10 а continuous system which Our consideration of фе control problem is relevant 10 а continuous system which
has а one-dimensional curve in its Poincaré section, e.g. Ше Réssler system. For such
systems we can formulate the control task as that of control at discrete moments of time
(the moments of intersection оё the Poincaré section) by using impulsive forces. The 53 intervals between these moments were used to calculate and to form the necessary control
force. Note (аг а similar approach is widely used in control technology. The main limitation of our present control approach
lies
in
the necessity of intervals between these moments were used to calculate and to form the necessary control
force. Note (аг а similar approach is widely used in control technology. References Reimann Р., апа Talkner Р./! Phys. Rev. Е. Vol. 44, 6348 (1991). 12. Reimann Р., апа Talkner Р./! Phys. Rev. Е. Vol. 44, 6348 (1991). 13. Badii R., Brun E., Finardi M., Flepp L., Holzner R., Parisi J., Re 13. Badii R., Brun E., Finardi M., Flepp L., Holzner R., Parisi J., Reyl C., and
Simonet
J. I/ Rev. Mod. Phys. Vol. 66, 1389 (1994). 13. Badii R., Brun E., Finardi M., Flepp L., Holzner R., Parisi J., Reyl C., and
Simonet
J. I/ Rev. Mod. Phys. Vol. 66, 1389 (1994). Received 12.09.2003 Physics Department, Saratov
State University, Russia
Department of Physics, Lancaster
University, LAI 4YB, UK Conclusion The main limitation of our present control approach
lies
in
the necessity of The main limitation of our present control approach
lies
in
the necessity of
studying the fluctuational dynamics of a given system prior to consideration of its control. Such
a study can be carried out by use of an extended map of the system, if model
equations are known, and/or experimentally by analysis of the fluctuational prehistory
distribution. A system model can be easily written down by determination оЁ the eigenvalue
of a stabilized unstable point: there are many effective methods of doing so [13]. We
thank D.G. Luchinsky and
V. Smelyansky for useful and stimulating
discussions and help. The research was supported by the Engineering and Physical
Sciences Research Council (UK) and INTAS (grant 01-867). References 1. Boccaletti 5., Grebogi C., Гаг Y.C., Mancini H., апа Maza D. // Phys. Rep. Vol. 329, 103 (2000). 2. Ott E., Grebogi C., апа Yorke J. // Phys. Rev. Lett. Vol. 64, 1196 (1990). 2. Ott E., Grebogi C., апа Yorke J. // Phys. Rev. Lett. Vol. 64, 1196 (1990)
3. Dykman M.1., McClintock P.V.E., Smelyanski V.N., Stein N.D., апа Stocks 2. Ott E., Grebogi C., апа Yorke J. // Phys. Rev. Lett. Vol. 64, 1196 (1990)
3. Dykman M.1., McClintock P.V.E., Smelyanski V.N., Stein N.D., апа Stocks 2. Ott E., Grebogi C., апа Yorke J. // Phys. Rev. Lett. Vol. 64, 1196 (1990). 3. Dykman M.1., McClintock P.V.E., Smelyanski V.N., Stein N.D., апа Stocks N 3. Dykman M.1., McClintock P.V.E., Smelyanski V.N., Stein N.D., апа Stocks N.G. . Rev. Lett. Vol. 68, 2718 (1992). 4. Graham R. апа Tel Т. /| Phys. Rev. Lett. Vol. 66, 3089 (1991). 3. Dykman M.1., McClintock P.V.E., Smelyanski V.N., Stein N.D., апа Stocks N.G. . Rev. Lett. Vol. 68, 2718 (1992). // Phys. Rev. Lett. Vol. 68, 2718 (1992). 4. Graham R. апа Tel Т. /| Phys. Rev. Lett. Vol. 66, 3089 (1991). 5. Grassberger Р./! J. Phys. А. Vol. 22, 3283 (1989). 6. Pontryagin L.S. The Mathematical Theory of Optimal Processes (Macmillan, 4. Graham R. апа Tel Т. /| Phys. Rev. Lett. Vol. 66, 3089 (1991). 5. Grassberger Р./! J. Phys. А. Vol. 22, 3283 (1989). 5. Grassberger Р./! J. Phys. А. Vol. 22, 3283 (1989). 6. Pontryagin L.S. The Mathematical Theory of Opti 6. Pontryagin L.S. The Mathematical Theory of Optimal Processes (Macmillan, 7. Smelyanskiy V.N., апа Dykman М.1. _ /! Phys. Rev. Е. Vol. 55, 2516 (1997). 8. Whittle P. Optimal Control: Basics апа Beyond (Wiley, 1996). 8. Whittle P. Optimal Control: Basics апа Beyond (Wiley, 1996). 9. Luchinsky D.G. I/ J. Phys. А. Vol. 30, L577 (1997). 9. Luchinsky D.G. I/ J. Phys. А. Vol. 30, L577 (1997). 10. Khovanov LA., Luchinsky D.G., Mannella R., апа 9. Luchinsky D.G. I/ J. Phys. А. Vol. 30, L577 (1997). 10. Khovanov LA., Luchinsky D.G., Mannella R., апа 10. Khovanov LA., Luchinsky D.G., Mannella R., апа McClintock P.V.E. [l Phys. Rev. Lett. Vol. 85, 2100 (2000). 11. Press W.H. et al. Numerical recipes: the art of scientific computing (Cambridge 11. Press W.H. et al. Numerical recipes: the art of scientific computing (Cambridge
University Press, Cambridge, 1989). 12. ОПТИМАЛЬНЫЙ КОНТРОЛЬ ФЛУКТУАЦИЙ B ПРИМЕНЕНИИ
К ПОДАВЛЕНИЮ ИНДУЦИРОВАННЫХ ШУМОМ НАРУШЕНИЙ
СТАБИЛИЗАЦИИ ХАОСА И.А. Хованов, Н.А. Хованова, P.V.E. McClintock Разрабатывается двойная стратегия управления хаосом
и флуктуациями. Индуцированные шумом нарушения стабилизации неустойчивых орбит в одно-
мерном логистическом отображении рассматриваются как большие флуктуации 54 от устойчивого состояния. Свойства больших флуктуаций проверяются путем
определения
и анализа оптимального
пути
и оптимального флуктуационного
воздействия, соответствующего нарушению стабилизации. Обсуждается проблема
управления индуцированных шумом больших флуктуаций,
и разрабатываются
методы управления. £ Khovanov Гвог Aleksandrovich was born оп October 1971, He was educated
in Physics Department of Saratov State University, gaining his undergraduate degree
in «radiophysics»
п
1993. He
got
а degree
of Candidate
оЁ Physical
апа
Mathematical Sciences (PhD) @ 1997 from Saratov University. Since 1996 he
worked
Assistant
of
nonlinear
dynamics
and
radiophysics
chair
оЁ
Saratov
University and from 1999 he is Assistant Professor of this chair. Scientific interests:
stochastic processes and nonlinear dynamics. E-mail: igor@chaos.ssu.runnet.ra E-mail: igor@chaos.ssu.runnet.ra ^ Khovanova Natalia Aleksandrovna was bom оп June
1972. She was
educated
т
Physics
Department
оЁ
Saratov
State
University,
gaining
his
undergraduate degree in «radiophysics» in 1994. She gained а degree оЁ Candidate
of Physical and Mathematical Sciences (PhD) from Saratov University т 1997. Since 1996 she worked Assistant оЁ general physics chair оЁ Saratov University and
from 1997 she is Assistant Professor of this chair. Scientific interests: stochastic
processes and nonlinear dynamics. Е-тай: khovanova@chaos.ssu.runnet.ru Е-тай: khovanova@chaos.ssu.runnet.ru #
. #
Peter Vaughan Elsmere McClintock was born in Omagh, N.Ireland, оп 17
October 1940. After being educated т Ireland, N. Rhodesia, W.Germany and
England, he read physics at Queen's University Belfast, gaining his BSc м 1962. His doctoral research
in Oxford, under H.M. Rosenberg, was оп spin-phonon
interactions in paramagnetic crystals аг very low temperatures, leading to а DPhil in
1966. During
his subsequent postdoctoral appointment (1966-1968)
at Duke
. University, N. Carolina, Henry Fairbank and Horst Meyer introduced him 10 the
superfluidity and other fascinating properties of liquid helium. Since 1968, when he
came
to Lancaster University, where he
is now Professor of Physics, he has
investigated several topics related to liquid helium, including a measurement of the
Landau critical velocity, studies of the creation and decay оё quantized vortices, апа
helium isotopic separation. He has also contributed 10 е exploration оё а range of fundamental problems in
stochastic nonlinear dynamics and applications to №е cardiovascular system. He holds а DSc from Queen's
University, Belfast, апа 15 а Fellow of the Institute оЁ Physics. E-mail: p.v.e.mcclintock@lancaster.ac.uk 55
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Restricting the distribution of visual attention reduces cybersickness
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Cognitive research
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© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
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regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. Abstract This study investigated whether increased attention to the central or peripheral visual field can reduce motion sick-
ness in virtual reality (VR). A recent study found that increased attention to the periphery during vection was cor-
related with lower self-reported motion sickness susceptibility, which suggests that peripheral attention might be
beneficial for avoiding cybersickness. We tested this experimentally by manipulating visual attention to central vs. peripheral fields during VR exposure. We also measured attention to the periphery during vection and motion sick-
ness susceptibility to attempt to replicate the previous results. In Experiment 1, task-relevant cues to target locations
were provided in the central or peripheral field during navigation in VR, and we found no differences in motion sick-
ness. In Experiment 2, attention to the center or periphery was manipulated with a dot-probe task during passive VR
exposure, and we found that motion sickness was greater in the condition that required attention to the periphery. In
both experiments, there was no correlation between baseline attentional allocation and self-reported motion sickness
susceptibility. Our results demonstrate that restricting attention to the central visual field can decrease cybersickness,
which is consistent with previous findings that cybersickness is greater with large FOV. Keywords Cybersickness, Simulator sickness, Virtual reality, Visually induced motion sickness, Visual attention, Misery
scale, SSQ, MSSQ Introduction Some recent research suggests that allocating attention
to the periphery may reduce motion sickness in virtual
reality, but this has not been directly tested. We tested
this experimentally by manipulating visual attention dur-
ing virtual reality exposure and measuring motion sick-
ness. Contrary to the hypothesized effect, we found that
motion sickness was greater with peripheral attention. We also failed to replicate the previous correlational find-
ings. Our findings potentially have both theoretical and
practical implications. Virtual reality (VR) exposure often results in visually
induced motion sickness (VIMS) symptoms, such as
oculomotor discomfort, eyestrain, and nausea (Gold-
ing, 1998; Weech et al., 2019). It has been estimated that
around 61–80% of the population will experience mild
to severe discomfort during VR interactions (Lawson,
2015). Motion sickness in VR has been termed “Cyber-
sickness,” “Simulator Sickness,” or “Virtual Reality Sick-
ness” (McCauley & Sharkey, 1992; Palmisano et al., 2017;
Saredakis et al., 2020). For consistency purposes, we will
adopt the term “Cybersickness” when referring to VIMS
in VR. According to the sensory conflict theory (Reason,
1978), cybersickness is the result of the sensory mis-
match between the visual and non-visual systems, with
the most prominent being the conflict between the visual
and vestibular inputs. When users experience simulated
movement in VR, they receive visual cues to self-motion *Correspondence:
Jeffrey Allen Saunders
jsaun@hku.hk
1 Department of Psychology, University of Hong Kong, Hong Kong, Hong
Kong Sai Ho Yip1 and Jeffrey Allen Saunders1* Sai Ho Yip1 and Jeffrey Allen Saunders1* Sai Ho Yip1 and Jeffrey Allen Saunders1* Cognitive Research: Principles
and Implications Cognitive Research: Principles
and Implications Cognitive Research: Principles
and Implications Yip and Saunders
Cognitive Research: Principles and Implications
https://doi.org/10.1186/s41235-023-00466-1 Yip and Saunders
Cognitive Research: Principles and Implications
https://doi.org/10.1186/s41235-023-00466-1 (2023) 8:18 *Correspondence:
Jeffrey Allen Saunders
jsaun@hku.hk
1 Department of Psychology, University of Hong Kong, Hong Kong, Hong
Kong Visual attention and cybersickness Wei et al. (2018) proposed that reallocation of visual
attention may help mitigate cybersickness and observed
some supporting correlational evidence. They meas-
ured the degree of attention allocation to the central and
peripheral visual fields during vection—a visually induced
sense of self-motion that is commonly experienced dur-
ing VR exposure (Weech et al., 2019)—and asked the
subjects to report their motion sickness susceptibility
using the Motion Sickness Susceptibility Questionnaire
Short-form (MSSQ-Short). Wei et al. (2018) found that
greater attention to the peripheral visual field (PVF) dur-
ing vection was correlated with lower self-rated general
susceptibility to motion sickness.i This explanation for FOV effects suggests that
increased attention to the CVF, rather than the PVF,
would reduce cybersickness. Forcing VR users to restrict
their attention to their CVF might decrease the contribu-
tion of peripheral motion information, similar to restrict-
ing FOV, and thereby reduce cybersickness. However, restricting attention to the CVF may not be
equivalent to removing peripheral information entirely,
and attention allocation might affect cybersickness in
other ways. It remains possible that removing periph-
eral motion cues can reduce motion sickness in VR, but
increased attention to the visual periphery can also miti-
gate cybersickness. Wei et al. (2018) attributed their findings to the con-
flict-reducing mechanism proposed by Brandt et al.,
(1998, 2002). When experiencing the same level of sen-
sory conflicts, different individuals may exhibit varying
motion sickness severity based on their ability to regu-
late visual and vestibular inputs. Those who exhibit fewer
VIMS symptoms when experiencing vection possess the
ability to downregulate vestibular inputs, while simulta-
neously strengthening the visual system signals. Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 2 of 18 would be expected to produce more cybersickness, which
is contrary to the empirical findings.f without corresponding vestibular cues (Weech et al.,
2019). It has been theorized that incongruent sensory
cues can trigger a response to possible poisoning, leading
to VIMS symptoms (Keshavarz & Hecht, 2012). i
A possible explanation for the effect of FOV on cyber-
sickness is that peripheral motion information increases
the visual–vestibular conflict that arises when a station-
ary observer is presented with simulated self-motion
(Weech et al., 2019). With large FOV, the visual cues to
self-motion would be stronger due to the peripheral
input, so there would be more conflict with non-visual
cues that specify that the observer is stationary.hf Current study: manipulating visual attention during a VR
task Although the results of Wei et al. (2018) suggest that vis-
ual attention to the PVF can reduce cybersickness, there
are some limitations to their study that make it difficult
to draw a strong conclusion. First, Wei et al. (2018) only
measured self-reported susceptibility to motion sickness
and did not measure actual motion sickness experienced
during vection. Second, Wei et al. (2018) did not manipu-
late their subjects’ visual attention, so the relationship
between visual attention and VIMS susceptibility was
merely correlational. To demonstrate a causal relation-
ship between visual attention and cybersickness, it would
be necessary to manipulate subjects’ visual attention allo-
cation when performing a VR task.h It has been hypothesized that people tend to rely on
their visual periphery more than the central visual field
(CVF) inputs to determine self-motion (Dichgans &
Brandt, 1978; Ungerleider, 1994). Wei et al. (2018) argue
that increased attention to the PVF will make visual sim-
ulations of self-motion more convincing and strengthen
the perception of self-motion. Increased attention to
visual information about self-motion could also reduce
attention to vestibular inputs. The combination of
strengthening the reliability of visual motion information
and downplaying vestibular signals might help people to
minimize the visual–vestibular conflict experienced dur-
ing vection. The present study tested the relationship between
attention allocation and cybersickness by manipulating
visual attention during VR exposure and directly meas-
uring experienced cybersickness. Subjects performed a
navigation task (Experiment 1) or passively viewed sim-
ulated motion (Experiment 2) in conditions that were
expected to produce some motion sickness symptoms. Separate conditions were designed to encourage atten-
tion to either central or peripheral vision, and subjects
rated their motion sickness using standard subjective
measures. Preregistrationh The methods and analysis plan were preregistered on
the Open Science Framework (OSF) before data collec-
tion: https://osf.io/rfzwt. One deviation from the pre-
registration is that we used the median response times,
estimated by the Hodges–Lehmann estimator, rather
than mean response times for our analysis of the SART
results. We used the robust measure to reduce the influ-
ence of outliers in response times. This choice did not
change any qualitative results. In the preregistration,
we stated that the SSQ scores would be transformed by
log10(SSQ + 10). We instead used an equivalent trans-
form log10(SSQ/10 + 1). The results are identical except
for a constant shift, which has no effect on statistical test
results. We also performed some exploratory analyses in
Experiment 1 that were not preregistered. There were no
other deviations from the preregistered plan. If heightened attention to the periphery during simu-
lated motion decreases cybersickness, as proposed by
Wei et al. (2018), this would predict: • H1: For the virtual reality exposure conditions, sub-
jects in the peripheral-cued condition would experi-
ence less cybersickness.f • H2: Individual differences in performance for PVF
vs CVF stimuli in the SART task would be negatively
correlated with self-reported motion sickness suscep-
tibility, with increased attention to PVF associated
with a decreased tendency toward motion sickness. • H3: Individual differences in SART performance
would also be negatively correlated with the overall
cybersickness experienced in the VR exposure condi-
tions. Experiment 1 In Experiment 1, we tested whether allocating atten-
tion to the peripheral visual field during virtual naviga-
tion reduces the severity of cybersickness. Attention was
manipulated by presenting task-relevant visual cues in
either the peripheral or central regions of the display, and
motion sickness in peripheral and central conditions was
compared. In addition to the virtual navigation task, sub-
jects performed the SART task and reported their motion
sickness susceptibility to test whether we could replicate
the correlation observed by Wei et al. (2018). We also attempted to replicate the finding by Wei et al. (2018) that attentional allocation during vection is cor-
related with general motion sickness susceptibility. In
addition to the VR exposure task, subjects completed
the Motion Sickness Susceptibility Questionnaire Short-
form (MSSQ-Short) to measure their VIMS susceptibility
and performed the Sustained Attention to Response Task
(SART) based on Wei et al. (2018). SART is a reaction
task that can measure the relative amount of attention
allocated to CVF and PVF during vection. Field of view and cybersicknessh The idea that more attention to the visual periphery
reduces cybersickness appears to conflict with the results
of other studies that have found that a large field of view
(FOV) increases cybersickness (Lin et al., 2002; Rebe-
nitsch & Owen, 2016; Saredakis et al., 2020; Seay et al.,
2002; Weech et al., 2019). Restricting the FOV removes
peripheral motion information and likely results in a
narrower range of attention. If attention to the periph-
eral motion helps to reduce cybersickness, a small FOV In Experiment 1, we manipulated visual attention
by presenting task-relevant visual cues in either the
peripheral or central regions of the displays. In the Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 3 of 18 peripheral-cued condition, targets were highlighted
when they were in the outer periphery of the visual dis-
plays, which is expected to increase attention to the PVF. In the central-cued condition, targets were highlighted
only when in the center of the visual displays, which
would tend to increase attention to the CVF. The visual
information about self-motion would not be affected by
the highlighting of targets, so any effects on cybersick-
ness could be attributed to differences in attentional allo-
cation. A drawback of this approach is that it is hard to
control fixation. In Experiment 2, we manipulated atten-
tion by superimposing a dot-probe task during exposure
to provide a stronger manipulation. tion to PVF associated with a greater tendency
toward motion sickness. • H3a: Individual differences in SART performance
would also be positively correlated with the overall
cybersickness experienced in the VR exposure condi-
tions. • H3a: Individual differences in SART performance
would also be positively correlated with the overall
cybersickness experienced in the VR exposure condi-
tions. Virtual navigation task For the virtual navigation task, subjects “moved” through
virtual environments with scattered treasure chests. They
were instructed to collect as many treasure chests as pos-
sible within a set amount of time (8 min). The chests were
partially hidden inside bushes but were highlighted in red
whenever they are in either the center or periphery of the
display, depending on the experimental condition.h The virtual environments used in this task were coded
with Unity version 2018.3.14f1 and presented using an
HTC Vive head-mounted display (HMD). The scenes
were rendered at a refresh rate of 90 Hz, with a resolu-
tion of 1080 × 1200 per eye (2160 × 1200 combined). The
software field of view (FOV) was set to match the field
of view of the displays. Heading movement was tracked
at 90 Hz and used to continuously update the simulated
views. Simulated movement through the environment
was controlled using the HTC Vive controller touchpad. The upper and lower parts of the trackpad were used to
control forward and backward simulated movement, and
the left and right parts of the trackpad were used to con-
trol simulated rotation. The forward/backward speed was
6 m/s, and the rotation rate was 40°/s. overall Type I error rate less than 5% with no adjust-
ment of the test alpha (i.e., the standard alpha of .05
is used to determine statistical significance). Allowing
the procedure to stop early when an interim test finds
a significant difference would increase the overall Type
I rate, but allowing the procedure to stop early when
an interim test finds no difference would decrease the
overall Type I rate. The stopping criteria were chosen
to balance these two effects. The procedure is similar
to some previously proposed methods that use p values
from interim tests to determine stopping: the compos-
ite-limited-adaptive-sequential test procedure (Botella
et al., 2006), and the variable-criteria sequential stop-
ping rule procedure (Fitts, 2010). Two attention allocation conditions were tested in a
within-subject design (Fig. 1–upper row). In the central-
cued condition, the chests were highlighted when they
are located inside a 10° diameter cone around the forward
direction of the head. In addition, subjects were verbally
encouraged to pay more attention to the CVF. A white
transparent reference point was provided, which allowed
the subjects to know where the center of the display was. Participants
S Alternatively, attending to the periphery during simu-
lated motion might produce more cybersickness than
attending to the central visual field. This would be con-
sistent with findings that cybersickness increases with
larger FOVs (Lin et al., 2002; Rebenitsch & Owen, 2016;
Saredakis et al., 2020; Weech et al., 2019). If so, this
would predict: Sixteen people participated in this experiment. The sam-
ple consisted of 7 males and 9 females, with ages between
21 and 24 years old (M = 22.4, SD = 1.09). Subjects were
recruited primarily through personal connections and
were paid $200 HKD as compensation. All subjects
reported that they had normal or corrected-to-normal
vision, and no history of impairment in vestibular or neu-
rological functioning.h • H1a: Subjects in the peripheral-cued exposure condi-
tion would experience more cybersickness.f The sample size was determined by a sequential
procedure, shown in Table 1. The interim test used to
determine stopping was a t test comparing the MISC
ratings in the peripheral-cued and central-cued condi-
tions. The stopping criteria were designed to keep the • H2a: Individual differences in performance for PVF
vs CVF stimuli would be positively correlated with
motion sickness susceptibility, with increased atten- Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 4 of 18 Page 4 of 18 Table 1 The sequential procedure used to determine sample
size
Interim N
p value
Action and interpretation
n = 16
p < .01
Stop, significant difference
p > .30
Stop, no significant difference
.01 ≤ p ≤ .30
Continue until n = 24
n = 24
p < .02
Stop, significant difference
p > .20
Stop, no significant difference
.02 ≤ p ≤ .20
Continue until n = 32
n = 32
p < .05
Stop, significant difference
p ≥ .05
Stop, no significant difference Sustained Attention to Response Task (SART) Sustained Attention to Response Task (SART)
For the Sustained Attention to Response Task (SART),
subjects fixated on a central point and responded when-
ever a dot of a certain color appeared. During the SART
task, subjects were presented with a rotating dot pattern Virtual navigation task For the peripheral-cued condition, the chests were only
highlighted when they are located more than 40° away
from the center measured horizontally, and subjects were
told to attend more to their PVF. For both attention allo-
cation conditions, chests were only highlighted when
they were within 50 m of the player. The procedure was designed to detect a medium-to-
large effect size with high efficiency. We had no prior
basis for estimating the effect size for the experimental
manipulation, and we planned to do a follow-up experi-
ment to investigate any effects or trends that were
observed in Experiment 1. The power and false-positive
rate of the procedure were estimated by performing
simulations, with 108 simulations per case. For the null
case, simulation results confirmed that the overall Type
I rate was less than 5%, with an average n = 19.3. Simu-
lations of nonzero effects found that the procedure has
94% power to detect an effect with dz = 0.7, with an
average n = 20.9, and 72% power to detect an effect with
dz = 0.5, with an average n = 23.1. The power as a func-
tion of effect size is approximately the same as using a
fixed sample size of n = 28. In Experiment 1, the proce-
dure stopped at the first interim stage (p = .608) with a
sample size of n = 16. To prevent subjects from remembering the chest loca-
tions across conditions, two similar virtual forests were
constructed. The only difference between the forests was
the specific locations of the trees, bushes, and chests. Each virtual forest consisted of 150 empty bushes, 39
bushes with a chest, and 185 trees. The order of the two
attention allocation conditions and pairing with the two
virtual forests were fully counterbalanced. Apparatus and stimuli Experiment 1 consisted of two tasks, the virtual naviga-
tion task and the Sustained Attention to Response Task
(SART) based on Wei et al. (2018). Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 5 of 18 Fig. 1 Screenshots from the central-cued and peripheral-cued conditions of Experiment 1 (top) and Experiment 2 (bottom). In Experiment 1,
subjects navigated in a virtual environment to find targets chests that were obscured by bushes. The chests were sometimes highlighted in red
depending on their position and the attentional cueing condition. In the central-cued condition (top left), targets were highlighted when their
direction was within 10° of the central direction and less than 50 m away. In the peripheral-cued condition (top right), targets were highlighted
when they were at least 40° to the left or right of the center and less than 50 m away. In Experiment 2, subjects passively viewed simulated
movement through an environment while performing dot-probe task. In the central-cued condition (bottom left), the superimposed dots
appeared within 5° of the center of the display. In the peripheral-cued condition (bottom right), the dots appeared in an annulus between 20 and
30° from the center Fig. 1 Screenshots from the central-cued and peripheral-cued conditions of Experiment 1 (top) and Experiment 2 (bottom). In Experiment 1,
subjects navigated in a virtual environment to find targets chests that were obscured by bushes. The chests were sometimes highlighted in red
depending on their position and the attentional cueing condition. In the central-cued condition (top left), targets were highlighted when their
direction was within 10° of the central direction and less than 50 m away. In the peripheral-cued condition (top right), targets were highlighted
when they were at least 40° to the left or right of the center and less than 50 m away. In Experiment 2, subjects passively viewed simulated
movement through an environment while performing dot-probe task. In the central-cued condition (bottom left), the superimposed dots
appeared within 5° of the center of the display. In the peripheral-cued condition (bottom right), the dots appeared in an annulus between 20 and
30° from the center Peripheral:
Fig. 2 The Sustained Attention to Response Task (SART). Subjects fixated at a center point and a field of random dots rotated around the center. At
random intervals, a red/green dot would appear either in the central region or the peripheral region Peripheral: Fig. was set to 72 cm, and the FOV of the projection area was
93.5° × 61.8°. The refresh rate was 60 Hz.
Static green/red dots either appeared inside the CVF
region (FOV: 0°–2.1°) or the PVF region (FOV: 7.9°–
24.9°) of the projection. Each colored dot was one SART
trial. Subjects were required to respond to the red dots
and ignore the green dots. The response time to each red Apparatus and stimuli There were 200 SART trials in total, split between the two
sessions. In each session, the SART trials were divided
into four different types (10 × Green-CVF, 10 × Green-
PVF, 40 × Red-CVF, 40 × Red-PVF) and presented in a
randomized order. dot was recorded and used for data analysis. The colored
dots were presented for a duration of 500 ms, and the
inter-trial interval varied between 1000 and 1500 ms. There were 200 SART trials in total, split between the two
sessions. In each session, the SART trials were divided
into four different types (10 × Green-CVF, 10 × Green-
PVF, 40 × Red-CVF, 40 × Red-PVF) and presented in a
randomized order. Attention allocation tendencyh The attention allocation tendency of individuals dur-
ing the SART task was quantified using the reaction
times to CVF and PVF stimuli. We first computed the
median response times to CVF and PVF stimuli using
the Hodges–Lehmann estimator, which is a robust esti-
mator of central tendency that is more efficient than the
sample median (Hodges & Lehmann, 1963). We then
computed the difference between response times to CVF
and PVF stimuli, ΔRT = RTCVF – RTPVF. Higher values of
ΔRT indicate relatively more attention to the PVF during
vection. Misery scale (MISC)h As in Wei et al. (2018), we used the Motion Sickness Sus-
ceptibility Questionnaire Short-form (Golding, 1998) to
measure subjects’ general susceptibility to motion sick-
ness. This self-report questionnaire consisted of 18 items. Each item measured the frequency of motion sickness
(i.e., sickness and nausea) when exposed to a particular
type of transportation/entertainment (e.g., small boat,
roundabout) on a scale of 0–3. The MSSQ can generate
a total score, child and adult subscale scores. The child
subscore indicates the motion sickness susceptibility
level before the age of 12, while the adult subscore repre-
sents the susceptibility over the last 10 years. The Misery Scale (Bos et al., 2005) served as the primary
indicator of cybersickness experienced during virtual
reality exposure. It is a fast single-item instrument that
monitors the course of cybersickness, without distract-
ing the subjects from the virtual experience (Chang et al.,
2020). The experimenter prompted the subjects to orally
report a MISC score every 2 min of VR exposure. A
MISC score can range from 0 to 10, with 0 indicating no
discomfort, 6 suggesting a slight sense of nausea, and 10
representing vomiting. The MISC scores used for the main analyses were from
one of the four exposure blocks, selected based on com-
pletion rate. We expected that some subjects would not
be able to complete all four exposure blocks. To ensure
that the subjects only experienced mild cybersickness,
the virtual navigation task was immediately stopped
whenever symptoms were rated as 6 or more on the
MISC scale. If only a small number of participants were
unable to complete all four exposure blocks (< 25% of
total subjects), we planned to use the MISC scores from
the last completed blocks for analysis. However, if a
larger number of subjects were unable to reach the final
block (25% or more of total subjects), MISC scores from
an earlier block would be used instead. We planned to
select the last block that at least 75% of subjects were able
to complete and use the MISC scores from that block for
analysis, or the MISC scores from the final completed
block for subjects who stopped earlier than the selected
block. Apparatus and stimuli 2 The Sustained Attention to Response Task (SART). Subjects fixated at a center point and a field of random dots rotated around the center. At
random intervals, a red/green dot would appear either in the central region or the peripheral region was set to 72 cm, and the FOV of the projection area was
93.5° × 61.8°. The refresh rate was 60 Hz. was set to 72 cm, and the FOV of the projection area was
93.5° × 61.8°. The refresh rate was 60 Hz. Static green/red dots either appeared inside the CVF
region (FOV: 0°–2.1°) or the PVF region (FOV: 7.9°–
24.9°) of the projection. Each colored dot was one SART
trial. Subjects were required to respond to the red dots
and ignore the green dots. The response time to each red to invoke vection (Fig. 2). The pattern consisted of
600–650 gray dots on a black background that rotated
anticlockwise at 32° per second. An additional gray dot
located at the center of the screen served as the fixation
marker, occupying 1.2° of the subjects’ FOV. The dis-
plays were presented with a BenQ HT4050 DLP Projec-
tor and a back-projection screen. The viewing distance h
Static green/red dots either appeared inside the CVF
region (FOV: 0°–2.1°) or the PVF region (FOV: 7.9°–
24.9°) of the projection. Each colored dot was one SART
trial. Subjects were required to respond to the red dots
and ignore the green dots. The response time to each red h
Static green/red dots either appeared inside the CVF
region (FOV: 0°–2.1°) or the PVF region (FOV: 7.9°–
24.9°) of the projection. Each colored dot was one SART
trial. Subjects were required to respond to the red dots
and ignore the green dots. The response time to each red Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 6 of 18 The SSQ scores were transformed and normal-
ized before performing statistical analysis. First, a
log transform was applied to the raw SSQ scores,
log10(SSQ/10 + 1), to reduce the skew of distributions. We further normalized the SSQ scores to compensate for
any pre-exposure symptoms by subtracting the pre-expo-
sure log-transformed SSQ scores from the post-exposure
log-transformed SSQ scores. dot was recorded and used for data analysis. The colored
dots were presented for a duration of 500 ms, and the
inter-trial interval varied between 1000 and 1500 ms. Procedureh This study was a two-day experiment. At the beginning
of the first session, we administered the Motion Sickness
Susceptibility Questionnaire Short-form (MSSQ-Short). Subjects then performed a block of SART trials. After
finishing the SART task, subjects were given a break to
recover from any motion sickness symptoms. They then
completed the pre-test Simulator Sickness Questionnaire
(SSQ) and Misery Scale (MISC), followed by the virtual
reality navigation task. The experimenter helped the sub-
ject put on the HMD and ensured that it was securely
attached and centered. After they completed the virtual
navigation, subjects completed the post-test SSQ. The
second experimental session was the same as the first ses-
sion except that the MSSQ-Short was not administered. Central‑cued vs. peripheral‑cued conditions (H1 and H1a) To test the main hypothesis of this study (H1 and H1a),
we conducted paired-sample t tests to compare the mean
cybersickness scores (MISC and SSQ) in the two atten-
tion allocation conditions. Statistical tests were con-
ducted on the raw MISC scores and the normalized and
transformed SSQ scores. Fig. 3 Percent of subjects who completed each of the virtual
navigation blocks in Experiment 1. The procedure was stopped if
subjects reported more than mild motion sickness symptoms (>6 on
MISC scale). Less than half of the subjects were able to complete the
full 8 min of exposure Q
The results did not reveal any reliable difference
between the cybersickness induced in the central-cued
and peripheral-cued conditions. Figure 4 plots the mean
MISC and SSQ scores for the two attention allocation
conditions. There was a trend toward less motion sick-
ness in the peripheral-cued condition, but this trend
was not statistically significant for either motion sick-
ness measure. There was no significant difference
between the mean MISC scores in the central-cued
condition (M = 2.125, SD = 2.217) and the peripheral-
cued condition (M = 1.813, SD = 1.797), t(15) = 0.524,
p = .608, dz = 0.131. Similarly, for the SSQ scores, there
was no significant difference between the change in
log10(SSQ-T/10 + 1)
in
the
central-cued
condition
(M = 0.328, SD = 0.196) and in peripheral-cued condition
(M = 0.276, SD = 0.283), t(15) = 0.635, p = .535, dz = 0.159. We also compared results from the SSQ subscales and
found no differences between the attentional allocation
conditions (nausea: t(15) = 0.544, p = .595, dz = 0.136; ocu-
lomotor disturbances: t(15) = 0.137, p = .893, dz = 0.034;
disorientation: t(15) = 1.249, p = .231, dz = 0.312). Overall,
our results provide no evidence that the attention manip-
ulation affected cybersickness. For the SART task, subjects were instructed to keep
their eyes on the fixation marker and press the “Shift”
key whenever a red dot appeared on the screen. A SART
block included 100 trials presented over a period of about
4 min. We limited the duration of the SART task to avoid
causing motion sickness symptoms. g
y
For the navigation task, subjects were given 8 min to
“collect" treasure chests scattered in the forest. Treas-
ure chests were collected by moving close to the chests,
which triggered an animation of the chest opening. Attention allocation tendency during vection y
Attention allocation tendency and MSSQ‑short (H2 and H2a)
We performed correlation analyses to test the relation-
ship between attention allocation tendency during the
SART task and self-reported motion sickness susceptibil-
ity (H2 and H2a), as measured by the MSSQ-Short total
scores and the two MSSQ-Short subscale scores (child
and adult). Based on the findings of Wei et al. (2018),
increased attention to the PVF was expected to be asso-
ciated with lower self-reported motion sickness suscep-
tibility. This was not observed. Figure 5 plots the score
from the three MSSQ-Short measures as a function of
the attentional allocation score (ΔRT). We did not find
a significant correlation between attention allocation Simulator Sickness Questionnaire (SSQ)h The Simulator Sickness Questionnaire (Kennedy et al.,
1993) was our secondary measurement of experienced
cybersickness. This self-report questionnaire is widely
used as a subjective indicator of cybersickness (Chang
et al., 2020; Weech et al., 2019). We administered the SSQ
to subjects immediately before and after VR exposure. The SSQ consists of 16 items, with each question captur-
ing the severity of a particular motion sickness symptom
(e.g., headache, nausea) on a scale of 0–3. Responses were
summed to obtain an SSQ total score, and scores for the
nausea, oculomotor, and disorientation subscales. Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 7 of 18 Percent completed
0%
25%
50%
75%
100%
Exp 1 - Virtual Navigation Completion Rate
2 Mins
4 Mins
6 Mins
8 Mins
Exposure Time
Fig. 3 Percent of subjects who completed each of the virtual
navigation blocks in Experiment 1. The procedure was stopped if
subjects reported more than mild motion sickness symptoms (>6 on
MISC scale). Less than half of the subjects were able to complete the
full 8 min of exposure Exp 1 - Virtual Navigation Completion Rate exposure blocks. The last block that was completed by at
least 75% of subjects was the 4-min block (87.5%, n = 14). Therefore, we used the MISC scores from the 4-min
block for all subjects that completed the second block,
and the MISC scores from the 2-min block for those who
stopped earlier. Central‑cued vs. peripheral‑cued conditions (H1 and H1a) Subjects remained seated when performing the virtual
navigation. To manipulate visual attention, central or
peripheral cues (i.e., chests being highlighted with a red
outline) were provided depending on the experimen-
tal condition. Every two minutes during the exposure,
subjects were asked to verbally report their MISC rat-
ing of cybersickness symptoms. The virtual task was ter-
minated immediately whenever the subjects reported
a MISC score ≥ 6, or by their request due to significant
discomfort. Before performing the virtual navigation, subjects per-
formed a short practice block to familiarize themselves
with the navigation and task. The virtual environment
for practice was a single room with four treasure chests. Subjects moved to collect the four treasure chests before
proceeding to the main navigation task. Cybersickness during VR Exposure
Virtual navigation completion rate Cybersickness during VR Exposure
Virtual navigation completion rate Before comparing the cybersickness in the two condi-
tions, we determined the exposure block to be used for
the analysis of MISC scores, following our preregistered
plan. Figure 3 shows the percentage of subjects that were
able to complete each of the four blocks. Only 43.75%
of the participants (n = 7) were able to complete all four Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 8 of 18 3.0
2.0
2.5
1.5
0.5
0
1.0
Exp 1 - MISC scores
Exp 1 - transformed SSQ scores
mean MISC scores
Central
cued
Peripheral
cued
Central
cued
Peripheral
cued
1.0
.75
.25
0
.50
mean log10(SSQ/10+1)
Pre
Post
Pre
Post
Fig. 4 Motion sickness in the central-cued (red) vs peripheral-cued (blue) conditions of Experiment 1. The left graph plots mean MISC scores. The
right graph plots mean SSQ scores after transforming by log10(SSQ/10 + 1). Pre-exposure SSQ scores are shown in gray. Error bars depict standard
errors of the mean 3.0
2.0
2.5
1.5
0.5
0
1.0
Exp 1 - MISC scores
mean MISC scores
Central
cued
Peripheral
cued Exp 1 - transformed SSQ scores Fig. 4 Motion sickness in the central-cued (red) vs peripheral-cued (blue) conditions of Experiment 1. The left graph plots mean MISC scores. The
right graph plots mean SSQ scores after transforming by log10(SSQ/10 + 1). Pre-exposure SSQ scores are shown in gray. Error bars depict standard
errors of the mean Exp 1 - Attention Allocation vs Motion Sickness Susceptibility 0
10
20
30
40
0
5
10
15
20
0
5
10
15
20
SART ∆RT (ms)
SART ∆RT (ms)
SART ∆RT (ms)
0
-50 -25
-75
0
0
0
1
-
-50 -25
-75
0
0
0
1
-
-50 -25
-75
-100
MSSQ-Total
MSSQ-Child
MSSQ-Adult
r = .052
p = .848
r = .052
p = .848
r = .049
p = .858
Exp 1 - Attention Allocation vs Motion Sickness Susceptibility
Fig. 5 Self-reported motion sickness susceptibility (MSSQ) of individual subjects in Experiment 1 plotted as a function of their attentional
allocation scores derived from SART. The attentional allocation score is the mean difference in reaction times for peripheral and central targets:
ΔRT = RTCVF − RTPVF. Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. Exp 1 - Attention Allocation vs Motion Sickness Susceptibility 0
5
10
15
20
SART ∆RT (ms)
0
-50 -25
-75
0
0
1
-
MSSQ-Child
r = .052
p = .848 0
5
10
15
20
SART ∆RT (ms)
0
-50 -25
-75
-100
MSSQ-Adult
r = .049
p = .858 0
10
20
30
40
SART ∆RT (ms)
0
-50 -25
-75
0
0
1
-
MSSQ-Total
r = .052
p = .848 Fig. 5 Self-reported motion sickness susceptibility (MSSQ) of individual subjects in Experiment 1 plotted as a function of their attentional
allocation scores derived from SART. The attentional allocation score is the mean difference in reaction times for peripheral and central targets:
ΔRT = RTCVF − RTPVF. Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. The left graph plots the
total MSSQ scores, and the middle and right graphs plot the MSSQ child and MSSQ adult subscores and the MSSQ-Short total scores (r(14) = .052, p = .848),
MSSQ-Short child subscores (r(14) = .052, p = .848), or
MSSQ-Short adult subscores (r(14) = .049, p = .858). The results showed no evidence for a linear relationship
between attention allocation tendency during vection
and self-reported motion sickness susceptibility scores. vection and the overall cybersickness experienced in
the virtual navigation task (H3 and H3a). Measures of
the overall cybersickness level for each subject were
computed by averaging the post-exposure MISC or
SSQ scores from the central-cued and peripheral-cued
conditions. We did not detect a correlation between attention allo-
cation scores (ΔRT) and the MISC scores (r(14) = − .233,
p = .385) or the SSQ scores (r(14) = − .194, p = .470). Fig-
ure 6 plots the two cybersickness measures as a function
of the attention allocation scores. Although there was a Cybersickness during VR Exposure
Virtual navigation completion rate The left graph plots the
total MSSQ scores, and the middle and right graphs plot the MSSQ child and MSSQ adult subscores Exp 1 - Motion Sickness Susceptibilty vs Experienced Cybersickness MSSQ-Total
0
20
40
30
10
0
1
2
3
4
5
MSSQ-Total
0
.25
.50
.75
1.00
1.25
0
20
40
30
10
MISC score
log10(SSQ/10+1)
r = .558
p = .025
r = .448
p = .082
MISC score
Transformed SSQ
p
p
y
p
y
Fig. 7 Cybersickness experienced by individual subjects in
Experiment 1 plotted as a function of self-reported motion sickness
susceptibility (MSSQ total). Lines show the regression fits. The left
graph plots the MISC scores and right graph plots the SSQ after
transforming by log10(SSQ/10 + 1) MSSQ-Total
0
20
40
30
10
0
1
2
3
4
5
MISC score
r = .558
p = .025
MISC score MSSQ-Total
0
.25
.50
.75
1.00
1.25
0
20
40
30
10
log10(SSQ/10+1)
r = .448
p = .082
Transformed SSQ Attention allocation tendency and cybersickness (H3
and H3a) We performed exploratory analyses to examine the rela-
tionship between attention allocation tendency during Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Yip and Saunders Cognitive Research: Principles and Implications Page 9 of 18 SART ∆RT (ms)
0
-50 -25
-75
-100
0
1
2
3
4
5
MISC score
SART ∆RT (ms)
0
.25
.50
.75
1.00
1.25
0
-50 -25
-75
-100
Transformed SSQ
MISC score
log10(SSQ/10+1)
r = –.23
p = .39
r = –.19
p = .47
Exp 1 - Attention Allocation vs Experienced Cybersickness
Fig. 6 Cybersickness experienced by individual subjects during
virtual navigation in Experiment 1 plotted as a function of their
attentional allocation scores derived from SART (ΔRT = RTCVF − RTPVF). Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. The left graph plots the MISC scores
and the right graph plots the SSQ scores after transforming by
log10(SSQ/10 + 1)
MSSQ-Total
0
20
40
30
10
0
1
2
3
4
5
MSSQ-Total
0
.25
.50
.75
1.00
1.25
0
20
40
30
10
MISC score
log10(SSQ/10+1)
r = .558
p = .025
r = .448
p = .082
MISC score
Transformed SSQ
Exp 1 - Motion Sickness Susceptibilty vs Experienced Cybersickness
Fig. 7 Cybersickness experienced by individual subjects in
Experiment 1 plotted as a function of self-reported motion sickness
susceptibility (MSSQ total). Lines show the regression fits. The left
graph plots the MISC scores and right graph plots the SSQ after
transforming by log10(SSQ/10 + 1) SART ∆RT (ms)
0
-50 -25
-75
-100
0
1
2
3
4
5
MISC score
SART ∆RT (ms)
0
.25
.50
.75
1.00
1.25
0
-50 -25
-75
-100
Transformed SSQ
MISC score
log10(SSQ/10+1)
r = –.23
p = .39
r = –.19
p = .47
Exp 1 - Attention Allocation vs Experienced Cybersickness
Fig. 6 Cybersickness experienced by individual subjects during
virtual navigation in Experiment 1 plotted as a function of their
attentional allocation scores derived from SART (ΔRT = RTCVF − RTPVF). Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. The left graph plots the MISC scores
and the right graph plots the SSQ scores after transforming by
log10(SSQ/10 + 1) Exp 1 - Attention Allocation vs Experienced Cybersickness moderately predictive of cybersickness in our virtual nav-
igation task. Visual attention allocation and motion sickness
susceptibility We were not able to replicate the results reported by Wei
et al. (2018). We did not observe a significant relationship
between the attention allocation scores and self-reported
motion sickness susceptibility. There was also no signifi-
cant correlation between the measures derived from the
SART task and experienced cybersickness. Fig. 7 Cybersickness experienced by individual subjects in
Experiment 1 plotted as a function of self-reported motion sickness
susceptibility (MSSQ total). Lines show the regression fits. The left
graph plots the MISC scores and right graph plots the SSQ after
transforming by log10(SSQ/10 + 1) p
y
Our inability to replicate the results by Wei et al. (2018)
could be due to the differences in the measure of atten-
tional allocation. In the original study, subjects per-
formed the SART during coherent background motion
that induces vection and also during incoherent motion. The incoherent motion condition was used as a baseline
when computing the measure of attention allocation. In
our Experiment 1, we only tested SART with the vec-
tion-inducing background motion, so our measure did
not normalize for any differences in attention allocation
during incoherent motion. If a tendency to attend to the
periphery during vection is associated with decreased
motion sickness susceptibility, either measure of atten-
tional allocation would be expected to show a negative
correlation. However, it is possible that our measure was
less sensitive. To test whether the difference in measures
could account for our failure to replicate Wei et al. (2018)
in Experiment 1, we performed a closer replication in
Experiment 2. Our inability to replicate the results by Wei et al. (2018)
could be due to the differences in the measure of atten-
tional allocation. In the original study, subjects per-
formed the SART during coherent background motion
that induces vection and also during incoherent motion. h negative trend for both MISC and SSQ scores, neither
showed a statistically significant relation to baseline
attention allocation tendency. Attention allocation tendency and cybersickness (H3
and H3a) SART ∆RT (ms)
0
-50 -25
-75
-100
0
1
2
3
4
5
MISC score
MISC score
r = –.23
p = .39 SART ∆RT (ms)
0
.25
.50
.75
1.00
1.25
0
-50 -25
-75
-100
Transformed SSQ
log10(SSQ/10+1)
r = –.19
p = .47 Manipulation of visual attention and cybersicknessf Manipulation of visual attention and cybersicknessf We found no difference between motion sickness ratings
in the two attention allocation conditions, using either
the MISC or SSQ scores. There was a small trend toward
lower cybersickness in the peripheral-cued condition,
but it was not statistically significant. Our findings do not
provide support for the hypothesis that more attention to
the PVF will alleviate cybersickness level. Fig. 6 Cybersickness experienced by individual subjects during
virtual navigation in Experiment 1 plotted as a function of their
attentional allocation scores derived from SART (ΔRT = RTCVF − RTPVF). Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. The left graph plots the MISC scores
and the right graph plots the SSQ scores after transforming by
log10(SSQ/10 + 1) However, our conclusions are limited by the fact that
the peripheral-cueing effect may have been temporary. For the peripheral-cued condition, it is possible that our
subjects quickly shifted their fixation to the cued location
whenever a chest was highlighted. If so, attention may
have only been briefly reallocated to the periphery in this
condition. In Experiment 2, we addressed this issue by
implementing a stronger manipulation of visual attention
allocation during virtual reality exposure. MSSQ‑short and cybersickness We performed additional exploratory analyses to test
whether MSSQ scores are predictive of experienced
cybersickness. Figure 7 plots the two measures of overall
cybersickness as a function of MSSQ-Short total scores. There was a significant positive correlation between
MSSQ-Short total scores and overall MISC scores,
r(14) = .558, p = .025, and a non-significant trend in the
same direction for the SSQ scores, r(14) = .448, p = .082. Overall, our results suggest that MSSQ-Short scores are Page 10 of 18 Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Apparatus and stimuli Experiment 2 consisted of two tasks: the virtual reality
exposure and the Sustained Attention to Response Task
(SART) based on Wei et al. (2018). Preregistrationh The methods and analysis plan were preregistered on the
Open Science Framework (OSF) before data collection:
https://osf.io/f7q8e. The only deviation was that we used
log10(SSQ/10 + 1) to transform the SSQ scores rather
than log10(SSQ + 10), which has no effect on the statisti-
cal test results. There were no other deviations from the
preregistered plan for Experiment 2. Two attention allocation conditions (Fig. 1—bottom
row) were tested in a within-subjects design. For the cen-
tral-cued condition, the white/black dots only appeared
in the central region of the HMD display (FOV: 0°–5°). The experimenter verbally encouraged the subjects to pay
more attention to the CVF in this condition, and a white
transparent reference point was provided to indicate the
center of the HMD display. For the peripheral-cued con-
dition, the targets appeared in the peripheral region of
the HMD display (FOV: 20°-30°) instead. No reference
point was provided, and the subjects were told to attend
more to their visual peripheral in this condition. The
presentation order of the two attention allocation condi-
tions was counterbalanced. Virtual reality exposure We also modified our method for measuring atten-
tion allocation during vection to more closely match the
method used by Wei et al. (2018). Wei et al. (2018) tested
the SART task with two types of background motion:
coherently rotating dots or incoherently rotating dots. Our Experiment 1 only included the coherently rotating
background. Experiment 2 tested both of the SART con-
ditions, which allowed us to compute the same attention
allocation measure used by Wei et al. (2018). For the VR exposure, subjects viewed a virtual roller-
coaster ride for a maximum duration of 8 min. The virtual
environment in Experiment 2 resembled a cartoon-like
rural region, populated by various ruins, hills, campsites,
trees, and bushes. The virtual scene was coded with Unity
version 2019.4.38f1 and presented with an HTC Vive
HMD. The environment was rendered at a resolution of
2160 × 1200 (1080 × 1200 per eye) at a 90 Hz refresh rate. During the exposure, subjects were “seated” in a self-
moving cart. They were given the ability to translate
head movements to the virtual environment. The cart
moved forward at a constant speed of 20 km/h, follow-
ing an invisible rail track with multiple horizontal turns. Through the ride, subjects were presented with a white/
black dot at a randomized 1500-2000 ms interval. Each
target remained visible on the display for 500 ms. Sub-
jects were instructed to press the “Shift” key when they
detect a white dot, but do nothing for the black dots. Experiment 2 correspond to an effect size of dz = 0.53. Our sample size
provided 90% power to detect an effect size of dz = 0.53
at an alpha level of .05. Our sample size also had at least
84% power to replicate the effect reported in Wei et al. (2018). Their study observed a correlation of r = − .479
between their measure of attention allocation based on
the SART task (TRT) and the total motion sickness sus-
ceptibility measure (MSSQ-T). In this follow-up study, we modified the virtual reality
exposure conditions to provide a stronger test of whether
allocating attention to the central or peripheral visual
field reduces cybersickness. For the virtual reality expo-
sure, we implemented a stronger manipulation of visual
attention allocation and also controlled the simulated
player movement. A dot-probe task resembling the SART
task was integrated into the virtual experience. Subjects
“rode” a virtual rollercoaster ride that was expected to
produce mild cybersickness. Throughout the exposure,
dots were periodically presented in either the central or
peripheral region of the display to encourage sustained
attention to the CVF or PVF, depending on the experi-
mental condition.i Participants Forty subjects participated in Experiment 2. Our sample
consisted of 10 males and 30 females, with ages between
18 and 23 years old (M = 19.075, SD = 1.289). Subjects
were recruited from the population of the University of
Hong Kong and were paid either $100 HKD or course
credits as compensation. We required all subjects to have
normal or corrected-to-normal vision, with no history of
vestibular or neurological functioning impairment.h The sample size was chosen to be able to reliably detect
a mean difference in MISC score of 1 or more and also
be able to replicate the main findings of Wei et al. (2018). The Misery Scale (MISC) is a 10-point self-administered
scale. If our attention manipulation changes the mean
MISC score by less than 1, it would have limited practical
utility. Based on the variability of MISC scores observed
in Experiment 1, a difference in MISC score of 1 would Cybersickness during VR exposure
Virtual reality exposure completion rateh In Experiment 2, we computed two measures of atten-
tion allocation tendency from the response times to CVF
and PVF stimuli in the SART task: The MISC scores used for analysis were chosen based
on the completion rate, as in Experiment 1. Figure 8
plots the percentage of subjects who completed each
exposure block. More than 75% of subjects (n = 31)
were able to complete all four exposure blocks, so we
used the MISC scores from each subject’s last com-
pleted block for analyses. For most subjects, this was
the MISC score from the final exposure block. RTnorm = (RTCVF,Coherent −RTCVF,Incoherent)
−(RTPVF,Coherent −RTPVF,Incoherent). The measure ΔRT is the difference between the median
response time to CVF and PVF stimuli presented with a
coherently moving background. This is the same measure
used in Experiment 1. The measure ΔRTnorm is the differ-
ence in median response times to CVF and PVF stimuli
after normalizing for the response times in the condition
with incoherent background motion. This is equivalent to
the attention allocation measure used by Wei et al. (2018). As in Experiment 1, we used the Hodges–Lehmann esti-
mator to compute the median response times. For both
measures, higher values indicate relatively more attention
to the PVF during vection. Measurements
Th The measures of motion sickness were the same as in
Experiment 1. As in the previous experiment, the SSQ
scores were log-transformed and normalized before sta-
tistical analyses, and the MISC scores used for analysis
were taken from the exposure block that resulted in at
least 75% completion. rather than just CRS. The two SART blocks were tested
in separate sessions in counterbalanced order. Sustained Attention to Response Task (SART)h The SART task in Experiment 2 was similar to the task
used in Experiment 1, except that the 200 SART trials Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 11 of 18 Percent completed
0%
25%
50%
75%
100%
Exp 2 - VR Exposure Completion Rate
2 Mins
4 Mins
6 Mins
8 Mins
Exposure Time
Fig. 8 Percent of subjects who completed each of the VR exposure
blocks in Experiment 2. The procedure was stopped if subjects
reported more than mild motion sickness symptoms (>6 on MISC
scale). Over 75% of the subjects were able to complete the full 8 min
of exposure Percent completed
0%
25%
50%
75%
100%
Exp 2 - VR Exposure Completion Rate
2 Mins
4 Mins
6 Mins
8 Mins
Exposure Time Exp 2 - VR Exposure Completion Rate were divided into two blocks with either coherently rotat-
ing stimuli (CRS) or incoherently rotating stimuli (IRS). The CRS stimuli would be expected to induce vection,
while the IRS stimuli would not. Each block consisted of 100 trials (10 × Green-CVF,
10 × Green-PVF, 40 × Red-CVF, 40 × Red-PVF). Trials in
the CRS block were identical to the ones in Experiment
1. For the IRS block, each gray dot had a different center
of rotation, which were randomly distributed inside an
invisible circular window (FOV: 0°–33.3°). The angular
velocity in the IRS block was set to 24°/s to ensure that
the mean rates of motion between the two blocks were
similar. Fig. 8 Percent of subjects who completed each of the VR exposure
blocks in Experiment 2. The procedure was stopped if subjects
reported more than mild motion sickness symptoms (>6 on MISC
scale). Over 75% of the subjects were able to complete the full 8 min
of exposure Central‑cued and peripheral‑cued (H1 and H1a) To test the main hypothesis of this study, we conducted
paired-sample t tests to compare the mean cybersick-
ness scores (MISC and SSQ) from the central-cued and
peripheral-cued conditions. As in Experiment 1, statis-
tical tests were performed on the raw MISC scores and
the transformed and normalized SSQ scores.h The results revealed that cybersickness was lower in
the central-cued condition than in the peripheral-cued
condition. Figure 9 shows the mean MISC and trans-
formed SSQ scores for the two attention allocation
conditions. The mean MISC score in the peripheral-
cued condition (M = 2.175, SD = 2.123) was significantly
higher than in the central-cued condition (M = 0.85,
SD = 1.122), t(39) = 4.38, p < .001, dz = 0.693. For the
SSQ scores, the same pattern was observed: The mean
change in log10(SSQ-T/10 + 1) was significantly larger in
the peripheral-cued condition (M = 0.318, SD = 0.280)
than
in
the
central-cued
condition
(M = 0.199,
SD = 0.268), t(39) = 3.302, p = .002, dz = 0.522. Further
analyses revealed a consistent pattern across all SSQ Procedureh The overall procedure was the same as in the previous
experiments. There were only two differences. In Experi-
ment 2, subjects experienced passive simulated motion
while performing a dot-probe task (see above), rather
than performing a navigation task. In addition, Experi-
ment 2 tested two types of SART trials, CRS and IRS, Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 12 of 18 3.0
2.0
2.5
1.5
0.5
0
1.0
Exp 2 - MISC scores
mean MISC scores
Central
cued
Peripheral
cued
1.0
.75
.25
.50
0
Exp 2 - transformed SSQ scores
mean log10(SSQ/10+1)
Central
cued
Peripheral
cued
Pre
Post
Pre
Post
Fig. 9 Motion sickness in the central-cued (red) vs peripheral-cued (blue) conditions of Experiment 2. The left graph plots mean MISC scores. The
right graph plots mean SSQ scores after transforming by log10(SSQ/10 + 1). Pre-exposure SSQ scores are shown in gray. Error bars depict standard
errors of the mean 3.0
2.0
2.5
1.5
0.5
0
1.0
Exp 2 - MISC scores
mean MISC scores
Central
cued
Peripheral
cued 1.0
.75
.25
.50
0
Exp 2 - transformed SSQ scores
mean log10(SSQ/10+1)
Central
cued
Peripheral
cued
Pre
Post
Pre
Post Fig. 9 Motion sickness in the central-cued (red) vs peripheral-cued (blue) conditions of Experiment 2. The left graph plots mean MISC scores. The
right graph plots mean SSQ scores after transforming by log10(SSQ/10 + 1). Pre-exposure SSQ scores are shown in gray. Error bars depict standard
errors of the mean MISC score in the peripheral-cued and central-cued
attention conditions was [0.718, 1.941]. Relative to the
mean MISC in the peripheral-cued condition (2.18),
the lower bound for the size of the difference would be
a 33% reduction in cybersickness in the central-cued
condition, and the upper bound would be a 90% reduc-
tion. For the SSQ data, the 95% HDI for the differences
between log10(SSQ-T/10 + 1) in the peripheral-cued and
central-cued conditions was [0.0453, 0.1901]. We con-
verted these differences to differences in raw SSQ total
scores using the mean post-test SSQ in the peripheral-
cued condition (16.7) as a baseline, and the resulting 95%
HDI for the difference in SSQ scores was [− 2.31, − 8.36]. Based on these results, the central-cued condition pro-
duced a 16–57% reduction in cybersickness as measured
by the SSQ total. Procedureh For both measures, the lower bounds
for the size of the effects would correspond to a meaning-
ful change in cybersickness. subscales, with all three subscales showing significantly
higher cybersickness in the peripheral-cued condition
(nausea: t(39) = 3.133, p = .003, dz = 0.495; oculomotor
disturbances: t(39) = 2.874, p = .007, dz = 0.454; disori-
entation: t(39) = 2.289, p = .028, dz = 0.362). Contrary to
Wei et al. (2018), our findings demonstrate that encour-
aging attention to the PVF during VR exposure leads to
more cybersickness than focused attention to the CVF
(supporting H1a). Bayesian analysis for H1 and H1a We performed additional Bayesian analyses to estimate
credible intervals for the differences between cyber-
sickness in the attentional cueing conditions. For each
measure, we estimated the posterior distribution for
differences using Bayes theorem, and then computed
the 95% highest density intervals (HDIs) of credible val-
ues. Noise was assumed to be normally distributed. We used non-informative priors for the unknown
parameters: a uniform distribution for mean differ-
ence and a Jeffreys prior for the variance. The poste-
rior distribution for mean differences was computed by
numerically integrating over the variance parameter:
P(m|{xi}) ~ ∫P({xi}|m,v) (1/v) dv. Using the estimated
posterior, we determined the 95% highest density inter-
val (HDI), which is the smallest interval containing 95%
of the posterior probability. For the SSQ, the HDIs were
computed from the normalized and log-transformed data
and then converted back to the original scale.h Attention allocation tendency during vection
Attention allocation tendency and MSSQ‑short (H Attention allocation tendency and MSSQ‑short (H2 and H2a)
We performed correlation analyses to examine the rela-
tionship between attention allocation during vection and
self-reported motion susceptibility (H2 and H2a). We
tested two measures derived from SART performance:
ΔRT, which was the measure used in Experiment 1, and
ΔRTnorm, which was used by Wei et al. (2018). Based on
the results of Wei et al. (2018), both attention allocation
measures would be expected to be negatively correlated
with the MSSQ-Short scores. The results indicate that attentional cueing produced
relatively large changes in experienced cybersickness. The estimated 95% HDI for the difference between the Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 13 of 18 0
10
20
30
40
0
5
10
15
20
0
5
10
15
20
0
10
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30
40
0
5
10
15
20
0
5
10
15
20
SART normalized
∆RT (ms)
SART normalized
∆RT (ms)
SART ∆RT (ms)
SART ∆RT (ms)
SART normalized
∆RT (ms)
SART ∆RT (ms)
0
-50 -25
0
0
1
-
5
7
-
0
50
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0
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0
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0
0
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5
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0
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25
r = 0.10
p = 0.544
r = 0.11
p = 0.487
r = 0.08
p = 0.619
r = .21
p = .192
r = .17
p = .286
r = .23
p = .148
Exp 2 - Attention Allocation vs Motion Sickness Susceptibility
MSSQ-Total
MSSQ-Child
MSSQ-Adult
Fig. 10 Self-reported motion sickness susceptibility (MSSQ) of individual subjects in Experiment 2 plotted as a function of their attentional
allocation scores derived from SART. The two rows use different measures of attentional allocation: the mean difference in reaction times for central
and peripheral targets with coherent background motion (top row), or the mean difference after normalizing for reaction times in the incoherent
motion conditions (bottom row). Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. Attention allocation tendency during vection
Attention allocation tendency and MSSQ‑short (H The left graph
plots the total MSSQ scores, and the middle and right graphs plot the MSSQ child and MSSQ adult subscores The results did not reveal any significant relationship
between attention allocation and MSSQ-Short scores,
regardless of the attentional allocation measure. Figure 10
plots the three MSSQ-Short measures as a function of
ΔRT (top row) and ΔRTnorm (bottom row). There was no
significant correlation between ΔRTnorm and the MSSQ-
Short total scores (r(38) = .211, p = .192), child subscores
(r(38) = .173, p = .286), or adult subscores (r(38) = .233,
p = .148). Similarly, there was no significant correlation
between ΔRT and MSSQ-Short total scores (r(38) = .099,
p = .544), child subscores (r(38) = .113, p = .487), or adult
subscores (r(38) = .081, p = .619). We were unable to
replicate the negative relationship between attention
allocation tendency during vection and self-reported
motion sickness susceptibility scores as reported by Wei
et al. (2018), and the small trends were in the opposite
direction. Attention allocation tendency during vection
Attention allocation tendency and MSSQ‑short (H The left graph
plots the total MSSQ scores, and the middle and right graphs plot the MSSQ child and MSSQ adult subscores Exp 2 - Attention Allocation vs Motion Sickness Susceptibility 0
5
10
15
20
SART ∆RT (ms)
0
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0
0
1
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5
7
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r = 0.11
p = 0.487
MSSQ-Child 0
5
10
15
20
SART ∆RT (ms)
0
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0
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1
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r = 0.08
p = 0.619
MSSQ-Adult 0
10
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40
SART ∆RT (ms)
0
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0
0
1
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5
7
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r = 0.10
p = 0.544
MSSQ-Total MSSQ-Adult SART ∆RT (ms) SART ∆RT (ms) 0
5
10
15
20
SART normalized
∆RT (ms)
SART ∆RT (ms)
0
50
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25
r = .17
p = .286 0
10
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30
40
SART normalized
∆RT (ms)
SART ∆RT (ms)
0
50
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25
r = .21
p = .192 0
5
10
15
20
SART normalized
(
)
0
50
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25
r = .23
p = .148 SART normalized
∆RT (ms) SART normalized
∆RT (ms) SART normalized
∆RT (ms) Fig. 10 Self-reported motion sickness susceptibility (MSSQ) of individual subjects in Experiment 2 plotted as a function of their attentional
allocation scores derived from SART. The two rows use different measures of attentional allocation: the mean difference in reaction times for central
and peripheral targets with coherent background motion (top row), or the mean difference after normalizing for reaction times in the incoherent
motion conditions (bottom row). Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. The left graph
plots the total MSSQ scores, and the middle and right graphs plot the MSSQ child and MSSQ adult subscores Fig. 10 Self-reported motion sickness susceptibility (MSSQ) of individual subjects in Experiment 2 plotted as a function of their attentional
allocation scores derived from SART. The two rows use different measures of attentional allocation: the mean difference in reaction times for central
and peripheral targets with coherent background motion (top row), or the mean difference after normalizing for reaction times in the incoherent
motion conditions (bottom row). Positive values of ΔRT correspond to more attention to the periphery. Lines show the regression fits. Bayesian analysis for H3 and H3a We also performed a Bayesian analysis to estimate 95%
credible intervals for the correlation between SART
scores and motion sickness. The posteriors and HDIs
were computed using JASP and assuming a uniform
prior. susceptibility in the direction predicted by Wei et al. (2018) was small, |r|< 0.23. The correlations reported
by Wei et al. (2018) were r = − .479 for the SART and
MSSQ total scores and r = − .595 for the SART score
and MSSQ adult subscores. Both of these are outside
the corresponding 95% HDIs from our data. The corre-
lation between SART and MSSQ child subscore was not
reported by Wei et al. (2018), as it was not significant. For the MISC scores, the 95% HDI for the correlation
with ∆RT was [− .302, .300], and with ∆RTnorm it was
[− .157, .433]. For SSQ, the 95% credible interval for
the correlation with ∆RT was [− .302, .300], and with
∆RTnorm it was [− .241, .359]. If there was correlation
between SART performance and experienced cyber-
sickness, our results indicate that the correlation was
likely to be within [− .302, .433]. Exp 2 - Motion Sickness Susceptibilty vs Experienced Cybersickness SART normalized
∆RT (ms) SART normalized
∆RT (ms) Fig. 11 Cybersickness experienced by individual subjects during
virtual navigation in Experiment 2 plotted as a function of their
attentional allocation scores. The two rows use different measures
of attentional allocation: the mean difference in reaction times for
central and peripheral targets with coherent background motion
(top row), or the mean difference after normalizing for reaction times
in the incoherent motion conditions (bottom row). Positive values
of ΔRT correspond to more attention to the periphery. Lines show
the regression fits. The left graph plots the MISC scores and the right
graph plots the SSQ scores after transforming by log10(SSQ/10 + 1) Bayesian analysis for H2 and H2a We performed an additional Bayesian analysis to estimate
95% confidence intervals of credible values for the corre-
lation between SART score and motion sickness suscep-
tibility. The posterior distributions were estimated using
JASP, with the default assumption of a uniform prior for
the correlation coefficient. fi
When using the measure of Wei et al. (2018) as an
indicator of attention allocation tendency (∆RTnorm), the
95% HDIs for correlations between SART and MSSQ-
Short scores were [− .105, .475] for MSSQ total, [− .142,
.445] for MSSQ child, and [− .083, .493] for MSSQ adult. Using the non-normalized measure of attention alloca-
tion (∆RT), the 95% HDI for the correlation with MSSQ
total score was [− .212, .385]. For the subscales, the 95%
credible intervals were [− .199, .397] for the MSSQ child
subscore, and [− .228, .370] for the MSSQ adult subscore. Based on these results, any correlation between atten-
tion allocation during vection and motion sickness Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 14 of 18 SART normalized
∆RT (ms)
SART ∆RT (ms)
0
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-75
-100
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SART normalized
∆RT (ms)
SART ∆RT (ms)
0
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1.00
1.25
0
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1.00
1.25
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0
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Transformed SSQ
MISC score
MISC score
log10(SSQ/10+1)
log10(SSQ/10+1)
r = .00
p > .99
r = .16
p = .33
r = .00
p = .99
r = .07
p = .68
Exp 2 - Attention Allocation vs Experienced Cybersickness
Fig. 11 Cybersickness experienced by individual subjects during
virtual navigation in Experiment 2 plotted as a function of their
attentional allocation scores. The two rows use different measures
of attentional allocation: the mean difference in reaction times for
central and peripheral targets with coherent background motion
(top row), or the mean difference after normalizing for reaction times
in the incoherent motion conditions (bottom row). Positive values
of ΔRT correspond to more attention to the periphery. Lines show
the regression fits. The left graph plots the MISC scores and the right
graph plots the SSQ scores after transforming by log10(SSQ/10 + 1) Exp 2 - Attention Allocation vs Experienced Cybersickness Exp 2 - Motion Sickness Susceptibilty vs Experienced Cybersickness Exp 2 - Motion Sickness Susceptibilty vs Experienced Cybersickness 2 - Attention Allocation vs Experienced Cybersickness Exp 2 - Motion Sickness Susceptibilty vs Experienced Cybersickness MSSQ Total
0
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MSSQ Total
0
.25
.50
.75
1.00
1.25
0
20
40
30
10
MISC score
log10(SSQ/10+1)
r = .55
p < .001
r = 0.51
p = 0.001
MISC score
Transformed SSQ
Exp 2 Motion Sickness Susceptibilty vs Experienced Cybersickness
Fig. 12 Cybersickness experienced by individual subjects in
Experiment 2 plotted as a function of self-reported motion sickness
susceptibility (MSSQ total). Lines show the regression fits. The left
graph plots the MISC scores and right graph plots the SSQ after
transforming by log10(SSQ/10 + 1) MSSQ Total
0
20
40
30
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0
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r = .55
p < .001
MISC score SART ∆RT (ms)
0
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0
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MISC score
r = .00
p > .99 SART ∆RT (ms)
0
.25
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Transformed SSQ
log10(SSQ/10+1)
r = .00
p = .99 MSSQ Total
0
.25
.50
.75
1.00
1.25
0
20
40
30
10
log10(SSQ/10+1)
r = 0.51
p = 0.001
Transformed SSQ Fig. 12 Cybersickness experienced by individual subjects in Fig. 12 Cybersickness experienced by individual subjects in
Experiment 2 plotted as a function of self-reported motion sickness
susceptibility (MSSQ total). Lines show the regression fits. The left
graph plots the MISC scores and right graph plots the SSQ after
transforming by log10(SSQ/10 + 1) SART ∆RT (ms) SART ∆RT (ms) SART normalized
∆RT (ms)
(
)
0
1
2
3
4
5
0
50
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25
MISC score
r = .16
p = .33 SART normalized
∆RT (ms)
0
.25
.50
.75
1.00
1.25
0
50
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25
log10(SSQ/10+1)
r = .07
p = .68 allocation measures. There was no significant correla-
tion between ∆RT and overall MISC (r(38) = − .001,
p = .996) or overall SSQ (r(38) = − .001, p = .993). There was also no correlation between ∆RTnorm and
overall MISC (r(38) = .158, p = .332) or overall SSQ
(r(38) = .067, p = .680). Overall, there did not appear
to be any relationship between the attention allocation
tendency during SART and the cybersickness experi-
enced during the virtual reality exposure. Visual attention allocation and motion sickness
susceptibility In Experiment 2, we were still unable to replicate the
findings of Wei et al. (2018) despite using the same meas-
ures and a larger sample size that had sufficient power. For both ∆RT (the attention allocation measure used
in Experiment 1) and ∆RTnorm (the attention allocation
measure used by Wei et al. (2018)), attention allocation
as measured by the SART was not predictive of self-
reported motion sickness susceptibility. Even using the
same measures as Wei et al. (2018) and a more closely
matched design, we did not replicate their main finding. The dot-probe task in the central-cued and periph-
eral-cued conditions might have differed in difficulty,
but it is unlikely that this explains the observed differ-
ence. Previous studies suggest that an increase in cogni-
tive load can lead to a decrease in motion sickness (Bos,
2015; Seno et al., 2011). As individuals become more
mentally occupied in sickness-inducing situations, such
as attempting to solve a challenging math question
during virtual navigation, this may distract them away
from the experienced symptoms. If there was a differ-
ence in task difficulty in our conditions, the peripheral-
cued condition would be the more challenging task
because there were more variations in the target loca-
tions. The peripheral-cued conditions would there-
fore be expected to produce less cybersickness, which
is in the opposite direction as the difference observed
in Experiment 2. Sepich et al. (2022) reported that
excessive cognitive load might instead elevate cyber-
sickness. However, we believe that neither the central-
cued nor peripheral-cued version of the dot-probe task
was overly demanding to our subjects, so a benefit of
increased cognitive load on cybersickness would still
be expected. Although cognitive load might have had
some effect on cybersickness, it is unlikely that this was
the cause of the reduced cybersickness with central
attention in our experiment. i
The results from our Bayesian analysis indicate that any
correlation between attention allocation and motion sick-
ness susceptibility in the expected direction was small. The lower bound of the 95% interval of credible values
was r = − .228, indicating that any negative relationship
that was present explained at most 5.2% of the variance. If we missed a negative correlation that was present, the
size of the effect is likely to be minimal. f
We also found no relationship between baseline atten-
tion allocation and experienced cybersickness. Manipulation of visual attention and cybersickness Manipulation of visual attention and cybersickness
Experiment 2 implemented a dot-probe task to encour-
age sustained attention to either the CVF or PVF during
VR exposure. With this manipulation, we detected a sig-
nificant difference in cybersickness between the atten-
tion-cueing conditions. The observed difference provides
evidence that the dot-probe task did affect attention
allocation. Encouraging subjects to focus more on their cen-
tral vision resulted in comparatively less cybersickness
than when attention to the periphery was encouraged. This difference was observed in all of the cybersickness
measures—MISC, SSQ, and SSQ subscales. This find-
ing contradicts the prediction made by Wei et al. (2018)
that attention to the periphery would reduce cybersick-
ness. On the other hand, it is consistent with previous
studies that have found that restricting the FOV reduces
cybersickness.h MSSQ‑short and cybersickness We performed correlation analyses to examine the rela-
tionship between attention allocation tendency during
the SART task and cybersickness experienced during
the VR exposure (H3 and H3a). As in Experiment 1, we
computed overall measures of cybersickness by aver-
aging the post-exposure MISC or SSQ scores from the
central-cued and peripheral-cued conditions. We performed additional exploratory analyses to
assess whether MSSQ-Short is an effective predic-
tor of cybersickness experienced in our VR exposure
conditions. Figure 12 plots the relationship between
MSSQ-Short total scores and the overall cybersick-
ness experienced during the exposure. Consistent with
the results from Experiment 1, we observed a signifi-
cant positive correlation between MSSQ-Short total
scores and overall MISC scores (r(38) = .536, p < .001), Figure 11 shows overall MISC and SSQ scores as a
function of ∆RT (top row) and ∆RTnorm (bottom row). The results were almost the same for the two attention Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 15 of 18 Page 15 of 18 as well as MSSQ-Short total scores and overall SSQ
scores (r(38) = .537, p < .001). Taken together, our
results suggest that the MSSQ-Short does have utility
for predicting individual differences in susceptibility to
cybersickness. as well as MSSQ-Short total scores and overall SSQ
scores (r(38) = .537, p < .001). Taken together, our
results suggest that the MSSQ-Short does have utility
for predicting individual differences in susceptibility to
cybersickness. It should be noted that our current findings may
have underestimated the actual effectiveness of our
manipulation in mitigating cybersickness due to a
potential floor effect. In Experiment 2, there were a
sizeable number of subjects who appeared to be highly
resilient to cybersickness. At least a quarter of our
sample (n = 10) did not experience any discomfort in
either of the attention-cueing conditions as measured
by MISC ratings. For users who are naturally not sus-
ceptible to cybersickness, any sickness-reducing inter-
vention would have little impact. The estimated effect
size observed in Experiment 2 was dz = 0.362 − 0.693,
depending on the measure. If our sample had been
composed entirely of cybersickness-susceptible indi-
viduals, the effect size would likely have been larger. Visual attention allocation and motion sickness
susceptibility Null
results were observed for both of the attention alloca-
tion measures (∆RT and ∆RTnorm). The results from the
Bayesian analyses indicate that any correlation between
attentional allocation and cybersickness was unlikely
to have a correlation of r > .433 or r < − .302. We cannot
rule out the possibility that a medium-sized correlation
(|r|= 0.3–0.4) was present but missed. Discussion Manipulation of visual attention and cybersickness General discussion Across experiments, we found no evidence that allo-
cating attention to the periphery reduces cybersick-
ness (H1). Based on the findings of Wei et al. (2018),
we hypothesized that reallocating visual attention to
the PVF during VR exposure would reduce experienced
cybersickness. A negative correlation between attention Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 16 of 18 Page 16 of 18 allocation tendency and overall experienced cybersick-
ness would also be expected (H3). Neither of these effects
was observed. We also failed to replicate the negative
correlation between attention allocation during vection
and self-reported motion sickness susceptibility reported
by Wei et al. (2018) (H2). Experiment 2 was designed to avoid the limitations of
Experiment 1. The dot-probe task provided a more reli-
able manipulation of attentional allocation. To perform
well, subjects would have to continuously attend to either
the CVF or PVF during the VR exposure. The observed
difference in cybersickness confirms that the manipula-
tion did have some effect. Experiment 2 also controlled
the simulated motion across conditions. Subjects were
“seated” in a self-driving cart during VR exposure, and
thus unable to slow down or pause in-game movements
when they begin to experience symptoms. These meth-
odological differences could explain why an effect of
attentional cueing on cybersickness was observed in
Experiment 2 but not in Experiment 1.f allocation tendency and overall experienced cybersick-
ness would also be expected (H3). Neither of these effects
was observed. We also failed to replicate the negative
correlation between attention allocation during vection
and self-reported motion sickness susceptibility reported
by Wei et al. (2018) (H2). Instead, we found evidence to support our main alter-
native hypothesis (H1a). Given that previous studies
found that restricted FOV can reduce cybersickness,
we hypothesized that encouraging attention to the
CVF, rather than the PVF, would reduce cybersickness
experienced in VR. Consistent with this hypothesis,
Experiment 2 found that cybersickness was lower in the
central-cued condition compared to the peripheral-cued
condition. A further prediction would be that attentional
allocation tendency would be positively correlated with
motion sickness susceptibility (H2a) and overall cyber-
sickness (H3a). These hypothesized correlations were not
observed in either experiment. p
p
A connection can be drawn between the effect of
attention reallocation and FOV on cybersickness. Manipulating visual attention to reduce cybersickness We manipulated visual attention allocation to CVF/PVF
using task-relevant visual cues (Experiment 1) or a dot-
probe task (Experiment 2). Experiment 1 did not find any
significant difference between the two attention-cueing
conditions, but Experiment 2 found that cybersickness
was reduced in the central-cued condition. One possible reason that Experiment 1 did not find a
detectable difference between the two attention-cueing
conditions is that the peripheral-cued condition did not
produce sustained visual attention to the periphery. In
Experiment 1, we used exogenous visual cues (i.e., high-
lighting the chests in red) to manipulate attention alloca-
tion in VR, which served as hints about the location of
the chests. Because the chests were distributed across
the environment, the cues would generally encourage a
wide allocation of attention. However, after being cued to
the location of a chest, subjects might quickly shift their
attention to focus on a single target chest, rather than
maintaining a wide allocation of attention. If the exog-
enous cues in the peripheral-cued conditions had only
transient effects on attention, then this could have pre-
vented any effects on cybersickness. General discussion Previ-
ous studies have attempted to control cybersickness by
reducing the in-game FOV (Lin et al., 2002; Rebenitsch
& Owen, 2016; Saredakis et al., 2020; Weech et al., 2019). The sensory conflict is minimized as restrictive FOV
removed the motion cues available in the visual periph-
ery. In Experiment 2, although periphery motion cues
remain available across the two conditions, the central-
cued condition encouraged the subjects to constantly
attend to their CVF, which would limit the attentional
resources that are available for peripheral motion cues. For both types of interventions, CVF attention cue-
ing and restrictive FOV, lowered cybersickness could be
explained by reduced processing of peripheral motion
cues. Baseline attention allocation tendency and motion
sicknessi In both experiments, we failed to replicate the findings by
Wei et al. (2018). No significant correlation was observed
between motion sickness susceptibility scores and the
two attention allocation measures (∆RT or ∆RTnorm).h The negative relationship between attention allocation
tendency during vection and motion sickness suscepti-
bility reported by Wei et al. (2018) may not reliable, or
might have been a false positive. In Experiment 1, the
failure to replicate might have been due to insufficient
power and some methodological differences. However,
Experiment 2 was a closer replication and well-powered
but still did not replicate the previous findings. We were
unable to detect any significant relationship between
MSSQ-Short and attention allocation tendency as meas-
ured by either ∆RT (the measure used in Experiment 1)
or ∆RTnorm (the measure used in Wei et al. (2018)). Fur-
thermore, the results from Experiment 2 indicate that
any negative relationship between attentional allocation f
Another factor that could have contributed to the null
finding in Experiment 1 is differences in experienced
motion. We allowed subjects to freely control their vir-
tual movement. Although we did not record the virtual
movement in Experiment 1, we noticed that some sub-
jects performed less active navigation as they experi-
enced discomfort, which may have been a strategy to
reduce cybersickness. If subjects altered their movement
in response to discomfort, this would tend to reduce any
differences between conditions. Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Page 17 of 18 specifically designed to measure visually induced motion
sickness susceptibility specifically might be preferred. tendency and motion sickness susceptibility was very
small: r > − .228 for ∆RT and r > − .142 for ∆RTnorm. We also did not observe any correlation between atten-
tion allocation during vection and overall experienced
cybersickness, which appears to conflict with the experi-
mental results from Experiment 2. In Experiment 2, we
found that cybersickness was reduced in the central-cued
condition. Given this finding, one might expect that peo-
ple with a natural allocation tendency toward the CVF
would be less likely to experience motion sickness during
VR exposure, which was not observed. Author contributions
B th
th
t ib t Both authors contributed to all aspects of the project with the exception of
data collection, which was performed by the first author. Availability of data and materials The data and materials are available at the public repository: https://osf.io/
8cbw9/ It has been suggested that the MSSQ may not be the
optimal tool for predicting visually induced motion sick-
ness, such as motion sickness induced by VR exposure. Keshavarz et al. (2019) pointed out that the MSSQ was
not specifically constructed to gauge one’s likelihood of
experiencing visually induced motion sickness, but rather
symptoms that are induced physically. The MSSQ derives
general motion sickness susceptibility from one’s his-
tory of discomfort in situations where physical motion is
expected, such as riding a boat. None of the MSSQ items
capture the incidence of motion sickness symptoms
in situations where strong physical motion is unlikely
to occur, such as watching a 3D movie. To accurately
predict cybersickness, alternative instruments that are Conclusion We discovered that reallocating attention to the central
visual field can reduce cybersickness symptoms. This
finding was observed in Experiment 2, which was a well-
powered experiment that avoided some methodological
limitations of Experiment 1. The effect of allocating attention to the CVF on cyber-
sickness may be comparable to the effect of restricting
FOV. Previous studies have found that restricting FOV
can reduce cybersickness (Lin et al., 2002; Rebenitsch &
Owen, 2016; Saredakis et al., 2020; Weech et al., 2019). Our results demonstrate that restricting attention to the
CVF can also reduce cybersickness. Both interventions
might reduce the severity of cybersickness by minimizing
the processing of peripheral motion cues. It is possible that the baseline level of attention alloca-
tion is not representative of the attentional distribution
when performing tasks in virtual reality. Allocation of
attention is known to be flexible and can be shifted with
various visual cues (Kean & Lambert, 2003). Therefore,
any context-relevant visual cues that manipulate visual
attention allocation, such as performing a dot-probe task
in VR or receiving an in-game notification on a newly
received side quest, could disrupt the effect of the default
attention allocation tendency. This could explain why the
default attention allocation tendency was not predictive
of experienced cybersickness in our studies, despite the
fact that our manipulation of attention affected cyber-
sickness in Experiment 2. We found no evidence that attention allocation ten-
dency predicts self-reported susceptibility to motion
sickness or experienced cybersickness during VR expo-
sure. Experiment 2 failed to replicate the findings of Wei
et al. (2018) despite using a closely matched method and
having good statistical power. Because visual attention
can be easily shifted with context-relevant visual cues,
the default attention allocation tendency may not be use-
ful for predicting cybersickness. Effectiveness of MSSQ‑short in predicting cybersickness
We performed exploratory analyses to assess the effec-
tiveness of MSSQ-Short in predicting cybersickness. Although both experiments found positive correlations
between MSSQ-Short and overall MISC/SSQ scores,
the amount of correlation was modest: r = .448 − .558. Anecdotally, we observed that multiple subjects rated
themselves as highly susceptible to motion sickness with
the MSSQ-Short but experienced minimal cybersickness
during the actual exposure. This raises the question of
whether the MSSQ-Short is a valid predictor of cyber-
sickness susceptibility. Funding
h This research was supported by a grant from the Hong Kong Research Grants
Council (GRF 17407914). Publication charges were supported by the HKU
Libraries Open Access Author Fund sponsored by the HKU Libraries. Competing interests
h
h
h The authors have no commercial relationships and no conflicts of interest. Consent for publication p
All subjects consented to publication of the results. All subjects consented to publication of the results. Ethical approval and consent to participate
h
d
d b
h The procedures were approved by the Human Research Ethics Committee of
the University of Hong Kong, and all participants gave informed consent. References Saredakis, D., Szpak, A., Birckhead, B., Keage, H. A., Rizzo, A., & Loetscher, T. (2020). Factors associated with virtual reality sickness in head-mounted
displays: A systematic review and meta-analysis. Frontiers in Human
Neuroscience. https://doi.org/10.3389/fnhum.2020.00096 Bos, J. E. (2015). Less sickness with more motion and/or mental distraction. Journal of Vestibular Research, 25(1), 23–33. https://doi.org/10.3233/
ves-150541 Bos, J. E., MacKinnon, S., & Patterson, A. (2005). Motion sickness symptoms in a
ship motion simulator: Effects of inside, outside and no view. Aerospace
Medicine and Human Performance, 76(12), 1111–1118. Seay, A. F., Krum, D. M., Hodges, L., & Ribarsky, W. (2002). Simulator sickness and
presence in a high field-of-view virtual environment. Proceedings of the
CHI’02 Extended Abstracts on Human Factors in Computing Systems. https://
doi.org/10.1145/506443.506596 Botella, J., Ximénez, C., Revuelta, J., & Suero, M. (2006). Optimization of sample
size in controlled experiments: The CLAST rule. Behavior Research Meth-
ods, 38(1), 65–76. https://doi.org/10.3758/BF03192751 Seno, T., Ito, H., & Sunaga, S. (2011). Attentional load inhibits vection. Attention,
Perception, & Psychophysics, 73(5), 1467–1476. https://doi.org/10.3758/
s13414-011-0129-3 Brandt, T., Bartenstein, P., Janek, A., & Dieterich, M. (1998). Reciprocal inhibitory
visual-vestibular interaction. Visual motion stimulation deactivates the
parieto-insular vestibular cortex. Brain: A Journal of Neurology, 121(9),
1749–1758. https://doi.org/10.1093/brain/121.9.1749 Sepich, N. C., Jasper, A., Fieffer, S., Gilbert, S. B., Dorneich, M. C., & Kelly, J. W. (2022). The impact of task workload on cybersickness. Frontiers in Virtual
Reality. https://doi.org/10.3389/frvir.2022.943409 Brandt, T., Glasauer, S., Stephan, T., Bense, S., Yousry, T. A., Deutschländer, A., &
Dieterich, M. (2002). Visual-vestibular and visuo-visual cortical interac-
tion: New insights from fMRI and PET. Annals of the New York Academy of
Sciences, 956(1), 230–241. https://doi.org/10.1111/j.1749-6632.2002.tb028
22.x Ungerleider, L. (1994). “What” and “where” in the human brain. Current Opinion
in Neurobiology, 4(2), 157–165. https://doi.org/10.1016/0959-4388(94)
90066-3 Weech, S., Kenny, S., & Barnett-Cowan, M. (2019). Presence and cybersickness
in virtual reality are negatively related: A review. Frontiers in Psychology. https://doi.org/10.3389/fpsyg.2019.00158 Chang, E., Kim, H. T., & Yoo, B. (2020). Virtual reality sickness: A review of causes
and measurements. International Journal of Human-Computer Interaction,
36(17), 1658–1682. https://doi.org/10.1080/10447318.2020.1778351f Wei, Y., Zheng, J., & So, R. H. (2018). Allocating less attention to central vision
during vection is correlated with less motion sickness. Ergonomics, 61(7),
933–946. https://doi.org/10.1080/00140139.2018.1427805 Dichgans, J., & Brandt, T. (1978). Visual-vestibular interaction: Effects on self-
motion perception and postural control. Perception. https://doi.org/10.
1007/978-3-642-46354-9_25fi Fitts, D. (2010). References Improved stopping rules for the design of efficient small-
sample experiments in biomedical and biobehavioral research. Behavior
Research Methods, 42(1), 3–22. https://doi.org/10.3758/BRM.42.1.3 Received: 27 August 2021 Accepted: 12 January 2023 Reason, J. T. (1978). Motion sickness adaptation: A neural mismatch model. Journal of the Royal Society of Medicine, 71(11), 819–829. https://doi.org/
10.1177/014107687807101109 Rebenitsch, L., & Owen, C. (2016). Review on cybersickness in applications and
visual displays. Virtual Reality, 20(2), 101–125. https://doi.org/10.1007/
s10055-016-0285-9 Preregistration The experiments were both preregistered on the Open Sciences Framework,
Experiment 1: https://osf.io/rfzwt, Experiment 2: https://osf.io/f7q8e. Page 18 of 18 Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Yip and Saunders Cognitive Research: Principles and Implications (2023) 8:18 Received: 27 August 2021 Accepted: 12 January 2023 Publisher’s Note
S
N Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. Golding, J. F. (1998). Motion sickness susceptibility questionnaire revised and
its relationship to other forms of sickness. Brain Research Bulletin, 47(5),
507–516. https://doi.org/10.1016/s0361-9230(98)00091-4 Hodges, J. L., & Lehmann, E. L. (1963). Estimates of location based on rank tests. The Annals of Mathematical Statistics, 34(2), 598–611. https://doi.org/10.
1214/aoms/1177704172 Kean, M., & Lambert, A. (2003). Orienting of visual attention based on periph-
eral information. In R. Radach, J. Hyona, & H. Deubel (Eds.), The Mind’s Eye:
Cognitive and Applied Aspects of Eye Movement Research (pp. 27–47). North
Holland. https://doi.org/10.1016/B978-044451020-4/50003-7. Kennedy, R. S., Lane, N. E., Berbaum, K. S., & Lilienthal, M. G. (1993). Simulator
sickness questionnaire: An enhanced method for quantifying simulator
sickness. The International Journal of Aviation Psychology, 3(3), 203–220. https://doi.org/10.1207/s15327108ijap0303_3 Keshavarz, B., & Hecht, H. (2012). Visually induced motion sickness and pres-
ence in videogames: The role of sound. Proceedings of the Human Factors
and Ergonomics Society Annual Meeting, 56(1), 1763–1767. https://doi.org/
10.1177/1071181312561354 Keshavarz, B., Saryazdi, R., Campos, J. L., & Golding, J. F. (2019). Introducing the
VIMSSQ: Measuring susceptibility to visually induced motion sickness. Proceedings of the Human Factors and Ergonomics Society Annual Meeting,
63(1), 2267–2271. https://doi.org/10.1177/1071181319631216 63(1), 2267–2271. https://doi.org/10.1177/1071181319631216 Lawson, B. (2015). Motion sickness symptomatology and origins. In K. S. Hale &
K. M. Stanney (Eds.), Handbook of Virtual Environments: Design, Implemen-
tation, and Applications (pp. 532–587). CRC Press. Lin, J. W., Duh, H. B., Parker, D. E., Abi-Rached, H., & Furness, T. A. (2002). Effects
of field of view on presence, enjoyment, memory, and simulator sickness in a
virtual environment. In Proceedings of the IEEE Proceedings of Virtual Reality,
2002 (pp. 164–171). Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/VR.2002.996519. McCauley, M. E., & Sharkey, T. J. (1992). Cybersickness: Perception of self-motion
in virtual environments. Presence: Teleoperators and Virtual Environments,
1(3), 311–318. https://doi.org/10.1162/pres.1992.1.3.311 Palmisano, S., Mursic, R., & Kim, J. (2017). Vection and cybersickness generated
by head-and-display motion in the Oculus Rift. Displays, 46, 1–8. https://
doi.org/10.1016/j.displa.2016.11.001
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Hybrid FES-exoskeleton control: Using MPC to distribute actuation for elbow and wrist movements
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Frontiers in neurorobotics
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Nathan Dunkelberger1, Jefrey Berning1, Eric M. Schearer2 and
Marcia K. O’Malley1* Nathan Dunkelberger1, Jefrey Berning1, Eric M. Schearer2 and
Marcia K. O’Malley1* 1Department of Mechanical Engineering, Mechatronics and Haptics Interfaces Laboratory, Rice
University, Houston, TX, United States, 2Center for Human Machine Systems, Department of Mechanical
Engineering, Cleveland State University, Cleveland, OH, United States Introduction: Individuals who have sufered a cervical spinal cord injury prioritize
the recovery of upper limb function for completing activities of daily living. Hybrid
FES-exoskeleton systems have the potential to assist this population by providing a
portable, powered, and wearable device; however, realization of this combination
of technologies has been challenging. In particular, it has been difcult to show
generalizability across motions, and to define optimal distribution of actuation,
given the complex nature of the combined dynamic system. Dunkelberger N, Berning J, Schearer EM and
O’Malley MK (2023) Hybrid FES-exoskeleton
control: Using MPC to distribute actuation for
elbow and wrist movements. Front. Neurorobot. 17:1127783. doi: 10.3389/fnbot.2023.1127783 Methods:
In this paper, we present a hybrid controller using a model
predictive control (MPC) formulation that combines the actuation of both an
exoskeleton and an FES system. The MPC cost function is designed to distribute
actuation on a single degree of freedom to favor FES control efort, reducing
exoskeleton power consumption, while ensuring smooth movements along
diferent trajectories. Our controller was tested with nine able-bodied participants
using FES surface stimulation paired with an upper limb powered exoskeleton. The hybrid controller was compared to an exoskeleton alone controller, and
we measured trajectory error and torque while moving the participant through
two elbow flexion/extension trajectories, and separately through two wrist
flexion/extension trajectories. COPYRIGHT
© 2023 Dunkelberger, Berning, Schearer and
O’Malley. This is an open-access article
distributed under the terms of the Creative
Commons Attribution License (CC BY). The use,
distribution or reproduction in other forums is
permitted, provided the original author(s) and
the copyright owner(s) are credited and that
the original publication in this journal is cited, in
accordance with accepted academic practice. No use, distribution or reproduction is
permitted which does not comply with these
terms. Results: The MPC-based hybrid controller showed a reduction in sum of squared
torques by an average of 48.7 and 57.9% on the elbow flexion/extension and
wrist flexion/extension joints respectively, with only small diferences in tracking
accuracy compared to the exoskeleton alone. model predictive control (MPC), hybrid control (HC), functional electrical stimulation
(FES), movement assistance, upper limb exoskeleton frontiersin.org TYPE Original Research
PUBLISHED 06 April 2023
DOI 10.3389/fnbot.2023.1127783 TYPE Original Research
PUBLISHED 06 April 2023
DOI 10.3389/fnbot.2023.1127783 Hybrid FES-exoskeleton control:
Using MPC to distribute actuation
for elbow and wrist movements OPEN ACCESS
EDITED BY
Emilio Trigili,
Sant’Anna School of Advanced Studies, Italy
REVIEWED BY
Mahdi Tavakoli,
University of Alberta, Canada
Nitin Sharma,
North Carolina State University, United States
*CORRESPONDENCE
Marcia K. O’Malley
omalleym@rice.edu
RECEIVED 20 December 2022
ACCEPTED 06 March 2023
PUBLISHED 06 April 2023
CITATION
Dunkelberger N, Berning J, Schearer EM and
O’Malley MK (2023) Hybrid FES-exoskeleton
control: Using MPC to distribute actuation for
elbow and wrist movements. Front. Neurorobot. 17:1127783. doi: 10.3389/fnbot.2023.1127783 REVIEWED BY
Mahdi Tavakoli,
University of Alberta, Canada
Nitin Sharma,
North Carolina State University, United States Nathan Dunkelberger1, Jefrey Berning1, Eric M. Schearer2 and
Marcia K. O’Malley1* Discussion:
To realize practical implementation of hybrid FES-exoskeleton
systems, the control strategy requires translation to multi-DOF movements,
achieving more consistent improvement across participants, and balancing
control to more fully leverage the muscles’ capabilities. 1. Introduction There are ∼291,000 people in the United States living with spinal cord injuries, and
the majority of these are cervical level injuries, resulting in tetraplegia (NSCISC, 2019). Injuries at such a high level of the spinal cord create severe arm and hand disabilities,
resulting in an inability to complete Activities of Daily Living (ADLs). As a result, 71% of
individuals with tetraplegia currently require assistance with ADLs (Collinger et al., 2013). Given this, it is not surprising that restoration of arm and hand function is a top priority
among people with tetraplegia due to cervical spinal cord injuries (SCI) (Anderson, 2004). With scarce rehabilitation and assistive technology options, these individuals are largely
dependent on full-time caregivers for feeding, grooming, and many other activities of daily Frontiers in Neurorobotics Frontiers in Neurorobotics 01 Dunkelberger et al. 10.3389/fnbot.2023.1127783 living. Regaining the ability to perform these tasks independently
will reduce requirements on caregivers and increase opportunities
for
individuals
to
return
to
social
participation
in
their
communities, both of which are highly correlated to quality
of life (Dijkers, 1997). FIGURE 1
An example future application of hybrid systems is shown for a
reach and grasp task. The incorporation of both FES and a robot
allows for a large portion of the movement to be provided by FES,
and the robot can provide small amounts of power to provide
minimal movement corrections. With the robot alone, all power for
the movement must be provided by the robot. Recovery of arm and hand function through rehabilitation can
be achieved for individuals with some residual muscle capability
(Dietz et al., 2002; Beekhuizen and Field-Fote, 2005), and there
are promising results that show that the same intensive robotic
rehabilitation that has been successful for inducing plasticity and
recovery following stroke (Reinkensmeyer et al., 2000; Charles
et al., 2005; Lum et al., 2012; Blank et al., 2014) can be effective
for SCI (Kadivar et al., 2012; Fitle et al., 2015; Francisco et al.,
2017; Frullo et al., 2017; Yozbatiran and Francisco, 2019). For those
without residual motor capability, however, or for those for whom
rehabilitation interventions have not been able to restore functional
movement, assistive technologies are a more viable option for
replacing lost function. 1. Introduction Such approaches incorporate mechanical
devices that are attached to the limb and have the capability to
move the limb or hand, or approaches that electrically stimulate the
existing muscles, causing muscle contraction and inducing motion
of the upper limb. FIGURE 1
An example future application of hybrid systems is shown for a
reach and grasp task. The incorporation of both FES and a robot
allows for a large portion of the movement to be provided by FES,
and the robot can provide small amounts of power to provide
minimal movement corrections. With the robot alone, all power for
the movement must be provided by the robot. Functional electrical stimulation (FES) is a promising assistive
technology to restore arm and hand function. By activating a
person’s own paralyzed muscles via surface electrodes placed on
the skin or surgically implanted electrodes, limb movements can
be generated. This approach requires very low energy consumption
and exhibits high embodiment by the person; however, FES
cannot produce sufficient torques to enable whole-arm reaching
movements in people with tetraplegia, as many muscles are
unresponsive to FES (Peckham et al., 1976; Mulcahey et al., 1999). Further, general multi-joint motions are notoriously hard to control
with FES even with the most advanced systems (Ajiboye et al.,
2017), often resulting in fine-tuned feed-forward implementations
due to the physiological delays in muscle response to applied
stimulation, and difficulty in accurately modeling the response
to muscle activation. Augmenting FES with an assistive robot
offers additional torque to support whole arm reaching while
also offering improved movement accuracy, but this comes at the
expense of increased bulkiness and decreased wearability of the
combined FES-robotic system. An optimal combination of FES
and an assistive robot would maximize the contribution of FES to
minimize size and power requirements of the robot (Dunkelberger
et al., 2020). is used to actuate another set (Varoto et al., 2008; Schulz et al.,
2011; Ajiboye et al., 2017). Typically the robot controls motions
that need precision or require larger torques and forces to support,
such as elbow flexion and extension, while FES is used for coarse
movements, such as grasping. For upper limb motions with coupled
degrees of freedom, such as shoulder, elbow, and wrist movements,
these existing control strategies pit FES against a robot-imposed
locked-joint, gravity, or single-joint motion constraint, essentially
wasting the free actuation from FES and transferring it to the
robot. Frontiers in Neurorobotics frontiersin.org 1. Introduction Recently, single-joint hybrid systems that do share actuation
on the same joint have been explored, but research has been
limited, testing only in the elbow flexion extension joint with
biceps electrodes in a minimum jerk trajectory (Wolf et al., 2017;
Burchielli et al., 2022), or in simulation (Bardi et al., 2021). In lower limb applications, more advanced hybrid control
algorithms have been explored, largely enabled by the repetitive
nature of gait motions (Bulea et al., 2014; del Ama et al., 2014;
Ha et al., 2016). These lower limb hybrid systems often use a
version of iterative learning control that takes advantage of the
repetitive movements to fine-tune control over several cycles. Some
recent research has begun to use model predictive control (MPC)
algorithms, which can be more readily adapted to non-cyclic
movements in the lower limbs (Kirsch et al., 2018; Bao et al., 2021),
and which are more similar to the non-cyclic movements required
of upper-limb movements. Results from these studies using MPC
have shown the ability to follow a step reference trajectory and
hold a position, and the algorithms should generalize to arbitrary
trajectories. This combination of FES with robotic devices is starting to
gain traction, and is termed hybrid FES-robot (or FES-exoskeleton)
control. A conceptual representation of using FES with a robot
is shown in Figure 1, where both robotic and FES action can
complement each other to assist in the completion of activities of
daily living. Many of the early approaches to bring this concept
to reality did not truly combine and coordinate the actuation
strategies for upper limb movements (Dunkelberger et al., 2020). Instead, each of the actuation types was used to achieve separate
functions. For example, robotic devices have been used to lock
degrees of freedom (Klauer et al., 2014; Ambrosini et al., 2017) or as
gravity compensation (Cannella et al., 2016) enabling the muscles
to relax and preventing fatigue. Other works have used robotic
support devices to actuate one set of degrees of freedom, while FES A truly shared approach for hybrid FES and robotic control
of upper limb reaching movements is needed to combine these
techniques in a manner that achieves generalized upper limb
movement assistance in an optimal manner. In this paper, we 02 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 10.3389/fnbot.2023.1127783 resulting torque and position profiles for the hybrid controller are
compared with an exoskeleton-alone controller in following two
different trajectories. 2.1. Participants Nine able-bodied participants (four female, avg age 22.9)
participated in a single session of the experiment after providing
informed consent. Three of the nine participants, who had
experience with FES prior to the initial experimental session,
also completed a second session of testing using the same
protocol at least 1 week after their first experimental session. The study was approved by the institutional review boards at
Rice University (IRB #FY2017-461) and Cleveland State University
(IRB #30213-SCH-HS). 2.4. Methods The study consists of several model characterization steps
related to each of the subsystems, followed by experimental testing
of the hybrid controller which makes use of these characterizations. First, the electrodes are placed in appropriate locations, and
comfortable ranges of stimulation are found. Recruitment curves
are characterized for each set of electrodes to define the relationship
between commanded pulse width and muscle activation level. Gaussian process regression models are created to characterize
torque output for each electrode based on the orientation of
the upper-limb. The mass properties of the participant’s arm are
then characterized so that a combined dynamic model can be
created for the arm-exoskeleton subsystem. The hybrid controller
is created using the characterizations of each of the components. These characterization steps are more completely described in
Sections 2.4.1–2.4.5. The hybrid controller is then compared
against an exoskeleton alone controller in a scenario of following
two trajectories for each DOF. 1. Introduction present a model-based control approach to hybrid FES-exoskeleton
control. Recent works have demonstrated the first steps toward
this vision. Wolf and Schearer (2022) demonstrated the use of
model-based algorithms to power FES in combination with gravity
compensation from a robot. Our group has also demonstrated
shared control of elbow flexion and extension movements with
FES and exoskeleton assistance acting in coordination to follow
a desired trajectory (Dunkelberger et al., 2022b). In that work,
we showed that a model-based controller for our upper limb
exoskeleton, which has knowledge of the expected contributions
of FES, requires significantly less robot torque than a standard
PD control algorithm, with minimal loss in trajectory following
accuracy. Here, we expand our initial demonstration along a
number of fronts. First, we present an MPC algorithm that removes
the integral term used previously and incorporates an additional
proportional-integral-derivative (PID) controller acting in parallel,
resulting in improved performance in both trajectory following and
reduction in torque requirements from the exoskeleton compared
to our initial controller. We incorporate a sophisticated model of
the user’s arm dynamics that accurately captures behavior across
the exoskeleton workspace. We experimentally demonstrate the
performance of the hybrid FES-exoskeleton controller in able-
bodied participants completing two trajectories for two degrees-
of-freedom of the exoskeleton (elbow flexion-extension and wrist
flexion-extension), and we compare the performance of the hybrid
controller to an exoskeleton-alone case, as illustrated in Figure 1. Finally, we examine longitudinal performance of the hybrid FES-
exoskeleton control for a subset of participants to determine how
performance changes 1 week after the initial experiment trials. Frontiers in Neurorobotics frontiersin.org 2.3. Materials The hybrid FES-exoskeleton system is comprised of two main
subsystems that provide actuation. The first subsystem, which
provides FES, is a transdermic electrical stimulation system (Trier
et al., 2001) which provides eight output channels of bipolar
stimulation. In this study, two channels are used for the elbow
flexion/extension joint, and two channels are used for the wrist
flexion/extension joint. To provide varying levels of output using
the FES subsystem, the amplitude and frequencies are kept at a
constant value for each channel, and the pulsewidth is varied. The second subsystem is the robot, the MAHI Open
Exoskeleton (Dunkelberger et al., 2022a). This robot provides
four DOFs of movement support, namely elbow flexion/extension,
forearm pronation/supination, wrist flexion/extension, and wrist
radial/ulnar deviation, and each of these joints line up with
the equivalent anatomical degree of freedom of a person using
the exoskeleton. These will also be referred to by joint number
throughout this paper, which are joints 1–4, respectively. The
exoskeleton has an adjustable counterweight to account for varying
arm masses, an adjustable slider to account for varying forearm
lengths, and an adjustable shoulder abduction angle to keep the
participant comfortable. The counterweight and forearm slider
parameters are adjusted for each subject at the beginning of the
experiment, and locked for the experiment duration. This shoulder
abduction angle was kept at a value of 30◦for all participants. 2.4.4. Gaussian process regression model creation 2.4.4. Gaussian process regression model creation
Th
l
d d
h
ll
h p
g
The last component needed to mathematically represent the
FES subsystem is a representation of the torque output based
on the arm joint configuration of the participant. A Gaussian
Process Regression (GPR) model is used to characterize this
relationship torque when each of the FES electrode pairs is at a
maximum activation as a function of the arm configuration. In
this case, the black-box representation of the GPR models also
implicitly capture some of the complex muscle dynamics. For
each of the degrees of freedom, eight evenly spaced positions
are taken between the minimum and maximum values that
each joint will see throughout the experiment. At each of
these positions, PD controllers on each of the individual robot
DOFs are used to keep the robot at the desired position. The
exoskeleton torque required to hold the pose when no muscles
are stimulated is recorded as τpassive. One electrode is increased
to its maximum activation, and the exoskeleton torque required
to hold that pose is recorded as τhold. We consider the difference
between the two values as the torque produced by the electrode
τrecord. 2.2. Procedure The goal of this study is to develop a new hybrid controller
that distributes actuation between an exoskeleton system and an
FES system. The goal of such a controller is that it can reduce the
power requirements in comparison to an exoskeleton alone system,
which can lead to more portable devices in the future that can
assist individuals with SCI in completing general activities of daily
living. To test the effectiveness, the developed hybrid controller is
used to provide movements on two different degrees of freedom
(DOF), elbow flexion/extension, and wrist flexion/extension. To
understand how this compares to available exoskeleton systems, the In
this
study,
the
elbow
flexion/extension
and
wrist
flexion/extension DOFs are tested independently. Each of the
experimental steps is performed with the elbow flexion/extension
joint and corresponding electrodes, followed by the wrist 03 Dunkelberger et al. 10.3389/fnbot.2023.1127783 performs four impulses at pwmax, followed by four linear ramps
between pwmin and pwmax, as shown in Figure 3. flexion/extension
joint
with
corresponding
electrodes. The
explanations that follow apply to both DOFs. The ramp deconvolution method is used (Durfee and MacLean,
1989) with the input of pulsewidth values and the corresponding
torques generated from the stimulation to generate smooth curves
to be characterized. The sigmoid is then fitted using Equation 3
with free parameters of c1 and c2, where pw∗and pw∗
max are defined
as pulsewidths normalized so that a pw∗value of 0, corresponds a
pwmin as defined in Equations 1, 2. Frontiers in Neurorobotics 2.4.2. Threshold identification Once the electrodes have been placed, the minimum and
maximum pulsewidth values that will be used for each participant
need to be identified. The robot and arm were moved to a neutral
configuration, and held there using independent PD controllers
on all joints. For each electrode placed, the minimum value that
produced a change in torque output in the PD controller is
considered the minimum pulse width value, pwmin. The discomfort
threshold is then found by increasing the pulsewidth until the
participant verbally indicates their maximum value which is still
comfortable. The maximum pulsewidth value used throughout
the experiment, pwmax, is taken as a slight reduction from the
discomfort threshold. A ramp from the pwmin to pwmax is then used
to verify that the participant remains comfortable throughout the
range, and that the pwmin is just below the threshold of providing
torque output. τrecord. (5) τrecord = τhold −τpassive
(5) 2.4.1. FES electrode placement The experimental protocol began by placing the electrodes on
the participants. Each of the electrode pairs were placed and tested
one at a time. A set of electrodes was placed as agonist/antagonist
pairs for each of the active degrees of freedom. This means for
the elbow flexion/extension joint, one set of electrodes was placed
to target elbow flexion, and another set was placed to target
elbow extension using two inch square electrodes. For the wrist
flexion/extension joint, one set of electrodes was placed to target
wrist flexion, and another set of electrodes was placed to target wrist
extension using one inch round electrodes. Electrode placement
locations for each of these movements were chosen based on pilot
testing based on which locations could reliably provide the desired
movement. These general chosen locations are shown in Figure 2. pw∗= pw −pwmin
(1)
pw∗
max = pwmax −pwmin
(2)
α∗=
c1
1 + e−c2(pw∗−pw∗max
2
)
−
c1
1 + e
c2pwmax
2
(3)
α = α∗
c1
(4) pw∗= pw −pwmin
(1)
pw∗
max = pwmax −pwmin
(2)
α∗=
c1
1 + e−c2(pw∗−pw∗max
2
)
−
c1
1 + e
c2pwmax
2
(3)
α = α∗
c1
(4) pw∗= pw −pwmin
(1)
pw∗
max = pwmax −pwmin
(2)
α∗=
c1
1 + e−c2(pw∗−pw∗max
2
)
−
c1
1 + e
c2pwmax
2
(3)
α = α∗
c1
(4) (1) (4) This equation results in a sigmoid with a minimum value of 0
and a maximum value of c1. The term c2 is related to the slope of the
function as it crosses the midpoint. To turn this characterization
into the standard definition of a recruitment curve which varies
from 0 to 1, α∗is divided by c1 to arrive at an equation for
activation, α. For the elbow flexion electrode placement, a reference electrode
was placed, and a Compex motor point pen was used to find a
specific point that generates biceps contraction, and the second
electrode was placed there. For the remaining electrodes, the pair
of electrodes were placed in a nominal location, and the pulse
width was increased slowly. The resulting movement with the
participant’s arm on a table was observed, and the electrodes
were adjusted if the desired movement was not produced. The
electrodes were then wrapped with medical bandage to ensure that
the electrodes stayed in the original location. frontiersin.org 2.4.3. Recruitment curve characterization (A) A participant with their arm in the robot in the experimental setup, with the axes of rotation for the active joints indicated by orange and red
arrows for the elbow flexion/extension and wrist flexion/extension joints respectively. (B) Placement of each of the four sets of electrodes. Electrodes
were placed over the biceps for elbow flexion over the triceps for elbow extension. Electrodes were placed on the flexor carpi ulnaris for wrist
flexion, and extensor carpi radialis longis and extensor carpi ulnaris muscles for wrist extension. FIGURE 3
(Left) Profiles of commanded pulsewidths, and resulting torque outputs due to stimulation from the wrist extension electrode in the recruitment
curve characterization process. (Right) Resulting characterized recruitment curve in the form of a sigmoid based on the ramp deconvolved data. FIGURE 3
(Left) Profiles of commanded pulsewidths, and resulting torque outputs due to stimulation from the wrist extension electrode in the recruitment
curve characterization process. (Right) Resulting characterized recruitment curve in the form of a sigmoid based on the ramp deconvolved data. FIGURE 3
(Left) Profiles of commanded pulsewidths, and resulting torque outputs due to stimulation from the wrist extension electrode in the recruitment
curve characterization process. (Right) Resulting characterized recruitment curve in the form of a sigmoid based on the ramp deconvolved data. 2.4.3. Recruitment curve characterization The
position
tested
and
τrecord
at
that
position
are
saved
as
training
data
for
the
tested
electrode. This
is
repeated
for
the
other
electrode
active
for
the
current
DOF, and at each of the other positions, three times in a
randomized order. The collected training points are then
used to generate a GPR model for each electrode using
Matlab’s
fitrgp
function. An
example
of
trained
GPR
models for elbow flexion/extension torque output resulting With the thresholds defined, a mathematical representation
between the pulsewidth range and muscle activation is found,
defined as a recruitment curve. Previous research has shown that
functional electrical stimulation produces a muscle recruitment
curve in the form of a sigmoid (Durfee and MacLean, 1989). To characterize this recruitment curve, the robot is again moved
to a neutral configuration, and held there using independent
PD controllers on each joint. Each of the electrodes sequentially 04 frontiersin.org 10.3389/fnbot.2023.1127783 Dunkelberger et al. FIGURE 2
(A) A participant with their arm in the robot in the experimental setup, with the axes of rotation for the active joints indicated by orange and red
arrows for the elbow flexion/extension and wrist flexion/extension joints respectively. (B) Placement of each of the four sets of electrodes. Electrodes
were placed over the biceps for elbow flexion over the triceps for elbow extension. Electrodes were placed on the flexor carpi ulnaris for wrist
flexion, and extensor carpi radialis longis and extensor carpi ulnaris muscles for wrist extension. FIGURE 3
(Left) Profiles of commanded pulsewidths, and resulting torque outputs due to stimulation from the wrist extension electrode in the recruitment
curve characterization process. (Right) Resulting characterized recruitment curve in the form of a sigmoid based on the ramp deconvolved data. FIGURE 2
(A) A participant with their arm in the robot in the experimental setup, with the axes of rotation for the active joints indicated by orange and red
arrows for the elbow flexion/extension and wrist flexion/extension joints respectively. (B) Placement of each of the four sets of electrodes. Electrodes
were placed over the biceps for elbow flexion over the triceps for elbow extension. Electrodes were placed on the flexor carpi ulnaris for wrist
flexion, and extensor carpi radialis longis and extensor carpi ulnaris muscles for wrist extension. Frontiers in Neurorobotics frontiersin.org 2.4.5. Arm model characterization GPR models are shown along with data points used to fit the model for the elbow flexion/extension joint for the elbow flexion and el
sion electrode. joints, this arm characterization process utilizes all four joints of the
exoskeleton to create a full dynamic model as shown in Equation 7,
which can then be reduced to the single-joint components for the
controller. velocities were filtered, and a finite difference derivative was
calculated to approximate the accelerations. With these values,
the difference between the left side and right side of Equation 7,
recorded and calculated torques respectively, could be found given
a guess of mass properties. The difference between these two values
at every time step is the error in the dynamic model, and this
error was used as the optimization criteria to estimate the mass
properties of the arm when combined with the mass properties
of the exoskeleton found in previous work (Dunkelberger et al.,
2022a). (7) τ = M(q)¨q + V(q, ˙q) + G(q) + Ff(˙q)
(7) τ = M(q)¨q + V(q, ˙q) + G(q) + Ff(˙q) In Equation 7, τ
∈
R4×1 is a vector consisting of the
torques at each joint. M ∈R4×4 is known as the mass matrix
and consists of different combinations of the mass and inertial
terms of each joint. V ∈R4×1 is the vector of centrifugal and
Coriolis terms. G ∈R4×1 is the gravity vector and gives the
affects of gravity on each joint, and Ff
∈R4×1 gives friction
on each joint. q is a vector of all joint positions, ˙q is a vector
of all joint velocities, and ¨q is a vector of all joint accelerations. M, V, G, and Ff were calculated using the same methods as
previous work (Dunkelberger et al., 2022a), but with the combined
arm and robot properties serving as lumped parameters in the
formulation. To keep the number of optimization variables small, the
problem was solved one joint at a time, starting with the most
distal joint, wrist radial/ulnar deviation. This joint was the first
to be optimized because for any given joint, only the more distal
joints impact the current mass property analysis. Each more
proximal joint was then optimized in order, ending with the
elbow flexion/extension joint. At each joint, the inertia about
the axis of rotation and the distances to the center of mass in
the other two axes were optimization variables. Frontiers in Neurorobotics frontiersin.org 2.4.5. Arm model characterization from the elbow flexion and elbow extension electrodes for
a single subject is shown in Figure 4. This results in the
following equation An accurate model of the dynamic system is needed for effective
MPC implementation. Previous work has developed a model of the
exoskeleton without an arm (Dunkelberger et al., 2022a). In this
study, an optimization problem was solved to find an estimate of
dynamic properties for the arm to be used with the exoskeleton
dynamic model, including masses, moments of inertia, and friction
components. τfes = P(q)α
(6) (6) where P(q) ∈R1×2 and where column i is an individual GPR
model that provides an estimated output torque when electrode set
i is at maximum stimulation, and the robot is at position q. Recall
that this is implemented for each joint separately, so there is one
P(q) that corresponds to the elbow flexion/extension joint and uses
the elbow flexion/extension position as an input, and one P(q) that
corresponds to the wrist flexion/extension joint and used the wrist
flexion/extension position as an input. where P(q) ∈R1×2 and where column i is an individual GPR
model that provides an estimated output torque when electrode set
i is at maximum stimulation, and the robot is at position q. Recall
that this is implemented for each joint separately, so there is one
P(q) that corresponds to the elbow flexion/extension joint and uses
the elbow flexion/extension position as an input, and one P(q) that
corresponds to the wrist flexion/extension joint and used the wrist
flexion/extension position as an input. To add theese dynamic properties of the arm to the dynamic
model of the exoskeleton, each joint in the arm was assumed to be
a rigid body rigidly connected to the corresponding joint on the
exoskeleton. With this assumption, the mass of each arm joint can
be added to the mass of the robot joint, and the inertia of each arm
joint can be combined with the inertia of each robot joint using
the parallel axis theorem. While this study mainly focuses on the
impact on the elbow flexion/extension and wrist flexion/extension 05 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 FIGURE 4
Fitted GPR models are shown along with data points used to fit the model for the elbow flexion/extension joint for the elbow flexion and elbow
extension electrode. 2.4.5. Arm model characterization Active joint
qhold_1
qhold_2
qhold_3
qhold_4
Elbow F/E
N/A
0◦
0◦
0◦
Wrist F/E
–30◦
–30◦
N/A
0◦ formulation of this optimization problem can be seen in Equations
8, 9. arg min
pd
ed =
M
X
t=1
(τcalc_d_t −τmeas_d_t)2
(8)
pd =
(
Iczz_d, rcx_d, rcy_d, rcx_d+1, Fk_d, Bd
if 1 ≤d ≤3
Iczz_d, rcx_d, rcy_d, Fk_d, Bd,
if d = 4
(9) (8) To develop our control problem, we define the following
quantities as the system state, x, system output, y, and and control
input, u, where C is the output matrix describing the variables we
can observe. (9) In these equations, pd represents the vector of parameters for a
given joint, d. A d of 1 represents the elbow flexion/extension joint
and d = 4 being the wrist radial ulnar/deviation joint, ed refers to
the torque error between the calculated torque, τcalc, and measured
torque, τmeas, t represents a given time step up to M total time steps,
Iczz is the moment of inertia about the axis of rotation taken about
the center of mass, and rcx, rcy, and rcz represent the distance from
the axis of rotation to the center of mass in the x, y, and z directions
respectively. x = [q, ˙q]T
(12)
C = I2
(13)
y = Cx
(14)
u = [τexo_mpc, α1, α2]T
(15) x = [q, ˙q]T
(12)
C = I2
(13)
y = Cx
(14)
u = [τexo_mpc, α1, α2]T
(15) (15) To use standard analysis techniques, we would like to have
our dynamics in the form of ˙x = f (x, u), which by definition
is the vector [˙q, ¨q]T. By solving Equation 11 for ¨q as follows,
we can obtain an explicit definition for the representation of
f (x, u). The optimization problem was solved using fmincon in
Matlab, with initial guesses of zero for all optimization variables. The optimal properties found using this method were combined
into the lumped arm and robot system used in the remainder of
this study. ¨q = 1
m(P(q)α + τexo_mpc −g sin(q −qeq) −ff (˙q))
(16) (16) 2.4.5. Arm model characterization When running
the optimization on any joint except wrist radial/ulnar deviation,
the next distal joint’s distance to the center of mass along the
distal joint’s axis of rotation was also included as an optimization
variable. This was added because this value does not appear in
the calculations for the joint moving, but does impact the more
proximal joints. Lastly, two optimization variables were added
to each joint corresponding to the joint kinetic and viscous
friction, which were considered to be added to the coefficients
previously characterized for the exoskeleton by itself. A constant
mass was assumed for each joint because the mass only appears
multiplied by the distance to the center of mass terms. The Equation 7 can be used to characterize the unknown arm
mass properties that appear in the equation, given experimentally
recorded values for τ, q, and ˙q. To collect these data for
characterization, the user’s arm was placed inside the robot and
secured. A chirp signal was used as a position reference for
the wrist radial/ulnar deviation joint while the other three joints
were commanded to remain stationary using independent PD
controllers. This process was then repeated for each more proximal
joint. The torque required to complete the motions and the
resulting joint positions and velocities were recorded. The recorded 06 frontiersin.org 10.3389/fnbot.2023.1127783 Dunkelberger et al. TABLE 1 Holding position of inactive joints throughout testing. For the DOF of interest, m represents the estimated lumped
inertia, g represents the gravitational effects, ff represents the
friction effects, and qeq represents the natural resting position of the
combined arm-robot system for the DOF of interest. In Equation
11, and throughout the remainder of the paper, all variables that
appear in equations are referring to a single DOF, and the values
of these variables are different in the elbow flexion/extension DOF
and the wrist flexion/extension DOF, but the symbolic expressions
apply to both DOFs. For example, when this equation is applied
to the elbow flexion/extension joint, q, ˙q, and ¨q are the position,
velocity, and acceleration of the robot elbow flexion/extension
joint, and α is the vector [α1, α2]T, which are the activation levels of
the electrodes placed to induce elbow flexion, and elbow extension. Active joint
qhold_1
qhold_2
qhold_3
qhold_4
Elbow F/E
N/A
0◦
0◦
0◦
Wrist F/E
–30◦
–30◦
N/A
0◦
formulation of this optimization problem can be seen in Equations
8, 9. frontiersin.org 2.5. Hybrid controller design From u, τexo_mpc is used directly, and α1 and α2 are
converted to pulsewidth commands to send to the stimulator using
Equation 4 which describes the recruitment curve. The general ideology behind the choice of gains in the hybrid
controller is as follows. The gains for Q represent the importance
for the controller to follow the desired trajectory, with higher gains
indicating better tracking, but less stable behavior if there are model
errors. The gains for Rm are chosen so that Rm_exo ≫Rm_fes, which
is the main method by which the hybrid control strategy reduces
exoskeleton torque compared to a strategy which only uses an
exoskeleton. Additionally, these gains are chosen such that (¯yi −
ri)TQ(¯yi−ri)≫uT
i Rmui, so that trajectory accuracy is not sacrificed
to allow for overall torque reduction. The gains for R are chosen so
that Rfes ≫Rexo so that the FES system, which has significant delay,
remains stable by mainly responding with low-frequency changes
in torque while the exoskeleton does mostly quick corrective
actions. This combination of chosen gains for R and Rm are
intended to have the general effect of the FES subsystem providing
low frequency, high amplitude torque, allowing it to provide a bulk
of the power requirement, yet maintain smooth motions despite
the time delay. The exoskeleton subsystem provides high frequency,
low amplitude torque, which provides necessary quick corrections
without requiring too much power consumption. As a reminder,
separate controllers are used for the elbow flexion/extension joint
and for the wrist flexion/extension joint, and the gains for each of
the two joints are created independently. To tune the gains for the MPC algorithm, Q and R were first
tuned to achieve smooth movements and low tracking error, with
Rm values kept at 0. Following this, the Rm gains were chosen
to achieve meaningful reduction in the exoskeleton torque, while
maintaining similar tracking accuracy. As Rm gains were tuned, Q
and R were further adjusted as necessary. To account for model error in the MPC formulation, a PID
controller using only exoskeleton torque is implemented in parallel
as shown in Figure 5. This has the effect of allowing the MPC
portion to control most of the action, while still providing a high
accuracy on the resulting trajectory tracking. 2.5. Hybrid controller design P(q)α + τexo_mpc = m¨q + g sin(q −qeq) + ff (˙q)
(11) (11) frontiersin.org Frontiers in Neurorobotics 07 frontiersin.org 10.3389/fnbot.2023.1127783 Dunkelberger et al. In this equation, the control input rate of change at timestep i is
defined as 1ui = ui−ui−1. Initial values for these gains were chosen
based on pilot studies that provided desired behavior as described
below. In Equation 24, k represents the current point in time, and
future discretized timesteps at time k + i are Ts seconds apart,
for N time steps. The dynamics at these future time points
are approximated using Euler integration as shown by the fist
constraint on the optimization problem, with the bars representing
that these are estimated values. The second constraint restricts
the activation level, α, of each electrode, e, to fall between 0 and
1. An additional constraint could be implemented to limit the
maximum allowable exoskeleton torque; however, in this study,
the torque required from the exoskeleton always remained below
the maximum allowable torque, which meant that this constraint
did not need to be implemented. The result of the optimization
is u(·) which represents the optimal control inputs over the time
prediction horizon, uk+1, uk+2, ..., uk+N. Q =
"
Qpos
0
0
Qvel
#
(21)
R =
Rexo
0
0
0
Rfes
0
0
0
Rfes
(22)
Rm =
Rm_exo
0
0
0
Rm_fes
0
0
0
Rm_fes
(23) Q =
"
Qpos
0
0
Qvel
#
(21)
R =
Rexo
0
0
0
Rfes
0
0
0
Rfes
(22)
Rm =
Rm_exo
0
0
0
Rm_fes
0
0
0
Rm_fes
(23) (21) (22) (23) This MPC formulation is created in C++ using the nonlinear
optimization framework CasADi (Andersson et al., 2019). The
solver for the dynamic problem is compiled into a dll file which
can be loaded at runtime and interfaced with the Interior Point
Solver, IPOPT (Wächter and Biegler, 2006), to solve the MPC
problem. This MPC problem is solved as fast as possible in a
separate thread, and each time a solution is found, the solution
of the minimization, u(·), is sent to the main thread, where those
successive control solutions are used until the next solution is
found. 2.5. Hybrid controller design To implement real time control, it is beneficial to use
a linearized form of the dynamics to reduce computation
time. We can then convert the dynamics to a linearized form
by calculating the Jacobian of the dynamics about time k
with respect to the input and output. The following gives a
estimate for the dynamic equations at time i, linearized at
time k. We first present the full four-DOF dynamics for the FES-
exoskeleton hybrid system, which we will then reduce to the single-
DOF dynamics for the control formulation. This is similar to the
dynamics of the robot and arm system in Equation 7, but the inputs
to the system arise from both the exoskeleton and the FES system,
so we separate the torque term into the two components. τfes + τexo = M(q)¨q + V(q, ˙q) + G(q) + Ff(˙q)
(10) (10) Ak = ∂f
∂x
x=xk,u=uk
(17)
Bk = ∂f
∂u
x=xk,u=uk
(18)
˙¯xi = Akxi+Bkui + ˙x|x=xk,u=uk
(19) (17) In this equation, τexo ∈R4×1 and τfes ∈R4×1 are torques
supplied along each of the robot joints due to robot torque outputs,
and torques provided by FES respectively. As in the previous sections, the control problem will be
described once, but the equations presented apply to either the
elbow flexion/extension or the wrist flexion/extension DOF. To
limit the full dynamics in Equation 10 to analyze a single DOF with
the rest of the joints remaining stationary, all inactive joints can be
constrained such that qj = qhold_j, ˙qj = 0, ¨qj = 0 for all joints j
that are inactive. Here, qhold_j is the holding position of joint j when
it is inactive, as shown in Table 1. This results with the following
equation to describe the dynamics of a single DOF system, either in
the elbow flexion/extension or wrist flexion/extension case. (19) These linearized dynamics are then used in the MPC
formulation. The
cost
function
is
as
follows,
where
i
represents
a
discrete
point
in
time
in
the
standard
MPC formulation. Ji = (ri −¯yi)TQ(ri −¯yi) + 1uT
i R1ui + uT
i Rmui
(20) (20) The matrices Q ∈R2×2, R ∈R3×3, and Rm ∈R3×3 are positive
diagonal matrices used to weight predicted trajectory error, control
input rate of change, and control input magnitude respectively. Frontiers in Neurorobotics 2.6. Experimental validation was followed by four wrist flexion/extension trials, again consisting
of each possible combination of trajectory and controller. This
sequence was repeated until all 40 total trials had been collected. Throughout each of the trials, position of the active DOF, total
exoskeleton torque commanded, and activation levels of electrodes
were collected at a rate of 1 kHz using a Quanser Q8-USB data
acquisition device. After
a
participant
completed
each
of
the
model
characterization steps and the MPC problem was generated,
the experimental validation was conducted. Participants were
assisted in completing two different trajectories in two different
conditions, using the hybrid controller that combined the FES
and exoskeleton action, and using the exoskeleton alone. The first
trajectory is referred to as the cup trajectory, and it is based on
a study that tracked healthy individuals’ joint-level movements
to move a cup to various target locations with differing grasps
(Valevicius et al., 2019). The movement profile for each of the
joints was taken independently and spaced so that it spanned
a useful and comfortable trajectory space for the exoskeleton
used in this study which was 30◦flexed to 90◦flexed from full
extension for elbow flexion/extension and 15◦extended to 45◦
flexed for wrist flexion/extension. The cup trajectory is useful to
observe how the hybrid controller behaves when following natural
motions that would be expected under normal use. The second
trajectory is referred to as the sinusoidal trajectory, and it is an
artificially created trajectory that is the summation of multiple
sinusoidal waves at different amplitudes and frequencies. This
trajectory was created to test the controllers’ ability to generalize
to different movements. The trajectories are relatively similar in
terms of difficulty for the elbow flexion/extension joint, but the
wrist flexion/extension joint movement is significantly easier in
the cup trajectory than the sinusoidal trajectory. Both trajectories
take 42.4 s to complete, which is four times the time it took an
average able-bodied individual to complete the cup trajectory in
Valevicius et al. (2019). A four times reduction was chosen because
the original trajectory moved through the workspace very quickly,
and this reduction empirically felt an appropriate length to safely
perform movements with a human in the robot. Visualizations of
these trajectories are shown in the results in Figures 8, 9. Three of the nine participants repeated the entire protocol
(including characterization steps) at least 1 week after they
completed the first set of data collection. 2.6. Experimental validation These data were collected
to provide insight into whether results remain similar between
sessions within the same participant, rather than only comparing
between participants. 2.5. Hybrid controller design FIGURE 5
Hybrid FES-exoskeleton control block diagram, showing how the diferent components of the hybrid controller work together to provide torque
commands to the robot and pulse width commands to the stimulator given a desired input trajectory. Frontiers in Neurorobotics 2.5. Hybrid controller design The torque provided
by the PID controller is defined as τexo_fb, and the gains for this
controller were chosen in pilot testing to achieve between 1 and
1.5◦RMS tracking error. In the tuning of this controller, the
gains were slowly increased, and tuned only after fully tuning
the MPC system independently, so that the controller dynamics
achieved from the MPC algorithm were the driving component. This additional controller does not change the output applied by the
FES subsystem, but the torque applied to the exoskeleton becomes Because the Rfes and Rm_fes gains place costs on activation levels
rather than FES torque outputs, in some cases, it was necessary to
adjust these values for each participant upon initial testing with the
hybrid controller to account for variations in torque productions
for the same activation level. To account for this, when the hybrid
controller was first tested in the experiment, these gains were
increased by a factor of two from the original values if there was
oscillatory behavior, or decreased by a factor of two if activation
levels were lower than expected. τexo_tot = τexo_mpc + τexo_fb
(25) (25) To test the effectiveness of the hybrid controller design, it is
compared against a purely exoskeleton controller, defined as the
exoskeleton alone control case. In this test case, the same general
structure is used with the MPC controller paired with a PID
controller, but Equation 15 becomes The final cost function used in the MPC implementation is as
follows. arg min
u(·)
Jtot =
N
X
i=1
Jk+i
(24)
subject to ¯yk+i+1 = ¯yk+i + ˙¯xk+iTs,
0 ≤αe ≤1, e = {1, 2} arg min
u(·)
Jtot =
N
X
i=1
Jk+i
(24)
subject to ¯yk+i+1 = ¯yk+i + ˙¯xk+iTs,
0 ≤αe ≤1, e = {1, 2} (24) u = [τexo]
(26) (26) which results in R and Rm being single values rather than matrices. which results in R and Rm being single values rather than matrices. frontiersin.org 08 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 FIGURE 5
Hybrid FES-exoskeleton control block diagram, showing how the diferent components of the hybrid controller work together to provide torque
commands to the robot and pulse width commands to the stimulator given a desired input trajectory. 2.7. Data analysis The primary objective of these experiments is to understand the
extent to which exoskeleton power consumption can be reduced
in a hybrid system compared to a exoskeleton alone system. We
compare power consumption by taking the sum of the squared
total exoskeleton torque throughout the trajectory for each of the
conditions tested as shown in Equation 27, averaged across each of
the five trials with that set of conditions. This value is labeled as
τss_exo for the exoskeleton alone control condition, and τss_hybrid for
the hybrid control condition. Because participants have different
arm sizes, and require the robot to be in different configurations,
it is expected that participants will require different amounts of
sum of squared torque from the system to move through the
cup and sinusoidal trajectories. To normalize the data to compare
across subjects, the reduction in sum of squared torque in the
hybrid control case compared to the exoskeleton alone control case
is shown by Equation 28. This allows us to analyze the varying
power consumption both between exoskeleton alone and hybrid
controllers, as well as how the relative controller performance
translates between two different trajectories. Each DOF was tested for ten trials on the cup trajectory, split
evenly between hybrid controller and exoskeleton alone controller,
and 10 trials on the sinusoidal trajectory, also split evenly between
hybrid controller and exoskeleton alone controller. While each
DOF was being tested, all other DOFs were kept at their qhold
values as shown in Table 1 using independent PD controllers
on those joints. Collection of the experimental data began by
running four elbow flexion/extension trials, consisting of one of
each possible combination of trajectory and controller type. This τss =
N
X
i=1
τ 2
exo_tot
(27)
%Imp = 100(1 −τss_exo −τss_hybrid
τss_exo
)
(28) (27) %Imp = 100(1 −τss_exo −τss_hybrid
τss_exo
)
(28) frontiersin.org 09 frontiersin.org Dunkelberger et al. Dunkelberger et al. 10.3389/fnbot.2023.1127783 10.3389/fnbot.2023.1127783 exoskeleton alone and hybrid controllers respectively. RMS errors
in the sinusoidal trajectory were 1.10 and 1.26◦for the exoskeleton
alone and hybrid controllers respectively. These results indicate
that there is a mean increase of 0.18◦in RMS error when using
the hybrid controller compared to using the exo alone controller
in the elbow flexion/extension joint. This difference was shown to
be statistically significant in the paired t-test, with p-values for each
of the trajectories < 0.01. In Equation 27, N is the number of data points collected. 2.7. Data analysis With
this representation, a value of %Imp = 0 would represent equal
amounts of torque being used in both control cases, which would
indicate no improvement, a value of %Imp > 0 would indicate a
reduction in power consumption using the hybrid controller with
a value of %Imp = 100 indicating no exoskeleton power was
consumed, and a value of %Imp < 0 would indicate that the hybrid
controller required more exoskeleton power than the exoskeleton
alone case. A paired t-test was performed to understand whether
there was a statistically significant difference between in the sum
of squared torque in the exoskeleton alone control case, and in the
hybrid control case for each of the trajectories. For the wrist flexion/extension joint, RMS errors in the cup
trajectory were 1.21 and 1.12◦for the exoskeleton alone and
hybrid controllers respectively. RMS errors in the sinusoidal
trajectory were 1.53 and 1.48◦for the exoskeleton alone and hybrid
controllers respectively. These results indicate that there is a mean
decrease of 0.07◦in RMS error when using the hybrid controller
compared to using the exoskeleton alone controller in the wrist
flexion/extension joint. This difference was again shown to be
statistically significant in the paired t-test, with p-values for each
of the trajectories again remaining < 0.01. The secondary objective of these experiments is to understand
how the tracking accuracy compares when using the two options
for controllers. The RMS tracking error is calculated as erms =
PN
i=1
p
(yi −ri)2
N
(29) (29) Figures 8, 9 show time series representations of torque profiles
for the best performing subject (represented by the △symbol in
Figures 6, 7) and movement profiles averaged across all subjects. In
the representative plots of torque profiles, the exoskeleton torque
used during the hybrid trials exhibits a smaller magnitude than
the exoskeleton torque used during exoskeleton alone trials. This
result shows that the hybrid controller is able to replace a significant
amount of the torque requirement from the exoskeleton with FES
torque. The plots for movement profiles demonstrate how well each
of the controllers are able to track the trajectory. In all combinations
of trajectories and DOFs, the trajectories almost entirely overlap
each other, showing similar accuracy regardless of controller. 2.7. Data analysis A paired t-test was performed to understand whether there was
a statistically significant difference between the RMS errors in the
exoskeleton alone control case, and in the hybrid control case for
each of the trajectories. One subject was unable to get any detectable torque output
from one of the electrodes on the wrist flexion/extension DOF,
and therefore, did not complete data collection for that DOF. Because of this, there are nine sets of data analyzed for the elbow
flexion/extension results, and eight sets of data analyzed for the
wrist flexion/extension results. The reduction in maximum torque for the torque profile
averaged across participants profiles across participants is also
analyzed, for the hybrid controller compared to the exoskeleton
alone controller. For this metric, it is interesting to observe both the
change in maximum and minimum values, as many cable-driven
systems would likely require one actuator for each agonist and
antagonist pair. In the elbow flexion/extension DOF, the maximum
torque was reduced by 44.2 and 43.7% in the cup and sinusoidal
trajectories respectively, and the minimum torque for the mean
profile was reduced by 31 and 27.1% for the cup and sinusoidal
trajectories respectively. In the wrist flexion/extension DOF, the
maximum torque was reduced by 67.1 and 65.3% in the cup and
sinusoidal trajectories respectively, and the minimum torque for
the mean profile was reduced by 36.9 and 36.6% for the cup and
sinusoidal trajectories respectively. 3. Results A summary of the sum of squared torque reduction findings
is presented in Figure 6 as boxplots with individual subject data
overlaid on top. These results show a mean sum of squared torque
reduction of 48.8 and 48.6% for the cup and sinusoidal trajectories
respectively for the elbow flexion/extension joint when comparing
the hybrid controller to the exoskeleton alone controller. These
values for individual participants spanned from 11.8 to 71.6%
for the cup trajectory, and from 8.8 to 77.2% for the sinusoidal
trajectory, with the lowest data point being an outlier. A mean
sum of squared torque reduction of 59.3 and 56.5% was shown
for the cup and sinusoidal trajectories respectively for the wrist
flexion/extension joint when comparing the hybrid controller
to the exoskeleton alone controller. These values for individual
participants spanned from 33.4 to 82.9% for the cup trajectory,
and from 39.3 to 79.0% for the sinusoidal trajectory. The statistical
tests showed that the sum of squared torques were significantly
lower in the hybrid control case compared to the exoskeleton alone
control case in both DOFs and in both trajectories, with p-values
being < 0.01 in both trajectories for the elbow flexion/extension
joint, and p-values being < 0.001 in both trajectories for the wrist
flexion/extension joint. Frontiers in Neurorobotics frontiersin.org Dunkelberger et al. 4. Discussion There is a need for devices to provide assistance in completing
activities of daily living for individuals with SCI. For this
population, return of upper-limb function is among their top
priorities (Anderson, 2004). Both FES and exoskeletons provide
some framework to assist with movement, but each of these
technologies has fundamental limitations preventing meaningful
assistance for the upper-limbs in activities of daily living. FES is
unable to provide accurate and repeatable movements by itself,
and using feedback control causes instability due to the inherent A summary of the trajectory tracking accuracy findings is
presented in Figure 7 as box plots with individual subject data
overlaid on top. For the elbow flexion/extension joint, mean
RMS errors in the cup trajectory were 1.04 and 1.24◦for the 10 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 FIGURE 6
Sum of squared torque reduction results are shown for all subjects for each trajectory for the elbow flexion/extension DOF (left) and wrist
flexion/extension DOF (right). The overlaid scatterplot shows individual subject results, with the same symbol representing a single subject across
figures. Points in green show the repeated data collection for the first three subjects, but repeated data collection does not contribute to boxplot
presentation. The purple “∗” above the plots represents a that there was a statistically significant diference in the sum of squared torque between the
hybrid and exoskeleton alone control cases. FIGURE 7
RMS error results are shown for all subjects for each trajectory and each controller type for the elbow flexion/extension DOF (left) and wrist
flexion/extension DOF (right). The overlaid scatterplot shows individual subject results, with the same symbol representing a single subject across
figures. Points in green show the repeated data collection for the first three subjects. The purple “∗” above the plots represents a that there was a
statistically significant diference in the RMS errors between the two control types. time delays in muscle response to stimulation. Exoskeletons
are able to provide accurate and repeatable movements, but
require bulky systems and large amounts of power to support
upper-limb movements against gravity. In this paper, we have
proposed a hybrid FES-exoskeleton controller that combines the
two technologies, with the goal of reducing power consumption
compared to a robot alone, and providing accurate movement,
similar to that of an exoskeleton alone. 4. Discussion This controller uses the FIGURE 6 FIGURE 6
Sum of squared torque reduction results are shown for all subjects for each trajectory for the elbow flexion/extension DOF (left) and wrist
flexion/extension DOF (right). The overlaid scatterplot shows individual subject results, with the same symbol representing a single subject across
figures. Points in green show the repeated data collection for the first three subjects, but repeated data collection does not contribute to boxplot
presentation. The purple “∗” above the plots represents a that there was a statistically significant diference in the sum of squared torque between the
hybrid and exoskeleton alone control cases. FIGURE 6
Sum of squared torque reduction results are shown for all subjects for each trajectory for the elbow flexion/extension DOF (left) and wrist
flexion/extension DOF (right). The overlaid scatterplot shows individual subject results, with the same symbol representing a single subject across
figures. Points in green show the repeated data collection for the first three subjects, but repeated data collection does not contribute to boxplot
presentation. The purple “∗” above the plots represents a that there was a statistically significant diference in the sum of squared torque between the
hybrid and exoskeleton alone control cases. FIGURE 7
RMS error results are shown for all subjects for each trajectory and each controller type for the elbow flexion/extension DOF (left) and wrist
flexion/extension DOF (right). The overlaid scatterplot shows individual subject results, with the same symbol representing a single subject across
figures. Points in green show the repeated data collection for the first three subjects. The purple “∗” above the plots represents a that there was a
statistically significant diference in the RMS errors between the two control types. RMS error results are shown for all subjects for each trajectory and each controller type for the elbow flexion/extension DOF (left) and wrist
flexion/extension DOF (right). The overlaid scatterplot shows individual subject results, with the same symbol representing a single subject across
figures. Points in green show the repeated data collection for the first three subjects. The purple “∗” above the plots represents a that there was a
statistically significant diference in the RMS errors between the two control types. proposed a hybrid FES-exoskeleton controller that combines the
two technologies, with the goal of reducing power consumption
compared to a robot alone, and providing accurate movement,
similar to that of an exoskeleton alone. Frontiers in Neurorobotics 4.1. Torque reduction An average reduction of 48.7 and 57.9% of sum of squared
torque was found on the elbow flexion/extension and wrist
flexion/extension DOFs respectively with the use of the hybrid
controller compared to the exoskeleton alone controller. These
results in the EFE joint are an improvement over the 32.1%
reduction found in our previous implementation using only the cup
trajectory (Dunkelberger et al., 2022b). This improvement shows
that the inclusion of the feedback controller instead of using an
integral term, and the incorporation of a more sophisticated arm
model, resulted in greater benefits in this hybrid control scheme,
while even extending to more generalized trajectory cases. This
shows promise for meaningful power consumption reduction for a
hybrid system when comparing to an exoskeleton alone controller. Practically, this could mean that a portable hybrid system could
be powered for roughly twice as long as an equivalent exoskeleton
alone system, given the same battery capacity. In the future, this
could lead to more portability and longevity in hybrid assistive
devices for impaired populations. It is worth noting the difference in tracking accuracy between
the cup and sinusoidal trajectories on the wrist flexion/extension
joint. Recall that the cup trajectory requires significantly less
movement, with an average velocity of 7.3 ◦/s compared to the
sinusoidal trajectory with an average velocity of 14.3 ◦/s. The
difference in difficulty between the trajectories is likely the cause for
more tracking error in the sinusoidal trajectory. Still, we see that the
general relationship of the hybrid controller having a 0.06◦RMSE
improvement is similar to the 0.09 degree RMSE improvement on
the cup trajectory. A benefit of the proposed control architecture is that the
feedback controller portion can be adjusted independently of
the model predictive control portion. This means that if a
specific movement needs high-precision, the gains of the feedback
controller can be modified in a straightforward manner to increase
accuracy, although it would result in an increase in exoskeleton
torque usage. Additionally, while this study focused on the
challenging task of tracking time-varying trajectories, it would
also be an interesting translation to modify the implementation to
achieve desired setpoint positions, where FES could be used for a
majority of the movement generation when it is far from the target,
and the exoskeleton could be used to fine-tune the position when it
is close to the desired setpoint. 4.3. Generalization across tasks The average reduction in minimum and maximum torques
shows potential for actuator sizes to be reduced while still achieving
the same resultant motion, which would result in less bulky assistive
robotic systems. In the future, this could be more directly tested by
artificially limiting the maximum torque of the exoskeleton joints
to observe how the FES can make up for the lack of torque. Many of the previous applications using FES for assistance
provide the stimulation using a pre-programmed profile for a
specific movement. An important feature of the proposed hybrid
controller is that it does not rely on knowing the desired trajectory
before use, and works with any given input trajectory. By testing
two different trajectories, we were able to observe how the
different outcome metrics varied in different movements. Tracking
performance across several tasks has been reported by a few studies
that use both FES and exoskeletons (Rohm et al., 2013; Memberg
et al., 2014; Ajiboye et al., 2017), but none of these studies use a
controller to distribute actuation between the two systems on the
same joint. 4.1. Torque reduction It is worth noting that while the participants are able-bodied
and can move their arm through the desired trajectories without
assistance, we should not expect to see a torque reduction of 100%. With FES we often cannot achieve the full capabilities of the user’s
muscles, and in this study, many of the participants were not able
to produce the maximum required torque solely through FES, even
at maximum activation. Additionally, FES is known to not provide
accurate or repeatable movements by itself, so at a minimum, the
exoskeleton needs to provide corrective torques to account for these
inaccuracies. 4. Discussion model predictive control cost function to leverage the strengths of
each of the subsystems, while minimizing the weaknesses of each. tracking, is ∼1 mm. For the wrist flexion/extension joint, the hybrid
controller had on average 0.09 and 0.05◦less RMS tracking error
on the cup and sinusoidal trajectories, respectively. Again, while
there is a small decrease in accuracy, the resultant trajectories are
very similar, as shown in Figure 9. These results demonstrate that
the hybrid controller is able to achieve similar tracking accuracies
to the exoskeleton alone controller in both of the individual
DOFs. 4. Discussion This controller uses the time delays in muscle response to stimulation. Exoskeletons
are able to provide accurate and repeatable movements, but
require bulky systems and large amounts of power to support
upper-limb movements against gravity. In this paper, we have Frontiers in Neurorobotics
11 11 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 FIGURE 8
Elbow flexion/extension joint exoskeleton torque profile for a single subject (top), and movement profiles averaged across subjects (bottom) are
shown for the two diferent trajectories, cup (left) and sinusoidal (right). In the plots, the blue line represents data for the exoskeleton alone
controller, and the yellow line represents data for the hybrid controller. FIGURE 9
Wrist flexion/extension joint exoskeleton torque profile from a single subject (top), and movement profiles averaged across subjects (bottom) are
shown for the two diferent trajectories, cup (left) and sinusoidal (right). In the plots, the blue line represents data for the exoskeleton alone
controller, and the yellow line represents data for the hybrid controller. Frontiers in Neurorobotics
12
frontiersin.org FIGURE 8
Elbow flexion/extension joint exoskeleton torque profile for a single subject (top), and movement profiles averaged across subjects (bottom) are
shown for the two diferent trajectories, cup (left) and sinusoidal (right). In the plots, the blue line represents data for the exoskeleton alone
controller, and the yellow line represents data for the hybrid controller. FIGURE 8
Elbow flexion/extension joint exoskeleton torque profile for a single subject (top), and movement profiles averaged across subjects (bottom) are
shown for the two diferent trajectories, cup (left) and sinusoidal (right). In the plots, the blue line represents data for the exoskeleton alone
controller, and the yellow line represents data for the hybrid controller. FIGURE 9
Wrist flexion/extension joint exoskeleton torque profile from a single subject (top), and movement profiles averaged across subjects (bottom) are
shown for the two diferent trajectories, cup (left) and sinusoidal (right). In the plots, the blue line represents data for the exoskeleton alone
controller, and the yellow line represents data for the hybrid controller. FIGURE 9 FIGURE 9
Wrist flexion/extension joint exoskeleton torque profile from a single subject (top), and movement profiles averaged across subjects (bottom) are
shown for the two diferent trajectories, cup (left) and sinusoidal (right). In the plots, the blue line represents data for the exoskeleton alone
controller, and the yellow line represents data for the hybrid controller. 12 Frontiers in Neurorobotics frontiersin.org 10.3389/fnbot.2023.1127783 10.3389/fnbot.2023.1127783 Dunkelberger et al. Frontiers in Neurorobotics frontiersin.org 4.2. Accuracy FES systems by themselves do not provide reliable repeatability
when trying to perform generalized movements. The goal of
hybrid FES and exoskeleton systems is to achieve trajectory-
following accuracies significantly better than FES systems by
themselves, ideally approaching accuracies that are achievable using
exoskeleton-alone systems. In the elbow flexion/extension joint,
the hybrid algorithm had on average 0.20 and 0.16◦more RMS
tracking error on the cup and sinusoidal trajectories, respectively,
when comparing the hybrid controller to the exoskeleton alone
controller. While this was a decrease in accuracy, this still resulted
in a very similar motion over the trajectory, as shown in Figure 8. To put this in perspective, for a forearm length of 30 cm, the
RMS error in positioning the wrist, given the error in angular The sum of squared torque reduction was similar between the
two trajectories for both the elbow flexion/extension DOF and the
wrist flexion/extension DOF. Along with the means and ranges
being the same, the general spacing of the participants within the
range of results remained the same between the two trajectories. This means that the benefits in power reduction did generalize
well to these different trajectories, and that users could expect
similar results on trajectories that require similar motions. It is
especially interesting that a similar level of sum of squared torque
reduction was found on the two different trajectories for the wrist 13 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 FIGURE 10
The maximum absolute values of the GPR predictions throughout the workspace for all participants are shown for each electrode, and for each DOF. This represents how diferent participants are able to achieve diferent levels of torque from FES when the participant is receiving maximum
stimulation. The symbols here correspond to the same symbols from Figures 6, 7. The maximum absolute values of the GPR predictions throughout the workspace for all participants are shown for each electrode, and for each DOF. This represents how diferent participants are able to achieve diferent levels of torque from FES when the participant is receiving maximum
stimulation. The symbols here correspond to the same symbols from Figures 6, 7. many of which are not modifiable. These variations in ability to
produce torques due to FES can be visualized across participants
in Figure 10, where the maximum absolute value that the GPR
model predicts that each participant can produce throughout the
workspace is shown. 4.2. Accuracy We can see that there are wide variations in
the predicted amount of FES torque production. As an example,
one participant cannot produce more than about 0.25 Nm of torque
throughout the entire workspace with either the elbow flexion or
elbow extension electrodes, but two other participants can produce
more than 3 Nm in both of these cases. With these differences
in mind, it is clear that some participants would never be able to
achieve high reductions in power consumption with this hybrid
control approach. To increase consistency between participants, it
would be interesting to test with implanted FES systems, which are
more reliable and targeted, and to model fatigue, which can help
modify the controller in real-time to account for it. flexion/extension joint, especially because one of the trajectories
was significantly more challenging than the other. While the elbow flexion/extension DOF saw similar tracking
accuracies in the two different trajectories when comparing
the two controllers, the wrist flexion/extension DOF did see a
difference in trajectory tracking accuracy on the two different
trajectories. Despite this, the relationship between the exoskeleton-
alone tracking accuracy and the hybrid tracking accuracy remained
similar in all cases, with the elbow flexion/extension DOF showing
average increase of 19.2 and 14.5% in RMS error on the cup and
sinusoidal trajectories respectively, and the wrist flexion/extension
DOF showing average reduction of 7.4 and 3.3% on the cup and
sinusoidal trajectories respectively. While not implemented in this paper, another benefit of this
proposed controller is the ability to intuitively adjust controller
behavior to generalize to different objectives of movement. If a
specific task requires high precision in a movement, the gains
of the Q matrix or feedback could be increased to favor more
accurate movement at a cost of more torque. If there is an onset
of fatigue, the weights of the Rm matrix can be adjusted to prefer
more exoskeleton torque, and allow the muscles to recover. When observing the results of the three participants who
performed the same protocol twice separated by at least a
week, we see that the results remained similar between the
two time points. The difference between sessions in sum of
squared torque reduction when comparing the hybrid controller
to the exoskeleton alone controller remained within 17% across
participants for the elbow flexion/extension DOF, and below
10% for the wrist flexion/extension DOF. 4.2. Accuracy The difference between
sessions in RMS tracking error for the hybrid controller compared
to the exoskeleton alone controller remained below 7% across
participants for the elbow flexion/extension DOF, and below
12% on the wrist flexion/extension DOF. It is encouraging that
even though it is difficult to generalize across participants, these
preliminary repeatability results seem to indicate that results
hold steady within users if the same implementation procedure
is followed during each use. It is important to note here
that the participants repeated the entire protocol, and it is
expected that the model that the FES production will change
(especially when using surface electrodes), meaning that the model Frontiers in Neurorobotics frontiersin.org Conflict of interest The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be
construed as a potential conflict of interest. Data availability statement The datasets presented in this study can be found in
online repositories. The names of the repository/repositories and
accession number(s) can be found at: https://github.com/mahilab/
SingleDofHybridControlDataFrontiers/releases. One participant had a particularly weak response to the
FES, with a very low response from the elbow flexion/extension
electrodes, and no response from the wrist flexion/extension
electrodes. This
difference
compared
to
the
remainder
of
participants
shows
the
importance
in
characterizing
each
individual’s FES behavior to understand the potential effectiveness
of using the proposed hybrid controller. Ethics statement The studies involving human participants were reviewed and
approved by Rice University IRB #FY2017-461 and Cleveland
State University IRB #30213-SCH-HS. The patients/participants
provided their written informed consent to participate in
this study. Funding Modeling of fatigue is another area of interest when using FES,
and has received much attention in the FES research community. While this study aimed to keep the stimulation time to a minimum
to reduce the effects of fatigue, there were likely at least some effects
of fatigue present in results. Modeling and compensating for fatigue
would be a meaningful addition to the hybrid controller to see
improved performance. This material is based upon work supported by the National
Science Foundation under Grants NSF CBET 2025130 and
2025142. Acknowledgments The overall results from this study show promise for power
reduction while maintaining high accuracy when performing
movements with a single-DOF through the implementation of the
hybrid FES-exoskeleton controller. Importantly, these algorithms
should translate to a multi-DOF use case with only small
modifications. To realize truly shared control for generalized
upper-limb movements, these algorithms should be tested in
multi-DOF circumstances to understand potential benefits and
complications in this scenario. We acknowledge the contributions of Skye A. Carlson and Kyra
C. Stovicek to the development of this study. 4.5. Future work An area of interest in observing the behavior of hybrid
systems would be to identify how maximum torque allowed by
the exoskeleton changes the resulting behavior in terms of torque
output and tracking error. We observed the maximum torque used
by the exoskeleton in this study, but it was not limited in any
particular way to influence controller behavior. We should expect
the controllers to behave differently if the maximum torques are
limited at the start, as the future-looking MPC controller is able to
predict a torque limit onset and proactively compensate for it. Frontiers in Neurorobotics 4.4. Consistency across participants While the results between trajectories were consistent within
participants, there is a significant distribution of results between
participants, especially for the sum of squared torque reduction
observed for the hybrid controller compared to the exoskeleton
alone controller. Even though all results showed improvement,
except for the single participant who could not achieve an FES
response in one of the wrist flexion/extension electrodes, some
participants had significantly better results than others. There are
many factors that can impact the effectiveness of FES, including
electrode placement, size of muscles, body fat levels, and fatigue, 14 frontiersin.org 10.3389/fnbot.2023.1127783 10.3389/fnbot.2023.1127783 Dunkelberger et al. will necessarily have to be tuned for each use, even for the
same participant. a hybrid FES-exoskeleton system. This control strategy reduced
exoskeleton torque for the hybrid system with similar tracking
accuracy compared to using the exoskeleton alone. To realize
practical implementation of hybrid FES-exoskeleton systems, the
control strategy requires translation to multi-DoF movements,
achieving more consistent improvement across participants, and
balancing control to more fully leverage the muscles’ capabilities. One factor of this controller implementation that does not
generalize across participants is that it relies on the relative
weighting between exoskeleton torque inputs and FES activation
levels. While the exoskeleton torque outputs are relatively
consistent across participants, the activation levels do not map
directly to torque outputs, because each participant produces a
different amount of torque, given an activation level. In this case,
the Rfes and Rm_fes parameters as defined in Equations 22, 23 must
be scaled for each participant, based on the torque outputs expected
from the GPR models. However, once the parameters are scaled
once they should only need to be modified if electrodes need to be
moved, or if fatigue occurs. Author contributions ND, JB, ES, and MO’M contributed to conception, design of
the study, and wrote sections of the manuscript. ND conducted
the experiments, performed the statistical analysis, and wrote the
first draft of the manuscript. All authors contributed to manuscript
revision, read, and approved the submitted version. frontiersin.org References Ajiboye, A. B., Willett, F. R., Young, D. R., Memberg, W. D., Murphy, B. A.,
Miller, J. P., et al. (2017). Restoration of reaching and grasping movements through
brain-controlled muscle stimulation in a person with tetraplegia: A proof-of-concept
demonstration. Lancet 389, 1821–1830. doi: 10.1016/S0140-6736(17)30601-3 electrical stimulation and exoskeleton assistance,” in 2022 International Conference on
Rehabilitation Robotics (ICORR) (Rotterdam), 1–6. electrical stimulation and exoskeleton assistance,” in 2022 International Conference on
Rehabilitation Robotics (ICORR) (Rotterdam), 1–6. Dunkelberger, N., Schearer, E. M., and O’Malley, M. K. (2020). A review
of methods for achieving upper limb movement following spinal cord injury
through hybrid muscle stimulation and robotic assistance. Exp. Neurol. 328, 113274. doi: 10.1016/j.expneurol.2020.113274 Ambrosini, E., Ferrante, S., Zajc, J., Bulgheroni, M., Baccinelli, W., D’Amico, E.,
et al. (2017). The combined action of a passive exoskeleton and an EMG-controlled
neuroprosthesis for upper limb stroke rehabilitation: First results of the RETRAINER
project. IEEE Int. Conf. Rehabil. Robot. 2017, 56–61. doi: 10.1109/ICORR.2017.8009221 Durfee, W. K., and MacLean, K. E. (1989). Methods for estimating isometric
recruitment curves of electrically stimulated muscle. IEEE Trans. Biomed. Eng. 36,
654–666. doi: 10.1109/10.32097 Anderson, K. D. (2004). Targeting recovery: Priorities of the spinal cord-injured
population. J. Neurotrauma 21, 1371–1383. doi: 10.1089/NEU.2004.21.1371 Fitle, K. D., Pehlivan, A. U., and O’Malley, M. K. (2015). “A robotic exoskeleton
for rehabilitation and assessment of the upper limb following incomplete spinal cord
injury,” in IEEE International Conference on Robotics and Automation (ICRA) (Seattle,
WA), 4960–4966. Andersson, J. A. E., Gillis, J., Horn, G., Rawlings, J. B., and Diehl, M. (2019). CasADi
– A software framework for nonlinear optimization and optimal control. Math. Progr. Comput. 11, 1–36. doi: 10.1007/s12532-018-0139-4 Bao, X., Sheng, Z., Dicianno, B. E., and Sharma, N. (2021). A tube-based
model predictive control method to regulate a knee joint with functional electrical
stimulation and electric motor assist. IEEE Trans. Contr. Syst. Technol. 29, 2180–2191. doi: 10.1109/TCST.2020.3034850 Francisco, G. E., Yozbatiran, N., Berliner, J., O’malley, M. K., Pehlivan, A. U.,
Kadivar, Z., et al. (2017). Robot-assisted training of arm and hand movement shows
functional improvements for incomplete cervical spinal cord injury. Am. J. Phys. Med. Rehabil. 96, S171–S177. doi: 10.1097/PHM.0000000000000815 Frullo, J. M., Elinger, J., Pehlivan, A. U., Fitle, K., Nedley, K., Francisco, G. E., et al. (2017). Effects of assist-as-needed upper extremity robotic therapy after incomplete
spinal cord injury: A parallel-group controlled trial. Front. Neurorobot. 11, 26. References doi: 10.3389/fnbot.2017.00026 Bardi, E., Dalla Gasperina, S., Pedrocchi, A., and Ambrosini, E. (2021). “Adaptive
cooperative control for hybrid fes-robotic upper limb devices: A simulation study,” in
2021 43rd Annual International Conference of the IEEE Engineering in Medicine and
Biology Society (EMBC) (Mexico), 6398–6401. Ha, K. H., Murray, S. A., and Goldfarb, M. (2016). An approach for the
cooperative control of fes with a powered exoskeleton during level walking for
persons with paraplegia. IEEE Trans. Neural Syst. Rehabil. Eng. 24, 455–466. doi: 10.1109/TNSRE.2015.2421052 Beekhuizen, K. S., and Field-Fote, E. C. (2005). Massed practice versus massed
practice with stimulation: Effects on upper extremity function and cortical plasticity
in individuals with incomplete cervical spinal cord injury. Neurorehabil. Neural Repair
19, 33–45. doi: 10.1177/1545968305274517 Kadivar, Z., Sullivan, J., Eng, D., Pehlivan, A., Malley, M., Yozbatiran, N., et al. (2012). RiceWrist robotic device for upper limb training: Feasibility study and case
report of two tetraplegic persons with spinal cord injury. Int. J. Biol. Eng. 2, 27–38. doi: 10.5923/j.ijbe.20120204.01 Blank, A. A., French, J. A., Pehlivan, A. U., and O’Malley, M. K. (2014). Current trends in robot-assisted upper-limb stroke rehabilitation: Promoting
patient engagement in therapy. Curr. Phys. Med. Rehabil. Rep. 2, 184–195. doi: 10.1007/s40141-014-0056-z Kirsch, N. A., Bao, X., Alibeji, N. A., Dicianno, B. E., and Sharma, N. (2018). Model-
based dynamic control allocation in a hybrid neuroprosthesis. IEEE Trans. Neural Syst. Rehabil. Eng. 26, 224–232. doi: 10.1109/TNSRE.2017.2756023 Bulea, T. C., Kobetic, R., Audu, M. L., Schnellenberger, J. R., Pinault, G.,
and Triolo, R. J. (2014). Forward stair descent with hybrid neuroprosthesis after
paralysis: Single case study demonstrating feasibility. J. Rehabil. Res. Dev. 51, 1077. doi: 10.1682/JRRD.2013.12.0257 Klauer, C., Schauer, T., Reichenfelser, W., Karner, J., Zwicker, S., Gandolla, M.,
et al. (2014). Feedback control of arm movements using neuro-muscular electrical
stimulation (NMES) combined with a lockable, passive exoskeleton for gravity
compensation. Front. Neurosci. 8, 1–16. doi: 10.3389/fnins.2014.00262 Burchielli, D., Lotti, N., Missiroli, F., Bokranz, C., Pedrocchi, A., Ambrosini, E., et
al. (2022). “Adaptive hybrid fes-force controller for arm exosuit,” in 2022 International
Conference on Rehabilitation Robotics (ICORR) (Rotterdam), 1–6. Lum, P. S., Godfrey, S. B., Brokaw, E. B., Holley, R. J., and Nichols, D. (2012). Robotic approaches for rehabilitation of hand function after stroke. Am. J. Phys. Med. Rehabil. 91, S242–S254. doi: 10.1097/PHM.0b013e31826bcedb Cannella, G., Laila, D. S., and T. Freeman, C. (2016). Design of a hybrid adaptive
support device for FES upper limb stroke rehabilitation. References New Trends Med. Serv. Robot. 38, 13–22. doi: 10.1007/978-3-319-23832-6_2 Memberg, W. D., Polasek, K. H., Hart, R. L., Bryden, A. M., Kilgore, K. L.,
Nemunaitis, G. A., et al. (2014). Implanted neuroprosthesis for restoring arm and
hand function in people with high level tetraplegia. Archiv. Phys. Med. Rehabil. 95,
1201–1211. doi: 10.1016/j.apmr.2014.01.028 Charles, S. K., Krebs, H. I., Volpe, B. T., Lynch, D., and Hogan, N. (2005). “Wrist
rehabilitation following stroke: Initial clinical results,” in International Conference on
Rehabilitation Robotics (ICORR) (Piscataway, NJ: IEEE), 13–16. Collinger, J. L., Boninger, M. L., Bruns, T. M., Curley, K., Wang, E., and Weber, D. J. (2013). Functional priorities, assistive technology, and brain-computer interfaces after
spinal cord injury. J. Rehabil. Res. Dev. 50, 145–160. doi: 10.1682/jrrd.2011.11.0213 Mulcahey,
M.,
Smith,
B.,
and
Betz,
R. (1999). Evaluation
of
the
lower
motor
neuron
integrity
of
upper
extremity
muscles
in
high
level
spinal
cord
injury. Spinal
Cord
37,
585. doi:
10.1038/sj.sc.310
0889 del Ama, A. J., Gil-Agudo, A., Pons, J. L., and Moreno, J. C. (2014). Hybrid FES-
robot cooperative control of ambulatory gait rehabilitation exoskeleton. J. Neuroeng. Rehabil. 11, 1–15. doi: 10.1186/1743-0003-11-27 NSCISC (2019). Spinal Cord Injury Facts and Figures at a Glance. Birmingham, AL:
National Spinal Cord Injury Statistical Center. Dietz, V., Müller, R., and Colombo, G. (2002). Locomotor activity in spinal man:
Significance of afferent input from joint and load receptors. Brain 125, 2626–2634. doi: 10.1093/brain/awf273 Peckham, P., Mortimer, J., and Marsolais, E. (1976). Upper and lower motor
neuron lesions in the upper extremity muscles of tetraplegics. Spinal Cord 14, 115–121. doi: 10.1038/sc.1976.19 Dijkers, M. (1997). Quality of life after spinal cord injury: A meta analysis of the
effects of disablement components. Spinal Cord 35, 829–840. doi: 10.1038/sj.sc.3100571 Reinkensmeyer, D. J., Kahn, L. E., Averbuch, M., McKenna-Cole, A., Schmit, B. D.,
and Rymer, W. Z. (2000). Understanding and treating arm movement impairment after
chronic brain injury: Progress with the ARM guide. J. Rehabil. Res. Dev. 37, 653–662. doi: 10.1007/s00115-016-0187-9 Dunkelberger, N., Berning, J., Dix, K. J., Ramirez, S. A., and O’Malley, M. K. (2022a). “Design, characterization, and simulation of the mahi open exoskeleton upper limb
robot (in review),” in IEEE/ASME International Conference on Advanced Intelligent
Mechatronics (Sapporo). Rohm, M., Schneiders, M., Müller, C., Kreilinger, A., Kaiser, V., Müller-Putz,
G. R., et al. (2013). Hybrid brain–computer interfaces and hybrid neuroprostheses for
restoration of upper limb functions in individuals with high-level spinal cord injury. Artif. Intell. Med. Publisher’s note In this paper, we presented a model-based control approach to
hybrid FES-exoskeleton control. We experimentally demonstrated
the benefits of using this model-based controller to distribute robot
and FES contributions to control elbow and wrist movements with All
claims
expressed
in
this
article
are
solely
those
of the authors and do not necessarily represent those of 15 frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 10.3389/fnbot.2023.1127783 Author disclaimer their
affiliated
organizations,
or
those
of
the
publisher,
the editors and the reviewers. Any product that may be
evaluated in this article, or claim that may be made by
its
manufacturer,
is
not
guaranteed
or
endorsed
by
the
publisher. Any opinions, findings, and conclusions or recommendations
expressed in this material are those of the authors and do not
necessarily reflect the views of the National Science Foundation. Frontiers in Neurorobotics Varoto, R., Barbarini, E. S., and Cliquet, A. Jr. (2008). A hybrid system
for upper limb movement restoration in quadriplegics. Artif. Org. 32, 725–729.
doi: 10.1111/j.1525-1594.2008.00597.x Valevicius, A. M., Boser, Q. A., Lavoie, E. B., Chapman, C. S., Pilarski, P. M., Hebert,
J. S., et al. (2019). Characterization of normative angular joint kinematics during two
functional upper limb tasks. Gait Post. 69, 176–186. doi: 10.1016/j.gaitpost.2019.01.037 Dunkelberger et al. Trier, S., Buckett, J., Campean, A., Miller, M., Montague, F., Vrabec, T., et al. (2001).
“A modular external control unit for functional electrical stimulation,” in Annual
Conference of the International Functional Electrical Stimulation Society (Cleveland,
OH). References 59, 133–142. doi: 10.1016/j.artmed.2013.07.004 Dunkelberger, N., Carlson, S. A., Berning, J., Stovicek, K. C., Schearer, E. M.,
and O’Malley„ M. K. (2022b). “Shared control of elbow movements with functional 16 Frontiers in Neurorobotics frontiersin.org Dunkelberger et al. 10.3389/fnbot.2023.1127783 10.3389/fnbot.2023.1127783 Schulz, S. B. S. R. W., Pylatiuk, C., and Reischl, M. (2011). “The hybrid fluidic
driven upper limb orthosis—Orthojacket,” in Proceedings of the 2011 MyoElectric
Controls/Powered Prosthetics Symposium Fredericton (New Brunswick). Wächter, A., and Biegler, L. T. (2006). On the implementation of an interior-point
filter line-search algorithm for large-scale nonlinear programming. Math. Progr. 106,
25–57. doi: 10.1007/s10107-004-0559-y Trier, S., Buckett, J., Campean, A., Miller, M., Montague, F., Vrabec, T., et al. (2001). “A modular external control unit for functional electrical stimulation,” in Annual
Conference of the International Functional Electrical Stimulation Society (Cleveland,
OH). Trier, S., Buckett, J., Campean, A., Miller, M., Montague, F., Vrabec, T., et al. (2001). “A modular external control unit for functional electrical stimulation,” in Annual
Conference of the International Functional Electrical Stimulation Society (Cleveland,
OH). Wolf, D., Dunkelberger, N., McDonald, C. G., Rudy, K., Beck, C., O’Malley, M. K.,
et al. (2017). “Combining functional electrical stimulation and a powered exoskeleton
to control elbow flexion,” in 2017 International Symposium on Wearable Robotics and
Rehabilitation (WeRob) (Houston, TX), 1–2. Wolf, D., and Schearer, E. (2022). Trajectory optimization and model predictive
control for functional electrical stimulation-controlled reaching. IEEE Robot. Automat. Lett. 7, 3093–8. doi: 10.1109/LRA.2022.3145946 Yozbatiran, N., and Francisco, G. E. (2019). Robot-assisted therapy for the
upper limb after cervical spinal cord injury. Phys. Med. Rehabil. Clin. 30, 367–384. doi: 10.1016/j.pmr.2018.12.008 Varoto, R., Barbarini, E. S., and Cliquet, A. Jr. (2008). A hybrid system
for upper limb movement restoration in quadriplegics. Artif. Org. 32, 725–729. doi: 10.1111/j.1525-1594.2008.00597.x 17 17 frontiersin.org Frontiers in Neurorobotics Frontiers in Neurorobotics
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UJI BEBERAPA VARIETAS DAN PEMBERIAN PUPUK BIOBOST TERHADAP PERTUMBUHAN DAN PRODUKSI BAWANG MERAH (Allium ascolonicum L.)
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BioLink Vol. 3 (2) Januari 2017 p-ISSN: 2356-458x e-ISSN:2597-5269 BioLink Vol. 3 (2) Januari 2017 p-ISSN: 2356-458x e-ISSN:2597-5269 p-ISSN: 2356-458x e-ISSN:2597-5269 *Corresponding author: Email : rafiqah22@ymail.com Penelitian ini bertujuan untuk mengetahui Uji Beberapa Varietas dan Pemberian Pupuk Bioboost Terhadap
Pertumbuhan dan Produksi Tanaman Bawang Merah (Allium ascolonicum L.). Rancangan yang digunakan dalam
penelitian ini adalah Rancangan Acak Kelompok, dengan 2 faktor yaitu. Faktor Uji Beberapa Varietas disimbolkan
dengan (V) terdiri dari 3 level yaitu : V1 = Varietas Lokal, V2 = Varietas Brebes, V3 = Varietas Filipina. Faktor
Pemberian Pupuk Bioboost disimbolkan dengan (B), yaitu: B0 = 0 cc/Liter air, B1 = 3,5 cc/Liter air, B2 = 5cc/Liter
air, B3 = 10 cc/Liter air. Dari hasil analisis sidik ragam bahwa akibat perlakuan beberapa varietas menunjukkan
pengaruh nyata pada tinggi tanaman umur 7 mst. Sedangkan pengaruh tidak nyata di jumpai pada pengamatan
tinggi tanaman umur 3,5 dan 9 mst. Jumlah anakan umur 3, 5, 7 dan 9 mst. Berat umbi per sampel dan berat umbi
per plot. Perlakuan pemberian pupuk Bioboost menunjukkan pengaruh nyata pada pengamatan berat umbi per
plot. Sedangkan pengaruh tidak nyata pada pengamatan tinggi tanaman umur 3, 5, 7 dan 9 mst, jumlah anakan
umur 3, 5, 7 dan 9 mst dan berat umbi per sampel. Perlakuan beberapa varietas dan pupuk Bioboost menunjukkan
pengaruh yang nyata pada pengamatan tinggi tanaman umur 7 dan 9 mst. Sedangkan pengaruh tidak nyata pada
pengamatan parameter tinggi tanaman umur 3 dan 5 mst, jumlah anakan umur 3, 5, 7 dan 9 mst, berat umbi per
sampel dan berat umbi per plot. Kata kunci : bawang merah, varietas, pupuk bioboost. Kata kunci : bawang merah, varietas, pupuk bioboost. Some Tests of Variety And Growing of Biobost Fertilizers on Growth
and Production of Onion (Allium ascolonicum L.) Rafiqah Amanda Lubis
Prodi Agroteknologi, Universitas Muhammadiyah Tapanuli Selatan,
Jl. Sutan Mohd. Arief No. 32, Padangsidimpuan PENDAHULUAN merupakan
suatu
sistem
yang
menerapkanteknologi ramah lingkungan
dalam mencapai sistem pertanian yang
lestari
dan
berkelanjutan
untuk
membangun kesuburan tanah jangka
panjang. Prinsip pertanian yang ramah
lingkungan
ini
menerapkan
usaha
budidaya yang dilakukan dengan prinsip
tidak
merusak
lingkungan
dan
mencemari lingkungan terkait dengan
aspek pemanfaatan sumber daya alam,
pembuangan limbah dan keamanan
lingkungan sekitarnya(Dinas Pertanian
Tanaman
Pangan
dan
Hortikultura
2007). Tanaman bawang merah (Allium
ascolonicum L) diyakini berasal dari
daerah
Asia
tengah,
yakni
sekitar
Bangladesh, India dan Pakistan. Bawang
merah dapat dikatakan sudah dikenal
oleh masyarakat sejak ribuan tahun
yang lalu, pada zaman Mesir kuno sudah
banyak orang menggunakan bawang
merah
untuk
pengobatan
(Widya,
2008). Bawang
merah
merupakan
komoditas sayuran yang sudah sejak
lama di usahakan oleh petani secara
intensif. Komoditas
pertanian
ini
merupakan sumber pendapatan dan
kesempatan kerja yang memberikan
kontribusi
cukup
tinggi
terhadap
perkembangan ekonomi suatu wilayah. Karena memiliki nilai ekonomi yang
cukup
tinggi
maka
pengusahaan
budidaya
bawang
merah
telah
menyebar hampir di setiap provinsi di
Indonesia terutama di Sumatera Utara. Meskipun minat petaniterhadap bawang
merah cukup kuat, namun dalam proses
pengusahaannya
masih
ditemui
berbagai kendala. Baik yang bersifat
teknis maupun ekonomis(Simatupang ,
2011). Pupuk Bioboost adalah pupuk
hayati karena kandungan yang terdapat
dalam bioboost adalah makhluk hidup
yaitu mikroba tanah, yaitu mikroba
penyubur tanah yang membuat pupuk
ini ramah lingkungan. Mikroba tersebut
bermanfaat
dalam
proses
biokimia
didalam tanah sehingga unsur hara
menjadi lebih mudah diserap akar
tanaman. Abstract This research aims was to know Test of Some Varieties and Provision of Bioboost Fertilizer on the Growth and
Production of Red Onion (Allium ascolonicum L.). The design used in this research is Randomized Block Design, with 2
factors is: Factor Test Some varieties symbolized with (V) consists of 3 levels: V1 = Local Variety, V2 = Varieties of
Brebes, V3 = Philippine Varieties. The Bioboost Fertilization Factor is symbolized by (B), is: B0 = 0 cc / Liter water, B1
= 3.5 cc / Liter water, B2 = 5cc / Liter water, B3 = 10 cc / Liter water. The result of analysis of variance that effect of
some varieties treatment showed real effect at plant height 7 mst. While the influence is not real in the observation on
the observation of plant height aged 3.5 and 9 mst. Number of tillers 3, 5, 7 and 9 mst. Tuber weight per sample and
weight of tuber per plot. Treatment of Bioboost fertilizer showed real effect on observation weight of tuber per plot. While the effect was not significant on the observation of plant height aged 3, 5, 7 and 9 mst, the number of tillers
aged 3, 5, 7 and 9 mst and tuber weight per sample. analysis of variance that due to the treatment of several varieties
and fertilizer Bioboost showed a real effect on observation of height of plant age 7 and 9 mst. While the effect was not
significant on observation of height parameters of plant age 3 and 5 mst, number of tillers age 3, 5, 7 and 9 mst, tuber
weight per sample and weight of tuber per plot. Keywords: red onion, varieties, bioboost fertilizer How to Cite: Lubis, R.A.,, (2017). Uji Varietas dan Pemberian Pupuk Biobost Terhadap
Pertumbuhan dan Produksi Bawang Merah (Allium ascolonicum L.), BioLink, Vol. 3 (2); Hal. 112-120 112 Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan
PENDAHULUAN
merupakan
suatu
sistem
yang Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan METODE PENELITIAN Penelitian dilaksanakan di lokasi
lahan
praktek
Fakultas
Pertanian
Universitas Muhammadiyah Tapanuli
Selatan, Penelitian ini dilaksanakan pada
bulan Juli 2016 dan selesai pada bulan
September 2016. Varietas bawang merah yang
ditanaman oleh petani kita di Indonesia
cukup banyak, antara lain sebagai
berikut: varietas bawang merah Medan,
varietas bima Brebes, varietas Philipine,
varietas
bawang
merah
Australia,
varietas bawang merah Bali dan lainnya
(Sumarni, 2005). HASIL DAN PEMBAHASAN Berdasarkan dari hasil analisis
sidik ragam bahwa perlakuan varietas
memberikan pengaruh yang tidak nyata
pada pengamatan 3, 5, dan 9 mst, tetapi
memberikan
pengaruh
nyata
pada
parameter tinggi tanaman umur 7 mst. Untuk
perlakuan
pemberian
pupuk
Bioboostmemberikan pengaruh yang
tidak nyata pada pengamatan tinggi
tanaman umur 3, 5, 7 dan 9 mst. Begitu
juga dengan interaksi kedua perlakuan
tersebut memberikan pengaruh tidak
nyata pada umur 3 dan 5 mst, tetapi
memberikan pengaruh nyata pada tinggi
tanaman umur 7 dan 9 mst. Daftar sidik
ragam dapat di lihat pada lampiran. Persiapan Lahan Penelitian Persiapan Lahan Penelitian Lahan yang digunakan sebagai
tempat penelitian terlebih dahulu
dibersihkan dari rumput – rumputan,
bebatuan dan kotoran lainya dengan
menggunakan
cangkul,
parang,
dan
babat. Selanjutnya
di
lakukan
pengolahan tanah, lahan yang di olah
di cangkul sedalam 30 cm. 4. Parameter Pengamatan 4. Parameter Pengamatan Tinggi
Tanaman
(cm),
Jumlah
anakan (anak), Berat umbi Pertanaman
Sampel (g), Berat umbi Per Plot (g). Tinggi
Tanaman
(cm),
Jumlah
anakan (anak), Berat umbi Pertanaman
Sampel (g), Berat umbi Per Plot (g). Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. 1. Penanaman Sebelum
penanaman
lakukan
seleksi akhir terhadap bibit yang hendak
ditanam. Bibit yang cacat, rusak, atau
terserang hama dan penyakit sebaiknya
dibuang. 2. Aplikasi perlakuan September 2016. Metode
penelitian
yang
digunakan
adalah
Rancangan
Acak
Kelompok (RAK) dengan dua faktorial
yaitu: Faktor beberapa varietas (V) dengan 3
level yaitu : Selain varietas, pemupukan juga
merupakan salah satu faktor yang
sangat penting untuk menunjang hasil
produksi
tanaman
bawang
merah,
dengan
sistem
pertanian
organik : Varietas Lokal V2
: Varietas Brebes : Varietas Brebes V3
: Varietas Filipina : Varietas Filipina 113 BioLink, Vol. 3 (2) Januari 2017: hal. 112-120 Faktor pemberian pupuk Bioboost (B)
dengan 4 level yaitu :
BO
: 0 cc/liter air
B1
: 3,5 cc/liter air
B2
: 5 cc/liter air
B3
: 10 cc/liter air Faktor pemberian pupuk Bioboost (B)
dengan 4 level yaitu :
BO
: 0 cc/liter air
B1
: 3,5 cc/liter air
B2
: 5 cc/liter air
B3
: 10 cc/liter air 3. Pemeliharaan
Pemeliharaan
meliputi:
Penyiraman, Penyulaman, Penyiangan,
Pengendalian
Hama
dan
Penyakit,
Pemanenan Pemeliharaan
meliputi:
Penyiraman, Penyulaman, Penyiangan,
Pengendalian
Hama
dan
Penyakit,
Pemanenan 2. Aplikasi perlakuan 2. Aplikasi perlakuan Pengaplikasian pupuk bioboost
setelah tanaman berumur 2 mst sesuai
dosis yang telah ditentukan. Pemupukan
dilakukan 4 kali sampai panen. Tabel 1.Pengaruh Varietas Terhadap Tinggi Tanaman PadaPada Umur 3, 5, 7 dan 9mst. 3 mst
5 mst
7 mst
9 mst
17.02a
23.24a
29.38a
34.90a
18.93a
23.34a
29.27b
35.67b
19.05a
24.36a
30.98a
36.00b
V3
Perlakuan Varietas
V1
V2
Tinggi Tanaman (cm)
Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. aruh Varietas Terhadap Tinggi Tanaman PadaPada Umur 3, 5, 7 dan 9mst. Tabel 1.Pengaruh Varietas Terhadap Tinggi Tanaman PadaPada Umur 3, 5, 7 da Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. 114 BioLink, Vol. 3 (2) Januari 2017: hal. 112-120 Tabel 2. Pengaruh Pupuk BioboostTerhadap Tinggi Tanaman Pada Umur 3, 5, 7 dan
9mst. 3 mst
5 mst
7 mst
9 mst
18.09a
23.00a
29.38a
34.68a
16.95a
23.49a
30.21a
35.97b
19.40a
24.37a
29.97a
35.33b
18.91a
23.73b
30.34a
36.12b
Tinggi Tanaman (cm)
B3
B2
Perlakuan Pupuk Bioboost
B0
B1
Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Tabel 2. Pengaruh Pupuk BioboostTerhadap Tinggi Tanaman Pada Umur 3, 5, 7 dan
9mst Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Tabel 3. Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost Terhadap
Tinggi Tanaman. B0
B1
B2
B3
V1
33.79a
36.50b
35.20b
36.46b
141,95
V2
35.55b
36.43b
35.15b
35.15b
142,28
V3
36.38b
34.90b
35.99b
36.75b
144,02
Total
105,72
107,83
106,34
108,36
-
Perlakuan Beberapa
Varietas
Perlakuan Pupuk Bioboost
Total Tabel 3. Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost Te
Tinggi Tanaman. . Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost Terhadap Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. 3, 5, dan 7, tetapi berpengaruh nyata
pada pengamatan jumlah anakan umur
9
mst. Interaksi
kedua
perlakuan
tersebut memberikan pengaruh pada
pengamatan jumlah anakan umur 3, 5, 7
dan 9. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan berbeda
nyata menurut uji DMRT 5%. 2. Aplikasi perlakuan Berdasarkan hasil analisis sidik
ragam bahwa perlakuan perbedaan
varietas menunjukkan pengaruh tidak
nyata pada pengamatan jumlah anakan
umur 3, 5, 7 dan 9 mst. Untuk perlakuan
pemberian
pupuk
Bioboost
menunjukkan pengaruh tidak nyata
pada pengamatan jumlah anakan umur
3, 5, dan 7, tetapi berpengaruh nyata
pada pengamatan jumlah anakan umur
9
mst. Interaksi
kedua
perlakuan
tersebut memberikan pengaruh pada
pengamatan jumlah anakan umur 3, 5, 7
dan 9. Tabel 7.Pengaruh Varietas Terhadap Jumlah Anakan Pada Perlakuan Pada Umur 3, 5, 7
dan 9 mst. Tabel 7.Pengaruh Varietas Terhadap Jumlah Anakan Pada Perlakuan Pada Umur 3, 5, 7
dan 9 mst. 3 mst
5 mst
7 mst
9 mst
2.08a
3.17a
4.17a
5.83a
2.17b
3.42b
4.33b
5.83a
2.00b
3.25bc
4.33a
5.92a
V3
Perlakuan Varietas
V1
V2
Jumlah Anakan
Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan berbeda
nyata menurut uji DMRT 5%. dan 9 mst. 3 mst
5 mst
7 mst
9 mst
2.08a
3.17a
4.17a
5.83a
2.17b
3.42b
4.33b
5.83a
2.00b
3.25bc
4.33a
5.92a
V3
Perlakuan Varietas
V1
V2
Jumlah Anakan 114 BioLink, Vol. 3 (2) Januari 2017: hal. 112-120 Tabel 8.Pengaruh Pupuk Bioboost TerhadapJumlah Anakan Pada Umur 3, 5, 7 dan 9mst. 3 mst
5 mst
7 mst
9 mst
2.00a
3.11a
4.22a
6.11a
2.00a
3.11a
4.11a
5.44a
2.22b
3.33b
4.33a
5.56b
2.11b
3.56b
4.44a
6.33b
Jumlah Anakan
B3
B2
Perlakuan Pupuk Bioboost
B0
B1 aruh Pupuk Bioboost TerhadapJumlah Anakan Pada Umur 3, 5, 7 dan 9mst. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Tabel 9. Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost Terhadap
Jumlah Anakan. B0
B1
B2
B3
V1
6.00a
5.67a
5.33a
6.33a
5,83
V2
6.33a
5.33a
5.33b
6.33b
6,06
V3
6.00b
5.33b
6.00b
6.33b
5,83
Total
18,33
16,33
16,66
18,99
-
Perlakuan
Beberapa
Perlakuan Pupuk Bioboost
Total
Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. uh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost Terhadap . Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost Terhadap
Anakan. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. tidak nyata pada pengamatan berat
umbi per sampel. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Pembahasan
Pengaruh
Beberapa
Varietas Terhadap Pertumbuhan dan
Produksi Tanaman bawang merah ataran tinggi untuk satu varietas sama
yang beradaptasi luas. Pengaruh tidak nyata karena adanya
perbedaan
pertumbuhan
dan
umur
tanaman bawang merah di lapangan
untuk
siap
dipanen
merupakan
manifestasi dari tanggapan tanaman
tersebut terhadap pengaruh lingkungan
dan yang paling menonjol adalah kondisi
agroklimat yang terjadi antara dataran
rendah dengan dataran tinggi, seperti
keadaan temperatur udara, evaporasi,
lamanya
penyinaran
matahari
dan
radiasi matahari yang diterima setiap
harinya, termasuk perbedaan curahhujan
antara musim kemarau dan musim
penghujan
di
dataran
rendah
dan
dataran tinggi. Perbedaan yang mencolok
dari unsur iklim tersebut antara dataran
rendah
dan
dataran
tinggi
adalah
perbedaan
temperatur
dan
cahaya
matahari. Hasil analisis sidik ragam bahwa
akibat
perlakuan
beberapa
varietas
menunjukkan
pengaruh
nyata
pada
tinggi tanaman umur 7 mst. Jumlah daun
3, 7, dan 9 mst. Sedangkan pengaruh
tidak nyata di jumpai pada pengamatan
tinggi tanaman umur 3,5 dan 9 mst. Jumlah daun umur 5 mst. Jumlah anakan
umur 3, 5, 7 dan 9 mst. Berat umbi per
sampel dan berat umbi per plot. Selanjutnya
Hermiati
(2000)
menyatakan
bahwa
setiap
varietas
memiliki
perbedaan
dalam
hal
kemampuannya untuk mempertahankan
hidup dan pertumbuhan individu dari
iklim yang berbeda. Faktor genetik
tanaman
dan
adaptasinya
terhadap
lingkungan menghasilkan pertumbuhan
yang berbeda-beda, hal ini dapat dilihat
varietas
memberi
pengaruh
nyata
terhadap
pertumbuhan
dan
hasil
tanaman bawang merah. 2. Aplikasi perlakuan Interaksi kedua
perlakuan menunjukkan pengaruh tidak
nyata pada berat umbi per sampel. tidak nyata pada pengamatan berat
umbi per sampel. Interaksi kedua
perlakuan menunjukkan pengaruh tidak
nyata pada berat umbi per sampel. Berdasarkan dari hasil analisis
sidik ragam bahwa perlakuan beberapa
varietas menunjukkan pengaruh tidak
nyata pada pengamatan berat umbi per
sampel. Untuk perlakuan pemberian
pupuk Bioboost menunjukkan pengaruh Tabel 10. Pengaruh VarietasTerhadap Rataan Berat Umbi Per Sampel. Berat Umbi Per Sampel
112.60a
122.29a
124.78a
V3
Perlakuan Varietas
V1
V2
Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Tabel 10. Pengaruh VarietasTerhadap Rataan Berat Umbi Per Sampel. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. 114 BioLink, Vol. 3 (2) Januari 2017: hal. 112-120 Tabel 11.Pengaruh Pupuk Bioboost Terhadap Rataan Berat Umbi Per Sampel. Berat Umbi Per Sampel
117.32a
113.51a
136.15a
112.57a
B3
B2
Perlakuan Pupuk Bioboost
B0
B1 Tabel 11.Pengaruh Pupuk Bioboost Terhadap Rataan Berat Umbi Per Sampel. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Tabel 12. Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboost
Terhadap Berat Umbi Per Sampel. B0
B1
B2
B3
V1
100.00a
112.10a
149.33a
89.92a
451,25
V2
118.41a
112.00a
135.00a
124.00a
489,41
V3
133.21a
118.00a
124.11a
123.77a
499,09
Total
351,62
342,10
408,10
337,69
-
Total
Perlakuan Varietas
Pelakuan Pupuk Bioboost
Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. el 12. Pengaruh Interaksi Beberapa Varietas dan Perlakuan Pupuk Bioboo
adap Berat Umbi Per Sampel. Keterangan: angka yang diikuti huruf yang sama pada kolom dan baris menunjukkan
tidak berbeda nyata menurut uji DMRT 5%. Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan
Pembahasan
Pengaruh
Beberapa
ataran tinggi untuk satu varietas sama Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan Pengaruh
Beberapa
Varietas
dan
Pemberian Pupuk Bioboost Terhadap
Pertumbuhan dan Produksi Bawang
merah Pengaruh
Beberapa
Varietas
dan
Pemberian Pupuk Bioboost Terhadap
Pertumbuhan dan Produksi Bawang
merah Pengaruh
tidak
nyata
pada
pengamatan pertumbuhan dan hasil
disebabkan karena kedua perlakuan
memberikan fungsinya masing – masing. Dan pengaruh keduanya juga disebabkan
oleh
faktor
lingkungan
dan
faktor
ketersediaan
unsur
hara
dan
juga
penyerapan unsur hara. Bentuk
respon
(tanggapan)terhadap
perubahan
lingkungan dapat bersifat positif dan
bersifat negatif yang secara sederhana
dapat
diartikan
peningkatan
dan
penurunan
ukuran
tanaman
(pertumbuhan)dan hasil panen sebagai
interaksi genetik dan faktor lingkungan
yang ditentukan oleh iklim, cuaca, suhu,
dan komposisi hara di dalam tanah
(Caudary, 1995, krug, 1997). Salah satu
faktor
yang
berpengaruh
terhadap
pertumbuhan dan produksi bawang
merah
adalah
pemupukan.Selama
pertumbuhannya
bawang
merah
memerlukan unsur hara yang cukup
khususnya
unsur
hara
fosfor
(P). (Belevins,
1994.,
Browter,
2000.,
Hardjowigeno, 1995) menyatakan fosfor
mempunyai
peran
penting
dalam
metabolisme
energi. Energi
yang
diperoleh dari proses fotosintesis dan
metabolisme
karbohidrat
disimpan
dalam bentuk fosfat yang digunakan
untuk pertumbuhan dan reproduksi
tanaman. Menurut
Redaksi
Agromedia
(2007) Meskipun unsur – unsur hara
terdapat dalam pupuk organik tergolong
sedikit , pupuk organik lebih ramah
lingkungan dibandingkan pupuk lainnya. Pengaruh tidak nyata pada interaksi
berat umbi per sampel dan berat umbi
per plot disebabkan pemupukan tidak
berpengaruhterhadap pemberian pupuk
Bioboost dalam meningkatkan berat
umbi pada tanaman bawang merah. Pengaruh Pupuk BioboostTerhadap
Pertumbuhan
dan Hasil
produksi
Tanaman Bawang Merah Pengaruh
tidak
nyata
akibat
perlakuan
beberapa
varietas
pada
pengamatan tinggi tanaman, disebabkan
karena adanya perbedaan varietas yang
dilakukan, yaitu V1 = Varietas Lokal, V2 =
Varietas Brebes, V3 = Varietas Filipina
dan pertumbuhan tanaman dibantu oleh
kandungan hara yang manpu melengkapi
kebutuhan metabolisme setiap tanaman. Pemupukan lewat daun lebih cepat
penyerapan haranya dibandingkan lewat
akar. Pupuk daun dapat memberikan
persediaan pada tanaman, walaupun
hara yang diberikan relatif sedikit, tetapi
bersifat kontinyu. Pemupukan sangat
erat kaitannya dengan fase pertumbuhan
vegetatif dan generatif. Beberapa varietas bawang merah
yang diusahakan di dataran rendah
umurnya
relatif
pendek,
bervariasi
antara 55 sampai 70 hari tergantung
pada varietas dan musim tanamnya. Penanaman bawang merah ke daerah
yang lebih tinggi menyebabkan tanaman
memiliki umur panen yang lebih panjang,
yaitu dapat mencapai umur 100 hari di MenurutLingga
dan
Marsono
(2007) menyatakan bahwa konsentrasi
pupuk merupakan faktor yang sangat
vital dan memiliki pengaruh yang besar
terhadap
keberhasilan
pemupukan
terutama pemupukan melalui daun. Oleh
sebab
itu
untuk
mendapatkan
pertumbuhan dan hasil optimal, harus
memperhatikan dosis dan konsentrasi
yang tepat. BioLink, Vol. 3 (2) Januari 2017: hal. 112-120 Didukung juga dengan Isdarmanto
(2009),
dengan
meningkatnya
produksivitas
metabolisme
maka
tanaman
akan
lebih
banyak
membutuhkan
unsur
hara
dan
meningkatnya penyerapan air, hal itu
berkaitan dengan pertumbuhan bagi
tanaman pada masa pertumbuhan dan
perkembangan
tanaman.Frekuensi
dengan pemberian pupuk dengan dosis
yang berbeda menyebabkan hasil yang
berbeda pula. tanaman dalam hal ini mengurangi susut
bobot umbi bawang merah (Soepardi,
1983). SIMPULAN Hasil analisis sidik ragam bahwa
akibat
perlakuan
pemberian
pupuk
Bioboost menunjukkan pengaruh nyata
pada jumlah daun umur 7 mst, dan berat
umbi per plot. Sedangkan pengaruh tidak
nyata pada tinggi tanaman umur 3, 5, 7
dan 9 mst, jumlah daun umur 3, 5 dan 9
mst, jumlah anakan umur 3, 5, 7 dan 9
mst dan berat umbi per sampel. Unsur P pada bawang merah
berperan
dalam
meningkatkan
perkembangan akar, sehingga dapat
mempermudah dan mempercepat unsur
hara tanah. Unsur p juga berfungsi dalam
meningkatkan
kualitas
dan
hasil Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan Rafiqah Amanda Lubis, Uji Beberapa Varietas dan Pemberian Pupuk Biobost terhadap Pertumbuhan dan Isdarmanto. 2009. Pengaruh Macam Pupuk
Organik dan Konsentrasi Pupuk Daun
Terhadap
Pertumbuhan
dan
hasil
Tanaman Cabai Merah (Capsicum annum
L) Dalam Budidaya Sistem Pot. [Skripsi]
Universitas sebelas maret. Surakarta Hasil analisis sidik ragam bahwa
akibat perlakuan beberapa varietas dan
pupuk Bioboost menunjukkan pengaruh
yang nyata pada tinggi tanaman umur 7
dan 9 mst, jumlah daun 5, 7 dan 9 mst. Sedangkan pengaruh tidak nyata pada
parameter tinggi tanaman umur 3 dan 5
mst, jumlah daun umur 3 mst, jumlah
anakan umur 3, 5, 7 dan 9 mst, berat
umbi per sampel dan berat umbi per plot. Krug. H. 1997. Environmental Influences On
Development. Growth and Yield. Pp. 101-
180 in the physiology Of Vegetable Crops
(HC Wien, ed.) CAB Internation. Oxon. Uk
New York. USA. Lingga, P. 2004. Petunjuk Penggunaan Pupuk
.Penebar Swadaya. Jakarta.. Lingga, P. 2008. Petunjuk Penggunaan Pupuk. Penebar Swadaya DAFTAR PUSTAKA Anonimus,
2015. Erecto
Bioboost
2. UD. Kembang Sewu Bekasi. Jabar. Marsono
dan
P. Lingga. 2007. Petunjuk
Penggunaan Pupuk. Penebar Swadaya,
Jakarta. 145 hlm. Arikunto, S. 2006. Metodelogi penelitian. Yogyakarta: Bina Aksara. Prabowo, 2007.Budidaya Bawang Merah. PT. Penebar Swadaya. Jakarta. Blevins, DG. 1994. Uptake. Translocation and
Function Of Essential Mineral Elements In
Crop Plant. Pp. 259 – 275 In Physiology and
Determination Of Grop Yield (Kj Booter. Jm Bennett. Tr Sinclair and GM. Paulsen,
eds). Raja, RL. 2007. Bawang Merah. PT. Panca
Anugrah Sakti. Tangerang. Rukmana,
2002.Bawang
Merah. Kanisius. Yogyakarta. Salisbury, F B dan C. W.Ross. 1995. Fisiologi
Tumbuhan. Terjemahan
dari
Plant
Physiology oleh D. R. Lukman dan
Sumaryono. ITB, Bandung. Brewter, Jl, 1997. Onions and Gaarlic, Pp. 581 –
619 in the physiology Of Vegetable Crops
(HC Wien, ed.) CAB Internation. Oxon. Uk
New York. USA. Simatupang , 2011.Budidaya Bawang Merah. Rinneka Cipta. Jakarta. Chaudary, Rc, 1995. Onions and Gaarlic, Pp. 581 –
619 in the physiology Of Vegetable Crops
(HC Wien, ed.) CAB Internation. Oxon. Uk
New York. USA. Soepardi. G. 1983. Sifat
dan
ciri
tanah. Departemen ilmu – ilmu Tanah. Fakultas
Pertanian Institut Pertanian Bogor. Sudaramonto, 2009. Bawang Merah. Delta
Media. Surakarta. Dinas Pertanian dan Kehutanan Kabupaten
Bantul. 2003. Prospek
Agribisnis
BawangMerah
Kabupaten
Bantul,
Yogyakarta. Sumarni, N., dan A, Hidayat. 2005. Budidaya
Bawang Merah. Balai Penelitian Tanaman
Sayuran. Psusat
Penelitian
dan
Pengembangan
Hortikulturadan
Pengembangan Pertanian. PTT Bawang
Merah No 3. gy
Dinas
pertanian,
Tanaman
Pangan
dan
Hortikultura. 2007. Pedoman Standar
Minimal BPP Model di Sumatera Barat,
Sumatera Barat. Sunarjono, H. H.2004. Bertanam 30 Jenis Sayur. Penebar Swadaya. Jakarta. Widya, Y 2009. Pedoman Bertanam Gomez, A. K and A.A, 2001. Prosedur Statistik
Untuk Penelitian Pertanian. UI Press . Jakarta. Hardjowigieno, S. 1995. Ilmu Tanah. Akademik
Pressindo. Jakarta. 233 hlm. Bawang Merah. Tim Bina Karya Tani. Bandung. Bawang Merah. Tim Bina Karya Tani. Bandung Hermiati. 2000. Pengantar Pemuliaan Tanaman. Universitas Padjadjaran, Bandung. BioLink, Vol. 3 (2) Januari 2017: hal. 112-120
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Um homem plural: sobre a “obra-vida” de Pierre Verger
|
Revista de antropologia
| 2,016
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cc-by
| 3,455
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Resenha SOUTY, Jérôme. Pierre Fatumbi Verger: do olhar livre ao conhecimento iniciático. São Paul
Editora Terceiro Nome, 2011, 446 pp. Tradução de Michel Colin. SOUTY, Jérôme. Pierre Fatumbi Verger: do olhar livre ao conhecimento iniciático. São Paulo,
Editora Terceiro Nome, 2011, 446 pp. Tradução de Michel Colin. Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... as personas que o habitavam pudessem enfim encontrar a paz (:381). Na formulação de
Souty, “A alteridade tornou-se pouco a pouco parte constitutiva de sua identidade. Verger
tornou-se outro, continuando a ser ele mesmo” (:381). O que parecia uma busca identitária
ao longo de toda a sua vida, revela-se, no livro de Souty, como uma existência múltipla. De maneira engenhosa, o autor mostra paulatinamente a coerência que havia por trás do
aparente paradoxo da vida de Verger. Ele era, nas palavras de Souty, um “intercessor”
(:387), uma pessoa entre duas culturas, cujo encontro com o outro tem a capacidade de
trazer à tona a real personalidade do sujeito. E, no caso de Verger, “querer ser outro
significa, em primeiro lugar, querer ser negro” (:254), o que faz com que sua busca da
África se confunda “com uma busca identitária” (:206). Não é de estranhar, portanto, que ele tenha encontrado acolhimento no modelo de
existência iorubá (cuja multiplicidade constitutiva não é paradoxal – :389), já que, como
nos conta Souty, “para os iorubás, o indivíduo é um ser compósito, feito de uma
pluralidade de elementos” (:390). Além disso, “a iniciação consiste também no acesso a um
melhor conhecimento de si mesmo” (:342). Inicia-se, portanto, para se tornar aquilo que na
verdade se é. Esse duplo pertencimento, no caso de Verger, serve como ferramenta de
análise antropológica, neste contexto particular no qual a iniciação serve ao mesmo tempo
como elemento de afirmação da identidade e como método de pesquisa. Seus estudos são,
notavelmente, feitos a partir “de dentro” e também “de fora”, termos muito utilizados para
se referir à relação que os pesquisadores de candomblé mantêm com a religião. Verger era
“de dentro”, pois iniciou-se; mas também era “de fora”, pois nunca se livrou do modo
europeu de pensar. Lamentava a sua falta de crença e mais ainda o fato de nunca ter entrado
em transe. Porém, a escolha (ainda que fruto do “acaso”) de Verger pelas religiões de matriz
africana condiz também com a sua falta de crença, já que estas se caracterizam
primeiramente pelo ato – Souty conta que certa vez, ao ser perguntado se acreditava no
candomblé, Verger respondeu: “vivo como se” (:362). Um homem plural:
sobre a “obra-vida” de Pierre Verger Clara Flaksman Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
claraflaksman@terra.com.br Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
claraflaksman@terra.com.br Pierre Verger dizia que virou etnógrafo “por acaso”: “se deixou guiar (...) pelo acaso e pelos
encontros” (:19). Porém, todos aqueles que conhecem um pouco do funcionamento das
religiões de matriz africana no Brasil sabem que, em sua lógica particular, não existe algo
como o acaso. As decisões que definem o destino de alguém não são tomadas
exclusivamente pela pessoa – ao menos pela pessoa como nós, ocidentais, a concebemos. No candomblé, o destino (odu) é determinado também pela vontade do(s) orixá(s) que
habita(m) a cabeça da pessoa; assim, não é de se estranhar que alguém venha a fazer o santo
contra a vontade, ou mesmo que seja levado a assumir um cargo dentro de um terreiro sem
assim o desejar. A vida de Verger, como nos conta Jerome Souty em seu livro Pierre Fatumbi Verger:
do olhar livre ao conhecimento iniciático, parece seguir à risca esse corolário. Recheada de
contradições, ele parece ter vivido muitas vidas em uma: ao mesmo tempo em que cresceu
em uma família burguesa, passou a vida com poucas posses; embora um francês cartesiano
que lamentava não ter crença alguma, iniciou-se em três vertentes das religiões africanas;
decidido a cometer suicídio aos quarenta anos, viveu quase cem. Ele morre enquanto Pierre
Verger e renasce como Fatumbi; posteriormente, volta a ser Pierre Verger e termina a vida
como Pierre Fatumbi Verger, nome que escolheu para a sua lápide, como se a unidade entre 300 Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... O livro de Souty, versão revista e adaptada de sua tese de doutorado defendida em
2005, na Ehess, em Paris, faz jus à complexidade e à multiplicidade da vida e da obra de
Verger. Sua minuciosa pesquisa incluiu um amplo levantamento bibliográfico, tanto dos
escritos acadêmicos de Verger quanto de correspondências trocadas por ele ao longo da
vida, além do seu grande arquivo fotográfico (algumas destas fotografias ilustram o livro,
espalhadas de maneira engenhosa ao longo dos capítulos, o que permite que o leitor de
certa maneira visualize aquilo que está sendo dito) e de entrevistas feitas tanto em Paris
quanto em Salvador ao longo dos anos de 1993 e 1994. Porém, chama a atenção o
conhecimento de Souty sobre o próprio tema das religiões de matriz africana no Brasil,
fruto de pesquisas feitas em Salvador e no Rio de Janeiro. Esse é um dos fatores que faz com
que um livro escrito sobre um autor sobre quem tanto já se escreveu traga um olhar (aqui
no sentido empregado por Souty, como metáfora para uma maneira mais ampla de ver o
mundo) novo e instigante. A primeira parte do livro trata do método de pesquisa de Verger, tanto na fotografia
quanto na etnografia, traçando um paralelo que se estende por todo o livro. O “olhar”, ou
melhor, a maneira de olhar de Verger era muito próxima em ambos os casos. Na fotografia,
sua opção por uma câmera rolleiflex traduz esse olhar: trata-se de uma câmera silenciosa,
que não é apontada diretamente para o sujeito (:57), o que permitia uma relação de
igualdade entre o fotógrafo e aquele que é fotografado (:58). Podemos perceber este mesmo
olhar em suas pesquisas etnográficas, empático e não intrusivo. Verger adiantou vários dos
temas que hoje são quase regra no método etnográfico da antropologia pós-colonial,
a saber, a não existência de hipótese previamente concebida, escrita descritiva mais que
explicativa, preocupação com a leitura nativa, respeito ao que é secreto. Devereux, por
exemplo, afirma que a informação obtida por Verger é fruto da “experiência
compartilhada” (:72). A todo momento, Souty deixa claro que o que parecia displicência da parte de
Verger (ou “acaso”) era, na verdade, um método próprio de organização (:183). Ao se
recusar a seguir o roteiro pré-estabelecido de um pesquisador, alcançando metas ou
respeitando uma temporalidade imposta, Verger construiu, respeitando seus princípios,
uma carreira acadêmica profícua. CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... Assim, nas religiões de matriz
africana – entre as quais um duplo pertencimento não caracteriza um problema –, Verger
pôde encontrar a identidade que, aparentemente, sempre buscou: um “indivíduo em
posição de entremeio” (:387), um “homem plural” (:388). Ao final do livro, Souty chama a
atenção para o fato de que “as ciências humanas (...) parecem carecer de ferramentas para
analisar esse grupo heterogêneo que reúne indivíduos em interface” (:387). Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 301 301 Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... etnográfica, a sensação que temos ao ler o livro de Souty é que Verger sempre fez o que
quis: “o único homem livre que eu conheço”, como se referiu a ele Théodore Monod (:45). A estrutura do livro é dividida em pequenas seções, cada uma com um título
significativo, que resume com eficiência o conteúdo da seção que segue. Por todo o livro,
a vida de Verger aparece entremeada à sua obra. Os dados efetivamente biográficos, sobre a
sua infância na França ou sua família, só aparecem de fato a partir da metade do livro,
o que reforça a ideia de indistinção entre vida pessoal e vida laboral. Assim, a história de
vida de Verger ganha um sentido subliminar que torna a leitura sobre a sua história mais
densa; fica clara a ideia de que a busca pessoal de Verger pautava sua obra e vice-versa. A indissociação entre vida e obra de Verger se reflete também em sua principal
teoria (e a única, segundo Souty, sobre a qual reivindicou autoria): a dos orixás como
arquétipos de personalidade. Souty defende que Verger tinha consciência de que foi levado
a formular esta teoria por razões pessoais: como na África os orixás são ancestrais
divinizados, e, portanto, presentes geneticamente em seus descendentes, como seria possível
que um branco, sem essa herança genética, pudesse trazer consigo essa presença? Verger
concluiu que os orixás têm uma dupla natureza, podendo ser tanto ancestrais divinizados
quanto arquétipos mais gerais da personalidade humana. Assim, um filho de Xangô poderia
ser tanto seu descendente direto (no caso africano) quanto ter uma personalidade
condizente com a do orixá (no caso brasileiro) (:162). Assim, durante a feitura, a pessoa
torna-se mais ela mesma, ainda que essa vontade não parta diretamente dela. Mas essa não foi a única contribuição importante de Verger para a antropologia das
religiões de matriz africana: é de sua autoria também a teoria do verbo atuante, que
identifica o poder performativo da linguagem no candomblé. Seus escritos sobre o transe e
sobre a noção de pessoa africana também foram fundamentais para os estudos sobre as
religiões de matriz africana, tendo papel fundamental em muitas das teorias de Bastide, de
quem foi colaborador assíduo. Durante todo o livro, podemos acompanhar o papel fundamental dos amigos na
vida de Verger, e ter a dimensão da importância destes em sua “obra-vida” e vice-versa. CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... Seja fotografando o que nunca havia sido fotografado,
ou mesmo debruçando-se sobre os arquivos da escravidão depois de tantos anos de pesquisa Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 302 CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... v. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016]
303 CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... similaridades com a África (:220). E opôs-se publicamente a Juana Elbein dos Santos, a
quem acusou de manipular dados para construir teorias “fechadas”. Souty levanta a hipótese
de que esta querela pode também ser vista como possível fruto de um parentesco simbólico
“demasiadamente estreito” (:270), já que Elbein era casada com Mestre Didi, filho de Mãe
Senhora, que havia iniciado Verger. Já o parentesco consanguíneo de Verger só nos é apresentado a partir da metade do
livro de Souty. Ali ficamos sabendo do sentimento de inadequação que o acompanhou por
toda a sua infância e da gradual perda de todos os membros de sua família no período entre
1914 e 1932. Quando a sua mãe morre, em 1932, ele parte em uma viagem praticamente
sem volta. Havia acabado de completar trinta anos, “sem diploma e nem emprego” (:240). Nesse mesmo ano, resolve que cometeria suicídio assim que completasse quarenta anos
(plano posteriormente abandonado, como se vê). Quando chega o dia marcado, 4 de
novembro de 1942, ele está em Cuzco, no Peru, e aparentemente se esquece de seu plano:
“frustrei minha morte” (:249). Porém, a quase morte marca o início de uma nova vida para Verger. De Cuzco, ele
segue viagem pelos Andes até que, em 1946, chega a Salvador (seguindo uma dica que
Bastide lhe dera) e permanece lá durante dois anos trabalhando como repórter fotográfico
para a revista O Cruzeiro. “Após quinze anos viajando pelo mundo, parece ter encontrado
seu lugar” (:257). Segundo Souty, na Bahia Verger conseguia conviver com os negros em pé
de igualdade, o que o levou a construir uma visão idealizada da cidade e, por conseguinte,
do candomblé, visto por ele como forma de manutenção e de resgate da autoestima dos
negros (:262). Em 1946 Verger embarca para a África, e na volta desta viagem, em 1948, dá o seu
primeiro bori com Mãe Senhora. Foi a partir da sua relação com o candomblé que Verger
foi acolhido pela população negra de Salvador, e por causa deste acolhimento (de um
branco europeu por uma religião de negros de origem africana) que ele desenvolveu a teoria
da dupla característica dos orixás. Souty analisa o processo iniciático de Verger com base na
teoria dos ritos de passagem de Van Gennep (separação, marginalização e agregação),
alternando as fases de suas iniciações com momentos de sua vida pessoal. CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... Métraux e Bastide o estimulam a enveredar-se na escrita (:146), e foi no diálogo com eles,
além de Leiris e Lydia Cabrera, que Verger formulou a maioria de suas ideias. Mas Verger
também construiu inimizades: desentendeu-se com Herskowits, já que este considerava o
desenvolvimento do candomblé baiano autônomo, enquanto Verger buscava conexões e Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 303 Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... Posteriormente, já como oju obá do Ilê Axé Opô Afonjá, ele inicia-se como babalaô
na região de Ketu, e ganha o nome de Fatumbi, “um segundo eu mesmo” segundo palavras
do próprio (:290). Em 1954 Verger lança o livro Dieux d'Afrique comparando imagens
feitas no Brasil e na África, iniciando a sua atuação como mensageiro transatlântico (:113). Verger buscava, mais do que atestar que esta ou aquela tradição era real, estabelecer um elo
entre as religiões tradicionais negras na África e no Brasil. Com este fim, transportou da
África para o Brasil (e também na direção inversa) objetos, histórias, documentos. Foi
baseado nessa dimensão da relação África-Brasil que Verger elegeu o candomblé ketu
(o “modelo cultural ioruba” – :181) como o legítimo representante desta tradição, o que
terminou por gerar controvérsias tanto dentro do próprio candomblé quanto na academia. Na análise de Souty sobre a “tradição” africana no Brasil, ele mostra como Verger, ao
mesmo tempo em que foi um dos artífices desta “invenção da tradição” (termo cunhado
por Hobsbawn e apropriado por Beatriz Góis Dantas e Stefania Capone numa espécie de
“denúncia” sobre a suposta influência de antropólogos e intelectuais nos terreiros de
candomblé), também se interessou pelos modelos de sincretismo existentes no Brasil (:195),
defendendo que o sincretismo entre o candomblé e o catolicismo seguia o modelo da
“justaposição sem oposição” (:197). Como destaca Souty, com propriedade, “entre destacar
a fidelidade e defender a ‘pureza’, a fronteira é tênue” (:181) e Verger foi criticado por ter
priorizado o modelo iorubá em detrimento das tradições fon e angola, e defendeu-se
afirmando que o modelo de culto iorubá era mais facilmente adaptável para o Brasil, pelo
fato de adorar também os elementos da natureza. Sobre isso, nos diz Souty que “para uma
apreciação justa, é necessário colocar-se a meio caminho entre essas duas interpretações e
não superestimar a influência dos trabalhos universitários na construção dos modelos rituais
e das tradições religiosas” (:204). O contraponto à visão sincrética do próprio Verger vem, segundo Souty, da sua
participação na fundação do terreiro de Balbino Daniel de Souza, mais conhecido como
Obarayi (:223). Ali, Verger leva a cabo sua visão do que seria um terreiro “tradicional” e
busca, com isso, implementar elementos já extintos das religiões africanas para legitimar
esse processo (:225). Aqui, Souty deixa clara a sua crítica a esse envolvimento de Verger
com a criação do terreiro de Obarayi. CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... Com isso,
consegue mostrar como esses dois aspectos da vida de Verger são indissociáveis: trata-se,
realmente, de uma “obra-vida”. Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016]
304 Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 304 304 Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... O livro de Souty segue, de alguma maneira, o estilo de Pierre Verger: ainda que sem
alarde, em um estilo mais descritivo que teórico, Souty apresenta, perto do final do livro,
uma teoria consistente sobre o segredo no candomblé (:327). Primeiramente, mostra-nos
como Verger se relacionou com a questão do segredo: apesar de ter se iniciado, como dizia,
para ter acesso ao segredo (e de ter usado a iniciação como método de pesquisa), Verger
nunca revelou a maioria das informações a que teve acesso, na maior parte das vezes por
iniciativa pessoal (:339). “Na obra etnográfica de Verger, há uma grande parte de silêncio”
(:328). É curioso que uma obra tão profícua como a de Verger tenha sido erigida sobre tal
dialética, mas, como nos lembra Souty, “o pilar sobre o qual repousa o saber oral iorubá é
também o depositário do segredo: aquele que conserva e transmite é também aquele que
esconde” (:334). Foi em cima dessa dupla reação que Verger construiu a sua obra:
“o silêncio foi bastante relativo. Sem (...) trair a lei do segredo, ele mostrou, escreveu e disse
muito” (:340). Mas Souty vai além da relação de Verger com o segredo: segundo ele, o segredo é
parte da experiência do candomblé justamente porque se relaciona a diversos aspectos de
sua prática. Sua presença tanto funciona, segundo Souty, como elemento de coesão do
grupo, quanto faz parte do processo de aprendizado. O candomblé estaria, podemos dizer,
impregnado pelo segredo. “O segredo participa diretamente da dinâmica de comunicação e
redistribuição da energia sagrada axé” (:349). Assim como o axé é o elemento fundamental
da dinâmica de funcionamento de um terreiro de candomblé, Souty defende que o segredo,
estando diretamente ligado a ele, seria também parte desta organização, ao mesmo tempo
como elemento diferenciador (entre os que sabem mais e menos) e de união (pois une o
grupo em torno de sua proteção) (:347). O segredo, além disso, aparece em camadas (:348):
Souty cita como exemplo o famoso testamento de Marcelina Obatossi, que, segundo ele,
“é revelador justamente pelo que não diz” (:351). CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... Segundo ele, “podemos considerar que
Verger participou tardiamente de certa ‘folclorização’ do culto” (:225). Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 305 305 v. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016]
306 CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... abandonavam a sua identidade cotidiana quando entravam nos terreiros, assumindo uma
posição de poder dentro daquela estrutura – poder que lhes era negado no dia a dia). Ou seja, que o pesquisador possa participar do grupo sem, no entanto, assumir uma postura
religiosa (:402). Porém, logo depois Souty afirma que, de lá para cá, “a iniciação do
pesquisador tornou-se assim uma coisa quase banal” (:404), “defendida e reivindicada como
um princípio metodológico que legitima a observação participante” (:403), chamando a
atenção, porém, para os riscos envolvidos neste processo (:411). Se o candomblé é, como vimos, uma religião do ato, do fazer, poderíamos dizer que
a antropologia de Verger é uma antropologia do fazer (:418). Souty defende que a obra de
Verger representa uma “revolução copernicana na antropologia” (:418), pois, ainda que sem
alarde, representou “uma crítica ao etnocentrismo ocidental, portanto ao logocentrismo e
ao escriptocentrismo” (:419). Verger “quis encontrar o outro, e não objetivá-lo” (:420), nos
diz Souty, e “teve o privilégio de viver várias vidas, de pertencer a vários mundos numa
única vida” (:422). E, ao chegar ao fim do livro, somos obrigados a concordar com ele. 1 O autor alterna o tratamento dado a Verger: em alguns momentos o chama de etnógrafo,
em outros de etnólogo. Sobre isso, convém lembrar que somente no Brasil o termo etnologia se
refere especificamente à etnologia indígena. CLARA FLAKSMAN. SOUTY. PIERRE FATUMBI VERGER: DO OLHAR LIVRE... O tema da metodologia é retomado ao fim do livro, quando a análise do método de
pesquisa de Verger (que Souty chama “antropologia iniciática” – :395) serve também como
mote para observações mais gerais sobre o método etnográfico, especialmente valiosas para
pesquisadores que trabalham com o tema das religiões de matriz africana que se deparam
com a questão da iniciação em seus locais de pesquisa. Souty chega a sugerir que se pense a
relação entre etnógrafo1 e o que ele denomina “objeto de estudo” nos moldes do princípio
de corte de Roger Bastide (que defendia que os participantes das religiões de matriz africana Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 306 Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] Notas 1 O autor alterna o tratamento dado a Verger: em alguns momentos o chama de etnógrafo,
em outros de etnólogo. Sobre isso, convém lembrar que somente no Brasil o termo etnologia se
refere especificamente à etnologia indígena. Rev. Antropol. São Paulo, Online, 59(1): 300-307 [abril/2016] 307
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Fabrication of weakly basic-functionalized poly (Styrene Co-Maleic Anhydride) hyper-cross-linked resins for the efficient adsorption organic acid
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Research Square (Research Square)
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cc-by
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Fabrication of weakly basic-
functionalized poly (Styrene Co-
Maleic Anhydride) hyper-cross-
linked resins for the efficient adsorption organic aci
d d Fabrication of weakly basic-
functionalized poly (Styrene Co-
Maleic Anhydride) hyper-cross-
linked resins for the efficient adsorption organic aci
d
Wang Yiqing
Shihua Zhong
(
zhongshihua@hunnu.edu.cn
)
at Key Laboratory of the Assembly and Application of Organic Functional Molecules ,Hunan Normal
University
Research Article
Keywords: Weakly basic resin, Anhydride, Suspension polymerization
Posted Date: November 21st, 2023
DOI: https://doi.org/10.21203/rs.3.rs-3507609/v1
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License.
Read Full License
Version of Record: A version of this preprint was published at Journal of Polymer Research on January
31st, 2024. See the published version at https://doi.org/10.1007/s10965-024-03890-z. Fabrication of weakly basic-
functionalized poly (Styrene Co-
Maleic Anhydride) hyper-cross-
linked resins for the efficient adsorption organic aci
d
Wang Yiqing
Shihua Zhong
(
zhongshihua@hunnu.edu.cn
)
at Key Laboratory of the Assembly and Application of Organic Functional Molecules ,Hunan Normal
University
Research Article
Keywords: Weakly basic resin, Anhydride, Suspension polymerization
Posted Date: November 21st, 2023
DOI: https://doi.org/10.21203/rs.3.rs-3507609/v1
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License
Version of Record: A version of this preprint was published at Journal of Polymer Research on January
31st, 2024. See the published version at https://doi.org/10.1007/s10965-024-03890-z. Research Article License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Version of Record: A version of this preprint was published at Journal of Polymer Research on January
31st, 2024. See the published version at https://doi.org/10.1007/s10965-024-03890-z. Page 1/18 Page 1/18 Abstract Herein, four hyper-cross-linked amide resins (DMDs) were synthesized by suspension polymerization and
amination reaction. In the process of suspension polymerization, divinylbenzene (DVB) and maleic
anhydride (MAH) with different feed ratios generated resins (DMHs) with different pore structures. After
N, N'-dimethyl-1,3-propanediamine (DMAPA) chemical functionalization of DMH, the weak base exchange
capacity of the product resins significantly increased, with the values of 1.01 mmol/g (DMD1), 1.15
mmol/g (DMD2), 1.22 mmol/g (DMD3), and 1.34 mmol/g (DMD4). Salicylic acid (SA), benzoic acid (BA),
gallic acid (GA), and phenol (PHE) were utilized as the adsorbates to investigate batch adsorption. At 288
K, the maximum capacity (qmax) of SA, BA, and GA on the DMD4 were 181.7 mg/g, 143.8 mg/g, and
145.2 mg/g, respectively. The adsorption of BA and GA attained the equilibrium within 100 min, and the
kinetic data can be described by the pseudo-second-order (PSO) rate model. This universal synthetic
method is of great importance for the fabrication of some other functionalized hyper-cross-linked
polymers, and this strategy was universal for the weakly basic functionalization of some other resins. 1. Introduction Hyper-cross-linked resin, also known as the third-generation resin, is an efficient adsorbent. According to
the polarity of the groups loaded on the surface of the resin, it can be divided into nonpolar, moderate
polar, and strong polar [1, 2]. Nonpolar adsorption resin frameworks without functional groups are mainly
adsorbed through their physical structures such as surface, pore volume (Vtotal), and pore size. However,
for moderate polar adsorption resins, their surfaces possess both hydrophobicity and hydrophilicity,
allowing them to adsorb nonpolar substances from polar solvents as well as polar substances from
nonpolar solvents [3, 4]. Their adsorption mainly relies on hydrophobic interactions and π - π stacking [5, 6]. Polar adsorption resins have polar functional groups on their surfaces, such as − COOH and − OH with O
atoms, −SH and − SO3H with S atoms, and − NH2 and − CONH2 with N atoms [7]. It is believed that the
main driving force is increased polarity matching through specific electrostatic interactions or hydrogen
bonds [8]. The porosity and polarity of hyper-cross-linked resin can be adjusted based on chemical reactions. However, synthesizing adsorption resins with high specific surface area (SBET) and Vtotal remains a
challenge. So far, three typical methods have been applied to improve the surface polarity of resins,
including inserting polar monomers into copolymers, adopting polar compounds as crosslinking agents,
and introducing polar aromatic compounds in Friedel-Crafts reactions. [9–12]. Moradi et al. [13] synthesized
porous phenyl hyper-cross-linked polymeric adsorbents with different morphological properties, which
possessed CO2 uptake capacity up to 167 mg/g, using small molecule cross-linking agents via Friedel -
Crafts alkylation reaction. You et al. [14] successfully synthesized modified hyper-cross-linked resins
containing pyridine and carboxylic acid groups (HCP-x) by changing the feed ratio of 4-VP and 4-VA
during polymerization, which effectively adjusted the SBET, Vtotal, and porosity. HCP-90, as the optimal
resin, had the largest SBET (742 m2/g), the smallest micropore volume (Vmicro, 0.07 cm3/g), and the best Page 2/18 adsorption performance (qmax, 777.9 mg/g). Sun et al. [15] chose the macroporous polystyrene adsorbent
NG-8 as a substrate and used 4-vinylpyridine (4VP) monomers to modify the vinyl suspended on the
adsorbent by graft polymerization, resulting in the adsorption capacity for 2-naphthalenesulfonic acid
(NSA) up to 1014 mg/g, which made the removal of aromatic sulfonic acids from wastewater promising. Cao et al. 1. Introduction And the DMH
and DMD resins were characterized and evaluated for the adsorption of different types of aromatic acids,
including adsorption kinetics, thermodynamics, selective adsorption, and regeneration properties. It has
great potential and guiding significance to be applied in the treatment of wastewater containing aromatic
acids. 1. Introduction [16] synthesized the HCPs with an excellent adsorption effect on phenol by inserting acetanilide
into the polymer skeleton of CMPS through two consecutive Friedel-Crafts alkylation reactions. Wu et al. [17] successfully prepared carbonyl functionalized HCLP by utilizing carbon tetrachloride as the cross-
linking agent through the Friedel-Crafts acylation reaction. Wang et al. [18] prepared the phenolic hydroxyl
functionalized HCPs, which contained a two-step alkylation reaction. The first step is that CMPS is
modified with DBP in order to load a hydroxyl group into the polymer skeleton, and the second step is the
molecular cross-linking reaction of CMPS. Among them, it is widely known that the best method of preparing the microspheric porous copolymers is
suspension polymerization. The application of different monomer types and relative molar ratios can
change the properties and structure of the resin. However, the traditional suspension polymerization
mostly used styrene, DVB, and some ester compounds as monomers and rarely adopted anhydride as
monomers [19–22]. Especially, acid anhydride is a very polar organic substance. In organic acid anhydride,
MAH is easily copolymerized with many monomers due to the fact that anhydride groups in polymers are
effective polymerization acylation reagents and are also expected to react with some compounds
including amines. Yukio et al. [23] used MAH, styrene (St), and DVB as the polar monomers to prepare
copolymer, which was effective in making the copolymer fine and spheroidal. Ogawa et al. [24] have
published the fabrication of styrene-maleic anhydride-DVB beads using glycerol as the continuous phase,
which had high selectivity for the adsorption of mercury ions. Tubituk et al. [25] applied the method of
suspension polymerization, which replaced water with glycerol as the dispersing medium and prepared
anhydride-styrene-DVB copolymer, ultimately obtaining porous MAn-St-DVB copolymers at relatively low
DVB concentration. In this work, four hyper-cross-linked amide resins (DMDs) were synthesized using DVB and MAH as the
monomers through suspension polymerization followed by the modification with DMAPA. And the DMH
and DMD resins were characterized and evaluated for the adsorption of different types of aromatic acids,
including adsorption kinetics, thermodynamics, selective adsorption, and regeneration properties. It has
great potential and guiding significance to be applied in the treatment of wastewater containing aromatic
acids. In this work, four hyper-cross-linked amide resins (DMDs) were synthesized using DVB and MAH as the
monomers through suspension polymerization followed by the modification with DMAPA. 2.1 Characterization of DMH and DMD In Fig. 1 (a), the FT-IR spectrum showed that the strong vibrations at 1720 cm− 1 and 1790 cm− 1 can be
assigned to C = O [26] stretching of DMH4 after suspension polymerization reaction. For DMD4, a new Page 3/18 broad characteristic peak at 3700 − 3150 cm− 1 (NH − groups) appeared. Besides, compared to DMH4,
DMD4 exhibited another strong adsorption peak at 1690 cm− 1, which was attributed to the considerable
− CONH2 stretching vibration of the amide. Noticeably, it can be seen in Table 1 that the weak base
exchange capacity increased significantly after the amination reaction, which verified that the amine had
been successfully uploaded to the resin skeleton. For DMH1, the capacity increased to 1.01 mmol/g, for
DMH2, the capacity increased to 1.15 mmol/g, for DMH3, the capacity increased to 1.22 mmol/g, and for
DMH4, the capacity increased to 1.34 mmol/g. Particularly, the weak base exchange amount increased
with increasing ratio of MAH, and DMD4 exhibited the highest weak base exchange capacity. In addition,
because of the hydrolysis reaction in the first step, which increased the amount of COOH − group, the
weak base exchange capacity ultimately improved slightly. It implied that the precursor resin was
successfully synthesized and realized the introduction of amide. In Fig. 1 (b), the XPS spectra indicated that the N species was present in DMD4 compared to DMH4. The
high-resolution C 1s revealed that the C = O [27, 28] configuration had migrated from 288.8 eV (DMH4) to
288.2 eV (DMD4). Moreover, as shown in Fig. 1 (c-d), the C − O configuration of DMH4 at 286.1 eV
apparently vanished, while another C − N configuration appeared for DMD4 with the binding energy at
287.4 eV. Besides, the O = C − O configuration of O 1s in Fig. 1 (e) vanished at 533.2 eV for DMD4. The
high-resolution N 1s in Fig. 1 (f) demonstrated that O = C − N and C − N configurations for DMD4 appeared
at 399.09 eV and 402.38 eV, respectively, confirming that the suspension polymerization and
ammonolysis were carried out stably. The N2 adsorption-desorption isotherms of the DMH and DMD resins were shown in Fig. 2, and Fig. 3
displayed the pore size distribution. And the relevant parameters of pore structure were measured and
summarized in Table 1, which revealed that both DMH and DMD were dominated by mesopores and
micropores. 2.1 Characterization of DMH and DMD However, the second
amination reaction dramatically increased the average pore size of the resins, transforming the structure
from abundant micropores to predominated mesopores, which made the pore canal become larger and
induced the water to be hardly preserved in the resin, resulting in a decrease in water content. The scanning electron microscopy (SEM) images of the resin samples (Fig. 4) were in accordance with
the phenomenon above. It can be seen that both DMD4 and DMH4 were regular spherical particles. Noticeably, inferring from obvious structures with an alternate dark and bright microstructure, DMD4
possessed the larger and more abundant pore structures, exhibiting superior adsorption performance. 2.1 Characterization of DMH and DMD According to Fig. 2, it can be seen that the N2 isotherm of DMH was much higher than DMD
at the high relative pressure, and the N2 isotherm of DMH1 was also higher than DMH4 in a considerable
range of pressure. In addition, DMH4 had the smallest SBET and Vtotal, with the values of 531.7 m2/g and
0.62 cm3/g, respectively. While DMH1 exhibited the largest SBET (575.4 m2/g) and Vtotal (1.16 cm3/g). For
DMD resins, DMD4 had the smallest SBET (448.9 m2/g) and Vtotal (0.61 cm3/g), and DMD1 possessed the
largest SBET (552.7 m2/g) and Vtotal (1.09 cm3/g). Therefore, the possible reason could be attributed to
the fact that as the suspension polymerization reaction occurred, more amount of MAH was introduced
to the resin skeleton, which caused the larger pore size and the smaller SBET under the influence of hole
filling. Moreover, after the following amination reaction, the SBET sharply decreased owing to the
introduction of DMAPA groups, which was related to the fact that the polar amino and amide groups
loaded on resin, leading to an increase of the polarity of the resin. Likewise, due to the introduction of
amino groups, the Vtotal increased. These experimental data strongly demonstrated the remarkable
increase of the pore size of the DMD resins, as well as the conspicuous enhancement of the
meso/macro-pores, following the amination reaction of the precursor resins. Page 4/18 Page 4/18 Table 1
The structure parameters of the resin
Resin
SBET (m2
/g)
Vtotal (cm3
/g)
Average pore size
(nm)
Weak base exchange
(mmol/g)
Water content
(wt.%)
DMH1
575.4
1.16
8.10
-
52.3
DMH2
564.3
0.88
6.49
-
49.8
DMH3
545.6
0.76
5.52
-
48.2
DMH4
531.7
0.62
4.72
-
47.8
DMD1
552.7
1.09
7.93
1.01
51.4
DMD2
519.2
0.84
6.97
1.15
50.6
DMD3
480.0
0.72
5.79
1.22
49.6
DMD4
448.9
0.61
5.32
1.34
48.1 Table 1 Table 1
The structure parameters of the resin In Table 1, it could be detected that the water content of DMH resin was slightly higher than that of DMD
resin. The possible reason may be assigned to the following fact. After the first suspension
polymerization, the precursor resins continuously occurred the hydrolysis reaction, producing the
hydrophilic COOH − group, which caused an obvious increase of the water content. 2.2 Equilibrium adsorption isotherms and Adsorption
kinetics After ammonolysis, the adsorption of aromatic acids by DMD resin mainly
relied on hydrogen bonding, acid-base interaction, hydrophobic interaction, and π-π interaction. In
particular, the presence of O and N atoms inside the amide bond significantly strengthened the hydrogen
bonding. On the other hand, the introduction of an alkaline amino group, which could react with aromatic
acid through acid-base interaction, furtherly boosted the adsorption capacity of the prepared resin. It was observed in Fig. 5 (a-c) that the adsorption capacity of the modified DMD resin remarkably
enhanced as the amount of MAH increased. Nevertheless, the adsorption of aromatic acids by the DMH
precursor resin decreased with the increase of MAH. For DMH, the major driving forces for adsorption
were hydrophobic interactions and π-π interactions. The synthesized resin containing hydrolyzable
anhydride groups after the first suspension polymerization reaction enhanced the hydrophilicity of the
resin, and reduced the SBET and Vtotal, ultimately resulting in a decrease in the adsorption amounts of
aromatic acids on the resin. After ammonolysis, the adsorption of aromatic acids by DMD resin mainly
relied on hydrogen bonding, acid-base interaction, hydrophobic interaction, and π-π interaction. In
particular, the presence of O and N atoms inside the amide bond significantly strengthened the hydrogen
bonding. On the other hand, the introduction of an alkaline amino group, which could react with aromatic
acid through acid-base interaction, furtherly boosted the adsorption capacity of the prepared resin. The Langmuir [29] and Freundlich [30] models were used to characterize the equilibrium data. Table S2-5 in
the Supporting Information displayed that two models were all suitable for depicting the adsorption
process. Moreover, it was evidently shown that the Freundlich model was more appropriate for
characterizing the adsorption of DMD4 for aromatic acids, consequently indicating that the adsorption
belonged to the multi-molecular layer adsorption. When SA was selected as an adsorbate, it was clear
that qmax followed an order of 288 K (193.7 mg/g) > 298 K (185.5 mg/g) > 308 K (178.7 mg/g),
suggesting an exothermic process. The qmax of DMD4 for SA at 288 K was predicted to be 193.7 mg/g,
which was comparable or superior to other reported data in the literature (Table 2). In addition, the
adsorption of BA, SA, and PHE on DMH4 had similar results in Fig. S2. 2.2 Equilibrium adsorption isotherms and Adsorption
kinetics Abundant nitrogen was embedded on the synthesized DMD resins, which were rich in pore structures. The
equilibrium isotherms of the resins in Fig. 5 (a-c) were determined at 288 K using aromatic acids as the
adsorbate, and Table S2-5 summarized the parameters KL, KF, n, and the correlation coefficients (R2). The
adsorption capacity of DMH and DMD for SA was displayed in Fig. 5 (a). For SA, the equilibrium
adsorption isotherms were ranked on the order of DMD4 (181.78 mg/g) > DMD3 (171.28 mg/g) > DMD2
(162.45 mg/g) > DMD1 (143.81 mg/g) > DMH1 (104.35 mg/g) > DMH2 (88.70 mg/g) > DMH3 (73.35
mg/g) > DMH4 (62.23 mg/g). Similarly, it was found that DMD4 exhibited optimal adsorption capacity for
BA and GA with the values of 145.86 mg/g and 145.28 mg/g, respectively. The adsorption capacity of Page 5/18 Page 5/18 DMH and DMD for PHE was shown in Fig. S1. It can be seen that the equilibrium capacities increased
sharply as the equilibrium concentration increased. With the structure of neighboring − OH and − COOH
groups, the SA molecule was capable of forming intramolecular hydrogen bonds, which hindered the
formation of hydrogen bonds with water molecules to some extent and facilitated the hydrophobic
interaction, further strengthening the adsorption capacity of SA on the resin. Noticeably, the adsorption of
PHE by resin mainly relied on hydrophobic action, hydrogen bonding, and acid-base action. PHE was a
weak organic acid with strong hydrophilicity, resulting in a significant reduction in hydrophobic and acid-
base effects, which further led to the poor adsorption capacity of PHE on DMD4 resin. Regarding to GA,
which contained three phenolic − OH groups, it was extremely hydrophilic, inducing a weaker hydrophobic
interaction. Hence, the adsorption of GA on DMH basically hardly occurred. It was observed in Fig. 5 (a-c) that the adsorption capacity of the modified DMD resin remarkably
enhanced as the amount of MAH increased. Nevertheless, the adsorption of aromatic acids by the DMH
precursor resin decreased with the increase of MAH. For DMH, the major driving forces for adsorption
were hydrophobic interactions and π-π interactions. The synthesized resin containing hydrolyzable
anhydride groups after the first suspension polymerization reaction enhanced the hydrophilicity of the
resin, and reduced the SBET and Vtotal, ultimately resulting in a decrease in the adsorption amounts of
aromatic acids on the resin. 2.2 Equilibrium adsorption isotherms and Adsorption
kinetics The adsorption equilibrium isotherms of SA, BA, and GA on DMD4 were measured at three different
temperatures of 288 K, 298 K, and 308 K, respectively. And the thermodynamic parameters for the
adsorption of DMD4 for SA, BA, GA, and PHE were obtained according to the Vant-Hoff equation [31]
(Table S6-9). Additionally, it demonstrated that regarding to SA, at 288K, the adsorption free energy (ΔG,
-9.13 kJ/mol), both entropy (ΔS) and enthalpy (ΔH) were negative, indicating that the process was
spontaneous and exothermic. BA, GA, and PHE had the same adsorption mechanisms as SA. Page 6/18 Page 6/18 Table 2
Comparison of adsorption capacities of SA on DMH4 and
DMD4 with some other adsorbents in the literature. Adsorbents
qm (mg∙g− 1)
References
CTAB-Mont
202.1
[32]
Zirconia-carbon composites
109
[33]
Sephabeads SP207
91.5
[34]
Sephabeads SP206
66.2
[34]
HJ-Y2
120.5
[35]
GQ-04
119.9
[36]
BPC
36.4
[37]
PDVB/PMAEMIPN
151.5
[38]
DMD4
181.7
This study Table 2 Table 2
Comparison of adsorption capacities of SA on DMH4 and
DMD4 with some other adsorbents in the literature. Selected DMH4 and DMD4 as model adsorbents, Fig. 6 illustrated the kinetic adsorption curves of SA, BA,
and GA. It revealed that the adsorption of BA and GA on DMD4 approached approximately 90% of the
equilibrium adsorption capacity within 100 min, while the adsorption of SA on DMD4 required longer time
(about 200 min), which might be attributed to the weak adsorption effect of the surface layer of the resin
for SA, resulting in the slow diffusion to the internal sites and the requirement of long time to reach the
adsorption equilibrium. The kinetics of adsorption of aromatic acids on the resin were analyzed by fitting
the data to pseudo-first-order (PFO) [39] and pseudo-second-order (PSO) [40] kinetic models. The findings
of the study in Table S10 and Fig. 6 (d-f) revealed that the adsorption process was more consistent with
PSO, which suggested that chemical adsorption was the major rate-determining step with the k2 value’s
order of 7.92 × 10− 4 g/(mg·min) (PHE) > 3.46 × 10− 4 g/(mg·min) (BA) > 1.47 × 10− 4 g/(mg·min) (GA) >
0.61 × 10− 4 g/(mg·min) (SA). It can be seen obviously that PHE was more likely to reach adsorption
equilibrium, which was assigned to low equilibrium adsorption capacity, the adsorption process only
completed the surface layer adsorption. 2.3 Factors affecting the adsorption of aromatic acids by
resins The impact of pH on the adsorption of aromatic acid on DMD4 was demonstrated in Fig. 7 (a), and the
original pH (SA with 2.64, PHE with 6.05, BA with 3.5, and GA with 3.65) of solution was found to be the
optimal condition for the adsorption of aromatic acids, proving that the molecular state was the most
conducive for the adsorption of aromatic acids. When NaOH was added to the original solution, the pH
increased and a large amount of H+ was consumed. Moreover, a large number of amino groups were
deprotonated, resulting in electrostatic repulsion between the resin and the anions of aromatic acids. On
the other hand, as the pH increased, the inhibition of adsorbate dissociation also weakened, and some
adsorbates no longer existed in molecular form, weakening hydrophobic interaction. Therefore, the
adsorption capacity decreased with the increase of pH value. When the pH decreased, the adsorption
capacity also decreased, which was due to the protonation of some functional groups and the
competition between the acid groups of SA and the added Cl−. In Fig. 7 (b), it was apparent that the electrolyte had a prominent impact on adsorption. The adsorption
capacity of DMD4 resin for aromatic acids exhibited a sharp reduction followed by a slow increase as the
concentration of Na2SO4 increased from 0.01 mol/L to 0.05 mol/L. The experimental results suggested
that many adsorption sites were initially occupied with anions of the electrolyte, resulting in a significant
decline in the adsorption capacity. The salt out effect was promoted with the addition of a large amount
of electrolytes, further enhancing the hydrophobic effect and ultimately leading to a slow increase in
adsorption capacity. Due to the fact that two adjacent active adsorption sites were provided to SO4
2−,
which consumed more amino groups, the decrease in adsorption capacity was more pronounced than
using NaCl. As shown in Fig. 7 (c), the desorption of the aromatic acid adsorbed on the resin was successfully
achieved by using the mixed solution of 0.1 mol/L NaOH and ethanol. After five repeated adsorption-
desorption cycles, the qmax of SA, BA, and GA decreased from 178.3 mg/g to 168.4 mg/g, from 135.2
mg/g to 123.8 mg/g, and from 133.6 mg/g to 114.0 mg/g, respectively. Notably, the adsorption rate of
DMD4 for aromatic acids remained over 90% even after five cycles, which suggested that the DMD4 resin
exhibited stable and outstanding regenerative capabilities. width of the pore channels of the resin, and consequently decreased the diffusion rate of the adsorbate
molecules. width of the pore channels of the resin, and consequently decreased the diffusion rate of the adsorbate
molecules. 2.2 Equilibrium adsorption isotherms and Adsorption
kinetics In comparison, as the equilibrium adsorption capacity continued
to increase, the surface adsorption sites of the modified resin were rapidly depleted so that the acids were
forced to diffuse to reach the inner active binding sites affected by diffusion resistance, causing the
decrease of the adsorption rate. The experimental data showed that the value of k2 when adsorption on
DMH4 was always greater than that by DMD4, indicating DMH4 achieved adsorption equilibrium earlier
than DMD4, which could be attributed to the introduction of an amino group after ammonolysis. That is,
the presence of the amino group not only impeded the adsorption of aromatic acid owing to spatial
hindrance, but also facilitated the formation of hydrogen bonds with water molecules, which reduced the Page 7/18 Page 7/18 2.4 The application of DMD4 for the separation and
extraction of alkaloids The adsorption of caffeine on DMD4 was studied in aqueous or isopropanol solutions. The results
indicated that DMD4 exhibited strong adsorption capacity of caffeine in aqueous solution (as shown in
Fig. S8), while it hardly adsorbed in isopropanol solution. This might be assigned to the inhibition of
hydrophobic and hydrogen bonding interactions under the influence of isopropanol. Caffeine contains
various organic acids, and removing these organic acids was of great significance in improving the purity
of caffeine. After removing organic acids in isopropanol solution, caffeine was extracted from aqueous
solution, and this screening method could be achieved using DMD4 resin. Obviously, this is of great
significance for guiding the purification of caffeine. 3. Conclusions In summary, MAH and DVB were used as the monomers and DMAPA was employed to amination
modified DMHs, resulting in the successful fabrication of weakly basic-functionalized hyper-cross-linked
resins. The DMDs owned plentiful weak base exchange capacity (1.01–1.34 mmol/g), high SBET (449–
552 m2/g) and Vtotal (0.61–1.69 cm3/g). The adsorption experiments demonstrated that the qmax of SA
at 288 K (181.7 mg/g) exceeded most synthetic adsorbents in the literature. The adsorption arrived at the
equilibrium within 100 min, and PSO model described the kinetic data well. The mixed solution of 0.01
mol/L NaOH and 75% ethanol can desorb and the polymers exhibited excellent regeneration and reuse
performance. 2.3 Factors affecting the adsorption of aromatic acids by
resins Figure 7 (d) investigated the adsorption of the resin for SA in isopropanol, with an adsorption capacity of
132.03 mg/g. Compared with the adsorption of SA on the resin in aqueous solution (193.7 mg/g) in
Fig. 5 (d), the adsorption amount was greatly reduced. This is because in isopropanol, the hydrophobic
interaction between the adsorbate and the resin was inhibited, and the hydrogen bonding was also
inhibited by the influence of alcohol, leading to a decrease in adsorption capacity. In addition, the
Freundlich model was more suitable for describing the isothermal adsorption process (Table S11), Page 8/18 demonstrating that the adsorption process was a multi-molecular layer adsorption. As Fig. 7 (d) and
Table S12 showed, the process of adsorption SA on DMD4 in the isopropanol solution also proved to be
spontaneous and exothermic, which was in accordance with the results in aqueous solution. The detailed adsorption mechanism was illustrated in Fig. 8. It was noted that the polarity of DMD was
much higher than that of DMH, and polarity action (interaction between aromatic acids and amino/amide
of DMD) was capable of strengthening the combination of the resins and polar compounds. The
experiments revealed that the adsorption process of large pore size DMD resin mainly relied on hydrogen
bonding, π - π stacking, acid-base interactions, and hydrophobic interactions for adsorption. On the other
hand, the amino groups uploaded after the amination reaction could promote adsorption through acid-
base interactions and hydrogen bond induction. Therefore, DMD4 can become a promising aromatic acid
adsorption resin through the appropriate adjustment of pore structure and amino loading. Funding The National Natural Science Foundation of China under Grant NO.51974374 and Open Foundation of
National &Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of
Resources under Grant NO. KF201804 were acknowledged for the financial support. The National Natural Science Foundation of China under Grant NO.51974374 and Open Foundation of
National &Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of
Resources under Grant NO. KF201804 were acknowledged for the financial support. The National Natural Science Foundation of China under Grant NO.51974374 and Open Foundation of
National &Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of
Resources under Grant NO. KF201804 were acknowledged for the financial support. Author Contributions Yiqing Wang performed the experiments and wrote the manuscript, Yiqing Wang and Shihua Zhong dealt
with the experimental data and revised the manuscript, Shihua Zhong was the supervisor. Page 9/18 Page 9/18 References 1. Zhang W, Ma F, Ma L, Zhou Y, Wang J (2020) Imidazolium-Functionalized Ionic Hypercrosslinked
Porous Polymers for Efficient Synthesis of Cyclic Carbonates from Simulated Flue Gas. Chemsuschem 13: 341-350 2. Fu Y, Huang X, Zhong S, Yi W, Li L (2019) A new chloromethylation method based on polystyrene-
divinylbenzene. Chemical Papers 73: 2183-2188 3. Peng X, Yang P, Dai K, Chen Y, Chen X, Zhuang W, Ying H, Wu J (2020) Synthesis, adsorption and
molecular simulation study of methylamine-modified hyper-cross-linked resins for efficient removal
of citric acid from aqueous solution. Scientific Reports 10: 9623 3. Peng X, Yang P, Dai K, Chen Y, Chen X, Zhuang W, Ying H, Wu J (2020) Synthesis, adsorption and
molecular simulation study of methylamine-modified hyper-cross-linked resins for efficient removal
of citric acid from aqueous solution. Scientific Reports 10: 9623 4. Rohr T, Knaus S, Gruber H, Sherrington D (2001) Preparation and Porosity Characterization of hyper-
cross-linked Polymer Resins Derived from Multifunctional (Meth)acrylate Monomers. Macromolecules 35: 97-105 5. Zhang W, Hong C, Pan B, Zhang Q, Jiang P, Jia K (2009) Sorption enhancement of 1-naphthol onto a
hydrophilic hyper-cross-linked polymer resin. Journal of Hazardous Materials 163: 53-57 6. Fu Y, Kong Y, Wang Y, Cao Y, Zhong S, Xu M, Lei T, Huang J (2023) Phenolic hydroxyl functionalized
hyper-crosslinked polymers and their efficient adsorption. Separation and Purification Technology
318: 123817 7. Liao H, Fu Y, Hu H, Zhu M, Xu M, Zhong S (2022) Boron Removal from Water and Wastewater using
New Polystyrene-Based Resin Grafted with Trometamol and 3-Amino-1, 2-propanediol. Journal of
The Chemical Society of Pakistan 44: 33-39 7. Liao H, Fu Y, Hu H, Zhu M, Xu M, Zhong S (2022) Boron Removal from Water and Wastewater using
New Polystyrene-Based Resin Grafted with Trometamol and 3-Amino-1, 2-propanediol. Journal of
The Chemical Society of Pakistan 44: 33-39 8. Kuang W, Liu Y, Huang J (2017) Phenol-modified hyper-cross-linked resins with almost all
micro/mesopores and their adsorption to aniline. Journal of Colloid and Interface Science 487: 31-37 8. Kuang W, Liu Y, Huang J (2017) Phenol-modified hyper-cross-linked resins with almost all
micro/mesopores and their adsorption to aniline. Journal of Colloid and Interface Science 487: 31-37 9. Yuan S, Zhang S, Zou W, Zhou Y, Zhou X (2008) Facile synthesis and characterization of novel
pseudo-hypercrosslinked resin. Chinese Chemical Letters 19: 611-614 9. References Yuan S, Zhang S, Zou W, Zhou Y, Zhou X (2008) Facile synthesis and characterization of novel
pseudo-hypercrosslinked resin. Chinese Chemical Letters 19: 611-614 10. Wang X, Fu Z, Yu N, Huang J (2016) A novel polar-modified post-cross-linked resin: Effect of the
porogens on the structure and adsorption performance. Journal of Colloid and Interface Science 466:
322-329 10. Wang X, Fu Z, Yu N, Huang J (2016) A novel polar-modified post-cross-linked resin: Effect of the
porogens on the structure and adsorption performance. Journal of Colloid and Interface Science 466:
322-329 11. Zeng X, Chen H, Zheng Y, Tao W, Fan Y, Huang L, Mei L (2012) Enhanced adsorption of puerarin onto
a novel hydrophilic and polar modified post-crosslinked resin from aqueous solution. Journal of
Colloid and Interface Science 385: 166-173 11. Zeng X, Chen H, Zheng Y, Tao W, Fan Y, Huang L, Mei L (2012) Enhanced adsorption of puerarin onto
a novel hydrophilic and polar modified post-crosslinked resin from aqueous solution. Journal of
Colloid and Interface Science 385: 166-173 Page 10/18
12. Castaldo R, Avolio R, Cocca M, Errico M, Avella M, Gentile G (2021) Amino-functionalized hyper-
crosslinked resins for enhanced adsorption of carbon dioxide and polar dyes. Chemical Engineering Page 10/18
12. Castaldo R, Avolio R, Cocca M, Errico M, Avella M, Gentile G (2021) Amino-functionalized hyper-
crosslinked resins for enhanced adsorption of carbon dioxide and polar dyes. Chemical Engineering Journal 418: 129463 Journal 418: 129463 13. Moradi M, Penchah H, Ghaemi A (2023) CO2 capture by benzene-based hypercrosslinked polymer
adsorbent: Artificial neural network and response surface methodology. The Canadian Journal of
Chemical Engineering 101: 5621-5642 14. You X, Wang Y, Han L, Liu Q, Fei Z, Chen X, Zhang Z, Tang J, Cui M, Qiao X (2023) Reinforced
Rhodamine B adsorption on the hyper-cross-linked resin co-modified by pyridine and carboxyl
groups. Microporous and Mesoporous Materials 349: 112423 15. Sun Y, Zheng W, Singh R, Chen L (2019) Grafting of Poly(4-vinylpyridine) onto a Macroporous Resin
for Sorption of 2-Naphthalenesulfonic Acid in Batch Experiments. Journal of Chemical and
Engineering Data 64: 3170-3178 15. Sun Y, Zheng W, Singh R, Chen L (2019) Grafting of Poly(4-vinylpyridine) onto a Macroporous Resin
for Sorption of 2-Naphthalenesulfonic Acid in Batch Experiments. Journal of Chemical and
Engineering Data 64: 3170-3178 16. Cao Y, Wang Y, Zhou F, Huang J, Xu M (2022) Acylamino-functionalized hyper crosslinked polymers
for efficient adsorption removal of phenol in aqueous solution. Separation and Purification
Technology 303: 122229 17. Ouyang Y, Wu D, Fu R (2013) Graphene oxide-supported two-dimensional microporous polystyrene. MRS Proceedings 1549: 25−29 17. Ouyang Y, Wu D, Fu R (2013) Graphene oxide-supported two-dimensional microporous polystyrene. MRS Proceedings 1549: 25−29 18. Wang Y, Shu Z, Zeng X, Kuang W, Huang J (2020) Fabrication of O-enriched HyperCrossLinked
Polymers and Their Adsorption of Aniline from Aqueous Solution. Industrial & Engineering Chemistry
Research 59: 11705-11712 19. Zhang J, Yuan M, Jia C (2022) Efficient adsorption separation of succinic acid with a novel resin
derived from styrene/methyl acrylate/vinyl acetate terpolymer. Reactive & Functional Polymers175:
105262 19. Zhang J, Yuan M, Jia C (2022) Efficient adsorption separation of succinic acid with a novel resin
derived from styrene/methyl acrylate/vinyl acetate terpolymer. Reactive & Functional Polymers175:
105262 20. Zhou Q, Wang M, Li A, Shuang C, Zhang M, Liu X, Wu L (2013) Preparation of a novel anion
exchange group modified hyper-crosslinked resin for the effective adsorption of both tetracycline and
humic acid. Frontiers of Environmental Science & Engineering 7: 412-419 21. Jalili K, Abbasi F, Ghasemi M, Haddadi E (2009) Preparation and Characterization of Expandable
St/MMA Copolymers Produced by Suspension Polymerization. Journal of Cellular Plastics 45: 197-
224 22. Xiao J, Lu Q, Cong H, Shen Y, Yu B (2021) Microporous poly(glycidyl methacrylate-co-ethylene glycol
dimethyl acrylate) microspheres: synthesis, functionalization and applications. Polymer Chemistry
12: 6050-6070 23. Journal 418: 129463 Mizutani Y, Matsuoka S (1981) Preparation of fine powdery copolymer of styrene—maleic
anhydride–DVB. Journal of Applied Polymer Science 26: 2113-2116 23. Mizutani Y, Matsuoka S (1981) Preparation of fine powdery copolymer of styrene—maleic
anhydride–DVB. Journal of Applied Polymer Science 26: 2113-2116 24. Ogawa N, Honmyo N, Harada K, Sugii A (1984) Preparation of spherical polymer beads of maleic
anhydride–styrene–DVB and metal sorption of its derivatives. Journal of Applied Polymer Science
29: 2851-2856 24. Ogawa N, Honmyo N, Harada K, Sugii A (1984) Preparation of spherical polymer beads of maleic
anhydride–styrene–DVB and metal sorption of its derivatives. Journal of Applied Polymer Science
29: 2851-2856 25. Okay O (1987) Porous maleic anhydride–styrene–DVB copolymer beads. Journal of Applied Polymer
Science 34: 307-317 25. Okay O (1987) Porous maleic anhydride–styrene–DVB copolymer beads. Journal of Applied Polymer
Science 34: 307-317 Page 11/18 26. Fu Y, Cao Y, Wang Y, Li M, Zhong S, Xu M, Lei T, Huang J (2023) Facile synthesis of 2,6-di-tert-
butylphenol modified polystyrene and its antioxidative properties as the heterogeneous antioxidant. Journal of Polymer Research 30: 27 26. Fu Y, Cao Y, Wang Y, Li M, Zhong S, Xu M, Lei T, Huang J (2023) Facile synthesis of 2,6-di-tert-
butylphenol modified polystyrene and its antioxidative properties as the heterogeneous antioxidant. Journal of Polymer Research 30: 27 27. Zhu M, Wang X, Huang Y, Yue L, Zhong S, Zeng L (2022) Synthesis of thiol‐functionalized resin and
its adsorption of heavy metal ions. Journal of Applied Polymer Science 139: e52976 27. Zhu M, Wang X, Huang Y, Yue L, Zhong S, Zeng L (2022) Synthesis of thiol‐functionalized resin and
its adsorption of heavy metal ions. Journal of Applied Polymer Science 139: e52976 28. Fu Y, Duan W, Chen J, Wang Y, Cao Y, Wang B, Zhong S, Xu M, Huang J, Lei T (2023) Synthesis of
sulfhydryl-functionalized polymers for the efficient adsorption of Pd2+ and Ag+ from aqueous
solution. Journal of polymer science 1 28. Fu Y, Duan W, Chen J, Wang Y, Cao Y, Wang B, Zhong S, Xu M, Huang J, Lei T (2023) Synthesis of
sulfhydryl-functionalized polymers for the efficient adsorption of Pd2+ and Ag+ from aqueous
solution. Journal of polymer science 1 29. Langmuir I (1917) The constitution and fundamental properties of solids and liquids. Journal of the
Franklin Institute183: 102-105 29. Langmuir I (1917) The constitution and fundamental properties of solids and liquids. Journal 418: 129463 Journal of the
Franklin Institute183: 102-105 30. Freundlich H (1906) Over the adsorption in solution. The Journal of Physical Chemistry A 57: 385-
470 30. Freundlich H (1906) Over the adsorption in solution. The Journal of Physical Chemistry A 57: 385-
470 31. Lima E, Hosseini-Bandegharaei A, Moreno-Piraján J, Anastopoulos I (2019) A critical review of the
estimation of the thermodynamic parameters on adsorption equilibria. Wrong use of equilibrium
constant in the Van't Hoof equation for calculation of thermodynamic parameters of adsorption. Journal of Molecular Liquids 273: 425−434 31. Lima E, Hosseini-Bandegharaei A, Moreno-Piraján J, Anastopoulos I (2019) A critical review of the
estimation of the thermodynamic parameters on adsorption equilibria. Wrong use of equilibrium
constant in the Van't Hoof equation for calculation of thermodynamic parameters of adsorption. Journal of Molecular Liquids 273: 425−434 32. Meng Z, Lv F, Zhang Y, Zhang Z, Ai S (2015) Modified Na-Montmorillonite With Quaternary
Ammonium Salts: Application for Removal of Salicylic Acid From Aqueous Solutions. CLEAN - Soil,
Air, Water 43: 1150–1156 32. Meng Z, Lv F, Zhang Y, Zhang Z, Ai S (2015) Modified Na-Montmorillonite With Quaternary
Ammonium Salts: Application for Removal of Salicylic Acid From Aqueous Solutions. CLEAN - Soil,
Air, Water 43: 1150–1156 33. Hasan Z, Cho D, Nam I, Chon C, Song H (2016) Hocheol Preparation of Calcined Zirconia-Carbon
Composite from Metal Organic Frameworks and Its Application to Adsorption of Crystal Violet and
Salicylic Acid. Materials 9: 261 33. Hasan Z, Cho D, Nam I, Chon C, Song H (2016) Hocheol Preparation of Calcined Zirconia-Carbon
Composite from Metal Organic Frameworks and Its Application to Adsorption of Crystal Violet and
Salicylic Acid. Materials 9: 261 34. Otero M, Grande C, Rodrigues A (2004) Adsorption of salicylic acid onto polymeric adsorbents and
activated charcoal. Reactive and Fuctional Polymers 60: 203–213 35. Wang X, Yuan X, Han S, Zha H, Sun X, Huang J, Liu Y (2013) Aniline modified hypercrosslinked
polystyrene resins and their adsorption equilibriums, kinetics and dynamics towards salicylic acid
from aqueous solutions. Chemical Engineering Journal 233: 124-131 36. Xiao G, Li H, Xu M (2013) Adsorption of Salicylic Acid in Aqueous Solution by a Water-Compatible
Hyper-Cross-Linked Resin Functionalized with Amino-Group. Journal of Applied Polymer Science
127: 3858-3863 37. Deokar S, Jadhav A, Pathak P, Mandavgane S (2022) Biochar from microwave pyrolysis of banana
peel: characterization and utilization for removal of benzoic and salicylic acid from aqueous
solutions. Scheme 1 Scheme 1 is available in the Supplementary Files section. Scheme 1 is available in the Supplementary Files section. Journal 418: 129463 Biomass Conversion and Biorefinery 37. Deokar S, Jadhav A, Pathak P, Mandavgane S (2022) Biochar from microwave pyrolysis of banana
peel: characterization and utilization for removal of benzoic and salicylic acid from aqueous
solutions. Biomass Conversion and Biorefinery 38. Xiao G, Wen R, Wei D (2016) Effects of the hydrophobicity of adsorbate on the adsorption of salicy
acid and 5-sulfosalicylic acid onto the hydrophobic-hydrophilic macroporous
polydivinylbenzene/polymethylacrylethylenediamine IPN. Fluid Phase Equilibria 421: 33-38 38. Xiao G, Wen R, Wei D (2016) Effects of the hydrophobicity of adsorbate on the adsorption of salicylic
acid and 5-sulfosalicylic acid onto the hydrophobic-hydrophilic macroporous
polydivinylbenzene/polymethylacrylethylenediamine IPN. Fluid Phase Equilibria 421: 33-38 Page 12/18
39. Lagergren S (1898) About the theory of so-called adsorption of soluble substances. Kungliga
Svenska Vetenskapsakademiens Handlingar 24: 1−39 Page 12/18
39. Lagergren S (1898) About the theory of so-called adsorption of soluble substances. Kungliga
Svenska Vetenskapsakademiens Handlingar 24: 1−39 Page 12/18 40. Ho Y (2006) Review of second-order models for adsorption systems[J]. Journal of Hazardous
Materials 136: 681−689 Figures Figure 1
FTIR spectra (a) of DMH4 and DMD4, XPS spectra of DMH4 (b) and DMD4 (c) and survey spectrum of
DMH4 and DMD4 C 1s (d), O 1s (e), N 1s (f) FTIR spectra (a) of DMH4 and DMD4, XPS spectra of DMH4 (b) and DMD4 (c) and survey spectrum of
DMH4 and DMD4 C 1s (d), O 1s (e), N 1s (f) Page 13/18 Page 13/18 Figure 2
N2 adsorption-desorption isotherms for eight resins Page 14/18
Figure 2
N2 adsorption-desorption isotherms for eight resins Figure 2 Figure 2 N2 adsorption-desorption isotherms for eight resins N2 adsorption-desorption isotherms for eight resins Page 14/18 Page 14/18 i
3 Page 15/18
Figure 3
The pore size distribution curves of eight resins
Figure 4
SEM of DMH4 (a-c) and DMD4 (d-f) Figure 3 The pore size distribution curves of eight resins Page 15/18
Figure 4
SEM of DMH4 (a-c) and DMD4 (d-f) Page 15/18
Figure 4
SEM of DMH4 (a-c) and DMD4 (d-f) Figure 4 SEM of DMH4 (a-c) and DMD4 (d-f) SEM of DMH4 (a-c) and DMD4 (d-f) Page 15/18 Figure 5
Adsorption of SA (a), BA (b), and GA (c) from aqueous solution by DMH and DMD resins at 288 K,
Adsorption isotherms of SA (d), BA (e), and GA (f) by DMD4 at different temperatures Figure 5 Figure 5 Adsorption of SA (a), BA (b), and GA (c) from aqueous solution by DMH and DMD resins at 288 K,
Adsorption isotherms of SA (d), BA (e), and GA (f) by DMD4 at different temperatures Page 16/18
Figure 6 Figure 6 Page 16/18 The adsorption kinetics of (a) SA, (b) BA, and (c) GA, PFO and PSO of kinetic curves for (d) SA, (e) BA,
and (f) GA The adsorption kinetics of (a) SA, (b) BA, and (c) GA, PFO and PSO of kinetic curves for (d) SA, (e) BA,
and (f) GA Figure 7
Effect of (a) pH on DMD4 adsorption of aromatic acid, (b) electrolyte and (c) Regenerative properties,
Adsorption isotherms of SA in isopropyl alcohol (d) by DMD4 at different temperatures Figure 8 Possible interaction between the DMD resin and the aromatic acids Figure 7 Effect of (a) pH on DMD4 adsorption of aromatic acid, (b) electrolyte and (c) Regenerative properties,
Adsorption isotherms of SA in isopropyl alcohol (d) by DMD4 at different temperatures Page 17/18 Figure 8 Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. Graphical.docx Highlights.docx Supplementaryinformation.docx scheme1.png Page 18/18 Page 18/18
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English
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Network pharmacology integrated molecular dynamics reveals the bioactive compounds and potential targets of Tinospora crispa Linn. as insulin sensitizer
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PLOS ONE PLOS ONE RESEARCH ARTICLE Editor: Usman Ali Ashfaq, Government College
University Faisalabad, PAKISTAN Editor: Usman Ali Ashfaq, Government College
University Faisalabad, PAKISTAN
Received: May 3, 2021
Accepted: November 4, 2021
Published: June 23, 2022 Editor: Usman Ali Ashfaq, Government College
University Faisalabad, PAKISTAN Editor: Usman Ali Ashfaq, Government College
University Faisalabad, PAKISTAN
Received: May 3, 2021
Accepted: November 4, 2021
Published: June 23, 2022 Received: May 3, 2021
Accepted: November 4, 2021
Published: June 23, 2022 Copyright: © 2022 Zuhri et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. Data Availability Statement: The link to the
requested data in a repository website https://doi. org/10.6084/m9.figshare.19782898. Ummu Mastna Zuhri1☯, Erni Hernawati Purwaningsih2☯, Fadilah FadilahID3,4☯*, Nancy
Dewi Yuliana5☯ Ummu Mastna Zuhri1☯, Erni Hernawati Purwaningsih2☯, Fadilah FadilahID3,4☯*, Nancy
Dewi Yuliana5☯ 1 Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
2 Department of Medical Pharmacy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia,
3 Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia,
4 Bioinformatics Core Facilities, IMERI Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia,
5 Department of Food Science and Technology, Bogor Agricultural University, Bogor, Indonesia a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 ☯These authors contributed equally to this work. * fadilah.msi@ui.ac.id OPEN ACCESS Insulin resistance is a metabolic disorder characterized by the decreased response to insu-
lin in muscle, liver, and adipose cells. This condition remains a complex phenomenon that
involves several genetic defects and environmental stresses. In the present study, we inves-
tigated the mechanism of known phytochemical constituents of Tinospora crispa and its
interaction with insulin-resistant target proteins by using network pharmacology, molecular
docking, and molecular dynamics (MD) simulation. Tinoscorside A, Makisterone C, Borape-
toside A and B, and β sitosterol consider the main phytoconstituents of Tinospora crispa by
its binding with active sites of main protein targets of insulin resistance potential therapy. Moreover, Tinoscorside A was revealed from the docking analysis as the ligand that binds
most strongly to the target protein, PI3K. This finding was strengthened by the results of MD
simulation, which stated that the conformational stability of the ligand-protein complex was
achieved at 15 ns and the formation of hydrogen bonds at the active site. In conclusion,
Tinospora crispa is one of the promising therapeutic agent in type 2 diabetes mellitus man-
agement. Regulation in glucose homeostasis, adipolysis, cell proliferation, and antiapopto-
sis are predicted to be the critical mechanism of Tinospora crispa as an insulin sensitizer. Citation: Zuhri UM, Purwaningsih EH, Fadilah F,
Yuliana ND (2022) Network pharmacology
integrated molecular dynamics reveals the
bioactive compounds and potential targets of
Tinospora crispa Linn. as insulin sensitizer. PLoS
ONE 17(6): e0251837. https://doi.org/10.1371/
journal.pone.0251837 Constructing database of known Tinospora crispa chemical constituents Data of chemical constituents in T. crispa was acquired from former research related to T. crispa constituent identification [4–12]. Database constructing the 2D structure was made in
sdf format were collected from PubChem, ChemSpider (http://www.chemspider.com/), or
drawn using MarvinSketch (https://chemaxon.com/products/marvin) [14]. Each 2D structure
then changed to a 3D structure using MarvinSketch and saved as PDB format [15]. The 2D
structure was needed for druggability analysis in each component, besides the 3D structure for
molecular docking analysis. Its compound’s drugability was predicted by the SwissADME
database (http://www.swissadme.ch/), including its drug-likeness based on Lipinsky rules of
five and its oral bioavailability prediction [16]. Competing interests: The authors have declared
that no competing interests exist. This approach aligns with the paradigm that has begun to change in natural product drug
discovery, the "herbal shotgun", which utilizes the synergy of multi constituents with varied
targets [3]. Research on antidiabetic drugs from Tinospora crispa (T. crispa) are still using the
"silver bullet" approach, which is oriented towards the single active principle with one target. As a result, the information obtained was not comprehensively explaining the activity of T. crispa, yet it was closer to the activity of specific metabolites contained in T. crispa [4–12]. Research on medicinal plants conducted by Wink et al. also supports the herbal shotgun
approach. It was reported that the combination of metabolite compounds in the medicinal
plant had a better effect than the single isolate of metabolite compound [13]. This fact requires
more recent research using the herbal shotgun approach so that the activity of medicinal plants
can be comprehensively reveal [3]. T. crispa as a multi-constituent preparation has not known its action mechanism in insulin
sensitization activity. It needs to be explored more extensively using a comprehensive approach
in silico prediction such as network pharmacology analysis. The current development of bioin-
formatics technology allows researchers to simultaneously predict the action mechanism of
medicinal plant constituents as a multicomponent therapeutic activity. This study aims to find a
significant therapeutic target in the pathogenesis of insulin resistance targeted by the active
compound of T. crispa. The known therapeutic target of compounds contained in T. crispa was
analyzed using network pharmacology to determine its potential activity as an insulin sensitizer. The most significant protein targets then verified its binding with T. crispa constituents by
molecular docking and molecular dynamics to verify its interactions (Fig 1). decision to publish, or preparation of the
manuscript.
Competing interests: The authors have declared
that no competing interests exist. decision to publish, or preparation of the
manuscript. to develop a potent drug in diabetes management [1]. Furthermore, drug monotherapy is chal-
lenging to provide the desired effect in controlling blood glucose levels in type 2 diabetes
patients. Combination therapy which has different mechanisms, is needed for maintaining the
requirement of therapeutic management. However, this strategy meets some disadvantages
regarding the increasing of drug side effects, toxicity, and interactions. Another alternative is
the search for a drug molecule that selectively modulates different targets and improving the
balance of efficacy and safety compared to single target agents [2]. Competing interests: The authors have declared
that no competing interests exist. Introduction Funding: This study was funded by Universitas
Indonesia research grants for doctoral students
through PUTI Grant with contract number NKB585/
UN2.RST/HKP05.00/2020 with Ummu Mastna
Zuhri as grant recipients. The funders had no role
in study design, data collection and analysis, Insulin resistance is a metabolic disorder characterized by the decreased response to insulin in
muscle, liver, and adipose cells. The normal insulin levels are unable to control glucose, lipids,
and energy homeostasis. This condition remains a complex phenomenon that involves several
genetic defects and environmental stresses, such as obesity. A complete understanding is
required to understand the entire itinerary and functional consequences of insulin resistance 1 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Constructing a database of protein target involved in insulin resistance Target proteins related to insulin resistance were retrieved from DisGeNET, UniProt, OMIM,
TTD, KEGG, and DrugBank database [17–21]. Data retrieval from DisGeNET were done with
the keyword "Insulin resistance" (CUI: C0021655) in the diseases search engine column. The
retrieved data was a summary of gene-disease associations that have been downloaded in xlsx
format (80 genes). Data retrieval from UniProt was done using the human disease option in
supporting data and input keyword "Diabetes mellitus, non-insulin-dependent" (DI-02060). 2 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Fig 1. General workflow of present work using network pharmacology and molecular docking analysis. https://doi.org/10.1371/journal.pone.0251837.g001 Fig 1. General workflow of present work using network pharmacology and molecular docking analysis. https://doi.org/10.1371/journal.pone.0251837.g001 Data were downloaded in tab file format (23 genes). Data from both data sources were merg-
ing in Cytoscape 3.7.2 software (https://cytoscape.org/) using UniProt ID as their identity to
eliminate double listed proteins [18, 22]. Data were downloaded in tab file format (23 genes). Data from both data sources were merg-
ing in Cytoscape 3.7.2 software (https://cytoscape.org/) using UniProt ID as their identity to
eliminate double listed proteins [18, 22]. Constructing target proteins of Tinospora crispa phytochemical
constituents The simplified molecular-input line-entry specification (SMILES) information of 56 TC constitu-
ents was submitted in SWISS Target Prediction (http://www.swisstargetprediction.ch/) Pharm-
Mapper to obtain its target prediction. Only human (Homo sapiens) target protein was set in the
data retrieval [23, 24]. Protein ID was aligned using UniProt ID to synchronize protein ID and
eliminate double listed protein [18]. The aligned target proteins ID were arranged in excel format
to be imported to Cytoscape 3.7.2, be visualized, and analyzed its degree of connectivity [22]. Prediction of significance target protein related insulin resistant Protein-protein interaction (PPI) was generated by submitting all UniProt IDs of the proteins
constructed from the previous step into the STRING database (https://string-db.org/) using 3 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer multiple proteins option [25]. Homo sapiens was set as the only organism, and the interaction
score confidence was set at the highest confidence (0.900). PPI data is then downloaded in tsv
format. Furthermore, the PPI network was analyzed using Cytoscape 3.7.2 software to discover
the rank of significance protein based on the degree of connectivity score [22]. Molecular docking Molecular docking was generated using AutoDock Vina (Molecular Graphics Laboratory, The
Scripps Research Institute) for initial screening of all T. crispa constituents followed by Auto-
Dock Tools 1.5.6 only for the top 3 constituents with the lowest binding energy [15, 27]. The
ligands were set as rigid structures with an active site was set visually at the centre of the cavity
docked by native ligand from each protein model. The grid box was adjusted at 40 x 40 x 40
Angstrom in x, y, and z-axis, respectively. Molecular docking was run in the Lamarckian
Genetic Algorithm after validation. Redocking the native ligand with its protein in specific
parameters with an RMSD value less than 2 Amstrong remains a valid docking parameter
[28]. The results were shown in the value of its lowest binding energy (kcal/mol) calculated by
total intermolecular energies, including hydrogen bonds energy, Van der Walls energy, deso-
lvation energy, and electrostatic energy. The more negative energy was, the better ligand-pro-
tein binding [29]. The result of ligan-protein complexes was visualized using PyMOL (https://
pymol.org/2/). The docking results were analyzed in LigPlot+ to evaluate the accurate binding
interaction between ligands and proteins [30]. Prediction of Tinospora crispa phytoconstituents target genes and their
intersection on insulin resistant related target All the phytochemical T. crispa compounds were predicted its target by SwissTargetPrediction
and PharmMapper [23, 24]. To comprehensively understand its molecular mechanism, all
compound-target data were visualized by Cytoscape 3.7.2 to reveal the interaction network
between compound-target. Furthermore, the network then merged with the PPI network to
discover a new network, a compound-target network of T. crispa targeted to insulin resistance. Ligand and protein preparation for in silico molecular docking Molecular docking was conducted towards the significant proteins in insulin resistance patho-
genesis and was targeted by constituents of T. crispa at once. Target proteins that meet the crite-
ria were PIK3R1, PTPN1, PPARG, INSR, EGFR, TNF, and AKT2. The 3D structure of T. crispa
constituents act as ligands (file type.pdb) were opened using AutoDock Tools 1.5.6. software
(Molecular Graphics Laboratory, The Scripps Research Institute) [15]. Water molecules were
removed, and chain contained active site was chosen. The chosen structure is then extracted
from its native ligand. The 3D crystal structures of target proteins were selected from Protein
Data Bank (PDB) (http://www.rcsb.org/pdb/) [26]. Protein structures with PDB accession num-
ber 3S2A were used for PIK3R1 target, 1LQF for PTPN1 target, 6O67 for PPARG target, 5E1S
for INSR, 6D8E for EGFR target, 5MU8 for TNF target, and 5D0E for AKT2 target. All protein
models were prepared by the addition of polar hydrogen and the addition of Gasteiger charges. Ligands were prepared with a torsion value less than 32. Both ligands and protein models were
saved as a pdbqt file. Preparation steps were done using AutoDock Tools 1.5.6 software. Protein-protein interaction networks related to insulin resistance 267 targets were documented to have relation to insulin resistance pathogenesis. All targets
were identified its interaction using STRING database [25]. Those interactions construct a PPI
network which is then assessed by Cytoscape 3.7.2 software for the degree of connectivity
value. The analysis results were displayed in Fig 2 in white to green gradation. The higher the
degree of a node (gene) in the network is marked with a darker green colour. The higher the
degree value indicates that the protein has a more significant role in the pathogenesis of insulin
resistance. The top degree ranks were INS, LEP, PI3K, PTPN1, IRS1, PPARG, IGF1, INSR,
CAV1, EGFR, IRS2, TNF, and AKT2, respectively. The degree rating of the entire PPI network
is shown in Fig 2. The exact degree value was shown in S1 Table. Database of Tinospora crispa phytoconstituents A total of 56 compounds were found in the literature related to T.crispa. 2D and 3D structures
of all compounds were collected from PubChem, ChemSpider, or drawn using Marvin Sketch
[14]. Its compounds druggability were predicted using SwissADME, including its drug-like-
ness based on Lipinsky rules of five and its oral bioavailability prediction (Table 1) [16]. The
molecular weight range from 135.13 to 714.71, with Adenine as the lightest molecule and Bora-
petoside H as the heaviest molecule. Predicted gastrointestinal absorption showed 34 of 56
compounds classified as highly absorbed in the GI tract. Drug likeness was assessed through
the Lipinski Rules of Five, with 37 compounds meet the five criteria required by Lipinski,
while 19 other compounds have violations of Lipinski’s rules of 1–3 violations. SWISS target prediction and DisGeNET identified that 56 constituents of T. crispa were
documented to have 5666 protein-specific targets [17, 23]. Those 5666 target proteins were
then analyzed by Cytoscape 3.7.2 to find out its intersection with insulin-resistant target pro-
tein [22]. Molecular dynamics simulation Molecular dynamics simulation was carried out using GROMACS (Groningen Machine for
Chemical Simulation) software package [31]. Previously docked complex ligand-protein was PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 4 / 15 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer subjected to 24 ns dynamic simulations in explicit water model using CHARMM36 for the
protein and CGenFF force field for the ligand [32, 33]. TIP3P model was used to represent sol-
vation on water molecules using a periodic cubic box with 1.0 nm minimum distance from
any atom in the protein to the walls of the cubic box [34]. The whole system was neutralized to
pH 7 by adding counter ions, followed by energy minimization, heating and equilibration by
running 100 ps of NVT (isothermal-isochoric) and NPT (isothermal-isobaric) ensemble. The
production step was carried out at 300K and around 1 atmospheric pressure for 24 ns with a
time step of 2 fs. Hydrogen bonds, root mean square deviation (RMSD) of protein (backbone
and side chains), as well as root mean square fluctuation (RMSF) of amino acid residues were
used to evaluate the ligand-protein interaction. The RMSD and RMSF were plotted using
GRACE v5.1.25. Interaction of lead compounds of Tinospora crispa on insulin resistant
related target proteins We conducted the molecular docking strategy to prove the underlying interactions between T. crispa predicted active phytoconstituents to insulin resistance. Molecular docking was con-
ducted on seven target proteins that meet the criteria of high connectivity value, targeted by T. crispa constituents and was involved in insulin resistance pathogenesis. Those targets were
PIK3R, PTPN1, PPARG, INSR, EGFR, TNF, and AKT2. The best docking interaction was
PI3K with Tinoscorside A as a ligand (binding energy -11.64), as shown in Table 2. Its binding 5 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer PLOS ONE Table 1. (Continued)
Molecule
Formula
MW (Dalton)
GI abs
Lipinski
Higenamine
C16H17NO3
271.31
High
0
Genkwanin
C16H12O5
284.26
High
0
Cycloeucalenol
C30H50O
426.72
Low
1
Columbamine
C20H20NO4
338.38
High
0
Borapetoside H
C33H46O17
714.71
Low
3
Borapetoside G
C26H32O12
536.53
Low
2
Apigenin
C15H10O5
270.24
High
0
Adenosine
C10H13N5O4
267.24
Low
0
Adenine
C5H5N5
135.13
High
0
https://doi.org/10.1371/journal.pone.0251837.t001 sketch map was shown in Fig 3 as well. The detailed docking scores of T. crispa targeted to 7
significance proteins were shown in S3 Table, and the docking sketch maps were shown in S1
Fig. The structures of the main constituents of T. crispa were shown in Fig 4. Molecular dynamics simulation
l
f
h
l
d
b l
d
l fl
b l
b
h d
k d
Table 1. (Continued)
Molecule
Formula
MW (Dalton)
GI abs
Lipinski
Higenamine
C16H17NO3
271.31
High
0
Genkwanin
C16H12O5
284.26
High
0
Cycloeucalenol
C30H50O
426.72
Low
1
Columbamine
C20H20NO4
338.38
High
0
Borapetoside H
C33H46O17
714.71
Low
3
Borapetoside G
C26H32O12
536.53
Low
2
Apigenin
C15H10O5
270.24
High
0
Adenosine
C10H13N5O4
267.24
Low
0
Adenine
C5H5N5
135.13
High
0
https://doi.org/10.1371/journal.pone.0251837.t001 sketch map was shown in Fig 3 as well. The detailed docking scores of T. crispa targeted to 7
significance proteins were shown in S3 Table, and the docking sketch maps were shown in S1
Fig. The structures of the main constituents of T. crispa were shown in Fig 4. sketch map was shown in Fig 3 as well. The detailed docking scores of T. crispa targeted to 7
significance proteins were shown in S3 Table, and the docking sketch maps were shown in S1
Fig. The structures of the main constituents of T. crispa were shown in Fig 4. sketch map was shown in Fig 3 as well. The detailed docking scores of T. crispa targeted to 7
significance proteins were shown in S3 Table, and the docking sketch maps were shown in S1
Fig. The structures of the main constituents of T. crispa were shown in Fig 4. PLOS ONE Table 1. Prediction of Tinospora crispa know phytoconstituents and its druggability [16]. Molecule
Formula
MW (Dalton)
GI abs
Lipinski
(-)-Secoisolariciresinol
C20H26O6
362.42
High
0
N-Acetylnornuciferine
C20H21NO3
323.39
High
0
N-cis-Feruloyltyramine
C18H19NO4
313.35
High
0
N-Formylanonaine
C18H15NO3
293.32
High
0
N-trans-Feruloyltyramine
C18H19NO4
313.35
High
0
Tembetarine
C20H26NO4
344.42
High
0
Tinoscorside A
C30H37NO13
619.61
Low
3
(-)-Litcubinine
C18H20NO4
314.36
High
0
Borapetol A
C20H24O7
376.4
High
0
Borapetol B
C21H26O7
390.43
High
0
Borapetoside A
C26H34O12
538.54
Low
2
Borapetoside B
C27H36O12
552.57
Low
2
Borapetoside C
C27H36O11
536.57
Low
2
Borapetoside D
C33H46O16
698.71
Low
3
Borapetoside E
C27H36O11
536.57
Low
2
Borapetoside F
C27H34O11
534.55
Low
2
Cycloeucalenone
C30H48O
424.7
Low
1
Dihydrodiscretamin
C19H18NO4
324.35
High
0
Luteolin 4’-methyl ether 7-glucoside
C22H22O11
462.4
Low
2
Makisterone C
C29H48O7
508.69
Low
2
N-acetylanonaine
C19H17NO3
307.34
High
0
N-acetylanornuciferine
C20H21NO3
323.39
High
0
N-formylanonaine
C18H15NO3
293.32
High
0
N-formylasimilobine 2-O-β-D-glucopyranoside
C24H29NO7
443.49
High
0
N-trans-caffeoyltyramine
C17H17NO4
299.32
High
0
Paprazine
C17H17NO3
283.32
High
0
Rumphioside A
C27H36O13
568.57
Low
2
Rumphioside B
C28H38O13
582.59
Low
2
(-)-Litcubinine
C18H29NO4
340.56
High
0
Berberine
C20H29NO4
347.45
High
0
Beta sitosterol
C29H50O
414.71
Low
1
Uridine
C9H12N2O6
244.2
Low
0
Tyramine
C8H11NO
137.18
High
0
Tinocrispol A
C21H24O7
388.41
High
0
Syringin
C17H24O9
372.37
Low
0
Syringaresinol
C22H26O8
418.44
High
0
Stigmasterol
C29H48O
412.69
Low
1
Secoisolariciresinol
C20H26O6
362.42
High
0
Salsolinol
C10H13NO2
179.22
High
0
Palmatine
C21H22NO4
352.4
High
0
Rumphiol E
C20H24O6
360.4
High
0
N-demethyl-N-formyldehydronornuciferine
C19H17NO3
307.34
High
0
Magnoflorine
C20H24NO4
342.41
High
0
Lysicamine
C18H13NO3
291.3
High
0
Luteolin 4’-methyl ether 7-glucoside
C22H22O11
462.4
Low
2
Luteolin 4’-methyl ether 3’-glucoside
C22H22O11
462.4
Low
2
Jatrorrhizine
C20H20NO4
338.38
High
0 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 6 / 15 Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 https://doi.org/10.1371/journal.pone.0251837.g002 Molecular dynamics simulation The maximum RMSF of the C alpha atom
is 2.5–3.0 nm, except the initial C alpha residue, which reaches 3.5 nm. Hydrogen bonds
between protein and ligand were ranged from 1–7 bonds in each frame (Fig 5C). There were
20 hydrogen bonds formed between protein-ligand during the MD simulation. The amino
acid residues involved in forming hydrogen bonds are Ala805, Ser806, Lys833, Asp841,
Tyr867, Glu880, Val882, Thr887, Asp964, and Lys890. The representation of the complex after
24 ns MD simulation was performed in Fig 5D. Molecular dynamics simulation To clarify the protein-ligand stability and protein structural flexibility between the docked
complex of PI3K and Tinoscorside, we performed a 24 ns MD simulation using GROMACS Fig 2. PPI network of protein related insulin resistance in Homo sapiens. The darker purple color and the bigger its nodes indicate
higher degree of protein in the network. htt
//d i
/10 1371/j
l
0251837 002 Fig 2. PPI network of protein related insulin resistance in Homo sapiens. The darker purple color and the bigger its nodes indicate
higher degree of protein in the network. https://doi.org/10.1371/journal.pone.0251837.g002 7 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Table 2. Docking scores of the lowest ligand-protein binding energy of T. crispa constituents and significant pro-
teins in insulin resistance. Target protein
Compound
Ki (nM)
The lowest binding energy (kcal/mol)
PI3K
Tinoscorside A
2.94
-11.64
INSR
Tinoscorside A
4.19
-11.43
AKT2
Makisterone C
5.17
-11.3
PPARG
Borapetoside A
51.96
-9.94
EGFR
Tinoscorside A
191.99
-9.16
PTPN1
Beta sitosterol
453.59
-8.65
TNF
Borapetoside B
1.62x103
-7.90
https://doi.org/10.1371/journal.pone.0251837.t002 Table 2. Docking scores of the lowest ligand-protein binding energy of T. crispa constituents and significant pro-
teins in insulin resistance. software. Protein and ligand root-mean-square deviation (RMSD) information of C alpha and
side chains of the complex are presented in Fig 5A. The root-mean-square fluctuation (RMSF)
of amino acid residues are presented in Fig 5B. RMSD calculation shows that the complex has
nearly constant RMSD since 15 ns MD production. The maximum RMSF of the C alpha atom
is 2.5–3.0 nm, except the initial C alpha residue, which reaches 3.5 nm. Hydrogen bonds
between protein and ligand were ranged from 1–7 bonds in each frame (Fig 5C). There were
20 hydrogen bonds formed between protein-ligand during the MD simulation. The amino
acid residues involved in forming hydrogen bonds are Ala805, Ser806, Lys833, Asp841,
Tyr867, Glu880, Val882, Thr887, Asp964, and Lys890. The representation of the complex after
24 ns MD simulation was performed in Fig 5D. software. Protein and ligand root-mean-square deviation (RMSD) information of C alpha and
side chains of the complex are presented in Fig 5A. The root-mean-square fluctuation (RMSF)
of amino acid residues are presented in Fig 5B. RMSD calculation shows that the complex has
nearly constant RMSD since 15 ns MD production. PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 Compound-target network To further discover the potential target and therapeutic pathway of T. crispa constituents in
ameliorating insulin resistance, the targets of insulin resistance were merged with the target of
T. crispa (Fig 6A). The compound-target network of T. crispa against insulin resistance was
shown in Fig 6C. After the network merging using Cytoscape 3.7.2, 30 T. crispa constituents
were reserved as the main active constituents in T. crispa treating insulin resistance. In addi-
tion, 22 targets were reserved as the main targets of TC in treating insulin resistance. Fig 3. Docking sketch map of Tinoscorside A interaction with the crystal structure of PI3K. (A) Pocket view of Tinoscorside A
binding with PI3K active site. (B) 2D docking pattern of Tinoscorside A with amino acids hydrogen bonds LYS833 and ASP964. Fig 3. Docking sketch map of Tinoscorside A interaction with the crystal structure of PI3K. (A) Pocket view of Tinoscorside A
binding with PI3K active site. (B) 2D docking pattern of Tinoscorside A with amino acids hydrogen bonds LYS833 and ASP964. g sketch map of Tinoscorside A interaction with the crystal structure of PI3K. (A) Pocket view of Tinoscorside A
I3K active site. (B) 2D docking pattern of Tinoscorside A with amino acids hydrogen bonds LYS833 and ASP964. https://doi.org/10.1371/journal.pone.0251837.g003 8 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Fig 4. Structure of active constituents prediction of T. crispa as insulin sensitizer. (A) Tinoscorside A (B) Makisterone C (C)
Borapetoside A (D) β Sitosterol (E) Borapetoside B. All structures were drawn using MarvinSketch based on the previous studies [6]. https //doi org/10 1371/journal pone 0251837 g004 Structure of active constituents prediction of T. crispa as insulin sensitizer. (A) Tinoscorside A (B) Makisterone C (C)
toside A (D) β Sitosterol (E) Borapetoside B. All structures were drawn using MarvinSketch based on the previous studies [6]. Fig 4. Structure of active constituents prediction of T. crispa as insulin sensitizer. (A) Tinoscorside A (B) Makisterone C (C)
Borapetoside A (D) β Sitosterol (E) Borapetoside B. All structures were drawn using MarvinSketch based on the previous studies [6]. https://doi.org/10.1371/journal.pone.0251837.g004 https://doi.org/10.1371/journal.pone.0251837.g004 https://doi.org/10.1371/journal.pone.0251837.g004 Fig 5. Molecular dynamics (MD) simulation analysis of Tinoscorside A with PI3K. (A) root-mean square deviation
(RMSD) of the complex against the initial crystal structure. PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 Discussion The present study tried to collect and investigate clues from the known phytoconstituents of T. crispa in ameliorating insulin resistance. Investigations were conducted using in silico
approaches, including network pharmacology, molecular docking, and molecular dynamics
simulation. We elucidated the potential therapeutic network of insulin resistance and inter-
sected this network with the T. crispa phytoconstituents potential target network. Both of the
networks were complicated networks with 5666 and 267 nodes. The intersection showed us
only the protein-related insulin resistance targeted by T. crispa constituents. From 267 targets,
there were only 22 target proteins that were targeted by T. crispa constituents. KEGG pathways analysis had indicated several signalling pathways, including insulin sig-
nalling, PI3K-Akt signalling, MAPK signalling, and TNF signalling pathway, that play vital
roles in the therapeutic mechanism of T. crispa as insulin sensitizer. Those signalling pathways
had close relative to glucose-lowering activity through the regulation of glucose homeostasis,
adipolysis, cell proliferation, and antiapoptosis. This showed that T. crispa, with its various sec-
ondary metabolites, had acted as an insulin sensitizer through different pathways (Fig 7). This
finding supports Wink et al. statement that the activity of a medicinal plant was due to syner-
gistic interactions of several phytoconstituents [13]. The network pharmacology approach pro-
vides an insight into prediction in the mode of action of a medicinal plant comprehensively
with multiple target therapies [35]. Network pharmacology analysis also informed that the
main phytoconstituents of T. cripa as insulin sensitizer were Tinoscorside A, Makisterone C,
Borapetoside A, Beta-sitosterol, and Borapetoside B. Based on former studies, Borapetoside A-C, and E may be the key of T. crispa constituents
as hypoglycaemic agents [7, 11, 12, 36, 37]. Lam et al reported, the isolated Borapetoside A and
C had significantly reduced plasma glucose levels but unable to increase insulin secretion in
MIN6 pancreatic beta cells [36]. It indicated that they had other mechanisms of hypoglycemic
activity. This study predicts the mechanism of action of Borapetoside A through activation of
PPARG and Borapetoside B through inhibition of TNF cytokines to bind to their receptor. Contrary to previous studies that indicated diterpenoids as active constituents, this study
presents Tinoscorside A (N-formylasimilobine 2-O-β-D-glucopyranosyl-(1!2)-β- D-gluco-
pyranoside) as a constituent of T. crispa which has the strongest docking binding with some
protein targets including PI3K, INSR, and EGFR respectively. Compound-target network The The blue graph represent RMSD of C alpha and the
turquoise one represent RMSD of the side-chain; (B) root-mean square fluctuation (RMSF) of the C alpha residue; (C)
The dynamics of hydrogen bond number along MD simulation; (D) the representative of the Tinoscorside A-PI3K
complex after 24 ns MD simulation. Fig 5. Molecular dynamics (MD) simulation analysis of Tinoscorside A with PI3K. (A) root-mean square deviation
(RMSD) of the complex against the initial crystal structure. The The blue graph represent RMSD of C alpha and the
turquoise one represent RMSD of the side-chain; (B) root-mean square fluctuation (RMSF) of the C alpha residue; (C)
The dynamics of hydrogen bond number along MD simulation; (D) the representative of the Tinoscorside A-PI3K
complex after 24 ns MD simulation. https://doi.org/10.1371/journal.pone.0251837.g005 9 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as ins
doi.org/10.1371/journal.pone.0251837
June 23, 2022 10 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Fig 6. (A) Intersection Venn diagram of T. crispa constituents and target protein related insulin resistance. There
were 30 constituents of T. crispa that were predicted to be targeted to insulin resistance target protein. (B) Intersection
Venn diagram between predicted target protein of T. crispa constituents, target proteins of insulin resistance
pathogenesis, and high degree of connection value of target proteins of insulin resistance. There were 7 target proteins
that meet the three intersections. In addition there were 22 proteins targeted by T. crispa constituents that were shown
visually in Fig 6C. (C) Compound-target network of T. crispa constituents targeted to insulin resistance pathogenesis. The blue dots represent T. crispa constituents, the yellow dots represent protein targets, and the connecting lines
represent compound-target interaction. https://doi.org/10.1371/journal.pone.0251837.g006 Moreover, 7 targets were revealed to have significant protein in insulin resistance pathogenesis
and also targeted by T. crispa constituents (Fig 6B). The complete T. crispa constituents and
their targets were shown in S2 Table. Moreover, 7 targets were revealed to have significant protein in insulin resistance pathogenesis
and also targeted by T. crispa constituents (Fig 6B). The complete T. crispa constituents and
their targets were shown in S2 Table. PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 Discussion Tinoscorsida A was a member
of aporphine alkaloid which has never been proven as part of active compounds of T. crispa in
reducing blood sugar level. This finding indicated that Tinoscorside A could be a potential glu-
cose lowering agent through multiple ways. The molecular dynamics analysis from the PI3K and Tinoscorside A as the ligand-protein
complex with the highest affinity, shows a stable conformation in water solvation under 300 K PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 11 / 15 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer Fig 7. Systematic prediction of 7 significant protein targets and therapeutic pathways of T. crispa constituents on insulin resistant. The highlighted nodes represent the significant targets of T. crispa and other nodes represent their related target on insulin resistant. All
the presented pathways were summarized by KEGG pathway database [21]. https://doi.org/10.1371/journal.pone.0251837.g007 Fig 7. Systematic prediction of 7 significant protein targets and therapeutic pathways of T. crispa constituents on insulin resistant. The highlighted nodes represent the significant targets of T. crispa and other nodes represent their related target on insulin resistant. All
the presented pathways were summarized by KEGG pathway database [21]. https://doi.org/10.1371/journal.pone.0251837.g007 https://doi.org/10.1371/journal.pone.0251837.g007 https://doi.org/10.1371/journal.pone.0251837.g007 temperature and 1 atmospheric pressure. It is in line with the docking analysis result. The for-
mation of 20 hydrogen bonds during the MD simulation indicates that the interaction has a
high affinity. Two of these bonds are hydrogen bonds reported in molecular docking. Both
bonds involve the amino acids Lys833 and Asp964. These two amino acids are active sites that
also interact with native ligands in the crystallographic structure of proteins. In addition to
these two residues, eight other amino acids are reported to be involved in the formation of
hydrogen bonds. Two of them are also included in active sites that interact with native ligands,
namely Tyr867 and Val882. In addition, this study also predicted that T. crispa had anti-
inflammatory activity through the TNF signalling pathway by inhibiting the binding between
TNFA and TNFR. S3 Table. Molecular docking result of T. crispa phytoconstituents to 7 selected target pro-
teins using AutoDock.
(DOCX) S3 Table. Molecular docking result of T. crispa phytoconstituents to 7 selected target pro-
teins using AutoDock. (DOCX) Conclusion The present study highlights the insulin-sensitizing role of T. crispa on insulin resistance path-
ogenesis by network pharmacology and molecular docking study. The role of T. crispa phyto-
constituents that served as plant extract with multiple constituents remains still undescribed. Our study provides valuable clues to reveal the prediction of their possible targets and mecha-
nistic pathways of T. crispa. The present study highlights the insulin-sensitizing role of T. crispa on insulin resistance pathogenesis by network pharmacology and molecular docking
study. The role of T. crispa phytoconstituents that served as plant extract with multiple constit-
uents remains still undescribed. Our study provides valuable clues to reveal the prediction of
their possible targets and mechanistic pathways of T. crispa. The result was shown that T. 12 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer crispa was a promising plant-based drug to be developed as an insulin sensitizer through mul-
tiple pathways, including glucose homeostasis, adipolysis, cell proliferation, and antiapoptosis. However, there are several limitations in the current study, including the limitation of the T. crispa phytoconstituents database that could be more phytoconstituents were not revealed yet
and the limitation of the database that serves the activity of the constituents as a single com-
pound neglecting the interaction of the multi-compound itself. Further study on the insulin-
sensitizing role of T. crispa and the underlying mechanism are still urgently to be investigated
in other methods such as in vitro, in vivo, and clinical study evaluation to verify this in silico
study. Data curation: Ummu Mastna Zuhri. Formal analysis: Ummu Mastna Zuhri, Fadilah Fadilah. Formal analysis: Ummu Mastna Zuhri, Fadilah Fadilah. Funding acquisition: Ummu Mastna Zuhri. Funding acquisition: Ummu Mastna Zuhri. Investigation: Ummu Mastna Zuhri, Erni Hernawati Purwaningsih. Methodology: Ummu Mastna Zuhri, Fadilah Fadilah. Methodology: Ummu Mastna Zuhri, Fadilah Fadilah. Software: Fadilah Fadilah. Supervision: Erni Hernawati Purwaningsih, Nancy Dewi Yuliana. Validation: Ummu Mastna Zuhri, Fadilah Fadilah. Visualization: Ummu Mastna Zuhri. Writing – original draft: Ummu Mastna Zuhri, Fadilah Fadilah. Writing – review & editing: Ummu Mastna Zuhri. Supporting information S1 Fig. Docking sketch map of best ligand-binding position of T.crispa phytoconstituents
and 7 selected target proteins in insulin resistance. (DOCX)
S1 Table. Degree ranking of insulin resistant related targets analyzed by Cytoscape 3.7.2. (DOCX)
S2 Table. 30 T. crispa phytoconstituents and its target proteins [17, 18, 24]. (DOCX)
S3 Table. Molecular docking result of T. crispa phytoconstituents to 7 selected target pro-
teins using AutoDock. (DOCX) S1 Fig. Docking sketch map of best ligand-binding position of T.crispa phytoconstituents
and 7 selected target proteins in insulin resistance. (DOCX) S1 Fig. Docking sketch map of best ligand-binding position of T.crispa phytoconstituents
and 7 selected target proteins in insulin resistance. (DOCX) S1 Table. Degree ranking of insulin resistant related targets analyzed by Cytoscape 3.7.2.
(DOCX) S1 Table. Degree ranking of insulin resistant related targets analyzed by Cytoscape 3.7.2. (DOCX) S2 Table. 30 T. crispa phytoconstituents and its target proteins [17, 18, 24]. (DOCX) Author Contributions Conceptualization: Ummu Mastna Zuhri, Erni Hernawati Purwaningsih, Nancy Dewi
Yuliana. Data curation: Ummu Mastna Zuhri. References 1. Pessin JE, Saltiel AR. Signaling pathways in insulin action: Molecular targets of insulin resistance. Vol. 106, Journal of Clinical Investigation. The American Society for Clinical Investigation; 2000. p. 165–9. 2. Artasensi A, Pedretti A, Vistoli G, Fumagalli L. Type 2 diabetes mellitus: A review of multi-target drugs. Molecules. 2020; 25(8):1–20. https://doi.org/10.3390/molecules25081987 PMID: 32340373 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 13 / 15 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer 3. Ulrich-Merzenich G, Zeitler H, Jobst D, Panek D, Vetter H, Wagner H. Application of the “-Omic-” tech-
nologies in phytomedicine. Phytomedicine. 2007; 14(1):70–82. https://doi.org/10.1016/j.phymed.2006. 11.011 PMID: 17188482 4. Fukuda N, Yonemitsu M KT. Isolation and structure elucidation of the five new furanoid diterpene glyco-
sides borapetoside C–G. Liebigs Ann der Chemie. 1993; 1993(5):491–5. 5. Lokman EF. The possible mechanisms by which borapetol B stimulates insulin release from rat islets. Int J Med Med Sci. 2014; 47(1):1461–8. 6. Ahmad W, Jantan I, Bukhari SNA. Tinospora crispa (L.) Hook. f. & Thomson: A review of its ethnobotan-
ical, phytochemical, and pharmacological aspects. Front Pharmacol. 2016; 7(MAR):1–19. 7. Ruan CT, Lam SH, Chi TC, Lee SS, Su MJ. Borapetoside C from Tinospora crispa improves insulin sen-
sitivity in diabetic mice. Phytomedicine. 2012; 19(8–9):719–24. https://doi.org/10.1016/j.phymed.2012. 03.009 PMID: 22579212 8. Thomas A, Rajesh EK, Kumar DS. The significance of Tinospora crispa in treatment of diabetes melli-
tus. Phyther Res. 2016; 30(3):357–66. https://doi.org/10.1002/ptr.5559 PMID: 26749336 9. Cachet X, Langrand J, Riffault-Valois L, Bouzidi C, Colas C, Dugay A, et al. Clerodane furanoditerpe-
noids as the probable cause of toxic hepatitis induced by Tinospora crispa. Sci Rep. 2018; 8(1):1–11. 10. Fukuda N, Yonemitsu M, Kimura T. Studies on the Constituents of the Stems of Tinospora tuberculata
BEUMEE. III. New Diterpenoids, Borapetoside B and Borapetol B. Chem Pharm Bull. 1986; 34
(7):2868–72. 11. Xu Y, Niu Y, Gao Y, Wang F, Qin W, Lu Y, et al. Borapetoside E, a clerodane diterpenoid extracted from
Tinospora crispa, improves hyperglycemia and hyperlipidemia in high-fat-diet-induced type 2 diabetes
mice. J Nat Prod. 2017; 80(8):2319–27. https://doi.org/10.1021/acs.jnatprod.7b00365 PMID: 28742368 12. Ruan CT, Lam SH, Lee SS, Su MJ. Hypoglycemic action of borapetoside A from the plant Tinospora
crispa in mice. Phytomedicine. 2013; 20:667–75. https://doi.org/10.1016/j.phymed.2013.02.009 PMID:
23523259 13. Wink M. Modes of Action of Herbal Medicines and Plant Secondary Metabolites. Medicines. 2015; 2
(3):251–86. https://doi.org/10.3390/medicines2030251 PMID: 28930211 14. PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 References Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, et al. PubChem 2019 update: Improved access to
chemical data. Nucleic Acids Res [Internet]. 2019 Jan 8 [cited 2019 Aug 28]; 47(D1):D1102–9. Available
from: https://academic.oup.com/nar/article/47/D1/D1102/5146201 https://doi.org/10.1093/nar/gky1033
PMID: 30371825 15. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and Auto-
DockTools4: Automated docking with selective receptor flexibility. J Comput Chem [Internet]. 2009 Dec
[cited 2019 Sep 20]; 30(16):2785–91. Available from: http://www.ncbi.nlm.nih.gov/pubmed/19399780
https://doi.org/10.1002/jcc.21256 PMID: 19399780 16. Daina A, Michielin O, Zoete V. SwissADME: A free web tool to evaluate pharmacokinetics, drug-like-
ness and medicinal chemistry friendliness of small molecules. Sci Rep [Internet]. 2017 [cited 2019 Oct
28]; 7:42717. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28256516 17. Piñero J, Ramı´rez-Anguita JM, Sau¨ch-Pitarch J, Ronzano F, Centeno E, Sanz F, et al. The DisGeNET
knowledge platform for disease genomics: 2019 update. Nucleic Acids Res [Internet]. 2019 Nov 4 [cited
2019 Dec 20]; 48(Database issue):D845–55. Available from: https://academic.oup.com/nar/advance-
article/doi/10.1093/nar/gkz1021/5611674 18. UniProt Consortium T. UniProt: the universal protein knowledgebase. Nucleic Acids Res [Internet]. 2018 Mar 16 [cited 2019 Apr 24]; 46(5):2699–2699. Available from: https://academic.oup.com/nar/
article/46/5/2699/4841658 https://doi.org/10.1093/nar/gky092 PMID: 29425356 19. Usman MS, Kusuma WA, Afendi FM, Heryanto R. Identification of significant proteins associated with
diabetes mellitus using network analysis of protein-protein interactions. Comput Eng Appl J. 2019; 8
(1):41–52. 20. Li YH, Yu CY, Li XX, Zhang P, Tang J, Yang Q, et al. Therapeutic target database update 2018:
Enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Res
[Internet]. 2017 [cited 2019 Aug 28]; 46(D1):D1121–7. Available from: http://www.ncbi.nlm.nih.gov/
pubmed/29140520 21. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome
variations in KEGG. Nucleic Acids Res. 2019; 47(D1):D590–5. https://doi.org/10.1093/nar/gky962
PMID: 30321428 22. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A Software Environ-
ment for Integrated Models. Genome Res [Internet]. 2003; 13(22):2498–504. Available from: http://ci. nii.ac.jp/naid/110001910481/ https://doi.org/10.1101/gr.1239303 PMID: 14597658 14 / 15 PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 PLOS ONE Network pharmacology integrated molecular docking prediction in Tinospora crispa Linn. as insulin sensitizer 23. Feller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V. Swiss Target Prediction: A web server
for target prediction of bioactive small molecules. Nucleic Acids Res [Internet]. 2014 Jul [cited 2019 Dec
6]; 42(Web Server issue):W32–8. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24792161 24. References Wang X, Shen Y, Wang S, Li S, Zhang W, Liu X, et al. PharmMapper 2017 update: A web server for
potential drug target identification with a comprehensive target pharmacophore database. Nucleic
Acids Res [Internet]. 2017 Jul 3 [cited 2019 Aug 28]; 45(W1):W356–60. Available from: http://www.ncbi. nlm.nih.gov/pubmed/28472422 https://doi.org/10.1093/nar/gkx374 PMID: 28472422 25. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: pro-
tein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res [Internet]. 2015
[cited 2019 Jul 3]; 43(Database issue):D447. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC4383874/ https://doi.org/10.1093/nar/gku1003 PMID: 25352553 26. Berman HM. The protein data bank. Nucleic Acids Res [Internet]. 2000 Jan 1 [cited 2020 Feb 13]; 28
(1):235–42. Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/28.1.235 27. Olson Arthur J. OT. AutoDock Vina: improving the speed and accuracy of docking with a new scoring
function, efficient optimization and multithreading. NIH Pubic Access. 2011; 31(2):455–61. 28. Hernndez-Santoyo A, Yair A, Altuzar V, Vivanco-Cid H, Mendoza-Barrer C. Protein-Protein and Pro-
tein-Ligand Docking. Protein Eng—Technol Appl. 2013;(May). 29. Fadilah F, Arsianti A, Kusmardi K, Tedjo A. Molecular docking studies of opened-chain analogues of
antimycin A3 as caspases inhibitors of apoptosis in colorectal cancer. Asian J Pharm Clin Res. 2016; 9
(3):8–10. 30. Laskowski RA, Swindells MB. LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model [Internet]. 2011 Oct 24 [cited 2021 Mar 15]; 51(10):2778–86. Available from: https://
pubmed.ncbi.nlm.nih.gov/21919503/ https://doi.org/10.1021/ci200227u PMID: 21919503 31. Abraham MJ, Murtola T, Schulz R, Pa´ll S, Smith JC, Hess B, et al. GROMACS: High performance
molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015
Sep 1; 1–2:19–25. 32. Soteras Gutie´rrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL, et al. Parametri-
zation of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein inter-
actions. Bioorg Med Chem. 2016 Oct 15; 24(20):4812–25. https://doi.org/10.1016/j.bmc.2016.06.034
PMID: 27353885 33. Yu W, He X, Vanommeslaeghe K, MacKerell AD. Extension of the CHARMM general force field to sulfo-
nyl-containing compounds and its utility in biomolecular simulations. J Comput Chem [Internet]. 2012
Dec 5 [cited 2021 Aug 18]; 33(31):2451–68. Available from: https://onlinelibrary.wiley.com/doi/full/10. 1002/jcc.23067 34. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential
functions for simulating liquid water. J Chem Phys [Internet]. 1998 Aug 31 [cited 2021 Aug 18]; 79
(2):926. Available from: https://aip.scitation.org/doi/abs/10.1063/1.445869 35. Hopkins AL. Network pharmacology: The next paradigm in drug discovery. Nat Chem Biol. PLOS ONE | https://doi.org/10.1371/journal.pone.0251837
June 23, 2022 References 2008; 4
(11):682–90. https://doi.org/10.1038/nchembio.118 PMID: 18936753 36. Lam SH, Ruan CT, Hsieh PH, Su MJ, Lee SS. Hypoglycemic diterpenoids from Tinospora crispa. J Nat
Prod. 2012; 75(2):153–9. https://doi.org/10.1021/np200692v PMID: 22283497 37. Lokman EF, Gu HF, Wan Mohamood W, Yusof M, Meng L, O¨ stenson C-G. Anti-diabetic effect of oral
borapetol B, isolated from the plant Tinospora crispa, by stimulating insuln resistance. Diabetologia. 2013; 56:1–7. 15 / 15
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RESUMO O objetivo deste artigo é apresentar uma proposta teórica para a formação de professores de
ciências e matemática na interface do agir comunicativo e as questões sociocientíficas. Defendemos neste trabalho, a necessidade da formação continuada de professores caso
tenhamos o interesse de desenvolver a formação científica escolar de alunos da Rede Oficial
de Ensino Básico. Para a formação de alunos competentes comunicativamente, ao final, da
escolarização
torna-se
necessária
a
formação
de
professores
competentes
argumentativamente. Para tanto, acreditamos que a teoria do agir comunicativo, de Jurgen
Habermas, venha a colaborar nesse sentido. Palavras-Chave: Ensino de Ciências, Formação de Professores, Agir Comunicativo,
Questões Sociocientíficas A Proposal for the Continuing Education of Science and Mathematics
Teachers at the Interface of the Communicative Action and the socio-
scientific issues Adriana Bortoletto1
Washington Luiz Pacheco de Carvalho2 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
1 Programa de Pós-Graduação em Educação para a Ciência – UNESP – Bauru
2 UNICAMP Key-Words: Science Teaching, Teacher Education, Action Communicative, Socio-scientific
Issues AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
UNICAMP 1 Programa de Pós-Graduação em Educação para a Ciência – UNESP – Bauru
2 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 INTRODUÇÃO A proposta deste artigo é estabelecer um diálogo teórico entre o tratamento das
questões sociocientíficas e a formação continuada de professores de Ciências e Matemática
pelo viés teórico-crítico da teoria do Agir Comunicativo de Jurgen Habermas. Isso porque há
um grande número de pesquisas no ensino de ciências, particularmente, na interface CTSA,
que argumentam sobre a necessidade de formação de aluno críticos, aptos para tomada de
decisões na sociedade científico-tecnológica contemporânea. De uma maneira geral, tais
pesquisas defendem a necessidade de os alunos compreenderem que as disciplinas científicas
escolares são fulcrais para o entendimento da evolução da ciência e tecnologia, inclusive, para
o entendimento das problemáticas advindas dos produtos que estão na interface entre ciência e
sociedade. Nessa direção, Kolsto (2000) afirma que é de fundamental importância a participação
da população nos debates em torno de questões que envolvam os produtos da ciência e
tecnologia. No entanto, para estar apto a estas discussões, torna-se necessário compreender
certos aspectos que caracterizam o fazer científico e o impacto do desenvolvimento científico-
tecnológico na sociedade contemporânea. Muitos destes aspectos estão relacionados com a
ideia de ciência para cidadania, a qual defende a necessidade de enfatizar a ciência como um
processo social, revelando o caráter humano, os valores envolvidos e os limites da ciência,
assim como defende uma formação em ciências que esteja fortemente ligada ao uso do
conhecimento científico escolar, bem como dos aspectos axiológicos da natureza da ciência, a
fim de potencializar a participação da população nos debates científicos e tecnológicos. Diante das necessidades formativas dos alunos, questionamos: em que medida os
professores de ciências e matemática legitimam as questões sociocientíficas e estão aptos a
implementá-las em sala de aula? Ou seja, em que medida a prática pedagógica dos professores
está voltada para os objetivos do ensino de ciências? 142
AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
Há uma grande preocupação dos professores da Rede Oficial de Ensino Básica em
“dar conta” do conteúdo, o que dificulta a inserção de estratégias com práticas argumentativas
no contexto de sala de aula, assim como, no diálogo entre os professores no cotidiano escolar. Para Giroux (1997), não há uma ênfase nos alunos para lerem o mundo criticamente, mas,
sim, em desenvolver habilidades de leitura de forma mecânica, a qual impede a produção de
sentido e significado sobre aquilo que é dado como factual. ABSTRACT The objective of this paper is to present a theoretical proposal for the training of teachers of
mathematics and science at the interface of communicative action and socio-scientific issues. In this paper we argue for the need for a continuous training of teachers if we are to be
interested in developing the scientific training of students from the public school system. To
form communicatively competent students, by the end of schooling, becomes necessary the
training of argumentatively competent teachers. Therefore, we believe that the theory of
communicative action by Jurgen Habermas, will cooperate to this end. Key-Words: Science Teaching, Teacher Education, Action Communicative, Socio-scientific
Issues AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho INTRODUÇÃO Não há um incentivo à
problematização das coisas que estão no mundo. A linguagem atua como mecanismo de 142 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto Washington Luiz Pacheco de Carvalho transmissão de informações. A racionalidade que orienta o discurso no contexto escolar é
instrumental e imperativa. Não há espaço para o exercício da argumentação crítica para
ocorrer o entendimento das tensões e obstáculos do cotidiano escolar e dos eventos do mundo
de uma maneira geral. A ausência de um espaço amplo de comunicação no ambiente escolar dificulta o
processo de formação entre professores, como nas relações aluno-professor e aluno-aluno. É
no processo comunicativo, livre de coerções, com o exercício efetivo da argumentação, que as
pessoas se entendem, entendem as coisas do mundo e promovem mudanças no status quo. Neste artigo, buscarmos discutir que, para o desenvolvimento da formação científica
escolar de alunos, é imprescindível a formação dos professores de ciências e matemática
frente aos mesmos objetivos. Diante disto, apresentamos a Teoria do Agir Comunicativo de
Jurgen Habermas como aporte teórico para a compreensão da prática discursiva docente e da
identificação das possíveis relações que os professores podem estabelecer com as escolas e os
saberes teóricos-pedagógicos, assim como com as questões sociocientíficas. AS QUESTÕES SOCIOCIENTÍFICAS O domínio das questões sociocientíficas possui uma estrutura teórica que permite o
desenvolvimento dos alunos quanto às questões morais e científicas por meio de processos
discursivos e interativos no contexto de sala de aula. Elas possuem como características os
seguintes pontos que são apontados por Ratcliffe e Grace (2003, p.2-3): • Tem base na ciência, e frequentemente se localiza na fronteira do conhecimento
científico; • Envolve a formação de opiniões, escolhas a nível pessoal ou social; • São frequentemente relatados pela mídia; • Possui informações incompletas e conflitos de evidências científicas; ossu
o
ações
co p etas e co
tos de ev dê c as c e t
cas;
• Possui dimensões locais ou globais ligadas a estruturas políticas e sociais; • Pode envolver elementos de desenvolvimento sustentável; • Pode requerer algum entendimento de probabilidade ou risco; • São tópicos frequentes na vida cotidiana; 143
AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
Assim, as questões sociocientíficas possuem uma estrutura teórico-pedagógica que
permite vislumbrar o desenvolvimento da argumentação, da natureza da ciência, o 143 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto entendimento das relações entre outras áreas do conhecimento humano com a dimensão
científica, a análise de informações de divulgação científica. Por outro lado, há uma
proximidade das questões sociocientíficas com as dimensões morais, as quais permitem que
os estudantes “tematizem o assunto e passem a refletir sobre algo que, aparentemente, parecia
trivial e previamente tido como definido” (GUIMARAES, 2010, p.06). As questões sociocientíficas são caracterizadas como temas científicos-tecnológicos de
fronteira da ciência, como por exemplo, pesquisas com células troncos, xenotransplantes,
aquecimento global, vacinas dentre outros. São temáticas que a priori não tem solução, mas
que o processo de entendimento exige dos cidadãos o uso do conhecimento científico escolar,
uma concepção de ciência como atividade humana, do raciocínio ético e moral e de
competência argumentativa. Zeidler et al. (2005) afirmam que realmente existe a necessidade de desenvolver a
proposta teórica para o domínio das questões sociocientíficas com o intuito de atender aos
objetivos de engajar a população em temas de ciência e tecnologia. AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 AS QUESTÕES SOCIOCIENTÍFICAS Porém, essa estrutura
teórica necessita ser suficientemente flexível a fim de potencializar o desenvolvimento dos
aspectos morais, da estrutura do conhecimento científico, emotivos e argumentativos
inerentes a um dilema. Os autores pontuam que a compreensão deste domínio de investigação
e o desenvolvimento de uma estrutura pedagógica permitiu o surgimento de quatro grandes
linhas de pesquisa: (1) natureza da ciência, (2) questões discursivas em sala de aula, (3)
questões culturais e (4) estudos de caso. A natureza da ciência caracteriza-se como um ponto importante das questões
sociocientíficas, pois, permite analisar a variedade de pontos de vistas epistemológicos que
muitos alunos utilizam para avaliar uma evidência científica, inferir ou elaborar uma hipótese
frente a uma problemática da ciência. Por outro lado, a dimensão discursiva está relacionada
com o potencial controverso destas questões, as quais potencializam o desenvolvimento da
prática discursiva em sala de aula, como por exemplo, a elaboração de argumentos. O
desenvolvimento de um processo argumentativo permite que o núcleo de crenças
epistemológicas e morais dos alunos sejam expostos por meio do uso de raciocínios lógicos
dedutivos. A exploração das estruturas argumentativas possibilita que os educandos percebam
as premissas que constituem a base do raciocínio e averiguem a plausibilidade frente à
questão que está sendo discutida. Quanto aos aspectos culturais, estes estão relacionados com
elementos que envolvem o respeito e a tolerância com a diversidade de perspectivas, muitas
destas, oriundas do núcleo de crenças pessoais. Por fim, os estudos de caso contribuem para 144 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto que os professores de ciências, assim como os alunos tenham consciência moral e
compromisso para o entendimento adequado das diferentes perspectivas que estão em jogo
numa questão sociocientífica, como também, avaliar em que medida outros setores da
sociedade determinam via dinheiro e poder os caminhos que percorrem certos
empreendimentos científicos controversos (ZEIDLER et al., 2005). Assim, é importante promover um ensino de ciências que leve em consideração as
seguintes características: processos de investigação, conflito, argumentação, compromisso,
tomada de decisão e engajamento frente à miríade de conhecimentos necessários para análise
e compreensão da temática. AS QUESTÕES SOCIOCIENTÍFICAS O exercício destes elementos pedagógicos permite que o
professor tenha entendimento de como ocorre a construção do conhecimento no contexto
escolar e a importância da linguagem como meio de entendimento dos fatos do mundo da
vida. As questões sociocientíficas permitem o desenvolvimento significativo dessas novas
estratégias cognitivas, assim como os conceitos científicos, políticos, morais e éticos
envolvidos potencializam o exercício da racionalidade de forma mais complexa, atendendo
não apenas à racionalidade instrumental, que possui um papel na construção do
conhecimento, mas também ao uso moral da racionalidade, ou seja, considerar quais aspectos
são importante para seleção dos melhores fins para todos. (LONGHI, 2005). Para poder avaliar uma temática na interface ciência-sociedade, torna-se necessário
utilizar certos questionamentos no intuito de sistematizar critérios e organizar a abordagem
metodológica no contexto de sala de aula. Por exemplo, é importante avaliar: a) a utilidade do
conhecimento proposto e as habilidades que serão realçadas para a formação do aluno; b) se o
conhecimento abordado proporciona o desenvolvimento da responsabilidade social e do
entendimento da articulação ciência e sociedade; c) se os conhecimentos matemáticos e
científicos intrínsecos a proposta são importantes na perspectiva histórica do conhecimento
humano; d) se os valores filosóficos presentes na temática são importantes para o
questionamento sobre a qualidade de vida, bem-estar, vida e morte (ZEIDLER; KEEFER,
2003). Nesse contexto, para estar coerente com os pressupostos de uma educação para
Ciência, é necessário desenvolver contextos de formação que possibilitem o entendimento dos
conhecimentos científicos, sociais, históricos, políticos e ético-morais que fazem parte de uma
concepção de natureza aberta da ciência, ou seja, desnaturalizada. Nessa perspectiva, pode-se 145 MAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS dizer que as questões sociocientíficas vão ao encontro de uma educação para ciência que
contribui para o processo de formação coletiva de atores sociais via prática comunicativa. dizer que as questões sociocientíficas vão ao encontro de uma educação para ciência que
contribui para o processo de formação coletiva de atores sociais via prática comunicativa. A TEORIA DO AGIR COMUNICATIVO 2012, p.141-160 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto Washington Luiz Pacheco de Carvalho importância da dimensão da cultura e seus aspectos funcionais no mundo da vida, quando
ocorrem dificuldades ou conflitos no processo de reprodução cultural que contribuem para a
perda de sentido ou crises de orientação e legitimação. Um exemplo disto seria a dificuldade
que os professores de ciências sentem na dinâmica entre professor-aluno e os saberes dos
alunos com relação aos saberes de senso comum do aluno. Ora, a dificuldade de
validação/legitimação dos saberes dos alunos via racionalidade comunicativa pelo professor
que declara o conhecimento escolar, potencializa a perda de sentido entre o saber do aluno e o
saber escolar, por conseguinte, há uma deterioração do real significado da escola, do
conhecimento escolar na vida do aluno. Estes aspectos sintomáticos dos conflitos que
obstaculizam a reprodução cultural são decorrentes das insuficiências dos saberes culturais
que os atores (no exemplo, os alunos) dispõem para articular e empreenderem um processo
argumentativo para o entendimento dos elementos que são válidos ou não numa determinada
situação. Já os aspectos funcionais da sociedade se articulam por meio das normatizações que
um grupo de pessoas legitima para poder praticar a coordenação de ações frente ao tema em
problematização. Além, do aspecto organizacional, as normas potencializam o fenômeno da
solidariedade coletiva, a qual está relacionada com uma ética discursiva, ou seja, que entre os
participantes ocorra o reconhecimento da fala do outro. Isto permite a estabilização das
identidades grupais via solidariedade coletiva. A não manutenção dos aspectos funcionais da
sociedade possibilita o surgimento de conflitos e anomia. Isso porque os participantes não
conseguem mais promover a coordenação de ações em novas situações com os elementos
normativos que antes organizavam e mantinham uma ética discursiva. Ora, a insuficiência
destas normatizações corrompe a solidariedade coletiva e desestabiliza as identidades grupais. As dimensões da cultura e da sociedade são responsáveis por assegurar vivências
experienciadas, as biografias das pessoas no mundo, como, também, a identificação de si para
com outro, a ética coletiva e o auto-reconhecimento como pessoa responsável no mundo que
participa de ações coletivas. A TEORIA DO AGIR COMUNICATIVO A Teoria do Agir Comunicativo concebe que a sociedade moderna contemporânea é
formada pelo mundo da vida e sistema. O mundo da vida é caracterizado como o espaço em que ocorrem as comunicações
livre de coerções, sem distorções. Local, no qual a linguagem não é utilizada como
instrumento de transmissão de informações. Mas, ao contrário, ela possui papel fundamental
na construção do conhecimento e na compreensão do mundo. Segundo Mühl (2003), a
linguagem é uma ação humana, faz parte da prática social, ação do sujeito no mundo como
mediadora das trocas intersubjetivas entres os atores sociais sob regras determinadas. Para Habermas (2012), a estrutura do mundo da vida é composta pela cultura,
sociedade e personalidade. Assim: A cultura constitui o estoque ou reserva de saber, do qual os participantes da
comunicação extraem interpretações no momento em que tentam se entender sobre
algo no mundo. Defino a sociedade por meio das ordens legítimas pelas quais os
participantes da comunicação regulam sua pertença a grupos sociais, assegurando a
solidariedade. Interpreto a personalidade como o conjunto de competências que
tornam o sujeito capaz de fala e de ação – portanto, que o colocam em condições de
participar de processos de entendimento, permitindo-lhe afirmar sua identidade. O
campo semântico dos conteúdos simbólicos, o espaço social e o tempo histórico
constituem as dimensões em que os atos comunicativos se realizam. As interações
que formam a rede prática comunicativa cotidiana configuram o meio pelo qual a
cultura, a sociedade e a pessoa se reproduzem. E tais processos de reprodução se
estendem às estruturas simbólicas do mundo da vida (HABERMAS, 2012, p. 253). 146
AMAZÔNIA Revista de Educação em Ciências e Matemáticas V 9
nº 17 jul 2012/dez 2012 p 141 160
As três estruturas que constituem o mundo da vida são interdependentes nos aspectos
funcionais. Por exemplo, a reprodução da dimensão cultural do mundo da vida é responsável
por manter a tradição e coerência daqueles “saberes” que foram constituídos ao longo do
tempo. É a manutenção cultural desses saberes, por meio do exercício da racionalidade
comunicativa, que permite o exercício da prática cotidiana. Torna-se possível constatar a 146 MAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 148
AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
3
O ato de fala na perspectiva habermasiana é caracterizado quando há pelo menos dois participantes
numa situação de diálogo. A TEORIA DO AGIR COMUNICATIVO Caso haja dificuldade em relação ao desenvolvimento e
significação das histórias de vida, de uma ética discursiva, como também, da responsabilidade
coletiva, é possível constatar aspectos sintomáticos das patologias psicológicas, como
alienação, depressões e outras. Estas patologias são manifestações da insuficiência dos atores
sociais em desenvolverem uma prática linguística intersubjetiva voltada para o entendimento. Ora, diante disto o sistema da personalidade (por exemplo, os professores da rede pública
básica de ensino) não consegue se manter, a não ser por meio de ações estratégicas como 147 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto Washington Luiz Pacheco de Carvalho autoproteção, por exemplo, as resistências de professores da rede básica de ensino em
problematizar a própria prática e romper processos tradicionalistas de ensino e aprendizagem. Assim, essas distinções são importantes para que haja o enfrentamento por meio de um
agir comunicativo das problemáticas decorrentes da invasão sistêmica no mundo da vida. Esse enfrentamento permite assegurar a integridade das estruturas do mundo da vida e evitar a
prevalência das patologias citadas acima. Para que ocorra a comunicação livre de coerções é imprescindível o uso das
pretensões de validade. Habermas (2012b), afirma que estas pretensões são regras tácitas ao
homem na sua relação com o mundo. Nesta perspectiva, a ideia de “regra” não está associada
a uma visão de mundo solipcista da existência do sujeito (LONGHI, 2005). Ao contrário
disto, o sujeito se torna existente a partir do momento em que se relaciona comunicativamente
com outros participantes por um principio ético discursivo, o qual está relacionado com as
pretensões de validade. O contexto comunicativo na perspectiva habermasiana, assim como a competência
comunicativa dos participantes, é orientado pelas pretensões de validade. Se considerarmos
uma situação em que um falante lança uma proposta sobre algum fato ou evento, as
pretensões de validade deverão ser consideradas. Logo, (...) a validade do ato de fala3 levado a cabo dependerá de esta ação se encontrar ou
não em conformidade com uma base normativa reconhecida. AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 3
O ato de fala na perspectiva habermasiana é caracterizado quando há pelo menos dois part
numa situação de diálogo. A TEORIA DO AGIR COMUNICATIVO Enquanto uma frase
gramatical cumpre as exigências da compreensibilidade, uma expressão bem
sucedida deverá satisfazer três pretensões de validade adicionais: ser considerada
verdadeira pelos participantes do ponto de vista em que representa algo que existe
no mundo, ser considerada sincera da perspectiva em que expressa uma intenção
do falante e, por fim, ser considerada acertada do ponto de vista em que se
encontre em conformidade com as expectativas socialmente reconhecidas
(HABERMAS, 2002, p.49). (...) a validade do ato de fala3 levado a cabo dependerá de esta ação se encontrar ou
não em conformidade com uma base normativa reconhecida. Enquanto uma frase
gramatical cumpre as exigências da compreensibilidade, uma expressão bem
sucedida deverá satisfazer três pretensões de validade adicionais: ser considerada
verdadeira pelos participantes do ponto de vista em que representa algo que existe
no mundo, ser considerada sincera da perspectiva em que expressa uma intenção
do falante e, por fim, ser considerada acertada do ponto de vista em que se
encontre em conformidade com as expectativas socialmente reconhecidas
(HABERMAS, 2002, p.49). Nesse contexto, Habermas (2002) entende por “competência comunicativa”, a
capacidade de o falante orientar a própria fala para o entendimento durante um contexto
comunicativo com diversos participantes. A fala orientada para o entendimento parte do
pressuposto de que o falante deverá ser capaz de estruturar uma frase de forma inteligível,
assim contribuindo para que o ouvinte possa compreender o ponto de vista externalizado pelo
falante; ao externalizar o seu ponto de vista, o falante expressa as intenções da proposta 148 ÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto Washington Luiz Pacheco de Carvalho formulada, no intuito de que o ouvinte possa confiar nas suas intenções; por fim, em cada ato
de fala durante o processo intersubjetivo há necessidade de o falante se orientar pelos valores
sociais aceitáveis, ou seja, atentar para as regras normativas do contexto comunicativo. Na perspectiva das pretensões de validade, os atos de fala4 compõem uma parte do
discurso e avaliam a força ilocutória5 de pontos de vista durante as relações interpessoais num
contexto comunicativo (HABERMAS, 2002). São estas relações intersubjetivas que se tornam
importantes no contexto da teoria da ação comunicativa. AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 A TEORIA DO AGIR COMUNICATIVO 5 A força ilocucionária está vinculada ao ato ilocucionário: não tem a intenção de
constatar uma situação, mas a de protestar ou de advertir sobre um determinado evento 149 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS
Adriana Bortoletto
Washington Luiz Pacheco de Carvalho
teorias, conceitos ou princípios da ciência, estamos apresentando atos de fala constativos; e,
por fim, se os participantes se reportam a aspectos pessoais no grupo, o ato de fala é
caracterizado como sendo expressivo. UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
Í Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho teorias, conceitos ou princípios da ciência, estamos apresentando atos de fala constativos; e,
por fim, se os participantes se reportam a aspectos pessoais no grupo, o ato de fala é
caracterizado como sendo expressivo. teorias, conceitos ou princípios da ciência, estamos apresentando atos de fala constativos; e,
por fim, se os participantes se reportam a aspectos pessoais no grupo, o ato de fala é
caracterizado como sendo expressivo. Quadro 1: Modos de Comunicação Fonte: (HABERMAS, 2002, p.88)
Modo de
Comunicação
Tipo de Ato de
Fala
Tema
Pretensão de
Validade Temática
Cognitivo
Constativo
Conteúdo
Proposicional
Verdade
Interativo
Regulativo
Relação
Interpessoal
Acerto e Adequação
Expressivo
Confissões
Intenções do
Falante
Veracidade Quadro 1: Modos de Comunicação Fonte: (HABERMAS, 2002, p.88) Cada tipo de ato de fala está relacionado com a forma como o ator-social faz uso da
razão para se relacionar e interpretar os fatos do mundo. Há três tipos de razões: Objetiva,
Social e Subjetiva. Estas razões são expressas pelo tipo de ato de fala que o indivíduo profere
em determinado contexto de comunicação e, por conseguinte, este ato de fala está vinculado a
uma pretensão de validade. Mundo
Razão
Tipo de Ato de
Fala
Pretensões de
Validade
Objetivo
Objetiva
Constativo
Verdade
Social
Social
Regulativo
Acerto de Normas e
Valores
Subjetivo
Subjetiva
Confissões
Veracidade/Sinceridade
Quadro 2: Usos das Razões Fonte: Autor. Quadro 2: Usos das Razões Fonte: Autor. A TEORIA DO AGIR COMUNICATIVO A grande ideia do conceito do agir comunicativo é que a linguagem tem a função de
coordenar ações, de socializar sujeitos de ação, além das ações orientadas para o consenso. Durante o processo de comunicação, há diferentes usos que os atores sociais fazem da
linguagem para buscar o entendimento sobre algo no mundo externo. Ao tentar compreender
fatos/eventos do mundo exterior de forma intersubjetiva, o sujeito se volta sobre si mesmo,
tornando-se objeto de si, empreendendo, assim, um processo de auto-reflexão, ao mesmo
tempo em que se apropria do mundo. Essa perspectiva intersubjetiva de compreensão de algo
do mundo é interpretada de maneira diferente pelos participantes de uma comunicação. Isso
permite que as diferentes visões de mundo contribuam para um processo de descentralização
egocêntrica que cada um tem de si e do mundo, desde que tenham como pressuposto a
consideração dos pontos de vista e interesses de cada participante envolvido no intuito de
alcançar um consenso. (HABERMAS, 2004). O ato de fala possui uma função importante para Habermas. Isso porque é por meio do
ato de fala que os participantes de uma discussão conseguem perceber as intenções dos outros
atores envolvidos no contexto comunicativo. O ato de fala representa uma ação, pois ao
pronunciar uma promessa ou um aviso o falante intervém no mundo. No entanto, é importante
considerar que, no contexto comunicativo, para existir o ato de fala, o falante deverá entender-
se com os outros participantes acerca de algo no mundo (HABERMAS, 2002). Ao considerarmos um contexto comunicativo, no qual se busca o entendimento, o ato
de fala possui características peculiares que estão relacionados com o uso que se faz da
linguagem. Por exemplo, se discutimos aspectos normativos da interação do grupo de atores
sociais estamos nos reportando a atos de fala regulativos; se estamos discutindo a respeito de 4 Ato de fala: toda ação que é realizada através do dizer. Isso porque todo ato de fala possui
uma intenção. A TEORIA DO AGIR COMUNICATIVO 150
AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V 9 – nº 17 - jul 2012/dez 2012 p 141-160
Quando o participante de uma discussão orientada para o entendimento faz uso
cognitivo/constatativo da linguagem, torna-se necessário que o falante forneça os
fundamentos que asseguram a validade cognitiva do ato de fala enunciado. “Os atos de fala
constatativos contêm a proposta que nos permite recorrer, se necessário, à fonte experimental
de onde o falante retira a certeza de que aquilo que afirma é verdade” (HABERMAS, 2002,
p.95). Caso as bases “teóricas” que fundamentam os atos de fala não sejam suficientes para 150 ÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto Washington Luiz Pacheco de Carvalho responder um questionamento ou esclarecer uma dúvida do ouvinte, torna-se necessário que
esta dúvida/problema venha ser problematizada(o) por meio do discurso teórico. Já no uso interativo/intersubjetivo da linguagem, o falante precisa fornecer
justificativas que assegurem as condições normativas/regulativas da importância do ato de
fala no contexto de uma discussão orientada para ação comunicativa. Porém, caso tais
justificativas não sejam suficientes, instaura-se um problema relacionado com as condições
normativas, assim com o objetivo de solucionar tal problemática, a discussão será
desenvolvida por meio do discurso prático. Por fim, no uso expressivo da linguagem, o falante necessita “provar” a veracidade
dos atos de fala por meio de esclarecer quais os fundamentos que realmente orientam as
intenções expressivas aos atos de fala (HABERMAS, 2002). Caso o falante não consiga
exprimir a ideia de veracidade para os ouvintes, a averiguação apenas será possível por meio
da observação da coerência comportamental do falante (HABERMAS, 2002). Logo, o que é
observado será se, após a enunciação de atos de fala expressivos, o falante de fato está
comprometido com aquilo que falou, ou seja, se foi cumprida. Podemos dizer que as pretensões de validade que caracterizam os usos cognitivo,
interativo/intersubjetivo e expressivo da linguagem e, por conseguinte, os atos de fala são as
seguintes: 1) PRETENSÕES DE VERDADE – obrigação de fornecer fundamentos;
Õ )
g ç
;
2) PRETENSÕES DE ACERTO – obrigação de fornecer justificações;
3) PRETENSÕES DE SINCERIDADE – obrigação de demonstrar a sua
fiabilidade. A TEORIA DO AGIR COMUNICATIVO g ç
2) PRETENSÕES DE ACERTO – obrigação de fornecer justificações;
Õ g ç
2) PRETENSÕES DE ACERTO – obrigação de fornecer justificações;
Õ 3) PRETENSÕES DE SINCERIDADE – obrigação de demonstrar a sua
fiabilidade. Domínios da
Realidade
Modos
de
Comunicação: Atitudes
Básicas
Pretensões
de Validade
Funções
Gerais do Discurso
“O” mundo de natureza
externa
Cognitivo:
atitude
objetivante
Verdade
Representação de Fatos
“Nosso”
mundo
de
sociedade
Interativo:
atitude
conformativa
Acerto
Estabelecimento
de
relações
interpessoais
legítimas
“Meu”
mundo
de
natureza interna
Expressivo:
atitude
expressiva
Sinceridade
Revelação
da
subjetividade do falante
Linguagem
----------
Inteligibilidade
---------- 151 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Enquanto o mundo da vida é regulado pelas pretensões de validade no intuito de
potencializar uma ação comunicativa voltada para o entendimento entre os atores
participantes, o sistema, pelo contrário, é regulado pelo dinheiro e poder. A linguagem, na
perspectiva do sistema, é instrumento para transmissão de informações. O uso da linguagem é
imperativo e não interacionista. O agir responsável pelo sistema é o teleológico, e a razão que
o orienta este agir, é a instrumental. AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS Atualmente, são inúmeras as manchetes nos meios de comunicação divulgando os
mais recentes produtos advindos da dimensão da ciência e tecnologia, principalmente, em
setores como biologia, química e física. Grande parte destes setores se relaciona com
temáticas que envolvem transgênicos, células-tronco, produção de energia, aquecimento
global, medicamentos, entre outros. Hoje, os movimentos nos setores de Ciência e Tecnologia têm como característica a
multidisciplinariedade, ou seja, para compreender as inovações nestas áreas é necessário se
apoiar nos conhecimentos da Física, Química, Biologia, Matemática, Economia e etc. A ideia
de um fazer científico neutro, à parte das consequências sociais é inviável. Sabemos que grandes indústrias, como a do tabaco e outras, investem em pesquisas
científicas para inovar e potencializar seus produtos no mercado capitalista. Assim, os
produtos da ciência têm um impacto social que pode ser construtivo ou destrutivo, possui um
valor. Porém, os pressupostos positivistas que orientam o fazer científico potencializam a
dicotomia entre a gênese do conhecimento e a validade social. Já que o positivismo assegura
que o método científico do fazer ciência não possui nenhuma relação com a dimensão
normativa. Ou seja, o método científico é a histórico (MÜHL, 2003). Esta separação entre o referencial metodológico positivista e as implicações sociais
levanta problemas graves sobre a legitimidade do produto científico-tecnológico. Para o
cientista positivista, fundamentações das decisões sociais para um determinado produto
científico não fazem parte do planejamento, a não ser quando estão atreladas a fatores
empíricos, que ressaltem o agir com respeito afins. AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 152 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Dessa forma, o positivismo mantém uma clara separação entre ser e dever-ser,
considerando que apenas o primeiro é suscetível de análise e planejamento racional. Com isso fica descartada a possibilidade de se pensar uma alternativa emancipativa
para a sociedade, pois, o máximo que se pode obter é um planejamento do destino
da humanidade, através de técnicas sociais adequadas (MÜHL, 2003, p.95). Nessa perspectiva, há uma redução dos aspectos morais da racionalidade implicando
na suspensão do processo de autorreflexão. O fazer científico-tecnológico se finda em ações
técnicas vinculadas aos imperativos de dinheiro e poder. A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS Se anteriormente o objetivo do
projeto iluminista era libertar o homem dos grilhões da escuridão, hoje, temos um
aprisionamento do homem em decorrência dos interesses sociais estarem determinados em
função da manutenção do sistema econômico (MÜHL, 2003). Assim, o conhecimento científico assume um caráter cientificista e passa a legitimar
uma ideologia que favorece o processo de manipulação e despolitização dos atores sociais. Isto ocorre em função da ausência de problematização das diferenças entre interesses e
necessidades coletivas e individuais. Assim, há o desenvolvimento de diversas patologias,
sendo uma delas: (...) a redução das possibilidades de reação contra o sistema por parte de grupos
sociais ou das classes, na medida em que o Estado desenvolve não somente
mecanismo de controle e da manipulação através da mass media, mas também,
políticas de compensação que asseguram a lealdade das massas (MÜHL, 2003,
p.96). (...) a redução das possibilidades de reação contra o sistema por parte de grupos
sociais ou das classes, na medida em que o Estado desenvolve não somente
mecanismo de controle e da manipulação através da mass media, mas também,
políticas de compensação que asseguram a lealdade das massas (MÜHL, 2003,
p.96). A apresentação e a formação da opinião pública em relação aos produtos da ciência e
da tecnologia determinam o aumento dos níveis de consumo, a crença de que a organização
da estrutura da sociedade, assim como de uma grande parte dos problemas que nelas eclodem
são de responsabilidade de tecnocratas e que, para a população, cabe apenas acatar as decisões
de especialistas, isso porque a felicidade e o bem-estar dela dependem exclusivamente dos
tecnocratas (MÜHL, 2003). Ora, diante disto, como podemos avaliar o impacto científico-tecnológico no nosso
mundo privado? A maneira como os produtos são apresentados para a população são livres de
conflitos ou controvérsias à primeira vista. Isto porque, segundo Ulrich Beck (1995), estamos
vivenciando uma sociedade de risco que surgiu em decorrência do próprio processo de
modernização, sendo esta, também, indiferente aos efeitos colaterais desta dinâmica
científico-tecnológica. 153 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS 2012, p.141-160 Adriana Bortoletto
Washington Luiz Pacheco de Carvalho UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto Washington Luiz Pacheco de Carvalho A ausência de um processo reflexivo sobre as necessidades e interesses do bem-estar
científico-tecnológico, ou seja, um comportamento hiperindividualista e de aceitação do que é
dito pelos especialistas, é o que corrobora o modo de ser da sociedade contemporânea. Um exemplo interessante para caracterizar o que seria a ideia de risco e a incerteza
frente a uma possível solução científico-tecnológica, seria o caso do campo eletromagnético,
produzido por aparelhos celulares e outros dispositivos de radiofrequência (televisores,
antenas de celulares e etc.). Ao se falar de uma educação para Ciência reconhece-se a necessidade de formação de
atores sociais que estejam aptos a exercer uma liberdade comunicativa frente às relações da
Ciência e Sociedade. Logo, pode-se dizer que a escola é o lócus em que ocorre a reprodução dos
conhecimentos construídos e reconstruídos ao longo da evolução da sociedade. A escola
possui uma identidade própria e uma função social pré-determinada. Cabe a ela “servir como
instância de formação intelectual e moral dos indivíduos e de formação técnica para o
atendimento das necessidades do mercado emergente, decorrente do desenvolvimento
industrial” (MUHL, p. 270, 2003). Segundo Longhi (2005), é possível reconhecer que a
escola possui a função de reproduzir as tradições culturais e outros valores do mundo
sistêmico, como, também, de assegurar o exercício da crítica frente aos novos fatos da
sociedade contemporânea e do conhecimento, buscando, por meio do agir comunicativo,
transformações dos significados coletivos e interpretativos dos fatos do mundo moderno. A função social da escola pode ser desvelada por meio da reprodução cultural do
conhecimento construído historicamente por meio de saberes selecionados e inseridos no
currículo escolar. Por outro lado, o exercício da crítica só se torna assegurado na inserção de
temáticas controversas no domínio do currículo. Ora, como exemplo de temática controversa,
temos as problemáticas ambientais, as drogas, a pobreza e as questões sociocientíficas. É nesse ponto em que a teoria do agir comunicativo potencializa a reflexão sobre as
questões sociocientíficas como sendo um recorte do pano fundo do mundo da vida que
necessita ser tematizado. 154
AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS 2012, p.141-160
No processo de tematização das questões sociocientíficas, segundo a teoria do agir
comunicativo, o ator social precisa fazer menção ao mundo objetivo (teorias, leis e
princípios), ao mundo social (normas nas interações sociais) e ao mundo subjetivo
(impressões pessoais, narrativas biográficas e etc.) no intuito de agir com responsabilidade e 154 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto autonomia sobre as coisas do mundo (SUTIL, 2009). Nesse processo, a linguagem é o meio
pelo qual os atores se reportam a cada um dos três mundos no intuito de alcançar um
consenso por meio do entendimento, o qual é regulado pelas pretensões de validez. Diante
disso, o consenso está vinculado com aquilo que os participantes de uma discussão procuram
ter em comum, ou seja, a constituição de um conhecimento sobre uma questão sociocientífica. Outro ponto importante da teoria da sociedade habermasiana, que vem contribuir com
a discussão das questões sociocientíficas, é sobre o uso da razão comunicativa. Há três
maneiras de utilizar a razão comunicativa pelos atores sociais no contexto comunicativo,
segundo Habermas. A primeira é o uso pragmático da razão, a segunda o uso ético da razão e
a terceira o uso moral da razão. O uso pragmático da razão comunicativa está orientado pelos
fins. Já o uso ético está orientado para aquilo que é bom para o indivíduo e para sociedade. Por fim, o uso moral da razão comunicativa está voltado para as questões de justiça, ou seja, o
que é correto. Ora, o que irá orientar os usos da razão pelos participantes são os interesses
envolvidos no contexto de comunicação (LONGHI, 2008). O entendimento dos usos da razão comunicativa é de importância fulcral no contexto
do ensino de ciências, particularmente, na dimensão das questões sociocientíficas. Isto porque
ele leva a discutir os impactos da ciência e tecnologia no mundo. O homem sempre buscou
discutir o que é bom e justo para todos. A cultura ocidental nunca abandonou o projeto de
encontrar uma ética e uma moral universal (LONGHI, 2008, p.77). As inovações na ciência e na tecnologia demandam ao homem a autorreflexão quantos
aos aspectos éticos e morais dos produtos científico-tecnológicos. A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS Há uma imensa dificuldade
em estabelecer critérios para uso da razão pragmática, ética e moral no contexto da sociedade
científico-tecnológica. Isto porque, os interesses e motivações que contribuem para o avanço
da ciência e da tecnologia, muitas vezes, estão vinculados aos imperativos corporativistas e
também à natureza dos produtos que são bons e justos para a promoção do bem-estar social
(HABERMAS, 2006; LONGHI, 2008). O uso pragmático, ético e moral da razão comunicativa diante dos avanços da
sociedade contemporânea permite que os atores sociais sejam movidos ao exercício da
autocompreensão frente aos conflitos e incertezas técnico-científicas. Segundo Longhi (2008),
o exercício da autocompreensão depende dos modelos interpretativos que estão articulados a
um determinado contexto cultural do sujeito. As interpretações que os sujeitos fazem sobre
determinado evento do mundo fazem parte da constituição da identidade do mesmo. É a 155 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho cultura, na qual o ator social está imerso, que irá orientar o próprio agir diante as situações do
mundo. Diante destas demandas sobre o que se deve fazer quanto aos impactos da ciência e
tecnologia na vida privada, como também no meio ambiente, é que se torna importante o uso
prático (ético e moral) da razão comunicativa, que não esteja fundamentado no sujeito, mas,
sim, num contexto intersubjetivo e solidário que garanta o enfrentamento coletivo deste
desafio da sociedade contemporânea. Esta perspectiva de enfrentamento permite que ocorra a constituição da vontade
coletiva dos atores sociais para deliberação de temas em comum. Isso permite a unificação da
razão prática com a vontade soberana de direitos humanos e democracia, pois, a vontade
coletiva do povo, é legítima para legislar (HABERMAS, 1990). A soberania popular só deve
poder manifestar-se ainda sob as condições discursivas de um processo, em si diferenciado,
de formação de opinião e de vontade (HABERMAS, 1990, p. 102). Logo, a formação de opinião e de vontade está intimamente relacionada com a ética
discursiva de Habermas, “a qual se refere aos pressupostos da comunicação que cada um de
nós intuitivamente fazemos sempre quando estamos dispostos de argumentar seriamente”
(DUTRA, 2005, p. 151). A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS Os pressupostos de comunicação, segundo o agir comunicativo, são as pretensões de
validade que orientam o contexto comunicativo para o consenso. Segundo Dutra (2005), à
própria facticidade do mundo, da aceitação e vigência subjaz um reconhecimento tácito destas
pretensões de validade. Isso porque, quando um falante se posiciona e apresenta uma
argumentação em relação ao tema em debate, pressupõe que todos o ouçam. A validação do
argumento proferido pelo falante dependerá das pretensões serem aceitas ou não pelos
participantes. A aceitabilidade ou não está vinculada ao principio do discurso teórico ou
prático. A compreensão desse processo é de suma importância e possibilita perceber o
potencial cognitivo em relação à ética discursiva, pois, no intuito de convencer os
participantes sobre a validade de uma opinião, é necessário sempre se reportar ao discurso
(prático ou moral) como forma de reconstruir os saberes proferidos para que estes estejam de
acordo com as pretensões de validez. Logo, a ética discursiva rebate o enfoque decisionista de
que não é preciso justificar as afirmações e opiniões proferidas. 156 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto Washington Luiz Pacheco de Carvalho O consenso em relação a um contexto comunicativo é o que permite a formação da
vontade. Esta vontade racional é constituída de processos argumentativos, sem coações, na
qual o que vale é o melhor argumento para a busca intersubjetiva e solidária da verdade. Esse
aprendizado ocorre socialmente e a escola é uma instituição com elevado potencial para que
os alunos experienciem este processo adquirindo conhecimentos necessários para
compreender o agir comunicativo. No entanto, os alunos não estão formados para agirem
racionalmente em função da competência linguística necessária para uma ética discursiva e a
prática do melhor argumento. Logo, eles são formados para isso. As questões sociocientíficas
possuem um importante papel nesta formação. Como foi discutido, as questões sociocientíficas possuem uma estrutura teórico-
pedagógica que contribui com o desenvolvimento dos alunos quanto à pratica discursiva, a
natureza da ciência, as dimensões éticas e morais e os diferentes aspectos culturais envolvidos
na temática. A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS É possível perceber que a temática sociocientífica se aproxima da teoria da ação
comunicativa como forma de tematização das coisas do mundo da vida e, por outro lado, uma
maneira de resistir às invasões sistêmicas que acabam potencializando as patologias da
modernidade, como, por exemplo, depressão, alienação, perda de sentido e esvaziamento
cultural. Ao levarmos as questões sociocientíficas para o contexto escolar, e se tomarmos como
pressuposto teórico as orientações do agir comunicativo, precisamos considerar que existe
uma assimetria de falas entre professor-aluno. Isso porque o professor aprioristicamente já é
um adulto, enquanto o aluno ainda perpassa um processo de formação moral. Diante disto, o
que temos é uma ação educativa no contexto das questões sociocientíficas. Segundo Longhi (2005), a ação educativa é subsidiada pelos pressupostos da teoria da
ação comunicativa, sendo que, na ação comunicativa, o objetivo da troca intersubjetiva é o
consenso alcançado intersubjetivamente por meio do entendimento via atos de fala, tendo
como regras de orientação comunicativa as pretensões de validez. Já na ação educativa, o
objetivo da interação intersubjetiva é a aprendizagem de um agir comunicativo, segundo os
pressupostos da teoria da ação comunicativa. Na teoria do agir comunicativo o telos é o consenso enquanto que o entendimento é
o meio, o instrumento por meio do qual é possível atingir o consenso. Na ação
educativa o telos é a aprendizagem das regras próprias do agir comunicativo,
enquanto que o processo educativo/formativo é o instrumento orientador do
processo de aquisição das regras próprias do agir comunicativo. Tanto no processo
do agir comunicativo quanto no processo de ação educativa é fundamental que o 157 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS
Adriana Bortoletto
Washington Luiz Pacheco de Carvalho
agir para o consenso e a ação para a formação estejam orientadas pelo entendimento
(LONGHI, p.138, 2005). UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOC OC
Í
CAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho agir para o consenso e a ação para a formação estejam orientadas pelo entendimento
(LONGHI, p.138, 2005). A ação educativa possui o caráter formativo que tem por objetivo orientar os alunos a
reconhecer e executar as ações guiadas pelo entendimento para obter um possível consenso. A CONTRIBUIÇÃO DA TEORIA DA AGIR COMUNICATIVO NO TRATAMENTO
DAS QUESTÕES SOCIOCIENTÍFICAS Nesse contexto, as assembleias de sala de aula e a elaboração de normas de convivência são
bons exemplos do exercício formativo do agir educativo. A vontade racional e a formação de
opinião dos alunos irão depender do nível de desenvolvimento dos alunos, do grau de
autonomia e a capacidade argumentativa dos mesmos. Logo, compete ao professor orientar as
ações comunicativas em sala de aula. O potencial formativo também está vinculado à
diferença de autonomia e à capacidade argumentativa do professor e dos alunos (LONGHI,
2005). CONSIDERAÇÕES FINAIS Há uma naturalização da formação continuada de professores por meio de cursos
tradicionais que têm por objetivo o treinamento de professores na dimensão conteudística. Devido a essa tradição, muitos professores possuem resistências a estratégias diferenciadas de
formação que potencializam a interação comunicativa no desenvolvimento de propostas
interdisciplinares, como, por exemplo, as questões sociocientíficas. Grande parte das resistências está associada à dificuldade de enfrentamento das
insuficiências formativas, sendo que elas podem estar vinculadas ao mundo subjetivo do
professor, ou seja, a natureza interna do mesmo, das suas crenças pessoais e/ou biografia. Por outro lado, podem ocorrer resistências quanto ao mundo objetivo, ou seja,
dificuldade de leitura, de entendimento de teorias tanto pedagógicas como o conteúdo
específico escolar. Quanto ao mundo social, alguns docentes pode ter dificuldade de enfrentar as
apresentações de seminários, em articular o conhecimento teórico disciplinar com os outros
participantes. 158
AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
Frente a essas adversidades, o discurso teórico caracterizado como sendo o momento
quando um participante levanta uma crítica frente aos aspectos teóricos do mundo objetivo
(por exemplo, os pressupostos teóricos das questões sociocientíficas) e estabelece um 158 MA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
ATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
OCIOCIENTÍFICAS
Adriana Bortoletto
Washington Luiz Pacheco de Carvalho
processo argumentativo, no qual o que vale é a força do melhor argumento, torna-se um
elemento fulcral para tematização das questões referentes à cultura. UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto
Washington Luiz Pacheco de Carvalho Adriana Bortoletto processo argumentativo, no qual o que vale é a força do melhor argumento, torna-se um
elemento fulcral para tematização das questões referentes à cultura. Quanto ao discurso prático, este é de extrema valia no intuito de tematizar junto aos
potenciais professores em formação a importância do compromisso com o grupo, da
articulação entre o falar e agir. O discurso prático surge sempre que algum participante
levanta uma crítica frente à pretensão de normas e direito em relação ao comprometimento
com o grupo, ou mesmo como forma de tematização das dificuldades do contexto de sala de
aula. CONSIDERAÇÕES FINAIS Por fim, a crítica terapêutica surge quando há necessidade de tematizar a conduta de
algum participante perante o grupo, por exemplo, quando há encenação (ação dramatúrgica)
no contexto formativo, o que acabava dificultando o processo de formativo. Para que ocorra uma formação de professores voltada para responsabilidade e
autonomia frente ao tratamento das questões sociocientíficas como qualquer outro tema, é
imprescindível a busca do equilíbrio entre os usos da razão objetiva, subjetiva e social. É com
base nesse equilíbrio que é possível desenvolver prática comunicativa entre professores
voltada para o entendimento. REFERÊNCIAS GIROUX, H. Os professores como intelectuais: rumo a uma pedagogia crítica da
aprendizagem. Tradução Daniel Bueno. Porto Alegre: Artmed, 1997. 270 p. GIROUX, H. Os professores como intelectuais: rumo a uma pedagogia crítica da
aprendizagem. Tradução Daniel Bueno. Porto Alegre: Artmed, 1997. 270 p. GUIMARÃES, Márcio Andrei. Raciocínio informal e a discussão de questões
sociocientíficas: o exemplo das células-tronco humanas. 2011. Tese (Doutorado em Educação
para a Ciência) Faculdade de Ciências, Universidade Estadual Paulista, Bauru, 2011. GIROUX, H. Os professores como intelectuais: rumo a uma pedagogia crítica da
aprendizagem. Tradução Daniel Bueno. Porto Alegre: Artmed, 1997. 270 p. GUIMARÃES, Márcio Andrei. Raciocínio informal e a discussão de questões
sociocientíficas: o exemplo das células-tronco humanas. 2011. Tese (Doutorado em Educação
para a Ciência) Faculdade de Ciências, Universidade Estadual Paulista, Bauru, 2011. GUIMARÃES, Márcio Andrei. Raciocínio informal e a discussão de questões
sociocientíficas: o exemplo das células-tronco humanas. 2011. Tese (Doutorado em Educação
para a Ciência) Faculdade de Ciências, Universidade Estadual Paulista, Bauru, 2011. HABERMAS, J. Racionalidade e Comunicação. Lisboa: Edições 70, 2002. HABERMAS, J. A ética da discussão e a questão da verdade. São Paulo: Martins Fontes,
2004. HABERMAS, J. Teoria da Ação Comunicativa I. São Paulo. Martins Fontes 2012 a. HABERMAS, J. Teoria da Ação Comunicativa II. São Paulo. Martins Fontes 2012b. MAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160 159 UMA PROPOSTA DE FORMAÇÃO CONTINUADA DE PROFESSORES DE CIÊNCIAS E
MATEMÁTICA NA INTERFACE DO AGIR COMUNICATIVO E DAS QUESTÕES
SOCIOCIENTÍFICAS Adriana Bortoletto
Washington Luiz Pacheco de Carvalho LONGHI, A. A ação educativa na perspectiva da teoria do agir comunicativo de Jürgen
Habermas: uma abordagem reflexiva. 2005 Tese de Doutorado. Faculdade de Educação. Universidade de Campinas, Campinas, 2005. LONGHI, A. A ação educativa na perspectiva da teoria do agir comunicativo de Jürgen
Habermas: uma abordagem reflexiva. 2005 Tese de Doutorado. Faculdade de Educação. Universidade de Campinas, Campinas, 2005. MÜHL, E. H. Habermas: ação pedagógica como agir comunicativo. Passo Fundo: UPF,
2003. RATCLIFFE M.; GRACE M. Science education for citizenship: teaching socioscientific
issues. Maidenhead: Open University Press, 2003 SADLER, T., ZEIDLER, D. Patterns of Informal Reasoning in the Context of Socioscientific
Decision Making. Journal Research in Science Teaching. n.01, v.42. 2005. SADLER, T. Informal Reasoning Regarding Socioscientific Issues: A Critical Review of
Research. Journal Research in Science Teaching. n.05.v.41, 2004. KOLSTO, S. REFERÊNCIAS Scientific Literacy for Citizenship: Tools for Dealing with the Science
Dimension of Controversial Socioscientific Issues. International Journal of Science
Education. v.85, n. 3, p. 291-310, 2001 ULRICH, B.; GIDDENS, A.; LASH, S. Modernização Reflexiva: Política, Tradição e Estética
na Ordem Social Moderna. São Paulo: UNESP, 1996. ZEIDLER, D.; SADLER, D. T.; SIMMONS, L.M.; HOWES, V.E Beyond STS: A Research-
Based Framework for Socioscientific Issues Education. International Journal of Science
Education. v.89, n.3, p. 357 – 377, 2005. ZEIDLER, D.; KEEFER, M. The Role of Moral Reasoning and the Status of Socioscientific
Issues in Science Education. In: ZEIDLER, D. (Org.) The Role of Moral Reasoning on
Socioscientific Issues and Discourse in Science Education. Dordrecht, The Netherlands:
Kluwer Academic Publishers, 2003, p. 07 – 40. 160 AMAZÔNIA - Revista de Educação em Ciências e Matemáticas V.9 – nº 17 - jul. 2012/dez. 2012, p.141-160
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Textbook outcome after major hepatectomy for perihilar cholangiocarcinoma — definitions and influencing factors
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Langenbeck's archives of surgery
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Abstract Purpose The concept of “textbook outcome” (TO) as composite quality measure depicting the ideal surgical has not yet
been defined for patients undergoing major hepatectomy (MH) for perihilar cholangiocarcinoma (PHC). This study sought
to propose a uniform definition through a systematic literature review as well as to identify patient- or procedure-related
factors influencing TO. l
Methods In this retrospective study, we analyzed all patients undergoing MH for PHC at our department between January
2005 and August 2019. After conducting a systematic literature search, we defined TO as the absence of 90-day mortal-
ity and major complications, no hospital readmission within 90 days after discharge, and no prolonged hospital stay (<75. percentile). A binary logistic regression analysis was performed to identify factors influencing TO. l
Results Of 283 patients, TO was achieved in 67 (24%) patients. Multivariate analysis revealed that preoperative biliary
drainage was associated with a decreased (OR= 0.405, 95% CI: 0.194–0.845, p=0.016) and left-sided-resection (OR= 1.899,
95% CI: 1.048–3.440, p=0.035) with increased odds for TO. Overall survival (OS) and DFS (disease-free survival) did not
differ significantly between the outcome groups (OS: p=0.280, DFS: p=0.735). However, there was a trend towards better
overall survival, especially in the late course with TO.ii Conclusion Our analysis proposed a uniform definition of TO after MH for PHC. We identified left hepatectomy as an inde-
pendent factor positively influencing TO. In patients where both right- and left-sided resections are feasible, this underlines
the importance of a careful selection of patients who are scheduled for right hepatectomy. Keywords Textbook outcome · Perihilar cholangiocarcinoma · Major hepatectomy * Moritz Schmelzle
moritz.schmelzle@charite.de Christian Benzing1 · Lena Marie Haiden1 · Felix Krenzien1 · Alexa Mieg1 · Annika Wolfsberger1 ·
Cecilia Filiz Atik1 · Nora Nevermann1 · Uli Fehrenbach2 · Wenzel Schöning1 · Moritz Schmelzle1 ·
Johann Pratschke1 Christian Benzing1 · Lena Marie Haiden1 · Felix Krenzien1 · Alexa Mieg1 · Annika Wolfsberger1 ·
Cecilia Filiz Atik1 · Nora Nevermann1 · Uli Fehrenbach2 · Wenzel Schöning1 · Moritz Schmelzle1 ·
Johann Pratschke1 Received: 9 November 2021 / Accepted: 9 February 2022
© The Author(s) 2022
/ Published online: 4 March 2022 ORIGINAL ARTICLE ORIGINAL ARTICLE ORIGINAL ARTICLE https://doi.org/10.1007/s00423-022-02467-y
Langenbeck's Archives of Surgery (2022) 407:1561–1573 https://doi.org/10.1007/s00423-022-02467-y
Langenbeck's Archives of Surgery (2022) 407:1561–1573 Histopathology In all cases, PHC was confirmed according to the histopatho-
logical reports of the resected specimen. Furthermore, data
on resection and lymph node status as well as perineural
sheath infiltration, microvascular infiltration, lymphangio-
sis carcinomatosa, and tumor differentiation were collected
from pathology reports. Based on the collected data and the
TNM classification valid at the time of resection, patients
were assigned to the appropriate tumor stage according
to the Union for International Cancer Control (UICC, 7th
edition). Patients and study design Patients undergoing MH in curative intent for PHC between
January 2005 and August 2019 at the Department of Surgery,
Campus Charité – Mitte and Campus Virchow Klinikum,
Charité – Universitätsmedizin Berlin were retrospectively
analyzed. This retrospective study was approved by the local
ethics committee (EA2/006/16 and EA1/358/16). Variables
included in the analysis were general patient characteristics
such as gender, age, American Association of Anesthesiolo-
gists (ASA) score, and body mass index (BMI). Periopera-
tive and histopathological data were recorded as well as data
on overall survival (OS) and disease-free survival (DFS). Postoperative morbidity as classified by Dindo-Clavien
during hospitalization, 30- and 90-day mortality, length of Surgical procedure All patients who underwent MH for PHC were included in
the analysis. The surgical resection was performed either as
a right or left sided major hepatectomy with extrahepatic
bile duct resection as described before [2, 3]. Biliary recon-
struction was performed as end-to-side hepaticojejunostomy. Patients with extrahepatic bile duct resection alone or mul-
tivisceral resections, e.g., hepatoduodenopancreatectomy
(HPD) were excluded from the analysis as well as patients
with intrahepatic or distant metastases or local peritoneal
carcinomatosis. Introduction Perihilar cholangiocarcinoma (PHC) is a rare malignant
tumor arising from the bile duct that is characterized by a
poor prognosis [1]. So far, major hepatectomy (MH) is the
only established, potentially curative treatment for patients
with PHC. Radical surgical approaches such as hilar en bloc
resection described by Neuhaus and colleagues were able to
increase overall survival rates in the last years [2, 3]. How-
ever, high postoperative morbidity and mortality still remain
unsatisfactory, despite advances in preoperative workup such
as portal vein embolization (PVE) and improvements in
perioperative management [4–6]. Diagnosis at an advanced
stage, which is often accompanied by bile duct obstruc-
tion, cholestasis, cholangitis, and poor liver function, and
radical surgical approaches are associated with morbidity Christian Benzing and Lena Marie Haiden contributed equally to
this work and share first authorship. Moritz Schmelzle and Johann Pratschke contributed equally to this
work and share senior authorship. * Moritz Schmelzle
moritz.schmelzle@charite.de
1
Department of Surgery, Campus Charité Mitte | Campus
Virchow‑Klinikum, Experimental Surgery and Regenerative
Medicine, Charité – Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany
2
Department of Radiology, Charité - Universitätsmedizin
Berlin, Berlin, Germany Christian Benzing and Lena Marie Haiden contributed equally to
this work and share first authorship. Moritz Schmelzle and Johann Pratschke contributed equally to this
work and share senior authorship. * Moritz Schmelzle
moritz.schmelzle@charite.de 1
Department of Surgery, Campus Charité Mitte | Campus
Virchow‑Klinikum, Experimental Surgery and Regenerative
Medicine, Charité – Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany 2
Department of Radiology, Charité - Universitätsmedizin
Berlin, Berlin, Germany (0121 3456789)
3 1562 Langenbeck's Archives of Surgery (2022) 407:1561–1573 hospital stay, and intensive care unit stay, respectively, were
recorded as well [21]. rates as high as 50–60% and substantial mortality rates
ranging between 5 and 18%, even in high-volume centers
[5, 7–11]. After resection, common complications are bile
leakage, septic, or vascular complications; however, post-
hepatectomy liver failure (PHLF) being associated with a
high associated mortality is feared the most [7, 12]. Preoperative management All patients who were referred to our institution for surgical
treatment underwent a highly individualized and detailed
workup. This routinely included computed tomography and/
or magnetic resonance imaging of the chest and abdomen
as well as endoscopic retrograde cholangiography (ERC). Biliary drainage with ERC and biliary stenting or percutane-
ous transhepatic cholangiodrainage (PTCD) was performed
when necessary. Routinely, Carbohydrate antigen 19-9 (CA
19-9) was measured before resection. On patients with sus-
pected peritoneal dissemination, diagnostic laparoscopy or
laparotomy was performed. g
y
[ ,
]
Recently, the concept of the “textbook outcome” (TO)
as composite quality measure depicting the ideal surgical
outcome has been used especially in complex oncological
surgery [13–16]. TO is achieved when certain predefined
desirable outcomes are simultaneously present in a patient’s
postoperative course representing a much more comprehen-
sive summary of a patient’s hospitalization than one singu-
lar outcome parameter such as mortality [17]. There is no
generally accepted definition of TO and different parameters
are used to define TO depending on the type of surgery or
tumor [18]. Traditional quality measures like postoperative
mortality (e.g., 90-day mortality), postoperative morbidity,
or length of stay (LOS) can often be found in the definition
of TO, but histopathological factors such as the presence
of an R0 resection are increasingly used as well [13, 19,
20]. As a comprehensive quality measure, TO can not only
be used by patients and health care providers for assessing
the quality of surgical care or hospital performance but also
by surgeons to optimize preoperative workup and surgical
care [19]. TO has not been established in PHC surgery yet
and TO rates as well as potentially influenceable patient-
and procedure-related factors TO are unknown. As it might
help improve surgical management and thus postoperative
morbidity and mortality, this study was conducted to define
TO after major liver resection for PHC, identify prognostic
factors predicting TO, and analyze the impact of achieving a
TO on overall survival (OS) and disease-free survival (DFS). Statistics Statistical analysis was performed using IBM SPSS Statis-
tics for Macintosh Version 25.0 (IBM Corp., Armonk, NY,
USA). A p-value < 0.05 was considered statistically signifi-
cant. Continuous parameters are presented as median and
range and statistically compared with the non-parametric
Mann-Whitney-U-test. Categorical data are displayed as
counts and percentages and are compared using the chi-
squared test or Fisher’s exact test, when necessary. To iden-
tify independent factors influencing TO, a binary logistic
regression analysis was performed. Results are reported
as odds ratio (OR) and 95% confidence interval (95% CI). Prognostic factors were included in the regression model
when a significant influence on TO was detected in univari-
ate analysis. The variables age and gender were included
in multivariate analysis regardless of significance. Sur-
vival was estimated with the Kaplan-Meier method and
compared between the outcome groups with the log-rank
test. Patients who died within 90 days of surgery were not
included in the survival analyses. A subgroup analysis was
performed with all patients surviving at least 30 months. Follow‑up Patients were followed up in the outpatient clinic or with
their general practitioner. Check-ups routinely included
testing of CA 19-9 serum levels and abdominal ultrasound,
CT, or MRI. Whether adjuvant chemotherapy was per-
formed was recorded as well. Definition of TO A total of 20 records were identified through database
searching. After removal of duplicates, 12 records were
screened for eligibility. After excluding sources that did
not meet the inclusion criteria, a total of 7 studies in HPB
surgery with TO as primary endpoint were identified for
the final review. Figure 1 summarizes the search algo-
rithm, whereas Table 1 and Table 2 give a summary on
included studies. All studies were retrospective and multi-
center studies that were published between 2019 and 2020. The smallest and largest series contained 687 and 21234
patients, respectively. Postoperative mortality, length of
stay, and hospital readmission were part of the TO defini-
tion in all seven studies. Four records [17, 19, 20, 24] used
30-day mortality and 30-day readmission, whereas three
studies [13, 22, 23] used a span of 90 days instead. His-
topathological criteria were used in four studies [13, 17,
19, 20] to define TO. This included tumor-free resection
margins in all four studies [13, 17, 19, 20] and absence of
lymph node metastases in one [20] study. Adjuvant chemo-
therapy and the need for postoperative transfusion were
part of the TO definition in two studies [17, 20]. One study
was not able to get detailed information on postoperative
morbidity and used LOS instead [20]. Specific complica-
tions such as bile leakage or postoperative pancreas fis-
tula were part of the TO definition on one study [24]. All
studies investigated TO rates for different tumor entities
or HPB procedures, and most studies sought to identify
TO-influencing factors after surgery (Table 2). Textbook outcome and postoperative course As TO had not yet been defined for major liver resection
for PHC, a systematic literature review was conducted to
evaluate common TO definitions used in HPB surgery. TO
was defined based on the results of this literature review
and common complications after PHC resection mentioned
in the established literature. The search terms “textbook
outcome” and “textbook oncologic outcome” were short-
ened to “textbook outcom*” and “textbook oncologic 3 1563 Langenbeck's Archives of Surgery (2022) 407:1561–1573 outcom*” and furthermore combined with the Boolean
operator AND the following search terms: “liver surgery,”
“hepatectomy,” “resection of liver,” “pancreatic surgery,”
“pancreaticoduodenectomy,” “resection of pancrea*,”
“hepatopancreatic surgery.” The publication period was
limited to the years 2010 to 2020. Only studies in Eng-
lish with TO as primary endpoint were considered. Study
designs such as reviews or meta-analyses were excluded. In addition, studies that investigated hepatic resections
performed laparoscopically were excluded. TO was
defined as the absence of 90-day mortality and major com-
plications (i.e., > grade II according to Dindo-Clavien),
no hospital readmission within 90 days after discharge,
and no prolonged hospital stay (i.e., <75. percentile). The
dichotomous textbook outcome was achieved when all four
abovementioned individual criteria were observed in one
patient after resection. Patients that could not be classified
as either TO or NTO due to missing data were excluded
from the analysis. outcom*” and furthermore combined with the Boolean
operator AND the following search terms: “liver surgery,”
“hepatectomy,” “resection of liver,” “pancreatic surgery,”
“pancreaticoduodenectomy,” “resection of pancrea*,”
“hepatopancreatic surgery.” The publication period was
limited to the years 2010 to 2020. Only studies in Eng-
lish with TO as primary endpoint were considered. Study
designs such as reviews or meta-analyses were excluded. In addition, studies that investigated hepatic resections
performed laparoscopically were excluded. TO was
defined as the absence of 90-day mortality and major com-
plications (i.e., > grade II according to Dindo-Clavien),
no hospital readmission within 90 days after discharge,
and no prolonged hospital stay (i.e., <75. percentile). The
dichotomous textbook outcome was achieved when all four
abovementioned individual criteria were observed in one
patient after resection. Patients that could not be classified
as either TO or NTO due to missing data were excluded
from the analysis. Patients’ characteristics In this study, two hundred and eighty-three patients who
underwent surgical resection for PHC in curative intent
between January 2005 and August 2019 and met the
inclusion criteria were analyzed. The cohort comprised
171 (60%) male and 112 (40%) female patients with a
mean age of 65 (33–86) years. The majority of patients
was grouped in either ASA 2 (56%, n=159) or ASA 3
(38%, n=107), thus suffering from pre-existing conditions. Table 3 summarizes all patient characteristics of the total
cohort. The majority of patients presented with Bismuth
Type IV PHC or advanced UICC stages (IIIB–IVA: 48%,
n=134). Tumor-free resection margins were achieved
in 68% (n=189) of all patients, whereas 48% (n=132)
patients had histopathologically confirmed local lymph
node metastases. Most patients presented with a moder-
ate tumor differentiation (G2: 68%, n=190). A total of 1 3 1564 Langenbeck's Archives of Surgery (2022) 407:1561–1573 Langenbeck s Archives of Surgery (2022) 407:1561–1573 g
g y (
) Fig. 1 Flowchart of search
algorithm Fig. 1 Flowchart of search
algorithm Fig. 1 Flowchart of search
algorithm Table 1 TO studies included in review TO textbook outcome, RA30 no 30-day readmission, LOS no prolonged hospital stay, 30DM no 30-day mortality, RA90 no 90-day readmission,
90DM no 90-day mortality, PK0 no postoperative complications according Dindo-Clavien [21], PK<III no major postoperative complications
according Dindo-Clavien (i.e., grade <III) [21], R0 tumor-free resection margin after resection, Tr0 no perioperative blood transfusion, PPF no
postoperative pancreas fistula, BL no bile leakage, PPH no post-pancreatectomy hemorrhage, aCT adjuvant chemotherapy, N0 absence of lymph
node metastasis
Author
Year of
publication
Study characteristics
Year of inclusion
Number of
patients
TO definition used
Heidsma et al. [13]
2020
Retrospective, multicenter
2000–2016
821
LOS, RA90, 90DM, R0, PK<III
Mehta et al. [22]
2020
Retrospective, multicenter
2013–2017
21234
LOS, RA90, 90DM, PK0
Merath et al. [17]
2019
Retrospective, multicenter
1993–2015
687
LOS, 30DM, RA30, R0, PK0, Tr0
Merath et al. [23]
2020
Retrospective, multicenter
2013–2015
13467
LOS, RA90, 90DM, PK0
Sweigert et al. [20]
2020
Retrospective, multicenter
2006–2015
18608
LOS, RA30, 30DM, aCT, N0, R0
Tsilimigras et al. [19]
2020
Retrospective, multicenter
2005–2017
1829
LOS, RA30, 30DM, R0, PK<III
Van Roessel et al. Patients’ characteristics [24]
2020
Retrospective, multicenter
2014–2017
3341
LOS, RA30, 30DM, BL, PK<III,
PPF, PPH TO textbook outcome, RA30 no 30-day readmission, LOS no prolonged hospital stay, 30DM no 30-day mortality, RA90 no 90-day readmission,
90DM no 90-day mortality, PK0 no postoperative complications according Dindo-Clavien [21], PK<III no major postoperative complications
according Dindo-Clavien (i.e., grade <III) [21], R0 tumor-free resection margin after resection, Tr0 no perioperative blood transfusion, PPF no
postoperative pancreas fistula, BL no bile leakage, PPH no post-pancreatectomy hemorrhage, aCT adjuvant chemotherapy, N0 absence of lymph
node metastasis 1 3 1565 Langenbeck's Archives of Surgery (2022) 407:1561–1573 Langenbeck's Archives of Surgery (2022) 407:1561–1573 Table 2 TO studies included in review
TO textbook outcome, DFS disease-free survival, HCC hepatocellular cholangiocarcinoma, ICC intrahepatic cholangiocarcinoma, OS overall
survival
Author
Tumor entity
Procedure
Primary endpoint
Heidsma et al. [13]
Pancreatic neuroendocrine tumor
Pancreatoduodenectomy, distal pan-
createctomy, enucleation
Incidence of TO, influence on DFS; TO
and different surgical approaches
Mehta et al. [22]
Malignant tumor of pancreas or liver
Minor or major liver resection, minor
or major pancreatic resection
Incidence of TO, TO rates according to
hospital type
Merath et al. [17]
ICC
Hepatectomy
Incidence of TO, factors associated
with TO, TO rates according to
hospital type
Merath et al. [23]
All indications for mentioned proce-
dure
Minor or major liver resection, minor
or major pancreatic resection
Incidence of TO, factors associated
with TO, TO and different surgical
approaches
Sweigert et al. [20]
Pancreatic adenocarcinoma
Pancreatoduodenectomy
Incidence of TO, factors associated
with TO, influence on OS
Tsilimigras et al. [19]
HCC, ICC
Hepatectomy
Incidence of TO, factors associated
with TO, influence on OS
Van Roessel et al. [24] All indications for mentioned proce-
dure
Pancreatoduodenectomy, distal pan-
createctomy
Incidence of TO, factors associated
with TO, TO rates according to
hospital type 114 patients (40%) were diagnosed with cholangitis preop-
eratively. Most patients underwent biliary drainage (86%,
n=243) before surgery. Portal vein embolization was part
of the preoperative workup in 46% (n=129) of patients, all
receiving right-sided resections. The majority of patients
underwent right-sided liver resection (63%, n=178) of
which 58% (n=165) were right trisectionectomies. Thirty-
seven percent (n=105) underwent left-sided liver resec-
tion, of which 23% (n=64) were left trisectionectomies. En
bloc portal vein resection was performed in 57% (n=162)
of cases. patients who did not (Table 4). Patients with TO showed
lower preoperative CA 19-9 levels (53 kU/l vs. Patients’ characteristics 95 kU/l,
p=0.047) and did less frequently undergo preoperative bil-
iary drainage (73% vs. 90%, p=0.001). Left-sided hepa-
tectomy was also associated with a higher TO rate when
compared to right hepatectomy (52% vs. 32%, p=0.003). With regard to right-sided resections only side and extent
of resection, TO is achieved in 18% (n=29) of right tri-
sectionectomies versus 23% (n=3) after standard major
hepatectomy (p=0.619). For left-sided resections, TO is
achieved in 33% (n=21) after left trisectionectomy vs. 34%
after standard major hepatectomy (n=14, p=0.888). Binary logistic regression analysis of factors
influencing textbook outcome Most patients suffered from postoperative complications
(90%, n=254), while major complications (grade IIIa–V)
occurred in 66% (n=186) [21]. Common complications
were infection (53%, n=150), pleural effusion (34%,
n=96), bile leakage (30%, n=86), and postoperative liver
failure (26%, n=74). Supplementary Table S1 gives an
overview of the specific postoperative complications. After resection, the median length of hospital stay was 23
(3–213) days. The 30-day and 90-day mortality were 8%
(n=22) and 15% (n=42). TO could be achieved in 24%
(n=67), severe postoperative complications where the
main reason not to be included in the TO group. From
all patients, 22% (n=61) had to be readmitted or had a
prolonged hospital stay (25%, n=72), thus not meeting
the TO criteria. Some differences in patients’ characteris-
tics were noted among patients who achieved TO versus To detect independent factors influencing TO, variables
shown in Table 5 that showed significant influence on TO
in univariable analysis were included in a binary regression
analysis model (Table 5). The regression analysis identi-
fied preoperative biliary drainage (OR= 0.405, 95% CI:
0.194–0.845, p=0.016) and left-sided-resection (OR= 1.899,
95% CI: 1.048–3.440, p=0.035), as independent factors
influencing TO, whereas left-sided resection was associated
with higher and preoperative biliary drainage with lower
odds of TO. Despite significant differences in univariable
analysis, tumor differentiation was not an independent pre-
dictor for TO (OR= 0.547, 95% CI: 0.263–1.137, p=0.106). The patient-related factors age, sex, and ASA score had no
impact on TO (age: p=0.392, sex: p=0.456, ASA: p=0.714). Binary logistic regression analysis of factors
influencing textbook outcome 1 3 Langenbeck's Archives of Surgery (2022) 407:1561–1573 1566 Table 3 Patient characteristics
Resected perihilar
cholangiocarcinoma
n = 283
Age1
65 (33–86)
BMI1
24.6 (16.0–38.3)
Gender (male)2
171 (60)
ASA score2
1
13 (5)
2
159 (56)
3
107 (38)
4
4 (1)
Bismuth-Corlette2
I
13 (5)
II
20 (7)
IIIa
72 (26)
IIIb
55 (20)
IV
116 (42)
UICC stage2
I
12 (4)
II
100 (36)
IIIa
32 (12)
IIIb
127 (46)
IVa
7 (2)
IVb
0 (0)
Resection margin2
R0
189 (68)
R1
89 (32)
Lymph node status2
N0
146 (53)
N+
132 (48)
Microvascular invasion2
Yes
48 (19)
No
206 (81)
Histopathological grading2
Grade 1
15 (5)
Grade 2
190 (68)
Grade 3
73 (26)
Perineural sheath infiltration2
Yes
207 (88)
No
28 (12)
Lymphangitis carcinomatosa2
Yes
100 (41)
No
147 (59)
T stage2
is
1 (0)
1
19 (7)
2a
81 (29)
2b
94 (33)
3
81 (29)
4
7 (3)
1 Data is presented as median and range; 2Data is presented as cou
and proportions (%)
Table 3 (continued)
Resected perihilar
cholangiocarcinoma
n = 283
Preoperative biliary drainage2
Yes
243 (86)
No
40 (14)
Portal vein embolization2
Yes
129 (46)
No
154 (54)
Preoperative cholangitis2
Yes
114 (40)
No
169 (60)
Resection side2
Left hepatectomy
105 (37)
Extended left hepatectomy
41 (15)
Left trisectionectomy
64 (23)
Right hepatectomy
178 (63)
Extended right hepatectomy
13 (5)
Right trisectionectomy
165 (58)
Portal vein resection2
Yes
162 (57)
No
121 (43)
Operating time (min)
385 (112–849)
Complications (Clavien-Dindo)2
None
29 (10)
I
12 (4)
II
56 (20)
IIIa
84 (30)
IIIb
51 (18)
IVa
6 (2)
IVb
1 (0)
V
44 (16)
Severe complications (grade IIIa–V)
186 (66)
Preoperative ALAT (U/l)
66 (9–1270)
Preoperative ASAT(U/l)
55 (13–3352)
CA 19-9 (kU/l)1
79 (1–32670)
ICU stay (days)1
4 (1–123)
Hospital stay (days)1
23 (3–213)
30-day mortality2
22 (8)
90-day mortality2
42 (15)
Hospital readmission
61 (22)
Prolonged hospital stay
72 (25)
Preoperative chemotherapy
Yes
10 (4)
No
273 (96)
Adjuvant chemotherapy
Yes
64 (23)
No
209 (77) Table 3 Patient characteristics 1 Data is presented as median and range; 2Data is presented as count
Table 3 (continued)
Resected perihilar
cholangiocarcinoma
n = 283
Preoperative biliary drainage2
Yes
243 (86)
No
40 (14)
Portal vein embolization2
Yes
129 (46)
No
154 (54)
Preoperative cholangitis2
Yes
114 (40)
No
169 (60)
Resection side2
Left hepatectomy
105 (37)
Extended left hepatectomy
41 (15)
Left trisectionectomy
64 (23)
Right hepatectomy
178 (63)
Extended right hepatectomy
13 (5)
Right trisectionectomy
165 (58)
Portal vein resection2
Yes
162 (57)
No
121 (43)
Operating time (min)
385 (112–849)
Complications (Clavien-Dindo)2
None
29 (10)
I
12 (4)
II
56 (20)
IIIa
84 (30)
IIIb
51 (18)
IVa
6 (2)
IVb
1 (0)
V
44 (16)
Severe complications (grade IIIa–V)
186 (66)
Preoperative ALAT (U/l)
66 (9–1270)
Preoperative ASAT(U/l)
55 (13–3352)
CA 19-9 (kU/l)1
79 (1–32670)
ICU stay (days)1
4 (1–123)
Hospital stay (days)1
23 (3–213)
30-day mortality2
22 (8)
90-day mortality2
42 (15)
Hospital readmission
61 (22)
Prolonged hospital stay
72 (25)
Preoperative chemotherapy
Yes
10 (4)
No
273 (96)
Adjuvant chemotherapy
Yes
64 (23)
No
209 (77) Resected per
cholangiocar
n = 283
Age1
65 (33–86)
BMI1
24.6 (16.0–3
Gender (male)2
171 (60)
ASA score2
1
13 (5)
2
159 (56)
3
107 (38)
4
4 (1)
Bismuth-Corlette2
I
13 (5)
II
20 (7)
IIIa
72 (26)
IIIb
55 (20)
IV
116 (42)
UICC stage2
I
12 (4)
II
100 (36)
IIIa
32 (12)
IIIb
127 (46)
IVa
7 (2)
IVb
0 (0)
Resection margin2
R0
189 (68)
R1
89 (32)
Lymph node status2
N0
146 (53)
N+
132 (48)
Microvascular invasion2
Yes
48 (19)
No
206 (81)
Histopathological grading2
Grade 1
15 (5)
Grade 2
190 (68)
Grade 3
73 (26)
Perineural sheath infiltration2
Yes
207 (88)
No
28 (12)
Lymphangitis carcinomatosa2
Yes
100 (41)
No
147 (59)
T stage2
is
1 (0)
1
19 (7)
2a
81 (29)
2b
94 (33)
3
81 (29)
4
7 (3) 1 1567 Langenbeck's Archives of Surgery (2022) 407:1561–1573 Age1
BMI1
Gender (male)2
ASA score2
1
2
3
4
Bismuth-Corlette2
I
II
IIIa
IIIb
IV
UICC stage2
I
II
IIIa
IIIb
IVa
Resection margin2
R0
R1
Lymph node status2
N0
N+
Microvascular invasion2
Yes
No
Histopathological grading2
Grade 1
Grade 2
Grade 3
Perineural sheath infiltration2
Yes
No
Lymphangitis carcinomatosa2
Yes
No
T stage2
is
1
2a
2b
3
4
Preoperative biliary drainage
Yes
No TO
NTO
p value
n = 67
n = 216
64 (38–81)
65 (33–86)
0.696
24.6 (16.0–35.0)
24.9 (16.0–38.3)
0.417
37 (55)
134 (62)
0.319
0.927
4 (6)
9 (4)
38 (57)
121 (56)
24 (36)
83 (38)
1 (2)
3 (1)
0.326
3 (5)
10 (5)
2 (3)
18 (9)
14 (21)
58 (28)
17 (26)
38 (18)
30 (46)
86 (41)
0.489
4 (6)
8 (4)
27 (40)
73 (35)
6 (9)
26 (12)
27 (40)
100 (47)
3 (5)
4 (2)
0.892
46 (69)
143 (68)
21 (31)
68 (32)
0.284
39 (58)
107 (51)
28 (42)
104 (49)
0.378
9 (15)
39 (20)
51 (85)
155 (80)
0.128
4 (6)
11 (5)
51 (77)
139 (66)
11 (17)
62 (29)
0.347
43 (84)
164 (89)
8 (16)
20 (11)
0.094
18 (31)
82 (57)
40 (69)
107 (43)
0.399
0 (0)
1 (0)
6 (9)
13 (6)
18 (27)
63 (29)
26 (39)
68 (32)
14 (21)
67 (31)
3 (5)
4 (2)
0.001
49 (73)
194 (90)
18 (27)
22 (10)
0.016 characteristics
tcome group
O)
Age1
BMI1
Gender (male)2
ASA score2
1
2
3
4
Bismuth-Corlette2
I
II
IIIa
IIIb
IV
UICC stage2
I
II
IIIa
IIIb
IVa
Resection margin2
R0
R1
Lymph node status2
N0
N+
Microvascular invasion2
Yes
No
Histopathological grading2
Grade 1
Grade 2
Grade 3
Perineural sheath infiltration2
Yes
No
Lymphangitis carcinomatosa2
Yes
No
T stage2
is
1
2a
2b
3
4
Preoperative biliary drainage
Yes
No Table 4 Patient characteristics
according to outcome group
(TO versus NTO) TO
NTO
p value
n = 67
n = 216
Age1
64 (38–81)
65 (33–86)
0.696
BMI1
24.6 (16.0–35.0)
24.9 (16.0–38.3)
0.417
Gender (male)2
37 (55)
134 (62)
0.319
ASA score2
0.927
1
4 (6)
9 (4)
2
38 (57)
121 (56)
3
24 (36)
83 (38)
4
1 (2)
3 (1)
Bismuth-Corlette2
0.326
I
3 (5)
10 (5)
II
2 (3)
18 (9)
IIIa
14 (21)
58 (28)
IIIb
17 (26)
38 (18)
IV
30 (46)
86 (41)
UICC stage2
0.489
I
4 (6)
8 (4)
II
27 (40)
73 (35)
IIIa
6 (9)
26 (12)
IIIb
27 (40)
100 (47)
IVa
3 (5)
4 (2)
Resection margin2
0.892
R0
46 (69)
143 (68)
R1
21 (31)
68 (32)
Lymph node status2
0.284
N0
39 (58)
107 (51)
N+
28 (42)
104 (49)
Microvascular invasion2
0.378
Yes
9 (15)
39 (20)
No
51 (85)
155 (80)
Histopathological grading2
0.128
Grade 1
4 (6)
11 (5)
Grade 2
51 (77)
139 (66)
Grade 3
11 (17)
62 (29)
Perineural sheath infiltration2
0.347
Yes
43 (84)
164 (89)
No
8 (16)
20 (11)
Lymphangitis carcinomatosa2
0.094
Yes
18 (31)
82 (57)
No
40 (69)
107 (43)
T stage2
0.399
is
0 (0)
1 (0)
1
6 (9)
13 (6)
2a
18 (27)
63 (29)
2b
26 (39)
68 (32)
3
14 (21)
67 (31)
4
3 (5)
4 (2)
Preoperative biliary drainage
0.001
Yes
49 (73)
194 (90) Langenbeck's Archives of Surgery (2022) 407:1561–1573 1568 Table 4 (continued) 1 Data is presented as median and range; 2Data is presented as count and proportions (%)
TO
NTO
p value
n = 67
n = 216
Yes
22 (33)
107 (50)
No
45 (67)
109 (50)
Preoperative cholangitis
0.571
Yes
25 (37)
89 (41)
No
42 (63)
127 (59)
Resection side2
0.003
Left hepatectomy
35 (52)
70 (32)
Extended left hepatectomy
14 (21)
27 (13)
Left trisectionectomy
21 (31)
43 (20)
Right hepatectomy
32 (49)
146 (68)
Extended right hepatectomy
3 (5)
10 (5)
Right trisectionectomy
29 (43)
136 (63)
Portal vein resection2
0.018
Yes
30 (45)
132 (61)
No
37 (55)
84 (39)
Operating time (min)
375 (232–547)
391 (112–849)
0.170
Severe complications (grade IIIa–V)
0 (0)
186 (86)
<0.001
Preoperative ALAT (U/l)1
68 (14–482)
66 (9–1270)
0.446
Preoperative ASAT (U/l)1
65 (17–430)
54 (13–3352)
0.919
CA 19-9 (kU/l)1
53 (1–32670)
95 (1–23049)
0.047
ICU stay (days)1
2 (2–18)
5 (1–123)
<0.001
Hospital stay (days)1
16 (7–37)
29 (3–213)
<0.001
Preoperative chemotherapy
0.300
Yes
1 (2)
9 (4)
No
66 (98)
207 (96)
Adjuvant chemotherapy
0.237
Yes
18 (29)
46 (22)
No
44 (71)
165 (78) Discussion 1 3 Langenbeck's Archives of Surgery (2022) 407:1561–1573 1569 Langenbeck's Archives of Surgery (2022) 407:1561–1573 Table 5 Univariable and
multivariable analysis of factors
influencing textbook outcome in
all resected patients All patients (n=283)
Variable
Univariable
Multivariable
OR (95% CI)
p value
OR (95% CI)
p value
Age
0.993 (0.968–1.018)
0.563
0.989 (0.963–1.015)
0.392
Gender (male)
0.755 (0.434–1.314)
0.320
0.800 (0.444–1.440)
0.456
Body mass index (kg/m2)
0.960 (0.892–1.034)
0.282
ASA (>2)
0.900 (0.511–1.583)
0.714
Preoperative ALAT (U/l)
1.000 (0.998–1.002)
0.825
Preoperative ASAT (U/l)
0.999 (0.997–1.001)
0.457
T stage (>2b)
0.694 (0.374–1.290)
0.248
UICC (>IIIA)
0.834 (0.480–1.449)
0.520
Preoperative CA 19-9 (kU/l)
1.000 (1.000–1.000)
0.999
Preoperative drainage (yes)
0.309 (0.154–0.620)
0.001
0.405 (0.194–0.845)
0.016
Resection side (left-sided resection)
2.281 (1.306–3.984)
0.004
1.899 (1.048–3.440)
0.035
Preoperative cholangitis (yes)
0.849 (0.483–1.494)
0.571
Histopathological grading (>G2)
0.484 (0.237–0.986)
0.046
0.547 (0.263–1.137)
0.106
Perineural sheath infiltration (Pn1)
0.655 (0.270–1.590)
0.350
Lymphovascular invasion (L1)
0.587 (0.314–1.098)
0.096
Microvascular invasion (V1)
0.701 (0.318–1.547)
0.379
Lymph node status (N+)
0.739 (0.424–1.287)
0.285 often develop more than one complication. Instead of
using “no morbidity” as a measure [23], major complica-
tions (≥IIIa according to Dindo-Clavien) were chosen as
a parameter in this analysis, because major complications
are frequently observed after MH for PHC [5, 21–23, 26]. Although R0 status was part of the TO definition in half of
the TO studies [13, 17, 19, 20], we decided not to include
it in the definition of TO in PHC surgery for several rea-
sons. First, the perihilar region is narrow and R1 resection
is not uncommon in PHC surgery [28–30] and patients
benefit from surgical resection even in case R1 status is
obtained. Second, especially in the subset of lymph node-
positive patients which counts up to almost 50%, survival
is independent of R status [30]. Third, PHC surgery is
characterized by high perioperative morbidity and mortal-
ity. Thus, TO should rather be defined by an uneventful
postoperative course than histopathological criteria. TO was defined as the absence of 90-day mortality and
major complications (i.e., > grade II according to Dindo-
Clavien), no hospital readmission within 90 days after dis-
charge, and no prolonged hospital stay (i.e., <75. percentile). According to the literature review, the exclusion criteria for
TO were 90-day mortality, severe complications (≥IIIa
according to Dindo-Clavien), unplanned readmission, and
prolonged hospital stay [21]. Discussion Median OS of all patients was 29 (24–35) months after
resection, whereas DFS was 22 (17–26) months. After
excluding patients who died within 90 days after resec-
tion, no significant difference between the two groups in
either OS (p=0.280) or DFS (p=0.735) analysis could be
detected. However, a trend towards better overall survival
in patients with TO especially in the late course could
be shown that failed to reach statistical significance. Sub-
group analyses of patients surviving at least 30 months
(Supplementary Table S2) after resection showed better
overall survival in patients with TO compared to patients
without TO (92 versus 60, p=0.039). There was no differ-
ence in DFS between patients surviving at least 30 months
(p=0.270, Figure 2A–D). In recent years, the concept of the TO as a quality meas-
ure depicting the ideal surgical outcome has been used in
complex oncological surgery, especially in the field of HBP
surgery. A recently published multi-center study by Mueller
et al. has examined the outcome after PHC surgery for so-
called benchmark cases [25]. This study marks an important
milestone in the field of PHC surgery since it provides a
definition of what is to be considered a benchmark case. However, this is the first study dealing with TO definitions in
PHC patients undergoing major hepatectomy. We were able
to identify relevant studies dealing with TO in the field of
HBP surgery and proposed a TO definition for PHC patients. Furthermore, we were able to identify left hepatectomy as a
factor that was independently associated with TO. Discussion Kaplan-Meier curves of (A) overall survival of all
resected patients with perihilar cholangiocarcinoma excluding 90-day
mortality according to outcome group; (B) overall survival of all
resected patients surviving >30 months according to outcome group;
(C) disease-free survival of all resected patients with perihilar chol-
angiocarcinoma excluding 90-day mortality according to outcome
group; and (D) disease-free survival of all resected patients with
perihilar cholangiocarcinoma surviving >30 months according to out-
come group (C) disease-free survival of all resected patients with perihilar chol-
angiocarcinoma excluding 90-day mortality according to outcome
group; and (D) disease-free survival of all resected patients with
perihilar cholangiocarcinoma surviving >30 months according to out-
come group Fig. 2 Overall survival and disease-free survival according to out-
come group. Kaplan-Meier curves of (A) overall survival of all
resected patients with perihilar cholangiocarcinoma excluding 90-day
mortality according to outcome group; (B) overall survival of all
resected patients surviving >30 months according to outcome group; improved OS and DFS if TO is achieved [13, 19, 20, 39]. There was no significant difference in survival between the
TO and NTO groups. However, in the long-term (beginning
from month 30), there was a clear trend towards a better OS
and DFS in the TO group compared to the NTO group. Rea-
sons for improved long-term survival when TO is achieved
may be a timely connection to adjuvant chemotherapy. This
can be delayed or not occur at all in patients with major
complications. In this work, a higher number of patients in
the TO group tended to receive adjuvant chemotherapy in
the overall cohort which can have a positive effect on OS and
DFS [40]. However, it is difficult to draw final conclusions
since exact follow-up data including the applied chemo-
therapy regimen, dose, and information on, e.g., premature
termination of adjuvant chemotherapy due to side effects
are missing in a relevant proportion of patients. In general,
recommendations for adjuvant chemotherapy included either
gemcitabine (± cisplatin) or fluorouracil/capecitabine. In the present work, left hepatectomy could be identified
as an independent factor favoring TO which is in line with
another study [19] compared with right hepatectomy. This
is due to a significantly smaller future liver remnant (FLR),
which is a risk factor for PHLF which consecutively leads to
increased postoperative mortality rates [7, 35]l As a second independent factor influencing TO, we found
that preoperative biliary drainage to be associated with not
achieving TO. Discussion When it comes to the defi-
nition of postoperative mortality, studies differ greatly, as
some used 30-day mortality, others 90-day mortality [13,
17, 22, 23, 26]. Defining postoperative mortality as 30-day
mortality may lead to an underestimation of the actual perio-
perative mortality after liver resection by up to 50%. After
an initial steep increase in postoperative mortality, a more
or less constant mortality rate is observed after 90 days [5,
27]. Indicators of postoperative morbidity reported in the
analyzed TO studies were length of hospital stay (LOS),
grade of complications, or specific complications. There is
a known high correlation between LOS and incidence of
complications [18]. Overall, a TO rate of 24% (n=67) was observed in the
present study. This is consistent with TO rates obtained
after surgical procedures in the field of HBP surgery [17,
19, 20]. Opposite to the findings in other studies [17, 19],
age was not found to be influencing TO in the present study. Poor histologic differentiation had a negative impact on the
development of a TO in the present study. In general, poor
grading is considered a risk for early tumor recurrence and
decreased OS [3, 31–33]. Additionally, however, these fac-
tors may also reflect an aggressive tumor biology indicat-
ing advanced tumor disease. This is related to frailty, which
leads to increased morbidity and mortality [34]. Nevertheless, there is a potential bias when only report-
ing LOS [18, 20]. LOS may not necessarily represent a
surgical quality measure, as it may be prolonged by exter-
nal factors such as inadequately ensured home care at dis-
charge and not morbidity-related [18] or cultural aspects
[5, 17]. For these reasons, a second morbidity measure
was added to the “prolonged hospital stay” parameter in
the present work. Specific complications to define TO as
used by van Roessel et al. were not used because patients 1 3 Langenbeck's Archives of Surgery (2022) 407:1561–1573 1570 In the present work left hepatectomy could be identified
improved OS and DFS if TO is achieved [13 19 20 39]
Fig. 2 Overall survival and disease-free survival according to out-
come group. 1 3 Discussion Similar to the results of this work, Zhang
et al. showed a significantly increased morbidity rate in
patients with biliary drainage [36]. This is likely attribut-
able to advanced disease as well as preoperative cholangitis;
thus, drainage should be considered a surrogate parameter
for advanced disease. The median overall survival in the current study in the
overall cohort was 29 (24–35) months, which is in line with
other studies (13–40 months) [10, 28, 29, 37, 38]. Some
previous studies in the field of HBP surgery have shown 1 3 1571 Langenbeck's Archives of Surgery (2022) 407:1561–1573 There are several limitations in the present study. First,
it is a retrospective analysis which can lead to bias. Second,
clear definitions of TO in PHC lack, so the comparability is
limited. However, this is the first study proposing a defini-
tion of TO in patients with PHC undergoing MH based on a
thorough literature review, which is evaluated and tested on
a large cohort of patients. 2. Neuhaus P, Thelen A, Jonas S, Puhl G, Denecke T, Veltzke-
Schlieker W, Seehofer D (2012) Oncological superiority of hilar
en bloc resection for the treatment of hilar cholangiocarcinoma. Ann Surg Oncol 19(5):1602–1608. https://doi.org/10.1245/
s10434-011-2077-5 3. Neuhaus P, Jonas S, Bechstein WO, Lohmann R, Radke C, Kling
N, Wex C, Lobeck H, Hintze R (1999) Extended resections for
hilar cholangiocarcinoma. Ann Surg 230(6):808–818; discussion
819. https://doi.org/10.1097/00000658-199912000-00010 4. Franken LC, Rassam F, van Lienden KP, Bennink RJ, Besselink
MG, Busch OR, Erdmann JI, van Gulik TM, Olthof PB (2020)
Effect of structured use of preoperative portal vein embolization
on outcomes after liver resection of perihilar cholangiocarcinoma. BJS Open 4(3):449–455. https://doi.org/10.1002/bjs5.50273 Conclusions p
p
g
j
5. Franken LC, Schreuder AM, Roos E, van Dieren S, Busch OR,
Besselink MG, van Gulik TM (2019) Morbidity and mortal-
ity after major liver resection in patients with perihilar cholan-
giocarcinoma: a systematic review and meta-analysis. Surgery
165(5):918–928. https://doi.org/10.1016/j.surg.2019.01.010 TO is a quality indicator that is not exclusively limited to
reporting mortality, but more comprehensively represents a
desired postoperative course. In the present study, we intro-
duced the composite quality measure TO into PHC. This is
of great importance in order to allow a comparison between
studies or centers. Therefore, there is a great need for a uni-
form and robust TO definition in future studies. We identi-
fied left hepatectomy as an independent factor positively
influencing TO. In cases with central tumors, where both
right- and left-sided resections are feasible, this underlines
the importance of a careful selection of patients who are
scheduled for right hepatectomy, which are superior in terms
of oncological radicality but associated with higher postop-
erative morbidity and mortality. 6. Olthof PB, Aldrighetti L, Alikhanov R, Cescon M, Groot
Koerkamp B, Jarnagin WR, Nadalin S, Pratschke J, Schmelze
M, Sparrelid E, Lang H, Guglielmi A, van Gulik TM (2020)
Portal vein embolization is associated with reduced liver failure
and mortality in high-risk resections for perihilar cholangiocarci-
noma. Ann Surg Oncol 27(7):2311–2318. https://doi.org/10.1245/
s10434-020-08258-3 7. Ribero D, Zimmitti G, Aloia TA, Shindoh J, Forchino F, Amisano
M, Passot G, Ferrero A, Vauthey J-N (2016) Preoperative cholan-
gitis and future liver remnant volume determine the risk of liver
failure in patients undergoing resection for hilar cholangiocarci-
noma. J Am Coll Surg 223(1):87–97. https://doi.org/10.1016/j.
jamcollsurg.2016.01.060 8. Lee EC, Park SJ, Han SS, Shim JR, Park HM, Lee SD, Kim
SH (2018) Risk prediction of post-hepatectomy liver failure in
patients with perihilar cholangiocarcinoma. J Gastroenterol Hepa-
tol 33(4):958–965. https://doi.org/10.1111/jgh.13966 Supplementary Information The online version contains supplemen-
tary material available at https://doi.org/10.1007/s00423-022-02467-y. Supplementary Information The online version contains supplemen-
tary material available at https://doi.org/10.1007/s00423-022-02467-y. 9. Yokoyama Y, Nagino M, Nimura Y (2007) Mechanism of
impaired hepatic regeneration in cholestatic liver. J Hepato-
Biliary-Pancreat Surg 14(2):159–166. https://doi.org/10.1007/
s00534-006-1125-1 Funding Open Access funding enabled and organized by Projekt
DEAL. Funding Open Access funding enabled and organized by Projekt
DEAL. Competing interests The authors declare no competing interests. Competing interests The authors declare no competing interests. Competing interests The authors declare no competing interests. Open Access This article is licensed under a Creative Commons Attri-
bution 4.0 International License, which permits use, sharing, adapta-
tion, distribution and reproduction in any medium or format, as long
as you give appropriate credit to the original author(s) and the source,
provide a link to the Creative Commons licence, and indicate if changes
were made. The images or other third party material in this article are
included in the article’s Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not included in
the article’s Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a
copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 11. Baton O, Azoulay D, Adam DVR, Castaing D (2007) Major hepa-
tectomy for hilar cholangiocarcinoma type 3 and 4: prognostic
factors and longterm outcomes. J Am Coll Surg 204(2):250–260. https://doi.org/10.1016/j.jamcollsurg.2006.10.028 12. Nagino M, Kamiya J, Uesaka K, Sano T, Yamamoto H, Hayakawa
N, Kanai M, Nimura Y (2001) Complications of hepatectomy
for hilar cholangiocarcinoma. World J Surg 25(10):1277–1283. https://doi.org/10.1007/s00268-001-0110-8 p
g
13. Heidsma CM, Hyer M, Tsilimigras DI, Rocha F, Abbott DE,
Fields R, Smith PM, Poultsides GA, Cho C, Maithel SK, Pawlik
TM (2020) Incidence and impact of textbook outcome among
patients undergoing resection of pancreatic neuroendocrine
tumors: results of the US Neuroendocrine Tumor Study Group. J
Surg Oncol 121(8):1201–1208. https://doi.org/10.1002/jso.25900 14. Salet N, Bremmer RH, Verhagen M, Ekkelenkamp VE, Hansen
BE, de Jonge PJF, de Man RA (2018) Is textbook outcome a valu-
able composite measure for short-term outcomes of gastrointesti-
nal treatments in the Netherlands using hospital information sys-
tem data? A retrospective cohort study. BMJ Open 8(2):e019405. https://doi.org/10.1136/bmjopen-2017-019405 1. Razumilava N, Gores GJ (2014) Cholangiocarcinoma. Lancet
383(9935):2168–2179. https://doi.org/10.1016/s0140-6736(13)
61903-0 Declarations 10. Olthof PB, Coelen RJS, Wiggers JK, Besselink MGH, Busch
ORC, van Gulik TM (2016) External biliary drainage following
major liver resection for perihilar cholangiocarcinoma: impact on
development of liver failure and biliary leakage. HPB 18(4):348–
353. https://doi.org/10.1016/j.hpb.2015.11.007 References Tsilimigras DI, Sahara K, Moris D, Mehta R, Paredes AZ, Ratti
F, Marques HP, Soubrane O, Lam V, Poultsides GA, Popescu I,
Alexandrescu S, Martel G, Workneh A, Guglielmi A, Hugh T,
Aldrighetti L, Weiss M, Bauer TW et al (2020) Assessing text-
book outcomes following liver surgery for primary liver cancer
over a 12-year time period at major hepatobiliary centers. Ann
Surg Oncol. https://doi.org/10.1245/s10434-020-08548-w 31. Groot Koerkamp B, Wiggers JK, Gonen M, Doussot A, Allen
PJ, Besselink MGH, Blumgart LH, Busch ORC, D'Angelica MI,
DeMatteo RP, Gouma DJ, Kingham TP, van Gulik TM, Jarnagin
WR (2015) Survival after resection of perihilar cholangiocar-
cinoma-development and external validation of a prognostic
nomogram. Ann Oncol 26(9):1930–1935. https://doi.org/10.
1093/annonc/mdv279 g
p
g
20. Sweigert PJ, Eguia E, Baker MS, Paredes AZ, Tsilimigras
DI, Dillhoff M, Ejaz A, Cloyd J, Tsung A, Pawlik TM (2020)
Assessment of textbook oncologic outcomes following pancrea-
ticoduodenectomy for pancreatic adenocarcinoma. J Surg Oncol
121(6):936–944. https://doi.org/10.1002/jso.25861 21. Dindo D, Demartines N, Clavien PA (2004) Classification
of surgical complications: a new proposal with evaluation in
a cohort of 6336 patients and results of a survey. Ann Surg
240(2):205–213. https://doi.org/10.1097/01.sla.0000133083.
54934.ae 32. Tang Z, Yang Y, Zhao Z, Wei K, Meng W, Li X (2018) The
clinicopathological factors associated with prognosis of patients
with resectable perihilar cholangiocarcinoma: a systematic
review and meta-analysis. Medicine (Baltimore) 97(34):e11999. https://doi.org/10.1097/md.0000000000011999 22. Mehta R, Tsilimigras DI, Paredes AZ, Sahara K, Dillhoff M,
Cloyd JM, Ejaz A, White S, Pawlik TM (2020) Dedicated can-
cer centers are more likely to achieve a textbook outcome fol-
lowing hepatopancreatic surgery. Ann Surg Oncol 27(6):1889–
1897. https://doi.org/10.1245/s10434-020-08279-yf 33. Groot Koerkamp B, Wiggers JK, Allen PJ, Besselink MG,
Blumgart LH, Busch OR, Coelen RJ, D'Angelica MI, DeMatteo
RP, Gouma DJ, Kingham TP, Jarnagin WR, van Gulik TM (2015)
Recurrence rate and pattern of perihilar cholangiocarcinoma
after curative intent resection. J Am Coll Surg 221(6):1041–
1049. https://doi.org/10.1016/j.jamcollsurg.2015.09.005 p
g
y
23. Merath K, Chen Q, Bagante F, Beal E, Akgul O, Dillhoff M,
Cloyd JM, Pawlik TM (2020) Textbook outcomes among medi-
care patients undergoing hepatopancreatic surgery. Ann Surg
271(6):1116–1123. https://doi.org/10.1097/sla.0000000000
003105 34. Ethun CG, Bilen MA, Jani AB, Maithel SK, Ogan K, Master VA
(2017) Frailty and cancer: implications for oncology surgery,
medical oncology, and radiation oncology. CA Cancer J Clin
67(5):362–377. https://doi.org/10.3322/caac.21406 24. References 1 3 3 Langenbeck's Archives of Surgery (2022) 407:1561–1573 1572 26. Mehta R, Paredes AZ, Tsilimigras DI, Moro A, Sahara K,
Farooq A, Dillhoff M, Cloyd JM, Tsung A, Ejaz A, Pawlik TM
(2020) Influence of hospital teaching status on the chance to
achieve a textbook outcome after hepatopancreatic surgery for
cancer among Medicare beneficiaries. Surgery 168(1):92–100. https://doi.org/10.1016/j.surg.2020.02.024 15. Denbo J, Anaya DA (2020) Textbook outcomes following liver
resection for cancer: a new standard for quality benchmarking and
patient decision making. Ann Surg Oncol. https://doi.org/10.1245/
s10434-020-08550-2 16. Busweiler LA, Schouwenburg MG, van Berge Henegouwen MI,
Kolfschoten NE, de Jong PC, Rozema T, Wijnhoven BP, van
Hillegersberg R, Wouters MW, van Sandick JW (2017) Textbook
outcome as a composite measure in oesophagogastric cancer sur-
gery. Br J Surg 104(6):742–750. https://doi.org/10.1002/bjs.10486 27. Mayo SC, Shore AD, Nathan H, Edil BH, Hirose K, Anders
RA, Wolfgang CL, Schulick RD, Choti MA, Pawlik TM (2011)
Refining the definition of perioperative mortality following
hepatectomy using death within 90 days as the standard crite-
rion. HPB (Oxford) 13(7):473–482. https://doi.org/10.1111/j.
1477-2574.2011.00326.x 17. Merath K, Chen Q, Bagante F, Alexandrescu S, Marques HP, Ald-
righetti L, Maithel SK, Pulitano C, Weiss MJ, Bauer TW, Shen F,
Poultsides GA, Soubrane O, Martel G, Koerkamp BG, Guglielmi
A, Itaru E, Cloyd JM, Pawlik TM (2019) A multi-institutional
international analysis of textbook outcomes among patients
undergoing curative-intent resection of intrahepatic cholangio-
carcinoma. JAMA Surg 154(6):e190571. https://doi.org/10.1001/
jamasurg.2019.0571 28. Ebata T, Mizuno T, Yokoyama Y, Igami T, Sugawara G, Nagino
M (2018) Surgical resection for Bismuth type IV perihilar chol-
angiocarcinoma. Br J Surg 105(7):829–838. https://doi.org/10.
1002/bjs.10556 29. Nagino M, Ebata T, Yokoyama Y, Igami T, Sugawara G, Taka-
hashi Y, Nimura Y (2013) Evolution of surgical treatment for
perihilar cholangiocarcinoma: a single-center 34-year review of
574 consecutive resections. Ann Surg 258(1):129–140. https://
doi.org/10.1097/SLA.0b013e3182708b57 j
g
18. Aiken T, Abbott DE (2020) Textbook oncologic outcome: a
promising summary metric of high-quality care, but are we on
the same page? J Surg Oncol 121(6):923–924. https://doi.org/
10.1002/jso.25872 30. Benzing C, Krenzien F, Mieg A, Wolfsberger A, Andreou A,
Nevermann N, Pelzer U, Fehrenbach U, Haiden LM, Öllinger
R, Schöning W, Schmelzle M, Pratschke J (2021) A tailored
approach in lymph node-positive perihilar cholangiocarcinoma. Langenbeck's Arch Surg 406(5):1499–1509. https://doi.org/10.
1007/s00423-021-02154-4 19. References van Roessel S, Mackay TM, van Dieren S, van der Schelling GP,
Nieuwenhuijs VB, Bosscha K, van der Harst E, van Dam RM,
Liem MSL, Festen S, Stommel MWJ, Roos D, Wit F, Mole-
naar IQ, de Meijer VE, Kazemier G, de Hingh I, van Santvoort
HC, Bonsing BA et al (2020) Textbook outcome: nationwide
analysis of a novel quality measure in pancreatic surgery. Ann
Surg 271(1):155–162. https://doi.org/10.1097/sla.0000000000
003451 35. Wiggers JK, Groot Koerkamp B, Cieslak KP, Doussot A, van
Klaveren D, Allen PJ, Besselink MG, Busch OR, D'Angelica
MI, DeMatteo RP, Gouma DJ, Kingham TP, van Gulik TM,
Jarnagin WR (2016) Postoperative mortality after liver resection
for perihilar cholangiocarcinoma: development of a risk score
and importance of biliary drainage of the future liver remnant. J Am Coll Surg 223(2):321–331.e321. https://doi.org/10.1016/j.
jamcollsurg.2016.03.035 25. Mueller M, Breuer E, Mizuno T, Bartsch F, Ratti F, Benzing
C, Ammar-Khodja N, Sugiura T, Takayashiki T, Hessheimer
A, Kim HS, Ruzzenente A, Ahn KS, Wong T, Bednarsch J,
D'Silva M, Koerkamp BG, Jeddou H, López-López V et al
(2021) Perihilar cholangiocarcinoma - novel benchmark values
for surgical and oncological outcomes from 24 expert centers. Ann Surg 274(5):780–788. https://doi.org/10.1097/sla.00000
00000005103 36. Zhang XF, Beal EW, Merath K, Ethun CG, Salem A, Weber
SM, Tran T, Poultsides G, Son AY, Hatzaras I, Jin L, Fields RC,
Weiss M, Scoggins C, Martin RCG, Isom CA, Idrees K, Mogal
HD, Shen P et al (2018) Oncologic effects of preoperative bil-
iary drainage in resectable hilar cholangiocarcinoma: percutane-
ous biliary drainage has no adverse effects on survival. J Surg
Oncol 117(6):1267–1277. https://doi.org/10.1002/jso.24945 1 3 Langenbeck's Archives of Surgery (2022) 407:1561–1573 1573 short-term outcomes and long-term survival after esophageal
and gastric cancer surgery. Ann Surg 270(5):868–876. https://
doi.org/10.1097/sla.0000000000003520 37. Sano T, Shimada K, Sakamoto Y, Yamamoto J, Yamasaki S,
Kosuge T (2006) One hundred two consecutive hepatobiliary
resections for perihilar cholangiocarcinoma with zero mortality. Ann Surg 244(2):240–247. https://doi.org/10.1097/01.sla.00002
17605.66519.38 40. g
40. Primrose JN, Fox RP, Palmer DH, Malik HZ, Prasad R, Mirza
D, Anthony A, Corrie P, Falk S, Finch-Jones M, Wasan H, Ross
P, Wall L, Wadsley J, Evans JTR, Stocken D, Praseedom R,
Ma YT, Davidson B et al (2019) Capecitabine compared with
observation in resected biliary tract cancer (BILCAP): a ran-
domised, controlled, multicentre, phase 3 study. Lancet Oncol
20(5):663–673. https://doi.org/10.1016/s1470-2045(18)30915-x 38. Publisher’s note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations. short-term outcomes and long-term survival after esophageal
and gastric cancer surgery. Ann Surg 270(5):868–876. https://
doi.org/10.1097/sla.0000000000003520 References Bednarsch J, Czigany Z, Lurje I, Tacke F, Strnad P, Ulmer TF,
Gaisa NT, Bruners P, Neumann UP, Lurje G (2020) Left- versus
right-sided hepatectomy with hilar en-bloc resection in perihilar
cholangiocarcinoma. HPB (Oxford) 22(3):437–444. https://doi.
org/10.1016/j.hpb.2019.07.003 g
j
p
39. van der Werf LR, Wijnhoven BPL, Fransen LFC, van Sandick
JW, Nieuwenhuijzen GAP, Busweiler LAD, van Hillegersberg
R, Wouters M, Luyer MDP, van Berge Henegouwen MI (2019)
A national cohort study evaluating the association between 1 3 1 3 3
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Formação docente e pedagogia triangular:
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Nível: Doutorado.
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Curso e/ou Programa: Programa de Pós-Graduação em Educação
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DOI: 10.30681/2236-3165 Richéle Timm dos Passos da Silvai RESUMO A formação docente é pauta significativa quando se trata em discutir a
educação como meio para a convivência hospitaleira. Os fundamentos sócio-
históricos e filosóficos que circundam a formação são basilares para a construção de
um sujeito crítico. Problematiza-se a perspectiva positivista frente ao modo de
interpretar a vida humana como uma perspectiva instrumental monolíngue e
monocultural. Essa compreensão colocou ênfase a apenas um aspecto da vida e
atribuiu status menor às compreensões e saberes que não coadunam com o escopo
unilateral da racionalidade. Restrita a esse padrão, a formação docente formata um
profissional tecnicista e, por isso mesmo, desconectado do mundo da vida. Esse,
idealiza uma concepção unilateral de escola, de aluno, de conhecimento e de formas
de ensinar e gerir a escola. A perspectiva estereotipada dificulta a compreensão do
Lebenswelt e de suas circunstancialidades. Os déficits na compreensão das
realidades vividas é aspecto importante para a formação docente sendo possível
detectar os malefícios que dificultam a dialogicidade entre as diferentes formas de
pensar e construir uma educação plural. Ante a inconformidade dos processos
formativos unilateralizantes e patologizante, o texto expõe, a partir de uma guinada Revista Even. Pedagóg. Número Regular: Estudos Decoloniais
Sinop, v. 13, n. 3 (34. ed.), p. 610-612, ago./dez. 2022 Revista Even. Pedagóg. Número Regular: Estudos Decoloniais
Sinop, v. 13, n. 3 (34. ed.), p. 610-612, ago./dez. 2022 Revista Even. Pedagóg. Número Regular: Estudos Decoloniais
Sinop, v. 13, n. 3 (34. ed.), p. 610-612, ago./dez. 2022 Revista Even. Pedagóg. d g g
Número Regular: Estudos Decoloniais d g g
Número Regular: Estudos Decoloniais g
inop, v. 13, n. 3 (34. ed.), p. 610-612, ago./dez. 2022 epistemológica o significado de uma pedagogia com base em uma triangularidade. Tal proposta parte do deslocamento do eixo gravitacional e geocultural do
Mediterrâneo ao Atlântico. A noção de triangularidade salienta que não há uma única
forma de compreender o mundo e consolidar vínculos. Daí, então, a necessidade de
se fazer uma justeza histórica e geo-cultural incluindo os olhares afro-ameríndios. A
compreensão dos diferentes saberes perpassa a formação de um docente na
perspectiva de uma justiça curricular prestada aos saberes até então não abordados
nos cursos. Eduardo Gruner abre caminho a uma compreensão na qual todos os
sujeitos possam falar e tenham a voz na construção de uma convivência hospitalaria. O universalismo apresentado como única proposta de compreensão curricular não
atende aos anseios de “todos”. RESUMO Assim, a noção de Lebenswelt permite elucidar o que
se entende por saber de mundo. Como diz Jovino Pizzi, la palabra saber hace
referencia a aspectos culturales y formas de vida, y no simplemente el dominio de
datos y aspectos cuantitativos. Ese saber compartido por los sujetos es reconocido en
un horizonte determinado, en donde las interacciones son vislumbradas através de
sus formas simbólicas y culturales de expresarse. São os saberes diversos que
rompem com a colonialidade do poder/saber que Aníbal Quijano menciona. Ao romper
com a unilateralidade da compreensão de mundo, a pedagogia triangular emprega um
caráter multifacetado, uma polissomia de vozes e de saberes que reforçam a
formação docente aberta à convivialidade. São os outros vértices do triângulo, outras
vozes, outros lugares, que se apresentam na história. Por isso, se trata de maneira
propositiva, uma transformação do modus operandi, ligada a outra conformação do
mapa político-econômico, filosófico e cultural-educativo. Os contornos dessa operam
na pluridiversidade de saberes, de compreensões nas maneiras de compreender o
mundo da vida étnico culturais. epistemológica o significado de uma pedagogia com base em uma triangularidade. Tal proposta parte do deslocamento do eixo gravitacional e geocultural do
Mediterrâneo ao Atlântico. A noção de triangularidade salienta que não há uma única
forma de compreender o mundo e consolidar vínculos. Daí, então, a necessidade de
se fazer uma justeza histórica e geo-cultural incluindo os olhares afro-ameríndios. A
compreensão dos diferentes saberes perpassa a formação de um docente na
perspectiva de uma justiça curricular prestada aos saberes até então não abordados
nos cursos. Eduardo Gruner abre caminho a uma compreensão na qual todos os
sujeitos possam falar e tenham a voz na construção de uma convivência hospitalaria. O universalismo apresentado como única proposta de compreensão curricular não
atende aos anseios de “todos”. Assim, a noção de Lebenswelt permite elucidar o que
se entende por saber de mundo. Como diz Jovino Pizzi, la palabra saber hace
referencia a aspectos culturales y formas de vida, y no simplemente el dominio de
datos y aspectos cuantitativos. Ese saber compartido por los sujetos es reconocido en
un horizonte determinado, en donde las interacciones son vislumbradas através de
sus formas simbólicas y culturales de expresarse. São os saberes diversos que
rompem com a colonialidade do poder/saber que Aníbal Quijano menciona. Página 612 – Richéle Timm dos Passos da Silva RESUMO Ao romper
com a unilateralidade da compreensão de mundo, a pedagogia triangular emprega um
caráter multifacetado, uma polissomia de vozes e de saberes que reforçam a
formação docente aberta à convivialidade. São os outros vértices do triângulo, outras
vozes, outros lugares, que se apresentam na história. Por isso, se trata de maneira
propositiva, uma transformação do modus operandi, ligada a outra conformação do
mapa político-econômico, filosófico e cultural-educativo. Os contornos dessa operam
na pluridiversidade de saberes, de compreensões nas maneiras de compreender o
mundo da vida étnico culturais. FORMAÇÃO DOCENTE E PEDAGOGIA TRIANGULAR: Os encontros e desencontros [...] – Página 611
Palavras-chave: Educação. Filosofia da Educação. Formação Docente. Pedagogia
Triangular. Recebido em: 30 de julho de 2022. Aprovado em: 23 de novembro de 2022. Link/DOI: https://periodicos.unemat.br/index.php/reps/article/view/6438/7328 Palavras-chave: Educação. Filosofia da Educação. Formação Docente. Pedagogia
Triangular. Triangular. FORMAÇÃO DOCENTE E PEDAGOGIA TRIANGULAR: Os encontros e desencontros [...] – Página 611
Recebido em: 30 de julho de 2022. Aprovado em: 23 de novembro de 2022. Link/DOI: https://periodicos.unemat.br/index.php/reps/article/view/6438/7328 FORMAÇÃO DOCENTE E PEDAGOGIA TRIANGULAR: Os encontros e desencontros [...] – Página 611 Revista Even. Pedagóg. Número Regular: Estudos Decoloniais
Sinop, v. 13, n. 3 (34. ed.), p. 610-612, ago./dez. 2022 Revista Even. Pedagóg. Número Regular: Estudos Decoloniais
Sinop, v. 13, n. 3 (34. ed.), p. 610-612, ago./dez. 2022 Revista Even. Pedagóg. Revista Even. Pedagóg. i Mestre em Educação pela Universidade Federal do Rio Grande do Sul (UFRGS-2013), Professora da
Faculdade de Educação da Universidade Federal de Pelotas (UFPel), Pesquisadora nos grupos: a)
Ética pós-metafísica e teorias da justiça: as novas democracias e os desafios da educação para a
justiça – UFPEL; b) Grupo de Estudos sobre Universidade (GEU/Unemat/UFMT) – UNEMAT e c) Grupo
de Pesquisa em Estudos Decoloniais - GPED – UFMS. Atua junto ao Observatório de Patologias
Sociais UFPel/Capes-Print. ii Este texto trata de uma abordagem teórico-prática estudada para a tese. A pesquisa do doutoramento
está em andamento e o objeto central da tese não está contido neste texto. Página 612 – Richéle Timm dos Passos da Silva
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https://openalex.org/W3005749394
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https://journal.ubpkarawang.ac.id/index.php/Akuntansi/article/download/878/769
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Pengaruh Audit Tenure, Rotasi Audit Dan Ukuran Kantor Akuntan Publik (KAP) Terhadap Kualitas Audit
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Jurnal buana akuntansi
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Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Jurnal Buana Akuntansi Kata Kunci: audit tenure, rotasi audit, ukuran KAP, kualitas audit Kata Kunci: audit tenure, rotasi audit, ukuran KAP, kualitas audit Abstract The purpose of this study was to examine the effect of audit tenure, audit rotation,
size of the public accounting firm and audit quality on large trading sector companies. Audit
tenure, audit rotation and the size of the public accounting firm as an independent variable. Audit quality as the dependent variable. This study uses the basic theory of agency theory. This study uses secondary data obtained from the Indonesia Stock Exchange (IDX) during
the period 2013-2017. The sampling process was carried out using the purposive sampling
method and this study used 100 observations. The analytical method for testing hypotheses is
logistic regression analysis. The results show that (1) audit tenure has a negative effect on
audit quality. (2) audit rotation does not affect audit quality, (3) the size of the public
accounting firm does not affect audit quality. Pengaruh Audit Tenure, Rotasi Audit Dan Ukuran Kantor
Akuntan Publik (KAP) Terhadap Kualitas Audit 1Carolus Askikarno Palalangan
2Johannes Baptista Halik
3Maria Yessica Halik
1carolus@ukipaulus ac id 1Carolus Askikarno Palalangan
2Johannes Baptista Halik
3Maria Yessica Halik
1carolus@ukipaulus.ac.id
1,2,3 Program Studi Akuntansi, Fakultas Ekonomi dan Bisnis, Universitas Kristen Indonesia Paulus Abstrak Tujuan dari penelitian ini adalah untuk menguji pengaruh audit tenure, rotasi
audit, ukuran kantor akuntan publik dan kualitas audit pada perusahaan sektor perdagangan
besar. Audit tenure, rotasi audit dan ukuran kantor akuntan publik sebagai variabel
independen. Kualitas audit sebagai variabel dependen. Penelitian ini menggunakan teori
dasar yaitu teori keagenan. Penelitian ini menggunakan data sekunder yang diperoleh dari
Bursa Efek Indonesia (BEI) selama periode 2013-2017. Proses pengambilan sampel dilakukan
dengan menggunakan metode purposive sampling dan penelitian ini menggunakan 100
observasi. Metode analisis untuk menguji hipotesis adalah analisis regresi logistik. Hasilnya
menunjukkan bahwa (1) audit tenure berpengaruh negatif terhadap kualitas audit. (2) rotasi
audit tidak berpengaruh terhadap kualitas audit, (3) ukuran kantor akuntan publik tidak
berpengaruh terhadap kualitas audit. Jurnal Buana Akuntansi pengambilan keputusan. Dalam menilai kewajaran suatu laporan keuangan yang
disajikan oleh perusahaan, diperlukan suatu proses untuk memperoleh serta
mengevaluasi laporan keuangan secara objektif yaitu melalui proses audit. Laporan
keuangan yang telah diaudit dapat memberikan jaminan yang tinggi akan
kewajaran laporan keuangan dibandingkan laporan keuangan yang tidak diaudit. Oleh karena itu auditor sebagai pelaku audit harus profesional dalam mengaudit
laporan keuangan sehingga audit laporan keuangan memiliki kualitas yang dapat
dipercaya oleh pihak internal dan eksternal perusahaan serta memperoleh
kepercayaan dalam menjalankan bisnis jasa akuntan publik sehingga auditor dapat
bertahan dan meningkatkan eksistensinya dalam dunia bisnis. Dalam mempertahankan eksistensi auditor dan untuk bertahan ditengah
persaingan yang ketat, khususnya dibidang bisnis pelayanan jasa akuntan publik
harus dapat menghimpun klien sebanyak mungkin dan mendapatkan kepercayaan
dari masyarakat luas, oleh karena itu menuntut para auditor tetap memiliki kualitas
audit yang baik (Putra, 2013) Kualitas audit adalah suatu nilai yang didapatkan atau hasil yang diperoleh
dari proses audit yang berpedoman pada standar auditing dan prosedur audit yang
telah ditetapkan yang menjadi pedoman pelaksanaan tugas dan tanggung jawab
profesi seorang auditor. Kualitas audit berhubungan dengan seberapa baik sebuah
pekerjaan diselesaikan dibandingkan dengan standar yang telah ditetapkan. Dengan
mengaudit laporan keuangan klien, auditor dapat menemukan pelanggaran yang
terjadi dalam sistem akuntansi klien dan melaporkannya dalam laporan keuangan
auditan, dimana dalam melaksanakan tugasnya tersebut auditor berpedoman pada
standar auditing dan kode etik akuntan publik. Kualitas audit yang ditetapkan
auditor digunakan untuk meningkatkan kepercayaan laporan keuangan pengguna
informasi akuntansi sehingga dapat mengurangi risiko informasi yang tidak
kredibel bagi pengguna laporan keuangan. g p
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g
Namun pada saat ini kepercayaan akan auditor semakin menurun
dikarenakan banyaknya kasus yang melibatkan auditor itu sendiri seperti yang
terjadi pada kantor akuntan publik mitra Ernest & Young (EY) di Indonesia yakni
KAP Purwantono, Suherman & Surya yang sepakat membayar denda senilai US$ 1
juta (sekitas Rp 13,3 Miliar) kepada regulator Amerika Serikat akibat divonis gagal
melakukan audit laporan keuangan kliennya. Kesepakatan itu diumumkan Badan
Pengawas Perusahaan Akuntan Publik AS (Publik Accounting Oversight Board
PCAOB) pada Kamis 9 Februari 2017 waktu Washington. Kasus ini merupakan
insiden terbaru yang menimpa kantor akuntan publik di negara berkembang yang
melanggar kode etik jaringan EY di Indonesia yang mengumumkan hasil audit atas
perusahaan telekomunikasi (ISAT) pada 2011 memberikan opini yang didasarkan
atas bukti yang tidak memadai. Temuan itu berawal ketika kantor akuntan mitra EY di AS melakukan kajian
atas hasil audit kantor akuntan di Indonesia. Pendahuluan Pada era globalisasi saat ini perkembangan dunia bisnis semakin besar dan
luas, khususnya dalam lingkup bisnis jasa akuntan publik yang semakin meningkat
seiring banyaknya perusahaan yang membutuhkan jasa audit laporan keuangan. Laporan keuangan merupakan catatan informasi keuangan perusahaan yang
menggambarkan kinerja perusahaan tersebut, sehingga kewajaran suatu laporan
keuangan sangat diperlukan bagi para pengguna laporan keuangan dalam 42 Carolus, Johannes, dan Maria
Vol. 4 No .2
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E-ISSN 2580-5452 Jurnal Buana Akuntansi dalam hal persewaan lebih dari 4 ribu unit tower seluler. Namun afiliasi EY di
Indonesia itu merilis laporan hasil audit dengan status wajar tanpa pengecualian. dalam hal persewaan lebih dari 4 ribu unit tower seluler. Namun afiliasi EY di
Indonesia itu merilis laporan hasil audit dengan status wajar tanpa pengecualian. PCAOB (The Publik Accounting Oversight Board) juga menyatakan tak lama
setelah dilakukan pemeriksaan atas audit laporan pada 2012 afiliasi EY di Indonesia
menciptakan belasan pekerjaan audit baru yang “tidak benar” sehingga
menghambat proses pemeriksaan PCAOB selain mengenakan denda US$ 1 juta juga
memberikan sanksi kepada dua auditor mitra EY yang terlibat dalam audit pada
2011, Roy Imam Wirahardja, senilai US$ 20.000 dan larangan praktik selama lima
tahun , mantan direktur EY Asia-Pasific James Randall Leali didenda US$ 10.000 dan
dilarang berpraktik selama satu tahun. g
p
Berdasarkan kasus KAP mitra EY di Indonesia dapat disimpulkan bahwa
auditor dalam melaksanakan tugas dan tanggung jawabnya belum dapat dikatakan
sebagai auditor profesional walaupun telah melaksanakan prosedur dan program
audit yang benar tetapi belum memiliki sikap independensi yang tinggi yaitu suatu
keadaan yang tidak terikat dengan pihak klien. Seorang
auditor
dapat
meningkatkan
sikap
profesionalnya
dalam
melaksanakan audit laporan keuangan dengan berpedoman pada standar audit
yang telah ditetapkan oleh Institut Akuntan Publik Indonesia (IAPI) yaitu standar
pekerjaan lapangan dan standar pelaporan, seorang auditor juga harus menerapkan
dan mematuhi prinsip dasar etika profesional, yaitu prinsip integritas, prinsip
objektivitas, prinsip kerahasiaan dan prinsip perilaku profesional (SPAP, 2013). Sesuai dengan kode etik profesi yang disusun oleh IFRS (International Federation
of Accountants) independensi merupakan bagian dari salah satu prinsip fundamental
kode etik profesi akuntansi yaitu objektivitas. Dalam kode etik profesi akuntansi,
objektivitas merupakan prinsip fundamental yang mensyaratkan seorang auditor
untuk tidak bias, bebas dari benturan kepentingan dan pengaruh lainnya yang
dapat yang dapat mengesampingkan profesional judgement. Dalam melaksanakan
audit, auditor harus memperhatikan dalam hal (1) merencanakan dan merancang
pendekatan audit; (2) memperoleh bukti untuk mendukung pengendalian khusus;
(3) memperoleh bukti melalui prosedur audit; (4) melaksanakan prosedur analitis
substantive; (5) melakukan pengujian rincian saldo; (6) melaksanakan pengujian
tambahan untuk penyajian dan pengungkapan; (7) mengumpulkan bukti akhir; (8)
mengeluarkan laporan audit (Indarto, 2011). g
p
(
)
Untuk menjaga independensi auditor, maka pemerintah mengeluarkan
aturan yang mengatur rotasi audit pada 2015 yaitu PP No.20/2015 tentang Praktik
Akuntan Publik. Dalam PP No.20/2015 pasal 11 ayat (1) dijelaskan bahwa akuntan
publik dalam melakukan audit atas suatu perusahaan berlaku selama 5 tahun buku
berturut-turut. Jurnal Buana Akuntansi Mereka menemukan bahwa hasil audit
atas perusahaan telekomunikasi itu tidak didukung oleh data yang akurat yakni 43 Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 Jurnal Buana Akuntansi mengeluarkan POJK No. 13 Tahun 2017 tentang Penggunaan Jasa Akuntan Publik
Dan Kantor Akuntan Publik Dalam Kegiatan Jasa Keuangan. Dalam peraturan
tersebut, bahwa institusi jasa keuangan wajib membatasi penggunaan jasa audit dari
AP paling lama 3 tahun buku berturut-turut. Sedangkan pembatasan penggunaan
jasa dari KAP tergantung pada hasil evaluasi Komite Audit. Selain itu, institusi jasa
keuangan harus menggunakan akuntan publik dan Kantor Akuntan Publik (KAP)
yang terdaftar di OJK. Pada umumnya kualitas audit bukan hanya dipengaruhi oleh faktor internal,
tetapi juga faktor eksternal seperti audit tenure, rotasi audit dan ukuran kantor
akuntan publik. Audit tenure adalah lamanya hubungan yang terjalin antara auditor
dan klien dalam mengaudit laporan keuangan. Menurut Hartadi (2012), audit tenure
adalah lamanya waktu auditor tersebut secara berturut-turut telah melakukan
pekerjaan audit terhadap suatu perusahaan. Dengan jangka waktu hubungan antara
klien dengan auditor maka dapat menimbulkan hubungan yang erat sehingga ada
kemungkinan auditor tidak bersikap independen. Dengan panjangnya audit tenure
maka untuk mengurangi resiko hilangnya independensi auditor maka dilakukan
rotasi audit. Rotasi audit yaitu pergantian KAP dalam mengaudit laporan keuangan klien. Menurut E Yuvisa I, dkk (2008) yaitu ketika hubungan klien dengan suatu kantor
akuntan berlangsung selama bertahun-tahun, klien dapat dipandang sebagai
sumber pendapatan bagi kantor akuntan publik secara terus menerus. Namun tidak
dapat dipungkiri dengan singkatnya masa perikatan antara audior dengan klien
dapat menimbulkan berbagai permasalahan seperti meningkatnya biaya perikatan
yang ditanggung oleh perusahaan klien karena dengan cepat menyelesaikan kontrak
dengan auditor juga audior akan lama mendalami dan menelusuri laporan
keuangan klien karena belum memahami secara luas akan perusahaan klien yang
bersangkutan. Oleh karena itu, diberlakukan adanya rotasi yang bersifat mandatory
dan valountery kantor akuntan publik supaya mengurangi dan menghindari
hubungan spesial yang terjalin antara klien dengan kantor akuntan publik. g
y
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Faktor yang ketiga yaitu ukuran kantor akuntan publik, kantor akuntan
publik terdiri dari KAP Big Four dan KAP Non Big four. Menurut Sulastono (2016:
33), kualitas auditor yang ada dalam kantor akuntan yang memiliki reputasi big four,
dianggap memiliki kecepatan, ketepatan dan memiliki sarana serta prasarana yang
lebih baik dari auditor kantor akuntan non big four. Jurnal Buana Akuntansi Setelah periode cooling-off selesai, maka AP dapat kembali
memberikan jasa audit pada perusahaan tersebut. Perusahaan yang dimaksud
dalam PP No. 20/2015 adalah industri di sektor pasar modal, bank umum, dana
pensiunan perusahaan asuransi/reasuransi atau BUMN, sebagaimana dijelaskan
pada pasal 11 ayat (2). Untuk memperketat pengawasan terhadap AP yang
melakukan audit terhadap perusahaan penyelenggara jasa keuangan, OJK 44 Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 Jurnal Buana Akuntansi Hal ini bertentangan dengan
kasus yang terjadi pada KAP Purwantono, Suherman & Surya yang merupakan
mitra Ernest & Young (EY) salah satu KAP Big Four yang mengaudit laporan
keuangan salah satu perusahaan telekomunikasi di Indonesia yang tidak memiliki
data yang akurat kemudian memberikan opini wajar tanpa pengecualian sehingga
KAP Purwanto, Suherman dan Surya diberikan sanksi berupa denda US$ 1juta dan
larangan melakukan praktik selama satu tahun. Penelitian ini mereplikasi penelitian terdahulu yaitu penelitian Ramdani
(2016) yang meneliti pengaruh fee audit, audit tenure, rotasi audit dan ukuran
perusahaan pada perusahaan sektor keuangan yang terdaftar di BEI tahun 2012- 45 Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 METODE PENELITIAN
Populasi Dan Sampel Populasi dan sampel penelitian ini adalah perusahaan perdagangan besar
yang terdaftar di Bursa Efek Indonesia (BEI) pada periode 2013-2017. Perusahaan
perdagangan besar dipilih karena merupakan salah satu sektor yang berpengaruh
dalam pertumbuhan ekonomi di Indonesia. Pada penelitian ini, populasi yang
digunakan adalah perusahaan perdagangan besar yang terdaftar di Bursa Efek
Indonesia (BEI) pada periode 2013 sampai 2017. Jumlah populasi dalam penelitian
ini sebanyak 37. Metode yang digunakan dalam penelitian ini adalah Purposive Sampling, yaitu
penetuan sampel dari populasi yang ada berdasarkan kriteria. Berdasarkan metode
tersebut, maka kriteria yang ditetapkan untuk penentuan sampel dalam penelitian
ini adalah sebagai berikut: 1. Perusahaan perdagangan besar yang terdaftar di Bursa Efek Indonesi
(BEI) selama tahun 2013-2017. 2. Perusahaan perdagangan besar yang menyediakan laporan keuangan,
annual report dan laporan yang telah diaudit oleh auditor independen
selama tahun 2013-2017. 3. Sektor keuangan yang selama tahun 2013-2017 tidak mengalami delisting
dari Bursa Efek Indonesia. Berdasarkan kriteria tersebut, maka penelitian memperoleh sampel sebanyak
20 perusahaan perdagangan besar yang menjadi sampel penelitian adalah 100 unit
yaitu 20 perusahaan x 5 tahun. Berdasarkan kriteria tersebut, maka penelitian memperoleh sampel sebanyak
20 perusahaan perdagangan besar yang menjadi sampel penelitian adalah 100 unit
yaitu 20 perusahaan x 5 tahun. Jurnal Buana Akuntansi 2014. Perbedaan penelitian ini dengan penelitian terdahulu yaitu hanya mengambil
tiga variabel bebas yaitu audit tenure, rotasi audit dan ukuran kantor akuntan
publik selain itu studi empiris dengan perusahaan yang berbeda dalam hal ini
menggunakan perusahaan perdagangan besar pada periode yang berbeda yaitu
tahun 2013-2017. 2014. Perbedaan penelitian ini dengan penelitian terdahulu yaitu hanya mengambil
tiga variabel bebas yaitu audit tenure, rotasi audit dan ukuran kantor akuntan
publik selain itu studi empiris dengan perusahaan yang berbeda dalam hal ini
menggunakan perusahaan perdagangan besar pada periode yang berbeda yaitu
tahun 2013-2017. Dalam penelitian ini, peneliti memakai studi pada perusahaan perdagangan
besar yang terdaftar di Bursa Efek Indonesia dikarenakan perusahaan perdagangan
besar memiliki pengaruh yang besar terhadap pertumbuhan ekonomi Indonesia. Berdasarkan uraian di atas, peneliti tertarik dan termotivasi melakukan penelitian
untuk mengetahui pengaruh audit tenure, rotasi audit dan ukuran kantor akuntan
publik terhadap kualitas audit. Berdasarkan hal tersebut, maka peneliti melakukan
penelitian yang berjudul “Pengaruh Audit Tenure, Rotasi Audit dan Ukuran Kantor
Akuntan Publik (KAP) terhadap Kualitas Audit”. Jenis Dan Sumber Data Jenis data yang digunakan dalam penelitian ini adalah data sekunder. Data
sekunder merupakan data yang diperoleh peneliti dari sumber yang sudah ada. Data sekunder didapatkan dari penelitian-penelitian terdahulu dan berbagai
literature-literatur yang dapat mendukung penelitian. 46 Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 Teknik Analisis Data Tujuan dari analisis data adalah untuk membuat kesimpulan atau menarik
kesimpulan mengenai karakteristik populasi berdasarkan data yang didapatkan dari
sampel biasanya ini dibuat berdasarkan pendugaan dan pengujian hipotesis. Metode analisis data penelitian ini menggunakan teknik analisis kuantitatif. Dalam
penelitian ini, analisis kuantitatif dilakukan dengan cara mengkuantifikasi data-data
penelitian sehingga menghasilkan informasi yang dibutuhkan dalam analisis. Analisis yang digunakan dalam penelitian ini adalah analisis model legit atau
regresi logistik (logistik regression) dengan bantuan IBM Statistikal Package for Social
Sciences (SPSS) versi 23. Menurut Ghozali (2011) logistik regression sebenarnya mirip
dengan analisis diskriminan yaitu menguji apakah probabilitas variabel terikat
dapat diprediksi dengan variabel bebasnya. Alasan menggunakan regresi logistik
adalah dalam analisis regresi logistik (Iogistic Regression) tidak memerlukan uji
asumsi multivariate normal distribution karena variabel bebas merupakan campuran
antara variabel kontinyu (metrik) dan kategorial (non-metrik) (Gozali, 2011). Menurut Winarno (2011) model logit (logistik regression) adalah model regresi
yang digunakan untuk menganalisis variabel dependen dengan kemungkinan
diantara 0 dan 1. Tahapan analisis regresi logistik (logistik regression) yaitu dengan
pengujian kelayakan model regresi, hipotesis, menilai kelayakan model regresi
(goodness of fit test), menilai model fit (overall model fit), uji regresi. Metode analisis
data yang digunakan yaitu statistik deskriptif yang digunakan untuk untuk
mendeskripsikan data yang telah terkumpul tanpa melakukan generalisasi. g
Teknik Pengumpulan Data Teknik pengumpulan data yang digunakan dalam penelitian ini yaitu metode
dokumentasi dan studi pustaka. Data sekunder dalam penelitian ini diperoleh
melalui metode dokumentasi. Metode dokumentasi dilakukan dengan cara
mengumpulkan, mencatat dan mengkaji data sekunder yang terdiri dari annual
report, laporan keuangan beserta laporan audit oleh auditor independen dari
perusahaan sektor keuangan yang listing dan dipublikasikan oleh Bursa Efek
Indonesia selama periode penelitian melalui Indonesia Stock Exchange (idx). Jurnal Buana Akuntansi Data sekunder yang digunakan dalam penelitian ini adalah laporan keuangan
perusahaan perdagangan besar yang telah diaudit. Yang didapatkan dengan
mengakses www.idx.co.id atau dari situs resmi masing-masing perusahaan. T k ik P
l
D t Jurnal Buana Akuntansi analisis statistik karena beberapa data yang dibutuhkan dari tahun tersebut tidak
digunakan, data tersebut hanya digunakan untuk melengkapi data tahun 2013. Data
yang digunakan yaitu diambil dari laporan keuangan dan annual report pada tahun
2013-2017 yang diakses melalui website www.idx.co.id. y
g
Adapun proses seleksi dari sampel yang didasarkan pada kriteria sebagai
berikut: Tabel 1: Tahapan Seleksi Sampel Dan Kriteria
No
Kriteria
Jumlah
1
Jumlah seluruh perusahaan sektor perdagangan
besar yang listing di BEI tahun 2013-2017
37
2
Perusahaan sektor perdagangan besar yang
tidak menerbitkan laporan keuangan, annual
report beserta laporan audit oleh auditor
independen selama tahun 2013-2017
(14)
3
Perusahaan sektor perdagangan besar yang
tidak memiliki data yang lengkap untuk
mendukung penelitian
(3)
4
Jumlah perusahaan sampel
20
5
Tahun pengamatan
5
6
Jumlah
perusahaan
sampel
selama
tahun
pengamatan
100 Tabel 1: Tahapan Seleksi Sampel Dan Kriteria
No
Kriteria
Jumlah
1
Jumlah seluruh perusahaan sektor perdagangan
besar yang listing di BEI tahun 2013-2017
37
2
Perusahaan sektor perdagangan besar yang
tidak menerbitkan laporan keuangan, annual
report beserta laporan audit oleh auditor
independen selama tahun 2013-2017
(14)
3
Perusahaan sektor perdagangan besar yang
tidak memiliki data yang lengkap untuk
mendukung penelitian
(3)
4
Jumlah perusahaan sampel
20
5
Tahun pengamatan
5
6
Jumlah
perusahaan
sampel
selama
tahun
pengamatan
100 Tabel 1: Tahapan Seleksi Sampel Dan Kriteria (14) (3) HASIL PENELITIAN DAN PEMBAHASAN Penelitian ini menggunakan populasi perusahaan sektor perdagangan besar
yang terdaftar di Bursa Efek Indonesia (BEI) selama tahun 2013-2017. Perusahaan
sektor perdagangan besar yang telah terdaftar di Bursa Efek Indonesia sebelum 1
Januari 2013 dan tidak dikeluarkan (delisting) selama periode penelitian. Pada
penelitian ini metode yang digunakan untuk penentuaan sampel adalah purposive
sampling. Penelitian ini mengambil sampel selama 5 tahun, yaitu dari tahun 2013-
2017, juga menggunakan tahun 2012 karena terdapat variabel yang membutuhkan
data dari tahun sebelumnya (t-1), namun data tahun 2012 tidak dimasukkan dalam 47 Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 Analisis Statistik Deskriptif p
Analisis statistik deskriptif digunakan untuk mengetahui deskripsi suatu data
yang dilihat dari nilai minimum, maksimum, rata-rata, dan standar deviasi
berdasarkan variabel spesialisasi auditor, rotasi audit, ukuran kantor akuntan
publik, kualitas audit. Berdasarkan analisis statistik deskriptif diperoleh gambaran
sampel sebagai berikut: p
g
Tabel 2: Statistik Deskriptif audit tenure, Rotasi Audit, Ukuran Kantor Akunt 48 Carolus, Johannes, dan Maria
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Jurnal Buana Akuntansi Carolus, Johannes, dan Maria
Vol. 4 No .2
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E-ISSN 2580-5452 Jurnal Buana Akuntansi p
p
Hasil Uji Kelayakan Model Regresi Hasil uji kelayakan model regresi diuji dengan menggunakan Hosmer and
Lemeshow Test. Berikut ini disajikan tabel hasil uji kelayakan model regresi: Tabel 5
Uji Kelayakan Model Regresi
Berdasarkan
tabel
5
menunjukkan bahwa nilai Chi-Square sebesar 3,089 dengan signifikansi (p) sebesar
0,877. Berdasarkan hasil tersebut, karena nilai signifikansi lebih besar dari 0,05
maka model dapat disimpulkan mampu memprediksi nilai observasinya (model
dapat dikatakan fit). Matriks Klasifikasi
Step
Chi-
square
Df
Sig. 1
3.089
7
.877 Tabel 5
Uji Kelayakan Model Regresi
tabel
5
Step
Chi-
square
Df
Sig. 1
3.089
7
.877 Tabel 5
Uji Kelayakan Model Regresi 5 menunjukkan bahwa nilai Chi-Square sebesar 3,089 dengan signifikansi (p) sebesar
0,877. Berdasarkan hasil tersebut, karena nilai signifikansi lebih besar dari 0,05
maka model dapat disimpulkan mampu memprediksi nilai observasinya (model
dapat dikatakan fit). Jurnal Buana Akuntansi Jurnal Buana Akuntansi Tabel 3
Hasil Uji Menilai Keseluruhan Model
Keterangan
-2 Log Likelihood
Block Number : 0
77,277
Block Number : 1
62,886 Tabel 3 Berdasarkan tabel di atas diketahui bahwa pengujian dilakukan dengan
membandiingkan nilai -2 log likelihood (-2LL) pada awal (block number 0) dengan nilai
-2 Log Likelihood (-2LL) pada akhir (Block Number=1). Nilai -2LL awal adalah sebesar
77,277. Setelah dimasukkan ketiga variabel independen, maka nilai -2LL akhir
mengalami penurunan menjadi 62,886. Penurunan Likelihood (-2LL) ini menunjukkan
model regresi yang lebih baik atau dengan kata lain model yang dihipotesiskan fit
dengan data. Hasil Uji Koefisien Determinasi ( Nagelkerke R Square)
Tabel 4
Hasil Uji Koefisien Determinasi
Step
-2 Log
likelihood
Cox & Snell
R Square
Nagelkerke
R Square
1
62.886a
.134
.249 Berdasarkan tabel 4, nilai statistik Nagelkerke R Square 0,249. Nilai
tersebut diinterpretasikan sebagai kemampuan audit tenure, rotasi audit, dan
ukuran kantor akuntan publik dalam mempengaruhi kualitas audit sebesar 24,9%,
sisanya 75,1 % dijelaskan oleh variabel-variabel atau faktor-faktor lain seperti fee
audit, spesialisasi auditor, ukuran perusahaan klien. p
p
Hasil Uji Kelayakan Model Regresi Jurnal Buana Akuntansi N
Minimu
m
Maximum
Mean
Std. Deviation
Kualitas
Audit
100
0
1
.13
.338
Audit Tenure
100
1
5
2.42
1.387
Rotasi Audit
100
0
1
.18
.386
Ukuran Kap
100
0
1
.48
.502
Valid N
(Listwise)
100 Publik, dan Kualitas Audit Publik, dan Kualitas Audit Berdasarkan tabel di atas dapat diketahui bahwa: Berdasarkan tabel di atas dapat diketahui bahwa: Jumlah unit analisis (N) dalam penelitian adalah sebanyak 100 unit analisis yang
terdiri dari 20 perusahaan sektor perdagangan besar yang terdaftar di Bursa Efek
Indonesia dari tahun 2013-2017. Variabel dependen berupa kualitas audit (Y) memiliki nilai minimum 0 dan
maksimum 1, sedangkan nilai rata-rata sebesar 0.13 dan standar deviasi sebesar
0,338. Nilai terkecil (minimum) diberikan kepada perusahaan yang tidak
menerima opini audit going concern sedangkan nilai terbesar (maximum)
diberikan kepada perusahaan yang mendapat opini going concern. Variabel independen yaitu Audit Tenure (X1) memiliki nilai minimum 1
dan nilai maksimum 5.sedangkan nilai rata-rata 2,42 dan standar deviasi 1,387. Nilai minimum menunjukkan masa perikatan sebesar 1 dan nilai maksimum
menunjukkan masa perikatan auditor dengan perusahaan sebesar 5. Variabel independen berupa Rotasi Audit (X2)pada perusahaan yang
menjadi sampel dalam penelitian ini memiliki nilai minimum sebesar 0 dan nilai
maksimum sebesar 1, sedangkan nilai rata-rata sebesar 0,18 dengan standar
deviasi sebesar 0,386.Nilai terkecil (minimum) diberikan kepada perusahaan yang
tidak melakukan rotasi audit sedangkan nilai terbesar (maximum) diberikan
kepada perusahaan yang melakukan rotasi audit. Variabel dependen berupa Ukuran Kantor Akuntan Publik (X3) pada
perusahaan yang menjadi sampel dalam penelitian ini memiliki nilai minimum
sebesar 0 dan nilai maksimum sebesar 1, sedangkan nilai rata-rata sebesar 0,48
dengan standar deviasi sebesar 0,502. Nilai terkecil (minimum) diberikan kepada
perusahaan yang tidak diaudit oleh KAP Big Four sedangkan nilai terbesar
(maximum) diberikan kepada perusahaan yang diaudit oleh KAP Big Four. Hasil Uji Kesesuaian Keseluruhan Model (Overall Model Fit) Berikut ini disajikan data hasil pengujian kesesuaian keseluruhan model
(overall model fit) berdasarkan pada fungsi likelihood. 49 Carolus, Johannes, dan Maria
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untuk memprediksi kemungkinan kualitas audit perusahaan dari opini audit 50 Carolus, Johannes, dan Maria
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Jurnal Buana Akuntansi Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 Jurnal Buana Akuntansi going concern dan opini audit non going concern. Hasil uji matriks klasifikasi dapat
dilihat pada tabel berikut: p
Tabel 6
Matriks Klasifikasi
Tabel
di
Observed
Predicted
K_AUDIT
Non
Going
Concer
n
Going
Concern
Percenta
ge
Correct
Step
0
K_AU
D
Non
Going
Concern
87
0
100.0
Going
Concern
13
0
0
Overall percentage
87,0 Tabel 6
Matriks Klasifikasi Tabel
di
atas
menunjukkan bahwa kekuatan dari kualitas audit dapat dilihat pada opini audit
non going concern dimana mendapatkan percentage correct sebesar 100% hal ini
menunjukkan model regresi yang digunakan ada sebanyak 87 laporan keuangan
(100%) yang diprediksi akan melihat kualitas audit dengan opini audit non going
concern. Kekuatan prediksi model perusahaan yang melihat kualitas audit dengan
going concern adalah 0% yang berarti bahwa model regresi yang digunakan tidak
ada perusahaan yang diprediksi akan melihat kualitas audit dengan opini audit
going concern dari total 13 laporan keuangan yang melihat dengan opini audit
going concern. Hasil Uji Regresi Logistik
Model regresi logistik yang terbentuk disajikan pada tabel di bawah ini:
Tabel 7
Hasil Uji Koefisien Regresi Logistik
B
S.E. Wald
df
Sig. Exp(B)
Step
1a
X1
-.843
.423
3.970
1
.046
.431
X2
.213
.733
.085
1
.771
1.238
X3
-
1.341
.842
2.537
1
.111
.262
Consta
nt
.033
.825
.002
1
.968
1.034
Hasil pengujian terhadap koefisien regresi logistik menghasilkan model
berikut ini:
Ln (p/1-p) = K_AUD = 0,033 - 0,843X1 + 0,213X2 – 1,341X3 + e Hasil Uji Regresi Logistik
Model regresi logistik yang terbentuk disajikan pada tabel di bawah ini:
Tabel 7
Hasil Uji Koefisien Regresi Logistik
B
S.E. Wald
df
Sig. Exp(B)
Step
1a
X1
-.843
.423
3.970
1
.046
.431
X2
.213
.733
.085
1
.771
1.238
X3
-
1.341
.842
2.537
1
.111
.262
Consta
nt
.033
.825
.002
1
.968
1.034
Hasil pengujian terhadap koefisien regresi logistik menghasilkan model
berikut ini:
Ln (p/1-p) = K_AUD = 0,033 - 0,843X1 + 0,213X2 – 1,341X3 + e j
g
g
Model regresi logistik yang terbentuk disajikan pada tabel di bawah ini:
Tabel 7 Hasil pengujian terhadap koefisien regresi logistik menghasilkan model
berikut ini:
Ln (p/1-p) = K_AUD = 0,033 - 0,843X1 + 0,213X2 – 1,341X3 + e 51 Carolus, Johannes, dan Maria
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E-ISSN 2580-5452 Jurnal Buana Akuntansi Berdasarkan tabel di atas menunjukan bahwa variabel independen yaitu
audit tenure memiliki koefisien negatif sebesar -0.843 dengan tingkat signifikansi g
g
g
g
0,046. Karena tingkat signifikansi (p) lebih kecil dari α = 5% maka hipotesis satu
(H ) diterima yang artinya audit tenure berpengaruh negatif terhadap kualitas audit 0,046. Karena tingkat signifikansi (p) lebih kecil dari α = 5% maka hipotesis
(H1) diterima yang artinya audit tenure berpengaruh negatif terhadap kualitas (
)
y
g
y
p
g
g
p
Variabel rotasi audit sebagai variabel independen memiliki koefisien sebesar
0.213 dengan tingkat signifikansi 0,771. Karena tingkat signifikansi (p) lebih besar
dari α = 5% maka hipotesis kedua (H2) tidak diterima yang artinya rotasi audit tidak
berpengaruh terhadap kualitas audit. p
g
p
Variabel ukuran KAP sebagai variabel independen memiliki koefisen negatif
sebesar -1.341 dengan tingkat signifikan 0,111. Karena tingkat signifikansinya lebih
besar dari α = 5%, hal ini berarti bahwa ukuran kantor akuntan publik tidak
berpengaruh terhadap kualitas audit maka hipotesis ketiga atau (H3) ditolak. Pembahasan Hasil pengujian hipotesis yang dikembangkan dalam penelitian ini secara
ringkas disajikan sebagai berikut: Hasil pengujian hipotesis yang dikembangkan dalam penelitian ini secar
kas disajikan sebagai berikut: Tabel 8
Hasil Pengujian Hipotesis
Hipotesis
Pernyataan
Hasil
H1
Audit tenure
berpengaruh negatif
dan signifikan
terhadap kualitas audit
Hipotesis
diterima
H2
Rotasi audit tidak
berpengaruh terhadap
kualitas audit
Hipotesis
ditolak
H3
Ukuran kantor
akuntan publik tidak
berpengaruh terhadap
kualitas audit
Hipotesis
ditolak Pengaruh Antara Audit Tenure Dengan Kualitas Audit Pengaruh Antara Audit Tenure Dengan Kualitas Audit g
g
Hasil uji koefisien regresi logistik menunjukkan bahwa audit tenure memiliki
koefisien negatif sebesar -0,843 dengan tingkat signifikansi yang dimiliki oleh variabel
audit tenure sebesar 0,046. Nilai signifikansi tersebut lebih kecil dari 0,05. Hal ini
berarti bahwa audit tenure berpengaruh negatif dan signifikan terhadap kualitas
audit. Dengan demikian dapat disimpulkan bahwa penelitian ini menerima H1. g
Penelitian ini sesuai dengan penelitian yang dilakukan oleh Giri (2010) yang
membuktikan bahwa variabel audit tenure berpengaruh negatif dan signifikan
terhadap kualitas audit, didukung juga oleh penelitian Panjaitan (2014) yang
menyatakan bahwa audit tenure berpengaruh negatif terhadap kualitas audit yang
artinya semakin lama perikatan KAP dengan klien maka akan memiliki kualitas audit
yang lebih rendah. Hal ini disebakan tenure biasanya dikaitkan dengan pengaruhnya
terhadap independensi auditor. Hubungan yang panjang antara KAP dan klien 52 Carolus, Johannes, dan Maria
Vol. 4 No .2
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E-ISSN 2580-5452 Jurnal Buana Akuntansi berpotensi untuk menimbulkan kedekatan antara mereka, hal tersebut dapat
menghalangi independensi auditor dan mengurangi kualitas audit (Al-Thuneibat et
al., 2011). Juga didukung oleh penelitian Nurintianti dan Purwanto (2017) bahwa
audit tenure berpengaruh negatif terhadap kualitas audit. Hal ini juga menyebabkan
audit tenure yang berlangsung
lama
membuat auditor kehilangan
sikap
profesionalismenya sehingga menjalankan proses audit berada dibawah pengaruh
manajemen sehingga jika terdapat kesalahan dari perusahaan maka sulit untuk
auditor mempublikasikannya karena auditor menganggap bisa saja perusahaan
memutuskan kontrak dalam mengaudit laporan keuangan klien sehingga akan
kehilangan pekerjaan. Dengan lamanya masa perikatan yang terjalin antara auditor
dan perusahaan maka akan berdampak pada menurunnya kualitas audit hal ini
disebabkan karena auditor telah memiliki hubungan emosional yang erat sehingga
terjalin keakraban yang memungkinkan menurunnya independensi auditor sehingga
berbagai kecurangan perusahaan dapat dimanipulasi oleh auditor sehingga kualitas
audit yang dihasilkan dapat menurunkan kepercayaan pengguna laporan keuangan. Juga dengan singkatnya masa perikatan auditor dengan klien akan berakibat pada
kurang efektifnya auditor dalam melaksanakan prosedur audit yang baik sehingga
memungkinkan melewati beberapa prosedur audit yang telah direncankan sehingga
kualitas audit menjadi rendah juga dengan singkatnya masa perikatan akan
menyulitkan auditor untuk memahami dan mendeteksi setiap kesalahan atau
penyimpangan yang dilakukan oleh auditor. berpotensi untuk menimbulkan kedekatan antara mereka, hal tersebut dapat
menghalangi independensi auditor dan mengurangi kualitas audit (Al-Thuneibat et
al., 2011). Juga didukung oleh penelitian Nurintianti dan Purwanto (2017) bahwa
audit tenure berpengaruh negatif terhadap kualitas audit. Hal ini juga menyebabkan
audit tenure yang berlangsung
lama
membuat auditor kehilangan
sikap
profesionalismenya sehingga menjalankan proses audit berada dibawah pengaruh
manajemen sehingga jika terdapat kesalahan dari perusahaan maka sulit untuk
auditor mempublikasikannya karena auditor menganggap bisa saja perusahaan
memutuskan kontrak dalam mengaudit laporan keuangan klien sehingga akan
kehilangan pekerjaan. Dengan lamanya masa perikatan yang terjalin antara auditor
dan perusahaan maka akan berdampak pada menurunnya kualitas audit hal ini
disebabkan karena auditor telah memiliki hubungan emosional yang erat sehingga
terjalin keakraban yang memungkinkan menurunnya independensi auditor sehingga
berbagai kecurangan perusahaan dapat dimanipulasi oleh auditor sehingga kualitas
audit yang dihasilkan dapat menurunkan kepercayaan pengguna laporan keuangan. Juga dengan singkatnya masa perikatan auditor dengan klien akan berakibat pada
kurang efektifnya auditor dalam melaksanakan prosedur audit yang baik sehingga
memungkinkan melewati beberapa prosedur audit yang telah direncankan sehingga
kualitas audit menjadi rendah juga dengan singkatnya masa perikatan akan
menyulitkan auditor untuk memahami dan mendeteksi setiap kesalahan atau
penyimpangan yang dilakukan oleh auditor. Pengaruh Rotasi Audit Terhadap Kualitas Audit g
p
Variabel rotasi audit sebagai variabel independen memiliki koefisien positif
sebesar 0,213 dengan signifikansi terhadap kualitas audit sebesar 0,771. Nilai
signifikansi tersebut lebih besar dari 0,05. Hal ini berarti bahwa rotasi audit tidak
memiliki pengaruh yang signifikan terhadap kualitas audit. Dengan demikian dapat
disimpulkan bahwa penelitian ini menolak H2 Penelitian ini sejalan dengan penelitian Hartadi (2012) yang menyatakan
bahwa rotasi audit tidak berpengaruh terhadap kualitas audit. Hal ini disebabkan
karena pasar sebenarnya tidak terlalu peduli apakah auditor yang menyatakan opini
pada laporan keuangan tahunan tersebut pernah dirotasi atau tidak. Hasil penelitian
ini mendukung penelitian Ramdani (2017) yang menyatakan bahwa rotasi audit tidak
berpengaruh terhadap kualitas audit sebab kurangnya kepedulian pelaku pasar
terhadap pergantian auditor dan tim auditnya masih baru sehingga pengalaman
auditnya masih baru. Juga sejalan dengan penelitian yang dilakukan Sofyana dan
Nugroho (2012) variabel rotasi audit tidak berpengaruh terhadap kualitas audit
dikarenakan independensi auditor, biaya yang cukup besar, waktu yang cukup lama
untuk KAP untuk mempelajari alur bisnis perusahaan dan juga perusahaan takut
akan terungkapnya semua kecurangan yang ada dan perusahaan memiliki
pengalaman terhadap KAP lain yang kinerjanya tidak memuaskan. Hal ini juga
disebabkan karena tingginya profesionalisme auditor tersebut yang bersikap
independen dalam melaksanakan audit, sehingga baik dilakukan rotasi audit atau 53 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Jurnal Buana Akuntansi tidak jika seorang auditor menjunjung tinggi independensi maka tidak akan
terpengaruh oleh hal-hal yang dapat mengurangi kualitas audit . Rotasi audit tidak
mempengaruhi kualitas audit juga disebabkan karena perusahaan menganggap
bahwa semua auditor akan berusaha semaksimal mungkin untuk memeriksa dan
memberikan opini sesuai dengan keadaan dari perusahaan karena klien merasa
bahwa baik sering mengganti auditor maupun lama akan sama karena semua auditor
menginginkan reputasi yang baik. Tetapi untuk menghindari hal-hal yang tidak
diinginkan maka terdapat dua alasan dalam melaksanakan rotasi audit yaitu
mandatory dan voluntary. ruh Ukuran Kantor Akuntan Publik Terhadap Kualitas Audit Pengaruh Ukuran Kantor Akuntan Publik Terhadap Kualitas Audit g
p
Variabel ukuran KAP sebagai variabel independen memiliki koefisen negatif
sebesar -1.341 dengan tingkat signifikansi 0,111. Nilai signifikansi tersebut lebih besar
dari 0,05. Hal ini berarti bahwa ukuran kantor akuntan publik yang dinyatakan dalam
KAP big four dan KAP non big four tidak memiliki pengaruh yang signifikan terhadap
kualitas audit. Dengan demikian dapat disimpulkan bahwa H3 ditolak. Hasil penelitian ini sesuai dengan penelitian yang dilakukan oleh Panjaitan dan
Chariri (2014); ukuran kantor akuntan publik tidak berpengaruh terhadap kualitas
audit atas pemeriksaan laporan keuangan pada perusahaan-perusahaan. Kantor
akuntan publik yang berafiliasi dengan KAP Big four tidak cenderung menghasilkan
kualitas audit yang lebih baik dari pada KAP yang tidak berafiliasi dengan KAP Big
four. Dari hasil penelitian dari Siregar dan Nindita, diperoleh beberapa kesimpulan
bahwa ukuran KAP tidak berpengaruh signifikan terhadap kualitas audit yang
diukur dengan nilai akrual dan ukuran KAP juga tidak memiliki pengaruh terhadap
probabilita penerbitan laporan audit going concern. Artinya bahwa tidak terdapat
perbedaan kualitas akrual bagi perusahaan yang diaudit oleh KAP yang besar, baik
itu KAP Big Four maupun KAP Non Big Four. Selain itu, penerbitan laporan audit
going concern pada perusahaan yang diaudit oleh KAP yang besar juga dapat
dikatakan seragam dengan KAP yang kecil. Secara keseluruhan disimpulkan bahwa
hasil pengujian belum dapat memberi bukti yang konsisten dengan penelitian
sebelumnya. Pengujian sensitifitas atas pengukuran ukuran KAP juga belum
memberikan bukti bahwa KAP yang lebih besar akan menghasilkan kualitas audit
yang lebih baik. Hal ini kemungkinan besar terjadi karena terdapat faktor-faktor yang
lebih mempengaruhi kualitas audit selain faktor ukuran KAP. Faktor tersebut adalah
kompetensi dan independensi. Apabila ukuran KAP yang besar tidak dibarengi
dengan kompetensi yang tinggi dari auditornya, kemampuan mendeteksi manajemen
laba serta kesangsian kelangsungan usaha pun akan rendah. Nindita: Pengaruh
Ukuran Kantor Akuntan Publik Terhadap Kualitas Audit 103 Akibatnya kualitas
akrual juga akan rendah. Begitu juga dengan independensi, KAP dengan ukuran
besar yang auditornya memiliki kompetensi yang tinggi akan membantu perusahaan
dalam melakukan manajemen laba apabila auditor tersebut kurang memiliki
independensi. Selain itu untuk bertahan dalam persaingan bisnis, kantor akuntan publik baik
big four maupun non big four akan berusaha semaksimal mungkin untuk 54 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Kesimpulan Penelitian ini dilakukan untuk mengetahui pengaruh audit tenure, rotasi
audit, dan ukuran kantor akuntan publik terhadap kualitas audit. Penelitian ini
menggunakan perusahaan sektor perdagangan besar yang terdaftar di Bursa Efek
Indonesia periode 2013-2017 sebagai populasi penelitian yaitu 37 perusahaan
sektor perdagangan besar dan 20 perusahaan yang memenuhi kriteria menjadi
sampel penelitian. p
p
Berdasarkan hasil penelitian ini, terdapat beberapa hal yang dapat
disimpulkan antara lain: 1 Hasil uji regresi logistik (logistic regression) menunjukkan bahwa audit
tenure berpengaruh negatif dan signifikan terhadap kualitas audit. Hasil
penelitian ini mendukung dari penelitian dari hasil penelitian yang
dilakukan oleh Giri (2010), Panjaitan (2014), Nurintiati dan Purwanto
(2018). 2 Hasil uji regresi logistik (logistic regression) menunjukkan bahwa rotasi
audit tidak berpengaruh terhadap kualitas audit. Hasil penelitian ini
didukung dari hasil penelitian yang dilakukan oleh Hartadi (2012),
Ramdani (2017), Sofyana dan Nugroho (2012) 3 Hasil uji regresi logistic (logistic regression) menunjukkan bahwa ukuran
kantor akuntan publik tidak berpengaruh terhadap kualitas audit,
penelitian ini didukung dari hasil penelitian yang dilakukan oleh Panjaitan
dan Chariri (2014). (
)
Saran Jurnal Buana Akuntansi memepertahankan eksistensinya dalam bisnis jasa akuntan publik sehingga mereka
akan bekerja sesuai dengan prosedur audit yang baik untuk menghasilkan laporan
audit yang berkualitas sehingga mendapatkan kepercayaan dari klien. memepertahankan eksistensinya dalam bisnis jasa akuntan publik sehingga mereka
akan bekerja sesuai dengan prosedur audit yang baik untuk menghasilkan laporan
audit yang berkualitas sehingga mendapatkan kepercayaan dari klien. Saran Beberapa saran yang dapat dipertimbangkan untuk peneliti selanjutnya
yang melakukan penelitian berkaitan dengan kualitas audit: 1 Bagi peneliti selanjutnya disarankan menambah variabel lain yang
berkaitan
erat secara
teori
terhadap variabel
kualitas
auditserta
memperluas ruang lingkup penelitian, agar hasil penelitian dapat
diperluas. Hal ini dimaksudkan agar hasil penentuan kualitas audit lebih
baik. 2 Penelitian ini hanya menggunakan sampel perusahaan sector perdagangan
besar. Peneliti selanjutnya dapat mempertimbangkan untuk memperluas
sampel penelitian dengan menggunakan sampel perusahaan dari seluruh
sektor terdaftar di BEI 55 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 DAFTAR PUSTAKA Al-Thuneibat, Ibrahim Isa, dan Ata Baker, 2011. “Do Audit tenure and Firm Size
Contribute to Audit Quality?” Journal of Accounting and Economics, Jordan. Atmaja, Lukas Setia. 2008. Teori dan Praktik Manajemen Keuangan. Yogyakkarta:
Penerbit Andi. Efraim, F. 2010. “Pengaruh Tenur KAP dan Reputasi KAP Terhadap Kualitas Audit:
Kasus Rotasi Wajib Auditor di Indonesia”. Simposium Nasional Akuntansi XIII
Purwokerto Giri, E. F.(2010). Pengaruh Tenur Kantor Akuntan Publik (KAP) dan Reputasi KAP
terhadap Kualitas Audit : Kasus Rotasi Wajib Auditor di Indonesia. Simposium
Nasional Akuntansi XIII Purwokerto,13-15 Oktober:1-26. Halim, Abdul. “Auditing (Dasar-Dasar Audit Laporan Keuangan)”, Jilid 1, UPP STIM
YKPN, Yogyakarta, 2008. Hamid, Abdul. “Pengaruh Tenur KAP dan Ukuran KAP terhadap Kualitas Audit”,
Fakultas Ekonomi Universitas Negeri Padang, 2013. Hartadi, Bambang. “Pengaruh Fee Audit, Rotasi KAP, dan Reputasi Auditor terhadap
Kualitas Audit di Bursa Efek Indonesia”, Jurnal Ekonomi dan Keuangan, Vol 16,
No. 1, hal 84-103, 2012. Hasbi, A.R.A. (2018). “Pengaruh Audit Tenure, Auditor Switching, Dan Company Size
Terhadap Kualitas Audit Pada Perusahaan Manufaktur Yang Terdaftar Di
Bursa Efek Indonesia Tahun 2012-2015”. (Skripsi). Universitas Islam Negeri
Alauiddin Makassar. Himawan, Ferdinandus. A dan Rara Emarila. “Pengaruh Persepsi Auditor atas
Kompetensi, Independensi dan Kualitas Audit terhadap Umur Kantor Akuntan Publik
(KAP) Di Jakarta”, Esensi Volume 13 No. 3, Jakarta, Desember, 2013 abarat, G. (2012). Pengaruh Pengalaman Time Budget Pressure dan Etika 6034. Jensen, M.C., & Meckling, W.H.(1976).Theory of the Firm: Managerial Behavior
Agency Cost, and Ownership Structure. Journal of Finance Economics, 3, 305-360. Diakses dari https://papers.ssrn.com. Kurniasih, Margi. (2014). Pengaruh Fee Audit, Audit Tenure, Dan Rotasi Audit
Terhadap Kualitas Audit (Studi Empiris pada Perusahaan Manufaktur Go 56 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Jurnal Buana Akuntansi Public yang Terdaftar di Bursa Efek Indonesia tahun 2008-2012). (skripsi). Universitas diponegoro. Public yang Terdaftar di Bursa Efek Indonesia tahun 2008-2012). (skripsi). Universitas diponegoro. Kurniasih, M,& Rohman, A. (2014). Pengaruh Fee Audit, Audit Tenure, dan Rotasi
Audit Terhadap Kualitas Audit. Diponegoro Journal of Accounting. Diakses dari
eprints.undip.ac.id. Mayasari, Ida. “Pengaruh Profesionalisme Auditor dan Masa Perikatan Audit Terhadap
Kualitas Audit”, Universitas Komputer Indonesia, Bandung, 2013. Mgbame, C.O., Eragbhe, E dan Osazuwa, N, “Audit Partner Tenure and Audit
Quality: An Emprical Analysis”, European Journal of Business and
Management, Vol. 4, No. 7, pp.154-159, 2012. Mulyadi (2010). Auditing (Edisi 6). Jakarta: Salemba Empat. Nuratama, I Putu. “Pengaruh Tenur dan Reputasi Kantor Akuntan Publik Pada Kualitas
Audit dengan Komite Audit Sebagai Variabel Moderasi”, Denpasar,2011. Nurintiati,A.A., & Purwanto, A, “Pengaruh Tenure Kap, Ukuran Kap, Spesialisasi
Auditor Dan Audit Fee Terhadap Kualitas Audit Dengan Moderasi Komite
Audit”, jurnal ilmiah akuntansi,Vol 6,No.1, pp 1-13, 2017 Panjaitan,C.M.dan Chariri, A.,(2014).”Pengaruh Tenure, Ukuran KAP Dan
Spesialisasi Auditor”, jurnal ilmiah akuntansi, Vol.3, No.3, pp. 1-12, 2014. Putra, I Gede Cahyadi. “Kualitas Audit Kantor Akuntan Publik di Bali Ditinjau dari
Time Budget Pressure Risiko Kesalahan, dan Kompleksitas Audit”, Jurnal
Ilmiah Akuntansi dan Humanika Jinah, Vol.2, No.2,pp. 765-784, 2013. Perdana, M. Hadi, (2014). Pengaruh Rotasi Kantor Akuntan Publik dan Rotasi
Akuntan Publik (Partner Auditor) Terhadap Kualitas Audit. Skripsi,
Universitas Diponegoro. Putri, T.M. (2014). Pengaruh Auditor Tenure, Ukuran Kantor Akuntan Publik, dan
Ukuran Perusahaan Klien terhadap Kualitas Audit (Studi Empiris pada
Perusahaan Maufaktur yang Terdaftar di BEI pada Tahun 2010-2012) (Skripsi). Universitas Diponegoro, Semarang. Radona, Bani, (2017). Analisis Pengaruh Audite Tenure, Audit Fee, Audit Switching,
Ukuran Perusahaan Dan Independensi Audit Terhadap Kualitas Audit. Skripsi. Universitas Sumatera Utara 57 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Carolus, Johannes, dan Maria
Vol. 4 No .2
ISSN 2528-1119
E-ISSN 2580-5452 Sofyana dan Gatot, “Analisis Pengaruh Praktik Rotasi Audit dan Masa Pemberian
Jasa Audit terhadap Kualitas Audit”, 2012. Jurnal Buana Akuntansi Ramdani, Rifky. (2016). Pengaruh Fee Audit, Audit Tenure, Rotasi Audit Dan
Ukuran Perusahaan Klien Terhadap Kualitas Audit pada Sektor Keuangan
yang Terdaftar di BEI Periode 2012-2014. (Skripsi). Universitas Islam Negeri
Jakarta Simangunsong, C. (2015). Faktor – Faktor yang Mempengaruhi Penerimaan Opini
Audit Going Concern pada Perusahaan Perbankan yang Terdaftar di Bursa
Efek Indonesia Tahun 2010 – 2012(Skripsi). Universitas Sumatera Utara. Medan Simanjuntak, Piter. (2008). Pengaruh Time Budget Pressure dan Resiko Kesalahan
terhadap Penurunan Kualitas Audit. Tesis. Universitas Diponegoro Semarang. Siregar, B.U. (2016). Pengaruh Audit Tenure, Reputasi Auditor, Spesialisasi Audit,
dan Ukuran Perusahaan terhadap Kualitas Audit Pada Perusahaan Property
dan Real Estate yang terdaftar di Bursa Efek Indonesia (BEI)(Skripsi). Universitas Sumatera Utara. Medan Sopian, Dani. 2014. Pengaruh Ukuran Kantor Akuntan Publik dan Masa Perikatan
Audit terhadap Kualitas Audit serta Implikasinya Terhadap Kualitas Laba. Jurnal Sains Manajemen & Akuntansi. Vol VI, No 1. Standar Profesional Akuntan
Publik.2013. Sofyana dan Gatot, “Analisis Pengaruh Praktik Rotasi Audit dan Masa Pemberian
Jasa Audit terhadap Kualitas Audit”, 2012. 58
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RETROFIT AND REPAIR OF REINFORCED CONCRETE WALLS WITH FRP: A REVIEW OF EXPERIMENTAL INVESTIGATIONS
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Zenodo (CERN European Organization for Nuclear Research)
| 2,023
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cc-by
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RETROFIT AND REPAIR OF REINFORCED CONCRETE WALLS
WITH FRP: A REVIEW OF EXPERIMENTAL INVESTIGATIONS
Jazalyn Dukes, National Institute of Standards and Technology, USA, Jazalyn.dukes@nist.gov
Siamak Sattar, National Institute of Standards and Technology, USA, siamak.sattar@nist.gov azalyn Dukes, National Institute of Standards and Technology, USA, Jazalyn.dukes@nist.gov
Siamak Sattar, National Institute of Standards and Technology, USA, siamak.sattar@nist.gov Retrofitted components; repair; experimental studies; database Retrofitted components; repair; experimental studies; database ABSTRACT Retrofit and repair of structures occur under differing circumstances but are both necessary to
improve existing building stock and increase resilience of communities against hazards. FRP is an
attractive option for both retrofit and repair because of its lightweight properties, corrosion resistant
qualities, and ease of application. This paper compiles a literature review on structural behavior of RC
shear walls after retrofit or repair with FRP. Details such as the FRP configuration, materials, and wall
shape of FRP-retrofitted shear walls are presented. This paper concludes with potential future research
topics to gain better understanding on the performance of FRP-retrofitted walls. INTRODUCTION Fiber-reinforced polymer (FRP) strengthening of concrete components has become an acceptable and
widely used method of retrofit and repair. However, there remain research areas where the
performance of these retrofitted systems has not been investigated. Goodwin et al. (2019) states that
one of the biggest research needs for FRP-retrofitted structures includes large-scale experiments. While reinforced concrete (RC) components such as columns wrapped in FRP have been studied for
over 30 years, components like FRP-retrofitted RC shear walls do not have the benefit of such an
extensive interest in experimental research. The goal of this review is to discuss available
experimental research on FRP-retrofitted and repaired shear walls, which was gathered as part of the
development of a database (Dukes & Sattar, 2021), and to highlight areas where research is needed. The authors distinguish retrofitted walls, which are walls that were untested prior to FRP addition, and
repaired walls, which were tested sometimes until failure, repaired, and then applied with an FRP
overlay, as the two types of wall tests that often have different goals and outcomes. Across the groups,
different characteristics of the walls, including FRP configuration, FRP material type, and wall
shapes, will be discussed. Conclusions are summarized in the final section, where additional research
needs are highlighted. FRP Application Purpose pp
p
We distinguish walls by the purpose of FRP application during testing. We refer to FRP-retrofitted
walls as walls that were tested only once after FRP was applied. This represents the scenario of
retrofitting an existing undamaged wall in a building before an event occurs. We refer to FRP-
repaired walls as walls that were tested or cycled as plain RC walls, then repaired with FRP. FRP-
repaired walls represent the scenario where an existing wall is damaged or degraded to the point of
needing repair. Over 40 % of the walls in the database were tested as retrofitted walls, and 30 % are
repaired and strengthened. Throughout the paper, the specimens discussed will be referred to in these
terms: retrofitted or repaired. WALL SHAPE Rectangular wall shapes are the dominant shape found in the database. These walls are planar walls
without barbells or pronounced boundary elements. As these wall types are easier to build and test in
the lab it is understandable why many research programs focused on this shape. However, this wall
shape does not represent all wall conditions found in existing buildings, which indicates a research
gap that should be explored. This section describes research studies that focused on non-rectangular
wall shapes. OVERVIEW OF FRP-RETROFITTED WALL DATABASE This review stems from the information gathered from an experimental database of FRP-retrofitted
RC shear walls developed at the National Institute of Standards and Technology (NIST) (Dukes &
Sattar, 2021). This database contains over 130 specimens from more than 30 publicly available
sources, such as journal articles, reports, and theses. The database is intended to be as comprehensive
as possible, providing details such as material properties of the concrete and FRP, geometric
properties, and loading and response information. During the development of the database, two major
categories were identified for grouping the test programs: whether there were openings in the walls,
and whether the walls were damaged prior to FRP application. Table 1 gives general statistics of the
types of wall specimens found in the database. The walls discussed in this paper fall under Subset A
and B groups, which are walls without openings that were either “retrofitted” or “repaired and
retrofitted” with FRP. 1 Table 1: Summary of types of walls found in FRP-retrofitted shear wall database
Wall Test and
Condition
Retrofit
No damage prior to FRP
Repair and Retrofit
Damage prior to FRP
No Openings
Subset A
Retrofit, no openings
40 %
Subset B
Repair, no openings
32 %
Openings
Subset C
Retrofit, with openings
12 %
Subset D
Repair, with openings
16 % Barbell walls Hwang et al. (2004) looked at the effectiveness of enhancing shear strength of seismically insufficient
RC partition walls with external carbon FRP (CFRP) materials. The research plan included
experimental and analytical studies of the specimens. The tests included six large scale specimens
with sizeable boundary elements or columns at each end, making the cross section of the wall a
barbell shape. The researchers tested the conditions of a retrofitted wall web without end anchors
(walls WF-12-FV and WF-12-FHV) and with end anchors (walls WF-12-FV-A and WF-12-FHV-A)
of the CFRP laminates. The identification of each specimen included the orientation of the laminates
(FV meaning vertical laminates, FHV meaning vertical and horizontal laminates) and presence of
anchors (with “-A” appended). The anchor system consisted of structural steel angles bolted to the
wall base and reaction beam. This allowed the CFRP reinforcement to be able to transfer the load to
the supports. The backbone envelope curves of the resulting cyclic testing in Figure 1 reveals that
anchorage improves the response of the retrofitted walls, while the retrofitted walls without anchors
showed almost no difference to the unretrofitted wall. The retrofitted walls with anchors WF-12-FV-
A and WF-12-FHV-A showed an increase of 88 % and 126 % in shear strength compared to the as-
built wall. The retrofitted walls without anchorage, WF-12-FV and WF-12-FHV, performed similarly
to the as-built wall, showing that the FRP retrofit in this case had little effect on the performance. 2 2 (b) Backbone response curves
0
500
1000
1500
2000
2500
3000
0
20
40
60
80
100
120
Shear Force (kN)
Deflection (mm)
WF-12
WF-12-FV
WF-12-FHV
WF-12-FV-A
WF-12-FHV-A (a) Illustration of retrofitted wall
specimen
(b) Backbone response curves
Figure 1: Envelope curves of the load-deflection response for all wall specimens in (source data from
Hwang et al. (2004))
0
500
1000
1500
2000
2500
3000
0
20
40
60
80
100
120
Shear Force (kN)
Deflection (mm)
WF-12
WF-12-FV
WF-12-FHV
WF-12-FV-A
WF-12-FHV-A (b) Backbone response curves specimen
Figure 1: Envelope curves of the load-deflection response for all wall specimens in (source data from
Hwang et al. (2004)) Li and Lim (2010) tested axially loaded RC walls with boundary elements to determine the
effectiveness of FRP as a repair method. Barbell walls The goal of the study was to investigate the seismic
performance of RC walls with limited transverse reinforcement, representing walls found in buildings
located in regions with low or moderate seismicity. Two sizes of walls, with aspect ratios of 1.125
(low-rise walls) and 1.625 (medium-rise walls), were subject to axial loading and cyclic loading to
simulate seismic loads until failure, then repaired with FRP materials and testing again. The original
specimens all failed in a similar mode, which was predominantly flexural failure. The FRP repair
configuration was based on the engineering judgement of the researchers. FRP sheets, consisting of
either all glass or a combination of glass and carbon fibers, were bonded in the horizontal and vertical
directions on both sides of the walls. The wall was confined by the addition of U-wraps around the
boundary elements, secured by grinding and rounding the corners of the wall. The FRP sheets were
also secured with glass FRP (GFRP) anchors located at various places along the length of the sheets. In the case of wall specimen MW2, a medium-rise wall was tested until failure, then repaired by
replacing concrete with mortar and injecting epoxy into cracks. The specimen was then strengthened
with a layer of vertical carbon FRP on both sides and along the edges of the wall, and a layer of
horizontal glass FRP along the web of the wall. The repaired wall was tested under the amended ID
RMW2. After the tests, the results showed that strength and ductility could be restored or improved
with the addition of FRP as a repair technique, as shown in Figure 2 for specimen MW2. The use of
CFRP showed an advantage in recovering strength over GFRP, which was used exclusively for the
other medium-rise wall specimen. The U-wraps used at the ends of the walls assisted in preventing
debonding of the jackets. However, there was debonding of L-shaped strips at the base of the walls,
which shows the potential difficulty of effectively anchoring critical regions, such as the base of
walls Figure 2: Hysteresis curves of reference wall MW-2 and retrofitted wall RMW-2 (source data from Li
and Lim (2010)) Figure 2: Hysteresis curves of reference wall MW-2 and retrofitted wall RMW-2 (source data from Li
and Lim (2010)) Other non-rectangular shapes g
p
Sonobe et al. (1999) tested columns with wing walls. These shapes have a symmetrical or
asymmetrical column in the center of two attached wing walls, as illustrated in Figure 3. This 3 experimental program consisted of 16 wall specimens that used both carbon and aramid fiber sheets
and included one repaired wall along with retrofitted walls. The wall design was based on a pre-1971
design code to represent old existing building stock. The testing variables included position of wing
walls to the column, width of wing walls, and the type and amount of FRP shear reinforcement. During testing, axial load was applied to each wall as well as reversed cyclic lateral loading. After
testing, nearly all of the specimens exhibited shear failures. It was concluded that both carbon and
aramid fibers enhanced the seismic behavior of these specimens, and that more fiber reinforcement
resulted in higher ultimate shear strengths, up to a limit. For specimens with three and four layers of
FRP, the researchers found similar ultimate shear strengths, which they attribute to there being a
limitation of retrofit effects with increasing layers of FRP. The authors proposed an equation to
evaluate the ultimate shear strength of columns with wing walls. As these test specimens are unlike
others in the database, which are mostly rectangular, it is unclear how these results would translate to
more typical retrofitted walls. Figure 3: Examples of wing wall specimens tested (adapted from Sonobe et al. (1999)) Figure 3: Examples of wing wall specimens tested (adapted from Sonobe et al. (1999)) Zhang et al. (2015) tested four nonrectangular repaired RC wall specimens. The tests included two L-
shaped walls, one specimen loaded parallel to one of the segments of the wall, and the other loaded in
the symmetrical axis; and two T-shaped walls that were loaded along the symmetrical axis but with
0.10 and 0.20 axial load ratios. The FRP repair was done on previously tested and damaged
specimens. Three of the specimens used a combination of glass and carbon fibers for the repair,
applying the carbon FRP to the plane of the wall parallel to the loading, and glass to the plane
perpendicular to the loading. Specimen LWR1, shown in Figure 4 (a) and (b) and was tested on the
symmetrical axis, was strengthened with only CFRP. The scheme of the FRP strengthening is shown
in Figure 4 (a) and (b). FRP MATERIAL Carbon and glass FRP are the most commonly used FRP materials in construction. Both carbon and
glass have been shown to improve strength and ductility in structures, and they perform well in certain
environmental conditions (Zaman et al., 2013; Dukes et al., 2022). Carbon FRP is usually preferred
because of the high modulus and strength, however glass is used as well, where lower costs are
desired and reduced strength is acceptable (Goodwin et al., 2019). Over 70 % of the specimens in the
database use carbon FRP, and around 15 % used glass FRP. For researchers or practitioners looking
for the performance of FRP materials other than carbon or glass on RC walls, the available research is
scarce. However, there were some examples of alternative FRP or composite use for retrofitting RC
shear walls. Some studies have shown the potential for natural fibers in FRP retrofits, as natural fibers can offer
similar performance to carbon or glass, with the added benefit of being sustainable, lower cost, and
more environmentally friendly. Di Luccio et al. (2017) tested retrofitted RC shear walls with the
natural fiber of flax. Among natural fibers, flax has potential for use in composite materials due to its
high tensile strength properties, but the characteristics can vary due to the type of species, location of
cultivation and even the position along the stem from which the fiber is taken. The researchers
compared RC wall performance of flax FRP retrofitted walls against walls retrofitted with carbon
FRP. The CFRP retrofitted walls were tested and reported by Qazi et al. (2013), which is described
later in this paper. The material properties of the CFRP include a Young’s modulus of 105 GPa, and
an ultimate strength of 820 MPa, while the FFRP had a Young’s modulus of 14 GPa and ultimate
strength of 120 MPa. The specimens were loaded under constant 90 kN vertical load, and cyclic
lateral load that grew 1 mm in amplitude every three cycles until failure. The configuration of each
specimen is illustrated in Figure 5. SLR4 CFRP-retrofitted specimen had one layer of bidirectional
CFRP, SLR6 specimen had one layer of unidirectional CFRP, and FRSL1-3 flax retrofitted specimens
had the number of layers indicated in Table 2. Other non-rectangular shapes Fiber anchors were also placed at the intersections of the wall elements to
prevent premature debonding of the FRP sheets. The results showed that all of the repaired walls were
able to recover most of the lateral strength of the original specimen, where the repaired walls were
within ± 20 % of the original peak lateral strength. The results showed that most of the repaired walls
maintained or gained ductility through the cyclic tests. The exception was specimen LWR1, the L-
shaped wall tested in the symmetrical axis, which lost lateral load capacity at an earlier cycle than the
original specimen. Figure 4 (c) shows the final hysteretic loops of the original and repaired test for
specimen LWR1. 4 (c) Backbone Response Curve (a) LWR1
FRP repair
elevation 1
(b) LWR1 FRP
repair elevation 2
(c) Backbone Response Curve
Figure 4: Backbone response curve of Specimen LWR1 before and after repair (source data from
Zhang et al. (2015)) elevation 1
Figure 4: Backbone response curve of Specimen LWR1 before and after repair (source data from
Zhang et al. (2015)) FRP MATERIAL As is shown in Table 2, the FRSL1 specimen, tested
with three layers of flax-FRP, showed an increase in strength but not in ultimate displacement
compared to the control specimen SL3. The other flax FRP-retrofitted walls (FRSL2 and FRSL3)
showed an improvement in both strength and ultimate displacement over the control. Compared to
specimens SLR4 and SLR6, ductility was also improved more substantially. These results, detailed in
Table 2, shows that flax-FRP may be to be a viable alternative with more studies and advanced
knowledge of the materials, including under different environmental conditions. 5 (a) SLR4/SLR6
CFRP retrofitted
specimen
(b) FRSL1 flax FRP
retrofitted wall
(c) FRSL2 flax FRP
retrofitted wall
(c) FRSL3 flax FRP
retrofitted wall
Figure 5: Configuration of RC walls retrofitted with composite materials (adapted from Di Luccio et
al. (2017))
Glass FRP
Flax FRP Figure 5: Configuration of RC walls retrofitted with composite materials (adapted from Di Luccio et
al. (2017)) Maximal loads and displacements for each wall specimen (source data from Di Luccio et al. (2017)) Table 2: Maximal loads and displacements for each wall specimen (source data from Di Luccio et
(2017))
Push Direction
Specimen
Type FRP
Layers
Max
Load
(kN)
Percent
change
Max
Disp. (mm)
Percent
change
SL3
None
-
27.75
-
20.56
-
SLR4
Carbon
1
36.01
+ 30
20.52
- 1
SLR6
Carbon
1
47.24
+ 70
14.57
- 30
FRSL1
Flax
3
55.25
+ 99
18.82
- 8
FRSL2
Flax
4
54.00
+ 94
22.92
+ 11
FRSL3
Flax +
Glass
2+2
68.5
+ 147
26.86
+ 31 Zhou et al. (2013) tested the capabilities of a new type of polymer matrix retrofit, called CarbonFlex,
which is a unique polymeric matrix composite system consisting of amino-based time-dependent
reacting compounds. Dhiradhamvit et al. (2011) detail the attributes of the material further. This
material was investigated because conventional CFRP materials perform in a brittle manner and have
low energy dissipation capability, where CarbonFlex was designed to sustain high strengths under
large deformations. The matrix has an internal energy dissipation mechanism, which can redirect the
damage path in extreme loading conditions. This results in stabilized crack propagation and ductile
mechanical failure. The researchers tested the material on a reinforced concrete wall with a
rectangular cross section that was cycled laterally until the wall had reached 40 % of the peak
strength. It was then repaired and retrofitted with the CarbonFlex material. FRP MATERIAL The retrofit consisted of
CarbonFlex cross-bracing strips placed in the diagonal directions on both sides of the wall, vertical
strips along the wall edges, horizontal strips along the top and bottom edges of the wall for anchorage,
and a full wrap around the wall with horizontal sheets. Comparison of the as-built wall to the repaired
and retrofitted wall shows increased confinement, improved strength on the negative side of the
backbone curve, improved ductility, and controlled crack propagation. The backbone curves are
shown in Figure 6. More tests are needed to show the potential of this material as a viable alternative
to typical CFRP applications. 6 6 Figure 6: Backbone curve response of as-built wall and a wall retrofitted with CarbonFlex (source
data from Zhou et al. (2013)) Figure 6: Backbone curve response of as-built wall and a wall retrofitted with CarbonFlex (source
data from Zhou et al. (2013)) Fully confined y
The majority of the walls in the database were retrofitted on both sides and confined around the
corners, either by continuous wrapping, or with C-shaped FRP wraps around the corners. The
configuration varied from full coverage on the faces of the walls, to intermittent strips or other type of
arrangement of FRP. The most common type of FRP retrofit was the full coverage wrapped around
the wall. Antoniades et al. (2003), El-Sokkary and Galal (2013), Ghoborah and Khalil (2004), and
Hwang et al. (2004), among others, wrapped the wall specimens covering the entire face with one or
more FRP layers. Differences appeared in the number of layers, orientation of the layers, and the use
of anchors. Layssi et al. (2012) wrapped wall specimens with one layer of CFRP to cover the plastic
hinge zone to prevent premature lap splice failure. Horizontal strips were placed above the plastic
hinge zone to the top of the wall, to improve the shear strength. Figure 7 (a) shows the retrofit
configuration. The results showed that the addition of the FRP confinement of the lap splice delayed
the premature brittle failure of that region. Comparison of the cumulative energy dissipated of the as-
built wall and the retrofitted walls (Figure 7 (b)) reveals that the FRP confinement effectively
increased the dissipated energy. (a) Illustration of FRP retrofit scheme
(b) Graph of dissipated energy between the
as-built specimen and the retrofitted
specimen
Figure 7: FRP retrofit for lap splice confinement of RC wall (source data from Layssi et al. (2012)) (b) Graph of dissipated energy between the
as-built specimen and the retrofitted
specimen p
Figure 7: FRP retrofit for lap splice confinement of RC wall (source data from Layssi et al. (2012)) FRP retrofit for lap splice confinement of RC wall (source data from Layssi et al. (2012)) Altin et al. (2013) explored the effects of different FRP configuration by varying the arrangement of
discrete FRP strips along the full length of the wall. Figure 8 shows the retrofit configuration of each
of the tested wall specimens. The purpose of the tests was to understand the influence of shear
strengthening for shear deficient wall specimens, under different CFRP configurations. Each retrofit
configuration was applied to both sides of the wall, and all strips were anchored using FRP fan Altin et al. Fully confined (2013) explored the effects of different FRP configuration by varying the arrangement of
discrete FRP strips along the full length of the wall. Figure 8 shows the retrofit configuration of each
of the tested wall specimens. The purpose of the tests was to understand the influence of shear
strengthening for shear deficient wall specimens, under different CFRP configurations. Each retrofit
configuration was applied to both sides of the wall, and all strips were anchored using FRP fan 7 anchors at spacings between 270 and 300 mm. Each specimen was cyclically loaded without axial
load applied until the specimen lost lateral load carrying capacity. The best performing retrofit scheme
was the horizontally placed strips, Specimen 2 in Figure 8 (a) and in the response curve of Figure 9. This specimen reached the highest lateral capacity and the highest lateral drift. The fan anchors also
proved to be essential in preventing debonding of the CFRP strips. The researchers concluded that
shear strengthening of shear deficient walls using CFRP strips was an effective technique and that
FRP configuration is important. . (a) Specimen 2
(b) Specimen 3
(c) Specimen 4
(d) Specimen 5
Figure 8: FRP strengthening congifurations of test wall specimens (adapted from Altin et al. (2013)) (b) Specimen 3 (b) Specimen 3 (b) Specimen 3 (c) Specimen 4 Figure 8: FRP strengthening congifurations of test wall specimens (adapted from Altin et al. (2013)) Figure 9: Backbone response envelopes of all specimens (source data from Altin et al. (2013))
-300
-200
-100
0
100
200
300
-3
-2
-1
0
1
2
3
Shear force (kN)
Top deflection (mm)
Specimen 1
Specimen 2
Specimen 3
Specimen 4
Specimen 5 Figure 9: Backbone response envelopes of all specimens (source data from Altin et al. (2013)) Two-sided retrofit Many of the walls tested were retrofitted on both sides, but without corners confined. Cruz Noguez et
al. (2015) retrofitted RC wall specimens on both sides without wrapping the corners to simulate a
minimally invasive field application where the edges may not be accessible. They used two types of
anchor systems to transfer loads from CFRP to the supporting elements: one system was an off the
shelf steel angle and bolt system, while the other system was an innovative mechanical tube system. The tested wall specimens were designed to modern standards as the purpose of the test was to
understand the performance of the FRP without influence from insufficient shear strength. Both
repaired walls and retrofitted walls were investigated. In comparing the two anchoring system used, it
was determined the tube system performed better than the steel angle system, as the tube system
maintains structural integrity throughout the loading process. However, both systems helped the FRP
retrofit to increase flexural strength of the specimens and regain or increase the stiffness of both
repaired and strengthened walls. This is illustrated in Figure 10, which shows the load-deformation
response envelope curves of Phase 2 (tube anchor) specimens both repaired and strengthened against
the control specimen. 8 Figure 10: Shear force-deflection response envelope curves for repaired and retrofitted walls (source
data from Cruz Noguez et al. (2015)) Figure 10: Shear force-deflection response envelope curves for repaired and retrofitted walls (source
data from Cruz Noguez et al. (2015)) Another method of strengthening explored by researchers includes retrofitting with strips of FRP
instead for full wall coverage. Qazi et al. (2013) investigated the behavior of slender RC walls under-
designed in flexure and subsequently retrofitted with FRP. The arrangement of the CFRP included
vertical strips along the sides and down the center of each face of the wall and intermittent horizontal
strips, as shown in Figure 5 (a). There were FRP fiber anchors embedded in the foundation block to
enable load transfer, and anchors embedded in the wall of some specimens to prevent debonding. The
variables in the strengthening scheme involved the size of the anchor, including anchors in the wall
panel, and the width of the center strip on the wall. The loading protocol for all specimens included
lateral cyclic loading, along with constant axial compression loading. Figure 11 shows the backbone
curves of the tested specimens. Two-sided retrofit When compared to the reference wall (SL4), the retrofitted specimens
displayed improved ultimate load capacity and displacement. SLR3 specimen, which included only
anchors at the foundation, displayed the greatest increase in ultimate displacement, while SLR6,
which included anchor throughout the wall panel, displayed the greatest increase in ultimate capacity. The researchers noted that the CFRP strips method limited crack propagation but not to the detriment
of limiting the ability to dissipate energy effectively. Figure 11: Hysteresis backbone envelope curves for the tested specimens (source data from Qazi et al. (2013)) Figure 11: Hysteresis backbone envelope curves for the tested specimens (source data from Qazi et al. (2013)) One-sided retrofit Of the many wall specimens included in the portion of the database with solid seismically tested FRP
repaired walls, only one study included a wall specimen with a one-sided retrofit. Antoniades et al. (2005) tested five specimens with 2-sided application, and only one specimen with a single sided
application of FRP. An illustration of the one-sided FRP retrofit is shown in Figure 12 (a). This study
researched code-compliant walls tested to failure, repaired conventionally with high strength mortar
and lap welding of fractured reinforcement, then wrapped with FRP jackets. The focus of this study
was to determine the performance of FRP retrofit on code-complaint walls and the use of a novel type
of anchorage for the FRP strips. GFRP was used for the wrapped and one-sided applications, while
CFRP was used on the wall edges to increase flexural strength. For this study, the results from the 9 tests of repaired walls were all similar, as the researchers noted that the single sided retrofitted wall
and the fully wrapped wall seem to have the same response and failure mode due to the walls failing
in flexure rather than shear. They concluded that while shear strength and stiffness could be improved
with an FRP-repaired wall, hysteretic behavior and dissipated energy was significantly lower than the
original specimens, as shown in Figure 12 (b). They also noted anchorage in critical regions such as
the base of the wall is difficult and concluded that the addition of plates or angles can assist in
preventing early peeling off of FRP anchorage. (a) Illustration of FRP
retrofit
(b) Backbone curves
Figure 12: Load-displacement curves for the original wall specimen and repaired and strengthened
with one-sided FRP (adapted from Antoniades et al. (2005)) Figure 12: Load-displacement curves for the original wall specimen and repaired and strengthened
with one-sided FRP (adapted from Antoniades et al. (2005)) CONCLUSIONS This literature review highlights the experimental studies that have been performed on FRP-retrofitted
reinforced concrete shear walls. The research is varied in terms of wall shape, FRP configuration,
FRP material, among other variables. However, there remains many areas of interest that may be
covered in future research studies, that would be beneficial for researchers and practitioners. Below
are observations of research gaps found in studying the database developed on these components, in
no particular order of importance. This literature review highlights the experimental studies that have been performed on FRP-ret
reinforced concrete shear walls. The research is varied in terms of wall shape, FRP configurati 1. The types of wall shapes present in the database are limited to mainly rectangular and barbell
shaped walls. Very few nonrectangular walls (such as L-shaped, C-shaped, and T-shaped
walls) retrofitted with FRP have been structurally tested in the lab. Research on more
nonrectangular walls would be helpful, if current practice in the field suggests FRP is used to
retrofit these types of walls. 2. Very few wall specimens were retrofitted on only one side of the wall, as the majority of
walls were retrofitted on both sides of the wall, either with full sheets or strips. This is a major
research gap as, often in the field, only one side of the wall is accessible. Research on one-
sided wall would greatly increase understanding of the performance of these components. 3. The main material types that were present in the studies are carbon and glass FRP. Very few
alternative material types were investigated. Also, glass FRP was usually in combination with
carbon FRP when used in experiments. It may be of interest to perform experiments on walls
retrofitted with glass only, or with alternative materials to advance the knowledge of
performance of new materials. 4. Most of the walls tested included anchors. However, anchor placement and types of
anchorage is still a topic of research that needs exploration. Many studies used steel angles at
foundations of walls, but there may be a need to investigate more fiber anchors or alternative
anchor types for the base and throughout wall panels. 4. Most of the walls tested included anchors. However, anchor placement and types of
anchorage is still a topic of research that needs exploration. CONFLICT OF INTEREST The authors declare that they have no conflicts of interest associated with the work presented in this
paper. ACKNOWLEDGEMENT ACKNOWLEDGEMENT
The authors thank fellow NIST researcher, Kevin Wong, for assistance with developing a graphic for
this paper. The authors thank fellow NIST researcher, Kevin Wong, for assistance with developing a graphic for
this paper. CONCLUSIONS Many studies used steel angles at
foundations of walls, but there may be a need to investigate more fiber anchors or alternative
anchor types for the base and throughout wall panels. 5. None of the walls in the database included weathering or degraded materials. This is
important to consider the long-term performance of retrofitted components. In some cases,
retrofitted walls are exposed to environmental conditions, so research studying the effects of 10 weathering or degradation on the retrofitted component (as opposed to just the FRP material)
would be useful to understand how these components perform over time. CONFLICT OF INTEREST
The authors declare that they have no conflicts of interest associated with the work presented in this
paper. CONFLICT OF INTEREST
The authors declare that they have no conflicts of interest associated with the work presented in this
paper. DATA AVAILABILITY DATA AVAILABILITY
Data on which this paper is based is available from the authors upon reasonable request. REFERENCES REFERENCES
Altin, S., Anil, O., Kopraman, Y., & Kara, M.E. (2013). “Hysteretic Behavior of RC Shear wall
Strengthened with CFRP strips." Composites: Part B. Vol 44 p 321-329. Antoniades, K., Salonikios, T., & Kappos, A. (2003). "Cyclic Tests on Seismically Damaged
Reinforced Concrete Walls Strengthened Using Fiber-Reinforced Polymer Reinforcement." ACI
Structural Journal, July-August 2003, Title no 100-S54 p 510-523 Antoniades, K., Salonikios, T., & Kappos, A. (2005). "Tests on Seismically Damaged Reinforced
Concrete Walls Repaired and Strengthened Using Fiber-Reinforced Polymers." Journal of
Composites for Construction. May/June 2005, Vol 9, No. 3. Cruz-Noguez, C.A., Lau, D.T., Sherwood, E.G., Hiotakis, S., Lombard, J., Foo, S., & Cheung, M. (2014). "Seismic Behavior of RC Shear Walls Strengthened for In-Plane Bending Using Externally
Bonded FRP Sheets." Journal of Composites for Construction, 19(1). Dhiradhamvit, K., Attard, T.L., and Zhou, H. (2011). “Development of a New Lightweight
‘Rubberized-Carbon’ Composite for Wood Home Protection.” Proceedings of ATINER Construction
Conference, Athens, Greece. June, 2011. Di Luccio, G., Michel, L., Ferrier, E., & Martinelli, E. (2017). "Seismic retrofitting of RC walls
externally strengthened by flax–FRP strips." Composites Part B: Engineering. Vol 127. Dukes, J. & Sattar, S. (2021). “Development of a Database of Experimental Tests on FRP Retrofitted
Reinforced Concrete Shear Walls.” 17th World Conference on Earthquake Engineering, Online,
September, 2021. Dukes, J., Goodwin, D., Sattar, S., & Sung, L. (2022). “Research Needs for Fiber Reinforced (FR)
Composite Retrofit Systems in Buildings and Infrastructure.” ACI Special Publication, 351, 110-128. El-Sokkary, H. & Galal, K.; (2013). “Seismic Behavior of RC Shear Walls Strengthened with Fiber-
Reinforced Polymer.” Journal of Composites for Construction. Ghobarah, A. & Khalil, A.A. (2004). “Seismic Rehabilitation of Reinforced Concrete Walls Using
Fibre Composites.” 13th World Conference on Earthquake Engineering, Vancouver, Canada, August,
2004. Goodwin, D., Sattar, S., Dukes, J., Kim, J.H., Sung, L., & Ferraris, C. (2019). “Research Needs
Concerning the Performance of Fiber Reinforced (FR) Composites Retrofit Systems for Buildings and
Infrastructure.” NIST Special Publication 1244. https://doi.org/10.6028/NIST.SP.1244 11 Hwang, S.-J., Tu, Y.-S., Yeh, Y.-H., & Chiou, T.-C. (2004). “Reinforced Concrete Partition Walls
Retrofitted with Carbon Fiber Reinforced Polymer.” 2004 ANCER Annual Meeting: Networking of
Young Earthquake Engineering Researchers and Professionals, ANCER. Layssi, H., Cook, W.D., & Mitchell, D. (2012). “Seismic Response and CFRP Retrofit of Poorly
Detailed Shear Walls.” Journal of Composites for Construction, Vol. 16, No. 3, June 1, 2012. Li, B., & Lim, C. L. (2010). Zhou, H., Attard, T.L., Zhao, B., Yu, J., Lu, W., & Tong, L. (2013). “Experimental study of retrofitted
reinforced concrete shear wall and concrete-encased steel girders using a new CarbonFlex composite
for damage stabilization.” Engineering Failure Analysis 35 (2013) 219-233. REFERENCES “Tests on Seismically Damaged Reinforced Concrete Structural Walls
Repaired Using Fiber-Reinforced Polymers.” Journal of Composites for Construction, 14(5), 597–
608. Sonobe, Y., Matsuzaki, Y., Nakamura, H., Iso, M., & Watanabe, M. (1999). "Experimental Study on
Reinforced Concrete Columns Having Wing Walls Retrofitted with Continuous Fiber Sheets"
American Concrete Institute Special Publication 188. Qazi, S., Michel, L., & Ferrier, E. (2013). "Mechanical behaviour of slender RC walls under seismic
loading strengthened with externally bonded CFRP." European Journal of Environmental and Civil
Engineering, 2013, Vol. 17, No. 6, 496–506. Zhang, Z., Li, B., & Qian, K. (2015). “Experimental Investigations on Seismically Damaged
Nonrectangular Reinforced-Concrete Structural Walls Repaired by FRPs.” Journal for Composites for
Construction 20(1). Zaman, A., Gutub, S., & Wafa, M. (2013). “A review on FRP composites applications and durability
concerns in the construction sector.” Journal of Reinforced Plastics and Composites, 32(23) 1966-
1988. Zhou, H., Attard, T.L., Zhao, B., Yu, J., Lu, W., & Tong, L. (2013). “Experimental study of retrofitted
reinforced concrete shear wall and concrete-encased steel girders using a new CarbonFlex composite
for damage stabilization.” Engineering Failure Analysis 35 (2013) 219-233. Zhou, H., Attard, T.L., Zhao, B., Yu, J., Lu, W., & Tong, L. (2013). “Experimental study of retrofitted
reinforced concrete shear wall and concrete-encased steel girders using a new CarbonFlex composite
for damage stabilization.” Engineering Failure Analysis 35 (2013) 219-233. 12
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Reporter PET Images Bortezomib Treatment-Mediated Suppression of Cancer Cell Proteasome Activity
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Scientific reports
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Reporter PET Images Bortezomib
Treatment-Mediated Suppression
of Cancer Cell Proteasome Activity Received: 30 January 2018
Accepted: 16 July 2018
Published: xx xx xxxx Jin Hee Lee1,2, Kyung-Ho Jung1,2, Cung Hoa Thien Quach1, Jin Won Park1,2,
Seung Hwan Moon1, Young Seok Cho1 & Kyung-Han Lee1,2 Proteasomal protein degradation is a promising target for cancer therapy. Here, we developed a
positron emission tomography (PET) technique based on the sodium-iodide symporter (NIS) gene
fused with the carboxyl-terminal of ornithine decarboxylase (cODC) that noninvasively images cancer
cells with inhibited proteasome activity. A retroviral vector was constructed in which the murine cODC
degron was fused to the human NIS gene (NIS-cODC). Transiently transduced CT26 and HT29 colon
cancer cells and stably expressing CT26/NIS-cODC cells were prepared. In cancer cells transiently
transduced with NIS-cODC, NIS expression and transport activity was low at baseline, but NIS protein
and 125I uptake was significantly increased by inhibition of proteasome activity with bortezomib. Stable CT26/NIS-cODC cells also showed increased cytosolic and membrane NIS by bortezomib, and
four different stable clones displayed bortezomib dose-dependent stimulation of 125I and 99mTc-04
−
uptake. Importantly, bortezomib dose-dependently suppressed survival of CT26/NIS-cODC clones
in a manner that closely correlated to the magnitudes of 125I and 99mTc-04
− uptake. CT26/NIS-cODC
tumors of bortezomib-treated mice demonstrated greater 124I uptake on PET images and increased NIS
expression on tissue staining compared to vehicle-injected animals. NIS-cODC PET imaging may allow
noninvasive quantitative monitoring of proteasome activity in cancer cells treated with bortezomib. Essential tumor-supporting machineries are an attractive target for cancer therapy1, and a key example is regu-
lated protein degradation that occurs predominantly via the 26S proteasome complex2,3. Cancer cells character-
istically have elevated proteasome activity4 because it offers a survival advantage by eliminating oncoproteins5. Indeed, treatment with proteasome inhibitors can induce cell cycle arrest and apoptotic death of cancer cells6,7. Therefore, the proteasome system is a promising target for cancer therapy and the ability to image its activity in
living bodies could contribute to the development of new anticancer drugs.i g
p
g
An opportunity to identify cells with reduced proteasome activity is provided by specific protein sequences
that are promptly recognized and eliminated through the proteasome system8. The C-terminal degron of mouse
ornithine decarboxylase (cODC) is promptly recognized by 26S proteasomes for rapid ubiquitin-independent
degradation9. Hence, in cancer cells, cODC-fused proteins undergo prompt degradation at baseline but accu-
mulate when proteasome activity is suppressed by treatment with proteasome inhibitors. Vlashi et al. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports 1Department of Nuclear Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine,
Seoul, Korea. 2Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.
Correspondence and requests for materials should be addressed to K.-H.L. (email: khnm.lee@samsung.com) Results
Proteasome inhibition of transduced cells increases NIS accumulation and substrate transp Proteasome inhibition of transduced cells increases NIS accumulation and substrate transport. Figure 1 illustrates our pQCXIN retroviral expression vector in which the carboxyl terminus 37 amino acids
of the murine cODC degron was fused to the NIS gene (NIS-cODC). The vector was first tested by transient
transfection in CT26 and HT29 colon cancer cells. Proteasome activity of these cells was completely abrogated
by treatment with bortezomib (Fig. 2A). Transfected CT26 cells showed very low NIS expression at baseline,
supporting the rapid degradation of NIS-cODC. However, 16 h inhibition of proteasome activity with 4 μM borte-
zomib induced a marked increase of NIS accumulation that was 17.5 ± 1.1 fold higher than non-transfected cells
(Fig. 2A). Furthermore, whereas NIS-cODC transfected cells displayed no increase or only mild increases in
radioiodine uptake at baseline, bortezomib stimulated 125I uptake to 594.8 ± 73.5% of control level for HT29 cells,
and 125I and 124I uptake to 272.4 ± 29.4% and 236.3 ± 22.8% for CT26 cells (Fig. 2B). Lower baseline uptake level
for HT29 compared to CT26 cells suggesting lower leakiness of expression might be explained by the 66.5 ± 1.4%
greater proteasome activity for HT29 compared to CT26 cells (Fig. 2A). NIS function in stably expressing CT26/NIS-cODC cells treated by bortezomib. We next pre-
pared CT26 cells stably expressing NIS-cODC (CT26/NIS-cODC cells) through clonal selection. Exposure of
four different CT26/NIS-cODC clones for 48 h with bortezomib caused dose-dependent increases of 99mTc-O4
−
and 125I uptake in a highly similar pattern (Fig. 3A). 99mTc-O4
− and 125I uptake reached 481.3 ± 57.0% and
478.8 ± 64.9% of untreated controls, respectively, by 25 nM bortezomib. Furthermore, 36 h treatment of CT26/
NIS-cODC cells (clone #9) induced a 76.3 ± 5.5-fold increase of total NIS protein by 200 nM bortezomib, and 10-
and 47-fold increases of membrane-localized NIS protein by 100 and 200 nM bortezomib, respectively (Fig. 3B). Using CT26/NIS-cODC cells (clone #9), we compared the in-vitro activity of the PET reporter system to pro-
teasome activity during treatment with graded doses of PS341. The results showed that proteasome activity was
substantially reduced to 24.8% of untreated level by 16 h treatment with 12.5 nM of PS341, and almost completely
inhibited by 25 nM or 50 nM (3.1% and 1.2% of untreated level, respectively). Reporter PET Images Bortezomib
Treatment-Mediated Suppression
of Cancer Cell Proteasome Activity We further investigated the capacity of the
NIS-cODC reporter to image tumors in mice treated with bortezomib with radioiodine PET. Reporter PET Images Bortezomib
Treatment-Mediated Suppression
of Cancer Cell Proteasome Activity previously
engineered cancer cells to stably express cODC-fused ZsGreen10, and cancer cells expressing this reporter were
tractable in mice treated with proteasome inhibitors11. However, this technique has limited usefulness for quanti-
tative monitoring of cancer cells in living bodies due to poor depth penetration of fluorescent signals.hf g
gl
g
The sodium iodide symporter (NIS) reporter can overcome this limitation and offers many additional advan-
tages for in vivo imaging12–14. In human tissues, Expression of this selective iodide carrier is limited to the thyroid,
salivary gland, gastric mucosa, and lactating mammary gland15. It does not influence underlying cell biochem-
istry, and by using species-specific sequences, it can avoid immune responses that are problematic with foreign
reporter proteins. Furthermore, NIS imaging tracers do not require radiochemical synthesis, and multiple types
of radioisotopes with a wide range of half-lives can be selected for positron emission tomography (PET) or
γ-camera imaging. Indeed, our group has previously shown NIS gene imaging useful for tracking various types
of cells in living bodies13,14,16. 1Department of Nuclear Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine,
Seoul, Korea. 2Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea. Correspondence and requests for materials should be addressed to K.-H.L. (email: khnm.lee@samsung.com) SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 1 www.nature.com/scientificreports/ Figure 1. NIS-cODC construct. Illustration of pQCXIN retroviral expression vector containing the carboxyl
terminal 37 amino acid sequence of the murine ornithine decarboxylase (cODC) degron fused to the human
sodium iodide symporter (NIS) gene. Figure 1. NIS-cODC construct. Illustration of pQCXIN retroviral expression vector containing the carboxyl
terminal 37 amino acid sequence of the murine ornithine decarboxylase (cODC) degron fused to the human
sodium iodide symporter (NIS) gene. In this study, we constructed a novel reporter system consisting of the human NIS gene fused to the cODC
degron. Cancer cells transiently or stably transfected with the construct were assessed for NIS expression and
substrate transport activity in response to proteasome inhibition. We further investigated the capacity of the
NIS-cODC reporter to image tumors in mice treated with bortezomib with radioiodine PET. In this study, we constructed a novel reporter system consisting of the human NIS gene fused to the cODC
degron. Cancer cells transiently or stably transfected with the construct were assessed for NIS expression and
substrate transport activity in response to proteasome inhibition. Results
Proteasome inhibition of transduced cells increases NIS accumulation and substrate transp Data are
mean ± standard deviation (SD) of fluorescent intensity of quadruplicate samples. Western blots for NIS and
β-actin (loading control) in CT26 cells at day 3 of NIS-cODC transfection (right). Blots were cropped with
single blot parts separated by space. For full length blot pictures, see Supplement Fig. 1. Bars are mean ± SD
of duplicate band intensities normalized to β-actin bands expressed as fold of controls. (B) HT29 cell uptake
of 125I (left) and CT26 cell uptake of 125I (middle) and 124I (right) at day 3 of NIS-cODC transfection after 16 h
treatment with bortezomib or vehicle. Bars are mean ± SD of % uptake of triplicate samples obtained from a
single experiment representative of 2 separate experiments. Figure 2. Cancer cells transiently expressing NIS-cODC. (A) Bortezomib (PS341) at 50 nM abrogated
proteasome activity in CT26 and HT29 colon cancer cells transiently expressing NIS-cODC (left). Data are
mean ± standard deviation (SD) of fluorescent intensity of quadruplicate samples. Western blots for NIS and
β-actin (loading control) in CT26 cells at day 3 of NIS-cODC transfection (right). Blots were cropped with
single blot parts separated by space. For full length blot pictures, see Supplement Fig. 1. Bars are mean ± SD
of duplicate band intensities normalized to β-actin bands expressed as fold of controls. (B) HT29 cell uptake
of 125I (left) and CT26 cell uptake of 125I (middle) and 124I (right) at day 3 of NIS-cODC transfection after 16 h
treatment with bortezomib or vehicle. Bars are mean ± SD of % uptake of triplicate samples obtained from a
single experiment representative of 2 separate experiments. to 25 nM bortezomib for 48 h and the magnitude of cell loss by treatment with 25 nM (r = 0.958, P < 0.05) or
50 nM bortezomib (r = 0.957, P < 0.05; Fig. 5B). 99mTc-O4
− uptake in cells exposed to 25 nM bortezomib for 48 h
faithfully recapitulated this close correlation with cell loss by treatment with 25 nM (r = 0.959, P < 0.05) or 50 nM
bortezomib (r = 0.980, P < 0.05; Fig. 5B). 124I PET imaging quantitatively monitors tumor response to bortezomib treatment. To inves-
tigate the usefulness of NIS-cODC reporter imaging for monitoring proteasome inhibitor response in vivo,
we prepared mice harboring subcutaneous CT26 or CT26/NIS-cODC tumors. PET/CT imaging showed that,
without bortezomib treatment, neither type of tumors took up significant amounts of 124I (Fig. Results
Proteasome inhibition of transduced cells increases NIS accumulation and substrate transp Under these conditions, NIS protein
level gradually increased to 303.4 ± 68.4%, 398.9 ± 42.4%, and 951.7 ± 36.4% of untreated control level. Similarly,
125I uptake level gradually increased to 124.1 ± 2.4%, 150.6 ± 13.2%, and 357.9 ± 14.1% of untreated control level
(Fig. 4A). Correlation analysis showed that NIS expression and 125I uptake increased exponentially as log pro-
teasome activity decreased. Furthermore, 125I uptake level showed a close linear relation to NIS expression level
(r = 0.98; P < 0.0001; Fig. 4B). Effects of bortezomib on NIS substrate uptake and survival of CT26/NIS-cODC cells. We next
tested the dose-dependent effects of bortezomib on the survival CT26/NIS-cODC and CT26 cells. After 72 h
treatment with 50 nM bortezomib, two CT26/NIS-cODC clones appeared to survive slightly better (52.7 ± 2.0
and 51.7 ± 2.0%) than CT26 cells (44.2 ± 2.8%; both P < 0.01), but two other clones showed no difference
(45.5 ± 1.5% and 48.1 ± 2.0%; Fig. 5A).ff g
Importantly, we compared bortezomib’s effect on NIS substrate transport and its effect on cell survival. In
four different stable CT26/NIS-cODC clones, there was a close correlation between 125I uptake in cells exposed SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 2 www.nature.com/scientificreports/ Figure 2. Cancer cells transiently expressing NIS-cODC. (A) Bortezomib (PS341) at 50 nM abrogated
proteasome activity in CT26 and HT29 colon cancer cells transiently expressing NIS-cODC (left). Data are
mean ± standard deviation (SD) of fluorescent intensity of quadruplicate samples. Western blots for NIS and
β-actin (loading control) in CT26 cells at day 3 of NIS-cODC transfection (right). Blots were cropped with
single blot parts separated by space. For full length blot pictures, see Supplement Fig. 1. Bars are mean ± SD
of duplicate band intensities normalized to β-actin bands expressed as fold of controls. (B) HT29 cell uptake
of 125I (left) and CT26 cell uptake of 125I (middle) and 124I (right) at day 3 of NIS-cODC transfection after 16 h
treatment with bortezomib or vehicle. Bars are mean ± SD of % uptake of triplicate samples obtained from a
single experiment representative of 2 separate experiments. Figure 2. Cancer cells transiently expressing NIS-cODC. (A) Bortezomib (PS341) at 50 nM abrogated t Figure 2. Cancer cells transiently expressing NIS-cODC. (A) Bortezomib (PS341) at 50 nM abrogated
proteasome activity in CT26 and HT29 colon cancer cells transiently expressing NIS-cODC (left). Results
Proteasome inhibition of transduced cells increases NIS accumulation and substrate transp Cropped blot parts
are separated by space. For full length blot pictures, see Supplement Fig. 2. NIS in CT26/NIS-cODC cells using
membrane protein (right). Blots were cropped to show representative blots. For full length blot pictures, see
Supplement Fig. 3. Bortezomib treatment was for 36 h. Bars on the left side are mean ± SD of duplicate band
intensities normalized to β-actin bands expressed as fold of controls. Figure 3. CT26 cells stably expressing NIS-cODC. (A) Effects of 48 h exposure to 12.5 or 25 nM bortezomib Figure 3. CT26 cells stably expressing NIS-cODC. (A) Effects of 48 h exposure to 12.5 or 25 nM bortezomib
on uptake of 99mTc-04
− (left) and 125I (right) on four different stable expressing CT26/NIS-cODC clones. Bars
are mean ± SD of % uptake of quadruplicate samples. ‡P < 0.001, †P < 0.005, compared to controls. (B) Western
blots for NIS and β-actin in CT26 and CT26/NIS-cODC cells using whole cell lysates (left). Cropped blot parts
are separated by space. For full length blot pictures, see Supplement Fig. 2. NIS in CT26/NIS-cODC cells using
membrane protein (right). Blots were cropped to show representative blots. For full length blot pictures, see
Supplement Fig. 3. Bortezomib treatment was for 36 h. Bars on the left side are mean ± SD of duplicate band
intensities normalized to β-actin bands expressed as fold of controls. Figure 3. CT26 cells stably expressing NIS-cODC. (A) Effects of 48 h exposure to 12.5 or 25 nM bortezomib
on uptake of 99mTc-04
− (left) and 125I (right) on four different stable expressing CT26/NIS-cODC clones. Bars
are mean ± SD of % uptake of quadruplicate samples. ‡P < 0.001, †P < 0.005, compared to controls. (B) Western
blots for NIS and β-actin in CT26 and CT26/NIS-cODC cells using whole cell lysates (left). Cropped blot parts
are separated by space. For full length blot pictures, see Supplement Fig. 2. NIS in CT26/NIS-cODC cells using
membrane protein (right). Blots were cropped to show representative blots. For full length blot pictures, see
Supplement Fig. 3. Bortezomib treatment was for 36 h. Bars on the left side are mean ± SD of duplicate band
intensities normalized to β-actin bands expressed as fold of controls. Results
Proteasome inhibition of transduced cells increases NIS accumulation and substrate transp 6A,B). However,
after treatment with just 2 doses of bortezomib, CT26/NIS-cODC tumors displayed significantly increased 124I
uptake (Fig. 6A,B). Immunohistochemistry confirmed high levels of NIS protein in tumors of this group, but very
small amounts of NIS in tumors of the other two groups (Fig. 7A). Quantitative PET analysis confirmed greater
tumor-to-background SUVmax ratios for bortezomib-treated CT26/NIS-cODC tumors (1.66 ± 0.33) compared
to CT26 tumors (1.16 ± 0.07, P = 0.008) or CT26/NIS-cODC tumors without treatment (1.20 ± 0.13, P = 0.008;
Fig. 7B). SUVmean ratios of uptake were also significantly greater for bortezomib-treated CT26/NIS-cODC tum-
ors (2.02 ± 0.53) compared to CT26 tumors (1.32 ± 0.14, P = 0.009) or CT26/NIS-cODC tumors without treat-
ment (1.32 ± 0.11, P = 0.012). Ex vivo measured tumor-to-muscle count ratios of extracted tissue reiterated these
results (2.99 ± 0.49 vs. 1.73 ± 0.22 and 2.17 ± 0.19, respectively; Fig. 7B). Correlation analysis verified a high
correlation between PET image-based SUVmax ratios and ex vivo measured tissue count ratios (rho = 0.864,
P < 0.0001; Fig. 7B). SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 3 www.nature.com/scientificreports/ Figure 3. CT26 cells stably expressing NIS-cODC. (A) Effects of 48 h exposure to 12.5 or 25 nM bortezomib
on uptake of 99mTc-04
− (left) and 125I (right) on four different stable expressing CT26/NIS-cODC clones. Bars
are mean ± SD of % uptake of quadruplicate samples. ‡P < 0.001, †P < 0.005, compared to controls. (B) Western
blots for NIS and β-actin in CT26 and CT26/NIS-cODC cells using whole cell lysates (left). Cropped blot parts
are separated by space. For full length blot pictures, see Supplement Fig. 2. NIS in CT26/NIS-cODC cells using
membrane protein (right). Blots were cropped to show representative blots. For full length blot pictures, see
Supplement Fig. 3. Bortezomib treatment was for 36 h. Bars on the left side are mean ± SD of duplicate band
intensities normalized to β-actin bands expressed as fold of controls. Figure 3. CT26 cells stably expressing NIS-cODC. (A) Effects of 48 h exposure to 12.5 or 25 nM bortezomib
on uptake of 99mTc-04
− (left) and 125I (right) on four different stable expressing CT26/NIS-cODC clones. Bars
are mean ± SD of % uptake of quadruplicate samples. ‡P < 0.001, †P < 0.005, compared to controls. (B) Western
blots for NIS and β-actin in CT26 and CT26/NIS-cODC cells using whole cell lysates (left). Discussion Our
results showed that graded concentrations of bortezomib resulted in substantial and dose-dependent reduc-
tions of cell number by bortezomib for both CT26 and CT26/NIS-cODC cells. In contrast to a previous study
where stable ZsGreen-cODC expression was found to be stressful for cancer cells11, we found that NIS-cODC
expression by itself did not exert cellular stress. Importantly, the amount of increase of NIS substrate transport
in bortezomib-treated CT26/NIS-cODC cells closely correlated to the magnitude of suppression in cell survival. This finding supports the possibility that the level of stimulated radioiodine uptake might help monitor cancer cell
response to proteasome inhibitor treatment. p
p
Finally, we investigated the ability of our reporter system to image inhibited proteasome activity in tumors of
living mice. For this purpose, CT26 cells conveniently produced a syngeneic tumor model in wild type BALB/c mice. PET/CT imaging of CT26/NIS-cODC tumors revealed significantly increased radioiodine uptake after only 2 doses
of bortezomib. This drug is considered a potent and specific proteasome inhibitor compared to the less specific and
weaker predecessors, making it suitable for in vivo application21. Bortezomib is the first-in-class therapeutic protea-
some inhibitor approved for human use, and several clinical studies have established its efficacy in multiple types of
refractory cancers22. In our experiments, CT26/NIS-cODC tumors of bortezomib-treated animals displayed clearly
increased radioiodine uptake on PET and showed strong NIS expression on tissue staining, which demonstrates the
capacity of our reporter to noninvasively image tumor response to proteasome inhibition. p
y
p
y
g
p
p
In clinical trials, bortezomib is administered at doses of up to 2 mg/m2 for a cumulative dose of 40 mg/
m2 23. Assuming a body-mass index of 25 kg/m2, these doses would amount to approximately 0.08 and 1.6 mg/
kg, respectively. Extrapolation of human doses to mice cannot be done based on body weight alone, because
species-dependent biochemical and functional systems alter pharmacokinetics. Small animals require larger drug
dose compared with humans on a weight basis, and for mice, a multiplication correction factor of 12.3 is recom-
mended24. In our case, this yields a single dose of approximately 1 mg/kg, which is the dose that we used. In a
previous study, Momose et al. imaged mice harboring HEK293 tumors that stably expressed ZsGreen-cODC after
injecting a single dose of bortezomib12. In their study, tumor fluorescence was greatest with 4 mg/kg bortezomib
and weak with 1 mg/kg. Discussion Construction of reporters that contain the cODC sequence provides a unique opportunity to monitor proteasome
activity. Although cODC-fused fluorescent reporters are useful for identifying cancer cells with poor proteasome
activity in vitro, poor signal penetrance limits their value for imaging living bodies. Here, we introduce a non-
invasive PET reporter system based on cODC-fused NIS that allows quantitative imaging of cancer cells with
suppressed proteasome activity in vivo.h The cODC consists of a 37-residue terminal-sequence that is recognized and rapidly degraded by the 26S pro-
teasome. Because this occurs in a ubiquitin-independent manner, no posttranslational modifications are required
for substrate preparation. Hence, cODC-tagged constructs readily act as substrates to probe proteasome-mediated
degradation in vitro as well as in vivo. This degradation tag functions autonomously and can be appended to other
proteins for proteasome targeting9. The cODC sequence is highly conserved, and tagging with the murine cODC
leads to efficient degradation of proteins from various species by mammalian proteasomes17.i fi
g
p
p
y
p
Although CT26 and HT29 cells are derived from colon tumors, they do not show significant endogenous NIS
expression13,18,19. In our study, we transduced cells with a retroviral vector driven by the CMV promoter, which results
in constitutive expression cODC-NIS, uninfluenced by the environment. In our study, CT26 and HT29 cells showed
complete abrogation of proteasome activity in response to bortezomib treatment. In accordance with the rapid deg-
radation of cODC-fused proteins under steady-state conditions, cells transiently transduced with NIS-cODC showed
very low NIS expression at baseline. However, the cells displayed a substantial increase of NIS protein when proteasome
activity was inhibited by bortezomib. The minimal amount of NIS-cODC protein at baseline allowed reporting of low
proteasome activity with increases of NIS-mediated uptake of radioiodine and radio-technetium substrates. p
y
p
Treatment of stably transfected CT26/NIS-cODC clones to bortezomib caused dose-dependent increases of
99mTc-O4
− and 125I uptakes. In clones 1 and 20, 125I uptake was higher by treatment with 25 nM of PS341 compared
to 12.5 nM, but 99mTc-O4
− uptake was not. Although the cause for this finding is not clear, it is noteworthy that
these 2 clones had apparently lower NIScODC transfection efficiency compared to clones 9 and 8. 99mTc-O4
− has
been reported to rapidly efflux out of cancer cells transfected with the NIS gene20. It might therefore be possible SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 4 www.nature.com/scientificreports/ Figure 4. Discussion Relation of NIS expression and radioiodine uptake to proteasome activity. (A) Proteasome activity
(left), NIS expression (middle) and 125I uptake (right) in CT26/NIS-cODC cells exposed for 16 h to graded
doses of bortezomib. Blots are cropped for representative blots and quantified as mean ± SD in fold of controls
of duplicate band intensities normalized to β-actin bands. For full length blot pictures, see Supplement Fig. 4. Bars on the right are mean ± SD of % uptake of triplicate samples. ‡P < 0.001, **P < 0.01, **P < 0.05, compared
to controls. (B) Correlations between NIS expression (left) or 125I uptake (middle) and log proteasome activity,
and between NIS expression and 125I uptake (right). Proteasome activity is measured as rate of increase in
fluorescent intensity (arbitrary units). Correlation coefficients (r) and P values are from regression analysis. Figure 4. Relation of NIS expression and radioiodine uptake to proteasome activity. (A) Proteasome activity Figure 4. Relation of NIS expression and radioiodine uptake to proteasome activity. (A) Proteasome activity
(left), NIS expression (middle) and 125I uptake (right) in CT26/NIS-cODC cells exposed for 16 h to graded
doses of bortezomib. Blots are cropped for representative blots and quantified as mean ± SD in fold of controls
of duplicate band intensities normalized to β-actin bands. For full length blot pictures, see Supplement Fig. 4. Bars on the right are mean ± SD of % uptake of triplicate samples. ‡P < 0.001, **P < 0.01, **P < 0.05, compared
to controls. (B) Correlations between NIS expression (left) or 125I uptake (middle) and log proteasome activity,
and between NIS expression and 125I uptake (right). Proteasome activity is measured as rate of increase in
fluorescent intensity (arbitrary units). Correlation coefficients (r) and P values are from regression analysis. that 99mTc-O4
− efflux in these cells is more rapid than that of radioiodine, causing less apparent differences in
99mTc-O4
− accumulation according to NIS expression in cancer cells with low transfection efficiency.h fi
The crucial role proteasomes play in degrading regulatory proteins that suppress cancer cell proliferation has
led to clinical trials of proteasome inhibitors for cancer treatment. The ability to monitor proteasome activity of
tumors in vivo can contribute to the development of new drugs that are more effective and apply to a broader
range of malignancies2,6,7. We investigated this issue in CT26 cells engineered to stably express NIS-cODC. Discussion Therefore, it is likely that higher doses of bortezomib would have resulted in higher levels
of tumor radioiodine uptake. SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 5 www.nature.com/scientificreports/ Figure 5. Treatment response of CT26/NIS-cODC clones and relation to NIS transport. (A) Surviving fraction
of clone #1 and #9 (left) or clone #8 and #20 (right) in comparison to CT26 cells after 72 h treatment with
graded doses of bortezomib. Bars are mean ± SD of % survival of quadruplicate samples. (B) Linear correlation
between 125I (left) or 99mTc-04
− uptake (right) at 48 h of exposure to 25 nM bortezomib and cytotoxic effects of
72 h treatment with 25 nM (top) or 50 nM bortezomib (bottom) in four different stable CT26/NIS-cODC clones. Bars are mean ± SD of % uptake of quadruplicate samples. Correlation coefficients (r) and P values are from
linear regression analysis of quadruplicate samples for each stable clone. Figure 5. Treatment response of CT26/NIS-cODC clones and relation to NIS transport. (A) Surviving fraction
of clone #1 and #9 (left) or clone #8 and #20 (right) in comparison to CT26 cells after 72 h treatment with
graded doses of bortezomib. Bars are mean ± SD of % survival of quadruplicate samples. (B) Linear correlation
between 125I (left) or 99mTc-04
− uptake (right) at 48 h of exposure to 25 nM bortezomib and cytotoxic effects of
72 h treatment with 25 nM (top) or 50 nM bortezomib (bottom) in four different stable CT26/NIS-cODC clones. Bars are mean ± SD of % uptake of quadruplicate samples. Correlation coefficients (r) and P values are from
linear regression analysis of quadruplicate samples for each stable clone. In our study, radioiodine uptake assessed in vivo by PET was highly accurate in comparison to uptake con-
firmed from extracted tissues. Whereas optical imaging of fluorescent signals is limited by depth of light pen-
etration and scatter, gamma rays generated from positron annihilation have high tissue penetrance. Hence, In our study, radioiodine uptake assessed in vivo by PET was highly accurate in comparison to uptake con-
firmed from extracted tissues. Whereas optical imaging of fluorescent signals is limited by depth of light pen-
etration and scatter, gamma rays generated from positron annihilation have high tissue penetrance. Hence, SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 6 www.nature.com/scientificreports/ Figure 6. PET/CT imaging of tumor response to Bortezomib treatment. Discussion (a,b) In vivo maximum intensity
projection (MIP) views (A), and coronal (B, top) and transaxial (b, bottom) tomographs of 124I PET/CT images
of mice harboring CT26 (left, arrow) or CT26/NIS-cODC tumors (arrows, middle and right). Animals with
CT26/NIS-cODC tumors were injected with 1 mg/kg bortezomib (PS341; right) or vehicle (DMSO; middle)
at 24 h and 12 h prior to PET imaging. Boxes in MIP views show ROIs placed on tumor and contralateral
background regions. Figure 6. PET/CT imaging of tumor response to Bortezomib treatment. (a,b) In vivo maximum intensity
projection (MIP) views (A), and coronal (B, top) and transaxial (b, bottom) tomographs of 124I PET/CT images
of mice harboring CT26 (left, arrow) or CT26/NIS-cODC tumors (arrows, middle and right). Animals with
CT26/NIS-cODC tumors were injected with 1 mg/kg bortezomib (PS341; right) or vehicle (DMSO; middle)
at 24 h and 12 h prior to PET imaging. Boxes in MIP views show ROIs placed on tumor and contralateral
background regions. these issues are not limiting for PET-based reporter imaging25. Therefore, our NIS reporter PET system may
provide highly accurate quantitative measurements and is expected to work just as well for deep seated orthotopic
tumor models as in subcutaneous tumor models. Together, our results demonstrate the potential usefulness of
NIS-cODC reporter PET for noninvasive monitoring of tumor response to proteasome inhibitors. p
g
p
p
A limitation of this study is that we did not compare radioiodine uptake level stimulated by bortezomib to
actual antitumor effects. Although this experiment was beyond the scope of the present study, which was to inves-
tigate the capacity of our reporter PET system to image proteasome inhibition, the issue deserves exploration in
future studies. In conclusion, we have developed a novel reporter PET technology based on the NIS gene fused with the
cODC degron, which allows robust monitoring of suppressed cancer cell proteasome activity in response to treat-
ment. Accumulation of NIS-cODC protein by low proteasome activity led to increased tumor radioiodine uptake
that was noninvasively imaged by PET in a quantitative manner. This technique may therefore be useful for non-
invasive monitoring of tumor response to proteasome inhibitors, which could facilitate new drug development. SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 7 www.nature.com/scientificreports/ Figure 7. Tumor NIS staining and radioiodine uptake level. (A) Immunohistochemistry for NIS expression
in tumor tissues extracted after imaging. Discussion (B) In vivo tumor-to-background SUVmax ratios obtained from PET
(left), and ex vivo tumor-to-muscle (tm/muscle) count ratios (middle). Bars are mean ± SD of values obtained
from mice with CT26 tumors (n = 5) and mice with CT26/NIS-cODC tumors treated with vehicle (n = 6)
or bortezomib (n = 8). Correlation between in vivo and ex vivo measured uptake indices with Spearman’s
correlation coefficient (rho; right). Figure 7. Tumor NIS staining and radioiodine uptake level. (A) Immunohistochemistry for NIS expression
in tumor tissues extracted after imaging. (B) In vivo tumor-to-background SUVmax ratios obtained from PET
(left), and ex vivo tumor-to-muscle (tm/muscle) count ratios (middle). Bars are mean ± SD of values obtained
from mice with CT26 tumors (n = 5) and mice with CT26/NIS-cODC tumors treated with vehicle (n = 6)
or bortezomib (n = 8). Correlation between in vivo and ex vivo measured uptake indices with Spearman’s
correlation coefficient (rho; right). Figure 7. Tumor NIS staining and radioiodine uptake level. (A) Immunohistochemistry for NIS expression
in tumor tissues extracted after imaging. (B) In vivo tumor-to-background SUVmax ratios obtained from PET
(left), and ex vivo tumor-to-muscle (tm/muscle) count ratios (middle). Bars are mean ± SD of values obtained
from mice with CT26 tumors (n = 5) and mice with CT26/NIS-cODC tumors treated with vehicle (n = 6)
or bortezomib (n = 8). Correlation between in vivo and ex vivo measured uptake indices with Spearman’s
correlation coefficient (rho; right). Materials and Methods
i
f h Construction of the NIS-cODC expression cassette and retroviral vector. The cODC sequence
directs the recognition site of the proteasome. A retroviral expression vector containing the cODC degron fused
to the ZsGreen gene (pQCXIN-ZsGreen-cODC) was a kind gift from Dr. Frank Pajonk (David Geffen School of
Medicine at University of California, LA). We removed the ZsGreen gene sequence from this vector by digestion
with Bam HI and Eco RI restriction enzymes (Takara, CA). The human NIS gene sequence cut out with identical
restriction enzymes was then cloned into the vector to produce pQCXIN-NIS-cODC, which expresses the NIS-
cODC fusion protein. The wild type human NIS that we used efficiently transports radioiodine in various in vitro
and in vivo systems13,14,16. This gene sequence is comprised of 2490 nucleotides that encode a protein of 643 amino
acids as previously described26. pQCXIN-NIS-cODC was transfected into PT67 packaging cells (Clontech, CA)
in high-glucose DMEM media (Lonza, Basel, Switzerland) to produce retroviral vectors. Cell culture and transient transfection. CT26 mouse colon cancer cells and HT29 human colon can-
cer cells from the American Type Culture Collection were maintained in RPMI (Lonza) supplemented with
10% fetal bovine serum (Serana, Germany) and 1% penicillin/streptomycin (Gibco Laboratories, Gaithersburg,
MD) at 37 °C and 5% CO2 in a humidified atmosphere. Cells were sub-cultured twice a week. To prepare tran-
sient transfectants, 5 × 104 cells were seeded into 24-well plates and transduced with pQCXIN-NIS-cODC or
empty pQCXIN plasmids (control) by adding 2 μg DNA per well mixed with 2 μl lipofectamine LTX (Invitrogen,
Carlsbad, CA) in opti-MEM (Gibco). Proteasome inhibition was performed by adding bortezomib (PS341;
Calbiochem, MA) to the culture media. Stably expressing cell lines. Stably-expressing CT26 cells were prepared because, unlike HT29 tumors
that require immune-deficient mice, CT26 tumors are conveniently generated in wild-type mice. CT26 cells were
infected with retroviral particles and selected 72 h later under 200 μg/ml geneticin (Gibco). Single-cell clones
expressing NIS-cODC (CT26/NIS-ODC cells) or ZsGreen-cODC (CT26/ZsGreen-cODC cells) were isolated
by plating dilute suspensions, and surviving clones were picked up, amplified in media containing geneticin, and
stored in liquid nitrogen. Immunoblotting for NIS proteins. Cells were lysed with cold protein extraction solution (PRO-PREP;
Intron, Korea) containing a protease inhibitor cocktail (Sigma Aldrich, St. Louis, MO). Membrane protein
was also prepared to assess membrane localized NIS. Materials and Methods
i
f h Proteasome activity was measured as rate
increase of fluorescent signals from Suc-LLVY-AMC degradation. Sulforhodamine B (SRB) survival assay. Surviving cell content was measured by SRB assays. Briefly,
cells seeded overnight on a 96-well plate were treated for the indicated durations of time, and cell monolayers
were fixed with 10% (wt/vol) trichloroacetic acid at 4 °C. After cells were stained with SRB dye (Sigma-Aldrich)
for 30 min, excess dye was removed by repeated washing with 1% (v/v) acetic acid. Protein-bound dye was finally
dissolved in 10 mM Tris base solution and subject to spectrophotometric measurement of absorbance at 510 nm
using a microplate reader. In vivo 124I PET imaging and ex vivo tumor uptake. Animal experiments were performed in accord-
ance with the National Institutes of Health Guide for Care and Use of Laboratory Animals, and approved by
the Institutional Animal Care and Use Committee of Samsung Medical Center. Three groups of tumor-bearing
animals were prepared in 8-week-old wild type male BALB/c mice by subcutaneous injection of 1 × 108 cancer
cells into the right shoulder region. The control group had tumors formed by non-transduced CT26 cells (n = 5). The second and third groups had CT26/NIS-cODC tumors and were intraperitoneally injected with DMSO vehi-
cle (n = 6) or 1 mg/kg bortezomib (n = 8), respectively, at 12 and 24 h prior to PET imaging. When tumor size
reached approximately 1.5 cm in diameter, animals were injected with 4 MBq of 124I through the tail vein. Imaging
was performed 1 h later under isoflurane anesthesia, using a small-animal PET/CT scanner (Inveon; Siemens,
Germany) without respiratory gating. PET imaging was followed by non-enhanced CT without attenuation cor-
rection. Care was taken to maintain an environment of 23–25 °C. A square ROI was placed on the tumor region with highest activity on coronal PET, and a mirrored ROI
was placed on the contralateral shoulder as background. Tumor-to-background ratios of mean and maxi-
mum standardized uptake values (SUVmean and SUVmax) were used as indices of uptake. Immediately after
PET imaging, animals were sacrificed by cervical dislocation. Tumor and background tissues were extracted,
weighed, and measured for 124I radioactivity on a high-energy γ-counter. Ex vivo measurements were expressed
as weight-corrected tumor-to-muscle count ratios. Immunohistochemistry staining of tissue sections for NIS expression. Materials and Methods
i
f h For this, cells were scrapped and homogenized in lysis
buffer containing sucrose (0.0856 g/mL), 10 mM N-(2-hydroxyethyl)piperazine-N’-(2-ethanesulfonic acid), 8 SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w www.nature.com/scientificreports/ 1 mM ethylenediaminetetraacetic acid, 10 μg/mL aprotinin, and 1 mM phenylmethylsulfonylfluoride. Following
removal of cell debris, the supernatant was incubated with 0.1 M Na2CO3 at 4 °C for 1 h. The samples were
filled with buffer containing sucrose (0.0856 g/mL), 10 mM HEPES, and 1 mM MgCl2 and then centrifuged at
42,000 rpm for 1 h at 4 °C. After centrifugation, the membrane fraction pellet was suspended in phosphate buff-
ered saline (PBS). (
)
Cell lysate (30 μg) or membrane fraction protein (10 μg) were separated by electrophoresis on a 10% sodium
dodecyl sulfate polyacrylamide gel, followed by transfer to a polyvinylidene difluoride membrane (Bio-RAD,
CA). The membrane was blocked with 5% nonfat milk in Tris-buffered saline and polysorbate-20 for 1 h at
room temperature and incubated overnight at 4 °C with primary antibodies against NIS or β-actin (Santa Cruz
Biotechnology, TX). Membranes were then incubated at room temperature for 1 h with secondary anti-rabbit IgG
antibody for NIS and anti-mouse IgG antibody for β-actin (Cell Signaling, MA). Immune reactive proteins were
detected by chemiluminescence, and band intensities were quantified on a GS-800 densitometer using Quantity
One software (Bio-Rad Laboratories). Cellular radioiodine and radio-technetium uptake measurements. Cells were incubated for 1 h
with 74 kBq 125I (Perkin Elmer, MA), 110 kBq 124I, or 740 kBq 99mTc-O4
− added to the culture media in 5% CO2 at
37 °C. Cells were rapidly washed twice with cold PBS, lysed with 0.1 N NaOH, and measured for cell-bound radi-
oactivity on a high energy γ-counter (Perkin-Elmer) for 124I or 99mTc-O4
− and γ-counter (Wallac) for 125I. Uptake
levels were normalized to protein content for each sample. Proteasome activity assay. To measure proteasome activity, 1.2 × 106 cells in 6-well plates were washed
and collected by scraping with 0.5% NP-40 in distilled water. After incubation for 30 min at −20 °C and centrifu-
gation at 13,000 rpm for 10 min at 4 °C, supernatants were measured for proteasome activity with a fluorometric
assay kit (Bio Vision, CA). Briefly, cell extracts were mixed with 100 μl assay buffer and 1 μl Suc-LLVY-7-amino-
4-methylcoumarin (Suc-LLVY-AMC) substrate. Fluorescence was measured at 350 nm excitation and 440 nm
emission wavelengths in a microplate reader at 37 °C for 30 min. Author Contributions K.H.L., J.H.L. and, K.H.J. designed experiments and analyzed data; J.H.L., C.H.T.Q. and J.W.P. performed
experiments. S.H.M. and Y.S.C. analyzed the data. J.H.L. and K.H.L. wrote the manuscript. All authors read,
provided feedback and approved the manuscript. References 13 Park J W et al Imaging early fate of cancer stem cells in mouse hindlimbs with sodium iodide symporter gene and I 124 PET Mol 12. Dadachova, E. & Carrasco, N. The Na/I symporter (NIS): imaging and therapeutic applications. Semin Nucl Med 34, 23–31 (2004). ,
,h
y
p
(
)
g
g
p
pp
,
(
)
3. Park, J. W. et al. Imaging early fate of cancer stem cells in mouse hindlimbs with sodium iodide symporter gene and I-124 PET. Mo
Imaging Biol 18, 748–757, https://doi.org/10.1007/s11307-016-0941-1 (2016).i h
13. Park, J. W. et al. Imaging early fate of cancer stem cells in mouse hindlimbs with sodium iodide
Imaging Biol 18, 748–757, https://doi.org/10.1007/s11307-016-0941-1 (2016).i g g
p
g
4. Quach, C. H. et al. Quantification of early adipose-derived stem cell survival: comparison between sodium iodide symporter and
enhanced green fluorescence protein imaging. Nucl Med Biol 39, 1251–1260, https://doi.org/10.1016/j.nucmedbio.2012.08.003 (2012) enhanced green fluorescence protein imaging. Nucl Med Biol 39, 1251 1260, https://doi.org/10.1016/j.nucmedbio.2012.08.003 (2012). 15. Dohán, O. et al. The sodium/iodide Symporter (NIS): characterization, regulation, and medical significance. Endocr Rev 24, 48–77,
https://doi.org/10.1210/er.2001-0029 (2003). gl
p
g g
p
g
j
15. Dohán, O. et al. The sodium/iodide Symporter (NIS): characterization, regulation, and medical significance. https://doi.org/10.1210/er.2001-0029 (2003). p
g
6. Jung, K. H. et al. Trypsinization severely perturbs radioiodide transport via membrane Na/I symporter proteolysis: implications fo
reporter gene imaging. Nucl Med Biol 36, 967–974, https://doi.org/10.1016/j.nucmedbio.2009.06.010 (2009).fi p
g
g
g
p
g
j
17. Takeuchi, J., Chen, H., Hoyt, M. A. & Coffino, P. Structural elements of the ubiquitin-independent proteasome degron of ornithine
decarboxylase. Biochem J 410, 401–407, https://doi.org/10.1042/BJ20071239 (2008). y
p
g
18. Mandell, R. B., Mandell, L. Z. & Link, C. J. Jr. Radioisotope concentrator gene therapy using the sodium/iodide symporter gene. Cancer Res 59, 661–668 (1999).hf 9. Jung, K. O. et al. Relationship between Apoptosis Imaging and Radioiodine Therapy in Tumor Cells with Different Sodium Iodide
Symporter Gene Expression. Mol Imaging 14, 7290201400050, https://doi.org/10.2310/7290.2014.00050 (2015).i 20. Chen, L. et al. 99mTc-pertechnetate uptake in hepatoma cells due to tissue-specific human sodium iodide symporter gene expression. Nucl Med Biol 33, 575–80 (2006).h ,
(
)
21. Seemuller, E. et al. Proteasome from Thermoplasma acidophilum: a threonine protease. Science 268, 579–582 (1995). 22. Manasanch, E. E. & Orlowski, R. Z. Proteasome inhibitors in cancer therapy. Nat Rev Clin Oncol 14, 417–433, https:/
org/10.1038/nrclinonc.2016.206 (2017). g
23. Lee, S. M. Acknowledgementsh g
The study was supported by the Basic Science Research Program through the National Research Foundation of
Korea (NRF) funded by the Ministry of Science, ICT, and Future Planning (NRF-2012R1A1A2041354 and NRF-
2015R1A2A2A01006419). g
The study was supported by the Basic Science Research Program through the National Research Foundation o
Korea (NRF) funded by the Ministry of Science ICT and Future Planning (NRF 2012R1A1A2041354 and NRF The study was supported by the Basic Science Research Program through the National Research Foundation of
Korea (NRF) funded by the Ministry of Science, ICT, and Future Planning (NRF-2012R1A1A2041354 and NRF-
2015R1A2A2A01006419). References 1. Dobbelstein, M. & Moll, U. Targeting tumour-supportive cellular machineries in anticancer drug development. Nat Rev Drug Discov
13, 179–196, https://doi.org/10.1038/nrd4201 (2014). 1. Dobbelstein, M. & Moll, U. Targeting tumour-supportive cellular machineries in anticancer drug development. Nat Rev Drug Discov
13, 179–196, https://doi.org/10.1038/nrd4201 (2014). p
g
(
)
2. Bedford, L., Lowe, J., Dick, L. R., Mayer, R. J. & Brownell, J. E. Ubiquitin-like protein conjugation and the ubiquitin-proteasome
system as drug targets. Nat Rev Drug Discov 10, 29–46, https://doi.org/10.1038/nrd3321 (2011).h p
g
2. Bedford, L., Lowe, J., Dick, L. R., Mayer, R. J. & Brownell, J. E. Ubiquitin-like protein conjugation and the ubiquitin-proteasome
system as drug targets. Nat Rev Drug Discov 10, 29–46, https://doi.org/10.1038/nrd3321 (2011).h y
g
g
g
p
g
3. Ciechanover, A. The ubiquitin-proteasome proteolytic pathway. Cell 79, 13–21 (1994). h
4. Loda, M. et al. Increased proteasome-dependent degradation of the cyclin-dependent kinase inhibitor p27 in aggressive colorecta
carcinomas. Nat Med 3, 231–234 (1997). 5. Oren, M. & Kotler, E. p53 mutations promote proteasomal activity. Nat Cell Biol 18, 833–835, https://doi.org/10.1038/ncb3392
(2016). (
)
6. Nalepa, G., Rolfe, M. & Harper, J. W. Drug discovery in the ubiquitin-proteasome system. Nat Rev Drug Discov 5, 596–613 (2006). 6. Nalepa, G., Rolfe, M. & Harper, J. W. Drug discovery in the ubiquitin proteasome system. Nat Rev Drug Discov 5, 596 613 (2006). 7 Adams J The proteasome: a suitable antineoplastic target Nat Rev Cancer 4 349 360 https://doi org/10 1038/nrc1361 (2004) p
p
g
y
q
p
y
g
7. Adams, J. The proteasome: a suitable antineoplastic target. Nat Rev Cancer 4, 349–360, https://doi.org/10.1038/nrc1361 (2004). h
p
p
g
p
g
8. Jariel-Encontre, I., Bossis, G. & Piechaczyk, M. Ubiquitin-independent degradation of proteins by the proteasome. Biochim Biophy
Acta 1786, 153–177, https://doi.org/10.1016/j.bbcan.2008.05.004 (2008). p
g
j
(
)
9. Hoyt, M. A., Zhang, M. & Coffino, P. Probing the ubiquitin/proteasome system with ornithine decarboxylase, a ubiquitin
independent substrate. Methods Enzymol 398, 399–413, https://doi.org/10.1016/S0076-6879(05)98033-6 (2005). p
y
p
g
0. Vlashi, E. et al. In vivo imaging, tracking, and targeting of cancer stem cells. J Natl Cancer Inst 101, 350–359, https://doi.org/10.1093
jnci/djn509 (2009).l j
j
1. Momose, I. et al. In vivo imaging of proteasome inhibition using a proteasome-sensitive fluorescent reporter. Cancer Sci 103
1730–1736, https://doi.org/10.1111/j.1349-7006.2012.02352.x (2012).h p
g
j
12. Dadachova, E. & Carrasco, N. The Na/I symporter (NIS): imaging and therapeutic applications. Semin Nucl Med 34, 23–31 (2004). References et al. Case Example of Dose Optimization Using Data From Bortezomib Dose-Finding Clinical Trials. J Clin Oncol 34,
1395–1401, https://doi.org/10.1200/JCO.2015.66.0662 (2016). p
g
4. Nair, A. B. & Jacob, S. A simple practice guide for dose conversion between animals and human. J Basic Clin Pharma 7, 27–31
https://doi.org/10.4103/0976-0105.177703 (2014). p
g
25. Doubrovin, M., Serganova, I., Mayer-Kuckuk, P., Ponomarev, V. & Blasberg, R. G. Multimodality in vivo molecular-genetic imaging. Bioconjug Chem 15, 1376–88 (2004). j g
(
)
26. Smanik, P. A. et al. Cloning of the human sodium lodide symporter. Biochem Biophys Res Commun 226, 339–345 (1996). Materials and Methods
i
f h After micro-sectioning
formalin-fixed and paraffin-embedded tissues at 4 μm thickness, heat-induced antigen retrieval was performed
for 3 min in pH 9.0 EDTA buffer (Dako). Sectioned slides were then incubated overnight with an anti–human NIS
rabbit polyclonal antibody (1:100 dilution; Santa Cruz Biotechnology) at 4 °C. This was followed by incubation
with HRP-labeled polymer-conjugated secondary antibodies against rabbit IgG (Dako, CA) for 30 min at room
temperature. A color reaction was induced using the ready-to-use 3,3′-diaminobenzidine substrate chromogen
solution (Dako) for 5 min, followed by washing with distilled water. Sections were lightly counterstained with
hematoxylin for 30 seconds before dehydration and mounting. Statistical analysis. Data are presented as mean ± standard deviation (SD). Significance of difference
between groups was analyzed by two-tailed unpaired Student’s t-tests for two groups and ANOVA with Tukey’s
post-hoc tests for three or more groups. Correlation was evaluated by linear regression or Spearman’s rank-order
analysis. P values < 0.05 were considered statistically significant. Data Availability. All data generated or analyzed during this study are included in this published article. SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 9 9 www.nature.com/scientificreports/ Additional Information Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-29642-w.h Competing Interests: The authors declare no competing interests. Competing Interests: The authors declare no competing interests. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps an
institutional affiliations. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and
institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. SCIeNTIfIC REPorTS | (2018) 8:12290 | DOI:10.1038/s41598-018-29642-w 10
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English
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Portable Measurement Systems Based on Microcontrollers to Test Durability of Structures: Mini-Review
|
Frontiers in built environment
| 2,020
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cc-by
| 4,768
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Portable Measurement Systems
Based on Microcontrollers to Test
Durability of Structures: Mini-Review
Crhistian C. Segura and Johann F. Osma*
Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota, Colombia Crhistian C. Segura and Johann F. Osma* Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota, Colombia Corrosion presence is a recurrent concern in buildings and structures that use steel
as their core or as reinforcement, due to the change of steel’s properties caused
by this phenomena. Therefore, methods to detect and quantify corrosion had been
developed; some are based on electrical and electrochemical measurements. On
reinforced concrete structures, sometimes there are exposed steel bars which are
visible, but on those, a visual inspection could determine corrosion presence. There
exist different options to measure the steel bars’ corrosion and its level. The more
straight forward consists of cutting through the concrete until the bar is exposed and
connecting a measurement device there. A disadvantage of this technique is that steel
has to be exposed to the environment during the measurement; as an alternative, novel
contact-less electrochemical techniques are getting more popular. Recent advances in
low-cost and portable electrochemical devices and embedded sensors can change how
the structures are tested. Moreover, there is a discussion about how those devices,
if developed for other fields as biosensors, can assist in other areas. This mini-review
also gives some hints of what the future trends could be due to the combination of
those areas. Edited by: Edited by:
Emilio Bastidas-Arteaga,
Université de Nantes, France Emilio Bastidas-Arteaga,
Université de Nantes, France Reviewed by:
Marija Kuster Maric,
University of Zagreb, Croatia
Antonio Formisano,
University of Naples Federico II, Italy
*Correspondence:
Johann F. Osma
jf.osma43@uniandes.edu.co Reviewed by:
Marija Kuster Maric,
University of Zagreb, Croatia
Antonio Formisano,
University of Naples Federico II, Italy *Correspondence:
Johann F. Osma
jf.osma43@uniandes.edu.co Keywords: portable device, cyclic voltammetry (CV), steel corrosion, electrochemical impedance spectroscopy
(EIS), corrosion MINI REVIEW
published: 04 December 2020
doi: 10.3389/fbuil.2020.563857 MINI REVIEW INTRODUCTION Specialty section:
This article was submitted to
Bridge Engineering,
a section of the journal
Frontiers in Built Environment From long ago, humans had been building bridges to connect cities, countries, and overcome
obstacles; the materials used in these constructions have changed over the times, from the stone
and wood to the modern bridges made of steel and concrete. These structures require periodical
maintenance to keep them well, but a common cause of problems in bridges is corrosion in
the steel bars due to the environment. In particular, the changes in temperature can cause small
dilatations and contractions; also, the rainfalls could raise the humidity. These factors increase the
probability that corrosion appears on the steel bars used during the construction. However, some
researchers had developed models to predict corrosion (Tuutti, 1982; Guo et al., 2019) that are
used to estimate the aging of a structure and the corrosion in advance. A fast approach to these
models is using a Finite Element Method (FEM) and simulating Reinforced Concrete behavior due
to corrosion as in Bossio et al. (2015). This corrosion could affect the durability of the steel and also
reduce its ability to sustain strain, reducing the stress threshold as modeled in Deng et al. (2018). Received: 19 May 2020
Accepted: 03 November 2020
Published: 04 December 2020 Keywords: portable device, cyclic voltammetry (CV), steel corrosion, electrochemical impedance spectroscopy
(EIS), corrosion Citation: Segura CC and Osma JF (2020)
Portable Measurement Systems
Based on Microcontrollers to Test
Durability of Structures: Mini-Review. Front. Built Environ. 6:563857. doi: 10.3389/fbuil.2020.563857 December 2020 | Volume 6 | Article 563857 Frontiers in Built Environment | www.frontiersin.org 1 Portable Measurement Systems for Structures Segura and Osma For example, the ultimate flexural capacity of reinforced concrete
elements is decreased due to the corrosion of steel, as pointed
out by Bossio et al. (2019b), they compared a set of experimental
data against a non-linear FEM model. Netherless, the seismic
capacity is directly affected by the corrosion level (Bossio
et al., 2019a) shows how the mechanical properties such as
ductility of the structure are affected, leading to structural failure
during an earthquake. However, some researchers (Bossio et al.,
2018) are working in a High-Performance Concrete (HPC)
that could aid the structure to sustain stress and improve the
structure ductility even in advanced corrosion levels. However,
reasearchers (Formisano et al., 2018, 2019) discussed the use of
non-destructive tests such as the leed hardness test to measure
steel properties. These tests use a penetration device, which
punctures a sample with a fixed force and measure the dent
on the steel. Which using conversion tables can achieve the
estimation of the material hardness. Otherwise Di Lorenzo et al. (2019) and Rizzo et al. (2019), present corrosion wastage models;
which could be used to predict corrosion in steel. The model
proposed by Rizzo et al. (2019) can estimate the corrosion depth
in structures made of wrought iron. Meanwhile, the model of
Di Lorenzo et al. (2019) based on experimental data obtained a
model calibrated with measurements on both mild carbon and
weathering steels. looking for rust or cracks in the structure, which could not give
an accurate measurement of corrosion and its level inside the
structure. On Mari´c et al. (2019), authors present some study
cases of bridges and how the use of non-destructive techniques
in routinary inspections can lead to more accuracy in find
steel corrosion and their level inside structures. The most used
technique is the Half-cell potential (HCP) (Poursaee, 2016),
which is used to detect corrosion resistance of steel bars using a
single contact point in the bar (electrode), and a second electrode
on the concrete surface (Kawaai et al., 2019). Another common
technique is linear-polarization-resistance (LPT). Citation: This technique
involves applying a small voltage (usually about 30 mV) above
and below its corrosion potential to the steel bar meanwhile
the current is measured; with this, the polarization resistance
(Rp) could be estimated, which is defined as the slope of the
current-potential curve. Also, making use of the Tafel plot
obtained, the corrosion rate could be estimated (Alexander and
Orazem, 2020a). This technique requires a direct connection to
the steel, which in some cases, implies digging across the concrete
to expose the steel. To avoid this situation, researchers had
explored the use of electrochemical analysis (Keddam et al., 2009;
Alexander and Orazem, 2020b), with contact-less measurements,
which could calculate steel corrosion using Electrochemical
Impedance Spectroscopy (EIS). Those tests are made with lab
potentiostats such as Gamry Reference 3000 (Gamry, USA) or
VersaSTAT 4.0 (Princeton Applied Research). For example, the ultimate flexural capacity of reinforced concrete
elements is decreased due to the corrosion of steel, as pointed
out by Bossio et al. (2019b), they compared a set of experimental
data against a non-linear FEM model. Netherless, the seismic
capacity is directly affected by the corrosion level (Bossio
et al., 2019a) shows how the mechanical properties such as
ductility of the structure are affected, leading to structural failure
during an earthquake. However, some researchers (Bossio et al.,
2018) are working in a High-Performance Concrete (HPC)
that could aid the structure to sustain stress and improve the
structure ductility even in advanced corrosion levels. However,
reasearchers (Formisano et al., 2018, 2019) discussed the use of
non-destructive tests such as the leed hardness test to measure
steel properties. These tests use a penetration device, which
punctures a sample with a fixed force and measure the dent
on the steel. Which using conversion tables can achieve the
estimation of the material hardness. Otherwise Di Lorenzo et al. (2019) and Rizzo et al. (2019), present corrosion wastage models;
which could be used to predict corrosion in steel. The model
proposed by Rizzo et al. (2019) can estimate the corrosion depth
in structures made of wrought iron. Meanwhile, the model of
Di Lorenzo et al. (2019) based on experimental data obtained a
model calibrated with measurements on both mild carbon and
weathering steels. There
exist
experimental
measurements
of
corrosion
propagation that use steel plates and a corrosion chamber that
simulate environmental conditions (Odrobinák and Gocál,
2018). ELECTRONIC TECHNIQUES AND
PORTABLE DEVICES There are currently attempts to reduce the size of electronic
measurement devices, while keeping their characteristics and
operation ranges. A field with a significant amount of these
devices is the biosensors, in which they research low-cost and
portable potentiostats suited for electrochemical tests. Some of
those devices can carry out most of the standard electrochemical
tests. For example, Segura and Osma (2017) developed a
miniaturized potentiostat that can do Cyclic Voltammetry (CV). With applied voltages from −1.65 to 1.65 V, measured currents
from 80 µA to 10 mA, and impedances in the range of 50 to 20
k. Other devices, like a low-cost amperometric device, can do Citation: Such conditions are set to induce accelerated corrosion
to model the behavior of steel of similar specifications on
bridges. Authors of Alexander and Beushausen (2019) present
a review of different ways to determine durability or service
life prediction of RC structures. However, it critiques some
of the current approaches and proposes the use of worldwide
specifications and models that improve those parameters. Some
common ions speed up the corrosion in the RC structures. One of the most studied is the Chloride ion, the penetration in
the concrete (Wang et al., 2018), how it interacts with cracked
concrete (Kušter Mari´c et al., 2020), and how it is transported
to the steel. These studies lead to models that can characterize
how the transport changes depending on the wetting/drying
cycles (van der Zanden et al., 2015; Kušter Mari´c et al., 2020). In this mini-review, standard corrosion detection methods are
presented, including commercial devices used; the third section
shows recent developments in terms of low-cost and portable
devices that meet similar criteria, also embedded sensors, and a
benchmark. Finally, the last section presents a vision of future
trends that gives hints about what problems these devices
could solve. The LPT analysis of reinforced concrete by EIS is used to
obtain the polarization resistance (Rp) of the bar; this is on
the EIS Nyquist charts. The typical impedance values could
vary from 100 to 10 k; this difference could vary by
electrodes distance and position, as described by Alexander and
Orazem (2020a), where the Rp measured in the same reinforced
concrete sample changed by 10 times due to the position of the
electrodes on the surface. However, the corrosion measurement
by impedance techniques could also test the effectiveness of
anti-corrosive coatings, testing coated and uncoated samples
(Alvarez-Pampliega et al., 2014; Raj et al., 2020) to test
anti-corrosive coats properties. Those tests and measurements
require an advanced electrochemical device such as the Autolab
PGSTAT302 and algorithms developed to extract the information
from the data like MATLAB. TYPICAL TECHNIQUES OF
MEASUREMENT FIGURE 1 | Some of the portable devices for electrochemical measurements. (A) Miniaturized Potentiostat (Segura and Osma, 2017). (B) Wireless potentiostat
(Steinberg et al., 2015). (C) USB Potentiostat Galvanostat (Dobbelaere, 2017). FIGURE 1 | Some of the portable devices for electrochemical measurements. (A) Miniaturized Potentiostat (Segura and Osma, 2017). (B) Wireless potentiostat
(Steinberg et al., 2015). (C) USB Potentiostat Galvanostat (Dobbelaere, 2017). FIGURE 1 | Some of the portable devices for electrochemical measurements. (A) Miniaturized Potentiostat (Segura and Osma, 2017). (B) Wireless potentiostat
(Steinberg et al., 2015). (C) USB Potentiostat Galvanostat (Dobbelaere, 2017). TABLE 1 | Comparison of commercial and low-cost devices. Voltage
supply
Techniques
supported
Operation Voltage
Communication
Size W × H
Price one device
USD
Current
measurement
capabilities
Miniaturized
Potentiostat (Segura
and Osma, 2017)
3.3 V
CV
−1.650 V to 1.650 V
USB
4.45 cm × 5.34 cm
N/A
10 µA to 10 mA
Wireless potentiostat
(Steinberg et al., 2015)
3.3 V
CA
−0.325 V to 0.900 V
NFC
8.00 cm × 5.00 cm
N/A
15 nA to 100 µA
USB Potentiostat
Galvanostat
(Dobbelaere, 2017)
5 V
CV
−8.00 V to +8.00 V
USB
5.00 cm × 5.00 cm
Below $100
2.5 µA to 25 mA
USB based sensor
(Bukkawar et al., 2019)
5 V
LSV
0.000 V to 3.300 V
USB
19.81 cm × 12.19 cm ∼$47
150 nA to 250 µA
Autolab PGSTAT101
120 V
SV, LSV, CV, ASV,
SWASV, CA
−10.00 V to 10.00 V
USB
9.00 cm × 21.00 cm
More than $2.000 10 nA to 100 mA
PalmSens3
Potentiostat/
Galvanostat/
Impedance Analyzer
5 V
SV, LSV, CV, ASV,
SWASV, CA, FRA/EIS:
10 µHz up to 1 MHz
−5.00 V to 5.00 V
Wireless Bluetooth or
USB
15.70 cm × 9.70 cm
More than $2.000 100 pA to 10 mA TABLE 1 | Comparison of commercial and low-cost devices. CVs with a voltage range from 0 V to 5 V, and current measures
up to 4.5 µA, with USB and Bluetooth connectivity (Agustini
et al., 2020). Some of them had EIS measurement capabilities
with a portable setup (Pruna et al., 2018; Barreiros dos Santos
et al., 2019; Jenkins et al., 2019), with voltage and current ranges
that could be used to measure corrosion. There are even open-
source projects which share all the information required to build
one of those portable devices. For example, Dobbelaere (2017)
presents a potentiostat/galvanostat, design, and fabrication. Frontiers in Built Environment | www.frontiersin.org TYPICAL TECHNIQUES OF
MEASUREMENT Also
Steinberg et al. (2015) developed an open-source potentiostat
ABE-Stat with the EIS technique; this technique could be used
on corrosion detection, as illustrated by Eid et al. (2020), Etim
et al. (2020), and Kenny and Katz (2020). Figure 1, presents
some of the portable devices mentioned in this section, those
devices are portable and their cost is a fraction of commercial
laboratory equipment. saltwater (Honglei et al., 2020). This effect had been studied
for a long time, leading to experimental data and simulations
(Chen et al., 2020). However, there exist researchers who are
working on the detection of the presence of chloride ions. For example, Torres-Luque et al. (2017) developed a chloride-
ion detector made to be placed inside the reinforced concrete
during the building process. This sensor detects and measures the
concentration of chloride-ions, using capacitors made of Calcium
Aluminate. Due to the geometrical disposition of the capacitors,
it had the potential to measure the corrosion direction. Furthermore, its low cost and small size make it possible to be
placed throughout the entirety of the bridge or structure. Table 1
presents a comparison between commercial devices and some of
the portable devices mentioned in this section. TYPICAL TECHNIQUES OF
MEASUREMENT For bridges made of reinforced concrete, it is necessary to
estimate the corrosion rate of steel embedded inside the concrete;
for this, several techniques had been developed throughout the
years. Usually, a routinary inspection consists of a visual test Frontiers in Built Environment | www.frontiersin.org December 2020 | Volume 6 | Article 563857 2 Portable Measurement Systems for Structures Segura and Osma FIGURE 1 | Some of the portable devices for electrochemical measurements. (A) Miniaturized Potentiostat (Segura and Osma, 2017). (B) Wireless potentiostat
(Steinberg et al., 2015). (C) USB Potentiostat Galvanostat (Dobbelaere, 2017). TABLE 1 | Comparison of commercial and low-cost devices. Voltage
supply
Techniques
supported
Operation Voltage
Communication
Size W × H
Price one device
USD
Current
measurement
capabilities
Miniaturized
Potentiostat (Segura
and Osma, 2017)
3.3 V
CV
−1.650 V to 1.650 V
USB
4.45 cm × 5.34 cm
N/A
10 µA to 10 mA
Wireless potentiostat
(Steinberg et al., 2015)
3.3 V
CA
−0.325 V to 0.900 V
NFC
8.00 cm × 5.00 cm
N/A
15 nA to 100 µA
USB Potentiostat
Galvanostat
(Dobbelaere, 2017)
5 V
CV
−8.00 V to +8.00 V
USB
5.00 cm × 5.00 cm
Below $100
2.5 µA to 25 mA
USB based sensor
(Bukkawar et al., 2019)
5 V
LSV
0.000 V to 3.300 V
USB
19.81 cm × 12.19 cm ∼$47
150 nA to 250 µA
Autolab PGSTAT101
120 V
SV, LSV, CV, ASV,
SWASV, CA
−10.00 V to 10.00 V
USB
9.00 cm × 21.00 cm
More than $2.000 10 nA to 100 mA
PalmSens3
Potentiostat/
Galvanostat/
Impedance Analyzer
5 V
SV, LSV, CV, ASV,
SWASV, CA, FRA/EIS:
10 µHz up to 1 MHz
−5.00 V to 5.00 V
Wireless Bluetooth or
USB
15.70 cm × 9.70 cm
More than $2.000 100 pA to 10 mA
CVs with a voltage range from 0 V to 5 V, and current measures
up to 4.5 µA, with USB and Bluetooth connectivity (Agustini
et al., 2020). Some of them had EIS measurement capabilities
saltwater (Honglei et al., 2020). This effect had been studied
for a long time, leading to experimental data and simulations
(Chen et al., 2020). However, there exist researchers who are FIGURE 1 | Some of the portable devices for electrochemical measurements. (A) Miniaturized Potentiostat (Segura and Osma, 2017). (B) Wireless potentiostat
(Steinberg et al., 2015). (C) USB Potentiostat Galvanostat (Dobbelaere, 2017). REFERENCES Bossio, A., Monetta, T., Bellucci, F., Lignola, G. P., and Prota, A. (2015). Modeling
of concrete cracking due to corrosion process of reinforcement bars. Cem. Concr. Res. 71, 78–92. doi: 10.1016/j.cemconres.2015.01.010 Agustini, D., Fedalto, L., Agustini, D., de Matos dos Santos, L. G., Banks, E. C.,
Bergamini, M. F., et al. (2020). A low cost, versatile and chromatographic device
for microfluidic amperometric analyses. Sens. Actuat. B Chem. 304:127117. doi: 10.1016/j.snb.2019.127117 Bukkawar, S., Sarwade, N., and Panse, M. (2019). Polyaniline assisted USB based
sensor for determination of benzene biomarker. Sens. Bio Sens. Res. 22:100260. doi: 10.1016/j.sbsr.2019.100260 Alexander, C. L., and Orazem, M. E. (2020a). Indirect impedance for corrosion
detection of external post-tensioned tendons: 2. multiple steel strands. Corros. Sci. 164:108330. doi: 10.1016/j.corsci.2019.108330 Chen, J., Zhang, W., Tang, Z., and Huang, Q. (2020). Experimental and
numerical
investigation
of
chloride-induced
reinforcement
corrosion
and
mortar
cover
cracking. Cem. Concr. Compos. 111:103620. doi: 10.1016/j.cemconcomp.2020.103620 Alexander, C. L., and Orazem, M. E. (2020b). Indirect electrochemical impedance
spectroscopy for corrosion detection in external post-tensioned tendons:
1. proof of concept. Corros. Sci. 164:108331. doi: 10.1016/j.corsci.2019. 108331 Deng, P., Zhang, C., Pei, S., and Jin, Z. (2018). Modeling the impact of corrosion
on seismic performance of multi-span simply-supported bridges. Constr. Build. Mater. 185, 193–205. doi: 10.1016/j.conbuildmat.2018.07.015 Alexander, M., and Beushausen, H. (2019). Durability, service life prediction, and
modelling for reinforced concrete structures – review and critique. Cem. Concr. Res. 122, 17–29. doi: 10.1016/j.cemconres.2019.04.018 Di Lorenzo, G., Rizzo, F., Formisano, A., Landolfo, R., and Guastaferro, A. (2019). Corrosion wastage models for steel structures: literature review and a
new interpretative formulation for wrought iron alloys. Key Eng. Mater. 813,
209–214. doi: 10.4028/www.scientific.net/KEM.813.209 Alvarez-Pampliega, A., Hauffman, T., Petrova, M., Breugelmans, T., Muselle, T.,
van de Bergh, K., et al. (2014). Corrosion study on Al-rich metal-coated
steel by odd random phase multisine electrochemical impedance spectroscopy. Electrochim. Acta 124, 165–175. doi: 10.1016/j.electacta.2013.09.159 209–214. doi: 10.4028/www.scientific.net/KEM.813.209 Dobbelaere, T. (2017). A USB-controlled potentiostat/galvanostat for thin-film
battery characterization. HardwareX 2, 34–49. doi: 10.1016/j.ohx.2017.08.001 Eid, J., Takenouti, H., Ait Saadi, B., and Taibi, S. (2020). Electrochemical studies of
steel rebar corrosion in clay: Application to a raw earth concrete. Corros. Sci. 168:108556. doi: 10.1016/j.corsci.2020.108556 Barreiros dos Santos, M., Queirós, R. B., Geraldes, Á., Marques, C., Vilas-
Boas, V., Dieguez, L., et al. (2019). Portable sensing system based on
electrochemical impedance spectroscopy for the simultaneous quantification of
free and total microcystin-LR in freshwaters. Biosens. Bioelectron. 142:111550. DISCUSSION However, other elements, such as embedded sensors, could
improve a portable device corrosion measurement. For example,
chloride-induced corrosion is a significant threat to reinforced
concrete (Sandra et al., 2020); this is common in places near Corrosion
and
electrochemical
tests,
in
general,
require
complicated and expensive devices and specialized laboratories. December 2020 | Volume 6 | Article 563857 3 Portable Measurement Systems for Structures Segura and Osma Nevertheless, due to recent advances in technology, some
researchers had developed their own low-cost and portable
devices, which gives technological independence. Additionally,
those custom made devices had small dimensions, making them
portable and a perfect choice for fieldwork. The portability also
refers to the supply voltage independence, which is usually of
5 V. This voltage could be easily provided by batteries or any
USB port from a laptop. Some of them even could be powered
remotely by NFC technology, which makes them perfect for
embedding inside the concrete, and carrying out measurements
in place, reporting data wirelessly to a smartphone or a laptop. This option could yield to obtain and process the data in situ,
which gives an advantage over the commonly used processes. Nevertheless, due to recent advances in technology, some
researchers had developed their own low-cost and portable
devices, which gives technological independence. Additionally,
those custom made devices had small dimensions, making them
portable and a perfect choice for fieldwork. The portability also
refers to the supply voltage independence, which is usually of
5 V. This voltage could be easily provided by batteries or any
USB port from a laptop. Some of them even could be powered
remotely by NFC technology, which makes them perfect for
embedding inside the concrete, and carrying out measurements
in place, reporting data wirelessly to a smartphone or a laptop. This option could yield to obtain and process the data in situ,
which gives an advantage over the commonly used processes. fast measurement of the status of the structure and how the
environment affects it over time. ACKNOWLEDGMENTS The authors acknowledge the support of the Los Andes
University and 727 Colciencias doctoral scholarships for their
support during the development of this system. Also, We thank
the Cleanroom laboratory and the Printed Circuit Board Facility
of the Electrical and Electronic Engineering Department at
Universidad de los Andes for access to the instruments and
technical support. AUTHOR CONTRIBUTIONS Both authors made substantial contributions to the present
review in equal shares. FUNDING This research was funded by the Colombian Ministry of
Education and the Administrative Department of Science,
Technology, and Innovation, Colciencias, through the program
for national doctorates, grant 727. Therefore, some commercial brands have also started
developing their own portable devices, but they still are
expensive. However, they have excellent specifications, and this
takes advantage of the know-how and the infrastructure that
backs them up. Nevertheless, there exists a gap when there
are large structures such as bridges or buildings, for which
it may be beneficial to have more readouts and even to had
embedded sensors and devices that allow continuous monitoring
of the corrosion. In the future, those low-cost devices could
be embedded in a large structure, and using IoT technologies
and lots of sensors, can create a mesh that could get a REFERENCES doi: 10.1016/j.bios.2019.111550 Etim, I. I. N., Dong, J., Wei, J., Nan, C., Pokharel, D. B., Umoh, A. J., et al. (2020). Effect of organic silicon quaternary ammonium salts on mitigating corrosion
of reinforced steel induced by SRB in mild alkaline simulated concrete pore
solution. J. Mater. Sci. Technol. doi: 10.1016/j.jmst.2019.10.006 Bossio, A., Fabbrocino, F., Monetta, T., Lignola, G., Prota, A., Manfredi, G., et al. (2019a). Corrosion effects on seismic capacity of reinforced concrete structures. Corros. Rev. 37, 45–56. doi: 10.1515/corrrev-2018-0044 Formisano, A., Chiumiento, G., and Di Lorenzo, G. (2018). Leeb hardness
experimental tests on carpentry steels: Surface treatment effect and empirical
correlation with strength. AIP Conf. Proc. 1978:450004. doi: 10.1063/1.5044058 Bossio, A., Imperatore, S., and Kioumarsi, M. (2019b). Ultimate flexural capacity
of reinforced concrete elements damaged by corrosion. Buildings 9:160. doi: 10.3390/buildings9070160 Formisano, A., Dessì, E. J., and Chiumiento, G. (2019). Non-destructive tests
on carpentry steels. Open Constr. Build. Tech. J. 13(Suppl. 2), 214–249. doi: 10.2174/1874836801913010214 Bossio, A., Lignola, G. P., and Prota, A. (2018). An overview of assessment and
retrofit of corroded reinforced concrete structures. Procedia Struct. Integr. 11,
394–401. doi: 10.1016/j.prostr.2018.11.051 Guo, Z., Ma, Y., Wang, L., and Zhang, J. (2019). Modelling guidelines
for corrosion-fatigue life prediction
of concrete bridges: Considering December 2020 | Volume 6 | Article 563857 Frontiers in Built Environment | www.frontiersin.org Portable Measurement Systems for Structures Segura and Osma polyethylenimine for enhanced corrosion protection of epoxy coated steel. Corros. Sci. 167:108548. doi: 10.1016/j.corsci.2020.108548 corrosion pit as a notch or crack. Eng. Fail. Anal. 105, 883–895. doi: 10.1016/j.engfailanal.2019.07.046 polyethylenimine for enhanced corrosion protection of epoxy coated steel. Corros. Sci. 167:108548. doi: 10.1016/j.corsci.2020.108548 corrosion pit as a notch or crack. Eng. Fail. Anal. 105, 883–895. doi: 10.1016/j.engfailanal.2019.07.046 Rizzo, F., Di Lorenzo, G., Formisano, A., and Landolfo, R. (2019). Time-dependent
corrosion wastage model for wrought iron structures. J. Mater. Civ. Eng. 31:04019165. doi: 10.1061/(ASCE)MT.1943-5533.0002710 Honglei, C., Zuquan, J., Tiejun, Z., Benzhen, W., Zhe, L., and Jian, L. (2020). Capillary suction induced water absorption and chloride transport in non-
saturated concrete: the influence of humidity, mineral admixtures and sulfate
ions. Constr. Build. Mater. 236:117581. doi: 10.1016/j.conbuildmat.2019.117581 Sandra, N., Kawaai, K., and Ujike, I. (2020). Influence of copper slag on
corrosion behavior of horizontal steel bars in reinforced concrete column
specimen due to Chloride-induced corrosion. Constr. Build. Mater. 255:119265. doi: 10.1016/j.conbuildmat.2020.119265 Jenkins, D. M., Lee, B. E., Jun, S., Reyes-De-Corcuera, J., and McLamore, E. S. (2019). REFERENCES ABE-Stat, a fully open-source and versatile wireless potentiostat project
including electrochemical impedance spectroscopy. J. Electrochem. Soc. 166,
B3056–B3065. doi: 10.1149/2.0061909jes doi: 10.1016/j.conbuildmat.2020.119265 Segura, C. C., and Osma, J. F. (2017). Miniaturization of cyclic voltammetry
electronic systems for remote biosensing. Int. J. Biosens. Bioelectron. 3, 297–299. doi: 10.15406/ijbsbe.2017.03.00068 Kawaai, K., Nishida, T., Saito, A., Ujike, I., and Fujioka, S. (2019). Corrosion
resistance of steel bars in mortar mixtures mixed with organic matter, microbial
or other. Cem. Concr. Res. 124:105822. doi: 10.1016/j.cemconres.2019.105822 Steinberg, M. D., Kassal, P., Kerekovi´c, I., and Steinberg, I. M. (2015). A wireless
potentiostat for mobile chemical sensing and biosensing. Talanta 143, 178–183. doi: 10.1016/j.talanta.2015.05.028 Keddam, M., Nóvoa, X. R., and Vivier, V. (2009). The concept of floating
electrode for contact-less electrochemical measurements: application to
reinforcing steel-bar corrosion in concrete. Corros. Sci. 51, 1795–1801. doi: 10.1016/j.corsci.2009.05.006 Torres-Luque, M., Osma, J. F., Sánchez-Silva, M., Bastidas-Arteaga, E., and
Schoefs, F. (2017). Chlordetect: commercial calcium aluminate based
conductimetric sensor for chloride presence detection. Sensors 17:2099. doi: 10.3390/s17092099 Kenny, A., and Katz, A. (2020). Steel-concrete interface influence on chloride
threshold for corrosion – empirical reinforcement to theory. Constr. Build. Mater. 244:118376. doi: 10.1016/j.conbuildmat.2020.118376 Tuutti, K. (1982). Corrosion of Steel in Concrete. Stockholm: Swedish Cement and
Concrete Research Institute. Kušter Mari´c, M., Ožbolt, J., Balabani´c G., Zhychkovska, O., and Gambarelli, S. (2020). Chloride transport in cracked concrete subjected to wetting – drying
cycles: numerical simulations and measurements on bridges exposed to de-
icing salts. Front. Built Environ. 6:561897. doi: 10.3389/fbuil.2020.561897 van der Zanden, A. J. J., Taher, A., and Arends, T. (2015). Modelling of
water and chloride transport in concrete during yearly wetting/drying
cycles. Constr. Build. Mater. 81, 120–129. doi: 10.1016/j.conbuildmat.2015. 02.012 Mari´c, M. K., Vlaši´c, A., Ivankovi´c, A. M., Bleiziffer, J., Srbi´c, M., and
Skokandi´c, D. (2019). Assessment of reinforcement corrosion and concrete
damage on bridges using non-destructive testing. Gradjevinar 71, 843–862. doi: 10.14256/JCE.2724.2019 Wang, X. H., Bastidas-Arteaga, E., and Gao, Y. (2018). Probabilistic analysis of
chloride penetration in reinforced concrete subjected to pre-exposure static
and fatigue loading and wetting-drying cycles. Eng. Fail. Anal. 84, 205–219. doi: 10.1016/j.engfailanal.2017.11.008 Odrobinák,
J.,
and
Gocál,
J. (2018). Experimental
measurement
of
structural
steel
corrosion. Procedia
Struct. Integr. 13,
1947–1954. doi: 10.1016/j.prostr.2018.12.266 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Poursaee, A. (2016). Frontiers in Built Environment | www.frontiersin.org December 2020 | Volume 6 | Article 563857 REFERENCES Corrosion measurement and evaluation techniques of
steel in concrete structures. Corr. Steel Concrete Struct. 2016, 169–191. doi: 10.1016/B978-1-78242-381-2.00009-2 Copyright © 2020 Segura and Osma. This is an open-access article distributed
under the terms of the Creative Commons Attribution License (CC BY). The use,
distribution or reproduction in other forums is permitted, provided the original
author(s) and the copyright owner(s) are credited and that the original publication
in this journal is cited, in accordance with accepted academic practice. No use,
distribution or reproduction is permitted which does not comply with these terms. Copyright © 2020 Segura and Osma. This is an open-access article distributed
under the terms of the Creative Commons Attribution License (CC BY). The use,
distribution or reproduction in other forums is permitted, provided the original
author(s) and the copyright owner(s) are credited and that the original publication
in this journal is cited, in accordance with accepted academic practice. No use,
distribution or reproduction is permitted which does not comply with these terms. Pruna, R., Palacio, F., Baraket, A., Zine, N., Streklas, A., Bausells, J., et al. (2018). A
low-cost and miniaturized potentiostat for sensing of biomolecular species such
as TNF-α by electrochemical impedance spectroscopy. Biosens. Bioelectron. 100, 533–540. doi: 10.1016/j.bios.2017.09.049 Raj, R., Morozov, Y., Calado, L.M., Taryba, M. G., Kahraman, R., Shakoor, R. A., et al. (2020). Calcium carbonate particles loaded with triethanolamineand Frontiers in Built Environment | www.frontiersin.org December 2020 | Volume 6 | Article 563857
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https://openalex.org/W2726998095
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https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-017-2564-2
|
English
| null |
A practical examination of RNA isolation methods for European pear (Pyrus communis)
|
BMC research notes
| 2,017
|
cc-by
| 5,414
|
© The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License
(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium,
provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license,
and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/
publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abstract Objective: With the goal of identifying fast, reliable, and broadly applicable RNA isolation methods in European pear
fruit for downstream transcriptome analysis, we evaluated several commercially available kit-based RNA isolation
methods, plus our modified version of a published cetyl trimethyl ammonium bromide (CTAB)-based method. Results: We confirmed previous work indicating chaotropic agent-based kits produced sufficient, high-quality RNA
in freshly harvested, mature ‘Bartlett’ fruit. However, RNA isolation from ‘d’Anjou’ pear peel and especially cortical tis-
sues of fruit stored for 11 months proved challenging to all but our modified CTAB-based method. Generally, more
RNA was recovered from peel tissues than cortical tissues. Less toxic dithiothreitol was confirmed to be an acceptable
reducing agent as its substitution for 2-mercaptoethanol often yielded high quality RNA. Finally, we present evidence
that erroneous signals in the 5S region of Bioanalyzer RNA size plot histograms, that interfered with RNA integrity
number calculation, were small RNA fragments that are reduced by simple cleanup procedures, not artifacts as previ-
ously reported. Keywords: RNA, Pyrus communis, 2-mercaptoethanol, Dithiothreitol, Cetyl-trimethyl-ammonium-bromide,
Bioanalyzer, RNA integrity number, ‘d’Anjou’, ‘Bartlett’ *Correspondence: loren.honaas@ars.usda.gov
US Department of Agriculture, Agricultural Research Service, Physiology
and Pathology of Tree Fruits Research Unit, Wenatchee, WA 98801, USA A practical examination of RNA isolation
methods for European pear (Pyrus communis) Loren Honaas* and Elena Kahn Honaas and Kahn BMC Res Notes (2017) 10:237
DOI 10.1186/s13104-017-2564-2 Honaas and Kahn BMC Res Notes (2017) 10:237
DOI 10.1186/s13104-017-2564-2 BMC Research Notes Open Access Sample analysis
l p
y
RNA was evaluated with a NanoDrop 2000 spectropho-
tometer (Thermo Fisher Scientific—http://www.nan-
odrop.com) to provide sample concentration, A260/280 and
A260/230. The Agilent Bioanalyzer (Agilent Technologies—
http://www.agilent.com), using the RNA Pico assay (cat#:
5067-1513) and following the manufacturers’ instruc-
tions, provided sample concentration, RNA integrity
number (RIN), and other detailed quality information. Data analysis Many samples were at or below the limit of detection
for the NanoDrop 2000, thus these data were excluded
from our analysis. Samples that had intact 18s and 28s
RNA, but had strong erroneous signals in the 5s region
(broad peaks of partially degraded and/or small RNAs—
see “Results and discussion” and Additional file 3) often
produced errors in the Bioanalyzer’s RIN estimation. We
manually adjusted the “5s Region Anomaly Threshold” in
the Agilent 2100 Expert software (version B.02.07) from
0.5 to 1.0 to override the error and produce a RIN value. Bioanalyzer profiles were examined for other anomalies
like bubbles (huge sharp peaks) or blank wells (presum-
ably blocked capillaries) and rerun as necessary. Sample
data were recorded in a custom database—an abbrevi-
ated version can be found in Additional file 2. Error bars
on plots in Fig. 2 are standard error of the mean. Introductionfi in interfering substances that accumulate during ripening
and result in low yields of RNA due to co-precipitation
with these substances [5–8]. This issue is especially com-
mon when using lysis buffers that contain chaotropic
agents [4, 9] such as those found broadly in commercially
available kits. However, high quality transcriptome data
that followed successful RNA isolation using the Qiagen
RNeasy Plant Kit™ [10] has been reported for pear (Pyrus
communis ‘Bartlett’). This study included developing fruit
up to harvest maturity that had entered the ethylene cli-
macteric, but did not include older fruit. Obtaining sufficient amounts of high quality RNA from
plant tissues is a primary hurdle to studying the tran-
scriptomes of plants. Many plant tissues are recalci-
trant to RNA extraction for a host of reasons including
abundant secondary metabolites and polysaccharides,
tough cell walls that may be lignified, high levels of native
RNase activity, and widely variable amounts of RNA [1]. Furthermore, readily available and convenient RNA kits
are often only evaluated on a few model plants, leaving
evaluation of these products to the researcher. Recent
surveys of RNA extraction methods [2–4] across many
plant species have typically used primarily young leaves,
as these are among the least recalcitrant and easiest to
obtain plant tissues. For postharvest fruit physiology, studying fruit pre-har-
vest through extended storage is routine [11–15], yet sur-
veys of the efficacy of various RNA extraction methods
for mature fruit that has been stored, especially for Euro-
pean pear (P. communis—e.g. ‘d’Anjou’, ‘Bartlett’) have not
been reported. To facilitate efforts for functional genom-
ics of tree fruit towards improving postharvest fruit qual-
ity [16], we present here a practical examination of pear
fruit RNA isolation methods including several commer-
cially available kits as well as a rapid and robust CTAB-
based method. We emphasize obtaining sufficient high Climacteric fruits of woody trees, including pear and
apple fruit, present challenges to RNA isolation like
those mentioned above, but especially due to increases Honaas and Kahn BMC Res Notes (2017) 10:237 Page 2 of 8 RNA cleanup RNA preparations from freshly harvested (“fresh”) d’Anjou
peel and cortex using the Macherey–Nagel NucleoSpin Plant
RNA Kit and our modified CTAB protocol were pooled and
processed with Zymo’s RNA Clean & Concentrator™-5 (cat#
R1015) following steps to exclude small RNA fragments
(<200 nt) and adhering to the manufactures instructions. Tissue processing quality RNA from small amounts of stored and freshly
harvested fruit tissue for sensitive transcriptome analy-
sis applications, including quantitative real time PCR
(qPCR) and transcriptome sequencing technologies, in
the context of postharvest fruit physiology. Fruits were washed with mild dish detergent and water,
then rinsed with deionized water. Fruit was peeled with
a standard vegetable peeler and peel tissues were flash
frozen in liquid nitrogen. Immediately following peeling,
the pear was cut in half, and roughly 1 cm sub-epidermal
cortical tissue from the equatorial region of the fruit was
minced finely and flash frozen in liquid nitrogen. Frozen
tissues were ground to a fine powder using a clean mor-
tar and pestle chilled with liquid nitrogen. Frozen tissue
powder was transferred to a pre-cooled specimen con-
tainer using a clean, pre-cooled spatula. The specimen
containers were immediately stored at −80 °C. To avoid
the tedious and inherently inaccurate estimation of small
frozen tissue masses we weighed 100 mg of frozen tis-
sue, and thereafter visually estimated an equivalent tissue
mass for each preparation in the interest of time. Materials and methods
Plant material ‘d’Anjou’ pears (Pyrus communis) were obtained from
Cashmere, WA on August 31 2015, stored at 33 °F in air
for 11 months, and are indicated as “stored”. ‘d’Anjou’
and ‘Bartlett’ pear (also P. communis) were obtained
from an experimental orchard located near Orondo, WA
on August 4 2016 (approximately commercial maturity
for ‘Bartlett’ and approximately 2 weeks before commer-
cial maturity for ‘d’Anjou’) and were indicated as “fresh”. ‘Gala’ apples were obtained at commercial maturity
August 15 2016 from a commercial orchard located near
Mattawa, WA. Commercially available kits tested We obtained commercially available kits (see list in
Table 1) for testing. For every kit we substituted dithi-
othreitol (DTT, VWR product # 0281-5 g) for 2-mercap-
toethanol (B-ME) based upon findings by Mommaerts
et al. [17] that the less toxic DTT was a suitable reduc-
ing agent during tissue lysis. The manufacturer’s instruc-
tions were followed for all kits, including recommended
elution volumes. Kit names and catalog numbers are
as follows: Macherey–Nagel NucleoSpin® RNA Plant
740949, Omega E.Z.N.A.® Total RNA Kit I R6834-00,
Omega E.Z.N.A.® HP Total RNA Kit R6812-00, Omega
E.Z.N.A.® Plant RNA Kit R6827-00, Qiagen RNeasy®
Plant Mini Kit 74903, Qiagen RNeasy® Plus Universal Kit
73404, Thermo Scientific GeneJET Plant RNA Purifica-
tion Mini Kit K0809, Zymo ZR Plant RNA MiniPrep™
R2024. Modified CTAB See Additional file 1 for the detailed CTAB protocol. This
protocol was modified from Gapper et al. [18] with the
following changes: (1) DTT was substituted for B-ME,
(2) the lysis (600 µL) and organic phase extraction (chlo-
roform 530 µL) volumes were reduced to accommodate
commonly available 1.7 mL microcentrifuge tubes, (3)
the organic phase extraction was centrifuged at 12,000×g
for 15 min at 4 °C, (4) we added an air drying step to
enhance ethanol removal and (5) allowed the elution to
incubate at RT for 1 min before centrifugation. Diethyl-
pyrocarbonate (DEPC) treated water was used to make
solutions used in this protocol and was prepared as
described in Sambrook et al. [19]. Honaas and Kahn BMC Res Notes (2017) 10:237 Page 3 of 8 Table 1 The kits tested plus the modified CTAB method are listed along with a summary of results
Pear fruit that was stored for 11 months is indicated as “stored” and freshly harvested pear and apple fruit is indicated as “fresh”. √ = RIN ≥7.5, yield per ~100 m
≥100 ng, OK = RIN ≥7.5 (or with clear 28s and 18s peaks) and yield 10–100 ng, poor = RIN 3–7.5 (or with clear 28s and 18s peaks) and/or yield <10 ng, X = RIN
and/or yield below detectable limit, – not tested
Method
Tissue
d’Anjou
peel stored
d’Anjou cortex
stored
d’Anjou
peel fresh
d’Anjou cor-
tex fresh
Bartlett peel
fresh
Bartlett cor-
tex fresh
Gala peel
fresh
Gala c
fresh
Macherey–Nagel
NucleoSpin RNA Plant
buffer RAI
Cat # 740949
X
X
–
–
–
–
–
–
Macherey–Nagel
NucleoSpin RNA Plant
buffer RAP
Cat # 740949
√a
OKc
√e
√g
√
√
√
√
Omega E.Z.N.A. HP Total RNA
Cat # R6812-00
√
X
–
–
–
–
–
–
Omega E.Z.N.A. Total RNA
Cat # R6834-00
√
X
–
–
–
–
–
–
Omega E.Z.N.A. Modified CTAB Plant RNA
Cat # R6827-00
X
Xnr
–
–
–
–
–
–
ThermoFisher
GeneJET Plant RNA
Cat # K0809
OK
X
–
–
–
–
–
–
Qiagen RNeasy
Plus Universal
Cat # 73404
X
Poor
–
–
√
√
–
–
Qiagen RNeasy
Plant buffer RLC
Cat # 74903
√
Poor
–
–
√*
√*
–
–
Qiagen RNeasy
Plant buffer RLT
Cat # 74903
OK
X
–
–
–
–
–
–
Zymo ZR
Plant RNA
Cat # R2024
X
X
–
–
–
–
–
–
CTAB
modified from
Gapper et al. [18]
√b
√d
√f
√h
√
√
√
√ Table 1 The kits tested plus the modified CTAB method are listed along with a summary of results Table 1 The kits tested plus the modified CTAB method are listed along with a summary of results √
X
–
–
–
–
–
– √
X
–
–
–
–
–
– X
Xnr
–
–
–
–
–
– Pear fruit that was stored for 11 months is indicated as “stored” and freshly harvested pear and apple fruit is indicated as “fresh”. √ = RIN ≥7.5, yield per ~100 mg
≥100 ng, OK = RIN ≥7.5 (or with clear 28s and 18s peaks) and yield 10–100 ng, poor = RIN 3–7.5 (or with clear 28s and 18s peaks) and/or yield <10 ng, X = RIN <3
and/or yield below detectable limit, – not tested Pear fruit that was stored for 11 months is indicated as “stored” and freshly harvested pear and apple fruit is indicated as “fresh”. √ = RIN ≥7.5, yield per ~100 mg
≥100 ng, OK = RIN ≥7.5 (or with clear 28s and 18s peaks) and yield 10–100 ng, poor = RIN 3–7.5 (or with clear 28s and 18s peaks) and/or yield <10 ng, X = RIN <3
and/or yield below detectable limit, – not tested Subscript letter indicates panel in Fig. 1 nr not replicated * Independently validated repeat of published result [10] * Independently validated repeat of published result [10] Results and discussion preparations were more or less of equivalent quality to
the next best Qiagen RNeasy Plant kit, yet yields were
more consistent and higher with the Macherey–Nagel
product for stored ‘d’Anjou’ cortical tissues. In addi-
tion to the best kit, we tested additional tissues with
our modified CTAB method. We selected these two
methods because in practice, use of a single method
for a range of tissues reduces confounding factors,
especially in the context of postharvest fruit physiol-
ogy where fruit is often stored for many months and
evaluated at multiple time points spanning the storage
period [11–15]. The sampling strategy was to evaluate the relatively
recalcitrant tissues first (stored d’Anjou pear fruit),
followed by less recalcitrant tissues (freshly harvested
mature pear and apple fruit). We included apple fruit
because the Gapper et al. [18] protocol, on which
ours was based, was used successfully on apples and
we wished to confirm our modified protocol was use-
ful for apple tissues as well. Based upon the results of
the tests in stored ‘d’Anjou’ fruit, the Macherey–Nagel
Nucleospin Plant kit was selected for additional test-
ing based on the observation that the low yielding Honaas and Kahn BMC Res Notes (2017) 10:237 Page 4 of 8 Page 4 of 8 Ribosomal RNA integrity (frequently estimated by the
RNA integrity number (RIN) [20]) has been shown to
be an excellent proxy for the integrity of other RNA spe-
cies present in total RNA preparations, namely mRNA
[21]. Furthermore, compared to estimates using samples
of equivalent high RNA integrity, relative gene expres-
sion measurements estimated with qPCR were shown
to become more divergent as RNA integrity decreased,
though Imbeaud et al. did find that interrogating simi-
larly degraded RNAs was a possible workaround for deal-
ing with partially degraded RNA samples [21]. It has also
been shown that successful transcriptome analysis by
second generation sequencing was correlated with RNA
integrity and A260/280 values [2, 22]. We therefore relied
on these metrics to predict success in downstream appli-
cations that target mRNA.i amplification) or amplification and cleanup of pooled
samples is part of a design, then the convenient Mach-
erey–Nagel NuleoSpin Plant or Qiagen RNeasy Plant kit
are attractive choices. The CTAB method is more scal-
able, though given input requirements for modern appli-
cations such as transcriptome sequencing (i.e. Results and discussion Illumina
TruSeq Stranded mRNA—http://www.illumina.com),
preparations yielding as little as 25 ng of total RNA may
be sufficient. This is especially relevant when the target
tissues are very small or hard to generate because a brute
force approach of processing large amounts of tissue may
not be practical or even possible. p
p
Estimations of RNA integrity, as determined by the RIN
(estimated during Bioanalyzer analysis), were hampered
by what we hypothesized were small fragments of RNA
(Fig. 2, C&G; Additional file 3). Jordon-Thaden and Chan-
derbali [2] speculated that broad peaks in the 5s region of
the RNA histogram (Additional file 3) were due to Bio-
analyzer marker contamination. Yet the kit chemistry has
been rigorously tested and the dyes are highly specific to
RNA (http://www.chem-agilent.com—Publication Num-
ber 5988-7650EN), making erroneous non-RNA signals
unlikely. To test this hypothesis, we chose 8 samples (4
pairs) to clean-up with Zymo’s RNA Clean & Concen-
trator-5, which is a kit that includes a step to selectively
remove small RNAs (<200 nt). Use of the clean-up pro-
cess resulted in a substantial reduction in the magnitude
of the broad peak seen in our RNA preps in the 5s region
(Additional file 3), supporting the hypothesis that this
erroneous signal was due, at least in part, to small RNA
fragments. These fragments may include intact small
RNAs as well as partially degraded RNAs. The erroneous
5s region signal seemed to interfere with RIN estimation
especially for samples at low concentrations (Additional
file 3). It may be possible to remove these fragments with
a similar cleanup scheme for the low yielding kits tested
here, but recovery of extremely low abundance samples
following cleanup may be difficult. Our CTAB method
did routinely produce some weak small RNA fragment
signals in the 5s region, but it was substantially less than
the kit-based methods (Fig. 1). g
Our modified CTAB protocol routinely produced
excellent quality RNA with RINs ≥8.3, A260/280 ≥1.67 and
the best yields across all tissue types ranging from 0.5 to
2 µg from ~100 mg fresh weight tissue (Table 1; Figs. 1,
2). The commercially available kits produced widely vari-
able results, though some were comparable to our bench-
mark CTAB method. Generally, peel tissues yielded more
and better quality RNA than cortical tissues, and younger
tissues than older, stored ones. Results and discussion This is not surprising
because fruit cortical tissues are specialized for storage
and, by mass, contain less RNA compared to peel. Gener-
ally older tissues are more recalcitrant to RNA extraction
than younger ones for a variety of reasons including pres-
ence of co-extracted secondary metabolites [1] and in
the case of climacteric fruit, increases in substances that
tend to co-precipitate with RNA [5–8]. Kits with alter-
nate buffers, such as the Macherey–Nagel NucleoSpin
Plant and Qiagen RNeasy Plant kits, tended to produce
better results using the alternate buffers (Table 1), which
make them attractive options compared to kits with no
alternates. Importantly, our CTAB based protocol was time equiv-
alent to the kits that were tested, though more equipment
intensive (e.g. requiring a fume hood for chloroform
handling, a refrigerated centrifuge and a water bath). We
eliminated intensive preparation of spatulas and mortars
and pestles by baking at 200 °C prior to use because native
plant RNase activity [23] renders these steps redundant
due to the processing of tissues with liquid N2 and the
strong denaturing conditions of lysis buffers. While we
did replace the reducing agent B-ME with the less toxic
DTT, verified as a suitable B-ME replacement by Mom-
maerts et al. [17], the CTAB method still included more
hazardous material compared to most kits tested, exclud-
ing the Qiagen RNeasy Plus Universal kit which includes
the QiaZol reagent and an organic extraction. However, if
yield is not a critical issue (e.g. cDNA synthesis for PCR Based on the results of our comparison, it is clear that
our short and reliable modified CTAB protocol would
be an excellent choice for European pear fruit at or near
harvest maturity through to fruit that had been stored
for an extended time. The Macherey–Nagel NucleoSpin
Kit and Qiagen RNeasy Plant kit represent the best of
the kits we tested—in part because of available alter-
nate lysis buffer chemistry. The kits are less robust than
our CTAB method, but with affordable and easy kit
based cleanup (e.g. Zymo RNA Clean & Concentrator),
the hurdles that low yields and partially degraded RNA
pose could be largely overcome. The input amount for all Honaas and Kahn BMC Res Notes (2017) 10:237 Page 5 of 8 Fig. 1 Kit based isolations and CTAB isolations yield intact RNA. Representative RNA profiles of similar tissues. Results and discussion The Y axis is arbitrary fluorescence
units (the Agilent Bioanalyzer uses an internal standard to calibrate fluorescence for each run) and the X axis is time. a, b d’Anjou peel stored, c, d
d’Anjou cortex stored, e, f d’Anjou peel fresh, g, h d’Anjou cortex fresh from 2 isolation methods. a, c, e, g Macherey–Nagel Nucleospin Plant Kit and
the modified CTAB protocol b, d, f, h. These plots are referenced by subscript in Table 1 Fig. 1 Kit based isolations and CTAB isolations yield intact RNA. Representative RNA profiles of similar tissues. The Y axis is arbitrary fluorescence
units (the Agilent Bioanalyzer uses an internal standard to calibrate fluorescence for each run) and the X axis is time. a, b d’Anjou peel stored, c, d
d’Anjou cortex stored, e, f d’Anjou peel fresh, g, h d’Anjou cortex fresh from 2 isolation methods. a, c, e, g Macherey–Nagel Nucleospin Plant Kit and
the modified CTAB protocol b, d, f, h. These plots are referenced by subscript in Table 1 Honaas and Kahn BMC Res Notes (2017) 10:237 Page 6 of 8 g. 2 Both yield and quality are variable within and across kit based methods, yet the modified CTAB protocol produces consistent high yield and
uality in stored ‘d’Anjou tissues. a RINs are higher and more consistent across methods for stored ‘d’Anjou’ peel than cortex. b Excluding proto-
ls with degraded RNA, yields are variable across kits with the highest yield using the CTAB protocol. c Excluding protocols with degraded RNA,
60/280− ratios were also variable across methods, with CTAB again producing the cleanest RNA. Error bars are standard error of the mean, where
plicable. Some data are missing due to very low yield or severely degraded individual samples. QRP RLC Qiagen RNeasy Plant using buffer RLC,
TAB our modified CTAB protocol see Additional file 1, OHP Omega EZNA HP total RNA, TF thermo fisher, MN RAP Macherey–Nagel NucleoSpin
ant using buffer RAP, OTR Omega EZNA total RNA, QRP RLT Qiagen RNeasy Plant using buffer RLT, MN RA1 Macherey–Nagel NucleoSpin Plant using
uffer RA1, ZR ZR plant RNA MiniPrep, OPR Omega EZNA plant RNA Kit 1, QRU Qiagen RNeasy plus universal Fig. 2 Both yield and quality are variable within and across kit based methods, yet the modified CTAB protocol produces consistent high yield and
quality in stored ‘d’Anjou tissues. Additional files 5. Lopez-Gomez R, Gomez-Lim MA. A method for extracting intact RNA
from fruits rich in polysaccharides using ripe mango mesocarp. HortSci-
ence. 1992;27(5):440–2. Additional file 1. Detailed protocol for our modified CTAB method. Additional file 2. Abbreviated database for all isolations done in this
study. Additional file 1. Detailed protocol for our modified CTAB method. Additional file 2. Abbreviated database for all isolations done in this
study. 6. Malnoy M, Reynoird JP, Mourgues F, Chevrea E, Simoneau P. A method
for isolating total RNA from pear leaves. Plant Mol Biol Rep. 2001;19:69. doi:10.1007/BF02824081. Additional file 3. Signal in the 5s region is likely due to small RNA
fragments and can interfere with RIN estimation. A, B are replicates of
RNA isolations from cortical fruit tissue of freshly harvested d’Anjou pear. C—samples shown in A, B were pooled, and processed with Zymo’s RNA
Clean & Concentrator Kit-5 in which we opted to remove RNA frag-
ments <200 nt. The arrows indicate the putative small RNA fragments
that are reduced during the cleanup (which is designed to remove small
RNA fragments). D—low yield RNA prep with clear 18s and 28s peaks and
low signal in the 5s region produces a RIN of 8.5, E—similarly low yielding
prep of RNA with clear 18S and 28S peaks but with high signal in the 5S
region produces a RIN of 2.8. The portion of intact mRNA in these preps
likely does not differ substantially. 7. Gasic K, Hernandez A, Korban SS. RNA extraction from different apple tis-
sues rich in polyphenols and polysaccharides for cDNA library construc-
tion. Plant Mol Biol Rep. 2004;22:437. doi:10.1007/BF02772687. 7. Gasic K, Hernandez A, Korban SS. RNA extraction from different apple tis-
sues rich in polyphenols and polysaccharides for cDNA library construc-
tion. Plant Mol Biol Rep. 2004;22:437. doi:10.1007/BF02772687. 8. Shellie KC, Meyer RD, Mirkov TE. Extraction of total RNA from melon
mesocarp tissue. HortScience. 1997;32(1):134. 8. Shellie KC, Meyer RD, Mirkov TE. Extraction of total RNA from melon
mesocarp tissue. HortScience. 1997;32(1):134. 9. Baker SS, Rugh CL, Kamalay JC. RNA and DNA isolation from recalcitrant
plant tissues. Biotechniques. 1990;9(3):268–72. 9. Baker SS, Rugh CL, Kamalay JC. RNA and DNA isolation from recalcitrant
plant tissues. Biotechniques. 1990;9(3):268–72. 10. Nham NT, de Freitas S, Macnish AJ, Carr KM, Kietikul T, Guilatco AJ, Jiang
C-Z, Zakharov F, Mitcham EJ. Funding This work was funded by the United States Department of Agriculture,
Agricultural Research Service (ARS) base funds and an Agricultural Research
Service Pacific/West Area Summer Research Employment Program award. 18. Gapper NE, Rudell DR, Giovannoni JJ, Watkins CB. Biomarker develop-
ment for external CO2 injury prediction in apples through exploration
of both transcriptome and DNA methylation changes. Ann Bot London. 2013. doi:10.1093/aobpla/plt021. 18. Gapper NE, Rudell DR, Giovannoni JJ, Watkins CB. Biomarker develop-
ment for external CO2 injury prediction in apples through exploration
of both transcriptome and DNA methylation changes. Ann Bot London. 2013. doi:10.1093/aobpla/plt021. 19. Sambrook J, Russel DW. Molecular cloning: a laboratory manual. 3rd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001. 19. Sambrook J, Russel DW. Molecular cloning: a laboratory manual. 3rd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001. Results and discussion Modified CTAB and TRIzol protocols
improve RNA extraction from chemically complex Embryophyta. Appl
Plant Sci. 2015;3(5):14000105. doi:10.3732/apps.1400105. methods tested here was around 100 mg, though when
processed with a successful method, the plant tissue
yielded 500 ng–2 µg of high quality clean RNA, which
is sufficient for a range of state-of-the-art transcriptome
analysis methods. 3. Yockteng R, Almeida AMR, Yee S, Andre T. A method for extracting
high-quality RNA from diverse plants for next-generation sequenc-
ing and gene expression analyses. Appl Plant Sci. 2013;1(12):1300070. doi:10.3732/apps.1300070. 4. Ghawana S, Paul A, Kumar H, Kumar A, Singh H, Bhardwaj AR, Singh
RS, Raizada J, Singh K, Kumar S. An RNA isolation system for plant
tissues rich in secondary metabolites. BMC Res Notes. 2011;4:85. doi:10.1186/1756-0500-4-85. Competing interests 16. Hertog M, Rudell DR, Pedreschi R, Schaffer RJ, Geeraerd AH, Nicolaï BM,
Ferguson I. Where systems biology meets postharvest. Postharvest Biol
Technol. 2011;62(3):223–37. doi:10.1016/j.postharvbio.2011.05.007. Abbreviations
CTAB
l
i CTAB: cetyl trimethyl ammonium bromide; DTT: dithiothreitol; RIN: RNA
integrity number. CTAB: cetyl trimethyl ammonium bromide; DTT: dithiothreitol; RIN: RNA
integrity number. 12. Mattheis J, Rudell D. Diphenylamine metabolism in ‘Braeburn’ apples
stored under conditions conducive to the development of internal
browning. J Agric Food Chem. 2008;56(9):3381–5. doi:10.1021/jf703768w. Additional files A transcriptome approach towards under-
standing the development of ripening capacity in ‘Bartlett’ pears (Pyrus
communis L.). BMC Genom. 2015;16:762. doi:10.1186/s12864-015-1939-9. 11. Watkins CB, Erkan M, Nock JF, Iungerman KA, Beaudry RM, Moran RE. Harvest date effects on maturity, quality, and storage disorders of ‘Honey-
crisp’ apples. HortScience. 2005;40(1):164–9. Authors’ contributions 13. Rudell DR, Mattheis JP, Hertog ML. Metabolomic change precedes apple
superficial scald symptoms. J Agric Food Chem. 2009;57(18):8459–66. doi:10.1021/jf901571g. LH conceived the work and designed the experiments. LH and EK conducted
the experiments, performed data analysis, wrote and revised the manuscript. Both authors read and approved the final manuscript. 14. Mellidou I, Buts K, Hatoum D, Ho QT, Johnston JW, Watkins CB, Schaffer RJ,
Gapper NE, Giovannoni JJ, Rudell DR, Hertog ML, Nicolai BM. Transcrip-
tomic events associated with internal browning of apple during posthar-
vest storage. BMC Plant Biol. 2014;14:328. doi:10.1186/s12870-014-0328-x. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. 20. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M,
Lightfoot S, Menzel W, Granzow M, Ragg T. The RIN: an RNA integrity
number for assigning integrity values to RNA measurements. BMC Mol
Biol. 2006;7:3. doi:10.1186/1471-2199-7-3. Received: 14 September 2016 Accepted: 20 June 2017 Received: 14 September 2016 Accepted: 20 June 2017 21. Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, Mueller
O, Schroeder A, Auffray C. Towards standardization of RNA quality assess-
ment using user-independent classifiers of microcapillary electrophoresis
traces. Nucleic Acids Res. 2005;33(6):e56. doi:10.1093/nar/gni054. 22. Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT,
Chase MW, Clarke ND, Covshoff S, dePamphilis CW, Edger PP, Goh F,
Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-
Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf
M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr, Surek B, Thomsen Availability of data and materials All data generated or analyzed during this study are included in this published
article [and its Additional files]. 17. Mommaerts K, Sanchez I, Betsou F, Mathieson W. Replacing
β-mercaptoethanol in RNA extractions. Anal Biochem. 2015;479:51–3. doi:10.1016/j.ab.2015.03.027. Acknowledgements
W
f l
Ni We are grateful to Nigel Gapper who shared his RNA method upon which
ours was based and also for his advice during its development. 15. Leisso RS, Gapper NE, Mattheis JP, Sullivan NL, Watkins CB, Giovannoni JJ,
Schaffer RJ, Johnston JW, Hanrahan I, Hertog ML, Nicolai BM, Rudell DR. Gene expression and metabolism preceding soft scald, a chilling injury
of ‘Honeycrisp’ apple fruit. BMC Genom. 2016;17(1):798. doi:10.1186/
s12864-016-3019-1. Competing interests
The authors declare that they have no competing interests. Competing interests
The authors declare that they have no competing interests. Results and discussion a RINs are higher and more consistent across methods for stored ‘d’Anjou’ peel than cortex. b Excluding proto-
cols with degraded RNA, yields are variable across kits with the highest yield using the CTAB protocol. c Excluding protocols with degraded RNA,
A260/280− ratios were also variable across methods, with CTAB again producing the cleanest RNA. Error bars are standard error of the mean, where
applicable. Some data are missing due to very low yield or severely degraded individual samples. QRP RLC Qiagen RNeasy Plant using buffer RLC,
CTAB our modified CTAB protocol see Additional file 1, OHP Omega EZNA HP total RNA, TF thermo fisher, MN RAP Macherey–Nagel NucleoSpin
Plant using buffer RAP, OTR Omega EZNA total RNA, QRP RLT Qiagen RNeasy Plant using buffer RLT, MN RA1 Macherey–Nagel NucleoSpin Plant using
buffer RA1, ZR ZR plant RNA MiniPrep, OPR Omega EZNA plant RNA Kit 1, QRU Qiagen RNeasy plus universal Fig. 2 Both yield and quality are variable within and across kit based methods, yet the modified CTAB protocol produces consistent high yield and
quality in stored ‘d’Anjou tissues. a RINs are higher and more consistent across methods for stored ‘d’Anjou’ peel than cortex. b Excluding proto-
cols with degraded RNA, yields are variable across kits with the highest yield using the CTAB protocol. c Excluding protocols with degraded RNA,
A260/280− ratios were also variable across methods, with CTAB again producing the cleanest RNA. Error bars are standard error of the mean, where
applicable. Some data are missing due to very low yield or severely degraded individual samples. QRP RLC Qiagen RNeasy Plant using buffer RLC,
CTAB our modified CTAB protocol see Additional file 1, OHP Omega EZNA HP total RNA, TF thermo fisher, MN RAP Macherey–Nagel NucleoSpin
Plant using buffer RAP, OTR Omega EZNA total RNA, QRP RLT Qiagen RNeasy Plant using buffer RLT, MN RA1 Macherey–Nagel NucleoSpin Plant using
buffer RA1, ZR ZR plant RNA MiniPrep, OPR Omega EZNA plant RNA Kit 1, QRU Qiagen RNeasy plus universal Page 7 of 8 Honaas and Kahn BMC Res Notes (2017) 10:237 2. Jordon-Thaden IE, Chanderbali AS. Modified CTAB and TRIzol protocols
improve RNA extraction from chemically complex Embryophyta. Appl
Plant Sci. 2015;3(5):14000105. doi:10.3732/apps.1400105. 2. Jordon-Thaden IE, Chanderbali AS. Modified CTAB and TRIzol protocols
improve RNA extraction from chemically complex Embryophyta. Appl
Plant Sci. 2015;3(5):14000105. doi:10.3732/apps.1400105. 2. Jordon-Thaden IE, Chanderbali AS. 23. Lessard P, Decroocq V, Thomas M. Extraction of RNA, cloning and subtrac-
tive hybridization. In: Clark MS, editor. Plant molecular biology—a labora-
tory manual. Berlin: Springer; 1997. p. 154–220. CJ, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK. Evaluating meth-
ods for isolating total RNA and predicting the success of sequencing phy-
logenetically diverse plant transcriptomes. PLoS ONE. 2012;7(11):e50226.
doi:10.1371/journal.pone.0050226. Honaas and Kahn BMC Res Notes (2017) 10:237 References References
1. MacRae E. Extraction of plant RNA. In: Hilario Elena, Mackay John, editors. Protocols for nucleic acid analysis by nonradioactive probes. Totawa:
Humana Press; 2007. p. 15–24. Page 8 of 8 Honaas and Kahn BMC Res Notes (2017) 10:237 CJ, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK. Evaluating meth-
ods for isolating total RNA and predicting the success of sequencing phy-
logenetically diverse plant transcriptomes. PLoS ONE. 2012;7(11):e50226. doi:10.1371/journal.pone.0050226. • We accept pre-submission inquiries
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English
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Impact of uncontrolled hypertension on 12-month clinical outcomes following below-the-knee arteries (BTK) interventions in patients with critical limb ischemia
|
Clinical hypertension
| 2,015
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cc-by
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© 2016 Im et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International
License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any
medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative
Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://
creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Im et al. Clinical Hypertension (2016) 22:9
DOI 10.1186/s40885-016-0044-y Im et al. Clinical Hypertension (2016) 22:9
DOI 10.1186/s40885-016-0044-y RESEARCH
Open Access
Impact of uncontrolled hypertension
on 12-month clinical outcomes following
below-the-knee arteries (BTK) interventions
in patients with critical limb ischemia
Sung Il Im1, Seung-Woon Rha2*, Byoung Geol Choi2, Se Yeon Choi2, Jae Joong Lee2, Sun ki Lee2, Ji Bak Kim2,
Jin Oh Na2, Cheol Ung Choi2, Hong Euy Lim2, Jin Won Kim2, Eung Ju Kim2, Chang Gyu Park2, Hong Seog Seo2
and Dong Joo Oh2 Abstract Background: Despite intensive anti-hypertensive treatment, overall control rates of only 30 ~ 50 % have been
reported in patients with hypertension (HTN). However, clinical significance and angiographic characteristics of
patients with uncontrolled HTN following Below-the-knee arteries (BTK) interventions in patients with critical limb
ischemia (CLI) are not clarified yet as compared to those with controlled HTN. Methods: A total 165 consecutive hypertensive patients with BTK lesions from August 2004 to November 2012
were enrolled for this study. Uncontrolled HTN was defined as a blood pressure of > 140 mmHg systolic and
90 mmHg diastolic under anti-hypertensive treatment. A total of 112 patients (67.8 %) had uncontrolled HTN. We
compared the clinical and angiographic characteristics of patients with uncontrolled HTN following BTK
interventions to those with controlled HTN at 12-month follow-up. Results: The baseline characteristics are well balanced between the two groups. At 12 months, there was no
difference in the incidence of mortality, target lesion revascularization (TLR), target extremity revascularization (TER),
and limb salvage rate in both groups. However, amputation rates were higher in patients with controlled HTN
(33.9 vs. 19.6 %, P = 0.045). Results: The baseline characteristics are well balanced between the two groups. At 12 months, there was no
difference in the incidence of mortality, target lesion revascularization (TLR), target extremity revascularization (TER),
and limb salvage rate in both groups. However, amputation rates were higher in patients with controlled HTN
(33.9 vs. 19.6 %, P = 0.045). Conclusion: Regardless of blood pressure control, HTN itself was an independent risk factor for BTK lesions, suggesting
more intensive medical therapy with close clinical follow up will be required for all BTK patients with HTN. Keywords: Uncontrolled hypertension, Below-the-knee artery (BTK) lesion, Peripheral angioplasty mortality from cardiovascular disease (CVD) and all
causes such as cerebrovascular diseases, renal disease,
and diabetes mellitus (DM). In addition, it is an inde-
pendent risk factor for mortality and morbidity in pa-
tients
with
CVD
[2–4]. Therefore,
the
clinical
importance of PAD has increasingly been acknowledged
in recent several years [5]. Impact of uncontrolled hypertension
on 12-month clinical outcomes following
below-the-knee arteries (BTK) interventions
in patients with critical limb ischemia Sung Il Im1, Seung-Woon Rha2*, Byoung Geol Choi2, Se Yeon Choi2, Jae Joong Lee2, Sun ki Lee2, Ji Bak Kim2,
Jin Oh Na2, Cheol Ung Choi2, Hong Euy Lim2, Jin Won Kim2, Eung Ju Kim2, Chang Gyu Park2, Hong Seog Seo2
and Dong Joo Oh2 * Correspondence: swrha617@yahoo.co.kr
2Cardiovascular Center, Korea University Guro Hospital, 80, Guro-dong,
Guro-gu, Seoul 152-703, South Korea
Full list of author information is available at the end of the article Study definition y
Hypertension was defined as either systolic or dia-
stolic elevation of blood pressure ≥140/90 mmHg or
ongoing antihypertensive pharmacological treatment. The physician measured blood pressure with sphyg-
momanometer with patients in a sitting posture, after
resting for at least 5 min with the cuff placed on the
arm. In each patient, the mean of two readings taken
at intervals of at least 2 min was used in the study. The blood pressures were measured for all patients
every three months from the enrollment. Uncon-
trolled HTN was defined as a blood pressure of >
140 mmHg systolic and 90 mmHg diastolic under
anti-hypertensive
treatment
including
patients
who
lack blood pressure control secondary to poor adher-
ence and/or an inadequate treatment regimen, as well
as those with true treatment resistance. Dyslipidemia
was defined as a total cholesterol level ≥200 mg/dL
or
current
treatment
with
lipid-lowering
drugs. Current
smoking
was
defined
as
active
smoking
within the past 12 months. Diabetes mellitus (DM)
was
defined
as
the
fasting
blood
glucose
level ≥
126 mg/dL, or use of oral hypoglycemic agents or in-
sulin. In the present study, if a patient’s past history,
medical records, present symptoms or medical exam-
ination results accorded with one of the following cri-
teria, the
patients
were diagnosed with
PAD: (1)
Claudication with ankle brachial indices < 0.90; (2) From August 2004 to November 2012, all consecutive
hypertensive patients with CLI undergoing angioplasty
of at least 1 BTK vessel at our center were screened for
enrollment. Inclusion criteria were the presence of
hypertension, CLI (Rutherford class 4 or greater), sten-
osis or occlusion ≥40 mm of at least 1 tibial vessel with
distal run-off to the foot, and agreement to 12-month
angiographic evaluation. The patients were excluded if they had one of the fol-
lowing conditions including advanced heart failure (New
York Heart Association class III or IV), serum creatin-
ine ≥3 mg/dL, life expectancy < 1 year, contraindication
to combined antiplatelet treatment, planned major am-
putation before angiography because these conditions
can be major causes of adverse cardiovascular events
and could serve as the bias of PAD and the patients
without HTN. Finally, a total 165 hypertensive patients (91.6 % of
total
subjects
underwent
PAG)
with
angiographic
proven PAD were enrolled for this study and under-
went peripheral angioplasty. Study population We performed peripheral angiography (PAG) in 180
consecutive patients (male 76.7 %, mean age 67.1 ±
10.9 years) who had typical or atypical claudication or
wound to confirm significant PAD at cardiovascular cen-
ter in Korea University Guro Hospital, Seoul, South
Korea. interventions up to 12 months in patients with HTN
according to presence of BP control. interventions up to 12 months in patients with HTN
according to presence of BP control. Background Hypertension (HTN) is probably the most common risk
factor of atherosclerotic cardiovascular disease. Athero-
sclerotic cardiovascular disease is the leading cause of
mortality in Western countries [1]. Peripheral arterial
disease (PAD), which is usually defined as atherosclerotic
occlusion of the arterial bed in the lower extremities, is
a major manifestation of systemic atherosclerosis. It is
well known that PAD is associated with increased risk of Critical limb ischemia (CLI), characterized by ischemic
rest pain or tissue loss, represent the most advanced
state of PAD, burdened by high morbidity and mortality. CLI generally occurs in high risk patients with several
risk factors including DM, older age, HTN with exten-
sive atherosclerotic disease of below-the-knee vessels. * Correspondence: swrha617@yahoo.co.kr
2Cardiovascular Center, Korea University Guro Hospital, 80, Guro-dong,
Guro-gu, Seoul 152-703, South Korea
Full list of author information is available at the end of the article Im et al. Clinical Hypertension (2016) 22:9 Page 2 of 12 Previous study also showed that PAD is significantly as-
sociated with systolic hypertension in the high risk
group [6]. interventions up to 12 months in patients with HTN
according to presence of BP control. Fig. 1 Flow chart HTN currently affects 25 % of adults and may
affect > 90 % of individuals during their lifetimes [7]. Therefore adequate control of blood pressure is of
public health importance. However, recent studies in-
dicated that 30 ~ 50 % of those with HTN are either
untreated or under-treated [8]. No previous study of
PAD has been performed in patients with uncon-
trolled HTN. Clinical significance and angiographic
characteristics of patients with uncontrolled HTN fol-
lowing Below-the-knee arteries (BTK) interventions in
patients with CLI are not clarified yet as compared to
those with controlled HTN. In this study, we sought to clarify the impact of uncon-
trolled HTN on clinical outcomes in patients with CLI fol-
lowing BTK interventions during 12 months follow-up. Study definition Those patients were di-
vided into two groups according to blood pressure
(BP) control (controlled HTN group; n = 53 patients,
uncontrolled
HTN
group;
n = 112
patients)
and
analyzed. The study flow chart was shown in Fig. 1. We compared the clinical and angiographic character-
istics,
and
major
clinical
outcomes
after
BTK Im et al. Clinical Hypertension (2016) 22:9 Page 3 of 12 Page 3 of 12 Claudication
with
findings
of
a
significant
lesion
(≥70 % diameter stenosis) in peripheral artery on
computed tomographic angiography (CTA) or invasive
angiography; (3) Symptomatic carotid, subclavian ar-
terial disease (≥70 % diameter stenosis) documented
by image studies including CTA or invasive angiog-
raphy. Insignificant CAD was defined as the ≤30 %
diameter stenosis in peripheral arteries documented
by
image
studies
including
CTA
or
invasive
angiography. Claudication
with
findings
of
a
significant
lesion
(≥70 % diameter stenosis) in peripheral artery on
computed tomographic angiography (CTA) or invasive
angiography; (3) Symptomatic carotid, subclavian ar-
terial disease (≥70 % diameter stenosis) documented
by image studies including CTA or invasive angiog-
raphy. Insignificant CAD was defined as the ≤30 %
diameter stenosis in peripheral arteries documented
by
image
studies
including
CTA
or
invasive
angiography. healthy surrounding tissue. All patients were sched-
uled to be readmitted for control peripheral angiog-
raphy
at
12
months. In
case
of
clinical
CLI
recurrence, angiography and repeat revascularization
were performed within 1 week from diagnosis. In pa-
tients undergoing clinically driven repeat angiography
of the target limb between 9 and 12 months who did
not show evidence of restenosis of the target lesion,
scheduled
angiography
at
12
months
was
not
performed. Study End points and definitions Before the intervention, immediately after the inter-
vention, and at follow-up, angiography of the target
vessel was performed in identical projections. The tar-
get lesion was identified by an image of the vascular
anatomy
and
specific
landmarks
(collaterals,
bone
landmarks), with a second image showing the inflated
balloons. These images were compared with follow-up
angiograms. The primary end point of the study was the com-
parison of the 12-month binary restenosis rates ac-
cording to BP control. Restenosis was defined by
angiography as a reduction in the luminal diameter >
50 % according to the worst angiographic view within
the treated lesion plus the 10-mm segments proximal
and distal to it. The
pre-specified
secondary
end
points
of
the
study were (1) clinically driven target lesion revascu-
larization (TLR) defined as repeat percutaneous inter-
vention
or
surgical
bypass
graft
resulting
from
angiographic evidence of restenosis at the level of
the treated lesion ±10 mm in the presence of at least
1 of the following criteria: recurrence of pain in the
foot at rest that increased in the supine position, re-
currence of foot lesion or evidence during follow-up
of foot lesion size decrease–increase behavior or ap-
pearance of a new foot lesion; (2) major amputation,
defined as unplanned amputation of the target limb
in which a prosthesis was required for standing or
walking, however, if the patients who refused the am-
putation, those patients were excluded from the ana-
lysis to reduce bias; and (3) target vessel occlusion
(by CTA or invasive angiography). Acquired angio-
grams were reviewed by 2 blinded investigators who
did not actively participate in recruitment and had
no knowledge of clinical status and randomization
group. Technical success was defined as restoration of dir-
ect flow in the target vessel with run-off to the foot
and a residual stenosis < 30 %. Clinical success was
defined as technical success without clinical events
during hospitalization. In patients with bilateral CLI,
an additional procedure for the revascularization of
the contralateral limb was planned in a different
session to limit the risk of x-ray exposure and con-
trast
induced
nephropathy,
maintaining
the
same
randomization arm. Study procedure y
After admission, the femoral, popliteal, dorsalis pedis
and posterior tibial arteries were palpated, and the ex-
tent of tissue loss was recorded as part of the pre-
procedural study. Angioplasties were performed with
crossover approach or an anterograde ipsilateral ap-
proach using 5 ~ 6 French sheaths. In case of failure
to recanalize by either intraluminal or subintimal ap-
proach, a retrograde approach was attempted. After
placing the sheath, intra-arterial heparin (70 IU/kg
heparin) was routinely administered via the vascular
sheath. A 0.014-in. guide wire was advanced into the
lesion and a balloon catheter of optimal size was in-
troduced. The appropriate balloon length and diam-
eter were determined by visual assessment. Balloon
inflation with normal pressure was maintained for at
least 120 s. All patients were taking aspirin 100 mg
daily at least 1 week prior to peripheral angioplasty. Post-intervention dual antiplatelet therapy with aspirin
100 mg and clopidogrel 75 mg once daily or add-
itional cilostazol 100 mg twice a day were given at
least for 4 weeks, and 100 mg aspirin was given daily
thereafter. Discussion The main findings of the present study are that despite
the patients with uncontrolled HTN had more proximal
target lesions, higher incidences of CTO and severe cal-
cifications, however, at 12 month follow-up, there was
no difference in the incidence of mortality, TLR, TER,
limb salvage rate in both groups following successful
BTK endovascular revascularization. Rather, the amputa-
tion rate was higher in patients with controlled HTN
compared to that of uncontrolled HTN. Therefore, it is
difficult to interpret the difference in the results of the
impact of BP control on mid-term clinical outcomes in
hypertensive patients with CLI following BTK interven-
tions. However, HTN itself was an independent risk fac-
tor for MALE in hypertensive CLI patients with BTK
lesions, suggesting more intensive medical therapy with
close clinical follow up will be required for all patients
with HTN in real world clinical practice. Coronary angiographic and clinical parameters were
shown in Table 2. There was no difference in coronary
angiographic characteristics between the two groups. The frequencies of beta blockers (BB), angiotensin
converting enzyme inhibitor (ACEi), angiotensin recep-
tor blocker (ARB), statins and antiplatelet drugs were
similar between the two groups on admission and
30 days after BTK interventions in Table 3. The procedural and peripheral angiographic character-
istics at baseline are shown in the Table 4. The most fre-
quently treated vessel was the anterior tibial artery. The
incidences of severe calcification, chronic total occlusion
(CTO) and proximal lesions were higher in the uncon-
trolled HTN group. However, Rutherford classifications,
ABI, lesion types, lesions length and procedural ap-
proach were similar between the two groups. Technical
and clinical successes were obtained in 94 % of all
patients. Previous study reported that the prevalence of PAD in
patients
with
HTN
is
higher
than
those
without
HTN.[4] Essential HTN is associated with impaired
regulation of vascular tone and endothelial dysfunction
in the peripheral artery [9]. Evidence from these studies
suggests that acetylcholine mediated as well as flow-
mediated dilation is impaired in essential HTN and that
the dysfunction in part is related to defects in the nitric
oxide system [10, 11]. Table 5 shows the procedural complications after
BTK interventions. There was no difference in pro-
cedural complications including arterio-venous (AV)
fistula,
pseudo-aneurysm,
access
site
hematoma,
gastro-intestinal (GI) bleeding, blood transfusion rates,
contrast
induced
nephropathy
and
arrhythmia
be-
tween the two groups. Follow-up Once discharged, patients were followed up in Korea
University Guro Hospital. Office visits were scheduled
every two weeks for first 2 months, once a month for
the third month, and then every 3 months. Minor
amputations planned before the interventions were
performed 2 to 4 weeks after revascularization an in-
cluded toe amputations resulting from necrosis or
infection of tissues and bones with preservation of Multivariate analyses was performed for the cumu-
lative 12-month prevalence of major adverse limb
events (MALE) including total death, major amputa-
tions, TLR, and repeat BTK interventions in both
groups. Im et al. Clinical Hypertension (2016) 22:9 Im et al. Clinical Hypertension (2016) 22:9 Page 4 of 12 Results The baseline clinical characteristics and laboratory find-
ings of patients are shown in Table 1. The most of vari-
ables including age, body mass index, dyslipidemia,
smoking history, chronic kidney disease, congestive heart
failure, and coronary artery disease were balanced be-
tween the two groups. There was no difference in base-
line laboratory findings between the two groups. Statistical analysis Clinical and peripheral angiographic data at 12 months
are presented in Table 6. There was no difference in the
incidence of mortality, myocardial infarction, cerebro-
vascular infarction in both groups. The incidences of
TLR, target extremity revascularization (TER), limb sal-
vage rate, binary restenosis, primary and secondary pa-
tency were also similar between the two groups at
12 months. And there was no patient who refused the
amputation, if the patients were indicated. However, all
patients with HTN (n = 165) had higher incidence of
MALE compared to those without HTN (n = 15) at
12 month follow-up (37.6 % vs. 6.7 %, P = 0.021). y
Data were analyzed according to the established stan-
dards descriptive statistics. Results were presented as
numbers (percentages) of patients or medians (inter-
quartile range) where applicable. Differences between
groups stratified by blood control status in patients with
HTN under anti-hypertensive medications were tested
by x2 test and the Fisher’s exact test for dichotomous
variables and the Mann–Whitney U test for continuous
variables. Then, differences in clinical outcome between
controlled HTN and Uncontrolled HTN groups were
assessed at 12-months follow-up. Results were adjusted
for age, gender and DM by logistic regression analysis. The difference in MALE between two groups during
follow-up period was assessed by the Kaplan-Meier
method by means of the log-rank test. All tests were 2-
tailed and a p value of <0.05 was considered statistically
significant. All statistical analysis was performed by
means of SPSS 18.0 (SPSS Inc., Chicago, Illinois). In univariate analysis, HTN, DM foot, regional wall mo-
tion abnormality of LV, mitral valve calcification, congest-
ive heart failure, chronic kidney disease and dialysis were
significantly associated with MALE in patients with CLI
after peripheral angioplasty at 12 months. In multivariate
analysis, HTN (P = 0.002), mitral valve calcification (P =
0.040) and dialysis (P = 0.029) were independent risk fac-
tors for MALE (Table 7) at 12 months. Kaplan-Meier curves showed that event free survivals
of MALE are similar in both groups at 12 month follow-
up (P = 0.456; Fig. 2). Discussion Guidelines published for the detection and treatment
of HTN (The joint National Committee on Prevention,
Detection, Evaluation and Treatment of high Blood Im et al. Clinical Hypertension (2016) 22:9 Page 5 of 12 Table 1 Baseline characteristics according to blood pressure control
Variable. Discussion Previous
meta-analyses
of
randomized
placebo-
controlled trials indicate that antihypertensive therapy in
patients with uncontrolled HTN reduces the risk of
major cardiovascular adverse events (stroke by 30 %,
coronary heart disease by 10 % to 20 %, congestive heart
failure by 40 %, and total mortality by 10 %) [13], which
can be conversely interpreted that uncontrolled HTN
can be very important risk factor for cardiovascular ad-
verse events. Although, it remains controversial whether
the risk of cardiovascular events is related solely to the
blood pressure achieved or also to the manner in which
it is achieved [7]. And recent study also reported that
the risk of PAD was increased with increasing HTN
grade (HTN grade 3, OR 1.62, P = 0.006) [14], and recent CLI represents the most severe stage of peripheral vas-
cular disease, with complications of limb loss [16, 17]. The clinical presentations range from rest pain, ischemic
ulcers to gangrene. Apart from the potential loss of limb
which is usually evident at presentation, the co-existent
cardiovascular morbidity and mortality presents an even
greater threat. Previous longitudinal follow-up studies
have been shown that HTN is amongst the most import-
ant risk factors for PAD along with increasing age,
smoking, DM and dyslipidemia [18–20]. Discussion Clinical Hypertension (2016) 22:9 Page 6 of 12 Table 1 Baseline characteristics according to blood pressure control (Continued)
Uric acid (mg/dL)
5.5 ± 1.8
5.6 ± 1.6
5.4 ± 1.8
0.559
Creatinine (mg/dL)
2.6 ± 3.1
2.8 ± 3.1
2.5 ± 3.0
0.595
Magnesium (mEq/L)
1.7 ± 0.2
1.7 ± 0.2
1.7 ± 0.3
0.615
Values are mean ± SD (range). HTN indicates hypertension group, Pts patients, AF atrial fibrillation, PTCA percutaneous transluminal coronary angioplasty, HDL high
dense lipoprotein, LDL low dense lipoprotein, hs-CRP high sensitive C-reactive protein Table 1 Baseline characteristics according to blood pressure control (Continued) Pressure, and European Society of Cardiology) recom-
mend PAD as evidence of clinical cardiovascular disease. Hypertensive patients with PAD need drug therapy no
matter which stages of hypertension they are in [12]. However, due to the lack of specific PAD symptoms,
clinical awareness of PAD is very low in the primary care
setting, which translates into missed opportunities to
treatment of HTN in hypertensive patients with PAD. Even though the hypertensive patients knew that they
had high blood pressure, 30 ~ 50 % of those with HTN
are either untreated or undertreated [8]. national review reported that the hypertensive patients
with major lower extremity amputations had higher inci-
dence of below the knee amputations than above the
knee amputations, which is suggesting that HTN can
affect smaller and more distal vessels of lower extrem-
ities [15]. Pressure, and European Society of Cardiology) recom-
mend PAD as evidence of clinical cardiovascular disease. Hypertensive patients with PAD need drug therapy no
matter which stages of hypertension they are in [12]. However, due to the lack of specific PAD symptoms,
clinical awareness of PAD is very low in the primary care
setting, which translates into missed opportunities to
treatment of HTN in hypertensive patients with PAD. Even though the hypertensive patients knew that they
had high blood pressure, 30 ~ 50 % of those with HTN
are either untreated or undertreated [8]. Therefore, we hypothesized that uncontrolled HTN
also can affect the mid or long term clinical outcomes
after BTK interventions in hypertensive patients with
CLI. This is the first study to compare the 12 months
clinical outcomes after BTK interventions in hyperten-
sive patients with according BP control. Discussion n%
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value
Baseline characteristics
Gender (Male)
128 (77.5)
43 (81.1)
85 (75.8)
0.550
Age (years)
68.2 ± 9.3
68.8 ± 10.2
67.9 ± 8.8
0.549
Body mass index (kg/m2)
23.2 ± 3.2
22.9 ± 3.4
23.3 ± 3.1
0.471
Diagnosis
Wound
135 (81.8)
44 (83)
91 (81.2)
0.783
Diabetic foot ulcer
124 (75.1)
41 (77.3)
83 (74.1)
0.652
Gangrene
11 (6.6)
3 (5.6)
8 (7.1)
1.000
Claudication
12 (7.2)
5 (9.4)
7 (6.2)
0.525
Resting pain
16 (9.6)
3 (5.6)
13 (11.6)
0.228
Blood pressure; BP (mmHg)
Systolic BP
151.7 ± 17.3
122.6 ± 13.2
165.4 ± 19.2
<0.001
Diastolic BP
76.2 ± 45.5
64.9 ± 12.4
81.5 ± 61.2
0.053
Heart rate
78.9 ± 14.7
79.1 ± 19.5
78.8 ± 12.4
0.911
Pulse pressure (mmHg)
78.6 ± 24.2
57.7 ± 0.8
83.8 ± 42.0
<0.001
Past medical and social history
Known HTN
116 (70.6)
35 (66.2)
81 (73.2)
0.399
Diabetes
152 (92.1)
49 (92.4)
103 (91.9)
1.000
Dyslipidemia
8 (4.8)
3 (5.6)
5 (4.4)
0.713
Cerebrovascular disease
32 (19.3)
9 (16.9)
23 (20.5)
0.676
Chronic kidney disease
55 (33.3)
20 (37.7)
35 (31.2)
0.480
Dialysis
41 (24.8)
15 (28.3)
26 (23.2)
0.563
Atrial fibrillation
15 (9.0)
5 (9.4)
10 (8.9)
1.000
Coronary artery disease
102 (61.8)
29 (54.7)
73 (65.1)
0.231
Myocardial infarction
10 (6.0)
3 (5.6)
7 (6.2)
1.000
PTCA
24 (14.5)
6 (11.3)
18 (16.0)
0.486
CABG
10 (6.0)
1 (1.8)
9 (8.0)
0.170
Smoking
66 (40.0)
21 (39.6)
45 (40.1)
1.000
Current smokers
35 (21.2)
13 (24.5)
22 (19.6)
0.542
Alcoholic
49 (29.6)
17 (32.0)
32 (28.5)
0.716
Current alcoholics
29 (17.5)
11 (20.7)
18 (16.0)
0.513
Laboratory findings
Fasting glucose (mg/dL)
144.2 ± 67.2
150.2 ± 71.9
141.2 ± 65.0
0.520
Hemoglobin A1c (%)
7.4 ± 1.4
7.3 ± 1.3
7.5 ± 1.4
0.318
Total cholesterol (mg/dL)
147.6 ± 44.7
146.6 ± 48.5
148.1 ± 42.9
0.842
Triglycerides (mg/dL)
129.6 ± 100.5
132.0 ± 53.0
128.4 ± 124.1
0.840
HDL cholesterol (mg/dL)
36.3 ± 11.5
35.9 ± 12.3
36.6 ± 11.2
0.725
LDL cholesterol (mg/dL)
90.0 ± 37.3
89.0 ± 38.2
90.5 ± 36.9
0.819
hsCRP (mg/L)
20.3 ± 38.6
25.3 ± 37.5
18.0 ± 39.1
0.439
Albumin (g/dL)
3.8 ± 1.6
4.1 ± 4.0
3.6 ± 0.5
0.400 Table 1 Baseline characteristics according to blood pressure control Im et al. Values are mean ± SD (range). HTN indicates hypertension group, Pts patients, CAG coronary angiography, 1VD 1 vessel disease, 2VD 2
disease, CTO chronic total occlusion, PCI percutaneous coronary intervention ge). HTN indicates hypertension group, Pts patients, CAG coronary angiography, 1VD 1 vessel disease, 2VD 2 vessel disease, 3VD 3 vess
occlusion, PCI percutaneous coronary intervention Discussion In this study, the peripheral angiographic characteris-
tics at baseline showed that the incidences of severe cal-
cification, CTO and proximal lesions were higher in the Table 2 Coronary angiographic and clinical parameters according to blood pressure control
Coronary artery disease
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value
Stents implantation
57 (34.5)
20 (37.7)
37 (33.0)
0.601
Routine CAG
138 (83.6)
31 (77.5)
107 (85.6)
0.226
Lesion site
Left main
13 (9.4)
3 (6.8)
10 (10.6)
0.550
Left artery descending artery
59 (42.7)
19 (43.1)
40 (42.5)
1.000
Left circumflex artery
49 (35.5)
16 (36.3)
33 (35.1)
1.000
Right coronary artery
49 (35.5)
14 (31.8)
35 (37.2)
0.572
Multi-vessel disease
56 (33.9)
19 (35.8)
37 (33.0)
0.728
1VD
41 (24.8)
9 (16.9)
32 (28.5)
2VD
34 (20.6)
13 (24.5)
21 (18.7)
3VD
22 (13.3)
6 (11.3)
16 (14.2)
CTO lesion
23 (13.9)
6 (11.3)
17 (15.1)
0.633
Onsite elective PCI
43 (26.0)
16 (30.1)
27 (24.1)
0.450
Values are mean ± SD (range). HTN indicates hypertension group, Pts patients, CAG coronary angiography, 1VD 1 vessel disease, 2VD 2 vessel disease, 3VD 3 vessel
disease, CTO chronic total occlusion, PCI percutaneous coronary intervention Im et al. Clinical Hypertension (2016) 22:9 Page 7 of 12 Table 3 Medications according to blood pressure control on admission and 30 days after BTK intervention
Variable. Discussion n%
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value
In-hospital medications
Aspirin
165 (100.0)
53 (100.0)
112 (100.0)
1.000
Clopidogrel
152 (92.1)
48 (90.5)
104 (92.8)
0.758
Cilostazol
81 (49)
28 (52.8)
53 (47.3)
0.617
Warfarin
12 (7.2)
3 (5.6)
9 (8.0)
0.753
Sarpogrelate
61 (36.9)
21 (39.6)
40 (35.7)
0.730
Diuretics
41 (24.8)
11 (20.7)
30 (26.7)
0.446
ß-blockers
58 (35.1)
21 (39.6)
37 (33)
0.485
Ca-blockers
84 (50.9)
29 (54.7)
55 (49.1)
0.510
ACE-inhibitors
36 (21.8)
10 (18.8)
26 (23.2)
0.687
ARBs
73 (44.2)
25 (47.1)
48 (42.8)
0.618
Statins
114 (69)
39 (73.5)
75 (66.9)
0.472
30 days medications
Aspirin
155 (93.9)
52 (98.1)
103 (91.9)
0.170
Clopidogrel
140 (84.8)
48 (90.5)
92 (82.1)
0.244
Cilostazol
54 (32.7)
20 (37.7)
34 (30.3)
0.377
Warfarin
10 (6.0)
3 (5.6)
7 (6.2)
1.000
Sarpogrelate
60 (36.3)
21 (39.6)
39 (34.8)
0.605
Values are mean ± SD (range). BTK indicates Below-the-knee, HTN hypertension, Pts patients, ACE angiotensin converting enzyme, ARB angiotensin II
receptor blocker uncontrolled HTN group, which is consistent with the
previous reports that severe HTN was more strongly as-
sociated with proximal disease [21], and the most im-
portant
factor
influencing
the
progression
of
atherosclerosis [22]. the knee lesions, more proximal lesion sites, total occlu-
sion type of lesions in both groups and most of the pa-
tients (>90 %) had diffuse long lesions (≥2 cm), which are
consistent with the characteristics of unrecognized lower
extremity peripheral artery disease in hypertensive adults
[14]. And in this study, all patients with HTN (n = 165)
had higher incidence of MALE compared to those without
HTN (n = 15) at 12 month follow-up (37.6 % vs. 6.7 %, P
= 0.021). In this regard, we can postulate that HTN itself
is an independent risk factor for BTK lesions in patients
with CLI, regardless of BP control. However, in this study, there was no difference in the
incidence of mortality, TLR, TER, limb salvage rate in
both groups at 12 months. Rather, amputation rate was
higher in patients with controlled HTN compared to
those with uncontrolled HTN (P = 0.045). Discussion Conversely,
the patients with uncontrolled HTN had a trend of
higher limb salvage rate than those with controlled HTN
(P = 0.059). Therefore, it is difficult to interpret this re-
sult. Our speculation and interpretations includes 1) dif-
ferences in amputation rates might be ‘by chance’ due to
relatively small number of study population, 2) signifi-
cant proportion of the controlled HTN pts might be as-
sociated with longer history of hypertension, causing
higher chance of advanced atherosclerosis and subse-
quent end organ damage, 3) despite of successful BTK
intervention, uncontrolled HTN group might have more
advanced wound condition that cannot be adjusted at
the time of presentation due to longer history of athero-
sclerotic vascular disease. g
Increased pulse pressure (PP) is known to be associ-
ated with arterial stiffness, leading to increased arterial
pulse wave velocity. This causes a faster reflection of sys-
tolic pulse waves from the peripheral artery and causes a
boost to late systolic BP, a greater fall in pressure in dia-
stole and an increased PP [23]. In hypertensive patients,
arterial compliance was reduced already with borderline
PAD and increasing arterial stiffness plays a major
pathophysiological role in the development of both in-
creased PP and atherosclerotic lesions in the peripheral
arteries [24]. In this study, the patients with uncon-
trolled HTN had increased PP compared to those with
controlled
HTN
(mean
PP;
83.8 ± 42.0
vs. 57.7 ±
0.8 mmHg, P < 0.001) as expected. However, there was
no significant correlation between PP and 12-month
clinical
outcomes
after
BTK
interventions
in Among those with CLI enrolled in this study, there were
common peripheral angiographic features regardless of BP
control in both groups. More than half patients had above Im et al. Clinical Hypertension (2016) 22:9 Page 8 of 12 Table 4 Peripheral angiographic and clinical parameters of target lesions according to blood pressure control
Variable. Study limitation This study has several obvious limitations. First, we used
retrospective analysis, although this study was performed
as a prospective study. However, this study results is still
meaningful due to the nature of study. We cannot per-
form randomized clinical trial with this exact title in
terms of ethical issues. Second, Uncontrolled HTN was defined as a blood
pressure of > 140 mmHg systolic and 90 mmHg diastolic
under anti-hypertensive treatment including patients
who lack blood pressure control secondary to poor ad-
herence and/or an inadequate treatment regimen, as well
as those with true treatment resistance, which can be
limitations due to the difference of pathophysiology be-
tween inadequate treatment and true treatment resist-
ance. However, in this study, we showed that regardless
of blood pressure control, HTN itself was an independ-
ent risk factor for MALE in CLI patients with BTK le-
sions. Third, there
are
small
numbers of
patients
without HTN, which could be too small to compare with
those with HTN. However, this study is retrospective ob-
servational study for the patients who underwent the
peripheral angioplasties. Therefore, we could not enroll hypertensive patients with CLI according to BP control
(P = 0.497). hypertensive patients with CLI according to BP control
(P = 0.497). hypertensive patients with CLI according to BP control
(P = 0.497). the patients without hypertension as a control group. Further a prospective study should be considered to get
final conclusion. Fourth, similar to many other trials in interventional
cardiology, this was not a blinded study. In addition, pa-
tients were enrolled only in a single, high volume center
that might have unique patient referral pattern and
interventional technique. Fifth, even though we mini-
mized the confounding effects from the baseline biases
with multivariate logistic analysis, it is possible that
some potential confounders might have crept in. Sixth,
this study had no financial support, and no external
angiography was available for adjudication of the end
points. However, the size of the observed effect of un-
controlled HTN in the BTK lesions leaves few chances
for these results to be controverted in a multicenter, ran-
domized study. Finally, clinical results achieved by an in-
tegrated multidisciplinary approach to CLI in well-
organized specialized center may not be reproduced in
patients with uncontrolled HTN in other centers with
different organization. Discussion n%
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value
Ankle-brachial index
0.65 ± 0.4
0.72 ± 0.48
0.62 ± 0.4
0.159
Rutherford classifications (Limb)
5.01 ± 1.48
5.12 ± 1.41
4.95 ± 1.52
0.453
Limb site
Right
108 (65.4)
35 (66.0)
73 (65.1)
1.000
Left
93 (56.3)
31 (58.4)
62 (55.3)
0.739
Both
36 (21.8)
13 (24.5)
23 (20.5)
0.552
Lesion locations
Above the knee - Pts
82 (49.6)
25 (47.1)
57 (50.8)
0.739
Above the knee - Limb
88 (43.7)
26 (39.3)
62 (45.9)
0.450
lliac - Pts
10 (6.0)
4 (7.5)
6 (5.3)
0.728
lliac - Limb
10 (4.9)
4 (6.0)
6 (4.4)
0.732
Femoral - Pts
77 (46.6)
24 (45.2)
53 (47.3)
0.868
Femoral - Limb
83 (41.2)
25 (37.8)
58 (42.9)
0.543
Popliteal - Pts
20 (12.1)
5 (9.4)
15 (13.3)
0.612
Popliteal - Limb
21 (10.4)
6 (9.0)
15 (11.1)
0.808
Below the knee - Pts
Below the knee - Limb
Tibial - Pts
156 (94.5)
49 (92.4)
107 (95.5)
0.470
Tibial - Limb
183 (91.0)
57 (86.3)
126 (93.3)
0.119
ATA - Pts
119 (72.1)
37 (69.8)
82 (73.2)
0.711
ATA - Limb
140 (69.6)
43 (65.1)
97 (71.8)
0.333
PTA - Pts
74 (44.8)
25 (47.1)
49 (43.7)
0.739
PTA - Limb
76 (37.8)
26 (39.3)
50 (37.0)
0.759
Peroneal - Pts
44 (26.6)
16 (30.1)
28 (25.0)
0.572
Peroneal - Limb
47 (23.3)
17 (25.7)
30 (22.2)
0.598
Lesion site
Proximal
151 (61.3)
45 (50.0)
106 (67.9)
0.007
Mid
30 (12.1)
15 (16.6)
15 (9.6)
0.110
Distal
24 (9.7)
12 (13.3)
12 (7.6)
0.182
Ostium
42 (17)
19 (21.1)
23 (14.7)
0.221
Lesion type
Concentric
38 (15.4)
16 (17.7)
22 (14.1)
0.467
Eccentric
61 (24.7)
20 (22.2)
41 (26.2)
0.541
Total occlusion
147 (59.7)
54 (60.0)
93 (59.6)
1.000
Lesion characteristics
CTO
119 (48.3)
35 (38.8)
84 (53.8)
0.025
Diffuse (≥2 cm)
231 (93.9)
83 (92.2)
148 (94.8)
0.418
Calcification
119 (48.3)
36 (40.0)
83 (53.2)
0.048
Procedure
SubIntimal approach
57 (23.1)
23 (25.5)
34 (21.7)
0.532
POBA
228 (92.6)
84 (93.3)
144 (92.3)
1.000
Stent type
18 (7.3)
6 (6.6)
12 (7.6)
1.000
S
l
(
)
(
)
(
) Im et al. Values are mean ± SD (range). HTN indicates hypertension group, Pts patients, AV arterio-venous, G.I. gastrointestinal Discussion Clinical Hypertension (2016) 22:9 Page 9 of 12 Table 4 Peripheral angiographic and clinical parameters of target lesions according to blood pressure control (Continued)
Xpert
14 (5.6)
3 (3.3)
11 (7.0)
Chromis deep
2 (0.8)
2 (2.2)
0 (0.0)
Maris deep
1 (0.4)
0 (0.0)
1 (0.6)
Technical Success
230 (93.4)
82 (91.1)
148 (94.8)
0.287
Clinical Success
232 (94.3)
85 (94.4)
147 (94.2)
1.000
Values are mean ± SD (range). HTN indicates hypertension group, Pts patients, ATA anterior tibial artery, PTA posterior tibial artery, CTO chronic total occlusion,
POBA plain old balloon angioplasty al angiographic and clinical parameters of target lesions according to blood pressure control (Continued) Conclusions Even though the patients with uncontrolled HTN had
more proximal target lesions, higher incidences of CTO
and severe calcifications, there was no difference in the Table 5 Periprocedural complications according to blood pressure control
Type of complications
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value
AV fistula
1 (0.6)
1 (1.8)
0 (0.0)
0.321
Pseudo-aneurysm
2 (1.2)
1 (1.8)
1 (0.8)
0.541
Access site hematoma
minor (<4 cm)
4 (2.4)
1 (1.8)
3 (2.6)
1.000
Major (≥4 cm)
14 (8.4)
4 (7.5)
10 (8.9)
1.000
G.I. bleeding
4 (2.4)
0 (0.0)
4 (3.5)
0.307
Transfusion
91 (55.1)
31 (58.4)
60 (53.5)
0.617
Transfusion (Unit)
5.81 ± 10.4
6.9 ± 11.2
5.2 ± 10.0
0.325
Acute renal failure
4 (2.4)
1 (1.8)
3 (2.6)
1.000
Congestive heart failure
3 (1.8)
1 (1.8)
2 (1.7)
1.000
Arrhythmia
4 (2.4)
2 (3.7)
2 (1.7)
0.594
Values are mean ± SD (range). HTN indicates hypertension group, Pts patients, AV arterio-venous, G.I. gastrointestinal Im et al. Clinical Hypertension (2016) 22:9 Page 10 of 12 Table 6 Clinical outcomes following BTK interventions in patients with CLI according to blood pressure control at 12 months
Variable. Conclusions n%
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value
12-months clinical outcomes
Mortality
9 (5.4)
2 (3.7)
7 (6.2)
0.720
Cardiac death
5 (3.0)
1 (1.8)
4 (3.5)
1.000
TLR, Pts
18 (10.9)
6 (11.3)
12 (10.7)
0.907
TLR, Limb
21 (10.4)
6 (9)
15 (11.1)
0.808
TER, Pts
20 (12.1)
7 (13.2)
13 (11.6)
0.769
TER, Limb
25 (12.4)
7 (10.6)
18 (13.3)
0.655
Non TER
7 (4.2)
3 (5.7)
4 (3.6)
0.534
Amputations - Pts
40 (24.2)
18 (33.9)
22 (19.6)
0.045
Amputations - Limb
41 (20.3)
19 (28.7)
22 (16.2)
0.061
Major
above the knee
0 (0.0)
0 (0.0)
0 (0.0)
1.000
above the ankle - Pts
10 (6.0)
7 (13.2)
3 (2.6)
0.013
above the ankle - Limb
10 (4.9)
7 (10.6)
3 (2.2)
0.016
minor (below the ankle) - Pts
30 (18.1)
11 (20.7)
19 (16.9)
0.556
minor (below the ankle) - Limb
31 (15.4)
12 (18.1)
19 (14)
0.533
Myocardial infarction
2 (1.2)
1 (1.8)
1 (0.8)
0.541
PTCA
7 (4.2)
3 (5.6)
4 (3.5)
0.682
Cerebrovascular accidents
1 (0.6)
0 (0.0)
1 (0.8)
1.000
Limb salvage
147/156 (94.2)
45/51 (88.2)
102/105 (97.1)
0.059
Angiogram to follow-up
55 (33.3)
18 (33.9)
37 (33)
0.906
CT
21 (38.1)
8 (44.4)
13 (35.1)
0.505
PAG
42 (76.3)
13 (72.2)
29 (78.3)
0.738
Binary restenosis
35 (63.6)
11 (61.1)
24 (64.8)
0.786
Total re-occlusion
29 (52.7)
8 (44.4)
21 (56.7)
0.391
Primary patency
20 (36.3)
7 (38.8)
13 (35.1)
0.786
Secondary patency
39 (70.9)
11 (61.1)
28 (75.6)
0.264
Non-Total occlusion; Runoff (≥1) included
Collateral, to distal
53 (96.3)
17 (94.4)
36 (97.2)
1.000
Values are mean ± SD (range). BTK indicates Below-the-knee artery, CLI critical limb ischemia, HTN hypertension, Pts patients, TLR target lesion revascularization,
TER target extremity revascularization, PTCA percutaneous transluminal coronary angioplasty, CT computed tomography, PAG follow-up invasive
peripheral angiography Table 6 Clinical outcomes following BTK interventions in patients with CLI according to blood pressure control at 12 months
Variable. References 1. Yusuf S, Reddy S, Ounpuu S, Anand S. Global burden of cardiovascular
diseases: Part II: variations in cardiovascular disease by specific ethnic
groups and geographic regions and prevention strategies. Circulation. 2001;104:2855–64. 1. Yusuf S, Reddy S, Ounpuu S, Anand S. Global burden of cardiovascular
diseases: Part II: variations in cardiovascular disease by specific ethnic
groups and geographic regions and prevention strategies. Circulation. 2001;104:2855–64. 2. Kennedy M, Solomon C, Manolio TA, Criqui MH, Newman AB, Polak JF, et al. Risk factors for declining ankle-brachial index in men and women 65 years or
older: the Cardiovascular Health Study. Arch Intern Med. 2005;165:1896–902. 3. Lee AJ, Price JF, Russell MJ, Smith FB, van Wijk MC, Fowkes FG. Improved
prediction of fatal myocardial infarction using the ankle brachial index in
addition to conventional risk factors: the Edinburgh Artery Study. Circulation. 2004;110:3075–80. 4. Yang X, Sun K, Zhang W, Wu H, Zhang H, Hui R. Prevalence of and risk
factors for peripheral arterial disease in the patients with hypertension
among Han Chinese. J Vasc Surg. 2007;46:296–302. 5. Farkas K, Jarai Z, Kolossvary E, Ludanyi A, Clement DL, Kiss I, et al. High
prevalence of peripheral arterial disease in hypertensive patients: the
Evaluation of Ankle-Brachial Index in Hungarian Hypertensives screening
program. J Hypertens. 2012;30:1526–32. 6. Newman AB. Peripheral arterial disease: insights from population studies of
older adults. J Am Geriatr Soc. 2000;48:1157–62. 7. Wang TJ, Vasan RS. Epidemiology of uncontrolled hypertension in the
United States. Circulation. 2005;112:1651–62. Fig. 2 Kaplan-Meier analysis for survival free from MALE in both
study groups 8. Hajjar I, Kotchen TA. Trends in prevalence, awareness, treatment, and control of
hypertension in the United States, 1988–2000. JAMA. 2003;290:199–206. 9. Taddei S, Virdis A, Mattei P, Ghiadoni L, Fasolo CB, Sudano I, et al. Hypertension causes premature aging of endothelial function in humans. Hypertension. 1997;29:736–43. 9. Taddei S, Virdis A, Mattei P, Ghiadoni L, Fasolo CB, Sudano I, et al. Hypertension causes premature aging of endothelial function in humans. Hypertension. 1997;29:736–43. incidence of major adverse events following BTK inter-
ventions in both groups at 12 months. Rather, the ampu-
tation rates were higher in patients with controlled HTN
compared to those of uncontrolled HTN and there were
common peripheral angiographic features regardless of
BP control in both groups. Conclusions n%
Total (n = 165 Pts) (n = 201 Limb)
(n = 246 Lesion)
Controlled HTN (n = 53 Pts)
(n = 66 Limb) (n = 90 Lesion)
Uncontrolled HTN (n = 112 Pts)
(n = 135 Limb) (n = 156 Lesion)
P Value Values are mean ± SD (range). BTK indicates Below-the-knee artery, CLI critical limb ischemia, HTN hypertension, Pts patients, TLR target lesion revascularization,
TER target extremity revascularization, PTCA percutaneous transluminal coronary angioplasty, CT computed tomography, PAG follow-up invasive
peripheral angiography Table 7 Univariate and multivariate Cox analyses for MALE in patients with CLI after peripheral angioplasty at 12-month follow-up
Univariate analysis
Multivariate analysis
Variable. N (%)
OR (95 % CI)
P-Value
OR (95 % C.I)
P-Value
Hypertension (itself)
2.093 (1.106 – 4.098)
0.017
3.867 (1.625 – 9.199)
0.002
DM foot
1.903 (0.935 – 3.876)
0.076
RWMA
2.342 (1.190 – 4.608)
0.014
Mitral valve calcification
3.029 (1.297 – 7.073)
0.010
2.915 (1.048 – 8.107)
0.040
CHF
2.342 (1.190 – 4.608)
0.014
CKD
1.966 (1.049 – 3.685)
0.035
Dialysis
3.000 (1.496 – 6.014)
0.002
5.221 (1.184 – 23.02)
0.029
OR odds ratio, CI confidence interval, DM diabetes mellitus, RWMA reginonal wall motion abnormality, CHF congestive heart failure-systolic, CKD chronic
kidney disease Table 7 Univariate and multivariate Cox analyses for MALE in patients with CLI after peripheral angioplasty a
Univariate analysis
Multivariate analys Page 11 of 12 Page 11 of 12 Page 11 of 12 Im et al. Clinical Hypertension (2016) 22:9 Fig. 2 Kaplan-Meier analysis for survival free from MALE in both
study groups Received: 30 October 2015 Accepted: 21 January 2016 Acknowledgements 21. Chen Q, Smith CY, Bailey KR, Wennberg PW, Kullo IJ. Disease location is
associated with survival in patients with peripheral arterial disease. J Am
Heart Assoc. 2013;2, e000304. This study was supported by the funding of Korean Society of Hypertension
(2012). 22. Nosenko NS, Nosenko EM, Dadova LV, Sidorenko BA. The risk factors and
predictors of the clinically significant progression of atherosclerosis in
patients with chronic lower extremity ischemia. Ter Arkh. 2010;82:56–60. 22. Nosenko NS, Nosenko EM, Dadova LV, Sidorenko BA. The risk factors and
predictors of the clinically significant progression of atherosclerosis in
patients with chronic lower extremity ischemia. Ter Arkh. 2010;82:56–60. Competing interests
The authors declare that they have no competing interests. Competing interests
The authors declare that they have no competing interests. 17. Ryu HM, Kim JS, Ko YG, Hong MK, Jang Y, Choi D. Clinical outcomes of
infrapopliteal angioplasty in patients with critical limb ischemia. Korean
circulation journal. 2012;42:259–65. 17. Ryu HM, Kim JS, Ko YG, Hong MK, Jang Y, Choi D. Clinical outcomes of
infrapopliteal angioplasty in patients with critical limb ischemia. Korean
circulation journal. 2012;42:259–65. p
g
The authors declare that they have no competing interests. 18. Hooi JD, Kester AD, Stoffers HE, Overdijk MM, van Ree JW, Knottnerus JA. Incidence of and risk factors for asymptomatic peripheral arterial occlusive
disease: a longitudinal study. Am J Epidemiol. 2001;153:666–72. 18. Hooi JD, Kester AD, Stoffers HE, Overdijk MM, van Ree JW, Knottnerus JA. Incidence of and risk factors for asymptomatic peripheral arterial occlusive
disease: a longitudinal study. Am J Epidemiol. 2001;153:666–72. References Regardless of blood pressure
control, HTN itself was an independent risk factor for
MALE in CLI patients with BTK lesions, suggesting
more intensive medical therapy with close clinical follow
up will be required in real world clinical practice. 10. Taddei S, Virdis A, Ghiadoni L, Magagna A, Pasini AF, Garbin U, et al. Effect
of calcium antagonist or beta blockade treatment on nitric oxide-
dependent vasodilation and oxidative stress in essential hypertensive
patients. J Hypertens. 2001;19:1379–86. 10. Taddei S, Virdis A, Ghiadoni L, Magagna A, Pasini AF, Garbin U, et al. Effect
of calcium antagonist or beta blockade treatment on nitric oxide-
dependent vasodilation and oxidative stress in essential hypertensive
patients. J Hypertens. 2001;19:1379–86. 11. Ferguson DW. Regular aerobic exercise augments endothelium-dependent
vascular relaxation in normotensive and hypertensive subjects: role of
endothelium-derived nitric oxide. Circulation. 2000;102:E119–20. 11. Ferguson DW. Regular aerobic exercise augments endothelium-dependent
vascular relaxation in normotensive and hypertensive subjects: role of
endothelium-derived nitric oxide. Circulation. 2000;102:E119–20. 12. Cuddy ML. Treatment of hypertension: guidelines from JNC 7 (the seventh
report of the Joint National Committee on Prevention, Detection, Evaluation,
and Treatment of High Blood Pressure 1). J Pract Nurs. 2005;55:17–21. quiz 2–3. 12. Cuddy ML. Treatment of hypertension: guidelines from JNC 7 (the seventh
report of the Joint National Committee on Prevention, Detection, Evaluation,
and Treatment of High Blood Pressure 1). J Pract Nurs. 2005;55:17–21. quiz 2–3 13. Psaty BM, Lumley T, Furberg CD, Schellenbaum G, Pahor M, Alderman MH,
et al. Health outcomes associated with various antihypertensive therapies
used as first-line agents: a network meta-analysis. JAMA. 2003;289:2534–44. 13. Psaty BM, Lumley T, Furberg CD, Schellenbaum G, Pahor M, Alderman MH,
et al. Health outcomes associated with various antihypertensive therapies
used as first-line agents: a network meta-analysis. JAMA. 2003;289:2534–44. Authors’ contributions SI Im and SW Rha were involved with research concept, data collection, data
analysis, interpretation of results and writing of manuscript. BG Choi, SY Choi,
SK Lee, JB Kim contributed to the research concept, interpretation of results
and review of manuscript. JO Na, CU Choi, HE Lim, CG Park, HS Seo and DJ
Oh were involved with the research concept, data analysis and drafting of
manuscript. All authors reviewed and approved the final manuscript. 19. Resnick HE, Lindsay RS, McDermott MM, Devereux RB, Jones KL, Fabsitz RR, et al. Relationship of high and low ankle brachial index to all-cause and cardiovascular
disease mortality: the Strong Heart Study. Circulation. 2004;109:733–9. 20. Tapp RJ, Balkau B, Shaw JE, Valensi P, Cailleau M, Eschwege E, et al. Association
of glucose metabolism, smoking and cardiovascular risk factors with incident
peripheral arterial disease: the DESIR study. Atherosclerosis. 2007;190:84–9. 21. Chen Q, Smith CY, Bailey KR, Wennberg PW, Kullo IJ. Disease location is
associated with survival in patients with peripheral arterial disease. J Am
Heart Assoc. 2013;2, e000304. Consent 14. He M, Qin X, Cui Y, Cai Y, Sun L, Xu X, et al. Prevalence of unrecognized
lower extremity peripheral arterial disease and the associated factors in
chinese hypertensive adults. Am J Cardiol. 2012;110:1692–8. 14. He M, Qin X, Cui Y, Cai Y, Sun L, Xu X, et al. Prevalence of unrecognized
lower extremity peripheral arterial disease and the associated factors in
chinese hypertensive adults. Am J Cardiol. 2012;110:1692–8. Written informed consent was obtained from the patient
for the publication of this report and any accompanying
images. yp
15. Zayed M, Bech F, Hernandez-Boussard T. National review of factors influencing
disparities and types of major lower extremity amputations. Ann Vasc Surg. 2013. 15. Zayed M, Bech F, Hernandez-Boussard T. National review of factors influencing
disparities and types of major lower extremity amputations. Ann Vasc Surg. 2013. 16. Pua U, Wong DE. Angioplasty in critical limb ischaemia: one-year limb
salvage results. Ann Acad Med Singapore. 2008;37:224–9. 16. Pua U, Wong DE. Angioplasty in critical limb ischaemia: one-year limb
salvage results. Ann Acad Med Singapore. 2008;37:224–9. oscillometric blood pressure monitor and a sphygmomanometer.
Hypertension. 2000;36:484–8.
24.
Korhonen PE, Syvanen KT, Vesalainen RK, Kantola IM, Kautiainen H,
Jarvenpaa S, et al. Ankle-brachial index is lower in hypertensive than in
normotensive individuals in a cardiovascular risk population. J Hypertens.
2009;27:2036–43. Im et al. Clinical Hypertension (2016) 22:9 Author details
1Di i i
f C d 1Division of Cardiology, Department of Internal Medicine, Kosin University
Gospel Hospital, Busan, South Korea. 2Cardiovascular Center, Korea University
Guro Hospital, 80, Guro-dong, Guro-gu, Seoul 152-703, South Korea. 23. van Popele NM, Bos WJ, de Beer NA, van Der Kuip DA, Hofman A, Grobbee DE,
et al. Arterial stiffness as underlying mechanism of disagreement between an 23. van Popele NM, Bos WJ, de Beer NA, van Der Kuip DA, Hofman A, Grobbee DE,
et al. Arterial stiffness as underlying mechanism of disagreement between an Page 12 of 12 Im et al. Clinical Hypertension (2016) 22:9 • We accept pre-submission inquiries
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0200781&type=printable
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English
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Global land use implications of dietary trends
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Editor: Andre´s Viña, Michigan State University,
UNITED STATES Received: March 7, 2018
Accepted: July 3, 2018
Published: August 8, 2018 Copyright: © 2018 Rizvi et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited. RESEARCH ARTICLE
Global land use implications of dietary trends
Sarah Rizvi1, Chris Pagnutti1, Evan Fraser2, Chris T. Bauch3, Madhur Anand1*
1 School of Environmental Science, University of Guelph, Guelph, Ontario, Canada, 2 Department of
Geography, University of Guelph, Guelph, Ontario, Canada, 3 Department of Applied Mathematics,
University of Waterloo, Waterloo, Ontario, Canada a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 Sarah Rizvi1, Chris Pagnutti1, Evan Fraser2, Chris T. Bauch3, Madhur Anand1* 1 School of Environmental Science, University of Guelph, Guelph, Ontario, Canada, 2 Department of
Geography, University of Guelph, Guelph, Ontario, Canada, 3 Department of Applied Mathematics,
University of Waterloo, Waterloo, Ontario, Canada a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 * manand@uoguelph.ca * manand@uoguelph.ca Introduction Increasing pressures on land and other natural resources such as water is largely attributed to
the increase in demand for agricultural products [1]. The agricultural sector is extremely
resource-intensive and continues to transform itself as populations grow. Global food produc-
tion is the largest user of fresh water and uses approximately 38% of the land on Earth [1,2]. An
estimated 62% of the remaining global land surface is either unsuitable for cultivation on
account of soil, climate topography, or urban development (30%) or is covered in natural land
states like forests (32%), so very little land is available for agricultural expansion that does not
destroy native land states. Hence, more efficient agricultural production is urgently needed [3]. However, approximately 12% of the world remains undernourished [2]. According to esti-
mates from the Food and Agriculture Organization of the United Nations (FAO), the world
will need to produce 70% more food by 2050 to meet increased demand [3]. The global food
system is at a point of change where a thorough understanding of the relationship between
food consumption patterns, agricultural production and distribution is required to improve Increasing pressures on land and other natural resources such as water is largely attributed to
the increase in demand for agricultural products [1]. The agricultural sector is extremely
resource-intensive and continues to transform itself as populations grow. Global food produc-
tion is the largest user of fresh water and uses approximately 38% of the land on Earth [1,2]. An
estimated 62% of the remaining global land surface is either unsuitable for cultivation on
account of soil, climate topography, or urban development (30%) or is covered in natural land
states like forests (32%), so very little land is available for agricultural expansion that does not
destroy native land states. Hence, more efficient agricultural production is urgently needed [3]. Data Availability Statement: All of the data we
used for the analysis are publicly available on the
USDA website (https://health.gov/
dietaryguidelines/dga2010/dietaryguidelines2010. pdf) and the UN FAO website (http://www.fao.org/
faostat/en). Funding: The research was supported by a Natural
Sciences and Engineering Research Council
(NSERC) of Canada Discovery Grant to Madhur
Anand. The funders had no role in study design,
data collection and analysis, decision to publish, or
preparation of the manuscript. However, approximately 12% of the world remains undernourished [2]. OPEN ACCESS
Citation: Rizvi S, Pagnutti C, Fraser E, Bauch CT,
Anand M (2018) Global land use implications of
dietary trends. PLoS ONE 13(8): e0200781. https://
doi.org/10.1371/journal.pone.0200781 OPEN ACCESS
Citation: Rizvi S, Pagnutti C, Fraser E, Bauch CT,
Anand M (2018) Global land use implications of
dietary trends. PLoS ONE 13(8): e0200781. https://
doi.org/10.1371/journal.pone.0200781 Editor: Andre´s Viña, Michigan State University,
UNITED STATES Abstract a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 Global food security and agricultural land management represent two urgent and intimately
related challenges that humans must face. We quantify the changes in the global agricultural
land footprint if the world were to adhere to the dietary guidelines put forth by the United States
Department of Agriculture (USDA), while accounting for the land use change incurred by
import/export required to meet those guidelines. We analyze data at country, continental, and
global levels. USDA guidelines are viewed as an improvement on the current land-intensive
diet of the average American, but despite this our results show that global adherence to the
guidelines would require 1 gigahectare of additional land—roughly the size of Canada–under
current agricultural practice. The results also show a strong divide between Eastern and
Western hemispheres, with many Western hemisphere countries showing net land sparing
under a USDA guideline diet, while many Eastern hemisphere countries show net land use
increase under a USDA guideline diet. We conclude that national dietary guidelines should be
developed using not just health but also global land use and equity as criteria. Because global
lands are a limited resource, national dietary guidelines also need to be coordinated interna-
tionally, in much the same way greenhouse gas emissions are increasingly coordinated. RESEARCH ARTICLE
Global land use implications of dietary trends RESEARCH ARTICLE Global land use implications of dietary trends the overall sustainability of the system [4]. It has become important now more than ever to
make global agricultural production both sustainable and equitable. Competing interests: The authors have declared
that no competing interests exist. Competing interests: The authors have declared
that no competing interests exist. The global distribution of diet may play a major role in achieving this goal. Food consump-
tion patterns vary widely between countries. Average caloric intake in least developed, devel-
oping, and industrialised countries varies widely; 2,120, 2,640, and 3,430 kcal per person per
day, respectively [5,6]. In many developing countries the average intake is even lower than
2,120 kcal per person per day, resulting in undernourishment [3]. National dietary guidelines provide guidance on what constitutes a healthy diet, especially
in industrialised countries where individuals have access to a wide choice of foods. The United
States Department of Agriculture (USDA) released The Dietary Guidelines for Americans, 2010
(“USDA guidelines” hereafter) to promote a healthy diet low in calories and saturated fats. The
dietary guidelines are divided by food groups and daily caloric intake levels depending on age,
sex, and physiological status (Table 1) [7]. Comparing the recommended food group servings
to current agricultural outputs and dietary practice reported in food balance sheets from the
FAO—both in the United States and many other industrialised countries—shows a mismatch
between current and guideline diets. For instance, in North America, the consumption of
land-intensive foods like meat is higher than the USDA guidelines recommend, and consump-
tion of land-sparing foods like vegetables is too low [8,9]. It is well known that there is not enough land for land-intensive diets such as those cur-
rently practiced in the United States to be applied globally [3]. However, it is not known
whether the healthier and less land-intensive diets such as described in the USDA guidelines
would have the same limitation. This could result in net land sparing attributable to countries
such as the United States where meat consumption declines under a USDA guideline diet. At
the same time, land use attributable to the poorest countries would increase, as individuals
gain the calories required to avoid malnourishment. This would clearly make global diets
more equitable, but it is not clear what the net effect on land use would be. Therefore, in this paper we build on the global land use change literature, which explores
both the drivers and consequences of how human decisions affect landscapes [10,11], to
address the question: Is there enough land worldwide under current agricultural practice for
every country to adhere to the USDA guidelines? Introduction According to esti-
mates from the Food and Agriculture Organization of the United Nations (FAO), the world
will need to produce 70% more food by 2050 to meet increased demand [3]. The global food
system is at a point of change where a thorough understanding of the relationship between
food consumption patterns, agricultural production and distribution is required to improve PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 1 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends Table 1. Daily recommended caloric intake of each food group as outlined by the United States Department of Agriculture Food Guide. Table adapted from the
USDA Dietary Guidelines for Americans 2010 [7]. Food groups are divided into 6 categories with servings determined by caloric levels. The caloric levels are assigned based
on sex, physiological status and age. Daily Calorie Level
Food Group
1000
1200
1400
1600
1800
2000
2200
2400
2600
2800
3000
3200
(Servings)
Fruit (Cups)
1.0
1.0
1.5
1.5
1.5
2.0
2.0
2.0
2.0
2.5
2.5
2.5
Vegetables (Cups)
1.0
1.5
1.5
2.0
2.5
2.5
3.0
3.0
3.5
3.5
4.0
4.0
Grains
3.0
4.0
5.0
5.0
6.0
6.0
7.0
8.0
9.0
10.0
10.0
10.0
Whole-grain portion (oz-eq)
1.5
2.0
2.5
3.0
3.0
3.0
3.5
4.0
4.5
5.0
5.0
5.0
Meat and Beans (oz-eq)
2.0
3.0
4.0
5.0
5.0
5.5
6.0
6.5
6.5
7.0
7.0
7.0
Milk (cups)
2.0
2.0
2.0
3.0
3.0
3.0
3.0
3.0
3.0
3.0
3.0
3.0
Oils (tsp)
3.0
4.0
4.0
5.0
5.0
6.0
6.0
7.0
8.0
8.0
10.0
10.0
Discretionary calorie allowance
165
171
171
132
195
267
290
362
410
426
512
648
https://doi.org/10.1371/journal.pone.0200781.t001 Table 1. Daily recommended caloric intake of each food group as outlined by the United States Department of Agriculture Food Guide. Table adapted from the
USDA Dietary Guidelines for Americans 2010 [7]. Food groups are divided into 6 categories with servings determined by caloric levels. The caloric levels are assigned based
on sex, physiological status and age. Next we took the recommended daily serving sizes of each food group based assuming an
intake of 2000 kcal/day and converted those to masses using the food balance sheets handbook
given by the FAO [13]. For each country we multiplied each of these masses by 365 (days)
times the population of the country to get the quantity of each food group that would be
required in order for that country to adhere to the USDA guidelines in a year. A country’s sur-
plus of each food group was taken to be the actual food supply for each food group minus the
corresponding quantity that would be required to meet the USDA guidelines. A negative sur-
plus is interpreted as a deficit, meaning that the country would need more food from that
group to follow the guidelines. Methods We used the USDA guidelines because they are comprehensive and well articulated (Table 1)
[7]. Also, many lower-income countries are beginning to adopt a more westernized lifestyle
including a diet similar to that expressed in the USDA guidelines, so the study is consistent
with ongoing global dietary trends. We used the FAOSTAT database [2] to compile the food supply quantity for each of the
commodity aggregates listed in Table 1 and grouped them according to the major food groups
recognized in the USDA MyPyramid model: fruits, vegetables, grains, meat/protein, dairy, oils
and discretional [7]. For beverages, oils, sugar, butter and stimulants we converted the pro-
cessed quantities to equivalent primary quantities (e.g. wine to grapes, beer to barley, butter to
milk etc.) using conversion factors given by the FAO [12]. The food supply quantity derived
from the domestic supply and reported in the Food Balance Sheets includes production plus
imports minus exports. Thus, when calculating domestic land use, we subtracted the imported
quantity to determine domestic land used for growing food. We also used these data to com-
pute the import dependency ratio, defined as the ratio of the import quantity to the domestic
supply quantity, for each country and each commodity. This ratio is used at a later step of the
analysis (see below). 2 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global analysis On a global scale it is apparent that certain food groups are driving most changes in agriculture. We observe that if the world were to alter its food consumption to meet the USDA guidelines,
there would need to be a dramatic and unsustainable increase in agricultural lands (Fig 1). Overall, for the world to meet the guidelines, additional land is required for fruits, dairy
and oils and discretional products (Fig 1). In contrast, significant amounts of land would be
spared in the meat, vegetables and grain sectors. This trend is common to most continents
except Africa (Fig A in S1 Appendix). In total for all food groups, approximately 1 gigahectare
(Gha) of additional land is required to meet the guidelines (Fig 1, “all groups”, 2010 data
point). 1 Gha of land is roughly the size of Canada and exceeds the amount of fertile land cur-
rently available worldwide. Hence, the current USDA guidelines do not go far enough in terms
of setting up a globally sustainable dietary practice. Our analysis also shows temporal trends in land spared or required under the guidelines
(Fig 1). Required land has been steadfastly increasing since 1960 (Fig 1, “all groups”) due to
increasing global population. Global land use implications of dietary trends data and estimated the amount of land required for the guideline diet, given the observed
(lower) historical population sizes and agricultural activity until 2010. Hence, the resulting
data point for each year represents the amount of land spared or required in that year, if the
given country had been adhering to the USDA guidelines. Although we generated these esti-
mates for 1960 to 2010 to evaluate past trends, the values for 2010 are most relevant to the cur-
rent situation and generate a lower bound for possible future land requirements. Hence we
focus on the 2010 estimates for our conclusions. PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 For each country the surplus of each food group was divided into two parts: one that was
produced within that country (domestic), and one that was produced outside of that country
(displaced) according to the import dependency ratio [13]. To meet the dietary guidelines, we
allow that imports may be increased, exports may be changed to domestic production, and
domestic production may be expanded where possible. For example, suppose a country’s
domestic supply is X tonnes of some commodity and it imports Y tonnes of the same com-
modity. The import dependency ratio is then Y/X. Now suppose that the amount of that com-
modity required by that country to meet the guidelines is Z tonnes. The surplus is given by S =
X+Y-Z. We assume the surplus can be divided into two parts according to the domestic part Sd
= S(1-Y/X) and the imported (displaced) part Si = S(Y/X). For the domestic portion of the surplus, the change in agricultural land area within that
country that is required to meet the USDA guidelines was taken to be the domestic surplus Sd
divided by that country’s combined yield of all commodities in the given food group (Table A
in S1 Appendix) [2,7]. The change in agricultural land area outside of that country was com-
puted in the same way, but using the displaced surplus Si and the world average yields. Yields
for crops can be found in the FAOSTAT database. For livestock products we estimated yield in
terms of production per hectare of land. The details of the calculations and the corresponding
Python script appear in Supporting Information (Text A and B in S1 Appendix). The code we
used for the analysis is also available on Github (https://github.com/Pacopag/faolyzer). Using this approach, we converted the USDA guidelines to land area required for the guide-
line diet at the level of country, continent, and world. We wished to estimate a conservative
lower bound on the amount of land needed to meet the guidelines, if countries were to switch
to the USDA guidelines in 2010. Hence, instead of relying on model-based projections for
future demographics and possible dietary trends, we used historical FAOSTAT country-level 3 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends Fig 1. There is not enough land in the world to allow everyone to eat a USDA guideline diet. Plot shows net amount of land spared (or
required) to meet the USDA Dietary Guidelines for Americans 2010, by year for (a) all food groups, and for (b) oils, (c) grains, (d) meat and
pulses, (e) vegetables, (f) fruits, (g) dairy, and (h) discretional. Red depicts the amount of land spared or required based only on domestic
production while the blue line combines domestic land and displaced land (land use a country generates elsewhere by relying on food
imports) to depict a total amount of land spared (or required). A net positive value for land spared means less land would be required
under a change to a USDA guideline diet, while a net negative value means more land would be required to meet the guidelines (a “land
deficit”). The gap between domestic and total land spared for all groups is nonzero due to discrepancies in the FAO dataset; the two curves
should match one another. htt
//d i
/10 1371/j
l
0200781 001 s not enough land in the world to allow everyone to eat a USDA guideline diet. Plot shows net amount of land spared (or Fig 1. There is not enough land in the world to allow everyone to eat a USDA guideline diet. Plot shows net am Fig 1. There is not enough land in the world to allow everyone to eat a USDA guideline diet. Plot shows net amount of land spared (or
required) to meet the USDA Dietary Guidelines for Americans 2010, by year for (a) all food groups, and for (b) oils, (c) grains, (d) meat and
pulses, (e) vegetables, (f) fruits, (g) dairy, and (h) discretional. Red depicts the amount of land spared or required based only on domestic
production while the blue line combines domestic land and displaced land (land use a country generates elsewhere by relying on food
imports) to depict a total amount of land spared (or required). A net positive value for land spared means less land would be required
under a change to a USDA guideline diet, while a net negative value means more land would be required to meet the guidelines (a “land
deficit”). PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Analysis by continent The challenges of providing stable access to adequate food are exacerbated by inequitable die-
tary patterns of over- and under-consumption between countries and continents. Some of
these issues become apparent when we analyze data at the continental level, at which notable
common trends in consumption patterns and the associated land requirements emerge. For
instance, North America and the European Union displace more land than any other conti-
nents, due to food imports (Fig 2). If North and South America shifted to USDA guidelines,
they would spare a moderate amount of land from changing to a less land-intensive diet. In
contrast, Africa, Eastern Europe, the European Union and Oceania would cause a large land
deficit. The impact of Asia shifting to USDA guidelines would be almost neutral, although the
historical trend suggests this will not be the case in the near future. The fact that the European
Union (where malnourishment is currently uncommon) would cause a land deficit by shifting
to the USDA guidelines suggests that the guidelines are unsustainable when it comes to land-
intensive foods like meat. For most decades, Asia would have caused a net land deficit by shifting to the USDA guide-
lines, since it was (and remains) a relatively under-nourished part of the world (Fig 2B). An
inflection point appears in the Asian dataset in 1980, when countries like China and India
began liberalizing their economies. Most notable are increases in land use for meat and grains
as Asia slowly begins to adopt a more westernized diet (Fig A in S1 Appendix). This suggests
that while Asia has increased land use rapidly, equity in resource distribution at the sub-conti-
nental level is imbalanced. For instance, one third of Indians are undernourished and continue
to live under food insecurity [3]. Inequities in global trading and extension services as well as
poor infrastructure trap populations in Asia in poverty. However, future improvements 4 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 The gap between domestic and total land spared for all groups is nonzero due to discrepancies in the FAO dataset; the two curves
should match one another. https://doi.org/10.1371/journal.pone.0200781.g001 towards equal land use change may better harness agricultural yields to align the Asian diet
with those of wealthier and more sustainable areas of the world, such as the European Union. Africa would require more land to meet the guidelines than any other continent. In fact,
most of the additional land required to meet the guidelines globally would be the result of die-
tary shifts in Africa. This is not surprising because undernourishment is widespread in Africa 5 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends [14]. However, an inflection point,
mies, occurs in 1990 (Fig 2C). Almo
Fig 2. Continents differ widely in land spared (or required) u
required) to meet the Dietary Guidelines in each continent, by y
Europe, (f) South America, (g) North America and (h) Oceania
domestic production while the blue line combines domestic lan
food imports) to depict a total amount of land spared (or requir
required under a change to a USDA guideline diet, while a net n
(a “land deficit”). https://doi.org/10.1371/journal.pone.0200781.g002 USDA guideline diet. Plot shows net amount of land spared (or
r (a) the world, (b) Asia, (c) Africa, (d) European Union, (e) Easter
depicts the amount of land spared or required based only on
displaced land (land use a country generates elsewhere by relying o
net positive value for land spared means less land would be
ve value means more land would be required to meet the guideline Fig 2. Continents differ widely in land spared (or required) under USDA guideline diet. Plot shows net amount of land spared (or
required) to meet the Dietary Guidelines in each continent, by year for (a) the world, (b) Asia, (c) Africa, (d) European Union, (e) Eastern
Europe, (f) South America, (g) North America and (h) Oceania. Red depicts the amount of land spared or required based only on
domestic production while the blue line combines domestic land and displaced land (land use a country generates elsewhere by relying on
food imports) to depict a total amount of land spared (or required). PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 World map We also created a world map with our results, showing net land spared or required for each
country to shift to a USDA guideline diet as of 2010 (Fig 3) [17]. Countries in blue or teal col-
ours could reduce global land use by shifting to a USDA guideline diet (net positive land
spared), while countries in green, red or yellow would cause an increase in land use (net nega-
tive land spared). Although 1 gigahectare of extra land would be required globally for a guide-
line diet (Fig 1), the world map shows how the results are much more variable at the country
level. The countries that can spare the most land are the USA, Brazil and Australia. In contrast,
the countries that require the most land to meet the guidelines are Mozambique, Saudi Arabia,
and India. Global economic disparity is often described in terms of the gap between the Global
North and the Global South. In contrast, our country-level map shows a strong hemispheric
divide: the western hemisphere would largely spare global lands by shifting to a USDA guide-
line diet, whereas the eastern hemisphere would largely use up more global lands under such a
diet. The Western hemisphere would spare significant amounts of land under a USDA diet
largely due to current very high levels of meat consumption, via grain grown to feed livestock. Global land use implications of dietary trends than what is available), Africa also stands the most to gain with respect to growing agricultural
yields [15]. Thus, although it is not currently possible to bring the African diet in line with that
of the USA or the European Union without a net growth in agricultural lands, future improve-
ments in agricultural practices in Africa may help to close the gap. The European Union would also require a significant amount of land to meet the USDA
guidelines. Almost all of the additional land needed would be the result of increased dairy and
fruit land use, a trend common to most of Europe (Fig A in S1 Appendix). We note that dis-
placed land (from buying food imports) contributes strongly to European Union land use, and
exceeds displaced land use in North America (Fig 2D). Interestingly, the land requirements for
the European Union indicate the need for more displaced lands than domestic land. This sug-
gests that an American diet is unsustainable from a land use perspective, domestically speaking. Land use in Eastern Europe has fluctuated significantly over time (Fig 2E). After the late
1980s, a land use deficit developed in the Eastern Europe dataset, and has largely persisted in
recent years. Therefore, in order to meet the USDA guidelines, Eastern Europe would require
a large amount of new land. North America can spare a significant amount of land, should the USDA guidelines be fol-
lowed. The stems largely from meat, grain and vegetable land use (Fig A in S1 Appendix) [16]. Land use for meat is greater in North America than any other continent, and as a result, land
use displacement in North America is also significant (Fig 2G). South America can also spare a significant amount of land by meeting the guidelines,
mostly from land sparing due to meat and grains, followed by vegetables and discretional
products. South America shows a steady increase in land use since 1984 (Fig 2F). This trend is
overwhelmingly due to rapid increases in land use for meat. Thus, reducing meat consumption
in South America shows strong potential for sparing land (Fig A in S1 Appendix). Finally,
Oceania can spare a small amount of land if the guidelines are met, primarily from meat,
grains and vegetables (Fig 2H; Fig A in S1 Appendix). A net positive value for land spared means less land would be
required under a change to a USDA guideline diet, while a net negative value means more land would be required to meet the guidelines
(a “land deficit”). https://doi.org/10.1371/journal.pone.0200781.g002 SDA guideline diet Plot shows net amount of land spared (or Fig 2. Continents differ widely in land spared (or required) under USDA guideline diet. Plot shows net amount of land spared (or
required) to meet the Dietary Guidelines in each continent by year for (a) the world (b) Asia (c) Africa (d) European Union (e) Eastern nents differ widely in land spared (or required) under USDA guideline diet. Plot shows net amount of land spared (or g
y
p
q
g
p
required) to meet the Dietary Guidelines in each continent, by year for (a) the world, (b) Asia, (c) Africa, (d) European Union, (e) Eastern
Europe, (f) South America, (g) North America and (h) Oceania. Red depicts the amount of land spared or required based only on
domestic production while the blue line combines domestic land and displaced land (land use a country generates elsewhere by relying on
food imports) to depict a total amount of land spared (or required). A net positive value for land spared means less land would be
required under a change to a USDA guideline diet, while a net negative value means more land would be required to meet the guidelines
(a “land deficit”). [14]. However, an inflection point, probably corresponding to growth in some African econo-
mies, occurs in 1990 (Fig 2C). Almost all of the additional land required to meet the guidelines
would be the result of increased dairy consumption (Fig A in S1 Appendix). Although the
extra land required to meet the guidelines in Africa is impossibly large (more land is needed [14]. However, an inflection point, probably corresponding to growth in some African econo-
mies, occurs in 1990 (Fig 2C). Almost all of the additional land required to meet the guidelines
would be the result of increased dairy consumption (Fig A in S1 Appendix). Although the
extra land required to meet the guidelines in Africa is impossibly large (more land is needed 6 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Discussion Currently, the world is in the midst of a “nutrition transition” that is marked by rapid changes
in the composition and quantity of our diet [18]. In particular, around the world, diets are
becoming more dominated by livestock, sugar, and saturated fat, and this is linked with the ris-
ing tide of obesity and diabetes [19]. These emerging diets are also linked with excessive land 7 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends Fig 3. A western/eastern hemispheric divide in land spared versus land required by a USDA guideline diet. Land spared or required in 2010 by country, in millions of
hectares (MHa). According to the scale, countries that would reduce global land use by changing to a USDA guideline diet (net positive land spared) are indicated in blue
and teal, while countries that would require extra land to meet the guidelines (net negative land spared) are indicated in red, yellow or green. The map was created by the
authors from FAOSTAT data using the Google Maps API (https://developers.google.com/maps/ with Apache License Version 2.0) [17]. Fig 3. A western/eastern hemispheric divide in land spared versus land required by a USDA guideline diet. Land spared or required in 2010 by country, in millions of
hectares (MHa). According to the scale, countries that would reduce global land use by changing to a USDA guideline diet (net positive land spared) are indicated in blue
and teal, while countries that would require extra land to meet the guidelines (net negative land spared) are indicated in red, yellow or green. The map was created by the
authors from FAOSTAT data using the Google Maps API (https://developers.google.com/maps/ with Apache License Version 2.0) [17]. https://doi.org/10.1371/journal.pone.0200781.g003 https://doi.org/10.1371/journal.pone.0200781.g003 https://doi.org/10.1371/journal.pone.0200781.g003 use and greenhouse gas emissions, the unsustainable use of water, and the loss of biodiversity
[20]. Against this background of both unsustainable and unhealthy diets [21,22], nutritional
guidelines such as those offered by the USDA show us what a balanced diet ought to look like. g
y
g
Unfortunately, our analysis shows that there is not enough land for the world to adhere
to the USDA guidelines under current agricultural practices. One gigahectare of fertile
land–roughly the size of Canada—would be required. This is despite the fact that the USDA
guideline diet is already less land-intensive than the current US diet. Our analysis also
revealed a hemispheric divide. PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends sustainable and equitable from a global land use perspective are part of the solution. In this
way we build on the literature of the global land use community that discusses the challenge
of maintaining ecosystem services while producing enough food to meet the global demand
for nutrition [11]. The easy availability of FAO data helps makes this plausible. However, it is worthwhile noting that reformulating national dietary guidelines with con-
sideration of global land use also needs to account for cultural and economic variation in food
sources. For instance, in the Global South, coarse grains (millet and sorghum), legumes, and
game hunting are an important part of many diets [23]. However, these food sources are gen-
erally under-represented in datasets, suggesting more efforts should be targeted toward their
data collection in order for land use estimation to become more accurate. This is an important
area for future research. A full accounting of land use implications of dietary shifts including
the full range of cultural and economic dietary heterogeneity is beyond the scope of our manu-
script, since our more limited goal was only to establish why national-level dietary guidelines
must go beyond nutritional health as a criterion to include land use as well, with the USDA
guidelines representing an example of an unsustainable model. The looming global land deficit suggested through this analysis is echoed by similar work
on water [1,24]. Briefly, this literature points out that we also face the potential for widespread
water shortages and that to avert such a crisis new paradigms are needed to conserve water
and develop drought resistant crops and livestock. Another approach to reduce water use is
through international trade to ensure that the food produced in regions where water is abun-
dant can be traded with regions where water is scarce [25,26]. Sometimes this is called the
trade in “virtual water” [27]. Our analysis was also broken down by continent and country. Recent dietary trends in
Africa and Asia (Fig 2) show movement toward the UDSA guidelines, as reflected in other
research on evolving diets in these regions [28]. China, India, and Saudi Arabia have changed
most drastically in recent years with an increase in agricultural land use. Pakistan, along with
India, is responding to growing consumer demand for more western diets by increasing beef
production [29]. PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Discussion North America, South America and Oceania could spare sig-
nificant amounts of land if they moved to the less meat-intensive (and consequently, grain-
intensive) diet in the USDA guidelines. In contrast, Africa, the European Union and Asia
would require a significant expansion of agricultural lands to support a USDA guideline
diet. Further to this point, the fact that Europe is sparing land by avoiding a USDA guideline
diet suggests that there may be sustainable ways to improve diets in the poorest countries
avoid malnourishment, while also sparing land compared to the USDA guideline diet. Feed-
ing the world while preserving natural land states and their ecosystem services is a complex
problem that may require applying multiple solutions. We, therefore, conclude that revising
national dietary guidelines to create dietary goals that are not just healthier but also more 8 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Supporting information S1 Appendix. Text A and B, Tables A and B, Fig A. (PDF) S1 Appendix. Text A and B, Tables A and B, Fig A. (PDF) S1 Appendix. Text A and B, Tables A and B, Fig A. (PDF) Acknowledgments This research was supported by an NSERC Discovery Grant to M.A. This project is associated
with the University of Guelph’s Food from Thought Initiative that is funded through the Can-
ada First Research Excellent Fund. Global land use implications of dietary trends studies to the overall accuracy of our findings. However, previous studies have compared
results derived from FAOSTAT to remote sensing data [32] and IPCC data [33] for instance,
finding fair but imperfect agreement between the data sources. Our finding that there is not
enough land for the world to shift to a USDA guideline diet would likely not change if errors
in the FAOSTAT dataset were removed. Therefore, our recommendation that national dietary
guidelines should take global land use into consideration would likely also not change. Our analysis concerns only masses and caloric values of food products, but a more detailed
analysis would include more specific breakdowns of nutrients, fats and proteins. Similarly, dif-
fering demographics and their individual nutritional requirements were not accounted for. The FAO trade matrix could also be used in conjunction with country-specific yields to
improve estimation of country-level land use, instead of using global average yields. These are
valuable areas for future research. Future research could also study the impact of real or potential dietary shifts on greenhouse
gas emissions. Global agricultural production accounts for nearly 30% of total greenhouse gas
(GHG) emissions [31]. Livestock alone are responsible for 18% of GHG emissions, which is
higher than the share of GHG emissions from transportation [29]. Hence, a shift to less meat
consumption would also reduce GHG emissions. Other topics for future research include the
effects of food lost during storage and transportation and (more importantly) food lost
through waste and disposal. Food loss is significant around the world, thus reducing food loss
could also help spare land. The implication of our results is that countries should coordinate their formulation of dietary
guidelines such that they are based not only on health considerations but also consideration of
sustainable global land use, equity, and natural ecosystem conservation. Moreover, given that
international agricultural trade is growing and global lands are increasingly in demand for
growing food, international coordination should incentivize country-level improvements in
dietary habits that result in global land sparing, similar to how countries are beginning to coor-
dinate reductions in their greenhouse gas emissions. Of particular interest in Asia is China, which is rapidly increasing production
in several sectors, largely contributing to Asia’s rapid agricultural growth rate (Fig A in S1
Appendix) [28]. Humans will have to deal with growing inequities as growing land use for
meat consumption by rich countries causes rising food costs for staples such as pulses and
grains and thus harms the poor and under-nourished remainder [30,31]. It is important to note that our analysis made simplifying assumptions and did not include
all factors that could influence dietary and land use trends in coming years Our estimate is
conservative since we relied upon recent historical data rather than attempting to project into
the future using population models. The world’s population will continue increasing for years
to come, creating stronger challenges than our analysis has described. On the other hand, by
avoiding future projections, we also neglected new technologies and possible future increases
in agricultural yield in continents like Africa. The FAOSTAT dataset is a secondary data source and relies largely upon data collected
from member countries. Therefore, it is subject to variable accuracy. This is reflected in our
own analyses. For instance, at the global level, there should be no discrepancy between “total”
and “domestic” land spared because total imports should, by definition, match total exports at
the agglomerated global level. However, Fig 1A suggests a discrepancy between these two val-
ues of approximately 20% in 2010. This error could be due to a combination of factors, such as
anomalous data points; differences between reported imports and exports (for instance, if a
country under-reports imports or exports due to black market activity); or discrepancy
between the FAO production data and the food balance sheets. We did not attempt country-
level case studies to validate our results since it would be difficult to generalize from case PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 9 / 12 Author Contributions Conceptualization: Madhur Anand. Data curation: Chris Pagnutti, Chris T. Bauch, Madhur Anand. Data curation: Chris Pagnutti, Chris T. Bauch, Madhur Anand. Formal analysis: Sarah Rizvi, Chris Pagnutti, Chris T. Bauch, Madhur Anand. Funding acquisition: Madhur Anand. Investigation: Sarah Rizvi, Evan Fraser, Madhur Anand. Methodology: Sarah Rizvi, Chris Pagnutti, Chris T. Bauch, Madhur Anand. Project administration: Madhur Anand. Formal analysis: Sarah Rizvi, Chris Pagnutti, Chris T. Bauch, Madhur Anand. 10 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends Resources: Chris Pagnutti, Chris T. Bauch, Madhur Anand. Software: Chris Pagnutti. Supervision: Madhur Anand. Validation: Chris Pagnutti, Madhur Anand. Visualization: Chris Pagnutti. Writing – original draft: Sarah Rizvi, Chris T. Bauch, Madhur Anand. Writing – review & editing: Evan Fraser, Chris T. Bauch, Madhur Anand. Resources: Chris Pagnutti, Chris T. Bauch, Madhur Anand. Writing – original draft: Sarah Rizvi, Chris T. Bauch, Madhur Anand. Writing – review & editing: Evan Fraser, Chris T. Bauch, Madhur Anand. References 1. Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S. Agricultural sustainability and intensive pro-
duction practices. Nature 418(6898), 671–677 (2002). https://doi.org/10.1038/nature01014 PMID:
12167873 2. Food and Agricultural Organization of the United Nations (FAO). Food Balance Sheets [Online]. http://
www.fao.org/faostat/en/#data/FBS (2017). 3. Moomaw W, Griffin T, Kurczak K, Lomax J. The Critical Role of Global Food Consumption Patterns in
Achieving Sustainable Food Systems and Food for All, A UNEP Discussion Paper, United Nations Envi-
ronment Programme, Division of Technology, Industry and Economics, Paris, France (2012). 4. Heller MC, Keoleian GA. Assessing the sustainability of the US food system: a life cycle perspective. Agricultural Systems 76(3), 1007–1041 (2003). 5. Kearney J. Food consumption trends and drivers. Philosophical transactions of the Royal Society of
London. Series B, Biological sciences 365(1554), 2793–807 (2010). 6. Young CE, Kantor LS. Moving Toward the Food Guide Pyramid. In: America’s Eating Habits: Changes
and Consequences, pp. 403–423 (1999). https://www.researchgate.net/profile/Elizabeth_Frazao/
publication/23516801_America’s_Eating_Habits_Changes_and_Consequences/links/
54dce3840cf282895a3b3014.pdf#page=424 7. Department of Agriculture U.S. and U.S. Department of Health and Human Services. Dietary Guidelines
for Americans 2010, 7th Edition ( Washington, DC: U.S. Government Printing Office, 2010). 8. Buzby JC, Wells HF, Vocke G. Possible Implications for U.S. Agriculture From Adoption of Select Die-
tary Guidelines. USDA Economic Research Service, Research Report #31 (2006). https://
ageconsearch.umn.edu/bitstream/7230/2/er060031.pdf 9. Kantor L. Many Americans are not meeting food guide pyramid dietary recommendations. Food
Review: The Magazine of Food Economics 19.1 (1996). http://agris.fao.org/agris-search/search/
display.do?f=2012/OV/OV201207846007846.xml;US19970113057 10. Verburg PH, Crossman N, Ellis EC, Heinimann A, Hostert P, Mertz O, et al. Land system science
and sustainable development of the earth system: A global land project perspective. Anthropocene
12, 29–41 (2015). 11. Lambin EF, Meyfroidt P. Global land use change, economic globalization, and the looming land scarcity. Proceedings of the National Academy of Sciences 108(9), 3465–3472 (2011). 12. Food and Agriculture Organization of the United Nations. Technical Conversion Factors for Agricultural
Commodities [Online] (2000). http://www.fao.org/economic/the-statistics-division-ess/methodology/
methodology-systems/technical-conversion-factors-for-agricultural-commodities/ar/ 13. Kelly A, Becker W, Helsing E. Food balance sheets. WHO regional publications. European series 34,
39–48 (2001). 14. IFPRI. Global Hunger Index. http://www.ifpri.org/sites/default/files/publications/ghi12.pdf (2012). 15. Deveze J. Challenges for African Agriculture. ( The World Bank, 2011). https://openknowledge. worldbank.org/handle/10986/12478 16. Duxbury JM, Welch RM. Agriculture and dietary guidelines. Food Policy 24(2–3), 197–209 (1999). 17. Google Maps API. Apache License Version 2.0. Retrieved 18 September 2017. https://developers. google.com/maps/ (2014). 18. Popkin BM. The nutrition transition and obesity in the developing world. References The Journal of nutrition 131(3),
871S–873S (2001). https://doi.org/10.1093/jn/131.3.871S PMID: 11238777 11 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 Global land use implications of dietary trends 19. Popkin BM, Adair LS, Ng SW. Global nutrition transition and the pandemic of obesity in developing
countries. Nutrition reviews 70(1), 3–21 (2012). https://doi.org/10.1111/j.1753-4887.2011.00456.x
PMID: 22221213 20. Steinfeld H, Gerber P, Wassenaar T, Castel V, Rosales M, De Haan C. Livestock’s long shadow. FAO,
Rome, 2006. 21. Fraser E, Legwegoh A, Krishna KC, CoDyre M, Dias G, Hazen S, et al. Biotechnology or organic? Extensive or intensive? Global or local? A critical review of potential pathways to resolve the global food
crisis. Trends in Food Science & Technology 48, 78–87 (2016). 22. Popkin BM. Relationship between shifts in food system dynamics and acceleration of the global nutrition
transition. Nutrition reviews 75(2), 73–82 (2017). https://doi.org/10.1093/nutrit/nuw064 PMID:
28395033 23. Akatama L, Mustalahti I. 7 Reducing emissions from deforestation and forest degradation (REDD+). Local Climate Change and Society, p.125 (2014). 24. Ruttan VW. Productivity growth in world agriculture: sources and constraints. Journal of Economic Per-
spectives 16(4), 161–184 (2002). 25. De Fraiture C, Wichelns D. Satisfying future water demands for agriculture. Agricultural water manage-
ment, 97(4), 502–511 (2010). 26. Hanjra MA, Qureshi ME. Global water crisis and future food security in an era of climate change. Food
Policy 35(5), pp.365–377 (2010). 27. Hoekstra AY, Hung PQ. Virtual water trade. A quantification of virtual water flows between nations in
relation to international crop trade. Value of water research report series, 11, p.166 (2002). 28. Kastner T, Rivas MJI, Koch W, Nonhebel S. Global changes in diets and the consequences for land
requirements for food. Proceedings of the National Academy of Sciences of the United States of Amer-
ica 109(18), 6868–72 (2012). https://doi.org/10.1073/pnas.1117054109 PMID: 22509032 29. Food and Agriculture Organization of the United Nations. The state of food and agriculture. http://www. fao.org/catalog/inter-e.htm (2009). 30. Pimentel D, Pimentel M. Sustainability of meat-based and plant-based diets and the Environment 78,
660–663 (2003). 31. Idso CD. Estimates of Global Food Production in the Year 2050: Will We Produce Enough to Ade-
quately Feed the World? Center for the Study of Carbon Dioxide and Global Change. www.co2science. org (2011). 32. Liu X, Yu L, Li W, Peng D, Zhong L, Li L, et al. Comparison of country-level cropland areas between
ESA-CCI land cover maps and FAOSTAT data. PLOS ONE | https://doi.org/10.1371/journal.pone.0200781
August 8, 2018 References International Journal of Remote Sensing, pp.1–15
(2018). https://doi.org/10.1080/01431161.2018.1465613 33. Tubiello FN, Salvatore M, Rossi S, Ferrara A, Fitton N, Smith P. The FAOSTAT database of green-
house gas emissions from agriculture. Environmental Research Letters 8(1), p.015009 (2013). 12 / 12
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https://openalex.org/W2211503916
|
https://digital.library.unt.edu/ark:/67531/metadc1363347/m2/1/high_res_d/10167734.pdf
|
English
| null |
NIST cooperative laboratory for OSI routing technology
| null | 1,994
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public-domain
| 14,573
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*This
material
is based
upon work
supported
in part by the National
Science
Foundation
under
Grant
Number
NCR-9120054
and the Department
of Energy
under
contract
number
DE-AI05-92ER25114 *This
material
is based
upon work
supported
in part by the National
Science
Foundation
under
Grant
Number
NCR-9120054
and the Department
of Energy
under
contract
number
DE-AI05-92ER25114
1
M AS'I"
E
-q/ SMTP: dougm@nist.gov
X.400:/g=doug/s=montgomery/prmd=gov+nist/admd=attmail/c=us
+1-301-975-3630
May 23, 1994 SMTP: dougm@nist.gov
X.400:/g=doug/s=montgomery/prmd=gov+nist/admd=attmail/c=us
+1-301-975-3630
May 23, 1994 SMTP: dougm@nist.gov
X.400:/g=doug/s=montgomery/prmd=gov+nist/admd=attmail/c=us
+1-301-975-3630
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IIIIt_
ItlIIN
llllI_llllla Contents 1
Program
of Work
3
2
NIST IS-IS lnteroperability
Testing
3
3
Interoperability
Testing Methodology
5
3.1
Evaluation of Interoperability
........................... 5
3.2
Protocol Functions Tested
............................. 6
4
Specific Testing Sessions
7
4.1
August 1991 DIS-level Implementation Testing
.................. 7
4.2
February 1992 IS-level Implementation Testing
.................. 9
4.3
Spring 1992 Interop Demonstration
........................ 12
4.4
Fall 1992 Interop Demonstration
Hot Stage
.................... 12
5
Conclusions
13
List of Figures
1
August 1991 Open Lab: Initial Configuration
................... 9
2
February 1192 Open Lab: Initial Configuration
.................. 11
3
Spring 1992 Intcrop Demonstration:
Initial Configuration
.............. 14
4
Fall 1992 Interop Demonstration
Hot Stage: Initial Configuration
......... 15
List of Tables
1
NIST Lab Sessions for ISIS Interoperability Testing ................ 4 "DOE/ER/25114-1 2 DISCLAIMER This report was prepareda_ an account of work sponsored by an agency of the United States
Government. Neither the_nited
States Government nor any agency thereof, nor any of their
employees, makes any warranty, express or implied, or assumes any legal liability or responsi-
bility for the accuracy, completeness, or usefulness of any information, apparatus, product, or
process disclosed, or represents that its use would not infringe privately owned rights. Refer-
ence herein to any specific,commercial product, process, or service by trade name, trademark,
manufacturer,
or otherwise does not necessarily constitute or imply its endorsement, recom-
mendation, or favoring by the United States Government or any agency thereof. The views
and opinions of authors expressed herein do not necessarily state or reflect those of the
United States Government or any agency thereof. 1 1 List of Tables "DOE/ER/25114--1 3 1
Program
of Work The National Institute of Standards andTechnology (NIST) has established acooperative laboratory
program[5] to provide an experimental conformance,
informal interoperability,
and product evalu-
ation testbed facility for emerging OSI-based routing technology. This ongoing NIST program of
work has multiple objectives: 1. Establish a cooperative research program with participants
from industry, academia,
and
government interested in fostering conformant, interoperable
OSI routing products. 1. Establish a cooperative research program with participants
from industry, academia,
and
government interested in fostering conformant, interoperable
OSI routing products. 2. Provide an open testbed facility for OSI routing products. 2. Provide an open testbed facility for OSI routing products. 3. Foster mature commercially available OSI routing products. 4. Refine and promote base standard specifications of OSI-based routing protocols. 5. Research and develop methodologies
and prototype
tools to support conformance
testing,
interoperability
testing, and product level evaluation of OSI routing technology. 5. Research and develop methodologies
and prototype
tools to support conformance
testing,
interoperability
testing, and product level evaluation of OSI routing technology. To date, the principal activities of this project have been focused on testing of the OSI IS-IS [4]
routing protocol and the integrated IS-IS (I-IS-IS) [1] extensions for support of IP. These testing
efforts have focused upon two areas: • Research and development of methodologies and prototype tools to support conformance test-
ing of routing protocols. This activity resulted in the development of aprototype conformance
test system for the IS-IS routing protocol [6]. The NIST IS-IS Multi-Party
Conformance
Test System has been used to conduct experimental conformance
testing, for the purpose of
test system development, with implementations
from several vendors. • Conducting
informal
multi-vendor
interoperability
tests of emerging
commercial
imple-
mentations. This effort focused on facilitating several "open labs" and private sessions of
interoperability
testing of IS-IS implementations. • Conducting
informal
multi-vendor
interoperability
tests of emerging
commercial
imple-
mentations. This effort focused on facilitating several "open labs" and private sessions of
interoperability
testing of IS-IS implementations. The remainder of this report discusses this interoperability
testing activity. The remainder of this report discusses this interoperability
testing activity. 2
NIST IS-IS Interoperability
Testing NIST has established a standing laboratory facility for testing OSI routing technology. Use of this
facility has included several "open labs" in which several implementors
have attended week long
testing/debugging
sessions. Several other individual, private testing sessions have been conducted
for organizations wanting to test new implementations
in a multi-vendor
environment. Table 1
summarizes these lab activities by noting the organizations and implementations
that participated, "DOE/ER/25114-1
4 • ' 4 "DOE/ER/25114-1 the number of intermediate
systems (ISs) involved in testing, and the general purpose and focus of
each testing session. Implementors
have used the NIST laboratory on site and through remote access to the systems
in the lab. In instances in which implementor
support was unavailable
NIST staff operated the
equipment under test. Implementors
have used the NIST laboratory on site and through remote access to the systems
in the lab. In instances in which implementor
support was unavailable
NIST staff operated the
equipment under test. [
.... Date
Participants
.......# of ISs
Session Purpose
August
12-16 1991
3Com,
.... 11
Earlytestingof emerging implementations of
DEC, Proteon,
the Draft International Standard (DIS- 10589). WeUfleet, Uinv
of Wisconsin
February 24-28 1992
3Corn,
DEC,
13
Testing
of implementations
of the Intema-
Fibercom, Pro-
tional Standard (ISO- 10589). teon, WeUfleet,
Cisco,
Retix,
Novell
May 1992
3Corn,
i 3
Participants in NiST testing demonstrate ISIS
DEC, Proteon,
interoperability
at Spring 92 Interop. Cisco, Phase2,
Novell,
Fibercom
October 1992
3Com,
DEC,
10
Hot
stage testing for Fall 1992 Interop Inte-
Cisco,
Pro-
grated ISIS demonstration. teon, Phase2
March 1993 - March 1994
standing
im-
9-13
Standing
laboratory
facility
in which NIST
plementations:
conducts
individual
testing
of new imple-
3Corn,
Cisco,
mentations. Organizations
that have used
DEC, Proteon,
this service include IBM, SMC, and Phase2
WeUfleet. Networks. ... Table I: NIST Lab Sessions for ISIS Interoperability
Testing Over the course of these sessions NIST ISIS interoperability
testing has involved various partici-
pants and activities. The following provides a broad summary of the scope of the activities: • Router Implementations
- NIST testing has involved 22 distinct ISs, representing
17 distinct
models/products
from 13 distinct vendors/implementors
(3Corn, Cisco,
DEC, Fibercom,
IBM, NoveU, Phase2 Networks, Retix, Proteon, SMC, University of Wisconsin,
Wellfleet). The r_ge
of products tested has spanned the spectrum from PC-based LAN routers to FDDI
capable backbone routers. 3
Interoperability
Testing Methodology NIST ISIS interoperability
testing is conducted on a informal basis. The primary
objectives of
the testing is to foster mature commercial implementations
of OSI-based routing technology
and
to refine protocol specifications. No notions of official NIST certification
or endorsement
are
associated with this activity. While the primary focus of the testing is IS-IS and I-IS-IS functionality, the testing also addresses
aspects of the operation of the corresponding:data
(i.e., CLNP and IP) and supporting
protocols
(i.e., ES-IS, ICMP). The interoperability
testing sessions consist of several test scenarios that focus on subsets of the
protocol functionality. Within each scenario,
individual
tests are executed
by perturbing:
the
physical configuration of the testbed, the logical configuration of ISs, and/or the flow of data traffic
across the testbed. ractical results of NIST's OSI routing testing are being disseminated in several ways: 1. Fostering
commercial
implementations
- NIST staff works closely with implementors
to
provide direct diagnostic feed back during testing. NIST's standing OSI routing lab has been
extensively used to provide testing of emerging new implementations. 1. Fostering
commercial
implementations
- NIST staff works closely with implementors
to
provide direct diagnostic feed back during testing. NIST's standing OSI routing lab has been
extensively used to provide testing of emerging new implementations. 2. Refining base and functional
standards
- Several design and specification errors have been
found in the IS-IS base standard and Integrated IS-IS RFC during the testing sessions. NIST
staff have actively participated
in the relevant ANSI, ISO, OIW, and IETF standards bodies
to document such errors and to contribute solutions. 2. Refining base and functional
standards
- Several design and specification errors have been
found in the IS-IS base standard and Integrated IS-IS RFC during the testing sessions. NIST
staff have actively participated
in the relevant ANSI, ISO, OIW, and IETF standards bodies
to document such errors and to contribute solutions. 3. Progressing
standards
- NIST I-IS-IS interoperability
testing fulfilled an important part of
the IETF criteria [3] for routing protocol standardization. A separate report [2] has been
developed and submitted as part of this standards process. 2
NIST IS-IS Interoperability
Testing • Subnetwork
Technologies
- IS-IS routers have been connected using LANs (802.3,802.5,
and FDDI), point-to-point
links (PPP, LAPB, and proprietary)
and X.25. To date, only
the various LAN technologies
have been thoroughly
tested with significant
multi-vendor
interconnections. 'DOE/ER/25114--1 5 5 • Host Environment
- The testing environment
has employed ESs from 7 vendors (3Com,
Apple, DEC, HP Packard, NCR, Novell, Sun Microsystems). These ESs have been used to
test the interaction
between host protocols (ES-IS, CLNP, IP, ICMP) and the IS-IS routing
protocol. • Host Environment
- The testing environment
has employed ESs from 7 vendors (3Com,
Apple, DEC, HP Packard, NCR, Novell, Sun Microsystems). These ESs have been used to
test the interaction
between host protocols (ES-IS, CLNP, IP, ICMP) and the IS-IS routing
protocol. The practical results of NIST's OSI routing testing are being disseminated in several ways: The practical results of NIST's OSI routing testing are being disseminated in several ways: 3.1
Evaluation
of Interoperability Evaluations of the results of interoperability
tests are made using various of techniques. First order
observation of the protocols under test are usually made using the console/management
capabilities
of individual ISs and protocol analyzers attached to appropriate subnets. Second order observations
are made using data streamz between ESs positioned
throughout the testbed. Observations
of the
following attributes are typically made during testing: 5 "DOE/ER/25114-1 6 • Reachability
- Examination of individual IS forwarding tables using console/management
interface. Observations
of duplex data streams between ESs (e.g. ECHO/PING,
remote
login, file transfer). • Reachability
- Examination of individual IS forwarding tables using console/management
interface. Observations
of duplex data streams between ESs (e.g. ECHO/PING,
remote
login, file transfer). , Convergence
Time - Maintenance
of Transport level connections
during routing conver-
gence. Observations of rate controlled ECHO/PING
sessions. , Convergence
Time - Maintenance
of Transport level connections
during routing conver-
gence. Observations of rate controlled ECHO/PING
sessions. , Convergence
Time - Maintenance
of Transport level connections
during routing conver-
gence. Observations of rate controlled ECHO/PING
sessions. • Protocol
Stability
- Observations
of protocol analyzers during reconfigurations
and stable
periods. • Protocol Efficiency - No serious attempt has been assess protocol efficiency. Casual obser-
vations are made using statistics maintained by individual ISs and utilization measurements
on protocol analyzers. • Protocol Efficiency - No serious attempt has been assess protocol efficiency. Casual obser-
vations are made using statistics maintained by individual ISs and utilization measurements
on protocol analyzers. 3.2
Protocol
Functions
Tested Individual interoperability
tests are selected to exercise specific protocol functions. The functions
addressed by NIST testing include: Individual interoperability
tests are selected to exercise specific protocol functions. The functions
addressed by NIST testing include: • IS Adjacencies
- L1/L2 IS adjacency acquisition. Primarily
tested on LANs, issues tested
include: area boundaries, area address computation,
protocols suppoI_ed, authentication. Configurations of 10, or more, ISs adjacencies on a single lan have been tested at L1 and L2. Configurations of 10, or more, ISs adjacencies on a single lan have been tested at L1 and L2. • Designated
IS (DIS) Election
- L1/L2 LAN DIS functions. Issues tested include:
DIS pri-
ority election, resignation, crash, pseudo node generation and sequence number processing. • Designated
IS (DIS) Election
- L1/L2 LAN DIS functions. Issues tested include:
DIS pri-
ority election, resignation, crash, pseudo node generation and sequence number processing. • Link State Data Base Maintenance
- L1/L2 update process functions. Issues tested in-
cluded: event driven and periodic LSP generation, sequence number LSP processing,
LSP
propagation, LSP lifetime control. • Link State Data Base Maintenance
- L1/L2 update process functions. Issues tested in-
cluded: event driven and periodic LSP generation, sequence number LSP processing,
LSP
propagation, LSP lifetime control. • ES Adjacencies
- L1/ES-IS functions. Issues tested include:
dynamic ES adjacencies, area
boundaries, manual ES adjacencies, ES poll. • ES Adjacencies
- L1/ES-IS functions. Issues tested include:
dynamic ES adjacencies, area
boundaries, manual ES adjacencies, ES poll. Configurations with _30 multi-vendor ES neighbors have been tested at L1. • L1 Route Computation
- L1 decision process functions. Issues addressed include: minimum
cost paths, routing to dynamic and manual ES neighbors, computation of nearest L2 IS, equal
cost multipaths, path pruning, overloaded ISs, multiple metrics. Configurations with 10, or more, equal cost paths have been tested. • L1 Route Computation
- L1 decision process functions. Issues addressed include: minimum
cost paths, routing to dynamic and manual ES neighbors, computation of nearest L2 IS, equal
cost multipaths, path pruning, overloaded ISs, multiple metrics. cost paths, routing to dynamic and manual ES neighbors, computation of nearest L2 IS, equal
cost multipaths, path pruning, overloaded ISs, multiple metrics. Configurations with 10, or more, equal cost paths have been tested. Configurations with 10, or more, equal cost paths have been tested. • Reachable
Address Prefix (RAP)s - L2 RAP configuration and processing. Configurations with 10, or more, areas within a domain have been tested. 3.2
Protocol
Functions
Tested Issues addressed
include: intemal and extemal metrics, RAP reporting in LSPs, default routes. • Reachable
Address Prefix (RAP)s - L2 RAP configuration and processing. Issues addressed
include: intemal and extemal metrics, RAP reporting in LSPs, default routes. • L2 Route Computation-
L2 decision process functions. Issues addressed include:
area
routes, prefix routes, path preference,
attached flag, partition detection. • L2 Route Computation-
L2 decision process functions. Issues addressed include:
area
routes, prefix routes, path preference,
attached flag, partition detection. Configurations with 10, or more, areas within a domain have been tested. Configurations with 10, or more, areas within a domain have been tested. 6 7 "19OE/ER/25114--1 • CLNP/IP Forwarding and other protocol Interactions
- Issues addressed include:
route
switching, error notifications, ES redirection. • CLNP/IP Forwarding and other protocol Interactions
- Issues addressed include:
route
switching, error notifications, ES redirection. • CLNP/IP Forwarding and other protocol Interactions
- Issues addressed include:
route
switching, error notifications, ES redirection. • CLNP/IP Forwarding and other protocol Interactions
- Issues addressed include:
route
switching, error notifications, ES redirection. 4
Specific Testing Sessions Participation in NIST interoperability
testing has varied over time. Likewise,
the maturity of the
implementations
tested has varied as new participants joined later sessions. In the sections that
follow the results and observations of various sessions are documented. These results document
the implementations
and specification errors/issues
that were found during the session. In many
instances, implementation
errors were corrected and retested during a single session. In instances
in which an implementation
and/or specification issue was raised in multiple sessions, it is typically
only documented once. 4.1
August 1991 DIS-level Implementation
Testing The first open lab was conducted August 12-16 1991 for the purpose of testing early implementations
of the Draft International Standard (DIS) version of the IS-IS standard. The participants
in this
session were: 3Corn, DEC, Proteon, Wellfleet, and Uinv of Wisconsin (WISIS in GATED, running
on a BSD 4.4 micro vax). For most of the participants
the implementations
under test were
relatively immature. The initial configuration for this testing session is depicted in figure 1. Testing primarily focused
upon 802.3 LAN tests. Hardware interface problems prevented
successful testing on the FDDI
LAN. The testing covered the basic LAN capabilities, level 1 and level 2 routing test scenarios. The following implementation
issues/errors
were found during testing: 1. Multiple LSPs - Some implementations
did not process multiple LSPs from the same system
correctly. Once systems began generating non-zero numbered LSPs these systems displayed
various problems in LSDB synchronization. 2. Unexpected
PDU Encodings
- Several simple PDU parsing errors were found. Implemen-
tations that made novel use of the PDU encoding rules (e.g., that place IS neighbors
one
per TLV option, use non contiguous LSP numbers) revealed some less than general parsing
assumptions in implementations. 3. DIS/Pseudo
Node Operation
- Several implementation
issues and errors were discovered
with DIS/pseudo node procedures, including: 3. DIS/Pseudo
Node Operation
- Several implementation
issues and errors were discovered
with DIS/pseudo node procedures, including: (a) Non DISs systems generating CSNs and responding to PSNs. (b) Systems not generating Pseudo Node PDUs correctly. (c) Systems not adjusting IIH Hello timers when DIS. 8 "DOE/ER/25114-1 (d) Few systems implement the ES poll function. (d) Few systems implement the ES poll function. (d) Few systems implement the ES poll function. 4. Area Address
Computation
- Errors were found in the computation of area addresses. Some
implementations
only reported the set of manual area addresses. 4. Area Address
Computation
- Errors were found in the computation of area addresses. Some
implementations
only reported the set of manual area addresses. 5. LSDB Synchronization
- Several implementations
had errors in synchronizing
LSP se-
quence numbers after a restart (e.g., either ignored previous sequence number in old LSPs,
or counted by 1 up to the correct number). 6. L1 Routing
L2 IS - Several implementation
errors were noted related to the use of L2
attached bit and computation
of the nearest L2 IS. Some implementations
did not correctly
set the attached bit, some set the attached bit when configured
Ll-only,
others did not
recognize changes in attached status of remote ISs during L1 SPF. Some systems did not perform background SPF computations. 7. L2 Routing
- Some errors were found in implementation
of path precedence
rules and
Reachable Address Prefix (RAP) processing
of interesting
prefixes (e.g., use of odd RAP
lengths, use of RAPs with IDI padding rules). 8. ES-IS Redirection
- Some errors were found in the ES-IS redirect function (e.g., redirecting
ISs, improper RD PDU encodings). 8. ES-IS Redirection
- Some errors were found in the ES-IS redirect function (e.g., redirecting
ISs, improper RD PDU encodings). The following specification issues/errors were found during testing: 1. Precedence of Routing Protocols - Questions arose relating to the relative precedence
of
IS-IS and ES-IS derived routing information. Some implementations
assign routes derived
from ES-IS a higher precedence than those computed by IS-IS. That is, CLNP PDUs are
delivered to ESs over the subnets to which they are directly attached while other IS-IS paths
with lesser cost exist. 1. Precedence of Routing Protocols - Questions arose relating to the relative precedence
of
IS-IS and ES-IS derived routing information. Some implementations
assign routes derived
from ES-IS a higher precedence than those computed by IS-IS. That is, CLNP PDUs are
delivered to ESs over the subnets to which they are directly attached while other IS-IS paths
with lesser cost exist. 2. Redirection
Based
Upon RAPs
- It was noted that issuing
a redirect
as the result of
forwarding based upon a RAP may require the NET of the next hop. This information
is not
specified as part of the RAP configuration information. It was also noted that if an NET was specified, the SNPA and the "liveness" of the RAP next
hop could be determined using the ES-IS protocol. 2. Redirection
Based
Upon RAPs
- It was noted that issuing
a redirect
as the result of
forwarding based upon a RAP may require the NET of the next hop. This information
is not
specified as part of the RAP configuration information. It was also noted that if an NET was specified, the SNPA and the "liveness" of the RAP next
hop could be determined using the ES-IS protocol. 3. ES Poll - Some implementors that did not implement the ES poll function did so intentionally
noting that few ESs support the ESCT option upon which the function is based. It was noted that for the ES poll function to be effective ESCT processing
must be supported
by ESs. Without such support, the ES Poll function may do more harm then good. Figure 1: August 1991 Open Lab: Initial Configuration Figure 1: August 1991 Open Lab: Initial Configuration 1. Authentication features. 2. Link state database overload features. 4.2
February
1992 IS-level Implementation
Testing The second open lab was conducted February 24-28 1992 for the purpose of testing implementations
of the recently finalized international standard version IS-IS. The participants in this session were:
3Com, DEC, Fibercom, Proteon, Wellfleet, Cisco, Re"tLx,NoveU. The initial configuration for this testing session is depicted in figure 2. Testing primarily focused
upon 802.3, and FDDI tAN tests. The te_ting covered the basic LAN capabilities, level 1and level 2
routing test scenarios. The maturity level of the implementations,
including those participating
for
the first time, was significantly higher than in the previous open lab. This allowed more time for
testing additional, secondary features of the protocol, including: 1. Authentication features. 2. Link state database overload features. 3. Partition Repair. 'DOE/ER/25114-1 10 • • During this open-lab session, the NIST IS-IS Multi-party Conformance Test Systems was demon-
strated operating upon vendor implementations. Experimental
conformance
test suites for the
subnetwork and update processes were executed. The following implementation
issues/errors
were found during testing: 1. Circuit State Changes
- Some implementations
are unable to determine the status of circuits
ha some situations (e.g., serial circuits marked extemal). Some implementations
failed to
reflect changes in circuit states in their LSPs (e.g., failure of event driven LSP to drop IS
neighbors or RAPs lost due to circuit state changes). 2. Munti-pathing-
Configurations
with up to 10 equal cost multipaths
revealed
some SPF
spanning tree algorithm implementation/scaling
errors. 2. Munti-pathing-
Configurations
with up to 10 equal cost multipaths
revealed
some SPF
spanning tree algorithm implementation/scaling
errors. 3. Overloaded
ISs - Some implementations
completely ignore LSDB overload state in ISs. In
those that recognized the state, there were differences in hnplementation
of this feature (see
specification issues below). The following specification issues/errors
were found during testing: 1. RH Padding
- Discrepancies in configured data link block sizes on FDDI initially prevented
IS adjacency
acquisition. The ISs with the smaller configured
data link block size was
capable of receiving larger IIHs, but the other IS would reject IIHs that were padded to a
smaller block size than its own. Questions arose regarding whether PAD length checks are required upon receipt of IIHs. Questions arose regarding whether PAD length checks are required upon receipt of IIHs. 2. Area Addresses
- Questions arose as to the use of computed
area addresses in uses other
than IS-IS PDUs. In particular questions arose as to: 2. Area Addresses
Questions arose as to the use of computed
area addresses in uses other
than IS-IS PDUs. In particular questions arose as to:
(a) If dynamic ES adjacencies should be rejected if they match a manual area address that
has been dropped. (b) For the purposes
of forwarding
and lowest NET computation
some interpretations
varied, with different implementations
using:the manual area addresses, the computed
area addresses, the union of both. (a) If dynamic ES adjacencies should be rejected if they match a manual area address that
has been dropped. (b) For the purposes
of forwarding
and lowest NET computation
some interpretations (a) If dynamic ES adjacencies should be rejected if they match a manual area address that
has been dropped. (b) For the purposes
of forwarding
and lowest NET computation
some interpretations
varied, with different implementations
using:the manual area addresses, the computed
area addresses, the union of both. 3. Routing Through
an Overloaded
IS - There were some questions regarding the description
of SPF computation in the presence of anoverloaded IS. While the text implies that one should
consider ES adjacencies on the other side of an overloaded ISs, some implementations
will
not compute the SPF through the overloaded IS to the pseudo node (which contains the LSP
for the dynamic ES adjacencies). Such implementations
will only compute routes to the the
manual ES adjacencies of an over loaded IS. 4. Partition
Repair - In attempting to test the partition repair function it became obvious that
the description cf partition repair forwarding had the real potential for routing loops. 4.3
Spring
1992
Interop
Demonstration The participants in NIST interoperability testing activities demonstrated multi-vendor IS-IS inter-
operability
at the spring 1992 Interop conference. The demonstration
was conducted within the
NIST booth, with periodic (i.e., after hours) interoperability
testing with the shownet routers. The
participants in this demonstration were: 3Corn, DEC, Cisco, Proteon, and Phase 2 Networks. The testbed configuration for this demonstration is depicted in figure 3. The demonstration consisted
primarily of L1/L2 route switching demonstrations across 802.3, and FDDI LAN tests. During the course of this demonstration one specification issue was raised: 1. DIS TOS Support - Questions arose as to whether the DIS should report support for all
metrics in its pseudo node LSPs. Failure to do so causes some SPF implementations
to
abandon TOS paths that actually are contiguous. 1. DIS TOS Support - Questions arose as to whether the DIS should report support for all
metrics in its pseudo node LSPs. Failure to do so causes some SPF implementations
to
abandon TOS paths that actually are contiguous. The following specification issues/errors
were found during testing: In the two sets of modifications to the standard to add descriptions
of precedence
of routes
and to make partition repair optional, the standard created a potential looping condition in
areas in which only some ISs implement partition repair. 4. Partition
Repair - In attempting to test the partition repair function it became obvious that
the description cf partition repair forwarding had the real potential for routing loops. In the two sets of modifications to the standard to add descriptions
of precedence
of routes
and to make partition repair optional, the standard created a potential looping condition in
areas in which only some ISs implement partition repair. 10 "-DOE/ER/25114-1 11 5. Attached Bit in Single Area Domains - In testing inter-area routing and computation of the
nearest L2 IS discussion arose as to the inability to support single area domains with external
RAPs. In particular, an L2 IS with RAPs (e.g., default prefix) but no area routes will not
identify itself as attached. identify itself as attached. It was felt that this was a deficiency in the protocol. @
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Figure 2: February 1192 Open Lab: Initial Configuration It was felt that this was a deficiency in the protocol. It was felt that this was a deficiency in the protocol. Figure 2: February 1192 Open Lab: Initial Configuration 11 11 DOE/ER_5114--1 12 4.4
Fall
1992 Interop
Demonstration
Hot Stage An open lab was conducted in October 1992 for the purpose of hot staging the fall 1992 Interop
integrated IS-IS multi-vendor demonstration. The direct participants in this session were: 3Com,
DEC, Cisco, Proteon, and Phase 2 Networks. Most of the participants
in this session had recently
added integrated support to their existing IS-IS implementations. The initial configuration
for this testing session is depicted
in figure 2 (shaded boxes indicate
IP-capable
integrated ISIS implementations). Testing primarily
focused upon 802.3, and FDDI
LAN tests. The testing scenarios covered the basic LAN capabilities,
level 1 level 2 routing test scenarios. Given maturity level of the OSI capabilities
of the implementations
under test, most effort was
directed at testing those iP capabi!ities required for the upcoming Interop demonstration. The following implementation
issues/errors
were found during testing: The following implementation
issues/errors
were found during testing: The following implementation
issues/errors
were found during testing: 1. L2 Reachability Summarization-
Some implementations reported configured address sum-
maries when there was no corresponding
internal reachability. 2. Nearest
L2 IS and L1 Default Routes - Some implementations
did not correctly establish
a default route to the nearest L2 IS. Also, some implementations
did not replace the route to
the nearest L2 IS with announced L1 default routes. 1. Precedence
of Routes - There was some questions
regarding the relative precedence
of
I-IS-IS derived routes and directly attached interfaces.
In particular, some implementations The following specification issueserrors
were found during testing: nce
of Routes - There was some questions
regarding the relative precedence
of 1. Precedence
of Routes - There was some questions
regarding the relative precedence
of
I-IS-IS derived routes and directly attached interfaces. In particular, some implementations 1. Precedence
of Routes - There was some questions
regarding the relative precedence
of
I-IS-IS derived routes and directly attached interfaces. In particular, some implementations nce
of Routes - There was some questions
regarding the relative precedence
of
derived routes and directly attached interfaces. In particular, some implementations 12 13 "DOE/ER/25114--I chose to treat local direct interfaces
at a higher priority than I-IS-IS derived routes. Thus,
longer-match
or lesser cost I-IS-IS derived routes are ignored when the destination
appears
to be on the locally attached _bnet. chose to treat local direct interfaces
at a higher priority than I-IS-IS derived routes. Thus,
longer-match
or lesser cost I-IS-IS derived routes are ignored when the destination
appears
to be on the locally attached _bnet. 2. Reporting
Interfaces
on Which
I-IS-IS
is disabled
- Questions arose as to whether an
interface over which I-IS-IS is not operating should be reported as reachable? 2. Reporting
Interfaces
on Which
I-IS-IS
is disabled
- Questions arose as to whether an
interface over which I-IS-IS is not operating should be reported as reachable? 5
Conclusions The NIST Cooperative
Laboratory
for OSI Routing Technology
project has provided valuable
contributions
to the development
of OSI-based
routing technology. The testing efforts of the
project have resulted in the refinement of base specifications of OSI-based routing specifications
and contributed to the development of mature commercially available products. [6] Debra Tang, Jinsheng Liu, and Jean-Philippe
Favreau.
The IS-IS Multi-Party
Conformance
Test System. Technical Report CSL/SNA-
92/7, NIST, 1992. Gunner
(Internet-Draft
expires
end
September
1994)
[Page
i] References [1] R. Callon. Use of OSI IS-IS for Routing in TCP/IP and Dual Environments. RFC 1195,
Network Working Group, December
1990. [2] Chris Gunner and Doug Montgomery. Experience with the Integrated IS-IS Protocol. Intemet
Draft &aft-ieff-isis-opexp-00.txt,
IETF/ISIS Working Group, March 1994. [3] Robert Hinden. Intemet Engineering
Task Force: Internet Routing Protocol Standardization
Criteria. RFC 1264, Network Working Group, October 1991. [4] ISO/IEC. Intermediate
System to Intermediate
System Intra-Domain
Routeing Information
Exchange Protocol for use in Conjunction with the Protocol for Providing the Connectionless-
mode Network Service (ISO 8473). Intemational
Standard 10589,ISO/IEC
JTC 1, Switzerland,
1991. [5] Doug Montgomery. NIST Cooperative Laboratory for OSI Routing Technology-
Project Plan. Technical Report (available as ftp://osi.ncsl.rfist.gov/pub/norl/isis-interop/norl.project_plan.ps,
and from author), NIST, 1990. [6] Debra Tang, Jinsheng Liu, and Jean-Philippe
Favreau. The IS-IS Multi-Party
Conformance
Test System. Technical Report CSL/SNA-
92/7, NIST, 1992. 13 14 "'DOE/ER/25114-I DOE/ER/25114-I
14
Shownet=47000580FFF8000001000
Figure 3: Spring 1992 Interop Demonstration:
Initial Configuration
14 Shownet=47000580FFF8000001000 Shownet=47000580FFF8000001000 Figure 3: Spring 1992 Interop Demonstration:
Initial Configuration 14 14 15 "DOE/ER/25114-1 @
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Figure 4: Fall 1992 Interop Demonstration Hot Stage: Initial Configuration Figure 4: Fall 1992 Interop Demonstration Hot Stage: Initial Configuration 15 15 ISiS
Working
Group
Internet-draft Chris
Gunner
Digital
Equipment
Corp. Doug
Montgomery
National
Institute
of
Standards
and
Technology
(NIST)
March
1994 Doug
Montgomery
National
Institute
of
Standards
and
Technology
(NIST) March
1994 Experience
with
the
Integrated
ISIS
Protocol
(draft
-iet
f-is
is - opexp-
00. txt
) Table
of
Contents Table
of
Contents
I. Status
of
this
Memo
2
2. Abstract
2
3. Introduction
2
3. I. General
Requirements
3
3.2. Specific
Requirements
for
Draft
Standard
4
4. Documentation
5
5. MIB
6
6. Security
architeuture
7
7. Implementations
7
8. Operational
Experience
8
8. i. Case
A
9
8.2. Case
B
i0
8.3. Case
C
ii
8.4. Case
D
12
9. Interoperability
Testing
12
9.1°
Interoperability
Testing
Methodology
12
9.1.i. Protocol
Functions
Tested
13
9.1.2. Evaluation
of
Interoperability
14
9.2. Testing
Sessions
14
9.2.1. August
1991
DiS-level
Implementation
Testing
15
9.2.2. February
1992
IS-level
Implementation
Testing
17
9.2.3. Spring
1992
Interop
Demonstration
20
9.2.4. Fall
1992
Interop
Demonstration
Hot
Stage
21
I0. References
23
ii. Acknowledgements
23
12. Working
Group
Information
24
13. Author's
Address
24
Gunner
(Internet-Draft
expires
end
September
1994)
[Page
i] I. Status
of
this
Memo 9. Interoperability
Testing p
y
g
9.1°
Interoperability
Testing
Methodology g
12. Working
Group
Information 3. i.
General
Requirements 3. i. General
Requirements 3. i. General
Requirements i. Documents
specifying
the
Protocol
and
its
Usage. This
may
be
one
or
more
documents. The
specifications
for
the
routing
protocol
must
be
well
written
such
that
independent,
interoperable
implementations
can
be
developed
solely
based
on
the
specification. For
example,
it
should
be
possible
to
develop
an
interoperable
implementation
without
consulting
the
original
developers
of
the
routing
protocol. 2. A
Management
Information
Base
(MIB)
must
be
written
for
the
protocol. Routing
protocols,
like
all
other
Internet
protocols,
need
a
MIB
defined
so
they
can
be
remotely
managed. 3. A
security
architecture
of
the
protocol
must
be
defined. The
security
architecture
must
include
mechanisms
for
authenticating
routing
messages
and
may
include
other
forms
of
protection. 4. Generally,
a
number
of
interoperable
implementations
must
exist. At
least
two
must
be
written
independently. 4. Generally,
a
number
of
interoperable
implementations
must
exist. At
least
two
must
be
written
independently. 5. There
must
be
evidence
that
all
features
of
the
protocol
have
been
tested,
running
between
at
least
two
implementations. This
must
include
that
all
of
the
security
features
have
been
demonstrated
to
operate,
and
that
the
mechanisms
defined
in
the
protocol
actually
provide
the
intended
protection. 6. There
must
be
operational
experience
with
the
routing
protocol. The
level
of
operational
experience
required
is
dependent
on
which
level
of
standardization
is
requested. All
significant
features
of
the
protocol
must
be
exercised. In
the
case
of
an
Interior
Gateway
Protocol
(IGP),
both
interior
and
exterior
routes
must
be
carried
(unless
another
mechanism
is
provided
for
the
exterior
routes). In
the
case
of
a
Exterior
Gateway
Protocol
(EGP),
it
must
carry
the
full
complement
of
exterior
routes. 7. Two
reports
must
be
submitted
to
the
IESG
via
the
Routing
Area
Director. The
first
report
must
document
how
requirements
I)
through
6)
of
this
document
have
been
satisfied. It
must
include: 7. Two
reports
must
be
submitted
to
the
IESG
via
the
Routing
Area
Director. The
first
report
must
document
how
requirements
I)
through
6)
of
this
document
have
been
satisfied. It
must
include: 7. a. Implementation
experience. [Page
3] [Page
3] Gunner Internet-Draft
Experience
with
Integrated
ISIS March
1994 March
1994 how
Integrated
ISIS
satisfies
these
requirements. a.
Implementation
experience. Internet-Draft
Experience
with
Integrated
ISIS
March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft Standard
and
it
being
submitted
for
Draft
Standard. The
revised
documents
should
include
a
section
summarizing
the
changes
made. 2. The
Management
Information
Base
(MIB)
must
be
at
the
Proposed
Standard
level
of
standardization. 2. The
Management
Information
Base
(MIB)
must
be
at
the
Proposed
Standard
level
of
standardization. 3. There
must
be
significant
operational
experience. This
must
include
running
in
a
moderate
number
of
touters
configured
in
a
moderately
complex
topology,
and
must
be
part
of
the
operational
Internet. All
significant
features
of
the
protocol
must
be
exercised. In
the
case
of
an
Interior
Gateway
Protocol
(IGP),
both
interior
and
exterior
routes
must
be
carried
(unless
another
mechanism
is
provided
for
the
exterior
routes). In
the
case
of
a
Exterior
Gateway
Protocol
(EGP),
it
must
carry
the
full
complement
of
exterior
routes. 3. There
must
be
significant
operational
experience. This
must
include
running
in
a
moderate
number
of
touters
configured
in
a
moderately
complex
topology,
and
must
be
part
of
the
operational
Internet. All
significant
features
of
the
protocol
must
be
exercised. In
the
case
of
an
Interior
Gateway
Protocol
(IGP),
both
interior
and
exterior
routes
must
be
carried
(unless
another
mechanism
is
provided
for
the
exterior
routes). In
the
case
of
a
Exterior
Gateway
Protocol
(EGP),
it
must
carry
the
full
complement
of
exterior
routes. 4.
Documentation The
Integrated
ISIS
protocol
is
an
extension
of
the
ISIS
protocol
defined
by
ISO
10589. The
first
definition
of
Integrated
ISIS
which
was
documented
in
RFC
I195
was
based
on
the
DP
version
of
the
ISO
standard. In
developing
Integrated
ISIS
some
revisions
to
the
ISO
standard
were
suggested
and
defined
in
RFC
1195. These
were
incorporated
into
ISO
10589
with
the
result
that
the
definitions
in
RFC
1195
were
no
longer
necessary. Hence
an
Internet
Draft
exists
for
Integrated
ISIS
which
defines
the
protocol
as
derived
from
the
ISO
10589
version
of
ISIS. The
details
of
what
changed
between
RFC
1195
and
the
Internet
Draft
are
described
in
[4]. The
implementations
and
testing
described
in
this
document
were
all
based
on
the
RFC
1195
definition
of
the
Integrated
additions
to
the
base
protocol. They
were
initially
based
on
the
DIS
10589
definition
of
the
base
ISIS
protocol. Subsequent
implementations
and
testing
were
based
on
the
standard
ISO
10589
definition
of
the
base
protocol
(see
section
9.1
for
details). The
Integrated
ISIS
protocol
Was
developed
by
the
ISIS
Working
Group
of
the
Internet
Engineering
Task
Force
(IETF)
. This
Working
Group
has
a
mailing
list,
isis@merit.edu,
where
discussions
of
protocol
features
and
operation
are
held. The
ISiS
Working
Group
also
meets
during
the
quarterly
Internet
Engineering
Task
Force
conferences. Reports
of
these
meetings
are
published
in
the
IETF's
Proceedings. Management
Information
Base
(MIB)
for
the
protocol
has
been [Page
5] Internet-Draft
Experience
with
Integrated
ISIS March
1994 b. Reference
to
the
MIB
for
the
protocol. c. Description
of
the
authentication
mechanisms
in
the
protocol. d. List
of
implementations
including
origin
of
code. e. Test
scenarios
and
test
results
showing
that
all
features
of
the
protocols
have
been
tested. f. Description
of
operational
experience. This
must
include
topology,
environment,
time
and
duration,
implementations
involved,
and
overall
results
and
conclusions
gained
from
the
operational
experience. The
second
report
must
summarize
the
key
features
of
the
protocol
and
analyze
how
the
protocol
will
perform
and
scale
in
the
Internet. The
intent
of
this
requirement
is
to
understand
t_e
boundary
conditions
of
the
routing
protocol. The
new
routing
protocol
must
be
compared
with
the
existing
routing
protocols
(e.g.,
RIP,
EGP,
etc.)
as
appropriate. The
report
should
answer
several
questions: g. What
are
the
key
features
and
algorithms
of
the
protocol? h. How
much
link
bandwidth,
router
memory
and
router
CPU
cycles
does
the
protocol
consume
under
normal
conditions? i. For
these
metrics,
how
does
the
usage
scale
as
the
routing
environment
grows? This
should
include
topologies
at
least
an
order
of
magnitude
larger
than
the
current
environment. j. What
are
the
limits
of
the
protocol
for
these
metrics? (I.e.,
when
will
the
routing
protocol
break?) k. For
what
environments
is
the
protocol
well
suited,
and
for
what
,is
it
not
suitable? k. For
what
environments
is
the
protocol
well
suited,
and for
what
_,is
it
not
suitable? The
IESG
will
forward
to
the
IAB
its
recon_nendation
for
advancement
of
the
new
routing
protocol
based
on
its
evaluation
of
protocol
specifications
and
these
reports. The
IESG
will
forward
to
the
IAB
its
recon_nendation
for
advancement
of
the
new
routing
protocol
based
on
its
evaluation
of
protocol
specifications
and
these
reports. 3.2. Specific
Requirements
for
Draft
Standard i. Revisions
to
the
Protocol
and
Usage
documents
showing
changes
and
clarifications
made
based
on
experience
gained
in
the
time
between
when
the
protocol
was
made
a
Proposed i. Revisions
to
the
Protocol
and
Usage
documents
showing
changes
and
clarifications
made
based
on
experience
gained
in
the
time
between
when
the
protocol
was
made
a
Proposed [Page
4] Gunner Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS March
1994 March
1994 Internet-Draft Internet-Draft
Experience
with
Integrated
ISIS developed
and
published
as
an
Internet
Draft
[3]. There
have
been
4
revisions
of
this
MIB. For
more
information
see
section
5
of
this
document. There
is
a
public-domain
implementation
of
Integrated
ISIS
available
from
the
University
of
Wisconsin. This
implementation
has
been
incorporated
into
the
public-domain
gated
program. Gunner [Page
5] March
1994 March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS March
1994 Internet-Draft 2
groups
(i0
objects)
must
be
supported
if
the
instance
supports
the
authentication
functions 1
group
(i0
objects)
must
be
supported
if
the
instance
supports
the
partition
repair
function 1
group
(i0
objects)
must
be
supported
if
the
instance
supports
the
partition
repair
function 2
groups
(36
objects)
may
be
supportea
if
the
instance
wishes
to
support
static
route
configuration 7.
Implementations There
are
multiple
interoperable
implementations
of
Integrated
ISIS
currently
available. This
section
gives
a
brief
overview
of
the
six
implementations
that
are
known
to
have
taken
part
in
interoperability
testing. Other
implementations
also
exist
or
are
in
development. The
six
implementations
that
are
known
to
have
undergone
interoperability
testing
are
(listed
in
alphabetical
order)
: -
3com. This
implementation
was
wholly
developed
by
3com. I [Page
7] 6.
Security
architecture Integrated
ISIS
provides
the
option
of
carrying
authentication
information
in
all
the
protocol's
packets. The
encoding
is
extensible
to
multiple
authentication
mechanisms. However,
currently
the
only
defined
mechanism
is
a
simple
password,
transmitted
without
encryption. This
use
of
a
simple
password
does
not
provide
useful
protection
against
intentional
misbehaviour. Rather,
this
should
be
thought
of
as
a
weak
protection
against
accidental
errors
such
as
misconfiguration. The
protocol
and
MIB
permit
separate
passwords
for
each
circuit,
each
area
and
the
domain. Also,
although
only
a
single
password
can
be
configured
for
inclusion
in
transmitted
packets,
a
set
of
passwords
can
be
configured
for
reception. This
makes
migration
from
one
password
to
another
simple. The
process
is
to
add
the
new
password
to
the
reception
set
on
each
router
in
turn,
then
change
the
transmission
password
on
each
router
in
turn
and
finally
to
remove
the
old
password
from
the
reception
set
on
each
router. During
this
process
no
change
in
the
routing
topology
need
occur. Since
the
encoding
of
the
authentication
option
is
extensible
to
other
mechanisms,
the
protocol
can
be
enhanced
in
a
backwards
compatible
fashion
to
support
stronger
authentication
should
that
be
required. 5.
MIB 5. MIB A
Management
Information
Base
for
Integrated
ISIS
has
been
published
as
an
Internet
Draft
[3]. The
latest
draft
is
the
fourth
version
of
the
MIB. The
MIB
is
based
on
the
managed
object
definitions
defined
in
ISO's
GDMO
and
contained
in
IS0
10589
and
parts
of
ISO
10733
with
additions
to
support
the
IP
functionality
of
Integrated
ISIS. A
design
goal
of
the
MIB
was
that
it
provide
equivalent
functionality
as
that
in
the
ISO
standards. This
results
in
a
large
MIB
since
the
ISO
standards
provide
richer
functionality
than
that
traditionally
found
in
MIBs,
for
example,
the
ability
to
dynamically
create
and
delete
table
rows
and
generally
provide
full
configuration
control. The
MIB
provides
complete
management
for
both
the
base
ISIS
protocol
and
the
Integrated
ISIS
protocol A
partial
implementation
of
the
MIB
has
been
developed
by
Novell
(level
1
and
OSI
only). A
second
implementation
(OSI
only)
has
been
developed
by
Lachman
Technology
Inc. The
MIB
provides
full
configuration
and
monitoring
control
for
the
protocol. It
supports
multiple
instances
of
the
protocol
running
on
the
same
system. The
MIB
consists
of
17
groups
and
211
objects
of
which: e
MIB
consists
of
17
groups
and
211
objects
of
which: -
4
groups
(104
objects
)
are
mandatory -
13
are
optional
depending
on
the
functions
supported
by
the
instance
of
the
protocol: 5
groups
(29
objects)
must
be
supported
if
the
instance
supports
IP 2
groups
(14
objects)
must
be
supported
if
the
instance
supports
OSI
at
level
1 1
group
(8
objects)
must
be
supported
if
the
instance
supports
OSI
at
level
2 [Page
6] Gunner [Page
6] [Page
6] Internet-Draft
Experience
with
Integrated
ISIS status,
there
are
multiple
interoperable
independent
implementations
of
Integrated
ISIS,
namely
those
from
3com, p
g
,
y
,
Cisco,
Digital,
Phase
2
Networks,
Proteon
and
the
University
Wisconsin. 8.
Operational
Experience This
section
describes
some
examples
of
significant
operational
experience
with
the
protocol. Since
Integrated
ISIS
is
a
derivation
of
the
ISIS
protocol,
most
of
the
core
algorithms
and
protocol
are
common
to
both
ISIS
and
Integrated
ISIS. However, [Page
8] [Page
8] [Page
8] Internet-Draft
Experience
with
Integrated
ISIS March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft has
participated
in
the
Interop
fall
'92
demonstration
and
NIST
interoperability
testing. -
Cisco. This
implementation
was
wholly
developed
by
Cisco. It
has
participated
in
the
Interop
fall
'92
demonstration
and
NIST
interoperability
testing. -
Cisco. This
implementation
was
wholly
developed
by
Cisco. It
has
participated
in
the
Interop
fall
'92
demonstration
and
NIST
interoperability
testing. -
Digital. This
implementation
was
wholly
developed
by
Digital. It
has
participated
in
the
Interop
fall
' 92
Memonstration
and
NIST
interoperability
testing. -
Phase
2
Networks. This
implementation
was
wholly
developed
by
Phase
2
Networks. It
has
participated
in
the
Interop
Fall
'92
demonstration
and
NIST
interoperability
testing. -
Phase
2
Networks. This
implementation
was
wholly
developed
by
Phase
2
Networks. It
has
participated
in
the
Interop
Fall
'92
demonstration
and
NIST
interoperability
testing. Proteon. This
implementation
was
wholly
developed
by -
Proteon. This
implementation
was
wholly
developed
by
Proteon. It
has
participated
in
the
Interop
Fall
'92
demonstration
and
NIST
interoperability
testing. -
Proteon. This
implementation
was
wholly
developed
by
Proteon. It
has
participated
in
the
Interop
Fall
'92 Proteon. This
implementation
was
wholly
developed
by
Proteon. It
has
participated
in
the
Interop
Fall
'92 Proteon. It
has
participated
in
the
Interop
Fal
demonstration
and
NIST
interoperability
testing. -
University
of
Wisconsin. This
implementation
was
developed
wholly
by
the
University
of
Wisconsin. It
has
participated
in
the
early
ISIS
testing
conducted
by
NIST. This
version
is
in
the
public
domain
and
has
been
incorporated
into
gated. In
addition
to
these
there
are
implementations
of
the
base
ISIS
protocol
which
have
participated
in
interoperability
testing
at
NIST. These
are: -
Wellfleet -
Fibercom -
Ret
ix -
Novell -
Novell Note
that,
as
required
by
the
IAB/IESG
for
Draft
standard
status,
there
are
multiple
interoperable
independent Note
that,
as
required
by
the
IAB/IESG
for
Draft
standard
status,
there
are
multiple
interoperable
independent Note
that,
as
required
by
the
IAB/IESG
for
Draft
standard
status,
there
are
multiple
interoperable
independent
implementations
of
Integrated
ISIS,
namely
those
from
3com,
Cisco,
Digital,
Phase
2
Networks,
Proteon
and
the
University
of
Wisconsin. status,
there
are
multiple
interoperable
independent
implementations
of
Integrated
ISIS,
namely
those
from
3com,
Cisco,
Digital,
Phase
2
Networks,
Proteon
and
the
University
of
Wisconsin. 8.1.
Case
A This
deployment
in
a
large
research
network
has
been
following
a
migration
plan
from
DECnet
Phase
IV
and
IP
to
DECnet
Phase
V
and
IP
over
the
last
few
years. Currently
I
ISIS
is
in
use
only
on
Digital
touters
of
which
there
are
approximately
38
split
into
12
level
2
routers
and
26
level
1
routers. These
are
in
two
different
areas
with
6
level
2
and
5
level
1
routers
in
one
area
and
6
level
2
and
21
level
1
routers
in
the
other
area. Note
that
all
level
2
routers
are
also
level
1
touters. A
small
number
of
the
level
1
routers
are
currently
running
ISIS
(i.e. not
Integrated
ISIS)
even
though
they
are
in
the
same
area
as
the
I
ISIS
routers. This
is
technically
in
violation
of
the
topology
restriction
defined
in
RFC
1195
which
states
that
all
routers
in
an
area
or
all
the
level
2
touters
must
be
either
ISIS
only
or
be
I
ISIS
only. The
reason
for
this
restriction
is
that
an
ISIS
only
router
that
was
on
the
path
between
two
I
ISIS
touters
would
not
be
able
to
forward
IP
packets
sent
to
it
consistently
with
the
I
ISIS
touters
(if
at
all). In
this
network
the
ISIS
only
touters
are
only
at
stubs
of
the
area
where
there
is
no
IP
traffic
to
be
routed
and
this
has
proved
to
work
correctly. There
are
approximately
600
endnodes
in
each
of
the
two
areas. Most
of
these
run
DECnet
Phase
IV
and
IP
and
some
run
DECnet
Phase
V
and
IP. The
network
migration
is
currently
in
the
stage
of
migrating
a
larger
number
of
Cisco
routers
to
also
run
I
ISIS
so
that
at
the
end
of
this
stage
there
will
be
approximately
130
routers
running
I
ISIS. The
current
network
topology
for
the
Digital
I
ISIS
touters
is
a
partial
mesh
of
Ethernet
and
point
to
point
links
(at
various
speeds:
19.2kbps,
64kbps,
128kbps,
256kbps,
512
kbps). In
some
cases
the
touters
running
I
ISIS
are
configured
to
not
announce
teachability
to
any
IP
Addresses. This
was
done
to [Page
9] [Page
9] [Page
9] Gunner March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft Internet-Draft
Experience
with
Integrated
ISIS the
operational
experience
reported
here
is
restricted
to
deployments
using
Integrated
ISIS
(those
using
ISIS
are
not
considered). The
interoperability
testing
includes
both
ISIS
and
Integrated
ISIS
testing
since
most
aspects
of
the
ISIS
testing
are
relevant
to
showing
that
Integrated
ISIS
is
interoperable. As
can
be
seen
from
the
sections
below,
the
protocol
has
been
in
use
in
some
reasonable
size
networks
for
a
significant
time. in
no
case
has
there
been
a
significant
problem
with
the
protocol. Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft avoid
the
subnets
to
which
the
router
attached
being
announced
into
the
I
ISIS
domain. These
subnets
were
being
announced
by
other
routers
using
other
IP
routing
protocols
already. In
these
cases
these
touters
forwarded
IP
traffic
as
expected. The
network
also
currently
has
a
larger
number
(70
or
so)
routers
(mostly
Ciscos)
which
are
doing
IP
routing
using
Cisco's
IGRP. Exchange
of
IP
routes
between
the
IGRP
and
I
ISIS
touters
is
done
either
using
RIP,
since
that
is
a
protocol
common
to
both,
or
using
static
routes. In
the
RIP
case
the
I
ISIS
domain
propagates
all
its
routes
into
RIP
while
the
IGRP
domain
propagates
just
a
default
route
into
the
I
ISIS
domain. The
IGRP
domain
is
connected
to
the
Internet. One
problem
that
this
network
had
was
in
managing
the
default
route
within
an
area. A
restriction
of
the
Digital
touters
meant
that
a
default
route
originated
on
a
level
2
router
was
always
at
level
2,
while
on
a
level
1
router
it
was
always
at
level
i. Because
of
the
precedence
of
routes
in
I
ISIS
this
meant
that
for
that
area,
the
default
route
at
level
1
was
always
preferred,
regardless
of
metric,
over
the
default
route
at
level
2. This
is
the
opposite
of
what
would
normally
be
required. This
is
not
really
a
problem
with
the
I
ISIS
protocol
but
indicates
the
flexibility
that
is
required
in
the
configuration
controls
for
the
touters. In
this
case
implementations
should
make
sure
they
permit
the
configuration
of
which
level
routes
are
announced
into
on
a
level
2
router. The
use
of
I
ISIS
in
this
network
has
been
operational
for
approximately
6
months. 8.2.
Case
B This
commercial
deployment
has
21
Digital
routers
all
running
Integrated
ISIS. All
touters
are
Configured
as
level
2. Note
that
all
level
2
routers
are
also
level
1
routers. A
main
Ethernet
LAN
has
eight
I
ISIS
touters
attached
together
with
10
other
IP-only
routers
(from
various
vendors:
Cisco,
3Com,
Sun)
which
exchange
RIP
with
most
of
the
Digital
I
ISIS
touters. The
other
touters
are
connected
through
a
mix
of
56kbps
and
384kbps
point
to
point
links
in
a
partial
mesh
such
that
no
single
link
failure
will
partition
the
network. At
each
of
the
13
branch
sites
there
is
an
Ethernet
LAN. All
the
point-to-point
links
use
the
DDCMP
data
link
protocol
over
which
I
ISIS
uses
the
same
point-to-point
subnetwork
convergence
functions
as
over
an
HDLC
link. Throughout
the
network
there
are
approximately
900
endnodes
of
various
types:
15
OSI,
200
DECnet
Phase
IV,
500
IP,
200
IPX
(whose
traffic
is
tunnelled
through
IP). [Page
I0] [Page
I0] Gunner Gunner March
1994 March
1994 March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS 8.3.
Case
C This
commercial
deployment
includes
Digital
touters
running
Integrated
ISIS
and
routers
from
Cisco,
Wellfleet
and
NSC
running
IP
only. The
network
is
a
partial
mesh
of
Ethernet,
FDDI
and
point
to
point
links
(at
256kbps
and
512kbps). There
are
over
2000
endnodes
in
the
network
mostly
running
IP
and/or
DECnet
Phase
IV
with
50SI
endsystems. All
the
I
ISIS
touters
are
configured
as
level
2. Note
that
all
level
2
touters
are
also
level
1
touters. Static
IP
routes
are
used
between
some
I
ISIS
touters
and
some
IP-only
touters. In
some
cases
the
circuit
metrics
were
changed
from
their
default
values
to
create
the
desired
traffic
patterns. Convergence
of
the
protocol
after
link
failures
has
not
been
a
problem. There
are
approximately
28
IP
subnets
with
varying
subnet
masks
in
use. s
network
is
not
connected
to
the
Internet. This
network
is
not
connected
to
the
Internet. [Page
II] [Page
II] Gunner Internet-Draft
Experience
with
Integrated
ISIS
March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft The
network
has
14
sites,
each
of
which
has
a
separate
OSI
Area
Address
and
a
separate
IP
subnet
address
(using
a
single
subnetted
class
B
network
address
with
a
single
network-wide
subnet
mask). The
I
ISIS
touters
that
exchange
RIP
with
the
IP-only
routers
operate
RIP
in
send
and
receive
mode
and
propagate
routes
from
I
ISIS
to
RIP
and
from
RIP
to
I
ISIS. They
are
configured
to
accept
the
default
route
from
RIP
but
not
to
announce
it
in
RIP. The
network
has
a
single
connection
to
the
Internet
via
an
endnode. Therefore
there
is
no
route
propagation
to
or
from
the
Internet. The
average
traffic
load
over
the
network
(including
all
network
protocols)
is
approximately
300Mbytes
per
day. The
overall
network
uptime
has
been
over
99%. Link
failures
have
averaged
one
per
month. These
failures
have
not
caused
any
problems
with
the
applications. There
have
been
a
few
designated
router
changeovers
(caused
by
manual
intervention
rather
than
failure). During
a
changeover
there
has
been
no
problem
with
the
applications. The
changeover
process
completes
within
a
few
seconds. This
network
has
now
been
operational
for
two
years. 9.
Interoperability
Testing There
have
been
four
testing
sessions
of
the
protocol
hosted
by
NIST. These
are
described
in
detail
in
the
sections
below. For
the
first
three
sessions,
only
the
base
ISIS
protocol
was
tested. The
fourth
session
was
conducted
prior
to
the
Fall
'92
Interop
demonstration
and
included
testing
I
ISIS. The
information
in
this
section
is
derived
from
reference
[9]. The
information
in
this
section
is
derived
from
reference
[9] The
following
provides
a
broad
summary
of
the
scope
of
the
interoperability
testing
activities
: -
NIST
testing
has
involved
21
distinct
ISs,
representing
16
distinct
models/products
from
11
distinct
vendors/implementors
(3Corn,
Cisco,
Digital,
Fibercom,
IBM,
Novell,
Phase2
Networks,
Retix,
Proteon,
University
of
Wisconsin,
Wellfleet). The
range
of
products
tested
has
spanned
the
spectrum
from
PC-based
LAN
routers
to
FDDI
capable
backbone
touters. -
IS-IS
routers
have
been
connected
using
LANs
(802_3,
802.5,
and
FDDI),
point-to-point
links
(PPP,
LAPB,
and
proprietary)
and
X.25. To
date,
only
the
various
LAN
technologies
have
been
thoroughly
tested
with
significant
multi-vendor
interconnections. -
The
testing
environment
has
employed
ESs
from
7
vendors
(3Com,
Apple,
Digital,
Hewlett-Packard,
NCR,
Novell,
Sun
Microsystems)
. These
ESs
have
been
used
to
test
the
interaction
between
host
protocol_
(ES-IS,
CLNP,
IP,
ICMP)
and
the
IS-IS
routing
protocol. 9.1. Interoperability
Testing
Methodology 8.4.
Case
D This
commercial
deployment
has
15
Digital
routers. These
are
interconnected
via
a
mix
of
64kbps
and
2Mbps
WAN
links. All
routers
are
running
Integrated
ISIS. The
network
has
been
operational
for
over
8 months. Gunner March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS This
network
has
now
been
operational
for
over
1
year 9.1.
Interoperability
Testing
Methodology NIST
ISIS
interoperability
testing
has
been
conducted
on
an
informal
basis. The
primary
objectives
of
the
testing
has
been
to
foster
mature
commercial
implementations
of
OSI-based
routing [Page
12 ] [Page
12 ] Gunner March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft technology. No
notions
of
official
NIST
certification
or
endorsement
are
associated
with
this
activity. While
the
primary
focus
of
the
testing
has
been
IS-IS
functionality,
the
testing
also
addresses
aspects
of
the
operation
of
the
corresponding
data
(i.e
,
CLNP
and
IP)
and
supporting
protocols
(i.e.,
ES-IS,
ICMP,
ARP). The
interoperability
testing
sessions
consist
of
several
test
scenarios
that
focus
on
subsets
of
the
protocol
functionality. Within
each
scenario,
individual
tests
are
executed
by
manually
altering:
the
physical
configuration
of
the
testbed,
the
logical
configuration
of
ISs,
and/or
the
flow
of
data
traffic
across
the
testbed. 9.1.1.
Protocol
Functions
Tested 9.1.1. Protocol
Functions
Tested Individual
interoperability
tests
are
selected
to
exercise
specific
protocol
functions. The
functions
addressed
by
NIST
testing
include: -
IS
Adjacencies
-
LI/L2
IS
adjacency
acquisition. Primarily
tested
on
LANs,
issues
tested
include:
area
boundaries,
area
address
Computation,
protocols
supported,
authentication. Configurations
of
I0,
or
more,
ISs
adjacencies
on
a
single
fan
have
been
tested
at
L1
and
L2. -
IS
Adjacencies
-
LI/L2
IS
adjacency
acquisition. Primarily
tested
on
LANs,
issues
tested
include:
area
boundaries,
area
address
Computation,
protocols
supported,
authentication. Configurations
of
I0,
or
more,
ISs
adjacencies
on
a
single
fan
have
been
tested
at
L1
and
L2. -
Designated
IS
(DIS)
Election
-
LI/L2
LAN
DIS
functions. Issues
tested
include:
DIS
priority
election,
resignation,
crash,
pseudo
node
generation
and
sequ&nce
number
processing. -
Designated
IS
(DIS)
Election
-
LI/L2
LAN
DIS
functions. Issues
tested
include:
DIS
priority
election,
resignation,
crash,
pseudo
node
generation
and
sequ&nce
number
processing. Link
State
Data
Base
Maintenance
-
LI/L2
update
process
functions. Issues
tested
included:
event
driven
and
periodic
LSP
generation,
sequence
number
LSP
processing,
LSP
propagation,
LSP
lifetime
control. -
Link
State
Data
Base
Maintenance
-
LI/L2
update
process
functions. Issues
tested
included:
event
driven
and
periodic
LSP
generation,
sequence
number
LSP
processing,
LSP
propagation,
LSP
lifetime
control. -
ES
Adjacencies
_
LI/ES_IS
functions. Issues
tested
include:
dynamic
ES
adjacencies,
area
boundaries,
manual
ES
adjacencies,
ES
poll. Configurations
with
approximately
30
multi-vendor
ES
neighbors
have
been
tested
at
LI. -
ES
Adjacencies
_
LI/ES_IS
functions. Issues
tested
include:
dynamic
ES
adjacencies,
area
boundaries,
manual
ES
adjacencies,
ES
poll. Configurations
with
approximately
30
multi-vendor
ES
neighbors
have
been
tested
at
LI. -
L1
Route
Computation
-
L1
decision
process
functions. Issues
addressed
include:
minimum
cost
paths,
routing
to
dynamic
and
manual
ES
neighbors,
computation
of
nearest
L2
IS,
equal
cost
multipaths,
path
pruning,
overloaded
ISs,
multiple
metrics. Configurations
with
I0,
or
more,
equal
cost
paths
have
been
tested. -
L1
Route
Computation
-
L1
decision
process
functions. Issues
addressed
include:
minimum
cost
paths,
routing
to
dynamic
and
manual
ES
neighbors,
computation
of
nearest
L2
IS,
equal
cost
multipaths,
path
pruning,
overloaded
ISs,
multiple
metrics. Configurations
with
I0,
or
more,
equal
cost
paths
have
been
tested. [Page
13] [Page
13] Gunner Gunner Internet-Draft
Experience
with
Integrated
ISIS March
1994 Internet-Draft -
Reachable
Address
Prefix
(RAP)s
-
L2
RAP
configuration
and
processing. 9.1.1.
Protocol
Functions
Tested Issues
addressed
include:
internal
and
external
metrics,
RAP
reporting
in
LSPs,
default
routes. -
L2
Route
Computation
-
L2
decision
process
functions. Issues
addressed
include:
area
routes,
prefix
routes,
path
preference,
attached
flag,
partition
detection. Configurations
with
10,
or
more,
areas
within
a
domain
have
been
tested. p
,
g,
p
Configurations
with
10,
or
more,
areas
within
a
domain
have
been
tested. -
CLNP/IP
Forwarding
and
other
protocol
Interactions
-
Issues
addressed
include:
route
switching,
error
notifications,
ES
redirection. 9.1.2.
Evaluation
of
Interoperability Evaluations
of
the
results
of
interoperability
tests
are
made
using
various
techniques. First
order
observation
of
the
protocols
under
test
are
usually
made
using
the
console/management
capabilities
of
individual
ISs
and
protocol
analyzers
attached
to
appropriate
subnets. Second
order
observations
are
made
using
data
streams
between
ESs
positioned
throughout
the
testbed. Observations
of
the
following
attributes
are
typically
made
during
testing: Evaluations
of
the
results
of
interoperability
tests
are
made
using
various
techniques. First
order
observation
of
the
protocols
under
test
are
usually
made
using
the using
various
techniques. First
order
observation
protocols
under
test
are
usually
made
using
the console/management
capabilities
of
individual
ISs
and
protocol
analyzers
attached
to
appropriate
subnets. Second
order
observations
are
made
using
data
streams
between
ESs
positioned
throughout
the
testbed. Observations
of
the
following
attributes
are
typically
made
during
testing: -
Reachability
- Examination
of
individual
IS
forwarding
tables
using
console/management
interface. Observations
of
duplex
data
streams
between
ESs
(e.g. ECHO/PING,
remote
login,
file
transfer). -
Reachability
- Examination
of
individual
IS
forwarding
tables
using
console/management
interface. Observations
of
duplex
data
streams
between
ESs
(e.g. ECHO/PING,
remote
login,
file
transfer). -
Convergence
Time
- Maintenance
of
Transport
level
connections
during
routing
convergence. Observations
of
rate
controlled
ECHO/PING
sessions. -
Protocol
Stability
-
Observations
of
protocol
analyzers
during
reconfigurations
and
stable
periods. -
Protocol
Stability
-
Observations
of
protocol
analyzers
during
reconfigurations
and
stable
periods. -
Protocol
Efficiency
- No
serious
attempt
has
been
made
to
assess
protocol
efficiency. Casual
observations
are
made
using
statistics
maintained
by
individual
ISs
and
utilization
measurements
on
protocol
analyzers. 9.2.
Testing
Sessions Participation
in
NIST
interoperability
testing
has
varied
over
time. Likewise,
the
maturity
of
the
implementations
tested
has
varied
as
new
participants
joined
later
sessions. In
the
sections
that
follow
the
results
and
observations
of
various [Page
14] [Page
14] Gunner March
1994 March
1994 Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft Internet-Draft
Experience
with
Integrated
ISIS sessions
are
documented. These
results
document
the
implementations
and
specification
errors/issues
that
were
found
during
the
session. In
many
instances,
implementation
errors
were
corrected
and
retested
during
a
single
session. In
instances
in
which
an
issue
was
raised
in
multiple
sessions,
it
is
typically
only
documented
once. g
g
stances
in
which
an
issue
was
raised
in
multiple
sessions,
it
typically
only
documented
once. 9.2.1. August
1991
DIS-level
Implementation
Testing Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft
Experience
with
Integrated
ISIS computation
of
area
addresses. Some
implementations
only
reported
the
set
of
manual
area
addresses. computation
of
area
addresses. Some
implementations
only
reported
the
set
of
manual
area
addresses. -
LSDB
Synchronization
-
Several
implementations
had
errors
in
synchronizing
LSP
sequence
numbers
after
a
restart
(e.g.,
either
ignored
previous
sequence
number
in
old
LSPs,
or
counted
by
1
up
to
the
correct
number). -
L1
Routing
L2
IS
-
Several
implementation
_rrors
were
noted
related
to
the
u&e
of
L2
attached
bit
and
computation
of
the
nearest
L2
IS. Some
implementations
did
not
correctly
set
the
attached
bit,
some
set
the
attached
bit
when
configured
Ll-only,
others
did
not
recognize
changes
in
attached
status
of
remote
ISs
during
L1
SPF. Some
systems
did
not
perform
background
SPF
confutations. -
L1
Routing
L2
IS
-
Several
implementation
_rrors
were
noted
related
to
the
u&e
of
L2
attached
bit
and
computation
of
the
nearest
L2
IS. Some
implementations
did
not
correctly
set
the
attached
bit,
some
set
the
attached
bit
when
configured
Ll-only,
others
did
not
recognize
changes
in
attached
status
of
remote
ISs
during
L1
SPF. Some
systems
did
not
perform
background
SPF
confutations. -
L2
Routing
-
Some
errors
were
found
in
implementation
of
path
precedence
rules
and
Reachable
Address
Prefix
(RAP)
processing
of
interesting
prefixes
(e.g.,
use
of
odd
RAP
lengths,
use
of
RAPs
with
IDI
padding
rules). -
ES-IS
Redirection
-
Some
errors
were
found
in
the
ES-IS
redirect
function
(e.g.,
redirecting
ISs,
improper
RD
PDU
encodings). -
ES-IS
Redirection
-
Some
errors
were
found
in
the
ES-IS
redirect
function
(e.g.,
redirecting
ISs,
improper
RD
PDU
encodings). The
following
specification
issues/errors
were
found
during
testing: The
following
specification
issues/errors
were
found
during
testing: -
Precedence
of
Routing
Protocols
-
Questions
arose
relating
to
the
relative
precedence
of
IS-IS
and
ES-IS
derived
routing
information. Some
implementations
assign
routes
derived
from
ES-IS
a
higher
precedence
than
those
computed
by
IS-IS. That
is,
CLNP
PDUs
are
delivered
to
ESs
over
the
subnets
to
which
they
are
directly
attached
while
other
IS-IS
paths
with
lesser
cost
exist. This
is
not
strictly
an
ISIS
problem
since
ISIS
is
clear
about
how
it
does
SPF
computation
to
end
systems. Internet-Draft
Experience
with
Integrated
ISIS This
is
an
implementation
choice
for
a
router
which
may
provide
the
ability
to
treat
ESIS
as
a
source
of
routes
to
end
systems
as
well
as
ISIS
and
then
also
provide
preference
controls. Unlike
the
case
with
IP
routes
where
there
may
be
multiple
sources
of
the
same
route,
in
the
OSI
case,
there
are
only
ESIS
and
ISIS
sources
(and
manual
adjacency
configuration). if
ISIS
is
treated
as
the
sole
source
of
routes
for
forwarding
then
this
is
sufficient
since
both
ESIS
and
manual
adjacency
information
is
fed
into
the
local
LSPs
of
the
router
which
are
used
in
the
SPF
computation. In
other
words
there
is
no
real
need
to
provide
extra
preference
controls
between
these
route
sources. [Page
16] [Page
16] 9.2.1.
August
1991
DIS-level
Implementation
Testing The
first
open
lab
was
conducted
August
12-16
1991
for
the
purpose
of
testing
early
implementations
of
the
Draft
International
Standard
(DIS)
for
IS-IS. The
participants
in
this
session
were:
3Com,
Digital,
Proteon,
Wellfleet,
and
University
of
Wisconsin
(WISIS
in
GATED,
running
on
a
BSD
4.4
microvax). For
most
of
the
participants
the
implementations
under
test
were
relatively
immature. Testing
primarily
focused
upon
802.3
LAN
tests. Hardware
interface
problems
prevented
successful
testing
on
the
FDDI
LAN. The
testing
covered
the
basic
LAN
capabilities,
level
1
and
level
2
routing
test
scenarios. The
following
implementation
issues/errors
were
found
during
testing: -
Multiple
LSPs
-
Some
implementations
did
not
process
multiple
LSPs
from
the
same
system
correctly. Once
systems
began
generating
non-zero
numbered
LSPs
these
systems
displayed
various
problems
in
LSDB
synchronization. -
Unexpected
PDU
Encodings
-
Several
simple
PDU
parsing
errors
were
found. Implementations
that
made
novel
use
of
the
PDU
encoding
rules
(e.g.,
that
place
IS
neighbors
one
per
TLV
option,
use
non
contiguous
LSP
numbers)
revealed
some
less
than
general
parsing
assumptions
in
implementations. -
DIS/Pseudo
Node
Operation
-
Several
implementation
issues
were
discovered
with
DiS/pseudo
Node
procedures,
including: Non
DIS
systems
generating
CSNs
and
responding
to
PSNs. Non
DIS
systems
generating
CSNs
and
responding
to
PSNs. Systems
not
generating
Pseudo
Node
PDUs
correctly. Systems
not
adjusting
IIH
Hello
timers
when
DIS. Few
systems
implement
the
ES
poll
function. Non
DIS
systems
generating
CSNs
and
responding
to
PSNs. Systems
not
generating
Pseudo
Node
PDUs
correctly. Systems
not
adjusting
IIH
Hello
timers
when
DIS. Few
systems
implement
the
ES
poll
function. Systems
not
generating
Pseudo
Node
PDUs
correctly. -
Area
Address
Computation
-
Errors
were
found
in
the [P age
15 ] [P age
15 ] Gunner [P age
15 ] 9.2.2.
February
1992
IS-level
Implementation
Testing The
second
open
lab
was
conducted
February
24-28
1992
for
the
purpose
of
testing
implementations
of
the
recently
finalized
International
Standard
(IS)
version
IS-IS. The
participants
in
this
session
were:
3Com,
Digital,
Fibercom,
Proteon,
Wellfleet,
Cisco,
Retix,
Novell. Testing
primarily
focused
upon
802.3,
and
FDDI
LAN
tests. The
testing
covered
the
basic
LAN
capabilities,
level
1
and
level
2
routing
test
scenarios. The
maturity
level
of
the
implementations,
including
those
participating
for
the
first
time,
was
significantly
higher
than
in
the
previous
open
lab. This
allowed
more
time
for
testing
additional,
secondary
features
of
the
protocol,
including: [Page
17] [Page
17] Experience
with
Integrated
ISIS Internet-Draft -
Redirection
Based
Upon
RAPs
-
It
was
noted
that
issuing
redirect
as
the
result
of
forwarding
based
upon
a
RAP
may
require
the
Network
Entity
Title
(NET)
of
the
next
hop. This
information
is
not
specified
as
part
of
the
RAP
configuration
information. It
was
also
noted
that
if
an
NET
was
specified,
the
SNPA
and
the
"liveness"
of
the
RAP
next
hop
could
be
determined
using
the
ES-XS
protocol. The
next
hop's
NET
must
be
included
in
a
Redirect
if
the
next
hop
is
a
router. This
requires
that
the
base
ISIS
standard
have
an
additional
attribute
in
the
Reachable
Address
managed
object
which
is
set
to
the
NET
of
the
next
hop. It
is
proposed
that
a
defect
report
be
submitted
against
the
base
ISIS
standard
which
details
adding
this
attribute. This
attribute
also
needs
to
be
added
to
the
ISIS
MIB. ES
Poll
-
Some
implementors
that
did
not
implement
the
ES
poll
function
did
so
intentionally
noting
that
few
ESs
support
the
ESCT
option
upon
which
the
function
is
based. It
was
noted
that
for
the
ES
poll
function
to
be
effective
ESCT
processing
must
be
supported
by
ESs. The
problem
with
ESs
not
supporting
the
option
is
that
during
a
poll
the
router
will
adjust
the
timer
for
ES
adjacencies
on
the
assumption
that
ESs
will
respond
to
the
poll. If
they
do
not
process
the
ESCT
option
then
their
adjacencies
will
be
timed
out
by
the
router
and
then
reformed
later
when
the
ESs
send
out
their
normal
frequency
ES
Hellos. One
resolution
to
this
problem
is
to
have
a
management
parameter
per
LAN
circuit
which
determines
whether
to
use
ES
Polling
on
that
circuit
or
not. 9.2.2. February
1992
IS-level
Implementation
Testing Gunner Gunner Gunner Internet-Draft Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft Internet-Draft Internet-Draft
Experience
with
Integrated
ISIS March
1994 Internet-Draft
Experience
with
Integrated
ISIS -
Authentication
features. -
Overloaded
ISs. -
Partition
Repair. -
Partition
Repair. During
this
open-lab
session,
the
NIST
IS-IS
Multiparty
Conformance
Test
Systems
was
demonstrated
operating
upon
vendor
implementations. Experimental
conformance
test
suites
for
the
subnetwork
and
update
processes
were
executed. The
following
implementation
issues/errors
were
found
during
testing: -
Circuit
State
Changes
-
Some
implementations
were
unable
to
determine
the
status
of
circuits
in
some
situations
(e.g.,
serial
circuits
marked
external). Some
implementations
failed
to
reflect
changes
in
circuit
states
in
their
LSPs
(e.g.,
failure
of
event
driven
LSP
to
drop
IS
neighbors
or
RAPs
lost
due
to
circuit
state
changes). -
Multi-pathing
-
Configurations
with
up
to
I0
equal
cost
multipaths
revealed
some
SPF
implementation/scaling
errors. -
Multi-pathing
-
Configurations
with
up
to
I0
equal
cost
multipaths
revealed
some
SPF
implementation/scaling
errors. -
Overloaded
ISs
-
Some
implementations
completely
ignore
LSDB
overload
state
in
ISs. In
those
that
recognized
the
state,
there
were
differences
in
implementation
of
this
feature
(see
specification
issues
below)° The
following
specification
issues/errors
were
found
during
testing: The
following
specification
issues/errors
were
found
during
testing: -
IIH
Padding
-
Discrepancies
in
configured
data
link
block
sizes
on
FDDI
initially
prevented
IS
adjacency
acquisition. The
ISs
with
the
smaller
configured
data
link
block
size
was
capable
of
receiving
larger
IIHs,
but
the
other
IS
would
reject
IIHs
that
Were
padded
to
a
smaller
block
size
than
its
own. Questionsarose
regarding
whether
PAD
length
checks
are
required
upon
receipt
of
IIHs. The
base
ISIS
standard
should
be
clarified
to
state
that
no
check
is
made
on
the
padded
length
of
received
IIHs. The
purpose
of
the
padding
is
to
ensure
that
ISIS
protocol
packets
of
maximum
size
can
traverse
the
transmission
path
between
the
neighbors
(which
may
be
an
extended
LAN
made
up
of
different
media). It
is
not
necessary
that
neighbors
have
the
same
data
link
block
size. Area
Addresses
-
Questions
arose
as
to
the
use
of
computed
area
addresses
in
uses
other
than
IS-IS
PDUs. In Gunner [Page
18] [Page
18] Experience
with
Integrated
ISIS March
1994 March
1994 Experience
with
Integrated
ISIS Internet-Draft Experience
with
Integrated
ISIS Experience
with
Integrated
ISIS algorithm
in
the
base
standard
is
not
ambiguous
about
this
but
it
would
be
reasonable
to
add
some
clarifying
text
to
explain
the
behaviour. What
happens
is
that
the
end
systems
will
be
reachable
through
non-overloaded
routers
on
the
LAN,
but
will
not
be
reachable
through
the
designated
router
itself
(which
is
overloaded). This
is
because
the
designated
router
is
setting
the
"infinite
hippity
cost"
bit
in
its
pseudonode
LSPs
and
its
own
LSPs. Therefore
a
path
through
the
designated
router
is
not
computed
because
its
teachability
to
the
pseudonode
is
blocked. Partition
Repair
-
In
attempting
to
test
the
partition
repair
function
it
became
obvious
that
the
description
of
partition
repair
forwarding
had
the
real
potential
for
routing
loops. In
the
two
sets
of
modifications
to
the
standard
to
add
descriptions
of
precedence
of
routes
and
make
partition
repair
optional
the
standard
created
a
potential
looping
condition
in
areas
in
which
only
some
ISs
implement
partition
repair. This
problem
has
been
clarified
in
the
base
ISIS
standard
through
the
submission
of
defect
reports
which
have
been
agreed
as
part
of
Technical
Corrigenda
1
and
2
[6
and
7]. Attached
Bit
in
Single
Area
Domains
-
In
testing
inter-area
routing
and
computation
of
the
nearest
L2
IS
discussion
arose
as
to
the
inability
to
support
single
area
domains
with
external
RAPs. In
particular,
an
L2
IS
with
RAPs
(e.g.,
default
prefix)
but
no
area
routes
will
not
identify
itself
as
attached. It
was
felt
that
this
was
a
deficiency
in
the
protocol. This
has
been
clarified
in
the
base
ISiS
standard
through
the
submission
of
a
Defect
Report
which
has
been
agreed
as
part
of
Technical
Corrigendum
1
[6]. The
presence
of
any
Reachable
Address
Prefix
causes
the
level
2
router
to
consider
itself
as
"attached". 9.2.3. Spring
1992
Interop
Demonstration Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft particular
questions
arose
as
to: If
dynamic
ES
adjacencies
should
be
rejected
if
they
match
a
manual
area
address
that
has
been
dropped. If
a
manual
area
address
is
dropped
from
the
area
this
indicates
a
configuration
error
since
the
result
will
be
that
teachability
to
some
systems
may
be
lost,
since
that
area
address
will
not
be
announced
at
level
2. The
base
ISIS
standard
is
clear
that
acceptance
of
dynamic
ES
adjacencies
is
based
on
the
configured
manual
area
addresses
and
not
the
set
of
manual
area
addresses
that
may
result
after
some
have
been
dropped. This
means
that
within
the
area
these
end
systems
will
be
reachable
but
they
will
not
be
reachable
from
outside
the
area. For
the
purposes
of
forwarding
and
lowest
NET
computation
some
interpretations
varied,
with
different
implementations
using:
the
manual
area
addresses,
the
computed
area
addresses,
the
union
of
both. The
base
ISIS
standard
could
be
clarified
to
make
it
easier
to
understand
exactly
which
area
addresses
are
used
in
each
case
although
it
is
currently
accurately
defined. Some
of
the
confusion
arises
from
the
use
of
the
term
"manuaiAreaAddresses"
to
be
both
the
local
router's
configured
area
addresses
and
those
of
another
router
that
a
router
receives
in
LSPs. -
Routing
Through
an
Overloaded
IS
-
There
were
some
questions
regarding
the
description
of
SPF
computation
in
the
presence
of
an
overloaded
IS. While
the
text
implies
that
one
should
consider
ES
adjacencies
on
the
other
side
of
an
overloaded
IS,
some
implementations
will
not
compute
the
SPF
through
the
overloaded
IS
to
the
pseudo
node
(which
contains
the
LSP
for
the
dynamic
ES
adjacencies)
. Such
implementations
will
only
compute
routes
to
the
the
manual
ES
adjacencies
of
an
overloaded
IS. The
purpose
of
including
ES
adjacencies
of
an
overloaded
router
in
the
SPF
computation
is
really
just
to
maintain
a
path
to
the
overloaded
router
itself,
since
a
router
announces
its
own
ID
as
reachable
in
its
level
1
LSP
ES
neighbor
options. This
path
is
needed
so
that
management
traffic
can
reach
the
overloaded
router. During
overload,
reachability
to
other
systems
in
the
area
or
domain
is
affected
and
it
doesn't
seem
worthwhile
adding
extra
complexity
to
the
SPF
computation
to
try
and
keep
reachability
to
end
systems
through
the
pseudonode. The
SPF [Page
19] [Page
19] Gunner Internet-Draft 9.2.3.
Spring
1992
Interop
Demonstration The
participants
in
NIST
interoperability
testing
activities
demonstrated
multi-vendor
IS-IS
interoperability
at
the
spring
1992
Interop
conference. The
demonstration
was
conducted
within
the
NIST
booth,
with
periodic
(i.e.,
after
hours)
int_roperability
testing
with
the
shownet
routers. The
participants
in
this
demonstration
were:
3Corn,
Digital,
Cisco,
Proteon,
and
Phase
2
Networks. participants
in
this
demonstration
were:
3Corn,
Digital,
Cisco,
Proteon,
and
Phase
2
Networks. The
demonstration
consisted
primarily
of
LI/L2
route
switching Internet-Draft
Experience
with
Integrated
ISIS Internet-Draft Internet-Draft March
1994 demonstrations
across
802.3,
and
FDDI
LAN
tests. During
the
course
of
this
demonstration
one
specification
issue
was
raised: -
DIS
TOS
Support
-
Questions
arose
as
to
whether
the
DIS
should
report
support
for
all
metrics
in
its
pseudo
node
LSPs. Failure
to
do
so
causes
some
SPF
implementations
to
abandon
TOS
paths
that
actually
are
contiguous. -
DIS
TOS
Support
-
Questions
arose
as
to
whether
the
DIS
should
report
support
for
all
metrics
in
its
pseudo
node
LSPs. Failure
to
do
so
causes
some
SPF
implementations
to
abandon
TOS
paths
that
actually
are
contiguous. The
problem
here
is
that
the
designated
router
announces
reachability
to
end
systems
on
the
LAN
on
behalf
of
other
touters
on
the
same
LAN,
but
the
TOS
supported
by
the
touters
may
be
different. Since
all
touters
must
support
the
default
TOS,
there
will
always
be
a
default
TOS
path. However,
if
there
were
a
path
at
a
non-default
TOS
that
were
contiguous
except
for
the
final
pseudonode
hop
then
that
non-default
TOS
path
could
not
be
used
-
the
default
TOS
path
would
be
used. One
solution
to
this
wouldbe
to
have
the
designated
router
announce
teachability
at
all
TOS
to
the
LAN
end
systems
in
its
pseudonode
LSPs
even
if
that
router
is
not
configured
to
support
one
or
more
of
those
TOS. Since
the
announced
cost
in
these
LSPs
is
always
zero,
there
is
no
problem
of
choosing
the
cost
to
use
when
doing
this. This
would
permit
fully
contiguous
TOS
paths
to
the
LAN
end
systems. If
the
designated
router
should
receive
a
data
packet
at
non-default
TOS
that
needs
to
be
forwarded
to
a
LAN
end
system
then
it
will
effectively
do
so
using
a
default
TOS
path
for
the
last
hop. This
does
not
cause
any
problem
since
this
is
guaranteed
to
be
only
a
last
hop. An
alternative
is
to
have
the
designated
IS
only
report
those
TOS
it
is
configured
to
support,
so
that
even
though
a
non-default
TOS
route
exists
to
the
DIS,
the
default
TOS
route
will
be
used
to
ESs
reported
by
the
DIS. If
users
really
want
to
use
the
non-default
TOS
routes
then
they
would
have
to
boost
the
Designated
Router
p';iority
of
those
routers
that
support
the
desired
TOS. Gunner [Page
20] Gunner [Page
20] [Page
20] Internet-Draft
Experience
with
Integrated
ISIS It
is
proposed
to
adopt
the
first
solution
and
to
make
that
a
defect
report
Oll the
base
ISIS
standard. . Fall
1992
Interop
Demonstration
Hot
Stage 9.2.4. Fall
1992
Interop
Demonstration
Hot
Stage An
open
lab
was
conducted
in
October
1992
for
the
purpose
of
hot
staging
the
fall
1992
Interop
integrated
IS-IS
multi-vendor
demonstration. The
direct
participants
in
this
session
were: [Page
21] [Page
21] [Page
21] Gunner Gunner Internet-Draft
Experience
with
Integrated
ISIS 3Corn, Digital,
Cisco,
Proteon,
and
Phase
2
Networks. Most
of
the
participants
in
this
session
had
recently
added
Integrated
support
to
their
existing
IS-IS
implementations. Testing
primarily
focused
upon
802.3,
and
FDDI
LAN
tests. The
testing
scenarios
covered
the
basic
LAN
capabilities,
level
1 level
2
routing
test
scenarios. Given
maturity
level
of
the
OSI
capabilities
of
the
implementations
under
test,
most
effort
was
directed
at
testing
those
IP
capabilities
required
for
the
upcoming
Interop
demonstration. The
following
_mplementation
issues/errors
were
found
during
testing: -
L2
Reachability
Summarization
-
Some
implementations
reported
configured
address
sununaries
when
there
was
no
corresponding
internal
reachability. -
Nearest
L2
IS
and
L1
Default
Routes
-
Some
implementation
did
not
correctly
establish
a
default
route
to
the
neares
L2
IS. Also,
some
implementations
did
not
replace
the
ro -
Nearest
L2
IS
and
L1
Default
Routes
-
Some
implementations
did
not
correctly
establish
a
default
route
to
the
nearest
L2
IS. Also,
some
implementations
did
not
replace
the
route
to
the
nearest
L2
IS
with
announced
L1
default
routes. L2
IS. Also,
some
implementations
did
not
replace
the
ro
to
the
nearest
L2
IS
with
announced
L1
default
routes. The
following
specification
issues/errors
were
found
during
testing: The
following
specification
issues/errors
were
found
during
testing: -
Precedence
of
Routes
-
There
were
some
questions
regarding
the
relative
precedence
of
I-IS-IS
derived
routes
and
directly
attached
interfaces. In
particular,
some
implementations
chose
to
treat
local
direct
interfaces
at
a
higher
priority
than
I-IS-IS
derived
routes. Thus,
longer-match
or
lesser
cost
I-IS-IS
derived
routes
are
ignored
when
the
destination
appears
to
be
on
the
locally
attached
subnet. -
Precedence
of
Routes
-
There
were
some
questions
regarding
the
relative
precedence
of
I-IS-IS
derived
routes
and
directly
attached
interfaces. In
particular,
some
implementations
chose
to
treat
local
direct
interfaces
at
a
higher
priority
than
I-IS-IS
derived
routes. Thus,
longer-match
or
lesser
cost
I-IS-IS
derived
routes
are
ignored
when
the
destination
appears
to
be
on
the
locally
attached
subnet. This
is
a
policy
that
needs
to
be
configured
on
each
router. Routes
to
local
interfaces
are
a
distinct
source
of
routes
for
the
router's
forwarding
table
from
those
routes
whose
source
is
I
ISIS. A
default
preference
for
these
would
have
local
interface
routes
preferred
to
I
ISIS
routes. But
a
router
may
provide
controls
to
alter
the
preference. Internet-Draft
Experience
with
Integrated
ISIS This
should
be
made
clear
in
the
I
ISIS
RFC
to
avoid
confusion. Reporting
Interfaces
on
Which
I-IS-IS
is
disabled
-
Questions
arose
as
to
whether
an
interface
over
which
I-IS-IS
is
not
operating
should
be
reported
as
reachable? This
is
similar
to
the
bullet
above. From
the
point
of
view Gunner [Page
22] [Page
22] March
1994 Internet-Draft Internet-Draft
Experience
with
Integrated
ISIS
March
1994
of
the
router,
the
local
interfaces
are
the
source
of
local
routes. Whether
these
are
announced
in
the
I
ISIS
protocol
may
be
under
the
user's
control
through
a
set
of
management
parameters. Normally
all
local
interface
routes
would
be
announced
in
I
ISIS. This
should
be
made
clear
in
the
I
ISIS
RFC
to
avoid
confusion. of
the
router,
the
local
interfaces
are
the
source
of
local
routes. Whether
these
are
announced
in
the
I
ISIS
protocol
may
be
under
the
user's
control
through
a
set
of
management
parameters. Normally
all
local
interface
routes
would
be
announced
in
I
ISIS. This
should
be
made
clear
in
the
I
ISIS
RFC
to
avoid
confusion. i0.
References [l]Callon,
R.W.,
"Use
of
OSI
IS-IS
for
Routing
in
TCP/IP
and
dual
environments",
RFC
1195,
December
1990. [l]Callon,
R.W.,
"Use
of
OSI
IS-IS
for
Routing
in
TCP/IP
and
dual
environments",
RFC
1195,
December
1990. [2]Callon,
R.W.,
"Use
of
OSI
IS-IS
for
Routing
in
TCP/IP
and
dual
environments",
Internet-draft
<draft-ietf-isis-tcpip-00{.ps,.txt},
January,
1993
(obsoletes
RFC
1195) [2]Callon,
R.W.,
"Use
of
OSI
IS-IS
for
Routing
in
TCP/IP
and
dual
environments",
Internet-draft
<draft-ietf-isis-tcpip-00{.ps,.txt},
January,
1993
(obsoletes
RFC
1195) [3]Gunner,
C.W.,
"Integrated
IS-IS
Management
Information
Base",
Internet-draft
<draft-file-name
tbs>,
date
- tbs,
year
-
tbs. [3]Gunner,
C.W.,
"Integrated
IS-IS
Management
Information
Base",
Internet-draft
<draft-file-name
tbs>,
date
- tbs,
year
-
tbs. [3]Gunner,
C.W.,
"Integrated
IS-IS
Management
Information
Base",
Internet-draft
<draft-file-name
tbs>,
date
- tbs,
year
-
tbs. [4]Gunner,
C.W.,
"Integrated
IS-IS
Protocol
Analysis"
Internet-draft
<draft-file-name
tbs>,
date
- tbs,
year
-
tbs. [4]Gunner,
C.W.,
"Integrated
IS-IS
Protocol
Analysis"
Internet-draft
<draft-file-name
tbs>,
date
- tbs,
year
-
tbs. [5] "Information
Technology
-
Telecommunications
and
information
exchange
between
systems
-
Intermediate
system
to
Intermediate
system
Intra-Domain
routelng
exchange
protocol
_or__---d-Con3unction
_{'-t-h-_Protocol
for
providing
the
Connectionless-mode
Network
Service
(ISO
8473)",
International
Standar-_-_0589
(ISO
submission
copy),
October
1991. [5] "Information
Technology
-
Telecommunications
and
information
exchange
between
systems
-
Intermediate
system
to
Intermediate
system
Intra-Domain
routelng
exchange
protocol
_or__---d-Con3unction
_{'-t-h-_Protocol
for
providing
the
Connectionless-mode
Network
Service
(ISO
8473)",
International
Standar-_-_0589
(ISO
submission
copy),
October
1991. [6]International
Standard
10589
-
Technical
Corrigendum
1 [6]International
Standard
10589
-
Technical
Corrigendum
1 [7]International
Standard
10589
-
Technical
Corrigendum
2 [7]International
Standard
10589
-
Technical
Corrigendum
2 [8] "Information
Technology
- Telocommunications
and
information
exchange
between
systems
-Elements
of
Management
Information
Related
to
OSI
Network
Layer
Standards",
International
Standard
10733
(ISO
submission
copy),
September
1992. [8] "Information
Technology
- Telocommunications
and
information
exchange
between
systems
-Elements
of
Management
Information
Related
to
OSI
Network
Layer
Standards",
International
Standard
10733
(ISO
submission
copy),
September
1992. [9]Montgomery,
D. "IS-IS
Interoperability
Testing
at
NIST",
Draft,
October
1993. [9]Montgomery,
D. "IS-IS
Interoperability
Testing
at
NIST",
Draft,
October
1993. 11. Acknowledgements Gunner
[Page
23] [Page
23] [Page
23] Gunner Internet-Draft
Experience
with
Integrated
ISIS March
1994 Internet-Draft Thanks
are
due
to
members
of
the
ISIS
working
group
of
the
Internet
Engineering
Task
Force
(IETF)
for
their
input
to
this
document. Doug
Montgomery
acknowledges
support
for
the
NIST
interoperability
testing
work
from
the
National
Science
Foundation
(Contract
No. NCR-9120054)
and
the
Department
of
Energy
(Contract
No. DE-AI05-92ER25114). 12.
Working
Group
Information The
current
co-chairs
of
the
ISIS
working
group
are: Ross
Callon
Wellfleet
Communications
Inc. 2 Federal
Street
Billerica
MA
01821
USA
Phone:
(508)
436
3936
Email:
rcallon@wellfleet.com
Chris
Gunner
Digital
Equipment
Corp. 550
King
Street
Littleton
MA
01460-1289
USA
Phone:
(508)
486
7792
Fax:
(508)
486
5279
Email:
gunner@dsmail.enet.dec.com Ross
Callon
Wellfleet
Communications
Inc. 2 Federal
Street
Billerica
MA
01821
USA
Phone:
(508)
436
3936
Email:
rcallon@wellfleet.com [Page
24 ] [Page
24 ] Internet-Draft
Experience
with
Integrated
ISIS
March
1994
(see
co-chair
information
above
for
mail,
etc.)
Doug
Montgomery
National
Institute
of
Standards
and
Technology
(NIST)
Phone:
(301)
975
3630
Fax:
(301)
590
0932
Email
:
dougm@osi,
ncsl. nist. gov Internet-Draft
Experience
with
Integrated
ISIS
March
1994 March
1994 (see
co-chair
information
above
for
mail,
etc.)
Doug
Montgomery
National
Institute
of
Standards
and
Technology
(NIST)
Phone:
(301)
975
3630
Fax:
(301)
590
0932
Email
:
dougm@osi,
ncsl. nist. gov (see
co-chair
information
above
for
mail,
etc.)
Doug
Montgomery
National
Institute
of
Standards
and
Technology
(NIST)
Phone:
(301)
975
3630
Fax:
(301)
590
0932
Email
:
dougm@osi,
ncsl. nist. gov Doug
Montgomery
National
Institute
of
Standards
and
Technology
(NIST) Gunner [Page
25] [Page
25]
|
https://openalex.org/W3023135170
|
https://europepmc.org/articles/pmc7198527?pdf=render
|
English
| null |
Intra-Day and Inter-Day Reliability of Measurements of the electromyographic signal on masseter and temporal muscles in patients with Down syndrome
|
Scientific reports
| 2,020
|
cc-by
| 6,068
|
www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Intra-Day and Inter-Day
Reliability of Measurements of
the electromyographic signal on
masseter and temporal muscles in
patients with Down syndrome
Lilian Chrystiane Giannasi1,3 ✉, Fabiano Politti2, Marignês T. S. Dutra1,
Vera L. S. Tenguan1, Gabriela R. C. Silva1, Gabriela P. Mancilha1, Daniel Batista da Silva1,
Luis Vicente Franco Oliveira3, Claudia Santos Oliveira3, Jose B. O. Amorim1,
Miguel Angel Castillo Salgado1 & Mônica F. Gomes1 The aim of the present study was to evaluate intra-day (test) and inter-day (re-test) reliability of
surface electromyography (sEMG) signals of the masseter and temporal muscles in patients with
Down syndrome (DS). We determined the reliability of sEMG variables in 33 patients with DS. EMG
signals were recorded at rest as well as during maximum voluntary clenching and maximum habitual
intercuspation (MHI). The signals were analyzed considering the amplitude in the root mean square
(RMS), mean frequency (MNF), median frequency (MDF) and approximate entropy (ApEn). The
intraclass correlation (ICC2,1) for the three trials recorded during MHI in the two sessions (test and retest)
revealed excellent intra-session and inter-session reliability (ICC2,1 = 0.76 to 0.97) for all sEMG variables
and muscles. In the rest position, excellent reliability was found for RMS and ApEn (ICC2,1 = 0.75 to 1.00)
and good to excellent reliability was found for MDF and MNF (ICC2,1 = 0.64 to 0.93). The intra-session
(test) and inter-session (re-test) analyses demonstrated the reliability of nonlinear sEMG variables of
the masticatory muscles in adults with Down Syndrome. Down syndrome (DS), also known as trisomy of chromosome 21 (HSA21), is the most common genetic altera-
tion, the prevalence of which ranges from six to 13 per every 10000 people in the general populatio1,2. This condi-
tion is associated with cognitive impairment, several comorbidities and emotional-social limitations, leading to
substantial medical and social costs3–6. Generalized muscular hypotonia is one of characteristics of DS, which, along with oral abnormalities, directly
affects oral functions, such as swallowing, speech and breathing (even during sleep, leading to obstructive sleep
apnea)7. The combination of abnormal masticatory muscle function (due to hypotonia) and altered skeletal devel-
opmental (e.g., discrepancy between alveolar arches, reduced maxillary length and midface retrusion) has several
consequences during the growth phase, such as oromotor incoordination (weak jaw-closing muscles, hypotonic-
ity of the tongue and inefficient lingual lateralization), difficulties during meals (choking, belching and food
spillage from the mouth), uncontrolled facial movements, mouth open at rest and mouth-breathing due to poor
muscle tonicity8–10. y
Some of these abnormal muscle functions, such as those in the muscles responsible for the sustaining and
moving the jaw (masseter and temporal) can be measured using surface electromyography (EMGs). However,
the selection of a measure for research or clinical use depends on several factors, such as reliability. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Variables
Baseline mean/SD
Age (years)
22.7 ± 6.5
Gender (female/male)
8/15
BMI (Kg/cm2)
28.5 ± 6.8
Neck circumference (cm)
40.3 ± 4.2
Abdomen circumference (cm)
93.7 ± 16.5
Table 1. Demographic and anthropometric data of 23 Down Syndrome patients. Note: BMI = body mass index. Variables
Baseline mean/SD
Age (years)
22.7 ± 6.5
Gender (female/male)
8/15
BMI (Kg/cm2)
28.5 ± 6.8
Neck circumference (cm)
40.3 ± 4.2
Abdomen circumference (cm)
93.7 ± 16.5
Table 1. Demographic and anthropometric data of 23 Down Syndrome patients. Note: BMI = body mass index. Table 1. Demographic and anthropometric data of 23 Down Syndrome patients. Note: BMI = body mass index. Table 1. Demographic and anthropometric data of 23 Down Syndrome patients. Note: BMI = body mass index evaluation of the complexity of sEMG variables of the masticatory muscles and can enable a better understanding
of neurophysiological conditions.h The root mean square (RMS) is a linear variable used to evaluate the excitability and activation of muscles
before and after therapy11,12. Median frequency (MDF) is another linear variable widely used to interpret spectral
characteristics of sEMG signals, reflecting muscle electrophysiology in different clinical conditions such as tem-
poromandibular disordes13, cerebral palsy14 and low back pain15. Nonlinear time-series analyses indicate features of motor control that are important for clinicians to meas-
ure16. Information entropy has been proposed as a measure of irregularity (nonlinear behavior) in biological
signals16–19. The measurement of entropy is reported to be a reliable method for characterizing neuromuscular
changes20 and approximate entropy (ApEn) enables a general understanding of the complexity of sEMG data21,22. In statistics, ApEn is used to establish the uncertainty or variability in a system. ApEn calculated from sEMG
signals is dependent on the variability in both amplitude and frequency and better represents this aspect than
amplitude or frequency alone21,22. As studies have demonstrated that nonlinear time-series analysis is more sen-
sitive to changes in myoelectrical signals in comparison to linear methods23,24, the use of ApEn to quantify the
irregularity or complexity of sEMG signals of the masseter and anterior temporal muscles in patients with DS
may be important to the quantification and understanding of the neurophysiological conditions of these muscles. y
p
qi
g
p y
g
However, the usefulness of sEMG data is dependent on the reproducibility of the signal detection method
both within and between recording sessions25. Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z Results
Th
l The sample was composed of 23 adults with DS (15 men and eight women) with a mean age of 22.7 ± 6.5 ye
mean body mass index (BMI) of 28.5 ± 6.8 kg/m2 and mean neck circumference of 40.3 ± 4.2 cm (Table 1).h The reliability of the sEMG variables was determined in all participants. Tables 2 and 3 displays the mean
(SD), ICC and SEM values for each sEMG measurement during MIH and in the rest position for each muscle. The ICCs for all sEMG parameters and muscles during MHI in the two sessions (test and retest) revealed excellent
intra-session and inter-session reliability (range: 0.76 to 0.97) (Table 2). In the rest position, excellent reliability
was found for RMS and ApEn (range: 0.75 to 1.00), whereas good to excellent reliability was found for MDF and
MFN (range: 0.64 to 0.93). www.nature.com/scientificreports/ This is a key factor to evaluating sEMG data in rehabilitation pro-
grams and clinical trials. Factors such as the preparation of the skin and positioning of the electrodes can exert an
influence on the results when sEMG data are collected on different days26,27, as occurs when signals are collected
before and after a clinical intervention. t
Although a number of studies have demonstrated the reliability and reproducibility of sEMG signals for the
evaluation of the masticatory muscles in both healthy and disabled patients17,21,28, to the best of our knowledge,
no studies have assessed the reliability of sEMG signals of the masticatory muscles or the reproducibility of sEMG
variables (linear and nonlinear) of the masseter and anterior temporal muscles in adults with DS. It is important
to determine the reproducibility of measuring sEMG signals (intra-session and inter-session reliability) prior to
suggesting the use of this technique as a tool for evaluating the efficacy of therapy designed to improve mastica-
tory muscle function in this population.h y
p p
Therefore, the aim of the present study was to determine the intra-session (test) and inter-session (re-test)
reliability of sEMG signals of the masseter and anterior temporal muscles in adults with DS. Intra-Day and Inter-Day
Reliability of Measurements of
the electromyographic signal on
masseter and temporal muscles in
patients with Down syndrome
Lilian Chrystiane Giannasi1,3 ✉, Fabiano Politti2, Marignês T. S. Dutra1,
Vera L. S. Tenguan1, Gabriela R. C. Silva1, Gabriela P. Mancilha1, Daniel Batista da Silva1,
Luis Vicente Franco Oliveira3, Claudia Santos Oliveira3, Jose B. O. Amorim1,
Miguel Angel Castillo Salgado1 & Mônica F. Gomes1 In clinical
practice, the combination of linear and nonlinear measures is important to the characterization, classification and 1Center of Biosciences Applied to Patients with Special Health Care Needs (CEBAPE), Institute of Science and
Technology, São José dos Campos Campus, São Paulo State University–UNESP, São Paulo, SP, Brazil. 2Nove de
Julho University, São Paulo, Brazil. 3Centro Universitário de Anápolis - UniEvangélica, São Paulo, Brazil. ✉e-mail:
odontogiannasi@uol.com.br Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z Discussionh The present study confirmed the reliability (calculated using the ICC and SEM) of different sEMG variables of
the masseter and anterior temporal muscles recorded during MHI and in the rest position in adults with DS. The
results of the linear (amplitude and frequency) and non-linear (ApEn) analyses revealed excellent intra-session
and inter-session reliability of sEMG signal readings during MIH (Table 2) as well as good to excellent reliability
in the rest position (Table 3).h These results are similar to those reported in a previous study involving patients with cerebral palsy, i.e., high
reproducibility for the data recorded during MIH and good to excellent reproducibility for data recorded in the
rest position17. A high degree of reliability during MHI has also been found for the anterior temporal and mas-
seter muscles in healthy patients29,30. These results demonstrate that sEMG activity recorded during MIH and at
rest can be used to quantify the effects of clinical interventions on the masseter and anterior temporal muscles.h The sEMG evaluation is diagnostically useful in identifying patients with pain-related temporomandibular
disorders31,32 or for the observation of muscle activity in the clinical setting30. Multiparameter sEMG analysis has
been used as a strategy to investigate the performance of the masticatory muscles following a stroke33,34, assess
pain patterns in the masticatory muscles35 and investigate the reproducibility of the evaluation of the masticatory
muscles in patients with cerebral palsy17. Discussionh Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z www.nature.com/scientificreports/ Test
Retest
Test/Retest
Mean (SD)
ICC2,1 (95%CI)
SEM
Mean (SD)
ICC2,1 (95%CI)
SEM
Mean (SD)
ICC2,1 (95%CI)
SEM
RMS MHI
RT
57.88 (33.26)
0.97 (0.93 to 0.99)
5.73
57.59 (36.46)
0.76 (0.51 to 0.89)
30.05
3.17 (3.81)
0.67 (0.36 to 0.85)
21.25
RM
57.55 (25.99)
0.90 (0.78 to 0.96)
8.27
57.27 (26.54)
0.84 (0.66 to 0.93)
10.60
2.92 (3.61)
0.78 (0.55 to 0.90)
12.28
LT
44.26 (32.79)
0.91 (0.90 to 0.96)
10.04
41.26 (26.26)
0.93 (0.84 to 0.97)
6.99
2.73 (2.32)
0.89 (0.76 to 0.95)
9.87
LM
48.29 (30.65)
0.86 (0.70 to 0.94)
11.45
48.56 (26.33)
0.85 (0.68 to 0.93)
10.14
3.64 (2.97)
0.82 (0.62 to 0.92)
11.99
FDM MHI
RT
164.82 (40.40)
0.93 (0.84 to 0.97)
10.31
165.49 (42.50)
0.95 (0.89 to 0.98)
9.00
71.82 (26.49)
0.95 (0.89 to 0.98)
8.97
RM
155.82 (39.24)
0.96 (0.91 to 0.98)
8.17
162.10 (38.18)
0.89 (0.76 to 0.95)
12.35
87.58 (26.84)
0.95 (0.89 to 0.98)
8.88
LT
119.14 (40.73)
0.92 (0.82 to 0.97)
11.77
124.54 (42.73)
0.95 (0.89 to 0.98)
10.35
72.01 (31.24)
0.94 (0.85 to 0.97)
10.53
LM
118.46 (43.44)
0.94 (0.86 to 0.97)
10.89
125.90 (40.78)
0.93 (0.84 to 0.97)
10.75
34.97 (29.99)
0.94 (0.86 to 0.97)
10.21
FM MHI
RT
182.56 (37.77)
0.95 (0.89 to 0.98)
8.63
181.69 (40.08)
0.97 (0.92 to 0.99)
7.33
105.28 (30.85)
0.96 (0.91 to 0.98)
7.59
RM
177.32 (36.90)
0.95 (0.88 to 0.98)
8.31
180.58 (36.27)
0.91 (0.90 to 0.96)
11.00
132.41 (37.19)
0.95 (0.89 to 0.98)
8.36
LT
139.66 (42.90)
0.94 (0.86 to 0.97)
10.48
148.83 (46.37)
0.95 (0.89 to 0.98)
10.69
116.33 (31.25)
0.94 (0.86 to 0.97)
10.41
LM
138.88 (38.68)
0.95 (0.89 to 0.98)
8.85
143.39 (40.39)
0.94 (0.86 to 0.97)
9.48
65.43 (4.83)
0.95 (0.89 to 0.98)
8.53
ApEn MHI
RT
1.20 (0.20)
0.86 (0.70 to 0.94)
0.08
1.20 (0.23)
0.85 (0.68 to 0.93)
0.09
1.39 (0.25)
0.89 (0.76 to 0.95)
0.07
RM
1.20 (0.19)
0.82 (0.62 to 0.92)
0.08
1.24 (0.20)
0.78 (0.55 to 0.90)
0.13
1.48 (0.28)
0.83 (0.64 to 0.92)
0.08
LT
1.09 (0.28)
0.88 (0.74 to 0.95)
0.10
1.15 (0.26)
0.89 (0.76 to 0.95)
0.09
1.60 (0.22)
0.88 (0.74 to 0.95)
0.10
LM
1.10 (0.22)
0.88 (0.74 to 0.95)
0.08
1.08 (0.24)
0.87 (0.77 to 0.94)
0.09
1.38 (0.22)
0.90 (0.77 to 0.96)
0.07
Table 2. Conclusionhi The present findings demonstrate the excellent reliability of surface electromyography variables (root mean
squared, mean frequency, median frequency and approximate entropy) of the masseter and anterior temporal
muscles in adults with Down Syndrome during maximum clenching effort as well as good to excellent reliability
of the median and mean frequency recorded in the rest position. Discussionh Intra-day (Test and Retest) and between-day (Test/Retest) reliability of EMG signal measurements in
MHI position. ApEn: approximate entropy. EMG: electromyographic. ICC: intraclass correlation coefficient. LT:
left temporal. LM: left masseter. MHI: maximum habitual intercuspation. MVC: maximal voluntary contraction. MDF: median frequency. MNF: mean frequency. RT: right temporal. RM: right masseter. RMS: root mean square. SEM: standard error of measurement. ZC: zero crossing. 95%CI: 95% confidence interval of the mean. Table 2. Intra-day (Test and Retest) and between-day (Test/Retest) reliability of EMG signal measurements in
MHI position. ApEn: approximate entropy. EMG: electromyographic. ICC: intraclass correlation coefficient. LT:
left temporal. LM: left masseter. MHI: maximum habitual intercuspation. MVC: maximal voluntary contraction. MDF: median frequency. MNF: mean frequency. RT: right temporal. RM: right masseter. RMS: root mean square. SEM: standard error of measurement. ZC: zero crossing. 95%CI: 95% confidence interval of the mean. Electromyographic components calculated in the time and frequency domains are the most widely used var-
iables for the study of masseter and anterior temporal muscle activity, whereas nonlinear components, such as
ApEn, remain under-investigated in clinical studies. This is an issue that needs to be better explored, as a change
in the entropy of the signal also reflects a qualitative change in the physiological system22. Specifically for ApEn,
the result is given between 0 and 2, with higher values reflecting greater irregularity within the time-series36–38. Thus, values near 2 indicate healthy muscle function. The excellent reliability found for ApEn under both test
conditions (MIH and rest) could be an important stimulus for future studies to use this sEMG parameter in the
evaluation of the effects of therapeutic interventions performed on the masseter and anterior temporal muscles. Materials and Methods Subjects. A convenience sample of adult patients with Down syndrome were evaluated at the Center
of Bioscience Applied to Persons with Special Care Needs (CEBAPE), Institute of Science and Technology –
UNESP/SJC, Brazil. The inclusion criteria were adult patients aged between 18–35 years-old, presenting snoring
and/or mild to moderate apnea/hypopnea index, preserved cognitive function (ability to understand and respond
to verbal commands necessary to perform this study, such as “open the mouth”, “close the mouth”, “ bite”, “relax”),
agreed to participate by free will and, the Awareness Term along with signed by patient or patient’s responsible. The exclusion criteria were body mass index (BMI) greater than 30, unsatisfactory dental health, not able to reach
the University when is needed, present psychiatric disease and have been submitted to physiotherapy, speech
therapy and/or orthodontic treatment at least 6 months before the beginning of this study.h py
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g
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This study received approval from the Human Research Ethics Committees of the Institute of Science and
Technology– UNESP/SJC, Brazil, CEPh 2.127.141 (process number CAAE 64173616.4.0000.0077). Instrumentation. The device used for the EMG acquisition was an eight-channel module (EMG System
do Brasil Ltda®) consisting of a conditioner with a band pass filter with cut-off frequencies at 20 to 500 Hz, an
amplifier gain of 1000 times and a common mode rejection ratio >120 dB. All data were acquired and processed
using a 16-bit analog to digital converter (EMG System do Brasil Ltda®) with a sampling frequency 2 kHz. Active
bipolar electrodes with a pre-amplification gain of 20x are included. Materials and Methods Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z www.nature.com/scientificreports/ Test
Retest
Inter day
Mean (SD)
ICC2,1 (95%CI)
SEM
Mean (SD)
ICC2,1 (95%CI)
SEM
Mean (SD)
ICC
SEM
RMS_rest
RT
3.31 (5.25)
0.99 (0.98 to 1.00)
0.41
3.03 (2.38)
0.98 (0.95 to 0.99)
0.35
3.17 (3.81)
0.95 (0.89 to 0.98)
0.91
RM
2.28 (1.19)
0.83 (0.64 to 0.92)
0.50
3.57 (6.04)
0.99 (0.98 to 1.00)
0.31
2.925 (3.61)
0.88 (0.74 to 0.95)
1.52
LT
2.96 (2.50)
0.87 (0.77 to 0.94)
0.89
2.51 (2.15)
0.99 (0.98 to 1.00)
0.23
2.73 (2.32)
0.95 (0.89 to 0.98)
0.53
LM
3.51 (2.39)
0.80 (0.58 to 0.91)
1.10
3.77 (3.56)
0.99 (0.98 to 1.00)
0.15
3.64 (2.97)
0.91 (0.89 to 0.96)
0.89
FDM rest
RT
69.18 (25.41)
0.80 (0.58 to 0.91)
11.59
74.46 (27.57)
0.86 (0.70 to 0.94)
10.69
71.82 (26.49)
0.66 (0.35 to 0.84)
15.97
RM
93.86 (26.07)
0.64 (0.32 to 0.83)
16.00
81.31 (27.62)
0.90 (0.78 to 0.96)
8.66
87.58 (26.84)
0.77 (0.53 to 0.90)
13.24
LT
72.29 (28.21)
0.85 (0.68 to 0.93)
11.16
71.74 (34.28)
0.89 (0.76 to 0.95)
11.30
72.01 (31.24)
0.77 (0.53 to 0.90)
14.95
LM
37.30 (29.84)
0.76 (0.51 to 0.89)
15.54
32.65 (30.15)
0.86 (0.69 to 0.94)
11.32
34.97 (29.99)
0.69 (0.40 to 0.86)
16.69
FM rest
RT
105.89 (29.29)
0.88 (0.74 to 0.95)
10.17
104.67 (32.42)
0.91 (0.90 to 0.96)
10.12
105.28 (30.85)
0.83 (0.64 to 0.92)
12.91
RM
137.29 (35.92)
0.82 (0.62 to 0.92)
15.38
127.53 (38.47)
0.93 (0.84 to 0.97)
132.41 (37.19)
0.75 (0.50 to 0.89)
19.02
LT
115.18 (27.87)
0.76 (0.51 to 0.89)
14.03
117.48 (34.63)
0.90 (0.78 to 0.96)
10.85
116.33 (31.25)
0.69 (0.40 to 0.86)
17.45
LM
64.28 (22.20)
0.68 (0.38 to 0.85)
12.60
66.59 (27.46)
0.90 (0.78 to 0.96)
8.90
65.43 (4.83)
0.75 (0.50 to 0.89)
12.39
ApEn rest
RT
1.40 (0.22)
0.83 (0.63 to 0.92)
0.09
1.38 (0.28)
0.91 (0.90 to 0.96)
0.08
1.39 (0.25)
0.83 (0.63 to 0.92)
0.10
RM
1.49 (0.28)
0.86 (0.70 to 0.94)
0.11
1.47 (0.29)
0.89 (0.76 to 0.95)
0.09
1.48 (0.28)
0.76 (0.51 to 0.89)
0.17
LT
1.59 (0.21)
0.75 (0.50 to 0.89)
0.11
1.62 (0.24)
0.89 (0.76 to 0.95)
0.08
1.60 (0.22)
0.82 (0.62 to 0.92)
0.10
LM
1.35 (0.18)
0.91 (0.90 to 0.96)
0.05
1.42 (0.27)
0.92 (0.82 to 0.97)
0.08
1.38 (0.22)
0.84 (0.66 to 0.93)
0.09
Table 3. Materials and Methods Intra-day (Test and Retest) and between-day (Test/Retest) reliability of EMG signal measurements in
rest position. ApEn: approximate entropy. EMG: electromyographic. ICC: intraclass correlation coefficient. LT:
left temporal. LM: left masseter. MHI: maximum habitual intercuspation. MVC: maximal voluntary contraction. MDF: median frequency. MNF: mean frequency. RT: right temporal. RM: right masseter. RMS: root mean square. SEM: standard error of measurement. ZC: zero crossing. 95%CI: 95% confidence interval of the mean. Table 3. Intra-day (Test and Retest) and between-day (Test/Retest) reliability of EMG signal measurements in
rest position. ApEn: approximate entropy. EMG: electromyographic. ICC: intraclass correlation coefficient. LT:
left temporal. LM: left masseter. MHI: maximum habitual intercuspation. MVC: maximal voluntary contraction. MDF: median frequency. MNF: mean frequency. RT: right temporal. RM: right masseter. RMS: root mean square. SEM: standard error of measurement. ZC: zero crossing. 95%CI: 95% confidence interval of the mean. Procedures. The participants visited the Physiology Laboratory on two different occasions, with a one-week
interval between visits. Sessions were held in a silent, well-lit recording room. The participant was instructed to
remain seated comfortably erect on a chair with eyes open, feet apart, shoulders relaxed and hands resting on
thighs, with the head on the Frankfort plane parallel to the ground. During the procedures, the participants did
not receive any visual feedback of the signals displayed on the computer. y
g
p y
p
A short training period was conducted prior to the tests to familiarize the participant with the tasks. Explanations concerning the procedures and electrode placement were given and the participant was trained to
bite as hard as possible with maximum voluntary clenching (MVC) effort with a cotton role between the arches
and maximum habitual intercuspation (MHI) effort with no material interposed between the teeth. p
(
)f
p
The sites for the placement of the electrodes were shaved and cleaned with a cotton ball soaked in 70% alcohol
to diminish impedance between the skin and electrode. Pre-gelled, self-adhesive, bipolar, disposable, Ag/AgCl
surface electrodes (MediTrace®) measuring 10 mm in diameter were positioned over the right masseter (RM), left
masseter (LM), right temporal (RT) and left temporal (LT) muscles with an inter-electrode distance of 20 mm in
the region of greatest tonus after the participant performed moderate intercuspation13. Bandage tape was used to
secure the electrodes further, with care taken to avoid micro movements. Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z Materials and Methods The grey
band shows three-second period selected (Patient with Down Syndrome – mean age: 22.7 ± 6.5 years; body
mass: 28.5 ± 6.8 kg/m2). ne-second window (total: three windows)17 and the average of the values among the three windows was used in
he reliability tests. ApEn (m, r, N) was calculated to quantify the regularity or complexity of the sEMG signals, with the embed-
ding dimension (m) and tolerance distance (r) set to m = 2 and r = 0.20 of the standard deviation (± SD) of the
data sequence and N = number of points to be analyzed36–38. This analysis returns a value between 0 and 2 (arbi-
trary units [au]), with higher values reflecting greater irregularity in the time series36–38.hih y
[
])
gl
g g
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The sEMG signals were processed using specific routines carried out in Matlab version 7.1 (The MathWorks
Inc., Natick, MA, USA). Data analysis. The Shapiro-Wilk test was used to determine the distribution of the data and data were
expressed as mean and SD. Intraclass correlation coefficients (ICCs) and the standard error of the mean (SEM)
was used to verify the reliability of each sEMG measure. Intra-session reliability was determined by computing
the intraclass correlation coefficient (ICC2,1) using only the first and second of the three measurements. Inter-day
reliability (ICC2,1) was determined by comparing the average (3 trails) of each sEMG activity index for each mus-
cle between the two sessions (test and retest). SEM was estimated by subtracting the ICCs value from one, taking
the square root of this value, and multiplying by the SD39. The ICCs was interpreted using the following criteria:
0.00 to 0.39 (poor), 0.40 to 0.59 (fair), 0.60 to 0.74 (good) and 0.75 to 1.00 excellent)40. The SEM was used to
express reliability in absolute values, with a lower SEM denoting greater reliability of the measurement, whereas a
high SEM indicates a high level of error and implies the non-reproducibility of the tested values. All d t
l
d
i
th St ti ti
l P
k
f
th S
i l S i
(SPSS) V
i
17 All data were analyzed using the Statistical Package for the Social Sciences (SPSS) Version 17. Ethic approval. Materials and Methods A rectangular metallic electrode meas-
uring 3 ×2 cm coated with Lectron II conductive gel (Pharmaceutical Innovations) to increase the conduction
capacity and impede interference from external noise was attached to the left wrist as a ground reference. p
y
pt
g
Readings were performed under three conditions: at rest, during MVC and during MHI. In session 1 (test),
three readings (10 seconds each) were performed in the rest position, followed by three readings (five seconds
each) during MVC with a two-minute interval between readings. After three minutes, three readings (five sec-
onds each) were performed during MIH with a two-minute interval between readings. The same procedures were
repeated after one week in session 2 (retest). Data processing. The sEMG signals obtained for the RT, RM, LT and LM muscles were processed using tra-
ditional linear analysis in the time (amplitude) and frequency domains as well as nonlinear analysis through the
calculation of the complexity of the sEMG signal17. For the analysis of MVC and MIH, the first and last seconds
of the five-second signals were discarded, resulting in three-second readings considered for each test. In contrast,
all 10 seconds of the signals captured in the rest position were considered (Fig. 1).h g
g
The amplitude of sEMG signal was determined considering root mean square (RMS) using a 200-ms moving
window. The mean RMS values of the three readings at rest and during MIH were normalized by the highest RMS
values obtained during the three MVC readings (µV/µV × 100: % MVC).h g
g
µ
µ
The power spectral density of the sEMG signals was calculated using Welch’s averaged periodogram with
a Hamming window length zero-padded to the length of 2048 points. Overlap was 50% of the window length. The mean frequency (MNF) and median frequency (MDF) of the power spectrum were calculated for each Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z www.nature.com/scientificreports/ Figure 1. Surface electromyography signal of the right temporal (RT), right masseter (RM), left temporal (LT)
and left masseter (LM) muscled during maximum habitual intercuspidation (MHI) and rest position. The grey
band shows three-second period selected (Patient with Down Syndrome – mean age: 22.7 ± 6.5 years; body
mass: 28.5 ± 6.8 kg/m2). Figure 1. Surface electromyography signal of the right temporal (RT), right masseter (RM), left temporal (LT)
and left masseter (LM) muscled during maximum habitual intercuspidation (MHI) and rest position. Materials and Methods All procedures performed in studies involving human participants were in accordance with
the ethical standards of the institutional research committee (Human Research Ethics Committees of the Institute
of Science and Technology– UNESP/SJC, Brazil, CEPh 2.127.141, process number CAAE 64173616.4.0000.0077)
and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Informed consent. Informed written consent, for adult with Down syndrome in this study, was obtained
from their parent/caregiver. Received: 3 September 2019; Accepted: 1 April 2020;
Published: xx xx xxxx Received: 3 September 2019; Accepted: 1 April 2020;
Published: xx xx xxxx Received: 3 September 2019; Accepted: 1 April 2020;
Published: xx xx xxxx Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z www.nature.com/scientificreports/ References Test-retest reliability of electromyographic variables of masseter and temporal muscles in patients with cerebral
palsy. Archives of Oral Biology. 59, 1352–8 (2014). p
y
f
gy
8. Costa, M., Goldberger, A. L. & Peng, C. K. Multiscale entropy to distinguish physiologic and synthetic RR time series. Computing in
Cardiology. 29, 137–40 (2000). 9. Costa, M., Goldberger, A. L. & Peng, C. K. Multiscale entropy analysis: a new measure of complexity loss in heart failure. Electrocardiol. 36(Suppl.), 39–40 (2003). 20. Goldberger, A. L., Peng, C. K. & Lipsitz, L. A. What is physiologic complexity and how does it change with aging and disease? Neurobiology of Aging. 23, 23–6 (2002).f gy f
g g
1. Sung, P. S., Zurcher, U. & Kaufman, M. Reliability difference between spectral and entropic measures of erector spinae muscle
fatigability. Journal of Electromyography and Kinesiology. 20, 25–30 (2010). g
y
f
y g
p y
gy
2. Sung, P. S. Nonlinear analysis of surface electromyography, EMG Methods for evaluating muscle and nerve function, Mr. Mark
Schwartz (Ed.), InTech, 793–802 (2012).l 23. Fattorini, L., Felici, F., Filligoi, G. C., Traballesi, M. & Farina, D. Influence of high motor unit synchronization levels on non-linear
and spectral variables of the surface EMG. Journal of Neuroscience Methods. 143, 133–9 (2005).t 4. Felici, F. et al. Linear and non-linear analysis of surface electromyograms in weight-lifters. European Journal Applied Physiology. 84
337–42 (2001). 5. Oskouei, A. H., Paulin, M. G. & Carman, A. B. Intra-session and inter-day reliability of forearm surface EMG during varying hand
grip forces. Journal Electromyography and Kinesiology. 23, 216–222 (2012). 6. Merletti, R. & Parker, P. A. Electromyography-physiology, engineering and noninvasive applications. New Jersey: John Wiley &
Sons; 2004.h 7. Veiersted, K. B. The reproducibility of test contractions for calibration of electromyographic measurements. European Journal o
Appllied Physiology and Occupational Physiology. 62, 91–98 (1991). pp
y
gy
p
y
gy
8. Lucareli, P. R. et al. Repeatability of a 3D multi-segment foot model during anterior and lateral step-down tests. Gait & Posture. 43
9–16 (2016). 9. Gonzalez, Y. et al. Reliability of electromyographic activity vs. bite-force from human masticatory muscles. European Journal of Ora
Sciences. 119, 219–224 (2011). 30. De Felício, C. M., Sidequersky, F. V., Tartaglia, G. M. & Sforza, C. Electromyographic standardized indices in healthy Brazilian young
adults and data reproducibility. Journal Oral Rehabilitation. 36, 558–577 (2009).h 1. Szyszka-Sommerfeld, L., Machoy, M., Lipski, M. & Wozniak, K. References 80, 861–69 (2010).f ,
(
)
1. Gianansi, L. C. et al. Effects of Neuromuscular Electrical Stimulation on the Masticatory Muscles and Physiologic Sleep Variables in
Adults with Cerebral Palsy: A Novel Therapeutic Approach. PLoS One. 6(10), e0128959 (2015).f cts of Neuromuscular Electrical Stimulation on the Masticatory Mu yh
p
pp
12. Silva, A. C. O. et al. Effect of Osteopathic Visceral Manipulation on Pain, Cervical Range of Motion, and Upper Trapezius Muscle i h
12. Silva, A. C. O. et al. Effect of Osteopathic Visceral Manipulation on Pain, Cervical Range of Motion, and Upper Trapezius Muscle
Activity in Patients with Chronic Nonspecific Neck Pain and Functional Dyspepsia: A Randomized Double Blind Placebo h
12. Silva, A. C. O. et al. Effect of Osteopathic Visceral Manipulation on Pain, Cervical Range of Motion, and Upper Trapezius Muscle
Activity in Patients with Chronic Nonspecific Neck Pain and Functional Dyspepsia: A Randomized, Double-Blind, Placebo-
Controlled Pilot Study Evidence-Based Compl and Alternative Medicine 6 e4929271 1–9 (2018) lva, A. C. O. et al. Effect of Osteopathic Visceral Manipulation on Pain, Cervical Range of Motion, and Upper Trapezius Muscle
ctivity in Patients with Chronic Nonspecific Neck Pain and Functional Dyspepsia: A Randomized, Double-Blind, Placebo-
ontrolled Pilot Study. Evidence-Based Compl and Alternative Medicine. 6, e4929271, 1–9 (2018). pi
y p p
tudy. Evidence-Based Compl and Alternative Medicine. 6, e4929271, p
., Kalytczak, M. M., Garcia, M. B. & Biasotto-Gonzalez, D. A. Ch 13. Politti, F., Casellato, C., Kalytczak, M. M., Garcia, M. B. & Biasotto-Gonzalez, D. A. Characteristics of EMG frequency bands in
temporomandibullar disorders patients. Journal of Electromyography and Kinesiology. 31, 119–125 (2016). 4. Lauer, R. T., Pierce, S. R., Tucker, C. A., Barbe, M. F. & Prosser, L. A. Age and Electromyographic Frequency Alterations during
Walking in Children with Cerebral Palsy. Gait & Poture. 31, 136–139 (2010). g
Children with Cerebral Palsy. Gait & Poture. 31, 136–139 (2010). g
y
5. Chiou, S. Y., Koutsos, E., Georgiou, P. & Strutton, P. H. Association between spectral characteristics of paraspinal muscles and
functional disability in patients with low back pain: a cohort study. BMJ Open. 8, e017091 (2018). y
p
p
y
p
16. Stergiou, N. & Decker, L. M. Human movement variability, nonlinear dynamics, and pathology: is there a connection? Human
Movement Science. 30, 869–88 (2011). 17. Giannasi, L. C. et al. References 1. Graaf, G. et al. Assessment of prevalence of persons with Down syndrome: a theory-based demographic model. Journal of Applied
Research in Intellectual Disabilities. 24, 247–262 (2011).h 1. Graaf, G. et al. Assessment of prevalence of persons with Down syndrome: a theory-based demographic model. Journal of Applied
Research in Intellectual Disabilities. 24, 247–262 (2011).h 2. Presson, A. P. et al. Current estimate of Down syndrome population prevalence in the United States. The Journal of Pediatrics. 163
1163–1168 (2013). y
p p
ph
f
1163–1168 (2013). 3 L
I T N
l
i
l h
f
D
d
h lif
P
i B
i R
h 197 101 121 (2012) (
)
3. Lott, I. T. Neurological phenotypes for Down syndrome across the life span. Progress in Brain Research. 197, 101–121 (2012). 4. Roizen, N. J. et al. A community cross-sectional survey of medical problems in 440 children with Down syndrome in New
State. The Journal of Pediatrics. 164, 871–75 (2014).h ,
J
y
y
p
y
State. The Journal of Pediatrics. 164, 871–75 (2014). d
Th b
d
(
) State. The Journal of Pediatrics. 164, 871–75 (2014). 5 Di
M D
d
Th b i i
i
i
d
N
R
i
N
i
13 844 858 (2012) h
f
5. Dierssen, M. Down syndrome: The brain in trisomic mode. Nature Reviews Neuroscience. 13, 844–858 (2012).h 6. Ballard, C., Mobley, W., Hardy, J., Williams, G. & Corbett, A. Dementia in down’s syndrome. The Lancet Neurology. 15, 622–636 (2016)
7. Lal, C., White, D. R., Joseph, J. E., van Bakergem, K. & LaRosa, A. Sleep-disordered breathing in Down syndrome. Chest. 147
570–579 (2015).hf (
)
8. Suharsini, M., Glinka, J. & Djokosalamoen, S. The effect of mastication muscular tone on facial size in patients with Down syndrome
Incisiva Dental Journal: Majalah Kedokteran Gigi Insisiva. 39(4), 161–64 (2006). 8. Suharsini, M., Glinka, J. & Djokosalamoen, S. The effect of mastication muscular tone on facial si
Incisiva Dental Journal: Majalah Kedokteran Gigi Insisiva. 39(4), 161–64 (2006). j
g
9. Faulks, D., Collado, V., Mazille, M. N., Veyrune, J. L. & Hennequin, M. Masticatory dysfunction in persons with Down’s syndrome. Part 1: a etiology and incidence. Journal of Oral Rehabilitation. 35, 854–62 (2008). gy
f
(
)
0. Suri, S., Tompson, B. D. & Cornfoot, L. Cranial base, maxillary and mandibular morphology in Down syndrome. The Angle
Orthodontist. Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z Acknowledgementsh g
This study was supported by Fundação De Amparo à Pesquisa do Estado de São Paulo- FAPESP, grant number
2017/06838-5. Competing interestsh g
The authors declare no competing interests. References The diagnostic value of electromyography in identifying patient
with pain-related temporomandibular disorders. Frontiers Neurology. 10, 180 (2019). p
p
gy
2. Nishi, S. E., Basri, R. & Alam, M. K. Uses of electromyography in dentistry: An overview with meta-analysis. European. Journal o
Dentistry. 10, 419–25 (2016). 33. Jian, C. et al. Multiparameter electromyographic analysis of the masticatory muscle activities in patients with brainstem stroke at
different head positions. Frontiers Neurology. 8, 221 (2017). f
34. Tang, X., Zhang, X., Gao, X., Chen, X. & Zhou, P. A novel interpretation of sample entropy in surface electromyographic examination
of complex neuromuscular alterations in subacute and chronic stroke. IEEE Transactions on Neural Systems and Rehabilitation
Engineering. 26, 1878–1888 (2018). 35. Álvarez-Méndez, A. M., Exposto, F. G., Castrillon, E. E. & Svensson, P. Systematic mapping of pressure pain thresholds of the
masseter and termporalis muscles and assessment of their diversity through the novel application of entropy. Journal Oral Facial
Pain Headache. 31, 362–371 (2017). 36. Inbar, G. F., Allin, J., Paiss, O. & Kranz, H. Monitoring surface EMG spectral changes by the zero crossing rate. Medical & Biological
Engineering & Computing. 24, 10–8 (1986). g
g
p
g
7. Pincus, S. M. Approximate entropy as a measure of system complexity. Proceedings of the National Academy of Sciences of the United
States of America. 88, 2297–301 (1991). 38. Pincus, S. M. & Goldberger, A. L. Physiological time-series analysis: what does regularity quantify? American Journal of Physiology. 266, H1643–56 (1994). (
)
39. Bruton, A., Conway, J. H. & Holgate, S. T. Reliability: what is it and how is it measured? Physiotherapy. 86, 94–9 (2000).i 40. Cicchetti, D. V. & Sparrow, S. S. Developing criteria for establishing inter-rater reliability of specific items: application to assessment
of adaptive behavior. American Journal of Mental Deficiency. 86, 127–37 (1981). Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z www.nature.com/scientificreports/ Author contributions All the authors contributed to the conception, design and performance of the study. L.C.G., F.P., M.A.C.S. and
M.F.G. provided the idea for the study, established the hypothesis and wrote the original proposal. L.C.G.,
V.L.S.T., G.R.C.S., G.P.M. and D.B.S. performed the acquisition of sEMG signals, patient electrode placement and
exported sEMG data. MTSD performed the data tabulation. J.B.O.A., L.C.G. and F.P. made the interpretation of
sEMG data. F.P. significantly contributed to sEMG signal and statistical analysis. J.B.O.A., L.V.F.O., C.S.O. and
L.C.G. were involved in critically revising the manuscript. M.A.C.S., L.C.G. and M.F.G. will supervise this study,
participate in its design and coordination and, will revise the manuscript that will lead to the final approval of the
current submission. All authors read and approved the final manuscript. The author J.C.R. will be responsible for
the screening of the patients that will be included in the study. Additional information Correspondence and requests for materials should be addressed to L.C.G. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the
copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2020 Scientific Reports | (2020) 10:7477 | https://doi.org/10.1038/s41598-020-63963-z
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Qeios · Definition, February 2, 2020 Open Peer Review on Qeios Open Peer Review on Qeios Canine Glioma National Cancer Institute National Cancer Institute Qeios ID: 51YLFD · https://doi.org/10.32388/51YLFD Source National Cancer Institute. Canine Glioma. NCI Thesaurus. Code C129297. National Cancer Institute. Canine Glioma. NCI Thesaurus. Code C129297. A brain or spinal cord tumor arising from glial cells that occurs in dogs. Qeios ID: 51YLFD · https://doi.org/10.32388/51YLFD 1/1
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To-Do and Not-To-Do in Model Studies of the Uptake, Fate and Metabolism of Metal-Containing Nanoparticles in Plants
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To cite this version: Justyna Wojcieszek, Javier Jiménez-Lamana, Lena Ruzik, Joanna Szpunar, Maciej Jarosz. To-Do and
Not-To-Do in Model Studies of the Uptake, Fate and Metabolism of Metal-Containing Nanoparticles
in Plants. Nanomaterials, 2020, 10 (8), pp.1480. 10.3390/nano10081480. hal-02943927 To-Do and Not-To-Do in Model Studies of the Uptake,
Fate and Metabolism of Metal-Containing Nanoparticles
in Plants Justyna Wojcieszek, Javier Jiménez-Lamana, Lena Ruzik, Joanna Szpunar,
Maciej Jarosz To cite this version:
Justyna Wojcieszek, Javier Jiménez-Lamana, Lena Ruzik, Joanna Szpunar, Maciej Jarosz. To-Do and
Not-To-Do in Model Studies of the Uptake, Fate and Metabolism of Metal-Containing Nanoparticles
in Plants. Nanomaterials, 2020, 10 (8), pp.1480. 10.3390/nano10081480. hal-02943927 Received: 6 July 2020; Accepted: 23 July 2020; Published: 28 July 2020 Abstract: Due to the increasing release of metal-containing nanoparticles into the environment,
the investigation of their interactions with plants has become a hot topic for many research fields. However, the obtention of reliable data requires a careful design of experimental model studies. The behavior of nanoparticles has to be comprehensively investigated; their stability in growth
media, bioaccumulation and characterization of their physicochemical forms taken-up by plants,
identification of the species created following their dissolution/oxidation, and finally, their localization
within plant tissues. On the basis of their strong expertise, the authors present guidelines for studies
of interactions between metal-containing nanoparticles and plants. Keywords: metal-containing nanoparticles; model plants; nano-bio interactions; transformations;
physico-chemical characterization; mass spectrometry HAL Id: hal-02943927
https://hal.science/hal-02943927v1
Submitted on 21 Sep 2020 L’archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
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lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers. nanomaterials nanomaterials Justyna Wojcieszek 1
, Javier Jiménez-Lamana 2,*
, Lena Ruzik 1, Joanna Szpunar 2
and
Maciej Jarosz 1 1
Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, 3 Noakowskiego str.,
00-664 Warsaw, Poland; jwojcieszek@ch.pw.edu.pl (J.W.); lenka@ch.pw.edu.pl (L.R.); mj@ch.pw.edu.pl (M.J.) 1
Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, 3 Noakowskiego str.,
00-664 Warsaw, Poland; jwojcieszek@ch.pw.edu.pl (J.W.); lenka@ch.pw.edu.pl (L.R.); mj@ch.pw.edu.pl (M.J.)
2
Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, Institute of Analytical and Physical Chemistry
for the Environment and Materials (IPREM), UMR 5254, 64053 Pau, France; joanna.szpunar@univ-pau.fr
*
Correspondence: j.jimenez-lamana@univ-pau.fr; Tel.: +33-540175090 1
Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, 3 Noakowskiego str.,
00-664 Warsaw, Poland; jwojcieszek@ch.pw.edu.pl (J.W.); lenka@ch.pw.edu.pl (L.R.); mj@ch.pw.edu.pl (M.J.)
2
Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, Institute of Analytical and Physical Chemistry
for the Environment and Materials (IPREM), UMR 5254, 64053 Pau, France; joanna.szpunar@univ-pau.fr
*
Correspondence: j.jimenez-lamana@univ-pau.fr; Tel.: +33-540175090 00 664 Warsaw, Poland; jwojcieszek@ch.pw.edu.pl (J.W.); lenka@ch.pw.edu.pl (L.R.); mj@ch.pw.edu.pl (M.J.)
2
Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, Institute of Analytical and Physical Chemistry
for the Environment and Materials (IPREM), UMR 5254, 64053 Pau, France; joanna.szpunar@univ-pau.fr
*
Correspondence: j.jimenez-lamana@univ-pau.fr; Tel.: +33-540175090 j
*
Correspondence: j.jimenez-lamana@univ-pau.fr; Tel.: +33-540175090
To-Do and Not-To-Do in Model Studies of the Uptake,
Fate and Metabolism of Metal-Containing
Nanoparticles in Plants Justyna Wojcieszek 1
, Javier Jiménez-Lamana 2,*
, Lena Ruzik 1, Joanna Szpunar 2
and
Maciej Jarosz 1 ustyna Wojcieszek 1
, Javier Jiménez-Lamana 2,*
, Lena Ruzik 1, Joanna Szpunar 2
and 1. Introduction On the other hand, metal-containing NPs may promote the
plant growth and seed germination. For example, exposure of tomato to strong irradiance and TiO2 NPs
resulted in better flower and fruit production, increased anthocyanin and carotenoids concentration and
high enzyme activity although rapid chlorophyll content decrease was also observed [11]. The uptake
and translocation of Fe3O4 NPs in Hordeum vulgare L. plants resulted in promoted gene expression and
increase of some phenological parameters such as chlorophyll, total soluble protein and number of
chloroplasts [9], although in Eichhornia crassipes plants a distinct decrease in chlorophyll content and
catalase activity and an increase of malondialdehyde (MDA) content was observed after Fe3O4 NPs
treatment at higher concentrations [19]. In this context, the comprehensive investigation of the behavior of metal-containing NPs throughout
the whole process of interaction with plants—uptake, bioaccumulation, and translocation—is needed. However, such a challenge can only be accomplished through a careful design of experiments, where
several factors must be taken into account, as well as through the use of several techniques that provide
complementary information. The use of each technique will depend on the specific behavior of each
metal-containing NPs (i.e., if they remain intact or they undergo dissolution and/or agglomeration) and
thus on their chemical and physical nature. A number of analytical techniques is being currently used for the analysis and characterization
of metal-containing NPs, such as transmission electron microscopy (TEM), scanning electron
microscopy (SEM), atomic force microscopy (AFM), X-ray diffraction (XRD), energy dispersive X-ray
spectroscopy (EDX), microbeam X-Ray Fluorescence (µ-XRF), microbeam X-ray absorption spectroscopy
(µ-XAS) [3,20]. Microscopy based techniques are a commonly accepted characterization tool, TEM being
the most widely used technique among them [4]. These techniques can provide information about
particle size, shape, and agglomeration of metal-containing NPs accumulated by plants at the cellular
and subcellular level [20]. However, the obtention of reliable data depends on statistical tools and a time
consuming sample preparation based on a drying process, which in addition can lead to aggregation
of NPs, especially in environmental samples [21]. On the other hand, synchrotron radiation (SR) based
techniques have great potential to investigate localization and speciation of metal-containing NPs
in plants. 1. Introduction The extensive use of metal-containing nanoparticles (NPs) in an increasing number of applications
is leading to their release into the environment, where they can interact with plants with unknown
effects [1]. This interaction may lead to some impact on plant physiological processes and eventually
to the bioaccumulation of NPs, and products of their metabolism, in the animal and human food chain. In the last years, the number of model studies focused on the investigation of interactions between
plant and engineered nanoparticles, especially metal-containing ones, has increased [2–4]. For example,
the bioaccumulation of silver nanoparticles (AgNPs) and aluminum oxide nanoparticles (Al2O3 NPs)
in roots of Lactuca sativa L. followed by their translocation to shoots has been demonstrated [5,6]. A similar behavior has been observed during the study of the uptake and translocation of lead sulfide
nanoparticles (PbS NPs), iron (III) oxide nanoparticles (Fe2O3 NPs) and magnetite nanoparticles (Fe3O4
NPs) in Zea mays L., Triticum aestivum L. and Hordeum vulgare L., respectively [7–9]. Contradictory
results have also been observed for the same type of metal-containing nanoparticles in different plants:
titanium oxide (TiO2 NPs) were not taken up by Coriandrum sativum L. [10], although their accumulation
and translocation in tomato [11] or radish plants [12] has been reported. On the other hand, NPs may
undergo different transformations after their accumulation in roots, followed by their translocation
to above-ground organs as it has been observed for selenium nanoparticles (Se NPs) and AgNPs in
garlic and Arabidopsis plants, respectively [13,14]. Finally, it is worth mentioning the accumulation
of AgNPs in stems of three different tree species was faster after foliar treatment compared to roots
treatment [15]. www.mdpi.com/journal/nanomaterials Nanomaterials 2020, 10, 1480; doi:10.3390/nano10081480 www.mdpi.com/journal/nanomaterials 2 of 16 Nanomaterials 2020, 10, 1480 After uptake and accumulation, metal-containing NPs can interact with plants at the cellular
and subcellular levels, facilitating changes to morphological and physiological states, which may be
suppressive or stimulatory [2]. For instance, Ag NPs caused oxidative stress and exhibited toxicity
when applied in higher concentrations to Allium cepa roots, regardless of surface coating used [16]. An increase of peroxidase, catalase, superoxide, dismutase activity, and inhibition in plant growth has
been detected in Lemna minor after copper oxide nanoparticles (CuO NPs) treatment [17]. It has also
been reported that the glutathione content and antioxidant power decreased significantly after Trigonella
foenum cultivation with Al2O3 NPs [18]. 1. Introduction The combination of high-resolution synchrotron x-ray fluorescence microscopy (SR-XFM),
offering multi-elemental detection down to the tens of nm, and spatially resolved XAS is a powerful
technique that can provide information about elemental composition, localization and chemical
speciation with minimal sample preparation and non-destructive analysis [22]. For instance, it has
been successfully applied to the study TiO2 NPs [23,24], AgNPs [23,25], zinc oxide nanoparticles
(ZnO NPs) [26,27] or cerium oxide nanoparticles (CeO2 NPs) [27] in different plants. The application
of these techniques to the study of interactions between NPs and plants has been recently reviewed by
Castillo-Michel et al. [22]. However, the majority of these techniques are inadequate for the characterization of NPs in
complex matrices at low concentrations. In this context, the use of analytical methods based on
the high-sensitive and element-specific technique of inductively coupled plasma mass spectrometry
(ICP-MS) allows NPs detection at environmentally relevant concentrations. Indeed, an analytical
tool that has become popular in these kinds of studies is Single Particle (SP) ICP-MS, thanks to a
combination of the benefits of ICP-MS, with those of a particle counting technique [28]. SP-ICP-MS can
provide information about the particle size, particle size distribution as well as quantitative information
about the metal in its dissolved and nanoparticulate form in a single analysis. Typically, the analysis of 3 of 16 Nanomaterials 2020, 10, 1480 a NP solution by SP-ICP-MS produces a time scan with two different types of signal: a steady signal at
low counts due to the background or the presence of the analyte in its dissolve form; and a number of
pulses above the background due to the presence of the analyte in its nanoparticulated form [29]. Authors present here a step-by-step guideline in order to obtain reliable data in metal-containing
NPs-plant interaction studies, including: the study of the stability of NPs in nutrient solutions used for
plant cultivation; the optimization of a procedure able to extract NPs from the plant matrix without
altering their properties; the analysis of NPs in plant tissues by monitoring their possible transformations;
the identification of new metal species created within the plant as a result of dissolution/oxidation
processes; the study of the spatial distribution of NPs in plant tissues. A flowchart with the necessary
steps in these kinds of studies is shown in Figure 1. 2. Transformation of Metal-Containing Nanoparticles in Growth Media Model studies carried out in order to get deeper insight about metal-containing NPs interactions
with plants include several steps. The first one involves the growth of plants in the presence of
metal/metal oxide NPs in a soil environment or in a hydroponic solution, being the latter the most used
in literature. Different media can be used for plant cultivation, for example, Murashige and Scoog,
Hoagland or Knop nutrient solution [30,31]. The composition of the nutrient solution may have a negative impact on the interpretation of the
results and may need to be adapted or modified. On the one hand, and due to the high sensitivity
of the analytical techniques used in this kind of study, the presence of the metal of interest even at
low concentration in the medium may lead to the occurrence of false positives when it comes to the
analysis of plant tissues. For instance, salts usually present in growth media, like ZnSO4, CuSO4 or
FeSO4, should be removed during the analysis of ZnO, CuO or Fe2O3 NPs, respectively. A possible
alternative could be the use of isotopically labeled metal NPs, which would allow the discrimination
from different metal sources. Isotopic labeling of NPs enables their sensitive tracing in the presence of
background elements in complex plant matrices [32]. On the other hand, special attention has to be
paid if metal compounds with complexing agents such as ethylenediaminetetraacetic acid (EDTA),
iminodiacetic acid (IMDA) or diethylenetriaminepentaacetic acid (DTPA) are added to a growth
solution. For example, the presence of EDTA, a very strong ligand, can bind metal ions potentially
released from the analyzed NPs and shift the equilibrium in the system, leading hence to biased results. In addition, the identification of metal-EDTA complexes created as a result of metal releasing from NPs
will not be useful information as this kind of compound cannot be formed inside plant tissues. In this
context, Fe-EDTA present in growth media like Knop nutrient solution must be replaced by another
salt, like FeSO4 [33]. Metal-containing NPs are reactive species that can interact with the surrounding environment. In this context, the stability of NPs in the growth medium used for plant cultivation needs to be
investigated before the cultivation and analysis of plants. These studies are usually performed by
spiking the nutrient solution with a suspension of metal-containing NPs followed by its analysis
immediately upon addition of the NPs suspension and over time. 1. Introduction Authors use their extensive experience with the
investigation of NPs of different chemical nature and properties to explain the different scenarios
stressing some critical points where special attention needs to be paid. It must be stated that the
guidelines described here apply to the experimental scheme shown in Figure 1, through the use of
different analytical techniques based on mass spectrometry, which has proven to give comprehensive
information. However, it must be highlighted that, besides the general rules draw in this manuscript,
each type of metal-containing NP has specific properties (size, shape, type of metal, coating, etc.) and
will require an individual study. 4 of 16 Nanomaterials 2020, 10, 1480 Figure 1. Flowchart presenting possible scenarios and steps to be carried out during studies of nanoparticles (NPs)–plant interactions. Figure 1. Flowchart presenting possible scenarios and steps to be carried out during studies of nanoparticles (NPs)–plant interactions. Figure 1. Flowchart presenting possible scenarios and steps to be carried out during studies of nanoparticles (NPs)–plant interactions. Nanomaterials 2020, 10, 1480 5 of 16 2. Transformation of Metal-Containing Nanoparticles in Growth Media The last analysis should be performed
at the endpoint time of the subsequent plant cultivation. This previous study is critical in model
studies of NPs-plants interaction in order to elucidate if the possible transformations of NPs take
place before or after their uptake by plants. In general, there are three possible scenarios according
to the transformations that NPs can undergo: (i) NPs remain unchanged in medium; (ii) NPs are
partially or totally dissolved; and (iii) NPs agglomerate over time. The occurrence (or not) and extent
of these transformations will depend on the nature of the NPs used and requires an individual and
specific study. For this purpose, SP-ICP-MS is a technique that can provide information about NP size
distribution and the physico-chemical form of the metal of interest in a single analysis, which makes it
an ideal tool to monitor possible NP transformation in growth medium. Examples of application of
SP-ICP-MS to the characterization of metal-containing nanoparticles in hydroponic solution under the
three mentioned scenarios are described below. The simplest situation that may happen during the study of the stability of NPs in a nutrient
solution is that they are stable during the whole cultivation period. In that case, the obtained size
distribution must be in good agreement with that obtained for the stock suspension [34]. Additionally,
in SP-ICP-MS, the absence of a high background signal (corresponding to the metal in its dissolved
from) and pulses of high intensity signal (corresponding to NPs of bigger sizes) will prove that NPs do
not undergo any transformation such as dissolution or agglomeration in nutrient solution used for
plant cultivation. As a consequence, any NPs transformation detected during the analysis of tissues of
treated plants, must be attributed to processes taking place inside plant tissues, after the uptake and
accumulation of NPs. However, growth medium can cause the dissolution of metal-containing NPs. It can happen
especially in the case of microelements that are present in high abundance in natural environments, 6 of 16 Nanomaterials 2020, 10, 1480 such as zinc or copper, usually present in different forms such as free ions, compounds with different
bioligands or as a component of rocks. This phenomenon can be easily identified thanks to the use of
SP-ICP-MS. 2. Transformation of Metal-Containing Nanoparticles in Growth Media In this case, on the time scans obtained during SP-ICP-MS analysis of growth medium,
a steady signal, i.e., characteristic of the dissolved form of the metal, is registered, whereas a significant
number of pulses proving the presence of NPs is observed after analysis of fresh NPs stock suspension. If only a steady signal is observed after analysis of growth medium, it leads to the conclusion that
plants are mainly taking up metal in its dissolved form and therefore the accumulation of NPs is
negligible. In the case of the presence of only the dissolved form of metal, speciation studies leading to
the quantification and identification of metal complexes formed inside the plant tissues must be carried
out, as it is explained in detail in Section 6 of this manuscript. The dissolution of NPs is time dependent
and can be partial, with both dissolved and particulate form of metal present in the growth medium. In this case, if both forms of metal are taken up by plants, both NP characterization by SP-ICP-MS as
well as speciation studies by the use of hyphenated techniques should be performed. If only metal
ions are taken up by plants, then characterization of NPs is not possible and the direction of the study
has to be changed. The dissolution rate of NPs strongly depends on media composition as well as on
the surface coating of NPs. It has been shown in different studies that bare nanoparticles are more
susceptible to transformation than coated NPs [35,36]. In the last scenario, NPs can undergo agglomeration as it was observed for some nanoparticles
based on metal oxides [12,37]. In this case, the extent of the agglomeration must be determined since it
may have an influence on the potential uptake by the plant. For instance, it can happen that the median
diameter of NPs shifts slightly toward bigger sizes after different times of incubation or that NP size
duplicate or triplicate, which leads to the conclusion that NPs can undergo agglomeration in a smaller
or bigger degree after different contact time with growth medium. In any case, the critical point is to
determine whether agglomerates of NPs created in a nutrient solution are taken up by plant tissues. Typically, only NPs at smaller sizes than those observed in the growth medium are accumulated in
plant leaves and roots [12,37,38]. 4. Extraction of Intact Nanoparticles Although analysis of total metal content provides a general idea of the metal bioaccumulation
by plants, when it comes to studies with metal-containing NPs, important information like the
physico-chemical form, the size distribution or the nanoparticle number concentration is lost after acid
digestion. The correct interpretation of the data strongly depends on the extraction of NPs from the
plant matrix preserving their native conditions. Therefore, the first important step in the analytical
procedure is to develop and optimize an efficient extraction process of NPs from plant material. Plant tissue matrix is generally made of some or all of the following components: macro and
micronutrients, vitamins, amino acids or other nitrogen supplements. In addition, the plant cell wall is
composed primarily of polysaccharides, cellulose being its major component, and it is organized into
paracrystalline structures inserted in a rich matrix of diverse polysaccharides, including hemicelluloses
and pectins, structural glycoproteins and lignin in certain tissues [44]. NPs can penetrate through the cell wall, so the digestion of polysaccharides is needed (for example,
pectin consists of four major polysaccharide domains: homogalacturonan (HGA), rhamnogalacturonan
I (RGI), rhamnogalacturonan II (RGII) and xylogalacturonan (XGA)) with the preservation of the NPs at
the same time. This can be done through the use of alkaline solutions or enzymes, for example, pectinase,
hemicellulase, and cellulase, which are perfectly suited for breaking down the polysaccharides found
in plant cell walls. Alkaline treatments with tetramethylammonium hydroxide (TMAH) have shown
a high-efficiency extraction of different NPs (Ag, Au, or carbon nanotubes) from tissues with a low
amount of salts remaining in solution after digestion [45]. It should be mentioned that an alkaline
treatment followed by SP-ICP-MS analysis could not be used for extracting AgNPs from tissue samples. This is important information regarding the changes in the state of AgNPs, most probably due to Ag+
precipitation and/or AgNPs aggregation [46]. Enzymatic digestion, which commonly works with mild conditions, i.e., at moderate temperatures
and pH conditions, can be an appealing sample pre-treatment for isolating NPs without their
degradation. The use of a multi-component enzyme mixture containing cellulase, hemicellulase,
and pectinase (Macerozyme R-10) was proposed by Dan et al. for isolating gold nanoparticles (AuNPs)
from roots of tomato plants [47]. In addition, a suitable extraction method should not only extract intact
NPs but also a representative amount of them. For this purpose, the mentioned enzymatic digestion
method was further developed by Jimenez-Lamana et al. [34]. 3. Sample Preparation and Total Content Determination After an investigation of NPs stability in nutrient solution, the cultivation of plants in the
presence of NPs and control plants is the next step to be carried out. Afterward, plants are divided
into different organs/tissues and subsequently grounded. The use of a pestle and mortar is highly
recommended. The translocation factor from roots to above-ground organs can be easily calculated at
this stage, by determining the total content of metal within the different plant organs. For this purpose,
mineralization processes with oxidizing acids and heating systems or microwave-assisted techniques
are commonly used for acid digestion of organic matrices [43], followed by quantitative analysis by
standalone ICP-MS or inductively coupled plasma optical emission spectrometry (ICP-OES). The choice
of the acid(s) used for the digestion of plant tissues will depend on the nature of the metal the NPs are
made of. Some metal-containing nanoparticles can dissolve under acidic conditions, mainly by the
use of concentrated nitric acid, but others will require different or additional reagents: aqua regia for
platinum nanoparticles (PtNPs) and palladium nanoparticles (PdNPs) [34,38]; hydrogen peroxide for
ZnO NPs and CeO2 NPs [33,37]; or hydrofluoric acid for TiO2 NPs. 2. Transformation of Metal-Containing Nanoparticles in Growth Media The occurrence of agglomeration processes can be avoided by the use
of coated-NPs and/or by the addition of some additional reagents such as organic acids or enzymes to
the solution used for plant cultivation. The former option is clearly advised, since the latter may be
problematic from the point of view of mimicking natural conditions and should be avoided as much
as possible. As it has been described on the three scenarios, is it important to monitor the possible transformation
processes of NPs in growth medium used during plant cultivation. The use of SP-ICP-MS can provide
clear information on whether NPs are stable or if they undergo different transformations such as
dissolution or agglomeration in a single analysis. Finally, it should be mentioned that the studies of the interaction between metal-containing NPs
and plants can also be performed in solid media, in order to mimic natural conditions, where NPs are
released into soil environments. Therefore, the stability of metal-containing NPs in a soil environment
must be investigated, not only to investigate the uptake by plants but also to understand the terrestrial
toxicity of NPs [39]. However, these studies are less convenient than those performed in a liquid
medium, since they imply an additional sample preparation step: the extraction of NPs from the solid
medium without changing their physico-chemical form. In this context, extractions with purified water
and with tetrasodium pyrophosphate (TSPP), with sonication to enhance particle dispersion, followed
by analysis by SP-ICP-MS have been proposed [40,41]. The type of media (liquid or solid) used for
plant cultivation may have a significant influence on NPs properties. For example, the bioavailability
and the effect of the silver ions released by AgNPs have been shown to be lower in a soil medium
compared with an agar medium [42]. In any case, regardless of the medium used for plant cultivation,
the fate and possible transformations of NPs must be monitored. Nanomaterials 2020, 10, 1480 7 of 16 7 of 16 4. Extraction of Intact Nanoparticles As it was demonstrated in this study,
different parameters (type of buffer used, amount of sample, amount of enzyme, sonication power,
sonication time, incubation time) need to be studied and optimized to obtain the highest number of
NPs from the different plant tissues. A typical enzymatic digestion procedure for the extraction of metal-containing NPs from plant
tissues is shown in Figure 2. It is important to highlight the use of well-grounded samples in order to 8 of 16 Nanomaterials 2020, 10, 1480 provide the maximum physical contact between sample and reagents. Ground samples are mixed
with citrate buffer and the mixture is next homogenized using an ultrasonic probe while the tube is
kept in ice. Milder procedures, like bath sonication or shaking, should be avoided, since they do not
provide a successful extraction of NPs from plant tissues. On the other hand, nominal powers of a
probe higher than 35% are not recommended, to avoid excessive heating of the sample. After the end
of homogenization, the enzyme solution is added. The samples are shaken in a water bath at 37 ◦C for
24 h. After the incubation, the obtained suspensions are filtered with a 0.45 µm syringe filter because
of the presence of a remaining solid after homogenization and incubation. Figure 2. Steps to be performed in a typical enzymatic digestion procedure. Figure 2. Steps to be performed in a typical enzymatic digestion procedure. Important precautions must be taken depending on the nature of the metal-containing NPs object
of the study. For instance, the sonication probe may leach significant amounts of titanium into the
suspension which, even at trace levels, may lead to the contamination of the plant samples and hence
the occurrence of false positives in studies of TiO2 NPs interactions with plants [12]. To avoid that,
a tissue grinder set can be used instead. The effect that the digestion procedure may have on NPs (dissolution and/or aggregation)
must be investigated. To do so, the same procedure must be performed on a suspension of the
metal-containing NPs followed by its analysis. As indicated above, the characterization and monitoring
of metal-containing NPs and the processes they may undergo can be easily carried out by SP-ICP-MS. In one single analysis, SP-ICP-MS can provide the necessary information to decide if the chosen
digestion protocol is suitable for extracting NPs from the plant tissues without altering their properties. 4. Extraction of Intact Nanoparticles Finally, the influence of the plant matrix can be additionally investigated by submitting control plant
tissues (i.e., cultivated in the absence of NPs) spiked with a suspension of metal-containing NPs to the
digestion procedure, obtaining the corresponding size distributions by SP-ICP-MS and comparing
with the original NP size distribution. It is important to mention that the use of a filtration step after the digestion procedure could imply
the loss of bigger NPs [12], leading to unreliable results. In that case, filtration should be discarded
and it is advisable to let the suspensions settle down after digestion for at least one hour and take the
supernatants to analyze. The use of centrifugation at this step is not recommended since NPs will also
settle down to the bottom of the suspension. 5. Uptake, Translocation and Biotransformation Once the stability of the metal-containing NPs suspension in the growth media and the suitability
of the digestion procedure has been investigated, the plant cultivation in the presence of NPs must be
carried out. During this process, a complementary evaluation by plant scientists should be carried out,
i.e., the tolerance of the plant to the NP concentration in terms of phytotoxic effects. Different factors,
such as color of plant tissues, biomass production or tissue hydration can be determined and compared
with those obtained for control plant samples. If possible, detailed tests for eventual phytotoxicity on
the cellular level should be undertaken. 9 of 16 Nanomaterials 2020, 10, 1480 As it was mentioned above, the total content of metal taken up by the plant does not provide
information about the form of element accumulated in plant tissues or about possible transformations
of NPs that can happen during uptake and transport. In this context, and in order to investigate
the physico-chemical form of metal accumulated inside plant tissues, SP-ICP-MS can be a valuable
tool. It is important to mention that in SP-ICP-MS, the dilution of the sample plays an important
role, in order to be able to detect signals produced by individual NPs. Typically, samples with NP
concentration around 1 × 108 NP L-1 are analyzed in SP-ICP-MS. This is especially important in the case
of roots, where higher NPs concentrations are expected. Different scenarios can be considered during
SP-ICP-MS analysis, depending on several factors such as the chemical nature of the metal-containing
NPs, type of plant or conditions of cultivation. Similarly to the investigation of metal-containing NPs stability in the growth media, unchanged
NPs can be taken up and accumulated in plants, i.e., no transformations such as agglomeration or
dissolution take place. This can be easily observed by a simple comparison of the size distributions
obtained in plant tissues with the one obtained for a fresh suspension of the metal-containing NPs. The presence of NPs in both roots and leaves presenting the same size distribution and nominal
diameter as the stock NPs suspension means that analyzed plant has an ability not only to uptake and
accumulate NPs in roots but also to translocate them to above ground organs. A different situation can be found when metal-containing NPs undergo agglomeration inside plant
tissues [34]. This phenomenon can be clearly seen when observing the size distribution obtained by
SP-ICP-MS. 5. Uptake, Translocation and Biotransformation If the agglomeration process occurs, two populations are observed on the size distribution:
a main one at sizes close to the nominal diameter, corresponding hence to unchanged NPs; and a second
population at larger sizes not observed during the analysis of stock suspension. In order to elucidate at
which step of the plant cultivation the metal-containing NPs undergo agglomeration, the particle size
distribution obtained in the roots must be compared with the one obtained previously in the stability
study in growth media. If no agglomeration is observed in the nutrient solution spiked with NPs,
the presence of second distribution at higher sizes will imply that NPs undergo agglomeration during
their uptake. On the other hand, agglomeration can already occur in a nutrient solution used for plant cultivation. Again, a comparison between NP size distributions obtained in plant tissues and those obtained in
the growth medium spiked by NPs over time must be performed. The key question here is whether
agglomerates eventually created in a nutrient solution are taken up by plant tissues. For example,
only smaller NPs may be taken up by plant roots, followed by the transport of intact NPs to stems
and leaves [12], suggesting that agglomerates are not taken up by plant tissues. This can be easily
recognized by a simple comparison of size distributions, since if only smaller NPs are taken up by plants,
size distributions obtained in roots after plant cultivation will present particles with lower diameters
in comparison with analysis of NPs suspension in growth medium. However, it can also happen,
despite the fact that only smaller NPs are taken up by roots, that bigger NPs are found in the analysis
of leaves and stems [37]. In this case, the results suggest that NPs can also undergo agglomeration at
the endpoint of their transportation, where nanoparticles are more locally concentrated and hence
agglomeration by contact is more likely to occur. The uptake of metal ions followed by re-precipitation
can also be considered as a pathway of NPs accumulation in plants, which was already suggested
during analysis of CeO2 NPs in three plant species by scanning transmission electron microscopy
(STEM) [48]. Finally, the dissolution of NPs can also be observed after SP-ICP-MS analysis, which resulted in a
steady signal on time scans, without pulses characteristic for particulate form of metal. Similarly to
the case of agglomeration, dissolution can appear at different stages of the experiment. 5. Uptake, Translocation and Biotransformation For instance,
partial dissolution of metal-containing NPs may occur inside plant tissues after their uptake as intact
NPs [38], which brings the opportunity to study both NPs characterization by SP-ICP-MS together
with metal speciation in plant tissues by the use of separation techniques coupled to mass spectrometry
detection [38]. 10 of 16 Nanomaterials 2020, 10, 1480 Figure 3 reflects how a simple comparison of size distributions obtained by SP-ICP-MS of
metal-containing NPs in growth medium, roots and leaves can provide useful information. Example 1
shows the case of NPs that agglomerate in growth medium, only smaller ones are taken up by the plant
and a re-agglomeration process occurs during transport to leaves. In example 2, agglomerates are not
taken up from medium either but NPs remain intact during transport. Finally, in example 3, NPs remain
unchanged in growth medium but they undergo agglomeration during uptake and/or transport. Figure 3. Comparison of size distributions obtained for metal-containing NPs in growth medium,
roots and leaves in 3 different scenarios. Figure 3. Comparison of size distributions obtained for metal-containing NPs in growth medium,
roots and leaves in 3 different scenarios. 6. Speciation Studies As it has been mentioned, metal-containing NPs may undergo partial or total dissolution in the
nutrient solution, leading to the uptake of metal ions by roots [33]. The analysis of the total metal
content in plant organs can provide preliminary conclusions about the physico-chemical form of NPs,
as the translocation factor of analyzed metal from roots to leaves is usually significantly higher if
dissolved metal is transported within the plant. If the dissolution of the metal-containing NPs in
growth medium is suspected, the cultivation of an additional set of plants treated with corresponding
metal salt at the same metal concentration is recommended. In this case, the comparison of total
metal content in plant tissues treated with metal salt and metal-containing NPs can give additional
information about the uptake mechanisms. In any case, and regardless of whether a dissolution process
takes place already in the growth medium used for plant cultivation or inside plant tissues after NPs
uptake and accumulation, the presence of the dissolved form of metal redirects the investigation
towards another direction. The key point is that the presence of the metal in its free form may lead to the formation of new
species inside the plant and hence studies on metal speciation to determine and identify these new
species are needed. For this purpose, the extraction of metal compounds formed in plant tissues
must be carried out in order to release them from solid matrix. If one-step extraction turns out to be
insufficient, additional steps should be applied, for example, by the use of enzymes such as pectinase
or cellulase. The use of these enzymes leads to an increase of extraction efficiency by degradation of the
plant cell wall, which allows the release of metal accumulated in this part of the tissue. The efficiency
of extraction can be determined by the digestion of each extract followed by metal content analysis
and comparison with the total metal concentration. It should be highlighted that, due to its different
chemical nature, procedure of extraction of metal compounds must be different than the digestion
procedure used for extraction of intact NPs from plant tissues. 6. Speciation Studies 11 of 16 Nanomaterials 2020, 10, 1480 Speciation analysis can be successfully performed by the use of hyphenated techniques, based on
the coupling of effective separation technique such as chromatography or electrophoresis to ICP-MS
for sensitive element-specific detection or/and to mass spectrometry with soft ionization (electrospray
(ESI) MS, matrix-assisted laser desorption/ionization (MALDI) MS) for identification of a compound
structure. For analysis of complicated matrix such as plant samples, an initial fractionation of extracted
compounds in terms of molecular mass can be performed by size exclusion chromatography (SEC)
coupled to ICP-MS. SEC is used for simple fractionation of metallocompounds according to their
molecular mass. In addition, SEC analyses are performed under mild conditions and without the
use of organic solvents, which is important to maintain the stability of metal species. However,
each peak obtained during SEC-ICP-MS analysis contains a significant number of metal compounds,
since resolution of SEC is rather low. Therefore, prior to the identification of extracted complexes,
a different technique that allows better separation of initially fractionated species, should be applied. One of the possible options is that after SEC-ICP-MS analysis, fractions corresponding to each peak
observed on the chromatograms can be collected, lyophilized and analyzed by hydrophilic interaction
chromatography (HILIC) coupled to ICP-MS [7], which provides a more efficient separation of metal
compounds, in terms of their polarity. Results obtained by using ICP-MS as an elemental detector
provide information about type and nature of extracted metal complexes, without information about the
ligands bound to the analyzed metal. Therefore, after characterization of the extracted metal species by
means of two-dimensional liquid chromatography coupled to ICP-MS, identification of the compounds
formed in plant tissues must be performed. For this purpose, tandem mass spectrometry (MS/MS) with
soft ionization such as ESI or MALDI is usually used by fragmentation of molecular ions and detection
of specific fragment ions. It can be performed by direct analysis of samples or after their separation
using chromatographic techniques. However, in the case of matrices that contain many different
compounds, the results obtained by direct MS/MS analysis can be complex to interpret. In order to
identify extracted metal complexes, HILIC chromatography coupled to high resolution electrospray
tandem mass spectrometry (ESI-MS/MS) is highly recommended to use. HILIC chromatography is
well suited to mass spectrometry detection, as typical eluents used in this separation technique contain
a high percentage of organic solvent in water or volatile buffer. 6. Speciation Studies The high resolution of state-of-the-art
ESI-MS together with high mass accuracy allow for automatic data mining in search for metal species
and organic compounds, based on their isotopic patterns and species mass defects. The mass spectrum
registered during analysis of extracted metal compounds must be searched for parent ions with a
specific isotopic pattern corresponding to analyzed metal (unless it is monoisotopic) and chosen
ions should be fragmented next for determination of species structure. Collision energy should be
optimized during analysis since it may occur that fragmentation is too strong or not strong enough
and contribution of the parent ion is too big. Thanks to this approach, the identification of extracted
complexes can be confirmed in terms of molecular mass, MS/MS fragmentation and by matching of the
registered isotopic patterns with the theoretical ones. If there is one major metal compound observed,
the quantification can be carried out by an external calibration curve and/or standard addition method. Finally, it should be highlighted that the use of hyphenated techniques for metal speciation
i
i
t i
ll
th
d t
ti
d id
tifi
ti
f
i
t l
l
t Finally, it should be highlighted that the use of hyphenated techniques for metal speciation
in various matrices allows the detection and identification of even minor metal complexes at
environmentally relevant concentrations. 7. Spatial Distribution The detection and characterization of NPs in above ground tissues demonstrates the ability of
plants to take up and translocate NPs. However, the exact pathways and mechanisms of uptake and
transport of NPs are still unclear. For example, damage of the physiological barriers of roots [4] or
penetration into the root epidermis and cortex through the apoplastic pathway have been suggested [49]. In this context, the study of the spatial distribution of metal-containing NPs in plant roots can help in
filling this gap. 12 of 16 12 of 16 Nanomaterials 2020, 10, 1480 The analytical techniques described so far are not able to provide this information. However,
Laser Ablation (LA) ICP-MS has proved to be a valuable analytical tool for bioimaging of metal species
in plant tissues [50]. This technique is based on the vaporization of a solid sample by using pulses
from a focused laser beam, the ablated material being transported to the ICP-MS in a gas flow of Ar or
He [51]. Even though LA-ICP-MS is not able to provide information about the physico-chemical form
of the metal analyzed, it can be successfully applied when the information about the presence of the
metal in its nanoparticulate form has been confirmed by another technique [37]. Sample preparation is
a critical step for the analysis of plant organs by LA-ICP-MS. Usually, thin layers of the plant tissue
are prepared with a microtome, which are directly mounted into glass slides. However, the sample
preparation procedure will depend on the shape and geometry of the analyzed organ. The analysis
performed by LA-ICP-MS can provide useful information about the localization of NPs inside the
tissue that will help to elucidate the uptake and transport mechanisms. For instance, the accumulation
and transport of CeO2 NPs by secondary roots from the bottom towards the central part of radish
roots was suggested after analysis by LA-ICP-MS [37]. LA-ICP-MS can also provide quantitative information but requires the use and availability of
matrix matching standards to constitute calibration curves and appropriate internal standards (IS)
to compensate signal variation during laser beam-sample interaction, transportation of the aerosol,
and instrumental drifts [52,53], making the analyses more complex. In addition, the use of a single
imaging technique like LA-ICP-MS may result insufficient in studies at low concentrations, where the
few observable NPs can be almost indistinguishable from naturally occurring NPs or other background
signals [54]. 7. Spatial Distribution It is then advisable, when possible, to combine the information obtained about spatial distribution
of metal nanoparticles by LA-ICP-MS, with the information obtained with other analytical techniques:
total metal determination (ICP-MS) and characterization of physico-chemical form (SP-ICP-MS). References Effects, uptake, and translocation
of aluminum oxide nanoparticles in lettuce: A comparison study to phytotoxic aluminum ions. Sci. Total
Environ. 2020, 719, 137393. [CrossRef] 6. Hayes, K.L.; Mui, J.; Song, B.; Shirzaei, E.; Eisenman, S.W.; Shef, J.B.; Kim, B. Effects, uptake, and translocation
of aluminum oxide nanoparticles in lettuce: A comparison study to phytotoxic aluminum ions. Sci. Total
Environ. 2020, 719, 137393. [CrossRef] 7. Ullah, H.; Li, X.; Peng, L.; Cai, Y.; Mielke, H.W. In vivo phytotoxicity, uptake, and translocation of
nanoparticles in maize (Zea mays L.) plants. Sci. Total Environ. 2020, 737, 139558. [CrossRef] 8. Al-amri, N.; Tombuloglu, H.; Slimani, Y.; Akhtar, S. Size effect of iron (III) oxide nanomaterials on the growth,
and their uptake and translocation in common wheat (Triticum aestivum L.). Ecotoxicol. Environ. Saf. 2020,
194, 110377. [CrossRef] 9. Tombuloglu, H.; Slimani, Y.; Tombuloglu, G.; Almessiere, M. Uptake and translocation of magnetite (Fe3O4)
nanoparticles and its impact on photosynthetic genes in barley (Hordeum vulgare L.). Chemosphere 2019, 226,
110–122. [CrossRef] 10. Hu, J.; Wu, X.; Wu, F.; Chen, W.; White, J.C.; Yang, Y.; Wang, B.; Xing, B.; Tao, S.; Wang, X. Potential application
of titanium dioxide nanoparticles to improve the nutritional quality of coriander (Coriandrum sativum L.). J. Hazard. Mater. 2020, 389, 121837. [CrossRef] 11. Ko, J.A.; Hwang, Y.S. Effects of nanoTiO2 on tomato plants under different irradiances. Environ. Pollut. 2019,
255, 113141. [CrossRef]
12
Wojcieszek J ; Jimenez Lamana J ; Ruzik L ; Asztemborska M ; Jarosz M ; Szpunar J Characterization of 255, 113141. [CrossRef]
12. Wojcieszek, J.; Jimenez-Lamana, J.; Ruzik, L.; Asztemborska, M.; Jarosz, M.; Szpunar, J. Characterization of
TiO2 NPs in radish (Raphanus sativus L.) by Single Particle ICP-QQQ-MS. Front. Environ. Sci. 2020, 8, 100. 2. Wojcieszek, J.; Jimenez-Lamana, J.; Ruzik, L.; Asztemborska, M.; Jarosz, M.; Szpunar, J. Characterizatio
TiO2 NPs in radish (Raphanus sativus L.) by Single Particle ICP-QQQ-MS. Front. Environ. Sci. 2020, 8, 10 13. Li, Y.; Zhu, N.; Liang, X.; Zheng, L.; Zhang, C.; Li, Y. A comparative study on the accumulation, translocation
and transformation of selenite, selenate, and SeNPs in a hydroponic-plant system. Ecotoxicol. Environ. Saf. 2020, 189, 109955. [CrossRef] [PubMed] 14. Bao, D.; Zheng, G.O.; Chen, Z. Characterization of silver nanoparticles internalized by Arabidopsis plants
using single particle ICP-MS analysis. Front. Plant Sci. 2016, 7, 1–8. [CrossRef] [PubMed] 15. obtained about the physico-chemical form of NPs inside plants, can provide new insights about
the uptake and translocation pathways. obtained about the physico-chemical form of NPs inside plants, can provide new insights about
the uptake and translocation pathways. Author Contributions: J.W. and J.J.-L. wrote and revised the original draft and prepared the final version of the
manuscript. L.R. contributed to the writing, revision and figure preparation. J.S. conceptualized, reviewed and
advised the work. M.J. has supervised and managed the funding resources. All authors have read and agreed to
the published version of the manuscript. Funding: This work was financially supported by Warsaw University of Technology and the National Science
Centre, Poland (grant No. 2015/18/M/ST4/00257) Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the design of the
study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to
publish the results. References 1. Ma, X.; Geiser-lee, J.; Deng, Y.; Kolmakov, A. Interactions between engineered nanoparticles (ENPs) and
plants: Phytotoxicity, uptake and accumulation. Sci. Total Environ. 2010, 408, 3053–3061. [CrossRef] [PubMed]
2
Khan M R ; Adam V; Rizvi T F ; Zhang B ; Ahamad F ; Josko I ; Zhu Y; Yang M ; Mao C 1. Ma, X.; Geiser-lee, J.; Deng, Y.; Kolmakov, A. Interactions between engineered nanoparticles (ENPs) and
plants: Phytotoxicity, uptake and accumulation. Sci. Total Environ. 2010, 408, 3053–3061. [CrossRef] [PubMed] 1. Ma, X.; Geiser-lee, J.; Deng, Y.; Kolmakov, A. Interactions between engineered nanoparticles (ENPs) and
plants: Phytotoxicity, uptake and accumulation. Sci. Total Environ. 2010, 408, 3053–3061. [CrossRef] [PubMed]
2. Khan, M.R.; Adam, V.; Rizvi, T.F.; Zhang, B.; Ahamad, F.; Josko, I.; Zhu, Y.; Yang, M.; Mao, C. Nanoparticle—Plant interactions: Two-way traffic. Small 2019. [CrossRef] [PubMed] 2. Khan, M.R.; Adam, V.; Rizvi, T.F.; Zhang, B.; Ahamad, F.; Josko, I.; Zhu, Y.; Yang, M.; M
Nanoparticle—Plant interactions: Two-way traffic. Small 2019. [CrossRef] [PubMed] 3. Shrivastava, M.; Srivastav, A.; Gandhi, S.; Rao, S.; Roychoudhury, A.; Kumar, A.; Singhal, R.K.; Kumar, S.;
Singh, S.D. Monitoring of engineered nanoparticles in soil-plant system: A review. Environ. Nanotechnol. Monit. Manag. 2019, 11, 100218. [CrossRef] 3. Shrivastava, M.; Srivastav, A.; Gandhi, S.; Rao, S.; Roychoudhury, A.; Kumar, A.; Singhal, R.K.; Kumar, S.;
Singh, S.D. Monitoring of engineered nanoparticles in soil-plant system: A review. Environ. Nanotechnol. Monit. Manag. 2019, 11, 100218. [CrossRef] 4. Lv, J.; Christie, P.; Zhang, S. Uptake, translocation, and transformation of metal-based nanoparticles in plants:
Recent advances and methodological challenges. Environ. Sci. Nano 2019, 6, 41–59. [CrossRef] 4. Lv, J.; Christie, P.; Zhang, S. Uptake, translocation, and transformation of metal-based nanoparticles in plants:
Recent advances and methodological challenges. Environ. Sci. Nano 2019, 6, 41–59. [CrossRef] 5. Torrent, L.; Iglesias, M.; Marguí, E.; Hidalgo, M.; Verdaguer, D.; Llorens, L.; Kodre, A.; Kavˇciˇc, A.;
Vogel-mikuš, K. Uptake, translocation and ligand of silver in Lactuca sativa exposed to silver nanoparticles
of different size, coatings and concentration. J. Hazard. Mater. 2020, 384, 121201. [CrossRef] 5. Torrent, L.; Iglesias, M.; Marguí, E.; Hidalgo, M.; Verdaguer, D.; Llorens, L.; Kodre, A.; Kavˇciˇc, A.;
Vogel-mikuš, K. Uptake, translocation and ligand of silver in Lactuca sativa exposed to silver nanoparticles
of different size, coatings and concentration. J. Hazard. Mater. 2020, 384, 121201. [CrossRef] 6. Hayes, K.L.; Mui, J.; Song, B.; Shirzaei, E.; Eisenman, S.W.; Shef, J.B.; Kim, B. 8. Conclusions The investigation of interactions between metal-containing NPs and plants requires several
steps that need to be carefully designed, each of them requiring a careful and individual evaluation
depending on the plant used in a model study, the cultivation conditions and especially the type
of metal NPs studied. In addition, for a correct characterization of metal-containing NPs at each
step and/or identification of new species created, a multi-technique approach is needed. Here we
summarize the most important recommendations developed along the text: -
The behavior of metal-containing NPs in the nutrient solution used for plant cultivation must
be investigated before starting the cultivation experiment. The occurrence of a transformation
process in the growth medium (agglomeration/dissolution) may influence the rest of the study. -
The behavior of metal-containing NPs in the nutrient solution used for plant cultivation must
be investigated before starting the cultivation experiment. The occurrence of a transformation
process in the growth medium (agglomeration/dissolution) may influence the rest of the study. -
NPs must be extracted from the plant material without altering their properties. The use of an
enzymatic digestion with an enzyme capable of digesting plant cell walls, like pectinase, cellulase
or hemicellulase is necessary. A cocktail of enzymes (e.g., Macerozyme R-10) is recommended. -
SP-ICP-MS has proved to be a useful tool for size characterization of metal-containing NPs in
plant tissues as well as to monitor possible NPs transformation inside the plants. -
The comparison of NPs size distributions in the nutrient solution, roots and above-ground
organs provides essential information about the mechanisms of uptake and translocation of
metal-containing NPs by plants. -
If NPs dissolution takes place, speciation studies leading to the identification of new metal
species created within plant tissues can be carried out by hyphenated techniques, which include
separation of extracted compounds by chromatography or electrophoresis, followed by their
characterization and/or identification by mass spectrometry. -
Additional information about the spatial location of metal following the uptake of NPs in tissues
can be obtained by laser ablation coupled to ICP-MS. This, in combination with the information -
Additional information about the spatial location of metal following the uptake of NPs in tissues
can be obtained by laser ablation coupled to ICP-MS. This, in combination with the information 13 of 16 Nanomaterials 2020, 10, 1480 References Cocozza, C.; Perone, A.; Giordano, C.; Salvatici, M.C.; Pignattelli, S.; Raio, A.; Schaub, M.; Sever, K.; Innes, J.L.;
Tognetti, R.; et al. Silver nanoparticles enter the tree stem faster through leaves than through roots. Tree Physiol. 2019, 39, 1251–1261. [CrossRef] [PubMed] 14 of 16 14 of 16 Nanomaterials 2020, 10, 1480 16. Souza, I.R.; Silva, L.R.; Fernandes, L.S.P.; Salgado, L.D.; Silva, H.C.; Assis, D.; Firak, D.S.; Bach, L.;
Santos-filho, R.; Voigt, C.L.; et al. Visible-light reduced silver nanoparticles’ toxicity in Allium cepa test. Environ. Pollut. 2020, 257, 113551. [CrossRef] [PubMed] 7. Song, G.; Hou, W.; Gao, Y.; Wang, Y.; Lin, L.; Zhang, Z.; Niu, Q.; Ma, R.; Mu, L.; Wang, H. Effects of C
nanoparticles on Lemna minor. Bot. Stud. 2016, 57, 1–8. [CrossRef] 18. Owji, H.; Hemmati, S.; Heidari, R.; Hakimzadeh, M. Effect of alumina ( Al2O3) nanoparticles and
macroparticles on Trigonella foenum—Graceum L. In vitro cultures: Assessment of growth parameters
and oxidative stress—Related responses. 3 Biotech 2019, 9, 1–12. [CrossRef] 19. Ding, Y.; Bai, X.; Ye, Z.; Ma, L.; Liang, L. Toxicological responses of Fe3O4 nanoparticles on Eichhornia crassipes
and associated plant transportation. Sci. Total Environ. 2019, 671, 558–567. [CrossRef] 20. Cristina, S.; Arruda, C.; Luiz, A.; Silva, D.; Moretto, R.; Antunes, R.; Aurélio, M.; Arruda, Z. Nanoparticles
applied to plant science: A review. Talanta 2015, 131, 693–705. [CrossRef] 21. Fabrega, J.; Luoma, S.N.; Tyler, C.R.; Galloway, T.S.; Lead, J.R. Silver nanoparticles: Behaviour and effects in
the aquatic environment. Environ. Int. 2011, 37, 517–531. [CrossRef] 22. Castillo-michel, H.A.; Larue, C.; Pradas, A.E.; Cotte, M.; Sarret, G. Practical review on the use of synchrotron
based micro- and nano- X-ray fluorescence mapping and X-ray absorption spectroscopy to investigate
the interactions between plants and engineered nanomaterials. Plant Physiol. Biochem. 2017, 110, 13–32. [CrossRef] [PubMed] 23. Larue, C.; Castillo-michel, H.; Stein, R.J.; Fayard, B.; Pouyet, E.; Villanova, J.; Magnin, V.; Pradas, A.; Trcera, N.;
Legros, S.; et al. Innovative combination of spectroscopic techniques to reveal nanoparticle fate in a crop
plant. Spectrochim. Acta Part B At. Spectrosc. 2016, 119, 17–24. [CrossRef] 24. Servin, A.D.; Castillo-Michel, H.; Hernandez-Viezcas, J.A.; Diaz, B.C.; Peralta-videa, J.R.; Gardea-torresdey, J.L. Synchrotron Micro-XRF and Micro-XANES confirmation of the uptake and translocation of TiO2 nanoparticles
in cucumber (Cucumis sativus) plants. Environ. Sci. Technol. 2012, 46, 7637–7643. [CrossRef] 25. Yin, L.; Cheng, Y.; Espinasse, B.; Colman, B.P.; Au, M.; Wiesner, M.; Rose, J.; Liu, J.; Bernhardt, E.S. References More than
the ions: The effects of silver nanoparticles on Lolium multiflorum. Environ. Sci. Technol. 2011, 45, 2360–2367. [CrossRef] [PubMed] 26. Hernandez-viezcas, J.A.; Castillo-michel, H.; Servin, A.D.; Peralta-videa, J.R.; Gardea-torresdey, J.L. Spectroscopic verification of zinc absorption and distribution in the desert plant Prosopis juliflora-velutina
(velvet mesquite) treated with ZnO nanoparticles. Chem. Eng. J. 2011, 170, 346–352. [CrossRef] [PubMed] 27. Hernandez-viezcas, J.A.; Castillo-michel, H.; Andrews, J.C.; Cotte, M.; Rico, C.; Peralta-videa, J.R.; Ge, Y.;
Priester, J.H.; Holden, A.; Gardea-torresdey, J.L. In situ synchrotron X-ray fluorescence mapping and
speciation of CeO2 and ZnO nanoparticles in soil cultivated soybean (Glycine max). ACS Nano 2013, 7,
1415–1423. [CrossRef] 28. Laborda, F.; Bolea, E.; Jiménez-Lamana, J. Single particle inductively coupled plasma mass spectrometry for
the analysis of inorganic engineered nanoparticles in environmental samples. Trends Environ. Anal. Chem. 2016, 9, 15–23. [CrossRef] 29. Laborda, F.; Bolea, E.; Jiménez-Lamana, J. Single particle inductively coupled plasma mass spectrometry:
A powerful tool for nanoanalysis. Anal. Chem. 2014, 86, 2270–2278. [CrossRef] 30. Murashige, T.; Skoog, F. A Revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol. Plant 1962, 15, 473–497. [CrossRef] 31. Hoagland, D.R.; Arnon, D.I. The water-culture method for growing plants without soil. Calif. Agric. Exp. Stn. Circ. 1949, 347, 32. 32. Nath, J.; Dror, I.; Landa, P.; Motkova, K.; Vanek, T.; Berkowitz, B. Isotopic labelling for sensitive detection of
nanoparticle uptake and translocation in plants from hydroponic medium and soil. Environ. Chem. 2019, 16,
391–400. [CrossRef] 33. Wojcieszek, J.; Jimenez-Lamana, J.; Bierla, K.; Asztemborska, M.; Ruzik, L.; Jarosz, M.; Szpunar, J. Elucidation
of the fate of zinc in model plants using single particle ICP-MS and ESI tandem MS. J. Anal. At. Spectrom. 2019, 34, 683–693. [CrossRef] 34. Jiménez-Lamana, J.; Wojcieszek, J.; Jakubiak, M.; Asztemborska, M.; Szpunar, J. Single particle ICP-MS
characterization of platinum nanoparticles uptake and bioaccumulation by Lepidium sativum and Sinapis alba
plants. J. Anal. At. Spectrom. 2016, 31, 2321–2329. [CrossRef] Nanomaterials 2020, 10, 1480 15 of 16 15 of 16 35. Knapen, D.; Bals, S.; Blust, R.; Adam, N. The uptake of ZnO and CuO nanoparticles in the water- flea Daphnia
magna under acute exposure scenarios. Environ. Pollut. 2014, 194, 130–137. [CrossRef] 36. Merdzan, V.; Domingos, R.F.; Monteiro, C.E.; Hadioui, M.; Wilkinson, K.J. The effects of different coatings
on zinc oxide nanoparticles and their influence on dissolution and bioaccumulation by the green alga,
C. reinhardtii. Sci. Total Environ. 2014, 488–489, 316–324. References [CrossRef] [PubMed] 37. Wojcieszek, J.; Jiménez-Lamana, J.; Bierła, K.; Ruzik, L.; Asztemborska, M.; Jarosz, M.; Szpunar, J. Uptake,
translocation, size characterization and localization of cerium oxide nanoparticles in radish (Raphanus sativus
L.). Sci. Total Environ. 2019, 683, 284–292. [CrossRef] 38. Ki´nska, K.; Jiménez-Lamana, J.; Kowalska, J.; Krasnod˛ebska-Ostr˛ega, B.; Szpunar, J. Study of the uptake and
bioaccumulation of palladium nanoparticles by Sinapis alba using single particle ICP-MS. Sci. Total Environ. 2018, 615, 1078–1085. [CrossRef] 39. Yang, J.; Cao, W.; Rui, Y. Interactions between nanoparticles and plants: Phytotoxicity and defense
mechanisms. J. Plant Interact. 2017, 12, 158–169. [CrossRef] 40. Schwertfeger, D.M.; Velicogna, J.R.; Jesmer, A.H.; Saatcioglu, S.; Mcshane, H.; Scroggins, R.P.; Princz, J.I. Extracting metallic nanoparticles from soils for quantitative analysis: method development using engineered
silver nanoparticles and SP-ICP-MS. Anal. Chem. 2017, 89, 2505–2513. [CrossRef] 41. Mahdi, K.N.M.; Peters, R.J.B.; Klumpp, E.; Bohme, S.; Ploeg, M.; Van Der Ritsema, C.; Geissen, V. Silver nanoparticles in soil: Aqueous extraction combined with single-particle ICP-MS for detection
and characterization. Environ. Nanotechnol. Monit. Manag. 2017, 7, 24–33. [CrossRef] 42. Lee, W.; Kwak, J.I; An, Y. Effect of silver nanoparticles in crop plants Phaseolus radiatus and Sorghum bicolor:
Media effect on phytotoxicity. Chemosphere 2012, 86, 491–499. [CrossRef] [PubMed] 43. Laborda, F.; Bolea, E.; Cepriá, G.; Gómez, M.T.; Jiménez, M.S.; Pérez-Arantegui, J.; Castillo, J.R. Detection,
characterization and quantification of inorganic engineered nanomaterials: A review of techniques and
methodological approaches for the analysis of complex samples. Anal. Chim. Acta 2016, 904, 10–32. [CrossRef]
[PubMed] 44. Stavolone, L.; Lionetti, V. Extracellular matrix in plants and animals: Hooks and locks for viruses. Front. Microbiol. 2017, 8, 1–8. [CrossRef] 45. Singh, G.; Stephan, C.; Westerhoff, P.; Carlander, D.; Duncan, T.V. Measurement Methods to Detect,
characterize, and quantify engineered nanomaterials in foods. Compr. Rev. Food Sci. Food Saf. 2014, 13,
693–704. [CrossRef] 46. Loeschner, K.; Navratilova, J.; Købler, C.; Mølhave, K.; Wagner, S.; Kammer, F. Von Der; Larsen, E.H. Detection
and characterization of silver nanoparticles in chicken meat by asymmetric flow field flow fractionation with
detection by conventional or single particle ICP-MS. Anal. Bioanal. Chem. 2013, 405, 8185–8195. [CrossRef] 47. Dan, Y.; Zhang, W.; Xue, R.; Ma, X.; Stephan, C.; Shi, H. Characterization of gold nanoparticle uptake by
tomato plants using enzymatic extraction followed by single-particle inductively coupled plasma-mass
spectrometry analysis. Environ. Sci. Technol. 2015, 49, 3007–3014. [CrossRef] 48. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/). References Schwabe, F.; Tanner, S.; Schulin, R.; Rotzetter, A.; Stark, W.; Quadt, A.; Von Nowack, B. Dissolved cerium
contributes to uptake of Ce in the three crop plants. Metallomics 2015, 7, 466–477. [CrossRef] 49. Zhao, L.; Peralta-videa, J.R.; Ren, M.; Varela-ramirez, A.; Li, C.; Hernandez-viezcas, J.A.; Aguilera, R.J.;
Gardea-torresdey, J.L. Transport of Zn in a sandy loam soil treated with ZnO NPs and uptake by corn plants:
Electron microprobe and confocal microscopy studies. Chem. Eng. J. 2012, 184, 1–8. [CrossRef] 50. Hansen, T.H.; de Ban, T.C.; Laursen, K.H.; Pedas, P.; Husted, S.; Schjoerring, J.K. Multielement plant tissue
analysis using ICP spectrometry. In Plant Mineral Nutrients: Methods in Molecular Biology (Methods and
Protocols); Maathuis, F., Ed.; Humana Press: Totowa, NJ, USA, 2013; p. 141. 51. Durrant, S.F. Laser ablation inductively coupled plasma mass spectrometry: Achievements, problems,
prospects. J. Anal. At. Spectrom. 1999, 14, 1385–1403. [CrossRef] 52. Becker, J.S.; Dietrich, R.C.; Matusch, A.; Pozebon, D.; Dressler, V.L. Quantitative images of metals in plant
tissues measured by laser ablation inductively coupled plasma mass spectrometry. Spectrochim. Acta Part B
At. Spectrosc. 2008, 63, 1248–1252. [CrossRef] 52. Becker, J.S.; Dietrich, R.C.; Matusch, A.; Pozebon, D.; Dressler, V.L. Quantitative images of metals in plant
tissues measured by laser ablation inductively coupled plasma mass spectrometry. Spectrochim. Acta Part B
At. Spectrosc. 2008, 63, 1248–1252. [CrossRef] 16 of 16 Nanomaterials 2020, 10, 1480 16 of 16 53. Grijalba, N.; Legrand, A.; Holler, V.; Bouvier-capely, C. A novel calibration strategy based on internal
standard—Spiked gelatine for quantitative bio-imaging by LA-ICP-MS: Application to renal localization and
quantification of uranium. Anal. Bioanal. Chem. 2020, 412, 3113–3122. [CrossRef] [PubMed] 53. Grijalba, N.; Legrand, A.; Holler, V.; Bouvier-capely, C. A novel calibration strategy based on internal
standard—Spiked gelatine for quantitative bio-imaging by LA-ICP-MS: Application to renal localization and
quantification of uranium. Anal. Bioanal. Chem. 2020, 412, 3113–3122. [CrossRef] [PubMed] 54. Avellan, A.; Schwab, F.; Masion, A.; Chaurand, P.; Borschneck, D.; Vidal, V.; Rose, J.; Santaella, C.; Levard, C. Nanoparticle uptake in plants: Gold nanomaterial localized in roots of arabidopsis thaliana by X-Ray
computed nanotomography and hyperspectral imaging. Environ. Sci. Technol. 2018, 51, 8682–8691. [CrossRef] [PubMed] 54. Avellan, A.; Schwab, F.; Masion, A.; Chaurand, P.; Borschneck, D.; Vidal, V.; Rose, J.; Santaella, C.; Levard, C. Nanoparticle uptake in plants: Gold nanomaterial localized in roots of arabidopsis thaliana by X-Ray
computed nanotomography and hyperspectral imaging. Environ. Sci. Technol. 2018, 51, 8682–8691. References [CrossRef] [PubMed] © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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The magic of small-molecule drugs during ex vivo expansion in adoptive cell therapy
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Frontiers in immunology
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TYPE Perspective
PUBLISHED 21 April 2023
DOI 10.3389/fimmu.2023.1154566 COPYRIGHT
© 2023 Zhang, Passang, Ravindranathan,
Bommireddy, Jajja, Yang, Selvaraj, Paulos and
Waller. This is an open-access article
distributed under the terms of the Creative
Commons Attribution License (CC BY). The
use, distribution or reproduction in other
forums is permitted, provided the original
author(s) and the copyright owner(s) are
credited and that the original publication in
this journal is cited, in accordance with
accepted academic practice. No use,
distribution or reproduction is permitted
which does not comply with these terms. CITATION
Zhang H, Passang T, Ravindranathan S,
Bommireddy R, Jajja MR, Yang L, Selvaraj P,
Paulos CM and Waller EK (2023) The magic
of small-molecule drugs during ex vivo
expansion in adoptive cell therapy.
Front. Immunol. 14:1154566.
doi: 10.3389/fimmu.2023.1154566 OPEN ACCESS OPEN ACCESS
EDITED BY
Beatriz Martı´n-Antonio,
University Hospital Fundacio´ n Jime´ nez
Dı´az, Spain
REVIEWED BY
Eduardo Anguita,
San Carlos University Clinical Hospital,
Spain
Carla Montesano,
University of Rome Tor Vergata, Italy
*CORRESPONDENCE
Hanwen Zhang
hanwen.zhang2@emory.edu
Edmund K. Waller
ewaller@emory.edu
SPECIALTY SECTION
This article was submitted to
Cancer Immunity
and Immunotherapy,
a section of the journal
Frontiers in Immunology
RECEIVED 30 January 2023
ACCEPTED 10 April 2023
PUBLISHED 21 April 2023
CITATION
Zhang H, Passang T, Ravindranathan S,
Bommireddy R, Jajja MR, Yang L, Selvaraj P
Paulos CM and Waller EK (2023) The magic
of small-molecule drugs during ex vivo
expansion in adoptive cell therapy. Front. Immunol. 14:1154566. doi: 10.3389/fimmu.2023.1154566 EDITED BY
Beatriz Martı´n-Antonio,
University Hospital Fundacio´ n Jime´ nez
Dı´az, Spain
REVIEWED BY
Eduardo Anguita,
San Carlos University Clinical Hospital,
Spain
Carla Montesano,
University of Rome Tor Vergata, Italy Hanwen Zhang 1*, Tenzin Passang 1, Sruthi Ravindranathan 1,
Ramireddy Bommireddy 2,3, Mohammad Raheel Jajja 4,
Lily Yang 3,5, Periasamy Selvaraj 2,3, Chrystal M. Paulos 3,5,6
and Edmund K. Waller 1,3* 1Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta,
GA, United States, 2Department of Pathology and Laboratory Medicine, Emory University School of
Medicine, Atlanta, GA, United States, 3Winship Cancer Institute, Emory University, Atlanta, GA, United
States, 4Departmert of Surgery, University of Alabama at Birmingham Heersink School of Medicine,
Birmingham, AL, United States, 5Department of Surgery, Emory University School of Medicine, Atlanta,
GA, United States, 6Department of Microbiology and Immunology, Emory University of School of
Medicine, Atlanta, GA, United States In the past decades, advances in the use of adoptive cellular therapy to treat
cancer have led to unprecedented responses in patients with relapsed/refractory
or late-stage malignancies. However, cellular exhaustion and senescence limit
the efficacy of FDA-approved T-cell therapies in patients with hematologic
malignancies and the widespread application of this approach in treating
patients with solid tumors. Investigators are addressing the current obstacles
by focusing on the manufacturing process of effector T cells, including
engineering approaches and ex vivo expansion strategies to regulate T-cell
differentiation. Here we reviewed the current small-molecule strategies to
enhance T-cell expansion, persistence, and functionality during ex vivo
manufacturing. We further discussed the synergistic benefits of the dual-
targeting approaches and proposed novel vasoactive intestinal peptide
receptor antagonists (VIPR-ANT) peptides as emerging candidates to enhance
cell-based immunotherapy. PI3K-AKT-mTOR pathway inhibitors The most frequent aberrations in cell signaling associated with
tumorigenesis, angiogenesis, cell growth, or metastasis are
hyperactive PI3K-AKT-mTOR pathways, exemplified by
activating mutations of PIK3CA and the loss of PTEN
functionality (54). Hence, the pharmaceutical industry has
dedicated significant effort to developing PI3K inhibitors (PI3Ki)
as targeted therapies. Mutational activation of PI3K signaling is
relatively rare in hematologic malignancies, yet PI3Kd inhibitors
(idelalisib, duvelisib) were approved as a therapy for B-cell
malignancies. Aside from suppressing tumor cell growth directly
via inhibiting intracellular PI3K signaling (55), the beneficial
clinical effects of PI3K inhibition in this setting may also be to
indirectly activate immune cells with anti-cancer cytotoxicity in the
tumor microenvironment. PI3Kg and PI3Kd are selectively
expressed in leukocytes and are essential in promoting glycolysis
and differentiation (56, 57). Indeed, while PI3K inhibitors may
dampen many immune cell functions, blocking regulatory T (Treg)
cell-mediated suppression of anti-tumor immune responses shows
promise in immunotherapy (58). Initially, pan-PI3K inhibitor
Pictilisib (GDC-0941) and PI3Ka/d/b inhibitor LY294002 were
found to delay terminal differentiation and preserve a reservoir of
memory T cells (TCM and TEM) (16, 17). Selective inhibition of
PI3Kd with idelalisib (CAL-101), but not PI3Ka or PI3Kb,
promoted the generation of naïve-like (CD45RA+CCR7+) and
undifferentiated CD8+ T cells phenotypes (CCR7+CD62L+,
CD127, Tcf7) that had enhanced proliferative potential, function,
and survival (16, 18). Idelalisib also preferentially inhibits human
regulatory T-cell function (59). Subsequent studies showed
idelalisib-treated T cells, or CAR T cells persisted longer and
engrafted better after adoptive transfer into tumor-bearing mice,
resulting in improved anti-tumor immunity (18, 19). These cells
expressed fewer exhaustion markers (i.e., lower PD1 expression
levels) and had a less senescent phenotype (CD27-CD28-) (21, 60). PI3Kg, first promoted as a selective immunotherapeutic target in
myeloid cells, was later found to be involved in remodeling T-cell
differentiation (22, 61, 62). Inhibition of PI3Kg and PI3Kd with
duvelisib (IPI-145) reprogramed terminal differentiation and the
metabolism of CAR T cells to enhance expansion, persistence, and
anti-tumor cytotoxicity (20). A recent phase 1 study
(NCT03274219) of bb21217, an anti-BCMA CART therapy based
on ide-cel that included the PI3K inhibitor bb007 during ex vivo
culture showed increased enrichment for CD27+/CCR7+ Tm cells,
depletion of CD57+ senescent cells, increased CD127 expression,
and higher peak in vivo CAR T expansion, resulting in improved T cell exhaustion is a homeostatic mechanism that protects the
organism against severe immunopathology from overwhelming
CD8 T cell responses (6). Introduction (15). More recently, adding small-molecule compounds targeting
tumor cell metabolic signaling pathways has also been explored to
enhance T-cell function and persistence. (Table 1). (15). More recently, adding small-molecule compounds targeting
tumor cell metabolic signaling pathways has also been explored to
enhance T-cell function and persistence. (Table 1). Adoptive T-cell therapy (ACT) is a form of cellular
immunotherapy in which tumor-reactive T cells recognize and
eliminate malignant cells after infusion into patients. Barnes and
Loutit initially proposed the ACT concept in 1956, describing the
graft-versus-leukemia (GvL) effect of allogeneic hematopoietic stem
cell transplantation (HSCT), which represents the earliest clinical
example of the adoptive transfer of T cells with anti-cancer activity
(1). In the past few decades, cell-based therapies with chimeric
antigen receptor (CAR) T cells, engineered T cell receptor (eTCR) T
cells, tumor-infiltrating lymphocytes (TILs), and other antigen-
specific T cells have rapidly developed and shown enormous
clinical potential. CAR T cell therapy, which involves the transfer
of allogeneic or autologous T cells modified to express a chimeric
antigen receptor (CAR), has gained FDA approval with studies
documenting durable remissions in patients with relapsed/
refractory (R/R) hematologic malignancies (2–4). However, many
patients fail to achieve long-lasting remission due to loss of CAR T
cell persistence and functionality (5). Hence, developing methods to
counteract T-cell exhaustion and improve functionality is essential
to improving ACT efficacy. OPEN ACCESS CITATION
Zhang H, Passang T, Ravindranathan S,
Bommireddy R, Jajja MR, Yang L, Selvaraj P,
Paulos CM and Waller EK (2023) The magic
of small-molecule drugs during ex vivo
expansion in adoptive cell therapy. Front. Immunol. 14:1154566. doi: 10.3389/fimmu.2023.1154566 COPYRIGHT
© 2023 Zhang, Passang, Ravindranathan,
Bommireddy, Jajja, Yang, Selvaraj, Paulos and
Waller. This is an open-access article
distributed under the terms of the Creative
Commons Attribution License (CC BY). The
use, distribution or reproduction in other
forums is permitted, provided the original
author(s) and the copyright owner(s) are
credited and that the original publication in
this journal is cited, in accordance with
accepted academic practice. No use,
distribution or reproduction is permitted
which does not comply with these terms. COPYRIGHT
© 2023 Zhang, Passang, Ravindranathan,
Bommireddy, Jajja, Yang, Selvaraj, Paulos and
Waller. This is an open-access article
distributed under the terms of the Creative
Commons Attribution License (CC BY). The
use, distribution or reproduction in other
forums is permitted, provided the original
author(s) and the copyright owner(s) are
credited and that the original publication in
this journal is cited, in accordance with
accepted academic practice. No use,
distribution or reproduction is permitted
which does not comply with these terms. adoptive cell therapy (ACT), chimeric antigen receptors (CAR), ex vivo manufacturing,
protein kinase inhibitor, PI3K, vasoactive intestinal peptide (VIP), small-molecule drugs,
peptide-based drugs Abbreviations: ACT, adoptive T-cell therapy; GvL, graft-versus-leukemia; GVHD, graft-versus-host disease;
HSCT, hematopoietic stem cell transplantation; CAR, chimeric antigen receptor; TCR, T cell receptor; BCR, B
cell receptor; TIL, tumor-infiltrating lymphocyte; CRS, cytokine release syndrome; VIP, vasoactive intestinal
peptide; VIPR-ANT, vasoactive intestinal peptide receptor antagonist; R/R, relapsed/refractory; ALL, acute
lymphocytic leukemia; AML, acute myeloid leukemia; CLL, chronic lymphocytic leukemia; DLBCL, diffuse
large B-cell lymphoma; NHL, non-Hodgkin’s lymphoma; PDAC, pancreatic ductal adenocarcinoma; TNBC,
triple negative breast cancer; HNSCC, head and neck squamous cell carcinoma; MM, multiple myeloma;
GBM, glioblastoma; MRD, minimal residual disease; PFS, progression-free survival; PDX, patient-derived
xenograft; TMV, tumor membrane vesicle. Frontiers in Immunology frontiersin.org 01 Zhang et al. 10.3389/fimmu.2023.1154566 Frontiers in Immunology PI3K-AKT-mTOR pathway inhibitors Generally, exhausted T (Tex) cells have
decreased expression of effector cytokines and increased expression
of inhibitory immune checkpoint receptors such as PD-1, TIM-3,
LAG-3, TIGHT, and CTLA-4 (7). However, expression of these
molecules is also upregulated during early T cell activation,
presumably as a homeostatic mechanism that modulates
activation downstream of co-stimulatory signaling (8). T cell
exhaustion comprises a differentiative process of several stages,
accompanied by significant epigenetic reorganization and distinct
transcriptional signatures (9, 10). Namely, the expression of TCF1/
7, a transcription factor critical to maintaining immunological
memory, decreases during the transition from the plastic to the
irreversible and fixed dysfunctional chromatin state (11, 12). Manufacturing of modified T cells is a multi-step process (13). The focus of two main areas of optimizing T-cell therapies are
designing optimal genetic modifications of T cells and engineering
improved cell activation and culture processes during ex vivo T-cell
expansion (14). Adding clinically approved compounds, such as
monoclonal antibodies and small molecule inhibitors, during the
manufacture of cellular products might be a promising strategy to
overcome T-cell exhaustion and enhance T-cell cytotoxicity. Adding drugs ex vivo represents an alternative to in vivo
administration as part of a preconditioning regimen or therapy
concomitant with T-cell infusion. Preclinical testing of ex vivo
manufacturing and expansion approaches can identify strategies
that yield a more potent adoptive T-cell therapy product with
superior anti-tumor activity and persistence after infusion. Cultures media supplemented with gamma-chain cytokines
during ex vivo manufacturing, including IL-2, IL-7, IL-15, and IL-
21, leads to the expansion of CAR T cells with enhanced
proliferation, metabolic profiles, and less terminal differentiation Frontiers in Immunology 02 frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 TABLE 1 Summary of small-molecule drugs enhancing adoptive T cells ex vivo. PI3K-AKT-mTOR pathway inhibitors ia; CLL, chronic lymphocytic leukemia; DLBCL, diffuse large B-cell lymphoma; NHL, non-Hodgkin’s lymphoma; PDAC, pancreatic ductal adenocarcinoma; TNBC
; HNSCC, head and neck squamous cell carcinoma; MM, multiple myeloma; GBM, glioblastoma. clinical outcomes in MM patients (24, 63). Excitingly, duvelisib also
potently inhibits IL-6 production and cytokine release syndrome
(CRS) (23). Two clinical trials were initiated to verify enhanced
CAR T-cell functionality (NCT04890236, diffuse large B-cell
lymphoma (DLBCL)) and CRS prevention (NCT05044039, non-
Hodgkin lymphoma (NHL), acute lymphocytic leukemia (ALL)) in
Duvelisib-treated DLBCL patients. subsequently activated PLCg1, which amplified downstream TCR
signaling and facilitated T-cell activation and expansion (70). Clinically, long-term treatment with ibrutinib, an inhibitor that
forms irreversible covalent bonds to BTK, reversed CD8 T cell
exhaustion and protected T cells from proliferation-induced
senescence in chronic lymphocytic leukemia (B-CLL) patients. In
addition, T cells from ibrutinib-treated CLL patients have decreased
PD-1, TIM3, and LAG3 expression and increased antigen-specific
responses (71–73). Ibrutinib improved CAR T cell expansion in vitro
and promoted a less-differentiated less-exhausted naïve-like phenotype
by inhibiting interleukin-2-inducible T-cell kinase (ITK) (31, 32). To
date, several clinical trials are investigating the regimen of concurrent
administration of CAR T cells and ibrutinib in B-cell malignancies
(NCT02640209, NCT03960840). Concurrent ibrutinib therapy may
improve CD19 CAR T-cell engraftment, enhance anti-tumor efficacy,
and decrease CRS severity, leading to high rates of minimal residual
disease (MRD)-negative responses, but progression-free survival (PFS)
was unchanged (32–35). Second-generation BTKi acalanrutinib and
zanubritinib, which are more selective and well-tolerated, have also
been examined (74). Acalabrutinib improved CAR T-cell effector
function and prolonged survival of tumor-bearing mice when
combined with CAR T cells (36), while zanubrutinib lacked these
positive effects (37). Inhibiting the pathway downstream of PI3K showed a similar
effect as direct inhibition of PI3K. mTOR acts intrinsically through
the mTORC1 (mTOR complex 1) pathway to regulate memory T-
cell differentiation (64). The mTORC1 inhibitor rapamycin
promoted memory CD8 T-cell survival, maintenance of a less
differentiated phenotype, and improved the functional qualities of
CD8 T cells (CD127High CD62LHigh Bcl2High KLRG1Low) (64). Furthermore, rapamycin-pretreated EpCAM CAR T cells had
upregulated CXCR4, increased infiltration into the bone marrow,
and superior elimination of AML cells in leukemia xenograft mouse
models (25). Interestingly, CAR-T cell expansion in IL-15 preserved
the stem cell memory (Tscm) phenotype and improved metabolic
fitness, likely via mTORC1 suppression. Tyrosine kinase inhibitors (TKI) Dasatinib, a second-generation tyrosine kinase inhibitor (TKI),
was initially approved by FDA to treat Ph+ chronic myeloid
leukemia (CML) (75). A recent study showed that dasatinib
prevents or reverses CD28/CAR T and 4-1BB/CA T cell
differentiation and exhaustion during ex vivo expansion, resulting
in profoundly enhanced therapeutic efficacy and in vivo persistence
(38). Multiple pathways are involved in this process, including Src
phosphorylation, JAK/STAT, MAPK, and PI3K/AKT (38, 76). Epigenetic modulators Epigenetic modulators represent another promising strategy to
enhance T-cell function based on the epigenetic remodeling and
chromatin transitions discovered during the process of T-cell
exhaustion. DNA methyltransferases and histone deacetylases
(HDACs) are activated during T-cell differentiation, resulting in high
levels of DNA and histone methylation in exhausted T cells (7, 9). Recent studies revealed that decitabine, a clinical DNA methylation
inhibitor, enhances anti-tumor activities, cytokine production, and
CAR T cell proliferation in both in vitro and in vivo non-Hodgkin
lymphoma (NHL) models (39). Decitabine also promotes the PI3K-AKT-mTOR pathway inhibitors However, the inclusion of
IL-7 and/or IL-21 in addition to IL15 reduced the beneficial effects
of IL-15 on the phenotype and anti-tumor potency of CAR-T (65). Akt functions as a critical signaling node to maintain T cell survival
during the effector-to-memory cell transition (66). Like rapamycin,
Akt inhibitors, notably Akt-inhibitor VIII and GDC-0068,
enhanced the expansion of tumor-specific lymphocytes and
promoted the ex vivo generation of stem cell memory-like CD8+
T cells (CD62Lhigh CCR7high CXCR4high) with a unique metabolic
profile and cytokine polyfunctionality (26–29). A pre-clinical study
utilizing EpCAM CAR T in a T murine AML model showed that
Akt inhibition (MK2206) at the initial stage of CAR T manufacture
enhanced the expansion of CAR T cells and CART efficacy in vivo
(30). Overall, targeting PI3K-AKT-mTOR signaling shows
therapeutic potential in improving adoptive T-cell therapy. PI3K
inhibition produces a more profound TCF1/7 upregulation than
other small molecular TK inhibitors and may elucidate better anti-
tumor efficacy in vivo (18). Frontiers in Immunology PI3K-AKT-mTOR pathway inhibitors Compound
Names
Target
T Cell Product
Tumor Model
CRS
Protein Kinase Inhibitors
GDC-0941
Pictilisib
pan-PI3K
gp100-TCR (16)
Melanoma
LY294002
PI3K a/d/b
CD33-CAR (17)
AML
CAL-101
Idelalisib
PI3K d
gp100-TCR (18)
CD19-CAR (19, 20)
CD5-CAR (21)
Meso-CAR (22)
Melanoma
CLL
DLBCL
Melanoma
IPI-145
Duvelisib
PI3K d/g
gp100-TCR (22)
Meso-CAR (22)
CD19-CAR (20)
Melanoma
CLL
Lower (23)
IPI-549
Eganelisib
PI3K g
gp100-TCR (22)
Meso-CAR (22)
Melanoma
TGR-1202
Umbralisib
PI3K d
gp100-TCR (22)
Meso-CAR (22)
Melanoma
bb007
PI3K
BCMA-CAR (24)
MM
Rapamycin
Sirolimus
mTORC1
EpCAM-CAR (25)
AML
Akt inhibitor VIII
Akt
TIL (26)
gp100-TCR (26)
CD19-CAR (27, 28)
MiHA-specific (29)
Melanoma
Melanoma
ALL
GDC-0068
Ipatasertib
Akt
MiHA-specific (29)
MK2206
Akt
EpCAM-CAR (30)
Colon Cancer
Ibrutinib
BTK
CD19-CAR (31–36)
CLL, NHL, ALL
Lower (33)
Acalanrutinib
BTK
CD19-CAR (36)
ALL
Zanubritinib
BTK
CD19-CAR (37)
B-malignancy
Dasatinib
TK
CD19-CAR (38)
ALL
Epigenetic modulators
Decitabine
DNMT
CD19-CAR (39)
CD20-CAR (39)
NY-ESO-1-TCR (40)
ALL
ALL
AML
Panobinostat
HDAC
Her2-CAR (41)
gp100-TCR (41)
PDAC
PDAC
SAHA
HDAC
B7-H3-CAR (42)
TNBC, HNSCC
Sulforaphane
HDAC
Meso-CAR (43)
Lung Cancer
JQ1
BRD4
CD19-CAR (44, 45)
HLA-A2/MART127-35-TCR (44)
ALL
Melanoma
Immunomodulators
Lenalidomide
Myeloma-specific (46)
CS1-CAR (47)
BCMA-CAR (48)
CD23-CAR (49)
WT1-CAR (50)
CD133-CAR (51)
HER2-CAR (51)
EGFRvIII-CAR (52)
CD19-CAR (53)
MM
MM
MM
CLL
Wilms Tumor
Glioma
Breast Cancer
GBM
DLBCL
Peptide-based modulators
(
d) TABLE 1 Summary of small-molecule drugs enhancing adoptive T cells ex vivo. TABLE 1 Summary of small-molecule drugs enhancing adoptive T cells ex vivo. (Continued) 03 Frontiers in Immunology frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 TABLE 1 Continued
Compound
Names
Target
T Cell Product
Tumor Model
CRS
VIPhyb
VPAC1/2
CD5 (21)
TMV-cultured
DLBCL
Colon Cancer
ANT308
VPAC1/2
T cells
AML, acute myeloid leukemia; CLL, chronic lymphocytic leukemia; DLBCL, diffuse large B-cell lymphoma; NHL, non-Hodgkin’s lymphoma; PDAC, pancreatic ductal adenocarcinoma; TNBC,
triple negative breast cancer; HNSCC, head and neck squamous cell carcinoma; MM, multiple myeloma; GBM, glioblastoma. Compound
Names
Target
T Cell Product
Tumor Model
CRS
VIPhyb
VPAC1/2
CD5 (21)
TMV-cultured
DLBCL
Colon Cancer
ANT308
VPAC1/2
T cells
AML, acute myeloid leukemia; CLL, chronic lymphocytic leukemia; DLBCL, diffuse large B-cell lymphoma; NHL, non-Hodgkin’s lymphoma; PDAC, pancreatic ductal adenocarcinoma; TNBC,
triple negative breast cancer; HNSCC, head and neck squamous cell carcinoma; MM, multiple myeloma; GBM, glioblastoma. AML, acute myeloid leukemia; CLL, chronic lymphocytic leukemia; DLBCL, diffuse large B-cell lymphoma; NHL, non-Hodgkin’s lymphoma; PD
triple negative breast cancer; HNSCC, head and neck squamous cell carcinoma; MM, multiple myeloma; GBM, glioblastoma. BTK inhibitors (BTKi) Bruton’s tyrosine kinase (BTK) is a nonreceptor tyrosine kinase
initially discovered as a critical component of B cell receptor (BCR)
signal transduction in both healthy and malignant B lymphocytes (67,
68). The clinical role of BTK extends beyond its effects on normal and
malignant B cells. PI3Kg can activate BTK to promote phospholipase C
(PLC) g-dependent signaling in hematopoietic cells, including myeloid
cells (69). A recent study suggested a regulatory role for BTK in T-cell
activation. After TCR engagement, BTK was activated and Frontiers in Immunology 04 frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 induces vasodilation and hypotension (83, 84). The
immunosuppressive properties of VIP were described in the
early 2000s by Delgado, who noted that VIP promoted the
survival of Th2 effectors, the generation of memory Th2 cells,
and enhanced Treg function (85–87). More recent studies
showed that VIP enhances M2 macrophage polarization and
promotes macrophages with a less-inflammatory physiologic
profile that promotes tissue repair (88–90). We recently noted
that VIP produced by activated T cells limits their proliferation
in vitro (91), and VIP produced by donor plasmacytoid
dendritic cells (pDCs) limits Graft-versus-Host Disease
(GVHD) in vivo (92). The emerging immunoregulatory role of
VIP on innate and adaptive immune functions makes it a
candidate immunotherapy target. maintenance of effector function and the memory phenotype of NY-
ESO-1-specific eTCR T cells leading to greater anti-AML efficacy (40). Likewise, HDAC inhibitors panobinostat, SAHA, and sulforaphane
promote the generation of T cells with a central memory phenotype
and reduce expression of immunosuppressive markers (PD-1, CTLA-
4, TET2) in CAR T-cell, resulting in enhanced anti-tumor response in
solid tumor models (41–43). BRD4 is a member epigenetic modulator of the bromodomain
and extra terminal motif (BET) subfamily. BRD4 promotes TEM
CD8 T-cell differentiation by regulating BATF expression. Treatment of CAR T cells with BET inhibitor JQ1 promoted the
expansion of less differentiated TSCM and TCM, downregulated PD-1
and TET2 exhaustion marker expression, improved persistence and
effector function, and augmented T-cell mediated anti-tumor effect
in leukemia models (44, 45). Interestingly, the commonly used PI3K
inhibitor LY294002 is also an inhibitor of BET bromodomains (77). VIP-hybrid (VIPhyb) is a VIP-receptor antagonist synthesized
by replacing the six N-terminal residues of VIP with highly charged
residues from the N-terminal peptide sequence of neurotensin (93). VIPhyb acts as a competitive antagonist, binding to VIP receptors
VPAC1 and VPAC2 without activating the downstream VIP-
receptor signaling pathway (94). Immune modulators Immunomodulatory imide drugs (IMiDs) are thalidomide analogs
with pleiotropic anti-myeloma properties. IMiDs act directly on
malignant cells and indirectly via enhancing T and NK cell effector
functions (78). Early in vitro studies showed that IMiDs induced T-cell
proliferation, IL-2 and IFN-g secretion, and myeloma-specific T-cell
responses (46, 79). Myeloma patients treated with lenalidomide had
increased numbers of central (TCM) and effector (TEM) memory CD8 T
cells with decreased PD-1 expression (80). However, the effect of IMiDs
on Treg remains uncertain (81). In general, favorable clinical outcomes
with lenalidomide were observed from either induction or post-
autologous stem cell transplant (ASCT) consolidation and
maintenance (81). Aligned with previous findings, lenalidomide-
treated CAR T cells acquired a memory phenotype, enhanced
polyfunctional cytokine secretion, and increased immune synapse
formation (47). CS1 CAR T cells expanded in vitro with
lenalidomide had improved anti-tumor efficacy and in vivo
persistence in murine myeloma models (47). Preclinical studies
showed treatment with lenalidomide during the early phase of in
vivo CAR T cell expansion recapitulated the effects of ex vivo
lenalidomide exposure in multiple hematologic and solid tumor
mouse models (48–52). As expected, several clinical trials
investigating the combination of CAR T cells with lenalidomide have
been initiated (NCT03070327, NCT05032820, NCT04923893,
NCT04002401). Preliminary data has shown that early lenalidomide
infusion enhances CAR T-cell response in patients with R/R DLBCL
(53, 82). Idelalisib and VIPhyb Previously, our team has shown that idelalisib and VIPhyb
synergically increased the transduction and expansion of anti-CD5
CAR T cells manufactured from DLBCL patients (21). The addition
of idelalisib and VIPhyb to cultured T cells reduced terminal
differentiation, enhanced cytokine expression, and preserved
expression of costimulatory molecules CD27 and CD28 (21). These agents target distinct signaling pathways, and their
combinatorial synergy might be applicable for manufacturing
CAR T therapy in patients with hematological and in adoptive T
cell for patients with solid tumor malignancies. However, applying
adoptive T cell therapy to solid tumor patients is constrained by the BTK inhibitors (BTKi) In the past decade, our group
showed that inhibiting VIP signaling could enhance CD8 T-cell
proliferation and function, leading to favorable T-cell-dependent
anti-viral and anti-cancer responses in murine models of CMV
infection and acute leukemia, respectively (91, 95–98). To further
improve the efficacy of VIP-receptor antagonists as immuno-
modulatory drugs, we have developed a series of peptides,
including ANT008, ANT308, and ANT195, that are predicted to
have increased binding affinity to human VIP receptors VPAC1 and
VPAC2 and have enhanced ability to elicit T cell-dependent
antileukemia responses in mice (Li unpublished). Recently, we
published that VIP-receptor antagonists (ANT008, ANT308) were
synergistic when added to anti-PD1 antibodies in enhancing T-cell
mediated anti-tumor response to multiple murine models of
pancreatic ductal carcinoma (PDAC) (99). These exciting findings
validated using VIP-receptor antagonists as anti-cancer
immunotherapy agents. In addition, we further investigated the
feasibility of using VIP-receptor antagonists in adoptive T-
cell therapy. VIP-receptor antagonists (VIPR-ANT) Vasoactive intestinal peptide (VIP) is a 28-amino acid
neuropeptide isolated in 1970 from porcine duodenum that Frontiers in Immunology 05 frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 10.3389/fimmu.2023.1154566 low frequency of tumor-infiltrating lymphocytes and the high
molecular heterogeneity of solid tumors lacking expression of
public (shared) tumor antigens. Therefore, we tested the
feasibility of expanding patient tumor-specific T cells ex vivo by
adding idelalisib and VIPhyb, using matched tumor and PBMCs from consented metastatic colon cancer patients. The source of
tumor antigens were tumor membrane vesicles (TMVs)
manufactured from that patient’s tumor and decorated with IL-12
and B7-1 (100, 101). Activating TMV-stimulated autologous T cells
in the presence of idelalisib, VIPhyb, and anti-CD3 Dyna beads B
C
D
A
FIGURE 1
Pharmacological blockade of PI3K and VIPR signaling improves T-cell expansion and function in vivo ((A) adoptive antigen-specific T cells in
metastatic colon cancer PDX model) and in vitro ((B–D), human T cells). (A) Left: Increased IFN-g secreting CD8+ T cells using decorated TMV with
VIPhyb and idelalisib (CRCLM-02, n=1); Right: Decreased tumor growth in PDX (CRCLM-02 and CRCLM-04) mice receiving T cells expanded with
beads+TMV+drugs. ANOVA was used to determine significance. The standard error (SE) was shown. (B) Total CD3+ T cells, the actively proliferating
Ki67+CD3+ subset, CD4+CD3+ T cells, and CD8+CD3+ T cells are synergistically expanded in vitro by the combination of ANT308 and duvelisib. The mean +/- SD fold increase in cell expansion over control cultures containing neither added ANT308 nor duvelisib is shown (n=4), with color
shading according to the relative increase. The pair of concentrations yielded the maximal increase in mean fold expansion is shown with a yellow
border around the cell. (C) Frequencies of CD27+CD28+ T cells in cultures with duvelisib and ANT308 led to the highest average expansion for that
subset of T cells (n=4). An example of gating is on the left. (D) ANT308 and duvelisib demonstrated synergy in decreasing PD1+, Lag3+, Tim3+, and
PD1+Lag3+Tim3+ cells (n=4). Figures were plotted with Microsoft Excel and Prism 9. Paired two-sided student t-test was used to determine
significance. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. A B
A A B B D C
D C D D C FIGURE 1
Pharmacological blockade of PI3K and VIPR signaling improves T-cell expansion and function in vivo ((A) adoptive antigen-specific T cells in
metastatic colon cancer PDX model) and in vitro ((B–D), human T cells). Data availability statement expanded cancer-specific T cells (Figure S1). After 14 days of ex vivo
culture, T cells expanded with decorated TMV, VIPhyb, and
idelalisib had 25% of IFN gamma-expressing CD8 T cells
compared to 13% IFN gamma-expressing CD8 T cells cultured
with IL12/B7-1 decorated TMV without VIPhyb and idelalisib
(Figure 1A). Notably, this effect was not observed in CD4 T cells,
which may attribute to the lack of VPAC1 expression in CD4 subset
(Passang unpublished). The tumor-antigen-stimulated T cells
expanded with VIPhyb and idelalisib were more effective in
controlling the growth of patient-derived colon cancer xenografts
(PDX) following infusion into tumor-bearing immunodeficient
NSG mice than T cells expanded with TMV but without the
addition of VIPhyb + idelalisib, or T cells expanded with neither
TMV nor VIPhyb plus idelalisib (Figure 1A). The raw data supporting the conclusions of this article will be
made available by the authors, without undue reservation. Funding The cancer immunotherapy research in EW’s laboratory is
funded by The Katz Foundation (PI: Waller), Robert W. Woodruff Health Sciences Fund (PI: Waller), The Coulter
Foundation (project 60934), NIGMS MARC program
(#T34GM105550), the National Institutes of Health (NIH) fund
(1R01AI145231-01A1, PI: Waller). The in vivo studies in NSG mice
were also funded by the NIH grant (R01 CA202846, PI: Yang). Concluding remarks The field of cell-based immunotherapy is growing
exponentially. However, efforts are still needed to improve the
clinical response rate. Recent studies have focused on developing
strategies to optimize efficiency in manufacturing T-cells for ACT
therapy and the efficacy of T cells in vivo. We have reviewed current
strategies to enhance T-cell expansion, persistence, and
functionality during ex vivo manufacturing. Moreover, we further
discussed the synergistic benefits of approaches that target multiple
signaling pathways. Besides the conventional small-molecule drugs,
novel VIPR-ANT peptides are promising immunotherapeutic
candidates. Future studies will define the immunoregulatory role
of VIP in ACT and its feasibility in clinical application. Ethics statement The animal study was reviewed and approved by Emory
University Institutional Animal Care and Use Committee. Acknowledgments We thank healthy volunteers and patients for blood and tumor
sample donation. We thank current and former colleagues for
contributing to the adoptive T-cell therapy research. We thank
Metaclipse Therapeutics Corporation for providing purified GPI-
IL-12 and GPI-B7-1 molecules. VIP-receptor antagonists (VIPR-ANT) (A) Left: Increased IFN-g secreting CD8+ T cells using decorated TMV with
VIPhyb and idelalisib (CRCLM-02, n=1); Right: Decreased tumor growth in PDX (CRCLM-02 and CRCLM-04) mice receiving T cells expanded with
beads+TMV+drugs. ANOVA was used to determine significance. The standard error (SE) was shown. (B) Total CD3+ T cells, the actively proliferating
Ki67+CD3+ subset, CD4+CD3+ T cells, and CD8+CD3+ T cells are synergistically expanded in vitro by the combination of ANT308 and duvelisib. The mean +/- SD fold increase in cell expansion over control cultures containing neither added ANT308 nor duvelisib is shown (n=4), with color
shading according to the relative increase. The pair of concentrations yielded the maximal increase in mean fold expansion is shown with a yellow
border around the cell. (C) Frequencies of CD27+CD28+ T cells in cultures with duvelisib and ANT308 led to the highest average expansion for that
subset of T cells (n=4). An example of gating is on the left. (D) ANT308 and duvelisib demonstrated synergy in decreasing PD1+, Lag3+, Tim3+, and
PD1+Lag3+Tim3+ cells (n=4). Figures were plotted with Microsoft Excel and Prism 9. Paired two-sided student t-test was used to determine
significance. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. 06 Frontiers in Immunology frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 Duvelisib and ANT308 Later we investigated the synergy effect of PI3Kg/d inhibitor
duvelisib and leading VIPR-ANT peptide ANT308. The actively
proliferating T cells (Ki67+CD3+), CD4+, and CD8+ T-cell subsets
synergistically expanded in vitro with the combinatorial use of
duvelisib and ANT308 (Figure 1B). We also found that ANT308 as
a single agent, could promote a less senescent T-cell phenotype
(CD27+CD28+), decrease exhausted T cells (PD1+Lag3+Tim3+) and
reduce the expression of PD-1, LAG3, and TIM3. Adding duvelisib
to T cells cultured with ANT308 or ANT195 synergistically
enhanced the expansion of central memory T cells. The
percentage of T cells co-expressing CD27 and CD28 increased
from 2.59% to 7.16% with single-agent ANT308 (3 mM) and
12.5% with single-agent duvelisib (1 µM). The percentage of
CD27+CD28+ T cells further increased to 40.83% with the
combination of ANT308 and duvelisib (Figure 1C). Similarly, the
percentage of T cells with an exhausted phenotype
(PD1+Lag3+Tim3+) decreased from 37.8% in control cultures with
neither ANT308 nor duvelisib, to 22.53% with only ANT308, to
12.56% with single-agent Duvelisib. Adding both drugs together
further decreased the frequency of exhausted T cells to 5.93%
(Figure 1D). Comparable synergistic effects of adding the VIP-
receptor antagonist ANT195 to duvelisib effect were observed
(Figures S2-3). Author contributions HZ conceived, drafted, and wrote the manuscript. TP performed
the in vitro experiments and provided the data of T-cells treated with
Duvelisib and ANT308. SR led the adoptive T cell therapy project in
metastatic colon cancer and conducted in vivo PDX-model
experiments. RB and PS produced TMV and incorporated the
molecules by protein transfer. MJ and LY established the PDX
model. CP critically reviewed and revised the manuscript. EW edited
and revised the manuscript and provided funding support. All authors
contributed to the article and approved the submitted version. Publisher’s note The Supplementary Material for this article can be found online at:
https://www.frontiersin.org/articles/10.3389/fimmu.2023.1154566/
full#supplementary-material All claims expressed in this article are solely those of the authors
and do not necessarily represent those of their affiliated References The dual PI3Kdg inhibitor duvelisib potently inhibits IL-6 production and cytokine
release syndrome (CRS) while maintaining CAR-T function in vitro and. In Vivo. Blood
(2020) 136:1–2. doi: 10.1182/blood-2020-139904 7. Gumber D, Wang LD. Improving CAR-T immunotherapy: overcoming the
challenges of T cell exhaustion. EBioMedicine (2022) 77:103941. doi: 10.1016/
j.ebiom.2022.103941 24. Alsina M, Shah N, Raje NS, Jagannath S, Madduri D, Kaufman JL, et al. Updated
results from the phase I CRB-402 study of anti-bcma CAR-T cell therapy bb21217 in
patients with relapsed and refractory multiple myeloma: correlation of expansion and
duration of response with T cell phenotypes. Blood (2020) 136:25–6. doi: 10.1182/
blood-2020-140410 8. Jiang W, He Y, He W, Wu G, Zhou X, Sheng Q, et al. Exhausted CD8+T cells in
the tumor immune microenvironment: new pathways to therapy. Front Immunol
(2020) 11:622509. doi: 10.3389/fimmu.2020.622509 25. Nian Z, Zheng X, Dou Y, Du X, Zhou L, Fu B, et al. Rapamycin pretreatment
rescues the bone marrow AML cell elimination capacity of CAR-T cells. Clin Cancer
Res (2021) 27:6026–38. doi: 10.1158/1078-0432.CCR-21-0452 9. Beltra JC, Manne S, Abdel-Hakeem MS, Kurachi M, Giles JR, Chen Z, et al. Developmental relationships of four exhausted CD8(+) T cell subsets reveals
underlying transcriptional and epigenetic landscape control mechanisms. Immunity
(2020) 52:825–841.e828. doi: 10.1016/j.immuni.2020.04.014 26. Crompton JG, Sukumar M, Roychoudhuri R, Clever D, Gros A, Eil RL, et al. Akt
inhibition enhances expansion of potent tumor-specific lymphocytes with memory cell
characteristics. Cancer Res (2015) 75:296–305. doi: 10.1158/0008-5472.CAN-14-2277 10. Chu T, Zehn D. Charting the roadmap of T cell exhaustion. Immunity (2020)
52:724–6. doi: 10.1016/j.immuni.2020.04.019 27. Klebanoff CA, Crompton JG, Leonardi AJ, Yamamoto TN, Chandran SS, Eil RL,
et al. Inhibition of AKT signaling uncouples T cell differentiation from expansion for
receptor-engineered adoptive immunotherapy. JCI Insight (2017) 2(23):e95103. doi:
10.1172/jci.insight.95103 11. Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, et al. Chromatin
states define tumour-specific T cell dysfunction and reprogramming. Nature (2017)
545:452–6. doi: 10.1038/nature22367 12. Zhang J, Lyu T, Cao Y, Feng H. Role of TCF-1 in differentiation, exhaustion, and
memory of CD8(+) T cells: a review. FASEB J (2021) 35:e21549. doi: 10.1096/
fj.202002566R 28. Urak R, Walter M, Lim L, Wong CW, Budde LE, Thomas S, et al. Ex vivo akt
inhibition promotes the generation of potent CD19CAR T cells for adoptive
immunotherapy. J ImmunoTherapy Cancer (2017) 5:26. doi: 10.1186/s40425-017-
0227-4 13. Conflict of interest Intellectual property related to the use of peptide antagonists to
vasoactive intestinal polypeptides to treat cancer is the subject of US
patent applications, which are licensed to Cambium Oncology,
LLC. EW is a co-founder and has equity in Cambium Oncology. Duvelisb was a commercial product of Verastem Oncology now a
product of Secura Bio. EW was on the Verastem Scientific Advisory
Board. PS holds shares in Metaclipse Therapeutics Corporation, a
company that is planning to use GPI-anchored molecules to Frontiers in Immunology 07 frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 organizations, or those of the publisher, the editors and the
reviewers. Any product that may be evaluated in this article, or
claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. develop a membrane-based TMV cancer vaccine in the future. A
conflict-of-interest management plan has been reviewed and
approved by Emory University. The remaining authors declare that the research was conducted
in the absence of any commercial or financial relationships that
could be construed as a potential conflict of interest. References 19. Stock S, Übelhart R, Schubert ML, Fan F, He B, Hoffmann JM, et al. Idelalisib for
optimized CD19-specific chimeric antigen receptor T cells in chronic lymphocytic
leukemia patients. Int J Cancer (2019) 145:1312–24. doi: 10.1002/ijc.32201 1. Barnes DW, Corp MJ, Loutit JF, Neal FE. Treatment of murine leukaemia with X
rays and homologous bone marrow; preliminary communication. Br Med J (1956)
2:626–7. doi: 10.1136/bmj.2.4993.626 2. Neelapu SS, Locke FL, Bartlett NL, Lekakis LJ, Miklos DB, Jacobson CA, et al. Axicabtagene ciloleucel CAR T-cell therapy in refractory Large b-cell lymphoma. N
Engl J Med (2017) 377:2531–44. doi: 10.1056/NEJMoa1707447 20. Funk CR, Wang S, Chen KZ, Waller A, Sharma A, Edgar CL, et al. PI3Kd/g
inhibition promotes human CART cell epigenetic and metabolic reprogramming to
enhance antitumor cytotoxicity. Blood (2022) 139:523–37. doi: 10.1182/
blood.2021011597 3. Schuster SJ, Bishop MR, Tam CS, Waller EK, Borchmann P, McGuirk JP, et al. Tisagenlecleucel in adult relapsed or refractory diffuse Large b-cell lymphoma. N Engl J
Med (2019) 380:45–56. doi: 10.1056/NEJMoa1804980 21. Petersen CT, Hassan M, Morris AB, Jeffery J, Lee K, Jagirdar N, et al. Improving
T-cell expansion and function for adoptive T-cell therapy using ex vivo treatment with
PI3Kd inhibitors and VIP antagonists. Blood Adv (2018) 2:210–23. doi: 10.1182/
bloodadvances.2017011254 21. Petersen CT, Hassan M, Morris AB, Jeffery J, Lee K, Jagirdar N, et al. Improving
T-cell expansion and function for adoptive T-cell therapy using ex vivo treatment with
PI3Kd inhibitors and VIP antagonists. Blood Adv (2018) 2:210–23. doi: 10.1182/
bloodadvances.2017011254 4. Gill S, Brudno JN. CAR T-cell therapy in hematologic malignancies: clinical role,
toxicity, and unanswered questions. Am Soc Clin Oncol Educ Book (2021), e246–65. doi:
10.1200/EDBK_320085 22. Dwyer CJ, Arhontoulis DC, Rangel Rivera GO, Knochelmann HM, Smith AS,
Wyatt MM, et al. Ex vivo blockade of PI3K gamma or delta signaling enhances the
antitumor potency of adoptively transferred CD8(+) T cells. Eur J Immunol (2020)
50:1386–99. doi: 10.1002/eji.201948455 5. Shah NN, Fry TJ. Mechanisms of resistance to CAR T cell therapy. Nat Rev Clin
Oncol (2019) 16:372–85. doi: 10.1038/s41571-019-0184-6 6. Cornberg M, Kenney LL, Chen AT, Waggoner SN, Kim SK, Dienes HP, et al. Clonal exhaustion as a mechanism to protect against severe immunopathology and
death from an overwhelming CD8 T cell response. Front Immunol (2013) 4:475. doi:
10.3389/fimmu.2013.00475 23. Amatya PN, Carter AJ, Ritchey JK, Niswonger J, Cooper ML, Pachter JA, et al. References Anti-CD19
CAR T cells in combination with ibrutinib for the treatment of chronic lymphocytic
leukemia. Blood Adv (2022) 6:5774–85. doi: 10.1182/bloodadvances.2022007317 56. Handi J, Patterson S, Levings M. The role of the PI3K signaling pathway in CD4+ T
cell differentiation and function. Front Immunol (2012) 3. doi: 10.3389/fimmu.2012.00245 57. Kim EH, Suresh M. Role of PI3K/Akt signaling in memory CD8 T cell
differentiation. Front Immunol (2013) 4. doi: 10.3389/fimmu.2013.00020 35. Liu M, Deng H, Mu J, Li Q, Pu Y, Jiang Y, et al. Ibrutinib improves the efficacy of
anti-CD19-CAR T-cell therapy in patients with refractory non-Hodgkin lymphoma. Cancer Sci (2021) 112:2642–51. doi: 10.1111/cas.14915 58. Ali K, Soond DR, Pineiro R, Hagemann T, Pearce W, Lim EL, et al. Inactivation
of PI(3)K p110d breaks regulatory T-cell-mediated immune tolerance to cancer. Nature
(2014) 510:407–11. doi: 10.1038/nature13444 36. Qin JS, Johnstone TG, Baturevych A, Hause RJ, Ragan SP, Clouser CR, et al. Antitumor potency of an anti-CD19 chimeric antigen receptor T-cell therapy,
lisocabtagene maraleucel in combination with ibrutinib or acalabrutinib. J
Immunother (2020) 43:107–20. doi: 10.1097/CJI.0000000000000307 59. Chellappa S, Kushekhar K, Munthe LA, Tjønnfjord GE, Aandahl EM,
Okkenhaug K, et al. The PI3K p110d isoform inhibitor idelalisib preferentially
inhibits human regulatory T cell function. J Immunol (2019) 202:1397–405. doi: 10.4049/jimmunol.1701703 37. Ye X, Liu M, Lv C, Li Y, Chen L, Zhang J, et al. Synergistic effects of zanubrutinib
combined with CD19 CAR-T cells in raji cells in vitro and in vivo. Technol Cancer Res
Treat (2022) 21:15330338221133224. doi: 10.1177/15330338221133224 60. Worel N, Grabmeier-Pfistershammer K, Kratzer B, Schlager M, Tanzmann A,
Rottal A, et al. The frequency of differentiated CD3(+)CD27(-)CD28(-) T cells predicts
response to CART cell therapy in diffuse large b-cell lymphoma. Front Immunol (2022)
13:1004703. doi: 10.3389/fimmu.2022.1004703 38. Zhang H, Hu Y, Shao M, Teng X, Jiang P, Wang X, et al. Dasatinib enhances
anti-leukemia efficacy of chimeric antigen receptor T cells by inhibiting cell
differentiation and exhaustion. J Hematol Oncol (2021) 14:113. doi: 10.1186/s13045-
021-01117-y 61. Kaneda MM, Messer KS, Ralainirina N, Li H, Leem CJ, Gorjestani S, et al. PI3Kg
is a molecular switch that controls immune suppression. Nature (2016) 539:437–42. doi: 10.1038/nature19834 39. Wang Y, Tong C, Dai H, Wu Z, Han X, Guo Y, et al. Low-dose decitabine
priming endows CAR T cells with enhanced and persistent antitumour potential via
epigenetic reprogramming. Nat Commun (2021) 12:409. doi: 10.1038/s41467-020-
20696-x 62. References Kagoya Y, Nakatsugawa M, Yamashita Y, Ochi T, Guo T, Anczurowski M, et al. BET bromodomain inhibition enhances T cell persistence and function in adoptive
immunotherapy models. J Clin Invest (2016) 126:3479–94. doi: 10.1172/JCI86437 67. Pal Singh S, Dammeijer F, Hendriks RW. Role of bruton’s tyrosine kinase in b
cells and malignancies. Mol Cancer (2018) 17:57. doi: 10.1186/s12943-018-0779-z 68. Hendriks RW, Yuvaraj S, Kil LP. Targeting bruton's tyrosine kinase in b cell
malignancies. Nat Rev Cancer (2014) 14:219–32. doi: 10.1038/nrc3702 45. Kong W, Dimitri A, Wang W, Jung IY, Ott CJ, Fasolino M, et al. BET
bromodomain protein inhibition reverses chimeric antigen receptor extinction and
reinvigorates exhausted T cells in chronic lymphocytic leukemia. J Clin Invest (2021)
131(16):e145459. doi: 10.1172/JCI145459 69. Gunderson AJ, Kaneda MM, Tsujikawa T, Nguyen AV, Affara NI, Ruffell B, et al. Bruton tyrosine kinase-dependent immune cell cross-talk drives pancreas cancer. Cancer Discovery (2016) 6:270–85. doi: 10.1158/2159-8290.CD-15-0827 46. Krämer I, Engelhardt M, Fichtner S, Neuber B, Medenhoff S, Bertsch U, et al. Lenalidomide enhances myeloma-specific T-cell responses. Vivo vitro. Oncoimmunology (2016) 5:e1139662. doi: 10.1080/2162402X.2016.1139662 70. Xia S, Liu X, Cao X, Xu S. T-Cell expression of bruton’s tyrosine kinase promotes
autoreactive T-cell activation and exacerbates aplastic anemia. Cell Mol Immunol
(2020) 17:1042–52. doi: 10.1038/s41423-019-0270-9 47. Wang X, Walter M, Urak R, Weng L, Huynh C, Lim L, et al. Lenalidomide
enhances the function of CS1 chimeric antigen receptor–redirected T cells against
multiple myeloma. Clin Cancer Res (2018) 24:106–19. doi: 10.1158/1078-0432.CCR-17-
0344 71. Parry HM, Mirajkar N, Cutmore N, Zuo J, Long H, Kwok M, et al. Long-term
ibrutinib therapy reverses CD8+ T cell exhaustion in b cell chronic lymphocytic
leukaemia. Front Immunol (2019) 10. doi: 10.3389/fimmu.2019.02832 72. Davis JE, Sharpe C, Mason K, Tam CS, Koldej RM, Ritchie DS, et al. Ibrutinib
protects T cells in patients with CLL from proliferation-induced senescence. J Trans
Med (2021) 19:473. doi: 10.1186/s12967-021-03136-2 48. Works M, Soni N, Hauskins C, Sierra C, Baturevych A, Jones JC, et al. Anti–b-
cell maturation antigen chimeric antigen receptor T cell function against multiple
myeloma is enhanced in the presence of lenalidomide. Mol Cancer Ther (2019)
18:2246–57. doi: 10.1158/1535-7163.MCT-18-1146 73. Baptista MJ, Baskar S, Gaglione EM, Keyvanfar K, Ahn IE, Wiestner A, et al. Select
antitumor cytotoxic CD8(+) T clonotypes expand in patients with chronic lymphocytic
leukemia treated with ibrutinib. Clin Cancer Res (2021) 27:4624–33. doi: 10.1158/1078-
0432.CCR-20-4894 49. References De Henau O, Rausch M, Winkler D, Campesato LF, Liu C, Cymerman DH, et al. Overcoming resistance to checkpoint blockade therapy by targeting PI3Kg in myeloid
cells. Nature (2016) 539:443–7. doi: 10.1038/nature20554 40. Kang S, Wang L, Xu L, Wang R, Kang Q, Gao X, et al. Decitabine enhances
targeting of AML cells by NY-ESO-1-specific TCR-T cells and promotes the
maintenance of effector function and the memory phenotype. Oncogene (2022)
41:4696–708. doi: 10.1038/s41388-022-02455-y
41. Ali AI, Wang M, von Scheidt B, Dominguez PM, Harrison AJ, Tantalo DGM,
et al. A histone deacetylase inhibitor, panobinostat, enhances chimeric antigen receptor
T-cell antitumor effect against pancreatic cancer. Clin Cancer Res (2021) 27:6222–34. doi: 10.1158/1078-0432.CCR-21-1141 40. Kang S, Wang L, Xu L, Wang R, Kang Q, Gao X, et al. Decitabine enhances
targeting of AML cells by NY-ESO-1-specific TCR-T cells and promotes the
maintenance of effector function and the memory phenotype. Oncogene (2022)
41:4696–708. doi: 10.1038/s41388-022-02455-y 63. Chandrasekaran S, Funk CR, Kleber T, Paulos CM, Shanmugam M, Waller EK. Strategies to overcome failures in T-cell immunotherapies by targeting PI3K-d and -g. Front Immunol (2021) 12:718621. doi: 10.3389/fimmu.2021.718621 64. Araki K, Turner AP, Shaffer VO, Gangappa S, Keller SA, Bachmann MF, et al. mTOR regulates memory CD8 T-cell differentiation. Nature (2009) 460:108–12. doi: 10.1038/nature08155 41. Ali AI, Wang M, von Scheidt B, Dominguez PM, Harrison AJ, Tantalo DGM,
et al. A histone deacetylase inhibitor, panobinostat, enhances chimeric antigen receptor
T-cell antitumor effect against pancreatic cancer. Clin Cancer Res (2021) 27:6222–34. doi: 10.1158/1078-0432.CCR-21-1141 65. Alizadeh D, Wong RA, Yang X, Wang D, Pecoraro JR, Kuo C-F, et al. IL15
enhances CAR-T cell antitumor activity by reducing mTORC1 activity and preserving
their stem cell memory phenotype. Cancer Immunol Res (2019) 7:759–72. doi: 10.1158/
2326-6066.CIR-18-0466 42. Lei X, Ou Z, Yang Z, Zhong J, Zhu Y, Tian J, et al. A pan-histone deacetylase
inhibitor enhances the antitumor activity of B7-H3–specific CAR T cells in solid
tumors. Clin Cancer Res (2021) 27:3757–71. doi: 10.1158/1078-0432.CCR-20-2487 66. Rogel A, Willoughby JE, Buchan SL, Leonard HJ, Thirdborough SM, Al-Shamkhani
A. Akt signaling is critical for memory CD8(+) T-cell development and tumor immune
surveillance. Proc Natl Acad Sci U.S.A. (2017) 114:E1178–e1187. doi: 10.1073/
pnas.1611299114 43. Shen C, Zhang Z, Tian Y, Li F, Zhou L, Jiang W, et al. Sulforaphane enhances the
antitumor response of chimeric antigen receptor T cells by regulating PD-1/PD-L1
pathway. BMC Med (2021) 19:283. doi: 10.1186/s12916-021-02161-8 44. References Blache U, Popp G, Dünkel A, Koehl U, Fricke S. Potential solutions for
manufacture of CAR T cells in cancer immunotherapy. Nat Commun (2022)
13:5225. doi: 10.1038/s41467-022-32866-0 29. Mousset CM, Hobo W, Ji Y, Fredrix H, De Giorgi V, Allison RD, et al. Ex vivo
AKT-inhibition facilitates generation of polyfunctional stem cell memory-like CD8+ T
cells for adoptive immunotherapy. OncoImmunology (2018) 7:e1488565. doi: 10.1080/
2162402X.2018.1488565 14. Liu Y, An L, Huang R, Xiong J, Yang H, Wang X, et al. Strategies to enhance
CAR-T persistence. biomark Res (2022) 10:86. doi: 10.1186/s40364-022-00434-9 30. Zhang Q, Ding J, Sun S, Liu H, Lu M, Wei X, et al. Akt inhibition at the initial
stage of CAR-T preparation enhances the CAR-positive expression rate, memory
phenotype and. Vivo efficacy. Am J Cancer Res (2019) 9:2379–96. 15. Dwyer CJ, Knochelmann HM, Smith AS, Wyatt MM, Rangel Rivera GO,
Arhontoulis DC, et al. Fueling cancer immunotherapy with common gamma chain
cytokines. Front Immunol (2019) 10:263. doi: 10.3389/fimmu.2019.00263 31. Fan F, Yoo HJ, Stock S, Wang L, Liu Y, Schubert M-L, et al. Ibrutinib for
improved chimeric antigen receptor T-cell production for chronic lymphocytic
leukemia patients. Int J Cancer (2021) 148:419–28. doi: 10.1002/ijc.33212 16. Abu Eid R, Ahmad S, Lin Y, Webb M, Berrong Z, Shrimali R, et al. Enhanced
therapeutic efficacy and memory of tumor-specific CD8 T cells by ex vivo PI3K-d
inhibition. Cancer Res (2017) 77:4135–45. doi: 10.1158/0008-5472.CAN-16-1925 32. Fraietta JA, Beckwith KA, Patel PR, Ruella M, Zheng Z, Barrett DM, et al. Ibrutinib enhances chimeric antigen receptor T-cell engraftment and efficacy in
leukemia. Blood (2016) 127:1117–27. doi: 10.1182/blood-2015-11-679134 17. Zheng W, O’Hear CE, Alli R, Basham JH, Abdelsamed HA, Palmer LE, et al. PI3K orchestration of the in vivo persistence of chimeric antigen receptor-modified T
cells. Leukemia (2018) 32:1157–67. doi: 10.1038/s41375-017-0008-6 18. Bowers JS, Majchrzak K, Nelson MH, Aksoy BA, Wyatt MM, Smith AS, et al. PI3Kd inhibition enhances the antitumor fitness of adoptively transferred CD8(+) T
cells. Front Immunol (2017) 8:1221. doi: 10.3389/fimmu.2017.01221 33. Gauthier J, Hirayama AV, Purushe J, Hay KA, Lymp J, Li DH, et al. Feasibility
and efficacy of CD19-targeted CAR T cells with concurrent ibrutinib for CLL after
ibrutinib failure. Blood (2020) 135:1650–60. doi: 10.1182/blood.2019002936 Frontiers in Immunology 08 frontiersin.org Zhang et al. 10.3389/fimmu.2023.1154566 10.3389/fimmu.2023.1154566 Zhang et al. 34. Gill S, Vides V, Frey NV, Hexner EO, Metzger S, O'Brien M, et al. References Tettamanti S, Rotiroti MC, Giordano Attianese GMP, Arcangeli S, Zhang R,
Banerjee P, et al. Lenalidomide enhances CD23.CAR T cell therapy in chronic
lymphocytic leukemia. Leukemia Lymphoma (2022) 63:1566–79. doi: 10.1080/
10428194.2022.2043299 74. Wen T, Wang J, Shi Y, Qian H, Liu P. Inhibitors targeting bruton’s tyrosine
kinase in cancers: drug development advances. Leukemia (2021) 35:312–32. doi:
10.1038/s41375-020-01072-6 50. Zhang L, Jin G, Chen Z, Yu C, Li Y, Li Y, et al. Lenalidomide improves the
antitumor activity of CAR-T cells directed toward the intracellular wilms tumor 1
antigen. Hematology (2021) 26:818–26. doi: 10.1080/16078454.2021.1981534 75. Vener C, Banzi R, Ambrogi F, Ferrero A, Saglio G, Pravettoni G, et al. First-line
imatinib vs second- and third-generation TKIs for chronic-phase CML: a systematic review
and meta-analysis. Blood Adv (2020) 4:2723–35. doi: 10.1182/bloodadvances.2019001329 51. Wang Z, Zhou G, Risu N, Fu J, Zou Y, Tang J, et al. Lenalidomide enhances
CAR-T cell activity against solid tumor cells. Cell Transplant (2020)
29:0963689720920825. doi: 10.1177/0963689720920825 76. Schade AE, Schieven GL, Townsend R, Jankowska AM, Susulic V, Zhang R, et al. Dasatinib, a small-molecule protein tyrosine kinase inhibitor, inhibits T-cell activation
and proliferation. Blood (2008) 111:1366–77. doi: 10.1182/blood-2007-04-084814 52. Kuramitsu S, Ohno M, Ohka F, Shiina S, Yamamichi A, Kato A, et al. Lenalidomide enhances the function of chimeric antigen receptor T cells against the
epidermal growth factor receptor variant III by enhancing immune synapses. Cancer
Gene Ther (2015) 22:487–95. doi: 10.1038/cgt.2015.47 77. Dittmann A, Werner T, Chung CW, Savitski MM, Fälth Savitski M, Grandi P,
et al. The commonly used PI3-kinase probe LY294002 is an inhibitor of BET
bromodomains. ACS Chem Biol (2014) 9:495–502. doi: 10.1021/cb400789e 53. Thieblemont C, Chevret S, Allain V, Di Blasi R, Morin F, Vercellino L, et al. Lenalidomide enhance CAR T-cells response in patients with Refractory/Relapsed
Large b cell lymphoma experiencing progression after infusion. Blood (2020) 136:16–7. doi: 10.1182/blood-2020-136279 78. Quach H, Ritchie D, Stewart AK, Neeson P, Harrison S, Smyth MJ, et al. Mechanism of action of immunomodulatory drugs (IMiDS) in multiple myeloma. Leukemia (2010) 24:22–32. doi: 10.1038/leu.2009.236 54. Okkenhaug K, Graupera M, Vanhaesebroeck B. Targeting PI3K in cancer:
impact on tumor cells, their protective stroma, angiogenesis, and immunotherapy. Cancer Discovery (2016) 6:1090–105. doi: 10.1158/2159-8290.CD-16-0716 79. Davies FE, Raje N, Hideshima T, Lentzsch S, Young G, Tai Y-T, et al. Thalidomide and immunomodulatory derivatives augment natural killer cell
cytotoxicity in multiple myeloma. Blood (2001) 98:210–6. doi: 10.1182/blood.V98.1.210 55. References Pharmacological inhibition of
VIP signaling enhances antiviral immunity and improves survival in murine
cytomegalovirus-infected allogeneic bone marrow transplant recipients. Blood (2013)
121:2347–51. doi: 10.1182/blood-2012-06-437640 85. Delgado M. VIP: A very important peptide in T helper differentiation. Trends
Immunol (2003) 24:221–4. doi: 10.1016/S1471-4906(03)00069-3 86. Delgado M, Ganea D. Vasoactive intestinal peptide: a neuropeptide with pleiotropic
immune functions. Amino Acids (2013) 45:25–39. doi: 10.1007/s00726-011-1184-8 97. Li JM, Darlak KA, Southerland L, Hossain MS, Jaye DL, Josephson CD, et al. VIPhyb, an antagonist of vasoactive intestinal peptide receptor, enhances cellular
antiviral immunity in murine cytomegalovirus infected mice. PloS One (2013) 8:
e63381. doi: 10.1371/journal.pone.0063381 87. Delgado M, Pozo D, Ganea D. The significance of vasoactive intestinal peptide
in immunomodulation. Pharmacol Rev (2004) 56:249–90. doi: 10.1124/pr.56.2.7 88. Carrión M, Pérez-Garcı́a S, Martı́nez C, Juarranz Y, Estrada-Capetillo L, Puig-
Kröger A, et al. VIP Impairs acquisition of the macrophage proinflammatory
polarization profile. J Leukoc Biol (2016) 100:1385–93. doi: 10.1189/jlb.3A0116-032RR 98. Petersen CT, Li JM, Waller EK. Administration of a vasoactive intestinal peptide
antagonist enhances the autologous anti-leukemia T cell response in murine models of
acute leukemia. Oncoimmunology (2017) 6:e1304336. doi: 10.1080/
2162402X.2017.1304336 98. Petersen CT, Li JM, Waller EK. Administration of a vasoactive intestinal peptide
antagonist enhances the autologous anti-leukemia T cell response in murine models of
acute leukemia. Oncoimmunology (2017) 6:e1304336. doi: 10.1080/
2162402X.2017.1304336 89. Kittikulsuth W, Nakano D, Kitada K, Uyama T, Ueda N, Asano E, et al. Vasoactive
intestinal peptide blockade suppresses tumor growth by regulating macrophage polarization and
function in CT26 tumor-bearing mice. Sci Rep (2023) 13:927. doi: 10.1038/s41598-023-28073-6 99. Ravindranathan S, Passang T, Li J-M, Wang S, Dhamsania R, Ware MB, et al. Targeting vasoactive intestinal peptide-mediated signaling enhances response to
immune checkpoint therapy in pancreatic ductal adenocarcinoma. Nat Commun
(2022) 13:6418. doi: 10.1038/s41467-022-34242-4 90. Azevedo MCS, Fonseca AC, Colavite PM, Melchiades JL, Tabanez AP, Codo AC,
et al. Macrophage polarization and alveolar bone healing outcome: despite a significant M2
polarizing effect, VIP and PACAP treatments present a minor impact in alveolar bone
healing in homeostatic conditions. Front Immunol (2021) 12:782566. doi: 10.3389/
fimmu.2021.782566 100. Bommireddy R, Munoz LE, Kumari A, Huang L, Fan Y, Monterroza L,
et al. Tumor membrane vesicle vaccine augments the efficacy of anti-PD1 antibody
in immune checkpoint inhibitor-resistant squamous cell carcinoma models of
head and neck cancer. Vaccines (Basel) (2020) 8(2):182. doi: 10.3390/
vaccines8020182 91. References Okkenhaug K, Burger JA. PI3K signaling in normal b cells and chronic
lymphocytic leukemia (CLL). Curr Top Microbiol Immunol (2016) 393:123–42. doi: 10.1007/82_2015_484 80. Busch A, Zeh D, Janzen V, Mügge LO, Wolf D, Fingerhut L, et al. Treatment with
lenalidomide induces immunoactivating and counter-regulatory immunosuppressive
changes in myeloma patients. Clin Exp Immunol (2014) 177:439–53. doi: 10.1111/cei.12343 Frontiers in Immunology 09 frontiersin.org Zhang et al. Zhang et al. 10.3389/fimmu.2023.1154566 81. D'Souza C, Prince HM, Neeson PJ. Understanding the role of T-cells in the
antimyeloma effect of immunomodulatory drugs. Front Immunol (2021) 12. doi: 10.3389/
fimmu.2021.632399 93. Gozes I, McCune SK, Jacobson L, Warren D, Moody TW, Fridkin M, et al. An
antagonist to vasoactive intestinal peptide affects cellular functions in the central
nervous system. J Pharmacol Exp Ther (1991) 257:959–66. 82. Lemoine J, Morin F, Di Blasi R, Vercellino L, Cuffel A, Benlachgar N, et al. Lenalidomide exposure at time of CAR T-cells expansion enhances response of
Refractory/Relapsed aggressive Large b-cell lymphomas. Blood (2021) 138:1433–3. doi: 10.1182/blood-2021-151109 94. Zia H, Hida T, Jakowlew S, Birrer M, Gozes Y, Reubi JC, et al. Breast cancer
growth is inhibited by vasoactive intestinal peptide (VIP) hybrid, a synthetic VIP
receptor antagonist. Cancer Res (1996) 56:3486–9. 82. Lemoine J, Morin F, Di Blasi R, Vercellino L, Cuffel A, Benlachgar N, et al. Lenalidomide exposure at time of CAR T-cells expansion enhances response of
Refractory/Relapsed aggressive Large b-cell lymphomas. Blood (2021) 138:1433–3. doi: 10.1182/blood-2021-151109 95. Li JM, Southerland L, Hossain MS, Giver CR, Wang Y, Darlak K, et al. Absence
of vasoactive intestinal peptide expression in hematopoietic cells enhances Th1
polarization and antiviral immunity in mice. J Immunol (2011) 187:1057–65. doi:
10.4049/jimmunol.1100686 95. Li JM, Southerland L, Hossain MS, Giver CR, Wang Y, Darlak K, et al. Absence
of vasoactive intestinal peptide expression in hematopoietic cells enhances Th1
polarization and antiviral immunity in mice. J Immunol (2011) 187:1057–65. doi:
10.4049/jimmunol.1100686 83. Said SI, Mutt V. Potent peripheral and splanchnic vasodilator peptide from
normal gut. Nature (1970) 225:863–4. doi: 10.1038/225863a0 84. Said SI, Mutt V. Polypeptide with broad biological activity: isolation from small
intestine. Science (1970) 169:1217–8. doi: 10.1126/science.169.3951.1217 96. Li JM, Hossain MS, Southerland L, Waller EK. Pharmacological inhibition of
VIP signaling enhances antiviral immunity and improves survival in murine
cytomegalovirus-infected allogeneic bone marrow transplant recipients. Blood (2013)
121:2347–51. doi: 10.1182/blood-2012-06-437640 96. Li JM, Hossain MS, Southerland L, Waller EK. References Li JM, Petersen CT, Li JX, Panjwani R, Chandra DJ, Giver CR, et al. Modulation of
immune checkpoints and graft-versus-Leukemia in allogeneic transplants by antagonizing
vasoactive intestinal peptide signaling. Cancer Res (2016) 76:6802–15. doi: 10.1158/0008-
5472.CAN-16-0427 101. Pack CD, Bommireddy R, Munoz LE, Patel JM, Bozeman EN, Dey P, et al. Tumor membrane-based vaccine immunotherapy in combination with anti-CTLA-4
antibody confers protection against immune checkpoint resistant murine triple-
negative breast cancer. Hum Vaccin Immunother (2020) 16:3184–93. doi: 10.1080/
21645515.2020.1754691 92. Zhu J, Wang Y, Li J, Das PK, Zhang H, Passang T, et al. Donor plasmacytoid
dendritic cells limit graft-versus-host disease through vasoactive intestinal polypeptide
expression. Blood (2022) 140:1431–47. doi: 10.1182/blood.2021012561 10 Frontiers in Immunology frontiersin.org
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Oral Lichen Planus in a 50-Year-Old Male Patient: A Case Report
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■ Abstract This paper presents the case of a 50-year-old heavy smoker male with multiple oral white lesions complaining of mild
burning sensation in his mouth while consuming acidic foods and liquids. Intraoral examination revealed non-scrapable
large white plaque-like lesions with slightly erythematous background on both right and left sides of jugal mucosa, and a
white plaque with papillae atrophy at the right lateral border of the tongue. The diagnosis of lichen planus was confirmed
through histopathological assessment. Topical corticosteroids were prescribed and symptoms improvement was achieved
after two months. Regular annual long-term follow-ups were requested to monitor the disease activity and to exclude any
malignant transformation. Keywords: oral, lichen planus, biopsy, histological examination, topical corticosteroid Submitted: 10 July 2022, Accepted: 26 July 2022, Published: 29 July 2022 Submitted: 10 July 2022, Accepted: 26 July 2022, Published: 29 July 2022 Copyright © 2022 Aoun G. This is an open access article distributed under the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Volume 2 Volume 2 Case Reports
Research Practices
in
&
MEDICINE
I S S N : 2 7 7 1 - 4 8 4 5 CASE REPORT Corresponding Author: Georges Aoun, e-mail: dr.georgesaoun@gmail.com Corresponding Author: Georges Aoun, e-mail: dr.georgesaoun@gmail.com Oral Lichen Planus in a 50-Year-Old
Male Patient: A Case Report
Georges Aoun1, Samira Haddad2, and Georgina El-Ghoul3 1Department of Oral Medicine and Maxillofacial Radiology, Faculty of Dental Medicine, Lebanese University, Beirut, Lebanon
2Private practice, Oral Medicine, Lebanon 3Department of Periodontology, Faculty of Dental Medicine, Saint Joseph University, Beirut, Lebanon www.crrpm.org Introduction Intraoral photograph showing the white lesion with
papillae atrophy at the right lateral border of the tongue cause the perturbation of the lining epithelial basement
membrane integrity [4]. Drugs such as antimalarials,
ACEIs, thiazide diuretics, NSAIDs, quinidine, beta-
blockers, tumor necrosis factor alpha (TNFα) inhibitors
[5], as well as contact allergens, and viruses, especially
the hepatitis C virus (HCV), have all been reported
to be possibly associated with development of LP [6,
7]. Additionally, OLP has been linked to a variety of
metals found in dental restorations including mercury,
copper, and gold [8]. Clinically, LP appears as pruritic, violaceous papules
and plaques most frequently found on the wrists, lower
back, and ankles [6]. A specific lattice-like network of
white lines called Wickham striae could be observed
overlying the lesions [3]. On the other hand, six types of
OLP, namely reticular, papular, plaque-like, atrophic/
erosive, ulcerative, and bullous can be identified [9]. The jugal mucosa, the tongue and the gingiva are
frequently involved although other sites may be rarely
affected [10]. OLP may present alone or associated with
skin lesions. It is often asymptomatic. However, it may
be complicated by painful erosions; burning sensation
may also occur. Microscopically, it is characterized by
lymphocytic infiltrate and vacuolar degeneration of the
epithelial basal layer [3]. Figure 2. Intraoral photograph showing the white lesion with
papillae atrophy at the right lateral border of the tongue and formation of parakeratosis foci. Rich band-like
inflammatory infiltrate consisting of mononuclear
cells was identified in the lamina propria, just below
the epithelium with perturbation of the basement
membrane integrity. This histological aspect was
consistent with OLP. The diagnosis of OLP was confirmed and since
the case presented mild symptoms, topical use of
corticosteroids (twice daily for 2 months) was prescribed
and symptoms improvement was achieved. Regular
annual long-term follow-ups were requested to monitor
the disease activity and to exclude any malignant
transformation. The prevalence of cutaneous LP is around 0.2% to
1% of adults globally [11]. OLP is more frequent and
reported in 1% to 4% of the population, with female to
male ratio of 1.5:1. Most of LP cases develop between
the ages of 30 and 60 [12]. While LP is not usually
considered to have a racial predilection, some studies
have suggested a higher incidence of the disease in
African-Americans, Indian and Arabian descents [13,
14]. Introduction A 50-year-old male was referred by his dentist to
our specialized oral medicine clinic for evaluation of
multiple oral white lesions. Mild burning sensation
while having acidic foods and liquids was his chief
complaint. Medical history was unremarkable, and
physical examination revealed no extra-oral abnormal
findings. He was a heavy smoker (30 cigarettes per day)
for more than 20 years. On clinical examination, the
patient presented non-scrapable large white plaque-
like lesions with slightly erythematous background on
both right and left sides of jugal mucosa. Additionally,
at the right lateral border of the tongue, a white plaque
with papillae atrophy was noticed (Figures 1 and 2). O
ral lichen planus (OLP) is a chronic inflammatory
disease that affects the mucous membrane of the
oral cavity. It belongs to the mucosal counterpart
of cutaneous lichen planus [LP] [1, 2]. The two major
clinical forms of OLP are reticular and erosive. Typically, the lesions are multiple, symmetrical,
and appear on different sites of the oral cavity [1]. It
is more common in the 4th decade of life with slight
female predilection [2]. LP of the skin is habitually self-
limiting and resolves within 6 months in over 50% of
cases and in up to 85% within 18 months. By contrast,
nail or scalp LPs as well as OLP are often chronic and
may be refractory to treatment [3]. Persistent lesions
are considered premalignant. Therefore, patients
should be followed up regularly for both, adjustment
of treatment, and screening for the development of
malignancies [3]. In this report, we present the case of
a 50-year-old male diagnosed with OLP. O Based on the clinical presentation and the
accompanying symptoms a provisional diagnosis of
OLP was given. The lesions were biopsied under local
anesthesia, fixed in 10% neutral buffered formalin, and
sent for histological examination. The histopathology
report disclosed a thickened stratified epithelium,
with irregular acanthosis and hyperparakeratosis Volume 2 Issue 3 72 www.crrpm.org 73 Oral Lichen Planus in a 50-Year-Old Male Patient: A Case Report Oral Lichen Planus in a 50-Year-Old Male Patient: A Case Report Figure 1. Intraoral photographs showing the bilateral (A: left; B: right) jugal white lesions. al (A: left; B: right) jugal white lesions. l (A: left; B: right) jugal white lesions. Figure 1. Intraoral photographs showing the bilater Figure 1. Intraoral photographs showing the bilateral (A: left; B: right) jugal white lesions. Figure 2. Introduction Additionally, a familial component of up to 10% of
first-degree relatives has been proposed [15]. ■ References 1. Vlad CS, Vlad DC, Popescu R, Borugă VM, Istrate SL,
et al. Oral lichen planus - case report. Rom J Morphol
Embryol. 2020; 61(2): 563-567. 2. Lavanya N, Jayanthi P, Rao UK, Ranganathan K. Oral
lichen planus: An update on pathogenesis and treatment. Journal of oral and maxillofacial pathology: JOMFP. 2011
May;15(2):127. 10. Ismail SB, Kumar SK, Zain RB. Oral lichen planus
and lichenoid reactions: etiopathogenesis, diagnosis,
management and malignant transformation. Journal of oral
science. 2007;49(2):89-106. 3. Boch K, Langan EA, Kridin K, Zillikens D, Ludwig RJ, et
al. Lichen planus. Front Med (Lausanne). 2021; 8: 737813. 11. Boyd AS, Neldner KH. Lichen planus. Journal of the
American Academy of Dermatology. 1991 Oct 1;25(4):593-
619. 4. Chaitanya NC, Chintada S, Kandi P, Kanikella S,
Kammari A, Waghamare RS. Zinc therapy in treatment
of symptomatic oral lichen planus. Indian Dermatology
Online Journal. 2019 Mar;10(2):174. 12. Laurence Le Cleach MD, Chosidow O. Lichen Planus. N
Engl J Med. 2012;366:723-32. 13. Balasubramaniam P, Ogboli M, Moss C. Lichen planus in
children: review of 26 cases. Clinical and Experimental
Dermatology: Clinical dermatology. 2008 Jul;33(4):457-9. 5. Asarch A, Gottlieb AB, Lee J, Masterpol KS, Scheinman
PL, Stadecker MJ, Massarotti EM, Bush ML. Lichen
planus–like eruptions: An emerging side effect of tumor
necrosis factor-α antagonists. Journal of the American
Academy of Dermatology. 2009 Jul 1;61(1):104-11. 14. Walton KE, Bowers EV, Drolet BA, Holland KE. Childhood
lichen planus: demographics of a US population. Pediatric
dermatology. 2010 Jan;27(1):34-8. 6. Alaizari NA, Al‐Maweri SA, Al‐Shamiri HM, Tarakji B,
Shugaa‐Addin B. Hepatitis C virus infections in oral lichen
planus: a systematic review and meta‐analysis. Australian
dental journal. 2016 Sep;61(3):282-7. 15. Kofoed ML, Wantzin GL. Familial lichen planus: More
frequent than previously suggested?. Journal of the American
Academy of Dermatology. 1985 Jul 1;13(1):50-4. 16. Ioannides D, Vakirlis E, Kemeny L, Marinovic B, Massone
C, Murphy R, Nast A, Ronnevig J, Ruzicka T, Cooper SM,
Trüeb RM. European S1 guidelines on the management of
lichen planus: a cooperation of the European Dermatology
Forum with the European Academy of Dermatology
and Venereology. Journal of the European Academy of
Dermatology and Venereology. 2020 Jul;34(7):1403-14. 7. Robledo-Sierra J, van der Waal I. How general dentists
could manage a patient with oral lichen planus. Medicina
oral, patologia oral y cirugia bucal. 2018 Mar;23(2):e189. 8. Dunsche A, Frank MP, Lüttges J, Açil Y, Brasch J,
Christophers E, Springer IN. Discussion Amphotericin B can be used several times daily (after
food consumption) to prevent secondary candida
infection. OLP may clear spontaneously within years,
but usually it presents a remitting and relapsing
course [3]. Long-term follow-up is indispensable to Discussion Lichen
planus
is
a
chronic
mucocutaneous
inflammatory lesion which may affect the skin, the
nails, the scalp, the lips, and other mucosal surfaces
including the oral mucosa, the esophagus, the pharynx,
and the genital mucosa (the glans penis, the vulvar
and vaginal mucosa, the labia majora, and the labia
minora) [3]. OLP is relatively frequent in adult
patients. Its etiology remains unknown, but stress,
drugs, dental fillings, genetic factors, immunity, and
hyper-sensitivity reactions can be contributing factors
to its pathogenesis [1]. Many studies have supposed
that OLP is a T cell-mediated autoimmune condition,
in which cytotoxic CD8+ T-cells that release different
cytokines like TNFα and interleukin-12 (IL-12) may The differential diagnosis includes lichenoid lesions
(drug related or caused by the contact with restorative
dental materials), leukoplakia, lupus erythematosus,
pemphigus vulgaris, mucous membrane pemphigoid,
secondary syphilis, traumatic patches, and candidiasis
[3]. OLP is habitually difficult to treat, especially when
wide erosions are present. Topical corticosteroids are
the treatment of choice. They can be applied twice daily
for 1 to 2 months, and then administered as required. Intralesional steroid injections are considered when ISSN: 2771-4845 Volume 2 Issue 3 Case Rep Res Prac Med (2022) 2(3):72-74 74 Aoun et al. observe disease activity and to rule out any potential
malignant transformation [3, 16]. observe disease activity and to rule out any potential
malignant transformation [3, 16]. lesions are particularly painful and fail to respond to
topical therapy [3, 16]. Systemic corticosteroids are
reserved for patients with severe erosive OLP [16]. Other systemic treatments are retinoids, cyclosporine,
azathioprine,
hydroxychloroquine,
methotrexate,
thalidomide,
and/or
use
of
topical
calcineurin
inhibitors [3, 16]. To reduce pain, mouthwash based on
a lidocaine solution may be helpful. Recently, low level
laser was used to decrease erosive OLP symptoms. Amphotericin B can be used several times daily (after
food consumption) to prevent secondary candida
infection. OLP may clear spontaneously within years,
but usually it presents a remitting and relapsing
course [3]. Long-term follow-up is indispensable to lesions are particularly painful and fail to respond to
topical therapy [3, 16]. Systemic corticosteroids are
reserved for patients with severe erosive OLP [16]. Other systemic treatments are retinoids, cyclosporine,
azathioprine,
hydroxychloroquine,
methotrexate,
thalidomide,
and/or
use
of
topical
calcineurin
inhibitors [3, 16]. To reduce pain, mouthwash based on
a lidocaine solution may be helpful. Recently, low level
laser was used to decrease erosive OLP symptoms. Conclusion OLP is an immune disease with unknown etiology. In order to improve its management, an early accurate
diagnosis through histological examination is needed. In our case, the clinical evolution was favorable after
the administration of topical corticosteroids. Regular
postoperative follow-ups are mandatory for optimum
treatment
outcome
and
recurrence/malignant
transformation prevention. 9. Chiang CP, Chang JY, Wang YP, Wu YH, Lu SY, Sun
A. Oral lichen planus–differential diagnoses, serum
autoantibodies, hematinic deficiencies, and management. Journal of the Formosan Medical Association. 2018 Sep
1;117(9):756-65. ■ References Lichenoid reactions of
murine mucosa associated with amalgam. British Journal
of Dermatology. 2003 Apr;148(4):741-8. ISSN: 2771-4845 Case Rep Res Prac Med (2022) 2(3):72-74 www.crrpm.org
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Differential-Evolution Control Parameter Optimization for Unmanned Aerial Vehicle Path Planning
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PloS one
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Differential-Evolution Control Parameter
Optimization for Unmanned Aerial Vehicle
Path Planning Kai Yit Kok, Parvathy Rajendran* School of Aerospace Engineering, Universiti Sains Malaysia, Engineering Campus, 14300 Nibong Tebal,
Pulau Pinang, Malaysia * aeparvathy@usm.my * aeparvathy@usm.my OPEN ACCESS Citation: Kok KY, Rajendran P (2016) Differential-
Evolution Control Parameter Optimization for
Unmanned Aerial Vehicle Path Planning. PLoS ONE
11(3): e0150558. doi:10.1371/journal.pone.0150558 Citation: Kok KY, Rajendran P (2016) Differential-
Evolution Control Parameter Optimization for
Unmanned Aerial Vehicle Path Planning. PLoS ONE
11(3): e0150558. doi:10.1371/journal.pone.0150558 Editor: Xiaosong Hu, Chongqing University, CHINA
Received: September 14, 2015
Accepted: February 14, 2016
Published: March 4, 2016 Copyright: © 2016 Kok, Rajendran. This is an open
access article distributed under the terms of the Copyright: © 2016 Kok, Rajendran. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. RESEARCH ARTICLE Abstract The differential evolution algorithm has been widely applied on unmanned aerial vehicle
(UAV) path planning. At present, four random tuning parameters exist for differential evolu-
tion algorithm, namely, population size, differential weight, crossover, and generation num-
ber. These tuning parameters are required, together with user setting on path and
computational cost weightage. However, the optimum settings of these tuning parameters
vary according to application. Instead of trial and error, this paper presents an optimization
method of differential evolution algorithm for tuning the parameters of UAV path planning. The parameters that this research focuses on are population size, differential weight, cross-
over, and generation number. The developed algorithm enables the user to simply define
the weightage desired between the path and computational cost to converge with the mini-
mum generation required based on user requirement. In conclusion, the proposed optimiza-
tion of tuning parameters in differential evolution algorithm for UAV path planning expedites
and improves the final output path and computational cost. OPEN ACCESS
Citation: Kok KY, Rajendran P (2016) Differential-
Evolution Control Parameter Optimization for
Unmanned Aerial Vehicle Path Planning. PLoS ONE
11(3): e0150558. doi:10.1371/journal.pone.0150558
Editor: Xiaosong Hu, Chongqing University, CHINA
Received: September 14, 2015
Accepted: February 14, 2016
Published: March 4, 2016
Copyright: © 2016 Kok, Rajendran. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. OPEN ACCESS
Citation: Kok KY, Rajendran P (2016) Differential-
Evolution Control Parameter Optimization for
Unmanned Aerial Vehicle Path Planning. PLoS ONE
11(3): e0150558. doi:10.1371/journal.pone.0150558
Editor: Xiaosong Hu, Chongqing University, CHINA
Received: September 14, 2015
Accepted: February 14, 2016
Published: March 4, 2016
Copyright: © 2016 Kok, Rajendran. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. Introduction Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. In recent years, unmanned aerial vehicles (UAVs) have received significant attention from the
military and commercial industries. Moreover, many studies have been conducted on UAV
development because of its wide variety of applications, including surveillance, traffic monitor-
ing, rescue mission, and aerial photography [1–12]. Aircraft path planning is a UAV operation
that aims to generate an optimum flight path from the starting coordinate to the destination
location. Data Availability Statement: All relevant data are
within the paper and its Supporting Information file. Data Availability Statement: All relevant data are
within the paper and its Supporting Information file. Funding: This study was supported by Universiti
Sains Malaysia; short term grant no. 304/PAERO/
60312047 and MYLAB-KPM grant no. 304/
PHUMANITI/650718. The funders had no role in
study design, data collection and analysis, decision to
publish, or preparation of the manuscript. Various algorithms are applicable for UAV path planning. This includes graph search algo-
rithm [13, 14], potential field based algorithm [15], probabilistic roadmap algorithm [16, 17],
rapidly-exploring random trees algorithm [18, 19], Dubin curve based algorithm [20, 21] and
evolutionary algorithm [22]. Each method has its own strengths and weaknesses over others. Graph search algorithms like Dijkstra, Bellman Ford and A are algorithms with straight for-
ward implementation. Yet, graph search algorithms are not efficient when they are used in
large search space environment. Competing Interests: The authors have declared
that no competing interests exist. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 1 / 12 DE Control Parameter Optimization for UAV Path Planning Hence, Differential evolution (DE) algorithm has often been used in UAV path planning
because of its good performance in addressing real-world optimization problems. DE a type of
evolutionary algorithm, which is a stochastic, population based optimization algorithm. Thus,
it may also be used in non-differential and non-linear optimization problems. In addition, DE
has good convergence properties with easy implementation into applications [23–25]. There are several control parameters in DE, namely the population size, differential weight,
and crossover. Obtaining an optimum value for these control parameters in DE is difficult and
requires trial and error because different applications require different optimum parameter set-
tings. DE performance is sensitive to the control parameter setting [26]. Furthermore, tuning the
control parameters is often time consuming [26, 27] and justifying the optimum performance of
DE is difficult. To overcome this issue, the use of mimetic algorithm in DE has been proposed
[28]. Furthermore, studies claim that dynamic control parameters in the DE perform better than
constant control parameters. However, most of these parameters conduct analyses by using
standard test functions and are rarely specific in a particular field [25, 27, 29, 30]. Zielinski [31]
has conducted a parameter study of DE by using the power allocation problem. In addition,
parameter optimization has been studied in other system such as power system using Genetic
algorithm and Kalman-based methods [32–36]. Data Availability Statement: All relevant data are
within the paper and its Supporting Information file. Besada-Portas [24] has presented a performance comparison method by using evolutionary
algorithms for UAV path planning. However, this method does not analyze the control param-
eters in detail. Thus, the optimum control parameter strategy of DE in UAV path planning is
unclear. In this study, we thoroughly investigate the effect of the control parameters in DE for
UAV path planning. Thus, the proposed DE control parameter optimization expedites and
improves in obtaining the desired path and computational cost for UAV path planning. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 Function Cost The function costs of UAV path planning include flight path distance, real-time computa-
tional time, minimum turning radius, power consumption, and threat area. However, only
the path distance and computational time are analyzed in this study. The other function
costs require study using a specific UAV model to ensure impartial comparison can be done. Yet, this limits application of the proposed DE model for a particular type of UAV. Thus, by
only optimizing path distance and computational time, the proposed method benefits all
types of UAV. Also, there are 5 parameters in DE algorithm, namely maximum generation number, length
of solution (number of waypoint in this case study), population size, differential weight and
crossover. Generally, solutions can evolve further when generation number is increased. The
length of solution decides the complexity of the problem while population size, differential
weight and crossover alter the performance of DE. Hence, this work analyzes the effect of pop-
ulation size, differential weight, and crossover on DE to obtain optimized range for those
parameters. Therefore, the UAV is assumed to carry sufficient power throughout the flight regardless of
the length of the flight with no threat area on a 3D terrain map. The UAV will also maintain a
minimum altitude of 100 m from the ground at each waypoint coordinate. The function cost
can be evaluated by using the following: J ¼
Xw
i¼1 li ;
ð1Þ ð1Þ where w is the number of waypoints and l is the length between the previous and current
location. where w is the number of waypoints and l is the length between the previous and current
location. Problem Formulation The main objective of path planning is to produce an optimum 3D flight path in both compu-
tational time and path distance from initial coordinate to target coordinate. To implement DE
in path planning with high search speed, the initial point is connected with the final point as
the virtual x-axis. Depending on the number of waypoint throughout the flight path, the virtual
x-axis is divided into the same number of intervals and forms a virtual y-axis at each point of
interval (Fig 1). The start and the goal for the desired path throughout the simulations are Fig 1. Transformation of coordinates system. doi:10.1371/journal.pone.0150558.g001 Fig 1. Transformation of coordinates system. doi:10.1371/journal.pone.0150558.g001 2 / 12 PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 DE Control Parameter Optimization for UAV Path Planning similar in Fig 1 which are [10, 90] and [90, 10] respectively. The map chosen for this study is
from an alpine region, where the mountains and hills are treated as the path obstacles. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 Principles of DE Algorithm DE was first proposed by renowned researchers Storn and Price [37]. Similar to genetic algo-
rithm (GA), DE involves selection, crossover, and mutation but in a different sequence. The
population is initialized by randomizing individuals within a search space. The population
then undergoes mutation, and an individual vGþ1
i
is generated by using the following equation
[38–43]: ð2Þ vGþ1
i
¼ xG
r1 þ F:ðxG
r2 xG
r3Þ ; r1 6¼ r2 6¼ r3; i ¼ 1; 2; . . . ; NP;
ð2Þ where x is an individual from the population r ϵ (1, NP), G is the generation or iteration, NP is
the population size, and F is the differential weight. However, not all particles from the muta-
tion will be used in the next operation, depending on crossover probability. Population with
trial individuals uG+1 is produced by the crossover process with the following condition: uGþ1
ij
¼
vGþ1
ij
; randij crossover
xG
ij
;
otherwise
j ¼ 1; 2; . . . ; D;
ð3Þ
( ð3Þ where randij is a random value between zero and one for the ith individual at the jth particle. Thereafter, the trial population will go through the selection process. Unlike GA, the selection
process of DE compares the current population and trial population. The individual with PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 3 / 12 NE | DOI:10.1371/journal.pone.0150558
March 4, 2016 DE Control Parameter Optimization for UAV Path Planning Fig 2. DE flowchart. doi:10.1371/journal.pone.0150558.g002 Fig 2. DE flowchart. doi:10.1371/journal.pone.0150558.g002 doi:10.1371/journal.pone.0150558.g002 lowest cost in the trial population will replace the individual of the current population: lowest cost in the trial population will replace the individual of the current population: xGþ1
i
¼
uGþ1
i
;
f ðuGþ1
i
Þ f ðxG
i Þ
xG
i ;
otherwise
:
ð4Þ
( ð4Þ The process is repeated from mutation to selection until the termination condition is met. Fig 2 demonstrates the flow of the DE algorithm. The process is repeated from mutation to selection until the termination condition is met. Fig 2 demonstrates the flow of the DE algorithm. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 Results and Discussions Furthermore, extra work is required to adjust the values within the search space. Results and Discussions To determine the effect of population size, differential weight, and crossover in DE, all combina-
tions of control parameter values are tested. The range of differential weight is set from 0.1 to 1. Both crossover and population size parameters are set from 10 to 100. The generation number is
from 100 to 1000. Furthermore, the number of waypoints is fixed at 50 in this investigation. However, similar to other evolutionary algorithms, DE output depends on certain random
probability to obtain better solutions; as a result, the output of DE is uncertain every time. Therefore, each combination simulation will be repeated 100 times to obtain the average out-
put performance of DE. The average path and computational cost at the 1000th generation with variations in differ-
ential weight and crossover at various NPs are given in Fig 3. Increasing the differential weight
will favor the reduction of the average path cost when the population size is small because it
increases the diversity of the population. However, an immoderate differential weight will
reduce the performance of DE. Moreover, a bigger population size tends to limit the optimum range of differential weight
because the diversity of the population is sufficient for bigger populations. An excessive differ-
ential weight will retard the decline of the average path cost. If the crossover increases, the opti-
mum differential weight prone will increase, particularly when the population size is small. Additionally, increasing both the crossover and differential weight increases the average
computational cost. The reason behind this effect is that more work is needed for higher 4 / 12 PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 DE Control Parameter Optimization for UAV Path Planning Fig 3. Average path and computational cost at the 1000th generation with variation between
differential weight and crossover at various population sizes of 10, 30, 50, 70, and 100 “Table A in S1
Dataset.” Fig 3. Average path and computational cost at the 1000th generation with variation between
differential weight and crossover at various population sizes of 10, 30, 50, 70, and 100 “Table A in S1
Dataset.” doi:10.1371/journal.pone.0150558.g003 crossover probability, whereas a high differential weight is prone to have values outside the
search space. Furthermore, extra work is required to adjust the values within the search space. crossover probability, whereas a high differential weight is prone to have values outside the
search space. Optimization of Differential Weight and Crossover According to the average path and computational cost given in Fig 3, the balanced value of the
differential weight at various crossover settings can be assumed at the interception point of the PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 5 / 12 DE Control Parameter Optimization for UAV Path Planning Fig 4. Estimation of optimum differential weight at NP = 10, G = 1000, and CR = 100%. doi:10.1371/journal.pone.0150558.g004 Fig 4. Estimation of optimum differential weight at NP = 10, G = 1000, and CR = 100%. doi:10.1371/journal.pone.0150558.g004 doi:10.1371/journal.pone.0150558.g004 average path cost and computational cost. This assumption is valid because increasing the dif-
ferential weight will reduce the average path cost to a certain level before it increases again with
a significant increase in computational cost. Fig 4 presents an example for obtaining the optimum differential weight at a population size
of 10, generation number of 1000, and crossover rate of 100%. Each interception point from all
combinations of crossover, population size, and generation number is recorded by using the
same method. Hence, the optimum differential weight for different crossover rates at various
population sizes from a generation number of 200 to 1000 is obtained. In each generation, the average computational cost of various crossovers for the same popu-
lation size is almost the same for all cases in the same generation number, as given in Fig 5. Fur-
thermore, the trend of the average path cost from various crossovers for the same population
size is a parabola with a minimum point. Thus, we assume that the optimum crossover with its
optimum differential weight can be determined at the lowest average path cost of a particular
population size. Fig 6 displays the optimum crossover value and differential weight for different
population sizes from a generation number of 100 to 1000. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 Overall Optimization of Control Parameters The optimum crossover has a tendency to decrease with increasing generation number,
whereas the optimum differential weight is the opposite. A larger population size will have
lower path cost and higher computational cost and vice versa (Fig 6). Moreover, a similar trend
between the average path and computational cost is shown in Fig 7. Thus, the interception point between both is identified as the balanced performance of the
DE algorithm. The optimum population size at various generation numbers is illustrated in
Fig 8. The figure indicates that the optimum population is almost consistent at the same level
when the generation number increases within the range. Therefore, the optimum population
size will not be affected evidently in these simulations from the initial stage to the convergence
stage. The optimum population size in relation to the maximum generation numbers may be
determined by using the following equation: P ¼ 0:006909 G þ 33:2:
ð5Þ ð5Þ P ¼ 0:006909 G þ 33:2:
ð5Þ The optimum differential weight and crossover along the generation number is shown in
Fig 9. At this instance, the number of generation is small when the optimum differential weight PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 6 / 12 DE Control Parameter Optimization for UAV Path Planning Fig 5. Average path and computational cost obtained with crossover rates on the optimum differential
weight over population sizes at various generations of 200, 400, 600, 800, and 1000 “Table B in S1
Dataset.”
doi:10 1371/journal pone 0150558 g005 Fig 5. Average path and computational cost obtained with crossover rates on the optimum differential
weight over population sizes at various generations of 200, 400, 600, 800, and 1000 “Table B in S1
Dataset.” doi:10.1371/journal.pone.0150558.g005 is small. As the generation number becomes larger, the optimum differential weight increases
with decreasing rate. However, the optimum crossover decreases as the generation number
grows with decreasing rate. Therefore, the optimum differential weight and crossover in 7 / 12 PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 DE Control Parameter Optimization for UAV Path Planning Fig 6. Optimum crossover and differential weight for various population sizes and generations
“Table C in S1 Dataset.”
doi:10.1371/journal.pone.0150558.g006
Fig 7. Average path and computational cost between various population sizes and generation
numbers at the optimum crossover and differential weight “Table D in S1 Dataset.”
doi:10.1371/journal.pone.0150558.g007 Fig 6. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 Overall Optimization of Control Parameters Optimum crossover and differential weight for various population sizes and generations
“Table C in S1 Dataset.” Fig 6. Optimum crossover and differential weight for various population sizes and generations
“Table C in S1 Dataset.”
d i 10 1371/j
l
0150558 006 Fig 6. Optimum crossover and differential weight for various population sizes and generations
“Table C in S1 Dataset.” doi:10.1371/journal.pone.0150558.g006 Fig 7. Average path and computational cost between various population sizes and generation
numbers at the optimum crossover and differential weight “Table D in S1 Dataset.”
d i 10 1371/j
l
0150558 007 doi:10.1371/journal.pone.0150558.g007 Fig 8. Optimum population size along generation number. doi:10.1371/journal.pone.0150558.g008 Fig 8. Optimum population size along generation number. doi:10.1371/journal.pone.0150558.g008 Fig 8. Optimum population size along generation number. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 8 / 12 DE Control Parameter Optimization for UAV Path Planning Fig 9. Optimum differential weight and crossover along generation number. doi:10.1371/journal.pone.0150558.g009 Fig 9. Optimum differential weight and crossover along generation number. Fig 9. Optimum differential weight and crossover along generation number. doi:10.1371/journal.pone.0150558.g009 doi:10.1371/journal.pone.0150558.g009 relation to the generation numbers may be determined by using Eqs (6) and (7), respectively,
F ¼ 1:858 1010G3 4:068 107G2 þ 0:0002821G þ 0:07939
ð6Þ
CR ¼ 80:55 8:864 102G þ 3:374 105G2 :
ð7Þ relation to the generation numbers may be determined by using Eqs (6) and (7), respectively,
F ¼ 1:858 1010G3 4:068 107G2 þ 0:0002821G þ 0:07939
ð6Þ ð6Þ ð7Þ The optimized setting of population size, differential weight and crossover using Eqs (5) till
(7) for different maximum generation number is shown in Table 1. This simplifies the need to
trial and error of the crucial parameters especially population size, differential weight and
crossover for the specific maximum generation number. As a result, the intended output to
obtain the desired path distance and computational time may be achieved for aircraft path
planning mission. Supporting Information S1 Dataset. Path and computational cost data of UAV path planning using DE. (XLSX) Conclusion Instead trial and error, an optimization of the DE algorithm for tuning the parameters of UAV
path planning is presented in this paper. The parameters focused are population size, differen-
tial weight, crossover, and generation number. In conclusion, the proposed optimization of the
tuning parameters in the DE algorithm for UAV path planning has enabled an expedited and
improved simulation of the final output path and computational cost. The developed algorithm
enables the user to simply define the weightage desired between the path and computational
cost to converge with the minimum generation required based on user requirement. Proposed DE Algorithm Optimization Result Average computational cost changes in % when compared to the optimized parameter setting
at maximum generation number of 1000 “Table F in S1 Dataset.” Fig 10. Average path cost changes in % when compared to the optimized parameter setting at
maximum generation number of 1000 “Table E in S1 Dataset.” Fig 10. Average path cost changes in % when compared to the optimized parameter setting at
maximum generation number of 1000 “Table E in S1 Dataset.” Fig 11. Average computational cost changes in % when compared to the optimized parameter setting
at maximum generation number of 1000 “Table F in S1 Dataset.” doi:10.1371/journal.pone.0150558.g011 the path distance cost, the computational time of optimized parameter setting were better than
all non-optimized parameter setting. In addition, some non-optimized parameter setting have
achieved more than 100% increment in computational time. This clearly indicates the impor-
tance for an optimized parameter setting in DE algorithm for aircraft path planning using opti-
mized setting based on maximum generation number. Proposed DE Algorithm Optimization Result The analyses on the effect of using and optimized DE algorithm are presented. In this occasion,
a simulation was done for a maximum generation number input value of 1000, to make a per-
formance comparison between the optimized parameter setting (i.e. shown in Table 1) and the
all other setting. Fig 10 illustrates the average path cost changes in percentage when compared
to the optimized parameter setting at maximum generation number of 1000. These analyses clearly indicates that the average path cost at optimized parameter setting is
better than all other setting, except for 3 combination setting (i.e. when Differential Weight is
0.2 and Crossover rate of 30, 40 and 50%). Still, the path cost at these non-optimized parameter
setting are only better in the range of 1–3%. Moreover, the average path cost at all other setting
are generally higher than optimized parameter setting, which may be by almost 200%. The average computational cost changes in percentage when compared to the optimized
parameter setting at maximum generation number of 1000 is shown in Fig 11. In contrast to mized setting of population size, differential weight & crossover at various maximum generation number. Table 1. Optimized setting of population size, differential weight & crossover at various maximum generation number. Generation
100
200
300
400
500
600
700
800
900
1000
Population
34
35
35
36
37
37
38
39
39
40
Differential Weight
0.10
0.12
0.13
0.14
0.14
0.14
0.14
0.14
0.14
0.14
Crossover (%)
72
64
57
51
45
40
35
31
28
26
doi:10.1371/journal.pone.0150558.t001 Table 1. Optimized setting of population size, differential weight & crossover at various maximum generatio Table 1. Optimized setting of population size, differential weight & crossov PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 9 / 12 DE Control Parameter Optimization for UAV Path Planning Fig 10. Average path cost changes in % when compared to the optimized parameter setting at
maximum generation number of 1000 “Table E in S1 Dataset.”
doi:10.1371/journal.pone.0150558.g010
Fig 11. Average computational cost changes in % when compared to the optimized parameter setting
at maximum generation number of 1000 “Table F in S1 Dataset.”
doi:10 1371/journal pone 0150558 g011 Fig 10. Average path cost changes in % when compared to the optimized parameter setting at
maximum generation number of 1000 “Table E in S1 Dataset.”
doi:10.1371/journal.pone.0150558.g010
Fig 11. References 1. Cayero J, Morcego B, Nejjari F. Modelling and adaptive backstepping control for TX-1570 UAV path
tracking. Aerospace Science and Technology. 2014; 39: 342–351. 2. Kontogiannis SG, Ekaterinaris JA. Design, performance evaluation and optimization of a UAV. Aero-
space Science and Technology. 2013; 29(1): 339–350. 3. Panagiotou P, Kaparos P. Yakinthos K. Winglet design and optimization for a MALE UAV using CFD. Aerospace Science and Technology. 2014; 39: 190–205. 4. Kownacki C. Design of an adaptive Kalman filter to eliminate measurement faults of a laser rangefinder
used in the UAV system. Aerospace Science and Technology. 2015; 41: 81–89. 5. Li Z, Liu Y, Walker R, Hayward R, Zhang J. Towards automatic power line detection for a UAV surveil-
lance system using pulse coupled neural filter and an improved Hough transform. Machine Vision and
Applications. 2010; 21(5): 677–686. 6. Coifman B, McCord M, Mishalani RG, Iswalt M, Ji Y. Roadway traffic monitoring from an unmanned
aerial vehicle. IEEE Proceedings-Intelligent Transport Systems. 2006; 153(1): 11–20. 7. Doherty P, Rudol P. A UAV search and rescue scenario with human body detection and geolocaliza-
tion. AI 2007: Advances in Artificial Intelligence. 2007; 4830: 1–13. 8. Rathinam S, Almeida P, Kim Z, Jackson S, Tinka A, Grossman W, et al. Autonomous searching and
tracking of a river using an UAV. American Control Conference, 2007 ACC'07; IEEE. doi: 10.1109/
ACC.2007.4282475 9. Semsch E, Jakob M, Pavlicek D, Pechoucek M. Autonomous UAV surveillance in complex urban envi-
ronments. Web Intelligence and Intelligent Agent Technologies, 2009 WI-IAT'09 IEEE/WIC/ACM Inter-
national Joint Conferences on: IET. doi: 10.1109/WI-IAT.2009.132 10. Ro K, Oh J, Dong L. Lessons Learned: Application of Small UAV for Urban Highway Traffic Monitoring. 45th AIAA Aerospace Sciences Meeting and Exhibit, Aerospace Sciences Meetings. 2007; doi: 10. 2514/6.2007–596 11. Bernard M, Kondak K, Maza I, Ollero A. Autonomous transportation and deployment with aerial robots
for search and rescue missions. J. Field Robotics. 2011, 28: 914–931. doi: 10.1002/rob.20401 12. Lin Y, Saripalli S. Road detection from aerial imagery. Robotics and Automation (ICRA), 2012 IEEE
International Conference on: IEEE. 2012; 3588–3593: doi: 10.1109/ICRA.2012.6225112 13. Qu Y, Pan Q, Yan J. Flight path planning of UAV based on heuristically search and genetic algorithms. Industrial Electronics Society, 2005 IECON 31st Annual Conference of IEEE. doi: 10.1109/IECON. 2005.1568876 14. Jun M, D’Andrea R. Path planning for unmanned aerial vehicles in uncertain and adversarial environ-
ments. Cooperative control: models, applications and algorithms. Author Contributions Conceived and designed the experiments: KYK PR. Performed the experiments: KYK. Ana-
lyzed the data: KYK PR. Contributed reagents/materials/analysis tools: KYK PR. Wrote the
paper: KYK PR. 10 / 12 PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 DE Control Parameter Optimization for UAV Path Planning PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 References 2003; doi: 10.1007/978-1-4757-
3758-5_6 15. Scherer S, Singh S, Chamberlain L, Elgersma M. Flying fast and low among obstacles: Methodology
and experiments. The International Journal of Robotics Research. 2008; 27(5): 549–574. 16. Pettersson PO, Doherty P. Probabilistic roadmap based path planning for an autonomous unmanned
helicopter. Journal of Intelligent & Fuzzy Systems: Applications in Engineering and Technology. 2006;
17(4): 395–405. 17. Hrabar S. 3D path planning and stereo-based obstacle avoidance for rotorcraft UAVs. Intelligent
Robots and Systems. 2008 IROS IEEE/RSJ International Conference on: IEEE. doi: 10.1109/IROS. 2008.4650775 18. Bry A, Roy N. Rapidly-exploring random belief trees for motion planning under uncertainty. Robotics
and Automation (ICRA), 2011 IEEE International Conference on. doi: 10.1109/ICRA.2011.5980508 19. Lin Y, Saripalli S. Sense and avoid for Unmanned Aerial Vehicles using ADS-B. Robotics and Automa-
tion (ICRA), 2015 IEEE International Conference on: IEEE. doi: 10.1109/ICRA.2015.7140098 20. Shanmugavel M, Tsourdos A, White B, Zbikowski R. 3D Dubins Sets Based Coordinated Path Planning
for Swarm of UAVs. AIAA Guidance, Navigation, and Control Conference and Exhibit, Guidance, Navi-
gation, and Control and Co-located Conferences. doi: 10.2514/6.2006–6211 21. Lin Y, Saripalli S. Path planning using 3D dubins curve for unmanned aerial vehicles. Unmanned Air-
craft Systems (ICUAS), 2014 International Conference on: IEEE. doi: 10.1109/ICUAS.2014.6842268 22. Ergezer H, Leblebicioğlu MK. 3D path planning for UAVs for maximum information collection. Unmanned Aircraft Systems (ICUAS), 2013 International Conference on; IEEE. doi: 10.1109/ICUAS. 2013.6564676 23. Fu Y, Ding M, Zhou C, Hu H. Route planning for unmanned aerial vehicle (UAV) on the sea using hybrid
differential evolution and quantum-behaved particle swarm optimization. Systems, Man, and Cybernet-
ics: Systems, IEEE Transactions on. 2013; 43(6): 1451–1465. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 11 / 12 DE Control Parameter Optimization for UAV Path Planning 24. Besada-Portas E, De La Torre L, Moreno A, Risco-Martín JL. On the performance comparison of multi-
objective evolutionary UAV path planners. Information Sciences. 2013; 238: 111–125. 25. Fan Q, Yan X. Self-adaptive differential evolution algorithm with discrete mutation control parameters. Expert Systems with Applications. 2015; 42(3): 1551–1572. 26. Gämperle R, Müller SD, Koumoutsakos P. A parameter study for differential evolution. Advances in
intelligent systems, fuzzy systems, evolutionary computation. 2002; 10: 293–298. 27. Qin AK, Huang VL, Suganthan PN. Differential evolution algorithm with strategy adaptation for global
numerical optimization. Evolutionary Computation, IEEE Transactions on. 2009; 13(2): 398–417. 28. Neri F, Tirronen V. References On memetic differential evolution frameworks: a study of advantages and limitations
in hybridization. Evolutionary Computation, 2008 CEC IEEE World Congress on Computational Intelli-
gence. doi: 10.1109/CEC.2008.4631082 29. Brest J, Zumer V, Maucec M. Self-adaptive differential evolution algorithm in constrained real-parame-
ter optimization. Evolutionary Computation, 2006 CEC IEEE Congress on. doi: 10.1109/CEC.2006. 1688311 30. Wang Y, Cai Z, Zhang Q. Differential evolution with composite trial vector generation strategies and
control parameters. Evolutionary Computation, IEEE Transactions on. 2011; 15(1): 55–66. 31. Zielinski K, Weitkemper P, Laur R, Kammeyer K-D. Parameter study for differential evolution using a
power allocation problem including interference cancellation. Evolutionary Computation, 2006 CEC
2006 IEEE Congress on. doi: 10.1109/CEC.2006.1688533 32. Zhang L, Wang Z, Hu X, Sun F, Dorrell DG. A comparative study of equivalent circuit models of ultraca-
pacitors for electric vehicles. Journal of Power Sources. 2015; 274: 899–906. 33. Zhang L, Hu X, Wang Z, Sun F, Dorrell DG. Experimental impedance investigation of an ultracapacitor
at different conditions for electric vehicle applications. Journal of Power Sources. 2015; 287: 129–138. 34. Zhang L, Wang Z, Sun F, Dorrell DG. Online parameter identification of ultracapacitor models using the
extended Kalman filter. Energies. 2014; 7(5): 3204–3217. 35. Hu X-S, Sun F-C, Zou Y. Online model identification of lithium-ion battery for electric vehicles. Journal
of Central South University of Technology. 2011; 18: 1525–1531. 36. Sun F, Hu X, Zou Y, Li S. Adaptive unscented Kalman filtering for state of charge estimation of a lith-
ium-ion battery for electric vehicles. Energy. 2011; 36(5): 3531–3540. 37. Storn R, Price K. Differential Evolution—A simple and efficient adaptive scheme for global optimization
over continuous spaces. Journal of Global Optimization. 1995; 11(4): 12. 38. Le-Anh L, Nguyen-Thoi T, Ho-Huu V, Dang-Trung H, Bui-Xuan T. Static and frequency optimization of
folded laminated composite plates using an adjusted Differential Evolution algorithm and a smoothed
triangular plate element. Composite Structures. 2015; 127: 382–394. 39. Gao L, Zhou Y, Li X, Pan Q, Yi W. Multi-objective optimization based reverse strategy with differential
evolution algorithm for constrained optimization problems. Expert Systems with Applications. 2015; 42
(14): 5976–5987. 40. Khan A, Jaffar MA, Shao L. A modified adaptive differential evolution algorithm for color image segmen-
tation. Knowledge and Information Systems. 2014; 43(3): 583–597. 41. Yi W, Gao L, Li X, Zhou Y. A new differential evolution algorithm with a hybrid mutation operator and
self-adapting control parameters for global optimization problems. Applied Intelligence. PLOS ONE | DOI:10.1371/journal.pone.0150558
March 4, 2016 References 2015; 42(4):
642–660. 42. Torres SP, Castro CA. Specialized differential evolution technique to solve the alternating current
model based transmission expansion planning problem. International Journal of Electrical Power &
Energy Systems. 2015; 68: 243–251. 43. Roque C, Martins P. Differential evolution optimization for the analysis of composite plates with radial
basis collocation meshless method. Composite Structures. 2015; 124: 317–326. 12 / 12
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DE VRU CH TBAARH EID VAN H E T G EBRU IK VAN HET
W A A R SC H IJN LIJK H E ID SB EG R IP IN D E CO N TRO LELEER
door Dr. H. A. ]. F. Misset
Probleemstelling
Het behoeft nauwelijks betoog, dat een verandering van de opvattingen met be
trekking tot de waarde die aan de interne controle in de accountantscontrole dient
te worden toegekend, een aanmerkelijke betekenis voor het aanzien en het belang
van het accountantsberoep zou kunnen hebben. In dit perspectief gezien lijkt het
ons alleszins gerechtvaardigd, opnieuw aandacht te schenken aan de beweging
van het laatste decennium, die in de volkomen structuur van de administratieve
organisatie, welke mede de interne controle omvat, een voldoende reden ziet, de
taak van de accountant te beperken 1). Het komt ons voor, dat de niet gebroken
kracht van deze beweging, ook na de overtuigende kritische analyse van de
betogen van haar aanhangers door Van Rietschoten en A. Mey in dit maandblad 2),
een voortzetting van de discussie wenselijk maakt. Dat deze wenselijkheid aan
wezig is, blijkt ook uit de artikelen van Louwers en Goudeket over de steekproef
in de accountantscontrole 3), welke weliswaar niet onmiddellijk zijn gericht op
het aantasten van de bestaande opvattingen omtrent de betekenis van de interne
controle, maar die toch van de veronderstelling uitgaan, dat juist de verbetering
van de administratieve organisatie een andere benadering door de accountant
mogelijk m aak t4).
In het volgende opstel willen wij onderzoeken of het gebruik van het waarschijnlijkheidsbegrip in de analyse van de betekenis der interne controle iets kan
bijdragen tot een verheldering van de fundamenten der controverse. Hoewel
onderzoekingen naar de logische grondslagen van technieken meermalen tot wei
nig vruchtbare beschouwingen leiden, menen wij, dat die toch in de bestaande
onoplosbaar lijkende controverse betreffende de optimale controletechniek ge
boden zijn. Alleen door onderzoekingen van dien aard kunnen tegengestelde
meningsuitingen een einde nemen.
1) A. A. de Jong, „Enige beschouwingen over de omvang en de techniek van de accountants
controle” , openbare les, Leiden 1950;
A. F. Tempelaar, „De eigen actie van de accountant bij het controleren van de jaarrekening” ,
M.A.B. 1951, blz. 321 e.v.;
G. Diephuis, „Enkele beschouwingen omtrent de functies en het arbeidsterrein van de openbare
accountant in Nederland” , openbare les, Groningen-Djakarta 1952;
G. Diephuis, „De „eigen actie” van de openbare accountant” , M.A.B. 1953, blz. 3 e.v.;
J. C. Wisse, „De taak van de public accountant bij de algemene controle” , M.A.B. 1953,
blz. 439 e.v.;
G. Diephuis, „Ontwikkelingstendenzen in de vaktechnische eisen bij de controle-arbeid van
de openbare accountant” , oratie, Groningen 1959;
G. Diephuis, „Functie en verantwoordelijkheid (als grondslagen van de taakbepaling van de
accountant)” , M.A.B. 1959, blz. 471 e.v.
2) A. M. van Rietschoten, „De betekenis van de interne controle voor de accountantscontrole” ,
M.A.B. 1954, blz. 239 e.v.;
A. Mey, „Interne controle en de techniek der accountantscontrole” , M.A.B. 1956, blz. 98 e.v.
3) P. C. Louwers, „De steekproef in de accountantscontrole” , M.A.B. 1958, blz. 230 e.v.,
blz. 391 e.v. en M.A.B. 1959, blz. 272 e.v.;
A. Goudeket, „De steekproef in de accountantscontrole” , M.A.B. 1959, blz. 485 e.v.
4) A. Goudeket, t.a.p., blz. 489.
mab
blz. 134
In technieken als de werktuigtechniek en de electrotechniek zijn de werk
wijzen een uitvloeisel van de toepassing van uitspraken of wetten, die in een
aantal wetenschappen en in het bijzonder in de natuurwetenschap zijn gefor
muleerd; de controletechniek onderscheidt zich wat haar wetenschappelijk fun
dament betreft, niet van de genoemde technieken en zij ontstaat, evenals deze,
uit de toepassing van wetenschappelijke uitspraken. In de volgende paragraaf
bespreken wij hoe de controletechniek een toepassing vormt van wetenschappe
lijke uitspraken van de bedrijfseconomie, de logica en de rekenkunde.
Nader grondslagenonderzoek
Teneinde het opstel te beperken, onderzoeken wij het gestelde probleem uitsluitend
voor de bedrijfshuishouding met een goederenbeweging, waar de accountant een
voortgezette periodieke controle verricht.
De handelingen van de leiding en de uitvoering leiden tot veranderingen in de
kwaliteit en de kwantiteit der produktiemiddelen die de bedrijfshuishouding voort
durend toevloeien en deze veranderingen hebben als resultaat hoeveelheden van
een of meer produkten, die op de afzetmarkt worden geruild. Het maatschappe
lijk verkeer verlangt een verklaring van deskundigen, niet ondergeschikt aan
belanghebbenden bij leiding en uitvoering, welke een beeld geeft van het samen
stel van handelingen en middelen in de bedrijfshuishouding. De functie die hieruit
voortvloeit, namelijk die van vertrouwensman van het maatschappelijk verkeer,
vormt de ruggegraat van het beroep van de accountant.
Men zou zich kunnen indenken, dat de vervulling van de genoemde functie
bestaat uit waarneming door de accountant van de handelingen die in de bedrijfs
huishouding op verschillende niveaus geschieden, en zijn waarneming van de ver
anderingen die de stroom van middelen hierdoor ondergaat. Deze methode om
kennis omtrent de werkelijkheid te verzamelen is geijkt voor tal van wetenschap
pen en technieken. Voor de techniek van de accountantscontrole is de waarde
van de optische controle echter beduidend geringer, omdat door de voortdurende
aanwezigheid van de accountant of zijn medewerkers op de verschillende plaatsen
in de bedrijfshuishouding, dus ook door zijn aanwezigheid bij de besprekingen van
de directie, zijn onafhankelijke status verloren zou gaan. Een ontwikkeling in die
zin vertoont de functie van de commissaris, die oorspronkelijk de vertrouwens
man van het maatschappelijk verkeer was, maar die zich meer en meer tot mede
bestuurder heeft ontwikkeld.
De optische controle van de accountant blijft beperkt tot de waarneming van
de toestand op bepaalde momenten in de bedrijfshuishouding, maar zij strekt
zich niet uit tot de waarneming van de veranderingen in de kapitaalgoederenstroom ten gevolge van handelingen van leiding en uitvoering. Dit laatste zou er,
zoals gezegd, onvermijdelijk toe leiden, dat de accountant zo nauw bij het beleid
wordt betrokken, dat hij mede op de stoel van de bestuurder komt te zitten. Het
komt ons voor, dat deze overweging het voornaamste bezwaar is tegen de waar
neming door de accountant van de handelingen zelve, meer dan zijn technische
ondeskundigheid. Voor zover de optische controle als waarnemingsinstrument
wel mogelijk is, bijvoorbeeld voor de samenstelling en de grootte van de voor
raden, dient men haar als een buitengewoon overtuigend waarnemingsmiddel,
m ab
blz. 135
ook voor de accountant, te beschouwen, gezien de positieve ervaringen die men
met dit middel in tal van wetenschappen en technieken heeft opgedaan 56).
De beperkte toepassing van de optische controle noopt de accountant ter aan
vulling van zijn controle tot het gebruik van andere middelen. Indien de ver
schijnselen zelve van waarneming zijn uitgesloten, zal de accountant, gelijk de
historicus, een interpretatie verrichten van de documenten, aantekeningen enz.,
die aanwezig zijn. Wel is de accountant, veelal in tegenstelling met de historicus,
in de positie het bewijsmateriaal dat ex post van de verschijnselen aanwezig zal
zijn, in kwaliteit en kwantiteit op te voeren. Dit is in het bijzonder het geval met
de voortgezette periodieke controle, ten behoeve waarvan de accountant de moge
lijkheid heeft, verbeteringen in de administratieve organisatie, waaronder de in
terne controle, door te voeren.
Het onderzoek is zowel bij de historicus als bij de accountant op een studie van
de documenten gericht teneinde aldus tot een voorstelling van de gang van zaken
te geraken, zoals die in het verleden werkelijk heeft plaats gevonden. Hiertoe zal
men in de geschiedwetenschap tot de oorspronkelijkste bronnen teruggaan en aan
de onmiddellijke gegevens de voorkeur geven boven de reeds tot een geschied
verhaal verwerkte gegevens °). Aangezien de grondslag van het onderzoek van de
accountant zich in dit opzicht niet onderscheidt van dat van de historicus, zal hij
uit dien hoofde op gelijke wijze te werk gaan. De accountant zal in zijn onderzoek
aan de documenten, zijnde de oorspronkelijke gegevens, een grotere waarde toe
kennen dan aan de beschrijving in de dag- en bijboeken, die aan de hand van deze
is verricht.
Verder dient het onderzoek naar het bewijsmateriaal onderling tegenstrijdige
uitspraken omtrent de aard en de omvang van een bepaald verschijnsel aan het
licht te brengen. Uit dit onderzoek naar de consistentie van het bewijsmateriaal
vloeit een vergelijking voort van de documenten onderling betreffende een gebeur
tenis en van de documenten met de verrichte aantekeningen in de administratie.
Ook hier onderscheidt zich het werk van de accountant wat de grondslag betreft
niet van dat van de geschiedschrijver.
Summa summarum zal de accountant, naast de optische controle van daarvoor
in aanmerking komende verschijnselen, documenten en aantekeningen van ge
beurtenissen waarnemen, die zich in de bedrijfshuishouding hebben voorgedaan;
deze waarnemingen impliceren een beoordeling van de echtheid van het bewijs
materiaal en een onderzoek naar de onderlinge consistentie van documenten en
aantekeningen inzake een verschijnsel.
Een juiste waardering van de betekenis, die de waarnemingen in het controle
onderzoek bezitten, is eerst mogelijk, indien wij onderzoeken in hoeverre de ac
countant van wetenschappelijke uitspraken of wetten gebruik maakt.
In de praktische uitvoering van zijn controle maakt hij gebruik van het comp
tabele systeem van aantekeningen in de bedrijfshuishouding, dat men met de
term boekhouding aanduidt. De aanwending van de boekhoudtechniek is geïncor
5) Deze opvatting ligt ten grondslag aan de behandeling van de voorraadcontrole in:
S. Klecrekoper, „D e voorraadcontrole in de literatuur” in „Vijfentwintig jaren maandblad voor
accountancy en bedrijfshuishoudkunde” , Purmerend 1950, blz. 579 e.v. en 607 e.v. (oorspronkelijk
in M.A.B. 1934 en 1935). De techniek van de voorraadcontrole, die Kleerekoper in deze artikelen
uiteenzet, is nu wel algemeen aanvaard in de kringen van de Nederlandse accountants.
6) J . Huizinga, „D e wetenschap der geschiedenis” , Haarlem 1937, blz. 122.
m ab
blz. 136
poreerd in de accountantscontrole, en enige wetten van de rekenkunde, waarop
de boekhoudtechniek berust, vormen dientengevolge een van de grondslagen van
de techniek van de accountantscontrole.
Hoewel de techniek van het boekhouden ongetwijfeld een vernuftige uitvinding
is, zijn de wetten van de rekenkunde, die eraan ten grondslag liggen, van uiterst
eenvoudige aard. Het zijn de wetten van optelling en aftrekking, die tezamen met
de axioma’s waaruit de boekingsregels voortvloeien, de kenmerken van deze
techniek bepalen 7). De conclusie dat het boekhouden een zelfs ongemeen sterk
wetenschappelijk fundament bezit, ligt zo voor de hand, dat boekhouders en an
dere gebruikers van deze techniek gemakkelijk geneigd zijn dit aspect over het
hoofd te zien.
Zolang de techniek der accountantscontrole haar enige grondslag in de boek
houdtechniek vindt, zal de accountant geen specifieke deskundigheid bezitten,
die hem onderscheidt van de boekhouder. Deze situatie is het kenmerk van de
eerste ontwikkeling van het accountantsberoep; met de ontwikkeling van de be
drijfseconomie zien wij echter tevens de deskundigheid en hiermede de taak van
de accountant veranderen 8).
De bedrijfseconomie ontpopt zich als wetenschap, zodra zij evenals andere
wetenschappen wetten formuleert. Uiteraard alleen, indien de deductie, die aan
de formulering ten grondslag ligt, einwandfrei is. Deze ontwikkeling is hier te
lande door Limperg tot stand gebracht. De bedrijfseconomische wetten betreffen
onder andere de organisatie, de financiering van de bedrijfshuishouding en de
berekening en doelmatigheid van de kosten. De controle van de accountant zal
zich mede uitstrekken tot de vraag of de wetten der bedrijfseconomie in de be
drijfshuishouding zijn toegepast. Zo niet, dan zal hij zulks in zijn verklaring
dienen te vermelden. Het maatschappelijk verkeer verlangt van de accountant
een toetsing van het concrete geval aan de bedrijfseconomische wetten en, omdat
een zodanige toetsing een bedrijfseconomische deskundigheid eist, heeft dit een
ontwikkeling van het beroep ten gevolge gehad, die naast comptabele kennis
bedrijfseconomische kennis verlangt.
De toepassing van de wetenschappelijke uitspraken van de rekenkunde en de
bedrijfseconomie in de techniek der accountantscontrole heeft geen betekenis,
zolang zij niet gepaard gaat met waarnemingen. In de accountantscontrole hebben
waarnemingen zonder gebruik van wetenschappelijke uitspraken weinig betekenis,
maar in deze techniek is, zoals in iedere techniek, het omgekeerde ondenkbaar,
namelijk deductieve analyse zonder waarnemingen. De aanwending van het mid
del der waarneming tezamen met dat der deductie smeedt de accountantscontrole
tot een machtig instrument in de voorlichting van het maatschappelijk verkeer.
Een goed voorbeeld van combinatie van inductie en deductie is de verbandscontrole: uit de inductie, die hier bestaat uit de waarneming van de omvang van
de inkopen en de begin- en de eindvoorraden volgt door deductie, namelijk de
toepassing van de wetten van optelling en aftrekking, de omvang van de verkopen;
7) De titel en inhoud van het werk van frater Luca Paciolo is een voorbeeld, dat het boek
houden in zijn kinderjaren tot de rekenkunde en aanverwante vakken werd geacht te behoren
(„Summa de Arithmetica, Geometria, Proportioni et Proportionalita” , Venetië 1494). Dit is een
ondersteuning van het argument, dat het boekhouden een toepassing van de rekenkunde is.
8) Hier te lande heeft de ontwikkeling van de bedrijfseconomie bijzonder bevruchtend gewerkt
op de techniek van de accountantscontrole. Dit is niet bevreemdend, indien wij in aanmerking
nemen, dat in Nederland de beste beoefenaren van de bedrijfseconomie tevens accountant waren.
mab
blz. 137
dit is een voorbeeld uit vele verschijnselen in de bedrijfshuishouding, waarop de
verbandscontrole kan worden toegepast. Zij wordt door vele accountants terecht
als een zeer belangrijk instrument van het onderzoek beschouwd, juist vanwege
haar gecombineerde toepassing van inductie en deductie.
Vervolgens een voorbeeld van toepassing van bedrijfseconomische wetten.
Leert de bedrijfseconomie, dat men de kostprijs op grond van de vervangings
waarde dient te berekenen, dan zal de accountant in de bedrijfshuishouding een
waarneming van de vervangingsprijzen en de techniek der produktie dienen te
verrichten om de leringen omtrent de kostprijs in de concrete situatie te verwer
kelijken. Hiermede zien wij weer ten behoeve van de controle een combinatie van
inductie en de toepassing van wetten, die het resultaat zijn van deductieve analyse.
Grondslagen van de theorie der waarschijnlijkheid
Hoewel de methodiek der accountantscontrole zowel de inductie als de deductie
als instrumenten bevat, is het toch onbetwistbaar, dat het vraagstuk van de ver
zameling van feitelijke gegevens, het inductieve deel der controle, sinds lang meer
de geesten in de accountantswereld bezighoudt dan de vraagstukken, die verband
houden met het zuiver redeneren. Een gang van zaken, welke ook volkomen
verklaarbaar is: blijkt eenmaal, gegeven de op waarneming gegronde hypothesen,
een onderzoek naar de deductieve samenhang der grootheden mogelijk, dan zal
twijfel aan de waarde hiervan, zelfs bij de ten gevolge van de aard van zijn werk
uiterst pragmatisch ingestelde accountant, niet licht opkomen. Wat daarentegen
de voor- en nadelen zijn van een vermeerdering of vermindering van het feiten
materiaal voor het resultaat van de controle, is lastig vast te stellen.
Dat de waardebepaling in het eerste geval geen moeilijkheden oplevert en wel in
het laatste, vormt, nog geheel afgezien van het specifieke karakter van de accoun
tantscontrole, een weerspiegeling van het algemene feit, dat de grondslagen der
inductie in vergelijking met die der deductieve logica nog zeer weinig ontwikkeld
zijn.
Ter toelichting van dit feit is het voor ons doel voldoende enige fundamentele
problemen met betrekking tot de inductie uiteen te zetten. Teneinde deze in een
duidelijk perspectief te plaatsen, is het wenselijk van de pogingen uit te gaan een
inductieve logica op te bouwen naar het beeld van de deductieve logica; hierbij
is het voor onze probleemstelling niet noodzakelijk, weinig vruchtbaar en ook
te tijdrovend, ons te verdiepen in de constructie zelve van de inductieve logica en
de verschillen, die hierin bij de verschillende logici optreden.
De vraag, die men met behulp van de inductieve logica tracht te beantwoorden,
is in welke mate een hypothese - verder voor te stellen door het symbool h - door
het bewijsmateriaal q 9) wordt bevestigd. Ter vorming van dit bewijsmateriaal
doet men waarnemingen, die men relevant acht voor de beoordeling van h, en
welke men samenvat in een rapport. Zeer belangrijk is, ook voor ons, dat men
de grens onderscheidt tussen de inductieve logica enerzijds en de politiek die men
volgt ter verzameling van het feitenmateriaal ter andere zijde.
Taak van de inductieve logica is, een logische redenering op te bouwen, die op
grond van het gegeven bewijsmateriaal q in het hierboven genoemde rapport vast
stelt in welke mate h door q wordt bevestigd. Met deze taak is men nog bijzonder
B) R. Carnap, „Logical Foundations of Probability” , Chicago 1950, biz. 20.
m ab
biz. 138
weinig gevorderd; ook over de grondslagen van de opbouw bestaat nog geen
overeenstemming 10). Hoe de logische redenering kan worden opgebouwd, be
spreken wij hier niet, maar wel merken wij op, dat men poogt een kwantitatieve
theorie op te bouwen, zodat men de degree of confirmation van h op grond van q
in een getal kan uitdrukken “ ). Duiden wij dit getal aan door het symbool z, dan
verstaat men onder de logische waarschijnlijkheid het getal z, dat de uitkomst van
de logische redenering is op grond van gegeven h en q 12). Wanneer wij in het
vervolg over waarschijnlijkheid spreken, hebben wij het oog op dit begrip der
logische waarschijnlijkheid. Men eist, dat z steeds tussen 0 en 1 zal liggen. Wij
komen op de moeilijkheden verbonden aan het opsporen van een passende functie
z hierna terug.
De inductieve logica gaat dus van een gegeven q uit, waarbij zij bij de beoor
deling van h aan de hand van q met alle aspecten van q rekening houdt. De be
doeling van de voorstanders van de inductieve logica is een logica te ontwikkelen,
die in opbouw en rigiditeit vergelijkbaar is met de deductieve logica. Daaren
boven dient men criteria te ontwikkelen, die verzekeren dat men de beschikking
krijgt over een optimale hoeveelheid feitenmateriaal. Dit probleem valt buiten
het gebied van de inductieve logica, aangezien deze een q met bepaalde inhoud
veronderstelt en het dan om de vraag gaat hoe de grootheid q samengesteld dient
te worden, dus welke feiten waargenomen moeten worden en in welke omvang.
De behandeling hiervan komt in de volgende paragraaf nader aan de orde.
Wij beperken ons te dezer plaatse tot beschouwingen over de grootheid z. Hoe
wel de inductieve logica, zoals gezegd, nog in het geheel niet tot wasdom is ge
komen, bestaat er wel overeenstemming over, dat bij een volledige of gedeeltelijke
waarneming van het in aanmerking komende feitenmateriaal de relatieve fre
quentie, waarmede een eigenschap optreedt, een belangrijke grootheid is in de
bepaling van de waarschijnlijkheid z 13). Is het aantal gebeurtenissen of toestan
den, dat men waarneemt, gelijk aan S en is Sv het aantal malen, dat men de eigen
schap V in de waargenomen massa S constateert, dan is
Sv
s
de relatieve frequen
tie, waarmede V in deze massa optreedt. Ceteris paribus, waaronder ook S, zal
Sv
de waarschijnlijkheid groter zijn naarmate de uitkomst ~
groter is.
Vele logici hebben de theorie der waarschijnlijkheid geheel gebaseerd op de
relatieve frequenties, waarmede eigenschappen optreden, welke opvatting echter
bepaalde hindernissen niet vermag op te ruimen, die op de weg ter vaststelling
der waarschijnlijkheid optreden 14). In hoeverre zulks het geval is, zal uit het
volgende nog blijken.
10) Carnap, op. cit., blz. 565.
11) Carnap, op. cit., blz. 23; verbeteringen van Carnap’s uitwerking in J. Kemeny, „A Logical
Measure Function” , Journal of Symbolic Logic 1953, blz. 289 e.v.
12) Een andere keuze der vaktermen, die tot een onderscheid tussen de degree of confirmation
en de waarschijnlijkheid leidt, in: K. R. Popper, „The Logic of Scientific Discovery” , blz. 251 e.v.;
het door hem ingevoerde onderscheid vertroebelt, dunkt ons, het inzicht in een aantal problemen
van de inductieve logica.
13) Niet alleen is dit de opvatting van de frequentie-theoretici, maar ook van Carnap: R.
Carnap, „The Continuüm of Inductive Methods” , Chicago 1952, blz. 24.
14) Vooral Von Mises en Reichenbach: R. von Mises, „Wahrscheinlichkeit, Statistik und
Wahrheit” , Wenen 1928, blz. 16 en H. Reichenbach, „Expericnce and Prediction” , Chicago 1938,
tweede druk 1947, blz. 300.Wij volstaan in het bovenstaande opstel met een beschouwing over
relatieve frequenties zonder de definitie van het waarschijnlijkheidsbegrip, dat Von Mises en
Reichenbach hanteren, uiteen te zetten en te bespreken. Voor ons doel is dit laatste niet nood
zakelijk'
mab
blz. 139
Wanneer wij in het volgende veronderstellen, dat de relatieve frequentie waar
mede eigenschappen optreden, een bepalende invloed op de hoogte hunner waar
schijnlijkheid heeft, is de vraag hoe de accountant een inzicht krijgt in de waar
schijnlijkheden van de in de verslaglegging opgenomen gebeurtenissen. De ac
countant zal, zoals gezegd, naast de waarneming van voorraden, documenten en
aantekeningen in de bedrijfshuishouding controleren in een omvang en op een
wijze, waarover wij in de volgende paragraaf nog nader spreken. Hier ter plaatse
is de vraag aan de orde, of het hem op grond van deze controle mogelijk is de
grootte van de waarschijnlijkheid vast te stellen, dat de gebeurtenissen in de ver
slagperiode zijn opgetreden, zoals zij in het verslag zijn weergegeven.
Onontkoombaar is, dat de accountant zich rekenschap geeft van de waarschijn
lijkheid dat de documenten enz. die hem worden voorgelegd, ook de feitelijke
gang van zaken in de bedrijfshuishouding weergeven. Hiermede komen wij wat
de bespreking van de grondslag van het accountantsberoep betreft, wel in medias
res. Wanneer op grond van de controle de waarschijnlijkheid, die de accountant
aan de hypothesen zou moeten toekennen, niet groot is, dan zou de omvang van
het vertrouwen in de uitkomsten van de arbeid van de accountant klein zijn, de
bestaansgrond van de functie beperkt en hierdoor de betekenis van het beroep
gering.
De waarschijnlijkheid, dat de documenten aan de accountant overgelegd in een
bedrijfshuishouding echt zijn - in de zin dat de erin vermelde tekens en zinnen
verschijnselen naar tijd en plaats aangeven, die ook werkelijk hebben plaats ge
vonden - hangt overeenkomstig het bovenstaande onder meer af van de relatieve
frequentie, dat de documenten die in de onderhavige bedrijfshuishouding aan
hem worden voorgelegd, echt zijn. Veelal zal de accountant niet in staat zijn
voor de afzonderlijke bedrijfshuishouding zelfs maar een vage indruk te vormen
van een dergelijke relatieve frequentie, maar wel zal hij door eigen praktijkerva
ring in een aantal bedrijfshuishoudingen en de overgeleverde ervaring van be
roepsgenoten tot bepaalde conclusies komen omtrent de frequentie van verval
singen in het algemeen.
Deze verzamelde ervaringen tonen aan, dat vervalsingen bij interne bewijsstuk
ken veelvuldiger voorkomen dan bij externe bewijsstukken en op deze grond
komt de accountant tot een rubricering van de documenten naar hun betrouwbaar
heid, die aan de echtheid der externe bewijsstukken een hogere waarschijnlijkheid
toekent dan aan de interne 15). Deze conclusie wordt tevens bevestigd door de
ductieve overwegingen, die berusten op de premisse, dat de vervalsing van externe
bewijsstukken een ingreep vereist, die meer tegen de code van eerlijkheid indruist,
welke in de maatschappij bestaat, dan de vervalsing van interne documenten.
Hier ligt de overweging van de accountant een zo groot gewicht aan de externe
documenten toe te kennen. Hoe hoog echter de waarschijnlijkheid is, dat de
documenten van de in het onderzoek betrokken bedrijfshuishouding echt zijn,
kan afgezien nog van andere overwegingen, door gebrek aan voldoende statistisch
15)
Reichenbach formuleert de invloed van de betrouwbaarheid op de waarschijnlijkheid als
volgt: „Why do we ascribe, say, a high probability to the statement that Napoleon had an attack
of illness during the battle of Leipzig, and a smaller probability to the statement that Caspar
Hauser was the son of a prince? It is because chronicles of different types report these statements:
one type is reliable because its statements, in frequent attempts at control, were confirmed; the
other is not reliable because attempts at control frequently led to the refutation of the statement” .
(Reichenbach, „Experience . . . . ” , blz. 307 e.v.).
mab
blz. 140
materiaal niet worden bepaald. Het gaat in het gegeven geval slechts om door de
ervaring gefundeerde indrukken van de accountant, die zijn hierboven besproken
comparatieve waarschijnlijkheidsoordelen wettigen.
Overigens dient men niet te vergeten, dat de ervaringen van de accountant
natuurlijk niet de vervalsingen omvatten, die hij niet heeft ontdekt en redelijker
wijze niet heeft kunnen ontdekken. Dit is een ander niet te omzeilen gebrek, inhe
rent aan de accountantscontrole, dat de exacte vaststelling van de waarschijnlijk
heid in de weg staat.
Dit gebrek aan statistisch materiaal verhindert een exacte beoordeling van de
waarde van de vaktechnische uitvoering der accountantscontrole, hetgeen haar
theoretische fundament niet zo hecht doet zijn als men wel zou wensen. Wel staat
de praktische betekenis van het werk van de accountant buiten kijf, maar de
onderhavige leemte bemoeilijkt het leggen van een kwantitatieve grondslag voor
zijn arbeid ten zeerste.
Voorts moeten wij bij onze beschouwingen over de waarschijnlijkheidstheorie
nog met de volgende moeilijkheden rekening houden, die eveneens belemmeringen
zijn voor de vorming van kwantitatieve grondslagen der controleleer. Men zal
hebben opgemerkt, dat wij in het bovenstaande verschillende relatieve frequenties
hebben genoemd, namelijk een relatieve frequentie betreffende de echtheid van
documenten in de bedrijfshuishouding die de accountant controleert, en een die,
wat hetzelfde verschijnsel betreft, meer in het algemeen betrekking heeft op een
niet nauwkeurig bepaalde verzameling van bedrijfshuishoudingen. In het accountantsberoep doet eerst een langdurige ervaring gefundeerde indrukken omtrent
de frequentie van het optreden van bepaalde verschijnselen ontstaan, zodat wij
hebben betoogd, dat de ontwikkeling van de grondslagen der vaktechniek meer
door het bewijsmateriaal, verzameld in een groot aantal bedrijfshuishoudingen
wordt bepaald dan door het bewijsmateriaal, verkregen in de bedrijfshuishouding,
die juist onderwerp van controle is. De constatering, dat de grondslagen der vak
techniek niet uit de ervaringen in de afzonderlijke bedrijfshuishoudingen worden
afgeleid, doch uit de algemene praktijkervaring, zal iedere vakgenoot beamen,
maar het is toch van belang, deze nader te bespreken, omdat waarschijnlijkheidstheoretische vraagstukken in het geding zijn.
Zeker is, dat de relatieve frequentie waarmede een eigenschap in het algemeen
voorkomt een factor voor het bepalen van de waarschijnlijkheid van het optreden
van deze eigenschap in het algemeen is en ten gevolge hiervan eveneens in de aan
het onderzoek onderworpen bedrijfshuishouding. De onderhavige relatieve fre
quentie vormt indirect bewijsmateriaal, dat de eigenschap zich in de genoemde
bedrijfshuishouding voordoet. Maar evenzo kan men zich voorstellen - gesteld
al dat men toegang tot de hiervoor vereiste gegevens zou hebben, hetgeen voor
de eigenschap van echtheid van documenten uitgesloten is - dat de relatieve fre
quentie van het optreden van de eigenschap in de betrokken bedrijfshuishouding
wordt vastgesteld. Dan heeft men naast de eerstgenoemde relatieve frequentie
nog een tweede, die meer in het bijzonder op de eigenschap, waarvan men de
waarschijnlijkheid wil vaststellen, betrekking heeft. De waarnemingen hiervoor
vormen het directe bewijsmateriaal voor de bevestiging van de hypothese, die
door de accountant voor de bijzondere bedrijfshuishouding wordt gesteld. Het
tweede getal staat in een directe relatie tot de eigenschap; hiermede vergeleken
heeft het eerste getal alleen betekenis voor de afzonderlijke bedrijfshuishouding
m ab
blz. 141
door van het algemene tot het bijzondere te besluiten, hetgeen een deductieve stap
is.
Bovendien kan men zich voorstellen de verzameling bedrijfshuishoudingen nog
naar een ander criterium in te delen, bijvoorbeeld naar bedrijfstak. Het is zeer
goed denkbaar, dat de relatieve frequentie van de eigenschap, waarvan men de
waarschijnlijkheid wil vaststellen, niet in ieder van de deelverzamelingen gelijk
is. Een wijziging van het criterium kan voorts de relatieve frequenties doen ver
anderen. Hier ontstaat opnieuw indirect bewijsmateriaal voor de beoordeling
van de hypothese, die door de accountant voor de bijzondere bedrijfshuishouding
is gesteld.
Stellen wij onszelf de vraag wat de waarschijnlijkheid is van de hypothese, dat
de in een bepaalde bedrijfshuishouding aan de accountant voorgelegde documen
ten ook de werkelijke gang van zaken weergeven, dan zullen wij bij de beant
woording zowel rekening dienen te houden met het directe bewijsmateriaal als
met het indirecte. Er ligt hier een probleem, niet alleen voor de accountant, hetgeen
wij met het volgende voorbeeld ontleend aan de fysica, adstrueren. Wanneer wij
de waarschijnlijkheid willen bepalen van de hypothese, dat de afstand die door
een vrij vallend lichaam wordt afgelegd, evenredig is met het kwadraat van de
tijd van de val, dan kunnen wij onmiddellijk op het gegeven geval betrekking
hebbende waarnemingen verrichten. Dit is het directe bewijsmateriaal, maar hier
moet het uiterst belangrijke indirecte bewijsmateriaal aan toegevoegd worden, dat
bestaat uit waarnemingen betreffende andere afleidingen van de dieper liggende
gravitatiewet van Newton. Dit voorbeeld kan met een onnoemelijk aantal andere
worden aangevuld.
Voor het hier gestelde probleem, namelijk uit het geheel van bewijsmateriaal,
direct en indirect, de waarschijnlijkheid van een hypothese af te leiden, heeft de
inductieve logica nog geen bevredigende oplossing gevonden 16). Hier is sprake
van een onvolkomenheid van de waarschijnlijkheidstheorie, die een nieuwe di
mensie toevoegt aan de reeds besproken moeilijkheden om te komen tot de kwan
titatieve vaststelling van de waarschijnlijkheid, dat vervalsingen van documen
ten optreden.
In dit verband dienen wij nog een ander verschijnsel te noemen, dat in zijn
betekenis zeer belangrijk kan zijn, namelijk het niet overleggen van documenten
aan de accountant. Hierdoor ontstaat voor de laatste een verkeerd beeld van de
werkelijkheid. Deze mogelijkheid, die voorzover geen bijzondere maatregelen zijn
getroffen, gemakkelijk is te verwezenlijken, zal de waarschijnlijkheid verminderen
van de hypothesen omtrent de gang van zaken in de bedrijfshuishouding, welke
aan het onderzoek onderworpen is. In welke mate zulks het geval is, hangt weer
af van de relatieve frequenties, waarmede het wederrechtelijk in bezit houden
door de leiding of de uitvoerenden, in het algemeen en in de bijzondere bedrijfs
huishouding geschiedt. Gelijke problemen bij de vaststelling van de waarschijn
lijkheid treden hier op als wij bij de vervalsing van documenten hebben behandeld.
16)
Een niet bevredigende poging van Reichenbach met behulp van direct en indirect sta
tistisch bewijsmateriaal de waarschijnlijkheid van een hypothese vast te stellen (Reichenbach,
„Experience. .. . ” , blz. 363 e.v.). In het in noot 9) genoemde werk van Carnap moet men een
poging zien door een rigoureuze formulering van de theorie de moeilijkheden uit de weg te ruimen;
zij heeft echter nog weinig tastbare resultaten opgeleverd. Een verbetering van Carnap’s werk
op een aantal punten bij J. Kemeny, „A Logical Measure Function” , Journal of Symbolic Logic
1953, blz. 289 e.v.
mab
blz. 142
Aangezien het niet overleggen van documenten aan de accountant gemakkelijker
uitvoerbaar is dan de vervalsing van documenten, ontstaat hierdoor het gevaar
van een aanzienlijke verlaging van de waarschijnlijkheid der hypothesen omtrent
de bedrijfsgang. Hieruit is de behoefte aan bijzondere maatregelen ontstaan, die
tot de interne controle behoren. Het gehele verschijnsel der interne controle zullen
wij in het volgende nader bespreken, maar hier kunnen wij reeds opmerken, dat
men met behulp van de interne controle onder andere het genoemde verschijnsel
van achterhouden van documenten tracht te elimineren, hetgeen geschiedt door
de registratie van eenzelfde feit door verschillende organen in de bedrijfshuishouding, organen bij voorkeur met tegengestelde belangen. Zo ontstaat een kwa
litatieve en kwantitatieve samenstelling van het bewijsmateriaal, die de waar
schijnlijkheid van een door de accountant gestelde hypothese, gegeven dit mate
riaal, zeker vergroot. Maar in welke mate de waarschijnlijkheid van de hypothese
hierdoor wordt vergroot, is zowel door de gebreken in het statistische materiaal,
die wij nog bespreken, als door de onvolkomenheden in de waarschijnlijkheidstheorie niet kwantitatief uit te drukken.
Ook op een andere dan de hiervoor besproken manier vindt de combinatie van
het directe met het indirecte bewijsmateriaal toepassing ter bevestiging van een
hypothese in de accountantscontrole. Wanneer wij opnieuw de verbandscontrole
ten tonele voeren, die wij eerder als voorbeeld van combinatie van inductie en
deductie hebben genoemd, dan is deze bij verder doordenken tevens een voorbeeld
van het verkrijgen van indirect bewijsmateriaal voor een hypothese. De omvang
van de verkopen wordt door een deductie afgeleid uit verrichte waarnemingen
omtrent inkopen en voorraden; hier zien wij dus dat het bewijsmateriaal verza
meld voor de staving van de hypothesen omtrent inkopen en voorraden, door een
deductieve afleiding van betekenis is voor de hypothese omtrent de aard en de
omvang van de verkopen.
Het directe bewijsmateriaal ter bevestiging van de hypothese omtrent de ver
kopen wordt ondersteund door bewijsmateriaal, dat voor de toetsing van andere
hypothesen bijeengebracht is. Hoewel het indirecte bewijsmateriaal voor de be
vestiging van de hypothese omtrent de omvang van de verkopen uiterst belang
rijk is, aangezien het ontstaat uit de controle van externe bescheiden en de op
tische controle, is het kwantitatieve effect hiervan op de hoogte der waarschijnlijk
heid niet uit te drukken.
Niet alleen toetst het bewijsmateriaal, dat verzameld is omtrent de inkopen
en de voorraden, de hypothese omtrent de verkopen, maar ook omgekeerd zal
het directe bewijsmateriaal omtrent de verkopen indirect van betekenis zijn voor
de bevestiging van de hypothese omtrent inkopen en voorraden. Alleen is deze
betekenis kleiner, doordat het directe bewijsmateriaal, dat bijeengebracht wordt
aangaande de verkopen, geheel uit documenten en aantekeningen bestaat, die door
de bedrijfshuishouding zelve zijn geproduceerd.
Wij hebben vroeger geconstateerd, dat de verbandscontrole een belangrijk
instrument is, voor welke uitspraak wij thans een nadere rechtvaardiging hebben
gevonden. De verbandscontrole stelt ons in staat, de waarschijnlijkheid van iedere
hypothese in verband met de waarschijnlijkheid van andere hypothesen omtrent
de bedrijfsgang te beoordelen. Hierdoor wordt het bewijsmateriaal ter bevestiging
van de hypothese aanzienlijk verbreed, hetgeen het waarschijnlijkheidsoordeel
aanmerkelijk aan waarde doet winnen. Deze werkwijze is in overeenstemming
mab
blz. 143
met de algemene wetenschappelijke methode van onderzoek, die Duhem voor de
natuurkundige als volgt formuleert:17)
„ ...........Ie physicien ne peut jamais soumettre au controle de Pexpérience
une hypothèse isolée, mais seulement tout un ensemble d’hypothèses...........”
Wanneer wij het voorgaande samenvatten, komen wij tot de volgende algemene
conclusies. In het bijzonder de optische controle, aangezien deze de accountant
onmiddellijk de feitelijke situatie doet leren kennen, en verder de controle aan de
hand van externe bescheiden, verzekeren het ontstaan van een zo breed mogelijke
basis voor het vellen van een waarschijnlijkheidsoordeel. De keuze der hypothesen
dient zo te geschieden, dat men ter verzekering van een zo hoog mogelijke waar
schijnlijkheid een maximaal gebruik maakt van deze controlemiddelen. Tevens
dient de accountant een zodanig aantal hypothesen te toetsen, dat de andere
controlemiddelen en in het bijzonder de verbandscontrole, hem in staat stellen
het waarschijnlijkheidsoordeel omtrent ieder der hypothesen en hierdoor omtrent
de juistheid van het gehele verslag een stevig fundament te verschaffen. Hoe hoog
de waarschijnlijkheden zijn is echter niet exact te bepalen.
De richtlijnen, die het bovenstaande oplevert voor de techniek der accountants
controle, zijn in feite sinds lang aanvaard, maar het dunkt ons een verdieping
van het inzicht, deze te stoelen op waarschijnlijkheidstheoretische beschouwingen.
Uit deze blijkt ook duidelijk, welke onvermijdelijke onvolkomenheden men in
de grondslagen der controleleer dient te aanvaarden.
Teneinde de betekenis van de voorgaande bespiegelingen in hun volle omvang
te doorgronden, is het gewenst ze in het kader van de leer van het gewekte ver
trouwen te plaatsen. De normatieve kern van deze leer houdt in, dat de accoun
tant verplicht is, zijn arbeid zo te verrichten, dat hij de verwachtingen, welke hij
bij de verstandige leek opwekt, niet beschaamt; en, omgekeerd, de accountant
mag geen grotere verwachtingen opwekken dan door de verrichte arbeid wordt
gerechtvaardigd 18).
Dit richtsnoer is zonder enige twijfel noodzakelijk om de bestaansgrond van
de functie van de accountant, namelijk het vertrouwen in de doeltreffendheid van
zijn administratieve controle, in stand te houden.
De verstandige leek, die belang heeft bij de verklaring van de accountant, be
schouwt hem als administratief en bedrijfseconomisch deskundige en hij verlangt
van zijn arbeid niet meer dan uit deze deskundigheid voortvloeit. Mitsdien ver
wacht hij van de accountant niet, dat deze verantwoordelijkheid draagt voor ver
schijnselen, die deze niet door middel van het onderzoek van de administratie aan
het licht kan brengen. Een zodanige beperking van de arbeid van de accountant
beschouwt de verstandige leek als een uit de aard van diens verantwoordelijkheid
voortvloeiende beperking. Dat deze zienswijze ook door de accountant zelve als
een vanzelfsprekendheid wordt aanvaard, getuigt het nieuwe Reglement van
Arbeid, dat in tegenstelling met het oude, niet meer een expliciete formulering
van deze beperking nodig acht.
Maar zeker is, dat de beperking in de waarnemingen het oordeel van de ac
countant omtrent aard en omvang van de verschijnselen in de bedrijfshuishouding
17) P. Duhem, „L a théorie physique, son objet - sa structure” , Parijs 1906, tweede druk 1914,
blz. 284.
18) D it is Limperg’s formulering in „Vijfentwintig jaren maandblad. . . . ” , blz. 154 (oorspronke
lijk in M.A.B. 1933).
m ab
blz. 144
nooit met zekerheid doet vaststaan. Uit dien hoofde is zijn oordeel steeds een
waarschijnlijkheidsoordeel19), dat, zoals bleek, niet in een numerieke grootheid
kan worden uitgedrukt. Intussen behoeft dit gebrek aan exactheid de doeltref
fendheid van de actie van de accountant niet teniet te doen, maar dan dient aan
het volgende te zijn voldaan: de waarschijnlijkheid van de juistheid van zijn
oordeel, ook al houden wij met de besproken beperking rekening, moet groot zijn.
Anders zal de omvang van het vertrouwen in de uitkomsten klein zijn en hierdoor
de betekenis van het beroep gering. De grootte van de waarschijnlijkheid van de
juistheid van het oordeel des accountants zal niet alleen worden bepaald door de
stand van de ontwikkeling van de controletechniek en zijn deskundigheid deze
te hanteren, maar ook door het gebrek dat inherent is aan het beroep, namelijk
dat in het algemeen niet de handelingen zelve, doch de administratie onderwerp
van controle is.
Een bespreking van de taak van de accountant, met als inzet het waarschijnlijkheidsbegrip, is het meest doelmatig voor het volgroeide beroep 20). Een zodani
ge toestand is aanwezig, indien de accountant de vermogens van de controletech
niek geheel uitbuit, dat wil zeggen indien hij op grond van zijn deskundigheid
alle waarnemingen verricht die noodzakelijk zijn voor het verkrijgen van zijn
oordeel en verder alle wetenschappelijke uitspraken aanwendt, die in verband
met de controletechniek van toepassing zijn en waarvan wij hierboven een prin
cipiële behandeling hebben gegeven. Een hierop gefundeerde taakuitvoering zal
aan de verwachtingen van het maatschappelijk verkeer zo goed als mogelijk is
voldoen, maar bovendien zal het werkprogramma van de accountant met uitslui
ting van andere overwegingen worden bepaald door het objectieve gegeven van
het vermogen der controletechniek.
Ook wanneer de accountant zijn werkprogramma geheel door controletech
nische factoren laat bepalen, blijft zijn oordeel zoals hierboven bleek, een waar
schijnlijkheidsoordeel. Weliswaar zal een volkomen uitbuiting van het vermogen
der controletechniek door de accountant de waarschijnlijkheid van de onjuistheid
van het oordeel minimaliseren 21), maar een volkomen zekerheid ontstaat hierdoor
nimmer 22).
Waarnemingen in de voortgezette periodieke controle
Thans zijn wij zover gevorderd, dat wij onszelf de vraag kunnen stellen, hoever
de accountant zijn waarnemingen dient uit te strekken. Hierbij is het gewenst
steeds de relatie met de in de vorige paragraaf behandelde problemen, die aan de
vaststelling van waarschijnlijkheidsoordelen verbonden zijn, in gedachten te hou
den. In het voorgaande hebben wij betoogd, dat de accountant alle waarnemingen
moet verrichten, die voor het verkrijgen van zijn oordeel noodzakelijk zijn. Hoe
wel men het over dit uitgangspunt roerend eens is, blijkt het bijna onmogelijk te
zijn het elliptische karakter van deze uitspraak door het ontwerpen van een
passende techniek van uitvoering te elimineren.
Op ander gebied hanteert men voor het determineren van de omvang der
19) Ook H . Mey, „De toepassing van steekproeven door de accountant” , M.A.B. 1960, blz. 51.
20) Liraperg, t.a.p., blz. 160.
21) Zie ook P. J. H. J . Bos, „De structuur van de leer der accountantscontrole en haar toe
passing” , pre-advies accountantsdag 9 oktober 1954 in De accountant 1954, blz. 7.
22) In tegenstelling met Louwers, die de mogelijkheid van een zekerheidsoordeel veronderstelt
(Louwers, M.A.B. 1958, blz. 241).
m ab
blz. 145
waarnemingen veelvuldig het beginsel, dat de kosten verbonden aan het verza
melen van feitenmateriaal dienen op te wegen tegen de voordelen, die men hier
mede bereikt.
Wanneer een statisticus voor een zo juist mogelijke fundering van een besluit
een gedeelte van het universum waarneemt, kan hij de lengte van de steekproef
bepalen aan de hand van de vergelijking van de kosten die ontstaan door uit
breiding van de steekproef, en de vermindering van het verwachte verlies of de
toeneming van de verwachte opbrengst ten gevolge hiervan 23).
Dit is meestentijds een deugdelijk uitgangspunt, ook in overeenstemming met
de grondslag van het economische handelen, dat echter op het gebied der accoun
tantscontrole volkomen onbruikbaar is. Dat wij deze oude waarheid nog eens
naar voren halen, geschiedt vooral om de gedachten die zich tegenwoordig om
trent de beperking van de waarnemingen voordoen, aan een nader onderzoek te
onderwerpen. Vandaar dan ook dat het zeker nuttig is de principiële grond te
formuleren, die tot de onbruikbaarheid in de accountantscontrole leidt van het
criterium, dat een afweging van kosten en opbrengsten inhoudt. De kosten, ver
bonden aan de uitvoering van een bepaald besluit, en de hierdoor ontstane op
brengsten, zijn slechts dan rationeel te vergelijken, indien het in de beschouwing
betrokken orgaan, waarin de kosten optreden, ook de opbrengsten incasseert. Met
steekproefsgewijze uitgevoerde kwaliteits- en andere controles in de industrie is
dit duidelijk het geval; de bedrijfshuishouding draagt de kosten der waarneming
en geniet de opbrengsten, die het gevolg zijn van de meer of minder uitgebreide
informatie op grond van de waarnemingen.
Dit ligt bij de accountantscontrole anders, zolang wij althans uitgaan van het
probleem, zoals dit zich voor de individuele accountant openbaart. Deze draagt
wel de kosten van waarneming, maar geniet niet de opbrengsten of lijdt de ver
liezen, welke het gevolg zijn van de omvang en samenstelling van de waarneming.
Wel ontvangt hij een vergoeding van de gemaakte kosten, maar deze wordt bepaald
door de omvang van de verrichte arbeid, niet door de gevolgen van deze arbeid.
De vruchten, die de arbeid van de accountant afwerpt, worden geplukt door de
gebruikers van zijn verklaring. Een vergelijking van kosten en opbrengsten heeft
in dit geval geen zin, tenzij men als economische eenheid de gehele maatschappij
neemt. Van een maatschappelijk gezichtspunt uit kan in beginsel wel een vergelij
king plaatsvinden van de kosten der accountantscontrole en het nuttig effect, dat
het maatschappelijk verkeer hieraan ontleent; hierbij is dan afgezien van de - on
overkomelijke - moeilijkheden, die zouden optreden wanneer men het nuttig effect
wil meten. Zulk een vergelijking van offers en opbrengsten wordt in de maatschap
pij niet verricht, stellig wel vanwege de onmogelijkheid het nuttig effect te meten.
Zou dit laatste wel uitvoerbaar zijn, dan kan men zich een andere oplossing van
het probleem van de omvang van de waarnemingen van de accountantscontrole
indenken en ten gevolge hiervan een geheel verschillende ontwikkeling van de
beroepsopvattingen.
In feite heeft zich een groei van het beroep voorgedaan, die Limperg de veel
vuldig beschreven en hiervoor herhaalde leer van het gewekte vertrouwen in de
pen heeft gegeven. Limperg’s leer steunt op een ander criterium dan dat, hetwelk
23)
Zie voor een elementaire uiteenzetting H. Freudenthal, „Waarschijnlijkheid en statistiek” ,
Haarlem 1957, blz. 99 e.v.
mab
blz. 146
de vergelijking van kosten en opbrengsten inhoudt24). Aangezien een beoordeling
van de vruchten der accountantscontrole geheel buiten het gezichtsveld van de
accountant valt, treedt hiervoor in de plaats zijn beoordeling van de verwach
tingen, die men in het maatschappelijk verkeer omtrent de resultaten van zijn
arbeid koestert. Maar zodra de accountant dit als criterium aanvaardt, sluit dit
uit, dat hij vage indrukken die hij verzamelt omtrent de vruchten van zijn arbeid
in het maatschappelijk verkeer, als criterium gebruikt. De grondslag, die afweging
van kosten en opbrengsten inhoudt, verwerpt men ten gunste van een standpunt,
dat uitgaat van verwachtingen bij de verstandige leek 25).
Tegen deze achtergrond moet men de pogingen bezien een grondslag in de
volkomen controle te vinden voor het verrichten van steekproeven in plaats
van een volledige waarneming van het universum. In Nederland zijn in dit
opzicht twee bijzonder stimulerende en belangrijke artikelen van De Wolff be
schikbaar, welke verdienen door iedere vakgenoot te worden gelezen 26). Niet
alleen geven zij een uitwerking, die verder gaat dan gebruikelijk is in de Ameri
kaanse literatuur 27*), maar bovendien openbaren zij buitengewoon scherp de ver
onderstellingen, die aan de door De Wolff beschreven methode van steekproefs
gewijze controle ten grondslag liggen. Het is niet onze bedoeling van de statis
tische arbeid van De Wolff, welke in deze artikelen ligt besloten, een exposé te
geven; zulks zou ons opstel onnodig uitbreiden, aangezien een voortreffelijke
weergave van de voor de accountant essentiële grondslagen beschikbaar is in de
vorm van een artikel van de hand van H. Cohen 2S). Dit gedegen artikel bevat
voorts een toetsing van De Wolff’s statistische methode aan de grondslagen der
controleleer, waarvan wij het resultaat grosso modo onderschrijven. Vandaar dan
ook dat wij hier slechts de kern uit de steekproefmethode van De Wolff uiteen
zetten en voor het overige menen te kunnen volstaan met een verwijzing naar de
artikelen van De Wolff en Cohen 29).
De uitvoering van de steekproefmethode van De Wolff maakt de conclusie
mogelijk, dat het totale fraudebedrag (indien al fraude aanwezig is) kleiner is dan
een a priori toegelaten foutenfractie <pvan het totale bedrag der transacties. Indien
B de totale waarde van alle transacties aangeeft, dan duidt bij dit onderzoek
<p. B de bovengrens aan van het totale bedrag der niet ontdekte frauden. Er is een
zekere waarschijnlijkheid, dat de conclusie op grond van de uitvoering onjuist
2i) Evenzo Belle, die hieruit volkomen ten onrechte een argument tegen de leer van Limperg
putte (L. H . Belle, „Grondslagen der accountancy” , VGravenhage 1931, blz. 38 e.v.).
25) Het komt ons voor, dat de macro-economische beschouwingswijze van H. Mey, die berust
op een afweging door de gemeenschap van de offers der accountantscontrole en de waarde van
het vertrouwen een utopie is; voor een dergelijke numerieke afweging zijn vage indrukken te
enen male onvoldoende (H. Mey, t.a.p., blz. 53).
26) P. de Wolff, „Steekproeven bij administratieve controle” , Statistica Neerlandica 1956, blz. 35
e.v. en P. de Wolff, „Produktiviteitsverhoging bij accountantscontrole door toepassing van
gelaagde steekproeven” , Statistica Neerlandica 1959, blz. 215 e.v.
2I) Zie bijvoorbeeld L. L. Vance en J . Neter, „Statistical Sampling for Auditors and Accoun
tants” , New York - Londen 1956.
2S) H . Cohen, „Een ten behoeve van de administratieve controle ontworpen steekproefmethode” ,
M.A.B. 1958, blz. 2 e.v.
29)
Bij de bestudering van het artikel van Cohen moet men bij diens twijfel aan het bestaan
van wetmatigheden aangaande de gedaante der frequentiefunctie f(x) nog in aanmerking nemen,
dat de nadere onderzoekingen van De W olff (Statistica Neerlandica 1959, blz. 231) bepaald niet
zulk een wetmatigheid hebben bevestigd. Opmerkelijk is dit, dunkt ons, niet, aangezien men kan
verwachten dat de frequentie van verschillende grootten van betalingen van bedrijfstak tot
bedrijfstak en van bedrijfshuishouding tot bedrijfshuishouding door verschillen in structuur zal
uiteenlopen.
mab
blz. 147
is, welke eveneens a priori gekozen wordt. Dit is de waarschijnlijkheidsdrempel t.
Voorts moet aan een aanvaardingscriterium zijn voldaan, namelijk dat geen
enkele fraude in de steekproef wordt ontdekt. Wanneer zulks wel het geval i»>
wordt alsnog de gehele populatie gecontroleerd 30). In hoofdzaak 31) heeft De
Wolff het oog op gevallen gericht, waarin het zin heeft te hoge boekingen te ver
richten. Dit is denkbaar bij de boekingen van uitgaven in een kasboek; de teveel
geboekte bedragen kunnen door de kassier, eventueel in samenwerking met an
deren, worden ontvreemd. De Wolff’s methode onderscheidt transactiebedragen
boven een bepaalde grens, die volledig worden gecontroleerd en de overige, die
met een enkelvoudige of gelaagde steekproef32) worden onderzocht. De aan
merkelijke beperking van de controle, namelijk tot het verschijnsel van te hoge
boekingen en door uitsluitend boekingen boven een bepaald bedrag volledig te
controleren, bant het plagende Kleerekoper-probleem 33) uit, dit is het probleem
van het risico voor de accountant dat in de niet gecontroleerde administratieve han
delingen een geval van belangrijke fraude voorkomt. Het schijnt ons echter toe,
dat een dergelijke beperking van de doelstelling van het onderzoek althans in de
voortgezette periodieke controle niet aanvaardbaar is. Men behoeft bij onoorbare
praktijken niet alleen te denken aan ontvreemding van gelden, maar eveneens
en misschien vooral aan een misleidend beeld van de winst en kapitaal- en ver
mogenspositie.
Als voorbeeld diene, dat men tot een geflatteerd beeld van de winst in een
periode geraakt door de inkopen tot een te laag bedrag in de administratie op
te voeren, bijvoorbeeld om hiermede een toekomstig beroep op de vermogensmarkt
te doen slagen. Een integrale positieve detailcontrole kan ook die gevallen aan
het licht brengen, waarbij de bedragen van de inkoopfactuur te laag zijn geboekt;
De Wolff’s methode is hiertoe niet in staat, aangezien dit in strijd zou zijn met
de door hem gemaakte veronderstellingen. Toch is de controle noodzakelijk, d*t
de inkopen niet tegen een te laag bedrag in de inkoopadministratie zijn geregis
treerd. Immers, het middel van de verbandscontrole, dat de accountant met
betrekking tot de goederenbeweging hanteert, vermindert de mogelijkheid voor
de gecontroleerde de inkoopfacturen in het geheel niet over te leggen. Deze kan
dan nog door de bedragen van de inkoopfacturen te laag te boeken een verkeerd
beeld van het totale bedrag der inkopen geven, zonder dat zulks uit de verbands
controle met betrekking tot de goederenbeweging blijkt. N aast de negatieve con
trole op de inkopen, bestaande uit de toepassing van de verbandscontrole met de
uitgaande geldbeweging, vrachten, commissies, invoerrechten enz., vormt de in
tegrale positieve detailcontrole een middel ter vaststelling van deze misleiding
Uit dit voorbeeld blijkt nog eens, dat men zeer voorzichtig moet zijn met een
beperking van de doelstelling van het controleonderzoek op grond van een
meestal willekeurige begrenzing van onoorbaarheden, omdat dan mogelijkerwijze
30) De Wolff, Statistica Neerlandica 1959, blz. 217.
31) Aan het einde van zijn artikel in Statistica Neerlandica 1959 gaat De Wolff tot een ver
ruiming van de doelstelling van het onderzoek over, die echter de hierna volgende beschouwingen
niet aantast.
32) Deze laatste in Statistica Neerlandica 1959.
33) Deze uitdrukking is van H. Cohen in een bespreking van L. L. Vance en J. Neter, „Statistica!
Sampling for Auditors and Accountants” , M.A.B. 1957, blz. 258 e.v.; zie voor de uiteenzetting
van het probleem S. Kleerekoper, „De steekproeven als middel van accountantscontrole in de
literatuur” in „V ijf en twintig jaren maandblad. . . . ” , blz 565 (oorspronkelijk in M.A.B. 1933).
mab
blz. 148
bepaalde essentiële elementen niet in de controle worden opgenomen. De con
clusie hieruit is, dat de beperking van de doelstelling onzes inziens uit het gezichts
punt van de accountant niet aanvaardbaar is en dat men op deze wijze niet van
het Kleerekoper-probleem kan afraken.
De accountant, die de omvang van zijn arbeid laat bepalen door de verwach
tingen, die het maatschappelijk verkeer koestert, zal ook de introductie van de
grootheden y en s een huiveringwekkende gedachte vinden. Het niet-exacte cri
terium, dat de leer van het gewekte vertrouwen aanlegt, zal de beoordeling van
wat een doelmatige accountantscontrole aan vakarbeid eist, niet vergemakkelij
ken. Op de vraag welke verwachtingen belanghebbenden in het maatschappelijk
verkeer koesteren met betrekking tot de grootte van f en £, moet de accountant
het antwoord schuldig blijven. Maar bovendien is het uiterst twijfelachtig of de
verstandige leek zich bij het lezen van de accountantsverklaring rekenschap van
het bestaan van het vraagstuk van y e n t geeft, zodat men volstrekt niet van een
verwachting over de toelaatbare grootte van deze grootheden in het maatschap
pelijk verkeer kan spreken. Aangezien de accountant in een dergelijk geval het
Prinzip der Vorsicht als grondslag dient te nemen teneinde het vertrouwen dat
in hem wordt gesteld, niet te schokken, leidt dit ertoe dat hij wordt genoodzaakt,
de waarden van y en £ gelijk aan nul te stellen. Alleen op deze wijze komt een oor
deel van de accountant tot stand, dat geen verwachtingen bij de gebruikers van
zijn verklaring opwekt, die niet door zijn arbeid worden gedragen. Dan zal de
controle echter alle transacties omvatten, zodat men niet meer van een steekproef
kan spreken 34).
N a de hierboven gegeven beschouwing over de waarschijnlijkheidsdrempel is
het nuttig erop te wijzen, dat deze grootheid niet de enige is, die de waarschijn
lijkheid z of de degree of confirmation van de hypothese omtrent de foutenmarge
bepaalt, waarvoor £ is berekend. Zulks is al niet het geval, omdat de steekproef
die de accountant neemt, zich beperkt - met uitzondering van het onderzoek
naar de aanwezigheid der voorraden - tot de controle van de juiste administra
tieve verwerking van de documenten en dientengevolge geen informatie verstrekt,
of alle verschijnselen, welke zich in de bedrijfshuishouding hebben voorgedaan,
ook in de administratie zijn opgenomen. Afgezien nog van de voorgestelde be
perkingen van het onderzoek, is het ook om de volgende reden moeilijk, de invloed
van de waarschijnlijkheidsdrempel £ op de waarschijnlijkheid z van de hypothese
vast te stellen; de grootheid £ vormt slechts een deel van het gehele bewijsmate
riaal en wel uitsluitend het directe bewijsmateriaal ter bevestiging van h. Immers,
het bewijsmateriaal verzameld bijvoorbeeld ter bevestiging van de hypothesen
omtrent de verkopen en de voorraden zal door de verbandscontrole indirect van
betekenis zijn voor de bevestiging van de hypothese omtrent de inkopen. Bestaat
het bewijsmateriaal ter bevestiging van de hypothese omtrent de inkopen uit een
steekproef, dan is het bij de gegeven stand van de waarschijnlijkheidstheorie
onmogelijk, de waarde van dit bewijsmateriaal vast te stellen in verhouding tot
het indirecte bewijsmateriaal en de invloed hiervan op de waarschijnlijkheid z van
de hypothese omtrent de inkopen te bepalen.
Dit tot dusverre bestaande fundamentele gebrek in de logische grondslagen
der waarschijnlijkheidstheorie moet men mede in aanmerking nemen bij en als
diepere oorzaak zien van de reeds besproken moeilijkheden, die rijzen, wanneer
34) Cohen, t.a.p., blz. 5.
mab
blz. 149
de accountant zou trachten op grond van de leer van het gewekte vertrouwen een
toelaatbare grootte voor y en t te vinden. Deze factor veroorzaakt in samenhang
met de reeds genoemde, dat de accountant een weinig deugdelijke grondslag bezit
voor de toepassing van steekproeven.
Hoewel wij met de behandeling van de toepassing van de steekproef in de ac
countantscontrole zijpaden hebben betreden, menen wij toch dat deze zwerftocht
op grond van de twee volgende overwegingen gerechtvaardigd is. In de eerste
plaats vergroot de bespreking van de steekproef het inzicht in de problemen, die
rondom de vaststelling der waarschijnlijkheid rijzen. Vervolgens ondersteunt de
gegeven uiteenzetting het komende betoog inzake de volkomenheid der interne
controle, aangezien zij als conclusie heeft opgeleverd, dat de steekproef als in
strument in de voortgezette periodieke controle niet aanvaardbaar is. Zulks op
gronden die zich voordoen, ongeacht de volkomenheid of onvolkomenheid van de
interne controle.
De volkomenheid van de interne controle
In de discussie om de betekenis van de interne controle en de taak die hieruit voor
de accountant voortvloeit, is meermalen verdedigd, dat onder de premisse van
volkomen organisatie de accountant de positieve detailcontrole van de inkooptransacties achterwege kan laten 35*). Deze concrete aanwijzing hoe de accountant
zijn taak kan beperken, is door de verdedigers hiervan als voorbeeld van een
achterwege laten van positieve detailcontrole met de bescheiden bedoeld; meer
algemeen menen zij, dat de ontwikkeling van de interne controle veroorzaakt dat
de positieve controle aan de hand van de bescheiden op de achtergrond raak t30).
Ook wij zullen ons betoog aangaande de interne controle adstrueren aan de hand
van de controle van de inkopen, maar evenmin als bij de genoemde beroepsgeno
ten blijft bij ons de toepassing van de nog te ontwikkelen grondslagen met be
trekking tot de betekenis der interne controle beperkt tot de controle van de
ingaande goederenbeweging.
Teneinde de plaats van de interne controle in de organisatie van de bedrijfshuishouding en in de accountantscontrole te kunnen bepalen, is het noodzakelijk,
vanwege de onderling afwijkende meningen die hieromtrent bestaan, eerst het
begrip interne controle te definiëren. Onder interne controle verstaan wij alle
controle in de bedrijfshuishouding, ten dienste van de leiding3738), welke omschrij
ving A. Mey naar onze mening zeer treffend met de volgende woorden toelicht:
„H et impliceert dus alle automatisch werkende, uit de administratie vanzelf
ontstaande overeenstemmingen van data en cijfers, hetzij in het verband van
détailgegevens met corresponderende totalen, hetzij onderling in detailcijfers.
Tevens alle constatering van overeenstemmingen en alle vergelijkingen van
data en cijfers der verslaglegging onderling, als in toetsing aan justificatoire
bewijsstukken. Bovendien alle analysen en verklaring van verschillen bij
die vergelijkingen geconstateerd ofwel ontstaan bij de vergelijking van nor
matieve gegevens en werkelijke cijfers, zowel terzake van opbrengsten als
de kosten betreffende” 3S).
30) De Jong, t.a.p., blz. 25; Tempelaar, t.a.p., blz. 326; Dicphuis, „D e „eigen actie” . . . . ” , blz. 6;
Wisse, t.a.p., blz. 440.
3C) Diephuis, oratie, blz. 10 en 11.
37) Van Rietschoten, t.a.p., blz. 240 en A. Mey, t.a.p., blz. 101 c.v.
38j A. Mey, ibid., blz. 101.
mab
blz. 150
Het feit dat de interne controle een niet-verbijzonderde controle ten behoeve
van de leiding vormt, impliceert dat zij tot een onderdeel van de administratieve
organisatie is ontwikkeld. In een aantal gevallen is het ondenkbaar, dat de interne
controle voor een verbijzondering tot accountantscontrole in aanmerking kom t39).
Een voorbeeld hiervan is de uitsluiting van de bevoegdheid van één persoon in de
bedrijfshuishouding verbintenissen aan te gaan: slechts door de gezamenlijke han
deling van twee personen ontstaat deze bevoegdheid. Het element van controle
dat hierin is gelegen, is van nature en geheel afgezien van kostenoverwegingen
niet voor verbijzondering v atbaar40).
Thans gaan wij over naar de opvatting onder beroepsgenoten, dat de volkomen
heid of perfectie van de interne controle een reden vormt, de taak van de accoun
tant te beperken. Wanneer deze beroepsgenoten over volkomen of perfecte interne
controle spreken, bedoelen zij hiermede dat de interne controlemaatregelen van
zodanige aard en zodanige omvang zijn, dat de leiding zekerheid verkrijgt met
betrekking tot de juistheid van de verslaglegging omtrent de werkelijke gang van
zaken in de bedrijfshuishouding 41).
Het is duidelijk, dat als kanttekening bij de onderhavige opvatting de vraag
opkomt of de veronderstelling van volkomenheid der interne controle een aan
vaardbaar uitgangspunt vormt. Omdat de aanhangers van een beperking van de
taak uit hoofde van de volkomenheid der interne controle, de conclusie van hun
analyse als een norm voor de bepaling van de arbeid des accountants beschouwen,
is het een dwingende eis dat zij ook toetsen of de premisse in overeenstemming
met de werkelijkheid is. Het is bevreemdend, dat zij een zodanige confrontatie
niet verrichten en zij voetstoots aannemen dat er geen bezwaren zijn die de ver
werkelijking van de genoemde premisse in de weg staan. Het belang hiervan
noopt ons iets meer op dit probleem in te gaan. Ter verduidelijking van de voet
angels en klemmen die hier liggen, nemen wij een voorbeeld van interne controle
en wel de interne controle met betrekking tot de ingaande goederenbeweging.
De maatregelen van interne controle op dit onderdeel der goederenbeweging
betreffen de vaststelling van de hoeveelheid en de kwaliteit der goederen die zijn
ontvangen, het constateren van de overeenstemming van deze vaststelling met de
inkoopfactuur en evenzo het constateren van de overeenstemming met de bestel
ling die is verricht, de controle op de door de leverancier berekende prijs, het
narekenen van de inkoopfactuur enz. Hoe kan de accountant hier een beoordeling
omtrent de graad van volkomenheid der interne controle verkrijgen?
Omdat de accountantscontrole niet zover reikt dat de accountant de hande
lingen zelve van de functionarissen in de bedrijfshuishouding waarneemt, dus ook
niet de niet-verbijzonderde controlehandelingen, zal hij moeten volstaan met de
aantekeningen die omtrent de uitvoering van de interne controle in de administra
tie zijn gemaakt. Het constateren van overeenstemmingen, de prijscontrole en het
narekenen van facturen door functionarissen van de bedrijfshuishouding blijken
slechts uit bijvoorbeeld de parafen die zij in een blokstempel plaatsen, dat op de
inkoopfactuur is aangebracht. Deze parafen kan de accountant controleren en
verder kan hij ter beoordeling van de interne controle op de inkopen de aan
sluiting van de totalen van het goederenontvangstboek met die van het inkoop39) Uitvoerig hierover Van Rietschoten, t.a.p., blz. 241 e.v.
40) Van Rietschoten, ibid., blz. 241.
41) Zeer duidelijk is in dit opzicht Diephuis, „De „eigen actie” . . . . ” , blz. 3.
mab
blz. 151
boek, het voorraadboek en ook de rekening inkopen van het grootboek nagaan.
Ook kan hij geheel of steekproefsgewijze het werk van de interne controle, voor zo
ver mogelijk, herhalen. Een volledige uitvoering van alle genoemde werkzaam
heden ligt uiteraard niet in de bedoeling van de aanhangers van de beperking van
de taak van de accountant, omdat zulks niet een beperking maar een uitbreiding
van de werkzaamheden zou betekenen. De accountant zal dus in deze gedachten
gang minder doen dan wat hier boven als mogelijkheid ter beoordeling van de
interne controle is opgesomd.
Teneinde de voorstelling aangaande een beperkt werkprogramma te concreti
seren, veronderstellen wij, dat de waarnemingen ter controle van de inkopen
bestaan uit een onderzoek naar de juistheid van de tellingen en de totalen van de
genoemde boeken en de rekening inkopen en verder een steekproefsgewijze veri
ficatie van de parafen in het blokstempel op de inkoopfacturen. Bovendien een
steekproefsgewijze herhaling van de uitvoering van de maatregelen van interne
controle betreffende de inkopen, voor zover zulks in de macht van de accountant
ligt. Dit bewijsmateriaal (de grootheid q) heeft de volgende betekenis voor de
bevestiging van de gestelde hypothese omtrent de inkopen, bijvoorbeeld dat de
inkopen van goed a in kwaliteit b die in de periode c zijn ontvangen, gelijk zijn
aan x gulden.
Wanneer dit bewijsmateriaal q in elk opzicht de hypothese h bevestigt, namelijk
dat de inkopen van goed a in kwaliteit b die op datum c zijn ontvangen, gelijk
zijn aan x gulden, dan is deze hypothese de best mogelijke schatting, gegeven
deze q. De aldus gegeven schatting is een waarschijnlijkheidsoordeel. D at deze
hypothese ook werkelijkheidswaarde bezit, is hiermede niet gezegd.
Willen wij deze toetsen, dan dient de verificatie van de stelling te geschieden,
dat alle kennis die omtrent de feitelijke bedrijfsgang bekend is en die relevant is
voor de bepaling van de waarschijnlijkheid der hypothese, ook in de grootheid q
is opgenomen. De grootheid q behoeft niet juist het materiaal te bevatten, dat wij
hierboven hebben opgesomd; een gewijzigde samenstelling van de grootheid q
op grond van een ander werkprogramma, dienende ter beoordeling van de interne
controle, kan evenzeer voor een dergelijke toetsing in aanmerking komen. Ons
dunkt, dat geen diepgaand onderzoek noodzakelijk is om aan te tonen, dat iedere
grootheid q, afgeleid uit een werkprogramma dat de aantekeningen omtrent de
interne controle in de administratie steekproefsgewijze waarneemt, en de uit
voering van de maatregelen der interne controle eveneens steekproefsgewijze her
haalt, tal van elementen mist, die in de werkelijkheid van ongemeen grote beteke
nis zijn. Iedere accountant zal uit zijn beroepservaring weten, dat de volgende
overwegingen in elk algemeen controleonderzoek steeds bijzonder belangrijk zijn:
1. Een verandering in de organisatie vereist meermalen een wijziging in de interne
controlemaatregelen. Het is een ervaringsfeit, dat de leiding veelal onvoldoende
aandacht schenkt aan deze zijde van de administratieve organisatie. Weliswaar
ligt hier bij uitstek een taak voor de accountant, maar de dynamiek in de organi
satie veroorzaakt toch, dat het moeilijk is onder alle omstandigheden de passende
interne controle te waarborgen.
2. Het voldoen door functionarissen van de bedrijfshuishouding aan de formele
eisen, die betreffende de interne controle in de instructie zijn gesteld, houdt niet
in dat de interne controle ook werkelijk is uitgevoerd. Hoewel de parafen in het
blokstempel op de inkoopfactuur aanwezig zijn, kan toch de hand zijn gelicht met
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blz. 152
het constateren van overeenstemmingen, de prijscontrole, het narekenen van de
factuur enz. De oorzaken kunnen onachtzaamheid, ondeskundigheid of ook opzet
zijn. Indien de accountant ter controle van deze mogelijke gebreken de uitvoering
van de maatregelen van interne controle gedeeltelijk doubleert, ontstaat een toe
passing van de steekproef, die de bezwaren oproept die wij hiervoor hebben
genoemd. Weliswaar zal de accountant aan de hand van goed gekozen steek
proeven kunnen vaststellen dat een systeem van interne controle bestaat, maar
niet, dat over de gehele periode van onderzoek de interne controle overeenkomstig
de instructie integraal is toegepast.
Echter bezit de accountant zelfs niet steeds deze mogelijkheid van doublure van
de interne controle. Dit wordt duidelijk geïllustreerd door het hiervoor genoemde
voorbeeld, dat de interne controle de gezamenlijke handeling van twee personen
eist voor het doen ontstaan van de bevoegdheid verbintenissen af te sluiten. De
accountant kan wel het delegatieregister controleren, maar hiermede stelt hij niet
vast dat de vereiste werkwijze bij alle afgesloten verbintenissen ook is toegepast42).
3. De verhoudingen tussen uitvoering en leiding in de bedrijfshuishouding worden
grotendeels bepaald door het hiërarchische verband. Het kan niet uitgesloten
worden geacht, dat de leiding het gezag dat zij bezit, aanwendt om de materiële
inhoud van de interne controle teniet te doen 43). Dat zulks helaas meermalen
voorkomt, is alweer een ervaringsfeit waarmede iedere accountant in zijn prak
tijk wordt geconfronteerd. De toepassing van het instrument van de steekproeven
teneinde de opzettelijke verbreking der interne controle te ontdekken, biedt geen
uitweg, aangezien het Kleerekoper-probleem zich hier bij uitstek zal voordoen,
afgezien nog van de andere bezwaren en gesteld al dat een doublure van de interne
controle mogelijk is.
Wanneer wij deze overwegingen overzien, is het bijzonder duidelijk, dat het
beperkte werkprogramma slechts begrensde mogelijkheden bezit om de wellicht
niet altijd virulente, maar toch wel steeds latent aanwezige gebreken van de in
terne controle te elimineren. Indien de accountant met voldoende beleid, slag
vaardigheid en deskundigheid optreedt, zal de techniek der administratieve orga
nisatie hem in staat stellen het bezwaar, dat in het eerste punt genoemd is, te
overwinnen, maar deze kans van slagen ontbreekt te enen male ad 2. en 3.
Gaan wij na deze uitweiding betreffende de interne controle, terug naar de
grootheid q en de eis, dat alle kennis die relevant is voor de bepaling van de
waarschijnlijkheid der hypothese, in q moet worden opgenomen, dan is de con
clusie onontkoombaar dat wij aan deze eis in het boven uiteengezette werkpro
gramma van de accountant niet hebben voldaan.
Uit deze constatering volgt, dat voor de vorming van een juist oordeel omtrent
de hypothese met betrekking tot de inkopen, het onafwendbaar is de overwegin
gen sub 1., 2. en 3. in de grootheid q op te nemen. Hoewel iedere accountant
zal bevestigen, dat de gebreken van de interne controle in genoemde opzichten
meermalen aan het licht komen, is het nog heel iets anders dit ervaringsfeit in de
vorm van een waarschijnlijkheidsoordeel uit te drukken.
Daartoe zou immers naast de vervulling van andere voorwaarden nodig zijn,
dat de accountant een inzicht heeft in de relatieve frequenties, waarmede deze ge42) Van Rietschoten, ibid., blz. 241.
43) Van Rietschoten, t.a.p., blz. 250.
mab
blz. 153
breken optreden. Zelfs bij een werkprogramma, dat naar een doublure van de in
terne controle streeft, op de gebieden die hiervoor in aanmerking komen, zal de
accountant niet tot dit inzicht komen, omdat hij zoals uit de overwegingen sub 2.
en 3. blijkt slechts een beperkt waarnemingsveld heeft. Hij zal wel bij tijd en wijle
ontdekken dat hier gebreken liggen, maar hij kan door de aard van de technieken
die hij gebruikt niet een systematisch onderzoek naar de relatieve frequentie van
de gebreken instellen.
N aar ons oordeel is het de onbekendheid van de grootte der waarschijnlijkheid,
die de beweging ter beperking van de taak des accountants tot een betrekkelijk
sterke kracht maakt in de vorming van de beroepsopvattingen. Zou de waar
schijnlijkheid van de juistheid van het oordeel bij beperking van de taak wel cal
culeerbaar zijn en zou deze duidelijk lager liggen dan de waarschijnlijkheid die
zonder aantasting van de taak zou ontstaan, dan is er, dunkt ons, geen twijfel dat
de voorstanders van de beperking worden genoopt uiterst moeilijk verdedigbare
stellingen te betrekken. Elke verkleining van de waarschijnlijkheid van de juist
heid van het oordeel bergt immers het gevaar in zich van een vermindering van
de betekenis van het beroep ten gevolge van een mogelijk nadelige werking op
het vertrouwen.
Maar het feit van de onbekendheid met een deel van de bedrijfsgang, in casu
de integrale toepassing der interne controle, vormt geen deugdelijke overweging
het probleem dat hierin is gelegen dan maar te ecarteren. En dit is toch door de
voorstanders van een achterwege laten van de positieve detailcontrole met de
bescheiden gedaan, en wel met behulp van de premisse van de volkomen structuur
der interne controle. Het tekort in de kennis van de accountant, die hij zou dienen
te bezittten om de waarschijnlijkheden te berekenen, veroorzaakt, dat er geen
wetenschappelijke grondslag te vinden is voor de voorgestelde beperkingen in
de taak.
Voor een bevredigende wetenschappelijke grondslag ter oplossing van het
gestelde probleem zou immers aan een aantal voorwaarden dienen te worden
voldaan, namelijk een zodanige ontwikkeling van de theorie der logische waar
schijnlijkheid dat zij toegepast kan worden op concrete problemen, een exacte
meting van de verwachtingen die de spil zijn van de leer van het gewekte vertrou
wen, en zulk een verandering van de techniek der accountantscontrole, dat de ac
countant in staat is de bedrijfshandelingen zelve waar te nemen. Hoewel men niet
weet wat de toekomst in haar schoot verborgen houdt, ziet het er niet naar uit, dat
aan de eerste twee voorwaarden spoedig, zo ooit voldaan zal zijn. Het vervullen
van de laatste voorwaarde is zelfs uitgesloten, omdat dit in strijd zou zijn met de
bestaansgrond van de functie van de accountant, zoals wij hierboven hebben
betoogd.
Het is in dit verband aanbevelenswaardig een kort woord te wijden aan het
middel der budgettering en zijn betekenis voor de accountantscontrole. De voor
standers van de taakbeperking vertonen de neiging de controlemogelijkheden die
het budgetsysteem biedt te overschatten 4i). Men dreigt te vergeten, dat de be
groting een prognose is en niet een weergave van de werkelijkheid; zij kan naar
haar aard geen aanwijzing geven omtrent de omvang van de transacties, die in de
bedrijfshuishouding hebben plaatsgevonden.
De betrouwbaarheid van de bedrijfseconomische prognoses is meestal zo klein,
4‘1) Bijvoorbeeld in Diephuis, oratie, blz. 7 en 8.
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blz. 154
dat aan deze geen deugdelijke grondslag voor de controle op de uitvoering is te
ontlenen. Dit betekent niet, dat de begroting geen enkel belang heeft voor de
controle op de uitvoering. Wanneer namelijk de technische standaarden, die één
van de pijlers vormen van het systeem van begrotingen in de bedrijfshuishouding,
betrekkelijk geringe toleranties vertonen, is hieraan ex post een deugdelijke grond
slag voor de verbandscontrole als onderdeel van de accountantscontrole te ont
lenen. Deze controle betreft dan in het bijzonder de technische relaties in de
bedrijfshuishouding. Voor de vaststelling van de overige verschijnselen zal de
accountant behoefte hebben aan ander bewijsmateriaal. De bedrijfseconomische
normen, die in de begrotingen liggen besloten, hebben door de omvang van hun
toelaatbare afwijking voor de controle een zeer geringe betekenis, hetgeen overi
gens het belang van het budgetsysteem voor de taakbepaling, vaststelling van
verantwoordelijkheden en bedrijfseconomische analyse niet uitsluit.
De voorgaande uiteenzetting heeft als negatieve conclusie, dat een vertrouwen
van de accountant in de volkomenheid der interne controle te veel aan de zeker
heid doet ontbreken waarmede zijn oordeel tot stand komt. Dit impliceert alreeds,
dat een beperking van de controle door het achterwege laten van de positieve
detailcontrole met de externe bescheiden onwenselijk is.
Wij kunnen tot deze laatste gevolgtrekking ook op andere wijze komen, name
lijk door na te gaan hoe de uitkomst van de waarschijnlijkheid z wordt beïnvloed,
als wij in de grootheid q naast het bewijsmateriaal dat uit de verificatie van de
interne controle ontstaat, ook nog datgene opnemen dat uit de positieve detail
controle voortvloeit. De vraag is of deze uitbreiding van q kennis aan het bewijs
materiaal toevoegt, die relevant is voor de vaststelling van de waarschijnlijkheid
der hypothese h.
Voordat wij de waarschijnlijkheid van de hypothese omtrent de inkopen onder
zoeken, merken wij met nadruk op, dat de positieve detailcontrole met de be
scheiden niet alleen een verificatie van de ontvangen goederenhoeveelheden, maar
ook een verificatie van de inkoopbedragen inhoudt. Het is niet in te zien hoe de
controle van de inkoopprijs de positieve detailcontrole kan ontberen en met een
analyse van de prijsverschillenrekening kan volstaan. Het steunen door de ac
countant op de interne controle is hier al bijzonder zwak, omdat het middel van
de verbandscontrole slechts kan worden aangewend voor de samenhang met de
uitgaande geldbeweging en niet voor de samenhang met de goederenbeweging.
A. Mey heeft dit punt in zijn reeds genoemd opstel uitvoerig behandeld 45).
Wat draagt de positieve detailcontrole bij tot de vaststelling van de waarschijn
lijkheid van de hypothese, dat de inkopen van goed a in kwaliteit b die in de
periode c zijn ontvangen, gelijk zijn aan x gulden? Onjuistheden in het oordeel
van de accountant op grond van de positieve detailcontrole kunnen ontstaan,
afgezien van onvolkomenheid van zijn uitvoering, door falsificaties in de externe
bescheiden en door het feit, dat de leiding of uitvoering een gedeelte van de
externe stukken niet overlegt.
Hoewel het bewijsmateriaal q nu bestaat uit het resultaat van het hiervoor
besproken beperkte werkprogramma, uitgebreid met de integrale positieve detail
controle aan de hand van de externe stukken, sluit dit niettemin de vaststelling
van de waarschijnlijkheid der hypothese omtrent de inkopen uit. De aan de lezer
45) A. Mey, t.a.p., blz. 104 en 108.
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blz. 155
thans bekende oorzaken van dit euvel liggen in de onbekendheid van de relatieve
frequenties van de genoemde gebreken in de externe stukken en de gecompliceerde
samenstelling van het bewijsmateriaal. De relatieve frequenties van deze gebreken
zullen nochtans minder hoog zijn dan de relatieve frequentie, waarmede de door
breking der interne controle geschiedt, aangezien de vervalsing der externe stuk
ken moeilijker te verwezenlijken is. De waarschijnlijkheid der hypothese omtrent
de inkopen wordt hierdoor gunstig beïnvloed, waarin de grond ligt voor de toe
passing van de integrale positieve detailcontrole. Verder gaat het hanteren van
de positieve detailcontrole niet gepaard met het abandonneren van de werkzaam
heden van de accountant, die gericht zijn op de vaststelling van het bestaan van
een systeem van interne controle; het met de positieve detailcontrole uitgebreide
werkprogramma zal hierdoor een bredere basis voor het vellen van het waarschijnlijkheidsoordeel bieden dan het beperkte werkprogramma.
De gevolgtrekking kan als volgt luiden. De kennis die uit de positieve detail
controle voortvloeit, is bepaald relevant voor de bevestiging van de waarschijn
lijkheid en moet mitsdien in het bewijsmateriaal q worden opgenomen. Hoewel wij
de waarschijnlijkheid der hypothese h op grond van dit bewijsmateriaal niet exact
kunnen vaststellen, is een uitkomst voor de waarschijnlijkheid te verwachten die
dichter bij één ligt dan in het geval dat in het bewijsmateriaal de uitkomsten van
de positieve detailcontrole niet zijn opgenomen. Dit vloeit voort uit de beschreven
moeilijkheden die verbonden zijn aan een bewust onjuiste overlegging van be
scheiden door leiding en uitvoering, benevens uit het feit dat de accountant de
verificatie der interne controle bij positieve detailcontrole niet achterwege laat.
Conclusie
Uitgangspunt van onze uiteenzetting was, dat de accountant in zijn controle
onderzoek streeft naar een zo groot mogelijke waarschijnlijkheid van de juistheid
van zijn oordeel. Immers, de arbeid die hieruit voor de accountant ontstaat, buit
de vermogens der controletechniek zodanig uit, dat de verwachtingen die met
betrekking tot de verklaring van de accountant in het maatschappelijk verkeer
bestaan, niet worden teleurgesteld. De grondslag, waarop de leer van het gewekte
vertrouwen steunt, laat geen andere interpretatie toe.
Gebleken is, dat de theorie onmachtig is, de waarschijnlijkheid in een getal uit
te drukken, zodat het niet mogelijk is de effectiviteit van wisselingen in het werk
programma in een waarschijnlijkheidscoëfficient te determineren. Dit veroor
zaakt, dat het probleem van de omvang der controle moeilijk vatbaar is voor
een wetenschappelijke analyse, hetgeen de controverse hieromtrent slepende houdt.
Wel staat vast, dat de veronderstelling van de volkomen interne controle strij
dig met de werkelijkheid is, zodat een werkprogramma dat de positieve detail
controle op grond hiervan abandonneert niet aanvaardbaar is. Immers, door de
verwerping van de positieve detailcontrole ziet men van de verkrijging van kennis
af, die uitermate relevant is voor de bepaling van de waarschijnlijkheid. Hierdoor
verdwijnt de mogelijkheid tot een waarschijnlijkheid van een hypothese te komen,
die zo dicht mogelijk bij één ligt.
Wil het oordeel dat de accountant in zijn verklaring formuleert met betrekking
tot de verslaglegging van de bedrijfshuishouding met de grootst mogelijke waar
schijnlijkheid juist zijn, dan dient hij in het bijzonder de mogelijkheid van positieve
detailcontrole met externe bescheiden uit te buiten. De zekerheidsgraad die deze
m ab
blz. 156
waarneming oplevert is groter dan enige andere soort van waarneming met uit
zondering van de optische controle, en het is niet verantwoord deze mogelijkheid
te abandonneren. Wij hebben dit in het voorgaande aan de hand van een voorbeeld
betreffende de ingaande goederenbeweging laten zien. Dit was een comparatieve
analyse, die van de theorie der waarschijnlijkheid geen getallen verlangt.
Hiervoor is nodig, dat de accountant ter verificatie van de verschijnselen in de
bedrijfshuishouding de omvang en de aard van het bewijsmateriaal q zo samen
stelt, en de hypothesen zo kiest, dat naast de optische controle van de mogelijkheid
van positieve detailcontrole met externe bescheiden volledig gebruik wordt ge
maakt. Is dit eenmaal geschied, dan zal de verbandscontrole een zo hoog mogelijk
niveau van waarschijnlijkheid voor de gehele verslaglegging waarborgen 46).
46) N adat het onderhavige artikel was voltooid, verschenen twee bijdragen over steekproeven
in de accountantscontrole in dit tijdschrift, namelijk van de hand van A. Mey, „Retrospectieve
steekproeven in het controleprogramma van de public-accountant” in september 1961, blz. 317
e.v., en van A. van Heerden, „Steekproeven als middel van accountantscontrole” , in december
1961, blz. 453 e.v. De bezwaren, die A. Mey op blz. 320 en 321 aanvoert tegen de beperkte opzet
van De Wolff, ondersteunen ons bovenstaande betoog. De vergelijking, die de auteur trekt tussen
de methode van classificatie en de mathematische steekproef, lijkt ons van belang voor de verdere
discussie omtrent dit vraagstuk. Zodra de techniek van het afromen is gemetamorfoseerd in de
gelaagde steekproef met wiskundige grondslag, is een beter gefundeerd oordeel mogelijk aan
gaande de betekenis van deze techniek. Duidelijk blijkt ook uit Mey’s bespreking, dat een uit
breiding van de steekproeven boven de omvang waarover in het beroep eenstemmigheid heerst,
het gevaar doet ontstaan van een vermindering van de waarde van de accountantscontrole.
De guldenrangnummermethode van Van Heerden, die ontegenzeggelijk zeer elegant is en
daardoor de lust doet ontstaan haar in de controle toe te passen, vertoont de bezwaren, die wij
in het bovenstaande al in verband met de beschouwingen van De Wolff hebben besproken. Van
Heerden’s poging de omvang van de te verrichten steekproeven door een afweging van nut en
kosten te bepalen, is onzes inziens op grond van in het voorgaande ontwikkelde argumenten, vol
strekt onaanvaardbaar.
mab
blz. 157
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https://openalex.org/W2954161274
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https://figshare.com/articles/journal_contribution/Effectiveness_of_resistance_exercise_in_functional_fitness_in_women_with_primary_Sj_gren_s_syndrome_randomized_clinical_trial/8332640/1/files/15616460.pdf
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| null |
Effectiveness of resistance exercise in functional fitness in women with primary Sjögren’s syndrome: randomized clinical trial
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Scandinavian journal of rheumatology
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Consent Form You are being invited to participate in a research whose purpose is to improve fatigue in the individual with
Sjögren's Syndrome. Your participation is very important for performance of this research so we can improve our
knowledge about the treatment of this syndrome. In this study the patients will be divided randomly into 2 groups. One group will perform muscle
strengthening exercises; the other group will receive guidance on how to deal with the syndrome. The exercises will be
held at CEPE, Rue Marselhesa, 500, 9th floor, twice a week for one hour during 16 weeks. Patients who are randomized to the exercise group will perform an ergometric evaluation or Exercise
Electrocardiogram prior to the start of the program with a CEPE cardiologist, attesting to the volunteer's clinical
condition. The discomforts resulting from both the evaluations and the exercise program are mainly related to fatigue in
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Research Ethics Committee (RuaBotucatu, 572-1. 14, tel. 5571-1062). In this project the principal investigator is
Physical Educator Paulo Alexandre Minali. Compliance with Ethical Standards Compliance with Ethical Standards Consent Form Consent Form I, ________________________________________________________________,
declare to have been sufficiently informed about this research that seeks to improve fatigue in patients with primary
Sjögren's Syndrome. I discussed my decision to participate with the Physical Educator Professional and the purpose of
the study is clear, as well as its discomforts and risks, the assurance of medical care if there is any problem arising from
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https://www.frontiersin.org/articles/10.3389/fsurg.2021.704478/pdf
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Urgent Transcatheter Arterial Embolization for Wunderlich Syndrome With Hypovolemic Shock Secondary to Ruptured Renal Angiomyolipoma
|
Frontiers in surgery
| 2,021
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cc-by
| 5,771
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Urgent Transcatheter Arterial
Embolization for Wunderlich
Syndrome With Hypovolemic Shock
Secondary to Ruptured Renal
Angiomyolipoma
Maofeng Gong †, Zhengli Liu, Haobo Su, Boxiang Zhao, Jie Kong and Xu He*
Department of Vascular and Interventional Radiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China Department of Vascular and Interventional Radiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China Keywords: wunderlich syndrome, renal angiomyolipoma, arterial embolization, embolic materials, interventional
radiology ORIGINAL RESEARCH
published: 13 August 2021
doi: 10.3389/fsurg.2021.704478 †ORCID: †ORCID:
Maofeng Gong
orcid.org/0000-0002-4580-3232 †ORCID:
Maofeng Gong
orcid.org/0000-0002-4580-3232 Specialty section:
This article was submitted to
Vascular Surgery,
a section of the journal
Frontiers in Surgery Specialty section:
This article was submitted to
Vascular Surgery,
a section of the journal
Frontiers in Surgery
Received: 03 May 2021
Accepted: 06 July 2021
Published: 13 August 2021 Received: 03 May 2021
Accepted: 06 July 2021
Published: 13 August 2021 Purpose: Wunderlich syndrome (WS) with hypovolemic shock secondary to ruptured
renal angiomyolipoma (rAML) represents an urgent condition. Hence, we reported our
experience with transcatheter arterial embolization (TAE) using different embolic materials
under this condition. Edited by:
Konstantinos A. Filis,
National and Kapodistrian University
of Athens, Greece Reviewed by:
Georgios I. Karaolanis,
University Hospital of Ioannina, Greece
Chris Bakoyiannis,
Laiko General Hospital of
Athens, Greece Methods: This retrospective study consisted of 22 patients. Embolic materials including
particles, microcoils, and liquid embolic agents were selectively used based on the
decisions of interventional radiologists. Technical success was defined as the complete
occlusion of bleeding vessels on the final renal angiogram. Clinical success was defined
as the absence of re-hemorrhage needed for repeat endovascular or surgery treatment
after TAE. *Correspondence:
Xu He
hexunj@163.com Results: The articulated materials were used when WS presented without aneurysms; a
combination of particulate materials and microcoils or Glubran 2 alone were used for WS
with aneurysms. The technical success based on 24 episodes of TAEs in 22 patients
was 100% (24 of 24). Repeat TAE was achieved in two patients with hemorrhages
re-occurring two days after the initial embolization with microcoils alone. The clinical
success was 90.9% (20 of 22). No nontarget embolization or embolization-related
complications occurred during the TAE procedure. Of the patients, 27.3% (6 of 22)
experienced minor complications of post-embolization syndrome (PES). During a median
follow-up time of 34 months, no recurrent hemorrhage that required repeat endovascular
or surgical treatment for hemostasis occurred. Transcatheter Arterial Embolization
Procedure The embolic materials employed in the present study were
GSP (Alicon Pharm, Ltd., Hangzhou, China), PVA (Cook,
Bloomington, IN, USA), microspheres (Embosphere; Merit,
Rockland, MA, USA), microcoils (Cook, Bloomington, IN, USA),
or Glubran 2 R⃝(N-butyl-2 cyanoacrylate; GEM, Viareggio, Italy). The benefits and potential risks of TAE were explained to the
patients and/or their relatives, and detailed informed consent was
obtained from all patients. Patients presented with ruptured rAML are generally in
urgent conditions that require immediate treatment (2, 5). Historically, surgery was the first-line option. However, complete
or partial nephrectomy is now thought to be associated with
the risk of declining renal function and the loss of renal
parenchyma (6). In addition, nephron-sparing surgery is also
difficult to perform given the urgent condition and severe
tissue adhesion of hemorrhage (7). Therefore, selective nephron-
sparing transcatheter arterial embolization (TAE) is currently the
treatment of choice for rAML. It may avoid emergent radical
surgery (2, 5–7) and have prophylactic effects in preventing
future hemorrhage (8). p
The
choice
of
embolic
materials
was
proposed
by
interventional radiologists in our center. Two interventional
radiologists with 20-year experience performed all procedures. To identify and localize active bleeding sites and feeder arteries
of rAML, before embolization, an accurate overview angiogram
was performed under local anesthesia with a 5-French (F)
selective Simon catheter (Radifocus Angio-graphic Catheter;
Terumo, Leuven, Belgium) through a 5-F introducer (Radifocus
Introducer II Introducer Sheath; Terumo, Leuven, Belgium)
into the right femoral artery. After identifying the arterial tumor
feeders and bleeding site, a compatible 2.4-F microcatheter
(Progreat; Terumo, Leuven, Belgium) was then coaxially
positioned, ensuring that the microcatheter tip was as close as
possible to the target bleeding site. Under fluoroscopy control,
GSP, PVA, microspheres, or Glubran 2 R⃝was injected as slowly
as possible using thumb pressure and adjusted according to
embolic material propagation in the bleeding artery and target
arterial flow speed. If possible, it was continued until the feeding
bleeding vessels were completely occluded to avoid undesired
embolization of normal arterial branches and reduce infarcted
renal parenchyma loss as much as possible. For patients without
aneurysms, GSP, PVA, or microspheres were used solely. For
patients with aneurysms, GSP or PVA was used, followed by
microcoils according to the diameter of target vessel, to embolize
the feeder artery trunk. For patients who underwent failed
TAE with microcoils alone for pseudoaneurysms, rescue TAE
with microspheres was performed. Citation: Conclusion:
Urgent TAE with the selective use of different embolic materials is an
effective alternative to control WS with hypovolemic shock secondary to ruptured rAML. The condition of presenting with or without aneurysms may determine the embolic
materials employed. Gong M, Liu Z, Su H, Zhao B, Kong J
and He X (2021) Urgent Transcatheter
Arterial Embolization for Wunderlich
Syndrome With Hypovolemic Shock
Secondary to Ruptured Renal
Angiomyolipoma. Front. Surg. 8:704478. doi: 10.3389/fsurg.2021.704478 August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org Management of Ruptured Renal Angiomyolipoma Gong et al. INTRODUCTION used to identify the entity of the hemorrhage and eliminate
other underlying causes of WS. The diagnosis of WS with
hypovolemic shock secondary to ruptured AML was based on
clinical manifestations, decreased hemoglobin levels, and specific
radiologic characteristics on CT scan findings. Data collected
from the medical records included the control of hypovolemic
shock (technical success and clinical success), the varieties and
volumes of embolic material, complications, preintervention and
postintervention renal function, and AML size. Renal
angiomyolipoma
(rAML)
is
an
uncommon
hamartomatous neoplasm of the renal cortex. It consists of
tri-phasic tissue with fat, smooth muscle, and abnormal blood
vessels in varying proportions, and it usually occurs randomly or
in adjunctive with tuberous sclerosis (TSC) (1, 2). Despite being
benign, it can possibly grow larger over time, potentially leading
to various complications. Hemorrhage is a major complication
of rAML that can be severe or life threatening. It is found in
more than half of the patients (with tumors size >4 cm) (2, 3). Ruptured rAML may be the most common cause (accounting for
35–40%) of benign neoplasm for Wunderlich syndrome (WS),
which is a rare clinical condition classically characterized by the
Lenk’s triad (flank pain, flank mass, and hypovolemic shock)
(4, 5). Transcatheter Arterial Embolization
Procedure Glubran 2 was successfully
employed as a sole embolic material in patients under severe
coagulopathic condition [defined by an abnormal value for
prothrombin
time,
activated
partial
thromboplastin
time,
and/or a reduced platelet count (<50 × 109/L)]. At the end
of embolization, the microcatheter was withdrawn, and a final
renal angiogram through the 5-F Simon catheter was performed
to evaluate vessel occlusion. Patients with post-embolization
syndrome (PES), including aggravation of flank pain and
low-grade fever (37.6–37.9◦C), were given supportive treatment TAE for WS with hypovolemic shock secondary to ruptured
AML is perceived as a more formidable task because of the
usual urgency of the condition (7). Embolic materials used
mainly involved particles [such as gelatin sponge particles (GSP),
polyvinyl alcohols (PVA), microparticles, and microsphere],
coils, and liquid agents (such as ethanol, ethiodized oil, ethylene
vinyl alcohol copolymer, etc.) (2, 6–9). Each material has its
specific benefits and drawbacks, and there are no prospective
and comparative studies that establish strong recommendations
on which one to choose (9). In this paper, we present our
experience with TAE using different embolic materials, alone or
in combination, to treat WS with hypovolemic shock secondary
to ruptured rAML. Frontiers in Surgery | www.frontiersin.org Study Design This retrospective study was approved by both our institutional
review board and by the written consent of patients. This
study reviewed patients with WS secondary to rAML between
March 2012 and March 2020 at a single academic university
hospital, including 22 consecutive patients with hypovolemic
shock who subsequently experienced 24 episodes of TAEs. Of these, two patients received additional embolization with
microspheres in the second procedure. CT scans confirmed
that these patients had WS, and that their kidneys had lost
the normal morphological structure: the density of internal
rAML structures was heterogeneous, including multiple low-
density (fatty tissue) areas. A contrast-enhanced CT scan was Frontiers in Surgery | www.frontiersin.org August 2021 | Volume 8 | Article 704478 2 or Wunderlich syndrome (WS) with hypovolemic shock secondary to ruptured renal AML. RESULTS (tramadol injection for analgesia and ice bag for physical cooling
temperature) until the symptoms disappeared. The demographic, clinical characteristics, embolic materials
used, and outcome of the patients are shown in Table 1. The
study included 12 female and 10 male patients aged 37–90
years (mean, 56.3 ± 16.3 years). Two patients (9.1%) were
diagnosed with a TSC in other hospitals. All patients presented
with hypovolemic sock, accompanied with flank pain (81.8%)
and hematuria (59.1%). Study Design Whether
with Aneurysm
Embolization
Site
Sessions/
(Embolic materials)
GSP/PVA
Microcoils
Successb
Size (µm)
Numbers
Size
(mm)
Numbers
No
RUP
I/GSP
560–710
50 mg
-
-
Yes
No
LUP
I/GSP
560–710
100 mg
-
-
Yes
No
RMP
I/Microspheres
500–700
1 ml
-
-
Yes
Yes
LUP
I/Glubran 2
1:7
1.4 ml
-
-
Yes
Yes
LLP
I/(PVA+Microcoils)
350–560
40 mg
2*20,
2*30,
3*30
3
Yes
Yes
RLP
I/(PVA+Microcoils)
350–560
40 mg
2*20
3
Yes
Yes
LMP
I/(GSP+Microcoils)
700–900
30 mg
3*30,
4*30,
5*50
3
Yes
Yes
LUP
I/(PVA+Microcoils)
350–560
50 mg
2*30,
3*30,
4*20,
4*30
4
Yes
No
RMP
I/PVA
560–710
70 mg
-
-
Yes
Yes
LLP
I/Microcoils;
II/Microspheres
100–300
1 ml
2*20,
3*20
2
I No; II Yesc
Yes
RLP
I/Glubran 2
1:3
0.9 ml
-
-
Yes
No
RUP
I/GSP
560–710
40 mg
-
-
Yes
No
LLP
I/Microspheres
500–700
1 ml
-
-
Yes
Yes
LUP
I/Glubran 2
1:7
1.2 ml
-
-
Yes
No
RMP
I/GSP
560–710
100 mg
-
-
Yes
Yes
LUP
I/(PVA+Microcoils)
350–560
40 mg
2*20,
3*30,
3*30
3
Yes
Yes
LUP
I/Microcoils;
II/Microspheres
100–300
1.1 ml
2*30,
3*20
3
I No; II Yesc
Yes
LUP
I/(GSP+Microcoils)
700–900
20 mg
3*20,
4*30,
5*50
3
Yes
No
LUP
I/PVA
560–710
50 mg
-
-
Yes
Yes
RMP
I/(PVA+Microcoils)
350–560
60 mg
2*20,
3*20,
4*20,
4*30
4
Yes
Yes
RLP
I/(PVA+Microcoils)
350–560
30 mg
2*30
3
Yes
Yes
RLP
I/Glubran 2
1:3
0.8 ml
-
-
Yes
me; AML, angiomyolipoma; F, female; M, male; LUP, left upper pole; LLP, left lower pole; RUP, right upper pole; RMP, right middle pole; RLP, right lower pole; GSP, gelatin
orrhage recurrence 2 days after initial TAE. Technical success was achieved. The second clinical success was achieved. Management of Ruptured Renal Angiomyolipoma Gong et al. Definitions of Efficacy, Safety, and
Follow-Up The efficacy of TAE included both technical and clinical
evaluations. Technical efficacy was defined as the complete
occlusion of target bleeding vessels on the final renal angiogram,
while the clinical efficacy was defined as the absence of re-
hemorrhage needed for repeat endovascular or surgery treatment
after TAE (10). The safety of TAE was evaluated based on
complications that occurred mid-TAE, especially clinically or
technically adverse events mid-intervention. The renal function
was assessed by comparing serum creatinine (Scr) and blood urea
nitrogen (BUN) levels after one week of preintervention. One
week after treatment, renal function was retested and compared
with the function before TAE. During the follow-up, CT and/or
Doppler Ultrasound on the abdomen and clinical evaluations
were performed on an outpatient basis for all patients on the
first, third, and sixth months and at 6-month intervals thereafter
or sooner when clinically indicated. Any instances of recurrent
bleeding or post-TAE complications were recorded. Twenty-two patients received a total of 24 episodes of
TAEs. Of
these,
8
patients
(36.3%)
without
aneurysms
in
neoplasm
underwent
TAE
using
GSP
(560–710 µm),
microspheres (500–700 µm), and PVA (350–560 µm) alone. Eight
patients
(36.3%)
with
proven
aneurysm
formation
in neoplasm underwent median 40 mg initial PVA (350–
560 µm) or GSP (700–900 µm) embolization of bleeding
sites, and additional total 31 microcoils (range, 2–5 mm ×
20–50 mm) in the feeder artery trunk in a single session. Two
patients (9.1%) identified with pseudoaneurysms in AML
underwent microcoils (2 mm × 20 mm and 3 mm × 20 mm;
2 mm × 30 mm and 3 mm × 20 mm) embolization in feeder
trunk vessel alone; hematuria suddenly occurred two days
following TAE, accompanied with tachycardia and decreased
blood pressure, and disappeared after receiving rescue TAE
with microspheres (100–300 µm, Figure 1). Glubran 2 was
successful employed as a sole embolic material in 4 patients
(18.2%)
under
severe
coagulopathic
condition
(Figure 2),
the concentration ratios were 1:3 and 1:7, and total volume
injected
was
median
1.1 ml. Final
angiography
revealed
complete occlusion of all targeted vessels, and the technical
success of embolization was achieved in 100% of patients (22
of 22). Statistical Analyses (a) The left renal overview arteriography revealed a dysplastic and aneurysmal artery (white arrow); (b) Thumb pressure angiogram through the
microcatheter demonstrated rupture of the renal parenchyma and spilling of the contrast agent (white arrow); (c) The mixture of Glubran 2 and ethiodized oil
(concentration ratio 1:7) was injected as slowly as possible into the bleeding target arterial, cast filling dysplastic, and aneurysmal arteries (white arrow); (d) Completion
arteriography after TAE with Glubran 2 demonstrating AML devascularization and maximum preservation of the normal renal parenchyma. FIGURE 2 | A patient who encountered Wunderlich syndrome (WS) secondary to ruptured renal angiomyolipoma (rAML) underwent transcatheter arterial embolization
(TAE) using Glubran 2. (a) The left renal overview arteriography revealed a dysplastic and aneurysmal artery (white arrow); (b) Thumb pressure angiogram through the
microcatheter demonstrated rupture of the renal parenchyma and spilling of the contrast agent (white arrow); (c) The mixture of Glubran 2 and ethiodized oil
(concentration ratio 1:7) was injected as slowly as possible into the bleeding target arterial, cast filling dysplastic, and aneurysmal arteries (white arrow); (d) Completion
arteriography after TAE with Glubran 2 demonstrating AML devascularization and maximum preservation of the normal renal parenchyma. of flank pain and low-grade fever (37.6–37.9◦C). They received
conservative treatment for 3 days and recovered without
permanent complications. The amount of contrast material
and duration of fluoroscopy were 49.8 ± 11.8 ml (320 mg
I/ml; range, 30–70 ml) and 22.0 ± 5.0 min (range, 15–30 min),
respectively. There were no significant changes in Scr and
BUN levels pre-intervention and one week after embolization
(Figure 3) (P > 0.05). The renal function information was
assessed via the evaluated glomerular filtration rate (eGFR), and
mean levels before and one week after TAE were 83.2 ± 29.9
ml/min and 80.7 ± 31.5 ml/min, respectively, which was not a
significant difference (t = 0.5, 95% CI −6.6 to 11.5, P > 0.05). also experienced stable hemodynamic status and an increase in
blood pressure following TAE to 115.9 ± 11.3 mmHg (t = −13.1,
95% CI −41.1 to −29. 1, P < 0.001). Their anemia symptoms
improved after blood transfusion and TAE treatment. The clinical
success was achieved in 90.9% of patients (20 of 22). Twenty
patients were freed from re-hemorrhage after receiving TAE, and
repeat TAE with microspheres was achieved in two patients due
to hemorrhage re-occurring two days after initial embolization
with microcoils alone. Statistical Analyses SPSS statistical software package (version 23.0; SPSS statistical
software, Chicago, Illinois, USA) was used for all statistical
analyses. Continuous variables were expressed as the means
± standard deviation. Qualitative variables were presented
as percentages. When assessing the correlation between pre-
intervention and post-intervention variables, a paired t-test
was used. Findings with a P value < 0.05 were deemed
statistically significant. All patients in pre-intervention encountered hypovolemic
shock with mean systolic pressure 80.8 ± 9 mmHg. All patients FIGURE 1 | Collateral feeding arteries formed lead to clinical failure after embolization using microcoils alone. (a) Right renal arteriography reveals emerging collateral
feeding arteries (white arrow) arising from adjacent artery supply the distal portion of the initial bleeding artery; (b) The hemorrhage disappears following repeat
embolization with microspheres (100–300 µm). FIGURE 1 | Collateral feeding arteries formed lead to clinical failure after embolization using microcoils alone. (a) Right renal arteriography reveals emerging collateral
feeding arteries (white arrow) arising from adjacent artery supply the distal portion of the initial bleeding artery; (b) The hemorrhage disappears following repeat
embolization with microspheres (100–300 µm). August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org 4 Gong et al. Management of Ruptured Renal Angiomyolipoma GURE 2 | A patient who encountered Wunderlich syndrome (WS) secondary to ruptured renal angiomyolipoma (rAML) underwent transcatheter arterial embolization
AE) using Glubran 2. (a) The left renal overview arteriography revealed a dysplastic and aneurysmal artery (white arrow); (b) Thumb pressure angiogram through the
crocatheter demonstrated rupture of the renal parenchyma and spilling of the contrast agent (white arrow); (c) The mixture of Glubran 2 and ethiodized oil
oncentration ratio 1:7) was injected as slowly as possible into the bleeding target arterial, cast filling dysplastic, and aneurysmal arteries (white arrow); (d) Completion
teriography after TAE with Glubran 2 demonstrating AML devascularization and maximum preservation of the normal renal parenchyma. FIGURE 2 | A patient who encountered Wunderlich syndrome (WS) secondary to ruptured renal angiomyolipoma (rAML) underwent transcatheter arterial embolization
(TAE) using Glubran 2. Statistical Analyses WS with hypovolemic
shock secondary to AML are benign tumors with a ruptured
vascular component; thus, they behave like, and must be treated
as, part-bleeding site and part-aneurysm (8). Therefore, we
used particles to achieve hemorrhage stasis. Since the aneurysm
remains pressurized and at risk of rupture, coil placement was
the most efficient technique (13, 14); combination of occlusion
of the distal vascular bed with particles followed by microcoils
occlusion of the arterial inflow to prevent retrograde filling of the
aneurysm have been used in the present study. FIGURE 3 | The progression of renal function during a six-month follow-up
period. No significant changes in serum creatinine and urea nitrogen level
preintervention and postintervention during follow-up period (P > 0.05). FIGURE 3 | The progression of renal function during a six-month follow-up
period. No significant changes in serum creatinine and urea nitrogen level
preintervention and postintervention during follow-up period (P > 0.05). With a median of 34 months follow-up, neither hypovolemic
shock due to hemorrhage nor recurrent further ruptures of the
tumor were observed. Surgical treatment was avoided in all
patients, and renal function remained stable during the follow-
up period, with no significant change in Scr and BUN levels
noted in individual patients. The tumor size of the rAML was
observed using CT alone and CT adjunctive with ultrasound (US)
in 8 patients, showing that the mean maximum diameter of the
renal tumor on CT scan in the 22 patients reduced from 60.5 ±
12.7 mm to 45.8 ± 13.6 mm at the last follow-up visit, which was
significantly smaller (t = 7.77, 95% CI 10.4 to 18.8, P < 0.001,
Figure 4). The median duration of perirenal hemorrhage due to
WS was average 3 months (Figure 5). y
y
Glubran 2, a modified N-butyl-2 cyanoacrylate, seems to be
a potent alternative liquid embolic agent used for rAML to
stop hemorrhage. In our study, four patients with hypovolemic
shock WS secondary to rAML under coagulopathic condition
underwent successful hemostasis. Before TAE, in order to
improve presentation, Glubran 2 was thoroughly mixed with
ethiodized oil. Concentration ratios were 1:3 and 1:7, depending
on the arterial flow speed and the distance between the
microcatheter tip and the bleeding site. This material appears to
be a promising alternative under the condition of coagulopathy,
even though complete hemostasis is difficult to achieve. Statistical Analyses No
non-target
embolization
or
embolization-related
complications occurred during the TAE. Six patients (27.3%)
experienced minor complications of PES, including aggravation August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org 5 Management of Ruptured Renal Angiomyolipoma Gong et al. FIGURE 3 | The progression of renal function during a six-month follow-up
period. No significant changes in serum creatinine and urea nitrogen level
preintervention and postintervention during follow-up period (P > 0.05). subcapsular and/or perinephric spaces (3, 4). Literature showed
that 83% of cases presented with acute onset of flank pain, 19%
had hematuria, and 11% had symptoms and signs of hypovolemic
shock (11). The presence of all three symptoms is uncommon
(12). Enlarged rAML is at a high risk of rupture due to
abnormal elastin-poor tortuous vessels predisposed to aneurysm
formation causing WS, and heterogeneous proportion is often
altered on CT by hemorrhage within the lesion and perirenal
hemorrhage (2, 3, 11). Conservative treatment for WS may be
considered in hemodynamically stable patients; however, WS
within the context of hypovolemic shock may require an urgent
management strategy, for which there is no clear consensus in the
literature regarding the embolization technique and the choice
of embolic materials. Thus, we implemented the method of TAE
with different embolic materials under this condition. In a recent systematic review of WS, only 102 cases were
presented in 79 pieces of literature, which is insufficient for
studying the WS treatment (11). Although our study population
of 22 patients is not particularly big, we have shown that urgent
TAE has been effective for WS with hypovolemic shock secondary
to ruptured rAML. Patients who suffered from WS with
hemodynamic instability avoided further surgery after urgent
TAE, and the perirenal hemorrhage of WS could be absorbed
within three months during follow-up, without nephrectomy
or nephron-sparing surgery. The use of sole microcoils in TAE
for rAML has been debatable, as collaterals can potentially
form occlusion and make further embolization difficult when
hemorrhage re-occurrs (13, 14). In our study, two patients
required repeat embolization with microcoils as the only embolic
materials. Fortunately, rescue treatment was sucessful achieved
with small microspheres (100–300 µm). Although pulmonary or
renal dysfunction were reported in literatures (2, 15), whereas,
was not observed in the present study. Statistical Analyses Polymerization can occur immediately upon contact with blood,
leading to instant and complete vessel occlusion. Thus, Glubran 2
has advantages in coagulopathy due to its abilities of penetration
and the formation of an intravascular cast extending from the DISCUSSION WS, also known as spontaneous renal hemorrhage, was
first described by Wunderlich in 1,856 with a condition of
spontaneous renal hemorrhage with dissection of blood into the August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org 6 Gong et al. Management of Ruptured Renal Angiomyolipoma FIGURE 4 | The CT images of renal angiomyolipoma (rAML) size in preintervention and postintervention after transcatheter arterial embolization (TAE) (the same
patient as in Figure 2) were showed. An inhomogeneous endophytic renal mass with low-attenuating areas of intra-tumoral fat. (a–f) CT images obtained at pre-TAE,
and at follow-up period of 1 week, 1 month, 3 months, 6 months, and 12 months. A significant reduction in rAML size was depicted. FIGURE 4 | The CT images of renal angiomyolipoma (rAML) size in preintervention and postintervention after transcatheter arterial embolization (TAE) (the same
patient as in Figure 2) were showed. An inhomogeneous endophytic renal mass with low-attenuating areas of intra-tumoral fat. (a–f) CT images obtained at pre-TAE,
and at follow-up period of 1 week, 1 month, 3 months, 6 months, and 12 months. A significant reduction in rAML size was depicted. FIGURE 4 | The CT images of renal angiomyolipoma (rAML) size in preintervention and postintervention after transcatheter arterial embolization (TAE) (the same
patient as in Figure 2) were showed. An inhomogeneous endophytic renal mass with low-attenuating areas of intra-tumoral fat. (a–f) CT images obtained at pre-TAE,
and at follow-up period of 1 week, 1 month, 3 months, 6 months, and 12 months. A significant reduction in rAML size was depicted. FIGURE 5 | The CT findings of renal hemorrhage size owing to Wunderlich syndrome (WS) pre- and post-transcatheter arterial embolization (TAE) (the same patient
as in Figure 2) were listed. High-attenuating hemorrhagic areas were seen around the kidney. (a–f) CT image obtained at pre-TAE, and at follow-up period of 1 week,
1 month, 3 months, 6 months, and 12 months. A significant reduction in hemorrhage size was observed. FIGURE 5 | The CT findings of renal hemorrhage size owing to Wunderlich syndrome (WS) pre- and post-transcatheter arterial embolization (TAE) (the same patient
as in Figure 2) were listed. High-attenuating hemorrhagic areas were seen around the kidney. (a–f) CT image obtained at pre-TAE, and at follow-up period of 1 week,
1 month, 3 months, 6 months, and 12 months. A significant reduction in hemorrhage size was observed. DISCUSSION smaller, distal tumor vasculature to the proximal, larger blood
supply, along with its predictability and controllability (16). diameter of the tumor decreased to 45.8 ± 13.6 mm, which was
significantly smaller. Vessels on the tumor appeared to have
reduced in size disproportionally compared to the fat component,
which explains the variability in overall reduction of the AML smaller, distal tumor vasculature to the proximal, larger blood
supply, along with its predictability and controllability (16). In our study, the maximum diameter of AML before TAE was
60.5 ± 12.7 mm. With 34 months of follow-up, the maximum In our study, the maximum diameter of AML before TAE was
60.5 ± 12.7 mm. With 34 months of follow-up, the maximum August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org 7 Management of Ruptured Renal Angiomyolipoma Gong et al. sizes. The fat component appeared to be relatively insensitive
to embolization, whereas the vessel components responded well,
which indicated that the tumor shrinkage was mainly due to
the large reduction in vessel components and smooth muscle
atrophy (17). Because of the different proportions of blood
vessels, smooth muscles, and fat content in different tumors,
AML in our study were completely occluded. Therefore, the
size reduction correlated with the success of the procedure and
showed significantly reduced volume. sizes. The fat component appeared to be relatively insensitive
to embolization, whereas the vessel components responded well,
which indicated that the tumor shrinkage was mainly due to
the large reduction in vessel components and smooth muscle
atrophy (17). Because of the different proportions of blood
vessels, smooth muscles, and fat content in different tumors,
AML in our study were completely occluded. Therefore, the
size reduction correlated with the success of the procedure and
showed significantly reduced volume. In conclusion, urgent TAE with the selective use of
different embolic materials play an important role in controlling
the WS with hypovolemic shock secondary to ruptured
rAML. It causes little damage to renal function, results in
moderate complications, and reduces the need for immediate
radical surgery. We preferred particulate materials for WS
without aneurysms, a combination of particulate materials
and microcoils, or Glubran 2 alone for WS with aneurysms. Studies over a larger population are required to determine
these conclusions of WS with hypovolemic shock secondary to
ruptured rAML. DATA AVAILABILITY STATEMENT The original contributions presented in the study are included
in the article/supplementary material, further inquiries can be
directed to the corresponding author/s. ACKNOWLEDGMENTS We would like to thank Jie Sun, who is pursuing her Master of
Health Data Science at Harvard University, for her assistance of
English editing during the revision. DISCUSSION In terms of the safety of TAE with different embolic materials
for WS secondary to rAML, no complications occurred during
the mid-procedure related to TAE. PES, which is characterized
as the most frequent complication of embolization by fever and
flank pain, occurs in up to 36% of cases (18). In the present
study, 27.3% of patients experienced PES that presented as
aggravation of flank pain and low-grade fever, which were treated
conservatively; all the patients recovered without permanent
complications. It was demonstrated that AML would shrink
with liquefactive necrosis and tend to induce abscess formation
post-TAE (11). Additionally, there were no local infection
cases in our study with these modalities of embolization. The
preservation of renal function was a crucial factor in renal
embolization in this population given the benign nature of
the disease, the average age of diagnosis, and the emerging
body of evidence that has been associated with an improved
overall survival (7). In our study, renal function was not
affected. Therefore, we consider that TAE does not increase risk
of complications. AUTHOR CONTRIBUTIONS Previous studies on the treatment of WS are mostly anecdotal
case reports. To the best of our knowledge, our study may be
the sole study regarding embolization using different embolic
materials for the treatment of WS due to ruptured rAML. This may offer experience for future researchers. However,
our study had several limitations. First, it was performed
at a single center with a small patient pool. Second, no
comparative analysis in different embolic materials was made,
which could be an interesting issue. Third, cases in our study
were confirmed without the pathology before TAE due to an
emergent hypovolemic shock condition; whereas rAML was
clearly diagnosed by three senior radiologists based on typical
CT scan. MG contributed to project development, data collection,
manuscript writing/editing. ZL, HS, and BZ contributed
to
project
development,
data
collection,
data
analysis. BZ manuscript editing. JK and XH contributed to project
development. All authors contributed to the article and approved
the submitted version. ETHICS STATEMENT The studies involving human participants were reviewed and
approved by the institutional review board (IRB) of the Nanjing
First Hospital, Nanjing Medical University (Nanjing, China). The
patients/participants provided their written informed consent to
participate in this study. REFERENCES Angle JF, Siddiqi NH, Wallace MJ, Kundu S, Stokes L, Wojak JC, et al. Qua-lity
improvement guidelines for percutaneous transcatheter embolization: society
of interventional radiology standards of practice committee. J Vasc Interv
Radiol. (2010) 21:1479–86. doi: 10.1016/j.jvir.2010.06.014 18. Lenton J, Kessel D, Watkinson AF. Embolization of renal angiomyolipoma:
immediate complications and long-term outcomes. Clin Radiol. (2008)
63:864–70. doi: 10.1016/j.crad.2008.02.005 18. Lenton J, Kessel D, Watkinson AF. Embolization of renal angiomyolipoma:
immediate complications and long-term outcomes. Clin Radiol. (2008)
63:864–70. doi: 10.1016/j.crad.2008.02.005 j j
11. Murray TE, Doyle F, Lee M. Transarterial embolization of angiomyolipoma: a
systematic review. J Urol. (2015) 194:635–9. doi: 10.1016/j.juro.2015.04.081 11. Murray TE, Doyle F, Lee M. Transarterial embolization of angiomyolipoma: a
systematic review. J Urol. (2015) 194:635–9. doi: 10.1016/j.juro.2015.04.081 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. 12. Grubb SM, Stuart JI, Harper HM. Sudden onset flank pain: spontaneous renal
rup-ture. Am J Emerg Med. (2017) 35:e1–3. doi: 10.1016/j.ajem.2017.07.095 13. Lin L, Li X, Guan H, Wang J, Tong X, Yang M, et al. Renal function,
complica-tions, and outcomes of a reduction in tumor size after transarterial
embolization for renal angiomyolipomas: a meta-analysis. J Int Med Res. (2019) 47:1417–28. doi: 10.1177/0300060519834447 Publisher’s Note: All claims expressed in this article are solely those of the authors
and do not necessarily represent those of their affiliated organizations, or those of
the publisher, the editors and the reviewers. Any product that may be evaluated in
this article, or claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. 14. Patatas K, Robinson GJ, Ettles DF, Lakshminarayan R. Patterns of renal
angiomyo-lipoma regression post embolisation on medium- to long-term
follow-up. Br J Radi-ol. (2013) 86:20120633. doi: 10.1259/bjr.20120633 15. Lee F, Aaronson DS, Blaschko S, Barbosa P, Wu AK, Eisenberg M, et al. Selective arterial embolization of angiomyolipoma leading to pulm-onary
hypertension. Can J Urol. (2010) 17:5232–5. Copyright © 2021 Gong, Liu, Su, Zhao, Kong and He. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. REFERENCES 5. Yamakado
K,
Tanaka
N,
Nakagawa
T,
Kobayashi
S,
Yanagawa
M,
Takeda
K. Renal
angiomyolipoma:
relationships
between
tumor
size,
aneurysm
formation,
and
rupture. Radiology. (2002)
225:78–82. doi: 10.1148/radiol.2251011477 5. Yamakado
K,
Tanaka
N,
Nakagawa
T,
Kobayashi
S,
Yanagawa
M,
Takeda
K. Renal
angiomyolipoma:
relationships
between
tumor
size,
aneurysm
formation,
and
rupture. Radiology. (2002)
225:78–82. doi: 10.1148/radiol.2251011477 1. Oesterling
JE,
Fishman
EK,
Goldman
SM,
Marshall
FF. The
management
of
renal
angiomyolipoma. J
Urol. (1986)
135:1121–
4. doi: 10.1016/S0022-5347(17)46013-7 6. Northrup
H,
Krueger
DA. Tuberous
sclerosis
complex
diagnostic
criteria update: recommendations of the 2012 Iinternational Tuberous
Sclerosis
Complex
Consens-us
Conference. Pediatr
Neurol. (2013)
49:243–54. doi: 10.1016/j.pediatrneurol.2013.08.001 2. Duan XH, Zhang MF, Ren JZ, Han XW, Chen PF, Zhang K, et al. Urgent
trans-catheter arterial embolization for the treatment of ruptured renal
angiomyolipoma with spontaneous hemorrhage. Acta Radiol. (2016) 57:1360–
5. doi: 10.1177/0284185115588125 2. Duan XH, Zhang MF, Ren JZ, Han XW, Chen PF, Zhang K, et al. Urgent
trans-catheter arterial embolization for the treatment of ruptured renal
angiomyolipoma with spontaneous hemorrhage. Acta Radiol. (2016) 57:1360–
5. doi: 10.1177/0284185115588125 7. Jou YC, Chen WP, Huang CL. Urgent angioembolization with early elective
nephr-on-sparing surgery for spontaneously ruptured renal angiomyolipoma. J Chin Med Assoc. (2009) 72:450–2. doi: 10.1016/S1726-4901(09)70405-8 3. Katabathina VS, Katre R, Prasad SR, Surabhi VR, Shanbhogue AK, Sunnapwar
A. Wunderlich syndrome: cross-sectional imaging review. J Comput Assist
Tomogr. (2011) 35:425–33. doi: 10.1097/RCT.0b013e3182203c5e 3. Katabathina VS, Katre R, Prasad SR, Surabhi VR, Shanbhogue AK, Sunnapwar
A. Wunderlich syndrome: cross-sectional imaging review. J Comput Assist
Tomogr. (2011) 35:425–33. doi: 10.1097/RCT.0b013e3182203c5e 8. Hocquelet A, Cornelis F, Le Bras Y, Meyer M, Tricaud E, Lasserre AS, et al. Long-term results of preventive embolization of renal angio-myolipomas:
evaluation of predictive factors of volume decrease. Eur Radiol. (2014)
24:1785–93. doi: 10.1007/s00330-014-3244-4 4. Albi G. del Campo L, Tagarro D. Wunderlich’s syndrome: causes,
diagnosis and radiological management. Clin Radiol. (2002) 57:840–
5. doi: 10.1053/crad.2002.0981 August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org 8 Management of Ruptured Renal Angiomyolipoma Gong et al. 9. Kiefer RM, Stavropoulos SW. The role of interventional radiology techniques
in the management of renal angiomyolipomas. Curr Urol Rep. (2017)
18:36. doi: 10.1007/s11934-017-0687-6 17. Kato H, Kuwatsuru R, Inoue T, Okada S, Aida M, Yamashiro Y. Superselective transcatheter arterial embolization for large unruptured renal
angiomyolipoma in lymphangioleiomyomatosis. J Vasc Interv Radiol. (2018)
29:958–65. doi: 10.1016/j.jvir.2017.11.003 10. Frontiers in Surgery | www.frontiersin.org August 2021 | Volume 8 | Article 704478 REFERENCES No use, distribution or reproduction is permitted which does not comply with these
terms. 16. Sugawara
S,
Arai
Y,
Sone
M,
Ishiguchi
T,
Kitagawa
A,
Aramaki
T, et al. Phase II trial of trans-arterial embolization using an n-
Butyl-2-Cyanoacrylate/Lipiodol
mixture
(JIVROSG-0802). Cardiovasc
Intervent
Radiol. (2019)
42:534–41. doi:
10.1007/s00270-018-
2141-7 August 2021 | Volume 8 | Article 704478 Frontiers in Surgery | www.frontiersin.org 9
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https://openalex.org/W3154946920
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https://www.frontiersin.org/articles/10.3389/fcvm.2021.574360/pdf
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English
| null |
Chronic Thromboembolic Pulmonary Hypertension – What Have We Learned From Large Animal Models
|
Frontiers in cardiovascular medicine
| 2,021
|
cc-by
| 12,519
|
Edited by:
Nicola Montano,
University of Milan, Italy
Reviewed by:
Gaetano Ruocco,
Regina Montis Regalis Hospital, Italy
Abraham Rothman,
Children’s Heart Center Nevada,
United States Edited by:
Nicola Montano,
University of Milan, Italy *Correspondence:
Daphne Merkus
daphne.merkus@
med.uni-muenchen.de;
d.merkus@erasmusmc.nl *Correspondence:
Daphne Merkus
daphne.merkus@
med.uni-muenchen.de;
d.merkus@erasmusmc.nl Keywords: CTEPH, pulmonary hypertension, pulmonary vasculature, vascular resistence, large animal models,
swine models, arrhythmogenesis, cardiac remodeling Specialty section:
This article was submitted to
General Cardiovascular Medicine,
a section of the journal
Frontiers in Cardiovascular Medicine Kelly Stam 1, Sebastian Clauss 2,3,4, Yannick J. H. J. Taverne 5 and Daphne Merkus 1,3,4* 1 Department of Cardiology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands, 2 Department of
Medicine I, University Hospital Munich, Ludwig-Maximilians University Munich, Munich, Germany, 3 Institute of Surgical
Research at the Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Munich, Germany,
4 DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Munich Heart Alliance, Munich, Germany,
5 Department of Cardiothoracic Surgery, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands Chronic thrombo-embolic pulmonary hypertension (CTEPH) develops in a subset of
patients after acute pulmonary embolism. In CTEPH, pulmonary vascular resistance,
which is initially elevated due to the obstructions in the larger pulmonary arteries, is further
increased by pulmonary microvascular remodeling. The increased afterload of the right
ventricle (RV) leads to RV dilation and hypertrophy. This RV remodeling predisposes to
arrhythmogenesis and RV failure. Yet, mechanisms involved in pulmonary microvascular
remodeling, processes underlying the RV structural and functional adaptability in CTEPH
as well as determinants of the susceptibility to arrhythmias such as atrial fibrillation in the
context of CTEPH remain incompletely understood. Several large animal models with
critical clinical features of human CTEPH and subsequent RV remodeling have relatively
recently been developed in swine, sheep, and dogs. In this review we will discuss the
current knowledge on the processes underlying development and progression of CTEPH,
and on how animal models can help enlarge understanding of these processes. REVIEW
published: 16 April 2021
doi: 10.3389/fcvm.2021.574360 published: 16 April 2021
doi: 10.3389/fcvm.2021.574360 Keywords: CTEPH, pulmonary hypertension, pulmonary vasculature, vascular resistence, large animal models,
swine models, arrhythmogenesis, cardiac remodeling INTRODUCTION Chronic thrombo-embolic pulmonary hypertension (CTEPH) develops in a some patients after
acute pulmonary embolism (1, 2). In CTEPH, pulmonary vascular resistance, initially increases
due to the obstructions in the larger pulmonary arteries but is further elevated by pulmonary
microvascular remodeling (1–3). CTEPH is defined as a mean pulmonary artery pressure ≥25
mmHg at rest persisting for at least 6 weeks in patients with previous pulmonary artery embolism
(4). In addition to the increase in pressure, flow is redistributed toward the unobstructed parts of
the pulmonary vasculature, causing local alterations in shear stress. Altered shear stress combined
with systemic risk factors contribute to pathological processes like endothelial dysfunction,
inflammation, vasoconstriction, and impaired vasodilation (5). In addition, these processes
promote structural remodeling of both the obstructed and unobstructed pulmonary vasculature
(6, 7). This remodeling leads to increased pulmonary vascular resistance that in turn augments
afterload of the right ventricle (RV), thereby resulting in RV dilation and RV hypertrophy. Received: 19 June 2020
Accepted: 08 March 2021
Published: 16 April 2021 Chronic Thromboembolic Pulmonary
Hypertension – What Have We
Learned From Large Animal Models Kelly Stam 1, Sebastian Clauss 2,3,4, Yannick J. H. J. Taverne 5 and Daphne Merkus 1,3,4* LARGE ANIMAL MODELS OF CTEPH Over the past decades, the pathophysiology of CTEPH has been
studied in large animal models. Different embolization protocols
and materials including air, autologous blood clots, Sephadex
beads, and glue have been utilized in swine, sheep and dogs
(Table 1). Measurements in these models include measurement
of PAP, with either indwelling (chronic), or Swan Ganz catheters. Cardiac output and stroke volume was measured using either
the Swan Ganz catheter, a chronically implanted flow probe
or via echo, CMR or PV loop catheter (Tables 1, 2). The PV
loop catheter also allows measurement of right ventricular-
pulmonary arterial (RV-PA) coupling, a measure of how well
the right ventricle can cope with the increased afterload. In
the absence of a PV-loop catheter, RV-PA coupling can also be
assessed using the single beat method (59). Pulmonary embolism results in an acute increase in pulmonary
vascular resistance and a decrease in pulmonary vascular
compliance, both of which contribute to an increase in RV
afterload. CTEPH is defined as a persistent pulmonary artery
pressure (PAP) above 25 mmHg, with a pulmonary wedge
pressure below 15 mmHg, at rest for at least 3 months,
despite therapeutic anticoagulation in order to discriminate this
condition from “subacute” PE (4, 13–16). It is increasingly
recognized that patients that fail to meet the PH cut-offvalue of
25 mmHg, yet have complaints similar to CTEPH patients, may
have a milder form of the disease, so-called chronic thrombo-
embolic disease (CTED) (3, 8, 17, 18). Indeed, PAP above 19
mmHg at rest following embolism are already associated with
increased mortality at long term (15, 19). Mismatched perfusion
defects on a ventilation/perfusion scan and specific diagnostic
signs for CTEPH seen by multidetector CT angiography, MR
imaging or conventional pulmonary cineangiography, such as
ring-like stenoses, webs/slits and chronic total occlusions are
imaging hallmarks for CTEPH. Very few investigators succeeded in establishing CTEPH
during prolonged follow-up although the PAP increases acutely
upon embolization (51). Ideally, autologous thrombi should be to
induce CTEPH, in order to mimic the contribution of potential
factors released from and cells interacting with these thrombi. However, studies with autologous thrombi to induce CTEPH
have generally failed, which has initially been ascribed to a more
active fibrinolytic system in animals as compared to humans
(3, 60). Plasminogen activator inbibitor-1 was upregulated in
the endothelial cells lining the thrombus in humans (60). Citation: Stam K, Clauss S, Taverne YJHJ and
Merkus D (2021) Chronic
Thromboembolic Pulmonary
Hypertension – What Have We
Learned From Large Animal Models. Front. Cardiovasc. Med. 8:574360. doi: 10.3389/fcvm.2021.574360 April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 1 Large Animal Models of CTEPH Stam et al. The symptoms of CTEPH are similar to those of other
forms of PH, being shortness of breath, fatigue, syncope,
chest
pain,
palpitations,
and
reduced
exercise
capacity,
which
(together
with
unawareness
in
many
physicians’
daily practice) contribute to the late diagnosis in a large
number
of
patients. This
delayed
diagnosis
negatively
impacts the prognosis (30). Treatment options for CTEPH
are
limited
and,
even
when
treated,
the
disease
often
advances to right heart failure and even death. Proximal
obstructions can be removed with surgical interventions
such as pulmonary endarterectomy or balloon angioplasty
(31–33) although these can only be performed in eligible
patients. Therapeutic agents to modulate the pulmonary
vascular resistance are limited to date. Riociguat, which is a
soluble guanylyl cyclase stimulator, that activates the nitric
oxide (NO) pathway without endogenous NO, thus acting
as a vasodilator, inhibiting pulmonary smooth muscle cell
growth and antagonizes platelet inhibition (i.e., preventing clot
formation) is the only approved therapeutic agent in CTEPH to
date (15, 31, 34–36). The degree of RV structural remodeling and functional
adaptability
have
been
demonstrated
to
be
important
determinants of functional capacity and survival in patients
with CTEPH (8–10). In addition to RV remodeling, CTEPH is
a risk factor for development of arrhythmias, especially atrial
fibrillation (AF), which adds to the morbidity and mortality of
patients with CTEPH (11, 12). Yet, mechanisms involved in pulmonary microvascular
remodeling,
processes
underlying
the
RV
structural
and
functional adaptability in CTEPH as well as determinants of
the susceptibility to arrhythmias such as AF in the context of
CTEPH remain incompletely understood. Gathering knowledge
about these processes has proven notoriously difficult, at least in
part because (large) animal models with critical clinical features
of human CTEPH and subsequent RV remodeling have only
been developed relatively recently. In this review we will discuss
current knowledge on the processes underlying development
and progression of CTEPH, and on how porcine, canine and
ovine models can help enlarge understanding of these processes. Frontiers in Cardiovascular Medicine | www.frontiersin.org LARGE ANIMAL MODELS OF CTEPH Furthermore, a prothrombotic milieu, evidenced by elevated
levels of von Willebrand Factor and C-reactive protein is
associated with CTEPH in humans (60) and CTEPH severity and
prognosis correlate with circulating D-dimer levels (61). These
conditions are generally difficult to mimic in animal models. Nevertheless, inhibition of the fibrinolytic system in animals with
tranexamic acid did not result in successful establishment of
CTEPH in dogs (40). This failure to maintain high PAP during
follow-up suggests that many models resemble CTED (i.e., mean The prevalence of CTEPH is still largely unknown. CTEPH
develops in about 3–4% of patients after acute pulmonary
embolism and in up to 10% of patients with recurrent pulmonary
embolism (3, 20–22). The reported annual incidence of acute
pulmonary embolism ranges from 750 to 2,700 per million adults
(23–25). According to these numbers, the expected incidence of
CTEPH would be 22.5–108 per million adults, while the reported
numbers of diagnosed patients with CTEPH are substantially
smaller. Three countries assessed the CTEPH incidence through
nationwide registries. In the United Kingdom the CTEPH
incidence was 1.75 per million (26), in Spain it was 0.9 per
million adults (12) and in Germany it was 5.7 per million adults
(27). Between ∼300 and 400 patients were newly diagnosed with
CTEPH per year in France and Germany (28, 29). April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org Frontiers in Cardiovascular Medicine | www.frontiersin.org 2 olization techniques to create CTEPH/CTED, adapted from (37). LARGE ANIMAL MODELS OF CTEPH Large Animal Models of CTEPH Stam et al. TABLE 2 | Overview of RV-functional measurements in CTEPH/CTED models. Reference
RV function
assessment
Group
EDA or EDV
ESA or ESV
FAC or EF (%)
TAPSE (mm)
Ees/Ea
Fulton Index
Guihaire et al. (49)
Echo,
PV-loop
Sham
4.6 ± 0.6 cm2/m2a
NR
51 ± 8a
20 ± 2a
1.24 ± 0.17c
NR
CTEPH
11.0 ± 2.4 cm2/m2a
NR
25 ± 4a
14 ± 4a
0.66 ± 0.18c
NR
Aguero et al. (51)
3D-Echo
Sham
101.7 ± 4.5 mla
30.5 ± 2.9 mla
70.0 ± 2.7a
24.5 ± 2.4a
NR
0.40 ± 0.03
Embolisation
76.2 ± 14.1 mla
23.3 ± 4.1 mla
68.8 ± 7.0a
21.6 ± 2.9a
NR
0.41 ± 0.02
Embolisaiton
+ coil
104.4 ± 21.0 mla
43.3 ± 10.7 mla
58.8 ± 3.7a
18.8 ± 2.4a
NR
0.47 ± 0.06
Noly et al. (52)
Echo,
PV-loop
Sham
5.2 ± 0.2 cm2/m2a
NR
46 ± 2a
NR
1.39 ± 0.27c
NR
CTEPH
9.7 ± 0.6 cm2/m2a
NR
26 ± 1a
NR
0.71 ± 0.15c
Stam et al. (37)
Echo
Sham
554 ± 92 mm2a
207 ± 54 mm2a
54 ± 3a
24 ± 1a
NR
NR
CTEPH
714 ± 83 mm2a
304 ± 69 mm2a
43 ± 4a
20 ± 2a
NR
NR
Stam et al. (55)
CMR
Sham
1.89 ± 0.25 ml/kgb
0.78 ± 0.12 ml/kgb
59 ± 2b
NR
2.35 ± 0.23c
0.40 ± 0.03
CTEPH
2.31 ± 0.31 ml/kgb
1.24 ± 0.27 ml/kgb
48 ± 5b
NR
1.80 ± 0.15c
0.51 ± 0.03
Mulchrone et al. (57)
Echo, CMR
Sham
2.73 ± 0.06 ml/kgb
1.41 ± 0.07 ml/kgb
48 ± 5a
15 ± 1a
NR
NR
CTEPH
2.98 ± 0.02 ml/kgb
2.05 ± 0.06 ml/kgb
32 ± 5a
8.5 ± 1a
NR
NR
Loisel et al. (58)
Echo,
PV-loop
Sham
NR
NR
43.5 [33.8–45.4]a
21 [19.5–21]a
1.03 [0.92–1.05]c
NR
CTEPH
NR
NR
32.8 [29.5–36.5]a
15.5 [13.8–17.3]a
0.69 [0.56–0.83]c
NR
ameasured by echo; bmeasured by CMR; cmeasured by PV-loop; Ees/Ea, indexof RV-PA coupling; FAC, fractional area change; EF, ejection fraction; TAPSE, tricuspid annular plane
systolic excursion (mm); NR, not reported. TABLE 2 | Overview of RV-functional measurements in CTEPH/CTED models. PAP between 20 and 25 mmHg) more than CTEPH (mean PAP
≥25 mmHg). used in embolization experiments, would result in a pulmonary
vasculature that is ∼0.5 log order, or 3-fold, smaller than that
of humans. LARGE ANIMAL MODELS OF CTEPH The porcine pulmonary vasculature showed 10
branching orders of vessels larger than 160 µm in swine (67). The
number of 3rd order pulmonary small arteries (diameter 430 µm,
range 380–570 µ) was estimated to be 2,100, while 590 4th order
vessels (diameter 760 µm, range 660–990 µm) were estimated to
be present (67). These numbers exclude supernumerary vessels,
which are 1.6- (68) to 2.8-fold (69) more than conventional
arteries. Taking into account these supernumerary vessels, a total
of 5,460–7,980 arteries of order 3, and 1,530–2,240 arteries of
order 4 are present in the porcine lung. It should be noted however, that PAP is mostly assessed
under general anesthesia, which due to its cardiodepressive
effects, may have resulted in an underestimation of PAP. Prerequisites for successful induction of CTEPH appear to
include repeated embolization procedures (37, 38, 43, 45–
50, 54, 56, 57) and obstruction of at least 40–60% of the
pulmonary vasculature (62, 63). In these studies, pulmonary
artery pressure and pulmonary vascular resistance decreased
in between embolization procedures, but showed a slow but
progressive increase over time and remained elevated after
cessation of the embolisations. Obstruction of a large part of
the pulmonary vasculature has been performed in swine, by
combined ligation of the left pulmonary artery and progressive
embolization of the segmental arteries of the right lower lobe,
to mimic the proximal obstructions induced by thrombo-
emboli (47–50, 64). An alternative method is to use smaller
(micro)spheres to obstruct the pulmonary vasculature. The
relative amount of obstruction of the pulmonary vasculature can
be estimated by comparing the amount of microspheres infused
with the number of vascular branches of this size present in
the pulmonary vascular bed. The latter can be estimated from
the morphometrical description of the pulmonary vasculature,
which, in humans contains 15 Strahler orders, from the capillaries
to the main pulmonary artery (65). It has been proposed that the
pulmonary vascular bed of dogs (10 kg) and rats (500 g) are 1 and
3 log orders smaller than those of humans (66). Extrapolation
of these numbers to swine of 20 kg, the size most commonly In the porcine studies from our laboratory, CTEPH was
induced with multiple (up to 5) embolizations using an average of
9,000 microspheres of 600–710 µm in diameter per embolization
procedure, hence 45,000 microspheres in total (37, 55, 56). LARGE ANIMAL MODELS OF CTEPH material
Embolizations
(N)
N
PAP & CO
assessment
Anesthesia
during RHC
Recovery
period
PAP
(mmHg)
PVR (WU)
RVW/LVW
+ SW
V/Q scan/
angiography
x G50
Variable (16–30
weeks)
5
Catheter via
jugular; dye
dilution
None
>7 days
29 ± 4
8.3 ± 2.3
0.54e
NR
nuous)
12 days
5
Indwelling
catheters +
SG
None
1.5 h
23f ± 2
5.2f
0.38 ± 0.06
Perfusion
defects
us thrombi +
mic acid
2
10
SG
Halothane
32 days
20.3 ± 2
4.2a
NR
NR
x G50 (15 mg/kg)
3
8
SG
Ketamine
7 days
18 ± 3
4.3a,b
NR
NR
beads (3 mm)
4
5
SG
Halothane
6 months
17 ± 2
4.3a
NR
Perfusion
defects
nuous)
8 weeks
4
SG
None
7 days
34 ± 2.6
4.5 ± 0.9
0.36 ± 0.01
NR
ligation
1
10
Open thorax
cath &
Transonic CO
Pento barbital
5 weeks
16.2 ± 1.3
10.05c ± 0.69
NR
NR
x G50 (∼21.1 ± 0.5 g)
60
9
SG
none
1 day
35 ± 3
1.7 ± 0.2
0.42 ± 0.01
NR
x G50
4 (3–6)
9
SG
Midazolam
2 months
27 ± 3
2.2d ± 1.1
NR
NR
l + Left PA ligation
5
5
SG
NR
7 days
28.5 ± 1.7
9.8a
NR
Thrombi
l + Left PA ligation
5
5
SG + PV-loop
Isoflurane
6 weeks
41 ± 4
10.0a,c
NR
NR
l + Left PA ligation
5
13
SG + PV-loop
Isoflurane
7 days
34 ± 9
12.4a,c
NR
NR
l + Left PA ligation
5
5
SG
NR
7 weeks
27 ± 1.1
7.9 ± 0.6
NR
NR
x G50 (20 mg/kg)
6
6
SG
Propofol
14 days
16 ± 2
1.5b
0.41 ± 0.02
NR
x G50 (20 mg/kg) +
4
6
Propofol
1 month
23 ± 4
1.6b
0.47 ± 0.06
NR
l + Left PA ligation
5
5
SG + PV-loop
Propofol
14 weeks
26.8 ± 1.4
6.9 ± 0.6a,c
0.42 ± 0.05
NR
us thrombi (0.3*1 cm)
NR
13
Cath in PA
Propofol
14 days
25.2 ± 3.6
NR
NR
Perfusion
defects
beads (0.6–0.9 mm)
21–40
3
SG
Isoflurane
NR
36.6g ±
0.9
NR
NR
NR
beads (0.6–0.9 mm)
9–12
3
SG
Isoflurane
20 monthsh
47g
7.8
NR
Perfusion
defects
+ Microspheres
µm ∼9000 per
e
4 (2–5)
6
Indwelling
cath
none
4–5 weeks
39.5 ± 5.1
7.8 ± 3.4
0.51 ± 0.03
NR
x G50 (∼51250 ±
eres)
Every 3–4 days
(4–8 months)
4
Indwelling
cath
Propofol
14–84 days
34.3 ± 6.0
27.6 ± 5.0
NR
Perfusion
defects
l + Left PA ligation
5
6
SG + PV-loop
Propofol
6 weeks
26[23-28
6.6 [5.5–7.2]a,c
NR
NR
ed PVRi; cTotal pulmonary vascular resistance; dMedian (interquartile range) reported; eOnly reported 2/5 cases; fCalculated from cmH2O or cmH2O·L−1·min; gsystolic PAP;
resonance; CPET, cardiopulmonary exercise testing; CT, computed tomography; LVW, left ventricular weight; NR, not reported; PA, pulmonary artery; PAP, mean pulmonary
nary vascular resistance; RHC, right heart catheterization; RVW, right ventricular weight; SG, Swan-Ganz catheter; SW, septum weight; WU, Wood units. Frontiers in Cardiovascular Medicine | www.frontiersin.org PULMONARY MICROVASCULOPATHY IN
CTEPH CTEPH not only involves the obstructed pulmonary arteries,
but causes progressive microvascular remodeling of the non-
obstructed distal pulmonary small arteries, which is associated
with a further increase in resistance and decrease in compliance
(1, 70), and contributes to worsening of CTEPH. The exact time-
course of microvascular remodeling is unknown. It is difficult to
distinguish between an increase in resistance due to recurrent
embolizations and an increase in resistance due to microvascular
remodeling even in animal models. Nevertheless, pulmonary
vascular resistance continued to increase after cessation of the
embolization procedures in our swine model, which suggest
persistent remodeling of the distal vasculature (37, 56). Even after
cessation of the eNOS inhibitor, which may also have contributed
to a higher pulmonary vascular resistance by increasing
microvascular tone, the high pulmonary pressure and resistance
persisted (37, 56). This microvasculopathy was reversible upon
reperfusion of the obstructed left lung vasculature (50). NO
not
only
impacts
the
vasculature
directly,
but
also indirectly by inhibiting the production of the potent
vasoconstrictor ET. ET can induce vasoconstriction and vascular
remodeling and plasma levels of ET are higher in both animal
models (42, 56) and patients with CTEPH (50) and correlate
with clinical severity (79, 80). Although beneficial effects of ET
receptor antagonism (ERA) in preventing vasculopathy were
shown in dogs (42) conflicting results of ERA therapy have
been reported in CTEPH patients with some studies showing
positive effects (81–83), whereas, the randomized, double-blind,
placebo-controlled BENEFIT study, which investigated dual
ERA therapy with Bosentan, showed no statistically significant
effects of Bosentan in CTEPH patients (84). Increased microvascular wall thickness results in narrowing of
the lumen and stiffening of the pulmonary microvasculature. The
mechanisms behind the pulmonary microvascular remodeling
remain incompletely understood. A shift in balance of angiogenic
factors, with decreased VEGF and high levels of angiopoietin
1 and 2 have been reported (1). Furthermore, chronic
inflammation, evidenced by increased C-Reactive protein (CRP),
as well as interleukin (IL)-10, monocyte chemotactic protein-1
(MCP-1), macrophage inflammatory protein-1α (MIP-1α) and
matrix metalloproteinase (MMP)-9 was present in patients with
CTEPH (71–73), indicating that chronic inflammatory processes
may play a role in the microvasculopathy. In accordance with this
concept, studies in swine showed an elevation in IL-6 expression
in the unobstructed territory (50), while no change in IL-6
was found in obstructed territories (50) and a trend toward
an increase in mixed territories (56). LARGE ANIMAL MODELS OF CTEPH This number is much higher than the number of order 3
and 4 pulmonary small arteries present in the porcine lung
and hence should be able to obstruct a sufficiently large part
of the pulmonary vasculature. Despite this large number of
emboli, sustained CTEPH only developed when embolizations
were combined with chronic inhibition of eNOS, suggesting that
endothelial dysfunction is required for CTEPH to develop in
swine. These findings are in accordance with a study by Rothman
and co-workers, who used ceramic beads of similar size but failed
to induce sustained CTEPH in swine (54). Conversely, when
a similar protocol was used in dogs, CTEPH was successfully
induced in the absence of eNOS inhibition (54). Other studies
in dogs also show that repeated embolization (Sephadex beads April 2021 | Volume 8 | Article 574360 4 Large Animal Models of CTEPH Stam et al. CTEPH induces endothelial dysfunction, thereby predisposing to
pulmonary microvasculopathy. of 100–300 µm in diameter) does result in sustained CTEPH
(38, 57), but this requires a large number of embolizations over
a period of several months. A total of ∼50,000 beads was injected
over a period of several months (57), which is similar to the
number of beads required to induced sustained CTEPH in our
swine model. However, it should be noted that these smaller
beads penetrate deeper into the pulmonary vasculature, and that
the number of pulmonary small arteries increases with decreasing
size. Thus, in the human lung 67,400 vessels of order 5 (diameter
150 ± 20 µm), 285,000 vessels of order 6 (diameter 220 ± 30µm)
and 86,000 vessels of order 7 (diameter 350 ± 90µm) 86,000
vessels are present. Particularly when taking into account the
0.5 log-order fold difference between dogs and pigs, the relative
number of beads required to induce sustained CTEPH in dogs
seems to be smaller as compared to pigs. The structural changes in the pulmonary microvasculature are
accompanied by functional changes. These functional changes
can be assessed using isolated pulmonary small arteries in animal
models of CTEPH. These thicker wall of the non-obstructed
pulmonary small arteries results in exaggerated vasoconstriction
to both KCl and the thromboxane analog U46619 (56). In
addition, microvascular remodeling induced alterations in two
major endothelial signaling pathways, i.e., endothelin (ET) and
NO. NO sensitivity was increased in pulmonary small arteries
from swine with CTEPH. LARGE ANIMAL MODELS OF CTEPH This increase in NO sensitivity
was evidenced by an enhanced vasodilator response to the
NO-donor SNP. Furthermore, while the vasodilator response
to bradykinin was reduced, there was a similar attenuation
of bradykinin-induced vasodilation by eNOS-inhibition. The
increased NO sensitivity was therefore likely accompanied by
and/or a consequence of a decrease in NO production (56). Loss of NO is in accordance with data from CTEPH patients
showing reduced circulating NO levels and increased levels of
the endogenous eNOS-inhibitor asymmetric dimethyl arginine
(ADMA) (74). In addition, the vasodilator response to PDE5
inhibition with Sildenafil was reduced in isolated pulmonary
small arteries from swine with CTEPH as compared to healthy
controls (56). This reduced PDE5 activity likely reduced the
rate of cGMP breakdown and therefore may have contributed
to the increased NO-sensitivity. Furthermore, a reduction in
endogenous PDE5 activity may explain that PDE5 -inhibition
is less effective for treatment of CTEPH and underlines the
importance of intervening more upstream in the NO-pathway
either by administering NO (75) or stimulating soluable guanylyl
cyclase (sGC) by Riociguat, which has recently been approved for
therapeutic use in CTEPH (35, 76–78). Frontiers in Cardiovascular Medicine | www.frontiersin.org PULMONARY MICROVASCULOPATHY IN
CTEPH However, neither mRNA
expression of interferon-γ, TNF-α, nor expression of TGF-β were
altered in the lungs of swine with CTEPH (56). It is however likely
that a general systemic inflammatory phenotype in patients with The lack of clinical effect of ERA in CTEPH may be due
to a decreased sensitivity of the pulmonary microvasculature
to ET (56). This decreased sensitivity to ET was accompanied
by an increased ETA but decreased ETB contribution to ET-
induced vasoconstriction. These data were consistent with an
increased ETA/ETB gene expression ratio in lung tissue (56) as
well as with the increased ETA receptor expression in human
pulmonary endarterectomy tissues (85) and in the lungs of
swine with CTEPH (47, 50). These data from large animal
models and humans suggest that ET signaling is altered in
the pulmonary microvasculature in CTEPH. The loss of ETB Frontiers in Cardiovascular Medicine | www.frontiersin.org April 2021 | Volume 8 | Article 574360 5 Large Animal Models of CTEPH Stam et al. (48). RV structural and functional adaptability are important
determinants of functional capacity and survival in patients with
CTEPH (8–10). mediated vasoactive effects in isolated pulmonary small arteries
(56) suggests that specific ETA blockade alone would be more
therapeutically efficacious. Although the AMBER trial, which
investigated the ETA specific ERA Ambrisentan was terminated
early (ClinicalTrials.gov NCT02021292, NCT02060721), there
are ongoing studies to ETA specific ERAs such as Macitentan
(MERIT) which is an ERA with high specificity for ETA (86). Thus, reduced RV – PA coupling, which denotes the ratio
of RV contractility and RV afterload, is associated with a lower
exercise capacity (8) and patients with a dilated RV have a
worse prognosis compared to patients in which RV function and
geometry are preserved (90, 91). Thus, reduced RV – PA coupling, which denotes the ratio
of RV contractility and RV afterload, is associated with a lower
exercise capacity (8) and patients with a dilated RV have a
worse prognosis compared to patients in which RV function and
geometry are preserved (90, 91). ET can signal via two pathways, the first one being calcium-
dependent and involving phospholipase C (PLC)-mediated
activation of myosin-light chain kinase. The second pathway
is calcium-independent and encompasses RhoA-Rho-kinase
mediated inactivation of myosin phosphatase (87). Although the
Rho-kinase inhibitor Fasudil is therapeutically effective in some
patients with PAH (88), knowledge about this pathway in the
pathogenesis of CTEPH is limited. PULMONARY MICROVASCULOPATHY IN
CTEPH ET-induced vasoconstriction
was mediated in part through Rho-kinase in isolated pulmonary
small arteries from healthy swine, whereas, Rho-kinase inhibition
had no effect in pulmonary small arteries from swine with
CTEPH (56), implying that ET-induced vasoconstriction in
CTEPH is mediated through the PLC-pathway. These data
imply that microvascular constriction and remodeling occur
via different pathways in CTEPH than in PAH in which
the contribution of Rho-kinase was found to be augmented
(89). Hence, using Rho-kinase inhibitors to alleviate pulmonary
vasoconstriction and remodeling may not be efficacious in
CTEPH patients. It is increasingly recognized that in addition to RV systolic
dysfunction, RV diastolic dysfunction is associated with a worse
prognosis in patients with PAH (92). Diastolic dysfunction,
evidenced by an increase in stiffness, is also present in pigs
with type II pulmonary hypertension (93). Diastolic stiffness is
determined by passive myocyte stiffness as well as interstitial
fibrosis. Consistent with the findings in a rat model of pulmonary
artery banding (94), the mild RV dysfunction in swine with
CTEPH was characterized by an increase in the stifftitin isoform
N2BA but not with changes in myocardial fibrosis as measured
histologically. Furthermore, there was a change in the ratio
between Col1 and Col3 in the RV, suggesting relatively more
expression of the stiffCol1 isoform (55), which is consistent
with data from rats with PAH (94), and may have contributed
to a stiffer RV. Although, neither SERCA nor phospholamban
gene expression were changed in our CTEPH swine model, it is
possible that changes in their phosphorylation may play a role in
altered Ca2+ handling, which is in turn implied to play a role in
the development of RV dysfunction (93). Hence, future studies
in relevant large animal models should investigate contractile
function of individual cardiomyocytes as well as expression
and phosphorylation of the contractile and calcium handling
proteins SERCA, phospholamban, smooth muscle actin, titin,
and troponins. Cardiac Dimensions and Function The afterload of the RV increases during development and
progression of CTEPH. To cope with this increased afterload,
the RV exhibits structural and functional changes to augment
contractility
(Figure 1). RV
dilation
and
remodeling
are
dependent on the magnitude of the increase in afterload (51). The
effects of CTEPH on cardiac structure and function have been
examined using a variety of non-invasive, including ultrasound,
CMR, CT, and invasive (pressure volume relation, assessment
of RV-PA coupling) methods (for overview see Table 2). These
studies show RV dilation (increase in enddiastolic area or
volume) and a reduced contractile function, as evidenced by
a decrease in fractional area change or ejection fraction, a
decrease in TAPSE and a progessive decrease in RV-PA coupling
in animals with CTED and CTEPH (Figure 1, for results of
individual studies see Table 2). Frontiers in Cardiovascular Medicine | www.frontiersin.org Cardiac Inflammation, Oxidative Stress,
Apoptosis, and Angiogenesis p p
g
g
A key factor that distinguishes compensated RV remodeling from
RV failure is adequate myocardial perfusion (95). Angiogenesis
is required to enhance RV perfusion commensurate with the
increase in RV mass. Capillary density is preserved or even
increased in adaptive RV remodeling, whereas, it is reduced in
RV failure (95). Furthermore, RV maladaptive remodeling in
CTEPH and PAH is accomanied by a reduction in myocardial
perfusion reserve (96, 97). Conversely, capillary density was
either unaltered (52) or increased in swine with CTEPH (55, 58),
which is beneficial for myocardial perfusion and oxygenation,
and suggests a state of adaptive RV remodeling. Nevertheless,
HIF1α (52) and VEGFA-expression were higher in swine with
CTEPH (52, 55, 58), suggesting that there was still a need for
additional perfusion. Furthermore, VEGFA expression corelated
inversely with RV-PA coupling (55) and further increasing
capillary density using a therapeutic intervention with infusion
of endothelial progenitor cells into the right coronary artery
improved right ventricular function independent of changes
in PVR (58). Hence, future studies should address myocardial
perfusion and coronary flow reserve in different stages of RV RV remodeling is associated with cardiomyocyte hypertrophy,
interstitial fibrosis and changes in capillary density (48,
55). RV hypertrophy, both in terms of RV weight and
RV cardiomyocyte size was accompanied by activation of
both pro- and antiapoptotic gene expression (upregulation
of Caspase-3 and BCL2 mRNA, respectively). RV resting
function is generally preserved, but BNP expression is increased
(48, 49, 55), suggestive of an increased wall stress. The
increased BNP showed a negative correlation with stroke
volume and a positive correlation with global RV hypertrophy April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 6 Stam et al. Large Animal Models of CTEPH FIGURE 1 | Cardiac remodeling and reserve in CTEPH. Cardiac remodeling in CTEPH, and the effects of exercise on the cardiac reserve. CTED, chronic
thrombo-embolic disease; CTEPH, chronic thrombo-embolic pulmonary hypertension; RV-PA coupling: right ventricular-pulmonary artery coupling. FIGURE 1 | Cardiac remodeling and reserve in CTEPH. Cardiac remodeling in CTEPH, and the effects of exercise on the cardiac reserve. CTED, chronic
thrombo-embolic disease; CTEPH, chronic thrombo-embolic pulmonary hypertension; RV-PA coupling: right ventricular-pulmonary artery coupling. (mal) adaptation and assess whether RV adaptations is different
in CTED vs. CTEPH. the RV of swine with CTEPH are consistent with these data
(55). Cardiac Inflammation, Oxidative Stress,
Apoptosis, and Angiogenesis Interestingly, expression of NOX1 and NOX4 as well as
ROCK2 correlated inversely with RV-PA coupling, suggesting
that oxidative stress in the myocardium may contribute to
deterioration of RV-function (55). The transition from compensated RV remodeling to RV
failure is also associated with inflammation and activation of
the immune system (98–100). Although, the mRNA of genes
involved in immune modulation (TNF-α, IL-6, IFN-γ) was not
altered in the RV of swine with CTEPH, expression of TGF-
β was higher (52, 55). Activation of the TGF-β pathway is
known to play a pivotal role in the development of PH (101,
102). TGF-β pathway activation was further supported by the
higher expression PAI, a downstream target of TGF-β signaling
in these animals. Just like endothelin, activation of the TGF-
β pathway can result in activation of the Rho-kinase pathway
(103–105). Indeed, ROCK2 expression was upregulated in the
RV of swine with CTEPH. Importantly, ROCK2 activation is
involved in cardiac hypertrophy, oxidative stress, angiogenesis,
apoptosis, and fibrosis and may therefore present a major
deleterious factor in RV-remodeling (106–108) (Figure 2). In
addition, ROCK2 activation increases phosphorylation of protein
phosphatase 1 (PP1), which in turn regulates Ca2+ handling and
Ca2+ sensitivity in the cardiomyocytes (108). Hence, it remains to be investigated whether Rho-kinase
inhibition may prevent adverse cardiac remodeling despite
observations that it has no beneficial effects on pulmonary
vascular tone and remodeling. Furthermore, animal models may
be well-suited to further establish markers of RV dysfunction. Epidemiology and Clinical Implications p
gy
p
Although
arrhythmias
have
been
identified
as
relevant
contributors for morbidity and mortality in patients with
CTEPH, only little is known about the incidence and prevalence
of arrhythmias in this patient cohort (112–115). Besides the
very limited number of studies performed in general, these
studies also included patients with other etiologies leading to
pulmonary hypertension (in most cases PAH type 1) which
makes it challenging to provide data specifically in patients
with CTEPH. In general, supraventricular arrhythmias are more
common in patients with CTEPH than in the general population
ranging from 11.7 to 22% in retrospective studies (115, 116)
and from 13.4 to 25.1% in prospective studies (11). The most
common arrhythmias observed in these studies were atrial
fibrillation (AF) and atrial flutter (AFlut). Kanemoto studied 101
patients with PAH and observed arrhythmias in 17.8% (113). ROCK2 is also expressed in the coronary vasculature, where
it is associated with oxidative stress and NOX-expression (109). NOX1, NOX2, and NOX4 expression was elevated in the
right coronary artery of swine with RV pressure overload
due to pulmonary artery banding. The increased expression
of these NOX- isoforms was accompanied by oxidative stress
and endothelial dysfunction, notwithstanding unaltered eNOS
expression (110). Furthermore, an increase in circulating NOX4
has been shown in patients with PAH (111). The upregulation
of NOX1 and NOX4, and the unaltered eNOS expression in April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 7 Large Animal Models of CTEPH Stam et al. FIGURE 2 | Processes involved in RV remodeling in CTEPH and therapeutic interventions tested in animal models. FIGURE 2 | Processes involved in RV remodeling in CTEPH and therapeutic interventions tested in animal models. with a worse prognosis (11, 12). Overall, supraventricular
arrhythmias are associated with increased mortality in PAH
patients (3.81-fold increased hazard of death) (122). The most frequent arrhythmias in this cohort were (i) sinus
tachycardia (38%), (ii) sinus bradycardia (18%), and (iii) first
degree AV block (15%) with sinus tachycardia being significantly
associated with mortality. Ventricular arrhythmias such as
ventricular tachycardia (VT) or ventricular fibrillation (VF) have
been demonstrated only in about 8% of patients with PAH and
sudden cardiac death (SCD) (117). Epidemiology and Clinical Implications Due to the pathophysiologic
alterations in PAH and the observation of VF and VT in a rat
model of PAH (118, 119) one would expect a higher incidence
of VT/VF in PAH patients potentially indicating difficulties in
diagnosing ventricular arrhythmias due to a lack of permanent
ECG monitoring (e.g., implantable loop recorders) in such
patients (12). Even more frequent than specific arrhythmias
are ECG abnormalities in PAH patients. Tonelli and colleagues
evaluated ECGs over time in 50 patients with PAH and could
see a significantly increased heart rate as well as prolonged
PR interval, QRS duration and QTc duration in terminally
diseased patients (120) which was further confirmed by Rich
et al. (121). They also observed that none of the patients had
a “normal” ECG before death and demonstrated a correlation
between QRS/QTc prolongation and impaired RV function,
increased RV mass and poor prognosis with a QTC > 480 ms
being an independent predictor for mortality (120). Occurrence
of arrhythmias is associated with clinical decompensation,
although, it is incompletely understood whether arrhythmias
occur as a cause or consequence of clinical worsening or both. However, conversion to sinus rhythm improved clinical status
and in most cases reverses cardiac decompensation, whereas, the
presence of sustained supraventricular arrhythmias is associated Frontiers in Cardiovascular Medicine | www.frontiersin.org ADDED VALUE OF ANIMAL MODELS Exercise testing after pulmonary embolism is predictive of
development of PH and/or patient outcome in established
CTEPH (130–133). Both patients with CTED and CTEPH show
impaired exercise tolerance (8, 18, 134, 135). In accordance with
these human data, swine with CTEPH also showed evidence
of exercise intolerance (37, 55). This impaired exercise capacity
is principally caused by an exacerbated increase in PAP and
pulmonary vascular resistance during exercise, that further
increases RV afterload and the V/Q-mismatch in the lungs
(Figure 3) (90, 134, 135). CTEPH
is
associated
with
increased
mortality
and
therefore
a
clinically
highly
relevant
disease. The
underlying
pathophysiology
is
complex
and
currently
poorly
understood. Animal
models
are
invaluable
in
this regard to study causal mechanisms and to identify
potential targets for drug development or establishment of
diagnostic/prognostic biomarkers. In this context, CTEPH large animal models are of special
interest since chronic instrumentation or repeated measurements
are possible and they better resemble pathophysiologic hallmarks
of the human situation such as microvascular remodeling, as well
as remodeling and/or electrophysiologic alterations of the RV in
CTED as well as CTEPH (37, 55, 56, 139–141). g
Physiological dead space is increased in proportion to
the increase in PVR in CTEPH, resulting in a lower PaO2,
which results in a reduction in PaCO2, due to compensatory
hyperventilation (136). Similarly, the slightly lower PaO2 in
swine with CTEPH is consistent with dead space ventilation,
a mild V/Q mismatch, and a subsequent decrease in capillary
transit time at rest. However, PaCO2 was not altered in the
swine with CTEPH neither at rest, nor during exercise (37). This discrepancy in CO2 response may in part be due to the
observation that swine lack collateral ventilation and therefore
cannot equalize intraregional V/Q differences between alveoli. Furthermore, healthy quadrupeds already ventilate and perfuse
their entire lungs at rest (137), and hence cannot further
recruit hypoventilated lung areas and improve V/Q mismatch
by increasing ventilation. Thus, hyperventilation may not be
capable of reducing PaCO2 levels below normal as seen in
humans (37, 56). The lower PmvO2 observed in CTEPH is partly
a consequence of the lower PaO2 due to the V/Q mismatch, and
in part reflects the decreased blood flow due to a lower cardiac
index (CI), forcing the body to extract more oxygen. Arrhythmia Mechanisms In patients with PAH increased RV stretch, hypertrophy and
fibrosis have been demonstrated – well-known proarrhythmic
mechanisms
summarized
under
the
term
“structural
remodeling.” These structural alterations result in reduced
conduction velocity and the occurrence of re-entry (126). In addition to that, both in patients and a rat model for
PAH electrical alterations (so called electrical remodeling),
can be observed including
downregulation
of potassium
channels, connexin-43, or changes in calcium handling leading
to conduction slowing, QTc and action potential duration
prolongation,
or
afterdepolarizations
and
ectopic
activity
(119–129). All these mechanisms finally result in an increased
susceptibility of arrhythmias (126) but their relevance in CTEPH
remains to be established. During exercise at 4 km/h, the anaerobic threshold was
reached in swine with CTEPH and maximal body oxygen
consumption was reduced which is consistent with a reduced
exercise tolerance in CTEPH patients (18, 111, 132, 138). This
reduction in maximal oxygen consumption was principally due
to a decreased CI (27% lower as compared to healthy) and
to a lesser extent to a decreased arterial oxygen content (10%
lower as compared to healthy). Hence, exercise intolerance
in CTEPH is principally caused by the increased pulmonary
vascular resistance, which augments afterload of the RV, and
thereby limits the exercise induced increase in CI. The relative
contributions of cardiac and pulmonary dysfunction to the
exercise intolerance in patients with more severe RV dysfunction
remains to be established. Arrhythmia Mechanisms y
The increased vulnerability to arrhythmias in CTEPH is
incompletely understood. So far, our knowledge on CTEPH-
associated arrhythmogenesis is based on clinical findings
in patients. So far, no specific animal model for CTEPH
has been investigated with respect to arrhythmias, only in
the monocrotaline induced PAH models in rat and dog
arrhythmogenesis has been studied. Thus, only extrapolated
mechanistic
data
from
non-CTEPH
animal
models
or
patients/animal models with non-CTEPH RV dysfunction
or cardiac remodeling leading to the clinical phenotype
seen
in
CTEPH
patients
are
currently
available
and
a
specific
mechanistic
understanding
of
CTEPH-mediated
electrophysiologic alterations and arrhythmogenesis is lacking. Having this major limitation in mind several arrhythmia
mechanisms
have
been
suggested
in
CTEPH,
including
autonomic, electrical, or structural remodeling (12). Autonomic
remodeling in PAH results in decreased heart rate variability,
an overall increased sympathetic activity and an adrenergic
remodeling in the RV including downregulation of β1-, α-,
or dopaminergic receptors. This autonomic dysregulation
is clinically reflected by arrhythmias (123) but also by sinus
tachycardia which may be a reactive mechanism to maintain
RV output (124). The influence of the autonomic system on
arrhythmogenesis has been further demonstrated in a dog April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 8 Stam et al. Large Animal Models of CTEPH model of PAH (125). Eight weeks after dehydromonocrotaline
treatment
beagles
develop
PAH
and
show
an
increased
vulnerability to AF/AFlut. They could confirm a downregulation
of β1 receptors in RV, but in RA they found an upregulation and
an increased density of sympathetic nerves. Finally, they ablated
the ganglionated plexi which resulted in reduced AF/AFlut
inducibility and further confirms the important role of the
autonomic nervous system in PAH-associated arrhythmogenesis. In accordance with the studies in CTED and CTEPH patients
in 2015 (8, 18), the RV of swine with CTEPH was not able
to cope with this increased afterload evidenced by the limited
exercise-induced increase in stroke volume and CI (Figure 1). Furthermore, RV-PA coupling was reduced in swine with CTEPH
(49, 55, 64) and a correlation was found between reduced
coupling and a reduced SV reserve with dobutamine in swine
(49) as well as between afterload and RV-PA coupling (55). Importantly, recent studies in patients with CTEPH show that
RV-PA coupling correlates with exercise capacity (8), which in
turn is a strong predictor of clinical outcome (90). REFERENCES Hypertension: definition of pulmonary hypertension challenged? Nat Rev Cardiol. (2016) 13:250–1. doi: 10.1038/nrcardio.2016.44 7. Moser KM, Bloor CM. Pulmonary vascular lesions occurring in patients
with chronic major vessel thromboembolic pulmonary hypertension. Chest. (1993) 103:685–92. doi: 10.1378/chest.103.3.685 20. Ende-Verhaar YM, Cannegieter SC, Vonk Noordegraaf A, Delcroix M,
Pruszczyk P, Mairuhu AT, et al. Incidence of chronic thromboembolic
pulmonary hypertension after acute pulmonary embolism: a contemporary
view of the published literature. Eur Respir J. (2017) 49:1601792. doi: 10.1183/13993003.01792-2016 8. Claeys M, Claessen G, La Gerche A, Petit T, Belge C, Meyns B, et al. Impaired
cardiac reserve and abnormal vascular load limit exercise capacity in chronic
thromboembolic disease. JACC Cardiovasc Imaging. (2018) 12(8 Pt. 1):1444–
56. doi: 10.1016/j.jcmg.2018.07.021 21. Vavera Z, Vojacek J, Pudil R, Maly J, Elias P. Chronic thromboembolic
pulmonary hypertension after the first episode of pulmonary embolism? How often? Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. (2016)
160:125–9. doi: 10.5507/bp.2015.021 9. Hardziyenka
M,
Campian
ME,
Reesink
HJ,
Surie
S,
Bouma
BJ,
Groenink
M,
et
al. Right
ventricular
failure
following
chronic
pressure overload is associated with reduction in left ventricular mass:
evidence for atrophic remodeling. J Am Coll Cardiol. (2011) 57:921–8. doi: 10.1016/j.jacc.2010.08.648 22. Yang S, Yang Y, Zhai Z, Kuang T, Gong J, Zhang S, et al. Incidence
and risk factors of chronic thromboembolic pulmonary hypertension in
patients after acute pulmonary embolism. J Thorac Dis. (2015) 7:1927–38. doi: 10.21037/jtd.2018.07.106 10. van de Veerdonk MC, Bogaard HJ, Voelkel NF. The right ventricle
and
pulmonary
hypertension. Heart
Fail
Rev. (2016)
21:259–71. doi: 10.1007/s10741-016-9526-y 23. Konstantinides SV, Barco S, Lankeit M, Meyer G. Management of
pulmonary embolism: an update. J Am Coll Cardiol. (2016) 67:976–90. doi: 10.1016/j.jacc.2015.11.061 11. Olsson KM, Nickel NP, Tongers J, Hoeper MM. Atrial flutter and fibrillation
in patients with pulmonary hypertension. Int J Cardiol. (2013) 167:2300–5. doi: 10.1016/j.ijcard.2012.06.024 24. Raskob GE, Angchaisuksiri P, Blanco AN, Buller H, Gallus A, Hunt
BJ, et al. Thrombosis: a major contributor to global disease burden. Arterioscler Thromb Vasc Biol. (2014) 34:2363–71. doi: 10.1161/ATVBAHA. 114.304488 12. Cirulis MM, Ryan JJ, Archer SL. Pathophysiology, incidence, management,
and consequences of cardiac arrhythmia in pulmonary arterial hypertension
and chronic thromboembolic pulmonary hypertension. Pulm Circ. (2019)
9:1–15. doi: 10.1177/2045894019834890 25. Vonk Noordegraaf Boonstra A, Konings TC, Marques KM, Bogaard
HJ. [Diagnosis and treatment of pulmonary hypertension]. Diagnostiek
en behandeling van pulmonale hypertensie. Ned Tijdschr Geneeskd. (2014) 158:A7315. 13. REFERENCES for European Paediatric and Congenital Cardiology (AEPC), International
Society for Heart and Lung Transplantation (ISHLT). Eur Heart J. 37:67–119. doi: 10.1093/eurheartj/ehv317 for European Paediatric and Congenital Cardiology (AEPC), International
Society for Heart and Lung Transplantation (ISHLT). Eur Heart J. 37:67–119. doi: 10.1093/eurheartj/ehv317 1. Simonneau G, Torbicki A, Dorfmuller P, Kim N. The pathophysiology of
chronic thromboembolic pulmonary hypertension. Eur Respir Rev. (2017)
26:160112. doi: 10.1183/16000617.0112-2016 1. Simonneau G, Torbicki A, Dorfmuller P, Kim N. The pathophysiology of
chronic thromboembolic pulmonary hypertension. Eur Respir Rev. (2017)
26:160112. doi: 10.1183/16000617.0112-2016 14. Hoeper MM, Madani MM, Nakanishi N, Meyer B, Cebotari S, Rubin
LJ. Chronic thromboembolic pulmonary hypertension. Lancet Respir Med. (2014) 2:573–82. doi: 10.1016/S2213-2600(14)70089-X 2. Lang IM, Dorfmuller P, Vonk Noordegraaf A. The pathobiology of chronic
thromboembolic pulmonary hypertension. Ann Am Thorac Soc. (2016)
13(Suppl. 3):S215–21. doi: 10.1513/AnnalsATS.201509-620AS 2. Lang IM, Dorfmuller P, Vonk Noordegraaf A. The pathobiology of chronic
thromboembolic pulmonary hypertension. Ann Am Thorac Soc. (2016)
13(Suppl. 3):S215–21. doi: 10.1513/AnnalsATS.201509-620AS 15. Kim NH, Delcroix M, Jais X, Madani MM, Matsubara H, Mayer E, et
al. Chronic thromboembolic pulmonary hypertension. Eur Respir J. (2019)
53:1801915. doi: 10.1183/13993003.01915-2018 3. Lang
IM,
Campean
IA,
Sadushi-Kolici
R,
Badr-Eslam
R,
Gerges
C,
Skoro-Sajer
N. Chronic
thromboembolic
disease
and
chronic
thromboembolic pulmonary hypertension. Clin Chest Med. (2021) 42:81–90. doi: 10.1016/j.ccm.2020.11.014 16. Lang
IM,
Madani
M. Update
on
chronic
thromboembolic
pulmonary
hypertension. Circulation. (2014)
130:508–18. doi: 10.1161/CIRCULATIONAHA.114.009309 4. Hoeper MM, Bogaard HJ, Condliffe R, Frantz R, Khanna D, Kurzyna M, et
al. Definitions and diagnosis of pulmonary hypertension. J Am Coll Cardiol. (2013) 62:D42–50. doi: 10.1016/j.jacc.2013.10.032 4. Hoeper MM, Bogaard HJ, Condliffe R, Frantz R, Khanna D, Kurzyna M, et
al. Definitions and diagnosis of pulmonary hypertension. J Am Coll Cardiol. (2013) 62:D42–50. doi: 10.1016/j.jacc.2013.10.032 17. Axell RG, Messer SJ, White PA, McCabe C, Priest A, Statopoulou T, et
al. Ventriculo-arterial coupling detects occult RV dysfunction in chronic
thromboembolic pulmonary vascular disease. Physiol Rep. (2017) 5:e13227. doi: 10.14814/phy2.13227 5. Matthews DT, Hemnes AR. Current concepts in the pathogenesis of chronic
thromboembolic pulmonary hypertension. Pulm Circ. (2016) 6:145–54. doi: 10.1086/686011 18. Held
M,
Kolb
P,
Grun
M,
Jany
B,
Hubner
G,
Grgic
A,
et
al. Functional
characterization
of
patients
with
chronic
thromboembolic disease. Respiration. (2016) 91:503–9. doi: 10.1159/000
447247 6. Galie
N,
Kim
NH. Pulmonary
microvascular
disease
in
chronic
thromboembolic pulmonary hypertension. Proc Am Thorac Soc. (2006)
3:571–6. doi: 10.1513/pats.200605-113LR 19. Torbicki A. FUNDING novel anti-arrhythmic therapeutic approaches are more feasible
in larger animals since the electrical properties of the heart
are more similar to humans (compared to rodents) (140). Some innovative agents targeting pulmonary vasculature are
indeed currently under clinical investigation (ClinicalTrials.gov
NCT03689244, NCT01416636, NCT03809650, NCT03273257,
NCT02634203, NCT00910429) but have not been tested in large
animal models of CTEPH. This
work
was
supported
by
the
German
Center
for
Cardiovascular Research (DZHK; 81X2600210, 81X2600204,
81X3600208, 81X2600249 to SC, 81Z0600207 to DM), the LMU
Munich’s
Institutional
Strategy
LMUexcellent
within
the
framework of the German Excellence Initiative (to SC), the
Förderprogramm für Forschung und Lehre (FöFöLe; 962 to
SC), the Heinrich-and-Lotte-Mühlfenzl Stiftung (to SC), the
ERA-NET on Cardiovascular Diseases (ERA-CVD; 01KL1910
to SC), the Netherlands Cardiovascular Research Initiative,
an initiative with financial support from the Dutch Heart
Foundation (CVON2014-11, RECONNECT to DM), and the
Corona-Foundation (S199/10079/2019 to SC). This
work
was
supported
by
the
German
Center
for
Cardiovascular Research (DZHK; 81X2600210, 81X2600204,
81X3600208, 81X2600249 to SC, 81Z0600207 to DM), the LMU
Munich’s
Institutional
Strategy
LMUexcellent
within
the
framework of the German Excellence Initiative (to SC), the
Förderprogramm für Forschung und Lehre (FöFöLe; 962 to
SC), the Heinrich-and-Lotte-Mühlfenzl Stiftung (to SC), the
ERA-NET on Cardiovascular Diseases (ERA-CVD; 01KL1910
to SC), the Netherlands Cardiovascular Research Initiative,
an initiative with financial support from the Dutch Heart
Foundation (CVON2014-11, RECONNECT to DM), and the
Corona-Foundation (S199/10079/2019 to SC). AUTHOR CONTRIBUTIONS KS drafted the manuscript. SC, YT, and DM revised the
manuscript. All
authors
approved
the
final
version
of
the manuscript. ADDED VALUE OF ANIMAL MODELS Thus, those close-to-human large animal models (37, 55, 56,
139) allow to identify and to validate biomarkers (e.g., circulating
biomarkers in the blood, hemodynamic biomarkers or ECG
traits) to facilitate early detection of disease and/or disease
progression in patients which could lead to the development
of preventive strategies in the future as well. Also, in large
animal models interventions that interfere with microvascular
and/or RV remodeling and have direct clinical applicability (e.g.,
catheter-based approaches) are possible to get more insight in
the pathways involved in this remodeling and get more specific
targeted therapy for inoperable CTEPH patients or patients
with residual PH after surgery. An example of such treatment
to be tested for improvement of RV function based on swine
data is ROCK2 inhibition. Thus far, few studies in large animal
models have been performed to study the effect of therapeutic Frontiers in Cardiovascular Medicine | www.frontiersin.org Frontiers in Cardiovascular Medicine | www.frontiersin.org April 2021 | Volume 8 | Article 574360 9 Stam et al. Large Animal Models of CTEPH FIGURE 3 | Determinants of exercise intolerance in CTEPH. Processes involved in decreased exercise tolerance in CTEPH. PAP, pulmonary artery pressure; PVR,
pulmonary vascular resistance; RV, right ventricle; V/Q-mismatch, ventilation/perfusion-mismatch; PmvO2, mixed venous oxygen pressure; PaO2, arterial oxygen
pressure; PaCO2, arterial carbon dioxide pressure. FIGURE 3 | Determinants of exercise intolerance in CTEPH. Processes involved in decreased exercise tolerance in CTEPH. PAP, pulmonary artery pressure; PVR,
pulmonary vascular resistance; RV, right ventricle; V/Q-mismatch, ventilation/perfusion-mismatch; PmvO2, mixed venous oxygen pressure; PaO2, arterial oxygen
pressure; PaCO2, arterial carbon dioxide pressure. and possibly interventions of CTEPH (142) and shed more light
on the importance and implications of cardiopulmonary exercise
testing in CTED and CTEPH patients. Finally, electrophysiologic
evaluation beyond pure mechanistic concepts (which can be
obtained in rodents or small animals) and especially studying interventions. One study investigated lung revascularization (50)
and one study investigated the effect of endothelial progenitor
cells to improve RV perfusion (58) (see also above). In addition, animal models may also be used to delineate sex-
differences that are known to exist in development, progression April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 10 Large Animal Models of CTEPH Stam et al. REFERENCES Stam K, van Duin RWB, Uitterdijk A, Cai Z, Duncker DJ, Merkus D. Exercise
facilitates early recognition of cardiac and vascular remodeling in chronic
thromboembolic pulmonary hypertension in swine. Am J Physiol Heart Circ
Physiol. (2018) 314:H627–42. doi: 10.1152/ajpheart.00380.2017 56. Stam K, van Duin RW, Uitterdijk A, Krabbendam-Peters I, Sorop O, Danser
AHJ, et al. Pulmonary microvascular remodeling in chronic thrombo-
embolic pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol. (2018)
315:L951–64. doi: 10.1152/ajplung.00043.2018 38. Shelub, van Grondelle A, McCullough R, Hofmeister S, Reeves JT. A model
of embolic chronic pulmonary hypertension in the dog. J Appl Physiol Respir
Environ Exerc Physiol. (1984) 56:810–5. doi: 10.1152/jappl.1984.56.3.810 57. Mulchrone Kellihan HB, Forouzan O, Hacker TA, Bates ML, Francois
CJ, Chesler NC. A large animal model of right ventricular failure
due
to
chronic
thromboembolic
pulmonary
hypertension:
a
focus
on function. Front Cardiovasc Med. (2019) 5:189. doi: 10.3389/fcvm. 2018.00189 39. Perkett EA, Brigham KL, Meyrick B. Continuous air embolization into
sheep causes sustained pulmonary hypertension and increased pulmonary
vasoreactivity. Am J Pathol. (1988) 132:444–54. 40. Moser KM, Cantor JP, Olman M, Villespin I, Graif JL, Konopka R, et al. Chronic pulmonary thromboembolism in dogs treated with tranexamic acid. Circulation. (1991) 83:1371–9. doi: 10.1161/01.CIR.83.4.1371 58. Loisel F, Provost B, Guihaire J, Boulate D, Arouche N, Amsallem
M, et al. Autologous endothelial progenitor cell therapy improves
right ventricular function in a model of chronic thromboembolic
pulmonary hypertension. J Thorac Cardiovasc Surg. (2019) 157:655–66.e7. doi: 10.1016/j.jtcvs.2018.08.083 41. Weimann J, Zink W, Schnabel PA, Jakob H, Gebhard MM, Martin E, et al. Selective vasodilation by nitric oxide inhalation during sustained pulmonary
hypertension following recurrent microembolism in pigs. J Crit Care. (1999)
14:133–40. doi: 10.1016/S0883-9441(99)90026-6 59. Brimioulle
S,
Wauthy
P,
Naeije
R. Single-beat
evaluation
of
right
ventricular
contractility. Crit
Care
Med. (2005)
33:917–8. doi: 10.1097/01.CCM.0000156236.49988.31 42. Kim H, Yung GL, Marsh JJ, Konopka RG, Pedersen CA, Chiles PG, et al. Endothelin mediates pulmonary vascular remodelling in a canine model of
chronic embolic pulmonary hypertension. Eur Respir J. (2000) 15:640–8. doi: 10.1034/j.1399-3003.2000.15d04.x 60. Toshner
M,
Pepke-Zaba
J. Chronic
thromboembolic
pulmonary
hypertension:
time
for
research
in
pathophysiology
to
catch
up
with
developments
in
treatment. F1000Prime
Rep. (2014)
6:38. doi: 10.12703/P6-38 43. Zhou X, Wang D, Castro CY, Hawkins H, Lynch JE, Liu X, et al. A pulmonary
hypertension model induced by continuous pulmonary air embolization. J
Surg Res. (2011) 170:e11–6. doi: 10.1016/j.jss.2011.04.030 61. REFERENCES Galie N, Humbert M, Vachiery JL, Gibbs S, Lang I, Torbicki A, et al. 2015 ESC/ERS guidelines for the diagnosis and treatment of pulmonary
hypertension: the joint task force for the diagnosis and treatment of
pulmonary hypertension of the European Society of Cardiology (ESC)
and the European Respiratory Society (ERS): endorsed by: Association 26. Condliffe R, Kiely DG, Gibbs JS, Corris PA, Peacock AJ, Jenkins DP,
et al. Improved outcomes in medically and surgically treated chronic Frontiers in Cardiovascular Medicine | www.frontiersin.org Frontiers in Cardiovascular Medicine | www.frontiersin.org April 2021 | Volume 8 | Article 574360 11 Stam et al. Large Animal Models of CTEPH thromboembolic pulmonary hypertension. Am J Respir Crit Care Med. (2008) 177:1122–7. doi: 10.1164/rccm.200712-1841OC 46. Garcia-Alvarez A, Fernandez-Friera L, Garcia-Ruiz JM, Nuno-Ayala M,
Pereda D, Fernandez-Jimenez R, et al. Non-invasive monitoring of serial
changes in pulmonary vascular resistance and acute vasodilator testing
using cardiac magnetic resonance. J Am Coll Cardiol. (2013) 62:1621–31. doi: 10.1016/j.jacc.2013.07.037 27. Escribano-Subias P, Blanco I, Lopez-Meseguer M, Lopez-Guarch CJ,
Roman A, Morales P, et al. Survival in pulmonary hypertension in
Spain: insights from the Spanish registry. Eur Respir J. (2012) 40:596–603. doi: 10.1183/09031936.00101211 47. Mercier O, Tivane A, Dorfmuller P, de Perrot M, Raoux F, Decante B,
et al. Piglet model of chronic pulmonary hypertension. Pulm Circ. (2013)
3:908–15. doi: 10.1086/674757 28. Kramm T, Wilkens H, Fuge J, Schafers HJ, Guth S, Wiedenroth
CB, et al. Incidence and characteristics of chronic thromboembolic
pulmonary hypertension in Germany. Clin Res Cardiol. (2018) 107:548–53. doi: 10.1007/s00392-018-1215-5 48. Guihaire J, Haddad F, Boulate D, Capderou A, Decante B, Flecher
E, et al. Right ventricular plasticity in a porcine model of chronic
pressure
overload. J
Heart
Lung
Transplant. (2014)
33:194–202. doi: 10.1016/j.healun.2013.10.026 29. Simonneau
G,
Hoeper
MM. Evaluation
of
the
incidence
of
rare
diseases:
difficulties
and
uncertainties,
the
example
of
chronic
thromboembolic pulmonary hypertension. Eur Respir J. (2017) 49:1602522. doi: 10.1183/13993003.02522-2016 49. Guihaire J, Haddad F, Noly PE, Boulate D, Decante B, Dartevelle P, et al. Right
ventricular reserve in a piglet model of chronic pulmonary hypertension. Eur
Respir J. (2015) 45:709–17. doi: 10.1183/09031936.00081314 30. Klok FA, Barco S, Konstantinides SV, Dartevelle P, Fadel E, Jenkins D, et
al. Determinants of diagnostic delay in chronic thromboembolic pulmonary
hypertension: results from the European CTEPH registry. Eur Respir J. (2018) 52:1801687. doi: 10.1183/13993003.01687-2018 p
50. Boulate D, Perros F, Dorfmuller P, Arthur-Ataam J, Guihaire J, Lamrani
L, et al. REFERENCES Pulmonary microvascular lesions regress in reperfused chronic
thromboembolic pulmonary hypertension. J Heart Lung Transplant. (2015)
34:457–67. doi: 10.1016/j.healun.2014.07.005 31. Edward JA, Mandras S. An update on the management of chronic
thromboembolic pulmonary hypertension. Curr Probl Cardiol. (2017) 42:7–
38. doi: 10.1016/j.cpcardiol.2016.11.001 51. Aguero J, Ishikawa K, Fish KM, Hammoudi N, Hadri L, Garcia-Alvarez A, et
al. Combination proximal pulmonary artery coiling and distal embolization
induces chronic elevations in pulmonary artery pressure in Swine. PLoS
ONE. (2015) 10:e0124526. doi: 10.1371/journal.pone.0124526 32. Gall H, Preston IR, Hinzmann B, Heinz S, Jenkins D, Kim NH, et al. An international physician survey of chronic thromboembolic pulmonary
hypertension management. Pulm Circ. (2016) 6:472–82. doi: 10.1086/688084 52. Noly PE, Haddad F, Arthur-Ataam J, Langer N, Dorfmuller P, Loisel F,
et al. The importance of capillary density-stroke work mismatch for right
ventricular adaptation to chronic pressure overload. J Thorac Cardiovasc
Surg. (2017) 154:2070–9. doi: 10.1016/j.jtcvs.2017.05.102 33. Haythe
J. Chronic
thromboembolic
pulmonary
hypertension:
a
review of current practice. Prog Cardiovasc Dis. (2012) 55:134–43. doi: 10.1016/j.pcad.2012.07.005 34. Albani S, Biondi F, Stolfo D, Lo Giudice F, Sinagra G. Chronic
thromboembolic pulmonary hypertension (CTEPH): what do we know
about it? A comprehensive review of the literature. J Cardiovasc Med. (2019)
20:159–68. doi: 10.2459/JCM.0000000000000774 53. Tang CX, Yang GF, Schoepf UJ, Han ZH, Qi L, Zhao YE, et al. Chronic
thromboembolic pulmonary hypertension: comparison of dual-energy
computed tomography and single photon emission computed tomography
in canines. Eur J Radiol. (2016) 85:498–506. doi: 10.1016/j.ejrad.2015.11.035 g
y
g
g
nines. Eur J Radiol. (2016) 85:498–506. doi: 10.1016/j.ejrad.2015.11 35. Halank M, Hoeper MM, Ghofrani HA, Meyer FJ, Stahler G, Behr J, et al. Riociguat for pulmonary arterial hypertension and chronic thromboembolic
pulmonary hypertension: results from a phase II long-term extension study. Respir Med. (2017) 128:50–6. doi: 10.1016/j.rmed.2017.05.008 54. Rothman Wiencek RG, Davidson S, Evans WN, Restrepo H, Sarukhanov V,
Mann D. Challenges in the development of chronic pulmonary hypertension
models in large animals. Pulm Circ. (2017) 7:156–66. doi: 10.1086/
690099 55. Stam K, Cai Z, van der Velde N, van Duin R, Lam E, van der Velden
J. Cardiac remodeling in a swine model of chronic thrombo-embolic
pulmonary hypertension- comparison of right vs. left ventricle. J Physiol. (2019) 597:4465–80. doi: 10.1113/JP277896 36. Pepke-Zaba J, Ghofrani HA, Hoeper MM. Medical management of chronic
thromboembolic pulmonary hypertension. Eur Respir Rev. (2017) 26:160107. doi: 10.1183/16000617.0107-2016 37. REFERENCES Skoro-Sajer N, Gerges C, Gerges M, Panzenbock A, Jakowitsch J,
Kurz A, et al. Usefulness of thrombosis and inflammation biomarkers
in chronic thromboembolic pulmonary hypertension-sampling plasma
and surgical specimens. J Heart Lung Transplant. (2018) 37:1067–74. doi: 10.1016/j.healun.2018.04.003 44. Sage E, Mercier O, Herve P, Tu L, Dartevelle P, Eddahibi S, et al. Right lung
ischemia induces contralateral pulmonary vasculopathy in an animal model. J Thorac Cardiovasc Surg. (2012) 143:967–73. doi: 10.1016/j.jtcvs.2011.12.052 62. Azarian R, Wartski M, Collignon MA, Parent F, Herve P, Sors H, et al. Lung perfusion scans and hemodynamics in acute and chronic pulmonary
embolism. J Nucl Med. (1997) 38:980–3. 45. Pohlmann JR, Akay B, Camboni D, Koch KL, Mervak BM, Cook KE. A low
mortality model of chronic pulmonary hypertension in sheep. J Surg Res. (2012) 175:44–8. doi: 10.1016/j.jss.2011.02.049 April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org Frontiers in Cardiovascular Medicine | www.frontiersin.org 12 Stam et al. Large Animal Models of CTEPH 63. Fedullo PF, Auger WR, Kerr KM, Rubin LJ. Chronic thromboembolic
pulmonary
hypertension. N
Engl
J
Med. (2001)
345:1465–72. doi: 10.1056/NEJMra010902 81. Hirashiki Adachi S, Nakano Y, Kamimura Y, Shimokata S, Takeshita K,
Murohara T, et al. Effects of bosentan on peripheral endothelial function in
patients with pulmonary arterial hypertension or chronic thromboembolic
pulmonary hypertension. Pulm Circ. (2016) 6:168–73. doi: 10.1086/685715 64. Guihaire J, Haddad F, Boulate D, Decante B, Denault AY, Wu J, et al. Non-
invasive indices of right ventricular function are markers of ventricular-
arterial coupling rather than ventricular contractility: insights from a porcine
model of chronic pressure overload. Eur Heart J Cardiovasc Imaging. (2013)
14:1140–9. doi: 10.1093/ehjci/jet092 82. Hirashiki Adachi S, Nakano Y, Kono Y, Shimazu S, Shimizu S, Morimoto R,
et al. Cardiopulmonary exercise testing to evaluate the exercise capacity of
patients with inoperable chronic thromboembolic pulmonary hypertension:
an endothelin receptor antagonist improves the peak PETCO2. Life Sci. (2014) 118:397–403. doi: 10.1016/j.lfs.2014.03.009 65. Huang W, Yen RT, McLaurine M, Bledsoe G. Morphometry of the
human
pulmonary
vasculature. J
Appl
Physiol. (1996)
81:2123–33. doi: 10.1152/jappl.1996.81.5.2123 83. Nishikawa-Takahashi M, Ueno S, Kario K. Long-term advanced therapy
with bosentan improves symptoms and prevents deterioration of inoperable
chronic thromboembolic pulmonary hypertension. Life Sci. (2014) 118:410–
3. doi: 10.1016/j.lfs.2014.03.024 66. Townsley MI. Structure and composition of pulmonary arteries, capillaries,
and veins. Compr Physiol. (2012) 2:675–709. doi: 10.1002/cphy.c100081 67. REFERENCES Eur Respir J. (2014)
44:951–62. doi: 10.1183/09031936.00145013 89. Do e Z, Fukumoto Y, Takaki A, Tawara S, Ohashi J, Nakano M, et al. Evidence
for Rho-kinase activation in patients with pulmonary arterial hypertension. Circ J. (2009) 73:1731–9. doi: 10.1253/circj.CJ-09-0135 74. Skoro-Sajer N, Mittermayer F, Panzenboeck A, Bonderman D, Sadushi
R, Hitsch R, et al. Asymmetric dimethylarginine is increased in chronic
thromboembolic pulmonary hypertension. Am J Respir Crit Care Med. (2007) 176:1154–60. doi: 10.1164/rccm.200702-278OC 90. Blumberg FC, Arzt M, Lange T, Schroll S, Pfeifer M, Wensel R. Impact of right ventricular reserve on exercise capacity and survival in
patients with pulmonary hypertension. Eur J Heart Fail. (2013) 15:771–5. doi: 10.1093/eurjhf/hft044 91. Grosse Grosse C, Lang I. Evaluation of the CT imaging findings in patients
newly diagnosed with chronic thromboembolic pulmonary hypertension. PLoS ONE. (2018) 13:e0201468. doi: 10.1371/journal.pone.0201468 75. Abe S, Ishida K, Masuda M, Ueda H, Kohno H, Matsuura K, et
al. A prospective, randomized study of inhaled prostacyclin versus
nitric oxide in patients with residual pulmonary hypertension after
pulmonary endarterectomy. Gen Thorac Cardiovasc Surg. (2017) 65:153–9. doi: 10.1007/s11748-016-0724-2 92. Trip P, Rain S, Handoko ML, van der Bruggen C, Bogaard HJ,
Marcus
JT,
et
al. Clinical
relevance
of
right
ventricular
diastolic
stiffness in pulmonary hypertension. Eur Respir J. (2015) 45:1603–12. doi: 10.1183/09031936.00156714 76. Ghofrani HA, D’Armini AM, Grimminger F, Hoeper MM, Jansa P,
Kim NH, et al. Riociguat for the treatment of chronic thromboembolic
pulmonary
hypertension. N
Engl
J
Med. (2013)
369:319–29. doi: 10.1056/NEJMoa1209657 93. Aguero J, Ishikawa K, Hadri L, Santos-Gallego C, Fish K, Hammoudi N, et
al. Characterization of right ventricular remodeling and failure in a chronic
pulmonary hypertension model. Am J Physiol Heart Circ Physiol. (2014)
307:H1204–15. doi: 10.1152/ajpheart.00246.2014 77. Koress C, Swan K, Kadowitz P. Soluble guanylate cyclase stimulators
and activators: novel therapies for pulmonary vascular disease or a
different method of increasing cGMP? Curr Hypertens Rep. (2016) 18:42. doi: 10.1007/s11906-016-0645-6 94. Rain S, Andersen S, NajafiA, Gammelgaard Schultz J, da Silva Goncalves
Bos D, Handoko ML, et al. Right ventricular myocardial stiffness
in experimental pulmonary arterial hypertension: relative contribution
of fibrosis and myofibril stiffness. Circ Heart Fail. (2016) 9:e002636. doi: 10.1161/CIRCHEARTFAILURE.115.002636 78. Lian TY, Jiang X, Jing ZC. Riociguat: a soluble guanylate cyclase stimulator
for the treatment of pulmonary hypertension. Drug Des Devel Ther. (2017)
11:1195–207. doi: 10.2147/DDDT.S117277 79. Guo L, Yang Y, Liu J, Wang L, Li J, Wang Y, et al. REFERENCES Lee YC, Clark AR, Fuld MK, Haynes S, Divekar AA, Hoffman EA, et al. MDCT-based quantification of porcine pulmonary arterial morphometry
and self-similarity of arterial branching geometry. J Appl Physiol. (2013)
114:1191–201. doi: 10.1152/japplphysiol.00868.2012 84. Jais X, D’Armini AM, Jansa P, Torbicki A, Delcroix M, Ghofrani HA,
et al. Bosentan effects in iNopErable forms of chronIc thromboembolic
pulmonary hypertension study, bosentan for treatment of inoperable chronic
thromboembolic pulmonary hypertension: BENEFiT (Bosentan Effects in
iNopErable forms of chronIc thromboembolic pulmonary hypertension), a
randomized, placebo-controlled trial. J Am Coll Cardiol. (2008) 52:2127–34. doi: 10.1016/j.jacc.2008.08.059 68. Rendas Branthwaite M, Reid L. Growth of pulmonary circulation in normal
pig–structural analysis and cardiopulmonary function. J Appl Physiol Respir
Environ Exerc Physiol. (1978) 45:806–17. doi: 10.1152/jappl.1978.45.5.806 85. Southwood M, MacKenzie Ross RV, Kuc RE, Hagan G, Sheares KK,
Jenkins DP, et al. Endothelin ETA receptors predominate in chronic
thromboembolic pulmonary hypertension. Life Sci. (2016) 159:104–10. doi: 10.1016/j.lfs.2016.02.036 69. Burrowes
KS,
Hunter
PJ,
Tawhai
MH. Anatomically
based
finite
element models of the human pulmonary arterial and venous trees
including
supernumerary
vessels. J
Appl
Physiol. (2005)
99:731–8. doi: 10.1152/japplphysiol.01033.2004 70. Delcroix M, Vonk Noordegraaf A, Fadel E, Lang I, Simonneau G,
Naeije
R. Vascular
and
right
ventricular
remodelling
in
chronic
thromboembolic pulmonary hypertension. Eur Respir J. (2013) 41:224–32. doi: 10.1183/09031936.00047712 86. Ghofrani HA, Simonneau G, D’Armini AM, Fedullo P, Howard LS, Jais X,
et al. Macitentan for the treatment of inoperable chronic thromboembolic
pulmonary hypertension (MERIT-1): results from the multicentre, phase
2, randomised, double-blind, placebo-controlled study. Lancet Respir Med. (2017) 5:785–94. doi: 10.1183/1393003.congress-2017.OA1984 71. Langer F, Schramm R, Bauer M, Tscholl D, Kunihara T, Schafers HJ. Cytokine
response to pulmonary thromboendarterectomy. Chest. (2004) 126:135–41. doi: 10.1378/chest.126.1.135 g
87. Horinouchi T, Terada K, Higashi T, Miwa S. Endothelin receptor signaling:
new insight into its regulatory mechanisms. J Pharmacol Sci. (2013) 123:85–
101. doi: 10.1254/jphs.13R02CR 72. Quarck R, Wynants M, Ronisz A, Sepulveda MR, Wuytack F, Van
Raemdonck D, et al. Characterization of proximal pulmonary arterial cells
from chronic thromboembolic pulmonary hypertension patients. Respir Res. (2012) 13:27. doi: 10.1186/1465-9921-13-27 88. Fukumoto Y, Yamada N, Matsubara H, Mizoguchi M, Uchino K, Yao
A, et al. Double-blind, placebo-controlled clinical trial with a rho-kinase
inhibitor in pulmonary arterial hypertension. Circ J. (2013) 77:2619–25. doi: 10.1253/circj.CJ-13-0443 73. Zabini D, Heinemann A, Foris V, Nagaraj C, Nierlich P, Balint Z,
et al. Comprehensive analysis of inflammatory markers in chronic
thromboembolic pulmonary hypertension patients. REFERENCES Effects of
intrinsic and extrinsic cardiac nerves on atrial arrhythmia in experimental
pulmonary
artery
hypertension. Hypertension. (2015)
66:1042–9. doi: 10.1161/HYPERTENSIONAHA.115.05846 108. Hartmann S, Ridley AJ, Lutz S. The function of Rho-associated kinases
ROCK1 and ROCK2 in the pathogenesis of cardiovascular disease. Front
Pharmacol. (2015) 6:276. doi: 10.3389/fphar.2015.00276 126. Medi Kalman JM, Ling LH, Teh AW, Lee G, Lee G, Spence SJ, et al. Atrial
electrical and structural remodeling associated with longstanding pulmonary
hypertension and right ventricular hypertrophy in humans. J Cardiovasc
Electrophysiol. (2012) 23:614–20. doi: 10.1111/j.1540-8167.2011.02255.x 109. Chen IC, Tan MS, Wu BN, Chai CY, Yeh JL, Chou SH, et al. Statins ameliorate pulmonary hypertension secondary to left ventricular
dysfunction through the Rho-kinase pathway and NADPH oxidase. Pediatr
Pulmonol. (2017) 52:443–57. doi: 10.1002/ppul.23610 127. Benoist Stones R, Drinkhill M, Bernus O, White E. Arrhythmogenic
substrate in hearts of rats with monocrotaline-induced pulmonary
hypertension
and
right
ventricular
hypertrophy. Am
J
Physiol
Heart
Circ
Physiol. (2011)
300:H2230–7. doi:
10.1152/ajpheart. 01226.2010 110. Lu X, Dang CQ, Guo X, Molloi S, Wassall CD, Kemple MD, et al. Elevated oxidative stress and endothelial dysfunction in right coronary
artery of right ventricular hypertrophy. J Appl Physiol. (2011) 110:1674–81. doi: 10.1152/japplphysiol.00744.2009 128. Benoist D, Stones R, Drinkhill MJ, Benson AP, Yang Z, Cassan C, et
al. Cardiac arrhythmia mechanisms in rats with heart failure induced
by pulmonary hypertension. Am J Physiol Heart Circ Physiol. (2012)
302:H2381–95. doi: 10.1152/ajpheart.01084.2011 111. Godinas L, Sattler C, Lau EM, Jais X, Taniguchi Y, Jevnikar M, et al. Dead-
space ventilation is linked to exercise capacity and survival in distal chronic
thromboembolic pulmonary hypertension. J Heart Lung Transplant. (2017)
36:1234–42. doi: 10.1016/j.healun.2017.05.024 129. Tanaka Y, Takase B, Yao T, Ishihara M. Right ventricular electrical remodeling
and arrhythmogenic substrate in rat pulmonary hypertension. Am J Respir
Cell Mol Biol. (2013) 49:426–36. doi: 10.1165/rcmb.2012-0089OC 112. Anand V, Roy SS, Archer SL, Weir EK, Garg SK, Duval S, et al. Trends
and outcomes of pulmonary arterial hypertension-related hospitalizations
in the United States: analysis of the nationwide inpatient sample
database from 2001 through 2012. JAMA Cardiol. (2016) 1:1021–9. doi: 10.1001/jamacardio.2016.3591 130. Held M, Grun M, Holl R, Hubner G, Kaiser R, Karl S, et al. Cardiopulmonary
exercise testing to detect chronic thromboembolic pulmonary hypertension
in patients with normal echocardiography. Respiration. (2014) 87:379–87. doi: 10.1159/000358565 113. Kanemoto
N,
Sasamoto
H. Arrhythmias
in
primary
pulmonary
hypertension. Jpn Heart J. (1979) 20:765–75. doi: 10.1536/ihj.20.765 131. REFERENCES Molecular research in chronic thromboembolic
pulmonary
hypertension. Int
J
Mol
Sci. (2019)
20:784. doi: 10.3390/ijms20030784 102. Rol N, Kurakula KB, Happe C, Bogaard HJ, Goumans MJ. TGF-beta and
BMPR2 signaling in PAH: two black sheep in one family. Int J Mol Sci. (2018)
19:2585. doi: 10.3390/ijms19092585 120. Tonelli AR, Baumgartner M, Alkukhun L, Minai OA, Dweik RA. Electrocardiography at diagnosis and close to the time of death in pulmonary
arterial hypertension. Ann Noninvasive Electrocardiol. (2014) 19:258–65. doi: 10.1111/anec.12125 103. Shimizu T, Liao JK. Rho kinases and cardiac remodeling. Circ J. (2016)
80:1491–8. doi: 10.1253/circj.CJ-16-0433 121. Rich JD, Thenappan T, Freed B, Patel AR, Thisted RA, Childers R, et al. QTc prolongation is associated with impaired right ventricular function
and predicts mortality in pulmonary hypertension. Int J Cardiol. (2013)
167:669–76. doi: 10.1016/j.ijcard.2012.03.071 104. Tsai SH, Lu G, Xu X, Ren Y, Hein TW, Kuo L. Enhanced endothelin-
1/Rho-kinase
signalling
and
coronary
microvascular
dysfunction
in
hypertensive myocardial hypertrophy. Cardiovasc Res. (2017) 113:1329–37. doi: 10.1093/cvr/cvx103 122. Smith Genuardi MV, Koczo A, Zou RH, Thoma FW, Handen A,
Craig
E,
et
al. Atrial
arrhythmias
are
associated
with
increased
mortality in pulmonary arterial hypertension. Pulm Circ. (2018) 8:1–9. doi: 10.1177/2045894018790316 105. Zeidan Gan XT, Thomas A, Karmazyn M. Prevention of RhoA activation
and cofilin-mediated actin polymerization mediates the antihypertrophic
effect of adenosine receptor agonists in angiotensin II- and endothelin-
1-treated
cardiomyocytes. Mol
Cell
Biochem. (2014)
385:239–48. doi: 10.1007/s11010-013-1832-2 123. Folino AF, Bobbo F, Schiraldi C, Tona F, Romano S, Buja G, et al. Ventricular
arrhythmias and autonomic profile in patients with primary pulmonary
hypertension. Lung. (2003) 181:321–8. doi: 10.1007/s00408-003-1034-x 106. Sunamura S, Satoh K, Kurosawa R, Ohtsuki T, Kikuchi N, Elias-Al-Mamun
M, et al. Different roles of myocardial ROCK1 and ROCK2 in cardiac
dysfunction and postcapillary pulmonary hypertension in mice. Proc Natl
Acad Sci U S A. (2018) 115:E7129–38. doi: 10.1073/pnas.1721298115 124. Ciarka Doan V, Velez-Roa S R. Naeije, van de Borne P. Prognostic
significance of sympathetic nervous system activation in pulmonary
arterial hypertension. Am J Respir Crit Care Med. (2010) 181:1269–75. doi: 10.1164/rccm.200912-1856OC 107. Ikeda S, Satoh K, Kikuchi N, Miyata S, Suzuki K, Omura J, et al. Crucial role
of rho-kinase in pressure overload-induced right ventricular hypertrophy
and dysfunction in mice. Arterioscler Thromb Vasc Biol. (2014) 34:1260–71. doi: 10.1161/ATVBAHA.114.303320 125. Zhao Q, Deng H, Jiang X, Dai Z, Wang X, Wang X, et al. REFERENCES Differentially
expressed plasma microRNAs and the potential regulatory function of Let-
7b in chronic thromboembolic pulmonary hypertension. PLoS ONE. (2014)
9:e101055. doi: 10.1371/journal.pone.0101055 95. Frump AL, Bonnet S, de Jesus Perez VA, Lahm T. Emerging role of
angiogenesis in adaptive and maladaptive right ventricular remodeling
in pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol. (2018)
314:L443–60. doi: 10.1152/ajplung.00374.2017 80. Reesink HJ, Meijer RC, Lutter R, Boomsma F, Jansen HM, Kloek JJ,
et al. Hemodynamic and clinical correlates of endothelin-1 in chronic
thromboembolic pulmonary hypertension. Circ J. (2006) 70:1058–63. doi: 10.1253/circj.70.1058 96. van Wolferen SA, Marcus JT, Westerhof N, Spreeuwenberg MD, Marques
KM, Bronzwaer JG, et al. Right coronary artery flow impairment in
patients with pulmonary hypertension. Eur Heart J. (2008) 29:120–7. doi: 10.1093/eurheartj/ehm567 April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 13 Stam et al. Large Animal Models of CTEPH 97. Vogel-Claussen J, Skrok J, Shehata ML, Singh S, Sibley CT, Boyce DM,
et al. Right and left ventricular myocardial perfusion reserves correlate
with right ventricular function and pulmonary hemodynamics in patients
with pulmonary arterial hypertension. Radiology. (2011) 258:119–27. doi: 10.1148/radiol.10100725 116. Cannillo M, Grosso Marra W, Gili S, D’Ascenzo F, Morello M,
Mercante
L,
et
al. Supraventricular
arrhythmias
in
patients
with
pulmonary arterial hypertension. Am J Cardiol. (2015) 116:1883–9. doi: 10.1016/j.amjcard.2015.09.039 117. Hoeper MM, Galie N, Murali S, Olschewski H, Rubenfire M, Robbins
IM, et al. Outcome after cardiopulmonary resuscitation in patients with
pulmonary arterial hypertension. Am J Respir Crit Care Med. (2002)
165:341–4. doi: 10.1164/ajrccm.165.3.200109-0130c 98. Dewachter L, Dewachter C. Inflammation in right ventricular failure: does it
matter? Front Physiol. (2018) 9:1056. doi: 10.3389/fphys.2018.01056 99. Sun
XQ,
Abbate
A,
Bogaard
HJ. Role
of
cardiac
inflammation
in
right
ventricular
failure. Cardiovasc
Res. (2017)
113:1441–52. doi: 10.1093/cvr/cvx159 118. Strauss Sassi Y, Bueno-Beti C, Ilkan Z, Raad N, Cacheux M, Bisserier M, et al. Intra-tracheal gene delivery of aerosolized SERCA2a to the lung suppresses
ventricular arrhythmias in a model of pulmonary arterial hypertension. J Mol
Cell Cardiol. (2019) 127:20–30. doi: 10.1016/j.yjmcc.2018.11.017 100. Frangogiannis
NG. Fibroblasts
and
the
extracellular
matrix
in
right
ventricular
disease. Cardiovasc
Res. (2017)
113:1453–64. doi: 10.1093/cvr/cvx146 119. Umar S, Lee JH, de Lange E, Iorga A, Partow-Navid R, Bapat A, et al. Spontaneous ventricular fibrillation in right ventricular failure secondary
to chronic pulmonary hypertension. Circ Arrhythm Electrophysiol. (2012)
5:181–90. doi: 10.1161/CIRCEP.111.967265 101. Opitz Kirschner MB. REFERENCES Held M, Hesse A, Gott F, Holl R, Hubner G, Kolb P, et al. A symptom-
related monitoring program following pulmonary embolism for the early
detection of CTEPH: a prospective observational registry study. BMC Pulm
Med. (2014) 14:141. doi: 10.1186/1471-2466-14-141 114. Rajdev
Garan
H,
Biviano
A. Arrhythmias
in
pulmonary
arterial
hypertension. Prog
Cardiovasc
Dis. (2012)
55:180–6. doi: 10.1016/j.pcad.2012.06.002 115. Tongers J, Schwerdtfeger B, Klein G, Kempf T, Schaefer A, Knapp
JM,
et
al. Incidence
and
clinical
relevance
of
supraventricular
tachyarrhythmias
in
pulmonary
hypertension. Am
Heart
J. (2007)
153:127–32. doi: 10.1016/j.ahj.2006.09.008 132. Richter MJ, Pader P, Gall H, Reichenberger F, Seeger W, Mayer E, et
al. The prognostic relevance of oxygen uptake in inoperable chronic
thromboembolic pulmonary hypertension. Clin Respir J. (2015) 11:682–90. doi: 10.1111/crj.12399 April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 14 Stam et al. Large Animal Models of CTEPH 133. Hasler ED, Muller-Mottet S, Furian M, Saxer S, Huber LC, Maggiorini
M,
et
al. Pressure-flow
during
exercise
catheterization
predicts
survival
in
pulmonary
hypertension. Chest. (2016)
150:57–67. doi: 10.1016/j.chest.2016.02.634 140. Clauss S, Bleyer C, Schuttler D, Tomsits P, Renner S, Klymiuk N, et al. Animal
models of arrhythmia: classic electrophysiology to genetically modified
large animals. Nat Rev Cardiol. (2019) 16:457–75. doi: 10.1038/s41569-019-
0179-0 134. Claessen La Gerche A, Dymarkowski S, Claus P, Delcroix M, Heidbuchel H. Pulmonary vascular and right ventricular reserve in patients with normalized
resting hemodynamics after pulmonary endarterectomy. J Am Heart Assoc. (2015) 4:e001602. doi: 10.1161/JAHA.114.001602 141. Clauss
S,
Schuttler
D,
Bleyer
C,
Vlcek
J,
Shakarami
M,
Tomsits
P,
et
al. Characterization
of
a
porcine
model
of
atrial
arrhythmogenicity
in
the
context
of
ischaemic
heart
failure. PLoS
ONE. (2020)
15:e0232374. doi:
10.1371/journal.pone.02
32374 135. Claessen La Gerche A, Wielandts JY, Bogaert J, Van Cleemput J, Wuyts
W, Claus P, et al. Exercise pathophysiology and sildenafil effects in
chronic thromboembolic pulmonary hypertension. Heart. (2015) 101:637–
44. doi: 10.1136/heartjnl-2014-306851 142. Shigeta Tanabe N, Shimizu H, Hoshino S, Maruoka M, Sakao S, Tada Y, et al. Gender differences in chronic thromboembolic pulmonary hypertension in
Japan. Circ J. (2008) 72:2069–74. doi: 10.1253/circj.CJ-08-0377 136. Melot C, Naeije R. Pulmonary vascular diseases. Compr Physiol. (2011)
1:593–619. doi: 10.1002/cphy.c090014 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. 137. D. Frontiers in Cardiovascular Medicine | www.frontiersin.org REFERENCES Merkus, de Beer VJ, Houweling B, Duncker DJ. Control of pulmonary
vascular tone during exercise in health and pulmonary hypertension. Pharmacol Ther. (2008) 119:242–63. doi: 10.1016/j.pharmthera.2008.04.003 138. Iwase T, Nagaya N, Ando M, Satoh T, Sakamaki F, Kyotani S, et al. Acute and
chronic effects of surgical thromboendarterectomy on exercise capacity and
ventilatory efficiency in patients with chronic thromboembolic pulmonary
hypertension. Heart. (2001) 86:188–92. doi: 10.1136/heart.86.2.188 Copyright © 2021 Stam, Clauss, Taverne and Merkus. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these
terms. 139. Cai Z, Klein T, Geenen LW, Tu L, Tian S, van den Bosch AE, et al. Lower
plasma melatonin levels predict worse long-term survival in pulmonary
arterial hypertension. J Clin Med. (2020) 9:1248. doi: 10.3390/jcm9051248 April 2021 | Volume 8 | Article 574360 Frontiers in Cardiovascular Medicine | www.frontiersin.org 15
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What Is Our Understanding of the Influence of Gut Microbiota on the Pathophysiology of Parkinson’s Disease?
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Frontiers in neuroscience
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Capital Medical University, China Reviewed by:
Louise C. Parr-Brownlie,
University of Otago, New Zealand
Ernest Jennings,
James Cook University, Australia
Elodie Kip,
University of Otago, Dunedin,
New Zealand in collaboration with
reviewer LP *Correspondence:
Philip W. J. Burnet
phil.burnet@psych.ox.ac.uk Specialty section:
This article was submitted to
Neuropharmacology,
a section of the journal
Frontiers in Neuroscience Keywords: Parkinson’s, microbiota, microbiome, bacteria, gut, dysbiosis, neurodegenerative, gut–brain What Is Our Understanding of the
Influence of Gut Microbiota on the
Pathophysiology of Parkinson’s
Disease? Microbiota have increasingly become implicated in predisposition to human diseases,
including neurodegenerative disorders such as Parkinson’s disease (PD). Traditionally, a
central nervous system (CNS)-centric approach to understanding PD has predominated;
however, an association of the gut with PD has existed since Parkinson himself reported
the disease. The gut–brain axis refers to the bidirectional communication between
the gastrointestinal tract (GIT) and the brain. Gut microbiota dysbiosis, reported in
PD patients, may extend this to a microbiota–gut–brain axis. To date, mainly the
bacteriome has been investigated. The change in abundance of bacterial products
which accompanies dysbiosis is hypothesised to influence PD pathophysiology via
multiple mechanisms which broadly centre on inflammation, a cause of alpha-synuclein
(a-syn) misfolding. Two main routes are hypothesised by which gut microbiota can
influence PD pathophysiology, the neural and humoral routes. The neural route involves
a-syn misfolding peripherally in the enteric nerves which can then be transported to
the brain via the vagus nerve. The humoral route involves transportation of bacterial
products and proinflammatory cytokines from the gut via the circulation which can
cause central a-syn misfolding by inducing neuroinflammation. This article will assess
whether the current literature supports gut bacteria influencing PD pathophysiology via
both routes. MINI REVIEW MINI REVIEW
published: 26 August 2021
doi: 10.3389/fnins.2021.708587 INTRODUCTION Received: 12 May 2021
Accepted: 26 July 2021
Published: 26 August 2021 Parkinson’s disease (PD) is the second most common neurodegenerative disorder worldwide. Insoluble intracytoplasmic protein aggregates, primarily consisting of misfolded fibrillar alpha-
synuclein (a-syn), are PD neuropathological hallmarks. These aggregates [Lewy bodies (LBs) and
Lewy neurites (LNs)], are believed to cause the catecholaminergic (CA) and dopaminergic (DA)
neuronal loss which manifests as motor dysfunction (parkinsonism). Since PD motor symptoms
are not evident until approximately 60–70% of DA neurons in the substantia nigra pars compacta
(SNpc) are lost (Dauer and Przedborski, 2003), the gut–brain hypothesis may allow earlier
interventions to be made before the motor system becomes affected. Parkinson’s disease (PD) is the second most common neurodegenerative disorder worldwide. Insoluble intracytoplasmic protein aggregates, primarily consisting of misfolded fibrillar alpha-
synuclein (a-syn), are PD neuropathological hallmarks. These aggregates [Lewy bodies (LBs) and
Lewy neurites (LNs)], are believed to cause the catecholaminergic (CA) and dopaminergic (DA)
neuronal loss which manifests as motor dysfunction (parkinsonism). Since PD motor symptoms
are not evident until approximately 60–70% of DA neurons in the substantia nigra pars compacta
(SNpc) are lost (Dauer and Przedborski, 2003), the gut–brain hypothesis may allow earlier
interventions to be made before the motor system becomes affected. Pathophysiological Evidence The characteristic Lewy bodies (LBs) have also been observed in
the enteric nervous system (ENS) of PD patients (Wakabayashi
et al., 1988; Shannon et al., 2012b; Gold et al., 2013). Braak
et al. (2003) defined the caudo-rostral axis in the brain along
which a-syn pathology progresses and identified LBs and LNs
in the dorsal motor nucleus of the vagus (DMV) in PD post
mortem brain samples. This implicated the vagus nerve, and later
the ENS (Braak et al., 2006), in the spreading of PD pathology. Braak’s hypothesis states that retrograde transport of misfolded
a-syn occurs from projection neurons in the ENS to the central
nervous system (CNS), via the vagus nerve. The initial a-syn
misfolding was posited to be induced in the enteric nerves by an
exogenous, neurotropic pathogen (Lionnet et al., 2018). Indeed,
other studies have corroborated this hypothesis (Shannon et al.,
2012a; Stokholm et al., 2016). Various animal models have supported Braak’s hypothesis. Vagus nerve-mediated translocation of a-syn aggregations from
the gut to the brain was observed after injections of human
recombinant a-syn from PD patients into rats’ intestinal walls
(Holmqvist et al., 2014), or the peritoneal cavity of a-synuclein
overexpressing (ASO) mice (Breid et al., 2016). Furthermore,
injection of preformed fibrils (PFFs) into mouse gastrointestinal
tracts (GITs) led to DA neuronal loss in the SNpc and motor
symptoms after 7 months, with a-syn accumulation in anatomical
locations associated with more advanced Braak’s stages (Kim
et al., 2019). In this study, truncal vagotomy in the PFF-injected
mice prevented a-syn spreading to the brain and protected
against loss of DA neurons. Decreased risk of PD with truncal
vagotomy has also been observed in patients (Svensson et al.,
2015; Liu et al., 2017). Citation: Hill AE, Wade-Martins R and
Burnet PWJ (2021) What Is Our
Understanding of the Influence of Gut
Microbiota on the Pathophysiology
of Parkinson’s Disease? Front. Neurosci. 15:708587. doi: 10.3389/fnins.2021.708587 Hill AE, Wade-Martins R and
Burnet PWJ (2021) What Is Our
Understanding of the Influence of Gut
Microbiota on the Pathophysiology
of Parkinson’s Disease? Front. Neurosci. 15:708587. doi: 10.3389/fnins.2021.708587 August 2021 | Volume 15 | Article 708587 1 Frontiers in Neuroscience | www.frontiersin.org Hill et al. Gut Microbiota in Parkinson’s Disease Hill et al. The microorganisms in the gut are involved in gastrointestinal
(GI) homoeostasis, such as maintaining the integrity of the gut
epithelial barrier (Miraglia and Colla, 2019), and their abnormal
colonisation and function (dysbiosis) can lead to peripheral
and/or systemic inflammation (Chen et al., 2019) which may
facilitate PD pathophysiology by neural and humoral routes. and their products into the lamina propria, triggering further
inflammation. Both neural and humoral routes converge on
inflammation which, via oxidative stress, forms one way in
which a-syn misfolding can occur (Hashimoto et al., 1999; Lema
Tomé et al., 2013). Local inflammation facilitates peripheral a-syn
misfolding which propagates to the brain via the neural route. Systemic inflammation induces neuroinflammation in the brain
(Mogi et al., 1994) via the humoral route which causes a-syn
misfolding. A-syn can induce further oxidative stress, forming a
positive feedback loop which leads to neurodegeneration in the
brain (Dias et al., 2013; Chen et al., 2019). NEURAL AND HUMORAL ROUTES FOR
A-SYNUCLEIN MISFOLDING AND
AGGREGATION Dysbiosis may explain the association between PD and risk
factors known to influence microbiome composition, such as
pesticides and diet (Gorecki et al., 2019; Gubert et al., 2020). Studies in PD, discussed below, propose that changes in bacterial
products accompanying dysbiosis could contribute toward the
observed inflammation in PD patients (Devos et al., 2013; Chen
et al., 2019). Indeed, functional increases in intestinal epithelial
barrier permeability (Davies et al., 1996; Kelly et al., 2014)
and decreased expression of intestinal barrier tight junctions
(Edelblum and Turner, 2009; Clairembault et al., 2015; Perez-
Pardo et al., 2019) in PD have been attributed to inflammation. This increased permeability would allow translocation of bacteria EVIDENCE FOR GUT INVOLVEMENT IN
PARKINSON’S DISEASE Gastrointestinal symptoms have been shown to precede motor
symptoms by Parkinson himself (Parkinson, 2002). Non-
motor symptoms are thought to predate motor symptoms by
approximately a decade and increase the risk of developing PD
(Abbott et al., 2001; Adams-Carr et al., 2016). Prolonged colonic
transit time is present in up to 80% of PD patients (Jost, 1997)
with significantly higher constipation incidence also reported
compared to healthy controls (HCs) (Edwards et al., 1991; Chen
et al., 2015). Gut microbiota have been implicated since they can
aid in host nutrient metabolism and modulate gastrointestinal
motility (Miraglia and Colla, 2019). Neural Route Braak’s hypothesis forms the basis of the neural route. Dysbiosis
in the gut lumen leads to a-syn aggregation in enteric nerves. Indirectly, inflammation increases intestinal barrier permeability
and hence mucosal inflammation, from translocation of bacteria
and their products, which facilitates a-syn misfolding (Forsyth
et al., 2011; Lema Tomé et al., 2013; Kelly et al., 2014). Directly,
enteroendocrine cells (EECs) may propagate misfolded a-syn
from the lumen, along their neuropods, to enteric nerves via
functional synapses (Chandra et al., 2017). This may explain
how Braak’s luminal exogenous pathogen could directly cause
a-syn aggregation in the enteric nerves without violating the
gut epithelium. Peripheral misfolded a-syn is proposed to be
transported in a prion-like way between neurons, passing from
the enteric nerves to the vagus nerve to the brain, where
a-syn forms intracytoplasmic aggregates (Visanji et al., 2013). Exogenous a-syn fibrils enter neurons (Volpicelli-Daley et al.,
2011), seeding intracellular a-syn aggregation both in vitro (Luk
et al., 2009) and in vivo (Kordower et al., 2011; Holmqvist et al.,
2014; Okuzumi et al., 2018), and upon exiting these neurons
restarts the process (Lee et al., 2005). Frontiers in Neuroscience | www.frontiersin.org Humoral Route: Dysbiosis and
Inflammation Reductions in the butyrate-producing
families Lachnospiraceae and Prevotellaceae and bacterial genera
such as Blautia, Roseburia, Coprococcus, and Faecalibacterium
prausnitzii are most commonly found (Table 1). Decreased
faecal SCFA concentrations in PD have been documented (Unger
et al., 2016), which could increase local inflammation and in
turn peripheral a-syn misfolding, facilitating the neural route. Since SCFAs can maintain the integrity of the intestinal barrier
(Wang et al., 2012), their reduction could increase gut barrier
permeability, facilitating the passage of other bacterial products
and proinflammatory cytokines into the circulation, thereby
engaging the humoral system (Dalile et al., 2019). Moreover, in
normal physiology unmetabolised SCFAs can reach the systemic
circulation and cross the blood–brain barrier (BBB) (Mitchell
et al., 2011), following the humoral route, meaning that a lack of
SCFAs could directly contribute to neuroinflammation. However,
reports of SCFA-producing bacteria abundance are contradictory:
Prevotella is decreased across studies whilst Akkermansia is
increased, despite both containing mucin-degrading species
(Table 1). This same pattern has been identified in multiple
sclerosis (Freedman et al., 2018). Decreased Prevotella levels may
reflect a lack of mucin synthesis, linked to increased barrier
permeability (Bullich et al., 2019). Indeed, butyrate stimulates
mucin synthesis (Brown et al., 2011) and putative-butyrate-
producing (pBP) bacteria, such as F. prausnitzi and Roseburia,
are consistently decreased (Table 1). Akkermansia may function
as a double-edged sword: although mucin degradation is pro-
inflammatory, decreased mucin levels could negatively feedback
and increase other bacteria’s mucin synthesis (Bullich et al., 2019). Moreover, Akkermansia converts mucin degradation products
into SCFAs (Derrien et al., 2004). Therefore, without pBP bacteria
decreases, increased Akkermansia could be anti-inflammatory;
however, decreased pBP bacteria abundance could cause net
mucin degradation and increased barrier permeability. Bacterial amyloids are increasingly being implicated in PD
pathology via the neural route or exacerbating existing pathology
via the humoral route. Extracellular amyloid fibres, such as
curli, are produced by bacterial species including Escherichia
coli (Römling et al., 1998; Hufnagel et al., 2013). Since bacterial
amyloids can cross-seed amyloids from other bacterial species
to induce aggregation, they may also cross-seed human a-syn
in enteric nerves for propagation via the vagus nerve (Santos
et al., 2019). Evidence for this comes from a study which
exposed aged rats with human-a-syn-expressing-Caenorhabditis
elegans to curliated E. coli: rats had increased a-syn inclusions
in the gut and brain, accompanied by neuroinflammation (Chen
et al., 2016). Furthermore, administration of curliated E. Humoral Route: Dysbiosis and
Inflammation Bacterial products and proinflammatory cytokines in the
systemic circulation trigger neuroinflammation, inducing central
a-syn misfolding through oxidative stress (Hashimoto et al., 1999;
Lema Tomé et al., 2013). Although mechanistically distinct to
the neural route, the direction of pathology transfer remains the August 2021 | Volume 15 | Article 708587 Frontiers in Neuroscience | www.frontiersin.org Frontiers in Neuroscience | www.frontiersin.org 2 Gut Microbiota in Parkinson’s Disease Hill et al. The bacterial endotoxin, LPS, is also implicated in PD
pathogenesis and may arise from the enrichment of Gram-
negative-rich phyla such as Proteobacteria and Verrucomicrobia
(Table 1). Increased TLR4 (LPS-specific receptor) expression in
PD colonic biopsies (Perez-Pardo et al., 2019) and decreased
serum LPS-binding protein (LBP) concentrations in PD (Forsyth
et al., 2011; Hasegawa et al., 2015), also indicated LPS
involvement. Functional evidence comes from rotenone-treated
TLR4-KO mice which, compared to rotenone-treated WT mice,
had reduced inflammation (intestinal and of the brain) and
dysfunction (intestinal and motor) (Perez-Pardo et al., 2019). LPS can subvert the intestinal epithelial barrier both indirectly,
through induced proinflammatory cytokines, and directly
(Forsyth et al., 2011; Pawłowska and Sobieszcza´nska, 2017). LPS-
induced inflammation in the lamina propria facilitates the neural
route and, by entering the systemic circulation, LPS can directly
participate in the humoral route. Moreover, LPS can disrupt the
BBB (Kortekaas et al., 2005; Banks and Erickson, 2010), and in the
brain can activate microglial CD14/TLR4/LBP complexes (Rivest,
2003). This creates a positive feedback cycle whereby microglia
release proinflammatory cytokines, causing neuroinflammation
which results in neuronal death and release of a-syn which then
binds to TLR4 and/or TLR2 to further activate microglia and
astroglia (Fellner et al., 2013; Kim et al., 2013). This process can
mediate DA neuronal loss in the SN via oxidative stress (Qin et al.,
2007; Dias et al., 2013). same. The first study to link dysbiosis with PD demonstrated
significant differences in faecal bacterial taxa between PD
patients and HCs (Scheperjans et al., 2015). Many more case–
control studies, using faecal samples, have followed (Table 1). Although heterogeneity between results exists, the consensus
is that the dysbiosis observed represents a shift toward a
proinflammatory profile. Short-chain fatty acids (SCFAs) are produced by GI bacteria
when anaerobically fermenting dietary fibres. These SCFAs
(in particular butyrate, propionate and acetate) have anti-
inflammatory effects both locally and systemically (Millard et al.,
2002; Dalile et al., 2019). Frontiers in Neuroscience | www.frontiersin.org Humoral Route: Dysbiosis and
Inflammation (2017)
Family: Bifidobacteriaceae, Christensenellaceae, Lactobacillaceae,
Tissierellaceae, Verrucomicrobiaceae
Genus: Akkermansia, Lactobacillus, Bifidobacterium
Family: Lachnospiraceae, Pasteurellaceae
Hopfner et al. (2017)
Family: Lactobacillaceae*, Barnesiellaceae, Enterococcaceae
n/a
Petrov et al. (2017)
Genus: Bifidobacterium, Catabacter, Christensenella, Lactobacillus,
Oscillospira
Genus: Bacteroides, Dorea, Faecalibacterium, Prevotella
Li et al. (2017)
Phylum: Proteobacteria, Actinobacteria
Family: Enterobacteriaceae, Veillonellaceae, Erysipelotrichaceae,
Coriobacteriaceae, Streptococcaceae, Moraxellaceae, and
Enterococcaceae
Genus: Acidaminococcus, Acinetobacter, Enterococcus,
Escherichia–Shigella, Megamonas, Megasphaera, Proteus,
Streptococcus
Phylum: Bacteroidetes
Genus: Blautia, Faecalibacterium, Ruminococcus
Heintz-Buschart et al. (2018)
Phylum: Verrucomicrobia
Class: Verrucomicrobiae
Order: Verrucomicrobiales
Genus: Akkermansia
n/a
Lin et al. (2018)
Family: Eubacteriaceae, Bifidobacteriaceae, Aerococcaceae,
Desulfovibrionaceae
Phylum: Firmicutes, Tenericutes, Euryarchaeota
Family: Streptococcaceae, Methylobacteriaceae,
Comamonadaceae, Halomonadaceae, Hyphomonadaceae,
Brucellaceae, Xanthomonadaceae, Lachnospiraceae,
Actinomycetaceae, Sphingomonadaceae, Pasteurellaceae,
Micrococcaceae, Intrasporangiaceae, Methanobacteriaceae,
Idiomarinaceae, Brevibacteriaceae, Gemellaceae
Qian et al. (2018)
Genus: Clostridium IV, Sphingomonas, Holdemania, Clostridium XVIII,
Butyricicoccus, Anaerotruncus, Aquabacterium
n/a
Barichella et al. (2019)
Phylum: Proteobacteria, Verrucomicrobia
Family: Enterobacteriaceae, Verrucomicrobiaceae, Bifidobacteriaceae,
Christensenellaceae, Coriobacteriaceae, Lactobacillaceae
Genus: Akkermansia
Family: Lachnospiraceae
Li et al. (2019)
Family: Ruminococcaceae, Verrucomicrobiaceae,
Porphyromonadaceae, Hydrogenoanaerobacterium, Lachnospiraceae
NK4A
Family: Bacteroides, Prevotellaceae
Pietrucci et al. (2019)
Family: Lactobacillaceae, Enterobacteriaceae, Enterococcaceae
Family: Lachnospiraceae
Vidal-Martinez et al. (2020)
Family: Verrucomicrobiaceae
Genus: Akkermansia
n/a
Ren et al. (2020)
PD-MCI (mild cognitive impairment)
Vs. PD-NC (normal cognition) and HC:
Genus: Blautia, Ruminococcus
PD-NC vs. PD-MCI and HC:
Family: Rikenellaceae
Genus: Alistipes, Barnesiella, Butyricimonas, Odoribacter
n/a
Zhang et al. (2020)
Phylum: Firmicutes, Actinobacteria, Verrucomicrobia
Genus: Oscillospira, Akkermansia
Phylum: Bacteroidetes, Fusobacteria
Genus: Fusobacterium TABLE 1 | Table presenting results of statistically significant (p < 0.05) changes in abundance of bacterial taxa in faecal samples between Parkinson’s disease patients
(PD) and healthy controls (HCs). Studys
Increased in PD patient faeces
Decreased in PD patient faeces
Scheperjans et al. (2015)
Family: Lactobacillaceae, Verrucomicrobiaceae, Bradyrhizobiaceae,
Ruminococcaceae
Family: Prevotellaceae, Clostridiales i.s. IV
Keshavarzian et al. (2015)
Phylum: Bacteroidetes, Proteobacteria, Verrucomicrobia
Family: Bacteroidaceae, Clostridiaceae, Verrucomicrobiaceae
Genus: Akkermansia, Oscillospira, Bacteroides
Phylum: Firmicutes
Family: Lachnospiraceae, Coprobacillaceae
Genus: Blautia, Coprococcus, Dorea, Roseburia
Hasegawa et al. (2015)
Genus: Lactobacillus
Species: Bacteroides fragilis, Clostridium coccoides,
Clostridium leptum
Unger et al. (2016)
Family: Enterobacteriaceae
Genus: Bifidobacterium
Phylum: Bacteroidetes
Family: Lactobacillaceae, Enterococcaceae
Species: Faecalibacterium prausnitzii
Bedarf et al. (2017)
Phylum: Firmicutes, Verrucomicrobiaceae
Genus: Unclassified Firmicutes, Akkermansia
Family: Erysipelotrichaceae, Prevotellaceae
Genus: Eubacterium, Prevotella
Hill-Burns et al. (2017)
Family: Bifidobacteriaceae, Christensenellaceae, Lactobacillaceae,
Tissierellaceae, Verrucomicrobiaceae
Genus: Akkermansia, Lactobacillus, Bifidobacterium
Family: Lachnospiraceae, Pasteurellaceae
Hopfner et al. (2017)
Family: Lactobacillaceae*, Barnesiellaceae, Enterococcaceae
n/a
Petrov et al. (2017)
Genus: Bifidobacterium, Catabacter, Christensenella, Lactobacillus,
Oscillospira
Genus: Bacteroides, Dorea, Faecalibacterium, Prevotella
Li et al. Phylum: Bacteroidetes, Fusobacteria
Genus: Fusobacterium Humoral Route: Dysbiosis and
Inflammation coli
to ASO mice produced motor defects and GI dysfunction
in addition to increasing gut and brain a-syn aggregation
(Sampson et al., 2020). A role for bacterial amyloids in PD would presumably
require a significant increase in amyloid-synthesising bacteria. Although none of the studies summarised in Table 1 investigated
amyloid-synthesising bacteria, consistent enrichment of E. coli is
observed, though without changes in other amyloid-producing
bacteria such as Streptococcus mutans, Staphylococcus aureus,
and Mycobacterium tuberculosis. This potential discrepancy
may be resolved by hypotheses that bacterial amyloids from
different bacterial species induce cross-seeding in a strain-specific
manner, i.e., solely on a-syn (Friedland and Chapman, 2017),
meaning that even small quantities of bacterial amyloids could
initiate pathology. Molecular H2 is another bacterial fermentation product
which could be affected by dysbiosis. H2 has anti-inflammatory
and antioxidant properties (Ostojic, 2018). Reduced intestinal
H2 production in PD, through decreases of Clostridium and
Prevotella and species such as Bacteroides fragilis (Table 1),
may compromise the function of tissues which use it (such
as DA neurons) (Ostojic, 2018). Indeed, motor symptoms in
rodent lesion models of PD were prevented by H2S inhalation
and systemic administration of NaHS (an H2S donor), and DA
neuronal loss was reduced (Hu et al., 2010; Kida et al., 2011). Therefore, a decrease in H2 might predispose to DA neuronal loss
and hence PD pathology via the humoral route. Bacterial
amyloids
and
human
oligomeric
a-syn
are
recognised
by
the
host
immune
system
via
the
gut
mucosal
TLR2/TLR1
heterocomplex
(Tükel
et
al.,
2010; August 2021 | Volume 15 | Article 708587 3 Hill et al. Gut Microbiota in Parkinson’s Disease TABLE 1 | Table presenting results of statistically significant (p < 0.05) changes in abundance of bacterial taxa in faecal samples between Parkinson’s disease patients
(PD) and healthy controls (HCs). Studys
Increased in PD patient faeces
Decreased in PD patient faeces
Scheperjans et al. (2015)
Family: Lactobacillaceae, Verrucomicrobiaceae, Bradyrhizobiaceae,
Ruminococcaceae
Family: Prevotellaceae, Clostridiales i.s. IV
Keshavarzian et al. (2015)
Phylum: Bacteroidetes, Proteobacteria, Verrucomicrobia
Family: Bacteroidaceae, Clostridiaceae, Verrucomicrobiaceae
Genus: Akkermansia, Oscillospira, Bacteroides
Phylum: Firmicutes
Family: Lachnospiraceae, Coprobacillaceae
Genus: Blautia, Coprococcus, Dorea, Roseburia
Hasegawa et al. (2015)
Genus: Lactobacillus
Species: Bacteroides fragilis, Clostridium coccoides,
Clostridium leptum
Unger et al. (2016)
Family: Enterobacteriaceae
Genus: Bifidobacterium
Phylum: Bacteroidetes
Family: Lactobacillaceae, Enterococcaceae
Species: Faecalibacterium prausnitzii
Bedarf et al. (2017)
Phylum: Firmicutes, Verrucomicrobiaceae
Genus: Unclassified Firmicutes, Akkermansia
Family: Erysipelotrichaceae, Prevotellaceae
Genus: Eubacterium, Prevotella
Hill-Burns et al. August 2021 | Volume 15 | Article 708587 Cause or Consequence? It is difficult to discern whether dysbiosis is a cause or
consequence of PD. Although two longitudinal studies have
been conducted in PD patients, neither have reported significant
changes in microbial composition with progression (Minato
et al., 2017; Aho et al., 2019). Support for a causative role
comes from the association between PD risk and inflammatory
conditions where dysbiosis is also reported, such as irritable
bowel syndrome (IBS) and inflammatory bowel disease (IBD)
(Lai et al., 2014; Lin et al., 2016; Mertsalmi et al., 2017). Evidence for the ENS controlling microbial composition,
with the CNS modulating these ENS signals (Rolig et al.,
2017), suggests that dysbiosis is a consequence of PD. This
substantiates the hypothesis that loss of central DA neurons
initiates DMV degeneration which results in GI inflammation Humoral Route: Dysbiosis and
Inflammation Phylum: Bacteroidetes, Fusobacteria
Genus: Fusobacterium August 2021 | Volume 15 | Article 708587 August 2021 | Volume 15 | Article 708587 Frontiers in Neuroscience | www.frontiersin.org 4 Gut Microbiota in Parkinson’s Disease Hill et al. Nishimori et al., 2012; Hufnagel et al., 2013; Kim et al., 2013;
Daniele et al., 2015). This would initiate a local and central
immune
response
against
endogenous
a-syn
(Lindestam
Arlehamn et al., 2020), creating a proinflammatory environment
which could facilitate a-syn misfolding (Hufnagel et al., 2013;
Friedland and Chapman, 2017; Miraglia and Colla, 2019). et al., 2019). Future studies need to agree on a standardised
protocol, with more stringent inclusion/exclusion criteria, to
increase the reproducibility and hence the reliability of the
reported results. Humoral Route: Dysbiosis and
Inflammation (2017)
Phylum: Proteobacteria, Actinobacteria
Family: Enterobacteriaceae, Veillonellaceae, Erysipelotrichaceae,
Coriobacteriaceae, Streptococcaceae, Moraxellaceae, and
Enterococcaceae
Genus: Acidaminococcus, Acinetobacter, Enterococcus,
Escherichia–Shigella, Megamonas, Megasphaera, Proteus,
Streptococcus
Phylum: Bacteroidetes
Genus: Blautia, Faecalibacterium, Ruminococcus
Heintz-Buschart et al. (2018)
Phylum: Verrucomicrobia
Class: Verrucomicrobiae
Order: Verrucomicrobiales
Genus: Akkermansia
n/a
Lin et al. (2018)
Family: Eubacteriaceae, Bifidobacteriaceae, Aerococcaceae,
Desulfovibrionaceae
Phylum: Firmicutes, Tenericutes, Euryarchaeota
Family: Streptococcaceae, Methylobacteriaceae, TABLE 1 | Table presenting results of statistically significant (p < 0.05) changes in abundance of bacterial taxa in faeca
(PD) and healthy controls (HCs). Studys
Increased in PD patient faeces
Decreas
Scheperjans et al. (2015)
Family: Lactobacillaceae, Verrucomicrobiaceae, Bradyrhizobiaceae,
Ruminococcaceae
Family: P
Keshavarzian et al. (2015)
Phylum: Bacteroidetes, Proteobacteria, Verrucomicrobia
Family: Bacteroidaceae, Clostridiaceae, Verrucomicrobiaceae
Genus: Akkermansia, Oscillospira, Bacteroides
Phylum: F
Family: La
Genus: B
Hasegawa et al. (2015)
Genus: Lactobacillus
Species:
Clostridiu
Unger et al. (2016)
Family: Enterobacteriaceae
Genus: Bifidobacterium
Phylum: B
Family: La
Species:
Bedarf et al. (2017)
Phylum: Firmicutes, Verrucomicrobiaceae
Genus: Unclassified Firmicutes, Akkermansia
Family: E
Genus: E
Hill-Burns et al. (2017)
Family: Bifidobacteriaceae, Christensenellaceae, Lactobacillaceae,
Tissierellaceae, Verrucomicrobiaceae
Genus: Akkermansia, Lactobacillus, Bifidobacterium
Family: La
Hopfner et al. (2017)
Family: Lactobacillaceae*, Barnesiellaceae, Enterococcaceae
n/a
Petrov et al. (2017)
Genus: Bifidobacterium, Catabacter, Christensenella, Lactobacillus,
Oscillospira
Genus: B
Li et al. (2017)
Phylum: Proteobacteria, Actinobacteria
Family: Enterobacteriaceae, Veillonellaceae, Erysipelotrichaceae,
Coriobacteriaceae, Streptococcaceae, Moraxellaceae, and
Enterococcaceae
Genus: Acidaminococcus, Acinetobacter, Enterococcus,
Escherichia–Shigella, Megamonas, Megasphaera, Proteus,
Streptococcus
Phylum: B
Genus: B
Heintz-Buschart et al. (2018)
Phylum: Verrucomicrobia
Class: Verrucomicrobiae
Order: Verrucomicrobiales
Genus: Akkermansia
n/a
Lin et al. (2018)
Family: Eubacteriaceae, Bifidobacteriaceae, Aerococcaceae,
Desulfovibrionaceae
Phylum: F
Family: S
C n/a Idiomarinaceae
Qian et al. (2018)
Genus: Clostridium IV, Sphingomonas, Holdemania, Clostridium XVIII,
Butyricicoccus, Anaerotruncus, Aquabacterium
n/a
Barichella et al. (2019)
Phylum: Proteobacteria, Verrucomicrobia
Family: Enterobacteriaceae, Verrucomicrobiaceae, Bifidobacteriaceae,
Christensenellaceae, Coriobacteriaceae, Lactobacillaceae
Genus: Akkermansia
Family: Lachno
Li et al. (2019)
Family: Ruminococcaceae, Verrucomicrobiaceae,
Porphyromonadaceae, Hydrogenoanaerobacterium, Lachnospiraceae
NK4A
Family: Bactero
Pietrucci et al. (2019)
Family: Lactobacillaceae, Enterobacteriaceae, Enterococcaceae
Family: Lachno
Vidal-Martinez et al. (2020)
Family: Verrucomicrobiaceae
Genus: Akkermansia
n/a
Ren et al. (2020)
PD-MCI (mild cognitive impairment)
Vs. PD-NC (normal cognition) and HC:
Genus: Blautia, Ruminococcus
PD-NC vs. PD-MCI and HC:
Family: Rikenellaceae
Genus: Alistipes, Barnesiella, Butyricimonas, Odoribacter
n/a
Zhang et al. (2020)
Phylum: Firmicutes, Actinobacteria, Verrucomicrobia
Genus: Oscillospira, Akkermansia
Phylum: Bacte
Genus: Fusoba
*Further statistical analysis rendered change non-statistically significant. CONCLUSION Microbiota undoubtedly play a role in PD pathophysiology. Associative evidence from case–control studies and functional
evidence from animal models have provided support for
microbiota causing PD via the neural and humoral routes. PD is primarily considered a disease of old age, despite
pathogenesis preceding motor symptoms by years, with dysbiosis
conceivably acting to exacerbate inflammation. Whilst previously
gut dysbiosis was only considered as a consequence of
PD, it is now also accepted that bacterial products may
influence PD pathology through creating peripheral and systemic
inflammatory environments, increasing both peripheral a-syn
transport to the brain and neuroinflammation (Perez-Pardo
et al., 2017). However, it is still not clear what initially triggers
dysbiosis nor how inflammation would selectively cause a-syn
aggregation rather than, for example, aggregation of Aβ in
Alzheimer’s disease since inflammation is an underlying feature
of many neurodegenerative diseases. Other factors are most likely
implicated, such as gene mutations (e.g., in clearance mechanisms
for misfolded a-syn), since not every ageing person develops PD
or a neurodegenerative disease (Tran et al., 2020). Seminal evidence for the role of GIT microbiota in PD
pathogenesis comes from a study of germ-free (GF) ASO mice
by Sampson et al. (2016). These mice had reduced a-syn
pathology load, microglial activation and motor symptoms
compared to specific pathogen-free (SPF) ASO mice, implicating
gut microbiota in causing PD pathophysiology. Moreover, GF-
ASO mice transplanted with faecal microbiota from human PD
donors developed exacerbated motor symptoms compared to
those given HCs (Sampson et al., 2016). This translates the
associative evidence from Table 1 into causal evidence. Understanding the exact mechanisms by which dysbiosis
could lead to the neuropathological hallmarks of PD will
require case–control studies to shift from predominantly
bacterial abundance measures to whole metagenome sequencing
(Supplementary Table 1) which provides data on functional
changes in the microbiota as well as the levels of other microbes
such as yeasts and viruses (Scheperjans, 2016). Studies which
look set to strengthen evidence for gut bacteria involvement
are investigating the effects of antibiotic administration on
PD risk, since antibiotics alter gut bacteria composition
(Mertsalmi et al., 2020). HOW USEFUL ARE THESE STUDIES? Some common criticisms can be applied to these studies. Methodological differences, some of which are highlighted in
Supplementary Table 1, may explain some of the heterogeneity
between results. Many studies did not identify potential
confounders in statistical analyses which may have resulted
in false positive outcomes. For example, dietary differences
between PD and HC groups, which could account for differential
microbial composition (Graf et al., 2015), were not assessed. Sample handling methods (not listed), such as the time period
between collection and freezing of samples, also varied greatly
but were not considered as potential confounders (Haikal FIGURE 1 | Summary diagram of the main mechanisms by which gut microbiota dysbiosis (specifically of bacteria) may cause PD pathophysiology. Created with
BioRender.com. FIGURE 1 | Summary diagram of the main mechanisms by which gut microbiota dysbiosis (specifically of bacteria) may cause PD pathophysiology. Created with
BioRender.com. August 2021 | Volume 15 | Article 708587 Frontiers in Neuroscience | www.frontiersin.org Hill et al. Gut Microbiota in Parkinson’s Disease and hence dysbiosis (Ulusoy et al., 2017; Rolli-Derkinderen
et al., 2020). However, the decreased PD risk after vagotomy
would suggest pathology originating from a region innervated
by the vagus nerve, such as the GIT, refuting the CNS-
centric hypothesis (Svensson et al., 2015; Liu et al., 2017;
Kim et al., 2019). These opposing arguments could potentially
be reconciled by an emerging theory which suggests the
existence of different subtypes of PD: “PNS-first” or “CNS-first”
(Borghammer and Van Den Berge, 2019). If a-syn pathology
starts in the PNS in a subset of patients, early interventions
to manipulate gut microbiota could be performed to halt
the progression of neurodegeneration before motor system
involvement. Faecal microbiota transplantation (FMT) studies
in humans have produced varying results: whilst Xue et al. (2020) found improvements in clinical scoring scales (such
as UPDRS and NMSS), Huang et al. (2019) did not but
noted constipation alleviation. These studies’ sample sizes and
follow-up periods are too small to draw conclusions from,
however, a larger clinical trial is currently ongoing (Santens,
2021 – NCT03808389). Probiotics administration in PD patients
produced significant improvements (i.e., decreases in MDS-
UPDRS score) (Tamtaji et al., 2019) which has been supported
by DA neuron neuroprotective effects and decreased motor
impairment observed after probiotic administration in a PD
mouse model (Hsieh et al., 2020). AUTHOR CONTRIBUTIONS The routes linking gut microbiota to PD pathophysiology
are illustrated in Figure 1. The change in SCFA- and H2-
producing bacteria, which accompanies dysbiosis, initiates a local
proinflammatory environment which triggers a-syn misfolding
peripherally in the gut, thus facilitating the neural route. Bacterial amyloids may also induce peripheral a-syn misfolding
independently of inflammation. Peripheral misfolded a-syn can
be transported along the enteric nerves via the vagus nerve
to the brainstem. Once in the brain, a-syn progresses along
Braak’s caudo-rostral axis. Local inflammation from dysbiosis can
also increase the permeability of the gut brain barrier, allowing
bacterial products to enter the lamina propria which can generate
further inflammation. Some of these bacterial products (e.g., LPS) AH and PB made an equal contribution to the conceptualisation,
drafting of the manuscript, scientific content proof-reading. AH
drafted the final version of the document and constructed the
accompanying figure and table. RW-M provided a significant
contribution to clinical content and proof-reading. All authors
contributed to the article and approved the submitted version. HOW USEFUL ARE THESE STUDIES? and proinflammatory cytokines can enter the circulation from
the lamina propria, acting via the humoral route by generating
neuroinflammation which causes a-syn misfolding. Frontiers in Neuroscience | www.frontiersin.org REFERENCES Health Dis. 26:26164. doi: 10.3402/mehd.v26.26164 Bullich, C., Keshavarzian, A., Garssen, J., Kraneveld, A., and Perez-Pardo, P. (2019). Gut Vibes in Parkinson’s Disease: The Microbiota-Gut-Brain Axis. Mov. Disord. Clin. Pract. 6, 639–651. doi: 10.1002/mdc3.12840 Gubert, C., Kong, G., Renoir, T., and Hannan, A. J. (2020). Exercise, diet and
stress as modulators of gut microbiota: implications for neurodegenerative
diseases. Neurobiol. Dis. 134:104621. doi:
10.1016/j.nbd.2019.10
4621 Chandra, R., Hiniker, A., Kuo, Y. M., Nussbaum, R. L., and Liddle, R. A. (2017). α-Synuclein in gut endocrine cells and its implications for Parkinson’s disease. JCI Insight 2:e92295. doi: 10.1172/jci.insight.92295 Haikal, C., Chen, Q. Q., and Li, J. Y. (2019). Microbiome changes: an indicator
of Parkinson’s disease? Transl. Neurodegener. 8:38. doi: 10.1186/s40035-019-
0175-7 Chen, H., Zhao, E. J., Zhang, W., Lu, Y., Liu, R., Huang, X., et al. (2015). Meta-
analyses on prevalence of selected Parkinson’s non-motor symptoms before and
after diagnosis. Transl. Neurodegener. 4:1. doi: 10.1186/2047-9158-4-1 Hasegawa, S., Goto, S., Tsuji, H., Okuno, T., Asahara, T., Nomoto, K., et al. (2015). Intestinal dysbiosis and lowered serum lipopolysaccharide-binding
protein in Parkinson’s Disease. PLoS One 10:e0142164. doi: 10.1371/journal. pone.0142164 Chen, Q. Q., Haikal, C., Li, W., and Li, J. Y. (2019). Gut Inflammation in
Association With Pathogenesis of Parkinson’s Disease. Front. Mol. Neurosci. 12:218. doi: 10.3389/fnmol.2019.00218 Chen, S. G., Stribinskis, V., Rane, M. J., Demuth, D. R., Gozal, E., Roberts, A. M.,
et al. (2016). Exposure to the functional bacterial amyloid protein curli enhances
Alpha-Synuclein aggregation in aged Fischer 344 Rats and Caenorhabditis
elegans. Sci. Rep. 6:34477. doi: 10.1038/srep34477 Hashimoto, M., Hsu, L. J., Xia, Y., Takeda, A., Sisk, A., Sundsmo, M.,
et al. (1999). Oxidative stress induces amyloid-like aggregate formation
of NACP/alpha-synuclein in vitro. Neuroreport 10, 717–721. doi: 10.1097/
00001756-199903170-00011 Clairembault, T., Leclair-Visonneau, L., Coron, E., Bourreille, A., Le Dily, S.,
Vavasseur, F., et al. (2015). Structural alterations of the intestinal epithelial
barrier in Parkinson’s disease. Acta Neuropathol. Commun. 3:12. doi: 10.1186/
s40478-015-0196-0 Heintz-Buschart, A., Pandey, U., Wicke, T., Sixel-Döring, F., Janzen, A., Sittig-
Wiegand, E., et al. (2018). The nasal and gut microbiome in Parkinson’s disease
and idiopathic rapid eye movement sleep behavior disorder. Mov. Disord. 33,
88–98. doi: 10.1002/mds.27105 Dalile, B., Van Oudenhove, L., Vervliet, B., and Verbeke, K. (2019). The role
of short-chain fatty acids in microbiota-gut-brain communication. Nat. Rev. Gastroenterol. Hepatol. 16, 461–478. doi: 10.1038/s41575-019-0157-3 Hill-Burns, E. M., Debelius, J. W., Morton, J. T., Wissemann, W. T., Lewis,
M. R., Wallen, Z. REFERENCES doi: 10.1186/s13073-017-0428-y Fellner, L., Irschick, R., Schanda, K., Reindl, M., Klimaschewski, L., Poewe, W., et al. (2013). Toll-like receptor 4 is required for α-synuclein dependent activation of
microglia and astroglia. Glia 61, 349–360. doi: 10.1002/glia.22437 Forsyth, C. B., Shannon, K. M., Kordower, J. H., Voigt, R. M., Shaikh, M., Jaglin,
J. A., et al. (2011). Increased intestinal permeability correlates with sigmoid
mucosa alpha-synuclein staining and endotoxin exposure markers in early
Parkinson’s disease. PLoS One 6:e28032. doi: 10.1371/journal.pone.0028032 Borghammer, P., and Van Den Berge, N. (2019). Brain-First versus Gut-First
Parkinson’s Disease: A Hypothesis. J. Parkinsons Dis. 9, S281–S295. doi: 10. 3233/jpd-191721 Braak, H., de Vos, R. A., Bohl, J., and Del Tredici, K. (2006). Gastric alpha-
synuclein immunoreactive inclusions in Meissner’s and Auerbach’s plexuses in
cases staged for Parkinson’s disease-related brain pathology. Neurosci. Lett. 396,
67–72. doi: 10.1016/j.neulet.2005.11.012 Freedman, S. N., Shahi, S. K., and Mangalam, A. K. (2018). The "gut
feeling": breaking down the role of gut microbiome in multiple sclerosis. Neurotherapeutics 15, 109–125. doi: 10.1007/s13311-017-0588-x Friedland, R. P., and Chapman, M. R. (2017). The role of microbial amyloid
in neurodegeneration. PLoS Pathog. 13:e1006654. doi: 10.1371/journal.ppat. 1006654 Braak, H., Rüb, U., Gai, W. P., and Del Tredici, K. (2003). Idiopathic Parkinson’s
disease: possible routes by which vulnerable neuronal types may be subject
to neuroinvasion by an unknown pathogen. J. Neural Transm. 110, 517–536. doi: 10.1007/s00702-002-0808-2 Gold, A., Turkalp, Z. T., and Munoz, D. G. (2013). Enteric alpha-synuclein
expression is increased in Parkinson’s disease but not Alzheimer’s disease. Mov. Disord. 28, 237–240. doi: 10.1002/mds.25298 Breid, S., Bernis, M. E., Babila, J. T., Garza, M. C., Wille, H., and Tamgüney,
G. (2016). Neuroinvasion of α-synuclein prionoids after intraperitoneal and
intraglossal inoculation. J. Virol. 90, 9182–9193. doi: 10.1128/jvi.01399-16 Gorecki, A. M., Preskey, L., Bakeberg, M. C., Kenna, J. E., Gildenhuys, C.,
MacDougall, G., et al. (2019). Altered Gut Microbiome in Parkinson’s Disease
and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-
Expressing Mouse Model. Front. Neurosci. 13:839. doi: 10.3389/fnins.2019. 00839 Brown, C. T., Davis-Richardson, A. G., Giongo, A., Gano, K. A., Crabb, D. B.,
Mukherjee, N., et al. (2011). Gut microbiome metagenomics analysis suggests
a functional model for the development of autoimmunity for type 1 diabetes. PLoS One 6:e25792. doi: 10.1371/journal.pone.0025792 Graf, D., Di Cagno, R., Fåk, F., Flint, H. J., Nyman, M., Saarela, M., et al. (2015). Contribution of diet to the composition of the human gut microbiota. Microb. Ecol. REFERENCES Dauer, W., and Przedborski, S. (2003). Parkinson’s disease: mechanisms and
models. Neuron 39, 889–909. doi: 10.1016/s0896-6273(03)00568-3 Abbott, R. D., Petrovitch, H., White, L. R., Masaki, K. H., Tanner, C. M., Curb, J. D.,
et al. (2001). Frequency of bowel movements and the future risk of Parkinson’s
disease. Neurology 57, 456–462. doi: 10.1212/wnl.57.3.456 Davies, K. N., King, D., Billington, D., and Barrett, J. A. (1996). Intestinal
permeability and orocaecal transit time in elderly patients with Parkinson’s
disease. Postgrad. Med. J. 72, 164–167. doi: 10.1136/pgmj.72.845.164 et al. (2001). Frequency of bowel movements and the future risk of Parkinson’s
disease. Neurology 57, 456–462. doi: 10.1212/wnl.57.3.456 Derrien, M., Vaughan, E. E., Plugge, C. M., and de Vos, W. M. (2004). Akkermansia
muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int. J. Sys. Evol. Microbiol. 54, 1469–1476. doi: 10.1099/ijs.0.02873-0 Adams-Carr, K. L., Bestwick, J. P., Shribman, S., Lees, A., Schrag, A., and Noyce,
A. J. (2016). Constipation preceding Parkinson’s disease: a systematic review
and meta-analysis. J. Neurol. Neurosurg. Psychiatry 87, 710–716. doi: 10.1136/
jnnp-2015-311680 Devos, D., Lebouvier, T., Lardeux, B., Biraud, M., Rouaud, T., Pouclet, H., et al. (2013). Colonic inflammation in Parkinson’s disease. Neurobiol. Dis. 50, 42–48. doi: 10.1016/j.nbd.2012.09.007 Aho, V. T. E., Pereira, P. A. B., Voutilainen, S., Paulin, L., Pekkonen, E., Auvinen,
P., et al. (2019). Gut microbiota in Parkinson’s disease: temporal stability and
relations to disease progression. EBioMedicine 44, 691–707. doi: 10.1016/j. ebiom.2019.05.064 Dias, V., Junn, E., and Mouradian, M. M. (2013). The role of oxidative stress in
Parkinson’s disease. J. Parkinsons Dis. 3, 461–491. doi: 10.3233/jpd-130230 Banks, W. A., and Erickson, M. A. (2010). The blood-brain barrier and immune
function and dysfunction. Neurobiol. Dis. 37, 26–32. doi: 10.1016/j.nbd.2009. 07.031 Edelblum, K. L., and Turner, J. R. (2009). The tight junction in inflammatory
disease: communication breakdown. Curr. Opin. Pharmacol. 9, 715–720. doi:
10.1016/j.coph.2009.06.022 Barichella, M., Severgnini, M., Cilia, R., Cassani, E., Bolliri, C., Caronni, S.,
et al. (2019). Unraveling gut microbiota in Parkinson’s disease and atypical
parkinsonism. Mov. Disord. 34, 396–405. doi: 10.1002/mds.27581 Edwards, L. L., Pfeiffer, R. F., Quigley, E. M., Hofman, R., and Balluff, M. (1991). Gastrointestinal symptoms in Parkinson’s disease. Mov. Disord. 6, 151–156. doi: 10.1002/mds.870060211 Bedarf, J. R., Hildebrand, F., Coelho, L. P., Sunagawa, S., Bahram, M., Goeser, F.,
et al. (2017). Functional implications of microbial and viral gut metagenome
changes in early stage L-DOPA-naïve Parkinson’s disease patients. Genome
Med. 9:39. SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found
online
at:
https://www.frontiersin.org/articles/10.3389/fnins. 2021.708587/full#supplementary-material August 2021 | Volume 15 | Article 708587 Frontiers in Neuroscience | www.frontiersin.org Gut Microbiota in Parkinson’s Disease Hill et al. REFERENCES D., et al. (2017). Parkinson’s disease and Parkinson’s disease
medications have distinct signatures of the gut microbiome. Mov. Disord. 32,
739–749. doi: 10.1002/mds.26942 Daniele, S. G., Béraud, D., Davenport, C., Cheng, K., Yin, H., and Maguire-Zeiss,
K. A. (2015). Activation of MyD88-dependent TLR1/2 signaling by misfolded
α-synuclein, a protein linked to neurodegenerative disorders. Sci. Signal. 8:ra45. doi: 10.1126/scisignal.2005965 Holmqvist, S., Chutna, O., Bousset, L., Aldrin-Kirk, P., Li, W., Björklund, T., et al. (2014). Direct evidence of Parkinson pathology spread from the gastrointestinal August 2021 | Volume 15 | Article 708587 Frontiers in Neuroscience | www.frontiersin.org 7 Hill et al. Gut Microbiota in Parkinson’s Disease tract to the brain in rats. Acta Neuropathol. 128, 805–820. doi: 10.1007/s00401-
014-1343-6 Taiwanese Retrospective Cohort Study. Inflamm. Bowel Dis. 22, 1049–1055. doi: 10.1097/mib.0000000000000735 tract to the brain in rats. Acta Neuropathol. 128, 805–820. doi: 10.1007/s00401-
014-1343-6 Hopfner, F., Künstner, A., Müller, S. H., Künzel, S., Zeuner, K. E., Margraf, N. G.,
et al. (2017). Gut microbiota in Parkinson disease in a northern German cohort. Brain Res. 1667, 41–45. doi: 10.1016/j.brainres.2017.04.019 Lindestam Arlehamn, C. S., Dhanwani, R., Pham, J., Kuan, R., Frazier, A., Rezende
Dutra, J., et al. (2020). α-Synuclein-specific T cell reactivity is associated with
preclinical and early Parkinson’s disease. Nat. Commun. 11:1875. doi: 10.1038/
s41467-020-15626-w Hsieh, T.-H., Kuo, C.-W., Hsieh, K.-H., Shieh, M.-J., Peng, C.-W., Chen, Y.-C., et al. (2020). Probiotics alleviate the progressive deterioration of motor functions in
a mouse model of Parkinson’s Disease. Brain Sci. 10:206. Lionnet, A., Leclair-Visonneau, L., Neunlist, M., Murayama, S., Takao, M., Adler,
C. H., et al. (2018). Does Parkinson’s disease start in the gut? Acta Neuropathol. 135, 1–12. doi: 10.1007/s00401-017-1777-8 Hu, L. F., Lu, M., Tiong, C. X., Dawe, G. S., Hu, G., and Bian, J. S. (2010). Neuroprotective effects of hydrogen sulfide on Parkinson’s disease rat models. Aging Cell 9, 135–146. doi: 10.1111/j.1474-9726.2009.00543.x Liu, B., Fang, F., Pedersen, N. L., Tillander, A., Ludvigsson, J. F., Ekbom, A., et al. (2017). Vagotomy and Parkinson disease: a Swedish register-based matched-
cohort study. Neurology 88, 1996–2002. doi: 10.1212/wnl.0000000000003961 Huang, H., Xu, H., Luo, Q., He, J., Li, M., Chen, H., et al. (2019). Fecal microbiota
transplantation to treat Parkinson’s disease with constipation: a case report. Medicine 98:e16163. Luk, K. C., Song, C., O’Brien, P., Stieber, A., Branch, J. R., Brunden, K. R., et al. (2009). REFERENCES Exogenous alpha-synuclein fibrils seed the formation of Lewy body-
like intracellular inclusions in cultured cells. Proc. Natl. Acad. Sci. U. S. A. 106,
20051–20056. doi: 10.1073/pnas.0908005106 Hufnagel, D. A., Tükel, C., and Chapman, M. R. (2013). Disease to dirt: the
biology of microbial amyloids. PLoS Pathog. 9:e1003740. doi: 10.1371/journal. ppat.1003740 Mertsalmi, T. H., Aho, V. T. E., Pereira, P. A. B., Paulin, L., Pekkonen, E., Auvinen,
P., et al. (2017). More than constipation - bowel symptoms in Parkinson’s
disease and their connection to gut microbiota. Eur. J. Neurol. 24, 1375–1383. doi: 10.1111/ene.13398 Jost, W. H. (1997). Gastrointestinal motility problems in patients with Parkinson’s
disease. Effects of antiparkinsonian treatment and guidelines for management. Drugs Aging 10, 249–258. doi: 10.2165/00002512-199710040-00002 Mertsalmi, T. H., Pekkonen, E., and Scheperjans, F. (2020). Antibiotic exposure
and risk of Parkinson’s disease in Finland: a nationwide case-control study. Mov. Disord. 35, 431–442. doi: 10.1002/mds.27924 Kelly, L. P., Carvey, P. M., Keshavarzian, A., Shannon, K. M., Shaikh, M., Bakay,
R. A., et al. (2014). Progression of intestinal permeability changes and alpha-
synuclein expression in a mouse model of Parkinson’s disease. Mov. Disord. 29,
999–1009. doi: 10.1002/mds.25736 Millard, A. L., Mertes, P. M., Ittelet, D., Villard, F., Jeannesson, P., and Bernard,
J. (2002). Butyrate affects differentiation, maturation and function of human
monocyte-derived dendritic cells and macrophages. Clin. Exp. Immunol. 130,
245–255. doi: 10.1046/j.0009-9104.2002.01977.x Keshavarzian, A., Green, S. J., Engen, P. A., Voigt, R. M., Naqib, A., Forsyth, C. B.,
et al. (2015). Colonic bacterial composition in Parkinson’s disease. Mov. Disord. 30, 1351–1360. doi: 10.1002/mds.26307 Minato, T., Maeda, T., Fujisawa, Y., Tsuji, H., Nomoto, K., Ohno, K., et al. (2017). Progression of Parkinson’s disease is associated with gut dysbiosis: two-year
follow-up study. PLoS One 12:e0187307. doi: 10.1371/journal.pone.0187307 Kida, K., Yamada, M., Tokuda, K., Marutani, E., Kakinohana, M., Kaneki, M., et al. (2011). Inhaled hydrogen sulfide prevents neurodegeneration and movement
disorder in a mouse model of Parkinson’s disease. Antioxid. Redox Signal. 15,
343–352. doi: 10.1089/ars.2010.3671 Miraglia, F., and Colla, E. (2019). Microbiome, Parkinson’s disease and molecular
mimicry. Cells 8:222. doi: 10.3390/cells8030222 Kim, C., Ho, D. H., Suk, J. E., You, S., Michael, S., Kang, J., et al. (2013). Neuron-released oligomeric α-synuclein is an endogenous agonist of TLR2 for
paracrine activation of microglia. Nat. Commun. 4:1562. doi: 10.1038/ncom
ms2534 Mitchell, R. W., On, N. H., Del Bigio, M. R., Miller, D. W., and Hatch, G. M. (2011). REFERENCES Fatty acid transport protein expression in human brain and potential
role in fatty acid transport across human brain microvessel endothelial cells. J. Neurochem. 117, 735–746. doi: 10.1111/j.1471-4159.2011.07245.x Kim, S., Kwon, S. H., Kam, T. I., Panicker, N., Karuppagounder, S. S., Lee, S.,
et al. (2019). Transneuronal propagation of pathologic α-Synuclein from the
gut to the brain models Parkinson’s Disease. Neuron 103, 627–641.e7. doi:
10.1016/j.neuron.2019.05.035 Mogi, M., Harada, M., Kondo, T., Riederer, P., Inagaki, H., Minami, M.,
et al. (1994). Interleukin-1 beta, interleukin-6, epidermal growth factor and
transforming growth factor-alpha are elevated in the brain from parkinsonian
patients. Neurosci. Lett. 180, 147–150. doi: 10.1016/0304-3940(94)90508-8 Kordower, J. H., Dodiya, H. B., Kordower, A. M., Terpstra, B., Paumier, K.,
Madhavan, L., et al. (2011). Transfer of host-derived α synuclein to grafted
dopaminergic neurons in rat. Neurobiol. Dis. 43, 552–557. doi: 10.1016/j.nbd. 2011.05.001 Nishimori, J. H., Newman, T. N., Oppong, G. O., Rapsinski, G. J., Yen, J. H.,
Biesecker, S. G., et al. (2012). Microbial amyloids induce interleukin 17A (IL-
17A) and IL-22 responses via Toll-like receptor 2 activation in the intestinal
mucosa. Infect. Immun. 80, 4398–4408. doi: 10.1128/iai.00911-12 Kortekaas, R., Leenders, K. L., van Oostrom, J. C., Vaalburg, W., Bart, J., Willemsen,
A. T., et al. (2005). Blood-brain barrier dysfunction in parkinsonian midbrain
in vivo. Ann. Neurol. 57, 176–179. doi: 10.1002/ana.20369 Okuzumi, A., Kurosawa, M., Hatano, T., Takanashi, M., Nojiri, S., Fukuhara,
T., et al. (2018). Rapid dissemination of alpha-synuclein seeds through
neural circuits in an in vivo prion-like seeding experiment. Acta Neuropathol. Commun. 6:96. doi: 10.1186/s40478-018-0587-0 Lai, S. W., Liao, K. F., Lin, C. L., and Sung, F. C. (2014). Irritable bowel syndrome
correlates with increased risk of Parkinson’s disease in Taiwan. Eur. J. Epidemiol. 29, 57–62. doi: 10.1007/s10654-014-9878-3 Ostojic, S. M. (2018). Inadequate production of H(2) by gut microbiota and
Parkinson disease. Trends Endocrinol. Metab. 29, 286–288. doi: 10.1016/j.tem. 2018.02.006 Lee, H. J., Patel, S., and Lee, S. J. (2005). Intravesicular localization and exocytosis
of alpha-synuclein and its aggregates. J. Neurosci. 25, 6016–6024. doi: 10.1523/
jneurosci.0692-05.2005 Parkinson, J. (2002). An essay on the shaking palsy. 1817. J. Neuropsychiatry Clin. Neurosci. 14, 223–236. doi: 10.1176/jnp.14.2.223 Lema Tomé, C. M., Tyson, T., Rey, N. L., Grathwohl, S., Britschgi, M., and Brundin,
P. (2013). Inflammation and α-synuclein’s prion-like behavior in Parkinson’s
disease–is there a link? Mol. Neurobiol. 47, 561–574. doi: 10.1007/s12035-012-
8267-8 Pawłowska, B., and Sobieszcza´nska, B. M. (2017). REFERENCES Alteration of
the fecal microbiota in Chinese patients with Parkinson’s disease. Brain Behav. Immun. 70, 194–202. doi: 10.1016/j.bbi.2018.02.016 Tükel, C., Nishimori, J. H., Wilson, R. P., Winter, M. G., Keestra, A. M., van
Putten, J. P., et al. (2010). Toll-like receptors 1 and 2 cooperatively mediate
immune responses to curli, a common amyloid from enterobacterial biofilms. Cell Microbiol. 12, 1495–1505. doi: 10.1111/j.1462-5822.2010.01485.x Qin, L., Wu, X., Block, M. L., Liu, Y., Breese, G. R., Hong, J. S., et al. (2007). Systemic
LPS causes chronic neuroinflammation and progressive neurodegeneration. Glia 55, 453–462. doi: 10.1002/glia.20467 Ren, T., Gao, Y., Qiu, Y., Jiang, S., Zhang, Q., Zhang, J., et al. (2020). Gut microbiota
altered in mild cognitive impairment compared with normal cognition in
sporadic Parkinson’s disease. Front. Neurol. 11:137. doi: 10.3389/fneur.2020. 00137 Ulusoy, A., Phillips, R. J., Helwig, M., Klinkenberg, M., Powley, T. L., and Di Monte,
D. A. (2017). Brain-to-stomach transfer of α-synuclein via vagal preganglionic
projections. Acta Neuropathol. 133, 381–393. doi: 10.1007/s00401-016-1661-y Unger, M. M., Spiegel, J., Dillmann, K. U., Grundmann, D., Philippeit, H.,
Bürmann, J., et al. (2016). Short chain fatty acids and gut microbiota
differ between patients with Parkinson’s disease and age-matched controls. Parkinsonism
Relat. Disord. 32,
66–72. doi:
10.1016/j.parkreldis.2016. 08.019 Rivest, S. (2003). Molecular insights on the cerebral innate immune system. Brain
Behav. Immun. 17, 13–19. doi: 10.1016/s0889-1591(02)00055-7 Rolig, A. S., Mittge, E. K., Ganz, J., Troll, J. V., Melancon, E., Wiles, T. J., et al. (2017). The enteric nervous system promotes intestinal health by constraining
microbiota composition. PLoS Biol. 15:e2000689. doi: 10.1371/journal.pbio. 2000689 Vidal-Martinez, G., Chin, B., Camarillo, C., Herrera, G. V., Yang, B., Sarosiek, I.,
et al. (2020). A Pilot Microbiota Study in Parkinson’s Disease Patients versus
Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in
Parkinsonian and Multiple System Atrophy Mouse Models. J. Parkinsons Dis. 10, 185–192. doi: 10.3233/jpd-191693 Rolli-Derkinderen, M., Leclair-Visonneau, L., Bourreille, A., Coron, E., Neunlist,
M., and Derkinderen, P. (2020). Is Parkinson’s disease a chronic low-grade
inflammatory bowel disease? J. Neurol. 267, 2207–2213. doi: 10.1007/s00415-
019-09321-0 Visanji, N. P., Brooks, P. L., Hazrati, L. N., and Lang, A. E. (2013). The prion
hypothesis in Parkinson’s disease: braak to the future. Acta Neuropathol. Commun. 1:2. doi: 10.1186/2051-5960-1-2 Römling, U., Bian, Z., Hammar, M., Sierralta, W. D., and Normark, S. (1998). Curli
fibers are highly conserved between Salmonella typhimurium and Escherichia
coli with respect to operon structure and regulation. J. Bacteriol. 180, 722–731. REFERENCES doi: 10.1128/jb.180.3.722-731.1998 Volpicelli-Daley, L. A., Luk, K. C., Patel, T. P., Tanik, S. A., Riddle, D. M., Stieber,
A., et al. (2011). Exogenous α-synuclein fibrils induce Lewy body pathology
leading to synaptic dysfunction and neuron death. Neuron 72, 57–71. doi:
10.1016/j.neuron.2011.08.033 Sampson, T. R., Challis, C., Jain, N., Moiseyenko, A., Ladinsky, M. S., Shastri, G. G.,
et al. (2020). A gut bacterial amyloid promotes α-synuclein aggregation and
motor impairment in mice. elife 9:e53111. doi: 10.7554/eLife.53111 Wakabayashi, K., Takahashi, H., Takeda, S., Ohama, E., and Ikuta, F. (1988). Parkinson’s disease: the presence of Lewy bodies in Auerbach’s and Meissner’s
plexuses. Acta Neuropathol. 76, 217–221. doi: 10.1007/bf00687767 Sampson, T. R., Debelius, J. W., Thron, T., Janssen, S., Shastri, G. G., Ilhan, Z. E.,
et al. (2016). Gut microbiota regulate motor deficits and neuroinflammation in
a model of Parkinson’s disease. Cell 167, 1469–1480.e12. doi: 10.1016/j.cell.2016. 11.018 Wang, H. B., Wang, P. Y., Wang, X., Wan, Y. L., and Liu, Y. C. (2012). Butyrate enhances intestinal epithelial barrier function via up-regulation of
tight junction protein Claudin-1 transcription. Dig. Dis. Sci. 57, 3126–3135. doi: 10.1007/s10620-012-2259-4 Santens, P. (2021). Fecal Microbiota Transplantation for Parkinson’s Disease. Available online at: https://clinicaltrials.gov/ct2/show/NCT03808389/ (accessed
June 27, 2021). Xue, L.-J., Yang, X.-Z., Tong, Q., Shen, P., Ma, S.-J., Wu, S.-N., et al. (2020). Fecal
microbiota transplantation therapy for Parkinson’s disease: a preliminary study. Medicine 99:e22035. doi: 10.1097/md.0000000000022035 Santos, S. F., de Oliveira, H. L., Yamada, E. S., Neves, B. C., and Pereira, A. Jr. (2019). The gut and Parkinson’s disease-A bidirectional pathway. Front. Neurol. 10:574. doi: 10.3389/fneur.2019.00574 Zhang, F., Yue, L., Fang, X., Wang, G., Li, C., Sun, X., et al. (2020). Altered gut
microbiota in Parkinson’s disease patients/healthy spouses and its association
with clinical features. Parkinsonism Relat. Disord. 81, 84–88. doi: 10.1016/j. parkreldis.2020.10.034 Scheperjans, F. (2016). Gut microbiota, 1013 new pieces in the Parkinson’s disease
puzzle. Curr. Opin. Neurol. 29, 773–780. doi: 10.1097/wco.0000000000000389 Scheperjans, F., Aho, V., Pereira, P. A., Koskinen, K., Paulin, L., Pekkonen, E.,
et al. (2015). Gut microbiota are related to Parkinson’s disease and clinical
phenotype. Mov. Disord. 30, 350–358. doi: 10.1002/mds.26069 Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Shannon, K. M., Keshavarzian, A., Dodiya, H. B., Jakate, S., and Kordower, J. H. (2012a). REFERENCES Intestinal epithelial barrier: the
target for pathogenic Escherichia coli. Adv. Clin. Exp. Med. 26, 1437–1445. doi: 10.17219/acem/64883 Li, F., Wang, P., Chen, Z., Sui, X., Xie, X., and Zhang, J. (2019). Alteration of
the fecal microbiota in North-Eastern Han Chinese population with sporadic
Parkinson’s disease. Neurosci. Lett. 707:134297. doi: 10.1016/j.neulet.2019. 134297 Perez-Pardo, P., Dodiya, H. B., Engen, P. A., Forsyth, C. B., Huschens, A. M.,
Shaikh, M., et al. (2019). Role of TLR4 in the gut-brain axis in Parkinson’s
disease: a translational study from men to mice. Gut 68, 829–843. doi: 10.1136/
gutjnl-2018-316844 Li, W., Wu, X., Hu, X., Wang, T., Liang, S., Duan, Y., et al. (2017). Structural
changes of gut microbiota in Parkinson’s disease and its correlation with clinical
features. Sci. China Life Sci. 60, 1223–1233. doi: 10.1007/s11427-016-9001-4 Perez-Pardo, P., Hartog, M., Garssen, J., and Kraneveld, A. D. (2017). Microbes
tickling your tummy: the importance of the gut-brain axis in Parkinson’s
disease. Curr. Behav. Neurosci. Rep. 4, 361–368. doi: 10.1007/s40473-017-
0129-2 Lin, A., Zheng, W., He, Y., Tang, W., Wei, X., He, R., et al. (2018). Gut microbiota in
patients with Parkinson’s disease in southern China. Parkinsonism Relat. Disord. 53, 82–88. doi: 10.1016/j.parkreldis.2018.05.007 Petrov, V. A., Saltykova, I. V., Zhukova, I. A., Alifirova, V. M., Zhukova, N. G.,
Dorofeeva, Y. B., et al. (2017). Analysis of gut microbiota in patients with
Parkinson’s disease. Bull. Exp. Biol. Med. 162, 734–737. doi: 10.1007/s10517-
017-3700-7 Lin, J. C., Lin, C. S., Hsu, C. W., Lin, C. L., and Kao, C. H. (2016). Association
Between Parkinson’s Disease and Inflammatory Bowel Disease: a Nationwide August 2021 | Volume 15 | Article 708587 8 Frontiers in Neuroscience | www.frontiersin.org Hill et al. Gut Microbiota in Parkinson’s Disease administration in people with Parkinson’s disease: a randomized, double-blind,
placebo-controlled trial. Clin. Nutr. 38, 1031–1035. doi: 10.1016/j.clnu.2018.05. 018 administration in people with Parkinson’s disease: a randomized, double-blind,
placebo-controlled trial. Clin. Nutr. 38, 1031–1035. doi: 10.1016/j.clnu.2018.05. 018 Pietrucci, D., Cerroni, R., Unida, V., Farcomeni, A., Pierantozzi, M., Mercuri,
N. B., et al. (2019). Dysbiosis of gut microbiota in a selected population of
Parkinson’s patients. Parkinsonism Relat. Disord. 65, 124–130. doi: 10.1016/j. parkreldis.2019.06.003 Tran, J., Anastacio, H., and Bardy, C. (2020). Genetic predispositions of Parkinson’s
disease revealed in patient-derived brain cells. NPJ Parkinsons Dis. 6:8. doi:
10.1038/s41531-020-0110-8 Qian, Y., Yang, X., Xu, S., Wu, C., Song, Y., Qin, N., et al. (2018). Frontiers in Neuroscience | www.frontiersin.org REFERENCES Is alpha-synuclein in the colon a biomarker for premotor Parkinson’s
disease? Evidence from 3 cases. Mov. Disord. 27, 716–719. doi: 10.1002/mds. 25020 Publisher’s Note: All claims expressed in this article are solely those of the authors
and do not necessarily represent those of their affiliated organizations, or those of
the publisher, the editors and the reviewers. Any product that may be evaluated in
this article, or claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. Shannon, K. M., Keshavarzian, A., Mutlu, E., Dodiya, H. B., Daian, D., Jaglin,
J. A., et al. (2012b). Alpha-synuclein in colonic submucosa in early untreated
Parkinson’s disease. Mov. Disord. 27, 709–715. doi: 10.1002/mds.23838 Stokholm, M. G., Danielsen, E. H., Hamilton-Dutoit, S. J., and Borghammer, P. (2016). Pathological α-synuclein in gastrointestinal tissues from prodromal
Parkinson disease patients. Ann. Neurol. 79, 940–949. doi: 10.1002/ana.24648 Copyright © 2021 Hill, Wade-Martins and Burnet. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the
original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms. Svensson, E., Horváth-Puhó, E., Thomsen, R. W., Djurhuus, J. C., Pedersen, L.,
Borghammer, P., et al. (2015). Vagotomy and subsequent risk of Parkinson’s
disease. Ann. Neurol. 78, 522–529. doi: 10.1002/ana.24448 Tamtaji, O. R., Taghizadeh, M., Daneshvar Kakhaki, R., Kouchaki, E., Bahmani,
F., Borzabadi, S., et al. (2019). Clinical and metabolic response to probiotic August 2021 | Volume 15 | Article 708587 Frontiers in Neuroscience | www.frontiersin.org 9
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https://pubs.rsc.org/en/content/articlepdf/2018/sc/c8sc02753f
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English
| null |
Unravelling the origins of ice nucleation on organic crystals
|
Chemical science
| 2,018
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cc-by
| 12,863
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aDepartment of Chemistry and Centre for Scientic Computing, University of Warwick,
Gibbet Hill Road, Coventry CV4 7AL, UK. E-mail: g.sosso@warwick.ac.uk
bSchool of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
cChemistry, University of Leeds, Leeds LS2 9JT, UK
dThomas Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, UK
† Electronic
supplementary
information
(ESI)
available.
See
DOI:
10.1039/c8sc02753f
‡ School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
§ School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Cite this: Chem. Sci., 2018, 9, 8077 Gabriele C. Sosso,
*a Thomas F. Whale,
‡b Mark A. Holden,
§bc
Philipp Pedevilla,d Benjamin J. Murray
b and Angelos Michaelides
d All publication charges for this article
have been paid for by the Royal Society
of Chemistry Organic molecules such as steroids or amino acids form crystals that can facilitate the formation of ice –
arguably the most important phase transition on earth. However, the origin of the ice nucleating ability
of organic crystals is still largely unknown. Here, we combine experiments and simulations to unravel the
microscopic details of ice formation on cholesterol, a prototypical organic crystal widely used in
cryopreservation. We find that cholesterol – which is also a substantial component of cell membranes –
is an ice nucleating agent more potent than many inorganic substrates, including the mineral feldspar
(one of the most active ice nucleating materials in the atmosphere). Scanning electron microscopy
measurements reveal a variety of morphological features on the surfaces of cholesterol crystals: this
suggests that the topography of the surface is key to the broad range of ice nucleating activity observed
(from 4 to 20 C). In addition, we show via molecular simulations that cholesterol crystals aid the
formation of ice nuclei in a unconventional fashion. Rather than providing a template for a flat ice-like
contact layer (as found in the case of many inorganic substrates), the flexibility of the cholesterol surface
and its low density of hydrophilic functional groups leads to the formation of molecular cages involving
both water molecules and terminal hydroxyl groups of the cholesterol surface. These cages are made of
6- and, surprisingly, 5-membered hydrogen bonded rings of water and hydroxyl groups that favour the
nucleation of hexagonal as well as cubic ice (a rare occurrence). We argue that the phenomenal ice
nucleating activity of steroids such as cholesterol (and potentially of many other organic crystals) is due
to (i) the ability of flexible hydrophilic surfaces to form unconventional ice-templating structures and (ii)
the different nucleation sites offered by the diverse topography of the crystalline surfaces. These findings
clarify how exactly organic crystals promote the formation of ice, thus paving the way toward deeper
understanding of ice formation in soft and biological matter – with obvious reverberations on
atmospheric science and cryobiology. Received 22nd June 2018
Accepted 27th August 2018
DOI: 10.1039/c8sc02753f
rsc.li/chemical-science Unravelling the origins of ice nucleation on organic
crystals† Cite this: Chem. Sci., 2018, 9, 8077 1
Introduction about heterogeneous ice nucleation has come from the study of
atmospherically
relevant
ice
nucleating
agents:5
in
fact,
heterogeneous ice nucleation from supercooled water plays
a critical role in the glaciation of mixed phase clouds, which in
turn inuences the climate.8,9 A variety of substances are known
to nucleate ice efficiently in the atmosphere, including inor-
ganic species such as silver iodide,10 feldspar11–13 as well as
biological entities such as the bacterium Pseudomonas syrin-
gae14–16 or birch pollen.17 The freezing of liquid water into crystalline ice is a ubiquitous
phenomenon which is part of our everyday experience1 and has
countless reverberations in elds as diverse as cryobiology2–4
and
atmospheric
science.5,6
Strikingly,
the
overwhelming
majority of ice on earth forms heterogeneously, i.e. thanks to
the presence of substances, other than water itself, which
facilitate the ice nucleation process.5,7 Much of what is known Biological ice nucleating agents also play a key role in the
ever-growing eld of cryobiology: in fact, the formation of ice
in biological matter is the cornerstone of cryotherapy and
cryopreservation,4,18 i.e. the long-term storage of frozen bio-
logical material which is essential to enable cutting-edge
technologies such as regenerative medicine.19,20 A number of
organic crystals have been known to facilitate ice nucle-
ation,21,22 and molecular crystals of steroids such as choles-
terol (CHL)23 are used to boost the formation of ice when
cryopreserving
biological
material.2,24
Importantly,
CHL Chem. Sci., 2018, 9, 8077–8088 | 8077 This journal is © The Royal Society of Chemistry 2018 Edge Article
View Article Online View Article Online Chemical Science Edge Article hydrophilic surfaces to trigger the formation of unconventional
ice-templating
molecular
features. In
addition,
different
nucleation sites potentially offered by the diverse topography of
the crystal can further enhance the intrinsic ice nucleation
potential of CHL surfaces. This insight could help to under-
stand ice formation on a number of other organic compounds,
from amino acid crystals46,47 to bacterial fragments48,49 – as they
are all characterised by the presence of exible hydrophilic
surfaces displaying diverse topological features. In addition,
organic crystals such as cholesterol are positioned “in between”
inorganic and biological ice nucleating agents: they possess the
order and the crystalline surfaces of the former, and the
complexity and exibility of the latter. 2.1
ml-NIPI experiments and scanning electron microscopy
measurements The ice nucleation efficiency of CHLM was evaluated using an
adapted version of the ml Nucleation by Immersed Particles
Instrument (ml-NIPI) described in detail in ref. 50. To make the
at plates we dissolved 2 g of pure CHL (Sigma Aldrich) in
approximately 30 ml of hot (343 K) 95% ethanol (Sigma-
Aldrich). The CHL solution was then allowed to cool slowly,
causing crystallisation of large (up to approx. 1 cm across) at
plates of CHLM. Individual plates of CHLM of around 2 mm
diameter were then recovered by vacuum ltration on a lter
membrane and placed onto a thin (0.1 mm) glass plate. The
glass plate was then placed onto an EF600 Stirling cryocooler. A
Picus Biohit electronic pipette was then used to deposit 1 ml
droplets of MilliQ water onto the separated CHLM plates. The
EF600 cryocooler was then used to reduce the temperature of
the droplets at a rate of 1 K min1 freezing was monitored using
a camera. In this way the droplet fraction frozen curve presented
in Fig. 1a was built up. The data is the result of several cooling
runs as only about 10 droplets could be frozen per experiment. It was important that plates were not in contact as ice clearly
propagated across the CHL surface, triggering neighbouring
droplets aer an initial freezing events, when multiple droplets
were placed on a single plate. In this work, we bring together experiments and simulations
to take an ambitious step forward in furthering our under-
standing of ice formation on organic crystals. We focus on CHL,
due to its relevance in cryopreservation and its role within
cellular membrane, unravelling microscopic motivations for
heterogeneous ice nucleation likely to be shared by many other
organic crystals. We nd via micro-litre droplet nucleation
measurements
(ml-NIPI)
that
CHL
crystals
display
an
outstanding ice nucleation ability (stronger than most inor-
ganic ice nucleating agents), with freezing events initiating at
very mild supercooling DTS ¼ TMelt T ¼ 4 K down to DTS ¼ 20
K. Scanning electron microscopy suggests that the activity of
these crystals as ice nucleating agents across such a wide
temperature range could be due to the diverse topography of the
surface of the cholesterol crystals, which are likely to offer
a variety of different nucleation sites. 8078 | Chem. Sci., 2018, 9, 8077–8088 1
Introduction This work thus paves the
way to a molecular-level understanding of ice formation in
biological matter, tackling a substrate (CHL crystals) that
embeds unique features of very different classes of materials. molecules also represent a major component (up to 40%) of
animal cell membranes,25 thus prompting the question of
whether this steroid can play a role as ice nucleator in the
context of ice formation in biological matter. g
However, the microscopic details of heterogeneous ice
nucleation on CHL – and indeed on the vast majority of organic
and inorganic compounds alike – remain remarkably poorly
understood,7 although a substantial body of experimental work
has been devoted to assess the ice nucleation ability of biolog-
ical matter.22,26–32 In fact, the reason why many biological ice
nucleating agents display a far stronger ice nucleating activity
than most inorganic materials5,7 is still largely unknown. Partly,
this is because obtaining molecular-level insight into the
nucleation process is still a formidable challenge for experi-
ments, and only very recently simulations of heterogeneous ice
nucleation have become feasible,7,13,33–40 largely thanks to the
capabilities of the coarse grained mW water model.41 Indeed,
mW has played a pivotal role in enabling systematic investiga-
tions of ice nucleation on e.g. carbonaceous42 or hydroxylated
organic surfaces.43 However, fully atomistic water models and
enhanced sampling methods are oen required to take into
account the subtleties of the hydrogen bond network between
water and complex impurities.44,45 2.2
Molecular dynamics simulations The computational setup we have used is depicted in Fig. 3a. A
single layer of CHL molecules, cleaved along the (001) plane
(perpendicular to the normal to the slab) was prepared by
starting from the experimental cell parameters and lattice
positions.52 Specically, a CHLM crystal system made of two
mirroring slabs (intercalated by water molecules, in a ratio of
1 : 1) was cleaved along the (001) plane. The triclinic symmetry
of the system (space group P1) was preserved, and we have
constructed a 3 by 3 supercell with in-plane dimensions of 37.17
and 36.57 ˚A. We positioned 1923 water molecules randomly
atop this CHLM slab at the density of the TIP4P/Ice model53 at
300 K, and expanded the dimension of the simulation cell along rticle. Published on 27 August 2018. Downloaded on 1
his article is licensed under a Creative Commons Attrib Fig. 2
CHLM crystals display a diverse surface topography. SEM
images of CHLM crystals, which predominantly expose {001} surfaces
– consistent with what has been reported in ref. 54. It is quite clear that
these plates possess numerous topographical features. Fig. 1
CHLM crystals promote the formation of ice across a wide
range of temperatures. (a) Droplet fraction frozen as a function of
temperature for 1 ml water droplets placed onto a CHLM substrate. (b)
Ice-active surface site density ns (see text and Methods section) values
for the same data reported for CHLM (CHL) in panel (a), together with
ns values for kaolinite (KAO) from Herbert et al.,62 BCS376 feldspar (K-
FELD) from Atkinson et al.,11 graphene oxide (GRA) from Whale et al.63
and single-walled carbon nanotubes (SWCN) also from ref. 63. The
uncertainty in terms of temperature associated with the CHLM data is
0.4 K. The uncertainties associated with the values of ns have been
calculated using Monte-Carlo simulations of possible active ice
nucleation sites distributions, propagated with the uncertainty
associated with A – as described in Harrison et al.12 These
simulations generate a list of possible values for the number of
active sites per droplet for a given experiment, given the
observed freezing data. By repeating this process a great many
times, a distribution of the possible active site distributions that
can account for the freezing of each droplet is obtained. The
error bars for the CHLM ns data reported in Fig. 2.1
ml-NIPI experiments and scanning electron microscopy
measurements Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Edge Article
Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Edge Article Edge Article Chemical Science Chemical Science largest, the contribution of the uncertainty in surface area
amounts to approximately 25% of total uncertainty in ns(T),
with the Poisson uncertainty in the active site distribution
accounting for the remainder of the error bars. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Scanning electron microscopy (SEM) was performed on
CHLM plates. These were mounted on copper tape, then coated
with 2 nm of iridium. SEM was performed with an FEI Nova
NanoSEM 450 in high vacuum mode, using an Everhart–
Thornley Detector (ETD). Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. 2.1
ml-NIPI experiments and scanning electron microscopy
measurements In order to get a molec-
ular-level insight into the mechanism of ice formation on
CHL crystals, we harness enhanced sampling simulations,
focusing on the hydroxylated (001) face of cholesterol mono-
hydrate (CHLM) – the most relevant surface (and polymorph, as
discussed below) in biological scenarios. We nd that CHL
crystals facilitate the formation of ice in a non-conventional
fashion: in contrast to what has been observed in the case of
inorganic substrates such as e.g. carbonaceous particles42 or
clay minerals,45 the exibility of the CHLM surface and the large
spacing of its hydroxyl groups prevent the formation of a at,
ice-like layer of water molecules at the water–crystal interface. Instead, the hydroxyl groups participate in the formation of 5-
and 6-membered hydrogen bonded rings of water molecules
forming peculiar molecular “cages” that provide an effective
template for the nucleation of both cubic and hexagonal ice (a
rare occurrence). In order to calculate the (surface) density of the active ice
nucleation sites (ns, commonly used to compare the ice nucle-
ating efficiency of different substances5) on the CHLM surface
(reported in Fig. 1) we have used the following expression: nðTÞ
N
¼ 1 exp½nsðTÞA;
(1) (1) where n(T) is the number of droplets frozen at temperature T, N
is the total number of droplets in the experiment and A is the
surface area of nucleating agent per droplet. The value of A for
each droplet was measured using the image analysis soware
imageJ, customarily used to quantify particles size in biosci-
ences.51 The resulting estimate of the mean value of A is 1.82
0.46 mm2. As a whole, our ndings suggest that the formation of ice on
CHL crystals originates from the ability of their exible This journal is © The Royal Society of Chemistry 2018 8078 | Chem. Sci., 2018, 9, 8077–8088 Chemical Science
View Article Online Chemical Science
View Article Online View Article Online Fig. 1
CHLM crystals promote the formation of ice across a wid
range of temperatures. (a) Droplet fraction frozen as a function
temperature for 1 ml water droplets placed onto a CHLM substrate. (
Ice-active surface site density ns (see text and Methods section) valu
for the same data reported for CHLM (CHL) in panel (a), together wi
l
f
k
li i
(KAO) f
H
b
l
62 BCS376 f ld
(
Edge Article
Open Access Article. This journal is © The Royal Society of Chemistry 2018 2.2
Molecular dynamics simulations 1 are generated
by propagating this distribution with the uncertainty in surface
area of cholesterol per droplet and taking the 95% condence
interval of the resulting distribution. At high and low temper-
ature ends of the reported data, where the Poisson uncertainty
(i.e. the error originating from the Monte-Carlo simulations) is Fig. 2
CHLM crystals display a diverse surface topography. SEM
images of CHLM crystals, which predominantly expose {001} surfaces
– consistent with what has been reported in ref. 54. It is quite clear that
these plates possess numerous topographical features. This journal is © The Royal Society of Chemistry 2018 Chem. Sci., 2018, 9, 8077–8088 | 8079 Edge Article
View Article Online Edge Article
View Article Online View Article Online Chemical Science Fig. 3
Structuring of water on the (001) hydroxylated face of CHLM. (a)
Representative snapshot of a molecular dynamics simulation of
a water slab in contact with the (001) hydroxylated face of CHLM. The
inset at the bottom illustrates the arrangement of the hydroxyl group
on the CHLM surface; an hypothetical ice Ih (001) plane (blue) is
superimposed on part of the image to highlight the absence of
a structural match between –OH groups and ice. (b) Density profile of
oxygen atoms belonging to either the –OH hydroxyl groups of CHLM
molecules (OCHL) or water molecules (OH2O) along the z-axis parallel
to [001] direction, thus normal to the water–CHLM interface. The zero
of the x-axis corresponds to the average position of the OCHL atoms,
while the shaded area in green identifies the water–CHLM interface. Statistics have been accumulated over a 1.5 ms long simulation at 230
K. (c) Number of n-membered rings of hydrogen bonded water
molecules at the water–CHLM interface (Surf) or within the bulk of the
water slab (Bulk), normalised by the number of oxygen atoms in each
region. Note that at the water–CHLM interface oxygen atoms
belonging to the CHLM–OH hydroxyl groups have also been
considered when computing the rings statistics. The CHARMM36 (ref. 2.2
Molecular dynamics simulations 55) force eld was used to model the
CHL crystals, taking advantage of a recent update of this force
eld parameters explicitly with respect to CHL.56 In order to
mimic the experimental conditions, we have constrained the
system
at
the
experimental
lateral
dimensions
(detailed
together with the computational geometry in the ESI†), and we
have also restrained the positions of the hydrophobic tail of
each CHL molecule (specically, the carbon atoms C25, C26 and
C27, see the inset of Fig. S1 in the ESI†) by means of an
harmonic potential characterised by a spring constant of
10 000 kJ mol1. All the other atoms within the CHLM slab are
unconstrained. We have veried that the thermal expansion of
the crystal at 230 K (0.1% with respect to each lateral
dimension) does not alter the structure nor the dynamics of the
water–kaolinite interface. This setup is thus as close as we can
get to the realistic (001) hydrophilic surface of CHLM within the
CHARMM36 model. Implications of the exibility of the CHLM
slab are discussed in the ESI.† The interaction between the
water molecules have been modelled using the TIP4P/Ice
model,53 so that our results are consistent with the homoge-
neous simulations of ref. 57. The interaction parameters
between the clay and the water were obtained using the stan-
dard Lorentz–Berthelot mixing rules.58 ess Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Fig. 3
Structuring of water on the (001) hydroxylated face of CHLM. (a)
Representative snapshot of a molecular dynamics simulation of
a water slab in contact with the (001) hydroxylated face of CHLM. The
inset at the bottom illustrates the arrangement of the hydroxyl group
on the CHLM surface; an hypothetical ice Ih (001) plane (blue) is
superimposed on part of the image to highlight the absence of
a structural match between –OH groups and ice. (b) Density profile of
oxygen atoms belonging to either the –OH hydroxyl groups of CHLM
molecules (OCHL) or water molecules (OH2O) along the z-axis parallel
to [001] direction, thus normal to the water–CHLM interface. 2.2
Molecular dynamics simulations The slab considered in
this work presents the hydrophilic, –OH terminated heads of
the CHL molecules to the water, in agreement with experi-
mental insight.54 As we discuss in the main text, the interaction
between the hydroxyl groups (which display amphoteric char-
acteristics in terms of the hydrogen bond network) of CHL
molecules and water is responsible for the templating effect of
CHLM crystals which serves to promote ice nucleation. 3 2.2
Molecular dynamics simulations This setup allows for a physi-
cally meaningful equilibration of the water at the density of
interest at a given temperature, but suffers from two distinct
drawbacks: (i) the CHLM slab possesses a net dipole moment
which is not compensated throughout the simulation cell and
(ii) the presence of the water–vacuum interface can alter the
structure and the dynamics of the liquid lm. However, we have
previously addressed these issues in previous work dealing with
the hydroxylated (001) polar surface of the clay mineral
kaolinite,44,45 concluding that such details do not affect the
mechanism nor the kinetics of ice formation. In addition, the
water lm is thick enough to allow a bulk-like region to exist in
terms of both structure and dynamics. The effect of the water–
vacuum interface is therefore negligible. The slab considered in
this work presents the hydrophilic, –OH terminated heads of
the CHL molecules to the water, in agreement with experi-
mental insight.54 As we discuss in the main text, the interaction
between the hydroxyl groups (which display amphoteric char-
acteristics in terms of the hydrogen bond network) of CHL
molecules and water is responsible for the templating effect of
CHLM crystals which serves to promote ice nucleation. the normal to the slab to 100 ˚A. This setup allows for a physi-
cally meaningful equilibration of the water at the density of
interest at a given temperature, but suffers from two distinct
drawbacks: (i) the CHLM slab possesses a net dipole moment
which is not compensated throughout the simulation cell and
(ii) the presence of the water–vacuum interface can alter the
structure and the dynamics of the liquid lm. However, we have
previously addressed these issues in previous work dealing with
the hydroxylated (001) polar surface of the clay mineral
kaolinite,44,45 concluding that such details do not affect the
mechanism nor the kinetics of ice formation. In addition, the
water lm is thick enough to allow a bulk-like region to exist in
terms of both structure and dynamics. The effect of the water–
vacuum interface is therefore negligible. 2.2
Molecular dynamics simulations The zero
of the x-axis corresponds to the average position of the OCHL atoms,
while the shaded area in green identifies the water–CHLM interface. Statistics have been accumulated over a 1.5 ms long simulation at 230
K. (c) Number of n-membered rings of hydrogen bonded water
molecules at the water–CHLM interface (Surf) or within the bulk of the
water slab (Bulk), normalised by the number of oxygen atoms in each
region. Note that at the water–CHLM interface oxygen atoms
belonging to the CHLM–OH hydroxyl groups have also been
considered when computing the rings statistics. Extreme care must be taken in order to correctly reproduce the
structure and the dynamics of the water–CHLM interface. The
Forward Flux Sampling (FFS) simulations reported in this work
rely on a massive collection of unbiased Molecular Dynamics
(MD) runs, all of which have been performed using the GRO-
MACS package, version 4.6.7. The code was compiled in single-
precision, in order to alleviate the huge computational work-
load needed to converge the FFS algorithm and because we have
taken advantage of GPU acceleration, which is not available in the
double-precision version. The equations of motions were inte-
grated using a leap-frog integrator with a time step of 2 fs. The van
der Waals (non bonded) interactions were considered up to 10 ˚A,
where a switching function was used to bring them to zero at 12
˚A. Electrostatic interactions have been dealt with by means of an
Ewald summation up to 12 ˚A. The NVT ensemble was sampled at
230 K using a stochastic velocity rescaling thermostat59 with a very
weak coupling constant of 4 ps in order to avoid temperature
gradients throughout the system. The geometry of the water
molecules (TIP4P/Ice being a rigid model) was constrained using
the SETTLE algorithm60 while the P_LINCS algorithm61 was used
to constrain the O–H bonds within the clay. We have veried that
these settings reproduce the dynamical properties of water re-
ported in ref. 57. The system was equilibrated at 300 K for 10 ns,
before being quenched to 230 K over 50 ns. This is the starting
point for the calculation of the initial ux rate for the FFS algo-
rithm, which lasted about 1.5 ms and thus allowed us to investi-
gate the water–CHLM interface as well (see e.g. Fig. 3). the normal to the slab to 100 ˚A. 3.2
The role of surface topography As noted above the spread of freezing temperatures we report for
CHLM is very broad. This behaviour suggests that the nucleation
behaviour of CHLM is spatially heterogeneous, i.e. different
parts of the surface nucleate ice with differing efficiency. This is
commonly known as site specic nucleation behaviour,62,70,71,73 As noted above the spread of freezing temperatures we report for
CHLM is very broad. This behaviour suggests that the nucleation
behaviour of CHLM is spatially heterogeneous, i.e. different
parts of the surface nucleate ice with differing efficiency. This is
commonly known as site specic nucleation behaviour,62,70,71,73
and it can be appreciated to a lesser extent for the other ice
nucleating agents considered in Fig. 1b. However, it is inter-
esting to note that CHLM crystals seem to lead to two different
ice nucleation regimes, as can be inferred from Fig. 1b (note the
two different slopes characterising ns as a function of tempera-
ture). As it is becoming increasingly clear that the topography of
the ice nucleating agents must play an important role in the
heterogeneous nucleation of ice from liquid water,40,74,75 we
suspect that structural differences between the crystalline areas
covered by the water droplets are responsible for the wide spread
in nucleation temperatures observed. This hypothesis is sup-
ported by the scanning electron microscope (SEM) images of the
(001) face of CHLM reported in Fig. 2. While the crystalline
plates appear as mostly at and smooth within the resolution of
100 mm, it is clear that there exist numerous defects, which can
potentially
present
opportunities
for
complicated
surface
geometries to occur. How exactly the nanometric structure of
crystalline ice nucleating agents affects the kinetics of ice
formation is still an open question (see e.g. ref. 40 and 32). In
fact, it would be expected that an atomically smooth and
homogeneous CHL surface would nucleate ice with a single
nucleation rate and hence within a far narrower range of
temperatures than that reported in Fig. 1. The role of specic
defects and broadly speaking of the surface morphology to ice
formation on CHL – and the vast majority of biological nucle-
ating agents – it thus remains yet to be fully understood. For
instance, it is not immediately clear why CHLM crystals are
much more effective than feldspar in promoting the formation
of ice. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM.
This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. In Fig. 1a we report the fraction of frozen droplets as a function
of temperature for CHLM. It can be seen that CHLM can induce
ice nucleation at temperatures as warm as 269 K. This agrees with
previous studies which have reported high nucleation tempera-
tures for CHL in the immersion mode.2,24 In here, we investigate
the ice nucleating ability of CHLM as a function of supercooling. As shown in Fig. 1a, the spread of nucleation temperatures for the
CHLM sheets is very broad, with some of them freezing at
temperatures as low as 252 K. To allow for a comparison of the
efficiency of ice nucleation by CHLM with other known nucleating
species we have calculated the ice-active surface site density (ns)
for CHLM on the basis of the size of the contact patch of the water
droplets with the CHL plates. As explained in greater detail in the
Methods section, ns is a site specic measure of ice nucleation
efficiency which does not take into account the time dependence
of ice nucleation, on the basis that the impact of time dependence
on heterogeneous ice nucleation is generally minimal.62,70,71 We
have compared the ice nucleating efficiency of CHLM with that of
e.g. kaolinite powder,62 which has commonly been regarded as an
efficient ice nucleating agent in the past72 and of BCS 376 feldspar
powder, which is known to nucleate ice highly efficiently11 and
was likely responsible for earlier observations of efficient ice
nucleation in kaolinite samples. It can be seen that CHLM
nucleates ice far more efficiently than kaolinite and more effi-
ciently even than the feldspar at warm temperatures. Thus, CHLM
has the potential to be a highly efficient ice nucleating agent in
immersion mode across a wide range of temperatures – which is Edge Article Chemical Science CHL can crystallise into two different polymorphs, namely
anhydrous64 (CHLA) and CHLM.52 The latter is the most relevant
to ice formation, as it spontaneously forms in aqueous envi-
ronments.52,54,65–68
Conveniently,
CHLM
crystallises
from
a mixture of 95% ethanol and 5% water as plates with the (001)
surface forming the at surface of the plates.66 The platy crystal
habit of CHLM is characteristic of CHLM as opposed to CHLA,
which tends to crystallise as needles. CHLM crystals display
a layered structure: bilayers of CHL molecules are stacked along
the [001] direction, and facile cleavage along the (001) planes
leads to surfaces exposing either a –CH3 terminated, hydro-
phobic surface or a –OH terminated, hydrophilic surface. Atomic and chemical force microscopy measurements indicate
that in aqueous and organic solution conditions, the hydro-
philic (001) surface is most abundantly found, in the form of
largely homogeneous crystalline faces.54 Early experimental
evidence suggested substantial ice nucleation activity of CHLM
at very mild supercooling (DTS ¼ 5 K).21,23,69 The ice nucleation
efficiency of CHLM was evaluated using an adapted version of
the ml-Nucleation by Immersed Particles Instrument (ml-NIPI)
experiments ml-NIPI described in detail in ref. 50. Experi-
ments were performed by placing droplets directly onto
a surface of crystalline CHLM. We used an electronic pipette to
place 1 ml droplets of water onto the (001) plane of plates of
CHLM. The water droplets were then cooled down at a rate of 1
K min1 and freezing monitored using a camera. In this way the
fraction of frozen droplets can be determined as a function of
temperature. Note that as the crystalline surface is submerged
in liquid water these experiments are conducted at 100% rela-
tive humidity – i.e. in “immersion mode”.70 the scenario typically encountered when dealing with cryobio-
logical applications. This journal is © The Royal Society of Chemistry 2018 3.1
Cholesterol promotes the formation of ice across a wide
range of temperatures We start by experimentally investigating the ice nucleating
ability of cholesterol crystals – as a function of supercooling. This journal is © The Royal Society of Chemistry 2018 8080 | Chem. Sci., 2018, 9, 8077–8088 View Article Online Edge Article 3.2
The role of surface topography In the next section, we will address this issue by showing
that in addition to the topography of the surface, the formation
of a peculiar hydrogen bond network at the water–CHLM inter-
face is key in determining the ice nucleating ability of this
compound. 3.3
The cholesterol–water interface This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Interestingly, despite the presence of the hydroxyl groups,
the density prole of the oxygen atoms of the water molecules
on CHLM reported in Fig. 3b resembles that for water at
hydrophobic walls.77 The enhancement (30% in Fig. 3b) of the
density, within the rst peak of the prole, compared to its
value in the bulk of the water slab, is much smaller than that
(typically a factor four or six) observed for e.g. water in contact
with hydrophilic walls – or indeed water on kaolinite. This is
because, the outer layer of the CHLM crystals is much more
mobile/exible than that of kaolinite: this is not surprising, as
we are comparing a molecular organic crystal (held together by
van der Waals interactions) with a (covalently bonded) clay
mineral. Importantly, it is reasonable to assume that a similar
degree of exibility characterises the majority of organic crystals
containing long molecules such as steroids. This is relevant to
ice formation because, as discussed in e.g. ref. 43, the structural
uctuations of organic/biological ice nucleating particles can
strongly affect the kinetics of ice nucleation. In fact, we have
shown in ref. 45 that the same argument holds in the case of
kaolinite as well: for instance, a “frozen” kaolinite surface
(atoms are kept xed during MD simulations) leads to non-
physically fast ice nucleation rates. We note that the emergence of these cages is the reason why
we have chosen to consider as the “interfacial layer” those water Fig. 4
The formation of unconventional ice-templating molecula
structures: hydrogen bonded cages. (a) A hydroxyl group (purple) o
CHLM participates into a hydrogen bonded cage of water molecules
(b) A single hydrogen bonded cage (top view), which constitutes the
building block of cubic ice (panel (c), side view). Note that these cages
are made of both 6-membered (panel (d), side view) and 5-membered
(panel (e), side view) hydrogen bonded rings, involving water mole-
cules as well as a hydroxyl group provided by the CHLM surface. 3.3
The cholesterol–water interface In order to investigate the molecular-level details of the CHLM–
water
interface,
we
have
performed
unbiased
molecular
dynamics simulations at strong supercooling (DTS ¼ 42 K)
employing the CHARMM36 (ref. 55 and 56) and the TIP4P/Ice53
force elds for CHL and water molecules respectively. Compu-
tational details and results concerning the validation of our
computational setup are reported in the Methods section and in
the ESI† respectively, while the computational geometry is
depicted in Fig. 3a. A water slab (40 ˚A thick) is in contact with the hydroxylated
(001) surface of CHLM (CHLMOH
001 ), modelled as a single layer of
CHL molecules. This surface is hydrophilic, due to the presence This journal is © The Royal Society of Chemistry 2018 Chem. Sci., 2018, 9, 8077–8088 | 8081 Edge Article
View Article Online Chemical Science occurrence of these rings is actually even more pronounced in
the proximity of the CHLM–water interface (red/orange points/
curve in Fig. 3c). Surprisingly, there is also an increase in the
number of 5-membered water/hydroxyl rings at the crystal–
liquid interface. Pentagonal rings are thought to frustrate the
homogeneous formation of ice;79 however, in this case both 6-
and 5-membered rings alike contribute to the formation of ice-
like uctuations such as the “cage” shown in Fig. 4a. These
cages are indeed the building blocks of ice Ic (see Fig. 4b and c),
and involve hydrogen bonds between water molecules and
hydroxyl groups, as depicted in Fig. 4d and e. Thus, in this
heterogeneous
nucleation
scenario,
the
presence
of
5-
membered rings in not detrimental; on the contrary, they lead
to the formation of ice-like uctuations of the water network at
the water–CHLMOH
001
interface. of amphoteric hydroxyl groups. As CHL molecules are relatively
bulky and the crystal is held together by weak electrostatic
interactions only, the arrangement of these –OH groups on the
CHLM surface is characterised by a broad distribution of large
OH–OH distances, ranging from 5.1 to 7.1 ˚A – as illustrated in
Fig. 3a. Such a pattern of hydroxyl groups does not straight-
forwardly match any particular low-index Miller surface of
either hexagonal or cubic ice. This is relevant, as a good struc-
tural match between a substrate and ice38 has traditionally been
considered as a “requirement” of an effective ice nucleating
agent.76 Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. 3.3
The cholesterol–water interface This is particularly relevant for CHL,
which
is
a
substantial
component
of
animal
cellular
membranes25 and could thus contribute to promote the
heterogeneous formation of ice in biological matter – a possi-
bility we will investigate in future work. In this respect, it is
interesting to note that very recent simulations81 suggest that
ice can bind to antifreeze proteins via “anchored clathrate”
motifs not dissimilar to the molecular cages discussed above. From the very early stages of the nucleation process, we
observe a strong preference for ice to form at the water–
CHLMOH
001 interface – as opposed to within the bulk of the water
slab. In fact, 75% of the pre-critical ice nuclei we observe as
natural uctuations of the supercooled water network (l ¼ 0) sit
on top of the CHLMOH
001
surface. The calculated growth proba-
bility P(l|l0) as a function of lambda, together with the fraction
of ice nuclei that can be found at the water–CHLMOH
001 interface
are reported in the ESI (Fig. S2b†). By the time the FFS algorithm
has reached l ¼ 125, no nuclei within the bulk of the water slab
survive. We have observed a similar trend in the case of ice
nucleation on the hydroxylated (001) basal face of kaolinite,44
but the fraction of ice nuclei at the water–kaolinite interface at
the initial stages of the FFS algorithm was much smaller
(25%). This suggests that pre-critical ice-like uctuations,
which we have recently investigated in the broader context of
heterogeneous crystal nucleation,95 are much more likely to
occur at the surface of CHLM compared to kaolinite. The
mechanism
of
ice
nucleation
at
the
water–
CHLMOH
001
interface is illustrated in Fig. 5: the early stages
involve the formation of elongated, almost one dimensional,
linear, chain-like ice nuclei preferentially along specic direc-
tions (see ESI†), due to the particular arrangement of the –OH
hydroxyl groups on the CHLMOH
001
surface. However, larger
nuclei (corresponding to increasing values of l) progressively
assume a more isotropic shape, as indicated by the evolution of
the asphericity parameter a (equal to 1 and 0 for a innitely
elongated rod and a perfect sphere respectively) as a function of
l. 3.3
The cholesterol–water interface Because of this exibility of the CHL molecules and the low-
density of hydroxyl groups at the water–CHLM interface, we did
not observe (within a 200 ns time scale) the formation of an
ordered, ice-like over-layer of water molecules, in contrast with
what is generally found in the case of idealised crystalline
surfaces,78 carbonaceous particles42 or kaolinite crystals.44,45 In
fact, most inorganic substrates are characterised by surfaces
where atomic/molecular species are tightly packed, and can
thus potentially provide a high density of functional groups for
supercooled water to interact with, typically by forming a more
or less ordered overlayer sitting on top of the crystalline surface. In the case of the water–CHLM interface, however, water
molecules can partially inltrate the outer layer of the CHLM
surface (see Fig. 3a and b) due to the relatively large spacing
between the CHL molecules and the exibility of the surface
itself. As a net result, despite the absence of a at overlayer of
ice-like water molecules, the amphoteric character of the
hydroxyl groups does facilitate the formation of a network of
hydrogen bonded rings of water molecules as well as hydroxyl
groups, as illustrated in Fig. 3c. In particular, we observe the
emergence of 6-membered rings of hydrogen bonded water
molecules and hydroxyl groups. These rings are the building
blocks of both hexagonal (ice Ih) and cubic (ice Ic) ice, and are
the most abundant species in bulk water. Note that the Fig. 4
The formation of unconventional ice-templating molecular
structures: hydrogen bonded cages. (a) A hydroxyl group (purple) of
CHLM participates into a hydrogen bonded cage of water molecules. (b) A single hydrogen bonded cage (top view), which constitutes the
building block of cubic ice (panel (c), side view). Note that these cages
are made of both 6-membered (panel (d), side view) and 5-membered
(panel (e), side view) hydrogen bonded rings, involving water mole-
cules as well as a hydroxyl group provided by the CHLM surface. This journal is © The Royal Society of Chemistry 2018 8082 | Chem. Sci., 2018, 9, 8077–8088 Edge Article molecules within 5.0 ˚A from the average position of the oxygens
of the CHL hydroxyl groups – as illustrated by the shaded region
in Fig. 3b. As shown in e.g. ref. 80, the denition of this water
layer can have an impact on the analysis of the structure of – in
this case – the water–CHLM interface. 3.3
The cholesterol–water interface While the interfacial layer
can be chosen on the basis on indicators such as the rst or
second minimum of the density prole (see Fig. 3b), we have
found that the rather generous cutoffof 5.0 ˚A is sufficient to
accommodate the substantial extent of the hydrogen bonded
cages depicted in Fig. 4d and 3e. We have also veried that by
choosing the second minimum of the density prole (7 ˚A) our
results, including the trends within the rings statistics reported
in Fig. 3c, are basically unchanged. J ¼ Fl0
Y
Nl
i¼1
Pðli|li1Þ
(2) (2) In this way, the (exceedingly small) total probability P(lice|l0)
for a certain MD trajectory to reach the ice basin is decomposed
in a collection of (manageable) crossing probabilities which we
compute by a large number (103 to 105) of unbiased MD trial
runs from li1 to li. Further details about the FFS algorithm can
be found in the ESI.† We note that we have used the same water
model (TIP4P/Ice) at the same strong supercooling (DTS ¼ 42 K)
as employed previously to compute the homogeneous ice
nucleation rate and the heterogeneous ice nucleation rate on
kaolinite, a clay mineral of relevance to atmospheric science. As
such, we can compare directly our results with those of ref. 44
and 57. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Our
ndings
thus
contribute
the
growing
body
of
evidence40,43,78 that the structural mismatch argument alone
cannot be deemed as neither a sufficient nor a necessary criteria
to assess, let alone to predict, the ice nucleating ability of
a given substrate.38 This is bound to be especially true in the
case of biological ice nucleating agents such as macromole-
cules,17 where the notion itself of a lattice mismatch is ill
dened. In fact, we argue that organic crystals such as choles-
terol lie halfway in between inorganic (e.g. mineral crystals) and
biological (e.g. bacterial fragments) ice nucleating agents, as
they are characterised by the relatively at and (in this case)
–OH regularly patterned surfaces of the former while showing
the exibility of the latter. 3.3
The cholesterol–water interface At the same time, the 1D character of the nuclei evolves
toward a more compact geometry, with a signicant growth
along
the
[001]
direction
(z-axis)
normal
to
the
water–
CHLMOH
001
interface, as demonstrated by the trend of the
dimension DZ of the ice nuclei along that axis, also reported in
Fig. 5. The resulting morphology of the ice crystals, though,
remains to be investigated because of the emergence of nite
size effects. Overall, the evolution of the ice nuclei within the
early stage of ice nucleation at the water–CHLMOH
001
interface
possesses some similarities with the case of ice formation on
kaolinite,44 where ice nuclei spread into a 2D, planar geometry
before stacking additional ice layers along the normal to the This journal is © The Royal Society of Chemistry 2018 3.4
Ice nucleation mechanism and kinetics We note however that in order to probe
this aspect of CNT quantitatively, it would be desirable to
improve the current enhanced sampling techniques to take into
account milder supercooling – and thus larger critical ice
nuclei. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. The ice nucleation rate on the CHLMOH
001
surface obtained
from our FFS simulations is 10273 s1 m3, about 20 orders of
magnitude larger than the homogeneous ice nucleation rate at
the same supercooling – calculated via FFS simulations using
the same water model.57 This spectacular enhancement of the
kinetics of ice formation is due to the small heterogeneous
critical nucleus size N*
H, which we estimate (as discussed in
detail in the ESI†) to contain 250 50 water molecules –
a number consistent with the predictions of CNT (see ESI† and
ref. 44). Interestingly, these results are very similar to what we
have previously obtained in the case of ice formation on
kaolinite,44 where we calculated J ¼ 10262 s1 m3 and N*
H ¼
225 25. However, it has to be said that the FFS simulations
performed in this work (as opposed to the case of kaolinite44)
may be suffering from nite size effects (discussed in the ESI†),
which could both enhance the kinetics of ice nucleation (as the
ice nuclei feel the inuence of their periodic images) and/or
hamper the growth of ice crystals (as the simulation box most
likely does not match the periodicity of the growing ice crystal). Our estimates of J and N*
H have therefore to be taken with care. H
The
fact
that
the
kinetics
of
ice
formation
on
the
CHLMOH
001
surface seems to be comparable with that of an
inorganic crystal such as kaolinite is not entirely unexpected, as
the (001) hydroxylated surface of kaolinite also presents –OH
groups at the water–crystal interface which are capable of
templating the formation of ice-like structures. However,
supercooled water on kaolinite forms a dense, hexagonal
ordered overlayer of ice-like molecules sitting on top of the
hydroxyl groups,45 while, as we have discussed in the previous
section,
water
molecules
can
partially
inltrate
the
CHLMOH
001
surface to form 5- and 6-membered hydrogen
bonded rings, resulting in a much less ordered and way less
dense overlayer. 3.4
Ice nucleation mechanism and kinetics In order to characterise the mechanism as well as the kinetics of
ice nucleation on CHLMOH
001
we have performed forward ux
sampling
(FFS)
simulations.82–89
While
other
enhanced
sampling techniques are in principle available, such as meta-
dynamics,90 transition path sampling,91 and seeded molecular
dynamics,92 FFS represents a “gold standard” approach when
dealing with ice nucleation (see e.g. ref. 35, 44, 57, 89 and 93). This method involves partitioning the path from (in this case)
liquid water to ice, described by an order parameter l, into
a collection of interfaces li. Here, l corresponds to the number
of water molecules within the largest ice nucleus, which can be
located either in the bulk of the water slab or at the water–
CHLMOH
001
interface. A diffuse crystal–liquid interface has been
taken into account into the denition of l, which relies on local
bond order parameters (see ESI† and ref. 94), consistent with
ref. 44. Starting from the natural uctuations of liquid water
toward the ice phase, i.e. pre-critical ice nuclei as sampled
within ms long unbiased MD simulations, the nucleation rate J
can be obtained as the product of the ux Fl0 by which the
system reached the rst interface l0, times the product of the
sequence of the individual crossing probabilities P(li|li1): This journal is © The Royal Society of Chemistry 2018 Chem. Sci., 2018, 9, 8077–8088 | 8083 Edge Article
View Article Online Edge Article
View Article Online View Article Online Fig. 5
The
early
stages
of
ice
nucleation
at
the
water–
CHLMOH
001
interface involve non-spherical ice crystallites. Asphericity
parameter a and spatial extent of the ice nuclei along the direction
normal to the CHLM slab DZ as a function of l for ice nuclei at the
water–CHLMOH
001
interface. The insets correspond to top and side
views of typical ice nuclei forming at the water–CHLMOH
001
interface,
containing about 100 (top) and 245 (bottom) water molecules. Chemical Science
Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Chemical Science Chemical Science Chemical Science Fig. 5 and 3 in the ESI†), which are likely to be characterised by
a much smaller interfacial energy if compared to the hemi-
spherical shape predicated by CNT in the case of perfectly at,
featureless substrates. 3.4
Ice nucleation mechanism and kinetics As both substrates (kaolinite and CHLM) are
characterised by the presence of hydroxyl groups which facili-
tate the formation of ice, the much faster kinetics of ice
nucleation
we
have
observed
experimentally
for
CHLM
compared to kaolinite (especially at mild supercooling, Fig. 1b)
is likely to be due to the different surface topography of the two
compounds. Fig. 5
The
early
stages
of
ice
nucleation
at
the
water–
CHLMOH
001
interface involve non-spherical ice crystallites. Asphericity
parameter a and spatial extent of the ice nuclei along the direction
normal to the CHLM slab DZ as a function of l for ice nuclei at the
water–CHLMOH
001
interface. The insets correspond to top and side
views of typical ice nuclei forming at the water–CHLMOH
001
interface,
containing about 100 (top) and 245 (bottom) water molecules. water–kaolinite interface, once the critical nucleus has been
reached. Thus, these ndings suggest that the nature of the
early stages of heterogeneous ice nucleation at strong super-
cooling (DTS ¼ 42 K) has a strong anisotropic character, in stark
contrast with the assumptions prescribed by classical nucle-
ation theory (CNT).96 In fact, CNT does not take into account the molecular
structure nor the “chemistry” of the substrate: these aspects are
only implicitly included into the value of the contact angle of
the ice nuclei with respect to the substrate. However, micro-
scopic features such as the particular arrangement of the
hydroxyl groups on the CHLM surface can inuence the shape
and the energetics of the ice nuclei. In the case of ice on CHLM,
water molecules at the water–cholesterol interface nd conve-
nient to harness the directionality of the –OH pattern (see
Fig. 3a and 3 in the ESI†) to form anisotropic ice nuclei (see 4
Conclusions Interestingly, despite the predominance of ice Ic within the
growing ice nuclei, ice Ih can still form and grow along
a specic direction (the [111] of the cubic phase) on top of ice Ic
crystals (which in turn grow along the [100] direction,
normal to the plane of the water–CHLMOH
001
interface), as
illustrated in the insets (right side) of Fig. 6. The coexistence of
ice Ic and ice Ih is thus likely to result in ice Isd crystals at strong
supercooling. However, at milder supercooling ice Ih uctua-
tions are expected to become more relevant, and in fact
experimental evidence suggests that the macroscopic crystal-
line habit of ice crystals grown on CHLM at DT ¼ 2 K is indeed
that of ice Ih.22 Importantly, we did not observe such
a competition between ice Ic and ice Ih in the case of kaolinite,
where the cubic polytype is basically absent throughout the
whole nucleation process.44,45 In fact, we argue that, in the
case of CHLM crystals, different nucleation sites (whose exact
nature remains to be determined) could promote chiey ice Ic
or ice Ih according to the different degree of supercooling, thus
contributing to unravel the strong ice nucleating ability
of CHLM crystals along such a wide range of temperatures. This argument would suggest that the multi-component
nature of ice nucleation on biological matter could be at
least partially attributed to a greater variety of nucleation
sites – as well as the specic templating effect of functional By means of a blend of experiments and simulations, we have
unravelled the origins of ice nucleation on cholesterol (CHL),
a prototypical organic crystal of relevance to cryopreservation. Our results suggest that its exceptional ice nucleating activity
stems from the ability of its exible hydrophilic surface to form
unconventional
ice-templating
structures
–
specically,
hydrogen bonded cages comprising 6- as well as 5-membered
rings. In addition, the experimental evidence reported here
suggests that the intrinsic potential of cholesterol to nucleate
ice may potentially be enhanced by specic topological features
of
the
crystalline
habit. In
particular,
droplet
freezing
measurements show that cholesterol promotes the heteroge-
neous formation of ice across a wide range of temperatures
(from 4 to 20 C). In fact, we nd that CHLM crystals
nucleate ice far better than the mineral feldspar, which is one of
the most effective inorganic ice nucleating agents of relevance
to
atmospheric
science. 3.5
Competition between cubic and hexagonal ice At the strong supercooling considered here (DTS ¼ 42 K),
homogeneous ice nucleation results in a mixture of ice Ic and
ice Ih known as stacking disordered ice Isd.97–99 However, things
can be quite different in the heterogeneous case. For instance,
the hydroxylated (001) basal face of kaolinite promotes exclu-
sively the formation of the primary prism face of ice Ih.44,45 In the
case of the CHLMOH
001
surface, we observe both ice Ic and ice Ih This journal is © The Royal Society of Chemistry 2018 8084 | Chem. Sci., 2018, 9, 8077–8088 View Article Online Edge Article Chemical Science Chemical Science Fig. 6
Competition between cubic (blue/cyan spheres/sticks) and hexagonal (red/orange spheres/sticks) ice within the early stage of ice
nucleation at the water–CHLMOH
001 interface. The average number of double diamond and hexagonal cages (DDC and HC, the building block of
ice Ic and ice Ih respectively) is reported as a function of the order parameter l. Insets on the left show representative ice Ic and ice Ih fluctuations
(top view) at the first FFS interface (l ¼ 80). Insets on the right show representative ice nuclei at l ¼ 165 and 260, where the competition between
the two polymorphs becomes more evident. The dashed (green) lines/arrows indicate the crystallographic plane/direction along with ice Ih has
the possibility to grow on top of ice Ic. Fig. 6
Competition between cubic (blue/cyan spheres/sticks) and hexagonal (red/orange spheres/sticks) ice within the early stage of ice
nucleation at the water–CHLMOH
001 interface. The average number of double diamond and hexagonal cages (DDC and HC, the building block of
ice Ic and ice Ih respectively) is reported as a function of the order parameter l. Insets on the left show representative ice Ic and ice Ih fluctuations
(top view) at the first FFS interface (l ¼ 80). Insets on the right show representative ice nuclei at l ¼ 165 and 260, where the competition between
the two polymorphs becomes more evident. The dashed (green) lines/arrows indicate the crystallographic plane/direction along with ice Ih has
the possibility to grow on top of ice Ic. Fig. 6
Competition between cubic (blue/cyan spheres/sticks) and hexagonal (red/orange spheres/sticks) ice within the early stage of ice
nucleation at the water–CHLMOH
001 interface. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6
This article is licensed under a Creative Commons Attribution 3.0 Un nuclei at the very early stages of the nucleation process, as
depicted in the inset (leside) of Fig. 6. These ice-like uctua-
tions originate from the templating effect of the hydroxyl groups
on the CHLM surface, as illustrated in Fig. 4a–e (and Fig. S3 in
the ESI†). In principle, even if ice Ic nuclei are three times more
abundant than ice Ih nuclei at the rst FFS interface (l ¼ 80), we
would expect the formation of ice on the CHLMOH
001
surface to
proceed via the growth of ice Isd. In fact, as shown in Fig. 6, the
competition between the growth of two ice polytypes at 230 K
(i.e. DT ¼ 42 K) is dominated by ice Ic: by the time the ice nuclei
have reached a post-critical size (e.g. l ¼ 360), the average
number of Hexagonal Cages (HC,57 the building blocks of ice Ih)
is still about three times larger than that of DDC (Double Dia-
mond Cages,57 the building blocks of ice Ic). groups acting as hydrogen bond donor and/or acceptors with
respect to supercooled liquid water. Moreover, we have shown
in this work that some of these functional groups – such as the
hydroxyl groups characterising the water–CHLMOH
001
interface
– can even promote a different ice polytype at the same time,
possibly according to different supercooling. Finally, we note that, in agreement with previous simula-
tions of ice nucleation,43,45 the exibility of the CHLMOH
001 has an
impact on the extent and the structure of the ice-like uctua-
tions at the CHLMOH
001 –water interface, and that the anhydrous
crystalline phase of CHL also displays substantial ice nucleating
potential. These two aspects are both addressed in detail in the
ESI.† This journal is © The Royal Society of Chemistry 2018 3.5
Competition between cubic and hexagonal ice The average number of double diamond and hexagonal cages (DDC and HC, the building block of
ice Ic and ice Ih respectively) is reported as a function of the order parameter l. Insets on the left show representative ice Ic and ice Ih fluctuations
(top view) at the first FFS interface (l ¼ 80). Insets on the right show representative ice nuclei at l ¼ 165 and 260, where the competition between
the two polymorphs becomes more evident. The dashed (green) lines/arrows indicate the crystallographic plane/direction along with ice Ih has
the possibility to grow on top of ice Ic. 4
Conclusions Moreover,
electron
microscopy
measurements suggest that the broad range of freezing
temperatures we observe for CHLM crystals may be due to the
coexistence of diverse structural features of the crystalline
surface, which in turn can act as different nucleation sites. The
microscopic structure of the latter remains to be assessed, but This journal is © The Royal Society of Chemistry 2018 Chem. Sci., 2018, 9, 8077–8088 | 8085 Edge Article
View Article Online Chemical Science formation of stacking disordered ices. Thus, we argue that the
dramatic ice nucleation ability of certain organic materials may
be traced down not only to the formation of a network of
hydrogen bonds between water and the nucleation sites, but
also to the capability of specic surfaces to promote at the same
time different ice polytypes as a function of supercooling. In
order to verify this hypothesis, though, we would need to
investigate ice nucleation on CHLM at milder supercooling. To
this
end,
an
heterogeneous
seeded
molecular
dynamics
approach is currently being validated.102 Our results also
suggest that organic crystals sit in between inorganic and bio-
logical materials, when it comes to promoting the formation of
ice: substrates like CHLM are characterised by relatively at
surfaces exposing an array of amphoteric functional groups,
much like several inorganic ice nucleating agents (e.g. kaolinite,
feldspar, hydroxylated graphene), but the exibility of the
surface and the low density of such functional groups is typical
of biological nucleating agents such as macromolecules and
bacterial fragments. This is especially relevant in the case of
CHL, a molecule which is not only used in crystalline form as an
ice nucleating agent in cryopreservation applications, but that
signicantly contributes to the composition of animal cell
membranes as well. the possibility that different parts of the CHLM surface may
nucleate ice with different efficiency suggests that surface
topography can play an important role in determining the ice
nucleating ability of organic crystals. Surprisingly, we nd that CHLM crystals, despite being
exceptionally good ice nucleating agents, do not provide
a conventional template for ice to form. Specically, molecular
simulations reveal that, as opposed to what has been reported for
supercooled water in contact with simple model substrates (e.g. 4
Conclusions Lennard-Jones crystals, which allow to rapidly explore different
surface geometries78) and/or inorganic materials (such as carbo-
naceous particles,42 or clay minerals44,45), water on the (001)
hydroxylated surface of cholesterol monohydrate (the most
abundant interface in aqueous environments) does not form an
ordered, dense, ice-like overlayer. Instead, due to the exibility of
the CHLM surface and its relatively low density of hydroxyl
groups, water molecules partially inltrate the crystal, forming
a network of both 6- and 5-membered hydrogen bonded rings. The latter involve water molecules as well as hydroxyl groups
provided by CHL molecules. While some of these structural
features (particularly pentagonal rings) are known to hinder
homogeneous water freezing, we nd that they actually facilitate
the heterogeneous formation of both hexagonal and cubic ice on
CHLM crystals. In fact, enhanced sampling simulations suggest
the emergence of stacking disordered ice (a mixture of the two
polytypes) at the water–CHLM interface. This is in stark contrast
with what we have previously observed in the case of e.g. the clay
mineral kaolinite, where only the hexagonal polytype was
observed along the whole nucleation process.44 In fact, more
oen than not a given crystalline substrate nucleates exclusively
one of the two ice polytypes.7,13 Moreover, we nd that the
nucleation rate of ice on CHLM crystals is basically identical to
that we have previously calculated in the case of kaolinite – at the
same strong supercooling (DTS ¼ 42 K). Kaolinite and CHLM are
both characterised by an hydrogen bond network capable of
facilitating the formation of ice nuclei: thus, the substantial
difference in the ice nucleating ability we observe experimentally
for these two compounds is most likely rooted into their surface
topography. In fact, the ns data reported in Fig. 1b suggest that
two populations of potentially different ice nucleating sites may
coexist on the CHLM surface. The change in the slope of the
CHLM data is reminiscent of that observed for freezing spectra
for birch pollen,17,100 which has been attributed to the presence of
two different ice nucleating macromolecules.101 Similarly, we
argue that there may be two different broad classes of ice
nucleating sites on CHLM, represented by the two different
slopes in the freezing spectra. 4
Conclusions Due to the spatially sporadic
nature of the highly active sites, which are not present in every
millimetre diameter droplet, it seems likely that these two
different classes of ice nucleation sites are related to specic
defects or the diverse topography of the CHLM, rather than any
factors related to the bulk molecular structure of CHLM. In addition, the emergence of stacking disordered ice phases
during the heterogeneous formation of ice has been experi- In summary, the experiments and simulations presented in
this work indicate that cholesterol crystals are incredibly effi-
cient ice nucleating agents, active across a broad range of
supercooling. We show that such strong ice nucleating activity
is due to the intrinsic potential of the exible amphoteric
surfaces of CHLM to form unconventional ice-templating
molecular structures. It is likely that microscopic structural
features of the crystals could further enhance the ability of
CHLM (and potentially of other organic crystals) to form ice,
by offering a diverse array of nucleating sites. In fact, we
believe that for an ice nucleating agent to be very efficient,
a combination of interfacial “chemistry” and surface topog-
raphy is generally required. This interplay could thus be the
key to understand the heterogeneous formation of ice on
molecular organic crystals, and it may provide a starting point
for the investigation of ice in soand biological matter at the
molecular level. In particular, tailoring the microscopic
structure of the substrate and modifying the nature as well as
the density of hydrogen-bonding functional groups at the
water–substrate interface can be seen as two different routes to
engineer the ice nucleating ability of novel cryoprotectants,
the design of which, at the moment, largely relies on the
high-throughput screening of whole libraries of different
compounds. The absence of a proper structure-to-function
paradigm is perhaps the most pressing challenge in cryobi-
ology: this is why future work will be devoted to assess whether
and how hydrogen-bonding functional groups other than
hydroxyls would be equally effective to enhance the kinetics of
heterogeneous ice nucleation. In addition, the emergence of stacking disordered ice phases
during the heterogeneous formation of ice has been experi-
mentally observed,99 and consequently ascribed to different
crystal growth regimes. Our results offer the intriguing prospect
that the nucleation process itself may favour, in some cases, the 8086 | Chem. Sci., 2018, 9, 8077–8088 Edge Article Chemical Science Chemical Science D. A. Knopf, U. P¨oschl, M. Bonn and T. Weidner, Sci. Adv., 2016, 2, e1501630. References 27 K. A. Pratt,
P. J. DeMott,
J. R. French,
Z. Wang,
D. L. Westphal, A. J. Heymseld, C. H. Twohy, A. J. Prenni
and K. A. Prather, Nat. Geosci., 2009, 2, 398–401. 1 T. Bartels-Rausch, Nature, 2013, 494, 27–29. 28 C. Hoose, J. E. Kristj´ansson and S. M. Burrows, Environ. Res. Lett., 2010, 5, 024009. 2 E. Moc´e, E. Blanch, C. Tom´as and J. Graham, Reprod. Domest. Anim., 2010, 45, 57–66. 3 I. Massie, C. Selden, H. Hodgson, B. Fuller, S. Gibbons and
G. J. Morris, Tissue Eng., Part C, 2014, 20, 693–702. 29 B. Wang,
A. T. Lambe,
P. Massoli,
T. B. Onasch,
P. Davidovits, D. R. Worsnop and D. A. Knopf, J. Geophys. Res., 2012, 117, D16209. 4 J. Morris and E. Acton, Cryobiology, 2013, 66, 85–92. 30 P. L. Davies, Trends Biochem. Sci., 2014, 39, 548–555. 5 B. J. Murray, D. O'Sullivan, J. D. Atkinson and M. E. Webb,
Chem. Soc. Rev., 2012, 41, 6519–6554. 31 K. Liu, C. Wang, J. Ma, G. Shi, X. Yao, H. Fang, Y. Song and
J. Wang, Proc. Natl. Acad. Sci. U. S. A., 2016, 113, 14739–
14744. 6 B. Slater, A. Michaelides, C. G. Salzmann and U. Lohmann,
Bull. Am. Meteorol. Soc., 2015, 97, 1797–1802. 7 G. C. Sosso, J. Chen, S. J. Cox, M. Fitzner, P. Pedevilla, A. Zen
and A. Michaelides, Chem. Rev., 2016, 116, 7078–7116. 32 J. M. Campbell, F. C. Meldrum and H. K. Christenson, Proc. Natl. Acad. Sci. U. S. A., 2017, 114, 810–815. 33 S. A. Zielke, A. K. Bertram and G. N. Patey, J. Phys. Chem. B,
2016, 120, 1726–1734. 8 U. Lohmann and J. Feichter, Atmos. Chem. Phys., 2005, 5,
715–737. 9 I. Tan, T. Storelvmo and M. D. Zelinka, Science, 2016, 352,
224–227. 34 X.-X. Zhang, M. Chen and M. Fu, J. Chem. Phys., 2014, 141,
124709. 35 Y. Bi, R. Cabriolu and T. Li, J. Phys. Chem. C, 2016, 120,
1507–1514. 10 C. Marcolli, B. Nagare, A. Welti and U. Lohmann, Atmos. Chem. Phys., 2016, 16, 8915–8937. 36 A. Reinhardt and J. P. K. Doye, J. Chem. Phys., 2014, 141, 084501. 11 J. D. Atkinson, B. J. Murray, M. T. Woodhouse, T. F. Whale, 11 J. D. Atkinson, B. J. Murray, M. T. Woodhouse, T. F. Whale,
K. J. Baustian, K. S. Carslaw, S. Dobbie, D. O'Sullivan and
T. L. Malkin, Nature, 2013, 498, 355–358. 37 G. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 A
This article is licensed under a Creative Commons Attribution 3.0 Unported 21 N. Fukuta and B. J. Mason, J. Phys. Chem. Solids, 1963, 24,
715–718. 22 N. Fukuta, J. Atmos. Sci., 1966, 23, 191–196. 23 R. B. Head, Nature, 1961, 191, 1058–1059. 24 I. Massie, C. Selden, H. Hodgson and B. Fuller, Tissue Eng.,
Part C, 2011, 17, 765–774. 25 M. R. Krause and S. L. Regen, Acc. Chem. Res., 2014, 47,
3512–3521. 26 G. R. Edwards and L. F. Evans, J. Atmos. Sci., 1971, 28, 1443–1447. There are no conicts to declare. There are no conicts to declare. This journal is © The Royal Society of Chemistry 2018 8086 | Chem. Sci., 2018, 9, 8077–8088 View Article Online View Article Online Acknowledgements Adv., 2016, 2, e1501630. 17 B. G. Pummer, H. Bauer, J. Bernardi, S. Bleicher and This work was supported by the European Research Council
(ERC) under the European Union's Seventh Framework Pro-
gramme: Grant Agreement number 616121 (HeteroIce project
[AM, PP, GCS]), Grant Agreement number 713664 (CryoProtect
project [TFW, BJM]) and Grant Agreement number 648661
(MarineIce project [TFW, BJM]). MAH and BJM are also sup-
ported by the Engineering Physical Sciences Research Council
(EPSRC) via the Research Grant number EP/M003027/1. GCS
and PP acknowledge the use of the UCL Grace and Legion High
Performance Computing Facilities, the use of Emerald, a GPU-
accelerated High Performance Computer, made available by
the Science & Engineering South Consortium operated in part-
nership with the STFC Rutherford-Appleton Laboratory and the
use of ARCHER UK National Supercomputing Service (http://
www.archer.ac.uk) through the Materials Chemistry Consor-
tium via the EPSRC grant number EP/L000202. The Forward
Flux Sampling simulations were supported by a grant from the
Swiss National Supercomputing Centre (CSCS; project ID s758). 17 B. G. Pummer, H. Bauer, J. Bernardi, S. Bleicher and
H. Grothe, Atmos. Chem. Phys., 2012, 12, 2541–2550. 18 M. Bar Dolev, I. Braslavsky and P. L. Davies, Annu. Rev. Biochem., 2016, 85, 515–542. 19 W. Asghar, R. E. Assal, H. Shaee, R. M. Anchan and
U. Demirci, Biotechnol. J., 2014, 9, 895–903. s Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM.
This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Open Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. 20 A. Aijaz, M. Li, D. Smith, D. Khong, C. LeBlon, O. S. Fenton, 20 A. Aijaz, M. Li, D. Smith, D. Khong, C. LeBlon, O. S. Fenton,
R. M. Olabisi, S. Libutti, J. Tischeld, M. V. Maus, R. Deans,
R. N. Barcia, D. G. Anderson, J. Ritz, R. Preti and
B. Parekkadan, Nat. Biomed. Eng., 2018, 2, 362–376. pen Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM.
This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. A., 2002,
99, 12562–12566. 61 B. Hess,
H. Bekker,
H. J. C. Berendsen
and
J. G. E. M. Fraaije, J. Comput. Chem., 1997, 18, 1463–1472. 91 P. G. Bolhuis, D. Chandler, C. Dellago and P. L. Geissler,
Annu. Rev. Phys. Chem., 2002, 53, 291–318. 62 R. J. Herbert, B. J. Murray, T. F. Whale, S. J. Dobbie and
J. D. Atkinson, Atmos. Chem. Phys., 2014, 14, 8501–8520. 92 J. R. Espinosa, C. Vega, C. Valeriani and E. Sanz, J. Chem. Phys., 2016, 144, 034501. 63 T. F. Whale,
M. Rosillo-Lopez,
B. J. Murray
and
C. G. Salzmann, J. Phys. Chem. Lett., 2015, 6, 3012–3016. 93 A. Haji-Akbari, J. Chem. Phys., 2018, 149, 072303. 64 H. S. Shieh, L. G. Hoard and C. E. Nordman, Nature, 1977,
267, 287–289. 94 G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio and
M. Parrinello, J. Chem. Theory Comput., 2017, 13, 1317–1327. 65 C. R. Loomis, G. G. Shipley and D. M. Small, J. Lipid Res.,
1979, 20, 525–535. 95 M. Fitzner, G. C. Sosso, F. Pietrucci, S. Pipolo and
A. Michaelides, Nat. Commun., 2017, 8, 2257. 66 N. Garti, L. Karpuj and S. Sarig, J. Lipid Res., 1981, 22, 785–
791. 96 R. Cabriolu and T. Li, Phys. Rev. E, 2015, 91, 052402. 97 E. B. Moore and V. Molinero, Phys. Chem. Chem. Phys., 2011,
13, 20008. 67 H. Rapaport, I. Kuzmenko, S. Lafont, K. Kjaer, P. B. Howes,
J. Als-Nielsen, M. Lahav and L. Leiserowitz, Biophys. J., 2001,
81, 2729–2736. 98 T. C. Hansen, M. M. Koza, P. Lindner and W. F. Kuhs, J. Phys.: Condens. Matter, 2008, 20, 285105. 68 I. Solomonov, M. J. Weygand, K. Kjaer, H. Rapaport and
L. Leiserowitz, Biophys. J., 2005, 88, 1809–1817. 99 T. L. Malkin, B. J. Murray, C. G. Salzmann, V. Molinero,
S. J. Pickering and T. F. Whale, Phys. Chem. Chem. Phys.,
2014, 17, 60–76. 69 R. B. Head, J. Phys. Chem. Solids, 1962, 23, 1371–1378. 100 D. O'Sullivan, B. J. Murray, J. F. Ross, T. F. Whale,
H. C. Price, J. D. Atkinson, N. S. Umo and M. E. Webb,
Sci. Rep., 2015, 5, 8082. 70 G. Vali, P. J. DeMott, O. M¨ohler and T. F. Whale, Atmos. Chem. Phys., 2015, 15, 10263–10270. 71 G. Vali, Atmos. Chem. Phys., 2014, 14, 5271–5294. 101 S. Augustin,
H. Wex,
D. Niedermeier,
B. Pummer,
H. Grothe,
S. Hartmann,
L. Tomsche,
T. Clauss,
J. References Fraux and J. P. K. Doye, J. Chem. Phys., 2014, 141, 216101. 38 P. Pedevilla, M. Fitzner and A. Michaelides, Phys. Rev. B,
2017, 96, 115441. 12 A. D. Harrison, T. F. Whale, M. A. Carpenter, M. A. Holden,
L. Neve,
D. O'Sullivan,
J. Vergara
Temprado
and
B. J. Murray, Atmos. Chem. Phys., 2016, 16, 10927–10940. 39 L. Lupi, R. Hanscam, Y. Qiu and V. Molinero, J. Phys. Chem. Lett., 2017, 8, 4201–4205. 13 A. Kiselev,
F. Bachmann,
P. Pedevilla,
S. J. Cox,
A. Michaelides, D. Gerthsen and T. Leisner, Science, 2017,
355, 367–371. 40 Y. Bi, B. Cao and T. Li, Nat. Commun., 2017, 8, 15372. 41 V. Molinero and E. B. Moore, J. Phys. Chem. B, 2009, 113,
4008–4016. 14 L. R. Maki,
E. L. Galyan,
M.-M. Chang-Chien
and
D. R. Caldwell, Appl. Microbiol., 1974, 28, 456–459. 42 L. Lupi, A. Hudait and V. Molinero, J. Am. Chem. Soc., 2014,
136, 3156–3164. 15 J. Lindemann, G. J. Warren and T. V. Suslow, Science, 1986,
231, 536. 43 Y. Qiu, N. Odendahl, A. Hudait, R. Mason, A. K. Bertram,
F. Paesani, P. J. DeMott and V. Molinero, J. Am. Chem. Soc., 2017, 139, 3052–3064. 16 R. Pandey, K. Usui, R. A. Livingstone, S. A. Fischer,
J. Pfaendtner, E. H. G. Backus, Y. Nagata, J. Fr¨ohlich-
Nowoisky,
L. Schm¨user,
S. Mauri,
J. F. Scheel, 44 G. C. Sosso, T. Li, D. Donadio, G. A. Tribello and
A. Michaelides, J. Phys. Chem. Lett., 2016, 7, 2350–2355. This journal is © The Royal Society of Chemistry 2018 Chem. Sci., 2018, 9, 8077–8088 | 8087 View Article Online View Article Online Chemical Science Edge Article 75 T. F. Whale, M. A. Holden, A. N. Kulak, Y.-Y. Kim,
F. C. Meldrum, H. K. Christenson and B. J. Murray, Phys. Chem. Chem. Phys., 2017, 19, 31186–31193. 45 G. C. Sosso, G. A. Tribello, A. Zen, P. Pedevilla and
A. Michaelides, J. Chem. Phys., 2016, 145, 211927. 46 L. F. Evans, J. Atmos. Sci., 1966, 23, 751–752. 76 D. Turnbull and B. Vonnegut, Ind. Eng. Chem., 1952, 44,
1292–1298. 47 M. Gavish, J. L. Wang, M. Eisenstein, M. Lahav and
L. Leiserowitz, Science, 1992, 256, 815–818. 77 M. F. Harrach and B. Drossel, J. Chem. Phys., 2014, 140,
174501. 48 P. K. Wolber,
C. A. Deininger,
M. W. Southworth,
J. Vandekerckhove, M. v. Montagu and G. J. Warren, Proc. Natl. Acad. Sci. U. S. pen Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM.
This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. 78 M. Fitzner, G. C. Sosso, S. J. Cox and A. Michaelides, J. Am. Chem. Soc., 2015, 137, 13658–13669. 49 D. Gurian-Sherman and S. E. Lindow, FASEB J., 1993, 7,
1338–1343. 79 H. Shintani and H. Tanaka, Nat. Phys., 2006, 2, 200–206. 50 T. F. Whale, B. J. Murray, D. O'Sullivan, T. W. Wilson,
N. S. Umo, K. J. Baustian, J. D. Atkinson, D. A. Workneh
and G. J. Morris, Atmos. Meas. Tech., 2015, 8, 2437–2447. 80 P. Pedevilla, S. J. Cox, B. Slater and A. Michaelides, J. Phys. Chem. C, 2016, 120, 6704–6713. 81 A. Hudait, N. Odendahl, Y. Qiu, F. Paesani and V. Molinero,
J. Am. Chem. Soc., 2018, 140, 4905–4912. 51 C. A. Schneider, W. S. Rasband and K. W. Eliceiri, Nat. Methods, 2012, 9, 671–675. 82 R. J. Allen, C. Valeriani and P. Rein ten Wolde, J. Phys.:
Condens. Matter, 2009, 21, 463102. 52 B. M. Craven, Nature, 1976, 260, 727–729. 83 T. Li, D. Donadio, G. Russo and G. Galli, Phys. Chem. Chem. Phys., 2011, 13, 19807–19813. 53 J. L. F. Abascal, E. Sanz, R. G. Fern´andez and C. Vega, J. Chem. Phys., 2005, 122, 234511. y
84 T. Li, D. Donadio and G. Galli, Nat. Commun., 2013, 4, 1887. 54 R. S. Abendan and J. A. Swi, Langmuir, 2002, 18, 4847–4853. 85 C. Valeriani, E. Sanz and D. Frenkel, J. Chem. Phys., 2005,
122, 194501. 55 P. Bjelkmar, P. Larsson, M. A. Cuendet, B. Hess and
E. Lindahl, J. Chem. Theory Comput., 2010, 6, 459–466. 86 Z.-J. Wang, C. Valeriani and D. Frenkel, J. Phys. Chem. B,
2009, 113, 3776–3784. 56 J. B. Lim, B. Rogaski and J. B. Klauda, J. Phys. Chem. B, 2012,
116, 203–210. 87 Y. Bi and T. Li, J. Phys. Chem. B, 2014, 118, 13324–13332. 57 A. Haji-Akbari and P. G. Debenedetti, Proc. Natl. Acad. Sci. U. S. A., 2015, 112, 10582–10588. 88 M. M. Gianetti, A. Haji-Akbari, M. P. Longinotti and
P. G. Debenedetti, Phys. Chem. Chem. Phys., 2016, 18,
4102–4111. 58 H. A. Lorentz, Ann. Phys., 1881, 248, 127–136. 59 G. Bussi, D. Donadio and M. Parrinello, J. Chem. Phys.,
2007, 126, 014101. 89 A. Haji-Akbari and P. G. Debenedetti, Proc. Natl. Acad. Sci. U. S. A., 2017, 114, 3316–3321. 60 S. Miyamoto and P. A. Kollman, J. Comput. Chem., 1992, 13,
952–962. 90 A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U. S. References A., 1986, 83, 7256–7260. pen Access Article. Published on 27 August 2018. Downloaded on 10/24/2024 6:47:08 AM.
This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Voigtl˜Ad’nder, K. Ignatius and F. Stratmann, Atmos. Chem. Phys., 2013, 13, 10989–11003. 72 H. Pruppacher and J. Klett, Microphysics of clouds and
precipitation, 1997. 73 G. Vali, Atmos. Chem. Phys., 2008, 8, 5017–5031. 74 C. Gurganus, J. Charnawskas, A. Kostinski and R. Shaw,
Phys. Rev. Lett., 2014, 113, 235701. 102 P. Pedevilla, M. Fitzner, G. C. Sosso and A. Michaelides, J. Chem. Phys., 2018, 072327. This journal is © The Royal Society of Chemistry 2018 8088 | Chem. Sci., 2018, 9, 8077–8088
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Influence of the choice of insolation forcing on the results of a conceptual glacial cycle model
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Clim. Past, 18, 547–558, 2022
https://doi.org/10.5194/cp-18-547-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
Influence of the choice of insolation forcing on the
results of a conceptual glacial cycle model
Gaëlle Leloup1,2 and Didier Paillard2
1 Agence
Nationale pour la gestion des déchets radioactifs (ANDRA), 1 Rue Jean Monnet, 92290 Châtenay-Malabry, France
des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ-Université Paris-Saclay,
91198 Gif-sur-Yvette, France
2 Laboratoire
Correspondence: Gaëlle Leloup (gaelle.leloup@lsce.ipsl.fr)
Received: 6 September 2021 – Discussion started: 13 September 2021
Revised: 11 February 2022 – Accepted: 18 February 2022 – Published: 25 March 2022
Abstract. Over the Quaternary, ice volume variations
are “paced” by astronomy. However, the precise way in
which the astronomical parameters influence the glacial–
interglacial cycles is not clear. The origin of the 100 kyr cycles over the last 1 million years and of the switch from
40 to 100 kyr cycles over the Mid-Pleistocene Transition
(MPT) remain largely unexplained. By representing the climate system as oscillating between two states, glaciation
and deglaciation, switching once glaciation and deglaciation thresholds are crossed, the main features of the ice volume record can be reproduced (Parrenin and Paillard, 2012).
However, previous studies have only focused on the use of
a single summer insolation as input. Here, we use a simple conceptual model to test and discuss the influence of the
use of different summer insolation forcings, having different
contributions from precession and obliquity, on the model
results. We show that some features are robust. Specifically,
to be able to reproduce the frequency shift over the MPT,
while having all other model parameters fixed, the deglaciation threshold needs to increase over time, independently
of the summer insolation used as input. The quality of the
model–data agreement however depends on the chosen type
of summer insolation and time period considered.
1
Introduction
Palaeoclimate records over the Quaternary (last 2.6 Myr),
such as ice cores (Jouzel et al., 2007) or marine cores
(Lisiecki and Raymo, 2005) show a succession of oscillations. These oscillations are due to the build-up and retreat of
northern continental ice sheets, corresponding to respectively
cold and warm periods known as the glacial–interglacial cycles. Over the last 1 million years, there is an alternation of
long glaciations followed by quick deglaciations, leading to
cycles of a period of 100 kyr. Yet, in the earliest part of the
record, glacial–interglacial cycles are mostly dominated by a
frequency of 41 kyr with lower amplitudes. Spectral analysis
of the record (Hays et al., 1976) has revealed that astronomical frequencies are imprinted into the ice volume record,
suggesting a strong link between insolation and the glacial–
interglacial cycles.
The nature and physics of this link has been a central question since the discovery of previous warm and cold periods,
and long before the obtention of continuous δ 18 O records.
It is known that the variations of annual total energy are
of too-low an amplitude to explain such changes (Croll,
1864). Therefore, focus has been set on seasonal variations.
Croll (1864) assumed that glaciations were linked to colder
winters. In contrast, the idea that the decisive element for
glaciation was the presence of cold summers, due to reduced
summer insolation, at latitudes of the Northern Hemisphere
critical for ice sheet growth (65◦ N), was taken up by Milankovitch, who made it the key element of his ice age theory
(Berger, 2021). For conceptual models, this raises the question of which insolation to use as input. When summer insolation is used, this questions the definition of summer: should
it be defined as a specific single day, like the summer solstice; the astronomical summer between the two equinoxes;
or a fixed number of days around the solstice? The choice
leads to very different forcings with different contributions
from obliquity and precession. For Earth system models and
Published by Copernicus Publications on behalf of the European Geosciences Union.
548
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
climate models, insolation is computed at each time step for
each grid area, and such choice of the input forcing is not
needed. However, other modelling choices have to be made.
For instance, several parameterizations are used to represent
ice sheet surface melt (Robinson et al., 2010), like the positive degree day (PDD) method (Reeh, 1991), in which surface melt depends solely on air temperature, or the insolation
temperature melt (ITM) method (Van den Berg et al., 2008),
which takes into account the effect of both temperature and
insolation. In both cases, the translation of insolation local
and seasonal variations into ice sheet changes and ice age
cycles remains an open modelling question.
The obtention of 100 kyr cycles is not possible with a linear theory like that of Milankovitch (Hays et al., 1976; Imbrie
and Imbrie, 1980), and a form of non-linearity is needed. Indeed, there is no simple relation between insolation extrema
and ice volume extrema. One of the largest deglaciations (termination V) occurred when insolation variations were minimal. Conversely, insolation variations were maximal at termination III, whereas the transition was rather small. In addition, the amplitude of summer insolation variations is maximal every 400 kyr, but this frequency is absent from the
palaeoclimatic records. The 100 kyr cycles have been proposed to be linked to either eccentricity-driven variations of
precession (Raymo, 1997; Lisiecki, 2010), obliquity (Huybers and Wunsch, 2005; Liu et al., 2008), or both (Huybers, 2011; Parrenin and Paillard, 2012), to internal oscillations phase locked to the astronomical forcing (Saltzman
et al., 1984; Paillard, 1998; Gildor and Tziperman, 2000;
Tziperman et al., 2006), to internal oscillations independent
of the astronomical forcing (Saltzman and Sutera, 1987; Toggweiler, 2008) or to period-doubling bifurcation (Verbitsky
et al., 2018). Additionally, the Mid-Pleistocene Transition
(MPT) and the switch from a 41 kyr dominated record to a
100 kyr one remain mostly unexplained.
Several conceptual models have been developed to try to
solve these questions. Calder (1974) was the first to develop a
simple conceptual model, linking insolation and ice volume
variations. Imbrie and Imbrie (1980) also developed a conceptual model, where the rate of change was different in the
case of a warming or cooling climate. Paillard (1998) developed the idea that the glacial–interglacial cycles can be seen
as relaxation oscillations between multiple equilibria, like a
glaciation and a deglaciation state. It was suggested that the
criteria to trigger a deglaciation depends on both insolation
and ice volume, whereas insolation alone seems able to trigger glaciation (Parrenin and Paillard, 2003). Here, we adapt
and simplify the model of Parrenin and Paillard (2003) and
extend it over the whole Quaternary.
One of the critical questions for conceptual models is to
decide which insolation to use as input. Milankovitch’s work
utilized “caloric seasons” at 65◦ N, the half-year with the
highest insolation. This was also the case in Calder’s model,
which used caloric seasons at 50◦ N as input. Imbrie and
Imbrie (1980) used the July insolation. The use of summer
Clim. Past, 18, 547–558, 2022
insolation gradually shifted towards the use of the summer
solstice insolation, most probably as it is easier to compute
thanks to the tables provided by Berger (1978) and allows
one to obtain better fits for the more recent part of the records
(Paillard, 2015). More recently, Huybers (2006) suggested
that the integrated summer insolation (ISI) over a certain
threshold could be better, as it would more closely follow
PDDs, an important metric for ice sheet mass balance. Others
have also used combinations of orbital parameters as a forcing (Imbrie et al., 2011; Parrenin and Paillard, 2012). However, most models only use one type of insolation forcing and
do not consider the influence of other insolation forcing types
on the model results.
In our work, we will consider several summer insolation
forcings at 65◦ N (summer solstice insolation, caloric season and ISI over two different threshold values) in order to
study their influence on the model results. These different
summer insolation forcings have similar shape, but the respective contribution of obliquity and precession differ. The
different insolation forcings have different performances in
matching the data, depending on the time period considered.
However, we show that some features are independent of the
insolation forcing used as input. In particular, we are able to
reproduce a switch from 41 kyr oscillations before the MPT
to 100 kyr cycles afterwards, in agreement with the records
for all insolation forcings, by varying a single parameter: the
deglaciation threshold V0 , and keeping all the other model
parameters constant. This is similar to the results of Paillard
(1998), who obtained a frequency shift on the glacial cycles
by using a linearly increasing deglaciation threshold. This is
also coherent with the more recent results of Tzedakis et al.
(2017), who demonstrated that the particular sequence of interglacials that happened over the Quaternary and the frequency shift from 41 to 100 kyr could be explained with a
simple rule, taking into account a deglaciation threshold that
increases over time, leading to “skipped” insolation peaks
and longer cycles.
2
2.1
Conceptual model and methods
Conceptual model
The model used in our study is an adapted and simplified
version of the conceptual model of Parrenin and Paillard
(2003). For the glacial–interglacial cycles, it is not a new idea
that the climate system can be represented by relaxation oscillations between multiple equilibria, like a glaciation and
a deglaciation state (Paillard, 1998; Parrenin and Paillard,
2003, 2012). The aim of conceptual models is not to explicitly model and represent physical processes but rather to help
us understand critical aspects of the climate system. Here,
we do not intend to explicitly represent the numerous physical processes involved in ice sheet volume evolution, affecting surface mass balance, ice discharge to the ocean and bottom melt of grounded ice. Instead, we represent the climate
https://doi.org/10.5194/cp-18-547-2022
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
system with two distinct states of evolution: the “glaciation
state” (g) and “deglaciation state” (d). We make the assumption that the evolution of the ice sheet volume in these two
states can be simply described by two terms. The first one,
common to the glaciation and deglaciation states, is a linear relation to the summer insolation: when the insolation is
above average, the ice sheet melts, whereas when the insolation is low enough, the ice sheet grows. The second term, specific to the system state, represents an evolution trend linked
to the system state: a slow glaciation in (g) state and a rapid
deglaciation in (d) state.
In our model, the evolution of the ice volume in these two
states is described by
(
I
1
(g) dv
dt = − τi + τg
(1)
I
v ,
(d) dv
dt = − τi − τd
where v represents the normalized ice volume. τi , τd and τg
are time constants. I is the normalized summer insolation
forcing at 65◦ N. The implicit assumption is made that the
global ice volume changes are mainly driven by the Northern Hemisphere ice sheet waning and waxing, as we focus
on the effect of insolation changes at high northern latitudes.
This is not a limiting assumption as data suggest much lower
sea level variations due to the Antarctic ice sheet than due to
those of the Northern Hemisphere over glacial–interglacial
timescales. For example, the contribution of the Antarctic ice
sheet to the ∼ 120 m Last Glacial Maximum sea level drop
is estimated to be between 10 and 35 m sea level equivalent
(Lambeck et al., 2014). Other effects like thermal expansion,
small glaciers and ice caps are estimated to be around 3 to
4 m sea level equivalent. Furthermore, it has been suggested
(Jakob et al., 2020) that the growth of larger Northern Hemisphere ice sheets since the start of the Quaternary and the
associated sea level drop has a stabilizing effect on the East
Antarctic ice sheet, as it limits its exposure to warm ocean
waters.
A critical point is to define the criteria for the switch between the glaciation and deglaciation states. To enter the
deglaciation state, both ice volume and insolation seem to
play a role (Raymo, 1997; Parrenin and Paillard, 2003, 2012),
as terminations occur after considerable build-up of ice sheet
over the last 1 million years. To represent the role of both ice
volume and insolation in the triggering of deglaciations, the
condition to switch from (g) to (d) state uses a linear combination of ice volume and insolation. The deglaciation is triggered when the combination crosses a defined threshold V0 :
the deglaciation threshold. As in the work of Parrenin and
Paillard (2003), this allows transitions to occur with moderate insolation when the ice volume is large enough and reciprocally. Conversely, glacial inception seems to depend on
orbital forcing alone (Khodri et al., 2001; Ganopolski and
Calov, 2011). Therefore, the condition to switch from the
deglaciation state to the glaciation state is based on insolation only: it is possible to enter glaciation when the insolation
https://doi.org/10.5194/cp-18-547-2022
becomes low enough.
(d) to (g) : I < I0
(g) to (d) : I + v > V0
549
(2)
The idea that the deglaciation threshold is linked to both
insolation and ice volume is not new (Parrenin and Paillard,
2003, 2012), and is similar to that developed by Tzedakis
et al. (2017), where the threshold for a complete deglaciation decreases with time as the system accumulates instability, with ice sheets becoming more sensitive to insolation increase. As the ice sheet grows and extends to lower latitudes,
the insolation needed to reach a negative mass balance decreases. This idea has been confirmed with modelling studies (Abe-Ouchi et al., 2013). Several reasons can explain this
increase of instability over time: delayed bedrock rebound
and exposure to higher temperature as the ice sheet sinks
(Oerlemans, 1980; Pollard, 1982; Abe-Ouchi et al., 2013),
increase in basal sliding as the ice sheet grows and the base
becomes warmer as it is more isolated from the cold surface
temperature (MacAyeal, 1992; Marshall and Clark, 2002),
ice sheet margin calving (Pollard, 1982), decrease of the ice
sheet albedo due to either snow ageing (Gallée et al., 1992) or
increase of dust deposition as the ice sheet expands (Peltier
and Marshall, 1995; Ganopolski and Calov, 2011) and increase of atmospheric CO2 due to the release of deep ocean
carbon when the Antarctic ice sheet extends over the continental shelves (Paillard and Parrenin, 2004; Bouttes et al.,
2012).
2.2
Summer insolation
The conceptual model defined previously uses summer insolation as input. It is therefore important to consider which insolation should be used. Insolation is usually taken at 65◦ N,
a typical latitude for Northern Hemisphere ice sheets. Several articles have used the summer solstice daily insolation
at 65◦ N as input insolation forcing (Paillard, 1998; Parrenin
and Paillard, 2003). Others (Tzedakis et al., 2017) have used
the caloric season, as defined by Milankovitch (1941), defined as the half-year with the highest insolation. It is also
possible to use as input a linear combination of orbital parameters (Imbrie et al., 2011; Parrenin and Paillard, 2012).
Huybers (2006) also defined the integrated summer insolation (ISI) above a threshold.
Here, for the first time, we want to examine the effect of
this choice on the dynamics of a conceptual model. We therefore use four different summer insolation forcings, and compare the model results obtained with each of them. We use
the summer solstice insolation, the caloric season and ISI
above two different thresholds (300 and 400 W m−2 ). Experiments were also conducted for the summer solstice insolation at 50◦ N instead of 65◦ N, but these are not presented
here as they do not change the conclusions obtained with the
forcings at 65◦ N. We refer the reader to Sect. S1 in the Supplement for information on these experiments.
Clim. Past, 18, 547–558, 2022
550
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
These four insolation forcings differ, and have different
contributions from precession and obliquity, as can be seen
in Fig. 1. For example, the summer solstice insolation has
a low contribution from obliquity (41 kyr) compared to the
caloric season, or ISI above 300 W m−2 . The summer solstice
insolation and the caloric season were computed using the
AnalySeries software (Paillard et al., 1996). The ISI for a
threshold τ (noted as ISI above τ , or ISI(τ ) in this article)
was defined by Huybers (2006) as the sum of the insolation
on days exceeding this threshold.
X
ISI(τ ) =
βi (Wi · 86 400)
i
Here, Wi is the mean insolation of day i in W m−2 and βi
equals one if Wi > τ and zero otherwise.
To compute ISI(τ ), one first needs to compute the daily
insolation on day i, and then sum over the year for the days
exceeding the threshold. Here, we developed a Python code
based on the MATLAB code provided by Huybers (2006).
Unlike the insolation files provided by Huybers (2006),
which used the solution from Berger and Loutre (1991), we
use the orbital parameter value of the Laskar et al. (2004)
solution for the calculation. This results in slightly different
results for deeper time periods as the calculation of orbital
parameters also differ with these two estimations.
2.3
Optimal model parameters
The conceptual model relies on a small number of model parameters: τi , τg , τd and the two thresholds for the switch from
a glaciation state to a deglaciation state and the inverse: V0
and I0 . For all the simulations performed, we kept τi = 9 kyr,
τg = 30 kyr, τd = 12 kyr and I0 = 0, as these parameters gave
correct behaviour in previous studies (Parrenin and Paillard,
2003). No attempt was made to tune these parameters to
obtain a behaviour closer to the data: on the contrary, focus was set more towards the influence of the deglaciation
threshold parameter, V0 , on the model results. To compare
our model results to the data, we used the benthic δ 18 O stack
“LR04” (Lisiecki and Raymo, 2005) as a proxy for ice volume, considering that most of the δ 18 O changes of benthic
foraminifera represent changes in continental ice (Shackleton, 1967; Shackleton and Opdyke, 1973). Lower δ 18 O values correspond to lower ice volume. The model results and
the LR04 curve were normalized to facilitate their comparison. In the following, “data” refers to the normalized δ 18 O
stack curve LR04.
To estimate which model parameters lead to model results
closer to the data, the definition of an objective criteria is
needed. The choice of such a criteria is not straightforward,
and the use of different criteria could have led to slightly
different results. Our model is simple and does not aim at
precisely reproducing the ice volume evolution, but rather at
reproducing the main qualitative features, such as the shape
Clim. Past, 18, 547–558, 2022
and frequency of the oscillations. Therefore, we used a criteria based on the state of the system: glaciation or deglaciation. Similar results can be obtained using a simple correlation coefficient (see Sect. S2). The definition of the deglaciation state in the data is explained in Sect. 2.4. A critical point
is that our model should be able to deglaciate at the right
time, when a deglaciation is seen in the data. Conversely, the
model should not produce deglaciation at periods where the
data do not show deglaciation.
We defined a criteria for each of these two conditions,
and assembled them in a global criteria. To determine if
deglaciation is well reproduced by our model, we look at
the state of the model (glaciation or deglaciation) at the time
halfway between the start of the deglaciation and the end of
the deglaciation. If the model state at that time is deglaciation, the deglaciation is considered as correctly reproduced.
Otherwise, it is considered as a “missed” deglaciation. We
simply defined the criteria c1 as the fraction of deglaciations correctly reproduced. This criteria equals one when all
the deglaciations take place at the right time, meaning that
the model produces a deglaciation state every time deglaciation is seen in the data. To ensure that the model does not
deglaciate too often, we looked at insolation maxima that
are not associated with deglaciation in the data and ensured
the corresponding model state was glaciation. We decided to
look specifically at insolation maxima, as they are where the
model is the most likely to deglaciate when it should not. A
deglaciation seen in the model at a place where no deglaciation is seen in the data is considered as a “wrong transition”.
We defined the criteria c2 as c2 = 1 − w, with w the fraction of wrong transitions. The c2 criteria equals one when
the model does not deglaciate when it should not. To take
into account these two conditions, the overall accuracy criteria c is defined as c = c1 · c2 . It is equal to one when all
the deglaciations are correctly placed and when no additional
deglaciation compared to the data take place.
In order to study the evolution of the optimal deglaciation
threshold V0 over the Quaternary, it was divided into five
500 kyr periods. The V0 values that maximize the accuracy
criteria for each time period and insolation forcing are called
“optimal V0 ”. To determine the optimal V0 threshold corresponding to each period and insolation forcing, several simulations were carried out and the parameter values maximizing the accuracy criteria c were selected. More precisely, for
each insolation and period, 3500 simulations corresponding
to different V0 thresholds (from V0 = 1.0 to V0 = 8.0 with
a step of 0.1) and different initial conditions (initial volume
Vinit ranging from 0.0 to 5.0 with a step of 0.2, and the two
possible initial states – glaciation or deglaciation) were performed. The numerical integration of the model equations
was done with a fourth-order Runge–Kutta scheme.
For each insolation forcing, the best fit over the Quaternary is defined as the simulation over the whole Quaternary
(0 to 2500 ka) with V0 changing with time that is equal to
the corresponding optimal V0 at each time period. Additionhttps://doi.org/10.5194/cp-18-547-2022
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
551
Figure 1. (a) The four different summer insolation forcings at 65◦ N (summer solstice, caloric season, ISI above 300 W m−2 and ISI above
400 W m−2 ) displayed over the Quaternary. The insolation forcings are centred and normalized by their standard deviation. (b) Corresponding spectral analysis over the Quaternary, normalized by standard deviation.
ally, simulations were performed to determine the optimal V0
threshold obtained when the optimization procedure is carQ
ried out over the whole Quaternary. It is called V0 in the
following.
tion is taken as the first local minima below the interglacial
threshold of 3.68 ‰. The deglaciation periods in the data corresponding to the time between the deglaciation starts and
deglaciation ends are displayed with blue shading in Figs. 4
and 5.
2.4
3
Definition of the deglaciation state in the data
To calculate our accuracy criteria c and therefore determine
the optimal V0 threshold over a given period, a definition of
the deglaciation in the data is needed. We based our definition
on the interglacial classification developed by Tzedakis et al.
(2017). Tzedakis et al. (2017) differentiates interglacials,
continued interglacials and interstadials based on a detrended
version of the LR04 stack curve. A period is considered as an
interglacial if its isotopic δ 18 O is below a threshold (3.68 ‰).
Two interglacials are considered to be separated if they are
separated by a local maximum above a threshold (3.92 ‰).
This definition differs from the usual characterization of terminations, sometimes leading to several interglacials in the
same isotopic stage. The definition of Tzedakis et al. (2017)
is for interglacials, and as our focus is not on interglacial
periods but rather on deglaciations, we adapted it. We defined deglaciations as periods of decreasing δ 18 O (and thus,
ice volume, in our assumptions) preceding the interglacials.
The start of the deglaciation is taken as the last local maxima
above the threshold of 3.92 ‰, and the end of the deglaciahttps://doi.org/10.5194/cp-18-547-2022
3.1
Results and discussion
Optimal deglaciation threshold V0 and
corresponding accuracy
For each insolation, we computed the deglaciation threshold
V0 maximizing the accuracy for each of the five 500 kyr peQ
riods and the fixed V0 value maximizing the accuracy over
the whole Quaternary. The results are displayed in Fig. 2.
In some cases, several values of the deglaciation threshold
V0 lead to the same accuracy criteria, whereas in others there
is only one V0 value maximizing the accuracy. When several
V0 values are equivalent, the mean value was plotted and the
other possible values are represented with error bars.
Over the same time period, different insolation values lead
to slightly different optimal V0 thresholds. But the most striking feature is the increase of the optimal V0 threshold over
time, and more specifically for the last 1 million years, after the MPT. This feature is valid regardless of the insolation
Q
type. The optimal V0 over the whole Quaternary V0 is between 3.4 and 4 for each insolation type. It is a value in the
Clim. Past, 18, 547–558, 2022
552
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
Figure 3. Accuracy over the five 500 kyr periods for the four differFigure 2. Optimal deglaciation threshold V0 over the five 500 kyr
periods for the four different summer insolation forcings at 65◦ N
and optimal constant V0 threshold obtained when the optimization
Q
procedure is done over the whole Quaternary (V0 ). When several
values of the deglaciation threshold V0 maximize the accuracy criteria, the mean value is plotted and the other possible values are
represented with error bars.
middle of the highest values that best fit the latter part of the
record and the lowest values that best fit the earliest part of
the record.
For each insolation, the accuracy corresponding to the optimal V0 threshold for each time period as well as to the fixed
Q
V0 value maximizing the accuracy over the whole Quaternary is displayed in Fig. 3.
It is first noticeable that the accuracy is higher over the last
1 million-year period, regardless the input summer insolation
used. In the last 1 million years, the summer solstice insolation as input produces the best results. However, this is no
longer the case for older time periods: the solstice insolation
gives the worst results at the start of the Quaternary. The acQ
curacy obtained for the whole Quaternary period (fixed V0
value) is globally lower than the accuracy for each time peQ
riod. This is due to the fact that the V0 values obtained are
lower than the optimal V0 values in the later part of the Quaternary and higher than the optimal V0 values in the earliest
part of the Quaternary, leading to a poorer representation of
both of these periods.
In the earlier part of the Quaternary (periods earlier than
1.5 Ma), the results are less robust. This is due to increased
uncertainties in the LR04 record, and the associated definition of interglacial periods, which affects our accuracy criteria. In their classification, Tzedakis et al. (2017) stated that
the definition of the valley depth needed to separate several
interglacials was quite straightforward in the earlier part of
Clim. Past, 18, 547–558, 2022
ent summer insolation forcings at 65◦ N, and accuracy criteria over
the Quaternary when the optimization procedure is done over the
Q
whole Quaternary (constant V0 ).
the record, whereas for earlier time periods (ages older than
1.5 Ma), their method led to several “borderline cases”. Additionally, slightly different choices for the interglacial and
interstadial thresholds would have led to a different population of interglacial. For us, this would lead to a different
definition of deglaciation, and thus a different accuracy criteria. In addition, the resolution of the LR04 curve decreases
with increasing age (Lisiecki and Raymo, 2005), and for periods with lower resolution or more uncertain age matching,
the amplitude of the peaks might be reduced (Tzedakis et al.,
2017).
Moreover, the δ 18 O LR04 curve includes at the same time
an ice volume and deep water temperature component. Ice
volume and sea level reconstructions do exist (Bintanja et al.,
2005; Spratt and Lisiecki, 2016), but are however limited to
the more recent part of the Quaternary and do not allow for
the investigation of the pre-MPT period. The use of δ 18 O
as an ice volume proxy has already been largely debated
(Shackleton, 1967; Chappell and Shackleton, 1986; Shackleton and Opdyke, 1973; Clark et al., 2006), and recent studies (Elderfield et al., 2012) have shown that the temperature
component may be as large as 50 %. Furthermore, the stack
was tuned to insolation (Lisiecki and Raymo, 2005). We refer the reader to Raymo et al. (2018) for a review of possible
biases in the interpretation of the LR04 benthic δ 18 O stack as
an ice volume and sea level reconstruction. All these reasons
encourage us to remain at a qualitative level to fit the data.
The increase in the optimal deglaciation threshold V0 over
the MPT is however a robust feature that does not depend on
the input summer insolation forcing used. This is coherent
with the work of Paillard (1998) and Tzedakis et al. (2017),
https://doi.org/10.5194/cp-18-547-2022
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
who obtained a frequency shift from 41 to 100 kyr cycles
with an increasing deglaciation threshold. The classical hypothesis and possible physical meanings of the rise of the V0
threshold often imply a gradual cooling, due to lower pCO2
(Raymo, 1997; Paillard, 1998; Berger, 1978), but this idea is
not supported by more recent data, which do not show a gradual decrease in the pCO2 trend, but rather only a decrease
in minimal pCO2 values (Hönisch et al., 2009; Yan et al.,
2019). Other hypothesis imply a gradual erosion of a thick
regolith layer that exposed the ice sheet to a higher friction
bedrock, allowing for a thicker ice sheet to develop (Clark
and Pollard, 1998; Clark et al., 2006), or a sea ice switching
mechanism (Gildor and Tziperman, 2000).
The overall lowest accuracy in the older part of the record
suggests that our non-linear threshold model is less adapted
for this time period. Indeed, the ice volume might respond
more linearly to the insolation forcing before the MPT, as
some studies suggest (Tziperman and Gildor, 2003; Raymo
and Nisancioglu, 2003). In contrast, others (Ashkenazy and
Tziperman, 2004) have shown that the 41 kyr pre-MPT oscillations are in fact significantly asymmetric and therefore
suggested that oscillations both before and after the MPT
could be explained as the self-sustained variability of the climate system, phase locked to the astronomical forcing. In
our model, the deglaciation threshold V0 changes over time,
leading to an amplitude change of the cycles. However, it
cannot be excluded that the mechanisms behind the pre- and
post-MPT glacial cycles are structurally different, and that
they cannot be explained with the same physics and the same
equations in our model. Moreover, this kind of conceptual
model has mainly been constructed in order to explain the
non-linear features of the 100 kyr cycles, and it is therefore
not surprising that its agreement with the data on the preMPT period is less satisfying.
3.2
Best fit over the Quaternary
Our conceptual model is able to reproduce qualitatively well
the data (LR04 normalized curve) over the whole Quaternary.
The model’s best fit over the Quaternary for each insolation
forcing, as defined in Sect. 2.3, is displayed in Fig. 4. It is
able to reproduce the frequency shift from a dominant 41 kyr
period before 1 Ma to longer cycles afterwards, as observed
in the data, and thus by varying only one parameter during the whole simulation length: the deglaciation threshold
V0 . Like the previous model of Parrenin and Paillard (2003),
from which our model is adapted, ours quickly looses its sensitivity to the initial conditions (after no more than 200 kyr).
For every input forcing, longer cycles are obtained in the last
part of the Quaternary (last Myr). Figure 4 displays the results over the whole Quaternary with the V0 threshold being
set to its optimal value for each 500 kyr period, while Fig. 5
displays the results over the last 1 million years with the V0
threshold being set to its optimal value for the [0–1000] ka
period.
https://doi.org/10.5194/cp-18-547-2022
553
For the last 1 million years, it is possible to reproduce
all terminations with the right timing, apart from the last
deglaciation, for all insolation forcings, by using a single
value of the V0 threshold over this period. Some differences
are however noticeable between the different forcings. In particular the agreement for the ISI above 300 W m−2 forcing is
not as good as for the other forcings: termination V (around
420 ka) is triggered later compared to in the data, while termination III (around 240 ka) is triggered too early. For the ISI
above 300 W m−2 forcing, the range of V0 values that allow
us to correctly reproduce most of the terminations during the
last 1 million years is reduced (only values of V0 = 3.9–4.0),
whereas the results are more robust for the three other insolation forcings, with a broader range of working V0 values. The
ISI above 300 W m−2 forcing has a low precession component, which explains why it is less successful in reproducing
the data over the last 1 million years. Experiments with our
model setup have shown that a summer forcing with no precession component could not successfully reproduce the data
over the post-MPT period as accurately as the four forcings
presented here that contain both precession and obliquity (see
Sect. S3).
Despite the accurate timing of terminations, the spectral
analysis of the model results over the last 1 million years differs from the spectral analysis of the data. For all forcings
except the summer solstice insolation, obliquity continues to
dominate after the MPT. The spectral analysis shows secondary and third peaks of lower frequency, but does not show
a sharp 100 kyr cyclicity as in the LR04 record. Compared to
the data, all the model outputs over the post-MPT period have
a more pronounced obliquity and precession component and
a less pronounced 100 kyr component. This feature is most
probably due to the model formulation, and more specifically the direct dependence of ice volume evolution to insolation via the dV /dt = −I /τi term. This is one of the limits
of our conceptual model. While the criteria on the switch to
deglaciations allow us to reproduce the deglaciations at the
right timing, the direct dependance of ice volume change to
the insolation forcing is definitely too simplistic and probably produces an overestimated dependency of the ice evolution to the astronomical forcing for the latter part of the
record.
In the first part of the Quaternary (2.6 to 1 Ma), the spectral analysis of the data is dominated by a 41 kyr (obliquity)
peak. It is also the case for the model results, for each type
of insolation. However, the model outputs also show a precession component (19 to 23 kyr), especially for the summer solstice and the ISI above 400 W m−2 forcings, which
does not exist on the data. Although our model reproduces
the features of the record qualitatively well, there are some
noticeable model–data mismatches that occur for all insolation types around 1100 and 2030 ka. Additionally, the amplitude of the oscillations produced is slightly too high in the
older part of the Quaternary, especially when the ISI above
300 W m−2 is used.
Clim. Past, 18, 547–558, 2022
554
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
Figure 4. Best model fit over the whole Quaternary and corresponding spectral analysis. (b) presents the best fit of the model for the different
summer insolation used as input, compared to the data. The results for the summer solstice insolation, caloric season, ISI above 300 and ISI
above 400 W m−2 are displayed. The data (normalized LR04 curve) are in black. The blue shading presents deglaciation periods in the data
and the yellow shading deglaciation periods in the model. This results in a green shading when deglaciations are seen in the model and data
at the same time. (a) presents the spectral analysis of the best fit solution over the last 1 million years. (c) presents the spectral analysis over
the older part of the Quaternary (before 1 Ma).
On the oldest part of the Quaternary, the caloric season
forcing and the ISI above 300 W m−2 seem to perform better
in reproducing the frequency of the oscillations than the summer solstice insolation and ISI above 400 W m−2 . They correspond to the forcing with the strongest obliquity (41 kyr)
component, which might explain why they more successfully
represent this part of the record, which is dominated by obliquity.
Over the last 1 million years, the highest accuracy is obtained with the summer solstice insolation as input forcing
(c = 0.92 for the summer solstice insolation, c = 0.82 for the
caloric season and ISI above 400 W m−2 and c = 0.87 for the
ISI above 300 W m−2 ). This is mainly due to the fact that for
the three other forcings (caloric season, ISI above 300 and
ISI above 400 W m−2 ), the last deglaciation occurs one insolation peak too early, around 50 ka. However, if one computes the accuracy over the last 1 million years excluding
the last 100 kyr (period from 100 ka to 1000 ka), the accuracy is similar for all four forcings (0.92 for summer solstice,
caloric season and ISI above 400 W m−2 and 0.89 for ISI
above 300 W m−2 ). Figure 5 displays two different alternatives. For the first one (full line), the optimal V0 is calibrated
over the [100–1000] ka period and maintained for the whole
simulation (V0 = 5.0 for the summer solstice insolation, 4.5
for the caloric season, 4.0 for the ISI above 300 W m−2 and
4.6 for the ISI above 400 W m−2 ). Except with the summer
solstice insolation as input, the three other insolation forcings
Clim. Past, 18, 547–558, 2022
fail to accurately reproduce the last deglaciation, as the last
deglaciation occurs one insolation peak too early. The second
alternative (dashed line) is to raise the deglaciation threshold
V0 over the last cycle (raised to V0 = 5.5 from 100 ka onward). In this case, the model does accurately reproduce the
last deglaciation for all insolation forcings. This suggests that
we might need to further raise the V0 threshold in order to
model a theoretical “natural” future (without anthropogenic
influence) with longer cycles. A cycle is not enough to conclude about a trend, but this should be envisaged for future
natural scenarios. This is coherent with the idea of Paillard
(1998), who used a linearly increasing deglaciation threshold over the Quaternary.
3.3
Reflections about the future
To model future natural evolutions of the climate system,
possible evolutions of the V0 threshold should be considered.
However, we do not exclude the fact that variations of other
parameters, which were kept constant in this study, could
vary in the future. For instance, different I0 thresholds have
to be considered. The fate of the next thousands of years in
a natural scenario cannot be ascertained with our conceptual
model. Indeed, this depends on the onset (or not) of a glaciation, which is determined by the I0 parameter. In our model,
a broad range of I0 parameter values lead to satisfying results over the last 1 million years. These different values prohttps://doi.org/10.5194/cp-18-547-2022
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
555
Figure 5. Normalized model results over the last 1 million years, with the different summer insolation forcings: insolation at the summer
solstice, caloric season, ISI above 300 W m−2 and ISI above 400 W m−2 . The full coloured lines are the best fit computed over the 100–
1000 ka period for each input insolation. The dashed lines represent the same solution, but with an increased V0 threshold for the last
deglaciation. The data (normalized LR04 stack curve) are in black. The blue shading represents deglaciation periods in the data. The yellow
shading represents deglaciation periods in the model outputs (case of the increased V0 threshold). This results in a green shading when
deglaciations are seen in the model and data at the same time.
jected into the future lead either to, in one case, a glaciation
start at present, or, in the other case, a continued deglaciation, switching to a glaciation state only around 50 kyr after present at the next insolation minima. This is due to the
current particular astronomical configuration, with very low
eccentricity, which leads to high summer insolation minima,
where the threshold for glaciation might not be reached. This
is coherent with previous studies (Berger and Loutre, 2002;
Paillard, 2001), which suggested that without anthropogenic
forcing, the present interglacial might have lasted 50 kyr.
However, this exercise is purely academic, as we are
not taking into account the role of anthropogenic CO2 ,
which would affect the glaciation and deglaciation thresholds (Archer and Ganopolski, 2005; Talento and Ganopolski, 2021). Furthermore, our conceptual model cannot be
extended outside the Quaternary, as the ice volume variations considered are exclusively those of the Northern Hemisphere, and our model is, by construction, unable to represent
projected future Antarctic ice sheet mass loss.
4
Conclusions
We have used a conceptual model with very few tunable parameters that represents the climatic system with multiple
equilibria and relaxation oscillation. Only one parameter was
varied, the deglaciation threshold parameter V0 . We used different summer insolation as input for our conceptual model:
the summer solstice insolation, the caloric season and ISI
https://doi.org/10.5194/cp-18-547-2022
over two different thresholds. With all these forcings, which
have different contributions from obliquity and precession,
we are able to reproduce the features of the ice volume over
the whole Quaternary. More specifically, we are able to represent the MPT and the switch from a 41 kyr dominated
record to larger cycles by raising the deglaciation threshold
and keeping the other model parameters constant. This rise
in the deglaciation threshold is valid regardless of the type of
summer insolation forcing used as input. However, the data
agreement is less satisfying before the MPT. This suggests
the possibility that climate mechanisms might be structurally
different before and after the MPT, with a more linear behaviour in pre-MPT conditions. This highlights that models
are designed to answer rather specific questions, and a model
built specifically to explain 100 kyr cycles might be less efficient in a more linear setting. More generally, this kind of
glacial–interglacial conceptual model is designed to explain
the main features of the Quaternary time period characterized
by the waning and waxing of Northern Hemisphere ice sheets
under the influence of changing astronomical parameters. In
our case, this raises the question of which physical phenomena are responsible for making deglaciations “harder” to start
in the latest part of the Quaternary compared to the earliest
part. This kind of model is however unlikely to be directly applicable in a more general context, like during the Pliocene
and earlier periods, or in the context of future climates under
the long-term persistence of anthropogenic CO2 (Archer and
Ganopolski, 2005; Talento and Ganopolski, 2021). In order
Clim. Past, 18, 547–558, 2022
556
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
to tackle such questions, it would be critical to gain a deeper
understanding of the natural evolution of the other forcings
involved in the climate system and most notably of the dynamics of the carbon cycle. Conceptual models are likely to
pave the way in this direction (Paillard, 2017). Indeed, just
as in the case of the Quaternary, a full mechanistic simulation of the many processes at work is currently out of reach
and modelling work can only be very exploratory. Here, we
have shown that some robust features are required to explain
Quaternary ice age cycles. Similar conceptual modelling on
a wider temporal scope over the Cenozoic could help better
explain the connections between astronomical forcing, the
carbon cycle, ice sheets and the climate. This would help us
imagine what the Anthropocene might be like.
Code and data availability. The model code, insolation input
files, spectral analysis and code needed to reproduce the figures are
available for download: https://doi.org/10.5281/zenodo.6045532
(Leloup, 2022).
Supplement. The supplement related to this article is available
online at: https://doi.org/10.5194/cp-18-547-2022-supplement.
Author contributions. GL and DP designed the study. GL per-
formed the simulations, and also wrote the manuscript under the
supervision of DP.
Competing interests. The contact author has declared that nei-
ther they nor their co-author has any competing interests.
Disclaimer. Publisher’s note: Copernicus Publications remains
neutral with regard to jurisdictional claims in published maps and
institutional affiliations.
Special issue statement. This article is part of the special issue
“A century of Milankovic’s theory of climate changes: achievements and challenges (NPG/CP inter-journal SI)”. It is not associated with a conference.
Acknowledgements. We acknowledge the use of the LSCE stor-
age and computing facilities. We also thank the reviewers for their
helpful comments and suggestions.
Financial support. This research has been supported by ANDRA
(contract no. 20080970).
Clim. Past, 18, 547–558, 2022
Review statement. This paper was edited by Marie-France
Loutre and reviewed by Mikhail Verbitsky, Andrey Ganopolski, and
one anonymous referee.
References
Abe-Ouchi, A., Saito, F., Kawamura, K., Raymo, M., Okuno, J.,
Takahashi, K., and Blatter, H.: Insolation-driven 100,000-year
glacial cycles and hysteresis of ice-sheet volume, Nature, 500,
190–193, https://doi.org/10.1038/nature12374, 2013.
Archer, D. and Ganopolski, A.: A movable trigger: Fossil fuel CO2
and the onset of the next glaciation, Geochem. Geophy. Geosy.,
6, Q05003, https://doi.org/10.1029/2004GC000891, 2005.
Ashkenazy, Y. and Tziperman, E.: Are the 41 kyr glacial oscillations
a linear response to Milankovitch forcing?, Quaternary Sci. Rev.,
23, 1879–1890, https://doi.org/10.1016/j.quascirev.2004.04.008,
2004.
Berger, A.: Long-term variations of daily insolation and Quaternary
climatic changes, J. Atmos. Sci., 35, 2362–2367, 1978.
Berger, A.: Milankovitch, the father of paleoclimate modeling,
Clim. Past, 17, 1727–1733, https://doi.org/10.5194/cp-17-17272021, 2021.
Berger, A. and Loutre, M.-F.: Insolation values for the climate of
the last 10 million years, Quaternary Sci. Rev., 10, 297–317,
https://doi.org/10.1016/0277-3791(91)90033-Q, 1991.
Berger, A. and Loutre, M.-F.: Climate: An Exceptionally Long Interglacial Ahead?, Science, 297, 1287–1288,
https://doi.org/10.1126/science.1076120, 2002.
Bintanja, R., van de Wal, R., and Oerlemans, J.: Modelled atmospheric temperatures and global sea levels over the past million years, Nature, 437, 125–128,
https://doi.org/10.1038/nature03975, 2005.
Bouttes, N., Paillard, D., Roche, D. M., Waelbroeck, C., Kageyama,
M., Lourantou, A., Michel, E., and Bopp, L.: Impact of oceanic
processes on the carbon cycle during the last termination, Clim.
Past, 8, 149–170, https://doi.org/10.5194/cp-8-149-2012, 2012.
Calder, N.: Arithmetic of ice ages, Nature, 252, 216–218,
https://doi.org/10.1038/252216a0, 1974.
Chappell, J. and Shackleton, N. J.: Oxygen isotopes and sea level,
Nature, 324, 137–140, 1986.
Clark, P. and Pollard, D.: Origin of the Middle Pleistocene Transition by ice sheet erosion of regolith, Paleoceanography, 13, 1–9,
https://doi.org/10.1029/97PA02660, 1998.
Clark, P., Archer, D., Pollard, D., Blum, J. D., Rial, J., Brovkin, V.,
Mix, A., Pisias, N., and Roy, M.: The middle Pleistocene transition: characteristics, mechanisms, and implications for long-term
changes in atmospheric pCO2 , Quaternary Sci. Rev., 25, 3150–
3184, https://doi.org/10.1016/j.quascirev.2006.07.008, 2006.
Croll, J.: XIII. On the physical cause of the change of climate
during geological epochs, The London, Edinburgh, and Dublin
Philosophical Magazine and Journal of Science, 28, 121–137,
https://doi.org/10.1080/14786446408643733, 1864.
Elderfield, H., Ferretti, P., Greaves, M., Crowhurst, S., Mccave, I. N., Hodell, D., and Piotrowski, A. M.: Evolution of Ocean Temperature and Ice Volume Through the
Mid-Pleistocene Climate Transition, Science, 337, 704–709,
https://doi.org/10.1126/science.1221294, 2012.
Gallée, H., Van Yperselb, J. P., Fichefet, T., Marsiat, I., Tricot, C.,
and Berger, A.: Simulation of the last glacial cycle by a cou-
https://doi.org/10.5194/cp-18-547-2022
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
pled, sectorially averaged climate-ice sheet model: 2. Response
to insolation and CO2 variations, J. Geophys. Res.-Atmos., 97,
15713–15740, https://doi.org/10.1029/92JD01256, 1992.
Ganopolski, A. and Calov, R.: The role of orbital forcing, carbon
dioxide and regolith in 100 kyr glacial cycles, Clim. Past, 7,
1415–1425, https://doi.org/10.5194/cp-7-1415-2011, 2011.
Gildor, H. and Tziperman, E.: Sea ice as the glacial cycles’ Climate
switch: role of seasonal and orbital forcing, Paleoceanography,
15, 605–615, https://doi.org/10.1029/1999PA000461, 2000.
Hays, J., Imbrie, J., and Shackleton, N. J.: Variations in the Earth’s
Orbit: Pacemaker of the Ice Ages, Science, 194, 1121–1132,
https://doi.org/10.1126/science.194.4270.1121, 1976.
Hönisch, B., Hemming, N. G., Archer, D., Siddall, M., and
McManus, J. F.: Atmospheric Carbon Dioxide Concentration
Across the Mid-Pleistocene Transition, Science, 324, 1551–
1554, https://doi.org/10.1126/science.1171477, 2009.
Huybers, P.: Early Pleistocene glacial cycles and the integrated summer insolation forcing, Science, 313, 508–511,
https://doi.org/10.1126/science.1125249, 2006.
Huybers, P.: Combined obliquity and precession pacing
of late Pleistocene deglaciations, Nature, 480, 229–232,
https://doi.org/10.1038/nature10626, 2011.
Huybers, P. and Wunsch, C.: Obliquity pacing of the late
Pleistocene glacial terminations, Nature, 434, 491–494,
https://doi.org/10.1038/nature03401, 2005.
Imbrie, J. and Imbrie, J. Z.: Modeling the Climatic Response to Orbital Variations, Science, 207, 943–953,
https://doi.org/10.1126/science.207.4434.943, 1980.
Imbrie, J. Z., Imbrie-Moore, A., and Lisiecki, L. E.: A phase-space
model for Pleistocene ice volume, Earth Planet. Sci. Lett., 307,
94–102, 2011.
Jakob, K. A., Wilson, P. A., Pross, J., Ezard, T. H. G., Fiebig, J.,
Repschläger, J., and Friedrich, O.: A new sea-level record for the
Neogene/Quaternary boundary reveals transition to a more stable
East Antarctic Ice Sheet, P. Natl. Acad. Sci. USA, 117, 30980–
30987, https://doi.org/10.1073/pnas.2004209117, 2020.
Jouzel, J., Masson-Delmotte, V., Cattani, O., Dreyfus, G., Falourd,
S., Hoffmann, G., Minster, B., Nouet, J., Barnola, J., Chappellaz, J., Fischer, H., Gallet, J.-C., Johnsen, S., Leuenberger, M.,
Loulergue, L., Lüthi, D., Oerter, H., Parrenin, F., Raisbeck, G.,
and Wolff, E.: Orbital and Millennial Antarctic Climate Variability over the Past 800,000 Years, Science, 317, 793–796,
https://doi.org/10.1126/science.1141038, 2007.
Khodri, M., Leclainche, Y., Ramstein, G., Braconnot, P., Marti, O.,
and Cortijo, E.: Simulating the amplification of orbital forcing
by ocean feedbacks in the last glaciation, Nature, 410, 570–574,
2001.
Lambeck, K., Rouby, H., Purcell, A., Sun, Y., and Sambridge, M.:
Sea level and global ice volumes from the Last Glacial Maximum
to the Holocene, P. Natl. Acad. Sci. USA, 111, 15296–15303,
https://doi.org/10.1073/pnas.1411762111, 2014.
Laskar, J., Robutel, P., Joutel, F., Gastineau, M., Correia, A., and
Levrard, B.: A long-term numerical solution for the insolation
quantities of the Earth, Astron. Astrophys., 428, 261–285, 2004.
Leloup, G.: Data and code for results and figures in Climate of the
Past “Influence of the choice of insolation forcing on the results
of a conceptual glacial cycle model”, Zenodo [code and data set],
https://doi.org/10.5281/zenodo.6045532, 2022
https://doi.org/10.5194/cp-18-547-2022
557
Lisiecki, L. E.: Links between eccentricity forcing and the
100,000-year glacial cycle, Nat. Geosci., 3, 349–352,
https://doi.org/10.1038/ngeo828, 2010.
Lisiecki, L. E. and Raymo, M. E.: A Pliocene-Pleistocene stack of
57 globally distributed benthic δ 18 O records, Paleoceanography,
20, PA1003, 2005.
Liu, Z., Cleaveland, L., and Herbert, T.: Early onset
and origin of 100-kyr cycles in Pleistocene tropical
SST records, Earth Planet. Sci. Lett., 265, 703–715,
https://doi.org/10.1016/j.epsl.2007.11.016, 2008.
MacAyeal, D. R.: Irregular oscillations of the West Antarctic
ice sheet, Nature, 359, 29–32, https://doi.org/10.1038/359029a0,
1992.
Marshall, S. J. and Clark, P. U.: Basal temperature evolution of North American ice sheets and implications for
the 100-kyr cycle, Geophys. Res. Lett., 29, 67-1–67-4,
https://doi.org/10.1029/2002GL015192, 2002.
Milankovitch, M.: Kanon der Erdbestrahlung und seine Anwendung
auf das Eiszeitenproblem, Royal Serbian Academy Special Publication, 133, 1–633, 1941.
Oerlemans, J.: Model experiments on the 100,000-yr glacial cycle,
Nature, 287, 430–432, https://doi.org/10.1038/287430a0, 1980.
Paillard, D.: The timing of Pleistocene glaciations from a
simple multiple-state climate model, Nature, 391, 378–381,
https://doi.org/10.1038/34891, 1998.
Paillard, D.: Glacial cycles: toward a new paradigm, Rev. Geophys.,
39, 325–346, https://doi.org/10.1029/2000RG000091, 2001.
Paillard,
D.:
Quaternary
glaciations:
from
observations to theories, Quaternary Sci. Rev., 107, 11–24,
https://doi.org/10.1016/j.quascirev.2014.10.002, 2015.
Paillard, D.: The Plio-Pleistocene climatic evolution as a consequence of orbital forcing on the carbon cycle, Clim. Past, 13,
1259–1267, https://doi.org/10.5194/cp-13-1259-2017, 2017.
Paillard, D. and Parrenin, F.: The Antarctic ice sheet and the triggering of deglaciations, Earth Planet. Sci. Lett, 227, 263–271,
https://doi.org/10.1016/j.epsl.2004.08.023, 2004.
Paillard, D., Labeyrie, L., and Yiou, P.: Macintosh Program performs time-series analysis, Eos Transactions, AGU, 77, 379–379,
https://doi.org/10.1029/96EO00259, 1996.
Parrenin, F. and Paillard, D.: Amplitude and phase of glacial cycles
from a conceptual model, Earth Planet. Sci. Lett., 214, 243–250,
https://doi.org/10.1016/S0012-821X(03)00363-7, 2003.
Parrenin, F. and Paillard, D.: Terminations VI and VIII (∼ 530 and
∼ 720 kyr BP) tell us the importance of obliquity and precession in the triggering of deglaciations, Clim. Past, 8, 2031–2037,
https://doi.org/10.5194/cp-8-2031-2012, 2012.
Peltier, W. R. and Marshall, S.: Coupled energy-balance/ice-sheet
model simulations of the glacial cycle: A possible connection
between terminations and terrigenous dust, J. Geophys. Res.Atmos., 100, 14269–14289, https://doi.org/10.1029/95JD00015,
1995.
Pollard, D.: A simple ice sheet model yields realistic 100 kyr glacial
cycles, Nature, 296, 334–338, https://doi.org/10.1038/296334a0,
1982.
Raymo, M.: The timing of major climate terminations, Paleoceanography, 12, 577–585, https://doi.org/10.1029/97PA01169,
1997.
Clim. Past, 18, 547–558, 2022
558
G. Leloup and D. Paillard: Conceptual model for glacial–interglacial ice volume evolution
Raymo, M. E. and Nisancioglu, K. H.: The 41 kyr world: Milankovitch’s other unsolved mystery, Paleoceanography, 18,
1011, https://doi.org/10.1029/2002PA000791, 2003.
Raymo, M. E., Kozdon, R., David, E., Lisiecki, L., and Ford,
H. L.: The accuracy of mid-Pliocene δ 18 O-based ice volume
and sea level reconstructions, Earth-Sci. Rev., 177, 291–302,
https://doi.org/10.1016/j.earscirev.2017.11.022, 2018.
Reeh, N.: Parameterization of Melt Rate and Surface Temperature
on the Greenland Ice Sheet, Polarforschung, 59, 113–128, 1991.
Robinson, A., Calov, R., and Ganopolski, A.: An efficient regional
energy-moisture balance model for simulation of the Greenland
Ice Sheet response to climate change, The Cryosphere, 4, 129–
144, https://doi.org/10.5194/tc-4-129-2010, 2010.
Saltzman, B. and Sutera, A.: The Mid-Quaternary Climatic Transition as the Free Response of a Three-Variable Dynamical Model,
J. Atmos. Sci., 44, 236–241, https://doi.org/10.1175/15200469(1987)044<0236:TMQCTA>2.0.CO;2, 1987.
Saltzman, B., Hansen, A., and Maasch, K.: The Late
Quaternary Glaciations as the Response of a ThreeComponent Feedback System to Earth-Orbital Forcing, J.
Atmos. Sci., 41, 3380–3389, https://doi.org/10.1175/15200469(1984)041<3380:TLQGAT>2.0.CO;2, 1984.
Shackleton, N.: Oxygen Isotope Analyses and Pleistocene Temperatures Re-assessed, Nature, 215, 15–17,
https://doi.org/10.1038/215015a0, 1967.
Shackleton, N. J. and Opdyke, N. D.: Oxygen isotope and
palaeomagnetic stratigraphy of Equatorial Pacific core V28238: Oxygen isotope temperatures and ice volumes on a
105 year and 106 year scale, Quaternary Res., 3, 39–55,
https://doi.org/10.1016/0033-5894(73)90052-5, 1973.
Spratt, R. M. and Lisiecki, L. E.: A Late Pleistocene sea level stack,
Clim. Past, 12, 1079–1092, https://doi.org/10.5194/cp-12-10792016, 2016.
Clim. Past, 18, 547–558, 2022
Talento, S. and Ganopolski, A.: Reduced-complexity model for the
impact of anthropogenic CO2 emissions on future glacial cycles,
Earth Syst. Dynam., 12, 1275–1293, https://doi.org/10.5194/esd12-1275-2021, 2021.
Toggweiler, J. R.: Origin of the 100,000-year timescale in Antarctic temperatures and atmospheric CO2 , Paleoceanography, 23,
PA2211, https://doi.org/10.1029/2006PA001405, 2008.
Tzedakis, P., Crucifix, M., Mitsui, T., and Wolff, E. W.: A simple
rule to determine which insolation cycles lead to interglacials,
Nature, 542, 427–432, https://doi.org/10.1038/nature21364,
2017.
Tziperman, E. and Gildor, H.: On the mid-Pleistocene transition
to 100-kyr glacial cycles and the asymmetry between glaciation and deglaciation times, Paleoceanography, 18, 1-1–1-8,
https://doi.org/10.1029/2001pa000627, 2003.
Tziperman, E., Raymo, M. E., Huybers, P., and Wunsch, C.: Consequences of pacing the Pleistocene 100 kyr ice ages by nonlinear phase locking to Milankovitch forcing, Paleoceanography,
21, PA4206, https://doi.org/10.1029/2005PA001241, 2006.
Van den Berg, J., van de Wal, R., and Oerlemans, H.: A
mass balance model for the Eurasian Ice Sheet for the
last 120,000 years, Global Planet. Change, 61, 194–208,
https://doi.org/10.1016/j.gloplacha.2007.08.015, 2008.
Verbitsky, M. Y., Crucifix, M., and Volobuev, D. M.: A theory of
Pleistocene glacial rhythmicity, Earth Syst. Dynam., 9, 1025–
1043, https://doi.org/10.5194/esd-9-1025-2018, 2018.
Yan, Y., Bender, M. L., Brook, E. J., Clifford, H. M., Kemeny, P. C.,
Kurbatov, A. V., Mackay, S., Mayewski, P. A., Ng, J., Severinghaus, J. P., and Higgins, J. A.: Two-million-year-old snapshots
of atmospheric gases from Antarctic ice, Nature, 574, 663–666,
https://doi.org/10.1038/s41586-019-1692-3, 2019.
https://doi.org/10.5194/cp-18-547-2022
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Chest computed tomography severity score is a reliable predictor of mortality in patients with chronic obstructive pulmonary disease co-infected with COVID-19
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Alipour Khabir et al.
European Journal of Medical Research (2023) 28:346
https://doi.org/10.1186/s40001-023-01336-8 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346
https://doi.org/10.1186/s40001-023-01336-8 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346
https://doi.org/10.1186/s40001-023-01336-8 European Journal
of Medical Research Open Access Chest computed tomography severity score
is a reliable predictor of mortality in patients
with chronic obstructive pulmonary disease
co‑infected with COVID‑19 Yalda Alipour Khabir1† , Sevda Alipour Khabir1† , Hassan Anari2 , Bahman Mohammadzadeh2,
Saeed Hoseininia3 and Mohammad Reza Aslani3,4* Yalda Alipour Khabir1† , Sevda Alipour Khabir1† , Hassan Anari2 , Bahman Mohammadzadeh2,
Saeed Hoseininia3 and Mohammad Reza Aslani3,4* © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecom-
mons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Abstract Background Coronavirus disease 2019 (COVID-19) pandemic is considered a global health crisis. The data related
to chronic obstructive pulmonary disease (COPD) patients with COVID-19 are incomplete, especially the findings
of the chest computed tomography (CT). The aim of the current study was to investigate the severity of the disease
of COVID-19 in patients with COPD based on CT severity score and to evaluate its predictive power in the mortality
of patients. Methods In a retrospective study, demographic, clinical, and CT scan findings of COPD patients with COVID-19 were
extracted from March 2020 to February 2022. CT severity score was determined based on the extent and nature
of involvement of lungs in CT scan findings. By performing receiver operating characteristics (ROC) and Kaplan–Meier
survival analysis were determined the disease severity and survival probability. Results The most frequent radiological findings in chest CT scan included ground glass opacities (89.3%), consolida-
tions (51.8%), crazy-paving pattern (46.4%), and septal thickening (35.7%). The mean CT severity score of deceased
patients (34.61 ± 18.73) was significantly higher than recovered patients (16.71 ± 14.01, p < 0.001). Based on the ROC
and Kaplan–Meier survival curves, it was revealed that CT severity score was a valuable criteria in the diagnosis
of mortality in COPD patients with COVID-19. Conclusion The findings of this study revealed that the CT severity scoring in COPD patients with COVID-19 was val-
uable in identifying poor prognosis, although further studies are needed. Keywords COVID-19, Chronic obstructive pulmonary disease, Computed tomography Keywords COVID-19, Chronic obstructive pulmonary disease, Computed tomography †Yalda Alipour Khabir and Sevda Alipour Khabir contributed equally to this
work. *Correspondence:
Mohammad Reza Aslani
mraslani105@yahoo.com; mr.aslani@arums.ac.ir
Full list of author information is available at the end of the article *Correspondence:
Mohammad Reza Aslani
mraslani105@yahoo.com; mr.aslani@arums.ac.ir
Full list of author information is available at the end of the article *Correspondence:
Mohammad Reza Aslani
mraslani105@yahoo.com; mr.aslani@arums.ac.ir
Full list of author information is available at the end of the article Background severity score and to evaluate its predictive power in the
mortality of patients. ac g ou d
In December 2019, a novel beta-coronavirus, severe
acute respiratory syndrome coronavirus 2 (SARS-
CoV-2), emerged in Wuhan city, China. The infectious
disease caused by this novel coronavirus was named
“coronavirus disease 2019 (COVID-19)” by WHO in
February 2020. One month later in March 2020, WHO
officially declared the disease a globally pandemic and
COVID-19 has been a global health crisis for more than
two years [1]. The clinical spectrum of SARS-CoV-2
infection ranges from asymptomatic patients to criti-
cally ill ones with acute respiratory distress syndrome
and multiorgan dysfunction [2]. Male individuals,
elderly people, and patients with comorbidities such
as diabetes, hypertension, obesity, and cardiovascular
disease are at higher risk of poor COVID-19 outcomes
and require more attention [3–7]. Methodsh This was a single-center retrospective study conducted
on COPD patients diagnosed with COVID-19 who
were hospitalized in Ardabil Imam Khomeini hospital,
northwestern Iran from March 2020 to February 2022. All patients who underwent chest CT scan within 24 h
of admission in the radiology department of the hospi-
tal, included in this study. The diagnosis of COVID-19
was confirmed with a positive RT-PCR for SARS-CoV-2
based on nasopharyngeal and oropharyngeal swabs. Exclusion was determined by certain conditions: (a)
patients with a negative RT-PCR, (b) absence of CT
findings in mild patients, (c) inadequate quality of chest
CT images for analysis, and (d) age below 18 years. This
study was approved by the ethics committee (IR.ARUMS. REC.1400.312). Early in the SARS-CoV-2 pandemic there was a grow-
ing concern about the outcomes in chronic obstruc-
tive pulmonary disease (COPD) patients who developed
COVID-19. COPD, a common cause of disability and
death worldwide, is a persistent dysfunction of the lung
characterized by airflow limitation due to inflammation
of the airway and/or alveolar abnormalities. COVID-19
patients with preexisting COPD are among high-risk
groups due to various complications. These complica-
tions include virus-induced exacerbations, impaired lung
function, compromised immune responses, and upreg-
ulation of angiotensin-converting enzyme 2 (ACE-2)
receptor. ACE-2 receptor facilitates SARS-CoV-2 entry
into cells putting these patients at higher risk of COVID-
19 infection [8–13].f © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecom-
mons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Page 2 of 8 Data collection
l d Data including demographic information, duration of
hospitalization, inpatient department, comorbidities, and
outcome of the disease (recovered or dead) were obtained
from each patient’s electronic medical records. Comor-
bidities included hypertension, chronic kidney disease,
chronic liver disease, diabetes mellitus, and coronary
artery disease. Based on disease severity patients divided
into 3 groups, moderate, severe, and critical cases. Mod-
erate disease included patients with symptoms and signs
of pneumonia such as fever, cough, and dyspnea but no
signs of severe pneumonia; severe disease additionally
met the following criteria––oxygen saturation at rest ⩽
93% and arterial blood oxygen partial pressure (PaO2)/
oxygen concentration (FiO2) ⩽ 300 mmHg; and the criti-
cal disease included patients who were admitted to ICU,
were in need of mechanical ventilation, and had signs of
multiorgan failure. Chest computed tomography (CT) is an effective
modality for COVID-19 diagnosis and monitoring the
progression of the disease. Studies have discussed that
CT imaging has a sensitivity higher than RT-PCR (98%
compared to 71%); therefore, chest CT can be used as a
screening tool in suspected cases of COVID-19. Accord-
ing to previous studies, ground glass opacities and con-
solidations with peripheral and subpleural distribution
are two main CT findings in COVID-19 [14–19]. The
extent and nature of these findings are predictive of
prognosis [15]. There are several studies that use a chest
CT-based scoring system to determine the risk of dis-
ease deterioration and poor outcomes in patients with
COVID-19. These studies have demonstrated that higher
scores in patients’ CT are associated with higher mortal-
ity and severe forms of COVID-19 [18, 20–24]. However,
there are limited data on predictive value of a CT severity
score in COVID-19 patients who have preexisting COPD. Taking that into consideration, the aim of the current
study was to investigate the severity of the disease of
COVID-19 in patients with COPD history based on CT Statistical analysis Data were investigated with SPSS version 21 and Med-
Calc version 19.4.1 software. Normally distributed vari-
ables are expressed by mean ± standard deviation (SD)
and categorical variables by percentages. The t-test was
used to compare the continuous variables. As for the cat-
egorical variables the chi-squared test was used. For esti-
mating the optimal cut-off score, a Receiver Operating Chest CT findingshi Patient characteristics and outcomeh This study involved 56 patients: 26 (46.4%) men and 30
(53.6%) women, the mean age was 68.01 ± 12.08 years. All patients had an underlying COPD and all were diag-
nosed with COVID-19. The most frequent comorbidities
besides COPD were hypertension (39.3%), diabetes mel-
litus (21%), and cardiovascular disease (14.3%). Among patients 60.7% were classified as having mod-
erate disease, 7% as severe and 32.1% as critical. 62.5%
of patients were admitted in general wards, while 37.5%
were ICU patients. For clinical outcomes, 62.5% of
patients recovered from the disease and were discharged,
while 37.5% expired. Table 1 shows patients’ characteris-
tics in the survival and non-survival groups. Chest CT interpretation p
All patients’ chest CT images were evaluated by two
certified radiologists. Both radiologists were blinded to
the patients’ data and the final assessments were made
by consensus. Definitions of radiological findings were
based on the Fleischner Society recommendations, pub-
lished in 2008 [25]. In this study we used a chest CT
severity scoring system first proposed by Ooi et al.[26]
in 2004 for SARS. According to this system, each lung
was evaluated in 3 levels: upper (above the carina), mid-
dle (below the carina up to the upper limit of the pul-
monary vein), and lower (below the inferior pulmonary
vein). Each level was evaluated separately. Levels were
assessed in both nature and extents of the involvement. Page 3 of 8 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 For evaluating the nature of the involvement grading was
as follows: 1 for no pulmonary involvement; 2 for at least
75% GGO/crazy-paving pattern; 3 for a combination of
GGO/crazy-paving pattern and consolidation with less
than 75% involvement for each; and 4 for at least 75%
consolidation. Characteristics (ROC) curve analysis was performed
(according to Youden’s index for maximizing sensitivity
and specificity). Survival probability for CT severity score
was estimated using the means of the Kaplan–Meier
curves, with the endpoint being death. Cox proportional
hazards regression was performed for both univariate
and multivariate analyses. The P-value was considered
significant when less than 0.05 in all analyses. The score for evaluating the extent of involvement
ranged from 0 to 4 as follows: 0 for no involvement, 1 for
1–24%, 2 for 25–49%, 3 for 50–74%, and 4 for more than
75%. The score for each level was calculated by multiply-
ing these two scores, and final score was determined by
adding up the scores at these levels in both lungs (ranging
from 0 to 96). When present, other lung abnormalities
such as septal thickening, reticulation, air bronchogram,
pleural thickening, halo sign, lymphadenopathy, and
bronchiectasis were also described. Distribution of pul-
monary findings were classified as central, peripheral,
or diffuse. Findings were also described as unilateral or
bilateral. ndependent t-test was used to contrast the statistical differences between non-survival and survival COPD patients with COVID-19 Chest CT findingsh The most frequent radiological findings in chest CT scan
included ground glass opacities (89.3%), consolidations The most frequent radiological findings in chest CT scan
included ground glass opacities (89.3%), consolidations Table 1 Patient characteristics in the survival and non-survival patients
An independent t-test was used to contrast the statistical differences between non-survival and survival COPD patients with COVID-19
Variables
All patients (n = 56)
Survival (n = 35)
Non-survival (n = 21)
P-value
Age
Mean ± SD (year)
68.01 ± 12.08
65.65 ± 11.37
71.95 ± 12.47
0.77
Sex, N (%)
Male
26 (46.4)
17 (48)
9 (42)
0.67
Female
30 (53.6)
18 (51)
12 (57)
Comorbidities, N (%)
Cardiovascular
8 (14)
5 (14)
3 (14)
1
Myocardial infraction
2 (3)
2 (5)
0
0.26
Heart failure
4 (7)
3 (8)
1 (4)
0.59
Type 2 diabetes
12 (21)
5 (8)
7 (33)
0.09
Hypertension
22 (39)
13 (37)
9 (42)
0.67
Cerebrovascular attack
3 (5)
1 (2)
2 (9)
0.28
Kidney diseases
1 (1)
1 (2)
0
0.43
Hospital stay
Mean ± SD (day)
8 ± 6
6.2 ± 3.8
11.1 ± 7.6
0.000
Diseases severity, N (%)
0.000
Moderate
34 (60)
32 (91)
2 (9)
Severe
4 (7)
2 (5)
2 (9)
Critical
18 (32)
1 (2)
17 (80) Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Page 4 of 8 (51.8%), crazy-paving pattern (46.4%), and septal thick-
ening (35.7%). CT findings were mostly bilateral (78.6%)
and multi-focal (75%) and were distributed peripherally
(76.8%). Table 2 summarizes chest CT findings and their
distribution in the survival and death groups. Chest CT findingsh Table 3 Mean ± SD of CT severity scores in each level of the lung
Upper lobe: above the carina, middle lobe: below the carina up to the upper
limit of the pulmonary vein, and lower lobe: below the inferior pulmonary vein
Lung levels
Nature of the
involvement
Extent of the
involvement
Total score
Right upper level
1.64 ± 1.25
2.35 ± 0.99
4.30 ± 3.48
Right middle level
1.53 ± 1.12
2.35 ± 1.01
4.12 ± 3.25
Right lower level
1.55 ± 1.21
2.32 ± 1.01
4.25 ± 3.70
Total right lung
–
–
12.67 ± 9.44
Left upper level
1.23 ± 1.15
2.12 ± 1.01
3.23 ± 3.23
Left middle level
2.14 ± 0.99
1.32 ± 1.17
3.44 ± 3.17
Left lower level
2.17 ± 1.09
2.17 ± 1.09
4.12 ± 3.97
Total left lung
–
–
10.75 ± 9.29
Total lung
–
–
23.42 ± 18.04 Chest CT severity score Table 3 shows the CT severity score based on nature of
the involvement and extent of the involvement at differ-
ent levels (upper, middle, and lower levels) of both right
and left lungs as well as the whole lung. The mean CT
severity score in non-surviving patients (34.61 ± 18.73)
was
significantly
higher
than
surviving
patients
(16.71 ± 14.01, p < 0.001) (Table 4). In addition, the mean
score of patients hospitalized in ICU (36.66 ± 18.33) was
significantly higher than that of patients hospitalized in
the general department (15.48 ± 12.47, p < 0.001). Upper lobe: above the carina, middle lobe: below the carina up to the upper
limit of the pulmonary vein, and lower lobe: below the inferior pulmonary vein were upper level of left lung (> 3), middle level of left
lung (> 4), lower level of left lung (> 4), total level of left
lung (> 11), upper level of right lung (> 2), middle level of
right lung (> 3), lower level of right lung (> 4), total level An independent t-test was used to contrast the statistical differences between non-survival and survival patients Receiver operating characteristics (ROC)f Optimal cut-off points observed for CT severity score
predicated on the ROC curve for surviving assessment Table 2 Chest CT findings in survival and non-survival COVID-19 COPD patients
An independent t-test was used to contrast the statistical differences between non-survival and survival patients
Nature of the findings
Total patients (n = 56) N (%) Survival (n = 35) N (%)
Non-survival (n = 21) N (%)
P-value
Ground glass opacities
50 (89)
31 (88)
19 (90)
0.82
Vascular enlargement
5 (8)
1 (2)
4 (19)
0.04
Posterior predilection
21 (37)
15 (42)
6 (28)
0.28
Consolidation
29 (51)
16 (45)
13 (61)
0.24
Linear opacities
9 (16)
5(14)
4 (19)
0.63
Septal thickening
20 (35)
10 (28)
10 (47)
0.15
Reticulation
11 (19)
5 (14)
6 (28)
0.19
Crazy-paving pattern
26 (46)
13 (37)
13 (61)
0.07
Air bronchogram
6 (10)
2 (5)
4 (19)
0.11
Pleural thickening
3 (5)
2 (5)
1 (4)
0.87
Halo sign
3 (5)
3 (8)
0
0.16
Bronchiectasis
6 (10)
2 (5)
4 (19)
0.11
Nodules
5 (8)
4 (11)
1 (4)
0.39
Bronchial wall thickening
5 (8)
1 (2)
4 (19)
0.04
Pleural effusion
8 (14)
4 (11)
4 (19)
0.43
Pericardial effusion
1 (1)
1 (2)
0
0.43
Bilateral findings
44 (78)
25 (71)
19 (90)
0.09
Unilateral findings
9 (16)
8 (22)
1 (4)
0.07
Upper or middle lobe involvement
49 (87.5)
29 (82)
20 (95)
0.17
Lower lobe involvement
45 (80)
28 (80)
17 (80)
0.93
Central location
3 (5)
2 (5)
1 (4)
0.87
Peripheral location
43 (76)
27 (77)
16 (76)
0.93
Central and peripheral location
17 (30)
6 (17)
11 (52)
0.005
Single-focal lesion
6 (10)
5 (14)
1 (4)
0.26
Multi-focal lesion
42 (75)
26 (74)
16 (76)
0.87
Diffuse lesion
25 (44)
13 (37)
12 (57)
0.14 Table 2 Chest CT findings in survival and non-survival COVID-19 COPD patients Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Page 5 of 8 Table 4 Mean ± SD of CT severity scores in survival and non-
survival COVID-19 COPD patients
An independent t-test was used to contrast the statistical differences between
non-survival and survival COPD patients with COVID-19. Receiver operating characteristics (ROC)f Upper lobe: above the
carina, middle lobe: below the carina up to the upper limit of the pulmonary
vein, and lower lobe: below the inferior pulmonary vein An independent t-test was used to contrast the statistical differences between
non-survival and survival COPD patients with COVID-19. Upper lobe: above the
carina, middle lobe: below the carina up to the upper limit of the pulmonary
vein, and lower lobe: below the inferior pulmonary vein of right lung (> 10), and total level of lung (> 18) (Fig. 1A,
B, C and Table 5).i Moreover, significant AUC levels demonstrated in
regard to CT severity score were upper level of left lung
(0.760), middle level of left lung (0.682), lower level of left
lung (0.682), total level of left lung (0.754), upper level
of right lung (0.746), middle level of right lung (0.774),
lower level of right lung (0.717), total level of right lung
(0.773), and total level of lung (0.772) (Fig. 1A, B, C and
Table 5). During the coronavirus pandemic, the use of different
indicators to diagnose the disease prognosis in patients
with COVID-19 has been of interest. In our previous
study, systemic inflammation indices were used to diag-
nose the severity of the disease in COVID-19 patients
[32–35]. On the other hand, the effectiveness of severity
score in patients with COVID-19 has been reported in
some studies [18, 36–39]. The results of the current study
showed that CT severity score was a valuable measure in
diagnosing the severity of the disease in COPD patients
infected with SARS-CoV-2. Although all the levels of the
right and left lungs (upper, middle, and lower) based on
ROC and Kaplan–Meier curves were useful in diagnos-
ing the mortality of patients, the lower levels of the lungs
were very efficient. The Kaplan–Meier survival curve showed that higher
levels of lower level of left lung (HR = 2.643, 95% CI 1.023
to 6.830, P < 0.05) (Fig. 2A) and lower level of right lung
(HR = 2.856, 95% CI 1.116 to 7.307, P < 0.05) (Fig. 2B)
were significantly associated with shorter survival period. Multivariate Cox regression models identified that only
lower level of right lung (HR = 2.682, 95% CI 1.019 to
7.058, P < 0.05) was significantly associated with survival. Receiver operating characteristics (ROC)f Upper lobe: above the
carina, middle lobe: below the carina up to the upper limit of the pulmonary
vein, and lower lobe: below the inferior pulmonary vein
Lung levels
Survival (n = 35)
Non-survival (n = 21)
P-value
Right upper level
3.17 ± 3.11
6.19 ± 3.31
0.001
Right middle level
2.88 ± 2.59
6.19 ± 3.28
0.0001
Right lower level
3.14 ± 2.73
6.09 ± 4.39
0.003
Total right lung
9.20 ± 7.54
18.47 ± 9.60
0.0001
Left upper level
2.05 ± 2.43
5.19 ± 3.50
0.0001
Left middle level
2.54 ± 2.52
4.95 ± 3.61
0.005
Left lower level
3 ± 3.17
6 ± 4.51
0.005
Total left lung
7.51 ± 7.37
16.14 ± 9.80
0.0001
Total lung
16.71 ± 14.01
34.61 ± 18.73
0.0001 Table 4 Mean ± SD of CT severity scores in survival and non-
survival COVID-19 COPD patients a quantitative CT emphysema score to examine its asso-
ciation with clinical outcome in COPD and COVID-19
patients, which demonstrated that scores higher than 5%
are associated with disease severity. However, this study
did not include COVID-19 specific radiologic findings in
the scoring system [27]. According to current data COPD
is not a frequent comorbidity in COVID-19 patients [22,
28]. In contrast, some studies have demonstrated that
COPD patients were more susceptible to the critical form
of COVID-19 [29, 30]. This can be due to impaired lung
function in COPD patients and higher ACE-2 expression
in these patients which may facilitate viral entry.h The results of the current study revealed that the mean
CT score was higher in the non-survival patients in com-
parison to the survival group. Patients with severe and
critical disease also had higher CT scores than moderate
cases. This was in agreement with previous studies that
suggested higher CT scores in COVID-19 patients are
associated with higher mortality and increase the risk of
developing severe and critical types of the disease [21,
31]. In addition, it was found that GGO, a crazy-paving
pattern, and consolidations are the most frequent find-
ings in COPD patients with COVID-19 and the findings
are more predominant in peripheral and they are mostly
bilateral, which was consistent with recent studies [14,
16, 17, 19].f An independent t-test was used to contrast the statistical differences between
non-survival and survival COPD patients with COVID-19. Discussionh The most important findings of the current study were as
follows: 1- The mean CT severity score in patients who
died was detectably higher than those who recovered. 2-
Based on the ROC and Kaplan–Meier survival curves, it
was revealed that CT severity score was a valuable crite-
ria in the diagnosis of mortality in COPD patients with
COVID-19. 3- Results from multivariate Cox regression
model indicated that lower lung lobes severity score were
significantly associated with survival. fi
To our best knowledge, multivariate Cox regression
analysis showed that among the different levels of the
right and left lung (upper, middle, and lower), the lower
level of the right lung remained with survival. It seems
that in COPD patients with COVID-19, the involvement
of the lower parts of the lungs is associated with a poor
prognosis of the disease, which requires further studies.hh i
Many studies have been conducted to identify the role
of a quantitative CT scoring system in predicting disease
severity in COVID-19 patients. To the best of our knowl-
edge this is the first study that focuses on COPD patients
infected by SARS- CoV-2 to evaluate CT findings based
on a quantitative scoring system. A previous study used The limitations of the study were as follows: 1- This
study was conducted retrospectively and in a sin-
gle center. 2- The sample size for the evaluation of
COPD patients with COVID-19 was moderate, and a
large number of patients is required for more detailed Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Page 6 of 8 Page 6 of 8
ipour Khabir et al. European Journal of Medical Research (2023) 28:346
Fig. 1 Receiver operating characteristics curve of COPD patients with COVID-19 for CT severity score of A: left lung, B: right lung, and C: total
ung. Upper lobe: above the carina, middle lobe: below the carina up to the upper limit of the pulmonary vein, and lower lobe: below the inferior
pulmonary vein Fig. 1 Receiver operating characteristics curve of COPD patients with COVID-19 for CT severity score of A: left lung, B: right lung, and C: total
lung. Upper lobe: above the carina, middle lobe: below the carina up to the upper limit of the pulmonary vein, and lower lobe: below the inferior pulmonary vein Funding Funding
This study was supported by Ardabil University of Medical Sciences. Acknowledgements The authors would like to thank student’s research committee of Ardabil Uni-
versity of Medical Sciences that supported this research and also the radiology
department and all of their staff whom without their help this research could
not be proceeded. Availability of data and materials Availability of data and materials
The data sets used and/or analyzed during the current study are available
from the corresponding author on reasonable request. The data sets used and/or analyzed during the current study are available
from the corresponding author on reasonable request. Fig. 2 Kaplan–Meier survival curves during hospitalization
of COVID-19 COPD patients with different cut-off values of A:
lower level of left lung and B: lower level of right lung. Lower lobe:
below the inferior pulmonary vein Discussionh Upper lobe: above the carina, middle lobe: below the carina up to the upper limit of the pulmonary vein, and lower lobe: below the inferior
pulmonary vein Table 5 Receiver operating characteristics (ROC) curves and prognostic accuracy of CT severity score in COVID-19 COPD patients
Upper lobe: above the carina, middle lobe: below the carina up to the upper limit of the pulmonary vein, and lower lobe: below the inferior pulmonary vein
Variables
AUC
95% CI
p-Value
Cut-off
Sensitivity
Specificity (%)
Upper level of left lung
0.760
0.623 to 0.866
0.000
> 3
66.6
78.1
Middle level of left lung
0.682
0.539 to 0.803
0.020
> 4
52.3
84.3
Lower level of left lung
0.682
0.540 to 0.803
0.025
> 4
61.9
84.3
Total level of left lung
0.754
0.616 to 0.862
0.000
> 11
76.1
78.1
Upper level of right lung
0.746
0.607 to 0.885
0.000
> 2
85.7
56.2
Middle level of right lung
0.774
0.638 to 0.877
0.000
> 3
90.4
59.3
Lower level of right lung
0.717
0.577 to 0.832
0.005
> 4
61.9
81.2
Total level of right lung
0.773
0.637 to 0.877
0.000
> 10
85.7
62.5
Total level of lung
0.772
0.637 to 0.876
0.000
> 18
80.9
65.6 Table 5 Receiver operating characteristics (ROC) curves and prognostic accuracy of CT severity score in CO erating characteristics (ROC) curves and prognostic accuracy of CT severity score in COVID-19 COPD patients Page 7 of 8 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 investigations. 3- Although the CT severity score o
patients at admission is used to determine the progno
sis of the disease, but each patient may be hospitalized
Fig. 2 Kaplan–Meier survival curves during hospitalization
of COVID-19 COPD patients with different cut-off values of A:
lower level of left lung and B: lower level of right lung. Lower lobe:
below the inferior pulmonary vein Author contributions MRA, SAK, and YAK were involved in literature search, proposal writing,
data collection, analysis of data, interpreted the patient data, manuscript
preparation, and review of manuscript. HA, BM, and SH were involved in data
collection, interpreted the patient data regarding CT severity score diagnosis,
major contributor in writing the manuscript, and review of manuscript. All the
authors read and approved the final manuscript. Consent for publication
Not applicable. investigations. 3- Although the CT severity score of
patients at admission is used to determine the progno-
sis of the disease, but each patient may be hospitalized
with a different severity of the disease. 4- Different stages
of COPD may have influenced the results of the study,
which could not be evaluated due to the lack of spirome-
try findings. 5- Medicines used by patients to treat COPD
before hospitalization could not be reported due to lack
of registration. Conclusion COPD patients are particularly vulnerable to SARS-
CoV-2 infection as a result of their specific treatments
and accompanying illnesses. Establishing the intensity
of the disease at the start of hospitalization in COPD
patients can manage their treatment effectively. The
current study demonstrated that the CT severity scor-
ing system can be used as a beneficial tool for estimat-
ing disease severity and predict prognosis in COVID-19
COPD patients. Interestingly, the lower lobes of lung
involvement showed an excellent predictive power for
mortality rates in the case of COPD patients infected
with COVID-19. Abbreviations
ACE-2
Angiotensin-converting enzyme 2
COPD
Chronic obstructive pulmonary disease
CT
Computed tomography
COVID-19
Coronavirus disease 2019
ROC
Receiver operating characteristics
SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2 Competing interests The authors have declared no conflict of interest. Ethics approval and consent to participate Ethics approval and consent to participate
This study was approved by the ethics committee of Ardabil University of
Medical Science (IR.ARUMS.REC.1400.312). pp
p
p
This study was approved by the ethics committee of Ardabil University of
Medical Science (IR.ARUMS.REC.1400.312). References Suppression of pulmonary innate host defence in smokers. Thorax. 2009;64(2):144–9. 34. Hosseninia S, Ghobadi H, Garjani K, Hosseini SAH, Aslani MR. Aggre-
gate index of systemic inflammation (AISI) in admission as a reliable
predictor of mortality in COPD patients with COVID-19. BMC Pulm Med. 2023;23(1):107. 13. Mallia P, Message SD, Gielen V, Contoli M, Gray K, Kebadze T, et al. Experimental rhinovirus infection as a human model of chronic
obstructive pulmonary disease exacerbation. Am J Respir Crit Care Med. 2011;183(6):734–42. 35. Ghobadi H, Mohammadshahi J, Tarighi A, Hosseini SAH, Garjani K, Aslani
MR. Prognostic Value of Admission Neutrophil Count in Asthma Patients
with COVID-19: A Comparative Analysis with other Systemic Inflamma-
tion Indices for In-Hospital Mortality Prediction. Iran J Allergy Asthma
Immunol. 2023;1:1–8. 14. Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W, et al. Correlation of chest CT
and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a
report of 1014 cases. Radiology. 2020. https://doi.org/10.1148/radiol.
2020200642. 36. Salaffi F, Carotti M, Tardella M, Borgheresi A, Agostini A, Minorati D, et al. The role of a chest computed tomography severity score in coronavirus
disease 2019 pneumonia. Medicine. 2020;99(42): e22433. 15. Salaffi F, Carotti M, Tardella M, Borgheresi A, Agostini A, Minorati D, et al. The role of a chest computed tomography severity score in coronavirus
disease 2019 pneumonia. Medicine. 2020. https://doi.org/10.1097/MD.
0000000000022433. 37. Mruk B, Plucińska D, Walecki J, Półtorak-Szymczak G, Sklinda K. Chest
computed tomography (CT) severity scales in COVID-19 disease: a valida-
tion study. Med Sci Monit. 2021;27: e931283. 16. Chung M, Bernheim A, Mei X, Zhang N, Huang M, Zeng X, et al. CT imag-
ing features of 2019 novel coronavirus (2019-nCoV). Radiology. 2020. https://doi.org/10.1148/radiol.2020200230. 38. Çetin C, Karaaslan A, Akın Y, Arifoglu M, Rona G, Demirhan R. Relation-
ship of chest computed tomography score with disease severity and
laboratory values in children with COVID-19. J Paediatr Child Health. 2022;58(5):802–8. g
17. Shi H, Han X, Jiang N, Cao Y, Alwalid O, Gu J, et al. Radiological findings
from 81 patients with COVID-19 pneumonia in Wuhan, China: a descrip-
tive study. Lancet Infect Dis. 2020;20(4):425–34. 39. Saylik F, Akbulut T, Oguz M, Sipal A, Ormeci T. Association of echocardio-
graphic parameters with chest computed tomography score in patients
with COVID-19 disease. Adv Med Sci. 2021;66(2):403–10. y
18. Francone M, Iafrate F, Masci GM, Coco S, Cilia F, Manganaro L, et al. References y
y
2020. https://doi.org/10.1371/journal.pone.0241265. 1. Hu B, Guo H, Zhou P, Shi Z-L. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol. 2021;19(3):141–54. 1. Hu B, Guo H, Zhou P, Shi Z-L. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol. 2021;19(3):141–54. 1. Hu B, Guo H, Zhou P, Shi Z-L. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol. 2021;19(3):141–54. 23. Lyu P, Liu X, Zhang R, Shi L, Gao J. The performance of chest CT in evaluat-
ing the clinical severity of COVID-19 pneumonia: identifying critical cases
based on CT characteristics. Invest Radiol. 2020;55(7):412–21. 2. Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, et al. Epidemiological and
clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia
in Wuhan, China: a descriptive study. The lancet. 2020;395(10223):507–13. 2. Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, et al. Epidemiological and
clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia 24. Charpentier E, Soulat G, Fayol A, Hernigou A, Livrozet M, Grand T, et al. Visual lung damage CT score at hospital admission of COVID-19 patients
and 30-day mortality. Eur Radiol. 2021;31(11):8354–63. y
3. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of
patients infected with 2019 novel coronavirus in Wuhan. China The
lancet. 2020;395(10223):497–506. 25. Hansell DM, Bankier AA, MacMahon H, McLoud TC, Muller NL, Remy J. Fleischner society: glossary of terms for thoracic imaging. Radiology. 2008;246(3):697. 4. Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, et al. Clinical course and risk factors
for mortality of adult inpatients with COVID-19 in Wuhan, China: a retro-
spective cohort study. The lancet. 2020;395(10229):1054–62. 26. Ooi GC, Khong PL, Müller NL, Yiu WC, Zhou LJ, Ho JC, et al. Severe acute
respiratory syndrome: temporal lung changes at thin-section CT in 30
patients. Radiology. 2004;230(3):836–44. p
y
5. Wang Y, Lu X, Li Y, Chen H, Chen T, Su N, et al. Clinical course and out-
comes of 344 intensive care patients with COVID-19. Am J Respir Crit
Care Med. 2020;201(11):1430–4. 27. Lim J-K, Park B, Park J, Choi K-J, Jung C-Y, Kim YH, et al. Impact of com-
puted tomography-quantified emphysema score on clinical outcome in
patients with COVID-19. Int J Gen Med. 2021;14:3327–33. 6. Varga Z, Flammer AJ, Steiger P, Haberecker M, Andermatt R, Zinkernagel
AS, et al. References Endothelial cell infection and endotheliitis in COVID-19. The
Lancet. 2020;395(10234):1417–8. 28. Halpin DM, Faner R, Sibila O, Badia JR, Agusti A. Do chronic respiratory
diseases or their treatment affect the risk of SARS-CoV-2 infection? Lancet
Respir Med. 2020;8(5):436–8. 7. Simonnet A, Chetboun M, Poissy J, Raverdy V, Noulette J, Duhamel A,
et al. High prevalence of obesity in severe acute respiratory syndrome
coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation. Obesity. 2020;28(7):1195–9. 7. Simonnet A, Chetboun M, Poissy J, Raverdy V, Noulette J, Duhamel A,
et al. High prevalence of obesity in severe acute respiratory syndrome
coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation. Obesity. 2020;28(7):1195–9. 29. Lippi G, Henry BM. Chronic obstructive pulmonary disease is associated
with severe coronavirus disease 2019 (COVID-19). Respir Med. 2020;167:
105941. 8. Bafadhel M, McKenna S, Terry S, Mistry V, Reid C, Haldar P, et al. Acute
exacerbations of chronic obstructive pulmonary disease: identification
of biologic clusters and their biomarkers. Am J Respir Crit Care Med. 2011;184(6):662–71. 30. Wang B, Li R, Lu Z, Huang Y. Does comorbidity increase the risk of patients
with COVID-19: evidence from meta-analysis. Aging. 2020;12(7):6049. 31. Liu K, Chen Y, Lin R, Han K. Clinical features of COVID-19 in elderly
patients: a comparison with young and middle-aged patients. J Infect. 2020;80(6):e14–8. 9. Mathioudakis AG, Janssens W, Sivapalan P, Singanayagam A, Dransfield
MT, Jensen J-US, et al. Acute exacerbations of chronic obstructive pul-
monary disease: in search of diagnostic biomarkers and treatable traits. Thorax. 2020;75(6):520–7. 32. Ghobadi H, Mohammadshahi J, Javaheri N, Fouladi N, Mirzazadeh Y,
Aslani MR. Role of leukocytes and systemic inflammation indexes (NLR,
PLR, MLP, dNLR, NLPR, AISI, SIR-I, and SII) on admission predicts in-hospital
mortality in non-elderly and elderly COVID-19 patients. Front Med. 2022;9: 916453. 10. Leung JM, Yang CX, Tam A, Shaipanich T, Hackett T-L, Singhera GK, et al. ACE-2 expression in the small airway epithelia of smokers and COPD
patients: implications for COVID-19. Eur Respir J. 2020. https://doi.org/10.
1183/13993003.00688-2020. 33. Mohammadshahi J, Ghobadi H, Matinfar G, Boskabady MH, Aslani MR. Role of Lipid Profile and Its Relative ratios (Cholesterol/HDL-C, triglycer-
ide/HDL-C, LDL-C/HDL-C, WBC/HDL-C, and FBG/HDL-C) on admission
predicts in-hospital mortality COVID-19. J Lipids. 2023;2023:6329873. 11. Milne S, Yang CX, Timens W, Bossé Y, Sin DD. SARS-CoV-2 receptor ACE2
gene expression and RAAS inhibitors. Lancet Respir Med. 2020;8(6):e50–1. 12. Herr C, Beisswenger C, Hess C, Kandler K, Suttorp N, Welte T, et al. References Chest
CT score in COVID-19 patients: correlation with disease severity and
short-term prognosis. Eur Radiol. 2020;30(12):6808–17. 19. Xu X, Yu C, Qu J, Zhang L, Jiang S, Huang D, et al. Imaging and clinical
features of patients with 2019 novel coronavirus SARS-CoV-2. Eur J Nucl
Med Mol Imaging. 2020;47(5):1275–80. Received: 9 March 2023 Accepted: 1 September 2023 21. Li Y, Yang Z, Ai T, Wu S, Xia L. Association of “initial CT” findings with
mortality in older patients with coronavirus disease 2019 (COVID-19). Eur
Radiol. 2020;30(11):6186–93. 22. Emami A, Javanmardi F, Pirbonyeh N, Akbari A. Prevalence of underlying
diseases in hospitalized patients with COVID-19: a systematic review and
meta-analysis. Archives of academic emergency medicine. PLoS ONE. 2020. https://doi.org/10.1371/journal.pone.0241265. Author details 1 Students Research Committee, School of Medicine, Ardabil University
of Medical Sciences, Ardabil, Iran. 2 Department of Radiology, Faculty
of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran. 3 Lung
Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran. 4 Department of Physiology, Faculty of Medicine, Ardabil University of Medical
Sciences, Ardabil, Iran. Page 8 of 8 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Alipour Khabir et al. European Journal of Medical Research (2023) 28:346 Received: 9 March 2023 Accepted: 1 September 2023 Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. 20. Xiao J, Li X, Xie Y, Huang Z, Ding Y, Zhao S, et al. Maximum chest CT score
is associated with progression to severe illness in patients with COVID-19:
a retrospective study from Wuhan. China BMC Infect Dis. 2020;20(1):1–11.
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Population dynamics of epithelial-mesenchymal heterogeneity in cancer cells
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bioRxiv (Cold Spring Harbor Laboratory)
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This may be the author’s version of a work that was submitted/accepted
for publication in the following source: Jain, Paras, Bhatia, Sugandha, Thompson, Rik, & Jolly, Mohit Kumar
(2022)
Population Dynamics of Epithelial-Mesenchymal Heterogeneity in Cancer
Cells. Biomolecules, 12(3), Article number: 348. This file was downloaded from: https://eprints.qut.edu.au/228591/ c⃝2022 The Author(s) This work is covered by copyright. Unless the document is being made available under a
Creative Commons Licence, you must assume that re-use is limited to personal use and
that permission from the copyright owner must be obtained for all other uses. If the docu-
ment is available under a Creative Commons License (or other specified license) then refer
to the Licence for details of permitted re-use. It is a condition of access that users recog-
nise and abide by the legal requirements associated with these rights. If you believe that
this work infringes copyright please provide details by email to qut.copyright@qut.edu.au License: Creative Commons: Attribution 4.0 Notice: Please note that this document may not be the Version of Record
(i.e. published version) of the work. Author manuscript versions (as Sub-
mitted for peer review or as Accepted for publication after peer review) can
be identified by an absence of publisher branding and/or typeset appear-
ance. If there is any doubt, please refer to the published source. https://doi.org/10.3390/biom12030348 https://doi.org/10.3390/biom12030348 Article Paras Jain 1, Sugandha Bhatia 2,3,4, Erik W. Thompson 2,4,* and Mohit Kumar Jolly 1,* Paras Jain 1, Sugandha Bhatia 2,3,4, Erik W. Thompson 2,4,* and Mohit Kumar Jolly 1,* 1 Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
parasjain@iisc.ac.in 2 School of Biomedical Sciences, Faculty of Health, Queensland University of Technology,
Brisbane 4000, Australia; sugandhabhatia05@gmail.com ,
y
, Q
y
gy,
Brisbane 4000, Australia; sugandhabhatia05@gmail.com
3 The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland,
Woolloongabba 4102, Australia 3 The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland
Woolloongabba 4102, Australia 3 The University of Queensland Diamantina Institute, Faculty of Medicin
Woolloongabba 4102, Australia g
ranslational Research Institute, Woolloongabba 4102, Austra * Correspondence: e2.thompson@qut.edu.au (E.W.T.); mkjolly@iisc.ac.in (M.K.J.) * Correspondence: e2.thompson@qut.edu.au (E.W.T.); mkjolly@iisc.ac.in (M.K.J.) Abstract: Phenotypic heterogeneity is a hallmark of aggressive cancer behaviour and a clinical chal‐
lenge. Despite much characterisation of this heterogeneity at a multi‐omics level in many cancers,
we have a limited understanding of how this heterogeneity emerges spontaneously in an isogenic
cell population. Some longitudinal observations of dynamics in epithelial‐mesenchymal heteroge‐
neity, a canonical example of phenotypic heterogeneity, have offered us opportunities to quantify
the rates of phenotypic switching that may drive such heterogeneity. Here, we offer a mathematical
modeling framework that explains the salient features of population dynamics noted in PMC42‐LA
cells: (a) predominance of EpCAMhigh subpopulation, (b) re‐establishment of parental distributions
from the EpCAMhigh and EpCAMlow subpopulations, and (c) enhanced heterogeneity in clonal pop‐
ulations established from individual cells. Our framework proposes that fluctuations or noise in
content duplication and partitioning of SNAIL—an EMT‐inducing transcription factor—during cell
division can explain spontaneous phenotypic switching and consequent dynamic heterogeneity in
PMC42‐LA cells observed experimentally at both single‐cell and bulk level analysis. Together, we
propose that asymmetric cell division can be a potential mechanism for phenotypic heterogeneity. Citation: Jain, P.; Bhatia, S.;
Thompson, E.W.; Jolly, M.K. Population Dynamics of
Epithelial‐Mesenchymal
Heterogeneity in Cancer Cells. Biomolecules 2022, 12, 348. https://doi.org/10.3390/biom12030348
Academic Editor: Joe S. Mymryk
Received: 21 January 2022
Accepted: 18 February 2022
Published: 23 February 2022 Keywords: asymmetric cell division; epithelial‐mesenchymal heterogeneity; epithelial‐mesenchymal
plasticity; population dynamics Academic Editor: Joe S. Mymryk Population Dynamics of Epithelial‐Mesenchymal
Heterogeneity in Cancer Cells Paras Jain 1, Sugandha Bhatia 2,3,4, Erik W. Thompson 2,4,* and Mohit Kumar Jolly 1,* 1. Introduction For instance, any of the three (E, M, hybrid E/M) subpopulations isolated and cul‐
tured from prostate tumor cells (PKV cell line) could give rise to other subpopulations in
different proportions within two weeks in vitro [8]. Similarly, in vivo, subcutaneous trans‐
plantation of different SCC tumor subpopulations with varied EMT status led to a sus‐
tained co‐existence of diverse phenotypes in the corresponding tumors [9]. These trends
indicated the role of bidirectional phenotypic plasticity in promoting the emergence of E‐
M heterogeneity. The phenotypic distribution of a cell population can vary across cell lines and single‐
cell clones generated from a cell line. For example, in a study across six different breast
cancer cell lines, while four of them were largely homogenous in terms of relative levels
of EpCAM (Epithelial Cell Adhesion Molecule—a common epithelial marker), two of
them—HCC38 and HCC1143—had a 90:10 and 99:1 ratio of EpCAMhigh to EpCAMlow cells
respectively [19]. Similarly, the PMC42‐LA cell line comprised 80% EpCAMhigh cells and
20% EpCAMlow [20], with the latter showing canonical mesenchymal morphological (spin‐
dle‐shaped) and molecular (higher levels of EMT‐transcription factors SNAIL, SLUG,
ZEB1 and mesenchymal markers VIM and FN1) traits. When these two subpopulations
were segregated and cultured separately, they returned to an 80:20 parental population
distribution within 8 weeks. However, the single‐cell clones established from PMC42‐LA
showed a more diverse phenotypic distribution in terms of ratios of EpCAMhigh to Ep‐
CAMlow cells. Importantly, these different clones had varied migratory, invasive, tumor‐
initiating and drug resistance features, indicating that the ratio of cells in different pheno‐
types can influence the overall ‘fitness’ of the population for invasion‐metastasis cascade. Similar molecular and functional diversity for single‐cell clones was reported in another
breast cancer cell line SUM149PT [21]. However, how these different subpopulation ratios
are achieved and maintained remains elusive. Here, we show, using a mathematical modelling approach, that in a cell population
carrying the EMT regulatory network (miR‐200/ZEB/SNAIL) [22], noise or fluctuations in
processes of content duplication and partitioning of biomolecules can drive asymmetric
cell division and can explain the observations for PMC42‐LA system. We consider the
influence of these fluctuations on the inherited levels of EMT‐transcription factor SNAIL
by the two daughter cells. SNAIL regulates the levels of ZEB and miR‐200 in a cell that
collectively defines its EMT status [22,23]. 1. Introduction Intra‐tumor heterogeneity is a major roadblock that thwarts multiple therapeutic ap‐
proaches in the clinic [1]. It has earlier been largely thought of as existing at a genomic
level, i.e., co‐existence of many sub‐clonal populations. Single‐cell genomic analysis has
helped construct the lineage trees mirroring clonal evolution [2]. However, recent preclin‐
ical (in silico, in vitro, in vivo) and clinical observations have emphasised that besides
genetic heterogeneity, tumors exhibit substantial non‐genetic heterogeneity as well, often
referred to as phenotypic heterogeneity [3–5]. Non‐genetic heterogeneity can facilitate ‘bet
hedging’ in a cancer cell population, thus enhancing its fitness under stressed conditions
(immune attack, targeted therapy, etc.) and enabling the survival of subpopulations that
can eventually drive tumor relapse and/or metastasis [6,7]. Therefore, identifying the
mechanisms underlying non‐genetic heterogeneity is of fundamental importance. Publisher’s Note: MDPI stays neu‐
tral with regard to jurisdictional
claims in published maps and institu‐
tional affiliations. Copyright: © 2022 by the authors. Li‐
censee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and con‐
ditions of the Creative Commons At‐
tribution (CC BY) license (https://cre‐
ativecommons.org/licenses/by/4.0/). A canonical example of intra‐tumor phenotypic heterogeneity is along the epithelial‐
mesenchymal axis. Epithelial‐Mesenchymal Transition (EMT) and its reverse Mesenchy‐
mal‐Epithelial Transition (MET) were initially considered as binary processes, but recent
investigations across carcinomas, especially those at a single‐cell level, have demonstrated www.mdpi.com/journal/biomolecules Biomolecules 2022, 12, 348. https://doi.org/10.3390/biom12030348 Biomolecules 2022, 12, 348 2 of 20 2 of 20 that cancer cells can display many hybrid epithelial/mesenchymal (E/M) phenotypes in
vitro and in vivo, as well as in patient samples [8–16]. Depending upon the combination
of markers used in a specific study, cancer cells can be classified into two or more pheno‐
types—Epithelial (E), Mesenchymal (M) and the hybrid E/M one(s) [17]. However, most
studies focus on a static snapshot of E‐M heterogeneity, with little longitudinal data that
can help unravel the set of underlying mechanisms initiating and sustaining this hetero‐
geneity. g
y
A few investigations into the population dynamics of E‐M heterogeneity have re‐
vealed that when these phenotypically diverse subpopulations of cells are sorted by FACS
(Fluorescent activated cell sorting) and cultured independently, over time, they can often
give rise to other phenotypes in the parental population. These observations are reminis‐
cent of stochastic cell‐state transitions seen among cancer stem cells (CSCs) and non‐CSCs
[18]. 1. Introduction The extent of fluctuations in SNAIL levels has
been assumed to be proportional to SNAIL levels of the dividing parent cell. Due to the
fluctuations in its inherited levels, we can observe three cell division types: (1) symmetric
division—when both daughter cells have the same phenotype as the parent cell, (2) asym‐
metric division—when one daughter has a phenotype different than parent cell, and (3)
divergent division—when both daughters have a phenotype different than that of the par‐
ent. This phenomenon recapitulates the spontaneous phenotypic switching among sub‐
populations with varied EMT statuses. Our model simulations can explain the observa‐
tions in PMC42‐LA cells—(a) the dominance of EpCAMhigh subpopulation over EpCAMlow
subpopulation and (b) heterogeneity in EpCAM profile in single‐cell clones. Thus, our Biomolecules 2022, 12, 348 3 of 20 3 of 20 results propose a possible mechanism that may underlie how non‐genetic heterogeneity
is generated in an isogenic cancer cell population. results propose a possible mechanism that may underlie how non‐genetic heterogeneity
is generated in an isogenic cancer cell population. 2.1. Asymmetric Distribution of Molecular Content on Cell Division Following the method proposed earlier [24], we consider fluctuations in the levels of
cellular content during its inheritance by daughter cells on cell division. These fluctuations
arise due to both imperfect duplication during the cell cycle and later asymmetric parti‐
tioning to the daughter cells. We propose these fluctuations to be proportional to the
amount of the molecular content available in the dividing parent cell itself. Considering
𝑆𝑁𝐴𝐼𝐿
denotes SNAIL level in a cell right after its division. Now, during the cell cycle
SNAIL content will approximately double, so that right before the next cell division we
can write: 𝑆𝑁𝐴𝐼𝐿ൌ 2 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
(1) (1) where, 𝜂ଵ
ᇱ is a stochastic scaling factor that determines the fluctuation due to imperfect
molecule duplication. Next, when a parent cell partitions its molecular content to two daughter cells during
cell division, SNAIL levels in each daughter can be specified as: 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଵ
ൌ 𝑆𝑁𝐴𝐼𝐿
2
𝜂ଶ
ᇱ 𝑆𝑁𝐴𝐼𝐿 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଵ
ൌ 𝑆𝑁𝐴𝐼𝐿
2
𝜂ଶ
ᇱ 𝑆𝑁𝐴𝐼𝐿
On substituting 𝑆𝑁𝐴𝐼𝐿 from (1),
𝑁𝐴𝐼𝐿ௗ௨௧ଵ
ൌ 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
2
𝜂ଶ
ᇱ ሺ2 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
ሻ
(2) 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଵ
ൌ 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
2
𝜂ଶ
ᇱ ሺ2 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
ሻ
(2) (2) And, for the other daughter cell And, for the other daughter cell 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଶ
ൌ 𝑆𝑁𝐴𝐼𝐿
2
െ 𝜂ଶ
ᇱ 𝑆𝑁𝐴𝐼𝐿
On substituting 𝑆𝑁𝐴𝐼𝐿 from (1),
𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଶ
ൌ 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
2
െ 𝜂ଶ
ᇱ ሺ2 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ
ᇱ 𝑆𝑁𝐴𝐼𝐿
ሻ
(3) 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଶ
ൌ 𝑆𝑁𝐴𝐼𝐿
2
െ 𝜂ଶ
ᇱ 𝑆𝑁𝐴𝐼𝐿 (3) where, 𝜂ଶ
ᇱ another random scaling factor determining the fluctuation in SNAIL levels due
to partitioning at the time of cell division. We consider stochastic scaling factors 𝜂ଵ
ᇱ and 𝜂ଶ
ᇱ to be two independent normally
distributed random variables with zero means and 𝜂ଵ and 𝜂ଶ as standard deviations,
i.e., 𝜂ଵ
ᇱൌ 𝜂ଵ𝑁ଵሺ0,1ሻ and 𝜂ଶ
ᇱൌ 𝜂ଶ𝑁ଶሺ0,1ሻ 𝜂ଵ
ᇱൌ 𝜂ଵ𝑁ଵሺ0,1ሻ and 𝜂ଶ
ᇱൌ 𝜂ଶ𝑁ଶሺ0,1ሻ where, 𝑁ሺ0,1ሻ, 𝑖ൌ1, 2 represents a standard normal random variable. Hereafter, 𝜂ଵ
and 𝜂ଶ are referred to as scaling factors for noise in SNAIL molecules’ duplications &
partitioning, respectively. 2.1. Asymmetric Distribution of Molecular Content on Cell Division Thus, Equations (2) and (3) can be rewritten as: 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଵ
ൌ 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ𝑁ଵሺ0,1ሻ 𝑆𝑁𝐴𝐼𝐿
2
𝜂ଶ𝑁ଶሺ0,1ሻ ሺ2 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ𝑁ଵሺ0,1ሻ 𝑆𝑁𝐴𝐼𝐿
ሻ
(4) (4) 𝑆𝑁𝐴𝐼𝐿ௗ௨௧ଶ
ൌ 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ𝑁ଵሺ0,1ሻ 𝑆𝑁𝐴𝐼𝐿
2
െ 𝜂ଶ𝑁ଶሺ0,1ሻ ሺ2 𝑆𝑁𝐴𝐼𝐿
𝜂ଵ𝑁ଵሺ0,1ሻ 𝑆𝑁𝐴𝐼𝐿
ሻ
(5) (5) 𝜂ଵ𝑁ଵሺ0,1ሻ 𝑆𝑁𝐴𝐼𝐿
ሻ Biomolecules 2022, 12, 348 4 of 20 4 of 20 Equations (4) and (5) are used to assign SNAIL values to the daughter cells when a
cell division happens. Further, the same equations were used when stochastics effects
were included in the other players of the EMT network (ZEB, mZEB and miR200) at the
time of cell division. 𝐿ሺ𝜇ሻൌቀ𝑛
𝑖ቁ𝑙𝑀ሺ𝜇ሻ
ୀ
𝑌ሺ𝜇ሻൌቀ𝑛
𝑖ቁ𝛾𝑀ሺ𝜇ሻ
ୀ
𝑌ఓሺ𝜇ሻൌቀ𝑛
𝑖ቁ𝛾ఓ𝑀ሺ𝜇ሻ
ୀ
𝑀ሺ𝜇ሻൌ
൬𝜇
𝜇൰
൬1.0 𝜇
𝜇൰
2.2. Dynamics of Core EMT Regulatory Network The dynamics of a core regulatory circuit involving interaction in canonical epithelial
(miR200) and mesenchymal (mRNA ZEB and ZEB protein) markers was modelled to ex‐
plain EMT and MET, based on SNAIL levels [22]. miR200 and ZEB (mRNA and protein)
mutually repress each other, and SNAIL suppresses miR200 levels and activates ZEB at
the mRNA level. The steady state response of the circuit was analysed for a relevant bio‐
logical parameter set, which gave a bifurcation diagram showing distinct possible stable
ranges of ZEB and miR200 based on SNAIL levels as shown in Figure 1D. The ordinary
differential equations describing the regulation dynamics and model parameters have
been described in Tables 1 and 2 [22]. The system’s ODEs are listed below: 𝑑𝜇ଶ
𝑑𝑡
ൌ𝑔ఓమబబ𝐻൫𝑍, 𝜆
ఓమబబ൯𝐻൫𝑆, 𝜆ௌ
ఓమబబ൯െ𝑚𝑌ఓሺ𝜇ଶሻെ𝑘ఓమబబ𝜇ଶ 𝑑𝑚
𝑑𝑡ൌ𝑔ೋ𝐻൫𝑍, 𝜆
ೋ൯𝐻൫𝑆, 𝜆ௌ
ೋ൯െ𝑚𝑌ሺ𝜇ଶሻെ𝑘ೋ𝑚 𝑑𝑍
𝑑𝑡ൌ𝑔𝑚𝐿ሺ𝜇ଶሻെ𝑘𝑍 𝑑𝑆
𝑑𝑡ൌ0 Here, 𝜇ଶൌ [miR‐200], 𝑚ൌ [ZEB1 mRNA], 𝑍ൌ [ZEB1], and 𝑆ൌ [SNAI1]. [⋅] rep‐
resents the concentration of a molecular species within a cell. 𝐻 is the shifted Hill function. 𝐻ሺ𝐵, 𝜆ሻൌ𝜆
1.0 െ𝜆
1.0 ቀ𝐵
𝐵ቁ
ಳ The functions 𝑌ఓ, 𝑌, and 𝐿 describe the post‐transcriptional regulation of mRNA
activity by micro‐RNAs and have been described in [22]. 𝐿ሺ𝜇ሻൌቀ𝑛
𝑖ቁ𝑙𝑀ሺ𝜇ሻ
ୀ
𝑌ሺ𝜇ሻൌቀ𝑛
𝑖ቁ𝛾𝑀ሺ𝜇ሻ
ୀ
𝑌ఓሺ𝜇ሻൌቀ𝑛
𝑖ቁ𝛾ఓ𝑀ሺ𝜇ሻ
ୀ
𝑀ሺ𝜇ሻൌ
൬𝜇
𝜇൰
൬1.0 𝜇
𝜇൰
5 of 20 Biomolecules 2022, 12, 348 Here, 𝜇 is the concentration of the micro‐RNA and 𝑛 is the number of micro‐RNA
binding sites on the mRNA. For the inhibition of ZEB1 mRNA by miR‐200, 𝑛ൌ6 and
𝜇ൌ 𝜇ଶ
. The values of all kinetic parameters are listed in Tables 1 and 2. Figure 1. Model description for population growth accompanying E‐M heterogeneity. (A) Schematic
showing existing E‐M heterogeneity among cancer cells and their spontaneous phenotypic switch‐
ing. Here, each cell is depicted by a cell membrane enclosing a nucleus (oval object) and a biomole‐
cule/organelle (rectangular/dashed object) that are shown to be asymmetrically distributed in cer‐
tain cell division events. (B) Schematic for asymmetric distribution of biomolecules among daughter
cells as a potential cause of spontaneous phenotypic switching. (C) Each cell in the population is
assigned with a core EMT network. It can divide or die in a given time step depending upon dou‐
bling and death rates. When it divides, each daughter cell inherits parent SNAIL levels taking into
consideration of fluctuations in its content duplication and partitioning during cell division. 2.3.1. Generation of Population as per Initial Phenotypic Fraction 2.3.1. Generation of Population as per Initial Phenotypic Fraction Each cell in the system is represented by a set of four variables that hold the levels of
miR200, mRNA ZEB, ZEB protein and SNAIL protein for that cell. Random SNAIL values
are sampled from a log‐normal distribution with median 200 × 103 and coefficient of vari‐
ance 1 and all possible stable states corresponding to that SNAIL value are used to initial‐
ize the cells’ variables. For example, if sampled SNAIL = 200 K and as for this value all
three phenotype—E, E/M and M—are stable. So, three cells are initialised with steady state
values of all variables corresponding to each phenotype. Initialization of a cell from a phe‐
notypic state is stopped when its required count in the population is achieved. 2.3.3. Population Growth The population growth is simulated using Gillespie’s Stochastic Simulation (SSA) al‐
gorithm [25], where six events—three division and three death events for each phenotype
are considered. The propensity of occurrence of an event is determined by its average rate
as described above. The SSA algorithm tells what the next event will be and at what time
point. Now, if the next event is a division of a cell of the E phenotype and will occur at t1
time, then a cell is uniformly sampled from the pool of cells of that phenotype, and its
molecular levels are updated using ODEs for the time gap (t1–t0), where t0 is the time point
of last most recent event. Then, a new cell is initialised in the population with molecular
levels same as that of the parent E cell, but with perturbed SNAIL levels. Similarly, the
parent cell SNAIL levels are perturbed to account for the second daughter cell on division. For a cell death of a phenotype, a cell is uniformly sampled from the pool of cells of that
phenotype, and it is erased from the population. Molecular levels of all the other undi‐
vided/unaffected cells are updated using ODEs for the time gap (t1–t0). 2.3.2. Avg. Birth and Death Rate of Cells In the cell population, the division rate of cells of a particular phenotype follows the
logistic equation shown below: 𝑟ൌ𝑟
𝑁 ሺ1 െ𝑁௧௧
𝐾ሻ And the death rate of cells of a particular phenotype is as follows: 𝑑ൌ𝑑
𝑁 𝑑ൌ𝑑
𝑁 where,
𝑝ℎ𝑒𝑛: E, E/M, M
𝑟: avg. doubling rate
𝑑: death rate
𝑟
: max. average doubling rate of an individual cell
𝑑
: average death rate of an individual cell
𝑁: total cells of a phenotype
𝑁௧௧ : total cells in the population
K: Carrying capacity of the system 2.2. Dynamics of Core EMT Regulatory Network (D)
Different stable (blue curves) ZEB mRNA levels based on SNAIL levels. Low, medium and high
ZEB mRNA levels correspond to Epithelial (E), Hybrid (E/M), and Mesenchymal (M) phenotypes
respectively. This bifurcation diagram is for the miR‐200/ZEB feedback loop driven by SNAIL, as
adapted from Lu et al. PNAS 2013 [22]. (E) Schematic for in‐silico passaging; adapted from
htt
//f
/i
f
ll
lt
di h
d
10 D
b
2021 (F) F
li
f
ll Here, 𝜇 is the concentration of the micro‐RNA and 𝑛 is the number of micro‐RNA
binding sites on the mRNA. For the inhibition of ZEB1 mRNA by miR‐200, 𝑛ൌ6 and
𝜇ൌ 𝜇ଶ
. The values of all kinetic parameters are listed in Tables 1 and 2. Figure 1. Model description for population growth accompanying E‐M heterogeneity. (A) Schematic
showing existing E‐M heterogeneity among cancer cells and their spontaneous phenotypic switch‐
ing. Here, each cell is depicted by a cell membrane enclosing a nucleus (oval object) and a biomole‐
cule/organelle (rectangular/dashed object) that are shown to be asymmetrically distributed in cer‐
tain cell division events. (B) Schematic for asymmetric distribution of biomolecules among daughter
cells as a potential cause of spontaneous phenotypic switching. (C) Each cell in the population is
assigned with a core EMT network. It can divide or die in a given time step depending upon dou‐
bling and death rates. When it divides, each daughter cell inherits parent SNAIL levels taking into
consideration of fluctuations in its content duplication and partitioning during cell division. (D)
Different stable (blue curves) ZEB mRNA levels based on SNAIL levels. Low, medium and high
ZEB mRNA levels correspond to Epithelial (E), Hybrid (E/M), and Mesenchymal (M) phenotypes
respectively. This bifurcation diagram is for the miR‐200/ZEB feedback loop driven by SNAIL, as
adapted from Lu et al. PNAS 2013 [22]. (E) Schematic for in‐silico passaging; adapted from
https://freesvg.org/image‐of‐cell‐culture‐dish, accessed on 10 December 2021. (F) Formalism for cell
doubling and death rates for all three phenotypes (E, E/M, and M) of cells. Biomolecules 2022, 12, 348 6 of 20 2.3. Simulation of Population Dynamics 2.3. Simulation of Population Dynamics 3. Results 3.1. Dominance of Epithelial Cells in the Population over Time Irrespective of Initial Distribution o i a
e of Epi
e ia
e
i
e
opu a io
o e
i e I e pe i e of I i ia
i
i u io
Here, we have developed a population dynamics framework to explain the emer‐
gence of epithelial‐mesenchymal heterogeneity in a given population, and the contribu‐
tion of spontaneous state switching in enabling this heterogeneity (Figure 1A). Specifi‐
cally, we consider phenotypic switching to occur during cell division (Figure 1B), where
two factors can contribute to a daughter cell having a phenotype different than its parent
cell: noise or fluctuations in (i) content duplication and that in (ii) partitioning of biomol‐
ecules, particularly in SNAIL (depicted by 𝑓ሺ𝑆𝑁𝐴𝐼𝐿, 𝜂ଵ
ᇱ, 𝜂ଶ
ᇱሻ) (Figure 1C). (For more in‐
formation on formalism used to include content duplication and partitioning noise, please
refer to Methods Section 2.1). Each cell contains the ZEB1/miR‐200 feedback loop driven
by SNAIL, and the levels of these molecules define the state of each cell. Depending on
the levels of SNAIL, cells may acquire a phenotype among all the stable ones, as shown in
the bifurcation diagram (Figure 1D) [22]. At SNAIL = 150 K molecules, all cells can adopt
only an epithelial state (lower blue curve in Figure 1D); at SNAIL = 200 K molecules, a cell
can acquire any of the three states—epithelial (E; lower blue curve), mesenchymal (M; top
blue curve) or hybrid E/M (middle blue curve), while at SNAIL = 250 K molecules, all cells
adopt a mesenchymal state (top blue curve in Figure 1D). Thus, asymmetry in content
duplication and/or partitioning of SNAIL levels can alter the SNAIL values sufficiently
enough to allow a phenotypic switch. For instance, if one daughter cell has SNAIL = 250
K for a parent cell with SNAIL = 200 K, then the daughter cell will be mesenchymal in
nature irrespective of the phenotype of the parent cell (E, hybrid E/M or M). We have also
implemented in silico passaging to mimic the experimental protocol for conducting these
experiments, where 10% of the cell population is passaged maintaining the distribution of
cells in different phenotypes when the entire population reaches 80% of its carrying ca‐
pacity (Figure 1E). 2.4. Cell Doubling Quantification Images for PMC42‐LA cells were captured on PhaseFocus LiveCyte Image Scanner
(Phase Focus, Sheffield, UK) with 10× magnification; individual images were captured
every 11 min for a span of 48 h. Imaging selected regions of interest (ROI) were 750 × 750
μm. Sixty individual selected cells were randomly selected and then manually tracked
from cytokinesis of a cell to two daughter cells to next cytokinesis to determine the exact
cell doubling time. 7 of 20 Biomolecules 2022, 12, 348 Table 1. Kinetic parameters for the EMT circuit ODE model
Parameter
Value
Parameter
Value
𝒈𝝁𝟐𝟎𝟎
2.1 ൈ10ଷ 𝑚𝑜𝑙. ℎିଵ
𝒏𝒁
𝝁𝟐𝟎𝟎
3
𝒈𝒎𝒁
11.0 𝑚𝑜𝑙. ℎିଵ
𝒏𝑺
𝝁𝟐𝟎𝟎
2
𝒈𝒁
0.1 ൈ10ଷ ℎିଵ
𝒏𝒁
𝒎𝒁
2
𝒌𝝁𝟐𝟎𝟎
0.05 ℎିଵ
𝒏𝑺
𝒎𝒁
2
𝒌𝒎𝒁
0.5 ℎିଵ
𝝀𝒁
𝝁𝟐𝟎𝟎
0.1
𝒌𝒁
0.1 ℎିଵ
𝝀𝑺
𝝁𝟐𝟎𝟎
0.1
𝒁𝟎
𝝁𝟐𝟎𝟎
220.0 ൈ10ଷ 𝑚𝑜𝑙. 𝝀𝒁
𝒎𝒁
7.5
𝑺𝟎
𝝁𝟐𝟎𝟎
180.0 ൈ10ଷ 𝑚𝑜𝑙. 𝝀𝑺
𝒎𝒁
10.0
𝒁𝟎
𝒎𝒁
25.0 ൈ10ଷ𝑚𝑜𝑙. 𝝁𝟐𝟎𝟎
𝟎
10000
𝑺𝟎
𝒎𝒁
180.0 ൈ10ଷ 𝑚𝑜𝑙. Table 2. Kinetic parameters for the EMT circuit ODE model
No. Of Mirna
Binding Sites
0
1
2
3
4
5
6
𝒍𝒊
1.0
0.6
0.3
0.1
0.05
0.05
0.05
𝜸𝒎𝒊 ሺ𝒉ି𝟏ሻ
0.0
0.04
0.2
1.0
1.0
1.0
1.0
𝜸𝝁𝒊 ሺ𝒉ି𝟏ሻ
0.0
0.005
0.05
0.5
0.5
0.5
0.5
Here, 𝑚𝑜𝑙. ≡𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑒𝑠/𝑐𝑒𝑙𝑙
3. Results Table 1. Kinetic parameters for the EMT circuit ODE model Table 2. Kinetic parameters for the EMT circuit ODE model No. Of Mirna
Binding Sites
0
1
2
3
4
5
6
𝒍𝒊
1.0
0.6
0.3
0.1
0.05
0.05
0.05
𝜸𝒎𝒊 ሺ𝒉ି𝟏ሻ
0.0
0.04
0.2
1.0
1.0
1.0
1.0
𝜸𝝁𝒊 ሺ𝒉ି𝟏ሻ
0.0
0.005
0.05
0.5
0.5
0.5
0.5
Here, 𝑚𝑜𝑙. ≡𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑒𝑠/𝑐𝑒𝑙𝑙 3. Results Further, the division rate of each subpopulation of cells is considered
to follow the logistic growth rate, whereas the death rate is directly proportional to the
subpopulation size (Figure 1F). Together, these factors are incorporated in a population
dynamics model including cell division which may be accompanied by a phenotypic
switch (please see Methods sections 2.2, 2.3 for more details about the population dynam‐
ics model). Biomolecules 2022, 12, 348 8 of 20 8 of 20 Using this framework, we investigated how the population distribution emerged
over time as we started with different initial fractions, and whether we can recapitulate
the dominance of epithelial (EpCAMhigh) subpopulation over a mesenchymal (EpCAMlow)
one as seen experimentally (Figure 2A) [20]. We first experimentally quantified the dou‐
bling time of PMC42‐LA cells to be 22.67 ± 2.77 h (Figure 2A). We started our simulations
with four distinct initial conditions: (1) Epithelial dominated (initial fraction E: E/M: M =
0.7: 0.1: 0.2), (2) Mesenchymal dominated (initial fraction E: E/M: M = 0.2: 0.1: 0.7), Hybrid
dominated (initial fraction E: E/M: M = 0.1: 0.7: 0.2), and mixed fractions (initial fraction E:
E/M: M = 0.4: 0.2: 0.4). In these simulations, we considered an average doubling time of
the population to be 20 h, η1 (scaling factor for noise due to SNAIL molecules’ duplication)
= 0.2 and η2 (scaling factor for noise due to SNAIL molecules’ partitioning) = 0.1, and
tracked the population distribution as a function of time. This choice of values represents
typical coefficient of variance values in protein levels reported in human H1299 lung car‐
cinoma cells [26]. We observed that all the initial fractions converged to an epithelial dominant popu‐
lation over a period of 16 weeks (Figure 2B), i.e., greater than or equal to 80% population
being E (EpCAMhigh). Particularly, for a mixed initial fraction (E: E/M: M = 0.4: 0.2: 0.4),
most of the hybrid E/M cells switch phenotype either to E or M within 2 weeks of time,
after which population is mostly comprised of E and M cells, which eventually converges
to an epithelial dominant one. 3. Results Time to Attain Epithelial Dominance Depends on Initial Fractions, Doubling Times of
Phenotypes and the Extent of Stochastic Fluctuations during Cell Division 3. Results Concomitantly, there is also a shift in the distribution of
SNAIL levels, such that the range of SNAIL values observed tend to correspond to an
epithelial phenotype as well by week 16 and 32, as compared to week 0 (Figure 2C),
thereby explaining a gain in the epithelial‐dominated subpopulation as seen experimen‐
tally, i.e., the EpCAMhigh subpopulation constituting the majority of the PMC42‐LA cell
line [20]. Further experiments revealed that this population distribution can be repro‐
duced by the FACS‐sorted EpCAMhigh and EpCAMlow subpopulations when cultured in‐
dividually, thus reminiscent of our simulations showing the asymptotic dominance of ep‐
ithelial subpopulation irrespective of initial phenotypic distributions. Over longer simulation times in our model, the dominance of the epithelial fraction
grew even stronger (Figure S1A). Thus, while our model encapsulates the dominance of
EpCAMhigh subpopulation in PMC42‐LA cells, it cannot accurately reproduce the experi‐
mentally observed 80:20 EpCAMhigh: EpCAMlow ratio. This lacuna indicates the role of var‐
ious important factors (both cell‐autonomous and non‐cell‐autonomous: chromatin status
and cellular communication, for instance, respectively) which can influence stochastic
fluctuations during cell division induced spontaneous switching, thus altering this ratio. Nonetheless, our simple phenomenological model can reproduce salient features of pop‐
ulation dynamics reported in the PMC42‐LA cell line [20]. 9 of 20 Biomolecules 2022, 12, 348 Figure 2. Dominance of the epithelial (EpCAMhigh) phenotype in the population over time for mul‐
tiple initial distributions. (A) Phenotypic distribution of EpCAMhigh and EpCAMlow subpopulations
in PMC42‐LA cells (left—adapted from Bhatia et al. J Clin Med [20]), and their observed doubling
time distribution (right). (B) Changes in phenotypic fraction over time starting with different frac‐
tions of E, E/M, and M cells in the population. (C) Change in the distribution range of SNAIL levels
over 32 weeks for two different initial conditions. Average doubling time (DT) of each phenotype is
set to 20 h and scaling factors η1 and η2 to 0.2 and 0.1. The initial population size was 200 cells. Mean
and standard deviation calculated from 16 independent runs. Figure 2. Dominance of the epithelial (EpCAMhigh) phenotype in the population over time for mul‐ Figure 2. Dominance of the epithelial (EpCAMhigh) phenotype in the population over time for mul‐
tiple initial distributions. (A) Phenotypic distribution of EpCAMhigh and EpCAMlow subpopulations
in PMC42‐LA cells (left—adapted from Bhatia et al. J Clin Med [20]), and their observed doubling
time distribution (right). 3. Results (B) Changes in phenotypic fraction over time starting with different frac‐
tions of E, E/M, and M cells in the population. (C) Change in the distribution range of SNAIL levels
over 32 weeks for two different initial conditions. Average doubling time (DT) of each phenotype is
set to 20 h and scaling factors η1 and η2 to 0.2 and 0.1. The initial population size was 200 cells. Mean
and standard deviation calculated from 16 independent runs. ip e i i ia
i
i u io
(A)
e o ypi
i
i u io
o Ep A
a
Ep A
u popu a io
in PMC42‐LA cells (left—adapted from Bhatia et al. J Clin Med [20]), and their observed doubling
time distribution (right). (B) Changes in phenotypic fraction over time starting with different frac‐
tions of E, E/M, and M cells in the population. (C) Change in the distribution range of SNAIL levels
over 32 weeks for two different initial conditions. Average doubling time (DT) of each phenotype is
set to 20 h and scaling factors η1 and η2 to 0.2 and 0.1. The initial population size was 200 cells. Mean
and standard deviation calculated from 16 independent runs. To assess how fluctuations in other players of the EMT network (miR‐200, ZEB) in‐
fluence population dynamics, we introduced stochasticity in their content duplication and
partitioning during cell division, rather than just in SNAIL levels. The population dynam‐
ics for this scenario, using the parameters and initial fractions described above, gave qual‐
itatively similar results of epithelial dominance over mesenchymal, though the time taken
to gain this dominance was shorter in this case (Figure S1B–C), indicating that additional
noise can accelerate the system dynamics. These results suggest that accounting for asym‐
metry in the levels of SNAIL is sufficient to capture the qualitative population dynamics
for PMC42‐LA cells. The dominance of the epithelial phenotype in a population over time irrespective of
initial fractions of phenotypes points towards the possibility that hybrid E/M and mesen‐
chymal cells switch more frequently to epithelial as compared to epithelial states switch‐
ing to hybrid E/M and mesenchymal. This one‐sided higher switching rate can be ex‐
plained by the multiplicative nature of noise considered (lower levels of SNAIL in epithe‐
lial cells invoke further fewer fluctuations during division) and have been quantified later. 3.2. 3.2. Time to Attain Epithelial Dominance Depends on Initial Fractions, Doubling Times of
Phenotypes and the Extent of Stochastic Fluctuations during Cell Division Upon simulating the population dynamics starting with purely E and purely M phe‐
notypes, we noticed differences in the mean epithelial (E) fraction at week 16 (Figure 3A). When starting with the purely M phenotype, it took 16 weeks to arrive at an epithelial‐
dominant population as compared to starting with the hybrid E/M (8–12 weeks) or fully E
ones. This trend raised the possibility that while initial phenotypic distribution may not
alter the steady state itself, it can change the time taken to arrive at it. For the scenario
starting with purely hybrid E/M cells, within 4 weeks the population structure had ap‐ Biomolecules 2022, 12, 348 10 of 20 10 of 20 proximately 60–70% epithelial cells, thus its dynamics post the 4 week timepoint is under‐
standably similar to that seen for E:E/M:M = 0.7:0.1:0.2 scenario (compare middle panel in
Figure 3A with the top left panel in Figure 2B). Figure 3A with the top left panel in Figure 2B). Figure 3. Time to attain dominance of E cells depends on initial fraction and average doubling tim
of phenotypes, and the extent of molecular fluctuations. (A) Temporal changes in phenotypic d
tribution for purely E, E/M, and M initial population. (B) Temporal changes in phenotypic distrib
tion when there is heterogeneity in average doubling time (DT) among phenotypes. DT(E/M, M
DT ratio * DT(E). η1 = 0.2, and η2 = 0.1. (C) Temporal changes in phenotypic distribution for fixed
and varying η2 values. Here, DT(E, E/M, M) = 20 h. (D) Same as (C) but with varying η1 and fixed
values. In all, except (A), initial fractions of (1) Mix of E/M and M, and (2) pure E phenotypes
considered. The initial population size was 200 cells. Mean and standard deviation calculated fro
16 independent runs. Besides initial phenotypic distribution, another factor that can impact the populati
d
i
i
d
bli
i
(DT) S
f
id
d h
DT f
E E/ Figure 3. Time to attain dominance of E cells depends on initial fraction and average doubling times
of phenotypes, and the extent of molecular fluctuations. (A) Temporal changes in phenotypic dis‐
tribution for purely E, E/M, and M initial population. (B) Temporal changes in phenotypic distribu‐
tion when there is heterogeneity in average doubling time (DT) among phenotypes. DT(E/M, M) =
DT ratio * DT(E). η1 = 0.2, and η2 = 0.1. 3.2. Time to Attain Epithelial Dominance Depends on Initial Fractions, Doubling Times of
Phenotypes and the Extent of Stochastic Fluctuations during Cell Division (C) Temporal changes in phenotypic distribution for fixed η1
and varying η2 values. Here, DT(E, E/M, M) = 20 h. (D) Same as (C) but with varying η1 and fixed η2
values. In all, except (A), initial fractions of (1) Mix of E/M and M, and (2) pure E phenotypes are
considered. The initial population size was 200 cells. Mean and standard deviation calculated from
16 independent runs. Besides initial phenotypic distribution, another factor that can impact the population
dynamics is average doubling time (DT). So far, we considered the same DT for E, E/M,
and M phenotypes. However, experimental evidence suggests the slowing down of pro‐
liferation rate of cells undergoing EMT [20,27]. Thus, we considered the case of increased
DT during EMT, by keeping the average DT of E/M and M phenotypes as 1.5, 2, and 2.5 Biomolecules 2022, 12, 348 11 of 20 11 of 20 times more than that of the E phenotype. We observed that the population maintained its
epithelial dominance, and converged to a stable phenotypic distribution faster than in the
case when all cells doubled at the same rate (Figure 3B), irrespective of the initial condi‐
tion. This trend can be explained by a higher resilience of E cells to switch to a hybrid E/M
or M phenotype during cell division, now coupled with their higher proliferation rate,
thereby offering the epithelial subpopulation an additional advantage to amplify their
population fraction. Importantly, this trend was already seen at the DT of hybrid E/M and
M cells being 1.5 times that of the E cells, hence indicating that a 50% increase in doubling
time for cells undergoing EMT may be sufficient in influencing the population structure. The slight initial decrease in the epithelial fraction noticed for the purely E case (Figure
3A,B) can be explained by appreciating that SNAIL levels for the initial cell population
were sampled from a log‐normal distribution, whose median was centred on the SNAIL
level where all phenotypes were stable (tristable region in Figure 1D); therefore, the cells
were highly susceptible to undergo phenotypic switching within the first few cell divi‐
sions. Despite this initial dip, an epithelial dominant population emerged eventually. p
p
p
p p
g
y
Next, we investigated how the extent of stochastic fluctuations in SNAIL molecules
being duplicated and partitioned (η1 and η2 respectively) influenced phenotypic distribu‐
tion over time. 3.2. Time to Attain Epithelial Dominance Depends on Initial Fractions, Doubling Times of
Phenotypes and the Extent of Stochastic Fluctuations during Cell Division When we varied η2, while maintaining the values of η1 = 0.2 and average
population DT = 20 h, we noticed that for the mesenchymal dominated initial fraction
(E:E/M:M = 0:0.2:0.8), the fraction of epithelial cells was higher for a higher η2 value for
the same time point (Figure 3C, left). However, not much observable effect on this fraction
was noticed when starting with an epithelial dominated population (Figure 3C, right). Similar observations were made when we varied η1 instead of varying η2 (Figure 3D). Thus, amplifying fluctuations in either duplication or partitioning of SNAIL molecules
seemed to enhance the chance of phenotypic switching for an M cell much more than for
an E cell. When we accounted for heterogeneity in average DT along with increasing fluc‐
tuations in SNAIL levels during cell division, the fast proliferating and relatively stable E
cells grew much faster than the slow proliferating and more plastic E/M and M cells, en‐
riching for epithelial cells (Figure S2A–D). Finally, we analysed how the population dynamics were altered when average DT
was increased for all phenotypes, given the experimentally observed average DT can often
depend on the confluency of cells in a petri dish. Thus, for this, we simulated population
dynamics keeping the average DT of all three phenotypes as 30 h, which led to overall
slower dynamics (Figure S2E). Instead of plotting against absolute time units, we also took
the number of cell cycles as the x‐axis, whose one unit is the population’s average DT. This
helped to compare the overall changes in phenotypic fractions between DT of 20 and 30 h
scenarios. We found that given an equal number of cell cycles, the changes in the E frac‐
tions were similar (Figure S2F). These observations help us to conclude that even if all
cells, on average, divided slower, the population growth and phenotypic switching tra‐
jectory would be similar to when cells divided faster when normalised with average DT. 3.3. Phenotypic Switching Probability and Rate in Cell Division Events Depends on the Cells’
Location on E‐M Axis After characterising the population dynamics at various time points as a function of
different model parameters, we wanted to better understand it from a cell division per‐
spective. In our framework, a cell can undergo one of the three division types: (1) sym‐
metric division—when both daughter cells have the same phenotype as the parent cell,
(2) asymmetric division—when one daughter has a phenotype different than the parent,
and (3) divergent division—when both daughters have a phenotype different than the
parent (Figure 4A). To quantify the probability of cells undergoing one of the three divi‐
sion types, we analysed certain cells occupying possible stable phenotypes spread across
the SNAIL ranges (Figure 4B). Iterating cell division events at a given SNAIL value, we
tracked the phenotypes of daughter cells, at specific η1 and η2 values, thus calculating
different division probabilities over an ensemble of iterations. At η1 = 0.2, η2 = 0.1, in Biomolecules 2022, 12, 348 12 of 20 12 of 20 SNAIL levels regions where either E or M phenotypes were the only stable state (mono‐
stable regions in bifurcation diagram—Figure 4B; SNAIL = 100 K, 300 K), more than 90%
events were of symmetric division (Figure 4C). However, as the SNAIL levels corre‐
sponded to a multi‐stable region (SNAIL values = 150 K, 250 K), there was an increasing
tendency to undergo asymmetric division, which was higher for M than for E cells. In
different bi‐stable regions (SNAIL = 189 K for {E, M} and SNAIL = 219 K for {E/M, M}),
with further increasing probability of asymmetric division, the divergent division also be‐
came more prominent and was the most dominant division for hybrid E/M cells (Figure
4C). This trend explains the sudden drop in hybrid E/M fraction of population to very low
levels within two weeks, when starting from a hybrid dominant population (Figure 3A). Further, in the tri‐stable region (SNAIL = 206 K for {E, E/M, M}), the probabilities for both
divergent and asymmetric division were increased (Figure 4C). Put together, the proba‐
bility of phenotypic switching at cell division is the highest in the tri‐stable region (inter‐
mediate SNAIL levels ~200 K) and decreases for cells as their corresponding SNAIL levels
either increase or decrease. Next, we quantified these probabilities for varying η1 and η2 values. 3.3. Phenotypic Switching Probability and Rate in Cell Division Events Depends on the Cells’
Location on E‐M Axis While η1 = 0 re‐
sulted in either asymmetric or symmetric division of E and M cells across SNAIL levels
(i.e., preventing divergent division), η2 = 0 leads to only symmetric and divergent divi‐
sions for these two phenotypes (i.e., preventing asymmetric division) (Figure S3A,B). Ad‐
ditionally, higher values of η1 and η2 amplify the chances of divergent and asymmetric
division, respectively, across SNAIL ranges (increasing η1 in Figure S3A,C,E and increas‐
ing η2 in Figure S3B,D,F). Thus, η1 and η2—the factors that represent noise during cell
division—can alter the probabilities of undergoing symmetric, asymmetric and divergent
division types for a cell with a SNAIL level (Figure S3). We observed that cells with SNAIL levels well away from the multi‐stable pheno‐
typic regions have mostly undergone symmetric division. However, when we started
with such a homogenous or largely homogeneous population and tracked the phenotypes
of daughter cells over multiple cell cycles, we noted phenotypic switching in which at
least one daughter cell took a different phenotype (Figure 3). Thus, we quantified how
many cell divisions it took for a cell to give rise to one of the cells in its progeny with a
different phenotype than its own. We observed the progeny up to 12 generations/cell cy‐
cles. We saw that the cells with SNAIL levels in a multi‐stable region switch phenotype
within one or two cell cycles (Figure 4D). We also noticed a skew between the resilience
of E and M cells to phenotypic switching in their mono‐stable regions, i.e., E cells required
more cell cycles to give rise to a non‐similar progeny cell than the M cells did (compare
the behavior seen at SNAIL = 300 K and SNAIL = 250 K with that at SNAIL = 100 K and
SNAIL = 150 K in Figure 4D). This difference may underlie the phenomenon of E cells
dominating over E/M and M cells in the population over time. However, this skew van‐
ished in the bi‐stable and tri‐stable regions, where all three phenotypes became equally
susceptible to undergo asymmetric switching within a few generations/cell cycles (SNAIL
= 189 K, 206 K, 219 K in Figure 4D). 13 of 20 Biomolecules 2022, 12, 348 Figure 4. Phenotypic switching probability and its rate at cell division depends on the location of a
cell on E‐M axis. (A) Schematic of different possible cell division types. 3.3. Phenotypic Switching Probability and Rate in Cell Division Events Depends on the Cells’
Location on E‐M Axis (B) Different ranges of
SNAIL where E, E/M, and M phenotypes are stable. (C) Probabilities of an E, E/M or M cell to un‐
dergo one among the three division types (A) when its SNAIL levels lie in different regions in bi‐
furcation diagram (B). (D) Number of cell cycles (generations) required to make first asymmetric or
divergent division when a parent E, E/M or M cells’ SNAIL level lied in different regions in bifurca‐
ti
di
(B) ( h
ti
i
i i
t) M
d t
d
d d
i ti
l
l t d f
10
d 16 Figure 4. Phenotypic switching probability and its rate at cell division depends on the location of a
cell on E‐M axis. (A) Schematic of different possible cell division types. (B) Different ranges of
SNAIL where E, E/M, and M phenotypes are stable. (C) Probabilities of an E, E/M or M cell to un‐
dergo one among the three division types (A) when its SNAIL levels lie in different regions in bi‐
furcation diagram (B). (D) Number of cell cycles (generations) required to make first asymmetric or
divergent division when a parent E, E/M or M cells’ SNAIL level lied in different regions in bifurca‐
tion diagram (B) (schematic given in inset). Mean and standard deviation was calculated from 10 and 16
independent runs in (C,D), respectively. In (C), each run includes 100 iterations. η1 = 0.2, η2 = 0.1. We also examined how η1 and η2 values varied the number of cell cycles over which
progeny diversification was observed. An increase in either η1 and η2 caused faster switch‐
ing for all phenotypes of cells, i.e., a smaller number of cell divisions was required, on
average, for a cell to give rise to a different phenotype (increasing η1 in Figure S4A–C and
increasing η2 in Figure S4D–F). However, η2 contributed more as compared to η1 (compare
Figure S4A–C with Figure S4D–F; quantified in Figures S5 and S6). 3.4. Heterogeneity in E Fraction at Initial Time Points among Single Cell Clones So far, we have focused on population dynamics when starting with an initial cell
population; however, heterogeneity has also been observed experimentally in single‐cell
clones established from cell lines [20,21]. For instance, in distinct single‐cell clones estab‐
lished from PMC42‐LA, varying distributions of EpCAMhigh: EpCAMlow subpopulations
were seen after the initial two passages (Figure 5A) [20]. We interrogated whether our
model could reproduce this heterogeneous behavior. 14 of 20 14 of 20 Biomolecules 2022, 12, 348 We performed a population dynamics simulation starting with a single E, E/M and
M cell, maintaining η1 = 0.2, η2 = 0.1, and average DT as 20 h. We observed heterogeneity
in the E fraction at week 4 when multiple such single cell simulation runs were performed
(Figure 5B). Thus, as a proof of principle, our model could recapitulate the experimentally
observed heterogeneity in the EpCAMlow fraction. In these simulations for single‐cell
clones, at the week 4 time point, the heterogeneity in the fraction of E cells was the highest
when the seeding cell was mesenchymal (M). Among the M clones, the highest E fraction
noticed was close to the highest E fraction noticed for single‐cell clones established from
the E or E/M initial phenotype. However, in M clones, we observed instances where the E
fraction was as low as 27% (Figure 5B). To examine this heterogeneous behaviour of individual clones more closely, we
probed the levels of SNAIL in the seeding (individual) cell for each of these clones. This
led us to identify the range of SNAIL levels in the individual cells that were all ‘cultured’
in silico to develop a clone (Figure 5C). From this range, we identified representative
SNAIL values and independently established single‐cell clones from them. Interestingly,
the single‐cell clones showed heterogeneity in the E fraction at 4 weeks, despite being
seeded with the same SNAIL level (Figure 5D), reminiscent of stochastic effects at lower
(cell) numbers. Additionally, as expected, the average E fraction decreases as seeding
SNAIL levels are increased (compare the average E fraction at SNAIL = 600 K vs. that at
SNAIL = 50 K in Figure 5D). Another feature we noticed is that the clones established from
cells with the same initial phenotype (M), but different initial SNAIL levels had varying E
fractions at week 4 (compare the average E fraction at SNAIL = 206 K vs. that at SNAIL =
600 K in Figure 5D). 3.4. Heterogeneity in E Fraction at Initial Time Points among Single Cell Clones This extent of diversity is less when the initial cell belongs to an epi‐
thelial or a hybrid E/M phenotype. This difference between the extent of variability no‐
ticed can possibly explain why we see more heterogeneity in the E fraction when starting
from an initially mesenchymal cell as compared to an initially epithelial or hybrid E/M
one (Figure 5B–D). Finally, when we continued the single‐cell (clonal) simulations for a longer duration,
we observed a decrease in heterogeneity in the E fractions with time (Figure 5E). Further,
the E fraction for all single cell clones increased overall. This difference in short‐term vs. long‐term behavior can be possibly rationalised by our population dynamics simulations
earlier showing predominance of epithelial phenotypes irrespective of initial phenotypic
distributions (Figures 2B and 3A) if we consider the clonal distribution noticed at week 4
as the initial condition for simulations being continued until week 16 or later. 15 of
Figure 5. Heterogeneity in the E fraction among single cell clones at initial stages of culture. (A
Experimentally observed heterogeneity in EpCAM profiling of single cell clones from PMC42‐L
cells (adapted from Bhatia et al. J Clin Med [20]). (B) Variability in the E fraction observed on sim
lating population dynamics starting with single E, E/M and M cell. Each dot represents the E fractio
at 4th week in an independent single cell simulation run. (C) E fraction in a single cell clone at 4
week plotted against the seeding (parent) cells’ SNAIL level. (D) Spread of the E fraction at 4th wee
of single cells clones when the seeding cells were initialised with certain SNAIL levels spannin
mono‐, bi‐, and tri‐stable regions of bifurcation diagram (Figure 4B). Mean and standard deviatio
calculated from 20 independent runs (E) Temporal dynamics extension of single cell simulation run
in (B). All results are with η1 = 0.2 and η2 = 0.1, and DT(E, E/M, M) = 20 h. 15 of 20 Biomolecules 2022, 12, 348 Figure 5. Heterogeneity in the E fraction among single cell clones at initial stages of culture. (A)
Experimentally observed heterogeneity in EpCAM profiling of single cell clones from PMC42‐LA
cells (adapted from Bhatia et al. J Clin Med [20]). (B) Variability in the E fraction observed on simu‐
lating population dynamics starting with single E, E/M and M cell. 4. Discussion Understanding the molecular mechanisms underlying epithelial‐mesenchymal plas‐
ticity and heterogeneity can contribute to better therapeutic strategies [28]. These mecha‐
nisms can be context‐specific with varying degrees of contribution to genetic and/or non‐
genetic heterogeneity. Epigenetic alterations, for instance, can govern the rate of bidirec‐
tional switching among the phenotypes, enabling reversible or irreversible EMT, as well
as driving resistance to undergo EMT [29–31]. Cell‐cell communication through autocrine
and/or paracrine signaling with other tumor cells as well as stromal cells can also shape
the E‐M phenotypic heterogeneity patterns in a population [19,32–34]. Another contrib‐
uting factor can be differential activation of many signaling pathways implicated in EMT,
thus generating a varied phenotypic repertoire of states in the multi‐dimensional EMT
landscape [35–39]. Here, we highlight one other possible reason driving E‐M heterogene‐
ity—phenotypic switching due to asymmetric cell division driven by noise in the pro‐
cesses of content duplication and in the partitioning of biomolecules. We investigate the
influence of such fluctuations on levels of SNAIL—a driver of miR‐200/ZEB feedback
loop—during cell division in determining the phenotypic distribution of population, but
our framework is applicable to investigate the population dynamics emerging from stochastic
partitioning of molecules involved in other multi‐stable EMT networks [40,41] as well. p
g
Asymmetric cell division is an evolutionarily conserved mechanism used by prokar‐
yotes, as well as eukaryotes to generate cell‐to‐cell heterogeneity, and mediate cell‐fate
decisions [42,43]. This phenomenon has been observed in multiple cancers, particularly
relating to cancer stem cell (CSC) differentiation [44–46]. Glioma CSCs can differentiate
into either glial or neural cells by asymmetric partitioning of CD144 and Numb levels
during cell division [45]. Similarly, colon CSCs can have asymmetric partitioning of
ALDH1 and CK20 levels, leading to cell differentiation [44]. The frequency of asymmetric
division depends on micro‐environmental conditions such as growth factors in the case
of glioma CSCs, and on regulatory molecules such as Notch and miR‐34a in colon CSCs. Consequent heterogeneity in molecular content among cells can lead to different signaling
responses, as measured by distinct IFN‐γ and oncostatin M response in fibroblasts [47],
and can lead to the presence of rare drug‐resistant cells, such as those seen in melanoma
[48]. Not only biomolecules (RNAs, proteins) but also entire organelles, such as mitochon‐
dria and membrane lipids can be asymmetrically partitioned, with implications in cell
division rates and/or stemness traits [49,50]. 3.4. Heterogeneity in E Fraction at Initial Time Points among Single Cell Clones Each dot represents the E fraction
at 4th week in an independent single cell simulation run. (C) E fraction in a single cell clone at 4th
week plotted against the seeding (parent) cells’ SNAIL level. (D) Spread of the E fraction at 4th week
of single cells clones when the seeding cells were initialised with certain SNAIL levels spanning
mono‐, bi‐, and tri‐stable regions of bifurcation diagram (Figure 4B). Mean and standard deviation
calculated from 20 independent runs (E) Temporal dynamics extension of single cell simulation runs
in (B). All results are with η1 = 0.2 and η2 = 0.1, and DT(E, E/M, M) = 20 h. Figure 5. Heterogeneity in the E fraction among single cell clones at initial stages of culture. (A)
Experimentally observed heterogeneity in EpCAM profiling of single cell clones from PMC42‐LA
cells (adapted from Bhatia et al. J Clin Med [20]). (B) Variability in the E fraction observed on simu‐
lating population dynamics starting with single E, E/M and M cell. Each dot represents the E fraction
at 4th week in an independent single cell simulation run. (C) E fraction in a single cell clone at 4th
week plotted against the seeding (parent) cells’ SNAIL level. (D) Spread of the E fraction at 4th week
of single cells clones when the seeding cells were initialised with certain SNAIL levels spanning
mono‐, bi‐, and tri‐stable regions of bifurcation diagram (Figure 4B). Mean and standard deviation
calculated from 20 independent runs (E) Temporal dynamics extension of single cell simulation runs
in (B). All results are with η1 = 0.2 and η2 = 0.1, and DT(E, E/M, M) = 20 h. Biomolecules 2022, 12, 348 16 of 20 16 of 20 4. Discussion In the EMT literature, to the best of our
knowledge, the asymmetric partitioning of cell‐fate determinant transcription factors
(here, SNAIL) has not yet been reported experimentally, but the frequency of the modes
of cell division (symmetric division, asymmetric division, divergent division) has been
shown to vary with EMT induction [51]. Although our modeling framework does not yet
specifically incorporate molecular mechanisms regulating this phenomenon [42], our re‐
sults suggest that one possible consequence of fluctuations during cell division can be
phenotypic switching and heterogeneity among subpopulations. Recent reports in glioblas‐
toma have demonstrated that asymmetric enrichment of EGFR and p75NTR in a daughter cell
during cell division conferred enhanced resistance to the standard‐of‐care therapies, such as
radiation and temozolomide [52]. While we do not yet know about differences, if any, in the
drug resistance features of EpCAMhigh and EpCAMlow sub‐populations in PMC42‐LA cells, the
varied drug‐resistance features seen in single‐cell clones established from PMC42‐LA [20] can
be a putative outcome of underlying asymmetric cell division. Approximately 10–30% of cells
undergoing TGFβ‐driven EMT were seen to exhibit asymmetric cell division, as traced by
NUMB distribution in daughter cells [51], but whether this asymmetry led to phenotypic
switching was not tracked per se. Therefore, our model suggests that blocking cell division
can be a possible way to restrict phenotypic plasticity and/or heterogeneity. Preliminary ex‐
perimental observations made recently support this prediction by our model [51]. Our model can recapitulate the observations for the PMC42‐LA system, an epithelial‐
dominant subline. However, what mechanisms may explain phenotypic heterogeneity in
a mesenchymal‐dominant population, such as EM3 or M clone from SUM149 cell line [21], Biomolecules 2022, 12, 348 17 of 20 17 of 20 remains to be investigated further. One factor that can alter the model outcomes is the
way noise during cell division is incorporated. We have considered multiplicative noise
(fluctuations in SNAIL proportional to its levels); however, our previous effort encapsu‐
lating additive noise (constant magnitude of fluctuations in SNAIL, irrespective of its levels)
could explain the spontaneous phenotypic switching observations in the prostate cancer PKV
cell line [24]. Whether cancer cells exhibit additive or multiplicative noise during cell division
remains unknown experimentally. Further, this noise and/or its consequences can be influ‐
enced by mutually dependent factors, such as chromatin status and diffusible cytokines [53]. These factors have not yet been explicitly incorporated into our framework. 4. Discussion y
p
y
p
Despite the above‐mentioned limitations, our model recapitulates various observa‐
tions for the PMC42‐LA system: (a) stable dominance of the EpCAMhigh subpopulation,
(b) repopulation of parental distributions starting with only one subpopulation, and (c)
enhanced heterogeneity in EpCAMhigh: EpCAMlow ratio of cells in single‐cell derived
clones. We predict that these single‐cell derived clones converge to EpCAMhigh dominant
distribution in longer time‐scales, a prediction that remains to be experimentally verified. Thus, we demonstrate that during cell division, stochasticity in content duplication and
partitioning of molecules involved in EMT can lead to spontaneous state switching, and
therefore, generate non‐genetic heterogeneity. g
g
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Future efforts are directed towards integrating continuous stochastic fluctuations in
EMT drivers with asymmetric cell division which happens at discrete time‐steps [54]. Ad‐
dressing these questions will involve mathematical models that can decode the emergent
dynamics at multiple scales—regulatory levels (transcriptional, epigenetic), length (intra‐
cellular, non‐cell‐autonomous effects by cytokines) and time (cell division, chromatin re‐
modelling, stochastic gene expression). References References 1. Biswas, A.; De, S. Drivers of dynamic intratumor heterogeneity and phenotypic plasticity. Am. J. Physiol.‐Cell Physiol. 2021,
320, C750–C760. https://doi.org/10.1152/ajpcell.00575.2020. 1. Biswas, A.; De, S. Drivers of dynamic intratumor heterogeneity and phenotypic plasticity. Am. J. Physiol.‐Cell Physiol. 2021,
320, C750–C760. https://doi.org/10.1152/ajpcell.00575.2020. p
g
jp
2. Shlyakhtina, Y.; Moran, K.L.; Portal, M.M. Genetic and Non‐Genetic Mechanisms Underlying Cancer
2021, 13, 1380. https://doi.org/10.3390/cancers13061380. ,
,
p
g
3. Jolly, M.K.; Celià‐Terrassa, T. Dynamics of Phenotypic Heterogeneity Associated with EMT and Stemness during Cancer
Progression. J. Clin. Med. 2019, 8, 1542. https://doi.org/10.3390/jcm8101542. p
g
3. Jolly, M.K.; Celià‐Terrassa, T. Dynamics of Phenotypic Heterogeneity Associated with EMT and Stemness during Cancer
Progression. J. Clin. Med. 2019, 8, 1542. https://doi.org/10.3390/jcm8101542. g
J
p
g
j
4. Sharma, A.; Merritt, E.; Hu, X.; Cruz, A.; Jiang, C.; Sarkodie, H.; Zhou, Z.; Malhotra, J.; Riedlinger, G.M.; De, S. Non‐Ge‐
netic Intra‐Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics
in Lung Tumors. Cell Rep. 2019, 29, 2164–2174. g
J
p
g
j
4. Sharma, A.; Merritt, E.; Hu, X.; Cruz, A.; Jiang, C.; Sarkodie, H.; Zhou, Z.; Malhotra, J.; Riedlinger, G.M.; De, S. Non‐Ge‐
netic Intra‐Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics
in Lung Tumors. Cell Rep. 2019, 29, 2164–2174. g
p
5. Lewis, A.C.; Kats, L.M. Non‐genetic heterogeneity, altered cell fate and differentiation therapy. EMBO
e12670. https://doi.org/10.15252/emmm.202012670. p
Kats, L.M. Non‐genetic heterogeneity, altered cell fate and differentiation therapy. EMBO Mol. Med. 2021,
s://doi.org/10.15252/emmm.202012670. 6. Su, Y.; Wei, W.; Robert, L.; Xue, M.; Tsoi, J.; Garcia‐diaz, A.; Homet, B.M.; Kim, J.; Ng, R.H.; Lee, J.W.; et al. Single‐cell
analysis resolves the cell state transition and signaling dynamics associated with melanoma drug‐induced resistance. Proc. Natl. Acad. Sci. USA 2017, 114, 13679–13684. https://doi.org/10.1073/pnas.1712064115. 6. Su, Y.; Wei, W.; Robert, L.; Xue, M.; Tsoi, J.; Garcia‐diaz, A.; Homet, B.M.; Kim, J.; Ng, R.H.; Lee, J.W.; et al. Single‐cell
analysis resolves the cell state transition and signaling dynamics associated with melanoma drug‐induced resistance. Proc. Natl. Acad. Sci. USA 2017, 114, 13679–13684. https://doi.org/10.1073/pnas.1712064115. p
g
p
Jolly, M.K.; Kulkarni, P.; Weninger, K.; Orban, J.; Levine, H. Phenotypic plasticity, bet‐hedging, and andr
ence in prostate cancer: Role of non‐genetic heterogeneity. Front. Oncol. 2018, 8, 50. https://doi.org/10.3389 8. Ruscetti, M.; Dadashian, E.L.; Guo, W.; Quach, B.; Mulholland, D.J.; Park, J.W.; Tran, L.M.; Kobayashi, N.; Bianchi‐Frias,
D.; Xing, Y.; et al. References HDAC inhibition impedes epithelial‐mesenchymal plasticity and suppresses metastatic, castration‐re‐
sistant prostate cancer. Oncogene 2016, 35, 3781–3795. https://doi.org/10.1038/onc.2015.444. p
g
p
g
9. Pastushenko, I.; Brisebarre, A.; Sifrim, A.; Fioramonti, M.; Revenco, T.; Boumahdi, S.; Van Keymeulen, A.; Brown, D.;
Moers, V.; Lemaire, S.; et al. Identification of the tumour transition states occurring during EMT. Nature 2018, 556, 463–
468. https://doi.org/10.1038/s41586‐018‐0040‐3. p
g
10. Rios, A.C.; Capaldo, B.D.; Vaillant, F.; Pal, B.; van Ineveld, R.; Dawson, C.A.; Chen, Y.; Nolan, E.; Fu, N.Y.; Jackling, F.C.; et
al. Intraclonal Plasticity in Mammary Tumors Revealed through Large‐Scale Single‐Cell Resolution 3D Imaging. Cancer
Cell 2019, 35, 618–632. https://doi.org/10.1016/j.ccell.2019.02.010. p
g
j
11. Biddle, A.; Liang, X.; Gammon, L.; Fazil, B.; Harper, L.J.; Emich, H.; Costea, D.E.; Mackenzie, I.C. Cancer stem cells in
squamous cell carcinoma switch between two distinct phenotypes that are preferentially migratory or proliferative. Cancer
Res. 2011, 71, 5317–5326. https://doi.org/10.1158/0008‐5472.CAN‐11‐1059. p
g
12. Yu, M.; Bardia, A.; Wittner, B.S.; Stott, S.L.; Smas, M.E.; Ting, D.T.; Isakoff, S.J.; Ciciliano, J.C.; Wells, M.N.; Shah, A.M.; et
al. Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition. Science 2013, 339,
580–584. https://doi.org/10.1126/science.1228522. 13. Deshmukh, A.P.; Vasaikar, S.V.; Tomczak, K.; Tripathi, S.; Den Hollander, P.; Arslan, E.; Chakraborty, P.; Soundararajan,
R.; Jolly, M.K.; Rai, K.; et al. Identification of EMT signaling cross‐talk and gene regulatory networks by single‐cell RNA
sequencing. Proc. Natl. Acad. Sci. USA 2021, 118, e2102050118. https://doi.org/10.73/pnas.2102050118. q
g
p
g
p
14. Karacosta, L.G.; Anchang, B.; Ignatiadis, N.; Kimmey, S.C.; Benson, J.A.; Shrager, J.B.; Tibshirani, R.; Bendall, S.C.; Plevri‐
tis, S.K. Mapping Lung Cancer Epithelial‐Mesenchymal Transition States and Trajectories with Single‐Cell Resolution. Nat. Commun. 2019, 10, 5587. https://doi.org/10.1101/570341. p
g
15. George, J.T.; Jolly, M.K.; Xu, S.; Somarelli, J.A.; Levine, H. Survival outcomes in cancer patients predicted by a partial EMT
gene expression scoring metric. Cancer Res. 2017, 77, 6415–6428. https://doi.org/10.1158/0008‐5472.CAN‐16‐3521. 16. Bhatia, S.; Monkman, J.; Blick, T.; Duijf, P.H.; Nagaraj, S.H.; Thompson, E.W. Multi‐Omics Characterization of the Sponta‐ p
g
15. George, J.T.; Jolly, M.K.; Xu, S.; Somarelli, J.A.; Levine, H. Survival outcomes in cancer patients predicted by a partial EMT
gene expression scoring metric. Cancer Res. 2017, 77, 6415–6428. https://doi.org/10.1158/0008‐5472.CAN‐16‐3521. 15. George, J.T.; Jolly, M.K.; Xu, S.; Somarelli, J.A.; Levine, H. Survival outcomes in cancer patients predicted by a partial EMT
gene expression scoring metric. Cancer Res. 2017, 77, 6415–6428. https://doi.org/10.1158/0008‐5472.CAN‐16‐3521. 16. 5. Conclusions Proportional noise/fluctuations in duplication and distribution of the parent cell SNAIL’s
level during cell division can possibly explain the experimentally observed population‐level
dynamics of epithelial‐mesenchymal heterogeneity in PMC42‐LA cells. Future endeavors
would involve incorporating the regulatory mechanism of asymmetric division and analysing
the contributions of various stochastic and deterministic (regulatory) processes to it. Another
direction would be to consider an integration of asymmetric cell division with other pheno‐
type stabilising mechanisms, such as epigenetics and cell‐cell communication. Supplementary Materials:The following supporting information can be downloaded at:
www.mdpi.com/xxx; Figure S1: Longer time simulations and similarities between effects of fluctu‐
ation in SNAIL and all players in core EMT network during cell division; Figure S2: Temporal
changes in E fraction for combinations of avg. doubling time (DT) ratio, η1, and η2 values; and higher
cell doubling time; Figure S3: Phenotypic switching probability for various scaling factors (η1 and
η2) values across SNAIL levels; Figure S4: Average cell cycles/generations required for first asym‐
metric switching for various scaling factors (η1 and η2) values across SNAIL levels; Figure S5: Sta‐
tistical analysis of differences in minimum cell cycles for required asymmetric division by a cell of
given phenotype and SNAIL level on varying η1 and keeping η2 fixed (0.1); Figure S6: Statistical
analysis of differences in minimum cell cycles required for asymmetric division for a cell of given
phenotype and SNAIL level on keeping η1 fixed (0.2) and varying η2. Author Contributions: P.J. performed simulations, S.B. performed experiments, E.W.T. and M.K.J. conceived and supervised research. All authors contributed to data analysis and writing of the man‐
uscript. All authors have read and agreed to the published version of the manuscript. Funding: This work was supported by Ramanujan Fellowship awarded by SERB, DST, Government
of India to MKJ (SB/S2/RJN‐049/2018) and by InfoSys Foundation, Bangalore. The Translational Re‐
search Institute receives funding from the Australian Government. Data Availability Statement: The data on PMC42‐LA cell doubling time and the codes for population
dynamics simulations are available on https://github.com/Paras‐Jain20/EMT‐Population‐Dynamics. Conflicts of Interest: The authors declare no conflict of interest. 18 of 20 18 of 20 Biomolecules 2022, 12, 348 References Sigal, A.; Milo, R.; Cohen, A.; Geva‐Zatorsky, N.; Klein, Y.; Liron, Y.; Rosenfeld, N.; Danon, T.; Perzov, N.; Alon, U. Varia‐
bility and memory of protein levels in human cells. Nature 2006, 444, 643–646. https://doi.org/10.1038/nature05316. y
y
p
p
g
27. Vega, S.; Morales, A.V.; Ocaña, O.H.; Valdés, F.; Fabregat, I.; Nieto, M.A. Snail blocks the cell cycle an
to cell death. Genes Dev. 2004, 18, 1131–1143. https://doi.org/10.1101/gad.294104. p
g
g
28. Jonckheere, S.; Adams, J.; De Groote, D.; Campbell, K.; Berx, G.; Goossens, S. Epithelial‐Mesenchymal Transition (EMT) as
a Therapeutic Target. Cells Tissues Organs 2021, in press. https://doi.org/10.1159/000512218. 29. Eichelberger, L.; Saini, M.; Moreno, H.D.; Klein, C.; Bartsch, J.M.; Falcone, M.; Reitberger, M.; Espinet, E.; Vogel, V.; Graf,
E.; et al. Maintenance of epithelial traits and resistance to mesenchymal reprogramming promote proliferation in meta‐
static breast cancer. bioRxiv 2020. https://doi.org/10.1101/2020.03.19.998823. p
g
30. Serresi, M.; Kertalli, S.; Li, L.; Schmitt, M.J.; Dramaretska, Y.; Wierikx, J.; Hulsman, D.; Gargiulo, G. Functional antagonism
of chromatin modulators regulates epithelial‐mesenchymal transition. Sci. Adv. 2021, 7, eabd7974. https://doi.org/10.1126/sciadv.abd7974. p
g
31. Jia, W.; Tripathi, S.; Chakraborty, P.; Chedere, A.; Rangarajan, A.; Levine, H.; Jolly, M.K. Epigenetic feedback and stochas‐
tic partitioning during cell division can drive resistance to EMT. Oncotarget 2020, 11, 2611–2624. https://doi.org/10.18632/oncotarget.27651. p
g
g
32. Bocci, F.; Gearhart‐Serna, L.; Boareto, M.; Riberio, M.; Ben‐Jacob, E.; Devi, G.R.; Levine, H.; Onuchic, J.N.; Jolly, M.K. To‐
ward understanding cancer stem cell heterogeneity in the tumor microenvironment. Proc. Natl. Acad. Sci. USA 2019, 116,
148–157. https://doi.org/10.1073/pnas.1815345116. 33. Scheel, C.; Eaton, E.N.; Li, S.H.J.; Chaffer, C.L.; Reinhardt, F.; Kah, K.J.; Bell, G.; Guo, W.; Rubin, J.; Richardson, A.L.; et al. Paracrine and autocrine signals induce and maintain mesenchymal and stem cell states in the breast. Cell 2011, 145, 926–
940. https://doi.org/10.1016/j.cell.2011.04.029. p
g
j
34. Li, X.; Jolly, M.K.; George, J.T.; Pienta, K.J.; Levine, H. Computational Modeling of the Crosstalk Between Macrophage
Polarization and Tumor Cell Plasticity in the Tumor Microenvironment. Front. Oncol. 2019, 9, 10. https://doi.org/10.3389/fonc.2019.00010. p
g
35. Watanabe, K.; Panchy, N.; Noguchi, S.; Suzuki, H.; Hong, T. Combinatorial perturbation analysis reveals divergent regula‐
tions of mesenchymal genes during epithelial‐to‐mesenchymal transition. NPJ Syst. Biol. Appl. 2019, 5, 21. https://doi.org/10.1038/s41540‐019‐0097‐0. p //
g/
/
36. Steinway, S.N.; Zañudo, J.G.T.; Michel, P.J.; Feith, D.J.; Loughran, T.P.; Albert, R. Combinatorial interventions inhibit
TGFβ‐driven epithelial‐to‐mesenchymal transition and support hybrid cellular phenotypes. NPJ Syst. Biol. Appl. References Bhatia, S.; Monkman, J.; Blick, T.; Duijf, P.H.; Nagaraj, S.H.; Thompson, E.W. Multi‐Omics Characterization of the Sponta‐
neous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines. J. Clin. Med. 2019, 8, 1253. https://doi.org/10.3390/jcm8081253. gene expression scoring metric. Cancer Res. 2017, 77, 6415 6428. https://doi.org/10.1158/0008 5472.CAN 16 3521. 16. Bhatia, S.; Monkman, J.; Blick, T.; Duijf, P.H.; Nagaraj, S.H.; Thompson, E.W. Multi‐Omics Characterization of the Sponta‐
neous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines. J. Clin. Med. 2019, 8, 1253. https://doi.org/10.3390/jcm8081253. 17. Jolly, M.K.; Somarelli, J.A.; Sheth, M.; Biddle, A.; Tripathi, S.C.; Armstrong, A.J.; Hanash, S.M.; Bapat, S.A.; Rangarajan, A.;
Levine, H. Hybrid epithelial/mesenchymal phenotypes promote metastasis and therapy resistance across carcinomas. Pharmacol. Ther. 2019, 194, 161–184. https://doi.org/10.1016/j.pharmthera.2018.09.007. 18. Gupta, P.B.; Fillmore, C.M.; Jiang, G.; Shapira, S.D.; Tao, K.; Kuperwasser, C.; Lander, E.S. Stochastic state transitions give
rise to phenotypic equilibrium in populations of cancer cells. Cell 2011, 146, 633–644. https://doi.org/10.1016/j.cell.2011.07.026. p
g
j
19. Yamamoto, M.; Sakane, K.; Tominaga, K.; Gotoh, N.; Niwa, T.; Kikuchi, Y.; Tada, K.; Goshima, N.; Semba, K.; Inoue, J.I. Intratumoral bidirectional transitions between epithelial and mesenchymal cells in triple‐negative breast cancer. Cancer
Sci. 2017, 108, 1210–1222. https://doi.org/10.1111/cas.13246. p
g
20. Bhatia, S.; Monkman, J.; Blick, T.; Pinto, C.; Waltham, A.; Nagaraj, S.H.; Thompson, E.W. Interrogation of Phenotypic Plas‐
ticity between Epithelial and Mesenchymal States in Breast Cancer. J. Clin. Med. 2019, 8, 893. https://doi.org/10.3390/jcm8060893. p
g
j
21. Brown, M.S.; Abdollahi, B.; Wilkins, O.M.; Chakraborty, P.; Ognjenovic, N.B.; Muller, K.E.; Kumar Jolly, M.; Hassanpour,
S.; Pattabiraman, D.R. Dynamic plasticity within the EMT spectrum, rather than static mesenchymal traits, drives tumor
heterogeneity and metastatic progression of breast cancers. bioRxiv 2021. https://doi.org/10.1101/2021.03.17.434993. g
y
p
g
p
g
22. Lu, M.; Jolly, M.K.; Levine, H.; Onuchic, J.N.; Ben‐Jacob, E. MicroRNA‐based regulation of epithelial‐hybrid‐mesenchymal
fate determination. Proc. Natl. Acad. Sci. USA 2013, 110, 18144–18149. https://doi.org/10.1073/pnas.1318192110. 19 of 20 19 of 20 Biomolecules 2022, 12, 348 23. Brabletz, S.; Brabletz, T. The ZEB/miR‐200 feedback loop‐‐a motor of cellular plasticity in development and cancer? EMBO
Rep. 2010, 11, 670–677. https://doi.org/10.1038/embor.2010.117. p
p
g
24. Tripathi, S.; Chakraborty, P.; Levine, H.; Jolly, M.K. A mechanism for epithelial‐mesenchymal heterogeneity in a popula‐
tion of cancer cells. PLoS Comput. Biol. 2020, 16, e1007619. https://doi.org/10.1101/592691. 25. In Proceedings of theGillespie, D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977, 81,
2340–2361. https://doi.org/10.1021/j100540a008. 26. References 2015, 1,
15014. https://doi.org/10.1038/npjsba.2015.14. p //
g/
/ pj
37. Cook, D.P.; Vanderhyden, B.C. Context specificity of the EMT transcriptional response. Nat. Commun. 2020, 11, 2142. https://doi.org/10.1038/s41467‐020‐16066‐2. p
g
38. Hari, K.; Sabuwala, B.; Subramani, B.V.; La Porta, C.A.M.; Zapperi, S.; Font‐Clos, F.; Jolly, M.K. Identifying inhibitors of
epithelial–mesenchymal plasticity using a network topology‐based approach. NPJ Syst. Biol. Appl. 2020, 6, 15. https://doi.org/10.1038/s41540‐020‐0132‐1. p
g
39. Cook, D.P.; Vanderhyden, B.C. Transcriptional census of epithelial‐mesenchymal plasticity in cancer. Sci. Adv. 2022, 8,
eabi7640. https://doi.org/10.1126/sciadv.abi7640. 40. Xin, Y.; Cummins, B.; Gedeon, T. Multistability in the epithelial‐mesenchymal transition network. BMC Bioinform. 2020, 21,
71. https://doi.org/10.1186/s12859‐020‐3413‐1. 41. Li, C.; Balazsi, G. A landscape view on the interplay between EMT and cancer metastasis. NPJ Syst. Biol. Appl. 2018, 4, 34. https://doi.org/10.1038/s41540‐018‐0068‐x. g
Cabernard, C. Principles and mechanisms of asymmetric cell division. Development 2020, 147, dev167650. rg/10.1242/dev.167650. p
g
42. Sunchu, B.; Cabernard, C. Principles and mechanisms of asymmetric cell division. Development 2020, 1
https://doi.org/10.1242/dev.167650. 43. Huh, D.; Paulsson, J. Non‐genetic heterogeneity from stochastic partitioning at cell division. Nat. Genet. 2011, 43, 95–100. https://doi.org/10.1038/ng.729. 44. Bu, P.; Wang, L.; Chen, K.Y.; Srinivasan, T.; Murthy, P.K.L.; Tung, K.L.; Varanko, A.K.; Chen, H.J.; Ai, Y.; King, S.; et al. A
miR‐34a‐Numb Feedforward Loop Triggered by Inflammation Regulates Asymmetric Stem Cell Division in Intestine and
Colon Cancer. Cell Stem Cell 2016, 18, 189–202. https://doi.org/10.1016/j.stem.2016.01.006. p
g
j
45. Lathia, J.D.; Hitomi, M.; Gallagher, J.; Gadani, S.P.; Adkins, J.; Vasanji, A.; Liu, L.; Eyler, C.E.; Heddleston, J.M.; Wu, Q.; et
al. Distribution of CD133 reveals glioma stem cells self‐renew through symmetric and asymmetric cell divisions. Cell
Death Dis. 2011, 2, e200. https://doi.org/10.1038/cddis.2011.80. 46. Izumi, H.; Kaneko, Y. Evidence of asymmetric cell division and centrosome inheritance in human neuroblastoma cells. Proc. Natl. Acad. Sci. USA 2012, 109, 18048–18053. https://doi.org/10.1073/pnas.1205525109. Biomolecules 2022, 12, 348 20 of 20 20 of 20 47. Topolewski, P.; Zakrzewska, K.E.; Walczak, J.; Towski, K.; Muller‐Newen, G.; Singh, A.; Komorowski, M. Phenotypic vari‐
ability, not noise, accounts for most of the cell‐to‐cell heterogeneity in IFN‐γ and oncostatin M signaling responses. Sci. Signal. 2022, 15. https://doi.org/10.1126/scisignal.abd9303. 48. Shaffer, S.M.; Dunagin, M.C.; Torborg, S.R.; Torre, E.A.; Emert, B.; Krepler, C.; Beqiri, M.; Sproesser, K.; Brafford, P.A.;
Xiao, M.; et al. Rare cell variability and drug‐induced reprogramming as a mode of cancer drug resistance. Nature 2017,
546, 431–435. https://doi.org/10.1038/nature22794. 49. Peruzzi, G.; Miotto, M.; Maggio, R.; Ruocco, G.; Gosti, G. References Asymmetric binomial statistics explains organelle partitioning
variance in cancer cell proliferation. Commun. Phys. 2021, 4, 188. https://doi.org/10.1038/s42005‐021‐00690‐5. 50. Döhla, J.; Kuuluvainen, E.; Gebert, N.; Amaral, A.; Englund, J.I.; Gopalakrishnan, S.; Konovalova, S.; Nieminen, A.I.;
Salminen, E.S.; Torregrosa Muñumer, R.; et al. Metabolic determination of cell fate through selective inheritance of mito‐
chondria. Nat. Cell Biol. 2022, 24, 148–154. https://doi.org/10.1038/s41556‐021‐00837‐0. Salminen, E.S.; Torregrosa Muñumer, R.; et al. Metabolic determination of cell fate through selective inheritance of mito‐
chondria. Nat. Cell Biol. 2022, 24, 148–154. https://doi.org/10.1038/s41556‐021‐00837‐0. p
g
51. den Hollander, P.; Vasaikar, S.; Castaneda, M.; Joseph, R.; Deshmukh, A.P.; Zhou, T.; Pietila, M.; Fu, C.; Symmans, W.F.;
Soundararajan, R.; et al. Acquisition of cancer stem cell properties during EMT requires cell division. bioRxiv 2021. https://doi.org/10.1101/2021.07.01.449976. p
g
52. Hitomi, M.; Chumakova, A.P.; Silver, D.J.; Knudsen, A.M.; Pontius, W.D.; Murphy, S.; Anand, N.; Kristensen, B.W.; La‐
thia, J.D. Asymmetric cell division promotes therapeutic resistance in glioblastoma stem cells. JCI Insight 2021, 6, e130510. https://doi.org/10.1172/JCI.INSIGHT.130510. p
g
53. Gregory, P.A.; Bracken, C.P.; Smith, E.; Bert, A.G.; Wright, J. a; Roslan, S.; Morris, M.; Wyatt, L.; Farshid, G.; Lim, Y.‐Y.; et
al. An autocrine TGF‐beta/ZEB/miR‐200 signaling network regulates establishment and maintenance of epithelial‐mesen‐
chymal transition. Mol. Biol. Cell 2011, 22, 1686–1698. https://doi.org/10.1091/mbc.E11‐02‐0103. y
,
,
p
g
54. Baptista, I.S.C.; Ribeiro, A.S. Stochastic models coupling gene expression and partitioning in cell division in Escherichia
coli. BioSystems 2020, 193–194, 104154. https://doi.org/10.1016/j.biosystems.2020.104154.
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English
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A Machine-learning Parsimonious Multivariable Predictive Model of Mortality Risk in Patients With Covid-19
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Research Square (Research Square)
| 2,021
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cc-by
| 7,710
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A machine‑learning parsimonious
multivariable predictive model
of mortality risk in patients
with Covid‑19
OPEN Rita Murri1*, Jacopo Lenkowicz2, Carlotta Masciocchi2, Chiara Iacomini2,
Massimo Fantoni1, Andrea Damiani3, Antonio Marchetti2, Paolo Domenico Angelo Sergi2,
Giovanni Arcuri2, Alfredo Cesario2, Stefano Patarnello2, Massimo Antonelli1,
Rocco Bellantone1, Roberto Bernabei1, Stefania Boccia1, Paolo Calabresi1,
Andrea Cambieri2, Roberto Cauda1, Cesare Colosimo1, Filippo Crea1, Ruggero De Maria3,
Valerio De Stefano1, Francesco Franceschi1, Antonio Gasbarrini1, Ornella Parolini3,
Luca Richeldi1, Maurizio Sanguinetti1, Andrea Urbani1, Maurizio Zega2, Giovanni Scambia1,
Vincenzo Valentini1 & The Gemelli against Covid Group* The COVID-19 pandemic is impressively challenging the healthcare system. Several prognostic models
have been validated but few of them are implemented in daily practice. The objective of the study
was to validate a machine-learning risk prediction model using easy-to-obtain parameters to help
to identify patients with COVID-19 who are at higher risk of death. The training cohort included all
patients admitted to Fondazione Policlinico Gemelli with COVID-19 from March 5, 2020, to November
5, 2020. Afterward, the model was tested on all patients admitted to the same hospital with COVID-19
from November 6, 2020, to February 5, 2021. The primary outcome was in-hospital case-fatality risk. The out-of-sample performance of the model was estimated from the training set in terms of Area
under the Receiving Operator Curve (AUROC) and classification matrix statistics by averaging the
results of fivefold cross validation repeated 3-times and comparing the results with those obtained
on the test set. An explanation analysis of the model, based on the SHapley Additive exPlanations
(SHAP), is also presented. To assess the subsequent time evolution, the change in paO2/FiO2 (P/F)
at 48 h after the baseline measurement was plotted against its baseline value. Among the 921
patients included in the training cohort, 120 died (13%). Variables selected for the model were age,
platelet count, SpO2, blood urea nitrogen (BUN), hemoglobin, C-reactive protein, neutrophil count,
and sodium. The results of the fivefold cross-validation repeated 3-times gave AUROC of 0.87, and
statistics of the classification matrix to the Youden index as follows: sensitivity 0.840, specificity 0.774,
negative predictive value 0.971. Then, the model was tested on a new population (n = 1463) in which
the case-fatality rate was 22.6%. The test model showed AUROC 0.818, sensitivity 0.813, specificity
0.650, negative predictive value 0.922. Considering the first quartile of the predicted risk score
(low-risk score group), the case-fatality rate was 1.6%, 17.8% in the second and third quartile (high-
risk score group) and 53.5% in the fourth quartile (very high-risk score group). www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports 1Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro
Cuore, Rome, Italy. 2Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. 3Università Cattolica Sacro
Cuore, Rome, Italy. *A list of authors and their affiliations appears at the end of the paper. *email: rita.murri@
policlinicogemelli.it Scientific Reports | (2021) 11:21136 Materials and methodsh Study population. The study cohort included all patients admitted to Fondazione Policlinico Gemelli with
COVID-19 from March 5, 2020 to February 5, 2021. The diagnosis of SARS-CoV-2 infection was considered
when the reverse transcription polymerase chain reaction (PCR) of the SARS-CoV-2 assay was detected from
nasopharyngeal swab. For each patient, time 0 was considered the date of hospitalization for SARS-CoV-2 infec-
tion. Data collection. Patient data included demographics, comorbidities, vital signs, and laboratory char-
acteristics, as well as exposure history, medical history, symptoms at onset, treatment, and outcome data on
admission and during hospitalization. Pre-existing conditions collected were diabetes, hypertension, chronic
heart disease, chronic respiratory disease, chronic kidney disease, mild to severe liver disease, pancreatitis, neu-
rological impairment, connective tissue disease, transplantation, HIV infection, and malignancy. Vital signs
included heart rate, respiratory rate, oxygen saturation by pulse oximetry (SpO2), temperature, body weight,
and body mass index (BMI). Laboratory parameters included hematologic variables (white blood cells [WBC],
neutrophils, lymphocytes, and eosinophils, platelet count, hematocrit), blood urea nitrogen (BUN); creatinine;
total bilirubin; creatine kinase; glucose; sodium; potassium; C-reactive protein; procalcitonine, D-dimer; fer-
ritin; lactate dehydrogenase (LDH); arterial blood oxygen partial pressure (paO2) and inspired oxygen fraction
(FiO2), paO2/FiO2 ratio (P/F). SpO2 was grouped into three categories according to the interquartile range:
SpO2 less than 94% (first quartile), SpO2 between 94 and 97.0% (second and third quartile), SpO2 greater than
97.0% (fourth quartile). All data were extracted from the electronic medical records of all patients. To obtain
structural information from unstructured texts (such as clinical diary, radiology reports etc.), Natural Language
Processing (NLP) algorithms were applied, based on text mining procedures such as: sentence/word tokeniza-
tion; rule-based approach supported by annotations defined by the clinical SMEs, and using semantic/syntactic
corrections where necessary. Outcome. The primary outcome was in-hospital case-fatality rate. Predictors. Candidate predictors were included when previously shown to be related to mortality in
COVID-19 patients or other respiratory diseases (such as bacterial pneumonia) or possibly related because of
clinical plausibility. Statistical analysis. To capture the risk of death associated with early hospitalization, we developed a pre-
dictive model including only laboratory variables and oxygen saturation at the time of SARS-Cov2 infection. The rationale behind this choice was to provide a tool for early risk assessment. reasonable to assume that the model is also applicable in not-hospitalized persons, only appropriate
studies can assess the accuracy of the model also for persons at home. A rapid spread of SARS-CoV-2, the agent of coronavirus disease 2019 (COVID-19), has been observed first in
China since early January 2020 and then in Italy since the last days of February 20201. At this time, the number
of COVID-19 cases and related deaths continue to increase. Patients hospitalized with COVID-19 had a relevant
rate of clinical deterioration. A first large study on more than 1000 patients with COVID-19 in China reported
the need for transfer to an intensive care unit (ICU) in 5% of patients admitted with COVID-19, 2.3% mechani-
cal ventilation; 1.4% died2. Other studies have reported a rate around 5% of people admitted as critically ill3,4. Case fatality rate in persons with COVID-19 range from < 1 to 15%5,6. This implies a staggering challenge for the
healthcare system. Unfortunately, treatment options are currently scarce, and as hospital resources are shrinking,
systems to target respiratory support and other hospital resources to the highest-risk population, such as the
ICU, is a priority. Several predictive models of adverse clinical outcomes in people with COVID-197–13 as well as
a systematic review14 have been published. Having a clinical algorithm to predict patients who can benefit most
from available resources is a valuable aid for decision making and capacity allocation. However, few models have
tested the predictive value of simple and readily available parameters. The objective of this study was to generate
and validate a machine-learning risk prediction model using parameters that are easily available to help identify
patients with COVID-19 who are at higher risk of death. A machine‑learning parsimonious
multivariable predictive model
of mortality risk in patients
with Covid‑19
OPEN The three risk score
groups showed good discrimination for the P/F value at admission, and a positive correlation was
found for the low-risk class to P/F at 48 h after admission (adjusted R-squared = 0.48). We developed
a predictive model of death for people with SARS-CoV-2 infection by including only easy-to-obtain
variables (abnormal blood count, BUN, C-reactive protein, sodium and lower SpO2). It demonstrated
good accuracy and high power of discrimination. The simplicity of the model makes the risk prediction
applicable for patients in the Emergency Department, or during hospitalization. Although it is 1Sezione di Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro
Cuore, Rome, Italy. 2Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. 3Università Cattolica Sacro
Cuore, Rome, Italy. *A list of authors and their affiliations appears at the end of the paper. *email: rita.murri@
policlinicogemelli.it | https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 www.nature.com/scientificreports/ Resultsh The eligible training cohort included a total of 1126 patients with confirmed COVID-19 admitted from 5 March,
2020, to 5 November, 2020. In this cohort, the in-hospital mortality rate was 13.0%. Characteristics of the study
population are shown in Table 1. Survivors differed from nonsurvivors for being younger, having few preexisting medical conditions (specifi-
cally, lower rates of diabetes, hypertension, cardiovascular diseases, chronic respiratory diseases, renal failure,
solid tumors, and arteriopathy), more cough and diarrhea at onset but less dyspnea, a longer time from symptoms
onset to hospitalization, a higher P/F, albumin and hemoglobin value, a higher platelet count, lower WBC and
lymphocyte count, a lower creatinine, BUN, C-reactive protein, and D-dimer.t y
p
y
p
From an initial dataset of 1126 patient records, a total of 921 complete records were included. After the feature
selection phase, the selected variables were age (relative selection frequency [RSF] 100%), platelet count (RSF
97%), SpO2 (RSF 80%), BUN (RSF 72%), hemoglobin (RSF 71%), C-reactive protein (RSF 68%), neutrophil count
(RSF 60%), and sodium (RSF 58%). These variables were used to fit the logistic regression model. The estimated
coefficients of the logistic model are shown in Table 2, along with p values. Each variable in the model is associ-
ated with a distribution of importance values among all instances of the dataset (patients), ordered by the value
of the variable from low to high. It emerges, for example, that a lower value of platelet count is associated with a
higher risk of death, whereas higher values of BUN, C-reactive protein, neutrophils and age are associated with
a higher risk of death. The sodium variable was subdivided according to the interquartile range: in this three-
category version of the variable (low, normal, high), it can be seen that the “low sodium” group (≤ 136 mmol/l)
does not impact death for this cohort of patients, whereas the ”high sodium” class (≥ 141 mmol/l) does. Simi-
larly, SpO2 < 94% has a greater impact in the model than the variable representing SpO2 values between 94 and
97. Figure 1 is a representation of the importance of the variables in the model based on the SHAP framework.hii g
p
p
The overall statistical significance of the model according to chi-squared residual deviance test was confirmed
with a p-value zero. www.nature.com/scientificreports/ their added contribution to the model in terms of information criterion to minimize model redundancy. The
model was trained on the first 8 months of data (March 5, 2020–November 5, 2020), and tested on the next
3 months of data (November 6, 2020–February 5 2021). The out-of-sample performance of the model was
estimated from the training set in terms of area under the receiving operator curve (AUROC) and classification
matrix statistics by averaging the results of the fivefold cross validation repeated 3-times and comparing the
results with those obtained on the test set. Finally, an analysis of lift and gain graphs is presented to identify seg-
ments of outcome probability where the model proves particularly useful compared to having no model at all. A
model explanation analysis, based on the SHapley Additive exPlanations (SHAP) framework, is also presented
to derive information about the contribution of individual variables to the model beyond that obtained from
simple logistic regression coefficients.it p
g
gfi
Baseline laboratory variables for each patient were included by taking the first value after the date-time of
hospital admission; only variables with less than 5% of missing values were retained for further analysis, and the
final training cohort was selected by choosing the complete records only. This set of variables, along with age
and sex, and study outcome, were given as input to a routine of 100-iteration of AIC-based stepwise selection
on 80% subsets of the randomly partitioned training data, and characteristics selected at least 50 times were
considered to train the final logistic regression model. A level of 0.05 was considered significant for statistical
testing. Statistical analysis was done with R version 3.6. Data were stored in SAS Viya V.03.05 and accessed
through R with SWAT library version 1.5.0. g
y
According to TRIPOD guidelines15, the study should be considered a TRIPOD 2b because it involves a
chronological division between training and testing data from a single institution. Ethical approval. This study was approved by Ethics Committees of the Fondazione Policlinico Gemelli
(IRB 3447). All research was performed in accordance with relevant guidelines/regulations and it was conducted
in accordance to the Declaration of Helsinki. Written informed consent was waived because of the rapid emer-
gence of this infectious disease (Comitato Etico Policlinico Gemelli; comitato.etico@policlinicogemelli.it). Materials and methodsh The variables for the model are
routinely collected, available within a very short time after presentation, and the literature has reported their
association with an increased likelihood of death; moreover, they could also be available at home through home
services. In this way, an estimate of risk can be obtained at the time of hospital admission, and actions on the
management of critical versus non-critical patients can be readily taken by hospital staff from the patient’s initial
clinical status as well as its evolution in a relatively short time frame. A binary logistic regression was applied to
express the risk of death in analytical terms, and possibly use it in risk assessment tools based on model coeffi-
cients alone. We have chosen to use a logistic regression model because it has both a simple analytical expression
and a straightforward interpretation in terms of regression coefficients; other machine learning techniques can
have in general higher or slightly higher performances, but at the cost of less technical transferability and clinical
explainability, at least in our setting. p
y
g
Candidate predictors were selected through a combination of prior domain knowledge and a data-driven
approach: for example, cut-off values to classify SpO2 and sodium were heuristically defined by the interquartile
range, confirmed by a-priori medical knowledge. Overall feature selection was conducted iteratively based on Scientific Reports | (2021) 11:21136 | https://doi.org/10.1038/s41598-021-99905-6 www.nature.com/scientificreports/ Resultsh The fivefold cross-validation repeated 3-times resulted in an AUROC of 0.87, and the sta-
tistics of the classification matrix at the Youden index as follows: sensitivity 0.840, specificity 0.774, negative
predictive value 0.971. The model was then tested on the cohort of patients admitted between November 6, 2020,
and February 5, 2021, (n = 1463), recording the model variable of interest and the clinical outcome. In this cohort
of patients, the mortality rate was 22.6%. The model test results in terms of AUROC statistics and confounding
matrix are AUROC 0.818, sensitivity 0.813, specificity 0.650, negative predictive value 0.922 (Table 3; Fig. 2). To get a quantification of how the model performs in different segments of probability outputs compared to a
random classifier, a gain and lift curve analysis is shown (Fig. 3). Moreover, the lift plot on the testing data in
Fig. 3 shows that for the first decile of predictions, the model performs more than 3 times better than random
guessing based on prevalence only. Specifically, when considering the first quartile of the predicted risk score on
the test set, it contains 6 death events out of 366 total predictions in that risk group. Similarly, the highest 25% of
risk scores on the test set contain 196 actual death events, which is more than 50% of the population classified in
that risk group (Table 4). A calibration analysis was performed on the testing set to produce the calibration plot
of Suppl. Fig. Y. A linear regression fit on the calibration points sampled at every 5 percentiles of the predicted
outcome probabilities estimated an intercept of − 4.57 ± 2.12 and a slope of 1.12 ± 0.03 for the regression line
with an adjusted R-squared of 0.89. Brier score on the testing set predictions was 0.12. j
q
g
p
A decision curve analysis was conducted on the testing set to assess model utility compared to baseline strate-
gies of considering “no high-risk” or “all high risk”. Suppl. Fig. W shows the decision curve for thresholds in the
range 0–0.5: the curve associated to the model is always higher or substantially higher than the baseline strategies. https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 | www.nature.com/scientificreports/ Table 1. Characteristics of patients included in the training and testing subsets. SD standard deviation, IQR
interquartile range, BMI body mass index, P/F paO2/FiO2 ratio. Table 1. Characteristics of patients included in the training and testing subsets. SD standard deviation, IQR
interquartile range, BMI body mass index, P/F paO2/FiO2 ratio. Resultsh Characteristics
Training
Test
All patients (N = 921)
Alive (n = 801)
Died (n = 120)
All patients (N = 1463)
Alive (n = 1131)
Died (n = 332)
Demographics
Age, median (SD)
68.0 (15.9)
64.0 (15.4)
84.0 (10.1)
70.0 (18.2)
65.0 (18.5)
80.0 (11.3)
Male
566 (61.4%)
501 (62.5%)
65 (54.2%)
798 (54.5%)
596 (52.7%)
202 (60.8%)
BMI, median (IQR)
26.0 (24.2; 29.1)
26.1 (24.2; 28.7)
26.0 (23.5; 29.3)
26.1 (24.2; 28.2)
26.1 (24.2; 28.2)
26.1 (23.9; 28.1)
Coexisting conditions
Any
685 (74.4%)
574 (71.7%)
111 (92.5%)
1127 (77.0%)
827 (73.1%)
300 (90.4%)
Current or former smoker
24 (2.6%)
23 (2.9%)
1 (0.8%)
23 (1.6%)
20 (1.8%)
3 (0.9%)
Arteriopathy
8 (0.9%)
4 (0.5%)
4 (3.3%)
13 (0.9%)
5 (0.4%)
8 (2.4%)
Chronic liver disease
11 (1.2%)
10 (1.2%)
1 (0.8%)
14 (1.0%)
9 (0.8%)
5 (1.5%)
Cirrhosis
6 (0.7%)
3 (0.4%)
3 (2.5%)
12 (0.8%)
8 (0.7%)
4 (1.2%)
Diabetes
149 (16.2%)
120 (15.0%)
29 (24.2%)
279 (19.1%)
206 (18.2%)
73 (22.0%)
Dyslipidemia
78 (8.5%)
70 (8.7%)
8 (6.7%)
106 (7.2%)
80 (7.1%)
26 (7.8%)
Hiv
27 (2.9%)
26 (3.2%)
1 (0.8%)
22 (1.5%)
18 (1.6%)
4 (1.2%)
Myocardial infarction
116 (12.6%)
87 (10.9%)
29 (24.2%)
227 (15.5%)
148 (13.1%)
79 (23.8%)
Kidney failure
44 (4.8%)
32 (4.0%)
12 (10.0%)
107 (7.3%)
53 (4.7%)
54 (16.3%)
Hypertension
374 (40.6%)
315 (39.3%)
59 (49.2%)
636 (43.5%)
480 (42.4%)
156 (47.0%)
Autoimmune disease
41 (4.5%)
38 (4.7%)
3 (2.5%)
62 (4.2%)
48 (4.2%)
14 (4.2%)
Hematologic neoplasm
6 (0.7%)
4 (0.5%)
2 (1.7%)
29 (2.0%)
16 (1.4%)
13 (3.9%)
Neurologic impairment
102 (11.1%)
59 (7.4%)
43 (35.8%)
171 (11.7%)
101 (8.9%)
70 (21.1%)
Pancreatitis
5 (0.5%)
5 (0.6%)
0 (0.0%)
13 (0.9%)
8 (0.7%)
5 (1.5%)
Cardiovascular pathology
155 (16.8%)
118 (14.7%)
37 (30.8%)
295 (20.2%)
182 (16.1%)
113 (34.0%)
Lung pathology
108 (11.7%)
81 (10.1%)
27 (22.5%)
162 (11.1%)
97 (8.6%)
65 (19.6%)
Radiotherapy
15 (1.6%)
13 (1.6%)
2 (1.7%)
43 (2.9%)
28 (2.5%)
15 (4.5%)
Heart failure
44 (4.8%)
27 (3.4%)
17 (14.2%)
84 (5.7%)
39 (3.4%)
45 (13.6%)
Transplantation
6 (0.7%)
5 (0.6%)
1 (0.8%)
22 (1.5%)
13 (1.1%)
9 (2.7%)
Tumor
236 (25.6%)
188 (23.5%)
48 (40.0%)
544 (37.2%)
406 (35.9%)
138 (41.6%)
Hepatic ulcer
15 (1.6%)
11 (1.4%)
4 (3.3%)
30 (2.1%)
16 (1.4%)
14 (4.2%)
Symptoms at admission
Any
807 (87.6%)
706 (88.1%)
101 (84.2%)
1162 (79.4%)
887 (78.4%)
275 (82.8%)
Cough
344 (37.4%)
327 (40.8%)
17 (14.2%)
366 (25.0%)
309 (27.3%)
57 (17.2%)
Dyspnea
503 (54.6%)
429 (53.6%)
74 (61.7%)
755 (51.6%)
542 (47.9%)
213 (64.2%)
Fever
712 (77.3%)
632 (78.9%)
80 (66.7%)
949 (64.9%)
744 (65.8%)
205 (61.7%)
Nausea or vomiting
47 (5.1%)
43 (5.4%)
4 (3.3%)
65 (4.4%)
53 (4.7%)
12 (3.6%)
Diarrhea
99 (10.7%)
97 (12.1%)
2 (1.7%)
93 (6.4%)
80 (7.1%)
13 (3.9%)
Time from symptom onset
to admission, median
(IQR)
7 (3; 10)
7 (3; 10)
3 (2; 7)
7 (3; 10)
7 (3; 11)
5 (2; 9.5)
Vital signs on the day of admission, median (IQR)
Temperature, °C
37.0 (36.0; 38.3)
37.1 (36.0; 38.4)
36.8 (36.0; 37.9)
36.5 (36.0; 37.9)
36.8 (36; 37.6)
36.3 (36.0; 37.9)
Systolic blood pressure,
mmHg
130.0 (118.0; 143.0)
130 (120; 142)
122 (108; 140)
130.0 (118.0; 145.0)
131.0 (120.0; 145.0)
123.5 (110.0; 145.0)
Heart rate, /min
80.0 (71.0; 88.0)
78.0 (70.0; 88.0)
83.0 (72.0; 90.0)
80.0 (73.0; 90.0)
80.0 (74.0; 90.0)
80.0 (72.0; 90.0)
Laboratory findings on the day of admission, median (IQR)
White blood cell count, /μl
7.0 (5.1; 9.5)
6.9 (5.0; 9.3)
8.1 (5.3; 10.5)
8.1 (5.9; 11.5)
7.9 (6.0; 11.5)
8.5 (5.6; 11.5)
Lymphocyte count, /μl
1.1 (0.8; 1.5)
1.1 (0.8; 1.5)
1.1 (0.7; 1.5)
1.0 (0.7; 1.5)
1.1 (0.8; 1.5)
0.9 (0.6; 1.3)
Hemoglobin level, g/dl
14.3 (13.1; 15.3)
14.5 (13.4; 15.3)
12.9 (11.6; 14.4)
14.1 (12.5; 15.2)
14.3 (12.9; 15.3)
13.3 (11.2; 14.6)
Platelets, μl
198.0 (158.0; 257.0)
202.0 (160.0; 263.0)
176.0 (143.0; 214.0)
204.0 (154.0; 273.0)
207.0 (162.0; 278.0)
196.5 (140.0; 253.5)
Creatinine level, mg/dl
0.9 (0.8; 1.1)
0.9 (0.8; 1.1)
1.1 (0.9; 1.6)
1.0 (0.8; 1.4)
0.9 (0.8; 1.2)
1.3 (0.9; 2.0)
d-Dimer level, ng/ml
740.5 (400.0; 1396.0)
695.0 (380.0; 1314.0)
1158.0 (863.0; 2872.0)
853.0 (468.0; 2031.0)
718.0 (396.0; 1488.0)
1715.5 (811.5; 3667.0)
C-reactive protein level,
mg/l
60.4 (23.5; 130.0)
58.0 (22.1; 130.0)
80.4 (38.7; 129.9)
77.4 (32.6; 143.1)
66.4 (25.5; 132.7)
99.9 (61.7; 164.3)
Urea nitrogen, mg/dl
18.0 (15.0; 24.0)
17.0 (14.0; 22.0)
27.0 (20.0; 38.0)
22.0 (17.0; 32.0)
20.0 (16.0; 27.0)
34.0 (23.0; 50.0)
Albumin, g/l
33.0 (30.0; 37.0)
33.0 (30.0; 37.0)
31.0 (26.0; 35.0)
31.0 (28.0; 35.0)
33.0 (29.0; 36.0)
29.0 (26.0; 32.0)
Vitamin D, ng/ml
15.7 (10.7; 20.1)
15.8 (10.7; 20.1)
12.8 (12.8; 12.8)
16.4 (13.2; 28.4)
19.3 (13.2; 28.4)
15.6 (14.3; 22.8)
P/F
290.5 (201.4; 361.9)
297.4 (208.2; 366.7)
248.3 (164.5; 351.7)
228.8 (159.5; 323.0)
249.8 (182.0; 332.8)
166.4 (104.0; 250.0) https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Table 2. Logistic regression model at the start of hospitalization for SARS-CoV-2 infection. Variables
Coefficient
P value
Intercept
− 8.022163
3.34e−09****
Age (continuous)
0.090299
9.32e-15****
Hemoglobin (continous)
− 0.124580
0.03666*
Blood urea nitrogen (continuous)
0.016342
0.00956**
Platelet count (continuous)
− 0.004924
0.00057***
C-reactive protein (continuous)
0.003086
0.04838*
Neutrophils (continuous)
0.092127
0.00203**
Sodium ≤ 136 mmol/l
0.015663
0.95494
Sodium ≥ 141 mmol/l
0.720771
0.01388*
SpO2 94.4–97.0%
0.501530
0.15757
SpO2 ≤ 94.3%
1.060584
0.00521** Table 2. Logistic regression model at the start of hospitalization for SARS-CoV-2 infection. Variables
Coefficient
P value
Intercept
− 8.022163
3.34e−09****
Age (continuous)
0.090299
9.32e-15****
Hemoglobin (continous)
− 0.124580
0.03666*
Blood urea nitrogen (continuous)
0.016342
0.00956**
Platelet count (continuous)
− 0.004924
0.00057***
C-reactive protein (continuous)
0.003086
0.04838*
Neutrophils (continuous)
0.092127
0.00203**
Sodium ≤ 136 mmol/l
0.015663
0.95494
Sodium ≥ 141 mmol/l
0.720771
0.01388*
SpO2 94.4–97.0%
0.501530
0.15757
SpO2 ≤ 94.3%
1.060584
0.00521** Table 2. Logistic regression model at the start of hospitalization for SARS-CoV-2 infection. Table 2. Logistic regression model at the start of hospitalization for SARS-CoV-2 infection. Figure 1. SHAP (SHapley additive exPlanations) framework for the features in the logistic model. Figure 1. SHAP (SHapley additive exPlanations) framework for the features in the logistic model. Figure 1. SHAP (SHapley additive exPlanations) framework for the features in the logistic model. Table 3. Classification matrix and statistics at training set Youden classification threshold on training (cross-
validation) and test data. AUROC area under the receiver operating characteristics, PPV positive predictive
value, NPV negative predictive value, TN true negative, FN false negative, TP true positive, FP false positive. Dataset
AUROC
Sensitivity
Specificity
PPV
NPV
TN
FN
TP
FP
Training set (cross validation)
0.870
0.840
0.766
0.341
0.971
639
19
100
193
Testing set
0.818
0.813
0.650
0.405
0.922
734
62
270
397 Table 3. Classification matrix and statistics at training set Youden classification threshold on training (cross-
validation) and test data. AUROC area under the receiver operating characteristics, PPV positive predictive
value, NPV negative predictive value, TN true negative, FN false negative, TP true positive, FP false positive. Dataset
AUROC
Sensitivity
Specificity
PPV
NPV
TN
FN
TP
FP
Training set (cross validation)
0.870
0.840
0.766
0.341
0.971
639
19
100
193
Testing set
0.818
0.813
0.650
0.405
0.922
734
62
270
397 Table 3. Classification matrix and statistics at training set Youden classification threshold on training (cross-
validation) and test data. www.nature.com/scientificreports/ AUROC area under the receiver operating characteristics, PPV positive predictive
value, NPV negative predictive value, TN true negative, FN false negative, TP true positive, FP false positive. Table 3. Classification matrix and statistics at training set Youden classification threshold on training (cross-
validation) and test data. AUROC area under the receiver operating characteristics, PPV positive predictive
value, NPV negative predictive value, TN true negative, FN false negative, TP true positive, FP false positive. Also, a zoomed-in version of the graph was produced in Suppl. Fig. Z to highlight the first risk threshold we
identified (0.02) for the risk classes. Evolution of respiratory condition by initial risk group. In addition to having an instrument capable
of distinguish between low-risk, high-risk and very high-risk cases with a fair degree of accuracy, we evaluated
the evolution of the different groups of patients in the first few hours after hospital admission. Considering the
cohort of patients used for model training and taking the first available value of P/F within 24 h of hospital
admission, the three model-defined risk groups had a mean value of P/F of 301, 273, 273 for low-risk, high-risk
and very high-risk, respectively. A t test between the low-risk group versus the other two categories showed a
statistically significant difference. To assess the subsequent time course, the change in P/F at 48 h after the base- https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 | www.nature.com/scientificreports/ Figure 2. Receiver operator characteristics (ROC) on training set (left) and testing set (right). Figure 2. Receiver operator characteristics (ROC) on training set (left) and testing set (right). Figure 3. Cumulative gain and lift charts on testing data. Figure 3. Cumulative gain and lift charts on testing data. Table 4. Risk groups as defined from gains and lift chart analysis on the test data by applying the threshold
Risk group
Number of patients
Lower threshold
Higher threshold
Death prevalence (%)
Mild risk (< 25th percentile)
366
0.000
0.019
1.6
High risk (25–75th percentile)
731
0.019
0.270
17.8
Very high risk (> 75th percentile)
366
0.270
1.000
53.5 Table 4. Risk groups as defined from gains and lift chart analysis on the test data by applying the thresholds
defined on the trained data. line measurement can be plotted against its baseline value (Fig. 4). In the low-risk group, the P/F following the
admission to hospital did not worsen over the following 48 h (adjusted R squared of 0.48). www.nature.com/scientificreports/ In the very high-risk
group the P/F tends to a single value independently from the baseline value (adjusted R squared of 0). Adoption in clinical practice. The risk of death score for each patient with SARS-CoV-2 infection was
made available to clinicians along with real-time predictions directly on the Electronic Health Record (Fig. 5). https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 4. Scatter plot of baseline P/F value and its variation at 48 h for the three groups of risk class patients
according to the logistic regression model. The line of best linear fit is reported for ease of visualization. Figure 4. Scatter plot of baseline P/F value and its variation at 48 h for the three groups of risk class patients
according to the logistic regression model. The line of best linear fit is reported for ease of visualization. Figure 4. Scatter plot of baseline P/F value and its variation at 48 h for the three groups of risk class patients
according to the logistic regression model. The line of best linear fit is reported for ease of visualization. Figure 5. Example of the availability on HER of the risk score of death at admission for a patient with SARS-
CoV-2 infection. Figure 5. Example of the availability on HER of the risk score of death at admission for a patient with SARS-
CoV-2 infection. www.nature.com/scientificreports/ Unfortunately, such calculators require data entry that is cumbersome in a busy clinical prac-
tice. Real-time processing of the model directly from the EHR provides an immediate and seamless calculation,
a score that can be used to support clinical decision making and support prioritization, especially when the
healthcare system is overloaded. Other predictive models have been published previously, many of which report age, hematologic meas-
ures, C-reactive protein and spO2 as the main variables explaining the predictive model7,8. Most of the pub-
lished studies focused on very critically ill people21. Our results confirm and extend those of other large cohort
studies7–13 demonstrating the predictive value of renal function20,22,23 and, particularly, of blood urea nitrogen
for mortality14,24,25. In addition, we share 4 of 9 variables from a machine-learning-based study with the largest
included population14. Many models make particular use of easy-to-collect variables26,27.h p p
y
p
y
The model of the present study shares some variables among those included in CURB-65, a well-validated and
widely used score for predicting mortality in persons with community-acquired pneumonia28, with an AUROC
of 0.72 (0.71–0.73) in patients with COVID-1914. Age and BUN are included in both CURB-65 and our predic-
tive model. whereas respiratory function was described by respiratory rate in CURB-65 and SpO2 in our model. The variables in the present model also share many parameters with other risk scores used to predict mortality in
patients with sepsis, such as the widely used SOFA score29, probably reflecting a clinical presentation of COVID-
19 very close to sepsis. These findings may help highlight the complex pathogenesis of the SARS-CoV-2 infection.f hi
To date, published models implementing machine learning techniques for statistical analysis used very differ-
ent techniques (support vector machine27, artificial neural networks, decision trees, partial least squares discri-
minant analysis, K nearest neighbour algorithm22,30,31, ensemble, Gaussian process, linear, Naïve Bayes22, random
forest, catboost, and extreme gradient boosting31) indicating good ability to predict mortality. In our study, we
proposed a simple classifier model based on logistic regression which can be easily exported on different soft-
ware environments and has a neat clinical explainability in terms of regression coefficients, while still maintain
a satisfying out-of-sample performance. In addition, we enhanced even more the model readability by using the
Shapley additive explanations (SHAP) framework to make the individual variables contribution to the overall
prediction available and understandable in real-time to physicians along with the model’s risk score. www.nature.com/scientificreports/ death of 1.6%, high-risk, with a prevalence of death of 17.8%, and very high-risk with a prevalence of death of
53.5%. Our model includes only easy-to-obtain variables: its simplicity makes the risk prediction applicable for
different purposes for patients in the Emergency Department, or during the hospitalization. For example, when
the calculated individual risk of death is low, the physician may choose to monitor the patient and send him/her
back home, whereas high risk estimates suggest more aggressive monitoring or resource allocation or may be
useful in anticipating organizational needs in terms of intensive, sub-intensive, and rehabilitation rooms and staff
allocation. Safely discharging patients from the Emergency Department is of a great benefit in saving beds for
other critically ill patients. Such a parsimonious model is exploitable even in medically resource-limited settings. death of 1.6%, high-risk, with a prevalence of death of 17.8%, and very high-risk with a prevalence of death of
53.5%. Our model includes only easy-to-obtain variables: its simplicity makes the risk prediction applicable for
different purposes for patients in the Emergency Department, or during the hospitalization. For example, when
the calculated individual risk of death is low, the physician may choose to monitor the patient and send him/her
back home, whereas high risk estimates suggest more aggressive monitoring or resource allocation or may be
useful in anticipating organizational needs in terms of intensive, sub-intensive, and rehabilitation rooms and staff
allocation. Safely discharging patients from the Emergency Department is of a great benefit in saving beds for
other critically ill patients. Such a parsimonious model is exploitable even in medically resource-limited settings.h y
p
p
p
y
g
The discriminatory performance of the model is very high and testing of the model on a new cohort of the
very newly diagnosed patients confirmed its validation. The model also demonstrated good accuracy in predict-
ing respiratory evolution when P/F at baseline and at 48 h were considered.h g
p
y
The two major strengths of the present study are the parsimonious inclusion of simple and easy-to-obtain
variables, also available in primary care settings, and the immediate translation of a mathematical model into a
comprehensible and implementable number in EHR for clinical decision making in daily practice. p
p
g
y p
Several published studies provide a computational tool or Web-based calculator for easy use in a variety of
settings10,11,16–20. Discussion Given the high rate of patients with complications of SARS-CoV-2 infection, prioritization of patients who
need higher levels of care or immediate medical attention is critical. In the present study on a total of 2384
patients hospitalized with COVID-19, of whom 18.9% died, we presented an artificial intelligence-driven clinical
algorithm to predict risk of death. The algorithm showed that abnormal blood counts (hemoglobin, platelets,
neutrophils), high levels of BUN, C-reactive protein, sodium and lower SpO2 were associated with an increased
risk of death. From the model, we were able to identify three risk level groups: low-risk, with a prevalence of https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 | www.nature.com/scientificreports/ Scientific Reports | (2021) 11:21136 | References
h
d p
g
25. Pan, P. et al. Prognostic assessment of COVID-19 in the intensive care unit by machine learning methods: Model developm
and validation. J. Med. Internet Res. 22(11), e23128 (2020). 26. Famiglini, L., Bini, G., Carobene, A., Campagner, A. & Cabitza, F. Prediction of ICU admission for COVID-19 patients: A Machine
Learning approach based on Complete Blood Count data. In 2021 IEEE 34th International Symposium on Computer-Based Medical
Systems (CBMS), 2021, pp 160–165.f 27. Booth, A. L., Abels, E. & McCaffrey, P. Development of a prognostic model for mortality in COVID-19 infection using machine
learning. Mod. Pathol. 34(3), 522–531 (2021).i g
8. Lim, W. S. et al. Defining community acquired pneumonia severity on presentation to hospital: An international derivation and
validation study. Thorax 58(5), 377–382. https://doi.org/10.1136/thorax.58.5.377 (2003). yh
g
29. Raith, E. P. et al. Prognostic accuracy of the SOFA score, SIRS criteria, and qSOFA score for in-hospital mortality among adults
with suspected infection admitted to the intensive care unit. JAMA 317(3), 290–300. https://doi.org/10.1001/jama.2016.20328
(2017). (
)
0. Cobre, A. F. et al. Diagnosis and prediction of COVID-19 severity: Can biochemical tests and machine learning be used as prog-
nostic indicators?. Comput. Biol. Med. 134, 104531 (2021). p
(
)
1. Fernandes, F. T. et al. A multipurpose machine learning approach to predict COVID-19 negative prognosis in São Paulo, Brazil
Sci. Rep. 11(1), 3343. https://doi.org/10.1038/s41598-021-82885-y (2021).i p
p
g
y
32. Asch, D. A. et al. Variation in US hospital mortality rates for patients admitted with COVID-19 during the first 6 months of the
pandemic. JAMA Intern. Med. https://doi.org/10.1001/jamainternmed.2020.8193 (2020). www.nature.com/scientificreports/ www.nature.com/scientificreports/ Received: 20 May 2021; Accepted: 2 September 2021 Received: 20 May 2021; Accepted: 2 September 2021 References
h
d Predicting CoVID-19 community mortality risk using machine learning and develop-
ment of an online prognostic tool. PeerJ 8, e10083. https://doi.org/10.7717/peerj.10083 (2020). 9. Das, A. K., Mishra, S. & Saraswathy, G. S. Predicting CoVID-19 community mortality risk using machine learning and develop-
ment of an online prognostic tool. PeerJ 8, e10083. https://doi.org/10.7717/peerj.10083 (2020). ,
,
,
y,
g
y
y
g
g
ment of an online prognostic tool. PeerJ 8, e10083. https://doi.org/10.7717/peerj.10083 (2020). 20. Jimenez-Solem, E. et al. Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European
cohort of 5594 patients. Sci. Rep. 11(1), 3246. https://doi.org/10.1038/s41598-021-81844-x (2021). 1. Rodríguez, A. et al. Deploying unsupervised clustering analysis to derive clinical phenotypes and risk factors associated with
mortality risk in 2022 critically ill patients with COVID-19 in Spain. Crit. Care. 25(1), 63. https://doi.org/10.1186/s13054-021-
03487-8 (2021). 21. Rodríguez, A. et al. Deploying unsupervised clustering analysis to derive clinical phenotypes and risk factors associated with
mortality risk in 2022 critically ill patients with COVID-19 in Spain. Crit. Care. 25(1), 63. https://doi.org/10.1186/s13054-021-
03487-8 (2021). 22. Subudhi, S. et al. Comparing machine learning algorithms for predicting ICU admission and mortality in COVID-19. NPJ Digit. 03487-8 (2021). 22. Subudhi, S. et al. Comparing machine learning algorithms for predicting ICU admission and mortality in COVID-19. NPJ Digit. Med. 4, 87 (2021). 22. Subudhi, S. et al. Comparing machine learning algorithms for predicting ICU admission and mortality in COVID-19. NPJ D
Med. 4, 87 (2021). ,
(
)
23. Schöning, V. et al. Development and validation of a prognostic COVID-19 severity assessment (COSA) score and machine learning
models for patient triage at a tertiary hospital. J. Transl. Med. 19(1), 56. https://doi.org/10.1186/s12967-021-02720-w (2021). 3. Schöning, V. et al. Development and validation of a prognostic COVID-19 severity assessment (COSA) score and machine learning
d l f
i
i
i
h
i l J T
l M d 19(1) 56 h
//d i
/10 1186/ 12967 021 02720
(2021) 3. Schöning, V. et al. Development and validation of a prognostic COVID 19 severity assessment (COSA) score and machine learning
models for patient triage at a tertiary hospital. J. Transl. Med. 19(1), 56. https://doi.org/10.1186/s12967-021-02720-w (2021). 24. Henry, B. M., de Oliveira, M. H. S., Benoit, S., Plebani, M. & Lippi, G. Hematologic, biochemical and immune biomarker abnor-
malities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): A meta-analysis. Clin. Chem. Lab. Med. 58(7), 1021–1028. https://doi.org/10.1515/cclm-2020-0369 (2020). References
h
d Factors associated with death in critically ill patients with coronavirus disease 2019 in the US. JAMA Intern. Med
180(11), 1–12. https://doi.org/10.1001/jamainternmed.2020.3596 (2020). 9. Gupta, S. et al. Factors associated with death in critically ill patients with coronavirus disease 2019 in the US. JAMA Int
180(11), 1–12. https://doi.org/10.1001/jamainternmed.2020.3596 (2020). 10. Liang, W. et al. Development and validation of a clinical risk score to predict the occurrence of critical illness in hospitalized
patients with COVID-19. JAMA Intern. Med. 180(8), 1081–1089. https://doi.org/10.1001/jamainternmed.2020.2033 (2020). 11. Razavian, N. et al. A validated, real-time prediction model for favorable outcomes in hospitalized COVID-19 patients. NPJ Digit. Med. 6(3), 130. https://doi.org/10.1038/s41746-020-00343-x (2020). p
g
2. Wynants, L. et al. Prediction models for diagnosis and prognosis of covid-19 infection: Systematic review and critical appraisal
BMJ 7(369), m1328. https://doi.org/10.1136/bmj.m1328 (2020).h 13. Bennett, T. D. et al. The national COVID cohort collaborative: Clinical characterization and early severity prediction. medRxiv
https://doi.org/10.1101/2021.01.12.21249511 (2021).i 14. Knight, S. R. et al. Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisa-
tion Protocol: Development and validation of the 4C Mortality Score. BMJ 9(370), m3339. https://doi.org/10.1136/bmj.m3339
CURB-65 (2020). 15. https://www.equator-network.org/reporting-guidelines/tripod-statement/. g
g g
16. Sardar, R., Sharma, A. & Gupta, D. Machine learning assisted prediction of prognostic biomarkers associated with COVID
using clinical and proteomics data. Front. Genet. 20(12), 636441. https://doi.org/10.3389/fgene.2021.636441 (2021). 17 W
S H
t l D
l
d
lid i
f
b b
d
COVID 19 i k
di i
d l A
J M d S i h
/ 17. Woo, S. H. et al. Development and validation of a web-based sever
org/10.1016/j.amjms.2021.04.001 (2021) (Epub ahead of print). 17. Woo, S. H. et al. Development and validation of a web-based severe COVID-19 risk prediction model. Am. J. Med. Sci. https://doi.
org/10.1016/j.amjms.2021.04.001 (2021) (Epub ahead of print). org/10.1016/j.amjms.2021.04.001 (2021) (Epub ahead of print) 8. Chowdhury, M. E. H. et al. An early warning tool for predicting mortality risk of COVID-19 patients using machine learning
Cognit. Comput. 21, 1–16. https://doi.org/10.1007/s12559-020-09812-7 (2021). g
p
p
g
(
)
19. Das, A. K., Mishra, S. & Saraswathy, G. S. Predicting CoVID-19 community mortality risk using machine learning and deve
f
li
i
l P
J 8
10083 h
//d i
/10 7717/
j 10083 (2020) g
p
p
g
(
)
19. Das, A. K., Mishra, S. & Saraswathy, G. S. References
h
d References
1. https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6. 1. https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6. 1. https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6. 2. Guan, W. J. et al. Clinical characteristics of coronavirus disease 2019 in China. N. Engl. J. Med. 382(18), 1708–1720. https://doi
org/10.1056/NEJMoa2002032 (2020) (Epub 2020 Feb 28). g
J
(
) ( p
)
3. Wu, Z. & McGoogan, J. M. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in
China: Summary of a report of 72 314 cases from the Chinese Center for disease control and prevention. JAMA 323(13), 1239–1242. https://doi.org/10.1001/jama.2020.2648 (2020). g
p
3. Wu, Z. & McGoogan, J. M. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in
China: Summary of a report of 72 314 cases from the Chinese Center for disease control and prevention. JAMA 323(13), 1239–1242
https://doi.org/10.1001/jama.2020.2648 (2020). p
g
j
(
)
4. Coronavirus disease 2019 (COVID-19). https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html. p
g
j
4. Coronavirus disease 2019 (COVID-19). https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html. 5. Chen, T. et al. Clinical characteristics of 113 deceased patients with coronavirus disease 2019: Retrospective study. BMJ 26(368)
m1091. https://doi.org/10.1136/bmj.m1091 (2020). p
g
j
(
)
6. Zhou, F. et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective
cohort study. Lancet 395(10229), 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3 (2020) (Epub 2020 Mar 11).i 6. Zhou, F. et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective
cohort study. Lancet 395(10229), 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3 (2020) (Epub 2020 Mar 11).i y
p
g
p
7. Castro, V. M., McCoy, T. H. & Perlis, R. H. Laboratory findings associated with severe illness and mortality among hospitalized
individuals with coronavirus disease 2019 in Eastern Massachusetts. JAMA Netw. Open. 3(10), e2023934. https://doi.org/10.1001/
jamanetworkopen.2020.23934 (2020). 7. Castro, V. M., McCoy, T. H. & Perlis, R. H. Laboratory findings associated with severe illness and mortality among hospitalized
individuals with coronavirus disease 2019 in Eastern Massachusetts. JAMA Netw. Open. 3(10), e2023934. https://doi.org/10.1001
jamanetworkopen.2020.23934 (2020). j
p
8. Berenguer, J. et al. Characteristics and predictors of death among 4035 consecutively hospitalized patients with COVID-19 in
Spain. Clin. Microbiol. Infect. 26(11), 1525–1536. https://doi.org/10.1016/j.cmi.2020.07.024 (2020) (Epub 2020 Aug 4). p
f
p
g
j
p
g
9. Gupta, S. et al. Factors associated with death in critically ill patients with coronavirus disease 2019 in the US. JAMA Intern. 180(11) 1 12 h
//d i
/10 1001/j
i
d 2020 3 96 (2020) 9. Gupta, S. et al. www.nature.com/scientificreports/ Machine
learning methods can synthesize data from thousands of patients to generate tailored predictions for each new
patient in real time. In addition, model explanations used in our study such as Shapley additive explanations
(SHAP)25,27 were made available and understandable to physicians along with real-time predictions.h y
g
The present study includes several limitations: the scalability and the interoperability of the entire data archi-
tecture must be demonstrated in other centers and clinical settings. Moreover, the impact of clinical implementa-
tion of this predictive model in daily clinical life has not yet been demonstrated. Studies demonstrating changes
in clinical management based on model prediction are strongly warranted.h The two greatest strengths of the present study are the parsimonious inclusion of simple and easy-to-obtain
variables, also available in primary care settings, and the immediate translation of a mathematical model into a
comprehensible and implementable number in EHR for clinical decision-making in daily practice. Indeed, for
each patient who tested positive to PCR for SARS-CoV2, hospital IT made available to us in near real-time the
patient’s data in a pseudo-anonimyzed manner on a dedicated environment. We were able to access this data
and send back to the server the model risk score, the risk class, and the importance of the variables for each
particular prediction. This output information was entered into the EMR software interface of the emergency
and infectious disease, through an automated procedure, for on-line consultation in the wards. g
p
Currently, containing the COVID-19 epidemic is an urgent global priority. Dealing with a severe pandemic
disease such as COVID-19 is also very challenging because rapidly changing variables (vaccination, new SARS-
CoV-2 variants, saturation of hospital capacity) alter the risk of death over time32. Our predictive model is prag-
matic and effective in identifying individuals at particularly high risk for a poorer hospital course. Computational
infrastructure could enhance this process, and data repository, updated in real time, can continuously inform the
planning of diagnostic and treatment strategies. Future randomised trials should be conducted to demonstrate
whether the current use of the death risk score will improve final patient outcomes. Predictive models can help
provide appropriate care and optimize the use of limited resources, such as during a pandemic. Finally, sharing large amounts of data among centers around the world can be a formidable response to the
tremendous challenge of the COVID-19 pandemic. Scientific Reports | (2021) 11:21136 | https://doi.org/10.1038/s41598-021-99905-6 Author contributions R.M., J.L., S.P. and V.V. conceived of the presented idea and drafted the manuscript. J.L., N.D.C., C.M., C.I., S.P.,
A.D., A.M., P.D.A.S. extracted and analysed the data. All other authors contributed equally, discussed the results
and concurred to the final manuscript. https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 | www.nature.com/scientificreports/ Competing interests
The authors declare no competing interests. Additional information
Supplementary Information The online version contains supplementary material available at https://doi.org/
10.1038/s41598-021-99905-6. Correspondence and requests for materials should be addressed to R.M. Correspondence and requests for materials should be addressed to R.M. Reprints and permissions information is available at www.nature.com/reprints. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
nstitutional affiliations. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps
institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4.0 International
License, which permits use, sharing, adaptation, distribution and reproduction in any medium or
format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the
Creative Commons licence, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2021 The Gemelli against Covid Group Alessandro Armuzzi1, Marta Barba3, Silvia Baroni1, Silvia Bellesi2, Annarita Bentivoglio1,
Luigi Marzio Biasucci1, Federico Biscetti1, Marcello Candelli2, Gennaro Capalbo2, Paola
Cattani1, Patrizia Chiusolo1, Antonella Cingolani1, Giuseppe Corbo1, Marcello Covino1,
Angela Maria Cozzolino3, Marilena D’Alfonso2, Giulia De Angelis1, Gennaro De Pascale1,
Giovanni Frisullo1, Maurizio Gabrielli1, Giovanni Gambassi1, Matteo Garcovich2, Elisa
Gremese1, Domenico Luca Grieco1, Amerigo Iaconelli2, Raffaele Iorio1, Francesco Landi1,
Annarita Larici1, Giovanna Liuzzo1, Riccardo Maviglia1, Luca Miele1, Massimo Montalto1,
Luigi Natale1, Nicola Nicolotti2, Veronica Ojetti1, Maurizio Pompili1, Brunella Posteraro1,
Gianni Rapaccini1, Riccardo Rinaldi2, Elena Rossi1, Angelo Santoliquido1, Simona Sica1,
Enrica Tamburrini1, Luciana Teofili1, Antonia Testa1, Alberto Tosoni1, Carlo Trani1, Francesco
Varone1 & Lorenzo Zileri Dal Verme1 https://doi.org/10.1038/s41598-021-99905-6 Scientific Reports | (2021) 11:21136 |
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https://openalex.org/W2525358694
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http://publikationen.ub.uni-frankfurt.de/files/42222/Stiebing_022087.pdf
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English
| null |
A lepton spectrometer for studies of fundamental atomic processes at HESR at FAIR
|
Journal of physics. Conference series
| 2,015
|
cc-by
| 751
|
A lepton spectrometer for studies of fundamental atomic processes
at HESR at FAIR *Goethe Universität Frankfurt, Germany, †GSI Darmstadt, Germany, ‡Justus-Liebig-Universität Gießen, Germany,
&Friedrich-Schiller-Universität Jena, Germany, §Helmholtz-Institut Jena, Germany Synopsis A lepton spectrometer for the study of atomic processes in relativistic collisions of very heavy highly charged
ions has been designed for experiments at the HESR storage ring at the FAIR facility. Figure 1: Simulated positron energy spectrum for
NCDR emitted at an angle of θ = 0° for 2.37 GeV/u
U92+ +Ar collisions. Projectile energies of up to 5 GeV/u for very
heavy highly ionized ions (up to e.g. U92+) ena-
ble the study of electron-positron pair produc-
tion processes in extremely strong transient
electric and magnetic fields. Under these condi-
tions, those reaction channels, where the elec-
tron of the dynamically created e+/e--pair is cap-
tured into the vacant K-shell of the projectile,
become interesting channels of observation. For
the specific case of collisions of U92+ on Ar,
accessible at HESR, two fundamental processes
can be contrasted here [1]: (a) Bound-free pair production (BFPP): (a) Bound-free pair production (BFPP):
U92+ + Ar → U91+ + Ar* + e+ and Figure 1: Simulated positron energy spectrum for
NCDR emitted at an angle of θ = 0° for 2.37 GeV/u
U92+ +Ar collisions. Figure 1: Simulated positron energy spectrum for
NCDR emitted at an angle of θ = 0° for 2.37 GeV/u
U92+ +Ar collisions. (b) Negative continuum dielectronic
recombination (NCDR):
U92+ + Ar → U90+ + [Ar+]* + e+. Figure 2: 3D Transport simulations [4] of leptons
(three kinetic energies centered at 6.5 MeV±4%,
with an emission angular spread of Δθ= 2.5°). While in BFPP the electron is directly cap-
tured into the projectile bound state, the hitherto
unobserved NCDR process results in the cap-
ture of two electrons (one from the e+/e—pair
and one from the excited target atom) into the
projectile. Therefore, both processes can be
separated by their ejectile’s charge states. The
relativistic kinematics facilitates experimental
studies by essentially focusing the emitted e+
into a small forward cone. In fig.1, the expected
positron-spectrum of NCDR at an ion energy of
2,37 GeV/u is shown. The simulation bases on
calculations by Artemyev et al. [2], using the
argon Compton profiles of Biggs et al. [3]. Figure 2: 3D Transport simulations [4] of leptons
(three kinetic energies centered at 6.5 MeV±4%,
with an emission angular spread of Δθ= 2.5°). A lepton spectrometer for studies of fundamental atomic processes
at HESR at FAIR A (Q-2D-Q) spectrometer, consisting of two
magnetic dipole sectors (60°) combined with
magnetic quadrupole singlets at the entrance
and the exit has been designed and simulated by
3D-FE calculations [4] (see fig. 2). Position
resolving stacks of ΔE-E scintillation detectors
will be installed in the focal plane. The e+/e--
annihilation radiation is detected in an array of
photon scintillation detectors. XXIX International Conference on Photonic, Electronic, and Atomic Collisions (ICPEAC2015)
IOP Publishing
Journal of Physics: Conference Series 635 (2015) 022087
doi:10.1088/1742-6596/635/2/022087 XXIX International Conference on Photonic, Electronic, and Atomic Collisions (ICPEAC2015)
IOP P
Journal of Physics: Conference Series 635 (2015) 022087
doi:10.1088/1742-6596/635/2 Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution
of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.
Published under licence by IOP Publishing Ltd
1 [1] P.-M. Hillenbrand et al., Experimental concepts
of positron spectroscopy at HESR, Phys. Scr., sub-
mitted (2015).
[2] Artemyev A N, Shabaev V M, Stöhlker T and
Surzhykov A S; Phys. Rev. A79(3), 032713 (2009).
[3] Biggs F, Mendelsohn L and Mann J; Atomic
Data Nuclear Data Tables 16(3), 201(1975).
[4]Computer simulation Technology, www.cst.com
.Supported by Helmholtz-CAS Joint Research Group
HCJRG-108 and by the Federal Ministry of Education and
Research, FRG, (Contract No. 05P12RFFAH). XXIX International Conference on Photonic, Electronic, and Atomic Collisions (ICPEAC2015)
IOP Publishing
Journal of Physics: Conference Series 635 (2015) 022087
doi:10.1088/1742-6596/635/2/022087 XXIX International Conference on Photonic, Electronic, and Atomic Collisions (ICPEAC2015)
IOP Publishing
Journal of Physics: Conference Series 635 (2015) 022087
doi:10.1088/1742-6596/635/2/022087 References [1] P.-M. Hillenbrand et al., Experimental concepts
of positron spectroscopy at HESR, Phys. Scr., sub-
mitted (2015). 1 E-mail: stiebing@em.uni-frankfurt.de
2 E-mail: p.m.hillenbrand@gsi.de Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution
of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Published under licence by IOP Publishing Ltd
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Clinical Applications of Esophageal Impedance Monitoring and High-Resolution Manometry
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Curr Gastroenterol Rep (2012) 14:197–205
DOI 10.1007/s11894-012-0253-9 Curr Gastroenterol Rep (2012) 14:197–205
DOI 10.1007/s11894-012-0253-9 ESOPHAGUS (MF VELA, SECTION EDITOR) B. F. Kessing (*): A. J. P. M. Smout: A. J. Bredenoord
Department of Gastroenterology and Hepatology,
Academic Medical Center Amsterdam,
Meibergdreef 9,
1105 AZ Amsterdam, The Netherlands
e-mail: b.f.kessing@amc.uva.nl Clinical Applications of Esophageal Impedance Monitoring
and High-Resolution Manometry Boudewijn F. Kessing & André J. P. M. Smout &
Albert J. Bredenoord Published online: 21 February 2012
# The Author(s) 2012. This article is published with open access at Springerlink.com Published online: 21 February 2012 Published online: 21 February 2012
# The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Esophageal impedance monitoring and high-
resolution manometry (HRM) are useful tools in the diag-
nostic work-up of patients with upper gastrointestinal com-
plaints. Impedance monitoring increases the diagnostic yield
for gastroesophageal reflux disease in adults and children
and has become the gold standard in the diagnostic work-up
of reflux symptoms. Its role in the work-up for belching
disorders and rumination seems promising. HRM is superior
to other diagnostic tools for the evaluation of achalasia and
contributes to a more specific classification of esophageal
disorders in patients with non-obstructive dysphagia. The
role of HRM in patients with dysphagia after laparoscopic
placement of an adjustable gastric band seems promising. Future studies will further determine the clinical implica-
tions of the new insights which have been acquired with
these techniques. This review aims to describe the clinical
applications of impedance monitoring and HRM. Introduction Esophageal manometry is being performed in humans since
the early 1950s [1]. Since then, esophageal manometry has
greatly increased our understanding of esophageal function
and is currently a widely performed technique to assess
esophageal function. Conventional manometry assemblies
detect pressure using a catheter with several water-perfused
sideholes and with or without the addition of a, so called,
sleeve sensor or solid state pressure transducers [2]. How-
ever, conventional manometry catheters are limited by gaps
between the pressure sensors which are several centimeters
long. To overcome this limitation, manometry catheters with
smaller spacings between sideholes were developed, the so
called high-resolution manometry (HRM) catheters. The
current HRM catheters are no longer water-perfused but
are equipped with intraluminal pressure transducers. With
HRM, the clinician can simultaneously measure from hypo-
pharynx to stomach which renders time-consuming pull-
through techniques obsolete. Although measuring pressure
at more levels provides more information, interpreting this
many signals can be challenging. Therefore, esophageal
pressure topography was adopted for the presentation of
HRM data [3] (Fig. 1a). This technique assigns color to
specific pressure levels which are than presented in a spa-
tiotemporal plot. These pressure topography plots are more
intuitive and easier learned by clinicians [4]. Keywords Esophagus . Motility. Impedance . IIM . High-resolution manometry. Manometry. HRM . HREPT. Gastroesophageal reflux disease . Eosinophilic esophagitis . Fundoplication . Achalasia . Functional gastrointestinal
disorder. Rumination syndrome . Adjustable gastric band . LABG . Belching . Aerophagia . Non-obstructive
dysphagia . Children Johnson and deMeester introduced ambulatory pH-
monitoring for the detection of reflux episodes in 1975 [5]. Since its introduction, pH-metry has become a commonly
used technique for the evaluation of patients with symptoms
suggestive of GERD. In 1991, impedance monitoring was
introduced as a new technique to detect flow of fluids and
gas through hollow viscera [6]. Esophageal impedance
monitoring is based on the concept of measuring the Curr Gastroenterol Rep (2012) 14:197–205 198 Fig. 1 HRM plots of the esophagus. a Anatomical landmarks which
can be identified with the use of HRM. b Assessment of LES relaxa-
tion using the integrated relaxation pressure (IRP). c Identification of
peristaltic landmarks using the 20-mmHg and 30-mmHg isobaric con-
tour lines. d Assessment of peristaltic function Fig. 1 HRM plots of the esophagus. a Anatomical landmarks which
can be identified with the use of HRM. b Assessment of LES relaxa-
tion using the integrated relaxation pressure (IRP). Introduction c Identification of peristaltic landmarks using the 20-mmHg and 30-mmHg isobaric con-
tour lines. d Assessment of peristaltic function peristaltic landmarks using the 20-mmHg and 30-mmHg isobaric con-
tour lines. d Assessment of peristaltic function Fig. 1 HRM plots of the esophagus. a Anatomical landmarks which
can be identified with the use of HRM. b Assessment of LES relaxa-
tion using the integrated relaxation pressure (IRP). c Identification of peristaltic landmarks using the 20-mmHg and 30-mmHg isobaric con-
tour lines. d Assessment of peristaltic function more recently, catheters in which these techniques are com-
bined into a single catheter have become commercially
available. Furthermore, the acquired impedance data can
be visualized as color plots which are projected over the
pressure topography plots acquired by HRM. resistance/impedance of an alternating electric current which
is generated between pairs of electrodes mounted on a non-
conductive catheter. When the esophagus is empty the cath-
eter is in contact with the collapsed walls thus forming the
medium between the sensors, this level is referred to as the
baseline impedance level. The conductivity of fluids such as
saline or gastric juice is high and the impedance level
decreases if these substances form the medium between
the electrodes. The conductivity of air is almost infinitely
low which results in a high impedance if the medium be-
tween the electrodes consists of air. Placement of a series of
electrodes along the catheter also enables one to evaluate the
direction and velocity in which the gaseous or liquid medi-
um is transported through the esophagus. Therefore, with
esophageal impedance monitoring, the nature and move-
ment of a substance in the esophagus can be detected. This review aims to describe the clinical applications of
esophageal impedance monitoring and HRM. Furthermore,
we aim to stipulate novel insights which have emerged from
using the application of techniques. Non-obstructive Dysphagia Fox et al. described that the close spacing of pressure
sensors at the HRM catheter allows the clinician to identify
isolated hypotensive segments in the peristaltic contraction
[16]. These isolated hypotensive segments are caused by a
delay and/or spatial gap between the contraction of the
striated muscle in the proximal esophagus and the initiation
of the smooth muscle in the distal esophagus. This region in
the esophagus is commonly referred to as the transition zone
[17]. With the use of concurrent video-fluoroscopy it was
demonstrated that the presence of a hypotensive segment
can predict the success of bolus transport [16]. Moreover, a
hypotensive segment >5 cm in length is uniformly associat-
ed with incomplete bolus clearance [18•]. Whereas transi-
tion zone defects are far less common than distal peristaltic
abnormalities or abnormalities at the EGJ they may be
related to dysphagia in a minority of patients [17]. Abnormalities of the force of the distal esophageal
contraction can be classified as hypotensive, absent or
hypertensive peristalsis. Hypotensive or absent peristalsis
can be easily recognized using the isobaric contour lines
(Fig. 1d). The threshold for hypotensive sections, also
known as peristaltic pressure breaks, was recently classi-
fied as breaks >2 cm (20-mmHg isobaric contour) or 3 cm in
length (30-mmHg isobaric contour) [18•]. The distal esopha-
geal contraction is further characterized for the vigor of con-
traction using a newly developed measure, the distal
contractile integral (DCI). The DCI integrates the length,
contractile vigor, and duration of contraction of the distal
esophageal segment contraction [11]. The first feature which is used to determine the transmis-
sion of peristalsis is the contractile front velocity (CFV)
(Fig. 1d). Conceptually, the CFV is calculated from the
slope of the line connecting the proximal margin of distal
contraction and the distal margin of the distal contraction
(Fig. 1c). A second feature of peristaltic transmission is the
so-called contractile deceleration point which was recently
proposed by Pandolfino et al. [13] (Fig. 1d). Conceptually,
the contractile deceleration point demarcates the point at
which the initial fast distal peristaltic velocity ends and the
subsequent slow progressing distal peristalsis commences. A third feature of peristaltic transmission is the distal latency
which determines the timing of the contractile deceleration
point relative to the swallow [12] (Fig. 1d). Interpretation of Data When HRM was introduced in clinical practice, the Spechler
and Castell classification of esophageal disorders was the gold
standard for assessing manometric data [8]. However, this
classification is based on conventional manometric data and
it soon became clear that it fell short in the analysis of the
complex data-set which is acquired by HRM. Therefore,
specific criteria for the interpretation of HRM were developed The concept of a simultaneous measurement of reflux
episodes and pressure dates back to the late 1950s when it
was described by Tuttle and Grossman [7]. More recently,
the technique of HRM and impedance monitoring have also
been combined. Although assemblies consisting of a sepa-
rate HRM catheter and an impedance catheter can be used, 199 Curr Gastroenterol Rep (2012) 14:197–205 [9]. This resulted in the so-called “Chicago classification,”
named after the city in which these criteria were developed. [9]. This resulted in the so-called “Chicago classification,”
named after the city in which these criteria were developed. The novel manometric criteria defined by the Chicago
Classification could potentially result in a decreased repro-
ducibility. However, Bogte et al. found that these novel
HRM criteria yield reproducible results [15]. Furthermore,
the reproducibility of LES resting and relaxation pressure
assessed with HRM is better than with conventional
manometry. With HRM several new features were added to the anal-
ysis of esophageal pressure data. The integrated relaxation
pressure (IRP) is a more complex measurement of degluti-
tive esophagogastric junction (EGJ) relaxation than the end-
expiratory nadir pressure [10] (Fig. 1b). Conceptually, the
IRP is the lowest average pressure for 4 contiguous or non-
contiguous seconds during deglutitive EGJ relaxation [11]. This measure of deglutitive EGJ relaxation exhibited 98%
sensitivity and 96% specificity for distinguishing well de-
fined achalasia patients from control subjects and patients
with other diagnoses [10]. Below, we will discuss new insights gained with high-
resolution manometry. Reflux Disease Reflux Disease Reflux Disease By far the largest application of esophageal impedance
monitoring in clinical practice is in the diagnostic work-up
of patients with GERD symptoms. Impedance monitoring
detects retrograde flow in the esophagus whereas pH mon-
itoring detects reflux events as a drop in the pH-level
(Fig. 2). Compared to impedance monitoring, detection of
reflux with pH monitoring is clearly inferior [28]. This is
mainly attributable to the detection of weakly acidic reflux
by impedance monitoring since impedance measures fluid
flow instead of change in pH. Therefore, with the use of
impedance monitoring, the clinician can correlate an in-
creased number of reflux symptoms with a reflux episode
[29, 30]. The latter increases the diagnostic yield in patients
with GERD and shows that the use of pH-metry alone will
result in an underestimation of GERD and an overestimation
of functional dyspepsia and functional heartburn [29, 30]. Therefore, the use of combined pH-impedance monitoring is
currently considered as the gold standard for the detection of
reflux episodes and is becoming available in an increasing
number of centers. The clinical relevance of identifying the achalasia sub-
type was demonstrated by a recent study by Pratap et al. who demonstrated that patients with type II achalasia re-
spond best to treatment followed by type I and type III [24]. Non-obstructive Dysphagia The close spacing of pressure sensors at the HRM catheter
also allows one to differentiate between the pressure generated
by the lower esophageal sphincter (LES) and the crural dia-
phragm if a hiatal hernia is present. This spatial separation of
the LES and the crural diaphragm in patients with a hiatal
hernia is observed as a double high-pressure zone compared to
a single high-pressure zone in subjects without a hiatal hernia
[19]. Scherer et al. demonstrated that, in a hiatus hernia
patient, EGJ obstruction is not always caused by the LES
but can also be caused by dysrelaxation of the crural dia-
phragm [20]. However, whether this information changes
therapeutic outcome needs to be determined by future studies. A recent study by Pandolfino et al. aimed to apply the
CFV and distal latency to refine the diagnosis of distal
esophageal spasm [14]. These authors observed that a large
heterogeneous group of patients can be identified as having
distal esophageal spasm based on the criterion of simulta-
neous contraction. However, most of the patients with si-
multaneous contractions do not have a clinical presentation
suggestive of esophageal spasm [14]. Therefore, the authors
proposed that only esophageal spasms characterized by a
short distal latency and spastic achalasia are considered
as pathological [14]. Future studies will determine
whether this new classification will result in different
clinical outcomes. The diagnostic work-up for non-obstructive dysphagia
can be troublesome due to the lack of agreement between
objective measurements of esophageal function and the lack
of bolus transit assessment as measured by conventional
manometry and subjective perception of bolus passage
[21•]. This suggests that increased bolus passage perception
in patients without mechanical obstruction might be due to
esophageal hypersensitivity thereby limiting the use of
esophageal function tests using conventional manometry in
patients with non-obstructive dysphagia [21•]. However, the
clinical application of HRM has resulted in a more specific
classification of esophageal disorders and future research
will determine whether this has clinical implications. Curr Gastroenterol Rep (2012) 14:197–205 200 patients undergoing gastric banding or in patients with side
effects of LAGB placement. Achalasia Eosinophilic Esophagitis A recent study by Roman et al. evaluated the use of HRM in
48 patients with eosinophilic esophagitis [27]. Using high-
resolution manometry, 37% of patients with eosinophilic
esophagitis were classified as having abnormal esophageal
motility. Pan-esophageal pressurization was present in 17%
of patients with eosinophilic esophagitis and 2% of GERD
patients while compartmentalized pressurization was pres-
ent in 19% of patients with eosinophilic esophagitis. In
theory, pan-esophageal pressurization in patients with eo-
sinophilic esophagitis could be the result of decreased com-
pliance of the esophagus. These patterns were not seen in
control subjects. Although motility disorders were more
frequent in patients with eosinophilic esophagitis than in
controls, the prevalence and type were similar to those
observed in GERD patients [27]. These results suggest that
there is no clinical indication for HRM in patients with
eosinophilic esophagitis. Furthermore, HRM has prompted the recognition of three
different subtypes of achalasia which are achalasia with min-
imal esophageal pressurization (type I, classic), achalasia with
esophageal compression (type II) and achalasia with spasm
(type III) [22]. However, it can be argued that these subtypes
can also be recognized with conventional manometry. With the use of intraluminal ultrasonography a longitu-
dinal muscle contraction of the distal esophagus was recent-
ly identified as the cause of pan-esophageal pressurization in
type II achalasia [23]. Furthermore, esophageal emptying
occurs intermittently during periods of pan-esophageal pres-
surization [23]. Patients with achalasia of types I and III
have no emptying or relatively normal emptying during
most swallows, respectively [23]. This suggests that, in
achalasia patients, esophageal emptying results from
swallow-induced longitudinal muscle contraction of the dis-
tal esophagus, which increases esophageal pressure and
allows flow across the non-relaxed EGJ [23]. Achalasia Ghosh et al. described that with the use of HRM substantial
shortening of the esophagus can be observed in achalasia
patients [10]. If conventional manometry is used in these
patients the movement of the EGJ between pressure sensors
can result in a pseudorelaxation. This suggests that the use
of HRM may result in an improved sensitivity for the
diagnosis of achalasia when compared to conventional ma-
nometry [10]. Bariatric Surgery Future studies are warranted to deter-
mine the clinical relevance of the baseline impedance level. ambulatory pH-impedance monitoring should preferably be
performed after cessation of PPI therapy [31]. However, a
different study by Pritchett and colleagues suggested that
impedance-pH on PPI may be best to study refractory [57]. Recent guidelines therefore suggest that the choice of on-
PPI or off-PPI should rely heavily on the pretest probability
of GERD and the question that needs to be answered [58]. Obviously, more research is warranted in this area to pro-
vide a definitive algorithm for reflux monitoring in GERD. Anti-reflux surgery, also known as surgical fundoplica-
tion, is a widely performed intervention for GERD. Besides
decreasing the number of acid reflux episodes, anti-reflux
surgery also reduces the number of weakly acidic reflux
episodes [32]. Therefore, one could suggest that GERD
patients with symptoms due to weakly acidic reflux epi-
sodes are also suitable candidates for anti-reflux surgery. This would favor pH-impedance monitoring over pH-
metry in the pre-operative work up of GERD patients. Whereas the detection of reflux episodes with pH-metry
can be easily detected as a pH-drop <4, the detection of
reflux episodes with impedance monitoring can be some-
what more troublesome. Several studies have assessed inter-
observer variability for the detection of reflux episodes with
impedance monitoring in the same center, however, a multi-
center study has not yet been performed in adults. A recent
multi-center study by Loots et al. assessed inter observer
variability in impedance tracings of children and found only
moderate agreement between the observers [38]. A different
approach which could potentially decrease inter-observer
variability is the use of an automatic analysis. The results
from studies which assessed the clinical use of the automatic
analysis show that this is a helpful tool which shows a high
correlation with a manual analysis [38, 39]. Despite the fact that reflux monitoring is a valuable
diagnostic tool, evidence for the use of pH-metry as a
preoperative predictor of surgical outcome has shown
conflicting evidence [33]. Furthermore, the quality and con-
sistency of the data on the use of pre-operative reflux mon-
itoring are mixed and the strength of the associations
remains unclear [33]. Moreover, the Symptom Association
Probability (SAP), which is a measure for the correlation
between symptoms and reflux episodes has not been shown
to be a preoperative predictor of surgical outcomes if mea-
sured by pH-metry [34]. Bariatric Surgery Laparoscopic placement of an adjustable gastric band
(LAGB) is a widely performed treatment for obesity. How-
ever, dysphagia, vomiting, and regurgitation are common
side effects of gastric banding. Several studies have aimed to
assess esophageal motility and clearance in symptomatic
LAGB patients using high resolution manometry [25, 26]. By comparing symptomatic patients with successfully trea-
ted patients, relevant parameters such as intra-bolus pressure
and lower esophageal contractile segment have been identi-
fied [25, 26]. It has been suggested that these parameters can
be used to determine whether the LAGB should be removed
[26]. However, whether HRM can replace the barium swal-
low, which is the current gold standard to determine flow
across the gastric band, cannot be concluded on the basis of
the available literature. Furthermore, it is also not known
whether a pre-surgical HRM can predict treatment outcome. Therefore, although the use of HRM looks promising, future
studies are warranted to determine its clinical application in Hemmink et al. assessed whether cessation of PPI could
further increase the diagnostic yield in patients with GERD
[31]. These authors found that the best chance to assess a
relationship between symptoms and reflux episodes is after
cessation of PPI. Therefore, these authors concluded that Curr Gastroenterol Rep (2012) 14:197–205 201 Fig. 2 Impedance tracings of a
wet swallow and a liquid reflux
episode. Wet swallows are
characterized by an antegrade
drop in impedance channels
whereas a reflux episode is
characterized by a retrograde
drop in impedance channels
after which a swallows clears
the refluxate and the impedance
levels return to their respective
baseline level integrity [35, 36, 37•]. Farré et al. demonstrated that baseline
impedance values remains lower after perfusion with acid in
rabbits [37•]. Furthermore, a positive correlation was found
between the transepithelial resistance of esophageal mucosa
and baseline impedance levels [37•]. A study from our
center showed a negative correlation between the acid ex-
posure time in the esophagus and the baseline impedance
levels [35]. Furthermore, even when the acid exposure time
was in the physiological range, GERD patients were char-
acterized by lower baseline impedance levels than controls
[35]. Moreover, PPI can increase low baseline impedance
levels in adults and children [35, 36]. These findings suggest
that baseline impedance is related to esophageal acid expo-
sure and could be a marker of reflux-induced changes to the
esophageal mucosa. Bariatric Surgery However, studies which specifically
assessed the role of pH-impedance monitoring as a preopera-
tive predictor of surgical outcome have not yet been per-
formed. Therefore, although pH-impedance monitoring is
the gold standard for the detection of reflux episodes, it
remains unclear whether pre-operative pH-impedance moni-
toring is better than pH-metry alone. Belching Disorders and Aerophagia The rumination syndrome is a functional gastroduodenal
disorder of unknown etiology characterized by persistent
or recurrent regurgitation of recently ingested food into the
mouth. Diagnosis of rumination is currently based on clin-
ical features as defined by the Rome III criteria [50]. The
pathophysiology is incompletely understood, but involves a
rise in intra-gastric pressure, generated by a voluntary, but
often unintentional, contraction of the abdominal wall mus-
culature causing retrograde movement of gastric contents
into the esophagus [51]. A large proportion of regurgitation
episodes in patients with the rumination syndrome are
weakly acidic, therefore, pH-impedance monitoring is supe-
rior to pH-metry for the detection of regurgitation episodes
in rumination patients [52]. Furthermore, with the use of
combined manometry-impedance monitoring Rommel et al. could differentiate between belching and rumination [53]. Although the number of patients with the rumination syn-
drome who are studied by HRM is still relatively small, the
first results suggest that HRM results in a more accurate
detection of rumination episodes [52]. Therefore, in case of
diagnostic uncertainty, manometric evaluation combined
with pH-impedance monitoring may confirm the diagnosis. Whether HRM is superior to conventional manometry in the
diagnostic work-up of the rumination syndrome needs to be
determined by future studies. Gastric belching is a physiological mechanism which ena-
bles venting of gas from the stomach to the esophagus in
order to prevent accumulation of excess gas in the stomach
or duodenum [40, 41]. With the use of esophageal imped-
ance monitoring a second mechanism of belching was iden-
tified in 2004, the so-called supragastric belch [42]. During
a supragastric belch, air is rapidly sucked into the esophagus
and is immediately followed by a rapid expulsion of air
without ever reaching the stomach. The clinical relevance of this differentiation between
supragastric belches and gastric belches was demonstrated
in patients with excessive belching as their main symptom
[42]. Bredenoord et al. demonstrated that these patients are
characterized by an increased frequency of supragastric
belches but not of gastric belches [42]. Moreover, a pilot
study in patients with excessive supragastric belching
revealed that speech therapy could decrease the severity of
belching symptoms [43]. Belching is a common symptom in GERD patients with
an incidence of 40% to 49%. Hemmink et al. showed that
supragastric belching can also occur in patients with GERD
[44]. Moreover, supragastric belching is associated with
troublesome belching symptoms in GERD patients. Reflux in Pediatric Patients During the work-up of reflux symptoms in children pH-
impedance monitoring is increasingly being performed. Studies revealed that a significant proportion of all reflux
episodes is weakly acidic and weakly acidic reflux episodes
are more prevalent than acid reflux episodes in infants with
symptoms [46, 47•]. Therefore, pH-impedance monitoring Between reflux episodes and swallows, the esophageal
lumen is collapsed and the resulting baseline impedance
level is determined by the esophageal wall. Several studies
hypothesized that impedance baseline measurements could
also be used to evaluate changes in esophageal mucosa 202 Curr Gastroenterol Rep (2012) 14:197–205 increases the diagnostic yield for GERD in children and is
superior to pH-metry [48]. With the use of impedance monitoring the clinician can
differentiate between supragastric belching, aerophagia and
gastric belching in patients with gas related symptoms such
as belching and abdominal bloating. This results in a more
accurate diagnosis and could possibly result in a more
specific treatment for selected patients. A recent study by Rosen et al. aimed to determine pre-
dictors of fundoplication outcome in children using pH-
impedance monitoring [49]. These authors found that no
single reflux marker predicted fundoplication outcome. Fur-
thermore, neither a positive symptom index nor a positive
symptom sensitivity index predicted postoperative improve-
ment. These results suggest that pH-impedance monitoring
in children may not be a useful tool in predicting fundopli-
cation outcome [49]. Belching Disorders and Aerophagia In the-
ory, supragastric belches could offer more specific treatment
options for GERD patients with troublesome belching
symptoms. Hemmink et al. also observed that supragastric
belches can precede reflux episodes and suggested that
supragastric belches could induce reflux episodes [44]. Studies which assess the role of speech therapy in this
specific group of GERD patients are currently being per-
formed in our center. Rumination Syndrome Rumination Syndrome Discussion Papers of particular interest, published recently, have been
highlighted as: The application of HRM has improved our understanding of
the esophagus and increases the diagnostic yield of manom-
etry. Furthermore, the design of the manometry assembly
and the presentation of the acquired data are easier to per-
form in clinical practice and easier learned by the clinician. •
Of importance 1. Butin JW, Olsen AM, Moersch HJ, Code CF. A study of esopha-
geal pressures in normal persons and patients with cardiospasm. Gastroenterology. 1953;23(2):278–93. The technique of HRM, the interpretation of the acquired
data and the classification of disease is constantly being
improved. Recently, 3D-HRM was developed which meas-
ures pressure with several radial pressure sensors at the
location of the EGJ [56]. 3D-HRM is currently only being
used in research and their clinical applications need to be
further explored. 2. Dent J. A new technique for continuous sphincter pressure mea-
surement. Gastroenterology. 1976;71(2):263–7. 3. Clouse RE, Staiano A. Topography of the esophageal peristaltic
pressure wave. Am J Physiol. 1991;261(4 Pt 1):G677–84. 4. Grübel C, Hiscock R, Hebbard G. Value of spatiotemporal repre-
sentation of manometric data. Clin Gastroenterol Hepatol. 2008;6
(5):525–30. pH-impedance monitoring has proven to be a diagnostic
tool which is superior to pH-metry in the diagnostic work-
up of adult and pediatric patients with GERD symptoms. Furthermore, the application of pH-impedance monitoring
with regard to belching complaints has already lead to more
specific treatment targets. Currently, evolving concepts re-
garding the use of baseline impedance levels and the role of
supragastric belching in patients with GERD are being
assessed. The outcomes of these studies will determine the
clinical relevance of these novel concepts and could expand
the clinical applications of impedance monitoring. 5. Johnson LF, Demeester TR. Twenty-four-hour pH monitoring of
the distal esophagus. A quantitative measure of gastroesophageal
reflux. Am J Gastroenterol. 1974;62(4):325–32. 6. Silny J. Intraluminal multiple electric impedance procedure for
measurement of gastrointestinal motility. J Gastrointest Motil. 1991;3:151–62. 7. Tuttle SG, Grossman MI. Detection of gastro-esophageal reflux by
simultaneous measurement of intraluminal pressure and pH. Proc
Soc Exp Biol Med. 1958;98(2):225–7. 8. Spechler SJ, Castell DO. Classification of oesophageal motility
abnormalities. Gut. 2001;49(1):145–51. 9. Pandolfino JE, Ghosh SK, Rice J, et al. Classifying esophageal
motility by pressure topography characteristics: a study of 400
patients and 75 controls. Am J Gastroenterol. 2008;103(1):27–37. 10. Ghosh SK, Pandolfino JE, Rice J, et al. Discussion Impaired deglutitive EGJ
relaxation in clinical esophageal manometry: a quantitative analy-
sis of 400 patients and 75 controls. Am J Physiol Gastrointest
Liver Physiol. 2007;293(4):G878–85. Potential competing interests
None. Open Access
This article is distributed under the terms of the Crea-
tive Commons Attribution License which permits any use, distribution,
and reproduction in any medium, provided the original author(s) and
the source are credited. Non-obstructive Dysphagia Combined manometry-impedance can be used to identify
esophageal function abnormalities in patients with non-
obstructive dysphagia [54]. The advantage of combined
HRM-impedance over conventional manometry is the abil-
ity to detect incomplete bolus clearance and combine this
information with a detailed assessment of peristalsis [12]. With the use of combined HRM-impedance it was shown
that incomplete bolus clearance occurs with failed peristalsis
or with pressure breaks in the peristaltic contraction [12]
(Fig. 1d). Moreover, pressure breaks in the peristaltic con-
traction are more frequent in patients with dysphagia com-
pared to control subjects [12]. Aerophagia is a disorder which is characterized by abdom-
inal bloating and abdominal distension due to an excessive
volume of intestinal gas [45]. With the use of impedance
monitoring an increased amount of air swallows was identi-
fied as a possible cause of the excessive intestinal gas. This
finding could, in theory, offer more specific treatment targets
and future studies will determine the clinical implications of
this finding. Curr Gastroenterol Rep (2012) 14:197–205 203 Financial support
A.J. Bredenoord is supported by The Netherlands
Organization for Scientific Research (NWO). A recent study by Burgess et al. applied this technique of
combined HRM-impedance monitoring and described that
little further information was gained compared to HRM alone
[55]. However, studies that assess the clinical relevance of
combined HRM and impedance monitoring with a focus on
bolus escape at the transition zone have not yet been per-
formed. Therefore, the currently available literature does not
support a clear clinical application of combined HRM-
impedance monitoring in patients with non-obstructive dys-
phagia at this moment. Conclusions 11. Pandolfino JE, Fox MR, Bredenoord AJ, Kahrilas PJ. High-
resolution manometry in clinical practice: utilizing pressure
topography to classify oesophageal motility abnormalities. Neurogastroenterol Motil. 2009;21(8):796–806. HRM and pH-impedance monitoring have lead to an im-
provement in diagnostics and classification of esophageal
disorders. Future studies will further determine the clinical
implications of the new insights which have been acquired
with these techniques. 12. Roman S, Lin Z, Pandolfino JE, Kahrilas PJ. Distal contraction
latency: a measure of propagation velocity optimized for esopha-
geal pressure topography studies. Am J Gastroenterol. 2011;106
(3):443–51. 13. Pandolfino JE, Leslie E, Luger D, et al. The contractile decelera-
tion point: an important physiologic landmark on oesophageal
pressure topography. Neurogastroenterol Motil. 2010;22(4):395–
400. e90. Disclosure
Dr. A. Bredenoord has been a consultant and honoraria
recipient for AstraZeneca, has received grant funding from Shire, and
payment for development of educational presentations from MMS
International; Dr. B.F. Kessing and A.J.P.M. Smout reported no poten-
tial conflicts of interest relevant to this article. 14. Pandolfino JE, Roman S, Carlson D, et al. Distal esophageal spasm
in high-resolution esophageal pressure topography: defining clin-
ical phenotypes. Gastroenterology. 2011;141(2):469–75. 204 Curr Gastroenterol Rep (2012) 14:197–205 32. Broeders JAJL, Bredenoord AJ, Hazebroek EJ, et al. Effects of
anti-reflux surgery on weakly acidic reflux and belching. Gut. 2011;60(4):435–41. 15. Bogte A, Bredenoord AJ, Oors J, Siersema PD, Smout AJPM. Reproducibility of esophageal high-resolution manometry. Neurogastroenterol Motil. 2011;23(7):e271–6. 16. Fox M, Hebbard G, Janiak P, et al. High-resolution manometry
predicts the success of oesophageal bolus transport and identifies
clinically important abnormalities not detected by conventional
manometry. Neurogastroenterol Motil. 2004;16(5):533–42. 33. Ip S, Tatsioni A, Conant A, et al. Predictors of clinical outcomes
following fundoplication for gastroesophageal reflux disease re-
main insufficiently defined: a systematic review. Am J
Gastroenterol. 2009;104(3):752–8. 17. Ghosh SK, Pandolfino JE, Kwiatek MA, Kahrilas PJ. Oesophageal
peristaltic transition zone defects: real but few and far between. Neurogastroenterol Motil. 2008;20(12):1283–90. 34. Broeders JA, Draaisma WA, Bredenoord AJ, et al. Impact of
symptom-reflux association analysis on long-term outcome after
Nissen fundoplication. Br J Surg. 2011;98(2):247–54. 35. Kessing BF, Bredenoord AJ, Weijenborg PW, et al. Esophageal
acid exposure decreases intraluminal baseline impedance levels. Am J Gastroenterol. 2011;106(12):2093–7. 18. • Roman S, Lin Z, Kwiatek MA, Pandolfino JE, Kahrilas PJ. Weak
peristalsis in esophageal pressure topography: classification and
association with Dysphagia. Am J Gastroenterol. 2011;106
(2):349–56. Conclusions This article defines novel criteria for the peristaltic
pressure breaks and correlates these findings to the clinical pre-
sentation of the patient.. 36. Loots CM, van Wijk MP, Smits MJ. Measurement of mucosal
conductivity using multichannel intraluminal impedance: a poten-
tial marker of mucosal integrity that is restored in infants receiving
acid suppression therapy. J Pediatr Gastroenterol Nutr. 2011;53
(1):120–3. 19. Bredenoord AJ, Weusten BLAM, Carmagnola S, Smout AJPM. Double-peaked high-pressure zone at the esophagogastric junction
in controls and in patients with a hiatal hernia: a study using high-
resolution manometry. Dig Dis Sci. 2004;49(7–8):1128–35. 37. • Farré R, Blondeau K, Clement D, et al. Evaluation of oesopha-
geal mucosa integrity by the intraluminal impedance technique. Gut. 2011;60(7):885–92. This article assesses whether the base-
line impedance level can be a novel marker for esophageal mucosa
integrity.. 20. Scherer JR, Kwiatek MA, Soper NJ, Pandolfino JE, Kahrilas PJ. Functional esophagogastric junction obstruction with intact peri-
stalsis: a heterogeneous syndrome sometimes akin to achalasia. J
Gastrointest Surg. 2009;13(12):2219–25. 38. Loots CM, van Wijk MP, Blondeau K, et al. Inter- and intra
observer variability in pH-impedance analysis between 10 experts
and automated analysis. J Pediatr. http://dx.doi.org/10.1016/j. jpeds.2011.08.017. 21. • Lazarescu A, Karamanolis G, Aprile L, et al. Perception of
dysphagia: lack of correlation with objective measurements of
esophageal function. Neurogastroenterol Motil. 2010;22
(12):1292–7. This article highlights the lack of correlation be-
tween objective findings and subjective complaints in patients with
non-obstructive dysphagia.. 39. Hemmink GJM, Bredenoord AJ, Aanen MC. Computer analysis of
24-h esophageal impedance signals. Scand J Gastroenterol. 2011;46(3):271–6. 22. Pandolfino JE, Kwiatek MA, Nealis T, et al. Achalasia: a new
clinically relevant classification by high-resolution manometry. Gastroenterology. 2008;135(5):1526–33. 40. Bredenoord A, Smout A. Physiologic and pathologic belching. Clin Gastroenterol Hepatol. 2007;5(7):772–5. 41. Wyman JB, Dent J, Heddle R, et al. Control of belching by the
lower oesophageal sphincter. Gut. 1990;31(6):639–46. 23. Hong SJ, Bhargava V, Jiang Y, Denboer D, Mittal RK. A
unique esophageal motor pattern that involves longitudinal
muscles is responsible for emptying in achalasia esophagus. Gastroenterology. 2010;139(1):102–11. 42. Bredenoord AJ, Weusten BLAM, Sifrim D, Timmer R, Smout
AJPM. Aerophagia, gastric, and supragastric belching: a study
using intraluminal electrical impedance monitoring. Gut. 2004;53
(11):1561–5. 24. Pratap N, Kalapala R, Darisetty S, et al. Achalasia cardia subtyping
by high-resolution manometry predicts the therapeutic outcome of
pneumatic balloon dilatation. J Neurogastroenterol Motil. 2011;17
(1):48–53. (
)
43. Conclusions Hemmink GJM, Ten Cate L, Bredenoord AJ, et al. Speech therapy
in patients with excessive supragastric belching–a pilot study. Neurogastroenterol Motil. 2010;22(1):24–8. e2-3. 44. Hemmink GJM, Bredenoord AJ, Weusten BLAM, Timmer R,
Smout AJPM. Supragastric belching in patients with reflux symp-
toms. Am J Gastroenterol. 2009;104(8):1992–7. 25. Burton PR, Brown WA, Laurie C, Hebbard G, O’Brien PE. Criteria
for assessing esophageal motility in laparoscopic adjustable gastric
band patients: the importance of the lower esophageal contractile
segment. Obes Surg. 2010;20(3):316–25. 45. Hemmink GJM, Weusten BLAM, Bredenoord AJ, Timmer R,
Smout AJPM. Aerophagia: excessive air swallowing demonstrated
by esophageal impedance monitoring. Clin Gastroenterol Hepatol. 2009;7(10):1127–9. 26. Cruiziat C, Roman S, Robert M, et al. High resolution esophageal
manometry evaluation in symptomatic patients after gastric band-
ing for morbid obesity. Dig Liver Dis. 2011;43(2):116–20. 46. van Wijk MP, Benninga MA, Omari TI. Role of the multichannel
intraluminal impedance technique in infants and children. J Pediatr
Gastroenterol Nutr. 2009;48(1):2–12. 27. Roman S, Hirano I, Kwiatek MA, et al. Manometric features of
eosinophilic esophagitis in esophageal pressure topography. Neurogastroenterol Motil. 2011;23(3):208–14. e111. 28. Aanen MC, Bredenoord AJ, Samsom M, Smout AJPM. Reliability
of oesophageal pH recording for the detection of gastro-
oesophageal reflux. Scand J Gastroenterol. 2008;43(12):1442–7. 47. • Pilic D, Fröhlich T, Nöh F, et al. Detection of gastroesophageal
reflux in children using combined multichannel intraluminal im-
pedance and pH measurement: data from the German Pediatric
Impedance Group. J Pediatr. 2011;158(4):650–4.e1. This article
describes the use of impedance monitoring in children and dem-
onstrates that pH-impedance monitoring is superior to pH-metry
alone. 29. Bredenoord AJ, Weusten BLAM, Timmer R, Conchillo JM, Smout
AJPM. Addition of esophageal impedance monitoring to pH mon-
itoring increases the yield of symptom association analysis in
patients off PPI therapy. Am J Gastroenterol. 2006;101(3):453–9. 48. Loots CM, Benninga MA, Davidson GP, Omari TI. Addition
of pH-impedance monitoring to standard pH monitoring
increases the yield of symptom association analysis in infants
and children with gastroesophageal reflux. J Pediatr. 2009;154
(2):248–52. 30. Savarino E, Marabotto E, Zentilin P, et al. The added value of
impedance-pH monitoring to Rome III criteria in distinguishing
functional heartburn from non-erosive reflux disease. Dig Liver
Dis. 2011;43(7):542–7. 31. Hemmink GJ, Bredenoord AJ, Weusten BL, et al. Esophageal pH-
impedance monitoring in patients with therapy-resistant reflux
symptoms: ‘on’ or ‘off’ proton pump inhibitor? Am J
Gastroenterol. 2008;103(10):2446–53. ( )
49. Conclusions Rosen R, Levine P, Lewis J, Mitchell P, Nurko S. Reflux events
detected by pH-MII do not determine fundoplication outcome. J
Pediatr Gastroenterol Nutr. 2010;50(3):251–5. Curr Gastroenterol Rep (2012) 14:197–205 205 evaluation of patients with non-obstructive Dysphagia. Am J
Gastroenterol. 2005;100(12):2624–32. 50. Foundation R. Guidelines–Rome III diagnostic criteria for func-
tional gastrointestinal disorders. J Gastrointestin Liver Dis. 2006;15(3):307–12. 55. Burgess NG, Wyeth JW. An audit of combined multichannel intra-
luminal impedance manometry in the assessment of dysphagia. J
Gastroenterol Hepatol. 2011;26:79–82. 51. Tack J, Blondeau K, Boecxstaens V, Rommel N. Review article: the
pathophysiology, differential diagnosis and management of rumina-
tion syndrome. Aliment Pharmacol Ther. 2011;33(7):782–8. 56. Kwiatek MA, Pandolfino JE, Kahrilas PJ. 3D-high resolution
manometry of the esophagogastric junction. Neurogastroenterol
Motil. 2011;23(11):e461–9. 52. Kessing BF, Govaert F, Masclee AAM, Conchillo JM. Impedance
measurements and high-resolution manometry help to better define
rumination episodes. Scand J Gastroenterol. 2011;46(11):1310–5. 57. Pritchett JM, Aslam M, Slaughter JC, Ness RM, Garrett CG, Vaezi
MF. Efficacy of esophageal impedance/pH monitoring in patients
with refractory gastroesophageal reflux disease, on and off therapy. Clin Gastroenterol Hepatol. 2009;7(7):743–8. 53. Rommel N, Tack J, Arts J, et al. Rumination or belching-
regurgitation? Differential diagnosis using oesophageal impedance-
manometry. Neurogastroenterol Motil. 2010;22(4):e97–104. Clin Gastroenterol Hepatol. 2009;7(7):743–8. y
g
( )
54. Conchillo JM, Nguyen NQ, Samsom M, Holloway RH, Smout
AJPM. Multichannel intraluminal impedance monitoring in the 58. Pandolfino JE, Vela MF. Esophageal-reflux monitoring. Gastrointest Endosc. 2009;69(4):917–30.
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Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state
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Abstract Citation: Ge H, Wu P, Qian H, Xie XS (2018)
Relatively slow stochastic gene-state switching in
the presence of positive feedback significantly
broadens the region of bimodality through
stabilizing the uninduced phenotypic state. PLoS
Comput Biol 14(3): e1006051. https://doi.org/
10.1371/journal.pcbi.1006051 Within an isogenic population, even in the same extracellular environment, individual cells
can exhibit various phenotypic states. The exact role of stochastic gene-state switching reg-
ulating the transition among these phenotypic states in a single cell is not fully understood,
especially in the presence of positive feedback. Recent high-precision single-cell measure-
ments showed that, at least in bacteria, switching in gene states is slow relative to the typical
rates of active transcription and translation. Hence using the lac operon as an archetype, in
such a region of operon-state switching, we present a fluctuating-rate model for this classi-
cal gene regulation module, incorporating the more realistic operon-state switching mecha-
nism that was recently elucidated. We found that the positive feedback mechanism induces
bistability (referred to as deterministic bistability), and that the parameter range for its occur-
rence is significantly broadened by stochastic operon-state switching. We further show that
in the absence of positive feedback, operon-state switching must be extremely slow to trig-
ger bistability by itself. However, in the presence of positive feedback, which stabilizes the
induced state, the relatively slow operon-state switching kinetics within the physiological
region are sufficient to stabilize the uninduced state, together generating a broadened
parameter region of bistability (referred to as stochastic bistability). We illustrate the oppo-
site phenotype-transition rate dependence upon the operon-state switching rates in the two
types of bistability, with the aid of a recently proposed rate formula for fluctuating-rate mod-
els. The rate formula also predicts a maximal transition rate in the intermediate region of
operon-state switching, which is validated by numerical simulations in our model. Overall,
our findings suggest a biological function of transcriptional “variations” among genetically
identical cells, for the emergence of bistability and transition between phenotypic states. Relatively slow stochastic gene-state switching
in the presence of positive feedback
significantly broadens the region of
bimodality through stabilizing the uninduced
phenotypic state Hao Ge1,2*, Pingping Wu3, Hong Qian4, Xiaoliang Sunney Xie1,5* a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 1 Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, P.R.China, 2 Beijing International
Center for Mathematical Research (BICMR), Peking University, Beijing, P.R.China, 3 School of Mathematical
Sciences and Centre for Computational Systems Biology, Fudan University, Shanghai, P.R.China,
4 Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of
America, 5 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts,
United States of America * haoge@pku.edu.cn(HG); xie@chemistry.harvard.edu(XSX) * haoge@pku.edu.cn(HG); xie@chemistry.harvard.edu(XSX) RESEARCH ARTICLE Editor: Daniel A Beard, University of Michigan,
UNITED STATES Received: June 20, 2017
Accepted: February 18, 2018
Published: March 12, 2018
Copyright: © 2018 Ge et al. This is an open access
article distributed under the terms of the Creative
Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in
any medium, provided the original author and
source are credited. Received: June 20, 2017
Accepted: February 18, 2018
Published: March 12, 2018 Copyright: © 2018 Ge et al. This is an open access
article distributed under the terms of the Creative
Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in
any medium, provided the original author and
source are credited. Data Availability Statement: All relevant data are
within the paper and its Supporting Information
files. Funding: HG is supported by NSFC grants
(10901040,21373021,11622101), the National
High Technology Research and Development
Program of China (863 Program) Funding: HG is supported by NSFC grants
(10901040,21373021,11622101), the National
High Technology Research and Development
Program of China (863 Program)
(2015AA020406), and the Foundation for the
Authors of National Excellent Doctoral
Dissertations of China (No. 201119). XSX is Funding: HG is supported by NSFC grants
(10901040,21373021,11622101), the National
High Technology Research and Development
Program of China (863 Program)
(2015AA020406), and the Foundation for the
Authors of National Excellent Doctoral
Dissertations of China (No. 201119). XSX is 1 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality supported by an NIH Pioneer Grant (No. 1DP1OD000277). The funders had no role in study
design, data collection and analysis, decision to
publish, or preparation of the manuscript. supported by an NIH Pioneer Grant (No. 1DP1OD000277). The funders had no role in study
design, data collection and analysis, decision to
publish, or preparation of the manuscript. Author summary Identifying the mechanism underlying the coexistence of multiple stable phenotypic states
has been a challenging scientific problem for more than half a century, and an appropriate
mathematical model at the single-cell level is also in high demand. Single-cell measure-
ments conducted in the past ten years have shown that gene-state switching is slow rela-
tive to the typical rates of active transcription and translation; hence the recently proposed
fluctuating-rate model is a good candidate for describing the single-cell dynamics. We use
the classic gene regulation module of the lac operon as an archetype and build a specific
fluctuating-rate model based on the recently identified operon-state switching mecha-
nism. This model is analyzed to dissect the interplay between positive feedback and the
stochastic switching of gene states in the emergence of bistability/multistablity and the
transition between phenotypic states. We show that relatively slow operon-state switching
stabilizes the uninduced state and that the positive feedback stabilizes the induced state. Thus, the parameter range for bistability is significantly broadened. In addition, recently
proposed landscape theory and rate formula predict opposite phenotype-transition rate
dependence on operon-state switching rates for the two types of bistability. Competing interests: The authors have declared
that no competing interests exist. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality stochastically and is relatively slow compared with the typical rates of active transcription and
translation. The stochastic operon-state switching of the lac operon has also been shown to be
crucial for the change in a cell’s phenotype [3, 13], which highlights the importance of single-
molecule events inside the cell. In terms of quantitative biochemical kinetics, the temporal evolution of the probability dis-
tribution of a well-mixed reaction system is governed by a Chemical Master Equation (CME)
[21], from which the corresponding stochastic trajectory of a single cell can be computationally
simulated. We have recently shown, using a toy model of gene regulation, that when the rate of
gene-state switching is low relative to the typical rates of active transcription and translation,
the full CME can be reduced to a single-molecule fluctuating-rate model, in which the dynam-
ics of mRNA and protein copy numbers at each given gene state follow deterministic dynamics
while transcription rates fluctuate due to stochastic gene-state switching [22], which is neces-
sary for spontaneous phenotypic state transitions. In the full Chemical Master Equation, the copy-number fluctuations of mRNA and protein
resulting from stochastic synthesis and degradation are present, which prevent us from study-
ing the role of only the stochastic gene-state switching. However, in fluctuating-rate models,
stochastic gene-state switching is the only source of randomness, the conclusions drawn from
which are much more clean and unambiguous. On the other hand, although numerical simu-
lations of full Chemical Master Equation can be practical, theoretical analysis is still difficult to
implement; while solid theoretical foundations have already been proposed for fluctuating-
rate models, which are also called piecewise deterministic Markov processes [22, 23]. The fluc-
tuating-rate model is easier to implement both theoretically and numerically. Therefore, it is a
good candidate for studying single-cell dynamics, especially towards investigating the role of
only the stochastic gene-state switching. So far, the exact role of stochastic gene-state switching that occurs during the transition
between phenotypic states in a single cell is unclear, especially in the presence of positive feed-
back. In the present study, we address this problem using the lac operon as an archetype. Recent experiments have shown that the switching of operon states of the lac operon is slow
compared with typical rates of active transcription and translation. Introduction Individual cells of a given genotype can exhibit various phenotypes. The phenotype of a cell
usually refers to distinct characteristics (static and dynamic, physical or chemical) and the
associative biological functions of the cell. Extending the central dogma of molecular biology,
it is now accepted that the behavior of a single cell is determined by both the genomic polynu-
cleic acid sequence and the dynamics of intracellular biochemical networks in space and time. The biochemical reactions inside cells serve as the immediate environment for the genome,
where genotypic information resides. It is only through intracellular biochemistry that extra-
cellular conditions can interact with genes. Based on this perspective, we propose the following: for a population of cells with identical
genomes and extracellular conditions, each phenotype can be represented by a cluster of sin-
gle-cell data defined as a peak (e.g., modal value) in the multi-dimensional histogram of bio-
molecular copy-numbers measured at steady state. In general, the peak is a sizable region in
the vast biochemical kinetic space, which is known as an attractor in chemical kinetics [1, 2]. Multiple peaks naturally discretize the space; at a given instance in time, a single cell can reside
in one of these discrete states. More interestingly, a homogeneous cell population responds to a varying environment
through changes in the distribution among discrete phenotypic states, rather than through
gradual adaptation to an intermediate state [3]. At a single-cell level, this observation is known
as all-or-none [4]. Furthermore, it has recently been shown that a steady-state multi-modal
distribution can be recovered after a subpopulation of cells under a peak is removed [5, 6],
indicating that dynamic interconversion between phenotypic states occurs within a single cell. In a sufficiently long time, each single cell is considered ergodic among the different pheno-
types. The coexistence of multiple phenotypic states diversifies clonal cells; and provides a
non-genetic evolutionary advantage for survival in unpredictable environments [7–9]. Recent experiments have revealed that the dynamics of a single cell are essentially stochas-
tic, as there is only a single copy of DNA inside a typical cell, which leads to stochastic mRNA
and protein production [10, 11]. Both transcriptional and translational events have been
shown to occur in stochastic bursts [10, 12–20] indicating that the gene state switches PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 2 / 24 Results The lac operon of E. coli, which involves multiple transcription factors, was the first complex
model of gene regulation to be elucidated. It consists of a promoter, a terminator, an operator
and three adjacent structural genes (lacZ, lacY, and lacA). lacZ encodes β-galactosidase, an
intracellular enzyme that catalyzes the transformation of the disaccharide lactose to glucose
and galactose, while lacY encodes β-galactoside permease, a membrane-bound transport pro-
tein that transports extracellular lactose into the cell. The lac operon remains inactive when
there is no extracellular lactose available, or if there is a more readily-available energy source,
such as glucose. However, it is rapidly activated when lactose is present(in the absence of glu-
cose), due to positive feedback. In the absence of lactose, the production of β-galactosidase is inhibited: an intracellular
regulatory protein known as the lactose repressor (lacI gene product) binds to the lac opera-
tor. In the presence of lactose, the repressor’s affinity for the lac operator is decreased by allo-
lactose, whose production from lactose is catalyzed by β-galactoside. As the repressor’s
affinity decreases, RNA polymerase transcribes the lac genes, leading to a high level of the
encoded proteins and consequent digestion of more lactose (Fig 1A). In wet-lab experiments,
inducers such as the lactose analog thiomethyl β-D-galactoside (TMG) are used instead of
lactose, because such inducers are not readily digested and therefore remain at a constant
concentration. The lac repressor molecule is a tetramer of identical subunits. Under repressed conditions,
one dimer binds to the major lac operator O1, and a second dimer binds to one of the weaker
auxiliary operators, O2 or O3, together forming a DNA loop. Choi et al. [3] have investigated
the molecular mechanism of the transition of E. coli cells from one phenotype to another
via lac operon. At intermediate inducer concentrations, a population of genetically identical
cells will exhibit two distinct phenotypes: fully induced cells and uninduced cells. Choi et al. observed a basal level of expression in uninduced cells as a result of the partial dissociation
of the tetrameric repressor from the operator O1 on looped DNA. In contrast, the rare occur-
rence of complete dissociation of the repressor results in large bursts of permease expression,
which trigger the induction of the lac operon. Therefore, stochastic single-molecule switching
between operon states is responsible for the change in the phenotype of the cell. Relatively slow stochastic gene-state switching significantly broadens bimodality rates vary with operon-state switching rates under each type of bistability. We also illustrate
that the maximal transition rates between different phenotypic states are achieved with an
intermediate rate of operon-state switching, which is a phenomenon that was predicted previ-
ously [27] and is explained using a recently proposed phenotype-transition rate formula. Finally but not the least, we not only explained the previously reported experimental dis-
coveries in the present study, but also further refined some earlier conclusions that were not as
precisely presented, such as the effect of DNA looping as well as the concept and quantification
of thresholds of phenotype transitions. Thus, in such a region of
operon-state switching, we propose to explore the single-molecule fluctuating-rate model in
quantitative detail, by incorporating the previous described operon-state switching mechanism
[3]. This mathematical model illustrates the emergence of discrete phenotypic states from
detailed nonlinear biochemical kinetics, and the robustness of such cellular states follows natu-
rally. Although in general, positive feedback is necessary for bistability in a biochemical net-
work, we show that the stochasticity in operon-state switching of an individual cell is able to
not only trigger stochastic transitions between phenotypic states, but also significantly broaden
the range of environmental parameters under which bistability occurs. The bistability that
occurs in the absence of stochasticity is called deterministic bistability, while the bistability
which occurs in the presence of stochasticity but beyond the parameter range of deterministic
bistability is called stochastic bistability. We further show that stochastic operon-state switching must be extremely slow to trigger
stochastic bistability (bimodal distribution) by itself in the absence of positive feedback. On
the other hand, positive feedback is known to be able to maintain a stable state [24–26], hence
with the help of positive feedback, the induced state is stabilized beyond the range of determin-
istic bistability, even when the rates of stochastic operon-state switching is only within the
physiological region. However, positive feedback is not able to stabilize the uninduced state
within the same parameter region. We show that the uninduced state is instead stabilized by
the relatively slow operon-state switching. Together, the mechanism of significantly broadened
parameter range of bistability is explained. We further predict how the phenotype-transition 3 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality Fig 1. Overview of the model. (A) Regulatory mechanism of the lac operon. Expression of permease increases the intracellular concentration of the inducer TMG
(thiomethyl β-D-galactoside), which removes the repressor LacI from the promoter, leading to increased expression of permease. Hence the repressor LacI and
permease LacY form a positive feedback loop. (B) Cartoon showing the dynamics of operon states. (C) Diagram of the Markovian jumping process of operon states. The O state denotes the free operon; the OR state denotes the operon bound to the repressor at the auxiliary lac operator O2 or O3(partial dissociation); the OR state
denotes the repressor bound to the operon at both the major and auxiliary lac operators; the ORIm state denotes the repressor bound to the operon at the auxiliary lac
operator O2 or O3 and to the inducer. Fig 1. Overview of the model. (A) Regulatory mechanism of the lac operon. Expression of permease increases the intracellular concentration of the inducer TMG
(thiomethyl β-D-galactoside), which removes the repressor LacI from the promoter, leading to increased expression of permease. Hence the repressor LacI and
permease LacY form a positive feedback loop. (B) Cartoon showing the dynamics of operon states. (C) Diagram of the Markovian jumping process of operon states. The O state denotes the free operon; the OR state denotes the operon bound to the repressor at the auxiliary lac operator O2 or O3(partial dissociation); the OR state
denotes the repressor bound to the operon at both the major and auxiliary lac operators; the ORIm state denotes the repressor bound to the operon at the auxiliary lac
operator O2 or O3 and to the inducer. https://doi.org/10.1371/journal.pcbi.1006051.g001 https://doi.org/10.1371/journal.pcbi.1006051.g001 The deterministic dynamics of all other chemical species under each operon state in the
fluctuating-rate model consist of several differential equations representing the temporal evo-
lution of mRNA, LacY polypeptides, and the intracellular inducer concentrations. The stochas-
tic kinetics of the operon states are described in Fig 1B and 1C, and are modeled by a simple
Markovian jumping process. Single-molecule fluctuating-rate model with recently identified operon-
state switching mechanism Stochastic gene-state switching is a major source of stochasticity inside a single cell [10, 13,
28], and even responsible for the phenotype transition [3]. By evoking the recently identified
stochastic gene-state switching mechanism, we propose a single-molecule fluctuating-rate
model for the lactose operon, introducing the fluctuating transcription rates into the determin-
istic dynamics described in previous studies [4, 29, 30]. 4 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow gene-state switching induces stochastic bistability with a
much broadened parameter range Positive feedback induces deterministic bistability. When stochastic operon-state
switching is very rapid, the dynamics of a single cell are well-described by a deterministic
mean-field equation (See Eq 3). Theoretical chemists refer to this as the adiabatic limit [27,
33]. Such systems exhibit bistability over a certain range of environmental parameters (i.e., co-
existence of two phenotypic states), as long as the synthesized gene product positively regulates
its own synthesis in a sigmoidal fashion [34]. Positive feedback increases protein levels, which
leads to a higher rate of synthesis and an even greater protein levels. However, positive feed-
back also implies lower protein levels resulting in reduced synthesis and a further decrease in
protein levels (with the presence of degradation). Therefore, there must exist a critical protein
level (threshold) in a single cell above which protein levels increase until complete saturation
(on-state or induced state) is reached and below which protein levels drop until nearly reach-
ing zero (off-state or uninduced state). Hence, there exist three steady states in the presence of
strong positive feedback: two stable states that are separated by an unstable state, which is
referred to as the “threshold” (or saddle point, similar to a transition state in molecular bio-
physics). When a system deviates from the unstable threshold, the deviation becomes even
greater due to positive feedback until the system reaches a stable steady state. This mechanism
is referred to as deterministic bistability, in contrast to the case below, which is caused by sto-
chastic fluctuations without a deterministic counterpart. In addition to the all-or-none bistable system, there is another common decision-making
mechanism in cells: the ultrasensitive system with a graded response. These mechanisms are
not incompatible with each other, and cells have the ability to convert one to the other and vise
versa [4]. Hence, a bifurcation diagram can be utilized to precisely represent the complete
range of environmental parameters over which the system is bistable. Fig 2A shows the steady-
state copy number of permease as a function of the extracellular concentration, Ie, of inducer
in the wild-type lac operon in the presence of positive feedback. The bifurcation diagram is
always accompanied by a hysteresis loop [34, 35]. In the absence of intrinsic stochasticity,
when the environmental parameter increases, the system remains in the off-state until it is no
longer stable. Relatively slow stochastic gene-state switching significantly broadens bimodality In addition, the repressor has 2 different binding constants (i.e. K and 1/K3, see S1 Text for
details) for the inducer, depending on whether the repressor is already bound to DNA [31, 32],
which are 10 to 100-fold apart. Accordingly, when inducer concentrations are below the lower
binding constant, there is weak concentration dependence of the complete dissociation rate,
whereas once the inducer concentration approaches the higher binding constant (100 μM), the
complete dissociation rate increases dramatically via the OR ! OR ! ORIm ! O pathway
shown in Fig 1B and 1C. This is the basic type of lac operon induction with which most molec-
ular biologists are familiar. However, the role of single-molecule fluctuations of DNA tran-
scription under intermediate concentrations of inducer was unclear prior to the work of Choi,
et al. [3]. The parameters of our model were obtained either directly from experimental measurements
or through fitting the predictions of the model to experimental data, as explained in S1 Text. The parameters of our model were obtained either directly from experimental measurements
or through fitting the predictions of the model to experimental data, as explained in S1 Text. The state O denotes the free operon; the state OR denotes the
operon with the repressor bound only at the auxiliary lac operator(partial dissociation); the
state OR denotes the operon with the repressor bound at both the major and auxiliary lac oper-
ators; and the state ORIm denotes the operon bound by both the repressor at the auxiliary lac
operator and inducer molecules. While the inducer is unlikely to interact with the fully bound
tetrameric repressor, it could conceivably bind to the inducer once a dimer head of the repres-
sor dissociates. Traditionally, the ORIm complex, which contains both the repressor and the inducers
bound on the operon, is omitted in mathematical models. Such an over-simplified model
cannot explain why the repressor binds stably to DNA in the absence of inducer, and is
released rapidly in the presence of inducer. Previous models, assuming either O + R ⇋OR or
O + R ⇋OR ⇋OR, imply that the rate of the complete dissociation of the repressor is inde-
pendent of the intracellular inducer concentration. However, data show that when the intracel-
lular inducer concentration is high, the frequency of complete dissociation can also be high
(0.01 minute−1) (Fig 2A in [3]). Alternatively, when the intracellular inducer concentration is
low, the frequency of complete dissociation events is low and shows very weak concentration
dependence (Fig 3D in [3]). Therefore it appears that the repressor also binds the inducer
when bound to the operon. 5 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality Relatively slow stochastic gene-state switching significantly broadens bimodality repressor bound to the operon in the absence of a DNA loop: 5 molec.−1 (D), 8 molec.−1 (E). (F) Stochastic hysteresis response of the
probability of induction for wild-type cells. Initial conditions: uninduced (blue line) or fully induced (red line) cells with a period of
T = 2000 min. The extracellular inducer concentration must exceed over 350μM to completely activate initially uninduced cells, whereas
it must decrease below 10μM to completely deactivate the initially induced cells. See S1 Text for parameter values. repressor bound to the operon in the absence of a DNA loop: 5 molec.−1 (D), 8 molec.−1 (E). (F) Stochastic hysteresis response of the
probability of induction for wild-type cells. Initial conditions: uninduced (blue line) or fully induced (red line) cells with a period of
T = 2000 min. The extracellular inducer concentration must exceed over 350μM to completely activate initially uninduced cells, whereas
it must decrease below 10μM to completely deactivate the initially induced cells. See S1 Text for parameter values. https://doi.org/10.1371/journal.pcbi.1006051.g002 https://doi.org/10.1371/journal.pcbi.1006051.g002 In addition to the extracellular inducer concentration, Ie, other parameters of the system
can also be tuned experimentally. For instance, an increase or decrease in the maximum
transcriptional rate can be achieved by increasing the number of operons in the cell or
changing the concentrations of other transcription factors. We computed the deterministic
bifurcation diagram (bistable or monostable) with both the active transcriptional rate, kM,
and the extracellular inducer concentration, Ie (Fig 2B). The system is bistable inside the
parameter region between the blue and brown lines and is monostable otherwise; it is an ana-
log of a first-order phase transition [36]. We show that the bistable range of extracellular
inducer concentrations becomes increasingly narrow and then disappears when kM either
increases or decreases from the value kM = 8min−1 for wild-type cells, which is known as the
cusp phenomenon [37]. In mutant strains that cannot transport lactose or the inducer into the cell, positive feedback
is disrupted. In this case, there is only one steady state (see Eq 3), which implies that positive
feedback is necessary for deterministic bistability (Fig 2C). Experiments have also indicated
that wild-type cells do not exhibit bistability without forming DNA loops as the repressor
bound to the operon [3]. However, our model demonstrates that bistability still exists without
DNA loops, although the range of bistability becomes much narrower and is therefore harder
to detect (Fig 2D and 2E). to detect (Fig 2D and 2E). Relatively slow operon state switching broadens the parameter range of bistability in
the presence of positive feedback. Spontaneous transitions between the on-state and the off-
state occur in a single cell. In mathematical models, stochasticity causes spontaneous transi-
tions in a deterministic bistable system and might also cause systems without deterministic
bistability to exhibit bistable phenomena, i.e., a bimodal distribution. To determine the param-
eter range for bistability in a stochastic system, we considered entire populations of cells start-
ing from either the on-state or the off-state at time zero and determined the fraction of cells in
the off state under different extracellular inducer concentrations after a certain amount of time
(Fig 2F, also see Materials and methods). This behavior is referred to as hysteresis and can be
directly measured in single-cell experiments [4]. In wild-type cells, we found that the range of
hysteresis was much wider than in the deterministic bistable system shown in Fig 2A. We then
directly simulated the copy-number distribution of permease, which confirmed the broadened
range of bistability (S2 Fig). The two induction curves presented in Fig 2F would merge and
the same fraction of phenotypic states would be achieved regardless of the different initial
states at which the cells start, only if the extracellular inducer concentration remains constant
for an extremely long period of time. For cellular phenotypes, this “extremely” long period of
time can be on the order of months or years, which completely beyond the relevant time scale
for cell division and typical experiments. This period is the origin of the ambiguity concerning
the threshold in the presence of stochasticity (see below). Furthermore, a cusp phenomenon similar to that shown in Fig 2B still exists in the presence
of intrinsic stochasticity, when the kM and Ie are considered. Bistability becomes more indis-
tinct when kM becomes either smaller or larger (S4 and S5 Figs). Therefore, the wild-type
value of kM is somewhat optimized. This phenomenon gives cells the opportunity to transition
between a hysteresis response system and an ultrasensitive graded response system. The cusp
phenomenon could be examined by replacing kM with other parameters in the system. Relatively slow gene-state switching induces stochastic bistability with a
much broadened parameter range Similarly, when the parameter decreases but remains within the bistable region,
the on-state remains stable, although the off-state reappears. Hysteresis protects the bistable
system from repeatedly transiting back and forth between the two phenotypic states when the
environmental parameter is near one of the critical values at which the bifurcations occur. Phe-
notype transitions involving hysteresis are driven by slow external modulation, while sponta-
neous transitions under fixed parameters require randomness. 6 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality Fig 2. Bistability with and without stochastic operon-state switching. (A) Deterministic bifurcation diagram for wild-type cells. There
are two saddle-node bifurcations occurring around Ie = 10μM and 59μM. (B) Deterministic bifurcation diagram containing both the
active transcriptional rate kM and the extracellular inducer concentration Ie. The wild-type cells exhibit deterministic bistability inside
the parameter region between the blue and brown lines and exhibit monostability otherwise. (C) Deterministic bifurcation diagram of
the mutant cells without positive feedback. (D)(E) Deterministic bifurcation diagrams with different association constants for the
| Fig 2. Bistability with and without stochastic operon-state switching. (A) Deterministic bifurcation diagram for wild-type cells. There
are two saddle-node bifurcations occurring around Ie = 10μM and 59μM. (B) Deterministic bifurcation diagram containing both the
active transcriptional rate kM and the extracellular inducer concentration Ie. The wild-type cells exhibit deterministic bistability inside
the parameter region between the blue and brown lines and exhibit monostability otherwise. (C) Deterministic bifurcation diagram of
the mutant cells without positive feedback. (D)(E) Deterministic bifurcation diagrams with different association constants for the PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 7 / 24 Relatively slow stochastic gene-state switching significantly broadens bimodality Stochastic bistability in the absence of positive feedback requires extremely slow
operon-state switching. It is known that stochasticity can induce bistability that has no mac-
roscopic counterpart and such a noise-induced bistability, called stochastic bistability, arises
from slow gene-state switching [33, 38–43]. Theoretical chemists refer to this scenario as
“non-adiabatic”, which is analogous to slow-moving nuclei in quantum mechanical atoms,
which is also similar to the quasi-static regime of enzyme kinetics [44]. This phenomenon is
purely stochastic; i.e., there is no determinstic bistability in the mean-field model that describes
in vitro biochemical experiments with large amounts of purified chemicals involving the same
parameters. However, in the absence of positive feedback, with the same parameters of wild-type cells,
we found that the stationary distribution was broad and did not exhibit distinct bistability (S3
Fig). This result implies that the operon-state switching inside a wild-type cell is not suffi-
ciently slow to exhibit bistability without positive feedback. We introduce the dimensionless parameter ω (See Material and methods), which character-
izes the rate of switching among multiple gene states. Mathematically, ω can be defined as the
ratio of switching rates among different gene states with respect to the wild-type rates or the
protein decay rate. We choose the former, in which ω = 1 corresponds to the wild-type rates. Further simulation showed that the switching rates among operon states must be at least 100-
1000 times slower than in the wild-type cells (ω = 0.01 −0.001) in order to trigger purely sto-
chastic bistability in the absence of positive feedback (Fig 3A–3C), which is rarely possible. Positive feedback and slow operon-state switching stabilize the induced and uninduced
states respectively. In the presence of positive feedback, it is beneficial to stabilize the
induced state as long as the extracellular inducer concentration is not too low, even when the
switching rates among operon states are within physiological regions (comparing Fig 3A and
3E with Fig 3D and 3F). In the induced state, the repressor is always fully dissociated from the
operon; once the operon is repressed, positive feedback keeps the intracellular inducer concen-
tration at a relatively high level; therefore, the repressor protein is forced to fully dissociate
from the operon rapidly, which stabilizes the induced state. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 8 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 We calculated the mean transition time between the fully repressed operon state and the
fully dissociated operon state of wild-type cells, under an intracellular inducer concentration
that is very high (induced state) or quite low (uninduced state) (Fig 4). The main pathways
underlying the induced state and the uninduced state are different (Fig 4A and 4B). Under the
uninduced state, the mean transition time (the reciprocal of rate) from the fully repressed
operon state to the fully dissociated operon state is quite long (Fig 4C), which stabilizes the
uninduced state, and the mean transition time backwards is much shorter (Fig 4E). On the
contrary, the mean transition time back and forth between the fully repressed operon state
and fully dissociated state in the induced state is also much shorter, which implies that the sta-
bility of the induced state can not be guaranteed by the stochastic switching between different
operon states. As the strength of stochasticity decreases, i.e. increasing the rates for stochastic switching
among operon states, the broadened parameter range for bistability in Fig 2F becomes nar-
rower and narrower, approaching the deterministic limit in Fig 2A (See S12 Fig). It is because
the rapid stochastic switching among operon states is not able to stabilize the uninduced state
any more outside the range of deterministic bistability. We also have tuned the strength of pos-
itive feedback, i.e. the parameter K, which is the equilibrium constant of the binding reaction
between the repressor and inducer. As the strength of positive feedback decreases, i.e. increas-
ing the parameter K, the capability of stabilizing the induced state also decreases (See S14 Fig). Together, positive feedback and stochastic operon-state switching significantly broaden the
parameter range of bistability. When the extracellular inducer concentration is low, positive 9 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality Fig 3. Positive feedback stabilizes the induced state. (A-C) Extremely slow operon-state switching is necessary to induce purely
stochastic bistability without positive feedback. (D-F) In the presence of positive feedback, the induced state is stabilized, and a bimodal
distribution emerges, even when operon-state switching rates are within the physiological region. https://doi.org/10.1371/journal.pcbi.1006051.g003 Fi 3 P
iti
f
db
k t bili
th i d
d t t
(A C) E
l
l
i hi
i
i d
l Fig 3. Positive feedback stabilizes the induced state. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Stochastic transition between different phenotypic states In addition to the mechanism of the emergence of bistability, we also sought to quantitatively
investigate the transition rates between different phenotypic states and the more detailed
molecular mechanisms that trigger them. How a single-molecule event determines the phenotype of a wild-type cell. There are
two kinds of bursts in the lac operon system: small bursts due to partial dissociation and large
bursts due to complete dissociation of the repressor from the operon. We confirmed previ-
ously reported experimental observations [3] (using the mathematical interpretations in the S1
Text and see S6 Fig): the size and frequency of small bursts are nearly independent of the intra-
cellular inducer concentration; and for large bursts, in the absence of positive feedback, size
always increases with the intracellular inducer concentration, while the frequency is invariant
under a low inducer concentration. How does a stochastic single-molecule event (i.e., a large burst) trigger phenotype transi-
tion? Time traces of permease showed that the stochastic full dissociation of the repressor
from the DNA could either successfully trigger phenotype transition or return to the unin-
duced state before arriving at the induced state (Fig 5A). The positive feedback mechanism of
the wild-type cell can significantly amlify the large burst, which dramatically increases the
probability of transition from the uninduced to the induced state (Fig 5B and S7 Fig). We cal-
culated the probability of successful induction of single cells initially in the uninduced state
after a single-molecule event(i.e., the repressor completely dissociating from the operon), as a
function of the extracellular inducer concentration (Fig 5C). Once the extracellular inducer
concentration reached 40μM, we found that the probability of induction was nearly 80%. We were also interested in the transition from the induced to the uninduced state. Once the
cell is induced, the intercellular concentration of the inducer is quite high, and the repressor
would always choose another pathway to dissociate rapidly from the operon (OR ! OR ! ORIm ! O in Fig 1C). These events make the induced state much more stable than the unin-
duced state, and contribute to much smaller fluctuations around the induced state than around
the uninduced state (Fig 4C and 4D). These predictions were also confirmed by our simulation
(S8 Fig). Stochastic threshold, time scales and quasi steady states. Another important quantity in
a bistable system is the barrier or threshold between the two phenotypic states. Relatively slow stochastic gene-state switching significantly broadens bimodality feedback cannot stabilize the induced state, whereas when the extracellular inducer concentra-
tion is high, positive feedback and slow fluctuations of operon states stabilize the induced and
uninduced states, respectively. This result explains why the broadened parameter range of bist-
ability can only be visualized on the right-hand-side of the deterministic bifurcation diagram
in Fig 2A. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 (A-C) Extremely slow operon-state switching is necessary to induce purely
stochastic bistability without positive feedback. (D-F) In the presence of positive feedback, the induced state is stabilized, and a bimodal
distribution emerges, even when operon-state switching rates are within the physiological region. https://doi.org/10.1371/journal.pcbi.1006051.g003 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 10 / 24 Fig 4. Major transit pathways and transition rates between fully repressed and fully dissociated operon states. (A, B) The major transit pathways
between fully repressed and fully dissociated operon states in the uninduced and induced phenotypic states. (C-F) Transition rates between fully
repressed and fully dissociated operon states in the uninduced and induced phenotypic states with very low and high intracellular inducer
concentrations respectively. The transition rates from the fully repressed operon state to the fully dissociated state in the uninduced phenotypic state
are the lowest, which stabilizes the uninduced state, even outside of the parameter range of deterministic bistability. https://doi.org/10.1371/journal.pcbi.1006051.g004
Relatively slow stochastic gene-state switching significantly broadens bimodality Relatively slow stochastic gene-state switching significantly broadens bimodality Fig 4. Major transit pathways and transition rates between fully repressed and fully dissociated operon states. (A, B) The major transit pathways
between fully repressed and fully dissociated operon states in the uninduced and induced phenotypic states. (C-F) Transition rates between fully
repressed and fully dissociated operon states in the uninduced and induced phenotypic states with very low and high intracellular inducer
concentrations respectively. The transition rates from the fully repressed operon state to the fully dissociated state in the uninduced phenotypic state
are the lowest, which stabilizes the uninduced state, even outside of the parameter range of deterministic bistability. https://doi.org/10.1371/journal.pcbi.1006051.g004 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 11 / 24 Stochastic transition between different phenotypic states The saddle
point of the mean-field model is generally regarded as the “deterministic” threshold, which is
an analog of the transition state in physical chemistry. In the presence of stochasticity, the defi-
nition of the threshold becomes vague. Choi et al. measured the single-cell time traces of fluorescence, normalized by cell size,
starting from different initial permease numbers, and they plotted the probability of induction
within 3 hours as a function of the initial permease number [3]. Then the threshold is deter-
mined through a Hill-type function fitting. However, the observed probability of induction in experiments is related to a quasi-steady
state rather than the final steady state, because it depends on the initial permease number
which is not a parameter but a dynamic variable of the system (Fig 2B in [3]). Because the tran-
sition rates between the different phenotypic states are low, the measured distribution is highly 12 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality Fig 5. Probability of induction by a single large burst and quasi-steady state. (A)Two typical single-cell tim
of permease levels. The first shows induction by a single full dissociation event of the repressor from the opero
while the second shows a failure to induce (right). (B) The large burst size in the presence of positive feedback
remarkably prolonged compared with the case without positive feedback. (C) Successful probability of inducti
complete dissociation event as a function of the extracellular inducer concentration. (D-G) Probability of indu
y
g
g
g
y Fig 5. Probability of induction by a single large burst and quasi-steady state. (A)Two typical single-cell time traces
of permease levels. The first shows induction by a single full dissociation event of the repressor from the operon (left),
while the second shows a failure to induce (right). (B) The large burst size in the presence of positive feedback is
remarkably prolonged compared with the case without positive feedback. (C) Successful probability of induction by a
complete dissociation event as a function of the extracellular inducer concentration. (D-G) Probability of induction Fig 5. Probability of induction by a single large burst and quasi-steady state. (A)Two typical single-cell time traces Fig 5. Probability of induction by a single large burst and quasi-steady state. (A)Two typical single-cell time traces
of permease levels. Relatively slow stochastic gene-state switching significantly broadens bimodality within different time windows starting from uninduced cells (blue) or induced cells (red); we determined the
stochastic threshold through mathematical fitting in the form of y ¼
xn
xnþKn for these curves. The deterministic threshold
is approximately 20(molec.), while the stochastic thresholds are larger and decrease when the time window is extended. The extracellular inducer concentration, Ie, is set to 40μM. within different time windows starting from uninduced cells (blue) or induced cells (red); we determined the
stochastic threshold through mathematical fitting in the form of y ¼
xn
xnþKn for these curves. The deterministic threshold
is approximately 20(molec.), while the stochastic thresholds are larger and decrease when the time window is extended. The extracellular inducer concentration, Ie, is set to 40μM. https://doi.org/10.1371/journal.pcbi.1006051.g005 dependent on the time window of the experiments and the initial state. Using our model simu-
lation, we rebuilt the experimental observations. We plotted the fraction of induced cells with
different time windows starting from uninduced or induced cells (red and blue curves in Fig
5D–5G). The estimated threshold decreases with the extension of the experimental time win-
dow, and is different from the deterministic threshold predicted from the corresponding
deterministic mean-field dynamics. It is clear that these two curves approach the same hori-
zontal line over time, indicating that the final steady-state distribution is independent of both
the time window and the initial state of the cell population. The difference between the quasi-steady state and the final steady state reveals why the
induced state dominates the final stationary distribution when the extracellular inducer con-
centration exceeds 40μM, according to estimated transition rates (data not shown), but it is
still possible to observe a distinct bimodal distribution at a reasonable time scale starting from
uninduced states when the extracellular inducer concentration exceeds 40μM (S2 Fig). The difference between the quasi-steady state and final steady state increases in the region
of deterministic bistability as the rate of gene-state switching increases. For example, when the
gene-state switching rate is 100 times faster, within a certain time scale (time = 2000 min), cells
will not become induced if they start in the uninduced state. However, it does exist on the
other side of the deterministic threshold, whose stability could be clearly demonstrated if the
cells start in the induced state (S9 Fig). Transition rates between phenotypic states and resonance phenomena. Stochastic transition between different phenotypic states The first shows induction by a single full dissociation event of the repressor from the operon (left),
while the second shows a failure to induce (right). (B) The large burst size in the presence of positive feedback is
remarkably prolonged compared with the case without positive feedback. (C) Successful probability of induction by a
complete dissociation event as a function of the extracellular inducer concentration. (D-G) Probability of induction PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 13 / 24 Once the gene-
state switching rates are not only slow compared to typical rates of active transcription and
translation, but also rapid compared with the time scale of cell division, a general rate formula
for phonotype transition in a fluctuating-rate model has been recently proposed [22]. The rate
formula is associated with the phenotypic landscape function, which is an analog of the energy
function at an equilibrium [22, 27, 39, 45–52]. The phenotypic landscape is defined as the negative logarithm of the steady-state probabil-
ity distribution pss(x) at the limit of infinite ω [22, 27, 39, 45, 47–50, 52], i.e., ðxÞ ¼ lim
o!1 1
o log pssðxÞ:
ð1Þ ð1Þ Here, ω serves as a Boltzmann factor [β = (kBT)−1] in thermal physics. However, this determin-
istic landscape ϕ(x) is not given a priori; it is an emergent property of the chemical kinetics of
a single cell. Furthermore, the most important feature of the function ϕ(x) is that the corre-
sponding mean-field deterministic dynamics in the large limit of ω, always decrease along ϕ(x)
(Fig 6A and 6B), which suggests that any local minimum of the function ϕ(x) corresponds to a
stable steady state of the deterministic model [22, 47]. Therefore, the necessary and sufficient
condition for deterministic bistability(i.e., two stable steady states predicted by the mean-field
model) is a double-welled deterministic landscape ϕ(x) (Fig 6A and 6B). Although the landscape function is not easily obtained, the most important consequence is
the transition rate formula from the i-th phenotype to the j-th one [22], i.e., kij ’ k0
ije oVij;
ð2Þ ð2Þ here the positive quantity Vij is referred to as the barrier term from the i-th phenotypic state PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 14 / 24 Relatively slow stochastic gene-state switching significantly broadens bimodality Fig 6. Transition rates between phenotypic states and the phenomenon of resonance. (A) Phenotypic landscape ϕ(x) in the region of
deterministic bistability. (B) Phenotypic landscape ϕ(x) outside the region of deterministic bistability. (C) The rate formula (2) is valid for the
parameter region of deterministic bistability with the fitted positive barrier V12 = 0.0550. Relatively slow stochastic gene-state switching significantly broadens bimodality deterministic bistability. (E) The transition rate increases and is finally saturated when the operon-state switching rate increases in the region
of purely stochastic bistability. (F) The mean phenotype transition time varies with the operon-state switching rates at Ie = 25μM. https://doi.org/10.1371/journal.pcbi.1006051.g006 deterministic bistability. (E) The transition rate increases and is finally saturated when the operon-state switching rate increases in the region
of purely stochastic bistability. (F) The mean phenotype transition time varies with the operon-state switching rates at Ie = 25μM. https://doi.org/10.1371/journal.pcbi.1006051.g006 https://doi.org/10.1371/journal.pcbi.1006051.g006 to the j-th phenotypic state, and k0
ij is a prefactor with units, all of which are independent of ω. From a dynamic perspective, this formula could also be understood through Kramers’ rate the-
ory, in which ω $ (kBT)−1 is proportional to the reciprocal of the fluctuation amplitude, and a
small T and large ω both represent small fluctuations. Theoretically, in the case of bistability,
the barrier terms V12 and V21 in formula (2) are the minimum of the differences in the local
maximum and minimum values, respectively, of the deterministic landscape ϕ along any tran-
sition path between the two phenotypic states [22]. Formula (2) is valid within the parameter region of deterministic bistability when ω is large. In this region, both phenotypic states are preserved within the large limit of ω. Additionally,
the forward and backward barriers between the phenotypic states are positive, and the transi-
tion rates therefore decrease exponentially with ω (Fig 6C). The transition rate from the
induced state to the uninduced state (* 10−7 min−1) is much lower than the forward transition
rate (* 10−4 min−1), which is beyond our computational capacity. However, due to established
mathematical theory [22, 53], the rate formula (2) is still valid. We found that the simulated stochastic transit time from the uninduced state to the
induced state exhibited an exponential distribution (S11 Fig). Additionally, when the gene-
state switching rates were sufficiently rapid, the typical transition pathway from the uninduced
state to the induced one is not the same as that of the wild-type by a single-molecule event, but
due to the accumulation of many times of full dissociation events (Fig 6D). Alternatively, in the parameter region of stochastic bistability, the two phenotypic states
merge within the large limit of ω, and the bimodal distribution gradually becomes unimodal
(S10 Fig). Thus, the transition between the two phenotypic states becomes relaxing towards
one unique phenotypic state. Accordingly, the transition rate increases with ω and reaches a
saturation value (Fig 6E), which is qualitatively different from the region of deterministic
bistability. We then numerically calculated the mean transition time dependent on the parameter ω in
the parameter region of deterministic bistability when Ie = 25μM. We showed that the transi-
tion rate from the uninduced state to the induced state reaches a maximum when the gene-
state switching rates are around the wild-type values (Fig 6F), which is referred to as a resonant
phenomenon [27, 42]. This occurs because, according to the rate in formula (2), the transition
rate between phenotypic states decreases exponentially when gene-state switching is rather
rapid. Meanwhile, when gene-state switching is very slow, it becomes the rate-limiting step for
the phenotype transition, which is also extremely low. (D) When the switching rates among different gene
states are sufficiently rapid, the phenotype transition from the uninduced state to the induced state must occur through the accumulation of
many complete dissociation events, rather than through a single dissociation event in wild-type cells, within the parameter region of Fig 6. Transition rates between phenotypic states and the phenomenon of resonance. (A) Phenotypic landscape ϕ(x) in the region of
deterministic bistability. (B) Phenotypic landscape ϕ(x) outside the region of deterministic bistability. (C) The rate formula (2) is valid for the
parameter region of deterministic bistability with the fitted positive barrier V12 = 0.0550. (D) When the switching rates among different gene
states are sufficiently rapid, the phenotype transition from the uninduced state to the induced state must occur through the accumulation of
many complete dissociation events, rather than through a single dissociation event in wild-type cells, within the parameter region of PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 15 / 24 Relatively slow stochastic gene-state switching significantly broadens bimodality state switching mechanism. The present study reveals the power of this type of model, which
will be used to investigate other questions regarding single-cell dynamics. We investigated the origin of the bimodal distribution of the lac operon in a realistic model
incorporating the recently discovered mechanism of operon-state switching. It has been
shown that either positive feedback or single-molecule fluctuations gives rise to bistability by
its own. However, we show here that the interplay of these two mechanisms makes the bimodal
distribution more realistic and reliable in the presence of environmental perturbations. With-
out positive feedback, the single-molecule kinetics of gene states are not sufficient slow, at least
in E. coli, to induce bistability, and without fluctuations of single DNA molecules, positive
feedback cannot stabilize the uninduced state when the extracellular inducer concentration is
high. The physiological region for the gene-state switching rates is therefore favorable and bal-
ances the two contradictory purposes of controlling stochasticity within a certain magnitude
and triggering phenotype transitions within a reasonable time scale. The stochastic model can quantify the relative stability (fractions in a population) of coex-
isting phenotypes, which cannot be achieved using a deterministic approach. However, the
time scale of the stochastically triggered spontaneous phenotype transition is quite long, which
prevents direct laboratory measurement of the relative stability (given the time window of a
typical experiment), due to inconsistencies between a quasi-steady state and the final steady
state. Such inconsistencies also mean that the concept of the threshold is not well-defined in a
stochastic scenario, which is considerably different from the deterministic threshold predicted
from the deterministic mean-field model. Recently, Razooky, et al. also investigated the interplay between positive feedback and rela-
tively slow gene-state switching kinetics in the transcriptional program controlling HIV’s fate
decision between active replication and viral latency, and found out that the positive feedback
shifts and expands the region of LTR bimodality [54]. However, the positive feedback in LTR
dynamics lacks cooperativity and cannot produce deterministic bistability by itself, which is
essentially different from the lac operon dynamics we studied here. Also the perspective we
used to explain the broadened bistability is different from [54]: their explanation more focused
on the mean-noise relation while ours more focus on the stability of each phenotypic states. In many experiments, people used minimal media for cells at 37˚C, making the E. Discussion Only a single copy of a DNA molecule exists inside a typical cell. Hence, the stochastic dynam-
ics of a single cell resulting from the fluctuating kinetics of single DNA molecule are a conse-
quence of fundamental physical and chemical laws. Still, individual cells can control the
stochastic kinetics of DNA molecules over a reasonable time scale and fluctuations due to bio-
chemical reactions can be even advantageous. Recent high-precision measurements performed
in single cells have revealed that stochastic gene-state switching is slow compared to typical
rates of active transcription and translation. The fluctuating-rate model is a good candidate for
the investigation of single-cell dynamics in this region because it only incorporates the gene- 16 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Model development Mean-field deterministic model. The model consists of several differential equations that
account for the temporal evolution of mRNA (M), the LacY polypeptide (Y), and the intracel-
lular inducer concentration. Here we take R to denote the concentration of the active (free) repressor while RT denotes
the total concentration of the repressor. Additionally Ie denotes the extracellular concentration
of thiomethyl β-D-galactoside (TMG), and I denotes the intracellular TMG concentration. y
g
The kinetic equations for the lac operon are y
g
The kinetic equations for the lac operon are R
RT
¼
K
K þ In ;
dM
dt
¼
kMpO gMM;
dY
dt
¼
kYM gYY;
dI
dt
¼
aklYbðIeÞ gII þ cðIe IÞ:
ð3Þ R
RT
¼
K
K þ In ;
dM
dt
¼
kMpO gMM;
dY
dt
¼
kYM gYY;
dI
dt
¼
aklYbðIeÞ gII þ cðIe IÞ:
ð3Þ ð3Þ where pO is the probability that the operon is free. Traditionally, pO is expressed as
a
1þ R
R0 ¼ a
KþIn
KþInþRT
R0 K, where a is the highest probability that can be archived when R = 0, and R0 is a
1þ R
R0 ¼ a
KþIn
KþInþRT
R0 K, where a is the highest probability that can be archived when R = 0, and R0 is the half saturation concentration of the repressor bound to TMG; however, after taking the
partial dissociation state into account in the present study, we believe that it should be modi-
fied (See Eq (6) and S1 Text). The Hill coefficient n is approximately 2 according to experi-
mental measurements [4]. Although there are 4 subunits in the repressor protein, K is the
equilibrium constant of the binding reaction between the repressor and inducer when not
bound to the operon. kM is the maximum transcription rate and γM represents the degradation
plus dilution rate. kY is the initial rate of translation for LacY transcripts. γY is the dilution and
degradation rate of LacY polypeptides. The variable α, which has two values, 0 or 1, denotes whether LacY is replaced by Tsr and
positive feedback is absent. The inducer could diffuse into the cell quickly, even in the absence
of permease; therefore, we denote c as the diffusion constant due to the difference in the
inducer concentrations across the cell membrane. Relatively slow stochastic gene-state switching significantly broadens bimodality organization, which is fundamentally different from the Watson-Crick genetic template-
copying mechanism. coli cells
grow slowly (doubling time is about one hour). In there experiments, a single copy or at most
two copies are reasonable. However, in a more natural environment, E. coli grows at most
commonly 20 −30 minutes doubling time, which implies more copies of operons. Hence we
also simulate the case with more than one copy of operons (see Materials and methods), and
find out that the qualitative results are exactly the same as the case with only a single copy of
operon (S13 Fig). On the other hand, in the main text, we model the lac operon under unnatural conditions,
i.e. using the unnatural lactose-analogue TMG, which is used in most of the experiments. We
also simulate the extended version of the model with lactose replacing TMG, in which an addi-
tional term representing the hydrolysis of allolactose is added (see Materials and methods). Under steady-state condition of extracellular lactose, the results are quite the same as those
from the main model in which we use TMG (S15 Fig). Finally, the notion of cell diversification of genetically identical phenotypes in biological
entities, due to stochastic gene expression, requires a mechanism for the inheritance of an
“intercellular biochemical” state through cell division. This issue has been discussed previ-
ously [55, 56]. Briefly, if the volume of a biochemical system doubles while maintaining
the same internal concentrations, the phenotypic state of the cell is maintained. Therefore,
the phenotype of a single cell can be preserved via growth and division into two daughter
cells. This epigenetic inheritance mechanism is based on dynamic biochemical self- PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 17 / 24 Relatively slow stochastic gene-state switching significantly broadens bimodality phenotypic states. The population behavior varies due to changes in the relative portion of the
two states, but no cell can exist in an intermediate state. Single-molecule fluctuating-rate model. The mean-field approach neither explains the
most recent experimental observations nor is consistent with the proposed stochastic mecha-
nism [3]. Therefore we developed a stochastic model that incorporates the stochastic single-
molecule operon-state switching. Most cells possess only one or two copies of any given gene. Hence, we separated the time
scales for operon-state switching and other evolutionary processes in the system, to introduce
a stochastic variable, η, which accounts for the regulation of transcriptional initiation by active
repressors. Single-molecule events(i.e., whether the operon is bound or unbound to a repres-
sor(s)) can be modeled by a simple Markovian jumping process (i.e., rate equations; see Fig 1B
and 1C). The switching rates between different operon states in wild-type cells are estimated and
provided in the S1 Text. We multiply each gene-state switching rate in Fig 1B and 1C by a
non-dimensionalized number, ω, which describes how rapid the switching rates are compared
with the wild-type. The parameter ω plays a central role in the investigation of phenotype-tran-
sition in the main text. In Fig 1B and 1C, OR and ORIm denote the partial dissociation state of DNA. Hence the
variable η is a stochastic trajectory that has only three values, 0, f and 1, which denote the tran-
scriptional levels when fully repressed (OR), partially dissociated (OR and ORIm) and
completely dissociated O, respectively. Finally, we obtain a three-dimensional differential equation that contains the variable η
mentioned above. dM
dt
¼
kMZ gMM;
dY
dt
¼
kYM gYY;
dI
dt
¼
aklYbðIeÞ gII þ cðIe IÞ:
ð5Þ ð5Þ In addition, the term pO in the deterministic model (3) is the mean of η: pO ¼ hZi ¼
1 þ f ðK1½R þ K1K3½RInÞ
1 þ K1½R þ K1K3½RIn þ K1K2½R ¼
K þ In þ f KK1RT þ RT
K4 In
K þ In þ KðK1 þ K1K2ÞRT þ RT
K4 In ;
ð6Þ ð6Þ where Ki = ri/r−i. Each repressor head is a dimer and can bind 0, 1, or 2 inducer molecules, and
we set n ’ 2 due to cooperativity [4]. Model development The inducer (TMG) could be also trans-
ported into the bacterium via a catalytic process in which permease plays a central role. Thus,
the inducer influx rate is assumed to be kIβ(Ie)Y. γI is the dilution and degradation rate of the
inducer. Here the form of β(Ie) is taken from [4], bðIeÞ
¼
I0:6
e :
ð4Þ ð4Þ The first equation in Eq 3 indicates that the kinetics of the repressor binding to TMG are
rapid; thus its kinetics yield an instantaneous fraction of the free repressor to total repressor
(rapid-equilibrium assumption) [4, 30]. As the concentration of TMG varies, the system generates either one or two stable steady
states, with a saddle-node bifurcation that separates the two phases. The existence of two stable
steady states is in accord with the all-or-none phenomenon observed in both population and
single-cell experiments [3, 57], by which we mean that a cell can exist in only one of the two PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 18 / 24 Relatively slow stochastic gene-state switching significantly broadens bimodality Quantifying bistability in the presence of stochasticity We define the bimodal steady-state distribution as bistability in the presence of stochasticity. However, it is quite time-consuming to obtain the exact steady-state distribution in simula-
tion, if it is bimodal. Luckily, if we only want to determine whether the steady-state distribu-
tion is bimodal or not, it is much easier. There is a fact that if the steady-state distribution is
unimodal, the simulated distribution will rapidly converge to the steady-state distribution,
while if the steady-state distribution is bimodal, the converging time is extremely long. Hence,
we can use the quasi-steady-state distribution and hysteresis response curves to determine
whether the system is bistable or not. We only need to simulate the system for a reasonably
long time, which is enough for making the system converge into the unimodal steady-state dis-
tribution if it is not bistable, or into the bimodal quasi-steady-state distribution if it is bistable. Hysteresis response curve follows the same idea. After a reasonably long time, if the simulated
distributions starting from induced state or uninduced state can not merge together, then it
implies bistability. Stochastic simulation method We used the standard exact method to simulate the dynamics of the operon developed by
Doob, Bortz et al., and Gillespie [58–61]. See the Supplementary Material in [22] for details. S1 Text. Mathematical derivations and calculations of parameters.
(PDF) S1 Text. Mathematical derivations and calculations of parameters. (PDF) S1 Fig. A two-state model of the central dogma without feedback. (TIF) S1 Fig. A two-state model of the central dogma without feedback.
(TIF) S2 Fig. Copy-number distributions for the permease protein in wild-type cells. We com-
pare the copy-number distribution of permease with different extracellular concentration of
inducers Ie and show that the Ie range of the bimodal distribution is much more broader than
that predicted in the deterministic bifurcation diagram(Fig 2A in the main text). (TIF) S2 Fig. Copy-number distributions for the permease protein in wild-type cells. We com-
pare the copy-number distribution of permease with different extracellular concentration of
inducers Ie and show that the Ie range of the bimodal distribution is much more broader than
that predicted in the deterministic bifurcation diagram(Fig 2A in the main text). (TIF) that predicted in the deterministic bifurcation diagram(Fig 2A in the main text). (TIF)
S3 Fig. Broad copy-number distributions for permease protein without positive feedback. (TIF)
S4 Fig. Copy-number distributions for permease protein under different values of Ie when
kM is small. (TIF)
S5 Fig. Copy-number distributions for permease protein under different values of Ie when
kM is large. (TIF)
S6 Fig. Size and frequency of small and large bursts without positive feedback, dependent
on the extracellular inducer concentration. (TIF)
S7 Fig. Copy-number distribution for the newly synthesized permease protein during a
single large burst with positive feedback, which is quite similar to exponential distribution. (TIF) Extended versions of the model Several extended versions of the fluctuating-rate model have also been investigated: (1)
Without feedback: set α to be zero; (2) Without DNA loop: there is only two operon states
O and OR; (3) In the case of multiple operons: independent n operons coupled only through
the intracellular M, Y, I, and the corresponding cell division time is set to be 50/n minutes,
which makes the parameters rI = 0.012nmin−1 and rY is equal to 0.1 + rI; (4) Lactose replac-
ing TMG: a term hyd
I
IþKI Y representing the hydrolysis of allolactose is added to the
right-hand-side of dI
dt. Simulated results from these extended versions are in the Supporting
Information. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 19 / 24 Supporting information pp
g
S1 Text. Mathematical derivations and calculations of parameters. (PDF)
S1 Fig. A two-state model of the central dogma without feedback. (TIF)
S2 Fig. Copy-number distributions for the permease protein in wild-type cells. We com-
pare the copy-number distribution of permease with different extracellular concentration of
inducers Ie and show that the Ie range of the bimodal distribution is much more broader than
that predicted in the deterministic bifurcation diagram(Fig 2A in the main text). (TIF)
S3 Fig. Broad copy-number distributions for permease protein without positive feedback. (TIF)
S4 Fig. Copy-number distributions for permease protein under different values of Ie when
kM is small. (TIF)
S5 Fig. Copy-number distributions for permease protein under different values of Ie when
kM is large. (TIF)
S6 Fig. Size and frequency of small and large bursts without positive feedback, dependent
on the extracellular inducer concentration. (TIF)
S7 Fig. Copy-number distribution for the newly synthesized permease protein during a
single large burst with positive feedback, which is quite similar to exponential distribution. (TIF) Acknowledgments We thank the past and present members of X.S.Xie’s group and particularly Dr. Paul Choi. We
also thank Dr. Biswajit Das for carefully reading the manuscript. We thank the past and present members of X.S.Xie’s group and particularly Dr. Paul Choi. We
also thank Dr. Biswajit Das for carefully reading the manuscript. S11 Fig. Nearly exponentially distributed transition time from the uninduced state to the
induced state in wild-type cells.
(TIF) S12 Fig. Stochastic hysteresis response of the probability of induction when tuning the
strengths of stochasticity. Initial conditions: uninduced (blue line) or fully induced (red line)
cells with a period of T = 2000 min. (TIF) S13 Fig. Bistability with and without stochastic operon-state switching when the number
of operons are more than one. (A)(B) Deterministic bifurcation diagram for wild-type cells in
which the number of operons is 2 or 6. (C)(D) Deterministic bifurcation diagrams for the
repressor bound to the operon in the absence of a DNA loop with association constant that
equals 5 molec.−1. (E) (F) Stochastic hysteresis response of the probability of induction. (TIF) S13 Fig. Bistability with and without stochastic operon-state switching when the number
of operons are more than one. (A)(B) Deterministic bifurcation diagram for wild-type cells in
which the number of operons is 2 or 6. (C)(D) Deterministic bifurcation diagrams for the
repressor bound to the operon in the absence of a DNA loop with association constant that
equals 5 molec.−1. (E) (F) Stochastic hysteresis response of the probability of induction. (TIF) S14 Fig. Bistability with and without stochastic operon-state switching tuning the strength
of positive feedback. (A)(B) Deterministic bifurcation diagram tuning the strength of positive
feedback. (C-F) Stationary distributions when tuning the strength of positive feedback. (TIF) S14 Fig. Bistability with and without stochastic operon-state switching tuning the strength
of positive feedback. (A)(B) Deterministic bifurcation diagram tuning the strength of positive
feedback. (C-F) Stationary distributions when tuning the strength of positive feedback. (TIF) S15 Fig. Bistability with and without stochastic operon-state switching when the dynamics
of inducer is replaced by that of lactose. (A-D) Deterministic bifurcation diagram in which
the dynamics of inducer is replaced by that of lactose. (E) (F) Stochastic hysteresis response of
the probability of induction. (TIF) S15 Fig. Bistability with and without stochastic operon-state switching when the dynamics
of inducer is replaced by that of lactose. (A-D) Deterministic bifurcation diagram in which
the dynamics of inducer is replaced by that of lactose. (E) (F) Stochastic hysteresis response of
the probability of induction. (TIF) S9 Fig. Copy-number distributions for the permease protein observed in the region of
deterministic bistability, varying with ω.
(TIF) S10 Fig. Copy-number distributions for the permease protein observed in the region of
purely stochastic bistability, varying with ω. (TIF) S4 Fig. Copy-number distributions for permease protein under different values of Ie when
kM is small.
(TIF) S6 Fig. Size and frequency of small and large bursts without positive feedback, dependent
on the extracellular inducer concentration. (TIF) S7 Fig. Copy-number distribution for the newly synthesized permease protein during a
single large burst with positive feedback, which is quite similar to exponential distribution
(TIF) 20 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Copy-number distributions for the permease protein observed in the region of
purely stochastic bistability, varying with ω. (TIF)
S11 Fig. Nearly exponentially distributed transition time from the uninduced state to the
induced state in wild-type cells. (TIF)
S12 Fig. Stochastic hysteresis response of the probability of induction when tuning the
strengths of stochasticity. Initial conditions: uninduced (blue line) or fully induced (red line)
cells with a period of T = 2000 min. (TIF)
S13 Fig. Bistability with and without stochastic operon-state switching when the number
of operons are more than one. (A)(B) Deterministic bifurcation diagram for wild-type cells in
which the number of operons is 2 or 6. (C)(D) Deterministic bifurcation diagrams for the
repressor bound to the operon in the absence of a DNA loop with association constant that
equals 5 molec.−1. (E) (F) Stochastic hysteresis response of the probability of induction. (TIF) Relatively slow stochastic gene-state switching significantly broadens bimodality S8 Fig. Will a single repressor rebinding event trigger the phenotype transition from the
induced state to the uninduced state? The uninduction probability nearly vanishes when the
extracellular inducer concentration is only slightly larger than about 40μM. (TIF)
S9 Fig. Copy-number distributions for the permease protein observed in the region of
deterministic bistability, varying with ω. (TIF)
S10 Fig. Copy-number distributions for the permease protein observed in the region of
purely stochastic bistability, varying with ω. (TIF)
S11 Fig. Nearly exponentially distributed transition time from the uninduced state to the
induced state in wild-type cells. (TIF)
S12 Fig. Stochastic hysteresis response of the probability of induction when tuning the
strengths of stochasticity. Initial conditions: uninduced (blue line) or fully induced (red line)
cells with a period of T = 2000 min. (TIF)
S13 Fig. Bistability with and without stochastic operon-state switching when the number
of operons are more than one. (A)(B) Deterministic bifurcation diagram for wild-type cells in
which the number of operons is 2 or 6. (C)(D) Deterministic bifurcation diagrams for the
repressor bound to the operon in the absence of a DNA loop with association constant that
equals 5 molec.−1. (E) (F) Stochastic hysteresis response of the probability of induction. (TIF)
S14 Fig. Bistability with and without stochastic operon-state switching tuning the strength
of positive feedback. (A)(B) Deterministic bifurcation diagram tuning the strength of positive
feedback. (C-F) Stationary distributions when tuning the strength of positive feedback. (TIF)
S15 Fig. Bistability with and without stochastic operon-state switching when the dynamics
of inducer is replaced by that of lactose. (A-D) Deterministic bifurcation diagram in which
the dynamics of inducer is replaced by that of lactose. (E) (F) Stochastic hysteresis response of
the probability of induction. (TIF)
S1 Table. Values of kinetic parameters in the fluctuating-rate model. (PDF)
Acknowledgments
We thank the past and present members of X.S.Xie’s group and particularly Dr. Paul Choi. We
also thank Dr. Biswajit Das for carefully reading the manuscript. Author Contributions
F
l
l
i
H
G S8 Fig. Will a single repressor rebinding event trigger the phenotype transition from the
induced state to the uninduced state? The uninduction probability nearly vanishes when the
extracellular inducer concentration is only slightly larger than about 40μM. (TIF)
S9 Fig. Copy-number distributions for the permease protein observed in the region of
deterministic bistability, varying with ω. (TIF)
S10 Fig. References 1. Huang S, Eichler G, Bar-Yam Y, Ingber DE. Cell fates as high-dimensional attractor states of a complex
gene regulatory network. Phys. Rev. Lett. 2005; 94: 128701. https://doi.org/10.1103/PhysRevLett.94. 128701 PMID: 15903968 2. Li Q, Wennborg A, Aurell E, Dekel E, Zou J, Xu Y, et al. Dynamics inside the cancer cell attractor reveal
cell heterogeneity, limits of stability and escape. Proc. Natl. Acad. Sci. USA 2016; 113: 2672–2677. https://doi.org/10.1073/pnas.1519210113 PMID: 26929366 3. Choi PJ, Cai L, Frieda K, Xie XS. A stochastic single-molecule event triggers phenotype switching of a
Bacteria cell. Science 2008; 322: 442–446. https://doi.org/10.1126/science.1161427 PMID: 18927393 4. Ozbudak EM, Thattai M, Lim HN, Shraiman BI, van Oudenaarden A. Multistability in the lactose utiliza-
tion network of Escherichia coli. Nature 2004; 427: 737–740. https://doi.org/10.1038/nature02298
PMID: 14973486 5. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage
choice in mammalian progenitor cells. Nature 2006; 453: 544–547. https://doi.org/10.1038/
nature06965 6. Gupta PB, Fillmore CM, Jiang GZ, Shapira SD, Tao K, Kuperwasser C, et al. Stochastic state transi-
tions give rise to phenotypic equilibrium in populations of cancer cells. Cell 2011; 146: 633–644. https://
doi.org/10.1016/j.cell.2011.08.030 PMID: 21854987 7. Acar M., Mettetal JT, van Oudenaarden A. Stochastic switching as a survival strategy in fluctuating envi-
ronments. Nat. Genetics 2008; 40: 471–475. https://doi.org/10.1038/ng.110 PMID: 18362885 8. Kirschner MW, Gerhart JC. The Plausibility of Life: Resolving Darwin’s Dilemma. New Haven: Yale
University Press; 2005. 9. Kussell E, Leibler S. Phenotypic diversity, population growth, and information in fluctuating environ-
ments. Science 2005; 309: 2075–2078. https://doi.org/10.1126/science.1114383 PMID: 16123265 10. Li GW, Xie XS. Central dogma at the single-molecule level in living cells. Nature 2011; 475: 308–315. https://doi.org/10.1038/nature10315 PMID: 21776076 11. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, et al. Quantifying E. coli proteome and tran-
scriptome with single-molecule sensitivity in single cells. Science 2010; 329: 533–538. https://doi.org/
10.1126/science.1188308 PMID: 20671182 12. Berg O. A model for the statistical fluctuations of protein numbers in a microbial population. J. Theor. Biol. 1978; 71: 587. https://doi.org/10.1016/0022-5193(78)90326-0 PMID: 96307 13. Bhogale P, Sorg R, Veening JW, Berg J. What makes the lac-pathway switch: identifying the fluctua-
tions that trigger phenotype switching in gene regulatory systems. Nucl. Acids Res. 2014; gku839. https://doi.org/10.1093/nar/gku839 PMID: 25245949 14. Cai L, Friedman N, Xie XS. Stochastic protein expression in individual cells at the single molecule level. Nature 2006; 440: 358–362. https://doi.org/10.1038/nature04599 PMID: 16541077 15. Relatively slow stochastic gene-state switching significantly broadens bimodality Resources: Hao Ge. Software: Hao Ge, Pingping Wu. Writing – original draft: Hao Ge. Writing – review & editing: Hao Ge, Hong Qian, Xiaoliang Sunney Xie. Resources: Hao Ge. Writing – original draft: Hao Ge. Writing – review & editing: Hao Ge, Hong Qian, Xiaoliang Sunney Xie. Writing – review & editing: Hao Ge, Hong Qian, Xiaoliang Sunney Xie. Author Contributions Formal analysis: Hao Ge. Formal analysis: Hao Ge. Investigation: Hao Ge, Pingping Wu, Hong Qian, Xiaoliang Sunney Xie. Project administration: Hao Ge. 21 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality 20. Yu J, Xiao J, Ren X, Lao K, Xie XS. Probing gene expression in live cells, one protein molecule at a
time. Science 2006; 311: 1600–1603. https://doi.org/10.1126/science.1119623 PMID: 16543458 21. Delbru¨ck M. Statistical fluctuations in autocatalytic reactions. J. Chem. Phys. 1940; 8: 120–124. https://
doi.org/10.1063/1.1750549 22. Ge H, Qian H, Xie XS. Stochastic phenotype transition of a single cell in an intermediate region of gene-
state switching. Phys. Rev. Lett. 2015; 114: 078101. https://doi.org/10.1103/PhysRevLett.114.078101
PMID: 25763973 23. Faggionato A, Gabrielli D, Ribezzi Crivellari M. Non-equilibrium thermodynamics of piecewise determin-
istic Markov Processes. J. Stat. Phys. 2009; 137: 259–304. https://doi.org/10.1007/s10955-009-9850-x 24. Igoshin OA, Brody MS, Price CW, Savageau MA. Distinctive topologies of partner-switching signaling
networks correlate with their physiological roles. J. Mol. Biol. 2007; 369: 1333–1352. https://doi.org/10. 1016/j.jmb.2007.04.021 PMID: 17498739 25. Park BO, Ahrends R, Teruel MN. Consecutive positive feedback loops create a bistable switch that con-
trols preadipocyte-to-adipocyte conversion. Cell Rep. 2012; 2: 976–90. https://doi.org/10.1016/j.celrep. 2012.08.038 PMID: 23063366 26. Ahrends R, Ota A, Kovary KM, Kudo T, Park BO, Teruel MN. Controlling low rates of cell differentiation
through noise and ultrahigh feedback. Science. 2014; 344: 1384–9. https://doi.org/10.1126/science. 1252079 PMID: 24948735 27. Walczak AM, Onuchic JN, Wolynes PG. Absolute rate theories of epigenetic stability. Proc. Natl. Acad. Sci. 2005; 102: 18926–18931. https://doi.org/10.1073/pnas.0509547102 PMID: 16361441 28. Ackers GK, Johnson AD, Shea MA. Qualitative model for gene regulation by λ phage repressor. Proc. Natl. Acad. Sci. 1982; 79: 1129–1133. https://doi.org/10.1073/pnas.79.4.1129 PMID: 6461856 29. Mettetal T, Muzzey D, Pedraza JM, Ozbudak EM, van Oudenaarden A. Predicting stochastic gene
expression dynamics in single cells. Proc. Natl. Acad. U.S.A. 2006; 103: 7304–7309. https://doi.org/10. 1073/pnas.0509874103 30. Santilla´n M, Mackey MC, Zeron ES. Origin of bistability in the lac operon. Biophys. J. 2007; 92: 3830–
3842. https://doi.org/10.1529/biophysj.106.101717 PMID: 17351004 31. Barkley MD, Riggs AD, Jobe A, Bourgeois S. Interaction of effecting ligands with lac repressor and
repressor-operator complex. Biochemistry 1975; 14: 1700. https://doi.org/10.1021/bi00679a024 PMID:
235964 32. Dunaway M, Olson JS, Rosenberg JM, Kallai OB, Dickerson RE, Matthews KS. Kinetic studies of
inducer binding to lac repressor operator complex. J. Biol. Chem. 1980; 255: 10115. PMID: 7000772 33. Karmakar R, Bose I. Graded and binary responses in stochastic gene expression. Phys. Biol. 2004; 1:
197–204. https://doi.org/10.1088/1478-3967/1/4/001 PMID: 16204839 34. Ferrell J, Xiong W. Bistability in cell signaling: How to make continuous processes discontinuous, and
reversible processes irreversible. References Eldar A, Elowitz M. Functional roles for noise in genetic circuits. Nature 2010; 467: 167. https://doi.org/
10.1038/nature09326 PMID: 20829787 16. Paulsson J, Ehrenberg M. Random signal fluctuations can reduce random fluctuations in regulated
components of chemical regulatory networks. Phys. Rev. Lett. 2000; 84(23): 5447–50. https://doi.org/
10.1103/PhysRevLett.84.5447 PMID: 10990965 17. Rigney D. Note on the kinetics and stochastics of induced protein synthesis as influenced by various
models for messenger RNA degradation. J. Theoret. Biol. 1979; 79: 247. https://doi.org/10.1016/0022-
5193(79)90250-9 18. Sepu´lveda LA, Xu H, Zhang J, Wang M, Golding I. Measurements of gene regulation in individual cells
reveals rapid switching between propomter states. Science 2016; 351: 1218–1222. https://doi.org/10. 1126/science.aad0635 PMID: 26965629 19. Suter D, Molina N, Gatfield D, Schneider K, Schibler U, Naef F. Mammalian genes are transcribed with
widely different bursting kinetics. Science 2011; 332: 472–474. https://doi.org/10.1126/science. 1198817 PMID: 21415320 22 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Relatively slow stochastic gene-state switching significantly broadens bimodality 44. Min W, Gopich IV, English BP, Kou SC, Xie XS, Szabo A. When does the Michaelis-Menten equation
hold for fluctuating enzymes? J. Phys. Chem. B 2006; 110: 20093–7. https://doi.org/10.1021/
jp065187g PMID: 17034179 45. Assaf M, Roberts E, Luthey-Schulten Z. Determining the stability of genetic switches: explicitly account-
ing for mRNA noise. Phys. Rev. Lett. 2011; 106: 248102. https://doi.org/10.1103/PhysRevLett.106. 248102 PMID: 21770603 46. Aurell E, Sneppen K. Epigenetics as a first exit problem. Phys. Rev. Lett. 2002; 88: 048101. https://doi. org/10.1103/PhysRevLett.88.048101 PMID: 11801174 47. Ge H, Qian H. Thermodynamic limit of a nonequilibrium steady state: Maxwell-type construction for a
bistable biochemical system. Phys. Rev. Lett. 2009; 103: 148103. https://doi.org/10.1103/
PhysRevLett.103.148103 PMID: 19905606 48. Lv C, Li X, Li F, Li TJ. Constructing the energy landscape for genetic switching system driven by intrinsic
noise. Plos One 2014; 9(2): e88167. https://doi.org/10.1371/journal.pone.0088167 PMID: 24551081 49. Wang J, Xu L, Wang E, Huang S. The potential landscape of genetic circuits imposes the arrow of time
in stem cell differentiation. Biophys. J. 2010; 99: 29–39. https://doi.org/10.1016/j.bpj.2010.03.058
PMID: 20655830 50. Zhou JX, Aliyu MDS, Aurell E, Huang S. Quasi-potential landscape in complex multi-stable systems. J. R. Soc. Interface 2012; 9: 3539–3553. https://doi.org/10.1098/rsif.2012.0434 PMID: 22933187 51. Zhou PJ, Li TJ. Construction of the landscape for multi-stable systems: Potential landscape, quasi-
potential, A-type integral and beyond. J. Chem. Phys. 2016; 144: 094109. https://doi.org/10.1063/1. 4943096 PMID: 26957159 52. Zhu XM, Yin L, Hood L, Ao P. Calculating biological behaviors of epigenetic states in the phage λ life
cycle. Funct. Integr. Genomics 2004; 4: 188–195. https://doi.org/10.1007/s10142-003-0095-5 PMID:
14762706 53. Freidlin MI, Wentzell AD. Random Perturbations of Dynamical Systems. New York: Springer; 1998. 54. Razooky BS, Cao YF, Hansen MK, Perelson AS, Simpso ML, Weinberger LS. Nonlatching positive
feedback enables robust bimodality by decoupling expression noise from the mean. PLOS Biol. 2017;
15(10): e2000841. https://doi.org/10.1371/journal.pbio.2000841 PMID: 29045398 55. Qian H. Cellular biology in terms of stochastic nonlinear biochemical dynamics: Emergent properties,
isogenetic variations and chemical system inheritability. J. Stat. Phys. 2010; 141: 990–1013. https://
doi.org/10.1007/s10955-010-0093-7 56. Qian H, Ge H. Mesoscopic biochemical basis of isogenetic inheritance and canalization: Stochasticity,
nonlinearity, and emergent landscape. Mol Cell Biomech. 2012; 9: 1–30. PMID: 22428359 57. Novick A, Weiner M. Enzyme induction as an all-or-none phenomenon. Proc. Natl. Acad. Sci. U.S.A. 1957; 43: 553–566. 58. Bortz AB, Kalos MH, Lebowitz JL. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 Chaos 2001; 11: 227–236. 35. Reluga TC, Qian H. Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling
switch. Phys. Rev. Lett. 2005; 94: 028101. https://doi.org/10.1103/PhysRevLett.94.028101 PMID:
15698232 36. Majdandzic A, Podobnik B, Buldyrev SV, Kenett DY, Havlin S, Stanley HE. Spontaneous recovery in
dynamical networks. Nat. Phys. 2014; 10: 34–38. https://doi.org/10.1038/nphys2819 37. Zeeman EC. Catastrophe Theory-Selected Papers 1972-1977. Reading, MA: Addison-Wesley; 1977. 38. Artyomov MN, Das J, Kardar M, Chakraborty AK. Purely stochastic binary decisions in cell signaling
models without underlying deterministic bistabilities. Proc. Natl. Acad. Sci. USA 2007; 104: 18958–
18963. https://doi.org/10.1073/pnas.0706110104 PMID: 18025473 39. Feng H, Han B, Wang J. Adiabatic and non-adiabatic non-equilibrium stochastic dynamics of single reg-
ulating genes. J. Phys. Chem. B 2011; 115: 1254–1261. https://doi.org/10.1021/jp109036y PMID:
21189036 40. Hornos JEM, Schultz D, Innocentini GCP, Wang J, Walczak AM, Onuchic JN, et al. Self-regulating
gene: an exact solution. Phys. Rev. E. 2005; 72: 051907. https://doi.org/10.1103/PhysRevE.72. 051907 41. Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression:from theories to pheno-
types. Nat Rev Genet. 2005; 6: 451–64. https://doi.org/10.1038/nrg1615 PMID: 15883588 42. Shi PZ, Qian H. A perturbation analysis of rate theory of self-regulating genes and signaling networks. J. Chem. Phys. 2011; 134: 065104. https://doi.org/10.1063/1.3535561 PMID: 21322737 43. To T, Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bist-
ability. Science 2010; 327: 1142–1145. https://doi.org/10.1126/science.1178962 PMID: 20185727 23 / 24 PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1006051
March 12, 2018 A new algorithm for Monte Carlo simulation of Ising spin systems. J. Comput. Phys. 1975; 17: 10–18. https://doi.org/10.1016/0021-9991(75)90060-1 59. Doob JL. Markoff chains-Denumerable case. Trans. Amer. Math. Soc. 1945; 58(3): 455–473. https://
doi.org/10.1090/S0002-9947-1945-0013857-4 60. Gillespie DT. A general method for numerically simulating the stochastic time evolution of coupled
chemical reactions. J. Comput. Phys. 1976; 22(4): 403–434. https://doi.org/10.1016/0021-9991(76)
90041-3 61. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977; 81(25):
2340–2361. https://doi.org/10.1021/j100540a008 24 / 24
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Stability of the Meat Protein Type I Collagen: Influence of pH, Ionic Strength, and Phenolic Antioxidant
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Received: 5 March 2020; Accepted: 8 April 2020; Published: 11 April 2020 Abstract: The water-holding capacity (WHC) is among the key factors in determining the quality
of meat and its value, which is strongly influenced by the content and quality of the connective
tissue proteins like collagen. Therefore, the factors that influence the proteins’ stability, e.g., pH, ionic
strength, and the antioxidants which are used to increase the meat shelf-life, also affect the WHC. The
interaction of collagen, whose structure is strongly influenced by the interaction with water molecules,
can be studied following the behavior of water diffusion by low-resolution 1H NMR experiments. The present study is addressed to study the collagen stability as a function of pH, ionic strength, and
phenolic antioxidants like catechin. The experimental study demonstrated how the 1H NMR time
domain (TD) experiments are able to evaluate the hydration properties of collagen, not only as a
function of ionic strength and pH, but also in determining the ability of catechin to interact both on
the surface of the collagen fibrils and inside the fibrillar domain. Keywords: meat; collagen; pH; ionic strength; catechin; 1H NMR; T2 relaxation Stability of the Meat Protein Type I Collagen:
Influence of pH, Ionic Strength, and
Phenolic Antioxidant Massimo Lucarini 1,*, Alessandra Durazzo 1
, Fabio Sciubba 2, Maria Enrica Di Cocco 2,
Raffaella Gianferri 2, Mosè Alise 3
, Antonello Santini 3
, Maurizio Delfini 2 and
Ginevra Lombardi-Boccia 1 Massimo Lucarini 1,*, Alessandra Durazzo 1
, Fabio Sciubba 2, Maria Enrica Di Cocco 2,
Raffaella Gianferri 2, Mosè Alise 3
, Antonello Santini 3
, Maurizio Delfini 2 and
Ginevra Lombardi-Boccia 1 1
CREA-Research Centre for Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy;
alessandra.durazzo@crea.gov.it (A.D.); g.lombardiboccia@crea.gov.it (G.L.-B.) 1
CREA-Research Centre for Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy;
alessandra.durazzo@crea.gov.it (A.D.); g.lombardiboccia@crea.gov.it (G.L.-B.) g
g
g
2
Department of Chemistry, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy;
Fabio.sciubba@uniroma1.it (F.S.); mariaenrica.dicocco@uniroma1.it (M.E.D.C.);
raffaella.gianferri@uniroma1.it (R.G.); maurizio.delfini@uniroma1.it (M.D.) g
3
Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Ital
alisemose@gmail.com (M.A.); asantini@unina.it (A.S.) g
*
Correspondence: massimo.lucarini@crea.gov.it; Tel.: +39-06-51494446
foods foods Foods 2020, 9, 480; doi:10.3390/foods9040480 foods foods 1. Introduction The water content of meat, approximately 75%, and the water-holding capacity (WHC) are both
key factors in determining the technological quality of meat and that of meat products [1,2]. Among the constituents of meat, proteins play a fundamental role in retaining water, [3] and,
consequently, the factors influencing the protein stability also affect the WHC [1]. The main proteins
responsible for the WHC in meat are myofibrils and the collagen of connective tissue. Myofibrillar
proteins are the most studied, since they are responsible for most of the water retained in the muscles. Collagen is ubiquitous in all vertebrates, and its structure is stabilized by extensive hydrogen bonds
where water molecules are a relevant part of the ordered hydrogen-bonding existing network [4]. Among the factors to be considered in the technological processes of the conversion of muscle into
meat, there are the pH, the ionic strength, and the antioxidant molecules, which are used to slow down
the oxidative process onset. Changes in the pH around the isoelectric point of the meat proteins causes a change in the net
charge (positive or negative) of proteins, determining a greater electrostatic repulsive force among Foods 2020, 9, 480; doi:10.3390/foods9040480 www.mdpi.com/journal/foods 2 of 10 Foods 2020, 9, 480 the protein chains, which leads to an increased swelling of the protein system with an increase in the
WHC. Similarly, the meat proteins’ electronic charge is also affected by the ionic strength that is able to
move the isoelectric point of the proteins, causing a different mobility of the water inside the protein
domain system. Oxidation of meat has a relevant effect on quality parameters, and for this reason,
antioxidant molecules are used to slow down this process. The use of natural antioxidants to prevent
and slow down the oxidation process in biological matrices is relevant. Proteins in biological matrices
are, together with lipids, one of the main targets of the oxidant compounds for both their reaction rate
and abundance [5,6]. Recently,
a mechanism for the antioxidant action of catechin,
a flavan-3-ol,
namely
(2R, 3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol, towards collagen, has been
proposed [7]. Madhan et al. [8], by using circular dichroism and Fourier transform infrared spectroscopy
(FTIR), reported how hydrogen bonding and hydrophobic interactions represent the main forces in
collagen stabilization due to the interaction with vegetal origin polyphenols. 2. Materials and Methods Collagen type I fibers from bovine Achilles tendon (BAT), (±) catechin and all reagents were
purchased from Sigma (Sigma Chemicals Co., St. Louise, MI, USA) and were used without further
purification for the experimental study. 1. Introduction The interaction of catechin
with the collagen could influence the WHC of the macromolecule; in fact, the molecular size of catechin
fits the ones of collagen pentafibrils. These last can then stabilize the collagen structure through inter
and intramolecular hydrogen bonds [8]. Collagen molecules can differ, not only in their molecular and
supramolecular structures, but also in their distributions in the tissues and their functions [9]. In this
study, attention has been mainly addressed to type I collagen, since it is ubiquitous in all vertebrates,
and it represents at least 90% of total collagen types [10]. Nuclear magnetic resonance time domain (NMR TD) is a nondestructive method that allows
the characterization of water mobility in addition to its distribution [11]. Many studies published
have correlated low-field 1H NMR measurements with the WHC. The transverse relaxation time (T2)
has been used to get information on the meat structure, with a high correlation with meat proteins’
properties [12]. Low-resolution 1H NMR has been used to characterize foods by determining both
the decay rate and the amplitude of the 1H NMR signal. The T2 relaxation curve in heterogeneous
systems is represented by a multiexponential decay curve that can be attributed to the presence in the
sample of elements with structural differences [13]. The decay rate of the 1H NMR signal is lower in
these systems compared to the one corresponding to bulk water and can be quantitatively rationalized. In this study, the dynamical properties of the water molecules present in the hydration network of
collagen by a systematic approach based on 1H NMR signal relaxation determinations have been
assessed. The behaviors of water dynamics under different experimental conditions that can occur in
meat products have been investigated by evaluating the water proton relaxation rates. Physiological
changes in the ionic strength and pH have been considered, as well as the effects of the interactions of
collagen with a small antioxidant molecule like catechin. Further information about collagen and water
dynamic behaviors have been obtained by transverse 1H NMR relaxation times and self-diffusion
measurements. To the authors’ knowledge, no other study has been up to today reported on the use of
1H NMR TD to assess the functional properties of collagen. 2.1. Study of Collagen Stability as Function of pH and Ionic Strength Three different solutions were prepared at pH 5.4, 6.2, and 7.0 and each of them with three different
ionic strengths (0.29, 0.45, and 0.71 M), for a total of nine buffer solutions. The range of pH and ionic strengths have been chosen and considered in order to represent the
variation of these parameters in the meat [14]. The buffer solutions were prepared using 50 mM citric
acid monohydrate (10.507 g/L) and trisodium dehydrate (14.707 g/L). pH was adjusted with 4 M NaOH Foods 2020, 9, 480 3 of 10 or 4 M HCl, and ionic strength (I) was adjusted by the addition of NaCl according to the following
Equations (1):
1 or 4 M HCl, and ionic strength (I) was adjusted by the addition of NaCl according to the following
Equations (1):
1 I = 1
2
X
CiZi2
(1) (1) where Ci stands for the concentration, and Zi stands for the ion charge. Considering our experim
he ion strength (I) was calculated by using the following Equation (2): where Ci stands for the concentration, and Zi stands for the ion charge. Considering our experiment,
the ion strength (I) was calculated by using the following Equation (2): I = 1
2([H2A]1 +
h
HA−2i
22 +
h
A−3i
32 + 2[NaCl])
(2) (2) Collagen was hydrated by adding a buffer solution to dried samples and left for two days at 4 ◦C
before 1H NMR experimental determinations. Collagen was hydrated by adding a buffer solution to dried samples and left for two days at 4 ◦C
before 1H NMR experimental determinations. 2.2. Catechin-Treated Collagen Collagen (2.5 mg/mL) was treated with catechin (0.001 M) for 24 h at room temperature (25 ◦C)
in the dark and without any shaking, as described in the supplementary material of a previously
published work by Lucarini et al. [7]. Catechin solutions were spectrophotometrically titrated at 280 nm
using a Cary 60 UV–Vis spectrophotometer (Agilent Technologies, Santa Clara, CA, USA) before and
after the collagen addition to estimate the catechin amount in the complex. Collagen-catechin complex sample was dialyzed for 24 h at 4 ◦C against distilled water. Dialysis
bag, manufactured by Spectrum Medical Industries and with a molecular weight cut-offless than 14KD,
were purchased from Fischer Scientific (Waltham, MA, USA). At the end of dialysis, the collagen-treated
samples were freeze-dried. After catechin treatment, the collagen color became slightly pink. 2.3. 1H NMR Time Domain (TD) Samples were hydrated by an addition of deionized distilled water or one of the nine buffer
solutions and left at 4 ◦C for two days to allow collagen hydration. The ratio buffer and dry collagen
matter was 3 (g/g). The hydrated samples were placed in 1H NMR tubes and immediately sealed. Measurements were performed with a Minispec mq 20-pulsed 1H NMR spectrometer (Bruker
Spectrospin Company, Silberstreifen, Germany) with an operating frequency of 20 MHz for protons
(magnetic field strength: 0.47 T). The NMR spectrometer was equipped with an external thermostat
(Julabo F25, Julabo Labortechnik GmbH, Seelbach, Germany) in order to maintain the selected
temperature conditions (t = 25 ◦C). Before the NMR measurements, the tube was placed into the 1H
NMR probe as long as needed for thermal equilibration (t = 15 min). Longitudinal relaxation measurements (T1) were performed by an inversion recovery (IR) se Transverse relaxation measurements (T2) were performed by a Carr-Purcell-Meiboom-Gill (CPMG)
sequence [15]. For each sample, 49 scans were acquired, with a recycle delay of 40 s. The decay of
the transverse magnetization was triexponential; the amplitudes and relaxation rates of the three
components were calculated by a nonlinear least-squares data fitting with a proprietary self-made
computer software based on the Marquardt algorithm [16]. Self-diffusion measurements were carried out using a standard Stejskal-Tanner (PFG spin-echo)
sequence [17]. 3. Results 3.1. 1H NMR Characterization of Type I Collagen 3.1.1. Time Domain Measurements 3.1.1. Time Domain Measurements The water properties of collagen recovered from the bovine Achilles tendon system were studied
by 1H NMR T2 relaxation measurements. 4 of 10 Foods 2020, 9, 480 Foods 2020, 9, 480 The CPMG decay data found for hydrated collagen samples were multicomponent, as generally
reported in compartmentalized or heterogeneous systems [18,19]. The sum of three exponentials gave
the best fit. As shown in Table 1, the three T2 values were 6 ± 1, 41 ± 7, and 447 ± 15 ms, with relative
fractions of 56 ± 5, 36 ± 4, and 8 ± 2%, respectively. Table 1. Transverse relaxation time (T2i), population (fi), and diffusion coefficient (Di) values
(mean ± standard deviation) related to each water fraction i obtained for hydrated collagen. Table 1. Transverse relaxation time (T2i), population (fi), and diffusion coefficient (Di) values
(mean ± standard deviation) related to each water fraction i obtained for hydrated collagen. Fraction i
1
2
3
T2i (ms)
6 ± 1
41 ± 7
447 ± 15
fi(%)
56 ± 5
36 ± 4
8 ± 2
Di (10−5cm2s−1)
0.71
1.22
2.31 Table 1 shows the three values of Di associated with the three water fractions. The Di values were
D1 = 0.71 × 10−5 cm2 s−1 for the fast-relaxing fraction 1, D2 = 1.22 × 10−5 cm2 s−1 for the intermediate
fraction 2, and D3 = 2.17 × 10−5 cm2 s−1 for the slow-relaxing fraction 3. We observed from relaxation
measurements in hydrated collagen that multiple water species were detectable (the water relaxation
curve was three exponential), with one component having the same relaxation time as pure water and
the others two characterized by a reduced T2. The three water fraction localizations were assigned
based on available literature data [18–20]. Considering the work by Kopp et al. [21], they describe a
protein solution which can be viewed as made by three different water environments: the buried water
molecules, the water hydration shell around the protein, and the bulk water [21]. In particular, the structural bonded water corresponds to unfreezable water molecules in line with
the collagen hydration models proposed [21,22]. They are linked by triple hydrogen bonds involving
hydroxyproline or by double hydrogen bonds in the available sites inside the triple helix [22]. 3. Results It has
been supposed, assuming non-interacting bonds, that four hydrogen bonds are involved in the linkage
of water at the protein–water interface, as it has been reported by Privalov [4]. A cross-relaxation and transverse relaxation 1H NMR study of partially hydrated collagen (h < 0.3),
at different temperatures and water activities, showed that T2 values of water protons were less than
300 ms [23]. In the experimental conditions of this research (CPMG echo time of 100 ms), the 1H NMR
signal cannot be assigned to this interstitial water fraction, whereas the water molecules localized in
the micro fibrils (between the triple helix of tropocollagen) mainly contribute to the shortest transverse
relaxation time (T21 = 6 ms). The intermediate T2 (T22 = 41 ms) was assigned to the water fraction
placed in the interfibrillar space. A part of this water fraction is related to the collagen structure and
provides water bridges between the collagen microfibrils [24]. The molecules of water present in fraction 2 are more mobile than those of fraction 1 but are
affected by the macromolecule, as confirmed by the small differences in the related diffusion coefficients
(D1 = 0.71 × 10−5 cm2/s and D2 = 1.22 × 10−5 cm2/s). These two slow-relaxing fractions are the hydration
water of the tropocollagen. The phenomenon of restriction explains their D1,2 values, whereas the
observed decrease is due to the so-called direct hydration effect [25]. For the third fraction, a long T2 (T23 = 447 ms) is reported, as well as a diffusion coefficient
(D3 = 2.31 × 10−5 cm2/s) close to the value for pure water, and corresponds to the “free” or “bulk”
water fraction. The best fit obtained for the longitudinal relaxation time T1 was monoexponential, with a value of
950 ms. The ratio T1/T2 was found >1.6. This result indicated that the motion of water molecules was
anisotropic and characterized by a distribution of correlation times [26]. That T1 was monoexponential is not anomalous, since in heterogeneous macromolecular systems,
T2 is almost exclusively considered. This is related to some experimental aspects in the measurement of
relaxation times: while T2 can be carefully and quickly determined by the CPMG sequence, an accurate
T1 determination can be challenging in heterogeneous systems, where, generally, T1 >> T2. 3. Results Since 5 of 10 Foods 2020, 9, 480 measuring the recovery curve of the longitudinal magnetization using the inversion recovery sequence
requires an adequate series of recovery delays and long repetition times (≥5 T1), to ensure complete
longitudinal relaxation, a number has often been measured low of the experimental points for T1
determination, and it has not always been possible, by deconvolution of the curve, to calculate the same
number of T1 components as those obtained from T2 measurements. Anyhow, the correspondence
of the T1 values with the T2 values and the ratio T1/T2 can be considered sufficient for the data
interpretation, since this ratio is potentially useful information for the assessment of the anisotropy
existing in heterogeneous systems [13]. Foods 2019, 8, x FOR PEER REVIEW
5 of 10
Anyhow, the correspondence of the T1 values with the T2 values and the ratio T1/T2 can be considered
sufficient for the data interpretation, since this ratio is potentially useful information for the Several works reported for water molecules not undergoing proton chemicals exchange a linear
relationship of the proton spin-spin relaxation time with the reciprocal of the temperature [27,28]. Indeed, a T2 minimum is expected if the chemical exchange mechanism is the main contribution to
relaxation. In a temperature range from 277 to 323 K, such a behavior has been displayed by the T23
component, as reported in Figure 1. assessment of the anisotropy existing in heterogeneous systems [13]. Several works reported for water molecules not undergoing proton chemicals exchange a linear
relationship of the proton spin-spin relaxation time with the reciprocal of the temperature [27,28]. Indeed, a T2 minimum is expected if the chemical exchange mechanism is the main contribution to
relaxation. In a temperature range from 277 to 323 K, such a behavior has been displayed by the T23
t
t d i
Fi
1 nt, as reported in Figure 1. Figure 1. Temperature dependence of the T23 values of the collagen sample. Figure 1. Temperature dependence of the T23 values of the collagen sample. Figure 1. Temperature dependence of the T23 values of the collagen sample. Figure 1. Temperature dependence of the T23 values of the collagen sample. 3. Results The presence of a T23 minimum, as function of temperature, indicates that proton relaxation
measurements of water in such a system can be interpreted based on an ongoing chemical exchange
process between water protons and hydrogen present on the hydroxyl groups of the polymer unit
side chains. The presence of a T23 minimum, as function of temperature, indicates that proton relaxation
measurements of water in such a system can be interpreted based on an ongoing chemical exchange
process between water protons and hydrogen present on the hydroxyl groups of the polymer unit
side chains. 3.1.2. Collagen Fibers as Affected by pH and Ionic Strength
3.1.2. Collagen Fibers as Affected by pH and Ionic Strength Nine buffer solutions at three pH values, 5.4, 6.2, and 7.0, were prepared at three different ionic
strengths: 0.29, 0.45, 0.71 M, as indicated in the Materials and Methods section. Prior to the 1H NMR
measurements, the collagen fibers were hydrated by adding the buffer to the dried sample and left
for two days at 4 °C. T2 relaxation times of hydrated collagen showed a triexponential decay with all
buffer systems studied. T21, T22, and T23 relaxation times at the three ionic strengths as a function of
pH are shown in Figures 2, 3 and 4, respectively. Both the ionic strength and pH affects significantly
the T2 relaxation times. Such behavior was displayed by each of the three ionic strengths studied
Nine buffer solutions at three pH values, 5.4, 6.2, and 7.0, were prepared at three different ionic
strengths: 0.29, 0.45, 0.71 M, as indicated in the Materials and Methods section. Prior to the 1H NMR
measurements, the collagen fibers were hydrated by adding the buffer to the dried sample and left
for two days at 4 ◦C. T2 relaxation times of hydrated collagen showed a triexponential decay with all
buffer systems studied. T21, T22, and T23 relaxation times at the three ionic strengths as a function of
pH are shown in Figures 2–4, respectively. Both the ionic strength and pH affects significantly the T2
relaxation times. Such behavior was displayed by each of the three ionic strengths studied solutions. 6 of 10
6 of 10 Foods 2020, 9, 480
Foods 2019, 8, x FOR ds 2019, 8, x FOR PEER REVIEW
6 o
Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic
strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic
strengths. Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic strengths. Figure 2. 3.1.2. Collagen Fibers as Affected by pH and Ionic Strength
3.1.2. Collagen Fibers as Affected by pH and Ionic Strength A strong effect of both the ionic strength and the pH on
the distribution of T2 relaxation times was observed as reported in Figures 2–4. g
g
the pH on the distribution of T2 relaxation times was observed as reported in Figures 2, 3, and 4. Significant increases in the T23 relaxation times, which correspond to the “free” or “bulk” water
fraction, with the increase of the ionic strength and pH were reported. Previous works, by
investigating the effect of increasing the ionic strength in myofibrils by means of 1H NMR T2
relaxation measurements, showed how T2 relaxation times increase in accordance with the ionic
strength [14,33,34]. The swelling of the collagen lattice with the increase of pH and ionic strength can
Significant increases in the T23 relaxation times, which correspond to the “free” or “bulk” water
fraction, with the increase of the ionic strength and pH were reported. Previous works, by investigating
the effect of increasing the ionic strength in myofibrils by means of 1H NMR T2 relaxation measurements,
showed how T2 relaxation times increase in accordance with the ionic strength [14,33,34]. The swelling
of the collagen lattice with the increase of pH and ionic strength can well explain the obtained
data [14,33,35]. well explain the obtained data [14,33,35]. These results confirm that the influence of pH changes on the fibrillar proteins’ net charge, and
consequently, filament spacing is largest around the pK—that is, around pH~5 for the myofibrillar
proteins; this support that the changes in relaxation time are related with the collagen lattice spacing,
as underlined in the work by Offer and Trinick [30]. Several studies reported how T2 relaxation
measured in muscle-based foods correlates with the total water content [36,37] and how T2 relaxation
times are influenced by the ionic strength and pH. Noticeably, the effect of increasing pH from 5.4 to
6.2 had higher impact on the T23 relaxation than of increasing pH from 6.2 to 7.0 (figure 4) when ionic
strength was 0.71 M. An evident effect of the ionic strength on T23 relaxation times was observed at
pH 6.2, when the ionic strength varies from 0.46 to 0.71 M. This indicates a correlation between ionic
strength and the degree of fibrillar swelling. 3.1.2. Collagen Fibers as Affected by pH and Ionic Strength
3.1.2. Collagen Fibers as Affected by pH and Ionic Strength Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic
strengths. Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic strengths. strengths. g
p
p
g
strengths. Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic
Figure 2. Relationship between the pH and T21 relaxation time in collagen at different ionic strengths. Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic
strengths. Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic strengths. g Fi
3 R l ti
hi
b t
th
H
d T
l
ti
ti
i
ll
t diff
t i
i
Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic
strengths
Figure 3. Relationship between the pH and T22 relaxation time in collagen at different ionic strengths. 7 of 10 7 of 10 Foods 2020, 9, 480 Figure 4. Relationship between the pH and T23 relaxation time in collagen at different ionic
h
Figure 4. Relationship between the pH and T23 relaxation time in collagen at different ionic strengths. Figure 4. Relationship between the pH and T23 relaxation time in collagen at different ionic
Figure 4. Relationship between the pH and T23 relaxation time in collagen at different ionic strengths. strengths. Both the ionic strength and pH are reported to influence the water-holding capacity [29–31]. This
behavior has been attributed to the effect of the pH on the net charge of the proteins, which
determines the amount of water in these structures [32]. A strong effect of both the ionic strength and
Both the ionic strength and pH are reported to influence the water-holding capacity [29–31]. This
behavior has been attributed to the effect of the pH on the net charge of the proteins, which determines
the amount of water in these structures [32]. 3.1.2. Collagen Fibers as Affected by pH and Ionic Strength
3.1.2. Collagen Fibers as Affected by pH and Ionic Strength Indeed, a major change in the T2 relaxation times at pH
7.0 was observed when the ionic strength was respectively 0.29 and 0.46 M respect to the increase
These results confirm that the influence of pH changes on the fibrillar proteins’ net charge, and
consequently, filament spacing is largest around the pK—that is, around pH~5 for the myofibrillar
proteins; this support that the changes in relaxation time are related with the collagen lattice spacing, as
underlined in the work by Offer and Trinick [30]. Several studies reported how T2 relaxation measured
in muscle-based foods correlates with the total water content [36,37] and how T2 relaxation times are
influenced by the ionic strength and pH. Noticeably, the effect of increasing pH from 5.4 to 6.2 had
higher impact on the T23 relaxation than of increasing pH from 6.2 to 7.0 (Figure 4) when ionic strength
was 0.71 M. An evident effect of the ionic strength on T23 relaxation times was observed at pH 6.2,
when the ionic strength varies from 0.46 to 0.71 M. This indicates a correlation between ionic strength
and the degree of fibrillar swelling. Indeed, a major change in the T2 relaxation times at pH 7.0 was
observed when the ionic strength was respectively 0.29 and 0.46 M respect to the increase showed at
0.71 M (Figure 4). g
p
y
p
wed at 0.71 M (figure 4). The myofibrillar swelling resulting from salting could be described hence by two main
The myofibrillar swelling resulting from salting could be described hence by two main mechanisms
ndicated by Offer and Trinick [30]; in particular: y
g
g
g
y
hanisms, as indicated by Offer and Trinick [30]; in particular:
(i) the bond of negatively charged ions and the increase of electrostatic repulsion between the
(i) the bond of negatively charged ions and the increase of electrostatic repulsion between the
ments, and ( )
g
y
g
p
filaments, and
(ii) the removal of one or more transverse structural constraints in the structure, allowing the
(ii) the removal of one or more transverse structural constraints in the structure, allowing the
filament lattice to expand. g
y
g
p
ments, and
(ii) the removal of one or more transverse structural constraints in the structure, allowing the
(ii) the removal of one or more transverse structural constraints in the structure, allowing the
ment lattice to expand. filament lattice to expand. 3.2. Characterization of Type I Collagen Modified with Catechin.
( g
)
3 2 Ch
t i
ti
f T
I C ll
M difi d
ith C t hi The water properties of collagen fiber systems modified with catechin were characterized using
1H NMR T2 relaxation measurements. 3.2. Characterization of Type I Collagen Modified with Catechin. The water properties of collagen fiber systems modified with catechin were characterized using
1H NMR T
l
i The CPMG decay of data from hydrated-modified collagen samples were multicomponent,
as expected. Additionally, in this case, the sum of three exponentials led to the best fit. The three T2
values thus obtained were compared with those found for the collagen fibers (see Table 1) and are
shown in Figure 5. 1H NMR T2 relaxation measurements. The CPMG decay of data from hydrated-modified collagen samples were multicomponent, as
expected. Additionally, in this case, the sum of three exponentials led to the best fit. The three T2
values thus obtained were compared with those found for the collagen fibers (see Table 1) and are
shown in Figure 5 Figure 5. A comparison among the three transverse relation time (T2) components of collagen (blue
columns) with those of collagen modified with catechin 0.01 M (green columns). Figure 5. A comparison among the three transverse relation time (T2) components of collagen (blue
columns) with those of collagen modified with catechin 0.01 M (green columns). Figure 5. A comparison among the three transverse relation time (T2) components of collagen (blue
columns) with those of collagen modified with catechin 0.01 M (green columns). Figure 5. A comparison among the three transverse relation time (T2) components of collagen (blue
columns) with those of collagen modified with catechin 0.01 M (green columns). Catechin strongly affects the T22 and T23 water relaxation times of collagen. As mentioned before,
the intermediate T22 was attributed to the water fraction in the interfibrillar space, and the third
fraction (T23) corresponded to the free water fraction. These results indicate that catechin has been
able to interact with collagen both on the fibrillar surface and inside the interfibrillar space. Water T23
relaxation value increases when the catechin is bound to the surface of collagen. This result could
indicate that water interacts less with the surface of the polymer due to the formation of a complex
between the catechin and collagen. Catechin strongly affects the T22 and T23 water relaxation times of collagen. 3.2. Characterization of Type I Collagen Modified with Catechin.
( g
)
3 2 Ch
t i
ti
f T
I C ll
M difi d
ith C t hi As mentioned before,
the intermediate T22 was attributed to the water fraction in the interfibrillar space, and the third
fraction (T23) corresponded to the free water fraction. These results indicate that catechin has been
able to interact with collagen both on the fibrillar surface and inside the interfibrillar space. Water
T23 relaxation value increases when the catechin is bound to the surface of collagen. This result could
indicate that water interacts less with the surface of the polymer due to the formation of a complex
between the catechin and collagen. 3.1.2. Collagen Fibers as Affected by pH and Ionic Strength
3.1.2. Collagen Fibers as Affected by pH and Ionic Strength Since the mechanism involving the removal of structural constraints in the collagen structure is a
Since the mechanism involving the removal of structural constraints in the collagen structure is a
significative element for the swelling, it is possible to hypothesize that an upper level for the degree of filament lattice to expand. Since the mechanism involving the removal of structural constraints in the collagen structure is a
Since the mechanism involving the removal of structural constraints in the collagen structure is a
significative element for the swelling, it is possible to hypothesize that an upper level for the degree of Foods 2020, 9, 480 8 of 10 swelling exists and that “saturation” is achieved in the ionic strength range between 0.46 and 0.71 M
(Figure 4). , ,
of swelling exists and that “saturation” is achieved in the ionic strength range between 0.46 and 0.71
M (figure 4) 3.2. Characterization of Type I Collagen Modified with Catechin. ( igu e )
3 2 Ch
t i
ti
f T
I C ll
M difi d
ith C t hi 4. Conclusions
4. Conclusions The present study demonstrates that 1H NMR TD can be used to study the water dynamics of
collagen thanks to its own longitudinal relaxation processes (T1 or spin-lattice) and transversal
relaxation (T2 or spin-spin). Therefore, this approach could improve the understanding of how meat-
processing factors can affect collagen swelling [38]. The spin-spin relaxation times reflect the
molecular mobility of the collagen chain in accordance with changes in its own chemical structure
also affecting meat quality traits related to the pH and ionic strength. Furthermore, the spin-spin
relaxation time component T23 can be correlated to the WHC of the collagen-hydrated molecule. In
fact, the composition and distribution of T23 fully represents the WHC: the higher the free water
percentage, the lower the water retained inside the polymer and, consequently, also the WHC. NMR relaxometry also allowed to investigate the interaction between collagen and catechin, an
The present study demonstrates that 1H NMR TD can be used to study the water dynamics
of collagen thanks to its own longitudinal relaxation processes (T1 or spin-lattice) and transversal
relaxation (T2 or spin-spin). Therefore, this approach could improve the understanding of how
meat-processing factors can affect collagen swelling [38]. The spin-spin relaxation times reflect the
molecular mobility of the collagen chain in accordance with changes in its own chemical structure also
affecting meat quality traits related to the pH and ionic strength. Furthermore, the spin-spin relaxation
time component T23 can be correlated to the WHC of the collagen-hydrated molecule. In fact, the
composition and distribution of T23 fully represents the WHC: the higher the free water percentage,
the lower the water retained inside the polymer and, consequently, also the WHC. Foods 2020, 9, 480 9 of 10 NMR relaxometry also allowed to investigate the interaction between collagen and catechin,
an antioxidant molecule used in meat processing. In a previous work [7], it has been shown, from mono-
and bi-dimensional proton NMR and 13C cross polarization magic angle spectroscopy experiments,
that collagen-catechin interactions preferentially occur between the catechin B ring and the collagen
proline and hydroxyproline amino acids. The results reported in this study can give further information
on the interaction between catechin and collagen, indicating that catechin is able to bind collagen both
on the fibrillar surface and inside the interfibrillar spaces of the polymer, giving a deeper insight in the
understanding of the interaction between catechin and collagen. References 1. Cheng, Q.; Sun, D.-W. Factors Affecting the Water Holding Capacity of Red Meat Products: A Review of
Recent Research Advances. Crit. Rev. Food Sci. Nutr. 2008, 48, 137–159. [CrossRef] [PubMed] 1. Cheng, Q.; Sun, D.-W. Factors Affecting the Water Holding Capacity of Red Meat Products: A Review of
Recent Research Advances. Crit. Rev. Food Sci. Nutr. 2008, 48, 137–159. [CrossRef] [PubMed] 2. Warner, R.D. The Eating Quality of Meat—IV Water-Holding Capacity and Juiciness. Chapter 14. In Lawrie’s
Meat Science, 8th ed.; Toldrà, F., Ed.; Woodhead Publishing: London, UK, 2017; pp. 419–459. [CrossRef] 2. Warner, R.D. The Eating Quality of Meat—IV Water-Holding Capacity and Juiciness. Chapter 14. In Lawrie’s
Meat Science, 8th ed.; Toldrà, F., Ed.; Woodhead Publishing: London, UK, 2017; pp. 419–459. [CrossRef] 3. Acton, J.C.; Ziegler, G.R.; Burge, D.L.; Froning, G.W. Functionality of muscle constituents in the processing of
comminuted meat products. C R C Crit. Rev. Food Sci. Nutr. 1983, 18, 99–121. [CrossRef] [PubMed] 3. Acton, J.C.; Ziegler, G.R.; Burge, D.L.; Froning, G.W. Functionality of muscle constituents in the processing of
comminuted meat products. C R C Crit. Rev. Food Sci. Nutr. 1983, 18, 99–121. [CrossRef] [PubMed] 4. Privalov, P.L. Stability of proteins: Proteins which do not present a single cooperative system. Adv. Protein
Chem. 1982, 35, 1–104. [PubMed] 4. Privalov, P.L. Stability of proteins: Proteins which do not present a single cooperative system. Adv. Protein
Chem. 1982, 35, 1–104. [PubMed] 5. Davies, M.J. Protein oxidation and peroxidation. Biochem. J. 2016, 473, 805–825. [CrossRef] 5. Davies, M.J. Protein oxidation and peroxidation. Biochem. J. 2016, 473, 805–825. [CrossRef] 6. Gebicki, J.M. Oxidative stress, free radicals and protein peroxides. Arch. Biochem. Biophys. 2016, 595, 33–39. [CrossRef] 6. Gebicki, J.M. Oxidative stress, free radicals and protein peroxides. Arch. Biochem. Biophys. 2016, 595, 33–39. [CrossRef] 7. Lucarini, M.; Sciubba, F.; Capitani, D.; Di Cocco, M.E.; D’Evoli, L.; Durazzo, A.; Delfini, M.; Ginevra, L.-B. Role of catechin on collagen type I stability upon oxidation: A NMR approach. Nat. Prod. Res. 2019, 34,
53–62. [CrossRef] 8. Madhan, B.; Subramanian, V.; Rao, J.R.; Nair, B.U.; Ramasami, T. Stabilization of collagen using plant
polyphenol: Role of catechin. Int. J. Boil. Macromol. 2005, 37, 47–53. [CrossRef] 9. Brinckmann, J. Collagens at a Glance. In Collagen. Topics in Current Chemistry; Brinckmann, J., Notbohm, H.,
Müller, P.K., Eds.; Springer: Berlin/Heidelberg, Germany, 2005; Volume 247. 10. Di Lullo, G.A.; Sweeney, S.M.; Korkko, J.; Ala-Kokko, L.; San Antonio, J.D. 4. Conclusions
4. Conclusions Author Contributions: M.L., M.D., and G.L.-B. conceived and designed the work; M.L., M.D., A.D., and A.S. wrote the work; M.L., R.G., and F.S. carried out the experimental work; M.E.D.C., M.L., F.S., and M.A. validated
and elaborated the data information and figures; M.L., A.D., F.S., M.E.D.C., R.G., M.A., A.S., M.D., and G.L.-B. made a substantial contribution to the revision of work and approved it for publication. All authors have read
and agreed to the published version of the manuscript. Funding: This research received no external funding Conflicts of Interest: The authors declare no conflicts of interest. Conflicts of Interest: The authors declare no conflicts of interest. References Mapping the ligand-binding sites
and disease-associated mutations on the most abundant protein in the human, type I collagen. J. Biol. Chem. 2002, 277, 4223–4231. [CrossRef] 11. Kadeˇrávek, P.; Bolik-Coulon, N.; Cousin, S.F.; Marquardsen, T.; Tyburn, J.M.; Dumez, J.N.; Ferrage, F. Protein
Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation. J. Phys. Chem. Lett. 2019, 10, 5917–5922. [CrossRef] y
2. Bertram, H.C.; Karlsson, A.H.; Rasmussen, M.; Pedersen, O.D.; Dønstrup, S.; Andersen, H.J. Origi
Multiexponential T2 Relaxation in Muscle Myowater. J. Agric. Food Chem. 2001, 49, 3092–3100. [CrossR 13. Gianferri, R.; Maioli, M.; Delfini, M.; Brosio, E. A low-resolution and high resolution nuclear magnetic
resonance integrated approach to investigate the physical structure and metabolic profile of Mozzarella di
Bufala Campana cheese. Int. Dairy J. 2007, 17, 167–176. [CrossRef] 14. Bertram, H.C.; Kristensen, M.; Andersen, H.J. Functionality of myofibrillar proteins as affected by pH, ionic
strength and heat-treatments. A low-field NMR study. Meat Sci. 2004, 68, 249–256. [CrossRef] 15. Meiboom, S.; Gill, D. Modified Spin-Echo Method for Measuring Nuclear Relaxation Times. Rev. Sci. Instrum. 1958, 29, 688–691. [CrossRef] Foods 2020, 9, 480 10 of 10 10 of 10 16. Marquardt, D.W. An algorithm for least-squares estimation of nonlinear parameters. J. Soc. Ind. Appl. Math. 1963, 11, 431–441. [CrossRef] 17. Stejskal, E.O.; Tanner, J.E. Spin diffusion measurements: Spin echoes in the presence of a time dependent
field gradient. J. Chem. Phys. 1965, 42, 288–292. [CrossRef] 18. Bjarnason, T.A.; Vavasour, I.M.; Chia, C.L.L.; MacKay, A.L. Characterization of the NMR behavior of white
matter in bovine brain. Magn. Reson. Med. 2005, 54, 1072–1081. [CrossRef] [PubMed] 19. Reiter, D.A.; Lin, P.-C.; Fishbein, K.; Spencer, R.G.S. Multicomponent T2 relaxation analysis in cartilage. Magn. Reson. Med. 2009, 61, 803–809. [CrossRef] 20. Martini, S.; Bonechi, C.; Foletti, A.; Rossi, C. Water-Protein Interactions: The Secret of Protein Dynamics. Sci. World J. 2013, 2013, 138916. [CrossRef] 21. Kopp, J.; Bonnet, M.; Renou, J.P. Effect of collagen crosslinking on collagen-water interactions (a DSC
investigation). Matrix 1989, 9, 443–450. [CrossRef] 22. Pineri, M.H.; Escoubes, M.; Roche, G. Water-collagen interactions: Calorimetric and mechanical experiments. Biopolymers 1978, 17, 2799–2815. [CrossRef] 23. Renou, J.P.; Bonnet, M.; Bielicki, G.; Rochdi, A.; Gatellier, P. NMR study of collagen-water inter
Biopolymers 1994, 34, 1615–1626. [CrossRef] [PubMed] 24. Migchelsen, C.; Berendsen, H.J.C. Proton exchange and molecular orientation of water in hydrated c
fibers. An NMR study of H2O and D2O. J. Chem. Phys. 1973, 59, 296–305. [CrossRef] 25. References Wang, J.H. Theory of the Self-diffusion of Water in Protein Solutions. A New Method for Studying the
Hydration and Shape of Protein Molecules. J. Am. Chem. Soc. 1954, 76, 4755–4763. [CrossRef] 26. Lechert, H.T. Water binding on starch: NMR studies on native and gelatinized starch. In Water Activity:
Influences on Food Quality; Rockland, L.B., Stewart, G.F., Eds.; Academic Press: New York, NY, USA, 1981;
pp. 223–245. 27. Goddard, Y.A.; Korb, J.-P.; Bryant, R.G. Water molecule contributions to proton spin–lattice relaxation in
rotationally immobilized proteins. J. Magn. Reson. 2009, 199, 68–74. [CrossRef] [PubMed] 28. Diakova, G.; Goddard, Y.; Korb, J.-P.; Bryan, R.G. Water-Proton-Spin-Lattice-Relaxation Dispersion of
Paramagnetic Protein Solutions. J. Magn. Reson. 2011, 208, 195–203. [CrossRef] [PubMed] 29. Bendall, J.R.; Swatland, H.J. A review of the relationships of pH with physical aspects of pork quali
Sci. 1988, 24, 85–126. [CrossRef] 30. Offer, G.; Trinick, J. On the mechanism of water holding in meat: The swelling and shrinking of my
Meat Sci. 1993, 8, 245–281. [CrossRef] 31. Chen, J.Y.; Piva, M.; Labuza, T.P. Evaluation of Water Binding Capacity (WBC) of Food Fiber Sources. J. Food
Sci. 1984, 49, 59–63. [CrossRef] 32. Hamm, R. Functional properties of the myofibrillar system and their measurements. In Muscle as Food;
Bechtel, P.J., Ed.; Academic Press: Orlando, FL, USA; Elsevier: Amsterdam, The Netherlands, 1986;
pp. 135–199. 33. Bertram, H.C.; Whittaker, A.K.; Andersen, H.J.; Karlsson, A.H. pH Dependence of the Progression in NMR
T2 Relaxation Times in Post-mortem Muscle. J. Agric. Food Chem. 2003, 51, 4072–4078. [CrossRef] 33. Bertram, H.C.; Whittaker, A.K.; Andersen, H.J.; Karlsson, A.H. pH Dependence of the Progression in NMR
T2 Relaxation Times in Post-mortem Muscle. J. Agric. Food Chem. 2003, 51, 4072–4078. [CrossRef] 34. Tornberg, E.; Nerbrink, O. Swelling of whole meat and myofibrils—as measured by pulse-NMR. In
Proceedings of the 30th European Meeting of meat Research Workers, Bristol, UK, 9–14 September 1984;
pp. 112–113. pp
35. Brownstein, K.R.; Tarr, C.E. Importance of classical diffusion in NMR studies of water in biological cells. Physol. Rev. A 1979, 19, 2446–2453. [CrossRef] 36. Brøndum, J.; Munck, L.; Henckel, P.; Karlsson, A.; Tornberg, E.; Engelsen, S.B. Prediction of waterholding
capacity and composition of porcine meat by comparative spectroscopy. Meat Sci. 2000, 55, 177–185. [CrossRef] 36. Brøndum, J.; Munck, L.; Henckel, P.; Karlsson, A.; Tornberg, E.; Engelsen, S.B. Prediction of waterholding
capacity and composition of porcine meat by comparative spectroscopy. Meat Sci. 2000, 55, 177–185. [CrossRef]
37. References Jepsen, S.M.; Pedersen, H.T.; Engelsen, S.B. Application of chemometrics to low-field 1H NMR relaxation
d
f
fih fl
h J S i F
d A
i
79 1793 1802 [C
R f] capacity and composition of porcine meat by comparative spectroscopy. Meat Sci. 2000, 55, 177 185. [CrossRef]
37. Jepsen, S.M.; Pedersen, H.T.; Engelsen, S.B. Application of chemometrics to low-field 1H NMR relaxation
data of intact fish flesh. J. Sci. Food Agric. 1999, 79, 1793–1802. [CrossRef] 38. Bertram, H.C. 1H NMR Relaxometry in Meat Science. In Modern Magnetic Resonance, 2nd ed.; Webb, G., Ed.;
Springer: Berlin, Germany, 2016; pp. 1–14. [CrossRef] © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
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Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu (1918–1941)
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Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941)
UDK
616-002.5(497.5Split):070]”1918/1940”
364:61](497.5Split)”1918/1940”
61-05Štampar, A.
Pregledni rad
Primljeno: 25. IV. 2019.
Prihvaćeno: 8. XI. 2019.
https://doi.org/10.33604/sl.13.25.4 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941)
UDK
616-002.5(497.5Split):070]”1918/1940”
364:61](497.5Split)”1918/1940”
61-05Štampar, A. Pregledni rad
Primljeno: 25. IV. 2019. Prihvaćeno: 8. XI. 2019. https://doi.org/10.33604/sl.13.25.4 Pregledni rad Pregledni rad Javno znanje o tuberkulozi i djelovanje
Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Ivanka Kuić
Sveučilišna knjižnica u Splitu
e-mail: kuicivanka@gmail.com SAŽETAK: Tuberkuloza je bila velik zdravstveni problem u Splitu između dvaju svjetskih
ratova (1918–1941). U zdravstvenom prosvjećivanju, kao jednoj od preventivnih metoda liječenja te opake
bolesti na tragu Štamparovih socijalno-medicinskih ideja, razbijanju predrasuda i senzibiliziranju jav-
nosti za suočavanje s posljedicama bolesti, važnu su ulogu imale znanstvene publikacije, časopisi i lokal-
ne novine. U radu se uspostavlja kontinuitet stvaranja zabilježenoga javnoga znanja, s posebnim osvr-
tom na ulogu masovnih medija: Novoga doba, važnoga političko-informativnoga dnevnika koji je izlazio
od 1918. do 22. travnja 1941., i Jadranskoga dnevnika, koji je izlazio između 1934. i 1938. Oba su dnevnika
uspješno obavljala društvenu funkciju informiranja, oblikovanja javnoga mišljenja i širenja znanja, pre-
noseći svu složenost i nužnost modernizacijskih praksi koje su mijenjale Split i činile ga modernim gra-
dom. Jedna od tih modernizacijskih praksi bila je i borba s tuberkulozom kao ozbiljnim socijalno- medi-
cinskim problemom. Ključne riječi: Andrija Štampar; tuberkuloza; socijalno-medicinske metode; Split 1918–1940.,
Novo doba, Jadranski dnevnik 1 »Danas, više nego ikad, stanje bolesti ili zdravlja, naše dijagnoze, usko su vezane uz troškove,
no ne realne nego one koji su određeni globalnim tržišnim nadmetanjima i ritmom „života“ slobodnoga Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) jetu globalizma i neoliberalnoga kapitalizma, u kojem su bolest i zdravlje na udaru
globalnih korporacija (primjerice farmaceutskih), ideologija koju je Štampar zastu-
pao i danas ostaje točka atrakcije hrvatske zdravstvene politike i mjesto prijepora
različitih pristupa organizaciji suvremene hrvatske medicinske prakse jer zastupa
interes čovjeka – ma tko on bio – u društvu u kojem živi. Središte je njegove ideolo-
gije, koju je oblikovao u jednom članku već 1911.,2 čovjek, njegovo zdravlje i fizička
snaga kao gospodarska vrijednost te socijalno-ekonomski uvjeti kao uvjeti čovjekova
života. Na krilima naprednjačke ideologije, koja u kontekstu tadašnjih prilika reflek-
tira društvenu potrebu za kulturnom i ekonomskom preobrazbom hrvatskoga druš-
tva, za napretkom i subjektivitetom svakoga pojedinca,3 Štampar je posebno posve-
ćen narodnom zdravlju i siromašnijim slojevima čiji život, socijalne i kulturne prilike
dobro poznaje. Načelo humanosti i humanizam, stavljanje čovjeka u središte druš-
tvena interesa temeljna su načela njegove profesionalne etike. Kako piše Grmek,
»Štampar je bio liječnik praktičar, ali ne na individualnoj razini; njegovi pacijenti bili
su ljudske zajednice«.4 Stoga ovom radu pristupamo istraživački, a u fokus istraživa-
nja stavljamo upravo sposobnost i integrativnu snagu Splita kao »ljudske zajednice«,
kao urbanističko-socijalne cjeline koja u istraživanom razdoblju postupno dobiva
konture modernoga grada i angažira se u saniranju takvih društvenih problema
kakva je bolest tuberkuloze. Kao jednu od važnih točaka socijalne medicine, koju
definira kao »socijalizovana znanstvena i praktična medicina«,5 tj. socijalne terapije,
on ističe socijalnu pedagogiju i popularizaciju te korištenje različitih tiskanih sred-
stava u širenju znanja o bolesti, higijenskom i racionalnom životu kao načinu suzbi-
janja socijalnih endemskih bolesti.6 jetu globalizma i neoliberalnoga kapitalizma, u kojem su bolest i zdravlje na udaru
globalnih korporacija (primjerice farmaceutskih), ideologija koju je Štampar zastu-
pao i danas ostaje točka atrakcije hrvatske zdravstvene politike i mjesto prijepora
različitih pristupa organizaciji suvremene hrvatske medicinske prakse jer zastupa
interes čovjeka – ma tko on bio – u društvu u kojem živi. Središte je njegove ideolo-
gije, koju je oblikovao u jednom članku već 1911.,2 čovjek, njegovo zdravlje i fizička
snaga kao gospodarska vrijednost te socijalno-ekonomski uvjeti kao uvjeti čovjekova
života. Na krilima naprednjačke ideologije, koja u kontekstu tadašnjih prilika reflek-
tira društvenu potrebu za kulturnom i ekonomskom preobrazbom hrvatskoga druš-
tva, za napretkom i subjektivitetom svakoga pojedinca,3 Štampar je posebno posve-
ćen narodnom zdravlju i siromašnijim slojevima čiji život, socijalne i kulturne prilike
dobro poznaje. 5 U pristupnom predavanju održanom na Medicinskom fakultetu u Zagrebu 1923. prigodom
izbora za profesora higijene i socijalne medicine Štampar je rekao: »Socijalna medicina je nauka koja se
bavi ispitivanjem međusobnog utjecaja socijalnih odnosa i patoloških pojava u narodu i pronalaženjem
mera socijalnog karaktera za unapređenje narodnog zdravlja.« U: U borbi za narodno zdravlje: izabrani
članci Andrije Štampara, str. 85. 6 »Popularizacija medicine je moćan faktor pri njezinu djelovanju. Općem širenju pučke pro-
svjete treba da pristupi i širenje pouka medicinskih. Izdavanjem poučnih, pučki dobro pisanih knjižica
zdravstvenog sadržaja, priređivanjem isto takvih predavanja, osnivanjem društava s tom svrhom, učinit
će se mnogo uspješnog i lijepog na području socijalne medicine.« A. Štampar: Socijalna medicina. U: U
borbi za narodno zdravlje: izabrani članci Andrije Štampara, str. 54. tržišta«. Sanja Špoljar-Vržina: Neoliberalno „zdravlje“, globalna bolest i Štamparova medicina, Društve-
na istraživanja, 17(2008) 6, str. 1000. 2 Andrija Štampar: Socijalna medicina. U: Mirko Dražen Grmek (prir.), U borbi za narodno
zdravlje: izabrani članci Andrije Štampara, Zagreb 1966, str. 51–54. 4 Mirko Dražen Grmek: Životni put Andrije Štampara, borca za unapređenje narodnog
zdravlja. U: U borbi za narodno zdravlje: izabrani članci Andrije Štampara, str. 14. Osnovne postavke Štamparove socijalne medicine I nakon šezdeset godina od smrti, Andrija Štampar ostaje i dalje velika i pomalo za-
tajena inspiracija hrvatske medicine i medicinske znanosti. Njegova misao i dalje je
predmet bavljenja povjesničara medicine, kulturnih povjesničara, sociologa, liječni-
ka koji praktično ostvaruju zadatke liječenja ljudi, kao i hrvatskoga društva u cjelini. Njegovu se socijalnu misao danas, nakon društvenih, političkih i socijalnih promje-
na kroz koje je prošlo naše društvo, sve više »konfrontira« s rastućim trendom komo-
difikacije naših tijela prema neoliberalnim tržišnim praksama.1 U suvremenom svi- 1 »Danas, više nego ikad, stanje bolesti ili zdravlja, naše dijagnoze, usko su vezane uz troškove,
no ne realne nego one koji su određeni globalnim tržišnim nadmetanjima i ritmom „života“ slobodnoga 87 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 3 Isto, str. 52. »Ako je ideal oslobađanje čovjeka u svakom pogledu duševnoga i tjelesnog života
prvi u idealima modernim, onda bi ideal zdravlja i fizičke snage morao biti odmah na drugom mjestu.« šta«. Sanja Špoljar-Vržina: Neoliberalno „zdravlje“, globalna bolest i Štamparova medicina, Društve
straživanja, 17(2008) 6, str. 1000. 9 U jednom članku Štampar socijalnu medicinu definira kao nauku »koja se bavi ispitivanjem
međusobnog utjecaja socijalnih odnosa i patoloških pojava u narodu i pronalaženjem mera socijalnog
karaktera za unapređenje narodnog zdravlja«. (»O socijalnoj medicini«. U: U borbi za narodno zdravlje:
izabrani članci Andrije Štampara, str. 85). 8 »Suzbijanje neznanja, širenje pismenosti i opšteg znanja, od većeg je značaja za unapređenje
narodnog zdravlja od mnogih čisto zdravstvenih ustanova.« Ibid., str. 100. 10 Misli se na članak »Borba protiv sušice«. Zvono, 1909., br. 14, str. 371–374; drugi spomenuti
članak je »Iz područja socijalne medicine: liječnik na selu«, Zvono, 1909., br. 16, str. 437–440. 11 Primjerak časopisa Zvono koji se čuva u Sveučilišnoj knjižnici, prema ex librisu, potječe iz
privatne knjižnice dr. Ante I. Štambuka. 7 Andrija Štampar: Naša ideologija. U: U borbi za narodno zdravlje: izabrani članci Andrije
Štampara, str. 99–101. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Načelo humanosti i humanizam, stavljanje čovjeka u središte druš-
tvena interesa temeljna su načela njegove profesionalne etike. Kako piše Grmek,
»Štampar je bio liječnik praktičar, ali ne na individualnoj razini; njegovi pacijenti bili
su ljudske zajednice«.4 Stoga ovom radu pristupamo istraživački, a u fokus istraživa-
nja stavljamo upravo sposobnost i integrativnu snagu Splita kao »ljudske zajednice«,
kao urbanističko-socijalne cjeline koja u istraživanom razdoblju postupno dobiva
konture modernoga grada i angažira se u saniranju takvih društvenih problema
kakva je bolest tuberkuloze. Kao jednu od važnih točaka socijalne medicine, koju
definira kao »socijalizovana znanstvena i praktična medicina«,5 tj. socijalne terapije,
on ističe socijalnu pedagogiju i popularizaciju te korištenje različitih tiskanih sred-
stava u širenju znanja o bolesti, higijenskom i racionalnom životu kao načinu suzbi-
janja socijalnih endemskih bolesti.6 tržišta«. Sanja Špoljar-Vržina: Neoliberalno „zdravlje“, globalna bolest i Štamparova medicina, Društve-
na istraživanja, 17(2008) 6, str. 1000. 2 Andrija Štampar: Socijalna medicina. U: Mirko Dražen Grmek (prir.), U borbi za narodno
zdravlje: izabrani članci Andrije Štampara, Zagreb 1966, str. 51–54. 4 Mirko Dražen Grmek: Životni put Andrije Štampara, borca za unapređenje narodnog
zdravlja. U: U borbi za narodno zdravlje: izabrani članci Andrije Štampara, str. 14. 88 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) tada moći suzbiti, ako se dobro upozna…«.12 Štampar smatra da se to može postići
širenjem znanja o bolesti jer »kako će onaj ići u bolnicu koji ne zna ništa o zdravlju i
bolesti, nego čeka da samo od sebe prođe«.13 Od tada je širenje znanja o bolesti i nači-
nima na koji se ona suzbija jedna od temeljnih postavki Štamparove socijalne medi-
cine koju su prihvatili i ugledni splitski liječnici u etatiziranim zdravstvenim ustano-
vama. Osvrćemo se na ovu knjigu i zato što u njoj iznosi i ideju o potrebi osnivanja
društava za očuvanje narodnoga zdravlja po ugledu na druge narode, pokretanja
»pučkih zdravstvenih novina«, zdravstvenoga prosvjećivanja, nasuprot tezi da »ne-
ukom svijetu nije dobro tumačiti bolesti, jer da se tim više škodi nego koristi«. Štam-
par smatra da se liječnici trebaju uključiti u zdravstveno prosvjećivanje i pisanjem
popularnih knjižica i članaka: »trebalo bi nam i ljudi, koji bi pravo pučki znali pisati,
da svatko može ono razumjeti, što napišu«. U uvodu također napominje: »Nije naime
dosta, da se knjiga napiše i izda nego treba da se čita«.14 Ta je jednostavno pisana
knjižica puna poslovičnih izreka o zdravlju, šireći Štamparevu misao i moderna zna-
nja i dostignuća medicine u liječenju tuberkuloze, držimo, bila diskurzivni preokret,
uzor i motiv splitskim liječnicima u borbi protiv tuberkuloze te otuda ima mjesta u
povijesti medicinske knjige u Splitu. Ona zasigurno ulazi u katalog temeljnih publi-
kacija koje su Split uvele u kampanju borbe protiv tuberkuloze. tada moći suzbiti, ako se dobro upozna…«.12 Štampar smatra da se to može postići
širenjem znanja o bolesti jer »kako će onaj ići u bolnicu koji ne zna ništa o zdravlju i
bolesti, nego čeka da samo od sebe prođe«.13 Od tada je širenje znanja o bolesti i nači-
nima na koji se ona suzbija jedna od temeljnih postavki Štamparove socijalne medi-
cine koju su prihvatili i ugledni splitski liječnici u etatiziranim zdravstvenim ustano-
vama. Osvrćemo se na ovu knjigu i zato što u njoj iznosi i ideju o potrebi osnivanja
društava za očuvanje narodnoga zdravlja po ugledu na druge narode, pokretanja
»pučkih zdravstvenih novina«, zdravstvenoga prosvjećivanja, nasuprot tezi da »ne-
ukom svijetu nije dobro tumačiti bolesti, jer da se tim više škodi nego koristi«. 12 Andrija Štampar: Pouke o zdravlju, Zagreb 1910., str. 6.
13 Isto, str. 30.
14 Pouke o zdravlju, str. 29–31.
15 Željko Dugac: Kako biti čist i zdrav: zdravstveno prosvjećivanje u međuratnoj Hrvatskoj, Zagreb
2010. Autor se u svojoj knjizi bavi iscrpno metodama zdravstvenoga prosvjećivanja u međuratnom peri-
odu. Također ističe da se zalaganje za uporabu pisanih materijala uočava odmah nakon Prvoga svjetsko-
ga rata, za što se zalagalo Povjerenstvo za suzbijanje tuberkuloze već 1919. u Zagrebu. »Provoditelji
zdravstveno-prosvjetnih akcija tiskane su materijale smatrali podesnim medijem za širenje svojih ideja,
ali je za njihovu upotrebu bilo potrebno ispuniti nekoliko važnih elemenata.« To je u prvom redu bila
pismenost, ali i dostupnost (str. 68). 15 Željko Dugac: Kako biti čist i zdrav: zdravstveno prosvjećivanje u međuratnoj Hrvatskoj, Zagreb
2010. Autor se u svojoj knjizi bavi iscrpno metodama zdravstvenoga prosvjećivanja u međuratnom peri-
odu. Također ističe da se zalaganje za uporabu pisanih materijala uočava odmah nakon Prvoga svjetsko-
ga rata, za što se zalagalo Povjerenstvo za suzbijanje tuberkuloze već 1919. u Zagrebu. »Provoditelji
zdravstveno-prosvjetnih akcija tiskane su materijale smatrali podesnim medijem za širenje svojih ideja,
ali je za njihovu upotrebu bilo potrebno ispuniti nekoliko važnih elemenata.« To je u prvom redu bila
pismenost, ali i dostupnost (str. 68). 14 Pouke o zdravlju, str. 29–31. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Povjerenje u znanje kao uvjet napretka i sretnijega života ideologija je koju
Štampar slijedi od studentskih dana. U članku »Naša ideologija«7 naglasio je znanje
kao najvažniji čimbenik borbe protiv bolesti.8 Ovo je doba socijalizacije i demokrati-
zacije medicine, naglašava u istom članku, kao rezultat velikih socijalnih pokreta i
napora reformatora, među koje ubraja i liječnike koji su se bavili narodnim zdrav-
ljem. Označivši zdravlje kao pozitivnu kulturnu činjenicu, demokratizacija znanja
postala je uvjet borbe za zdravlje. Ideju brige za narodno zdravlje Štampar je zastupao već početkom XX. stolje-
ća kao student medicine u Beču u člancima koje je objavljivao u nekim časopisima.9
U pokušaju da uspostavimo kontinuitet prisutnosti njegova ideala u Splitu i Dalma-
ciji i utjecaja koji je morao imati, treba svakako poći od serije članaka objavljenih
1909. u časopisu Zvono. U jednom od njih izvještava o modernim metodama borbe
protiv sušice u Njemačkoj, a u drugom10 je posvećen ulozi liječnika kao socijalnoga
radnika i prosvjetitelja. Biti liječnik na selu, smatra Štampar, zahtjevna je profesija,
zahtijeva veliko znanje, veće nego znanje liječnika u gradu i humanost, a liječnik i
učitelj mogu puno učiniti na području pučke prosvjete. Nije dovoljno biti dobar liječ-
nik nego treba biti i dobar čovjek. Literatura i pisana riječ za Štampara su uvijek bili
važan oslonac u radu, jedan od socijalnih uvjeta znanja. Na žalost, piše on, u Hrvat-
skoj nema popularne medicinske literature kao u drugim zemljama. Njegove su ide-
je već tada bile poznate javnosti Splita.11 Malu knjižicu Pouke o zdravlju objavio je
1910. i posvetio je u cijelosti borbi protiv tuberkuloze. Ta je knjižica također dospjela
do splitske stručne i druge javnosti i mogla se nabaviti u knjižari Vinka Jurića u
Splitu. U njoj je Štampar pokazao poznavanje i razumijevanje etiologije i prirode
tuberkuloze u Hrvatskoj, posebno u hrvatskom selu. U svojoj knjižici iznosi niz po-
uka o zdravom životu i ideju o zdravlju kao najvećem bogatstvu koje treba čuvati, što
čini srž njegove medicinske misli. Misao o znanju iznio je u nekoliko proročanskih
rečenica: »Znanje je moć. Tko više zna više može. U neznanju svašta se može dogo-
diti. Znanjem se i bolest suzbija. Ali nije dovoljno znati, treba i htjeti. Bolest će se tek 89 12 Andrija Štampar: Pouke o zdravlju, Zagreb 1910., str. 6.
13 Isto, str. 30.
14 Pouke o zdravlju, str. 29–31. 13 Isto, str. 30. 16 Miroslav Tuđman smatra da su tradicionalni stavovi informacijskih znanosti da je javno
znanje svijet objektivnih i istinitih informacija. To su stavovi koji vrijede za sredinu XX. stoljeća, ali
danas dolazi do dekonstrukcije toga svijeta pod utjecajem informacijske znanosti koja digitalnu infor-
maciju stavlja u središte znanja koja više ne funkcionira kao javno znanje i nema zadaću prenositi istini-
te i objektivne informacije. Vrijeme u kojem se nalazimo, način proizvodnje tekstova i objavljene infor-
macije kontekstualizirane zbiljom upućuje na činjenicu da je javno znanje još uvijek bilo objektivna i
istinita društvena forma. Vidi: Miroslav Tuđman: Je li informacijska znanost još uvijek društvena znanost?
http://infoz.ffzg.hr/infuture/2007/pdf/1-04%20Tudjman,%20Miroslav,%20Je%20li%20informacij-
ska%20znanost%20jos%20uvijek%20drustvena%20znanost.pdf (pristupljeno 2. I. 2019) 17 »Za formiranje javnog znanja presudna je instrumentalizacija svih funkcija, a posebno infor-
macijske funkcije. No i ova je forma znanja kulturno i filozofski uvjetovana jer polazi od pretpostavke o:
postojanju objektivnog znanja; autonomnoj egzistenciji objektivnog znanja neovisnoj od spoznajnog
sub jekta; podjeli rada i diferencijaciji socijalnih uloga na čemu se i zasniva rast informacijske infrastruk-
ture; egzistenciji javnog znanja kao autonomnog predmeta kojim se bave te službe, pa se govori o infor-
macijskom tržištu, informacijskoj ekonomiji, informacijskim proizvodima i uslugama itd.« Miroslav
Tuđman: Epistemološki postav informacijske znanosti, str. 108. https://www.researchgate.net/publicati-
on/281099573_Epistemologijski_postav_informacijske_znanosti_Epistemology_of_the_information_
science (pristupljeno 3. I. 2019). Vidi i: Stephen Downes: Connectivism and Connective Knowledge,
str. 315–316. https://www.downes.ca/files/books/Connective_Knowledge-19May2012.pdf (pristupljeno
3. I. 2019) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) ili organiziranoga djelovanja, većinom uz pomoć medija.16 Javno je znanje ono znanje
»kojem želimo podučiti našu djecu, to je ono što utjelovljuje kanon i prenosi se na
sljedeće generacije«.17 Prema tome, to je eksplicitna reprezentacija društvenoga zna-
nja u jeziku ili nekoj drugoj formi. Drugo je pitanje društvenih dimenzija znanja, tj. socijalnih uvjeta znanja.18 Možemo se stoga, nakon upoznavanja s medicinsko-teorij-
skim postavkama Andrije Štampara, zapitati u kakvim je relacijama bilo znanje liječ-
nika prema znanju naroda o zaraznim bolestima i tuberkulozi, te jesu li liječnici
sami mogli i uz kakve napore prosvjećivati nepismen i socijalno i ekonomski zapu-
šten narod, bez šire društvene akcije. Odgovor na to pitanje zahtijeva i poznavanje
nekih ključnih društvenih i socijalnih činjenica o Splitu koje bi omogućile bolje ra-
zumijevanje odnosa tadašnjih masovnih medija i stvarnosti te napora splitskih liječ-
nika koji su djelovali u smjeru Štamparovih uputa o sprječavanju bolesti. ili organiziranoga djelovanja, većinom uz pomoć medija.16 Javno je znanje ono znanje
»kojem želimo podučiti našu djecu, to je ono što utjelovljuje kanon i prenosi se na
sljedeće generacije«.17 Prema tome, to je eksplicitna reprezentacija društvenoga zna-
nja u jeziku ili nekoj drugoj formi. Drugo je pitanje društvenih dimenzija znanja, tj. socijalnih uvjeta znanja.18 Možemo se stoga, nakon upoznavanja s medicinsko-teorij-
skim postavkama Andrije Štampara, zapitati u kakvim je relacijama bilo znanje liječ-
nika prema znanju naroda o zaraznim bolestima i tuberkulozi, te jesu li liječnici
sami mogli i uz kakve napore prosvjećivati nepismen i socijalno i ekonomski zapu-
šten narod, bez šire društvene akcije. Odgovor na to pitanje zahtijeva i poznavanje
nekih ključnih društvenih i socijalnih činjenica o Splitu koje bi omogućile bolje ra-
zumijevanje odnosa tadašnjih masovnih medija i stvarnosti te napora splitskih liječ-
nika koji su djelovali u smjeru Štamparovih uputa o sprječavanju bolesti. Općenito se u međuratnom razdoblju Split nalazio u tranziciji prema otvore-
nom i modernom gradu. U promijenjenim društvenim uvjetima nove države, njego-
vi su razvojni potencijali dolazili do izražaja više zahvaljujući sposobnostima pojedi-
naca s »tehničkim i funkcionalnim kompetencijama«, dakle »odozdo«, nego pomoći
središta koje je s vremenom sve manje podržavalo splitske projekte. Položaj najvećega
grada na Jadranu, na koji je s pravom računao, mijenja se teritorijalnim podjelama u
Kraljevini SHS/Jugoslaviji, koje umanjuju njegovo značenje u širem okruženju. 18 Socijalni epistemolog Frederich Schmitt podrazumijeva »utjecaj društvenih odnosa, intere-
sa, uloga i institucija… Oduvijek se priznaje da socijalni uvjeti podupiru znanje tako što čine materijalno
mogućima opažanje, sjećanje i razmišljanje...«. John Greco i Ernest Sosa (prir.). Epistemologija: vodič u
teoriji znanja, Zagreb 2004. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Štam-
par smatra da se liječnici trebaju uključiti u zdravstveno prosvjećivanje i pisanjem
popularnih knjižica i članaka: »trebalo bi nam i ljudi, koji bi pravo pučki znali pisati,
da svatko može ono razumjeti, što napišu«. U uvodu također napominje: »Nije naime
dosta, da se knjiga napiše i izda nego treba da se čita«.14 Ta je jednostavno pisana
knjižica puna poslovičnih izreka o zdravlju, šireći Štamparevu misao i moderna zna-
nja i dostignuća medicine u liječenju tuberkuloze, držimo, bila diskurzivni preokret,
uzor i motiv splitskim liječnicima u borbi protiv tuberkuloze te otuda ima mjesta u
povijesti medicinske knjige u Splitu. Ona zasigurno ulazi u katalog temeljnih publi-
kacija koje su Split uvele u kampanju borbe protiv tuberkuloze. Andrija Štampar nije samo reformator sustava zdravstvene zaštite u smislu
metodologije i organizacije rada nego i ideolog koji je odredio etiku, vrijednosti, ori-
jentire i prioritete stručnoga rada. Kao reformator, on se u svojoj strategiji oslonio na
pisanu riječ15 i širenje informacija i znanja o zaraznim bolestima pisanim sredstvima,
dajući liječnicima konkretne zadatke prosvjećivanja i stvaranja korpusa javnoga zna-
nja na korist društva i pojedinca. Jezgra toga znanja, sudeći prema njegovim članci-
ma, trebaju biti istinite i objektivne informacije zasnovane na znanstvenim i praktič-
nim socijalno-medicinskim spoznajama i kontekstualizirane zbiljom jer su bez toga
ciljevi koje je postavio bili teško ostvarivi. Općenito se »javno znanje« definira kao
zabilježeno znanje koje je dostupno svima, koje se stvara u nekom društvenom pro-
storu kao rezultat međusobne komunikacije i interakcije pripadnika nekoga društva 90 19 Ivan Rogić, Ivan Čizmić: Modernizacija u Hrvatskoj i hrvatska odselidba, Zagreb 2011., str. 45–53.
Prema autorima, nakon 1918. oblikuje se jedna nadnacionalna strategija razvoja i nova dvostruka perifer-
nost kao osnovni problemi, što znači manjak državne potpore lokalnoj politici i projektima, što dovodi
do stratifikacije »poduzetničke moći« po nacionalnoj liniji, dok mala poduzeća koja ne mogu ponuditi
višak radnih mjesta i manjak osnovnoga obrazovanja većine stanovništva dovode do golemih socijalnih
razlika i produbljuje distancu grad – selo, ali u Splitu i grad-periferija, uza sva nastojanja uprave da se
oblikuje moderan grad koji urbanizacijski povezuje svoje dijelove. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) kon početnoga optimizma, odnos prema središnjoj vlasti radikaliziran je nemoguć-
nošću autonomnoga djelovanja u rješavanju brojnih socijalnih i gospodarskih prob-
lema i izostanku pomoći središnje vlade i planova (cementna industrija, industrija
konzerviranja ribe, i dr.) i ostvarenju municipalnih prava i identiteta. U okvir tih
problema ulaze i zdravstveni problemi o kojima ovdje pišemo. Koristeći se jezičnim
aparatom Ivana Rogića kada piše o hrvatskim modernizacijama, sažeto možemo reći
da je Split, zajedno s velikim zaleđem, živio u uvjetima »zapriječenosti«, »usporeno-
sti« i »nedovršenosti«: industrijalizacije, urbanizacije, samovoljne birokratizacije sre-
dišnjih vlasti. Kao grad bez velikih industrijskih poduzeća, Split nije mogao osigura-
ti prihvat doseljenih iz okolnih pasivnih mjesta koji sa sobom donose niz problema
pa i bolesti, niti im ponuditi radno mjesto i bolje uvjete života.19 Asanacija grada,
uređenje gradske infrastrukture te osnivanje potrebnih zdravstvenih ustanova i na
kraju početak gradnje bolnice 1931. godine koja nije dovršena do 1941., postupno i u
skladu s ekonomskim mogućnostima, omogućavali su rješavanje problema skučenih
i nezdravih splitskih područja, izvora svekolike zaraze i boleštine. U takvoj situaciji
lokalne su novine, posebno Novo doba i Jadranski dnevnik kao novine s dužim kon-
tinuitetom izlaženja, uvodeći novu društvenu praksu informiranja o zaraznim bole-
stima, upozorili javnost na razmjere problema sustavno pritišćući društvo i središte
vlasti, razvijajući suosjećanje pojedinaca prema oboljelima i siromašnima te postup-
no stvarajući uvjete za organizaciju korpusa javnoga znanja o problemu zaraznih
bolesti. To je znanje zasigurno imalo učinak na ponašanje stanovništva i na javno
djelovanje. kon početnoga optimizma, odnos prema središnjoj vlasti radikaliziran je nemoguć-
nošću autonomnoga djelovanja u rješavanju brojnih socijalnih i gospodarskih prob-
lema i izostanku pomoći središnje vlade i planova (cementna industrija, industrija
konzerviranja ribe, i dr.) i ostvarenju municipalnih prava i identiteta. U okvir tih
problema ulaze i zdravstveni problemi o kojima ovdje pišemo. Koristeći se jezičnim
aparatom Ivana Rogića kada piše o hrvatskim modernizacijama, sažeto možemo reći
da je Split, zajedno s velikim zaleđem, živio u uvjetima »zapriječenosti«, »usporeno-
sti« i »nedovršenosti«: industrijalizacije, urbanizacije, samovoljne birokratizacije sre-
dišnjih vlasti. Kao grad bez velikih industrijskih poduzeća, Split nije mogao osigura-
ti prihvat doseljenih iz okolnih pasivnih mjesta koji sa sobom donose niz problema
pa i bolesti, niti im ponuditi radno mjesto i bolje uvjete života.19 Asanacija grada,
uređenje gradske infrastrukture te osnivanje potrebnih zdravstvenih ustanova i na
kraju početak gradnje bolnice 1931. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) godine koja nije dovršena do 1941., postupno i u
skladu s ekonomskim mogućnostima, omogućavali su rješavanje problema skučenih
i nezdravih splitskih područja, izvora svekolike zaraze i boleštine. U takvoj situaciji
lokalne su novine, posebno Novo doba i Jadranski dnevnik kao novine s dužim kon-
tinuitetom izlaženja, uvodeći novu društvenu praksu informiranja o zaraznim bole-
stima, upozorili javnost na razmjere problema sustavno pritišćući društvo i središte
vlasti, razvijajući suosjećanje pojedinaca prema oboljelima i siromašnima te postup-
no stvarajući uvjete za organizaciju korpusa javnoga znanja o problemu zaraznih
bolesti. To je znanje zasigurno imalo učinak na ponašanje stanovništva i na javno
djelovanje. Stoga su deskripcija medijske pojavnosti (znanstvene publikacije, časopisi i
novine) procesa zdravstvenoga prosvjećivanja, u Splitu, u sučeljavanju s tuberkulo-
zom i drugim zaraznim bolestima, diskurzivna praksa kao proizvodnja tekstova,
način razmišljanja, odnosa i ponašanja te artikulacija toga problema kao stvarne
društvene i socijalne opasnosti po pojedinca i po društvo, srž ovoga istraživanja. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Na- 16 Miroslav Tuđman smatra da su tradicionalni stavovi informacijskih znanosti da je javno
znanje svijet objektivnih i istinitih informacija. To su stavovi koji vrijede za sredinu XX. stoljeća, ali
danas dolazi do dekonstrukcije toga svijeta pod utjecajem informacijske znanosti koja digitalnu infor-
maciju stavlja u središte znanja koja više ne funkcionira kao javno znanje i nema zadaću prenositi istini-
te i objektivne informacije. Vrijeme u kojem se nalazimo, način proizvodnje tekstova i objavljene infor-
macije kontekstualizirane zbiljom upućuje na činjenicu da je javno znanje još uvijek bilo objektivna i
istinita društvena forma. Vidi: Miroslav Tuđman: Je li informacijska znanost još uvijek društvena znanost? http://infoz.ffzg.hr/infuture/2007/pdf/1-04%20Tudjman,%20Miroslav,%20Je%20li%20informacij-
ska%20znanost%20jos%20uvijek%20drustvena%20znanost.pdf (pristupljeno 2. I. 2019) 18 Socijalni epistemolog Frederich Schmitt podrazumijeva »utjecaj društvenih odnosa, intere-
sa, uloga i institucija… Oduvijek se priznaje da socijalni uvjeti podupiru znanje tako što čine materijalno
mogućima opažanje, sjećanje i razmišljanje...«. John Greco i Ernest Sosa (prir.). Epistemologija: vodič u
teoriji znanja, Zagreb 2004. 91 23 U organizaciji besplatne liječničke službe sudjelovala je i Ženska zadruga u Splitu. Osnovala
je Savjetovalište za majke i dojenčad, gdje je besplatno primao pacijente dr. Kovačić, i Ambulatorij Mazzi
za siromahe, đake i činovnike, koji je vodio dr. Petković, a koje su primale pacijente dva puta tjedno.
Škola za zdravstveno promicanje također je djelovala uz Žensku zadrugu, a poslije je prenijela svoj djelo-
krug po manjim mjestima širom Dalmacije. Nove zdravstvene ustanove u Dalmaciji. U: Pučka prosvjeta,
1923., br. 8, str. 139. 20 Zdravka Jelaska Marijan: Grad i ljudi: Split 1918.-1941. Zagreb 2009., str. 25–29.
21 Ibid., str. 298–299. Prema podatcima Anagrafskoga zavoda, u Splitu je posljednjega dana
1923. od 28 684 stanovnika bilo 26,96% nepismenih, a posljednjega dana 1924. od 29 655 stanovnika
28,44% nepismenih. Primjetno je kolebanje u broju stanovnika.
22 O njegovu radu vidi: Ivana Marasović Šušnjara i sur., Doktor Josip Škarić (1887.-1975.) – pio-
nirski pothvati na polju javnog zdravstva na području Dalmacije u prvoj polovici 20. stoljeća. U: Acta
Med Croatica, 71(2017), str. 319–326. Posebno su dramatični njegovi opisi zapuštenosti bolesnika i kuća na
koje je nailazio u svom radu.
23 U organizaciji besplatne liječničke službe sudjelovala je i Ženska zadruga u Splitu. Osnovala
je Savjetovalište za majke i dojenčad, gdje je besplatno primao pacijente dr. Kovačić, i Ambulatorij Mazzi
za siromahe, đake i činovnike, koji je vodio dr. Petković, a koje su primale pacijente dva puta tjedno.
Škola za zdravstveno promicanje također je djelovala uz Žensku zadrugu, a poslije je prenijela svoj djelo-
krug po manjim mjestima širom Dalmacije. Nove zdravstvene ustanove u Dalmaciji. U: Pučka prosvjeta,
1923 b
8
139 20 Zdravka Jelaska Marijan: Grad i ljudi: Split 1918.-1941. Zagreb 2009., str. 25–29.
21 Ibid., str. 298–299. Prema podatcima Anagrafskoga zavoda, u Splitu je posljednjega dana
1923. od 28 684 stanovnika bilo 26,96% nepismenih, a posljednjega dana 1924. od 29 655 stanovnika
28,44% nepismenih. Primjetno je kolebanje u broju stanovnika.
22 O njegovu radu vidi: Ivana Marasović Šušnjara i sur., Doktor Josip Škarić (1887.-1975.) – pio-
nirski pothvati na polju javnog zdravstva na području Dalmacije u prvoj polovici 20. stoljeća. U: Acta
Med Croatica, 71(2017), str. 319–326. Posebno su dramatični njegovi opisi zapuštenosti bolesnika i kuća na
koje je nailazio u svom radu.
23 U organizaciji besplatne liječničke službe sudjelovala je i Ženska zadruga u Splitu Osnovala Tuberkuloza u Splitu i znanstvene publikacije Ulaskom u novu zajednicu, Kraljevinu SHS, Split nastavlja fazu produžene prve
modernizacije – urbane transformacije i postupne promjene svih vidova javnoga ži-
vota. Kao najveće urbano naselje, nakon gubitka Zadra i Rijeke ugovorom u Rapallu 92 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 1920., Split postaje političko, gospodarsko i kulturno središte Dalmacije. Split se i
demografski mijenja: iz zaleđa dolazi velik broj radnika u potrazi za poslom i boljim
uvjetima života, pa se njegovo stanovništvo povećava s 25 045, koliko je imao prema
popisu iz 1921., na 35 417 stanovnika prema popisu iz 1931. godine, do 46 001 stanov-
nika 1941.20 Usvajanjem Regulacijskoga plana otvorene su mogućnosti za urbanistič-
ku preobrazbu – gradnju stanova, zdravstvenih ustanova, javnih, znanstvenih i
obrazovnih ustanova i oblikovanje novoga lica grada. Međutim, mnoštvo problema,
ekonomsko i kulturno stanje stanovništva, posebice radnika i težaka, kao posljedice
Prvoga svjetskoga rata, gladi, društvenih i socijalnih problema, kulturne zapušteno-
sti, velike nepismenosti,21 raširenosti zaraznih bolesti, otežavali su brzo i učinkovito
rješavanje gradskih problema. Javno zdravstvo u toj situaciji moralo je što hitnije
djelovati. Zahvaljujući naporima Andrije Štampara i suradnji sa Zdravstvenim odje-
lom za Dalmaciju, prvi upravitelj kojega je bio liječnik Šime Ljubić, u Splitu su već
1922. osnovani Bakteriološka stanica, zaslugom liječnika Josipa Škarića,22 Institut za
proučavanje i suzbijanje malarije u Trogiru, koji je vodio liječnik Andrija Sfarčić,
Ambulanta za venerične i kožne bolesti koju je vodio Ivo Stalio, postavljeni su temelji
istraživačke, dijagnostičke i preventivno-profilaktičke prakse u Splitu. Godine 1923. osnovan je i Dispanzer za grudne bolesti. Sve su te ustanove pružale besplatnu liječ-
ničku pomoć.23 Njihovim spajanjem nastao je 1929. Higijenski zavod (danas Nastavni
zavod za javno zdravstvo Splitsko-dalmatinske županije), a njegov direktor također
je bio Josip Škarić. Teritorijalnim podjelama koje su u tom razdoblju provedene, Split
je bio sjedište Splitske oblasti (1922–29), Primorske banovine (1929–39), a od 1939. u
sastavu je Banovine Hrvatske. 1920., Split postaje političko, gospodarsko i kulturno središte Dalmacije. Split se i
demografski mijenja: iz zaleđa dolazi velik broj radnika u potrazi za poslom i boljim
uvjetima života, pa se njegovo stanovništvo povećava s 25 045, koliko je imao prema
popisu iz 1921., na 35 417 stanovnika prema popisu iz 1931. 22 O njegovu radu vidi: Ivana Marasović Šušnjara i sur., Doktor Josip Škarić (1887.-1975.) – pio-
nirski pothvati na polju javnog zdravstva na području Dalmacije u prvoj polovici 20. stoljeća. U: Acta
Med Croatica, 71(2017), str. 319–326. Posebno su dramatični njegovi opisi zapuštenosti bolesnika i kuća na
koje je nailazio u svom radu. ,
p
j
j
j
j
22 O njegovu radu vidi: Ivana Marasović Šušnjara i sur., Doktor Josip Škarić (1887.-1975.) – pio-
nirski pothvati na polju javnog zdravstva na području Dalmacije u prvoj polovici 20. stoljeća. U: Acta
Med Croatica, 71(2017), str. 319–326. Posebno su dramatični njegovi opisi zapuštenosti bolesnika i kuća na
koje je nailazio u svom radu.
23 U organizaciji besplatne liječničke službe sudjelovala je i Ženska zadruga u Splitu. Osnovala
je Savjetovalište za majke i dojenčad, gdje je besplatno primao pacijente dr. Kovačić, i Ambulatorij Mazzi
za siromahe, đake i činovnike, koji je vodio dr. Petković, a koje su primale pacijente dva puta tjedno. 24 Propisi za suzbijanje tuberkuloze: otpis C.K. Ministra predsjednika kao upravljača ministar-
stava unutrašnjih posala, dneva 14. jula 1902. br. 29949. Zadar 1902. U vezi s indirektnim mjerama, Mi-
nistarstvo preporučuje: »To je prije svega poučavanje najširih slojeva pučanstva o načinu kako postaje i
kako se suzbija tuberkuloza i kako se čovjek ima vladati kad je zdrav i kad oboli. To se može postići s
popularnim predavanjima i člancima liječnika ili kojih strukovnjaka i širenjem dobrih popularnih djela
za koje bi se imala postarati humanitarna društva«, str. 13. 26 Rafo Ferri: Tuberkuloza u Splitu i asanacija grada, Split 1925. Opširnije o Rafi Ferriju vidi u:
Zaslužni splitski liječnici u prošlosti od 1946. do 1947., Split 1999., str. 56–71. 25 O stanju zdravlja i teškim uvjetima života u Splitskoj oblasti nakon teške zime vrlo potresnu
izjavu dao je liječnik Ivo Petković, govoreći o strašnoj gladi od koje posebno pate djeca, nestašici novca i
pitke vode: Zdravstveno stanje u Splitskoj oblasti. Novo doba, (1929), br. 102, str. 5. Tuberkuloza u Splitu i znanstvene publikacije godine, do 46 001 stanov-
nika 1941.20 Usvajanjem Regulacijskoga plana otvorene su mogućnosti za urbanistič-
ku preobrazbu – gradnju stanova, zdravstvenih ustanova, javnih, znanstvenih i
obrazovnih ustanova i oblikovanje novoga lica grada. Međutim, mnoštvo problema,
ekonomsko i kulturno stanje stanovništva, posebice radnika i težaka, kao posljedice
Prvoga svjetskoga rata, gladi, društvenih i socijalnih problema, kulturne zapušteno-
sti, velike nepismenosti,21 raširenosti zaraznih bolesti, otežavali su brzo i učinkovito
rješavanje gradskih problema. Javno zdravstvo u toj situaciji moralo je što hitnije
djelovati. Zahvaljujući naporima Andrije Štampara i suradnji sa Zdravstvenim odje-
lom za Dalmaciju, prvi upravitelj kojega je bio liječnik Šime Ljubić, u Splitu su već
1922. osnovani Bakteriološka stanica, zaslugom liječnika Josipa Škarića,22 Institut za
proučavanje i suzbijanje malarije u Trogiru, koji je vodio liječnik Andrija Sfarčić,
Ambulanta za venerične i kožne bolesti koju je vodio Ivo Stalio, postavljeni su temelji
istraživačke, dijagnostičke i preventivno-profilaktičke prakse u Splitu. Godine 1923. osnovan je i Dispanzer za grudne bolesti. Sve su te ustanove pružale besplatnu liječ-
ničku pomoć.23 Njihovim spajanjem nastao je 1929. Higijenski zavod (danas Nastavni
zavod za javno zdravstvo Splitsko-dalmatinske županije), a njegov direktor također
je bio Josip Škarić. Teritorijalnim podjelama koje su u tom razdoblju provedene, Split
je bio sjedište Splitske oblasti (1922–29), Primorske banovine (1929–39), a od 1939. u
sastavu je Banovine Hrvatske. Ekonomska se situacija 1930-ih godina pogoršavala pod utjecajem svjetske
ekonomske krize. Zbog velikoga doseljavanja okolnoga stanovništva posebno je akut-
no bilo pitanje izgradnje novih stanova za radnike, poboljšanje uvjeta stanovanja i
saniranje zaraznih bolesti u središtu grada oko Dioklecijanove palače, opskrba pit- 93 27 Ibid., str. 20. U svojoj brošuri o tuberkulozi R. Ferri iznio je statistiku umrlih od tuberkuloze
u odnosu na »opći pomor«, ustvrdivši da je u 25 godina od tuberkuloze umrlo 2718 osoba, od kojih 75%
od plućne tuberkuloze. Prikazao je statističke pokazatelje umrlih od tuberkuloze od 1900. do 1924. Godi-
ne 1900. umrlih od tuberkuloze bilo je 16,69% te se krivulja postotaka od tada kretala uzlazno i silazno
da bi 1924. taj postotak iznosio 14,67%. U relaciji prema broju stanovnika taj je postotak 1900. iznosio
6,36%, a 1924. godine 3,74%, što pokazuje smanjivanje krivulje kao rezultat djelovanja zdravstvenih usta-
nova. Ibid., str. 9. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) preventivno-higijenske te institucionalne probleme s kojima se susreće Split u borbi
protiv tuberkuloze. Početkom XX. stoljeća tuberkuloza je bila raširena u cijelom
Splitu, pa je Ferri izradio kartu predjela u kojima je najraširenija i na taj način dao
putokaz za regulaciju i asanaciju gradskih predjela. Opisao je ostvarene i potrebne
asanacijske radnje te izradio »vodič« prirodnih prednosti Splita za boravak u prirodi
i zdrav život. Ta je knjižica bila namijenjena stručnoj javnosti, ali donosi niz zdrav-
stvenih preporuka i prednosti Splita koje mogu olakšati borbu protiv tuberkuloze,
koje su razumljive i intelektualnoj javnosti grada koja se kroz humanitarna društva i
na drugi način može boriti protiv te opake bolesti. Statistički je prikazao i kretanje
broja umrlih od tuberkuloze (u postotcima općega pomora i prema broju stanovni-
ka) kao ilustraciju relativnoga uspjeha u liječenju.27 Osnovni čimbenici, koji po njemu
djeluju na javno zdravlje, posebno posljednjih godina, ekonomsko su stanje pojedina-
ca, nehigijenski uvjeti stanovanja, posebice u pojedinim dijelovima Splita (Diokleci-
janova palača, Veli Varoš, Radunica) i uopće nehigijena. Analizirao je gradske napore
za asanaciju grada, uređenje ulica, proširenje vodovodne mreže i sl. te mogućnosti
institucionalnoga liječenja. U Splitu je 1923. osnovan Dispanzer za grudne bolesti
koji je obavljao velik broj pregleda, ali je bolnica imala nedovoljan broj kreveta i za
druge bolesnike i nije imala poseban odjel za liječenje tuberkuloznih bolesnika. Pita-
nje sanatorija bilo je otvoreno. Prema njegovoj procjeni svaka trideseta osoba boluje
od tuberkuloze, a umire oko stotinjak ljudi, većinom mlađih. Podatci koje je iznio
splitskoj su javnosti jasno pokazali kakav je problem tuberkuloza, senzibilizirali su
javnost i postali dio javnih spoznaja pred kojima se nije moglo »zatvoriti oči«, što nije
pokrenulo medijsku kampanju, ali je produbilo svijest i poglede na tuberkulozu te
zasigurno produktivno utjecalo na kasniju medijsku proizvodnju članaka. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) kom vodom i provođenje ostalih asanacijskih radova. Zarazne bolesti širile su se op-
ćom nehigijenom i neznanjem, a tuberkuloza je bila jedna od najraširenijih socijalnih
bolesti. Spoznaja o raširenosti tuberkuloze zabrinjavala je dalmatinske vlasti još u
doba Austro-Ugarske Monarhije. Njezina važnost kao socijalne bolesti u Dalmaciji
dolazi do izražaja nakon što su sanirane druge epidemije (kuga i malarija). Stoga je
1902. u Zadru tiskana knjižica Propisi o suzbijanju tuberkuloze, u kojoj je naveden niz
propisa koje je tadašnja vlast odredila u borbi protiv tuberkuloze. Uz izravne mjere
liječenja, predložen je i niz indirektnih kako bi se postigla željena svrha: ponajprije se
preporučivalo poučavanje najširih slojeva nizom predavanja, člancima i drugim po-
pularnim djelima liječnika ili drugih stručnjaka o načinu kako nastaje tuberkuloza,24
kako se suzbija i kako se treba ponašati onaj koji ima tuberkulozu, a u vezi s preven-
tivom preporučivalo se snažnije zdravstveno prosvjećivanje: širenje popularnih me-
dicinskih knjiga, suradnja škola, odgojnih zavoda i humanitarnih društava, prosvje-
titeljska uloga štampe i uopće svih odgovornih čimbenika u pojedinoj političkoj
oblasti. Štamparova je medicina od početka bila na tragu suvremenih medicinsko-
-preventivnih metoda liječenja u tretmanu problema tuberkuloze. Međutim, ono što
ističe vrijednost Štamparove knjižice i njegova modela liječenja baš je u tome što je
Štampar dobro poznavao teško ekonomsko, socijalno i kulturno stanje pojedinih sre-
dina u Hrvatskoj, posebice hrvatskih sela, u kojima se tuberkuloza masovno širila, te
je razumio ne samo uzroke bolesti nego i odnos bolesnika prema njoj (sram, prikri-
vanje, zapuštanje).25 Metodološka sličnost u pristupu liječenja i suzbijanja tuberkulo-
ze ovih dviju knjižice je očita: zajedničko im je to da se u suzbijanju tuberkuloze
oslanjaju, među ostalim, i na tiskane materijale kao važno sredstvo zdravstvenoga
prosvjećivanja. Treća knjiga, koja ulazi u korpus publikacija u kontinuitetu socijalno-medi-
cinske misli o tuberkulozi i javnoga znanja u Splitu, knjiga je dr. Rafe Ferrija26 (Ston,
24. II. 1899 – Split, 22. VIII. 1969), poznatoga splitskoga ftiziologa, Tuberkuloza u
Splitu i asanacija grada, objavljena 1925. godine kao prvo izdanje Dispanzera za
grudne bolesti u Splitu. U toj je knjizi Rafo Ferri vrlo studiozno opisao socijalne, 94 28 Novo doba, 3(1920), br. 264, str. 3 (22.11.); U Zagrebu je 1919. osnovano Povjerenstvo za suzbi-
janje tuberkuloze. U svom programu ističu: »Potrebno je da se naša javna štampa, a naročito periodični
časopisi, sistematski upućuju u suzbijanje tuberkuloze …Osim te periodične propagande, trebat će izda-
vati i priručnike za liječnike, medicinare, školske knjige i štiva i napokon sasma popularnu uputu za ši-
roko općinstvo…«. Željko Dugac: Zdravstveno prosvjećivanje protiv tuberkuloze, Medicus, str. 157. 31 U Splitu je postojala tradicija izdavanja pučkih listova. Časopis Pučka prosvjeta izlazio je kao
mjesečnik od 1921. do konca 1932. Bio je opći prosvjetni časopis koji je na neki način nastavljao tradiciju
pučke prosvjete časopisa Pučki list, što ga je također uređivao don Frane Ivanišević. Između dvaju ratova
to je bio jedini časopis za pučko prosvjećivanje koji je radio na podizanju kulturne razine svojih čitatelja
i na održavanju veza s Hrvatima izvan domovine. 32 Pučka prosvjeta, 1921, br. 5 (maj), str. 68–69. J. Arambašin tuberkulozi pristupa kao činjenici
koja ima negativne posljedice i na ukupni ekonomski razvoj države. Preračunato u financijske pokazate-
lje, pokazuje štetne posljedice neliječenja od tuberkuloze. Na kraju članka naglašava ciljeve zdravstvene
politike: »Eto za tim ide nauka o zdravlju: ona hoće da svaki naš čovjek dođe do znanja i do uvjerenja da 29 To su »Tuberkuloza uopće«, »Staralište za tuberkulozne«, »Škola na suncu za slabunjavu
djecu« i »Sanatorij na Brestovcu«. Novo doba, 4(1921), br. 5, str. 3 (8. I.). Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) suočavanju s tuberkulozom. Započela je i šira kampanja zdravstvenoga prosvjećiva-
nja u časopisima i novinama, osnovano je Društvo za borbu protiv tuberkuloze te
Liga za borbu protiv tuberkuloze Primorske banovine, što je, uz rad liječnika, omo-
gućilo i uključivanje građanstva kroz dobrotvorni rad. Tuberkuloza je na taj način
postala javno vidljiva bolest, bolest koja je iz sfere pojedinca i obitelji postala jav-
nozdravstveni problem. Osim knjigama i brošurama, Splićani su bili obavještavani i
educirani o socijalno-higijenskim problemima tuberkuloze, metodama liječenja i
uspjesima zdravstvene službe u popularnim časopisima i novinama te drugim sred-
stvima propagande: plakatima i prigodnim letcima, predavanjima i izložbama. suočavanju s tuberkulozom. Započela je i šira kampanja zdravstvenoga prosvjećiva-
nja u časopisima i novinama, osnovano je Društvo za borbu protiv tuberkuloze te
Liga za borbu protiv tuberkuloze Primorske banovine, što je, uz rad liječnika, omo-
gućilo i uključivanje građanstva kroz dobrotvorni rad. Tuberkuloza je na taj način
postala javno vidljiva bolest, bolest koja je iz sfere pojedinca i obitelji postala jav-
nozdravstveni problem. Osim knjigama i brošurama, Splićani su bili obavještavani i
educirani o socijalno-higijenskim problemima tuberkuloze, metodama liječenja i
uspjesima zdravstvene službe u popularnim časopisima i novinama te drugim sred-
stvima propagande: plakatima i prigodnim letcima, predavanjima i izložbama. Početak medijske kampanje možemo pratiti već od 1920., kad su, kako je zabi-
lježilo Novo doba održani tečajevi za usavršavanje liječnika u organizaciji Zdravstve-
noga odsjeka za Dalmaciju. Predavanja su bila iz područja socijalne medicine, bakte-
riologije, epidemiologije, tuberkuloze i drugih zaraznih bolesti.28 Sljedeće, 1921. godine zabilježeno je i da su u kinu Karaman prikazana četiri propagandna filma o
tuberkulozi koja je publici komentirao dr. Šime Ljubić.29 Obavještavanje o djelatnosti
Zdravstvenoga odsjeka, predavanjima, izložbama i sl. nastavljeno je u novinama i
dalje. Zdravstveni odjel organizirao je u ožujku 1922. antialkoholnu i antituberkuloz-
nu izložbu u svojim novim prostorima, aktivno provodeći zdravstvenu edukaciju na
tragu ideja A. Štampara. U dvije velike prostorije izložen je velik broj slika, plakata i
tablica o štetnom djelovanju tuberkuloze i alkohola. Liječnici Zdravstvenoga odjela u
Splitu objašnjavali su posjetiocima izložene materijale.30 U promociju djelovanja higijensko-zdravstvene službe u sprječavanju tuber-
kuloze vrlo rano se uključio popularni opći prosvjetni časopis Pučka prosvjeta.31 Već
1921. dr. Josip Arambašin objavio je članak »Korist učenja higijene«,32 na tragu pro- 29 To su »Tuberkuloza uopće«, »Staralište za tuberkulozne«, »Škola na suncu za slabunjavu
djecu« i »Sanatorij na Brestovcu«. Novo doba, 4(1921), br. 5, str. 3 (8. I.). 30 Novo doba, 5(1922), br. 60, str. 3 (14. III.) Splitski časopis Pučka prosvjeta u borbi za suzbijanje tuberkuloze
između dvaju ratova: početak kampanje Osnivanjem Ministarstva za narodno zdravlje (poslije Ministarstva narodnoga
zdravlja i socijalne politike) i organizacijom zdravstvene službe započela je nova
zdravstvena politika i omogućeno je smišljeno i organizirano njezino provođenje u
Kraljevini SHS, u čemu je aktivno sudjelovao i Andrija Štampar. Zdravstveni odsjek
za Dalmaciju, osnovan 1919., odmah po osnutku započeo je s edukacijom liječnika u 95 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 36 U članku »Tuberkuloza i prehrana« osvrće se na podatke o umiranju od tuberkuloze. »Poli-
tički kotar Split sa nešto više preko 100.000 duša imao je do g. 1919. godišnje preko 200 smrti od tuberku-
loze«, piše on. Nakon rata tuberkuloza nije posustala zbog »oskudijevanja i stradanja za vrijeme rata te
nemogućnost da se kroz tako kratko vrijeme osjetljivo stane na put tako velikom zlu, pošto svaki i manji
napredak na tom polju iziskuje ogromnih materijalnih žrtava…«. Pučka prosvjeta, 1923., br. 8, str. 133–134. 34 Branko Peričić u članku »Higijena stana« piše o svim važnim elementima higijene stana i
kuće. Nikakva kuća, makar najbolje uređena, drži on, ne može se smatrati higijenskom ako se ne drži
čistom. Pučka prosvjeta, 1923., br. 8, str. 125–127. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 31 U Splitu je postojala tradicija izdavanja pučkih listova. Časopis Pučka prosvjeta izlazio je kao
mjesečnik od 1921. do konca 1932. Bio je opći prosvjetni časopis koji je na neki način nastavljao tradiciju
pučke prosvjete časopisa Pučki list, što ga je također uređivao don Frane Ivanišević. Između dvaju ratova
to je bio jedini časopis za pučko prosvjećivanje koji je radio na podizanju kulturne razine svojih čitatelja
i na održavanju veza s Hrvatima izvan domovine. 32 Pučka prosvjeta, 1921, br. 5 (maj), str. 68–69. J. Arambašin tuberkulozi pristupa kao činjenici
koja ima negativne posljedice i na ukupni ekonomski razvoj države. Preračunato u financijske pokazate-
lje, pokazuje štetne posljedice neliječenja od tuberkuloze. Na kraju članka naglašava ciljeve zdravstvene
politike: »Eto za tim ide nauka o zdravlju: ona hoće da svaki naš čovjek dođe do znanja i do uvjerenja da 96 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) filaktičkih, socijalno-higijenskih preporuka A. Štampara. Broj 8 iz 1923. posvećen je
gotovo u cijelosti narodnom zdravlju. U nepotpisanom uvodniku, koji je vjerojatno
napisao dr. Josip Arambašin, naglašava se da je cilj toga broja »da podučimo naš na-
rod, osobito po selima kako mu je čuvati ovo blago što mu ga je Bog dao, …stara je
besjeda od davnih mudraca: u zdravom tijelu i pamet je zdrava«. Don Frane Ivaniše-
vić, urednik Prosvjete, kao župnik u Jesenicama imao je doticaj s narodom, poznavao
je njegove potrebe, znanje o bolesti i racionalnom životu, bio je u prilici besplatno
dijeliti časopis na čitanje. Članci objavljeni u tom broju pokazatelj su liječničkih na-
pora za ostvarenje ideala narodnoga zdravlja A. Štampara. Opširnije članke o različi-
tim dijagnostičko-terapeutskim i higijenskim problemima zaraznih bolesti objavili
su Vjera Škarica,33 Josip Arambašin, Branko Peričić,34 F. D. Marušić,35 A. Sfarčić pi-
sao je o suzbijanju malarije, Ivo Stalio o spolnim bolestima te Josip Berković,36 liječ-
nici u službi pojedinih odsjeka zdravstvene službe u Splitu. U svojim člancima pisali
su jasno i razumljivo, bez pretjerane uporabe stručnih termina, pristupačno svim
čitateljima, pa i onima koji su bili manje pismeni. 33 Vjera Škarica u članku »Prva hrana i dojenje« obraća se majkama, ističući vrijednost majčina
mlijeka kao hrane. »Majčina je dakle dužnost da doji svoje dijete ako joj je ikako moguće jer se majčino
mlijeko i srce ne daju nikako zamijeniti.« Pučka prosvjeta, br. 8, 1923., str. 118–119. 35 U članku »Djeca na moru« ističe se ljekovitost morske kupelji protiv mnogih bolesti, pa i
tuberkuloze, kao poziv moderne znanosti »povratite se prirodi«. Pučka prosvjeta, 1923., br. 8, str. 124–125. sve što potroši za poboljšanje zdravlja naplati mu se s velikom kamatom i da nauči kako se do toga dola-
zi…«. to potroši za poboljšanje zdravlja naplati mu se s velikom kamatom i da nauči kako se do toga dola- sve što potroši za poboljšanje zdravlja naplati mu se s velikom kamatom i da nauči kako se do toga dola-
zi…«.
33 Vjera Škarica u članku »Prva hrana i dojenje« obraća se majkama, ističući vrijednost majčina
mlijeka kao hrane. »Majčina je dakle dužnost da doji svoje dijete ako joj je ikako moguće jer se majčino
mlijeko i srce ne daju nikako zamijeniti.« Pučka prosvjeta, br. 8, 1923., str. 118–119.
34 Branko Peričić u članku »Higijena stana« piše o svim važnim elementima higijene stana i
kuće. Nikakva kuća, makar najbolje uređena, drži on, ne može se smatrati higijenskom ako se ne drži
čistom. Pučka prosvjeta, 1923., br. 8, str. 125–127.
35 U članku »Djeca na moru« ističe se ljekovitost morske kupelji protiv mnogih bolesti, pa i
tuberkuloze, kao poziv moderne znanosti »povratite se prirodi«. Pučka prosvjeta, 1923., br. 8, str. 124–125.
36 U članku »Tuberkuloza i prehrana« osvrće se na podatke o umiranju od tuberkuloze. »Poli-
tički kotar Split sa nešto više preko 100.000 duša imao je do g. 1919. godišnje preko 200 smrti od tuberku-
loze«, piše on. Nakon rata tuberkuloza nije posustala zbog »oskudijevanja i stradanja za vrijeme rata te
nemogućnost da se kroz tako kratko vrijeme osjetljivo stane na put tako velikom zlu, pošto svaki i manji
napredak na tom polju iziskuje ogromnih materijalnih žrtava…«. Pučka prosvjeta, 1923., br. 8, str. 133–134. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Pokazali su senzibilitet za zdrav-
stvene probleme, poznavanje stvarnoga ekonomskoga stanja i uvjeta života siromaš-
nih u Splitu i okolnim selima, razumijevanje da uspjeh u borbi protiv zaraznih bole-
sti, osobito tuberkuloze, nije samo medicinsko-terapeutski problem nego prije svega
ovisi »od asanacije socijalnih prilika, posebno od bolje prehrane«, zdravstvenoga
prosvjećivanja te o mogućnosti stvaranja bolničkih kapaciteta za izolaciju bolesnih. Pučka prosvjeta 1925. objavljuje oveći članak dr. Josipa Škarića, bliskoga surad-
nika Andrije Štampara od prvih dana djelovanja javnoga zdravstva u Splitu, o radu
Državne bakteriološke stanice, otvorene 1. ožujka 1922. Naveo je zapanjujući podatak
da se do njezina osnivanja krv na pregled slala u Beč ili Trst, a sada je to bilo moguće
u Splitu. Na kraju članka naglasio je zasluge A. Štampara koji je dao »temelj i smjer« to potroši za poboljšanje zdravlja naplati mu se s velikom kamatom i da nauči kako se do toga dola- 97 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) socijalno-zdravstvenoj organizaciji u Kraljevini SHS.37 Josip Berković se u članku
»Borba protiv sušice (tuberkuloze)« osvrće na uzroke bolesti koje također vidi u eko-
nomskim prilikama bolesnika te iznosi nekoliko podataka o poduzetim mjerama
koje su terapeutske, higijenske i propagandne. Liječnici su u profilaksi i prevenciji
tuberkuloze obavljali golem posao; od 1. VIII. 1923. do 31. XII. 1924. pregledali su 4184
novih bolesnika i otkrili 2506 slučajeva tuberkuloze, od kojih je 12% s otvorenim
procesom. Obišli su 1662 kuće i upoznali se sa stvarnim higijenskim uvjetima stano-
vanja, dijelili materijalnu pomoć i pomoć u hrani, podučavali stanovništvo i podije-
lili 7495 letaka.38 socijalno-zdravstvenoj organizaciji u Kraljevini SHS.37 Josip Berković se u članku
»Borba protiv sušice (tuberkuloze)« osvrće na uzroke bolesti koje također vidi u eko-
nomskim prilikama bolesnika te iznosi nekoliko podataka o poduzetim mjerama
koje su terapeutske, higijenske i propagandne. Liječnici su u profilaksi i prevenciji
tuberkuloze obavljali golem posao; od 1. VIII. 1923. do 31. XII. 1924. pregledali su 4184
novih bolesnika i otkrili 2506 slučajeva tuberkuloze, od kojih je 12% s otvorenim
procesom. Obišli su 1662 kuće i upoznali se sa stvarnim higijenskim uvjetima stano-
vanja, dijelili materijalnu pomoć i pomoć u hrani, podučavali stanovništvo i podije-
lili 7495 letaka.38 To su bili prvi propagandni koraci splitskih liječnika i dispanzerske službe,39
kojima je započelo zdravstveno prosvjećivanje, informiranje i stvaranje javnoga zna-
nja o stanju te bolesti. 39 Andrija Štampar posebno je naglašavao ulogu dispanzera već 1919. godine: »Glavna nam je
zadaća osnivanje dispanzera za tuberkulozu, koji će nam otkriti sva vrela zaraze i omogućiti jedino
ispravno socijalno djelovanje. Ti će dispanzeri ispitivati sve odnošaje jednog tuberkuloznog bolesnika,
provađati njegovu izolaciju u kući, potpomagati njegovu obitelj sanitarno i materijalno, vodit će brigu o
higijeni stana i na taj način sprečavati familijarnu infekciju.« Andrija Štampar: O zdravstvenoj politici.
U: U borbi za narodno zdravlje: izabrani članci Andrije Štampara, str. 69. 37 »Čitava pak zdravstvena organizacija je tako uređena da su se prvi svjetski ljekarski stručnja-
ci, a osobito Amerikanci izrazili da smo na tom polju pretekli sve po ratu nastale kao i mnoge od starih
država. Za taj ogroman napredak ide u prvom redu zasluga načelnika Ministarstva narodnog zdravlja
gosp. Prof. Štampara koji je dao temelj i smjer cjelokupnoj našoj socijalno-zdravstvenoj organizaciji«,
Pučka prosvjeta, 1925., br. 6, str. 96–98. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Tuberkuloza je, kao bolest od koje se umiralo, izazivala strah u
stanovništvu zbog neznanja o tome kako se prenosi i razvija te kako se treba odnosi-
ti prema tuberkuloznom bolesniku. Sve veći strah od tuberkuloze naveo je Branka
Nižetića da u članku »Tuberkuloza i općenite predrasude o njoj«40 objašnjava da je
osnovni problem u stvaranju nekih predrasuda o tuberkulozi neznanje koje podrža-
va strah od zaraze. Svoj članak završava s nekoliko propisa o čuvanju od zaraze koje
ulaze u korpus općenitih higijenskih preporuka. 38 Pučka prosvjeta, 1925., br. 3, str. 48–50. 40 Branko Nižetić: Kalendar »Jadran«, 1928., str. 70–73. 43 Između dva rata prema bibliografiji Hrvoja Morovića izlazila su 122 naslova novina s manjim
ili dužim vremenom izlaženjem. Velik broj naslova dolazio je iz različitih diskursnih sfera: zastupale su
političke stranke, interese pojedinih društvenih grupa i slojeva – radnika, činovnika, pomoraca, sport-
ske, kulturne i religijske teme, donoseći u javnost mnoštvo društvenih praksi i uvodeći Split u moderno
društvo u kojem se zrcali niz problema. Novo doba i Jadranski dnevnik, kao i sve druge novine, danas su
dokumenti života i transformacije Splita u moderan i otvoren grad. 44 Jean Baudrillard: Simulacija i zbilja, Zagreb 2013., str. 56–78. Navodimo ovom prilikom kao
važno mišljenje Stuarta Halla o komunikaciji putem medija: Hall drži da se o modelu komunikacije
razmišlja linearno, ali da ga je moguće promatrati i kao strukturu »koja nastaje i održava se artikulaci-
jom povezanih, ali odvojenih momenata proizvodnje, kruženja, distribucije, potrošnje, reprodukcije«.
To znači da se taj proces održava artikulacijom povezanih praksi i da je potrošnja ili recepcija poruke i
sama jedan trenutak proizvodnoga procesa u širem smislu. Stjuart Hol: Mediji i moć, str. 7–11. 41 Radi se doista o velikom broju članaka, od kojih smo odabrali samo neke kako bismo ilustri-
rali osnovnu temu rada. U svojoj ukupnosti svi ti tekstovi potvrđuju našu osnovnu tezu da su lokalne
novine imale snažnu i još nedovoljno prepoznatu ulogu u procesu informiranja i zdravstvenoga prosvje-
ćivanja stanovništva. 42 Opširnije o Novom dobu vidi u: Ivanka Kuić: Kulturna baština, 39(2013), str. 113–138. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) zdravstvenih mjera borbe za suzbijanje tuberkuloze, novine su imale važnu funkciju
jer su obavljale masovnu difuziju (prijenos, širenje) različitih informacija. Ta dva
dnevnika objavila su tijekom dvadesetak godina vrlo velik broj članaka različitih
novinskih žanrova (vijesti, osvrta, saopćenja, prikaza, intervjua)41 koji su obavještava-
li splitske čitatelje o svim temama iz područja zdravstvenoga prosvjećivanja i promi-
canja borbe za suzbijanje tuberkuloze, izravno promičući tu temu ili kontekstualno
u vezi s brojnim gradskim socijalnim problemima. Svakako se radilo o medijskoj re-
gulaciji stvarnosti i djelovanja građana s pozitivnim učinkom. Nije nam poznato jesu
li se i u drugim sredinama lokalne novine uključile u kampanju u takvim razmjeri-
ma, ali angažman splitskih novina na saniranju teškoga socijalno-zdravstvenoga
problema zasigurno zaslužuje pozornost. Informativno-političko novinstvo bilo je
razvijeno u Splitu još na prijelazu dvaju stoljeća. Nakon 1918. pokrenuto je Novo doba,
političko-informativni list,42 a poslije i još neki dnevnici koji su kraće izlazili, a među
kojima se posebno ističe Jadranski dnevnik, dubinski zahvaćajući brojne gradske kul-
turne i društvene probleme.43 Ova su dva dnevnika regulirajućom diskurzivnom
praksom dovela tuberkulozu u fokus javnosti. Novine su uvijek dio neke organizira-
ne društvene prakse, informiranja, propagiranja, zastupanja i sl. Neovisno o Baudril-
lardovoj kritici komunikacijskoga modela kao »modela simulacije komunikacije«,
činjenica je da su novine kao masovni mediji učinili da je tuberkuloza, koja je prije
Prvoga svjetskog rata većinom imala sporedni status, a njezino liječenje bilo privatna
obveza, postala predmet neprekinuta zanimanja i javni društveni problem i obveza. Sad je tuberkuloza, nekad bolest na margini javnoga interesa, »zadobila veliku difu-
zijsku moć što (joj) podaruje društvene i ‘historijske’ razmjere«.44 Ona je naime nadiš-
la značenje »gradske rubrike« i postala »moćna« tema forsirane medijske kampanje. Novine imaju moć nametnuti temu i postaviti ju na »dnevni red«; one su je učinile zdravstvenih mjera borbe za suzbijanje tuberkuloze, novine su imale važnu funkciju
jer su obavljale masovnu difuziju (prijenos, širenje) različitih informacija. Ta dva
dnevnika objavila su tijekom dvadesetak godina vrlo velik broj članaka različitih
novinskih žanrova (vijesti, osvrta, saopćenja, prikaza, intervjua)41 koji su obavještava-
li splitske čitatelje o svim temama iz područja zdravstvenoga prosvjećivanja i promi-
canja borbe za suzbijanje tuberkuloze, izravno promičući tu temu ili kontekstualno
u vezi s brojnim gradskim socijalnim problemima. Svakako se radilo o medijskoj re-
gulaciji stvarnosti i djelovanja građana s pozitivnim učinkom. Uloga lokalnih novina u kampanji za suzbijanje tuberkuloze U obavještavanje šire javnosti o tuberkulozi između dvaju ratova uključile su se u
velikoj mjeri i lokalne novine i razvile široku kampanju zdravstvenoga prosvjećiva-
nja javnosti i informiranja o radu zdravstvene službe i statističkim pokazateljima u
borbi protiv tuberkuloze. Analizirali smo napise u Novom dobu (1918–41) i Jadran-
skom dnevniku (1934–38), kao najznačajnijim novinama iz toga razdoblja koje su izla-
zile u Splitu. Na tragu Štamparovih uputa o promicanju socijalnih, higijenskih i 37 »Čitava pak zdravstvena organizacija je tako uređena da su se prvi svjetski ljekarski stručnja-
ci, a osobito Amerikanci izrazili da smo na tom polju pretekli sve po ratu nastale kao i mnoge od starih
država. Za taj ogroman napredak ide u prvom redu zasluga načelnika Ministarstva narodnog zdravlja
gosp. Prof. Štampara koji je dao temelj i smjer cjelokupnoj našoj socijalno-zdravstvenoj organizaciji«,
Pučka prosvjeta, 1925., br. 6, str. 96–98. 98 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Nije nam poznato jesu
li se i u drugim sredinama lokalne novine uključile u kampanju u takvim razmjeri-
ma, ali angažman splitskih novina na saniranju teškoga socijalno-zdravstvenoga
problema zasigurno zaslužuje pozornost. Informativno-političko novinstvo bilo je
razvijeno u Splitu još na prijelazu dvaju stoljeća. Nakon 1918. pokrenuto je Novo doba,
političko-informativni list,42 a poslije i još neki dnevnici koji su kraće izlazili, a među
kojima se posebno ističe Jadranski dnevnik, dubinski zahvaćajući brojne gradske kul-
turne i društvene probleme.43 Ova su dva dnevnika regulirajućom diskurzivnom
praksom dovela tuberkulozu u fokus javnosti. Novine su uvijek dio neke organizira-
ne društvene prakse, informiranja, propagiranja, zastupanja i sl. Neovisno o Baudril-
lardovoj kritici komunikacijskoga modela kao »modela simulacije komunikacije«,
činjenica je da su novine kao masovni mediji učinili da je tuberkuloza, koja je prije
Prvoga svjetskog rata većinom imala sporedni status, a njezino liječenje bilo privatna
obveza, postala predmet neprekinuta zanimanja i javni društveni problem i obveza. Sad je tuberkuloza, nekad bolest na margini javnoga interesa, »zadobila veliku difu-
zijsku moć što (joj) podaruje društvene i ‘historijske’ razmjere«.44 Ona je naime nadiš-
la značenje »gradske rubrike« i postala »moćna« tema forsirane medijske kampanje. Novine imaju moć nametnuti temu i postaviti ju na »dnevni red«; one su je učinile 41 Radi se doista o velikom broju članaka, od kojih smo odabrali samo neke kako bismo ilustri-
rali osnovnu temu rada. U svojoj ukupnosti svi ti tekstovi potvrđuju našu osnovnu tezu da su lokalne
novine imale snažnu i još nedovoljno prepoznatu ulogu u procesu informiranja i zdravstvenoga prosvje-
ćivanja stanovništva. 99 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 46 U teoriji medija postoji obiman katalog funkcija koje autori pridjeljuju masovnim medijima
u različitim periodima. Velik broj autora podržava tezu da »masovni mediji uvijek poprimaju oblik i
kolorit određenih društvenih i političkih struktura«. Za ovaj rad mogli bismo se pozvati na Harolda
Laswella, koji zastupa mišljenje da je funkcija medija: 1) promatranje i kontrola okruženja, 2) uspostava
odnosa između dijelova društva kao reakcija na zahtjev okruženja i 3) prijenos kulturne baštine na slje-
deću generaciju. U cjelini to je stabiliziranje sustava masovne komunikacije. U: Michael Kunczik, Astrid
Zipfel: Uvod u znanost o medijima i komunikologiju. Zagreb, 2006., str. 37. 45 Svakako treba napomenuti da je Split prije Prvoga svjetskog rata bio socijalno snažno podije-
ljen grad, što je bio dio njegova tadašnjega identiteta. Nakon rata i zahvaljujući gradskoj upravi, njegovi
se dijelovi sve više povezuju i socijaliziraju. U svemu tome su i lokalni mediji imali velike zasluge preno-
seći novi doživljaj grada kao cjeline svojim čitateljima. Tuberkuloza tako postaje gradski problem, a ne
problem njegovih siromašnih dijelova, što se vidi iz brojnih izvješća sa sastanaka i skupština njegovih
upravnih tijela. 47 Andrija Štampar: Pet godina socijalno-medicinskog rada u Kraljevini Srba, Hrvata i Slovena-
ca 1920-1925. U: U borbi za narodno zdravlje, str. 96.
48 Tuberkuloza u Splitu Novo doba 1929 br 207 str 2 (23 VIII ) 47 Andrija Štampar: Pet godina socijalno-medicinskog rada u Kraljevini Srba, Hrvata i Slovena-
-1925. U: U borbi za narodno zdravlje, str. 96. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) konfliktnom i kontinuirano politički zanimljivom u okviru zdravstvene politike koja
se provodila u Kraljevini SHS/Jugoslaviji, sudjelujući u procesu njezine socijalizacije
i demokratizacije, dajući širu sliku o tim procesima i zadobivajući moć da predstav-
ljaju i upravljaju društvenom stvarnosti.45 Danas je to zabilježeno znanje historijska
činjenica iz koje zaključujemo kako se Split kao zajednica odnosio prema tom najve-
ćem »društvenom zlu«.46 konfliktnom i kontinuirano politički zanimljivom u okviru zdravstvene politike koja
se provodila u Kraljevini SHS/Jugoslaviji, sudjelujući u procesu njezine socijalizacije
i demokratizacije, dajući širu sliku o tim procesima i zadobivajući moć da predstav-
ljaju i upravljaju društvenom stvarnosti.45 Danas je to zabilježeno znanje historijska
činjenica iz koje zaključujemo kako se Split kao zajednica odnosio prema tom najve-
ćem »društvenom zlu«.46 Splitski liječnici koji su »s velikom ljubavlju, požrtvovanjem, jednom novom
ideologijom žilavo radili zadnjih pet godina«47 na suzbijanju tuberkuloze nisu bili
vezani samo uz časopis Pučka prosvjeta. Bili su svjesni važnosti medijske promocije
problema. Godine 1929. objavljen je intervju s liječnikom Rafom Ferrijem, vodite-
ljem Dispanzera za grudne bolesti, o radu dispanzera i uspjesima u liječenju tuber-
kuloze. Tada je istaknuto da u Splitu godišnje umire oko 75 bolesnika od tuberkulo-
ze pluća, a to znači da ima oko 550 oboljelih, te da je taj broj zasigurno još veći jer ima
dosta naoko zdravih ljudi s prikrivenom latentnom bolešću. Ipak se u borbi s tuber-
kulozom smrtnost posljednjih godina smanjuje. Tako je prosječni mortalitet od tu-
berkuloze u Splitu oko 3%.48 Nalazimo još nekoliko njihovih članaka iz područja kojim su se bavili: dr. Ste-
van Simunović (voditelj Socijalno-medicinskoga odjeljenja Higijenskoga zavoda) ba-
vio se higijenom prehrane i napisao članak »Problemi ishrane naših sela« koji je tis-
kan neposredno prije prvoga sastanka Lige protiv tuberkuloze Primorske banovine,
osnovane 1931., koja je imala 62 člana. Pozivajući na mobilizaciju cijeloga naroda i
države u borbi protiv »podmuklog i upornog neprijatelja«, zaključuje da »oskudica
higijene, racionalnog rada, dovoljne ishrane i kulturnog shvaćanja sa svojim neha- 45 Svakako treba napomenuti da je Split prije Prvoga svjetskog rata bio socijalno snažno podije-
ljen grad, što je bio dio njegova tadašnjega identiteta. Nakon rata i zahvaljujući gradskoj upravi, njegovi
se dijelovi sve više povezuju i socijaliziraju. U svemu tome su i lokalni mediji imali velike zasluge preno-
seći novi doživljaj grada kao cjeline svojim čitateljima. 48 Tuberkuloza u Splitu. Novo doba, 1929., br. 207, str. 2 (23. VIII.) 51 Jadranski dnevnik, 2(1935), br. 122, str. 3 (25. V.). S. Antunović-Mikačić naglašava, kao i svi li-
ječnici, teške socijalne prilike u kojima žive pojedine obitelji, osobito one koje imaju bolesnika. Za ilustra-
ciju teškoća u borbi s bolešću navodi podatke iz tromjesečnog izvještaj Antituberkuloznoga dispanzera
u Splitu za 1935: od bolesnika s otvorenim procesom tuberkuloze,73 bolesnika imala su zasebnu sobu, 58
bolesnika bilo je s odraslima u sobi, 10 bolesnika bilo je s odraslima u krevetu, a 19 bolesnika bilo je s
maloljetnom djecom u sobi. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Tuberkuloza tako postaje gradski problem, a ne
problem njegovih siromašnih dijelova, što se vidi iz brojnih izvješća sa sastanaka i skupština njegovih
upravnih tijela. 48 Tuberkuloza u Splitu. Novo doba, 1929., br. 207, str. 2 (23. VIII.) 100 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) jem, stvaranju povoljne uvjete za širenje socijalnih bolesti a posebno tuberkuloze«.49
Napisao je i opširni članak o prvoj higijenskoj izložbi organiziranoj u Beogradu 1933. u kojem je opisao izložbe pojedinih odsjeka: za tuberkulozu, malariju i druge zarazne
bolesti, higijenu, zaštitu majke i djeteta i dr.50 jem, stvaranju povoljne uvjete za širenje socijalnih bolesti a posebno tuberkuloze«.49
Napisao je i opširni članak o prvoj higijenskoj izložbi organiziranoj u Beogradu 1933. u kojem je opisao izložbe pojedinih odsjeka: za tuberkulozu, malariju i druge zarazne
bolesti, higijenu, zaštitu majke i djeteta i dr.50 Dr. Smiljana Antunović-Mikačić, voditeljica Bakteriološko-epidemiološkoga
odjeljenja Higijenskoga zavoda, obraća se izravno ženama u članku »Žene i
tuberkuloza«.51 Polazeći od toga da je »jedino dobro bezimena čovjeka radna snaga i
zdravlje« sasvim nezaštićena od socijalnih bolesti, ona se obraća ženama s nekoliko
preporuka kako zaštititi djecu i obitelj jer žene mogu spriječiti širenje tuberkuloze
zaštitom djece od bolesnika, cijepljenjem, brigom o higijeni, o hrani, nadzorom kon-
takta djece s osobljem koje može biti bolesno, aktivnim zalaganjem za uređenje gra-
da, škola, parkova i jačanjem, s porukom »Mi žene – polovica čovječanstva, bez obzi-
ra na naš položaj i zvanje, jer naša su nam djeca jednako mila, pokažimo shvaćanja za
ovakve akutne probleme naše najbliže okoline i surađujmo na njemu aktivno«. Vrlo
opširan članak »Socijalno higijenska zaštita majke i djeteta«, koji nije izravno pove-
zan s tuberkulozom, navodimo kao primjer svijesti o potrebi zdravstvenoga prosvje-
ćivanja žena koje su čuvarice obiteljskoga zdravlja. Ona piše o modernim metodama
zaštite majke i djece u svijetu; osvrće se na stanje u Splitu i rad tradicionalnih usta-
nova socijalne skrbi koji nije zadovoljavajući. Iznosi podatke o mortalitetu djece u
splitskom kotaru u 1927. 49 Novo doba, 15(1932), br. 16, str. 3–4 (subotnji prilog, 16. I.). U svom članku dr. Simunić tvrdi:
»Našu državu u 10 godina tuberkuloza je koštala preko pola milijuna grobova i preko stotinu milijardi
dinara«. Pitanje ishrane pasivnih krajeva, nezaposlenosti radnika i socijalno osiguranje postaje predmet
rasprave socijalne sekcije poslaničkog kluba sa zaključkom da se rasprava proširi na parlamentarni klub.
U istom broju na naslovnoj stranici objavljeno izvješće sa sjednice. 52 Novo doba, 12(1929), br. 160, str. 7–8 (27. VI.) 50 Stevan Simunić. Velika higijenska izložba u Beogradu. Novo doba, (1933), br. 193, str. 11
(19. VIII.) 53 Novo doba, 18(1935), br. 120, str. 3 (23. V.) p
j
j p
g
j
p
p
p
U istom broju na naslovnoj stranici objavljeno izvješće sa sjednice.
50 Stevan Simunić. Velika higijenska izložba u Beogradu. Novo doba, (1933), br. 193, str. 11
(19. VIII.)
51 Jadranski dnevnik, 2(1935), br. 122, str. 3 (25. V.). S. Antunović-Mikačić naglašava, kao i svi li- Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) će riješiti ovaj problem ako pritom nedostaje dovoljan broj kreveta u bolnicama i sa-
natorijima, kao što je to bio slučaj u Splitu. će riješiti ovaj problem ako pritom nedostaje dovoljan broj kreveta u bolnicama i sa-
natorijima, kao što je to bio slučaj u Splitu. Novine su i 1930-ih godina nastavile bilježiti teme iz svih područja socijalne
medicine: izvještaje o narodnom zdravlju, zdravstvenom prosvjećivanju, prevenciji,
etiologiji tuberkuloze, djelatnosti medicinskih ustanova u području liječenja i zaštite
od bolesti i statističke pokazatelje Dispanzera za grudne bolesti, Higijenskoga zavoda
i Zdravstvenoga odsjeka grada Splita, promotivne aktivnosti, primjerice Antituber-
kulozni tjedan, koji su svake godine organizirali Društvo za borbu protiv tuberkulo-
ze i Higijenski zavod, u okviru kojega su držana predavanja, prikazivani filmovi i di-
jeljeni letci o zaštiti od bolesti i liječenju. Svi članci osim što su širili znanje o higijeni
i bolesti objavljivanjem statističkih pokazatelja upozoravali su na opasnost od bolesti. U članku o izvješću Dispanzera za grudne bolesti za 1933.54 naglašena je važnost
profilakse koju provode medicinske institucije. Redakcija je zamolila da Dispanzer do-
stavi podatke o radu u desetogodišnjem razdoblju te podatke o zaraznim bolestima za
1932: Dispanzer je u toj godini imao velik broj pregleda bolesnika i 150 diskretno regi-
striranih bolesnika od tuberkuloze, a pretpostavka je da ih ima oko 300 jer se svi ne
prijavljuju i nije obvezna prijava bolesti od tuberkuloze; umrla su 72 bolesnika od pluć-
ne tuberkuloze. Opisane su i druge aktivnosti, posjeti kućama, napori za odvajanje
bolesnih i zdravih, dijeljenje materijalne pomoći i sl. U tekstu se osjeća snažna senzibi-
liziranost autora i redakcije za prilike u kojima žive pojedine siromašne obitelji. Redovito je praćen rad gradskoga Zdravstvenog odsjeka, koji je primjerice
1934. u raspravi o stanju zdravlja u gradu i poduzimanju higijenskih mjera, prema
izvješću tadašnjega šefa saniteta dr. Mihovila Čulića, naglasio da je u gradu velik broj
zaraznih bolesti, posebice od tuberkuloze, a samo tijekom listopada 1934. od raznih
oblika tuberkuloze umrlo je 12 osoba.55 Tuberkuloza je najčešće u člancima označava-
na kao »naše najveće socijalno zlo«. Kao najveći problem označavani su higijena stana
i nedostatak dovoljnoga broja bolničkih kreveta za izolaciju bolesnika. Bolesnici zbog
siromaštva ostaju u obitelji, truju sve oko sebe i »u velikom broju slučajeva i vlastitu
malenu djecu«. Međutim, stanje se u Splitu ne popravlja. 54 Tuberkuloza u Splitu. Novo doba, 16(1933), br. 79, str. 6 (4. IV.)
55 Porast pučanstva u III. tromjesečju ove godine, Jadranski dnevnik, 3(1936), br. 232, str. 5
(18. XII.); vidi i Sjednica općinskog zdravstvenog odbora. Novo doba, 17(1934), br. 163, str. 5 (13.VII.)
56 Naše najveće zlo je tuberkuloza. Novo doba, (1939), br. 17, str. 3 (20. I.) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) koji iznosi 35%.52 Ljubo Šimunić u antituberkuloznom tjednu u članku »Oboljenje i borba pro-
tiv tuberkuloze kod djece i odraslih«53 jednostavno i poučno objašnjava povijest, etio-
logiju i obilježja tuberkuloze kao zarazne bolesti te kako se ona prenosi na djecu koja
vrlo lako obolijevaju od nje. Drži da samo zdravstvenim prosvjećivanjem nije mogu- 101 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 61 Jadranski dnevnik, 1(1934), br. 53, str. 4 (23. V.). Naglašavaju se postignuća gradskih vlasti u
rješavanju stambenih problema radnika u pojedinim dijelovima Splita, ali se istodobno upozorava na
nove takve probleme. 60 Glavni zadaci borbe protiv tuberkuloze: povodom osnivanja Jugoslovenske lige za borbu
protiv tuberkuloze, Novo doba, 15(1932), br. 95, str. 4 (23. IV.) 57 Anketa radi obvezne prijave tuberkuloze. Novo doba, 18(1935), br. 46, str. 6 (23. II.)
58 Borba protiv tuberkuloze. Jadranski dnevnik, 2(1935), br. 81, str. 5 (5. V.)
59 Čuvajte se tuberkuloze. Jadranski dnevnik, 2(1935), br. 121, str. 5 (24. V.) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Izvještaj sa sjednice Odsjeka
u siječnju 1939. o zaraznim bolestima pokazuje da tuberkuloza kao socijalno zlo ne
posustaje. Naime u 1938. registrirano je 297 bolesnika (moguće kao rezultat doseljava-
nja). Tom je prilikom istaknuto da liječenje jednoga tuberkuloznog bolesnika košta
između 10 i 20 tisuća dinara. Kao tri temeljna uvjeta za suzbijanje tuberkuloze istak-
nuta je higijena, nedostatak tuberkuloznoga odjeljenja i prehrambene prilike.56 102 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) 62 U Primorskoj banovini umire godišnje 2000 ljudi od tuberkuloze. Novo doba, 14(1931), br.
222, str. 5 (23. IX.). Broj od 2000 smrtnih slučajeva godišnje od tuberkuloze pojavljivao se u liječničkim
iskazima u nekoliko navrata. Moguće je da je bio donekle predimenzioniran. 62 U Primorskoj banovini umire godišnje 2000 ljudi od tuberkuloze. Novo doba, 14(1931), br.
222, str. 5 (23. IX.). Broj od 2000 smrtnih slučajeva godišnje od tuberkuloze pojavljivao se u liječničkim
iskazima u nekoliko navrata. Moguće je da je bio donekle predimenzioniran.
63 Rad na suzbijanju tuberkuloze u Splitu. Novo doba, 15(1932), br. 112, str. 6 (14. V.).
64 Skupština društva za borbu protiv tuberkuloze. Jadranski dnevnik, 2(1935), br. 140, str. 6 (17. VI.) 63 Rad na suzbijanju tuberkuloze u Splitu. Novo doba, 15(1932), br. 112, str. 6 (14. V.).
64 Skupština društva za borbu protiv tuberkuloze. Jadranski dnevnik, 2(1935), br. 140, str. 6 (17. VI.)
65 Akcija protiv tuberkuloze. Jadranski dnevnik, 3(1936), br. 117, str. 7 (20. V.) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Redakcija Novoga doba donosila je i obavijesti Ministarstva socijalne skrbi i
narodnoga zdravlja. Primila je zamolbu Odsjeka za suzbijanje tuberkuloze pri Mini-
starstvu socijalne skrbi da redovito objavljuje vijesti o broju slobodnih kreveta u lje-
čilištima te vijesti koje o tuberkulozi dostavlja Agencija Avala. Državne strukture
prepoznale su potrebu angažiranja sredstava masovne komunikacije u široj difuziji
informacija i znanja o stanju tuberkuloze i njihovu moć oblikovanja i reguliranja
javnoga ponašanja. Prilikom osnivanja Jugoslavenske lige za borbu protiv tuberkulo-
ze novine su objavile propagandni članak o glavnim zadatcima borbe protiv tuber-
kuloze. Po nalogu Ministarstva socijalne skrbi i narodnoga zdravlja održana je u
Splitu anketa o prijavi bolesnika od tuberkuloze. To je bila dvodnevna rasprava u
kojoj su sudjelovali liječnici koji neposredno djeluju u zaštiti od tuberkuloze. Ras-
pravljalo se o prednostima i posljedicama obvezne prijave pa je zaključno da bi se
obvezna prijava, zbog različitih kulturnih i socijalnih problema, mogla uvesti samo
u sredinama koje imaju dispanzere i kod liječnika koji besplatno liječe, ali ne i kod
privatnih liječnika.57 Prenijeli su priopćenje Ministarstva o tuberkulozi kod djece i u
12 točaka kako se može prepoznati simptome tuberkuloze kod male djece.58 Tijekom
antituberkuloznoga tjedna Dispanzer za grudne bolesti tiskao je nekoliko tisuća le-
taka i razaslao ga po cijeloj banovini. Tekst letka objavljen je u cijelosti.59 Objavljen je
i velik članak o glavnim zadacima borbe protiv tuberkuloze u povodu osnivanja Ju-
goslavenske borbe protiv tuberkuloze.60 Tuberkulozu se povezivalo i s književnim
djelima i sudbinama književnih junaka, sportom i drugim područjima socijalnih
praksi. Praćenje statističkih pokazatelja o broju oboljelih od tuberkuloze nastavljeno
je sve do konca opisanoga razdoblja. Mnoga područja Splita bila su rasadište nehigi-
jene i zaraze. U članku »Pred vratima Splita« upozorava se vlast kako se živi u split-
skoj okolici i u kakvim žalosnim ekonomskim i higijenskim uvjetima žive splitski
radnici. Naglašava se nastojanje Društva za suzbijanje tuberkuloze, kao i drugih dru-
štava, da pomognu bolesnima. U sklopu svojih aktivnosti Društvo je dijelilo plakate
po gradu sa sljedećim sadržajem: »Svaki četvrti čovjek umire kod nas od sušice. Kad
kašlješ, drži rupčić na ustima«.61 61 Jadranski dnevnik, 1(1934), br. 53, str. 4 (23. V.). Naglašavaju se postignuća gradskih vlasti u
rješavanju stambenih problema radnika u pojedinim dijelovima Splita, ali se istodobno upozorava na
nove takve probleme. 103 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Obavijesti o radu Društva tiskane su i u daljnjem periodu, a gotovo u svakom
broju Novoga doba tiskana je poruka: »Upisujte se u Društvo za borbu protiv tuber-
kuloze«. Društvo za borbu protiv tuberkuloze u Splitu Društvo za borbu protiv tuberkuloze osnovano je na tragu prakse koja je već uvelike
postojala u razvijenim zemljama Europe i na tragu preporuka Andrije Štampara. Nešto ranije takvo je društvo osnovano u Zagrebu. U travnju 1931., prema napisima
u Novom dobu, u krugu liječnika koji su radili oko Higijenskoga zavoda odlučili su
osnovati Društvo za borbu protiv tuberkuloze, što je značilo uključivanje širega gra-
đanstva u humanitarnu borbu protiv ovoga društvenoga problema. Promicateljni
odbor sastavio je proglas i razaslao ga na brojne adrese. U letku je stanovništvo upo-
zoreno na opasnost od tuberkuloze u svijetu i u Primorskoj banovini, u kojoj godiš-
nje od nje umire oko 2000 ljudi.62 Prema opširnom izvješću s prve godišnje skupštine
Društva, predsjednik Josip Arambašin, istaknuo je da je Društvo, s malim sredstvi-
ma od 9000 dinara, nemoćno učiniti više od zagovaranja podizanja »za slabunjavu
djecu škole na otvorenom, u prirodi« i to pod uvjetom da bude potpomognuto dr-
žavnim sredstvima i da i dalje promiče zdravstveno prosvjećivanje i zdravstveni od-
goj. Prema izvješću Rafe Ferrija, Društvo je imalo 456 članova u Splitu. Namjerava-
li su proširiti članstvo u i drugim sredinama. U godinu dana rada ipak su »udareni
… temelji za osnivanje jačeg fonda za suzbijanje tuberkuloze«. Zajedno s Higijenskim
zavodom organiziran je tjedan borbe protiv tuberkuloze, a s namjerom da se ta akci-
ja pokrene i u sljedećim godinama. Osim predsjednika Josipa Arambašina, potpred-
sjednika Josipa Škarića, tajnika Rafe Ferrija, blagajnika Mihovila Čulića, u upravi
Društva bila je kao potpredsjednica i Eleonora Tartaglia, supruga bana Ive Tarta-
glie, što je obećavalo novinsko praćenje rada Društva. U odbor Društva izabrani su
i drugi ugledni Splićani iz redova liječnika, učitelja, ravnatelja škola i drugih ustano-
va.63 Na skupštini održanoj 1935. istaknut je rad Društva na osnivanju šumske škole
na Marjanu, izgradnji dječjega igrališta i privremenoga bolničkoga paviljona za tu-
berkulozu u blizini nove bolnice.64 Na skupštini održanoj 1936., na kojoj je ponovno
birana ista uprava, istaknuto je da je rad Društva bio većinom usmjeren prema stva-
ranju fondova za izgradnju antituberkuloznoga dispanzera; sredstva su položena
kod Hipotekarne banke i mogu poslužiti u tu svrhu, ako do izgradnje dođe. Društvo
je pokušalo doći do privremenoga paviljona za tuberkulozu na području Firula, jer
u Splitu nije bilo dovoljno bolničkih kreveta za sve bolesnike kako bi ih se izoliralo iz
obitelji, ali na žalost ta akcija nije uspjela. 65 104 IZVORI Jadranski dnevnik, 1934–1938. Novo doba, 1918–1941. Jadranski dnevnik, 1934–1938. Novo doba, 1918–1941. Pučka prosvjeta, 1921–1932. Pučka prosvjeta, 1921–1932. Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Zaključak Promicanje zdravstvene edukacije putem novina, časopisa i popularno-znanstvenih
publikacija bila je vrlo važna metoda socijalno-zdravstvene prevencije tuberkuloze. Brojna izvješća o radu socijalno medicinske službe, statistički pokazatelji o broju bo-
lesnika od tuberkuloze, opisi teških uvjeta života radnika i uopće siromašnih slojeva
u Splitu i splitskom okruženju promovirali su problem oboljelih od tuberkuloze, sen-
zibilizirali javnost za njihove ljudske potrebe i, što je najvažnije, učinili dostupnim
barem minimalno znanje o higijeni, zaštiti od bolesti i zdravlju kao kulturnoj kate-
goriji modernoga doba. Uz to, u javnosti su istaknuti i neki drugi akteri, i njihove
potrebe, čija je sudbina do tada bila skrivena ili manje zanimljiva: primjerice potreba
zaštite male djece, uloga žene kao majke i čuvarice obiteljskoga zdravlja. Uspostavlja-
jući kontinuitet procesa promicanja zdravstvenoga prosvjećivanja putem različitih
medija i stvaranja javnoga znanja, ustvrdili smo da je taj proces u ovom obujmu bio
moguć najvećim dijelom zahvaljujući suradnji novinskih redakcija i novinama kao
medijima masovne komunikacije. Postavljajući pitanje kako je došlo do toga da su se masovni mediji komunika-
cije u tolikoj mjeri uključili u kampanju za suzbijanje tuberkuloze na vrijednostima
Štamparove medicinske misli, zaključili smo, ne zaobilazeći aktivan angažman
splitskih liječnika koji su prihvatili njegovu socijalno-medicinsku misao, ni rad
Društva za suzbijanje tuberkuloze kao građanske udruge, da je to, funkcionalistički
gledano, bio odgovor novina na zahtjev okoline da se u Splitu uspostavi odnos izme-
đu socijalno odvojenih dijelova zajednice i da se tadašnji tiskani mediji, stvarajući
pritisak prema središnjoj državnoj vlasti, na odgovarajući način aktivno uključe u
rješavanje akutnoga društvenog problema. Novine nisu samo prenosile informacije
nego su proizvodnjom članaka o tuberkulozi, na kraju komunikacijskoga lanca,
omogućile recepciju dostignutih znanja o sprječavanju zdravstvenih problema, po-
boljšanju zdravstvenih navika i daljnju reprodukciju informacija o stvarnom socijal-
nom stanju dijelova društva, razvijajući i snažno suosjećanje prema oboljelima i si-
romašnima. 105 Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Studia lexicographica, 13(2019) 25, STR. 87–107
Ivanka Kuić: Javno znanje o tuberkulozi i djelovanje Društva za suzbijanje tuberkuloze u Splitu
(1918–1941) Članci su dostupni pod licencijom Creative Commons: Imenovanje-Nekomercijalno
(https://creativecommons.org/licenses/by-nc/4.0/). Sadržaj smijete umnožavati, distribuirati, priopćavati
javnosti i prerađivati ga, uz obvezno navođenje autorstva, te ga koristiti samo u nekomercijalne svrhe. LITERATURA Baudrillard, Jean: Simulacija i zbilja, Zagreb: Naklada Jesenski i Turk–Hrvatsko sociološko društvo, 2 Dugac, Željko: Kako biti čist i zdrav: zdravstveno prosvjećivanje u Hrvatskoj, Zagreb: Srednja Europa, 2 Dugac, Željko: »Zdravstveno prosvjećivanje protiv tuberkuloze u međuratnoj Hrvatskoj«. Medicus,
14(2005) 1, str. 155–171. Hol, Stjuart: Mediji i moć, Beograd: Karpos, 2013. Hol, Stjuart: Mediji i moć, Beograd: Karpos, 2013. Ferri, Rafo: Tuberkuloza u Splitu i asanacija grada, Split: Splitska društvena tiskara, 1925. Grmek, Mirko Dražen: »Životni put Andrije Štampara, borca za unapređenje narodnog zdravlja«. U:
U borbi za narodno zdravlje: izabrani članci Andrije Štampara. Zagreb: Škola narodnog zdravlja
»Andrija Štampar«: Medicinski fakultet, 1966. Kraljević, Ljubomir (ur.): Zaslužni splitski liječnici u prošlosti od 1946. do 1975. godine, znanstveni skup,
Split 23. rujna 1996. u povodu stodvadesete obljetnice rođenja dr. Jakova Miličića (zbornik rado-
va), Split: Hrvatski liječnički zbor, Podružnica, 1999. Kuić, Ivanka: »Novo doba – najvažniji splitski i dalmatinski list između dva rata«. Kulturna baština,
39(2013), str. 113–138. Marasović Šušnjara, Ivana i dr.: »Doktor Josip Škarić (1887–1975). – pionirski pothvati na polju javnog
zdravstva na području Dalmacije u prvoj polovici 20. stoljeća«. Acta Med. Croatica, 71(2017),
str. 319–326. rijan Jelaska, Zdravka: Grad i ljudi: Split 1918.–1941., Zagreb: Hrvatski institut za povijest, 2009. Propisi za suzbijanje tuberkuloze: otpis C.K. Ministra predsjednika kao upravljača ministarstava unu-
trašnjih posala, dneva 14. jula 1902. br. 29949. Zadar 1902. Štampar, Andrija: Pouke o zdravlju, Zagreb: Društvo hrvatskih sveučilišnih građana za pouke analfa-
beta, 1910. Štampar, Andrija: »Socijalna medicina«. U: Mirko Dražen Grmek (prir.), U borbi za narodno zdravlje:
izabrani članci Andrije Štampara. Zagreb: Škola narodnog zdravlja »Andrija Štampar«–Medi-
cinski fakultet, 1966. Štampar, Andrija: »O zdravstvenoj politici«. U: Mirko Dražen Grmek (prir.), U borbi za narodno zdrav-
lje: izabrani članci Andrije Štampara, Zagreb: Škola narodnog zdravlja »Andrija Štampar«–Me-
dicinski fakultet, 1966. Štampar, Andrija: »O socijalnoj terapiji«. U: Mirko Dražen Grmek (prir.), U borbi za narodno zdravlje:
izabrani članci Andrije Štampara, Zagreb: Škola narodnog zdravlja »Andrija Štampar«–Medi-
cinski fakultet, 1966. Štampar, Andrija: »O socijalnoj medicini«. U: Mirko Dražen Grmek (prir.), U borbi za narodno zdravlje:
izabrani članci Andrije Štampara, Zagreb: Škola narodnog zdravlja »Andrija Štampar«–Medi-
cinski fakultet, 1966. Štampar, Andrija: »Pet godina socijalno-medicinskog rada u Kraljevini SHS«. U: Mirko Dražen Grmek
(prir.), U borbi za narodno zdravlje: izabrani članci Andrije Štampara, Zagreb: Škola narodnog
zdravlja »Andrija Štampar«–Medicinski fakultet, 1966. 106 PUBLIC KNOWLEDGE ABOUT TUBERCULOSIS AND THE ACTIVITIES OF THE
SOCIETY FOR THE ERADICATION OF TUBERCULOSIS IN SPLIT (1918–1941) Ivanka Kuić
University library in Split
kuicivanka@gmail.com ABSTRACT: Tuberculosis was a major health problem in Split between the two world wars. Scientific publications, journals, and local newspapers played an important role in health education as
one of the preventive treatment methods of this nefarious disease, which is based on Štampar’s socio-
medical ideas, as well as in shattering prejudices and raising popular awareness of how to face the con-
sequences of the disease. This paper establishes the existence of a continuity in the creation of recorded
public knowledge relevant to this topic, with particular reference to the role of mass media such as Novo
doba and Jadranski dnevnik. Novo doba was a very important political-informative weekly newspaper
published from 1918 until 22 April 1941. Jadranski dnevnik was published from 1934 to 1938. Both papers
successfully performed their social function of providing information, shaping public opinion, and
spreading knowledge, transferring all the complexity and necessity of modernisation practices that
were changing Split and making it into a modern city. Among these modernisation practices was the
struggle against tuberculosis as a serious socio-medical problem. Keywords: Andrija Štampar; tuberculosis; socio-medical methods; Split 1918–1940; Novo doba;
Jadranski dnevnik Članci su dostupni pod licencijom Creative Commons: Imenovanje-Nekomercijalno
(https://creativecommons.org/licenses/by-nc/4.0/). Sadržaj smijete umnožavati, distribuirati, priopćavati
javnosti i prerađivati ga, uz obvezno navođenje autorstva, te ga koristiti samo u nekomercijalne svrhe. 107
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Protekcjonizm regulacyjny we współczesnym handlu międzynarodowym
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DOI 10.14746/ssp.2018.2.5 DOI 10.14746/ssp.2018.2.5 Zdzisław W. Puślecki
Uniwersytet im. Adama Mickiewicza w Poznaniu 1 Artykuł przygotowano w ramach grantu OPUS, Narodowe Centrum Nauki
– NCN, Nr UMO – 2013/11/B/HS5/03572. Protekcjonizm regulacyjny we współczesnym
handlu międzynarodowym Streszczenie: Celem głównym opracowania jest przedstawienie protekcjonizmu
regulacyjnego zniekształcającego i ograniczającego współczesny handel międzyna-
rodowy. Ważna jest zatem harmonizacja i wzajemne uznawanie norm szczególnie
w zakresie barier technicznych i XXI wieku coraz większego znaczenia nabierają
porozumienia bilateralne. Obejmują one już ponad 70% handlu zliberalizowanego. Wyraźnie zwiększyła się rola grupy G20. Zarówno WTO, jak i grupa G20 powinny
wspólnie podejmować i koordynować wysiłki na rzecz zasad promujących nie tylko
handel międzynarodowy państw wysoko rozwiniętych, ale rozszerzających również
dostęp do rynku światowego państw rozwijających się. Poprzez wspieranie zasad
handlowych w systemie globalnym wzmacniać się będzie legitymizacja funkcjono-
wania grupy G20, a zreformowany system światowej wymiany handlowej i zmodyfi-
kowane zarządzanie tym systemem w ramach WTO z uwzględnieniem specyficznych
interesów poszczególnych państw może przyczyniać się do dalszego dynamicznego
rozwoju. Słowa kluczowe: biznes międzynarodowy, kryzys gospodarczy, protekcjonizm regu-
lacyjny, porozumienia bilateralne Wprowadzenie1 N
owe tendencje do wzrostu protekcjonizmu regulacyjnego we współ-
czesnym handlu międzynarodowym, także Unii Europejskiej roz-
szerzają się i stanowią poważne ograniczenia dla dalszego rozwoju zagra-
nicznych kontaktów biznesowych. Protekcjonizm regulacyjny dotychczas
jest słabo rozpoznawalny w zagranicznej polityce handlowej. Może on
wzrastać z powodu różnych przyczyn. Uzależnione jest to od celów jakie
stawiają sobie poszczególne państwa. Protekcjonizm regulacyjny w okre-
ślonym stopniu odnosi się do wzrastających w handlu międzynarodowym N ŚSP 2 ’18 ŚSP 2 ’18 66 Zdzisław W. Puślecki barier technicznych i fitosanitarnych. Należy zatem podejmować dzia-
łania w zakresie harmonizacji przepisów i zarządzeń oraz wzajemnego
uznawania różnego rodzaju norm w wymiarze narodowym. Z uwagi na to, że działania WTO w zmniejszaniu barier regulacyjnych
nie przynoszą odpowiednich rezultatów, z powodu ograniczonego wpły-
wu na kwestie polityki wewnętrznej poszczególnych państw, opierającej
się na własnych przepisach i rozporządzeniach, także w sferze zagranicz-
nej polityki handlowej, coraz większego znaczenia nabierają porozumie-
nia bilateralne. W obecnych warunkach rozwoju już około 70% handlu
zliberalizowanego wynika z efektów porozumień bilateralnych. Charak-
ter funkcjonowania WTO staje się więc coraz bardziej symboliczny. Ce-
lem opracowania jest przedstawienie istoty i negatywnego oddziaływania
protekcjonizmu regulacyjnego na współczesny handel międzynarodowy,
także Unii Europejskiej. 1. Nowe tendencje protekcjonistyczne Nowe tendencje do wzrostu protekcjonizmu handlowego we współ-
czesnym biznesie międzynarodowym, chociaż występowały wcześniej,
były także przedmiotem obrad grupy G20 w Baden Baden w marcu
2017 r. Dotyczy to również protekcjonizmu regulacyjnego (Puślecki,
2016b), który dotychczas jest słabo rozpoznawalny w zagranicznej po-
lityce handlowej. Protekcjonizm ten może wzrastać z powodu różnych
przyczyn (Lester, Barbee, 2013). Uzależnione jest to od celów, jakie stawiają
sobie poszczególne państwa. Warto zaznaczyć, że protekcjonizm regulacyjny
w określonym stopniu odnosi się do wzrastających w handlu międzynaro-
dowym barier technicznych i fitosanitarnych (Puślecki, 2016b). Protekcjonizm regulacyjny w szerszym zakresie obejmuje rozporządze-
nia i regulacje biurokratyczne poszczególnych państw, które są trudne do
zidentyfikowania. W celu zidentyfikowania wariantów mających na celu
pogłębienie wzajemnych stosunków handlowych i inwestycyjnych stosuje
się dwie metody, a mianowicie harmonizację i wzajemne uznawanie norm
(Lester, Barbee, 2013). Harmonizacja implikuje do sprowadzania regulacji
do pojedynczych dobrych praktyk Wzajemne uznawanie norm natomiast
może być osiągane poprzez zawieranie porozumień o wzajemnym uznawa-
niu lub odwzajemnianie się ewkwiwalentami reugulacyjnymi. Podkreślić należy, iż wskazane regulacje w znacznym stopniu utrud-
niają oraz zmniejszają swobodny przepływ towarów i usług. Wpływa- ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... 67 ją zatem na ograniczanie i zniekształcanie handlu międzynarodowego. Protekcjonizm regulacyjny był przede wszystkim przedmiotem rokowań
w sprawie proponowanego Transatlantyckiego Partnerstwa Handlowe-
go i Inwestycyjnego (TTIP) między Unią Europejską i USA (Puślecki,
2016b). Dotychczas jednak propozycje te, które miały zmniejszyć, po-
jawiające się w stosunkach transatlantyckich ograniczenia o charakterze
regulacyjnym, nie zostały wprowadzone w życie. Występujące tendencje protekcjonistyczne widoczne są także w Unii
Europejskiej. Komisja Europejska musi przede wszystkim stawić czoła
żądaniom unijnych rolników na rzecz większego interwencjonizmu pań-
stwowego. Szczególnym wyzwaniem jest zapewnienie globalnego bez-
pieczeństwa żywności. Nie jest bowiem jasne, czy większa produkcja UE
i wynikające z niej niższe globalne ceny żywności są pożądane w walce
z głodem i ubóstwem (Huges, Irfan, 2008). Problem polega na tym, że
najubożsi mają tendencję do konsumowania większej ilości żywności
niż jej produkowania, a niższe ceny żywności prawdopodobnie redukują
głód tylko w krótkiej perspektywie. Długofalowo natomiast niższe ceny
przyczyniają się do zmniejszania produkcji rolnej w krajach rozwijają-
cych się. Obniża to równocześnie koszty nisko wykwalifikowanej siły
roboczej, która jest licznie zatrudniana w rolnictwie i redukuje wzrost
ekonomiczny w państwach słabo rozwiniętych. W sumie wydaje się moż-
liwe, że zwiększony przez UE import żywności i konsekwentnie wyższe
ceny na rynku światowym są lepszym narzędziem walki z globalnym
ubóstwem. 1. Nowe tendencje protekcjonistyczne Jednakże w żadnym wypadku WPR w swym obecnym kształ-
cie nie przynosi rozwiązania tego problemu (Dwyer, Guyomard, 2006). Na początku 2010 r. ceny na artykuły rolne uległy zmniejszeniu, dla-
tego oczekiwany był wzrost subsydiów eksportowych, w szczególności
dla sektora mlecznego (Dwyer, Guyomard, 2006). Pojawiało się przy tym
pytanie: na czym polega problematyczność tych subsydiów? Otóż utrud-
niają one uczciwą konkurencję, ze szkodą dla produkcji i usług, a także
zakłócają produkcję rolną na korzyść tych produktów, które otrzymują
najwięcej wsparcia. Ponadto, obniżają światowe ceny rynkowe dla pro-
duktów rolnych i poprzez zniekształcanie handlu międzynarodowego
prowadzą do niekorzystnej sytuacji w krajach rozwijających się (Olson,
1986). Innym problemem są taryfy celne na produkty rolne, które przeciętnie
są ponad cztery razy wyższe niż opłaty na inne dobra. Wszystkie unijne
cła, które przekraczają 100%, dotyczą produktów rolnych, a dla izogluko-
zy osiągają nawet bardzo wysokie w granicach 604% należności. Głów- 68 ŚSP 2 ’18 Zdzisław W. Puślecki nym zarzutem wobec nich jest to, że zakłócają sygnały rynkowe, które
mogłyby kreować skuteczną alokacją środków ekonomicznych (Birch-
field, 2008). Należy podkreślić, że bez taryf celnych UE produkowałaby mniej
dóbr rolniczych, a więcej dóbr przemysłowych i usług. Przyniosłoby to
równocześnie więcej korzyści w międzynarodowej specjalizacji produk-
cji głównie poprzez skupianie się na tworzących wysoką wartość do-
daną segmentach, gdzie UE cieszy się względną przewagą. W dodatku
różnice w taryfach celnych pomiędzy produktami rolnymi prowadzą do
zniekształcania produkcji. W rezultacie europejscy rolnicy wytwarzają te
dobra, które są wysoce protegowane, a nie te, które są wewnętrznie kon-
kurencyjne. Nie bez znaczenia jest fakt, że rynki rolne z natury są niestabilne. Izolowanie europejskiego rynku od zewnętrznych szoków może wy-
glądać na dobry pomysł, lecz ceny krajowe mają tendencję do wyższej
niestabilności niż ceny rynku światowego, który gromadzi różnego ro-
dzaju ryzyko. Na przykład dobre plony w Kazachstanie czy w USA
mogą zrównoważyć zły sezon w Europie. Poprzez osłabianie transmisji
cenowych z relatywnie stabilnego rynku światowego taryfy celne mogą
właściwie zwiększać niestabilność cen w UE. Podkreślić również na-
leży, że unijne cła są często pobierane jako cła specyficzne, w postaci
stałej opłaty za kilogram, co oznacza, że stają się bardziej restrykcyjne,
kiedy ceny spadają, a mniej restrykcyjne podczas okresów wysokich
cen. W wyniku takiej sytuacji globalny popyt maleje w okresach wy-
sokiej podaży i na odwrót. Światowe rynki w rezultacie stają się mniej
efektywnymi buforami przeciwko krajowym szokom cenowym i sil-
niejszym źródłem zakłóceń w biznesie międzynarodowym artykułami
rolnymi. 1. Nowe tendencje protekcjonistyczne W rezultacie krzywdzi to przede wszystkim ubogich w krajach
rozwijających się (Huges, Irfan, 2008). Wspólna zewnętrzna taryfa celna UE, stosowana selektywnie wobec
wybranych towarów, może hamować liberalizację handlu międzynarodo-
wego, co często jest podkreślane przez partnerów handlowych z krajów
nienależących do tego europejskiego ugrupowania integracyjnego i jest
oznaką protekcjonizmu handlowego, który w warunkach kryzysowych,
jak to miało miejsce także w latach 2008–2010, ulega nasileniu. Ograni-
czenie unijnych selektywnych zewnętrznych taryf celnych byłoby więc
ważnym wkładem do światowego systemu handlowego, dostarczające-
go wysokich zysków nie tylko dla UE, ale też skutecznego narzędzia
w walce z globalnym ubóstwem. Należy także w tym miejscu podkre- 69 ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... ślić wysoki poziom subsydiowania budżetowego unijnego rolnictwa, co
w poważnym stopniu ogranicza możliwości eksportowe krajów najsła-
biej rozwiniętych i jest także oznaką protekcjonizmu handlowego. Ina-
czej natomiast sytuacja wygląda w bogatszych krajach rozwijających się,
które paradoksalnie przyjmują podobne działania, jakie stosuje UE pole-
gające na zwiększaniu subsydiowania budżetowego własnego rolnictwa
co w konsekwencji wpływa na wzrost zniekształceń światowej wymiany
handlowej. W okresie nowej prezydentury Donalda Trumpa nasiliły się także ten-
dencje protekcjonistyczne w USA, co jest oznaką swoistego izolacjoni-
zmu, czyli odchodzenia od polityki globalizacji w kierunku wzrostu zna-
czenia interesów narodowych. Podkreśla się to obecnie w koncepcjach
zagranicznej polityki ekonomicznej nowej administracji rządowej USA. Wyrazem tego jest wyjście Stanów Zjednoczonych z Partnerstwa Trans-
Pacyficznego (TPP) i renegocjacja porozumienia NAFTA (North Ameri-
can Free Trade Agreement) obejmującego integrację gospodarczą USA,
Kanady i Meksyku. 2. W kierunku reform WTO Kryzys gospodarki światowej zapoczątkowany kryzysem finanso-
wym w latach 2008–2010 i brak rezultatów Rundy Doha doprowadziły
do przekonania, że WTO powinna gruntownie zmienić swoje funkcjo-
nowanie i przyszłościowy, handel międzynarodowy (Birchfield, 2008). Równocześnie podkreślić należy, że kraje rozwijające się, aby uchronić
się przed szokami zewnętrznymi, powinny wyraźnie zmniejszyć swo-
ją zależność od rynku światowego i udoskonalić organizację produkcji
(Ragazzi, Egger, 2010). Zależność ta może być zmniejszona poprzez
wewnętrzną restrukturyzację i modernizację produkcji. Ponadto rządy
państw Azji, Afryki i Ameryki Łacińskiej winny ochraniać mniejszych
producentów przed konkurencją zagraniczną na przykład poprzez sto-
sowanie cen gwarantowanych (Ragazzi, Egger, 2010). Towarzyszyć
temu powinno ograniczanie subwencji eksportowych w krajach wy-
soko rozwiniętych takich jak Unia Europejska czy Stany Zjednoczone
prowadzących, do wyraźnego zniekształcania cen na rynku światowym
(Birchfield, 2008). Warto zauważyć, że współczesna polityka handlowa państw wysoko
rozwiniętych powoduje poważne szkody w krajach rozwijających się, 70 ŚSP 2 ’18 Zdzisław W. Puślecki szczególnie odczuwalne przez ubogich rolników oraz przemysł głównie
spożywczy (Elsing, 2002). Dumping subsydiowanej żywności wypiera
ich bowiem z rynków lokalnych oraz międzynarodowych. Ceny eks-
portowe UE stanowią prawie 2/3 kosztów produkcji pszenicy, około 1/2
w przypadku proszkowanego mleka i tylko 1/4 w przypadku cukru. Po-
dobnie ceny eksportowe USA tak samo jak UE są zaniżane. UE i USA
równocześnie zmuszają kraje rozwijające się do otwierania ich rynków
na eksportowane wysoce subsydiowane produkty rolne (Birchfield, 2008;
Olson, 1986). Nie bez znaczenia jest fakt, iż głównym celem reform WPR miało
być dostosowanie rolnictwa UE do regulacji WTO w międzynarodowym
handlu rolnym (Agriculture, 2006; Michałek, Wilkin, 2008; Christian,
2008). Jednakże zmniejszanie cen na artykuły rolne na rynku światowym
spowodowało obniżkę cen wewnętrznych UE na te towary w stosunku
do poziomu światowego. W związku z tym subsydia eksportowe zredu-
kowano z ok. 10 mld euro w roku 1992 r. do poziomu zbliżającego się
do 3 mld euro w roku 2010 (www.foeeurope.org). Dopłaty bezpośrednie
mogą jednak w dalszym ciągu prowadzić do pozornie zaniżonych cen
produktów rolnych, jak również żywności przetworzonej, nawet w przy-
padku braku ich powiązania z produkcją. Warto przy tym zaznaczyć, że
uniezależnione od produkcji subsydia bezpośrednie są dozwolone dzięki
regułom WTO – w odróżnieniu od dopłat eksportowych czy wspierania
cen, które Unia pomogła ustanowić. W rezultacie takiej sytuacji Unia
Europejska może dalej bez przeszkód eksportować żywność po cenach
znacznie niższych niż koszty produkcji. 2. W kierunku reform WTO W takich uwarunkowaniach rozwoju handlu międzynarodowego,
szczególnie w warunkach kryzysowych, kraje rozwijające się powinny
mieć możliwość obrony przed subsydiowaną konkurencyjną produkcją
rolną ze strony krajów wysoko rozwiniętych. Kraje rozwijające się nie
mają bowiem możliwości subsydiowania własnego rolnictwa w stopniu
zbliżonym do krajów bogatych. Podkreślić należy, że jedynym sposo-
bem gwarancji handlu międzynarodowego „fair play” (Stiglitz, Charl-
ton, 2007) jest zaprzestanie nacisków w stosunku do krajów rozwija-
jących się w kierunku ciągłego zmniejszania taryf celnych (Birchfield,
2008). Jest to równocześnie jedyny sposób na utrzymanie subsydiów
przez kraje zamożne. W przeciwnym razie, państwa rozwijające się
powinny mieć możliwość podwyższania taryf celnych do poziomów
przynajmniej współmiernych do stosowanych subsydiów w krajach bo-
gatych. 71 ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... W procesach zmian ważną rolę powinna odegrać WTO, która w prze-
ciwieństwie do GATT ma szersze kompetencje i może również doko-
nywać interwencji w wewnętrznych politykach gospodarczych swoich
członków, aby je dostosować do realizacji swoich celów i zadań (Nielson,
2003; Hoekman, Kostecki, 2001). Oprócz tego WTO może stosować sze-
reg własnych środków wynikających z jej funkcjonowania (Flory, 1999)
między innymi takich jak rozszerzanie specjalnych klauzul ochronnych,
wzajemne dostosowania cen krajowych i międzynarodowych, stabilizacja
cen eksportowych i innych mechanizmów stabilizujących ceny produk-
tów tropikalnych, olejów roślinnych, cukru i bawełny. Z powodu braku
Aktu Końcowego Rundy Doha rola WTO uległa jednak wyraźnemu osła-
bieniu. Nastąpił równocześnie wzrost znaczenia porozumień bilateral-
nych (Puślecki, 2016a), i Grupy G20. W tej sytuacji konieczna jest refor-
ma WTO. Powinna ona uwzględniać przede wszystkim potrzeby państw
rozwijających się, czyli likwidację zacofania gospodarczego i zależności
ekonomicznej od państw wysoko rozwiniętych. Należy podkreślić, że jest
to niezwykle ważne nowe zadanie i kierunek działań WTO. 3. Wzrost roli i znaczenia grupy G20 Kluczową rolę w stymulowaniu rozwoju sytuacji w biznesie między-
narodowym, w czasie kryzysu, odegrały sprawy podstawowe, w tym
nieoczekiwane zmiany warunków gospodarczych na świecie związa-
ne z gwałtownym wzrostem popytu na „emerging markets”, czyli we
wschodzących gospodarkach rynkowych (Task..., 2010), co powodo-
wało wyraźny wzrost nadwyżki budżetowej w tych państwach w po-
równaniu z państwami wysoko rozwiniętymi i światem ogółem (wy-
kres 1). Do innych czynników, którym również można przypisać pewną
rolę, należą niedobory dostaw i polityka monetarna, a także, zwłaszcza
w ostatnich latach, różne działania polityczne podejmowane ad hoc. W okresie poprzedzającym kryzys cen żywności z 2008 r. na ceny te
wpłynęły ograniczenia wywozowe, środki stosowane na granicach oraz
zmiany w zasadach składowania. Większe wykorzystanie gruntów rol-
nych do produkcji energii ze źródeł odnawialnych (Schreyer, Metz,
2009) wzmocniło powiązanie między zmianami cen artykułów rolnych
i cen energii. Zmiany cen stały się częstsze także w wyniku różnych
problemów strukturalnych związanych z łańcuchami podaży i dystry-
bucją poszczególnych towarów. 72 ŚSP 2 ’18 Zdzisław W. Puślecki Wykres 1. Nadwyżka budżetowa w gospodarkach wschodzących
– „emerging markets”, państwach wysoko rozwiniętych i na świecie
w latach 1925 i 2004
Procent PKB
1
0
–1
–2
–3
–4
–5
–6
–7
2
4
6
8
10
12
14
16
18
20
Świat 1925
Kraje wysokorozwinięte 2004
Kraje wschodzące 2004
Świat 2004
Źródło: Bordo et al. (2001), IMF World Economic Outlook, January 2009. Wykres 1. Nadwyżka budżetowa w gospodarkach wschodzących
– „emerging markets”, państwach wysoko rozwiniętych i na świecie Wykres 1. Nadwyżka budżetowa w gospodarkach wschodzących Wykres 1. Nadwyżka budżetowa w gospodarkach wschodzących
– „emerging markets”, państwach wysoko rozwiniętych i na świecie
w latach 1925 i 2004 – „emerging markets”, państwach wysoko rozwiniętych i na świecie
w latach 1925 i 2004 Procent PKB Źródło: Bordo et al. (2001), IMF World Economic Outlook, January 2009. Działania grupy G20 w kierunku zmniejszania niestabilności cen
na rynku światowym związane były z kryzysem finansowym, który
w latach 2008–2010 przekształcił się w kryzys ekonomiczny. Został
on zapoczątkowany w Stanach Zjednoczonych na rynku nierucho-
mości i przejawiał się poważnymi zaburzeniami w funkcjonowaniu
instytucji finansowych, a w tym systemu bankowego wraz z upad-
kiem banku Lehman Brothers. Warto przy tym zaznaczyć, że od czasu
wielkiej depresji z lat 1929–1933 nie odnotowywano takich spadków
światowej produkcji przemysłowej, na rynkach kapitałowych i w biz-
nesie międzynarodowym. Poniższe wykresy 2, 3 i 4 wskazują, że po-
czątkowe spadki w 2008 r. 3. Wzrost roli i znaczenia grupy G20 były nawet silniejsze i głębsze niż w czasie
wielkiej depresji końca lat dwudziestych i początku lat trzydziestych
XX wieku. 73 ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... Wykres 2. Światowa produkcja przemysłowa w czasie wielkiej depresji
i w latach 2008–2010
100
95
90
85
80
75
70
65
60
2
3
6
9
12
15
18
21
24
27
30
33
36
39
42
45
48
51
June 1929 = 100
April 2008 = 100
Jun09 Update
Months into the crisis
Źródło: B. Eichengreen, K. O’Rourke, What do the new data tell us, Vox 8 March 2010,
and A tale of two depressions: now and then, Vox, 6 April 2009, www.voxeu.org/index. php?q=node/324#jun09. Wykres 2. Światowa produkcja przemysłowa w czasie wielkiej depresji
i w latach 2008–2010
100
95
90
85
80
75
70
65
60
2
3
6
9
12
15
18
21
24
27
30
33
36
39
42
45
48
51
June 1929 = 100
April 2008 = 100
Jun09 Update
Months into the crisis
Ź Wykres 2. Światowa produkcja przemysłowa w czasie wielkiej depresji
i w latach 2008–2010 Months into the crisis Źródło: B. Eichengreen, K. O’Rourke, What do the new data tell us, Vox 8 March 2010,
and A tale of two depressions: now and then, Vox, 6 April 2009, www.voxeu.org/index. php?q=node/324#jun09. Źródło: B. Eichengreen, K. O’Rourke, What do the new data tell us, Vox 8 March 2010,
and A tale of two depressions: now and then, Vox, 6 April 2009, www.voxeu.org/index. php?q=node/324#jun09. Perturbacje na rynkach finansowych wystąpiły później także w wielu
innych państwach, zwłaszcza w tych, w których system bankowy i ubez-
pieczeniowy był najbardziej rozwinięty. Kryzys finansowy rozprzestrze-
nił się z kolei na realną sferę gospodarki, przy czym jego nasilenie przy-
padło na drugą połowę 2008 i pierwsze półrocze 2009 roku. Zmusiło to
rządy wielu państw do coraz silniejszego zaangażowania się w procesy
gospodarcze, a to z reguły oznaczało konieczność przygotowania planów
(pakietów) pomocowych jak to uczyniły na przykład Chiny. Należy za-
uważyć, że w 2008 r. podczas pierwszych oznak kryzysu finansowego
w USA i w Europie, rząd w Pekinie wprowadził gigantyczny pakiet sty-
mulacyjny, co pozwoliło utrzymać inwestycje w infrastrukturze na pozio-
mie z poprzednich lat (Broszkiewicz, 2012). Efekty rządowego wsparcia
dla gospodarki chińskiej widoczne były jeszcze w 2011 r. W tym roku ŚSP 2 ’18 ŚSP 2 ’18 74 Zdzisław W. Puślecki Chiny odnotowały bowiem wzrost PKB w wysokości 9,2 proc. 3. Wzrost roli i znaczenia grupy G20 Jednakże
już w czwartym kwartale 2011 r. dał się zauważyć spadek wzrostu PKB
do wysokości 8,9 proc. W tym czasie MFW prognozował na 2012 r. obni-
żenie tempa wzrostu PKB w Państwie Środka do poziomu 9,0 proc. Jest to
wprawdzie poziom, którego i tak świat zazdrościłby Chinom. W 2012 r. MFW obserwując sytuację w Europie skorygował jednak swoje szacunki
wzrostu PKB Chin do poziomu 8,5 proc. W 2012 r. przedstawiciel MFW
w Chinach ostrzegł także, że pogrążona w kryzysie Europa może w tym
roku pociągnąć Chiny w dół, a kosztować je to może nawet 4 punkty
procentowe wzrostu2. Radził również władzom chińskim, aby w 2012 r. zaczęły przygotowywać drugi pakiet stymulacyjny. Warto zaznaczyć, że
w 2017 r. wzrost gospodarczy w Chinach kształtował się na poziomie
około 6%, co i tak uznawane było za wzrost wysoki w stosunku do innych
państw świata. Wykres 3. Światowy rynek kapitałowy – giełda w czasie wielkiej depresji
i w latach 2008–2010
110
100
90
80
70
60
50
40
30
2
3
6
9
12
15
18
21
24
27
30
33
36
39
42
45
48
51
June 1929 = 100
April 2008 = 100
Jun09 Update
Months into the crisis
Źródło: Jak w wykresie 2. 2 Miało to miejsce w czasie seminarium naukowego w Pekinie na początku 2012 r. Wykres 3. Światowy rynek kapitałowy – giełda w czasie wielkiej depresji
i w latach 2008–2010
110
100
90
80
70
60
50
40
30
2
3
6
9
12
15
18
21
24
27
30
33
36
39
42
45
48
51
June 1929 = 100
April 2008 = 100
Jun09 Update
Months into the crisis Wykres 3. Światowy rynek kapitałowy – giełda w czasie wielkiej depresji
i w latach 2008–2010
110
100
90
June 1929 = 100
April 2008 = 100
Jun09 Update Wykres 3. Światowy rynek kapitałowy – giełda w czasie wielkiej depresji
i w latach 2008–2010 June 1929 = 100
April 2008 = 100
Jun09 Update Months into the crisis Źródło: Jak w wykresie 2. 2 Miało to miejsce w czasie seminarium naukowego w Pekinie na początku 2012 r. 2 Miało to miejsce w czasie seminarium naukowego w Pekinie na początku 2012 r. 2 Miało to miejsce w czasie seminarium naukowego w Pekinie na początku 2012 r. 75 ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... Powyższe zjawiska nie mogły pozostać bez wpływu na handel mię-
dzynarodowy. 3. Wzrost roli i znaczenia grupy G20 W warunkach kryzysowych pojawiła się realna groźba po-
wrotu do protekcjonizmu handlowego. Należało równocześnie oczekiwać
wyraźnego spadku międzynarodowych obrotów towarowych ze względu
na spadek produkcji przemysłowej (wykres 2). W ciągu 2009 r. wolumen
handlu światowego zmniejszył się o 12,2% (WTO, 2010a), a jego war-
tość aż o 23%, co oznaczało, iż był to największy spadek od zakończenia
drugiej wojny światowej. Wykres 4. Wielkość handlu światowego w czasie wielkiej depresji
i w latach 2008–2010
110
100
90
80
70
60
2
3
6
9
12
15
18
21
24
27
30
33
36
39
42
45
48
51
June 1929 = 100
April 2008 = 100
Jun09 Update
Months into the crisis
Ź ódł
J k
k
i 2 Wykres 4. Wielkość handlu światowego w czasie wielkiej depresji
i w latach 2008–2010 Źródło: Jak w wykresie 2. Źródło: Jak w wykresie 2. W kontekście rozważanych zagadnień pojawia się pytanie dlaczego
wskazany powyżej spadek wolumenu handlu międzynarodowego był aż
tak nagły i tak wysoki. Ekonomiści są zgodni w kwestii kilku kluczowych
wyjaśnień. Najważniejszym problemem było to, że rzeczywisty kryzys
instytucjonalny, a w jego ramach kryzys systemu bankowego doprowa-
dził do załamania popytu w Stanach Zjednoczonych, a później na całym
świecie. Ograniczyło to równocześnie zdolność kredytową międzynaro-
dowego systemu walutowego. Sektor bankowy i globalny łańcuch poda-
ży były przy tym istotnymi czynnikami wpływającymi na synchronizację
efektów kryzysu. Krótko mówiąc, konsumenci wyraźnie ograniczyli kon-
sumpcję. W biznesie międzynarodowym natomiast ograniczenia kredyto- ŚSP 2 ’18 76 Zdzisław W. Puślecki we wpływały na hamowanie decyzji dotyczących nowych przedsięwzięć
inwestycyjnych. Efekty kryzysu, powodujące spadek zatrudnienia, pro-
wadziły także do redukcji popytu. Dodatkowe statystyczne efekty osła-
bienia globalnego łańcucha podaży uwidoczniły się zatem w wyraźnym
spadku efektów handlu międzynarodowego (Kelton, 2012). W pierwszej połowie 2010 r. handel światowy wzrastał w szybkim tem-
pie, podobnie jak spadał w minionym 2009 r. W porównaniu roku do roku
wzrost ten był nawet silniejszy od rekordowego w 1950 r. (Kelton, 2012). Aczkolwiek, co warto podkreślić, na podstawie niskiej bazy wyjściowej
ekonomiści WTO już wcześniej przewidywali, że w 2010 r. wzrost handlu
międzynarodowego osiągnie 13,5% (WTO, 2010b) z rekordowo wysokim
poziomem wzrostu państw rozwijających SIĘ, przewyższającym nawet
poziom wzrostu państw wysoko rozwiniętych. Spowodowało to równocze-
śnie wyraźny wzrost łańcucha dostaw w biznesie międzynarodowym. Tak
więc wsparcie rządowe, przy pomocy zastosowanych środków interwen-
cyjnych doprowadziło do nieprawdopodobnego, trudnego do przewidzenia
wzrostu handlu międzynarodowego (Kelton, 2012). 3. Wzrost roli i znaczenia grupy G20 W toku rozważanych zagadnień dotyczących szybkiego wzrostu łań-
cucha dostaw i handlu światowego należy jednak wskazać dwa niebez-
pieczeństwa. Pierwsze polegało na tym, że dostosowania strukturalne do
zmian zachodzących w gospodarce światowej, jako konsekwencja recesji,
mogły doprowadzić do dodatkowych efektów w postaci nacisków politycz-
nych w kierunku wprowadzenia neomerkantylistycznej protekcjonistycznej
polityki handlowej. Mogły być one przy tym podobne do tych, które wy-
stąpiły w końcu lat siedemdziesiątych i na początku lat osiemdziesiątych
XX wieku. Drugie niebezpieczeństwo sprowadzało się natomiast do tego,
iż perspektywy dla reform światowego systemu handlowego, polegające
na rozszerzeniu koncesji państw wysoko rozwiniętych dla państw rozwi-
jających się, stawały się coraz mniej oczywiste (Kelton, 2012). W takich
okolicznościach test dla nowo ukonstytuowanej grupy G20, która uwzględ-
niała nowy układ sił w systemie międzynarodowym, potwierdzał jej legity-
mizację jako ważnej i wpływowej instytucji globalnej. Zakończenie Uogólniając należy stwierdzić, że rynek i wolny handel dobrze służą
poprawie ogólnego dobrobytu poszczególnych uczestników biznesu mię-
dzynarodowego. Jednakże w istniejących okolicznościach wynikających 77 ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... z aktualnych tendencji rozwoju gospodarki światowej i handlu międzyna-
rodowego, którym towarzyszy wzrost protekcjonizmu handlowego, trudno
spodziewać się szybkich i zadowalających efektów. Protekcjonizm mo-
tywowany jest szczególnie kwestiami społecznymi, co wskazuje na to, iż
ochrona płac i zatrudnienia jest nadal wiodącym argumentem współczesnej
ochrony handlowej. Widoczne jest to także w USA w czasie prezydentury
Donalda Trumpa, którego polityka prowadzi do osłabiania roli globalizacji
współczesnej gospodarki światowej i wchodzenia w erę postglobalizacji. Pomoc dla państw rozwijających się ze strony państw wysoko rozwi-
niętych powinna być znacznie szersza i bardziej odczuwalna, szczególnie
w zmniejszaniu barier handlowych na rynku światowym. Pozwoli to im
zwiększyć dochody, rozszerzyć napływ kapitału zagranicznego, dostęp do
nowych technologii oraz wykwalifikowanych kadr i dokonując równocześnie
zmian wewnętrznych, przyspieszyć rozwój gospodarczy. W konsekwencji
przyniesie to korzystne efekty dla całego biznesu międzynarodowego i wpły-
nie na osłabienie palącego obecnie problemu migracji międzynarodowych,
a szczególnie imigracji do Europy z państw azjatyckich i afrykańskich. W nowych uwarunkowaniach rozwoju biznesu międzynarodowe-
go wynikających z kryzysu gospodarki światowej, uwzględniać należy
wzrost znaczenia grupy G20. Bieżące problemy rozwoju biznesu między-
narodowego polegają na tym, że uwaga państw skierowana na tworzenie
bilateralnych porozumień handlowych prowadzi do utraty ich zdolności
do uwzględniania dotychczasowych zasad WTO i decyzji wynikających
z wielostronnych negocjacji handlowych. Przedłużający się brak końco-
wych rezultatów Rundy Doha osłabia równocześnie legitymizację funk-
cjonowania WTO, której charakter działania staje się coraz bardziej sym-
boliczny. Jej dalsze funkcjonowanie wymaga zatem istotnych reform. Warto także podkreślić, że w nowych uwarunkowaniach rozwojowych
wynikających z kryzysu, większość porozumień liberalizujących współ-
czesny handel międzynarodowy dokonuje się na poziomie dwustronnym,
a nie na poziomie wielostronnym. Dochodzi równocześnie do efektu
przesunięcia handlu międzynarodowego z wielostronnego na dwustron-
ny, który w wymiarze globalnym może być mniej korzystny. Bibliografia
Agricultural Trade and its Importance (2006), European Commission, Brussels. Birchfield V. (2008), Dueling Imperialsim or Principled Policies? A Comparative
Analysis of EU and US Aproaches to Trade and Development, w: North and Bibliografia
Agricultural Trade and its Importance (2006), European Commission, Brussels. Birchfield V. (2008), Dueling Imperialsim or Principled Policies? A Comparative
Analysis of EU and US Aproaches to Trade and Development, w: North and Bibliografia 78 ŚSP 2 ’18 ŚSP 2 ’18 Zdzisław W. Puślecki South in the World Political Economy, red. R Reuveny, W. R. Thompson,
Blackwell Publishing Ltd., Malden USA–Oxford UK–Carlton Victoria Aus-
tralia. Broszkiewicz M. (2012), Alternative Investment in China – a Solution for Investment
at a Time of the Modern Financial Crisis, „Ekonomia Economics” Publishing
House of Wrocław University of Economics, Wrocław, nr 3(20), s. 71–82. Christian H. (2008), Determinants of Agricultural Protection in an International Per-
spective: The Role of Political Institutions, 12th European Congress of Agri-
cultural Economists, Ghent. Dwyer I., Guyomard H. (2008), International trade, agricultural policy reform and
the multifunctionality of EU agriculture. A framework for analysis, w: Trade
Agreements, Multifunctionality and EU Agriculture, red. E. Kaditi, J. Swin-
nen, Centre for European Policy Studies, Brussels. Eichengreen B., O’Rourke K. (2010), What do the new data tell us, Vox 8 March, and
A tale of two depressions: now and then, Vox, 6 April 2009, www.voxeu.org/
index.php?q=node/324#jun09. Elsing M. (2006), The EU’s Common Commercial Policy, Macmillan, Burlington. Flory T. (1999), L’organisation mondiale du commerce. Droit institutionel et substan-
tiel, Etablissements Emile Bruylant, Bruxelles. Hoekman B. M., Kostecki M. M. (2001), The political economy of the world trading
system; the WTO and beyond, Oxford University Press, Oxford. Huges B. B., Irfan M. T. (2008), Assessing Strategies for Reducing Global Pover-
ty, w: North and South in the World Political Economy, red. R. Reuveny,
W. R. Thompson, Blackwell Publishing Ltd., Malden USA–Oxford UK–Carl-
ton Victoria Australia. Kelton M. (2012), Global Trade, w: R. Devetak, A. Burke, J. George, An Introduction
to International Relation, Cambridge University Press, New York. Lester S., Barbee I. (2013), The Challenge of Cooperation: Regulatory Trade Barriers
in the Transatlantic Trade and Investment Partnership, „Journal of International
Economic Law”, vol. 16, Issue 4, s. 847–867. Michałek J. J., Wilkin J. (2008), Wstępna ocena konsekwencji niepowodzenia sesji
ministerialnej Doha (lipiec 2008) dla instrumentów stosowanych w ramach
WPR, w: Polityka Unii Europejskiej po 2013 roku, UKIE, Warszawa 2008. Nielson D. L. (2003), Supplying Trade Reform: Political Institutions and Liberaliza-
tion in Middle-Income Presidetial Democracies, „American Journal of Poli-
tical Science” 47. Olson M. (1986), The Exploitation and Subsidization of Agriculture in Developing
and Developed Countries, w: Agriculture in a Turbulent World Economy, red. A. Maunder, U. Renborg, Aldershot, Gower, U.K. Puślecki Z. W. Bibliografia (2016a), Bilateral trade agreements and the rise of global supply cha-
ins, „Journal of Economic & Financial Studies”, USA, vol. 04. nr 05: October,
s. 17–23. 79 ŚSP 2 ’18
Protekcjonizm regulacyjny we współczesnym handlu... Puślecki Z. W. (2016b), Transatlantic Cooperation Regarding China, „US-China
Law Review”, David Publishing Company, New York, USA, vol. 13, nr 7,
July, s. 522–552. Ragazzi I., Egger M. (2010), Nach der Doha Runde. Elemente fuer eine neue WTO
Agenda, Dokument 19. Marz, http:/www.alliancesud.ch/de/publicatione-
n,downloads/dokument-19-2010-web.pdf. Schreyer M. L., Metz L., (2009), Europejska Wspólnota Energii Odnawialnej, Stu-
dium wykonalności, t. 3, Wydawca: Fundacja im. Heinricha Boella. Stiglitz J. E., Charlton A. (2007), Fair trade-szansa dla wszystkich, przeł. A. Szewor-
ski, PWN, Warszawa. Task Force on Commodity Futures Markets. Report to the G20, OICU/IOSCO, Tech-
nical Commitee of the International Organization of Securities Commission,
June 2010 (2010). www.iosco.org/library/pubdocs/pdf/IOSCOPD340.pdf,
maj 2012. World Trade Organization (2010a), International trade statistics 2010, WTO, Geneva. World Trade Organization (2010b), World trade report 2010: trade in natural re-
sources,
Geneva,
www.wto.org/english/res_e/booksp_e/anrep_e/world_
trade_report10_e.pdf. Data przekazania tekstu: 13.02.2018; data zaakceptowania tekstu: 7.03.2018. Summary The main goal of the study is to discuss regulatory protectionism that distorts
and restricts contemporary international trade. Therefore, it is important to harmo-
nize trade standards and recognize them internationally, especially with respect to
technical barriers. In the 21st century, bilateral agreements are becoming increasingly
important. They already account for over 70% of liberalized trade. The role of the
G20 group has clearly increased. Both the WTO and G20 should jointly undertake and
coordinate efforts to develop the principles that would promote not only international
trade of developed countries but also increase access of developing countries to the
global market. The promotion of global trade rules will increase the legitimacy of the
G20 group and the reformed global trade system whereas its modified management
within the WTO framework, which will take into account the specific interests of
individual countries, may contribute to further dynamic development. Key words: international business, economic crisis, regulatory protectionism, bilat-
eral agreements
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English
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Sciatica Caused by Nerve Root Entrapment Due to a Prominent Lumbosacral Ligament
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JBR-BTR
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cc-by
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Gossner, J 2015 Sciatica Caused by Nerve Root Entrapment Due to a
Prominent Lumbosacral Ligament. Journal of the Belgian Society of Radiology,
99(1), pp. 113–114, DOI: http://dx.doi.org/10.5334/jbr-btr.840 Competing Interests The author declares that they have no competing interests. IMAGES IN CLINICAL RADIOLOGY
Sciatica Caused by Nerve Root Entrapment Due
to a Prominent Lumbosacral Ligament J. Gossner* Figures A–D: A 61-year-old female patient presented at our hospital
with worsening sciatica of the right leg. Examination
revealed involvement of the fifth lumbar nerve root. Pain
was the leading complaint. A computed tomographic scan
of the lumbar spine was performed. At the disc level L5-S1
osteochondrosis and spondylarthrosis could be seen. There was no disc prolapse or formainal stenosis affect
ing the L5 root. A prominent lumbosacral ligament was
present on both sides on computed tomography as well
as on MRI (Fig. A, arrows). Coronal reformations revealed
direct contact of the lumbosacral ligament and the nerve
root (Figs. B, C). In contrast, there is no obvious contact
on the left (Fig. C). The right nerve root appeared slightly
edematous compared to the left side and the surrounding
fat tissue seemed minimally infiltrated (Fig. A). A possi
ble entrapment of the fifth nerve root on the right side
was suggested. To test this hypothesis, a CT guided selec
tive nerve root infiltration (local anesthetic and corticoid)
was performed on the next day resulting in improvement
of the patient’s pain (Fig. D). With further infiltrations
the patient experienced a significant and lasting pain
reduction. Figures A–D: been no clinical studies or case reports on this subject. In our case the above described morphologic features of
symptomatic entrapment were visible on the CT scan and
CT guided infiltration of the affected fifth lumbar nerve
root resulted in improvement of the patient sciatica. The
combination of morphologic findings and improvement
after selective nerve root infiltration favors the hypothesis
of a symptomatic entrapment of the fifth lumbar nerve
root due to a prominent lumbosacral ligament as a rare
cause of sciatica. Radiologist should be aware of this pos
sible differential diagnosis. been no clinical studies or case reports on this subject. In our case the above described morphologic features of
symptomatic entrapment were visible on the CT scan and
CT guided infiltration of the affected fifth lumbar nerve
root resulted in improvement of the patient sciatica. The
combination of morphologic findings and improvement
after selective nerve root infiltration favors the hypothesis
of a symptomatic entrapment of the fifth lumbar nerve
root due to a prominent lumbosacral ligament as a rare
cause of sciatica. Radiologist should be aware of this pos
sible differential diagnosis. Comment The lumbosacral ligament is a fibrous structure reaching
from the caudal parts of the transverse process and the
body of the fifth lumbar vertebrae to the ala of the sacral
bone. Briggs and Chandraraj observed in an anatomi
cal study, that in some cases the lumbosacral ligament
showed a contact to the underlying nerve root. In 9%
of the dissected patients the nerve root was compressed
and visibly flattened. Microscopic examination of these
nerves showed an increase in connective tissues, sugges
tive of chronic changes due to entrapment. In the patients
with compressed nerve roots the lumbosacral ligament
was also prominent, presumably due to a reactive hyper
trophy because of the degenerative disc disease and sub
sequent segmental microinstability. This cadaveric study
suggested a possible role of the lumbosacral ligament in
some patients with sciatica. But, until now, there have * Department of Clinical Radiology, Evangelisches Krankenhaus
Göttingen-Weende, Göttingen, Germany
Corresponding author: J. Gossner How to cite this article: Gossner, J 2015 Sciatica Caused by Nerve Root Entrapment Due to a Prominent Lumbosacral Ligament.
Journal of the Belgian Society of Radiology, 99(1), pp. 113–114, DOI: http://dx.doi.org/10.5334/jbr-btr.840 Gossner: Sciatica Caused by Nerve Root Entrapment Due to a Prominent Lumbosacral Ligament Reference 1. Briggs, CA and Chandraraj, S. Variations in the
lumbosacral ligament and associated changes in
the lumbosacral region resulting in compression
of the fifth dorsal root ganglion and spinal nerve. Clin Anat. 1995; 8: 339–346. DOI: http://dx.doi. org/10.1002/ca.980080506. PMid: 8535966. 1. Briggs, CA and Chandraraj, S. Variations in the
lumbosacral ligament and associated changes in
the lumbosacral region resulting in compression
of the fifth dorsal root ganglion and spinal nerve. Clin Anat. 1995; 8: 339–346. DOI: http://dx.doi. org/10.1002/ca.980080506. PMid: 8535966. 114 Gossner: Sciatica Caused by Nerve Root Entrapment Due to a Prominent Lumbosacral Ligament How to cite this article: Gossner, J 2015 Sciatica Caused by Nerve Root Entrapment Due to a Prominent Lumbosacral Ligament. Journal of the Belgian Society of Radiology, 99(1), pp. 113–114, DOI: http://dx.doi.org/10.5334/jbr-btr.840 How to cite this article: Gossner, J 2015 Sciatica Caused by Nerve Root Entrapment Due to a Prominent Lumbosacral Ligament. Journal of the Belgian Society of Radiology, 99(1), pp. 113–114, DOI: http://dx.doi.org/10.5334/jbr-btr.840 Published: 15 September 2015 Published: 15 September 2015 Copyright: © 2015 The Author(s). This is an open-access article distributed under the terms of the Creative Commons
Attribution 3.0 Unported License (CC-BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium,
provided the original author and source are credited. See http://creativecommons.org/licenses/by/3.0/. Journal of the Belgian Society of Radiology is a peer-reviewed open access journal
published by Ubiquity Press. OPEN ACCESS
Journal of the Belgian Society of Radiology is a peer-reviewed open access journal
published by Ubiquity Press. OPEN ACCESS
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English
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“I’ll be in a safe place”: a qualitative study of the decisions taken by people with advanced cancer to seek emergency department care
|
BMJ supportive & palliative care
| 2,016
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cc-by
| 9,991
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Citation for published version (APA):
Henson, L. A., Higginson, I. J., Daveson, B. A., Ellis-Smith, C., Koffman, J., Morgan, M., & Gao, W. (2016). 'I'll
be in a safe place': A qualitative study of the decisions taken by people with advanced cancer to seek
emergency department care. BMJ Open, 6(11), Article e012134. https://doi.org/10.1136/bmjopen-2016-012134 Citing this paper
Pl
h C t
g t
s pape
Please note that where the full-text provided on King's Research Portal is the Author Accepted Manuscript or Post-Print version this may
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again advised to check the publisher's website for any subsequent corrections. Citation for published version (APA):
Henson, L. A., Higginson, I. J., Daveson, B. A., Ellis-Smith, C., Koffman, J., Morgan, M., & Gao, W. (2016). 'I'll
be in a safe place': A qualitative study of the decisions taken by people with advanced cancer to seek
emergency department care. BMJ Open, 6(11), Article e012134. https://doi.org/10.1136/bmjopen-2016-012134 To cite: Henson LA,
Higginson IJ, Daveson BA,
et al. ‘I’ll be in a safe place’: a
qualitative study of the
decisions taken by people
with advanced cancer to seek
emergency department care.
BMJ Open 2016;6:e012134.
doi:10.1136/bmjopen-2016-
012134 Lesley A Henson,1 Irene J Higginson,1 Barbara A Daveson,1 Clare Ellis-Smith,1
Jonathan Koffman,1 Myfanwy Morgan,2 Wei Gao,1 on behalf of BuildCARE ABSTRACT
Objective: To explore the decisions of people with
advanced cancer and their caregivers to seek
emergency department (ED) care, and understand the
issues that influence the decision-making process. Design: Cross-sectional qualitative study incorporating
semistructured patient and caregiver interviews. Methods: Between December 2014 and July 2015,
semistructured interviews were conducted with 18
people with advanced cancer, all of whom had recently
attended the ED of a large university teaching hospital
located in south-east London; and six of their
caregivers. Interviews were audio recorded, transcribed
verbatim and analysed using a constant comparative
approach. Padgett and Brodsky’s modified version of
the ‘Behavioral Model of Health Services Use’ was used
as a framework to guide the study. Conclusions: These data provide healthcare
professionals and policymakers with a greater
understanding of how systems of care may be
developed to help reduce ED visits by people with
advanced cancer. In particular, our findings suggest
that the number of ED visits could be reduced with
greater end-of-life symptom support and education,
earlier collaboration between oncology and palliative
care, and with increased access to community
healthcare services. 1Faculty of Life Sciences &
Medicine, Division of
Palliative Care, Policy &
Rehabilitation, King’s College
London, London, UK
2Faculty of Life Sciences &
Medicine, Division of Health
& Social Care Research,
King’s College London,
London, UK General rights General rights
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Downloaded from Research Open Access ‘I’ll be in a safe place’: a qualitative
study of the decisions taken by people
with advanced cancer to seek
emergency department care ▸Prepublication history and
additional material is
available. To view please visit
the journal (http://dx.doi.org/
10.1136/bmjopen-2016-
012134). Received 1 April 2016
Revised 1 July 2016
Accepted 8 September 2016 Lesley A Henson,1 Irene J Higginson,1 Barbara A Daveson,1 Clare Ellis-Smith,1
Jonathan Koffman,1 Myfanwy Morgan,2 Wei Gao,1 on behalf of BuildCARE Strengths and limitations of this study ▪Understanding
what
influences
people
with
advanced cancer to seek emergency department
(ED) care is key to developing initiatives aimed at
reducing high attendance; to date, however, such
evidence is limited. To address this issue we
conducted a qualitative interview study exploring
the decision-making process of people with
advanced cancer and their caregivers to seek ED
care. ▸Prepublication history and
additional material is
available. To view please visit
the journal (http://dx.doi.org/
10.1136/bmjopen-2016-
012134). ▪Semistructured in-depth interviews were con-
ducted with 18 people with advanced cancer, all
of whom had recently attended the ED of a large
university teaching hospital located in south-east
London; and six of their caregivers. ▪We adopted a maximum variation (heterogeneity)
sampling strategy to identify people with a range
of characteristics and capture potentially richer
and more diverse data relevant to the research
question. Results: Issues influencing the decision-making
process included: (1) disease-related anxiety—those
with greater anxiety related to their cancer diagnosis
interpreted their symptoms as more severe and/or
requiring immediate attention; (2) prior patterns of
health-seeking behaviour—at times of crisis
participants defaulted to previously used services; (3)
feelings of safety and familiarity with the hospital setting Received 1 April 2016
Revised 1 July 2016
Accepted 8 September 2016 ▪Our study interviewed people who decided to
seek ED care. The decision-making process of
those who used alternative services was not
explored and is a limitation of this research. —many felt reassured by the presence of healthcare
professionals and monitoring of their condition; and,
(4) difficulties accessing community healthcare services
—especially urgently and/or out-of-hours. UK this is estimated at 10–20% of the
National
Health
Service
(NHS)
budget,
while in the USA it accounts for as much as
30% of the Medicare budget.1 2 This pattern
of spending is especially pronounced for
people with cancer. Despite the cancer tra-
jectory being highly predictable, costs escal-
ate at an exponential rate up to the time of
death,3
with
the
additional
costs
almost
entirely attributable to an increased use of
acute hospital services, in particular emer-
gency department (ED) visits and unplanned
hospital admissions.1 4 1Faculty of Life Sciences &
Medicine, Division of
Palliative Care, Policy &
Rehabilitation, King’s College
London, London, UK
2Faculty of Life Sciences &
Medicine, Division of Health
& Social Care Research,
King’s College London,
London, UK Participants Participants
were
adults
(≥18 years)
with
advanced
cancer who had recently attended, from their private
residence, the hospital’s ED; and where applicable their
main caregiver (see box 1). Most of the existing research on end-of-life ED use by
people with cancer has focused on quantifying attend-
ance and/or
identifying factors
associated
with an
increased risk of multiple visits in the last month of
life.16–18 While these studies have identified a number of
sociodemographic,
environmental
and
clinical
risk
factors (eg, sex, age, ethnicity, socioeconomic status and
type of cancer), evidence for why people with cancer
decide to attend the ED is limited.19
20 In order to
address this issue and help guide development of future
healthcare services, we conducted the following qualita-
tive study. The aim of our study was to explore the deci-
sions
of
people
with
advanced
cancer
and
their
caregivers to seek ED care, and understand the issues
that influence the decision-making process. METHODS ▪Adults (≥18 years). ▪Identified as their caregiver by an eligible patient recruited to
the study. Caregiver defined as an unpaid family member/close
friend involved in caring for the patient’s physical, emotional
and/or practical needs. This study is reported following the consolidated criteria
for reporting qualitative studies (COREQ).21 Setting A
large
university
teaching
hospital
in
south-east
London, serving an ethnically, socially and economically
diverse urban population of approximately two million. The hospital’s ED sees over 120 000 patients each year—
about 350 patients a day.28 Box 1
Study eligibility criteria Inclusion criteria: patients ▪Adults (≥18 years). ▪Diagnosed with advanced cancer by a qualified healthcare pro-
fessional involved in the patient’s care. Advanced cancer
defined as cancer that has invaded surrounding body tissues
and/or metastasised, and is not curable and is life-threatening. ▪Assessed as having a prognosis of weeks to short months by
a qualified healthcare professional involved in the patient’s
care. ▪Attended, from their private residence, the emergency depart-
ment (ED), within 2 weeks of screening for the study. Inclusion criteria: caregivers Inclusion criteria: caregivers Open Access initially developed to explain non-discriminative health-
care use among the general population, the model has
since been applied to a variety of services and popula-
tions.26 It has not, however, been used to examine the
uptake of healthcare services by people with advanced
cancer or at the end-of-life. In 1992, Padgett and
Brodsky27 modified the model, specifically to explain
non-urgent ED use. In this adapted version, three stages
of decision-making are identified: (1) problem recogni-
tion; (2) decision to seek medical care; and, (3) decision
to use the ED. Predisposing, enabling and need-based
factors—as per Andersen and Newman’s original model
—are
proposed
to
influence
each
of
these
three
stages.27 This modified version of the model was used as
a framework for our study. The model’s utility when
applied to a different population group—people with
advanced cancer—was also tested. However, evidence suggests this is not the case. Instead,
prolonged hospital admissions and/or multiple ED visits
in the last month of life are associated with greater phys-
ical distress, overall dissatisfaction with care and more
than a threefold increase in the likelihood of psychiatric
illness among bereaved relatives.5–7 Furthermore, for the
majority of people with cancer, acute hospital care is dia-
metrically
opposed
to
their
stated
preferences
for
end-of-life care.8 Most (64–84%) people with cancer
prefer to be cared for and die at home,9 surrounded by
their loved ones and free from the stressful environment
of an acute hospital.9–12 Reducing patients with cancer use of acute hospital
services towards the end-of-life therefore provides an
opportunity to improve overall care quality and reduce
healthcare costs. These clear individual and societal ben-
efits have motivated policymakers to introduce measures
to minimise acute hospitalisations. To date, however, the
impact of such initiatives has been limited; instead, the
number of people with cancer experiencing multiple
ED visits and/ or with prolonged hospital admissions
towards the end-of-life has risen.13 14 In England, most
ED visits represent self-presentations.15 Hence, if future
initiatives are to be successful, a more comprehensive
understanding of why people with cancer choose ED
care is required. Only then will it be possible to devise a
system of end-of-life care services that can effectively
serve the needs and preferences of people with cancer
and their families. Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 BACKGROUND The increased use of acute hospital ser-
vices towards the end-of-life would not be
such a concern if it improved outcomes for
patients
with
cancer
and
their
families. A large proportion of all healthcare expend-
iture in developed countries is consumed by
care for those in the last year of life; in the Correspondence to
Dr Lesley A Henson;
lesley.henson@kcl.ac.uk 1 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
on November 25, 2016 - Published by
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Downloaded from group.bmj.com
on November 25, 2016 - Published by
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on November 25, 2016 - Published by
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Downloaded from Open Access Theoretical framework Exclusion criteria: patients and caregivers Exclusion criteria: patients and caregivers ▪Participants incapable of providing informed consent. Many previous studies have explored patients’ use of
healthcare services22–25 and extant models of health-
seeking behaviour can be useful to guide future research
and investigation. The most widely acknowledged theory
of healthcare usage is the ‘Behavioral Model of Health
Services Use’ developed by Andersen in 1968 and subse-
quently published with Newman in 1973.22 Although ▪Patients attending the ED from nursing homes, care homes or
other institutionalised care settings. ▪Patients brought to the ED by representatives of Her Majesty’s
Prison Service and under their supervision. ▪Participants whose clinical team considers them to be too
unwell and/or distressed to participate in the study. Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 2 group.bmj.com
on November 25, 2016 - Published by
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Downloaded from group.bmj.com
on November 25, 2016 - Published by
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Downloaded from Open Access Open Access Recruitment of patients was through the hospital’s pal-
liative care and acute oncology teams. Between 16
December 2014 and 31 July 2015 both teams screened
all new referrals against the study’s eligibility criteria. The acute oncology team also screened all ED dis-
charges for people with advanced cancer who attended
the ED but were not admitted. Any eligible patients
identified were first approached by a clinical member of
the team who provided them with a leaflet about the
study
and
assessed
their
interest
in
participating
(patients already discharged were phoned at home). Those who expressed interest in the study were then
followed-up by a member of the research team, either
face-to-face or via the telephone. female). All interviews were audio recorded and field
notes were made during or immediately after each inter-
view. At the request of participants, caregiver interviews
were conducted jointly with patients apart from in one
case where the caregiver interview occurred immediately
following the patient interview. During the consenting
process LH explained that she was working with the pal-
liative care or acute oncology team to conduct a study
about people’s decisions to seek ED care. No further
information about the research team was offered. During interviews participants were asked to describe
the most recent time that they, or their family member/
close friend, attended the ED and the issues that influ-
enced
their
decision-making
process. Theoretical framework In
order
to
enhance the consistency and completeness of data col-
lected across cases, topic guides were developed (based
on the study’s theoretical framework27), piloted and
used during interviews (see online supplementary file 1
—patient interview topic guide; online supplementary
file 2—caregiver interview topic guide). Participants
were encouraged to talk in-depth about their thought
processes with prompts used to elicit further informa-
tion when required. p
Recruitment to research studies can be especially chal-
lenging in vulnerable population groups such as those
with advanced diseases. Issues such as gate keeping,
high symptom burden and a rapidly changing clinical
picture often result in poor recruitment and/or high
attrition rates.29 To help overcome some of these chal-
lenges the research and clinical teams collaborated
closely during the study period, with face-to-face meet-
ings at least twice weekly. This enabled prompt follow-up
of potential participants, most of whom were contacted
by the research team within 24 hours of them expressing
interest in the study. Additional strategies to reduce attri-
tion included flexibility around the interview setting and
timing, as well as the option to conduct joint patient
and caregiver interviews if preferred. Characteristics of participants Seven hundred and thirty-one patients were screened
for the study, of whom 67 met the eligibility criteria and
were approached regarding participation. Twenty-two
patients declined
to participate citing
reasons that
included ‘not interested’ and ‘didn’t feel up to it’. A
further 22 patients became too unwell or died in the
short time period between being approached about the
study and an interview being arranged. The final five
patients were excluded for other reasons, including
closure of a hospital ward because of a Norovirus RESULTS Recruitment of both patients and caregivers continued
until data saturation was achieved. Specifically, this was
the point when we were confident that the emerging
themes and constructs appeared to be fully represented
by the data collected. Additional interviews did not
result in a greater depth of understanding or the gener-
ation of new themes and/or constructs.31 Analysis Interviews were anonymised, transcribed verbatim and
analysed
using
a
constant
comparative
approach.32
Analysis began with open coding of the transcript where
meaningful words, phrases and statements were identi-
fied, followed by more detailed axial coding as items
emerged. These items were then grouped into themes
which became further refined as the analysis continued. Differences and similarities were explored within and
across interviews. Where new themes emerged, earlier
interviews were reanalysed to consider further and/or
alternative meaning, with particular attention paid to
non-confirmatory/divergent cases. We adopted a maximum variation (heterogeneity)
sampling strategy to identify people with a range of
characteristics and capture potentially richer and more
diverse
data
relevant
to
the
research
question.30
Sampling criteria were based on the findings of a
recently conducted systematic review exploring factors
associated with ED attendance by patients with cancer in
the last month of life, and were: sex; age; ethnicity;
socioeconomic status; type of cancer; and use of pallia-
tive care services.18 All interview transcripts were analysed by researcher
LH. To address issues of analytical rigour, credibility and
trustworthiness, a selection of interviews were also ana-
lysed by researchers CE-S and JK, and then reviewed
with LH. Where coding differed, areas were reconsid-
ered and discussed until consensus was reached regard-
ing interpretation and overall meaning. Caregivers were identified through patients enrolled
to the study, all of whom were asked if they had a family
member/close friend that helped care for any of their
physical, emotional and/or practical needs. For patients
who identified a caregiver, permission was sought for a
member of the research team to approach the caregiver
regarding study participation. Stage 1: problem recognition All participants described physical problems during
their interviews with a wide range of symptoms reported,
including
pain,
fevers,
breathlessness
and
seizures
(table 1). While most reported these physical symptoms
as central to their decision to seek medical care, it
became apparent that most experienced symptoms at
many other points in time for which they did not decide
to seek help. Instead it was participants’ perception, or
interpretation, of their symptom(s)—rather than the
symptom per se—which appeared to influence their
decision-making. y
g
No participants withdrew from the study, however two
interviews ended
early. In one case (ED03),
after
27 min, the patient felt unwell and unable to continue
with the interview. In the second case (ED16), the
patient found the study questions frustrating, in particu-
lar the level of detail being asked, and requested to stop
after 13 min. Eighteen of the 24 interviews were con-
ducted in hospital, 5 in participants’ homes and 1 in the
hospital’s Macmillan Information and Support Centre. No other persons apart from those involved in the study
were present during the interview process. Interviews
lasted an average of 31 min (range 13–57). The mean
number of days between the patient’s interview and
death was 90 (range 7–252) (Five patients remained
alive as of the 16 February 2016). Symptom interpretation varied considerably between
participants. Some interpreted their symptom(s) as
severe and felt compelled to seek medical care as soon
as possible. Others perceived their symptoms as mild, or
to be expected, and consequently did not decide to seek
medical care until another event triggered them to seek
help. Three concepts emerged as influencing partici-
pants’ symptom perception/interpretation: (1) anxiety
relating to their underlying cancer diagnosis; (2) prior
symptom
experiences;
and
(3)
education
and
knowledge. Characteristics of the 18 patient participants are pre-
sented in table 1. Interviews Each participant consented to a one off semistructured
interview with researcher LH (palliative care physician
(MBBS,
MRCP)
and
PhD
clinical
training
fellow; 3 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
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Downloaded from Open Access outbreak. A total of 18 patients were recruited to the
study (figure 1). morning of his ED visit he had struggled to get out of
bed. It was this feature—the pain limiting his mobility—
that triggered his decision to seek medical care. Among the 18 patients recruited, 10 identified a
family member/close friend as their main caregiver,
with
one
patient
identifying
two
family
members. Permission was given for eight of these individuals to be
approached about the study. One caregiver declined to
participate stating ‘they didn’t have enough time’ and
one was unable to consent; the remaining six were
enrolled to the study (figure 1). gg
Each of the decision-making stages, and the issues that
influenced them, are presented below. Accounts of the decision-making process g p
During each interview participants narrated their own
unique account of the events leading up to their ED
visit. In keeping with the study’s theoretical framework,27
participants’ overall decision-making was composed of
three key stages: (1) problem recognition; (2) decision
to seek medical care; and, (3) decision to use the ED. For
some
participants
these
decision-making
stages
occurred quickly (within minutes), while for others one
was deliberated to a greater extent than the other. For a
few participants the initial ‘problem recognition’ and
‘decision to seek medical care’ stages were so intuitive
that they struggled to recognise any decision-making at
this time. For example, patient ED16 began his interview
by describing back pain he had experienced in the days
leading up to his ED visit. When asked why he decided
to seek medical care, he struggled to describe his
decision-making further, instead repeating that pain was
the reason he sought help. Anxiety relating to underlying cancer diagnosis A number of participants conveyed narratives explaining
how their diagnosis of cancer felt like a ‘death sentence’
and was ‘always on their mind’. Any new symptom
experienced would be interpreted within this context. For example, patient ED02, a woman with colorectal
cancer, described how she immediately thought her
cancer was progressing when she developed pain. ED02 [patient]: it’s always going to trigger (Researcher:
Okay) is this thing growing? Is this get…is it getting out
of hand you know? (Researcher: Okay) You know, what
is, what is going to happen? Two patient characteristics appeared to influence par-
ticipants’ anxiety of their cancer: age; and religious or
spiritual beliefs. Compared to younger patients, older
patients tended to describe less anxiety related to their
cancer diagnosis and subsequently were less likely to per-
ceive a new symptom as always being cancer related. ED16 [patient]: Well the pain. Researcher: Okay, but you’d had it [the pain] for a few
days? ED16: Yeah. Researcher: So what changed? ED16: Well the pain. ED16 [patient]: Well the pain. Researcher: Okay, but you’d had it [the pain] for a few
days? y
ED16: Yeah. y
ED16: Yeah. Researcher: So when you fell onto the floor, that
[cancer] wasn’t something going through your mind? Later during the interview ED16 was able to elaborate
further. He explained that over a period of days his pain
got progressively worse to the extent that on the ED06 [patient]: When, when? Accounts of the decision-making process Researcher: When you slipped from the chair? Researcher: When you slipped from the chair? Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 4 group.bmj.com
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Downloaded from Open Access D06: Oh! Good God no! I was looking at the bloody
ootball score [laughs]. When…when I get to a state where I get like a bit o
wimp, I pray. ure 1
Flow diagram of patient and caregiver recruitment. *One patient identified two family members. ED, emergency
artment. Open Acc Figure 1
Flow diagram of patient and caregiver recruitment. *One patient identified two family members. ED, emergency
department Figure 1
Flow diagram of patient and caregiver recruitment. *One patient identified two family members. ED, emergency
department. ED06: Oh! Good God no! I was looking at the bloody
football score [laughs]. ED06: Oh! Good God no! I was looking at the bloody
football score [laughs]. When…when I get to a state where I get like a bit of a
wimp, I pray. When…when I get to a state where I get like a bit of a
wimp, I pray. Participants’
with
religious
or
spiritual
beliefs
described how their faith helped them cope with their
cancer diagnosis and any symptoms they experienced. Education and knowledge Several patients had received advice from healthcare
professionals regarding specific symptoms. This educa-
tion and knowledge influenced their interpretation of
how important certain symptoms were and whether or
not they decided to seek help. ED12 [patient]: …the reason I came in is because erm,
I’ve got cancer, and erm, I was erm being looked after at
XX Hospital team and they told me, erm if I’ve got a
temperature above erm I think it’s 37 point something
then I should go to my nearest A&E. I did have a tem-
perature of 38 point. I called them and the nurse said to
me I should make my way here just in-case I had an
infection. The levels of anxiety relating to having a diagnosis of
cancer was variable across individuals, as above, and did
not appear to differ between those who were and were
not receiving community palliative care. Participants
who received symptom advice/information from their
palliative care team did describe less anxiety regarding
new symptoms and several also reported seeking alterna-
tive sources of help before deciding to attend the ED. Prior symptom experience Participants’
recollections
of
previously
experienced
symptoms also influenced how they interpreted their
situation. Many considered a new symptom as ‘severe’
and/or ‘urgent’ if it was similar or related to symptoms
they had experienced around the time of their cancer ED18 [patient]: …my faith is very strong in in what I
believe, and, that really takes care of a lot of the…the
burden if I should say, (Researcher: Okay) you know. 5 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
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Downloaded from Open Access diagnosis. This was illustrated by patient ED10 who
explained how he had been diagnosed with metastatic
lung cancer after having a grand-mal seizure. Despite
experiencing many other symptoms since then, ED10
had not had another seizure until the week of his inter-
view when he developed a partial seizure of his arm and
decided to immediately seek help. ED10 described his
thoughts at this time: Table 1
Characteristics of patient participants
Type of cancer
N
Sex (male/
female)
Age in years
(mean (range))
Ethnicity (white
British/other)
Socioeconomic
status* (1–2/3–5)
Under community
palliative care prior to ED
visit (yes/no)
Reasons for ED attendance
Lung
4
3/1
70 (45–86)
3/1
3/1
1/3
Focal seizures; malaise; pain;
breathlessness and malaise. Haematological
malignancies
4
2/2
75 (59–90)
4/0
4/0
1/3
Pain; rectal bleeding; fever;
fever. Prostate, gynaecological
and urinary tract
4
2/2
72 (55–88)
3/1
4/0
2/2
Fall; pain; facial weakness
and malaise; haematuria. Gastrointestinal and
hepatocellular
3
1/2
59 (42–68)
1/2
2/1
1/2
Pain; pain fever and cough;
fever. Other
3
1/2
37 (19–47)
0/3
1/2
0/3
Pain; facial numbness and
headache; fever and pain. *Socioeconomic status derived from index of multiple deprivation (IMD) quintiles (1st—most deprived; 5th—least deprived) The IMD is an area based measure of deprivation that uses Lower ED10 [patient]: That decision came because of the past
experience. So we know its brain. (Researcher: Okay) So
our fear was it’s—it may have grown bigger and the pres-
sure could be you know imminent danger. Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 Stage 2: decision to seek medical care For those who interpreted their symptom(s) as severe,
their decision to seek medical care followed rapidly and
was often hard to separate from the initial problem rec-
ognition stage. However, for participants who did not
seek help immediately and instead accommodated or
managed their symptom(s), this second decision to seek
medical care appeared to occur later when for some
reason they were no longer able to tolerate, or accom-
modate, their symptom(s). Reasons for why this accom-
modation broke down included situations where the
symptom changed in character, started to interfere with
activities of daily living and/or persisted beyond an arbi-
trary time threshold. Patient ED25, a woman with
bladder cancer, explained how despite having experi-
enced
multiple
previous
episodes
of
cancer-related
haematuria, she decided to seek help for the most
recent occurrence because the bleeding became increas-
ingly severe and persisted beyond 3 days. 6 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
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Downloaded from Open Access Open Access important barrier to participants’ seeking help from
their general practitioner (GP) and often facilitated
their decision to instead attend the ED. ED25 [patient]: the bleeding just got heavier and heavier
and heavier and went on for about four days and didn’t
abate at all—it just got worse. ED25 [patient]: the bleeding just got heavier and heavier
and heavier and went on for about four days and didn’t
abate at all—it just got worse. In another example, patient ED18, a woman with
metastatic breast cancer, described how she had been
managing with back pain for several days. However, it
was when the pain became so severe that is started to
restrict her movements that she decided she needed
help. ED08 [daughter]: Can’t get hold of dad’s GP of a
weekend. (Researcher: Okay) (ED07 [patient]: No) I
can’t get hold of my GP in XX [local area of patient] of
a weekend so erm (Researcher: Okay) it goes through to
XX [out of hours service]. ED08 [daughter]: Can’t get hold of dad’s GP of a
weekend. (Researcher: Okay) (ED07 [patient]: No) I
can’t get hold of my GP in XX [local area of patient] of
a weekend so erm (Researcher: Okay) it goes through to
XX [out of hours service]. Stage 3: decision to use the ED Once participants had decided to seek medical care,
their decision to use the ED was explored. Four con-
cepts emerged as key to this stage of decision-making:
(1) availability and ease of access; (2) hospital facilities
and environment; (3) trust and healthcare provider con-
tinuity; and, (4) ability to abdicate responsibility. Community palliative care services were often not
called as participants felt they would be unable to
help in an emergency situation. Instead community
palliative care services were described as being able
to help with non-urgent issues and help facilitate com-
munication between services such as their GP and
oncology. Stage 2: decision to seek medical care A few participants described contacting other health-
care services prior to attending the ED, in most cases
telephoning their oncology nurse specialist or commu-
nity palliative care team. When probed further about
these decisions only one participant described calling
because she hoped this would result in some action that
could help her avoid attending the ED. The remaining
participants reported other reasons for calling their
oncology team. One patient explained that he called his
oncology team as a courtesy; he had been advised to call
them
with
any
new
symptoms. Another
patient
explained how calling the oncology team sometimes
expedited the hospital’s triage process, stating: ED18 [patient]: So it’s like certain movements I couldn’t
even do. (Researcher: Okay) Yeah, it like just trapped me
there. Sanctioning by family and/or healthcare professionals
was also described. During one interview, patient ED12
explained how her family would encourage her to seek
medical care for symptoms that she felt she was coping
with. At times their insistence was so great it would lead
to her seeking medical care. ED12 [patient]: Well they put pressure on me and some-
times to shut them up [laughs], just to shut them up, I
would call the nurse, yes they [family]…they…they influ-
enced me to call the nurse then yeah. To keep them
[family] happy you know and to stop nagging me. ED22 [patient]: Yes and the advantage of phoning ahead
is they sort of expect you, and therefore you might get
through a stage quicker. Availability and ease of access doi:10.1136/bmjopen-2016-012134 group.bmj.com
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Downloaded from ED13: Never see GP. Don’t see the point. When it came to seeking help, these relationships
influenced participants’ decision-making, especially at
times of crisis when participants defaulted to services
they had previously used and felt safe with. In the major-
ity of cases this ended up being the hospital—only one
patient described having a more trusting relationship
with their GP than with the hospital. ED10 [patient]: …Because I know what’s going on. I
have a slight idea, I have the fear that this could be this,
because we’ve done a lot of research, (Researcher: Okay)
on how things work. And now I’m on a few forums as
well and so I know cases where—what other people have
experienced. Trust and healthcare provider continuity During interviews several participants spent time talking
about their relationship with the hospital, which often
began around the time of their cancer diagnosis. Participants described how over months, or even years,
of investigations and treatment, relationships with hos-
pital professionals had developed. For many this process
had led to them becoming familiar with the hospital
and their clinical team. Many held feelings of trust or
‘belief’ in the care being provided by the hospital. ED08 [daughter]: Erm, and what am I supposed to do if
that happens? I’m not qualified in anything other than
just sort of being able to hold him tight (Researcher:
Mmm) and cuddle him. Abdicate responsibility When participants decided to attend the ED many also
described acute feelings of being unable to cope or
manage at home. In comparison, patient ED04 reported instinctively
‘knowing’ that her symptoms required hospital care
despite not having any specific treatments or tests in
mind. She said: ED25 [patient]: Because my big fear was—would be that,
you know…a giant clot is gonna form and I’m gonna be
yelling and screaming in somebody’s house or restaurant
get me to hospital you know. ED25 [patient]: Because my big fear was—would be that,
you know…a giant clot is gonna form and I’m gonna be
yelling and screaming in somebody’s house or restaurant
get me to hospital you know. ED04 [patient]: Well because I knew he [GP] couldn’t
do anything about it but get me to…to the hospital
because of all that, and I knew. He wouldn’t—they
couldn’t have done anything, only getting the ambulance
and coming here. By seeking help from the hospital participants were
enabled—and in many cases expected—to abdicate
responsibility for their care to healthcare professionals. The carer of one patient explained how she brought her
father to the ED because she had run out of options to
care for him at home. Trust and healthcare provider continuity Open Access ED05: Yeah we believe—that’s the word mum we believe
in XX [hospital] don’t we? ED05: Yeah we believe—that’s the word mum we believe
in XX [hospital] don’t we? Availability and ease of access In only one case was advice from the patient’s GP
sought prior to them attending the ED. During this
interview, ED17, son of ED16, explained that since his
father’s cancer diagnosis his GP would always make
himself available, even if his schedule was full. Both the availability of healthcare services and their ease
of access were important to participants when deciding
where to seek help. Participants preferred services
where they could receive care quickly and with little
stress or inconvenience. Overly complicated systems
were bypassed for more straightforward options, for
example, patient ED01 described how he chose to
attend the ED over an alternative healthcare service
because access to the latter often involved multiple steps
and time. By comparison, once he arrived at hospital,
healthcare professionals would come to him and the
responsibility for identifying and accessing the ‘right’
care was organised for him. ED17 [son]: He’s even gave him an open appointment
that if we need to see him we will see him. If the…if the
reception says there’s not a…a…a space in the normal
appointment times, he makes time at the end of the
surgery. This level of GP support meant that both ED16 and
ED17 felt they would always seek advice from their GP
prior to seeking help elsewhere; ED16 explained that
although he thought his father needed to be in hospital
he still decided to contact his GP first. ED01 [patient]: …they would have to go through
someone else to go through someone else (Researcher:
Mmm) do you know what…I wouldn’t want anything like
that. Erm or I might as well just come to hospital in that
case (Researcher: Okay) because eventually I’ll be in a
safe place and they’ll come to me. ED17 [son]: He [GP] would come at the end of the
surgery……Although to us at the time he needed to be
in there [hospital]. (Researcher: Okay) But as I…as I say
it’s…it’s easier going through the GP. ED17 [son]: He [GP] would come at the end of the
surgery……Although to us at the time he needed to be
in there [hospital]. (Researcher: Okay) But as I…as I say
it’s…it’s easier going through the GP. Trouble
accessing
appointments,
especially
those
which
were
urgent
and/or
out-of-hours,
was
an 7 Henson LA, et al. BMJ Open 2016;6:e012134. Hospital facilities and environment Hospital facilities and environment When deciding where to seek help from, participants
tended to favour care delivered in a hospital over other
less acute or community settings. They described feeling
comforted by the frequent monitoring of their condition
and the presence of healthcare professionals. ED04: We believe in it—first words are don’t take me any-
where (ED05: Yes) but XX [hospital]. (Researcher:
Okay) That is true. ED04: We believe in it—first words are don’t take me any-
where (ED05: Yes) but XX [hospital]. (Researcher:
Okay) That is true. In contrast to the hospital relationships that had devel-
oped, most participants described rarely seeing their GP
during this time. Some stated explicitly that their GP
had little or no role in the management of their cancer. ED19: …Like in the hospitals when you go they give you
lots of attention, lots of treat—you are under their eyes,
they come and check you, monitoring you. Several participants also described how the hospital
provided facilities and equipment that they considered
essential for the management of their symptoms. Many
held strong beliefs about the type and level of care their
condition required, for example, intravenous antibiotics,
which appeared to originate from a combination of their
clinical knowledge, previous healthcare experiences and/
or an instinctive feeling regarding the treatment they
required. None of the participants interviewed identified
alternative settings where inpatient care could have been
accessed. Patient ED10 explained how his decision to call
999 was based on both his previous symptom experiences
as well as his knowledge of his cancer. Researcher: …do you tend to see your GP more now or
less now? How do you feel? Researcher: …do you tend to see your GP more now or
less now? How do you feel? ED13 [patient]: Never see him. ED14 [wife]: Yeah, very rarely. ED14 [wife]: Yeah, very rarely. DISCUSSION This qualitative study provides new findings that help
explain why and how people with advanced cancer
decide to seek ED care. We have identified individual’s
symptom interpretation, their prior patterns of health-
seeking behaviour, feelings of safety and familiarity with
the hospital setting and difficulties accessing community
healthcare services as important issues influencing the
decision-making process. This qualitative study provides new findings that help
explain why and how people with advanced cancer
decide to seek ED care. We have identified individual’s
symptom interpretation, their prior patterns of health-
seeking behaviour, feelings of safety and familiarity with
the hospital setting and difficulties accessing community
healthcare services as important issues influencing the
decision-making process. ED05 [daughter]: It’s…it’s nice to come to a place that
you’re not frightened of. (Researcher: Yeah) You know,
that makes you feel good. ED04 [patient]: That’s right you believe in you know,
you’ve got to believe in it. 8 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
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Downloaded from Open Access Open Access studies.19 Integrating interventions to reduce anxiety
and/or enhance coping to current end-of-life support ser-
vices may be one approach towards modifying patient’s
symptom perception/interpretation. Understanding these
decision-making mechanisms is important for clinical
practice, especially at a policy level where the findings
may be used to inform services delivery and/or interven-
tion development. We suggest that rather than developing
policies/interventions that target a particular ‘high-risk’
patient group, for example, ethnic minority patients or
those of lower socioeconomic status, educating patients
regarding end-of-life symptoms is likely to be more effect-
ive through addressing the issues of symptom interpret-
ation and/or levels of distress. Indeed targeting patients
identified as having greater levels of anxiety regarding
their symptoms may be more effective and not exclusive
to those with specific predisposing factors. Consistent with our study’s theoretical framework, par-
ticipants described a three-stage process of decision-
making. The influence from predisposing, enabling and
need-based factors, did however vary from the original
framework, as illustrated in figure 2. g
Need-based factors were identified as the most import-
ant influence on patients’ problem recognition (stage 1). In particular, patients’ anxiety relating to their underlying
cancer diagnosis significantly influenced their symptom
perception in terms of meaning and severity. CONCLUSIONS Drawing on Padgett and Brodsky’s modified version of
the ‘Behavioral Model of Health Services Use’, this study
provides new evidence for why and how patients with
advanced cancer decide to seek ED care. Issues influen-
cing
the
decision-making
process
included:
(1)
disease-related anxiety; (2) prior patterns of health-
seeking behaviour; (3) feelings of safety and familiarity
with the hospital setting; and, (4) difficulties accessing
community
healthcare
services—especially
urgently
and/or out-of-hours. These insights provide healthcare
professionals and policymakers with a greater under-
standing of how systems of care may be developed to
help reduce ED visits made by people with advanced
cancer. In particular, our findings suggest that the
number of ED visits could be reduced with greater
end-of-life symptom support and education, earlier col-
laboration between oncology and palliative care and
with increased access to community healthcare services. q
The availability of community healthcare services was
also important in patients’ decision-making, with several
participants describing having ‘no alternative’ to attend-
ing the ED. In a recently published qualitative critical
incident study of people with advanced respiratory
disease, Karasouli et al19 found that the decisions of par-
ticipants to seek emergency hospital care were rein-
forced in those who had experienced difficulty accessing
support from community services. While access remains
critical, we found that the structure of community ser-
vices also needs consideration. Our study highlighted
key features of the hospital environment described as
important to participants, for example, many felt reas-
sured by the presence of healthcare staff to whom they
were also able to abdicate responsibility. Community ser-
vices need to develop in a way that allows them to meet
such preferences as expansion of existing services alone
may not necessarily translate into reduced acute hospital
service use. Increasing the number of inpatient hospice
beds may be one possible solution. Acknowledgements The authors acknowledge the additional support received
from Marie Curie Cancer Care and the Collaboration for Leadership in Applied
Health Research and Care (CLAHRC) South London, National Institute for Health
Research (NIHR). The CLAHRC is a partnership between King’s Health Partners,
St. George’s, University London, and St George’s Healthcare NHS Trust. Contributors IJH and BAD participated in conception and design. LH was
involved in data collection and writing of the manuscript with critical revisions
by all other authors. LH, CE-S, JK and MM participated in data analysis and
interpretation. All authors approved the final version of the manuscript. Open Access lifetime. Despite advances in oncology care and treat-
ment, 50% of those diagnosed will ultimately die from
their disease.35 For these patients, the current model of
healthcare delivery is one where as their disease pro-
gresses they transition from receiving exclusively onco-
logical care—a predominantly hospital-based specialty, to
mostly
palliative
care—more
community-based.36
37
Implementing this model of transition is, however, chal-
lenging. Studies have found that many oncologists are
reluctant to refer their patients to palliative care which
some perceive as ‘an alternative philosophy of care
incompatible with cancer therapy’ (Schenker et al, 2014,
pp. e41).38
Furthermore,
inaccurate
prognostication
often leads to an overestimate of survival,39 meaning that
many transitions to palliative care are often initiated too
late in a patients’ illness or do not happen at all.40
During interviews we observed that patients’ health-
seeking behaviour tended to favour hospital-based care. This preference occurred in part as a result of the exten-
sive hospital contact patients had experienced earlier in
their illness, along with very limited GP and community
service engagement during this time. Patients require
time to become familiar with new services and for their
patterns of health-seeking behaviour to change. Studies
showing an association between earlier palliative care
referral and fewer ED visits at the end-of-life,41 42 as well
as those that show less aggressive end-of-life care with
greater community healthcare contact43 further support
these findings. If the time between palliative care referral
and patient death is insufficient, patients are likely to con-
tinue to use services they are familiar with, especially at
times of crisis. New models of healthcare delivery that
encourage earlier integration between oncology and pal-
liative care are required to address this issue. by the researcher’s personal biases and/or experience. We attempted to address this by using a maximum vari-
ation sampling strategy and performing dual coding for
a selection of interviews. Although member checking of
the interview transcripts and/or study findings could
have further enhanced the rigour of our results, this was
unable to be performed due to the rapid deterioration
of many of the participants. The setting (London) of our study is likely to have influ-
enced some of our findings. Compared to other more
rural settings patients in London have greater access to
acute hospital care. Community healthcare services are
also known to vary by region. Open Access Some of our study findings
may therefore not be applicable to people living in differ-
ent environments, especially those in more rural settings. p
y
g
We also only interviewed patients who had decided to
seek ED care meaning that the decision-making process
of those who used alternative services was not explored. Future research exploring whether the issues identified
remain relevant to patients who choose community ser-
vices would provide further insight and understanding
of this topic. Finally, it is important to acknowledge that for many
people acute hospital
care does not represent an
adverse event. In many situations the ED is the most
appropriate setting for urgent care needs to be investi-
gated and managed, and the importance of providing
individualised patient-centered care, including ED care
if needed, should not be overlooked. DISCUSSION While pre-
disposing factors, such as age, also influenced problem
recognition, this effect appeared to act through patients’
symptom perception/interpretation. For example, we
found older patients were less likely to interpret symptom
(s) as a sign of illness and therefore less likely to recog-
nise them as a problem. A number of previous studies
have identified variation in patients with cancers’ ED
attendance based on differing sociodemographic (predis-
posing) factors.16–18 Our findings, however, suggest that
rather than these factors per se influencing patients’ ED
use, it is the variation in symptom perception among
these groups that ultimately determines the overall differ-
ences seen. This mechanism of action is further sup-
ported by previous studies that have identified variation
in symptom perception by patient sociodemographics,
including differences found across social class33 and eth-
nicity.34 Addressing the anxiety and other psychological
sequelae commonly experienced by patients with cancer
is an important component of high-quality holistic care. Evidence that people experience an increasing sense of
vulnerability and/or lack of control prior to seeking
emergency hospital care has been reported in similar While there was strong evidence for the influence of
need-based factors on patients’ problem recognition
(stage 1), our study did not support enabling factors as
also being influential. These were however, important to
both subsequent stages of decision-making: decision to
seek help (stage 2); and, decision to use the ED (stage 3)
(figure 2). In healthcare research enabling factors are
arguably the most important to consider since they repre-
sent the group of variables most amenable to change. Understanding
how
this
group
influences
patients’
health-seeking behaviour can therefore provide policy-
makers with better evidence to develop and/or modify
existing healthcare structures to improve patient out-
comes. Presently, in the UK, one in every two people will
be diagnosed with some form of cancer during their Figure 2
Model of factors influencing advanced cancer patients’ emergency department use. Factors in bold indicate those with
evidence from current study, factors in italic indicate those identified from previous studies. Figure 2
Model of factors influencing advanced cancer patients’ emergency department use. Factors in bold indicate those with
evidence from current study, factors in italic indicate those identified from previous studies. 9 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
on November 25, 2016 - Published by
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on November 25, 2016 - Published by
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Downloaded from Open Access Limitations There are limitations to this study. As with all qualitative
research it is possible that our findings were influenced 10 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
on November 25, 2016 - Published by
http://bmjopen.bmj.com/
Downloaded from group.bmj.com
on November 25, 2016 - Published by
http://bmjopen.bmj.com/
Downloaded from Open Access Open Access Funding BuildCARE is supported by Cicely Saunders International (CSI) and
The Atlantic Philanthropies, led by King’s College London, Cicely Saunders
Institute, Department of Palliative Care, Policy and Rehabilitation, UK. CI:
Higginson. Grant leads: Higginson, McCrone, Normand, Lawlor, Meier,
Morrison. Project Co-ordinator/PI: Daveson. Study arm PIs: Pantilat, Selman,
Normand, Ryan, McQuillan, Morrison, Daveson. We thank all collaborators
and advisors including service-users. BuildCARE members: Emma Bennett,
Francesca Cooper, Barbara Daveson, Susanne de Wolf-Linder, Mendwas
Dzingina, Clare Ellis-Smith, Catherine J Evans, Taja Ferguson, Lesley A Henson,
Irene J Higginson, Bridget Johnston, Paramjote Kaler, Pauline Kane, Peter
Lawlor, Paul McCrone, Regina McQuillan, Diane Meier, Sean Morrison, Fliss E
Murtagh, Charles Normand, Caty Pannell, Steve Pantilat, Ana Reison, Karen
Ryan, Lucy Selman, Melinda Smith, Katy Tobin, Rowena Vohora, Wei Gao. Funding BuildCARE is supported by Cicely Saunders International (CSI) and
The Atlantic Philanthropies, led by King’s College London, Cicely Saunders
Institute, Department of Palliative Care, Policy and Rehabilitation, UK. CI:
Higginson. Grant leads: Higginson, McCrone, Normand, Lawlor, Meier,
Morrison. Project Co-ordinator/PI: Daveson. Study arm PIs: Pantilat, Selman,
Normand, Ryan, McQuillan, Morrison, Daveson. We thank all collaborators
and advisors including service-users. BuildCARE members: Emma Bennett,
Francesca Cooper, Barbara Daveson, Susanne de Wolf-Linder, Mendwas
Dzingina, Clare Ellis-Smith, Catherine J Evans, Taja Ferguson, Lesley A Henson,
Irene J Higginson, Bridget Johnston, Paramjote Kaler, Pauline Kane, Peter
Lawlor, Paul McCrone, Regina McQuillan, Diane Meier, Sean Morrison, Fliss E
Murtagh, Charles Normand, Caty Pannell, Steve Pantilat, Ana Reison, Karen
Ryan, Lucy Selman, Melinda Smith, Katy Tobin, Rowena Vohora, Wei Gao. 16. Tang ST, Wu SC, Hung YN, et al. Determinants of aggressive
end-of-life care for Taiwanese cancer decedents, 2001 to 2006. J Clin Oncol 2009;27:4613–18. 17. Miesfeldt S, Murray K, Lucas L, et al. Association of age, gender,
and race with intensity of end-of-life care for medicare beneficiaries
with cancer. J Palliat Med 2012;15:548–54. ;
18. Henson LA, Gao W, Higginson IJ, et al. Emergency department
attendance by patients with cancer in their last month of life: a
systematic review and meta-analysis. J Clin Oncol 2015;33:370–6. y
y
19. REFERENCES 1. Georghiou T, Davies S, Davies A, et al. Understanding patterns of
health and social care at the end of life. Secondary Understanding
patterns of health and social care at the end of life [pdf], 2012. http://
www.nuffieldtrust.org.uk/sites/files/nuffield/publication/121016_
understanding_patterns_of_health_and_social_care_at_the_end_of_
life_summary_final.pdf 28. Emergency Patients. Secondary Emergency Patients [online], 2016. https://www.kch.nhs.uk/patientsvisitors/patients/emergency-patients 29. Jordhøy MS, Kaasa S, Fayers P, et al. Challenges in palliative care
research; recruitment, attrition and compliance: experience from a
randomized controlled trial. Palliat Med 1999;13:299–310. 30. Coyne IT. Sampling in qualitative research. Purposeful and
theoretical sampling; merging or clear boundaries? J Adv Nurs
1997;26:623–30. 2. Emanuel EJ. Cost savings at the end of life. What do the data show? JAMA 1996;275:1907–14. 3. Chastek B, Harley C, Kallich J, et al. Health care costs for patients
with cancer at the end of life. J Oncol Pract 2012;8:75s–80s. 31. Given LM. The Sage encyclopedia of qualitative research methods. Los Angeles: SAGE, 2008. 4. Huang J, Boyd C, Tyldesley S, et al. Time spent in hospital in the
last six months of life in patients who died of cancer in Ontario. J Clin Oncol 2002;20:1584–92. g
32. Elo S, Kyngäs H. The qualitative content analysis process. J Adv
Nurs 2008;62:107–15. 33. Koos EL. The health of Regionville. What the people thought and
did about it. New York: Columbia University Press, 1954. 5. Wright AA, Zhang BH, Ray A, et al. Associations between end-of-life
discussions, patient mental health, medical care near death, and
caregiver bereavement adjustment. JAMA 2008;300:1665–73. y
34. Stoeckle JD, Zola IK, Davidson GE. On going to see the doctor, the
contributions of the patient to the decision to seek medical aid. A
selective review. J Chronic Dis 1963;16:975–89. 6. Wright AA, Keating NL, Balboni TA, et al. Place of death:
correlations with quality of life of patients with cancer and predictors
of bereaved caregivers’ mental health. J Clin Oncol 2010;28:4457–64. T
JM Cl
id
BR C
V
l F
il
i 35. Cancer mortality projections for all cancers combined. Secondary
Cancer mortality projections for all cancers combined [online]. 2012. http://www.cancerresearchuk.org/cancer-info/cancerstats/mortality/
mortality-projections/ 7. Teno JM, Clarridge BR, Casey V, et al. Family perspectives on
end-of-life care at the last place of care. JAMA 2004;291:88–93. p
8. Higginson IJ, Sen-Gupta GJ. Place of care in advanced cancer: a
qualitative systematic literature review of patient preferences. J Palliat Med 2000;3:287–300. y p
j
36. Ferris FD, Bruera E, Cherny N, et al. REFERENCES Palliative cancer care a decade
later: accomplishments, the need, next steps—from the American
Society of Clinical Oncology. J Clin Oncol 2009;27:3052–8. 9. Gomes B, Higginson IJ, Calanzani N, et al. Preferences for place of
death if faced with advanced cancer: a population survey in
England, Flanders, Germany, Italy, the Netherlands, Portugal and
Spain. Ann Oncol 2012;23:2006–15. y
gy
;
37. Meier DE. Increased access to palliative care and hospice services:
opportunities to improve value in health care. Milbank Q
2011;89:343–80. ;
38. Schenker Y, Crowley-Matoka M, Dohan D, et al. Oncologist factors
that influence referrals to subspecialty palliative care clinics. J Oncol
Pract 2014;10:e37–44. p
10. Steinhauser AE, Christakis NA, Clipp EC, et al. Factors considered
important at the end of life by patients, family, physicians, and other
care providers. JAMA 2000;284:2476–82. ;
39. Christakis NA, Lamont EB. Extent and determinants of error in
physicians’ prognoses in terminally ill patients: prospective cohort
study. West J Med 2000;172:310–13. 11. Heyland DK, Dodek P, Rocker G, et al., Canadian Researchers
End-of-Life Network (CARENET). What matters most in end-of-life
care: perceptions of seriously ill patients and their family members. CMAJ 2006;174:627–33. y
40. Cheng WW, Willey J, Palmer JL, et al. Interval between palliative
care referral and death among patients treated at a comprehensive
cancer center. J Palliat Med 2005;8:1025–32. 12. Voogt E, van der Heide A, Rietjens JA, et al. Attitudes of patients
with incurable cancer toward medical treatment in the last phase of
life. J Clin Oncol 2005;23:2012–19. 41. Nevadunsky NS, Gordon S, Spoozak L, et al. The role and timing of
palliative medicine consultation for women with gynecologic
malignancies: association with end of life interventions and direct
hospital costs. Gynecol Oncol 2014;132:3–7. 13. Ho TH, Barbera L, Saskin R, et al. Trends in the aggressiveness of
end-of-life cancer care in the universal health care system of
Ontario, Canada. J Clin Oncol 2011;29:1587–91. p
y
42. Temel JS, Greer JA, Muzikansky A, et al. Early palliative care for
patients with metastatic non-small-cell lung cancer. New Engl J Med
2010;363:733–42. 14. Earle CC, Neville BA, Landrum MB, et al. Trends in the
aggressiveness of cancer care near the end of life. J Clin Oncol
2004;22:315–21. 43. Henson LA, Gomes B, Koffman J, et al. Factors associated with
aggressive end of life cancer care. Support Care Cancer
2016;24:1079–89. 15. Hospital Episode Statistics. Accident and emergency attendances in
England—2012-13. Limitations Karasouli E, Munday D, Bailey C, et al. Qualitative critical incident study
of patients’ experiences leading to emergency hospital admission with
advanced respiratory illness. BMJ open 2016;6:e009030. p
y
p
20. Bailey C, Hewison A, Karasouli E, et al. Hospital care following
emergency admission: a critical incident case study of the
experiences of patients with advanced lung cancer and Chronic
Obstructive Pulmonary Disease. J Clin Nurs 2016;25:2168–79. Competing interests None declared. Competing interests None declared. y
21. Tong A, Sainsbury P, Craig J. Consolidated criteria for reporting
qualitative research (COREQ): a 32-item checklist for interviews and
focus groups. Int J Qual Health Care 2007;19:349–57. Ethics approval UK National Research Ethics Service Committee South
Central—Berkshire (REC reference 14/SC/1207). g
p
22. Andersen R, Newman JF. Societal and individual determinants of
medical care utilization in the United States. Milbank Mem Fund
Q Health Soc 1973;51:95–124. Provenance and peer review Not commissioned; externally peer reviewed. Provenance and peer review Not commissioned; externally peer reviewed. 23. Zola IK. Culture and symptoms—an analysis of patients’ presenting
complaints. Am Sociol Rev 1966;31:615–30. Data sharing statement No additional data are available. Data sharing statement No additional data are available. p
;
24. Mckinlay JB. Social networks, lay consultation and help-seeking
behavior. Soc Forces 1973;51:275–92. Open Access This is an Open Access article distributed in accordance with
the terms of the Creative Commons Attribution (CC BY 4.0) license, which
permits others to distribute, remix, adapt and build upon this work, for
commercial use, provided the original work is properly cited. See: http://
creativecommons.org/licenses/by/4.0/ 25. Mechanic D. Sociological dimensions of illness behavior. Soc Sci
Med 1995;41:1207–16. 26. Babitsch B, Gohl D, von Lengerke T. Re-revisiting Andersen’s
Behavioral Model of Health Services Use: a systematic review of
studies from 1998-2011. Psychosoc Med 2012;9:Doc11. y
27. Padgett DK, Brodsky B. Psychosocial factors influencing non-urgent
use of the emergency room: a review of the literature and
recommendations for research and improved service delivery. Soc
Sci Med 1992;35:1189–97. REFERENCES Health and Social Care Information Centre,
2014:1–34. 11 Henson LA, et al. BMJ Open 2016;6:e012134. doi:10.1136/bmjopen-2016-012134 group.bmj.com
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http://repository.essex.ac.uk/29858/1/Reconfigurable%20Filtering%20of%20Neuro-Spike%20Communications%20Using%20Synthetically%20Engineered%20Logic%20Circuits.pdf
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English
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Reconfigurable Filtering of Neuro-Spike Communications Using Synthetically Engineered Logic Circuits
|
Frontiers in computational neuroscience
| 2,020
|
cc-by
| 12,637
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Edited by:
Shaohui Wang,
Louisiana College, United States Reviewed by:
Daya Shankar Gupta,
Camden County College,
United States
Keke Wang,
Embry-Riddle Aeronautical University,
Prescott, United States *Correspondence:
Geoflly L. Adonias
gadonias@tssg.org Reconfigurable Filtering of
Neuro-Spike Communications Using
Synthetically Engineered Logic
Circuits Geoflly L. Adonias 1*, Harun Siljak 2, Michael Taynnan Barros 3,4, Nicola Marchetti 2,
Mark White 5 and Sasitharan Balasubramaniam 1 Geoflly L. Adonias 1*, Harun Siljak 2, Michael Taynnan Barros 3,4, Nicola Marchetti 2,
Mark White 5 and Sasitharan Balasubramaniam 1 1 Telecommunications Software & Systems Group, Waterford Institute of Technology, Waterford, Ireland, 2 CONNECT Centre,
Trinity College Dublin, Dublin, Ireland, 3 CBIG at Biomeditech, Faculty of Medicine and Health Technology, Tampere University,
Tampere, Finland, 4 School of Computer Science and Electronic Engineering, University of Essex, Colchester,
United Kingdom, 5 Research, Innovation & Graduate Studies, Waterford Institute of Technology, Waterford, Ireland High-frequency firing activity can be induced either naturally in a healthy brain as
a result of the processing of sensory stimuli or as an uncontrolled synchronous
activity characterizing epileptic seizures. As part of this work, we investigate how logic
circuits that are engineered in neurons can be used to design spike filters, attenuating
high-frequency activity in a neuronal network that can be used to minimize the effects of
neurodegenerative disorders such as epilepsy. We propose a reconfigurable filter design
built from small neuronal networks that behave as digital logic circuits. We developed
a mathematical framework to obtain a transfer function derived from a linearization
process of the Hodgkin-Huxley model. Our results suggest that individual gates working
as the output of the logic circuits can be used as a reconfigurable filtering technique. Also, as part of the analysis, the analytical model showed similar levels of attenuation
in the frequency domain when compared to computational simulations by fine-tuning
the synaptic weight. The proposed approach can potentially lead to precise and tunable
treatments for neurological conditions that are inspired by communication theory. ORIGINAL RESEARCH
published: 15 October 2020
doi: 10.3389/fncom.2020.556628 1. INTRODUCTION Seizure dynamics with either spontaneous and recurrent profiles can occur even in healthy patients
during the processing of sensory stimuli or it could manifest itself as an uncontrolled synchronous
neural activity in large areas of the brain (Jirsa et al., 2014). Any disruption to the mechanisms
that inhibit action potential initiation or the stimulation of processes that facilitate membrane
excitation, can prompt seizures. Tackling this disease efficiently is an existing clinical issue where
new approaches are constantly being investigated in order to provide precise and reliable strategies
in inhibiting or disrupting seizure-triggering populations of neurons. For example, controlling
neuron firing threshold can most likely prevent seizure activity, which can often be achieved at
a single neuron level (Scharfman, 2007). Received: 28 April 2020
Accepted: 28 August 2020
Published: 15 October 2020 Keywords: neuron, Hodgkin-Huxley, linear model, transfer function, systems theory, epilepsy, filter Citation: (2014) used identical neurons to propose dynamic logic gates that
work based on their historical activities, interconnection profiles,
as well as the frequency of stimulation at their input terminals. In
our previous works (Adonias et al., 2019; Adonias et al., 2020),
we developed several logic gates arranged in groups of three
heterogeneous models of neurons, with two working as inputs
and one as the output, and performed a queueing-theoretical
analysis aiming at the study of such a complex network as a single
element behaving as the collective of those cells. Irrespective
of the tremendous efforts from the scientific community, these
works do not provide a framework of reconfigurable circuits that
could pave the way for more sophisticated approaches for neuron
control. Further investigation of novel neuronal electronic
components constructions is needed to develop bio-compatible
and reliable solutions that can address defective neuronal
networks. While the scientific community has been witnessing
remarkable progress in the manipulation and engineering of the
behavior of mammalian cells (Lienert et al., 2014), the existing
models do not yield analytical expressions that could be used
to model drug-induced filtering capabilities of a neuron and,
in particular, incorporating computing paradigms. The main
focus of this work is to lay the ground-work of analytical
models for digital filters that are designed and engineered
into neurons, potentially leading to the development of novel
epilepsy treatments. Previous studies on the firing response of neurons have
investigated the filtering capabilities either due to realistic
synaptic dynamics (Brunel et al., 2001; Moreno-Bote and Parga,
2004) or by naturally manipulating the resting potential of
voltage-dependent active conductances of a neuron enhancing its
temporal filtering properties (Fortune and Rose, 1997; Motanis
et al., 2018). On the other hand, existing analyses do not account
for the many molecular control mechanisms that may influence
the synaptic activity, e.g., drug. In the case of seizures, the
understanding of the drug-induced firing response may allow
further analysis on the impact of high-frequency firing on
the neural tissue as well as how to desynchronize or slow it
down. Frequency-domain analysis has been performed on top
of linear models of the Hodgkin-Huxley (HH) formalism to
investigate not only the transmission of information through
the use of subthreshold electrical stimulation (Khodaei and
Pierobon, 2016) but also the influence of axonal demyelination
on the propagation of action potentials (Chaubey and Goodwin,
2016). Citation: Adonias GL, Siljak H, Barros MT,
Marchetti N, White M and
Balasubramaniam S (2020)
Reconfigurable Filtering of
Neuro-Spike Communications Using
Synthetically Engineered
Logic Circuits. The development of techniques for the treatment of this type of neurodegenerative disorder is
challenging not only due to the complexity of the brain function and structure but also as a result
of the invasiveness and discomfort caused by today’s most common neurostimulation or surgery
approaches (Rolston et al., 2012). However, due to the lack of success in non-invasive approaches, Front. Comput. Neurosci. 14:556628. doi: 10.3389/fncom.2020.556628 October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 1 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. the immediate future epilepsy treatment will still see invasive
methods. This approach must achieve population-level control
with state-of-the-art technology in not only neuroengineering
but must also integrate other disciplines. Recent advancements
in nanotechnology, for instance, have been enabling the
development of novel devices at the nano-scale that are capable of
improving bio-compatibility. Nanotechnology-based treatment
also includes advantages in the treatment precision, patient
comfort as well as longer treatment lifetime. However, there
still remain numerous challenges in the use of nanotechnology. For example, the passage of chemicals through the blood-brain
barrier (BBB) is among the many challenges that disrupt the
efficiency of nanoparticles-mediated drug delivery functioning. Challenges still remain as to how nanoparticles that pass
through the BBB will diffuse toward specific neural populations. However, if the drug-loaded nanoparticles can be delivered at
sufficient concentrations and accurately to a specific location,
this can influence neural activities (Bennewitz and Saltzman,
2009; Veleti´c et al., 2019). As an example, drug delivery
targets specific neurodegeneration promoting factors (Feng et al.,
2019) by performing a drug-induced control over intracellular,
extracellular and synaptic properties that regulate spiking
activity (Blier and De Montigny, 1987). The manipulation of cellular activity, such as neuronal
spiking activity, using molecules complexes to mimic logic gates
and transistors has also been proposed in the literature. One
example is the work of Vogels and Abbott (2005), in which the
propagation of neuronal signals in networks of integrate-and-fire
models of neurons was investigated and they found that different
types of logic gates may arise within the network by either
strengthening or weakening specific synapses. Goldental et al. Citation: Although Hodgkin-Huxley is not the only neuron model
available in the literature, it is one of the most plausible models
for computational neuroscience (Long and Fang, 2010). Other
proposed models are, for example, integrate-and-fire, Izhikevich
and Fitzhugh-Nagumo models (Mishra and Majhi, 2019). In this work, we propose a mathematical framework aiming
at the interpretation of the filtering capabilities in small
populations of neurons that are engineered into a logic circuit
(Figure 1). The circuit aims to reduce the firing rates from its
inputs by performing the binary logic as well as integrating
reconfigurability, where the different logic circuit arrangements,
as well as logic gate types, can be tuned to change the filtering
properties. To achieve that in our mathematical framework,
we modify parameters on the logic circuit transfer function,
derived from the linear interpretation of the Hodgkin-Huxley
neuronal model. These parameters are related to neuronal
and synaptic properties of a neuro-spike communication, such
as conductances and weight, and can potentially be achieved FIGURE 1 | Engineered neuronal digital logic circuit, where each gate is composed of three neurons and each block Wi(s) represents one neuron as a transfer
function to enable communication metric analysis. FIGURE 1 | Engineered neuronal digital logic circuit, where each gate is composed of three neurons and each block Wi(s) represents one neuron as a transfer
function to enable communication metric analysis. October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org Frontiers in Computational Neuroscience | www.frontiersin.org 2 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. through the sustained administration of a specific drug. Our
mathematical framework is, from an application point-of-view, a
design platform for neuroscientists in creating filtering solutions
for smoothing out the effects of neurological diseases that require
the minimization of firing activity. The framework models the
effects of drug-induced molecular changes in models of neurons
aiming to control the neuronal activity of a synthetic engineered
cell, however, the fabrication and specifications of such a drug are
out of the scope of this paper. The contributions of this paper are
as follows: We aim to investigate the neuronal and synaptic properties
in constructing logic circuits that perform the filtering of spikes
in small populations from the somatosensory cortex. The cortex
is responsible for most of the signal processing performed by
the brain and comprises a rich variety of morpho-electrical types
of neuronal and non-neuronal cells. 2.1.1.1. Morpho-electrical characteristics
E
th
h ll
d i
thi
k 2.1.1.1. Morpho-electrical characteristics
Even though all neurons used in this work can assume different
morphological structure, it is exactly by analyzing their axonal
and dendritic ramification that we can have a good enough
categorization of their respective morphological types. Regardless
of their types, neurons in the cortical layer are considered of small
sizes (8 - 16 µm). Furthermore, inhibitory neurons can be better
identified by their axonal features while excitatory neurons can be
more easily classified based on their dendritic features (Markram
et al., 2015). Each morphological type (m-type) can fire different
spiking patterns and this may affect the gating capabilities of
neurons due to the fluctuations on precise spike timing. Markram
et al. (2015) categorized 11 different electrical types (e-types) of
neurons, hence, 11 different ways of firing a spike train generated
in response to an injected step current. Citation: We will take into account
these characteristics in the construction of our mathematical
framework that is used to design the circuits. 2.1. Neuronal Communication To be able to synthetically implement complex functions
inside the brain, we must control how the neurons exchange
information using the propagation of action potentials inside a
network of neurons. The number of excitatory and inhibitory
connections between neurons determines the spatio-temporal
dynamics of the action potentials propagation (Zhou et al.,
2018). Efficient coding and modulation of neuronal information
have been used to implement bio-computational approaches
in our previous work (Adonias et al., 2020). Bio-computing
can be created from neuronal networks that are engineered to
function as logic circuits through controlling the neuro-spike
communication and curbing the signal propagation dynamics
between the neurons. 2.1.1. Properties of a Neuron Neurons are divided into three main parts: dendrites, soma, and
axon. Dendrites receive stimuli from other cells and the way
these dendritic trees are projected onto neighboring neurons in
a network helps to classify neuron morphological types. The
axon passes stimuli forward to cells connected down the network
through its axon terminals and the soma is the main body of
the neuron. Each neuron’s response to a stimulus will dictate
the electrophysiological neuron type. The soma is where most
proteins and genes are produced and where stimuli are generated
and fired down the axon. • Neuronal logic circuits are built using computational models
of neurons and this arrangement is expected to be capable
of acting as digital filters, converging four inputs into one
output with a shift in attenuation driven by modifications to
the synaptic weight. • Neuronal logic circuits are built using computational models
of neurons and this arrangement is expected to be capable
of acting as digital filters, converging four inputs into one
output with a shift in attenuation driven by modifications to
the synaptic weight. • Neuronal logic circuits are built using computational models
of neurons and this arrangement is expected to be capable
of acting as digital filters, converging four inputs into one
output with a shift in attenuation driven by modifications to
the synaptic weight. • A mathematical framework is proposed paving the way
for the design of neuronal digital filters to help suppress
the destructive effects of neurodegenerative diseases. This
framework should enable the relationship between biophysical
models and drug design, facilitating scientists control over the
behavior of the filters. Besides the way dendrites are projected, the proteins
and genes that neurons express and their morphological
and electrophysiological characteristics are important for the
classification of different types of neurons. One of the most
comprehensive works on neuronal modeling, by Markram et al. (2015), classifies the neurons from the rat’s somatosensory cortex
based on their morpho-electrical properties (morphological and
electrical characteristics) as well as the cortical layer they belong
(columnar and laminar organization). • Analysis of the performance of the neuronal filters in terms
of accuracy and of signal power attenuated by the circuit. This
analysis gives an insight into how parameters such as weight
or frequency at the input would affect the performance of
such filters. The remainder of this paper is as follows, section 2.1 briefly
describes how neurons differ between each other and how they
communicate with one another. In section 2.2, we explain how
neurons can function as non-linear electronic circuits based
on the seminal work of Hodgkin and Huxley (1952) and we
also describe the process of linearization aiming to derive
a transfer function of the filter model. The filter design is
explained in section 2.3 which also covers how neurons are
represented as compartments and connected to form logic gates
and, consequently, to form logic circuits. In section 3, we present
the results that are discussed in section 4 and, finally, the
conclusions are presented in section 5. 2.1.1.2. Cortical organization
Th
b
l The cerebral cortex comprises six distinguished horizontal layers
of neurons, with each layer having particular characteristics such
as cell density and type, layer size, and thickness. This horizontal
configuration is also known as a “laminar” organization, where
the layers are identified as (1) Molecular layer, which contains
only a few scattered neurons and consists mostly of glial cells
and axonal and dendritic connections of neurons from other
layers; (2) External granular layer, containing several stellate
and small pyramidal neurons; (3) Pyramidal layer, contains
non-pyramidal and pyramidal cells of small and medium sizes; October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 3 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. e.g., connection probabilities between neurons, that influence
the signal propagation to converge into either a specific pattern
or flow. (4) Inner granular layer, predominantly populated with stellate
and pyramidal cells, this is the target of thalamic inputs; (5)
Ganglionic layer, containing large pyramidal cells that establish
connections with subcortical structures; and (6) Multiform layer,
populated by just a few large pyramidal neurons and a good
amount of multiform neurons, which sends information back to
the thalamus. All layers may contain inter-neurons bridging two
different brain regions. 2.1.2. Neuron-to-Neuron Communication 2.1.2. Neuron-to-Neuron Communication
The communication between a pair of neurons is done
through the diffusion of neurotransmitters in the synaptic
cleft; this process is triggered by an electrical impulse reaching
the axon terminals of the transmitting cell characterizing
an electrochemical signaling process known as the synapse. Action potentials propagate down the axon of the pre-synaptic
cell, which is the sender cell, and when reaching the axon
terminals also known as pre-synaptic terminals, it triggers the
release of vesicles containing neurotransmitters into the synaptic
cleft, which is the gap between a pre- and a post-synaptic
terminal, as illustrated in Figure 2. Those neurotransmitters The neurons are not just stacked one on top of another
suggesting a horizontal organization, indeed vertical connections
are also found in between the neurons from either the same or
different layers. This allows another type of classification known
as mini-columns (also called, micro-columns) with a diameter of
30–50 µm and when activated by peripheral stimuli, they are seen
as macro-columns, with a diameter of 0.4–0.5 mm (Peters, 2010). This will create network topologies with intrinsic characteristics, FIGURE 2 | Schematic of a synapse; action potentials traveling down the axon trigger the release of neurotransmitters into the cleft between pre- and post-synaptic
terminals, traveling toward neuroreceptors on the other end leading to changes on membrane conductance that can either excite or inhibit the post-synaptic neuron. FIGURE 2 | Schematic of a synapse; action potentials traveling down the axon trigger the release of neurotransmitters into the cleft between pre- and post-synaptic
terminals, traveling toward neuroreceptors on the other end leading to changes on membrane conductance that can either excite or inhibit the post-synaptic neuron. Frontiers in Computational Neuroscience | www.frontiersin.org Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 4 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. will probabilistically bind to neuro-receptors located at the
post-synaptic terminals, i.e., dendrites (Balevi and Akan, 2013),
triggering the exchange of ions through the membrane that
can either excite or inhibit the cell, depending on the type of
neurotransmitters that were received. In our work, we focus
on the synaptic weight between the pre- and post-synaptic
terminals. The synaptic weight is a measure of how much
influence the pre-synaptic stimuli have on the post-synaptic
cell and it is known to have its value best approximated to
the time integral of the synaptic conductance (Gardner, 1989). 2.1.2. Neuron-to-Neuron Communication Furthermore, the value of synaptic conductance in the post-
synaptic terminal is driven by the number of neurotransmitters
bound to neuroreceptors (Guillamon et al., 2006). We illustrate
the synaptic weight, in Figure 2, as red neurotransmitters which
should have their release from the pre-synaptic terminals induced
by the administration of a specific drug. that play an important role in determining its input and output
relationship. By sectioning the neuron into several compartment
models, we are able to account for the influence that individual
compartments have on the communication process of the
neuron. Even though we consider the same value of resting
potential for all compartments of the cell, there is some
discussion on whether different compartments have different
potentials when at rest (Hu and Bean, 2018). We aim to develop a transfer function for the neuron-
spike response, or output [V(s)], to a particular spike input
[I(s)]. Using a transfer function for each neuron which is
represented as a single compartment, we are able to efficiently
associate the configuration of the filters with the structure of
the neural network as well as the individual characteristics
of each neuron. On top of that, we also are able to focus
on frequency domain for an effective spike firing filtering. We rely on the electronic interpretation of the Hodgkin-
Huxley model of neuron action potentials, which is made
based on the neuronal cable theory assumptions on the static
ionic channels conductance. In this section, we provide the
details of the development of the transfer function, which
is built on the linearization process of the Hodgkin-Huxley
neuron model. In an excitatory synapse, the membrane potential of the
post-synaptic cell, which rests at approximately −65 mV, will
start depolarizing itself until it reaches a threshold, th, for
action potential initiation. On the other hand, if the synapse
is inhibitory, the membrane should get even more polarized
making it nearly impossible for the cell to fire a spike and not
allowing the propagation of any signal down the network from
the inhibited cell. After reaching th, the membrane potential
should increase toward a maximum peak of depolarization, and
then the cell will start the process of repolarization toward
its resting potential. 2.2.1. Hodgkin-Huxley Formalism
A
f
i
d i
i
1 2.2.1. Hodgkin-Huxley Formalism
As aforementioned in section 1, neurons can perform spike
filtering tasks either by manipulating ionic conductances,
such as sodium and potassium conductances, from within
the cell (Fortune and Rose, 1997) or by working on the
extracellular environment where the synapse occurs (Brunel
et al., 2001; Moreno-Bote and Parga, 2004). Furthermore, filtering
capabilities may vary according to the non-linearities of the
neuron’s activity and action potential propagation. In order to
design an efficient filtering process, we will need to eliminate
the non-linearities so we can directly link neurons properties to
the filtering behavior and adjust these properties according to
a desired filtering performance level. We consider the Hodgkin
and Huxley non-linear model (Pospischil et al., 2008) as our
basic model since it perfectly describes the influence of ionic
conductance and synaptic conductance in the propagation of
the action potentials. We assume that parts of the neuron
will constitute a compartment, which results in the electric 2.1.2. Neuron-to-Neuron Communication For a brief moment, the potential inside
the cell will cross the level of potential when at rest making
the membrane hyperpolarized, which is a period known as the
refractory period and it can be further subdivided as absolute and
relative. The absolute refractory period (ARP) lasts around 1–
2 ms during which the neuron is unable to fire again regardless
of the strength of the stimuli; then, it is followed by the relative
refractory period (RRP) during which a response in the potential
of the cell may be evoked depending on the strength of the
stimuli (Mishra and Majhi, 2019). 2.2.2. Hodgkin-Huxley Linear Model In order to derive a transfer function for the Hodgkin-Huxley
model, we must consider each neuron as a system that is
linear and time-invariant (LTI). If the system is non-linear, then
a linearization process should be done before any frequency
analysis is performed. For a more detailed analysis on the
procedures for linearization of the Hodgkin-Huxley model, the
reader is referred to Koch (2004), Mauro et al. (1970), Sabah and
Leibovic (1969), and Chandler et al. (1962). When an external stimulus, Iext, is presented, it triggers
either the activation or inactivation of the ionic channels that
allow the exchange of ions that result in depolarization (or
hyperpolarization when inhibitory) of the membrane of the cell. These dynamics are modeled as The
linearization
process
requires
that
we
reconsider
the electronic components in each neuron compartment to
adequately eliminate trivial relationships. Membranes with
specific types of voltage- and time-dependent conductances can
behave as if they had inductances even though neurobiology
does not possess any coil-like elements. This modification
will transform the behavior of non-linear components toward
linearization, resulting in a proportional relationship between the
voltage and current changes (Koch, 2004). CdV
dt = −Il −INa −IK + Iext,
(1) (1) where V is the membrane potential and Ix are the ionic currents
where x represents either a specific ion (Na, K) or the leak channel
(l). Those currents are described as Il = gl(V −El),
(2)
INa = gNam3h(V −ENa),
(3)
IK = gKn4(V −EK),
(4) Il = gl(V −El),
(2)
INa = gNam3h(V −ENa),
(3)
IK = gKn4(V −EK),
(4) (2) Every linearization process is performed for small variations
around a fixed point, hereafter denominated by δ, and in the
case of the Hodgkin-Huxley model, this fixed point should
be the steady-state (resting state) of the system. Because the
sodium activation generates a current component that flows in
an opposite direction compared to that of a passive current,
the branch concerning the sodium activation should have
components with negative values while the branches regarding
potassium activation and sodium inactivation should have
components with positive values (Sabah and Leibovic, 1969). 2.2. Electronic Interpretation of a Neuron
Model The main structures of a neuron, previously mentioned in
section 2.1.1, can assume different shapes and spatial structures FIGURE 3 | Hodgkin-Huxley (HH) model: (A) Electronic circuit representation and (B) Equivalent biological HH compartment; the lipid bilayer is modeled as C, the
conductances g represent how open or close the ionic gates are and the gradient of ions between the intra- and extra-cellular space define the reversal potentials E. FIGURE 3 | Hodgkin-Huxley (HH) model: (A) Electronic circuit representation and (B) Equivalent biological HH compartment; the lipid bilayer is modeled as C, the
conductances g represent how open or close the ionic gates are and the gradient of ions between the intra- and extra-cellular space define the reversal potentials E. Frontiers in Computational Neuroscience | www.frontiersin.org Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 5 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. circuit in Figure 3A when applying the conventional neural
cable theory. ionic channel can be studied as containing one or more physical
gates which can assume either a permissive or a non-permissive
state when controlling the flow of ions. The channel is open when
all gates are in the permissive state, and it is closed when all of
them are in the non-permissive state (Baxter and Byrne, 2014). Figure 3 depicts C as the membrane capacitance, each voltage-
gated ionic channel represented by its respective conductances
gNa and gK and the leak channel by the linear conductance
gl. The membrane capacitance is proportional to the surface
area of the neuron and, along with its resistance, dictates how
fast its potential responds to the ionic flow. The ratio between
intra- and extra-cellular ions define the reversal potentials ENa, K, l
establishing a gradient that will drive the flow of ions (Barreto and
Cressman, 2011). 2.2.2. Hodgkin-Huxley Linear Model gn =
4¯gKn3
∞(V −EK)
dαn
dV
r
−n∞
d(αn + βn)
dV
r
αn + βn
,
(27)
Ln =
1
gn(αn + βn),
(28)
gm =
3¯gNam2
∞h∞(V −ENa)
dαm
dV
r
−m∞
d(αm + βm)
dV
r
αm + βm
,
(29)
Lm =
1
gm(αm + βm),
(30)
gh =
¯gNam3
∞(V −ENa)
dαh
dV
r
−h∞
d(αh + βh)
dV
r
αh + βh
,
(31)
Lh =
1
gh(αh + βh). (32) gn =
4¯gKn3
∞(V −EK)
dαn
dV
r
−n∞
d(αn + βn)
dV
r
αn + βn
,
(27)
Ln =
1
gn(αn + βn),
(28)
gm =
3¯gNam2
∞h∞(V −ENa)
dαm
dV
r
−m∞
d(αm + βm)
dV
r
αm + βm
,
(29)
Lm =
1
gm(αm + βm),
(30)
gh =
¯gNam3
∞(V −ENa)
dαh
dV
r
−h∞
d(αh + βh)
dV
r
αh + βh
,
(31)
Lh =
1
gh(αh + βh). (32) Let us consider the membrane potential deviation, δV, around
some fixed potential. Thus, we can express the response of the
circuit to small-signal inputs as (27) (28) CdδV
dt
= Iext −δIl −δIK −δINa,
(14) (14) where δIl,Na,K are current variations at any given steady-state and
can be defined as δIl = glδV,
(15)
δIK = GKδV + 4gKn3
∞(V −EK)δn,
(16)
δINa = GNaδV + 3gNam2
∞h∞(V −ENa)δm
+ gNam3
∞(V −ENa)δh,
(17) (17) (32) where GK,Na are pure conductances of potassium and sodium and
GL the pure leak conductance expressed as Each channel has a probability of being open which represents
the fraction of gates in that channel that are in the permissive
state (Gerstner et al., 2014). The gating variables are described
by the coupling of the conductances gn,m,h and their respective
inductances Ln,m,h which are functions of the rate constants
representing the transition from permissive to non-permissive
state, α(V), and vice-versa, β(V) which should take a short period
of time, τ = [α(V) + β(V)]−1, to eventually reach a steady-state
value, α∞and β∞(Koslow and Subramaniam, 2005). Each channel has a probability of being open which represents
the fraction of gates in that channel that are in the permissive
state (Gerstner et al., 2014). 2.2.2. Hodgkin-Huxley Linear Model The
linear version of the circuit of Figure 3A is illustrated in Figure 4,
where C is the membrane capacitance, gn, gm, and gh are the
conductances of the inductive branches connected in series with (4) where m and h are the activation and inactivation variables of
the sodium channel, respectively, and n is the activation variable
of the potassium channel, following the conventional approach
described by Hodgkin and Huxley (1952) and stated as dm
dt = αm(V)(1 −m) −βm(V)m,
(5)
dh
dt = αh(V)(1 −h) −βh(V)h,
(6)
dn
dt = αn(V)(1 −n) −βn(V)n,
(7) (5) (6) (7) FIGURE 4 | Hodgkin-Huxley linear circuit model representation. in which the values of the rate constants αi and βi for the i-th
ionic channel can be defined as αm =
0.1(V + 40)
1 + e−(V+40)/10 ,
(8)
βm = 4e−(V+65)/20,
(9)
αh = 0.07e−(V+65)/20,
(10)
βh =
1
1 + e−(V+35)/10 ,
(11)
αn =
0.01(V + 55)
1 −e−(V+55)/10 ,
(12)
βn = 0.125e−(V+65)/80. (13) (8) (13) The membrane capacitance is proportional to the size of the cell,
and on the other hand, the bigger the cell diameter, the lower the
spontaneous firing rate (Sengupta et al., 2013). Furthermore, each The membrane capacitance is proportional to the size of the cell,
and on the other hand, the bigger the cell diameter, the lower the
spontaneous firing rate (Sengupta et al., 2013). Furthermore, each FIGURE 4 | Hodgkin-Huxley linear circuit model representation. Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 6 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. and the conductances, gn,m,h, and inductances, Ln,m,h, of the
inductive branches are defined as and the conductances, gn,m,h, and inductances, Ln,m,h, of the
inductive branches are defined as their respective inductances Ln, Lm, and Lh derived from the
linearization process and GT = GL + GK + GNa is the total pure
membrane conductance. their respective inductances Ln, Lm, and Lh derived from the
linearization process and GT = GL + GK + GNa is the total pure
membrane conductance. 2.2.2. Hodgkin-Huxley Linear Model The gating variables are described
by the coupling of the conductances gn,m,h and their respective
inductances Ln,m,h which are functions of the rate constants
representing the transition from permissive to non-permissive
state, α(V), and vice-versa, β(V) which should take a short period
of time, τ = [α(V) + β(V)]−1, to eventually reach a steady-state
value, α∞and β∞(Koslow and Subramaniam, 2005). GL = ¯gl,
(18)
GK = ¯gKn4
∞,
(19)
GNa = ¯gNam3
∞h∞,
(20) (20) where ¯gK,Na are the maximum attainable conductances, and δn,
δm, and δh are small variations around the steady-state of the
activation and inactivation variables n, m, and h which are written
as where ¯gK,Na are the maximum attainable conductances, and δn,
δm, and δh are small variations around the steady-state of the
activation and inactivation variables n, m, and h which are written
as Borrowing concepts from systems theory such as frequency
analysis of LTI systems, as a standard procedure for the analysis
of linear differential equations as simpler algebraic expressions
(see Nise, 2015), and the linearization of non-linear systems
for the reason previously mentioned at the beginning of this
section, we derived a transfer function in the Laplace domain for
the linear system from Figure 4. The relationship between the
different elements of the circuit and their respective impedance
and admittance values from the Laplace transforms are depicted
in Table 1. as as dδn
dt = dαn
dV δV −(αn + βn)δV −n∞
dαn
dt −dβn
dt
δV,
(21)
dδm
dt
= dαm
dV δV −(αm + βm)δV −m∞
dαm
dt
−dβm
dt
δV,
(22)
dδh
dt = dαh
dV δV −(αh + βh)δV −h∞
dαh
dt −dβh
dt
δV,
(23) (21) (21) Therefore, the relationship between the output and the
input of the system in the frequency domain is expressed as as a function of the derivative of the rate constants αn,m,h and
βn,m,h, and n∞, m∞, and h∞are the steady-state values of m, n,
and h defined as
n∞=
αn
αn + βn
,
(24)
m∞=
αm
αm + βm
,
(25)
h∞=
αh
αh + βh
,
(26)
TABLE 1 | Impedance relationships for capacitors, resistors, and inductors. October 2020 | Volume 14 | Article 556628 2.2.2. Hodgkin-Huxley Linear Model where s = σ + jω is a complex variable; j = √−1 and ω = 2πf ,
where f is the frequency in Hertz. Let us rewrite Equation (33) as W(s) = C−1
s
s2 + sC−1(GT + gn + gm + gh) + C−1(L−1
m + L−1
n
+ L−1
h )
. (34) Now, denoting γ = GT+gn+gm+gh and λ−1 = L−1
n +L−1
m +L−1
h
and performing a few algebraic manipulations, we end up with
the following transfer function for the filter model Now, denoting γ = GT+gn+gm+gh and λ−1 = L−1
n +L−1
m +L−1
h
and performing a few algebraic manipulations, we end up with
the following transfer function for the filter model W(s) = γ −1
C−1γ s
s2 + C−1γ s + λ−1C−1 . (35) (35) For frequency response analysis, we observe the behavior of
W(jω), i.e., substitute s = jω. For ω →0, W(jω) behaves
like ω; for ω →∞it behaves like
1
ω+1, i.e., in both cases it
tends to zero, and hence demonstrates the behavior of a second-
order band-pass filter (BPF). It corresponds to the canonical form
K(ω0/Q)s
s2+(ω0/Q)s+ω2
0 where K = γ −1 is the gain, Q = γ −1√
Cλ−1 is
the selectivity and ω0 =
√
λ−1C−1 is the peak frequency of the
filter. This agrees with findings from previous literature on the
matter (Plesser and Geisel, 1999) that concluded the periodicity
of a stimulus is optimally encoded by a neuron only in a specific
spectral window. Given that several factors such as connection probability,
type of cell, and different numbers of compartments (as
discussed in section 2.3.2) among different types of neurons may
influence its gating capabilities. This variation on the quantity of
compartments could also lead to variations on periods for the
action potential to reach the post-synaptic terminals and start
the synapse process. Furthermore, cells with bigger sizes of soma
may take more time and amount of stimuli to reach threshold
for action potential initiation (Sengupta et al., 2013), thus, also 2.3. Transfer Function Filter Design Given the transfer function for a neural compartment in the
previous section, we now progress toward a transfer function
for the spike filter. The filter is comprised of neurons that are
particularly chosen to have a network that will behave as a digital
gate and a small population that will behave as a circuit that
implements the filter. Our aim is to capture the relationship
between compartments as well as neuron connections so we
can build a transfer function for the filter while considering
neuron connection variables (synaptic conductance and synaptic
weight) that allow easy reconfiguration of the filtering process. The linearization process combined with the analysis of the
neuron communications is the driver of the filtering process,
which also allows the derivation of a filter transfer function which
is detailed below. FIGURE 5 | (A) Schematic of circuits A, B, and C and (B) The connection of
AND gates in cascade to circuit A. A1 refers to the arrangement described by
a single AND gate connected to the output of the circuit A and A2 refers to
another AND gate connected to the output of A1 arrangement, i.e., two AND
gates in cascade with circuit A. Analogous nomenclature is employed for both
circuits B, as in B1/B2 and C, as in C1/C2. 2.2.2. Hodgkin-Huxley Linear Model Component
Impedance
Admittance
Capacitor
1
Cs
Cs
Resistor
R
G = 1
R
Inductor
Ls
1
Ls
Frontiers in Computational Neuroscience | www.frontiersin.org
7
October 2020 | Volume 14 | Article 556628 TABLE 1 | Impedance relationships for capacitors, resistors, and inductors. as a function of the derivative of the rate constants αn,m,h and
βn,m,h, and n∞, m∞, and h∞are the steady-state values of m, n,
and h defined as Frontiers in Computational Neuroscience | www.frontiersin.org
7
October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org
7
October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. Figure 5A shows the three types of the circuit we have built
and analyzed in this work. From circuits A to C, the number
of OR gates is decreased; when compared to AND gates, OR
gates are quite permissive. In our previous study (Adonias et al.,
2020), we present an analysis on how signals from two input
neurons will need to be close to each other to amplify the action
potential of the output neuron in order to achieve maximum
AND-gating accuracy. The transformation from a purely OR-
formed logic circuit to a purely AND-formed one leads to the
confirmation of what the truth-tables suggest, i.e., fewer states
evoke spikes in the output and, consequently, the attenuation of
higher frequencies in the inputs. Figure 5B shows the connection
of AND gates in cascade, and this analysis is further discussed
in the section 4. Each of the circuits was analyzed with one
and two AND’s in cascade, hence the nomenclature of a letter
followed by a number, the letter refers to the type of circuit and
the number accounts for how many AND gates are connected
in cascade. Only two types of logic gates were used to build
the circuits, an AND composed of the cells L23-MC (Layer 2/3
Martinotti Cell), L23-NBC (Layer 2/3 Nest Basket Cell), and L1-
HAC (Layer 1 Horizontal Axon Cell); and an OR composed of
the cells L23-MC, L23-NBC, and L1-DAC (Layer 1 Descending
Axon Cell). These cells were picked because they showed the
best performance in our previous analysis on their individual
gating capabilities. 2.3.2. Compartmental Modeling
l 2.3.2. Compartmental Modeling
Neurons
are
very
complex
structures
with
numerous
ramifications and several factors that contribute to their highly
non-linear dynamism. Aiming to make the comprehension
of such a complex electrical behavior easier, one employs a
widely used technique called “compartmental modeling.” Since
different neurons have different morphologies, the mechanism
of determining the number of compartments will be based
on estimating the length of a specific neuronal structure. For
instance, a varying length of axon, which will reflect in different
quantities of compartment in series, where we will have a fixed
size for each segment of the axon representing one compartment. This is a very natural and elegant way to model dynamic
systems as multiple interconnected compartments where each
compartment is described by its own set of equations, carrying
the influence of one compartment to the next reproducing the
behavior of the whole neuron. Wi(s) = ζiγ −1
i
C−1
i
γis
s2 + C−1
i
γis + λ−1
i
C−1
i
, i = 1, . . . , 9
(36) Wi(s) = ζiγ −1
i
C−1
i
γis
s2 + C−1
i
γis + λ−1
i
C−1
i
, i = 1, . . . , 9
(36) (36) with symbols defined previously, and a new parameter ζi
describing the synaptic weight for the ith cell; ζi acts as a tunable
gain for the neurons. Using the parameters from (Mauro et al., 1970) aiming to
keep them within the physically sensible orders of magnitude,
we obtain the reference values of ¯γ = 0.0024, ¯λ = 119, ¯C = 1
and ¯ζ = 1, and the values for 9 cells were generated multiplying
these reference values by a uniformly distributed random variable
in the range (0, 1). This kind of distribution is widely used to
describe experiments where an arbitrary result should lie between
certain boundaries, and in our case boundaries are defined by
reasonable orders of magnitude around values made available by
previous studies; keeping exactly the same parameters for all cells
in the cascade is not realistic. 2.3.1. Biological Logic Gates and Circuits Synthetic biology is the technology that allows the control of
the neurons’ internal process in order to construct non-natural
activity and functioning of neurons, e.g., logic gates (Larouche
and Aguilar, 2018). Synthetic logic operations inspire scientists
to address the challenges posed by novel synthetic biomedical
systems, such as biocompatibility and long-term use. FIGURE 5 | (A) Schematic of circuits A, B, and C and (B) The connection of
AND gates in cascade to circuit A. A1 refers to the arrangement described by
a single AND gate connected to the output of the circuit A and A2 refers to
another AND gate connected to the output of A1 arrangement, i.e., two AND
gates in cascade with circuit A. Analogous nomenclature is employed for both
circuits B, as in B1/B2 and C, as in C1/C2. FIGURE 5 | (A) Schematic of circuits A, B, and C and (B) The connection of
AND gates in cascade to circuit A. A1 refers to the arrangement described by
a single AND gate connected to the output of the circuit A and A2 refers to
another AND gate connected to the output of A1 arrangement, i.e., two AND
gates in cascade with circuit A. Analogous nomenclature is employed for both
circuits B, as in B1/B2 and C, as in C1/C2. Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 8 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. affecting the way a neuronal logic gate would work regarding
a specific morphological neuronal type. For that reason, it is
safe to keep two cells fixed as inputs (as illustrated in Figure 1)
and then deploy an arrangement with which its performance
has been previously assessed, allowing us to be fairly certain
about how the synthetic gate or circuit should behave. Each
neuron is represented by a block, Wi(s) for the i-th neuron,
and its representation in the frequency domain is proposed in
Equation (35) and further detailed in section 2.3.2. frequency domain: two bandpass filters in series pass only the
frequencies that exist in both of their passbands. On the other
hand, a parallel connection has a set-union effect, a parallel
connection of filters will pass all the frequencies in both their
passbands. 2.3.1. Biological Logic Gates and Circuits As such, a large network (tree) of such compartments
with similar bands combined in a cell, and cells combined in a
group of cells will exhibit asymptotic bandpass behavior as well. Every single compartment, each represented by one transfer
function, is grouped in trees of three cells (Figure 1) forming a
logic gate; the three gates are connected into a tree of their own,
as illustrated in Figure 5A, forming a logic circuit. All of the cells
are represented with the same form of the transfer function, 2.3.2. Compartmental Modeling
l The total transfer function of this
system is Observing the neuron as a set of compartments described
by transfer functions equivalent to that of (35), the neuronal
morphology of a pyramidal cell, as illustrated in Figure 6A, (or
any cell for that matter) can be modeled as an electrical circuit as
shown in the topology of Figure 6B; the dendritic ramifications
are modeled as a combination of serial and parallel connections
terminating in the soma which is connected to the axon modeled
as a series of compartments; its interpretation in terms of filtering
is given in Figure 6C. The effect of a serial connection of two
compartments is one of set-intersection when observed in the W = ((W1 + W2)W3W7 + (W4 + W5)W6W8)W9,
( (37) FIGURE 6 | Compartmental neuron representation: (A) Natural topology of a pyramidal cell, (B) Electronic circuit compartments, and (C) Effects of serial and parallel
connections between compartments. FIGURE 6 | Compartmental neuron representation: (A) Natural topology of a pyramidal cell, (B) Electronic circuit compartments, and (C) Effects of serial and parallel
connections between compartments. October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 9 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. and its frequency response (Bode plot) for the relevant range of
frequencies in our applications (Wilson et al., 2004) is shown
in Figure 7B. relevant part of the spectrum. As such, the filter behaves as a low
pass filter for all practical considerations. g
Let us now observe three cases concerning the choice of
ζi values. In the first case, we keep all of them at unity and
consider it our base case for this part of the analysis (and to
keep it aligned with the rest of the paper, we call it Circuit B). In the second case, we double the values of ζ3 and ζ6, which
corresponds to the manipulation of the output cell for the two
input gates in Circuit A. In our linear model, this is equivalent
to doubling ζ9 and leaving everything else intact. Finally, in
the third case, we manipulate the output cell of the last gate
by halving its synaptic conductance (Circuit C). This effectively
means that the three cases are ζ9B = 1, ζ9A = 2, and ζ9C =
1/2, respectively. 2.3.2. Compartmental Modeling
l Since the tunable gain ζ9 of the gate W9, is
the tunable gain of the whole system W according to (37), its
change would offset the frequency response along the ordinate
axis, i.e., lower gains (lower conductance) would suppress the
unwanted frequencies in a better way, while higher gains would
do the opposite. This is demonstrated in Figure 7A. The process
of the analysis is summarized in Algorithm 1 and a summary
with all elements from both the original and linearized versions
of the Hodgkin-Huxley as well as the transfer function model is
presented in Table 2. 3. RESULTS In this section, we discuss the simulation results concerning
the reconfigurable logic gates as well as the circuits. For all
simulations, intrinsic parameters of the cell were kept at their
default values (such as the length and diameter of each of
their compartments) meaning that nothing concerning their
morphological properties was changed, the spike trains fed to
the input of the circuits followed a Poisson process and the
threshold for spike detection and data analysis was 0 mV where
any potential higher than that in a specific time slot would be
considered a bit “1,” characterizing the use of a simple On-
OffKeying (OOK) modulation which was implemented where
a spike is considered as a bit “1” and its absence a bit “0”
in each time slot. The cell models and information on their
respective connection probabilities between different pair of Algorithm 1 | Linear model filter analysis
Initialize:
Ŵ = {γ1, . . . , γ9} ∈(0, ¯γ )
3 = {λ1, . . . , λ9} ∈(0, ¯λ)
C = {C1, . . . , C9} ∈(0, ¯C)
Z = {ζ1, . . . , ζ9} ∈(0, ¯ζ)
for 1 ≤i ≤9 do
Wi ←ζiγ −1
i
C−1
i
γis
s2+C−1
i
γis+λ−1
i
C−1
i
end
WB ←((W1 + W2)W3W7 + (W4 + W5)W6W8)W9
WA ←2WB
WC ←0.5WB
Plot frequency response: WA, WB, WC Algorithm 1 | Linear model filter analysis Algorithm 1 | Linear model filter analysis Alternatively, as we suggested earlier, a single transfer function
of a compartment serves as an approximation of the entire system
due to the effects of repeated bandpass filtering in Figure 6C. In such case, we observe 20 dB/decade slope in the Bode plot
shown in Figure 7A (as compared to 80 dB/decade slope in
Figure 7B) and the same offset of 20 · log10 2 ≈6 dB in case
of halving/doubling the synaptic weight. Since the filter is of a
band-passing nature, it is only natural that, around the resonant
frequency, lower and higher frequency amplitudes should be
ideally attenuated toward zero. Thus, it is worth mentioning that
in both cases depicted here, the part of the frequency response
with the cusp is at very low frequencies, so it is not visible in the Plot frequency response: WA, WB, WC FIGURE 7 | Bode plots: (A) Single second-order bandpass filter approximation and (B) Filter structure from Equation (37). 3. RESULTS FIGURE 7 | Bode plots: (A) Single second-order bandpass filter approximation and (B) Filter structure from Equation (37). Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 10 10 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. TABLE 2 | Summary of elements described in the proposed model. Element
Description
C
Membrane capacitance
gNa, gK, gl
Sodium, potassium, and leak conductances
ENa, EK, El
Sodium, potassium, and leak reversal potentials
Iext
External stimulus
INa, IK, Il
Ionic current for the sodium, potassium, and leak channels
V
Membrane potential
m, h
Sodium activation and inactivation variables
n
Potassium activation variable
α, β
Rate constants for m, h, and n from permissive to
non-permissive state and vice-versa
δ
Small variation around the steady-state
GT
Total pure conductance
GNa, GK, GL
Sodium, potassium, and leak pure conductances
¯gNa, ¯gK, ¯gl
Maximum attainable sodium, potassium and leak
conductances
m∞, h∞, n∞
Steady-state values of m, h, and n
gm, gh, gn
Conductances of the inductive branches
Lm, Lh, Ln
Inductances of the ionic paths
W
Transfer function of the filter
K, Q, ω0
Gain, selectivity, and peak frequency of the filter
ζ
Synaptic weight TABLE 2 | Summary of elements described in the proposed model. where PY,E[Y] is the probability of Y given E[Y] in which Y is the
actual output and E[Y] is the expected output and Y & E[Y] ∈
{0, 1}. PY,E[Y] resembles the conditional probabilities in a binary
symmetric channel (BSC). Thus, P0,0 = 1 −P1,0, and P0,1 =
1 −P1,1. It is possible to calculate P1,1, for instance, by counting
the number of bits there are for each input-output combination. In other words, considering #Bi,j the number of times a bit i was
received when bit j was sent knowing that i & j ∈{0, 1}, then
P1,1 = #B1,1/(#B1,1 + #B0,1). Given the objective of obtaining a behavior similar to an OR
gate, the synaptic weight should be set to 0.06 µS, meaning that
the pre-synaptic stimuli will drive a higher influence on the
depolarization of the post-synaptic cell. On the other hand, for
an AND behavior, the weight is set to 0.03 µS, which reduces the
influence of a single spike and look to a response of the post-
synaptic neuron only when two spikes arrive very close to each
other in terms of time. 1https://github.com/gladonias/neuronal-filters 3.2. Neuronal Logic Circuits Once the reconfigurable behavior of the gates is assessed, they are
connected to other gates to form a logic circuit. The performance
is measured employing a ratio (frequency response), i.e., the
number of spikes (bits “1”) in the output divided by the
nominal input frequency, in Hertz. This ratio is also known as
the magnitude, or gain when evaluating the data in decibels. Following the approach for individual gates, the inputs are
random and the frequency is increased uniformly. Since the gates
showed similar accuracy when increasing the input frequency,
we picked the one analyzed in Figure 8A for our circuit analysis
with a reconfigurable logic gate, modifying only the output gate’s
synaptic properties. 3. RESULTS This is conducted so we have acceptable
levels of accuracy when compared to the expected outputs of
the gate. Figure 8 show similar responses when gates originally built to
be of a specific kind. This means either OR or AND gates can
change their configurations that drives their gating capabilities
by modifying the synaptic weight between the connections of the
input cells and the output cell. Although there is quite a visible
difference between the performance of AND and OR gates, even
at high frequencies (150 Hz), the accuracy of the reconfigurable
logic gates remains above 80%. neurons were obtained from the work of Markram et al. (2015),
and then we used NEURON and Python for simulation and
data analysis (Carnevale and Hines, 2009; Hines et al., 2009). The source-code of our simulations is publicly available on a
GitHub repository1. Frontiers in Computational Neuroscience | www.frontiersin.org 3.1. Reconfigurable Logic Gates In this work, we call “reconfigurable” logic gates, the gates that
work by changing the synaptic weight between the connections
of both input cells with the output cell in a neuronal logic gate
structure. Aiming to measure individual gate accuracy, the spike
trains in the inputs were randomly produced but we control
their frequency variation, in other words, for each simulation,
the frequency at all inputs was the same and any change in the
frequency was performed for all inputs of the gates meaning that
none of the simulations account for different frequency values
between different inputs in a single simulation. The accuracy is a
simple but powerful measure for the performance of the gates,
with which we intend to analyze the effects of the dynamics
of the cell on the output of the circuit when comparing this
output with the ideal response of the circuit derived from its
truth-table. The accuracy is calculated according to the following
equation (Hanisch and Pierobon, 2017): Figure 9A show the results for the circuits in Figure 5A. As
expected, Circuit C has a stronger attenuation of the signals
passing through it, and this is mainly due to the fact it is an
arrangement with three AND gates and, based on the truth table,
an AND gate only responds to stimuli if all its inputs are active
at the same time. The magnitude in decibels shown in Figure 9B
follow a standard presentation of the response of digital filters. In the non-linear case of the system, the filtering is even better
than what the linear model would promise, i.e., the suppression
of unwanted frequencies is better due to superexponential decay. Let us compare Figures 7B, 9B. The linear model suggests that
a constant difference of 6 dB is to be expected if the synaptic
weight of the output cell is halved (or doubled), and a linear,
constant amplitude drop. In the nonlinear model, we do observe
a 20 dB/decade drop and 6 dB difference at relevant frequencies,
but instead of a linear trend, we observe a convex response, which A(E[Y]; Y) =
P1,1 + P0,0
X
Y
X
E[Y]
PY,E[Y]
,
(38) (38) October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 11 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. 3.1. Reconfigurable Logic Gates FIGURE 8 | Analysis on reconfigurable logic gates with neurons of types (A) L23-MC, L23-NBC, and L1-DAC and (B) L23-MC, L23-NBC, and L1-HAC. FIGURE 8 | Analysis on reconfigurable logic gates with neurons of types (A) L23-MC, L23-NBC, and L1-DAC and (B) L23-MC, L23-NBC, and L1-HAC. FIGURE 9 | Effects of dynamic changes to the synaptic weight in circuits A, B, and C; (A) Frequency response and (B) Magnitude in decibels. helps in attenuating high frequencies faster than we would expect
from the linear model. This is because the linear model is accurate
in a neighborhood of the point at which it was linearized. circuit has a preferable frequency band for achieving maximum
efficiency. For frequencies lower than or equal to 80 Hz, Circuit
C seems the most efficient, especially at 60 Hz, while frequencies
around 100 Hz show Circuit B as the most efficient which is also
the band where it performs the best. Circuit A, on the other hand,
has its best performance for 120 Hz, and probably for higher
frequencies as well if the trend continues. Now, let us consider H(ν) as the response of an ideal low-pass
filter, and W(ν) the response of the proposed neuronal filter, the
counter-efficiency of W given H is calculated as ψ(W|H) =
Z νc
0
|W(ν) −H(ν)| dν +
Z νf
νc
|W(ν)| dν
(39) This shift in performance may allow us to control which
type of circuit we want to activate inside the brain depending
on which activity the subject is performing at the time, e.g.,
being awake or being asleep. These changes may be induced by
the intake of specific drugs that alter synaptic properties in a
neuronal connection. where νc is the cut-offfrequency and νf is the last evaluated
frequency (in this relationship, the lower the value, the more
efficient the filter is). Since, in terms of magnitude, a frequency
band when cut by an ideal filter should be attenuated toward
negative infinity (−∞), we have to pick a limit for the calculation
of the area under the curves. In our case, after a visual inspection,
the baseline for calculation chosen was −25 dB, because this is
the closest integer value to the lowest values of magnitude. Figure 11 shows a parallel analysis between the magnitude in
dB and the accuracy of the filters with AND gates in cascade. 3.1. Reconfigurable Logic Gates Each
circuit is identified by a pair of characters, the first is the letter
referring to the circuit analyzed, the second is how many AND
gates were connected in cascade. For example, A2 means Circuit
A with two AND gates in cascade, as illustrated in Figure 5B. Figure 10 depicts the counter-efficiency analysis performed
for the three circuits. As it is shown, for different frequency bands
we have some circuits performing better than others. Also, each The results suggest that, by increasing the number of gates in
cascade, we have to deal with attenuation in the network due to October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 12 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. FIGURE 10 | Counter-efficiency of the circuits when compared to ideal filters (the lower the value, the better the filter’s performance). FIGURE 10 | Counter-efficiency of the circuits when compared to ideal filters (the lower the value, the better the filter’s performance). GURE 10 | Counter-efficiency of the circuits when compared to ideal filters (the lower the value, the better the filter’s performance). FIGURE 11 | Parallel between Magnitude (dB) and accuracy of circuits (A) A, (B) B, and (C) C, with AND gates in cascade. FIGURE 11 | Parallel between Magnitude (dB) and accuracy of circuits (A) A, (B) B, and (C) C, with AND gates in cascade. the influence of a specific synaptic weight. This is due to
the proportional relationship that the weight has with each
synaptic connection that individually releases a certain amount
of neurotransmitters, hence, different neuron types may affect
the influence of a fixed value of synaptic weight. This explains
how the accuracy values fluctuate between different types of gates
and circuits as shown in Figure 11. Within a larger network
spatial dimension, the types of neurons may drive a higher
accuracy fluctuation since the network connection exhibits
different synaptic weights between each other. propagation caused by specific characteristics of the cell, such as
the connection probability; hence, the more gates in cascade the
worse the performance of the circuit. Also, even though the ratio
keeps going downwards, at some point, the accuracy will start to
shoot up. With careful evaluation, the dip in the accuracy along
mid-range frequencies is very low in terms of scale, showing a
difference of only around 0.03 on the values of accuracy. Frontiers in Computational Neuroscience | www.frontiersin.org 5. CONCLUSION In this work, we proposed a reconfigurable spike filtering design
using neuronal networks that behave as a digital logic circuit. This approach requires the cells to be sensitive to modifications
through chemicals delivered through several proposed methods
available in the literature. From the Hodgkin-Huxley action
potential model we developed a mathematical framework to
obtain the transfer function of the filter. This required a
linearization of the Hodgkin-Huxley model that changes the
cable theory simplification for each cell compartment. To
evaluate the system, we have used our transfer function as well as
the NEURON simulator to show how the frequency of operation,
logic circuit configuration as well as logic circuit size can affect the
accuracy and efficiency of the signal propagation. We observed
that all-ANDs circuit produces more accurate results concerning
their truth-table when compared to all-ORs. In addition, the
results show that each digital logic circuit is also reconfigurable
in terms of cut-offfrequency of the filter, by manipulating the
types of gates in the last layer of the circuit. Our results, therefore, suggest that neuronal logic circuits
can be used to construct also digital filters, filtering abnormal
high-frequency activity which can have many sources including
neurodegenerative diseases. A metric of counter-efficiency was
also proposed, which should show how far apart the real results
are from the ideal cases. We found that frequency bands were
found to be of optimal value for different types of circuits such
as 60 Hz for circuit C, 100 Hz for circuit B, and 120 Hz for
circuit A, as shown in Figure 10. Based on the presented results,
we demonstrate that by reconfiguring the gates inside the digital
filters we can shift the intensity with how we attenuate the spiking
frequency allowing an on-the-fly adaptation of the filtering tasks
depending on the activity that is being performed by the subject
where, for instance, circuit C should outperform both A and B for
frequencies lower than or equal to 80 Hz. We believe the proposed filter design and its mathematical
framework will contribute to synthetic biology approaches for
neurodegenerative disorders such as epilepsy, by showing how
the control of cellular communication inside a small population
can affect the propagation of signals. For future work, we plan
the use of non-neuronal cells, e.g. astrocytes, for the control
of gating operations and the assessment of neuronal filtering
capabilities at a network level. 5. CONCLUSION Treatment techniques based on
this method can be a radical new approach to reaching precision
and adaptable outcomes, inspired from electronic engineering as
well as communication engineering. Such techniques could tackle
at a single-cell level, neurons affected by seizure-induced high-
frequency firing or bypass neurons that have been affected by a
disease-induced neuronal death and degeneration, thus keeping
the neuronal pathway working at a performance as optimal
as possible. q
q
The envisioned application of the proposed mathematical
framework is for in-silico pharmacology and how it can be
used to provide advanced prediction supporting computational
strategies to test drugs. Since drug design and discovery
in neuroscience are very challenging, especially due to the
complexity of the brain and the significant impediment of the
blood-brain barrier (BBB) imposes on the delivery of therapeutic
agents to the brain. The success rate for approval by competent
authorities of such drugs is <10%. Such a low rate is attributed
not only to factors related to the disease itself, such as complexity,
slow development, and gradual onset but also, to the limited
availability of animal models with good predictive validity
and the limited understanding of the biological side of the
brain (Geerts et al., 2020). The system model derived from a
set of coupled neuron compartments can help push forward the
design of these neuronal filters and provide a platform for in silico
drug-induced treatments on top of engineered biological models
of neurons. A platform that could lead to cost-effective drug
development and analysis of potential bio-computational units
capable of enhancing signal processing in the brain, as well as DATA AVAILABILITY STATEMENT The original contributions presented in the study are included
in the article/supplementary material, further inquiries can be
directed to the corresponding author/s. 4. DISCUSSION With our model, we have mainly investigated the attenuation
on the spiking frequency for three different types of circuits in
which we decrease the number of OR gates by replacing them
with AND gates. We were also able to have the fine-tuning
synaptic properties showing a difference of around 5 dB in
performance between the curves in Figure 9B. Changes in the Synaptic weight plays a role in the influence of the pre-synaptic
stimuli and its impact on the post-synaptic neuron and has a
value proportional to the synaptic conductance (Gardner, 1989)
which is driven by the amount and type of neurotransmitters that
are being bound to the post-synaptic terminals. The higher the
connection probability between pairs of neurons, the stronger October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 13 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. synapse are also considered (Vogels and Abbott, 2005), either by
strengthening or weakening specific synaptic connections, logic
gates were built within a homogeneous network of integrate-and-
fire neurons. Moreover, the experiments conducted by Goldental
et al. (2014) followed a procedure that enforced stimulations
on neuronal circuits within a network of cortical cells in-vitro
and they do propose other types of gates such as XOR and
NOT. Furthermore, we increased the number of AND gates in
a cascade-like manner in order to confirm that the longer the line
of cascade gates, the more attenuated the signal should be if none
of those elements receives any kind of external stimuli despite
the spike coming from the circuit, and this result is depicted
in Figure 11. A peak value in the difference of around 8 dB
occurs in Circuit A, decreasing to around 5 dB in Circuit B and
there is a small difference in Circuit C. The transfer function
derived from the Hodgkin-Huxley linear model suggests a band-
pass behavior of the system (Plesser and Geisel, 1999) for very
low frequencies leaving us with a low-pass filter acting on higher
frequencies ranging from 5 to 150 Hz. Considering the time for
a spike to be fired that comprises depolarization, repolarization,
and refractory period, higher frequencies will lead to saturation
and non-realistic behavior of neuronal firing. predicting long-term effects of using a specific drug are potential
uses of the proposed mathematical framework. Frontiers in Computational Neuroscience | www.frontiersin.org REFERENCES doi: 10.1002/syn.890010511 Koslow, S., and Subramaniam, S. (2005). Databasing the Brain: From Data to
Knowledge (Neuroinformatics). Hoboken, NJ: Wiley. Larouche, J., and Aguilar, C. A. (2018). New technologies to enhance in vivo
reprogramming for regenerative medicine. Trends Biotechnol. 37, 604–617. doi: 10.1016/j.tibtech.2018.11.003 Brunel, N., Chance, F. S., Fourcaud, N., and Abbott, L. F. (2001). Effects of synaptic
noise and filtering on the frequency response of spiking neurons. Phys. Rev. Lett. 86, 2186–2189. doi: 10.1103/PhysRevLett.86.2186 Lienert, F., Lohmueller, J. J., Garg, A., and Silver, P. A. (2014). Synthetic biology
in mammalian cells: next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol. 15, 95–107. doi: 10.1038/nrm3738 Carnevale, N. T., and Hines, M. L. (2009). The NEURON Book, 1st Edn. New York,
NY: Cambridge University Press. Long, L. and Fang, G. (2010). “A review of biologically plausible neuron
models for spiking neural networks,” in AIAA Infotech@Aerospace 2010
(Atlanta, GA: America Institute of Aeronautics and Astronautics), 1–14. doi: 10.2514/6.2010-3540 Chandler, W., Fitzhugh, R., and Cole, K. S. (1962). Theoretical stability
properties
of
a
space-clamped
axon. Biophys. J. 2(Pt
1),
105–127. doi: 10.1016/S0006-3495(62)86844-1 Chaubey, S., and Goodwin, S. J. (2016). A unified frequency domain model to study
the effect of demyelination on axonal conduction. Biomed. Eng. Comput. Biol. 7:BECB.S38554. doi: 10.4137/BECB.S38554 Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M.,
Sanchez, C. A., et al. (2015). Reconstruction and simulation of neocortical
microcircuitry. Cell 163, 456–492. doi: 10.1016/j.cell.2015.09.029 Feng, T., Huang, X., Ni, R., Suen, W. L. L., and Chau, Y. (2019). “Nanoparticles for
drug delivery targeting neurodegeneration in brain and eye,” in Nanomaterials
for Drug Delivery and Therapy, ed A. M. Grumezescu (Norwich, NY: William
Andrew Publishing), 149–183. doi: 10.1016/B978-0-12-816505-8.00006-0 Mauro, A., Conti, F., Dodge, F., and Schor, R. (1970). Subthreshold behavior
and phenomenological impedance of the squid giant axon. J. Gen. Physiol. 55,
497–523. doi: 10.1085/jgp.55.4.497 Fortune, E. S., and Rose, G. J. (1997). Passive and active membrane properties
contribute to the temporal filtering properties of midbrain neurons in vivo. J. Neurosci. 17, 3815–3825. doi: 10.1523/JNEUROSCI.17-10-03815.1997 Mishra, A., and Majhi, S. K. (2019). A comprehensive survey of recent
developments in neuronal communication and computational neuroscience. J. Indus. Inform. Integr. 13, 40–54. doi: 10.1016/j.jii.2018.11.005 Gardner, D. (1989). Noise modulation of synaptic weights in a biological neural
network. Neural Netw. 2, 69–76. doi: 10.1016/0893-6080(89)90016-6 Moreno-Bote, R., and Parga, N. (2004). Role of synaptic filtering on the
firing response of simple model neurons. REFERENCES Hanisch, N., and Pierobon, M. (2017). “Digital modulation and achievable
information rates of thru-body haptic communications,” in Disruptive
Technologies
in
Sensors
and
Sensor
Systems,
Vol. 10206
(Anaheim,
CA:
International
Society
for
Optics
and
Photonics),
1020603. doi: 10.1117/12.2262842 Adonias, G. L., Yastrebova, A., Barros, M. T., Balasubramaniam, S., and
Koucheryavy, Y. (2019). “A logic gate model based on neuronal molecular
communication engineering,” in Proceedings of the 4th Workshop on Molecular
Communications (Linz), 15–16. Hines, M., Davison, A., and Muller, E. (2009). NEURON and python. Front. Neuroinform. 3:1. doi: 10.3389/neuro.11.001.2009 Adonias, G. L., Yastrebova, A., Barros, M. T., Koucheryavy, Y., Cleary, F., and
Balasubramaniam, S. (2020). Utilizing neurons for digital logic circuits: a
molecular communications analysis. IEEE Trans. NanoBiosci. 19, 224–236. doi: 10.1109/TNB.2020.2975942 Hodgkin, A. L., and Huxley, A. F. (1952). A quantitative description of membrane
current and its application to conduction and excitation in nerve. J. Physiol. 117, 500–544. doi: 10.1113/jphysiol.1952.sp004764 Balevi, E., and Akan, O. B. (2013). A physical channel model for nanoscale
neuro-spike
communications. IEEE
Trans. Commun. 61,
1178–1187. doi: 10.1109/TCOMM.2012.010213.110093 Hu, W., and Bean, B. P. (2018). Differential control of axonal and somatic resting
potential by voltage-dependent conductances in cortical layer 5 pyramidal
neurons. Neuron 97, 1315–1326.e3. doi: 10.1016/j.neuron.2018.02.016 Barreto,
E.,
and
Cressman,
J. R. (2011). Ion
concentration
dynamics
as
a mechanism for neuronal
bursting. J. Biol. Phys. 37, 361–373. doi: 10.1007/s10867-010-9212-6 Jirsa, V. K., Stacey, W. C., Quilichini, P. P., Ivanov, A. I., and Bernard,
C. (2014). On the nature of seizure dynamics. Brain 137, 2210–2230. doi: 10.1093/brain/awu133 Baxter, D. A., and Byrne, J. H. (2014). “Chapter 14: Dynamical properties of
excitable membranes,” in From Molecules to Networks, 3rd Edn, eds J. H. Byrne,
R. Heidelberger, and M. N. Waxham (Boston, MA: Academic Press), 409–442. doi: 10.1016/B978-0-12-397179-1.00014-2 Khodaei,
A.,
and
Pierobon,
M. (2016). “An
intra-body
linear
channel
model
based
on
neuronal
subthreshold
stimulation,”
in
2016
IEEE
International Conference on Communications (ICC) (Kuala Lumpur), 1–7. doi: 10.1109/ICC.2016.7511483 Bennewitz,
M. F.,
and
Saltzman,
W. M. (2009). Nanotechnology
for
delivery of drugs to the brain for epilepsy. Neurotherapeutics 6, 323–336. doi: 10.1016/j.nurt.2009.01.018 Koch, C. (2004). “Linearizing voltage-dependent currents,” in Biophysics of
Computation: Information Processing in Single Neurons, Computational
Neuroscience, ed M. Stryker (New York, NY: Oxford University Press), 232–247. Blier, P., and De Montigny, C. (1987). Modification of 5-HT neuron properties by
sustained administration of the 5-HT1A agonist gepirone: electrophysiological
studies in the rat brain. Synapse 1, 470–480. AUTHOR CONTRIBUTIONS GA performed the simulations and wrote the manuscript. HS
performed the control-theoretic analysis. GA, HS, and MB
performed the data analysis. SB, NM, MB, and MW led the work
development. All authors contributed to manuscript writing
and revision. All authors also have read and approved the
submitted version. October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 14 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. FUNDING for the CONNECT Research Centre (13/RC/2077) and the
FutureNeuro Research Centre (16/RC/3948). The work of MB
was supported by the European Union’s Horizon 2020 Research
and Innovation Programme through the Marie Skłodowska-
Curie Grant under Agreement 839553. This publication has emanated from research conducted with
the financial support of Science Foundation Ireland (SFI) and
is co-funded under the European Regional Development Fund This publication has emanated from research conducted with
the financial support of Science Foundation Ireland (SFI) and
is co-funded under the European Regional Development Fund REFERENCES Phys. Rev. Lett. 92:028102. doi: 10.1103/PhysRevLett.92.028102 Geerts, H., Wikswo, J., van der Graaf, P. H., Bai, J. P., Gaiteri, C., Bennett, D., et al. (2020). Quantitative systems pharmacology for neuroscience drug discovery
and development: current status, opportunities, and challenges. Pharmacometr. Syst. Pharmacol. 9, 5–20. doi: 10.1002/psp4.12478 Motanis, H., Seay, M. J., and Buonomano, D. V. (2018). Short-term synaptic
plasticity as a mechanism for sensory timing. Trends Neurosci. 41, 701–711. doi: 10.1016/j.tins.2018.08.001 Nise, N. S. (2015). Control Systems Engineering, 7th Edn. Pomona, CA: Wiley;
California State Politechnic University. Gerstner,
W.,
Kistler,
W. M.,
Naud,
R.,
and
Paninski,
L. (2014). Neuronal Dynamics: From Single Neurons to Networks and Models of
Cognition and Beyond. Cambridge, UK: Cambridge University Press. doi: 10.1017/CBO9781107447615 Peters, A. (2010). “Chapter 4: The morphology of minicolumns,” in The
Neurochemical Basis of Autism: From Molecules to Minicolumns, ed G. J. Blatt
(Boston, MA: Springer US), 45–68. doi: 10.1007/978-1-4419-1272-5_4 Goldental, A., Guberman, S., Vardi, R., and Kanter, I. (2014). A computational
paradigm for dynamic logic-gates in neuronal activity. Front. Comput. Neurosci. 8:52. doi: 10.3389/fncom.2014.00052 Plesser, H. E., and Geisel, T. (1999). Bandpass properties of integrate-fire neurons. Neurocomputing 26–27, 229–235. doi: 10.1016/S0925-2312(99)00076-4 Guillamon, A., McLaughlin, D. W., and Rinzel, J. (2006). Estimation of synaptic
conductances. J. Physiol. 100, 31–42. doi: 10.1016/j.jphysparis.2006.09.010 Pospischil, M., Toledo-Rodriguez, M., Monier, C., Piwkowska, Z., Bal, T.,
Frégnac, Y., et al. (2008). Minimal Hodgkin-Huxley type models for October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 15 Reconfigurable Synthetically Engineered Neuronal Filters Adonias et al. different classes of cortical and thalamic neurons. Biol. Cybern. 99, 427–441. doi: 10.1007/s00422-008-0263-8 different classes of cortical and thalamic neurons. Biol. Cybern. 99, 427–441. doi: 10.1007/s00422-008-0263-8 Vogels, T. P., and Abbott, L. F. (2005). Signal propagation and logic gating
in networks of integrate-and-fire neurons. J. Neurosci. 25, 10786–10795. doi: 10.1523/JNEUROSCI.3508-05.2005 Rolston, J. D., Englot, D. J., Wang, D. D., Shih, T., and Chang, E. F. (2012). Comparison of seizure control outcomes and the safety of vagus
nerve, thalamic deep brain, and responsive neurostimulation: evidence
from
randomized
controlled
trials. Neurosurg. Focus
FOC
32:E14. doi: 10.3171/2012.1.FOCUS11335 Wilson, C. J., Weyrick, A., Terman, D., Hallworth, N. E., and Bevan, M. D. (2004). A model of reverse spike frequency adaptation and repetitive
firing of subthalamic nucleus neurons. J. Neurophysiol. 91, 1963–1980. doi: 10.1152/jn.00924.2003 Sabah, N., and Leibovic, K. (1969). Subthreshold oscillatory responses of the
Hodgkin-Huxley cable model for the squid giant axon. Frontiers in Computational Neuroscience | www.frontiersin.org October 2020 | Volume 14 | Article 556628 REFERENCES Biophys. J. 9, 1206–1222. doi: 10.1016/S0006-3495(69)86446-5 Zhou, Y., Peng, Z., Seven, E. S., and Leblanc, R. M. (2018). Crossing the
blood-brain barrier with nanoparticles. J. Controll. Release 270, 290–303. doi: 10.1016/j.jconrel.2017.12.015 Scharfman, H. E. (2007). The neurobiology of epilepsy. Curr. Neurol. Neurosci. Rep. 7, 348–354. doi: 10.1007/s11910-007-0053-z Conflict of Interest: The authors declare that the research was conducted in the
absence of any commercial or financial relationships that could be construed as a
potential conflict of interest. Sengupta, B., Faisal, A. A., Laughlin, S. B., and Niven, J. E. (2013). The effect of cell size and channel density on neuronal information
encoding and energy efficiency. J. Cereb. Blood Flow Metab. 33, 1465–1473. doi: 10.1038/jcbfm.2013.103 Copyright © 2020 Adonias, Siljak, Barros, Marchetti, White and Balasubramaniam. This is an open-access article distributed under the terms of the Creative Commons
Attribution License (CC BY). The use, distribution or reproduction in other forums
is permitted, provided the original author(s) and the copyright owner(s) are credited
and that the original publication in this journal is cited, in accordance with accepted
academic practice. No use, distribution or reproduction is permitted which does not
comply with these terms. Veleti´c, M., Barros, M. T., Balasingham, I., and Balasubramaniam, S. (2019). “A molecular communication model of exosome-mediated brain drug
delivery,” in Proceedings of the Sixth Annual ACM International Conference
on Nanoscale Computing and Communication, NANOCOM’19 (New York,
NY: Association for Computing Machinery), 1–7. doi: 10.1145/3345312. 3345478 October 2020 | Volume 14 | Article 556628 Frontiers in Computational Neuroscience | www.frontiersin.org 16
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Innovation of New Product Development Process: A Case Study of Healthy Drink-Based Product Line in Indonesia’s Company
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1. Introduction Company or business organization must be able to adapt in order to survive. Businesses operate with the
knowledge that their competitors will inevitably come to the market with a product that changes the basis of
competition. The high level of competition is characterized by the increasing number of emerging similar
products at the marketplace. Competition among similar bussineses are getting more tremendous so company
must allocate adequate resources and strategy to maintain the level of competitiveness. One of most of
strategic decision in company to winning the competition is to develop a strategy of new product development
and innovation. Innovation it self, is a very broad concept that can be understood in a variety of ways. One of the more
comprehensive definitions is offered by Myers and Marquis (1969 in Trott 2005 ): Innovation is not a single action but a total process of interrelated sub processes. It is not just the
conception of a new idea, nor the invention of a new device, nor the development of a new market. The
process is all these things acting in an integrated fashion. p
g
g
g
f
The conception of innovation can be distinguished from invention by suggesting that innovation is
concerned with the commercial and practical application of ideas or inventions. Furthermore, the conception of new ideas is the starting point for innovation. A new idea by itself, while
interesting, is neither an invention nor an innovation, it is merely a concept or a thought or collection of thoughts. The process of converting intellectual thoughts into a tangible new artefact (usually a product or process) is an
invention (Trott 2005). This is where science and technology usually play a significant role. At this stage
inventions need to be combined with hard work by many different people to convert them into products that will
improve company performance. To summarise, then, innovation depends on inventions but inventions need to be
harnessed to commercial activities before they can contribute to the growth of an organisation. Thus: y
g
g
Innovation is the management of all the activities involved in the process of idea generation, technology
development, manufacturing and marketing of a new (or improved) product or manufacturing process
or equipment. Abstract Contemporary and performing organizations are under tremendous pressure to bring new products and to market
them quickly. However, the task of new product development requires significant investment and time in
addition to making various decisions during the NPD process. The aims of the study is to identify pattern and
model of new product development (NPD) process conducted by an Indonesia’s local company (“S” company),
particularly for healthy drink, “K” products line to meet best practice in NPD. The research was also conducted
to determine the factor(s) that promote and hinder innovation culture within the company, which can affect the
company’s competitiveness. Descriptive analysis of factors and determinants which support and hinder the
NPD process are provided using strategic assessment and alignment model. The mapping status of newess level
of products or portfolios, level of innovativeness and NPD stages are analysed using a Stage-Gate framework. The result found that the process of innovation and NPD in “S” company strongly associated with personal
figure of the CEO/top manager or top-down appraoch. The fact that informal NPD process in “S” company is
seemingly spontaneous, natural yet very flexible and highly dependent on CEO’s intuition. Keywords: new product development process, Indonesia, healthy drink, innovation
DOI 10 7176/EJBM/11 24 17 Publication date: August 31st 2019 Innovation of New Product Development Process: A Case Study
of Healthy Drink-Based Product Line in Indonesia’s Company
Rahmi Lestari Helmi
Research Center for Science Technology and Innovation Policy and Management
Indonesian Institute of Sciences (LIPI)
A building , 3rd fl. LIPI , Jl.Jend Gatot Subroto no. 10 Jakarta Indonesia Rahmi Lestari Helmi
Research Center for Science Technology and Innovation Policy and Management
Indonesian Institute of Sciences (LIPI)
A building , 3rd fl. LIPI , Jl.Jend Gatot Subroto no. 10 Jakarta Indonesia The research was financed by National Innovation System Research Incentive, Ministry Research and
Technology, Republic of Indonesia (SINAS Ristek )
Abstract The research was financed by National Innovation System Research Incentive, Ministry Research and
Technology, Republic of Indonesia (SINAS Ristek ) www.iiste.org www.iiste.org European Journal of Business and Management
ISSN 2222-1905 (Paper) ISSN 2222-2839 (Online)
DOI: 10.7176/EJBM
Vol.11, No.24, 2019 DOI: 10.7176/EJBM 1. Introduction y
g
g
Innovation is the management of all the activities involved in the process of idea generation, technology
development, manufacturing and marketing of a new (or improved) product or manufacturing process
or equipment. Based on the conception given above, innovation was defined as the application of knowledge. This notion
that lies at the heart of all types of innovations (e.g product, process, organization, production, or service
innovation) as desribed by Mattews & Manley (2009). It is noticeable that many studies have suggested that
product innovations are soon followed by process innovation in what they describe as an industry innovation
cycle. Furthermore, it is common to associate innovation with physical change, but many changes introduced
within organisations involve very little physical change. Rather, it is the activities performed by individuals that 148 European Journal of Business and Management
ISSN 2222-1905 (Paper) ISSN 2222-2839 (Online)
DOI: 10.7176/EJBM
Vol.11, No.24, 2019 European Journal of Business and Management www.iiste.org change. A good example of this is the adoption of so-called Japanese management techniques by automobile
manufacturers in Europe and the United States (Nonaka & Takeuchi 1995; Mathew & Manley, 2009; Lunvall
& Nielsen, 2007). change. A good example of this is the adoption of so-called Japanese management techniques by automobile
manufacturers in Europe and the United States (Nonaka & Takeuchi 1995; Mathew & Manley, 2009; Lunvall
& Nielsen, 2007). The NPD process is often described as a sequential linear process consisting of activities from idea
generation to product launch (Trott, 2005). Contemporary and performing organizations are under tremendous
pressure to bring new products and to market them quickly. However, the task of new product development
requires significant investment and time in addition to making various decisions during the NPD process. Ganguly et al. (2013) states new product development (NPD) is vital for all companies. Previous research
indicates that the success of new products is dependent upon how professionally the development process is
performed. In particular, the proficiency of NPD activities has a positive effect on product quality. On other hand,
NPD is one of the riskiest, yet most important, endevour of the modern corporation. Studies on accelerated product development may be categorized into four streams of research (Griffin, 2002
in Langerak, 2010). The first category encompasses grounded-theory approaches and small-sample studies
conducted to uncover the drivers of product development cycle time. 1. Introduction Many
national and multinational companies have invested in related product and brand name to seize the market share. “S” company is a well-kown local company industry's leading herbal extracts in Indonesia. The company
has implemented international standards in manufacturing activities, which include HACCP ISO 9001: 2008,
QS-9000, and OHSAS 18001. K product line, one of healthy product line/brand name, is targeted for export
market. K product line export market currently account for 31-40%, which includes Northern Europe, Asia,
Middle East, and Western Europe with total annual sales of the K brand have reached US $ 10 million-50
million (Helmi, 2015). Although the company have launched more than 100 brands and variants, K product line
is selected as an object of study case. The first consideration is, as energy drink, K line products are national
leading market and categorized as cash cow to company so company have to drive innovation and sustainable
new product development in order to maintain its position as market leader. Other consideration is related to
business competition. Technically, Competitor will be relatively easier to copy a me-too product formula so
there is possibility that competitors may shift current position of company in the market. Helmi (2015) also
noted that is as many as 34 product lines or brand name of energy drink are manufactured and distributed
nationwide. Market potential of energy drink, or healthy drink is considered a fast moving business. Many
national and multinational companies have invested in related product and brand name to seize the market share. The aims of the study is to identify pattern and model of NPD process conducted by an Indonesia’s local
company (PT S), mainly for healthy drink K products line to meet best practice in new product development. The research was also conducted to determine the factor(s) that support and hinder innovation culture within
the company, which can affect the company’s competitiveness. Although most new product may fail before and
after launching, an effective and efficient NPD process and resource allocation can minimise the risk of loss and
have opportunities to gain profit to cover the loss. 1. Introduction The output of these efforts are numerous
factors assumed to be associated with development cycle time, including project strategy features (e.g.,product
complexity, strategic intent, level of innovativeness, and technical difficulty), development process
characteristics (e.g., formality, stages, and structure), and organizational characteristics (e.g., team use and
assignment level, leadership style, size, and innovation level). The second category synthesizes these
exploratory findings to develop conceptual models and test the hypothesized influence(s) of accelerated product
development on project strategy, and process and organizational characteristics on development time. Other
studies have identified a number of organizational actions that firms can take to reduce development cycle time,
in particular improving the R&D–marketing–manufacturing interface by establishing cross-functional teams, and
simplifying the organizational structure. The third stream of research comprises studies that investigate the
outcomes of development cycle time reduction in terms of development costs, product quality, and project
success. The fourth category of research reflects on these divergent empirical results via its employment of
(mainly) the survey methodology to examine the moderating effects of contextual factors, such as uncertainty,
product innovativeness, new-product strategy, team improvisation, and customer participation. “S” company is a well-kown local company industry's leading herbal extracts in Indonesia. The company
has implemented international standards in manufacturing activities, which include HACCP ISO 9001: 2008,
QS-9000, and OHSAS 18001. K product line, one of healthy product line/brand name, is targeted for export
market. K product line export market currently account for 31-40%, which includes Northern Europe, Asia,
Middle East, and Western Europe with total annual sales of the K brand have reached US $ 10 million-50
million (Helmi, 2015). Although the company have launched more than 100 brands and variants, K product line
is selected as an object of study case. The first consideration is, as energy drink, K line products are national
leading market and categorized as cash cow to company so company have to drive innovation and sustainable
new product development in order to maintain its position as market leader. Other consideration is related to
business competition. Technically, Competitor will be relatively easier to copy a me-too product formula so
there is possibility that competitors may shift current position of company in the market. Helmi (2015) also
noted that is as many as 34 product lines or brand name of energy drink are manufactured and distributed
nationwide. Market potential of energy drink, or healthy drink is considered a fast moving business. 3. Result And Discussion 3.1 Innovativeness of “K” line Product f
There are a total of 25 product items under the “K” brand as shown in Table 1., Table 2. And Figure 1. Considering the life cycle of the similar food and beverage product, product items/variants which have
launched for more 5 years are not considered ‘new product’, meanwhile 11 out 25 product items categorised as
‘new product’. In spite of one item of traditional herb (or jamu) under “K” product line, was not necessarily a
new product at present, however, by the first time launched, the herb is categorized as highly innovative product. The company claimed the first four product item also a breakthrough product at that periode. The breakthrough
was in the way or method in preparing tradisional herbal medicine or traditional herb (‘jamu’). Consumer
usually take traditional herb with natural bitter taste. The innovator formulated the traditional herb to reduce the
bitterness, without reducing the efficacy of herbal medicine. ,
g
y
Table.1 Summary of new products portfolios derived from the “K” product line
Number of product
items/variants
Category
Launched
Innovativeness and successful/failure in
the market1)
4
traditional herbal
medicine/traditional herb
(Indonesia: ‘jamu’)
>5 years
• 1 out 4 is categorized as highly
innovative
• 1 out 4 is considered successful in the
marketplace
7
instant traditional herb drink
>5 years
-data not available -
1
food supplement
>5 years
-data not available -
2
healthy drink
>5 years
• 1 out 2 is categorized as moderately
innovative
• 1 out 2 is considered successful in the
marketplace
11
(KG1-KG11)
healthy drink
<5 years
• 1 out 11 product items are categorized as
moderate and 10 out 11 as low
• Product items are considered failure,
successful, very succesful, and quite
successful in the marketplace**) Note 1) criteria of successful successful, very succesful, and quite successful in the marketplace determined by
the company, which is based on selling point per per year of individual product item. Among total 4 product items of traditional herbs under “K”-product line, only one considered very
successful in the marketplace. The term of ‘successful’ (including’very successful’ and ‘quite successful’) or
‘failure’ is depend on number of sales in a certain period (sales data not available). achive cost reduction; and repositionings. p
g
Descriptive analysis of factors and determinants which support and hinder the NPD process are provided using
strategic assessment and alignment model (Ekstedt, et al.,2005; (Arnzten &Voransachai, 2008; Gmelin &
Seuring, 2014a). Primary and secondary data are collected during 2013-2015. A semi structured questionnaire are
developed in order to provide primary data. In-depth-interview with marketing manager and R & D manager in
the company are conducted to uncover the NPD process and pattern. Secondary data and information
concerning the products and company performance are obtained over the company’s annual report. 2. Methodology A case study of NPD process in local company (“S” company) is the subject of this research. The NPD analysis
focus on “K” product line, while “K” is brand name for a product line which consist of several product items
or variants. The intention of the study is to map factors and determinants affected the NPD process at PT S. The mapping status of newess level of products or portfolios, level of innovativeness and NPD stages are
analysed using framework described by Booz-Allen & Hamilton (Cooper, 2001: Broring et al., 2006). Kleinschmidt and Cooper (in Cooper, 2001) categorise three simple classes of new products in terms of
innovativeness: (1) highly innovative products, namely new-to-the-world products and innovative new product
lines to the company, (2) moderately innovative products, consisting of new lines to the firm, with products that
are not as innovative (that is, not new,] to the market), and new items in existing products line for firm, (3) low
innovativeness products, consisting of all others: modification to existing products, redesigned products to 149 European Journal of Business and Management ste.org achive cost reduction; and repositionings. 3.2 New Product of healty drink 3.2 New Product of healty drink The next category of product items under “K” product line is healthy drink/energy drink. The product which as
many as 14 product items were considered as moderately innovativeness as described by Kleinschmidt and
Cooper (Cooper 2001) . It indicates that the healthy drink or energy drink is new product under “K” product line,
following traditional herbs, instant traditional herbs and food supplement. The term ‘moderate’ indicates that
the product derived from existing “K” product line, or the same product line. g
NPD process in “S” company is initiated from 1980s so everage rate of new product launched per year is
2 (two). The sales of KG 1-KG12 (see table 1 and table 2) accounted for 85% of the “K” product line sales,
and contributing 40% of sales of the company (Helmi, et al, 2015). According to Figure 1, among a total 25 product items derived from “K” product line, 5 product items are
confirmed failure in the market place. However, the failure rate (proportion of number of new product failure (s)
and total number of product items) is relatively low. Unfortunately, no detailed information of company’s
portfolios has developed in last five year so the exact failure rate can not be determined. According to Figure 1, among a total 25 product items derived from “K” product line, 5 product items are
confirmed failure in the market place. However, the failure rate (proportion of number of new product failure (s)
and total number of product items) is relatively low. Unfortunately, no detailed information of company’s
portfolios has developed in last five year so the exact failure rate can not be determined. Some studies showed, at least three main causes of new product failure. The highest percentage of failure
may caused by inadequate market analysis and effort. Insufficient of faulty marketing research is what managers
cite most frequenty as the number one product failure. Brethauer (2002) and Cooper (2001) found that a lack of
thoroughness in identifying real needs in the marketplace, or in spotting early signs of competitors girding up to
take the offensive. The failure also triggered by assuming “the product would sell it self” and simply failed to
back the product’s launch with suffient marketing, selling and promotional resources. The second most common cause of new product failure is technical problem. 3. Result And Discussion The impact of products
innovativeness of new product success is not nearly as straightforward as expected by company while failure
rate do not necessarily steady increase (or steadily decrease) with increasing innovativeness. Furthermore, traditional herb product items were continue to improve and the company released up to 7
variants of instant traditional herb following regular traditional herbs. Unfortunately, in term of market, data
indicates successful or failure of the product in the market after launching is not available. The similar
explanation applies to the food supplement product items/variants. There was possibility that the product items
have failed in the market for some reasons. Thus, It implies to the company’s strategic decision whether the
product development discontinue or continue. The strategic decision, then highly depend on the market response
and sales of individual product item. 150 Table 2. Inovativeness category of “K” product line
Product item (code name)
Innovativeness category 1
Description of inovativeness
KB 2
Highly innovativeness
a new product that has never existed
in the market and for the company
KG1 2
Moderate innovativeness
a new product category of “K”
product line
KG2
Low innovativeness
Flavor and taste improvement from
existing
products,
repackaging,
modification to ready to drink (RTD)
formula,
KG3
Low innovativeness
KG4
Low innovativeness
KG5
Low innovativeness
KG6
Low innovativeness
KG7
Low innovativeness
KG8
Low innovativeness
KG9
Low innovativeness
KG10
Low innovativeness
KG11
Low innovativeness
KG12
Low innovativeness
Note 1) in accordance with Booz-Allen & Hamilton category (Cooper, 2001), 2) not including new product
category which launched for more than 5 years
Figure 1 Summary of new products & “K” Product Line Figure 1 Summary of new products & “K” Product Line 3.2 New Product of healty drink Difficulties in trying to
convert from laboratory or pilot–plant scale to full-scale production are common, while manufacturing glitches
and product quality problem frequently arise (Felekoglu et al., 2013; Ganguly, et al, 2013). In many cases, it’s a
failure to conduct the earlier phase more thoroughly-technical research, design, engineering-before moving to the 151 European Journal of Business and Management
ISSN 2222-1905 (Paper) ISSN 2222-2839 (Online)
DOI: 10.7176/EJBM
Vol.11, No.24, 2019 www.iiste.org commercialization phase. Other reason is, lack of understanding of customer’s requirement. The third cause of
product failure is bad timing. Timing issues is a key reason for failure. The penalties of moving too slowly, or
too fast, stem from, not only technical issues, but also from unorganized planning, executing and evaluating. commercialization phase. Other reason is, lack of understanding of customer’s requirement. The third cause of
product failure is bad timing. Timing issues is a key reason for failure. The penalties of moving too slowly, or
too fast, stem from, not only technical issues, but also from unorganized planning, executing and evaluating. ,
,
y
,
g
p
g,
g
g
Gmelin & Seuring (2014b) also stated that at least 4 (four) success factors in achieving sustainable new
product development; (1) cross-functional work, (2) top-management support, (3) market planning, and (4)
formalized process. Numerous new products failures result from not moving quickly enough, given a limited
window of opportunity. In case of “S company”, although most of the product item of “KG2-KG12” has the
same basic formula, not all the product items successful in the market. The case study uncovered the company
have set a low innovative strategy in “K” product line by following works such as flavor and taste improvement
from existing products, repackaging, and modification to ready to drink (RTD) formula. The strategy have been
taken to accelerate the NPD process, and minimalizing the failure rate. The NPD strategy was taken also to
assure a product launch timing. If not, it might be possible of shift in customer preferences during development
cycles; while the competitors moves more quickly with a new product and seize the marketshare. In term of
technical aspect, the failure of some “K” product items in the product line have indicated that NPD process
might not sharpen product differentiation among items so that customers in the market couldn’t recognize the
items as one product/item. 3.2 New Product of healty drink The facts was, beside the low proportion of product failure compared to the success,
the market failure of some “K” product items was unevitable, so it was critical process to provide a sufficient
market data or consumer preference, which would lead to a preferable product/variant. Even the failure rate was
moderately higher than existing items, revenue generated from the success product covered the overall NPD cost
of “K” product line 3.3 Stages of NPD process 3.3 Stages of NPD process The dynamic NPD in “S” company have been carried out since 1980s, and no formal NPD structure in the
company. The NPD process, as part of company strategy to lead the national market, is managed informally. In managing innovation process, a source of new product idea, most frequently generated from key person(s) in
the company. Informality of NPD in the company is indicated by several indicators. First, no written documents
or SOP or other formalized process dealing with the NPD process which can be used as guidance or manual. Second, inspite of the NPD planning usually established a year before, the company's flexibility in NPD
projects is relatively high. The third, idea of innovation and NPD in the company, is highly dependent to key
person (s). In order to understand the basic idea of NPD process in “S” company, the following reconstruction (Fig. 2 and Table 3) is developed by adapting the State-Gate system (Cooper, 2001): )
p
y
p
g
y
(
p
)
Figure 2. The simple steps reconstruction of NPD of KG2-KG12 Figure 2. The simple steps reconstruction of NPD of KG2-KG12 152 www.iiste.org Vol.11, No.24, 2019
Table 3. 3.3 Stages of NPD process State-Gate system interpretation of NPD of KG2-KG12
Stage
Main activity/process of new product
development
Constraint /challenging
Idea repository
•
Deriving source of ideas/inventions
derived
from
internal
and
external
organization
•
indentifying
detailed
description
on
internal-sourced ideas which generated
from key person in company
•
(if any) indentifying detailed description on
an external-sourced ideas which generated
from
outside
company
(customers,
suppliers, networks, or scientists from
universities and R&D organization)
•
Person
in
charge
(PIC):
Product
Development Manager (PDM)
• Highly intervension of key person (s) in
strategic
position/top-down
ideation
process
• bottom-up idea(s) might not be or less
accommodated
• The NPD planning is too flexible,
spontaneous, and could be changed
from the annual plan
Gate 1
Gate keeper: PDM and/or CEO
Stage 1:
Idea screening
& selection
• Initial screening to test the idea prior to
NPD process
• An initial idea screening was adjusted
through a smaller team’s feedback (the
small team represented division/position of
top management, marketing, R & D)
• Initial assessment in justifying further NPD
proccss within team (marketing team
provided data from customer feedback and
suppliers)
• Building an initial business case
• 'in-house' testing (technical assessment)
• PIC: Product Development Manager
• adjustment the scoping is highly
dependent on the small team’s ability in
data interpreting
• relevant
only
for
low
innovative
products, less relevant for moderate and
highly innovative products
Gate 2
Gate keeper: PDM and/or CEO
State 2: product
development
stage
• Involving the bigger-cross functional team
in company (marketing, R & D and
supporting team)
• ‘in house’ NPD testing involved other
employees (eg. “S” company have already have strategy formulation in NPD. The company tends to apply a simplyfied State-
Gate model in promoting NPD (“K” product line). The simplification of the model implies toward a quick, and
profitable innovation process. State-Gate model is a business process for value creation that is designed for 3.4 Driving force for NPD innovation in organization 3.3 Stages of NPD process Representation of the values were also performed by the prominent figure(s) as role
models on electronic or printed promotion medias. p
p
Ideally, company generates an organizational culture that nurture the NPD process with high-performance
teams, focus on customers and markets, excellent solutions, compliance, discipline, speed and quality. Despite
the promotion and marketing innovation strategies have implied to increase much more resources allocation than
NPD itself, the company have tendency to foster a dynamic and flexible relationship that is very supportive
toward innovation in organiation. The fact is, “S” company has no formal NPD process and guidelines, so the
company must formalize the process in order to increase efficient and effective NPD process. It can be
concluded that the informal style in the NPD is very spontaneous, flexible, and mostly top-down approach. The company fostering innovation culture in the organization by involving cross fuctional teams to
executing NPD who represent R & D, marketing, IT, HR, legal, design, promotion and finance. It was also
revealed that the key persons (CEO and/or R&D manager) is also innovator in “S” company. Even “S”
company is an Indonesia’s key player in traditional herb industry, it was managed as family enterprise. As the
company growth is geting bigger, the centrality of CEO in NPD process relatively unchanged and strongly
dominated the process. Thus, In the context of the NPD process, the CEO plays main role as intrapreneurship
and entrepreneurship. According to Pinchot (1995 in Iqbal et al, 2011), at least 8 characteristics of
intrapreneurship and entrepreneurship have ability in; (1) combining vision and action, (2) managing risk, (3)
coping with mistakes and failures, (4) determining a high internal standard for him/herself, (5) determining clear
objectives, (6) placing high priority on performance, (7) seeking the pleasure of the workload, and (8) managing
a hybrid company. In case of “S” company, the most prominent figure of the CEO is seemingly able to capture the market
opportunity through the values creation as described above. It was reflected by the NPD and innovation
marketing strategy He/she is able to integrate the NPD process in the company and convert the original ideas
into something concrete and workable so that it can be realized in a concrete new products. The figure also has a
capability to bridge the ideas and inventions generated by knowledge workers become valuable innovation and
profit. 3.3 Stages of NPD process sensory test)
• Technical testing and validating products
were carried out under limited scale
production
• PIC : R & D Manager
• more technical assessment to obtain
initial prototypes,
• no detailed market study or no market
related-activity test or selling of tests
conducted by the company prior to
launch of the product
Gate 3
Gate keeper: (PDM) and/or CEO
Stage 3:
product launch
• The stage involved a bigger cross functional
team (marketing, R & D, legal)
• Applying overall process in company : full
production and marketing process
• PIC: Marketing Manager
• highly dependent on the ability to
achieve initial market data/market
testing
Post
launch
Review
•
determining successful or failure NPD a
new product based on sales value in a
certain period
•
decision
making
process
to
continue/discontinue new product
• PIC: Marketing Manager
• Determining sales periode, marketing
efforts versus inovativeness/newess
level of NPD, the lower the
inovativeness, the shorter the testing
periode
3.4 Driving force for NPD innovation in organization
“S” company have already have strategy formulation in NPD. The company tends to apply a simplyfied State- 3.4 Driving force for NPD innovation in organization 153 European Journal of Business and Management European Journal of Business and Management
ISSN 2222-1905 (Paper) ISSN 2222-2839 (Online)
DOI: 10.7176/EJBM
Vol.11, No.24, 2019 www.iiste.org quick and profitable transformation of company’s best ideas into new products/services (Stosic &Radul, 2014). Based on the data of the NPD per year, top management aware that the survival strategy of the company
depends on product performance. The company realize that product innovation or NPD is not a ‘stand alone
strategy’ must be taken. Although the inovativeness of “K”-product line tends to a low level category, the
company have applied a combination of innovation strategies in improving company performance, namely
innovation in marketing and promotion. Interestingly, the promotion and marketing launched by the company
were through values proposition. Shared value of the company's reflects in its vision, mission and ambition. Philosophy of the values is closely related to the new products themselves, which are rooted from Indonesia's
local cultural traditions in dealing with health and prevent illness. The values which wanted to share by the
company on medias, mostly promote issues such as ‘the pride of being part of Indonesian, nationalism, local
wisdom, traditional art and culture, diversity, environtment, peace, humanity, healthy lifestyle, and Indonesia’s
spectacular panoramas. 3.3 Stages of NPD process Invention and ideas that worked in NPD process not limited sourced from the internal organization alone,
but can also come from the network and its external sources over the years. The nature of intrapreneurship and
entrepreneurship is also further gradually transmitted to other family members (who currently have strategic
positions in the company) due to intensive interaction in managing a family business. The companies should
make efforts so that the ability of intrapreneurship and entrepreneurship of the figure can be transmitted to other
employees. 3.5 Factors that hinder NPD innovation in organization 3.5 Factors that hinder NPD innovation in organization Kohne & Sawyer (2018) described that the main reason can be attributed failure of NPD innovation process is:
communication barriers between functional departments. An organization has to make sure that the regarding
departments interact efficiently with each other. Another explanation triggering the failure of the launch is the
lack of communication internally: between Chief Investment Officers and Chief Executive Officers, but it also
occurs between management and staff. In case of the “S” company, the low failure rate of NPD was faund
relatively low to moderate. Our finding was, the most contributor to NPD’s ideation orginated from a top-down
mechanism so communication barrier among top management level was deminish. However, future NPD
process in a long range of “S” company growth, the company should considered more on implementing a
bottom up mechanism. Over-reliance on inividual’s idea toward NPD process may lead declining in future
NPD performance. The NPD planning in “S” company is too flexible, spontaneous, and can be changeable so the company
should establish more formal structure of NPD in the organization. Too flexibility on NPD process may lead to
a ‘bad timing’ or delay the outcomes. The wider impact of ‘bad timing’ also lead to a big loss. There must be a
balance between flexible and formalized process of NPD (Felekoglu et al., 2013). The company’s formal NPD
process must be considered as tool to win the competition, while from technology point of view, the 154 European Journal of Business and Management European Journal of Business and Management
ISSN 2222-1905 (Paper) ISSN 2222-2839 (Online)
DOI: 10.7176/EJBM
Vol.11, No.24, 2019 www.iiste.org www.iiste.org healthy/energy drink formula is relatively easily imitized by competitor so the company have to emphasis on, not
only the NPD innovation it self. It indicate that the growth of healthy drink industry is very promising and
influenced by urban life style. According to the Ministry of Industry of Indonesia, recent data was recorded in
the third quarter of 2018 the growth of the food and beverage industry reached 8.67% or exceeded the national
economic growth of 5.27%. Over the past year, the food and beverage industry grew 9.23% per year (Pratama,
2018). 3.5 Factors that hinder NPD innovation in organization Furthermore, its critical point to asses of product life cycle, as part of NPD manajement in order to
minimize loss and anticipate ‘bad timing’ as stated by Gmelin & Seuring (2014b) p
g
y
g (
)
Regarding state gate intepretation of NPD process in “S” company, the problems and pitfalls identified in
three points, namely an inadequate market analysis, failure to understand customer need and wants, and
insufficient attention to the market place. Cooper (2001) stated that a lack of market orientation is consistently
cited as major reason for NPD failure. Simply stated, the company tent to omit many of critical marketing tasks,
particularly those in the early phase of project. Activities such as the detailed market study (to determine
customer need and to assess likely market acceptance) and test market or trial sell (to test the launch plan and
determine market penetration). Considering the existing size of the company, a cross functional team was very
limited, while too many NPD projects were conducted. The lack of time, money, and people is the root cause of
errors for product performance. 4. Conclusion The study case revealed that the success of “K” product items was on the innovation strategies, which applied an
integrated process of NPD, marketing and promoting.The process of NPD innovation in “S” company strongly
associated with personal figure of the CEO/top manager who is also an intrapreneur and innovator in the
organization. The fact that informal NPD process in “S” company is seemingly spontaneous, natural yet very
flexible and highly dependent on CEO’s intuition. Entrerprenership nature and at the same time strong
intrapreneurship of the central figure in the company are greatly influencing decision making in NPD innovation
in the company. The company applied the integrated strategy to allocated more resouces in marketing and
promotional innovation than the NPD innovation itself. The strategy was choosen in order to win competition in
the related market. Through the new products, the company share values to the customers by promoting issues
such as ‘the pride of being part of Indonesian, nationalism, local wisdom, traditional art and culture, diversity,
environtment, peace, humanity, healthy lifestyle, and Indonesia’s spectacular panoramas. In spite of tight competition in the next 5-10 years, the company should be able to formulate a more formal
guidelines and customized for a more comprehensive product development. The customized system can be
applied to accomodate the principles of NPD process: flexibility, fluidity, focus (priority and portfolio
management), facilitation and forever green (always to regenerate and repair) to support innovation in the
company. However, considering the existing size of the company, a cross functional team was very limited,
while too many NPD projects were conducted. A formal guidelines is also required to guide the process more
efficient and effective. The company is also expected to also provide opportunities to more employees
participation in the NPD innovation process through bottom-up approach. . References References
Arnzten, A.B. &Voransachai, L. (2008). Aligning knowledge process and innovation management capability in
a global business. Communication of the IBIMA, 6, 130-135. en, A.B. &Voransachai, L. (2008). Aligning knowledge process and innovation management capability
a global business. Communication of the IBIMA, 6, 130-135. Brethauer, Dale .(2002) New Product Development and Delivery.Ensuring Successful Products Through
Integrated Process Management, New York: American Management Association (AMACOM). Broring, S. Cloutier, L.M., & Leker, J. (2006). The front end of innovation in an area of industry. R and D
Management Journal, 36(5), 487-498. nger, H. ,J. Warschat, D. Fischer. (2000). Rapid product development-an overview. Computer in Indust
42: 99-108. Cooper, R.G. (2001) Winning at New products. Accelerating the Process from Idea to Launch, New York: Basic
Book . Ekstedt, M., Narcisa J., Leonel P., Enrique S.M., Norman V. (2005). Industrial information and control systems,
KTH -Rroyal an organization-wide approach for assessing strategic business and IT Alignment. PICMET Ganguly, K.,Satyabrata D. and P.K.Bandyopadhyay. (2013). Compressed new product development cycle & its
impact on outsourcing decisions in auto component industry. International Journal of Managing Value and
Supply Chains (IJMVSC),4(2), 25-37. pp y
(
) ( ),
Gmelin H., S. Seuring (2014a) Determinants of sustainable new product development. Journal of Cleaner
Production 69: 1-9. Gmelin H., S. Seuring (2014b). Achieving sustainable new product development by integrating product life-
cycle management capabilities. Int. J. Production Economics 154: 166-177. Felekoglu, B., Anja M.M., James M. (2013) Interaction in new product development: How the nature of the 155 European Journal of Business and Management
ISSN 2222-1905 (Paper) ISSN 2222-2839 (Online)
DOI: 10.7176/EJBM
Vol.11, No.24, 2019 www.iiste.org NPD process influences interaction between teams and management. Journal of Engi
Technology Management 30, 384-401. NPD process influences interaction between teams and management. Journal of Engineering and
Technology Management 30, 384-401. gy
g
Helmi, R.L (2015).Mengelola Inovasi Bidang Pangan Fungsional. Dalam: Diah AJ, editor . Peluang Adopsi
Inovasi Berbasis Data Paten di Bidang Pangan Fungsional . Jakarta:LIPI Press. Iqbal, M., Rasli A,,Heng, L.H, Ali, M.B.,Hassan, I. & Jolaee, A. (2011). Academic staff knowledge sharing
intentions and university innovation capability. African Journal of Business Management, 5(27),1105-
11059. Kohne, H.L & Sawyer, A. (2018). Process innovation: requirements and opportunities. European Journal of
Management Issues, 26 (1-2), 22-28 Langerak, F. (2010) Accelerated product development. In Wiley International Encyclopedia of Marketing
Jagdish N. Sheth and Naresh K. Malhotra: John Wiley & Sons Ltd H. (2007). References Knowledge sharing and firm innovation capability: an empirical study. International Journal
Manpower, 28(3/4):315-332. Lunvall, B. & Nielsen, P. (2007).Knowledge management and innovation performance. International Journal of
Manpower, 28(3/4), 207-223. p
,
(
),
Mattews, J. & Manley. K. (2009). Enhancing Research and Development: Designing Collaborative
Environments for Innovation. Queensland University of Technology. f
Q
y
gy
Nonaka & Takeuchi (1995). The Knowledge-Creating Company . How Japanese Companies Create the
Dynamic of Innovation. New York: Oxford University Press Stošić B. & Radul M. (2014).Possibilities of Opening Up the Stage-Gate Model. Romanian Statistical Review,
4:41-53. Trott, P. (2005) Innovation Management and New Product Development 3rd edition. London: Prentice Hall,
Pearson Education. Pratama W P (2018) Industri Minuman untuk Kesehatan Bakal Berkembang Ini Alasannya Pearson Education. Pratama., W.P. (2018). Industri Minuman untuk Kesehatan Bakal Berkembang, Ini Alasannya. Pratama., W.P. (2018). Industri Minuman untuk Kesehatan Bakal Berkembang, Ini Alasannya. https://ekonomi.bisnis.com/read/20181025/257/853355/industri-minuman-untuk-kesehatan-bakal-berkembang-
ini-alasannya. Accessed on August, 30th 2019. 156
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English
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Predicting COVID-19 Disease Progression and Patient Outcomes based on Temporal Deep Learning
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Research Square (Research Square)
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cc-by
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Sun et al. BMC Med Inform Decis Mak (2021) 21:45
https://doi.org/10.1186/s12911-020-01359-9 Sun et al. BMC Med Inform Decis Mak (2021) 21:45
https://doi.org/10.1186/s12911-020-01359-9 Predicting COVID-19 disease progression
and patient outcomes based on temporal deep
learning Chenxi Sun1,2, Shenda Hong3,4, Moxian Song1,2, Hongyan Li1,2* and Zhenjie Wang5* Chenxi Sun1,2, Shenda Hong3,4, Moxian Song1,2, Hongyan Li1,2* and Zhenjie Wang5* Abstract Background: The coronavirus disease 2019 (COVID-19) pandemic has caused health concerns worldwide since
December 2019. From the beginning of infection, patients will progress through different symptom stages, such as
fever, dyspnea or even death. Identifying disease progression and predicting patient outcome at an early stage helps
target treatment and resource allocation. However, there is no clear COVID-19 stage definition, and few studies have
addressed characterizing COVID-19 progression, making the need for this study evident. Methods: We proposed a temporal deep learning method, based on a time-aware long short-term memory
(T-LSTM) neural network and used an online open dataset, including blood samples of 485 patients from Wuhan,
China, to train the model. Our method can grasp the dynamic relations in irregularly sampled time series, which is
ignored by existing works. Specifically, our method predicted the outcome of COVID-19 patients by considering both
the biomarkers and the irregular time intervals. Then, we used the patient representations, extracted from T-LSTM
units, to subtype the patient stages and describe the disease progression of COVID-19. Results: Using our method, the accuracy of the outcome of prediction results was more than 90% at 12 days and 98,
95 and 93% at 3, 6, and 9 days, respectively. Most importantly, we found 4 stages of COVID-19 progression with differ-
ent patient statuses and mortality risks. We ranked 40 biomarkers related to disease and gave the reference values of
them for each stage. Top 5 is Lymph, LDH, hs-CRP, Indirect Bilirubin, Creatinine. Besides, we have found 3 complica-
tions - myocardial injury, liver function injury and renal function injury. Predicting which of the 4 stages the patient is
currently in can help doctors better assess and cure the patient. Conclusions: To combat the COVID-19 epidemic, this paper aims to help clinicians better assess and treat infected
patients, provide relevant researchers with potential disease progression patterns, and enable more effective use of
medical resources. Our method predicted patient outcomes with high accuracy and identified a four-stage disease
progression. We hope that the obtained results and patterns will aid in fighting the disease. Keywords: COVID-19, Disease progression, Outcome early prediction, Irregularly sampled time series, Time-aware
long short-term memory © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Background g
Coronavirus disease 2019 (COVID-19) outbreaks have
caused health concerns worldwide since December
2019; the disease was declared a pandemic by the World
Health Organization (WHO) on 11 March 2020 [1]. Over
seven million cases of COVID-19 have been reported *Correspondence: leehy@pku.edu.cn; zhenjie.wang@pku.edu.cn
1 School of Electronics Engineering and Computer Science, Peking University,
Beijing, People’s Republic of China
5 Institute of Population Research, Peking University, No.5 Yiheyuan Road,
Beijing 100871, People’s Republic of China
Full list of author information is available at the end of the article *Correspondence: leehy@pku.edu.cn; zhenjie.wang@pku.edu.cn
1 School of Electronics Engineering and Computer Science, Peking University,
Beijing, People’s Republic of China
5 Institute of Population Research, Peking University, No.5 Yiheyuan Road,
Beijing 100871, People’s Republic of China
Full list of author information is available at the end of the article © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Page 2 of 16 Page 2 of 16 learning methods for COVID-19 prediction tasks [17,
19–26]. However, these methods either use the simple
multi-layer perceptron for predicting or use the convolu-
tional structures for image classification. Both the above
methods ignored the temporal development of patient’s
status. In the real-world patient records, except for the
basic information, vital signs, test values and diagnoses
are both time series, especially for the blood samples of
COVID-19 patients, the data we used in this paper. worldwide, including more than 400,000 deaths (as of
15 June 2020) [2]. Even though the disease has been con-
trolled in certain countries, the WHO director warns the
pandemic is still ‘Speeding Up’ [3]. Because of its sudden
onset, many hospitals are still facing medical resource
shortages. For example, news in [4] reported a lack of
medical resources in New Delhi. In [5], Arizona has
experienced record-high hospital capacity as coronavirus
cases climb. A reasonable allocation of resources accord-
ing to patient condition is needed.h Recently, a deep learning method, recurrent neu-
ral network (RNN) [31] can efficiently model temporal
sequences. It uses recursion in the direction of sequence
evolution to learning the relations among past, present
and future. But the basic RNN has the long-term depend-
ency problems [32]. Meanwhile, RNN only process uni-
formly distributed longitudinal data while COVID-19
patient blood samples are distributed nonuniformly with
irregular time intervals between observations. Thus,
a method that can model this irregular time series of
COVID-19 patients is needed. The solution to this problem involves determining the
stages of disease progression by subtyping and predict-
ing the outcome of COVID-19 patients. Then, targeted
treatment and medical resource allocation can be carried
out for patients in different stages. Recent studies [6–11]
have used statistical methods to analyze COVID-19 pro-
gress by inpatient symptoms. However, different statisti-
cal results were obtained by considering different patient
groups and different symptoms. At present, there is no
clear division of the stages of COVID-19 progression. In this paper, we retrospectively analyzed the blood
samples of 485 patients from the region of Wuhan,
China. The medical records collected with standard case
report forms, including epidemiological, demographic,
clinical, laboratory and mortality outcome information,
from an online open dataset under an MIT license. We
applied a temporal deep learning method Time-aware
Long Short-term Unit (T-LSTM) to model the irregular
time series of COVID-19 patients. T-LSTM can predict
the mortality with more than 98% accuracy before 3 days. Meanwhile, we have discovered four stages of COVID-19
patients. According to the different stages, we gave the
analysis of the patient’s state and found the related bio-
markers and complications. Longitudinal disease analysis is the key to under-
standing disease progression, designing prognoses and
developing early diagnostic tools. The time dynam-
ics of disease can provide more information than static
symptom observation [12]. Considering the complex
patient states, the amount of interventions and the real-
time requirement, the data-driven machine learning
approaches by learning from electronic health records
are the desiderata to help clinicians [13]. Many existing works have used machine learning
methods for COVID-19 prediction tasks. We have sum-
marized them in Table 1. For example, in most method
of [27] and in [1, 14–19], authors used non-deep learning
methods, such as k-NN, LR, Cox, SVM and DT to classify
CT/X-ray images and predict the outcomes of COVID-19
patients. However, in terms of prediction accuracy, non-
deep learning is not as good as deep learning methods. Deep learning methods can train the parameters with
complex nonlinearity to learn the data structures and
have achieved state-of-the-art in many medical predic-
tion tasks [28–30]. Thus, many current works apply deep Methods In this section, we first introduce the COVID-19 dataset
and the data preprocessing process. Then, we describe
the methods for mortality prediction and disease pro-
gression in detail. Table 1 The conclusion of machine learning methods used in COVID-19 prediction tasks
We use the abbreviations of methods and the full names are listed in Table 1
Non-deep learning methods
Deep learning methods
Statistics
Regression
SVM
Decision tree
Basic NN
CNNs
RNNs
LDA [14]
NB [15]
k-NN [16]
LR [17, 18]
Cox [19]
[17]
RF [17]
XGBoost [1]
BPNN [17, 19, 20],
GRNN [21],
RBFNN [21],
PNN [21]
Basic CNN [22],
Transfer CNN [23],
GDCNN [24],
COVID-Net [25],
COVNet [26]
/ Table 1 The conclusion of machine learning methods used in COVID-19 prediction tasks We use the abbreviations of methods and the full names are listed in Table 1 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Page 3 of 16 Sun et al. BMC Med Inform Decis Mak Dataset description We also list the range and mean
value of each feature. In Fig. 1, we display the distribu-
tions of some features (age, gender, LHD, lymph and hs-
CRP) of survival class (0) and death class (1). the time series of LHD, lymph and hs-CRP of a 70-year-
old female patient during hospitalization. We can see
the time intervals between two observations are irregu-
lar, which could be a few minutes or even days.h The detailed statistical information of demographic
and 74 clinical laboratory test features is listed Table 2. Dataset description College, Huazhong University of Science and Technol-
ogy, Wuhan, China [33]. The dataset contains 80 char-
acteristics from 375 patients with 6120 records as a
training set and 110 patients with 757 records as a test
set. A case of sample is shown in Fig. 1. It draws lines of Blood index values can reflect a COVID-19 patient’s
physical condition [10]. COVID-19 patients’ blood
samples were collected between 10 January and 18
February 2020 at Tongji Hospital of Tongji Medical Fig. 1 Examples and statistics of COVID-19 dataset. The first block is a line chart of an example in dataset - a 70-year-old female patient. It draws the
time series of LHD, lymph and hs-CRP during hospitalization; The second block is the distributions of age, gender, LHD, lymph and hs-CRP of survival
class (0) and death class (1); The third block is the statistics about dataset. It contains the counts of time series length, the statistics of overall missing
rate and the statistics of each feature’s missing rate under different sampling rate Fig. 1 Examples and statistics of COVID-19 dataset. The first block is a line chart of an example in dataset - a 70-year-old female patient. It draws the
time series of LHD, lymph and hs-CRP during hospitalization; The second block is the distributions of age, gender, LHD, lymph and hs-CRP of survival
class (0) and death class (1); The third block is the statistics about dataset. It contains the counts of time series length, the statistics of overall missing
rate and the statistics of each feature’s missing rate under different sampling rate Fig. 1 Examples and statistics of COVID-19 dataset. The first block is a line chart of an example in dataset - a 70-year-old female patient. It draws the
time series of LHD, lymph and hs-CRP during hospitalization; The second block is the distributions of age, gender, LHD, lymph and hs-CRP of survival
class (0) and death class (1); The third block is the statistics about dataset. It contains the counts of time series length, the statistics of overall missing
rate and the statistics of each feature’s missing rate under different sampling rate Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Page 4 of 16 For example, in the dataset, the average age of patients
is 58.83, the survival rate is 53.6% and the ratio of male
to female is about 1.5:1. Dataset description Table 2 Demographic, laboratory and outcome information of 375 samples in training dataset
a Characteristics have three types - demographics (age and gender), outcomes (survival and mortality) and laboratory test (74 items)
Characteristicsa
Statisticsb
Characteristicsa
Statisticsb
Demographics
Outcomes
Age, mean (years)
58.83
Survival, count and rate
201, 53.6%
Gender
Male 224; Female 151
Mortality, count and rate
174, 46.4%
Lab test mean (min, max) patient’s last measurements
cTnI
747.76 (1.9, 43,905.19)
glucose
8.37 (2.43, 32.37)
Hemoglobin
124.89 (6.4, 178.0)
neutrophils count
7.03 (0.85, 31.43)
Serum chloride
102.73 (77.7, 138.2)
Direct bilirubin
9.5 (1.7, 216.3)
Prothrombin time
16.01 (11.69, 84.22)
Mean platelet volume
10.89 (9.04, 14.0)
procalcitonin
0.99 (0.02, 49.34)
ferritin
1634.37 (26.8, 42,402.91)
Eosinophils(%)
0.56 (0.0, 5.61)
RBCW-SD
41.78 (32.5, 83.3)
sIL-2R
961.52 (61.0, 5608.04)
Thrombin time
18.17 (13.0, 133.67)
Alkaline phosphatase
84.86 (37.18, 481.5)
Lymphocyte(%)
16.45 (0.6, 54.83)
albumin
33.06 (19.1, 45.07)
Anti-HCV
0.13 (0.03, 1.85)
basophil(%)
0.21 (0.0, 1.38)
D-D dimer
6.2 (0.21, 29.82)
Interleukin 10
12.5 (5.0, 500.0)
Total cholesterol
3.66 (0.66, 6.11)
Total bilirubin
16.28 (2.95, 276.0)
AST
56.53 (8.0, 1858.0)
Platelet count
187.78 (1.2, 472.5)
Uric acid
297.47 (57.0, 1001.0)
monocytes(%)
6.66 (0.62, 31.62)
HCO3-
22.59 (6.3, 29.7)
antithrombin
87.57 (20.0, 136.0)
calcium
2.1 (1.35, 2.5)
Interleukin 8
88.08 (5.0, 6385.85)
NT-proBNP
3166.26 (5.57, 70,000.0)
indirect bilirubin
6.85 (1.0, 79.3)
LDH
492.12 (143.0, 1867.0)
RDW
12.94 (10.91, 22.91)
platelet large cell ratio
31.63 (16.48, 54.1)
Neutrophils(%)
76.09 (15.9, 98.1)
Interleukin 6
130.37 (1.5, 5000.0)
Total protein
66.06 (36.7, 79.33)
FDP
44.29 (4.0, 182.4)
Anti-TP
0.17 (0.02, 8.74)
monocytes count
0.54 (0.08, 22.75)
Prothrombin activity
80.97 (16.3, 136.64)
PLT distribution width
12.97 (8.42, 25.3)
HBsAg
10.35 (0.0, 250.0)
globulin
32.96 (13.8, 46.04)
mean corpuscular volume
89.75 (62.3, 110.73)
γ-GT
51.79 (10.6, 555.25)
hematocrit
37.0 (19.9, 51.3)
INR
1.3 (0.86, 10.51)
WBC
15.18 (0.8, 1726.6)
basophil count(#)
0.02 (0.0, 0.12)
Tumor necrosis factorα
12.07 (4.0, 168.0)
2019-nCoV nucleic acid
−1.0 (−1.0, −1.0)
MCHC
344.17 (286.0, 464.33)
MCH
30.9 (20.8,47.67)
fibrinogen
4.38 (0.5, 8.89)
APTT
41.72 (25.59, 100.27)
Interleukin 1β
6.56 (5.0, 79.44)
hs-CRP
72.49 (0.2, 320.0)
Urea
9.74 (2.17, 68.4)
anti-HIV
0.1 (0.05, 0.26)
lymphocyte count
1.06 (0.13, 35.53)
serum sodium
141.06 (122.8, 171.4)
PH value
6.47 (5.0, 7.54)
thrombocytocrit
0.21 (0.05, 0.49)
Red blood cell count
7.58 (0.1, 749.5)
ESR
32.33 (2.0, 102.0)
Eosinophil count
0.03 (0.0, 0.33)
GPT
42.6 (5.0, 1508.0)
Corrected calcium
2.34 (1.78, 2.67)
eGFR
81.07 (2.0, 164.7)
Serum potassium
4.45 (3.1, 9.86)
creatinine
120.38 (39.25, 1497.0) oratory and outcome information of 375 samples in training dataset Table 2 Demographic, laboratory and outcome information of 375 sa Table 2 Demographic, laboratory and outcome information of 375 samples in training dataset b Statistics is statistical data for corresponding characteristics, such as rate, mean value and range. b Statistics is statistical data for corresponding characteristics, such as rate, mean value and range. The statistical methods are described in each column Dataset preprocessing T-LSTM can be formulated as: mr = Nmissing
Nall (1) CS
t−1 = tanh (WdCt−1 + bd)
Short-term memory
ˆCS
t−1 = CS
t−1 ∗g( t)
Discounted short-term memory
CT
t−1 = Ct−1 −CS
t−1
Long-term memory
C∗
t−1 = CT
t−1 −ˆCS
t−1
Adjusted previous memory
ft = σ
Wf xt + Uf ht−1 + bf
Forget gate
it = σ(Wixt + Uiht−1 + bi)
Input gate
∼
Ct = tanh (Wcxt + Ucht−1 + bo) Candidate memory
Ct = ft ∗C∗
t−1 + it ∗
∼
Ct
Current memory
ot = σ(Woxt + Uoht−1 + bo)
Output gate
ht = ot ∗tanh (Ct)
Current hidden state CS
t−1 = tanh (WdCt−1 + bd)
Short-term memory
ˆCS
t−1 = CS
t−1 ∗g( t)
Discounted short-term memory
CT
t−1 = Ct−1 −CS
t−1
Long-term memory
C∗
t−1 = CT
t−1 −ˆCS
t−1
Adjusted previous memory
ft = σ
Wf xt + Uf ht−1 + bf
Forget gate
it = σ(Wixt + Uiht−1 + bi)
Input gate
∼
Ct = tanh (Wcxt + Ucht−1 + bo) Candidate memory
Ct = ft ∗C∗
t−1 + it ∗
∼
Ct
Current memory
ot = σ(Woxt + Uoht−1 + bo)
Output gate
ht = ot ∗tanh (Ct)
Current hidden state (2)
CS
t−1 = tanh (WdCt−1 + bd)
Short-term memory
ˆCS
t−1 = CS
t−1 ∗g( t)
Discounted short-term memory
CT
t−1 = Ct−1 −CS
t−1
Long-term memory
C∗
t−1 = CT
t−1 −ˆCS
t−1
Adjusted previous memory
ft = σ
Wf xt + Uf ht−1 + bf
Forget gate
it = σ(Wixt + Uiht−1 + bi)
Input gate
∼
Ct = tanh (Wcxt + Ucht−1 + bo) Candidate memory
Ct = ft ∗C∗
t−1 + it ∗
∼
Ct
Current memory
ot = σ(Woxt + Uoht−1 + bo)
Output gate
ht = ot ∗tanh (Ct)
Current hidden state (2) Meanwhile, for feature selection, using all 74 laboratory
test features is unrealistic. To address the high missing
rate, repeated features and collection difficulties, we con-
sidered three key features: lactic dehydrogenase (LDH),
lymphocytes (lymph) and high-sensitivity C-reactive pro-
tein (hs-CRP). These features contain specific research
biomarkers of COVID-19 patients [33] and can be easily
collected in any hospital. Considering that only three fea-
tures may not achieve high prediction accuracy, we also
select 40 features (listed in Table 7) with missing rate less
than 30% for comparative experiment. In Eq. Dataset description The statistical methods are described Page 5 of 16 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak This COVID-19 blood test data is publicly available at
https://github.com/HAIRLAB/Pre_Surv_COVID_19. This COVID-19 blood test data is publicly available at
https://github.com/HAIRLAB/Pre_Surv_COVID_19. evolution, and all units are chained together. In basic
RNN (the second structure in Fig. 2), the current state
ht is affected by the previous state ht − 1 and the current
input xt and is described as ht = σ(Wxt + Uht − 1 + b),
where σ is an activation function, and W, U and b are
learnable parameters. Long Short-Term Memory (LSTM)
[32] (the third structure in Fig. 2) is a variant of RNN that
is adept at solving long-term dependency problems. A
standard LSTM unit consists of a forget gate ft, an input
gate it, memory cells Ct,
∼
Ct and an output gate ot. Dataset preprocessing 2, based on the basic LSTM, T-LSTM possesses
some new designs. CS
t−1 component learns the short-term
memory of sequence by learnable network parameters. CT
t−1 is the long-term memory calculated from the for-
mer memory cell Ct − 1 with getting rid of CS
t−1 . CS
t−1 is
adjusted to the discounted short-term memory ˆCS
t−1 by
the elapsed time function g(Δt). The previous memory
C∗
t−1 is changed to the complement subspace of CT
t−1
combined with ˆCS
t−1. In Eq. 2, based on the basic LSTM, T-LSTM possesses
some new designs. CS
t−1 component learns the short-term
memory of sequence by learnable network parameters. CT
t−1 is the long-term memory calculated from the for-
mer memory cell Ct − 1 with getting rid of CS
t−1 . CS
t−1 is
adjusted to the discounted short-term memory ˆCS
t−1 by
the elapsed time function g(Δt). The previous memory
C∗
t−1 is changed to the complement subspace of CT
t−1
combined with ˆCS
t−1. We use a log calculation for the elapsed time function. Δt describes the time gap between two records at two
sequential time steps t and t − 1. Tt is the actual time at
time step t. Dataset preprocessing First, we attempted to find a suitable time measurement
granularity. In the raw dataset, the lengths of sequences
are unequal and different sampling times result in miss-
ing data, with an 85% missing rate on average. The miss-
ing rate is expressed in Eq. 1. Nmissing means the number
of time points with missing data in one time series. Nall
means the number of time points in that time series. The
presence of vacancies has a large impact on data quality,
resulting in unstable predictions and other unpredictable
effects [34]. We used 3 days as the basic sampling inter-
val, reducing the average mr below 30%. The time series
length of raw data, the average missing rate and the miss-
ing rate for each feature are shown in Fig. 1. However, RNNs only process uniformly distributed
longitudinal data by assuming that the sequences have an
equal distribution of time differences. COVID-19 patient
blood samples are distributed nonuniformly. For exam-
ple, the time gap between two sequential records could
be hours or days. Time-aware Long Short-Term Memory
(T-LSTM) [35] (the fourth structure in Fig. 2) incorpo-
rates the elapsed time information into LSTM. It applies
a memory discount to capture the irregular temporal
dynamics. T‑LSTM Recurrent neural networks (RNNs) [31] (the first struc-
ture in Fig. 2) are deep network architectures designed
to model temporal sequences. They take sequence data
as input, recursion occurs in the direction of sequence (3)
g( t) =
1
log (e + t),
t = Tt −Tt−1 (3) Sun et al. BMC Med Inform Decis Mak (2021) 21:45 (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 6 of 16 A
l
i
d
h di
i
i
li i
l
d
d b
Fig. 2 Structures of the methods. The first block shows the structure of RNNs, including basic RNN, LSTM and our T-LSTM; The second block shows
the structure that how to use T-LSTM to complete the outcome prediction task (lower grey area) and disease progressing task (upper grey area) Fig. 2 Structures of the methods. The first block shows the structure of RNNs, including basic RNN, LSTM and our T-LSTM; The second block shows
the structure that how to use T-LSTM to complete the outcome prediction task (lower grey area) and disease progressing task (upper grey area) Fig. 2 Structures of the methods. The first block shows the structure of RNNs, including basic RNN, LSTM and our T-LSTM; The second block shows
the structure that how to use T-LSTM to complete the outcome prediction task (lower grey area) and disease progressing task (upper grey area) and each dimension is a clinical record represented by
a numeric vector. C ∈ {0, 1} is the outcome, where class 0
means death and class 1 means survival. The outcome
prediction task aims to predict patient outcomes by the
prediction function f : X → C Analysis strategyi We first describe the two tasks in this study and then
introduce the specific methods. The whole method pro-
cess is shown in Fig. 3. Task 1 (Outcome prediction) A set of labeled patient
data is represented as D = {(xi, ci) ∈(X, C)|i = 1, . . . , n}
. X
is
a
time
series
set
of
patients,
where
xi =
xt
i|t = 1, . . . , tonset
represents a patient’s records
over t time steps; specifically, xt
i is multivariate data, Task 2 (Temporal patient subtyping / Disease pro-
gression mining) The goal is to find patient groups
G = {gi| i = 0, …, m} with similar feature representa-
tion R =
rt
i |i = 0, . . . , n; t = 0, . . . , tonset
. rt
i is the Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Page 7 of 16 into two dimensions. 3) Obtaining the patient group set
G. As prior information about the patient groups was
not available, we acquired patient groups by applying an
unsupervised clustering method, the Density-Based Spa-
tial Clustering of Applications with Noise (DBSCAN)
[38], on rt. 4) Analysis of G and stages of disease progres-
sion. The mortality rate MR, and the average time dis-
tance TD were calculated as the analysis criteria. representation of clinical record xt
i at time t. Then, the
patient groups G distributed over time are used to analyze
the stages of disease progression In COVID-19 patient outcome prediction task,
T-LSTM is used to handle patient record sequences and
then make the prediction. The process is displayed in the
proposed method of Fig. 2, in the lower gray area. For a patient i, the input of T-LSTM at time
step
t
is
a
three-dimensional
feature
vector
xt
i =
vLDH, vlymphocytes, vhs−CRP,
with time gap Δt. The
output is the state representation si at the last time step. We
apply this outcome prediction task as a binary classification
task, with two classes: death and survival.h (5)
MR = Ndeath
Npatient (5) (6)
TD =
1
| gk |
xt
i ∈gk
Ttonset −Tt (6) The cross-entropy [36] is mainly used to measure the
difference between two probability distributions. We
expect our predicted distribution of patient outcomes
to be closer to the true distribution. Thus, we use the
cross-entropy loss function in Eq. 4. (See figure on next page.)
Fig. 3 The results of outcome prediction. The first line’s charts are the AUC-ROC of mortality prediction results using baselines; The second line’s
chart is the changes of accuracy and loss during training T-LSTM; The third line’s charts are the dimension experiments. They show the accuracy of
mortality prediction by using different representation dimensions and the effect of representation dimension reduction; The fourth line’s charts are
the effect when using DBSCAN Analysis strategyi Besides, when using
sigmoid active function, this loss can avoid the reduced
learning rate causing by traditional mean square error
loss when gradient decreases. Equation 5 expresses the mortality rate. Ndeath is the
number of patients with the death outcome and Npatient is
the total number of patients. Eq. 6 expresses the average
time distance. Tt means the current prediction time and
Ttonset means the time of outcome. ∣gk∣ is the number of
patients in group gk. (4)
L = LCE
C, ˆC
= −
xp(x)logq(x)
= −
n
i=1 ˆcilogci +
1 −ˆci
log(1 −ci) Evaluation metricsh The prediction results were evaluated by assessing the
area under the curve of the Receiver Operating Charac-
teristic (AUC-ROC). The ROC is a curve of the True Pos-
itive Rate (TPR) and the False Positive Rate (FPR). TN,
TP, FP and FN represent true positives, true negatives,
false positives and false negatives, respectively. (4) p(x) is the prior probability (true label vector) and q(x) is
the prediction probability (predicted results vector). Cor-
respondingly, ˆC is the real class of input data, and C rep-
resents the prediction class. In COVID-19 patient disease progression task, temporal
patient subtyping can uncover the dynamic characteristics
of diseases by significantly nuanced subtyping, which leads
to the potential stages of disease progression. We addressed
the issue by building a time stage reference and providing a
low-dimensional representation of each subject, encoding
his or her position with respect to this reference.h (7)
TPR =
TP
TP + FN
(8)
FPR =
FP
TN + FP (7) (8) The patient groups obtained by unsupervised cluster-
ing were evaluated by the Calinski-Harabaz Index (CH),
which measures the covariance of data within a class
and between classes. A larger CH value indicates a bet-
ter clustering performance. In Eq. 9, m is the number of
data and k is the number of groups. Bk and Wk respec-
tively represent the covariance matrices between groups
and within groups. The method structure is displayed in the upper gray
area of proposed method in Fig. 2. It has 4 steps: 1)
Acquisition of patient representation rt. We used the hid-
den state ht, extracted from every T-LSTM unit, as the
patient’s representation rt at time step t. 2) Dimension
reduction of rt. For better demonstration, we used the
t-distributed Stochastic Neighbor Embedding (t-SNE)
[37] method to reduce these high-dimensional vectors rt Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 8 of 16 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 9 of 16 Table 3 AUC-ROC of COVID-19 mortality prediction results by using baselines
a n days early: The models make prediction n days before the final death/survival time. Results We used the records of 375 patients as a training set; the
ratio of the training set to the verification set was 0.8:0.2. The records of 110 patients made up the test set. This
experiment was conducted on 5-fold cross-validation. The code implementation is publicly available at https://
github.com/scxhhh/COVID-19. Evaluation metricsh The values for each dimension are the
values of LDH, lymphocyte and hs-CRP in patients’ blood tests. Its output is the binary result 0/1. Here, 0 indicates survival and 1 indicates death. The hidden states in
its units are 64 dimensional, and the fully connected layer has 32 dimensions For measure and evaluate each feature, we use the aver-
age KL divergence (Average KL) between neighbor stages
gi, gi + 1. m is the number of groups. (9)
CH = tr(Bk)
tr(Wk)
m −k
k −1 (9) When we get the stages of COVID-19 patients, we used
Kullback-Leibler Divergence (KL divergence) to analyze
patient characteristics through each laboratory test fea-
ture. KL divergence can measure the degree of difference
between two probability distributions. For each feature,
we first establish the Gaussian distribution N
µ, σ 2
with
expected value μ and variance σ2 at each stage. Then, we
calculate the average KL divergence of the distribution of
adjacent stages. If the average KL divergence of a feature
is large, it more likely is a biomarker to distinguish differ-
ent stages. The basic KL divergence of distribution p(X)
and q(X) and the KL divergence of two univariate Gauss-
ian distributions are in Eq. 10 and 11. (12)
Average KL = 1
m
m−1
i=0
KLgi,gi+1 (12) Evaluation metricsh They use sequence data from day 0 to n days before the last time to predict
0 days earlya
3 days earlya
6 days early
9 days early
12 days early
Coxb
0.955 ± 0.06
0.992 ± 0.02
0.870 ±0.01
0.85 ±0.01
0.810 ±0.01
k-NNc
0.950 ± 0.02
0.909 ± 0.01
0.890 ±0.02
0.840 ±0.02
0.816 ±0.01
SVMd
0.969 ± 0.04
0.954 ± 0.02
0.930 ± 0.03
0.895 ±0.04
0.857 ±0.02
DTe
0.974 ±0.01
0.959 ± 0.03
0.924 ±0.00
0.897 ±0.01
0.869 ±0.03
BPNNf
0.980 ±0.02
0.954 ±0.05
0.933 ±0.0 1
0.894 ±0.02
0.878 ±0.03
PNNg
0.985 ±0.01
0.961 ±0.02
0.940 ±0.0 2
0.889 ±0.02
0.889 ±0.02
RNNh
0.985 ±0.01
0.960 ±0.01
0.931 ±0.00
0.910 ±0.02
0.871 ±0.01
LSTMi
0.990 ±0.01
0.961 ±0.02
0.937 ±0.02
0.920 ±0.03
0.897 ±0.03
T-LSTMj
0.997 ± 0.00
0.969 ± 0.01
0.947 ±0.03
0.921 ±0.03
0.914 ±0.02 Table 3 AUC-ROC of COVID-19 mortality prediction results by using baselines Support Vector Machines classify by solving the separation hyperplane which can divide the training data correctly and has the largest ge ecision tree is a simple classifier consisting of sequences of hierarchically organized binary decisions. It is used in [33] f BPNN: Back Propagation Neuron Network makes the signal and the error propagate forward and backward separately. It is used in [20]
g PNN: Probabilistic Neural Network is a forward propagation network and does not need back propagation to optimize parameters by using Bayesian decision-
making. It is used in [21] h RNN: Recurrent Neural Network have been introduced in the ‘T-LSTM’ section i LSTM: Long Short-Term Memory which we have introduced in the ‘T-LSTM’ section. Here, the hyperparameter setting is same as T-LSTM i LSTM: Long Short-Term Memory which we have introduced in the ‘T-LSTM’ section. Here, the hyperparameter setting is same as T- j T-LSTM: Time-aware LSTM is the model used in this paper. Its inputs are the three-dimensional vectors and the time intervals. The values for each dimension are the
values of LDH, lymphocyte and hs-CRP in patients’ blood tests. Its output is the binary result 0/1. Here, 0 indicates survival and 1 indicates death. The hidden states in
its units are 64 dimensional, and the fully connected layer has 32 dimensions j T-LSTM: Time-aware LSTM is the model used in this paper. Its inputs are the three-dimensional vectors and the time intervals. Baselines use Cox [19], k-NN [16], SVM [17], DT [1], BPNN [20],
PNN [21], RNN, LSTM and T-LSTM for COVID-19
mortality prediction. T-LSTM is our method. Further, we also select 40 features (listed in Table 7) as
the input of T-LSTM for comparative experiment. The
results in Table 5 indicate that learning a large number
of patient characteristics does not necessarily contrib-
ute to COVID-19 patient mortality prediction task. The
three biomarkers, LDH, lymph and hs-CRP can make the
results better. The AUC-ROC of using 3 features is 3%
higher than using 40 features on average. This is because
too many features will introduce redundant and irrel-
evant dependencies leading by redundant features. Baselines We use the related works summarized in Table 1 as com-
parison methods. Related works are divided into non-
deep learning methods and deep learning methods. We (10)
KL
p(X) | |q(X)) =
xiǫX
p(xi)log p(xi)
q(xi) (10) (11) Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 10 of 16 Page 10 of 16 Table 4 AUC-ROC of COVID-19 mortality prediction results
by using T-LSTM on different sets at different timestamps
a n days early: The model makes a prediction n days before the final death/
survival time. It uses sequence data from day 0 to n days before the last time to
predict
b We use the records of 375 patients as the training set; the ratio of training set
to verification set is 0.8:0.2. The records of 110 patients make up the test set. This
experiment is conducted on 5-fold cross-validation
Trainingb
Validationb
Testb
0 days earlya
0.996 ± 0.01
0.997 ± 0.01
0.997 ± 0.00
3 days early
0.989 ± 0.00
0.987 ± 0.01
0.969 ± 0.01
6 days early
0.960 ±0.01
0.957 ±0.0 2
0.947 ±0.03
9 days early
0.944 ±0.00
0.935 ± 0.01
0.921 ±0.03
12 days early
0.926 ± 0.01
0.924 ±0.0 2
0.914 ±0.02
15 days early
0.891 ± 0.01
0.883 ± 0.01
0.863 ±0.01
18 days early
0.852 ± 0.01
0.834 ±0.0 2
0.819 ±0.0 2 Table 4 AUC-ROC of COVID-19 mortality prediction results
by using T-LSTM on different sets at different timestamps learning, while too many dimensions lead to redundant
calculations and easy over-fitting. Considering result
accuracy, computational complexity and ease of repre-
sentation use in the following task, we decided to use 64
dimensional vectors to represent patients. Based on prediction results, we found: 1) Deep learning
approaches (T-LSTM, RNN, PNN and BPNN) has higher
COVID-19 outcome prediction accuracy than non-deep
learning approaches (Cox, k-NN, SVM and DT) as they
have completed the highly nonlinear feature transforma-
tion by neural junction structures. 2) RNN-based models
(T-LSTM and RNN) performance better on time series
data as they contain state connections for reproducing
time delays and output feedback connections for forming
a loop. 3) Time-aware model (T-LSTM) has the best per-
formance as it can model the time series with irregular
time intervals, which is a prominent feature of COVID-
19 blood sample dataset. Outcome prediction results Table 3 shows the results of COVID-19 mortality predic-
tion using baselines. The AUC-ROC is evaluated at 0, 3, 6,
9, 12, 15, and 18 days early. Here, the results are obtained
when the patient’s representations are 64 dimensional. The results indicate that our method T-LSTM performed
better than all of baselines no matter how early before the
onset times of patients. More precisely, using T-LSTM,
the outcome prediction accuracy is above 90% at 12 days
early and is approximately 97% accurate when predicting
3 days before the disease outcome. More detailed results
of train, validation and test sets using T-LSTM are listed
in Table 4.hii Disease progression results By implementing the four steps of disease progression
mining, we obtained the 4 stages in both the death class
(critical) and the survival class (general), shown in Fig. 4. For better visualization, we reduced the dimension
of the patient’s representation vector, the fifth figure
in Fig. 3 is the dimension reduction effect. We chose 2
dimensions due to low representation loss and clear
observation. Besides, the DBSCAN clustering effect
evaluated by the CH index is shown in the sixth and sev-
enth figures in Fig. 3. Different clustering effects can be
obtained by changing the cluster radius parameter ε. The
best CH index values for the death class and the survival
class are 680.07 and 44.24, respectively. The first four figures in Fig. 3 are the visualizes of pre-
diction results. The first two figures are the AUC-ROC of
prediction results of baselines and T-LSTM in different
earliness. The third figure is the changes of prediction
accuracy and cross-entropy loss when training the model. The fourth figure represents the relation of patient repre-
sentation dimension and AUC-ROC of prediction using
T-LSTM. Too few dimensions lead to incomplete feature Table 5 AUC-ROC of COVID-19 mortality prediction results by using T-LSTM with 40 or 3 laboratory testsb
a n days early: The model makes prediction n days before the final death/survival time. It uses sequence data from day 0 to n days before the last time to predict
b The inputs of T-LSTM are time series of 48 laboratory tests or 3 laboratory tests (LDH, lymph and hs-CRP)
0 days earlya
3 days earlya
6 days early
9 days early
12 days early
40 features
0.949 ± 0.01
0.920 ± 0.03
0.915 ± 0.01
0.910 ± 0.01
0.903 ± 0.01
3 features
0.997 ± 0.00
0.969 ± 0.01
0.947 ±0.03
0.921 ±0.03
0.914 ±0.02 Table 5 AUC-ROC of COVID-19 mortality prediction results by using T-LSTM with 40 or 3 laboratory testsb
a n days early: The model makes prediction n days before the final death/survival time. Table 5 AUC-ROC of COVID-19 mortality prediction results by using T-LSTM with 40 or 3 laboratory testsb
a n days early: The model makes prediction n days before the final death/survival time. It uses sequence data from day 0 to n days before the last time to predict
b The inputs of T-LSTM are time series of 48 laboratory tests or 3 laboratory tests (LDH, lymph and hs-CRP)
0 days earlya
3 days earlya
6 days early
9 days early
12 days early
40 features
0.949 ± 0.01
0.920 ± 0.03
0.915 ± 0.01
0.910 ± 0.01
0.903 ± 0.01
3 features
0.997 ± 0.00
0.969 ± 0.01
0.947 ±0.03
0.921 ±0.03
0.914 ±0.02 Disease progression results It uses sequence data from day 0 to n days before the last time to predict
b The inputs of T-LSTM are time series of 48 laboratory tests or 3 laboratory tests (LDH, lymph and hs-CRP)
0 days earlya
3 days earlya
6 days early
9 days early
12 days early
40 features
0.949 ± 0.01
0.920 ± 0.03
0.915 ± 0.01
0.910 ± 0.01
0.903 ± 0.01
3 features
0.997 ± 0.00
0.969 ± 0.01
0.947 ±0.03
0.921 ±0.03
0.914 ±0.02 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 11 of 16 Fig. 4 The result of COVID-19 progression. This figure shows the four stages of COVID-19 patients by using T-LSTM. The upper clusters are the
original clustering of data. The lower are the patient subtyping by using T-LSTM. We can find there are four clusters with distinct boundaries both in
death/critical class (red) and survival/general class (blue) Fig. 4 The result of COVID-19 progression. This figure shows the four stages of COVID-19 patients by using T-LSTM. The upper clusters are the
original clustering of data. The lower are the patient subtyping by using T-LSTM. We can find there are four clusters with distinct boundaries both in
death/critical class (red) and survival/general class (blue) Fig. 4 The result of COVID-19 progression. This figure shows the four stages of COVID-19 patients by using T-LSTM. The upper clusters are the
original clustering of data. The lower are the patient subtyping by using T-LSTM. We can find there are four clusters with distinct boundaries both in
death/critical class (red) and survival/general class (blue) Fig. 4 The result of COVID-19 progression. This figure shows the four stages of COVID-19 patients by using T-LSTM. The upper clusters are the
original clustering of data. The lower are the patient subtyping by using T-LSTM. We can find there are four clusters with distinct boundaries both in
death/critical class (red) and survival/general class (blue) Page 12 of 16 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. Disease progression results BMC Med Inform Decis Mak (2021) 21:45 Table 6 Feature statistics of patients in different stages
of COVID-19 disease progression
Survival class (general)
Mean value
Stage 1
Stage 2
Stage 3
Stage 4
Mortality rate (%)
7.57
0
1.91
0
Time distance (days)
22.65
14.08
7.98
2.75
Lymph (%)
16
18
21
31
LDH (U/l)
328
301
245
199
hs-CRP (mg/l)
43
39
21
3
Indirect Bilirubin (μmol/l)
7
6
4
3
Creatinine (μmoI/l)
98
75
89
76
INR
2
1
1
1
Serum Sodium (mmol/l)
138
139
140
137
eGFR (ml/min)
79
109
112
111
Serum Chlorine (mmol/l)
97
99
103
102
Albumin (g/l)
41
39
38
40
Death class (critical)
Mean value
Stage 1
Stage 2
Stage 3
Stage 4
Mortality rate (%)
76.32
88.76
91.28
100
Time distance (days)
26.96
18.76
9.32
2.05
Lymph (%)
15
10
9
4
LDH (U/l)
338
364
375
499
hs-CRP (mg/l)
48
55
69
84
Indirect Bilirubin (μmol/l)
8
9
14
23
Creatinine (μmoI/l)
104
106
120
125
INR
2
2
3
2
Serum Sodium (mmol/l)
140
140
135
129
eGFR (ml/min)
75
71
70
57
Serum Chloride (mmol/l)
96
103
104
105
Albumin (g/l)
40
32
33
32 Table 6 Feature statistics of patients in different stages
of COVID-19 disease progression In this case, both classes have four groups. Four stages
of COVID-19 patients are shown in Fig. 4. For each
stage, we calculate the mortality rate MR and the aver-
age time distance TD. For the death class, MR increases
over stages and is 100% at stage 4. For the survival class,
MR decreases over stages and is 0% in stage 4. TD in
both classes decreases, meaning that the 4 stages are dis-
tributed over time. Meanwhile, as the CH index of the
survival class is higher than that of the death class, the
survival class stages are relatively loosely distributed.i In Fig. 4, the first clustering is obtained by using bio-
markers directly and shows that reasonable stages could
not be found. In the first clustering, no stage is clustered
in the death class and the 2 stages in the survival class
have similar mortality rates and no time difference, as
the shade of blue indicates. However, using our method,
different stages have obvious differences, such as the
data point color deepening with the stages. Disease progression results Meanwhile,
as shown in the two insets, the class boundary is clearer
based on our method. The division of stages contains the potential charac-
teristics of COVID-19. Here, we present three findings. First, at the time of initial diagnosis, the COVID-19
infected patients’ physical conditions are similar, regard-
less of final survival or death. In Fig. 4, the distance
between stage 1 for the death class and the survival class
is small, and the two even overlap. This indicates that
outcome prediction is likely not accurate at the time of
infection. Second, the physical condition of patients who
eventually die changes less than that of those who even-
tually survive. We conclude this from CH index values,
where the CH value of the survival class is larger than
that for the death class. Third, mortality rate varies by
stage. For example, if the patient is classified into the
death class and is at stage 1, there is still hope of survival,
as shown by the green triangle sample in Fig. 4. However,
if the patient is in stage 3 or 4, he or she is very likely to
die. Based on estimating the current stage of a patient,
doctors will be given a reference, which can help them
assess a patient’s current situation. Based on that, doctors
can carry out targeted treatment and reasonable resource
allocation more easily. Thus, the ultimate goal of this
study, helping improve the quality of medical care, can be
achieved. Further, we calculated the average KL divergence
between adjoint stages of each features in 40 clinical lab-
oratory tests data. We ranked the average KL values. The
higher the ranking, the better the biomarkers can be used
to distinguish different stages. By ranking 40 biomark-
ers according to the degree of correlation with COVID-
19 (Table 7), we have found the biomarkers which are
more relevant to COVID-19. The top 10 are: Lymph,
LDH, hs-CRP, Indirect Bilirubin, Creatinine, INR, Serum
Sodium, eGFR, Serum Chlorine and Albumin. For each
marker, we gave its reference value in each stage, shown
in Table 6. Different markers have unique trends in dif-
ferent stages. Meanwhile, we calculated the mean values of 40 labo-
ratory test features in each stage, the feature values vary
with stages. Table 6 lists 10 of these features - Lymph,
LDH, hs-CRP, Indirect Bilirubin, Creatinine, INR,
Serum Sodium, eGFR, Serum Chlorine and Albumin. Disease progression results The changes of values through 4 stages are visualized in
Fig. 5. Under different classes, the trends of features are
different. Combining the correlation analysis with the refer-
ence value analysis, we found that the critical COVID-19
patients are usually accompanied by low values of lymph,
eGFR, albumin and Serum Sodium, high values of LDH,
hs-CRP, indirect bilirubin, creatinine and INR. For exam-
ple, in the critical stage 4, the average lymph (%) is just
4 and the average LDH (U/l) is up to 499. Besides, there Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 13 of 16 Fig. 5 Changes of features in different stages. This figure shows the changes of features (Mortality rate, Lymph, LDH, hs-CRP, Indirect Bilirubin,
Creatinine, INR, Serum Sodium, eGFR, Serum Chlorine and Albumin) through 4 stages. Under different classes, the trends of features are different Fig. 5 Changes of features in different stages. This figure shows the changes of features (Mortality rate, Lymph, LDH, hs-CRP, Indirect Bilirubin,
Creatinine, INR, Serum Sodium, eGFR, Serum Chlorine and Albumin) through 4 stages. Under different classes, the trends of features are different Fig. 5 Changes of features in different stages. This figure shows the changes of features (Mortality rate, Lymph, LDH, hs-CRP, Indirect Bilirubin,
Creatinine, INR, Serum Sodium, eGFR, Serum Chlorine and Albumin) through 4 stages. Under different classes, the trends of features are different Therefore, we expect to combine DL methods to study
and fight COVID-19.h are three major complications of COVID-19 patients -
myocardial injury, liver function injury and renal func-
tion injury. We got the conclusions separately through
the value of 1) LDH, 2) albumin and indirect bilirubin, 3)
serum sodium, serum chlorine and creatinine in different
stages. i
The states of COVID-19 patients in hospital are
dynamic time sequence processes. In addition to the
basic information of patients, the vital signs, diagno-
ses and other lab tests are all time series. Existing many
works [14–27, 41, 42] have achieved good results for
COVID-19 prediction tasks. But they paid little atten-
tion to analyze and model the characteristics of COVID-
19 patients’ time series. Dynamic time series modeling
can grasp the relationship between historical observa-
tions and current observations, and learn the potential
development mode of sequence, which is conducive to
more accurate prediction and representation. Disease progression results Besides,
we have found that the time series of COVID-19 patients Discussion In recent years, deep learning (DL) technology has been
widely used because of its superior performance in vari-
ous medical applications [28, 29], such as medical image
recognition [39] and medication recommendations
[40]. In the past year, the spread of COVID-19 has had
a peripheral effect on the global economy and health. Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak Page 14 of 16 Table 7 Ranking of average KL divergence values of top 40 features
Ranking
Feature
Average KL
Ranking
Feature
Average KL
1
Lymph
0.0421
21
Total Cholesterol
0.0041
2
LDH
0.0392
22
Interleukin 6
0.0032
3
hs-CRP
0.0376
23
I sIL-2R
0.0031
4
Indirect Bilirubin
0.0324
24
cTnI
0.0030
5
Creatinine
0.0302
25
RBCW-SD
0.0024
6
INR
0.0235
26
Uric Acid
0.0023
7
Serum Sodium
0.0232
27
Corrected Calcium
0.0022
8
eGFR
0.0225
28
Interleukin 8
0.0019
9
Serum Chloride
0.0224
29
Prothrombin Time
0.0018
10
Albumin
0.0193
30
Serum Potassium
0.0017
11
Globulin
0.0177
31
Interleukin 1β
0.0017
12
Hematocrit
0.0122
32
D-D dimer
0.0016
13
Hemoglobin
0.0091
33
FDP
0.0016
14
Fibrinogen
0.0079
34
Antithrombin
0.0015
15
γ-GT
0.0079
35
Procalcitonin
0.0010
16
ESR
0.0078
36
Platelet Count
0.0009
17
NT-proBNP
0.0074
37
WBC
0.0006
18
APTT
0.0053
38
Ferritin
0.0005
19
Eosinophils
0.0051
39
Interleukin 10
0.0004
20
basophil
0.0049
40
PLT
0.0004 Table 7 Ranking of average KL divergence values of top 40 features is irregularly sampled - Different time intervals exist in
adjacent observations. Every possible test is not regularly
measured during an admission. When a certain symptom
worsens, corresponding variables are examined more
frequently; when the symptom disappears, the corre-
sponding variables are no longer examined. These time
intervals will add a time sparsity factor when the intervals
between observations are large [13]. Therefore, it is nec-
essary not only to deal with time series, but also to deal
with irregular time series according to the characteristics
of COVID-19 patients. In this paper, we use time-aware
LSTM model solved this problem. patient outcomes with higher accuracy than baselines. The method can effectively predict whether the infected
patient will die or survive 12 days prior to disease out-
come with over 90% accuracy. The prediction accuracies
at 3-, 6-, and 9-days prior are 98, 95 and 93%, respectively. Conclusionsh The sudden outbreak and epidemic of COVID-19 has
led to worldwide suffering and shortages of medical
resources. In this paper, we propose T-LSTM to predict
patient outcomes with high accuracy - 98, 95 and 93%
at 3, 6, and 9 days, which will enable reasonable alloca-
tion of medical resources. T-LSTM can effectively model
the irregular sampled time series in blood test sam-
ples of COVID-19 patients and predict more accurately
than existing baselines. Meanwhile, we identified four
COVID-19 stages. We ranked 40 biomarkers according
to correlations to the outcomes of patients, gave the ref-
erence values of top 10 biomarkers for each stage. The
top 10 biomarkers are: Lymph, LDH, hs-CRP, Indirect
Bilirubin, Creatinine, INR, Serum Sodium, eGFR, Serum
Chlorine and Albumin. We also found 3 complications of
COVID-19, which are myocardial injury, liver function
injury and renal function injury. By analyzing patients’
life conditions at different stages, doctors can choose spe-
cific, targeted treatments. Future work will focus more
on the study of pathological characteristics of different
stages. Aiming at four stages, targeted treatments are
expected to be designed. Meanwhile, more real clinical
data are expected to be available for model validation and
the model will be used to mine the inherent hidden fea-
tures of other diseases. Availability of data and materials The code implementation is publicly available at https://github.com/scxhhh/
COVID-19. The data is from an online open dataset https://github.com/HAIRL
AB/Pre_Surv_COVID_19 under an MIT license (https://doi.org/10.5281/zenod
o.3758806). Funding This work was supported by the Scientific Research Foundation for the
Returned Overseas Chinese Scholars, State Education Ministry and UKRI’s
Global Challenge Research Fund (ES/P011055/1). This work was also sup-
ported by the National Key Research and Development Program of China (No. 2020YFB2103402). The funders had no role in study design, data collection,
analysis, the writing of the manuscript, or the decision to submit this article for
publication. Acknowledgments
h
d d This paper is dedicated to those who want to fight COVID-19. Discussion Second, the DL method is the black-box models which
are troubled by poor interpretability [46, 47], but clini-
cal settings prefer interpretable models. For example,
finding the appropriate prediction-related biomarkers
is important. Currently, certain studies have identified
suitable predictive biomarkers, such as the 3 biomarkers
in [33], which are regarded to have a significant impact
on patient mortality. For interpretability, our method
identified four disease stages distributed over time. This
interesting finding cannot be distinguished simply by
the value of biomarkers, as shown as the comparison of
two clustering results in Fig. 4. The discovered stages are
closely related to mortality and time of illness and can
help analyze the status of infected patients. This shows
that the DL method can explore new patterns in mul-
tidimensional space that cannot be demonstrated by a
simple variable value [48]. We also ranked 40 biomark-
ers according to the degree of correlation with COVID-
19 progression, which can provide interpretable results to
help doctors better understand the model. Deep learning methods have outstanding performance
in prediction tasks. If a doctor predicts survival or death
only by observing the biomarkers and using a threshold,
the accuracy is at or below 80% for early predictions. However, the clinical reference value of inaccurate results
is very low [43, 44]. The DL method has better perfor-
mance, and the time-aware aspect enables higher accu-
racy, as shown in Table 3. However, there are some concerns about the use of DL
methods in the high-risk tasks of healthcare. First, it may be risky to apply predictive methods
directly to clinical practice [45]. DL methods may be
assistive tools for doctors but not used to make deci-
sions directly. It is challenging for doctors to make
optimal decisions, a data-driven and high-accuracy pre-
diction method could help. In this paper, we can predict This study has three basic contributions. 1) we can
predict patient outcomes with higher accuracy than
all baselines. 2) We identified four stages of COVID-19 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Page 15 of 16 Page 15 of 16 Authors’ contributions C.S. and S.H. conceptualized the idea. S.H., Z.W. and H.L. initialized, conceived
and supervised the project. C. S, S.H. and M.S. collected data and implemented
the experiments. C. S, S. H, M.S. and Z.W. drafted the manuscript. All authors
provided a critical review of the manuscript and approved the final draft for
publication. All authors read and approved the final manuscript. Consent for publication
Not applicable. Not applicable. Abbreviations progression. The stages are closely related to mortal-
ity and time of illness and can help analyze the status of
infected patients. 3) We give the ranking of 40 biomark-
ers according to the degree of correlation with COVID-
19. Based on this, we found three major complications
of COVID-19 patients - myocardial injury, liver function
injury and renal function injury. COVID-19: Corona Virus Disease 2019; WHO: World Health Organization; LDH:
Lactic Dehydrogenase; hs-CRP: High-sensitivity C-reactive Protein; lymph:
Lymphocytes; DL: Deep Learning; RNN: Recurrent Neural Network; LSTM: Long
Short-Term Unit; T-LSTM: Time-aware Long Short-Term Memory; PNN: Proba-
bilistic Neural Network; RBFNN: Radial Basis Function Neural Network; GRNN:
Generalized Regression Neural Network; BPNN: Back Propagation Neuron
Network; DT: Decision Tree; RF: Random Forest; XGBoost: eXtreme Gradient
Boosting; SVM: Support Vector Machines; Cox: Cox’s Proportional Hazards
Regression; LR: Linear Regression; NB: Naive Bayes; LDA: Linear Discriminant
Analysis; t-SNE: t-distributed Stochastic Neighbor Embedding; DBSCAN:
Density-Based Spatial Clustering of Applications with Noise; MR: Mortality
Rate; TD: Average Time Distance; AUC-ROC: The Area Under the Curve of the
Receiver Operating Characteristic; CH: Calinski-Harabaz Index; KL divergence:
Kullback-Leibler Divergence. Further, there is room for further improvement. First,
because of the data limitations, our method may face risk
of bias, because data-driven methods are easily influenced
by different source of data. For example, the results may
vary when using different datasets [45]. Second, our cur-
rent interpretation is based on results, such as the degree
of association between biomarkers and disease. We hope
to give more explanations about the complex DL black-
box model, such as telling more specific effect of each
part of the model on the result. Meanwhile, we hope to
enlighten the relevant researchers to further study these
4 stages and present more clinical explanations. In par-
ticular, we expect to be able to give specific treatments
for different stages. Targeted treatment is significant for
both patient rehabilitation and the reasonable allocation
of medical resources. Ethics approval and consent to participate The original study was approved by the Ethics Committee of Tongji Hospital,
Tongji Medical College, Huazhong University of Science and Technology (Yan
Li, et al. “An interpretable mortality prediction model for COVID-19 patients.”
Nature Machine Intelligence). In the current study, the data used is from that
study as an online open dataset under an MIT license (https://doi.org/10.5281/
zenodo.3758806). Received: 17 July 2020 Accepted: 30 November 2020 References Williams RJ, Zipser D. A learning algorithm for continually running fully
recurrent neural networks. Neural Comput. 1998;1(2):270–80. 8. Yang X, et al. Clinical course and outcomes of critically ill patients with
SARS CoV-2 pneumonia in Wuhan, China: a single-centered, retrospec-
tive, observational study. Lancet Resp Med. 2020;8:475–81. 32. Hochreiter S, Schmidhuber J. Long short-term memory. Neural Computa-
tion. 1997;9(8):1735–80. 33. Yan L, Zhang HT, Goncalves J, et al. An interpretable mortality prediction
model for COVID-19 patients. Nat Mach Intell. 2020;2:283–8. 9. Zhou F, Yu T, Du R, et al. Clinical course and risk factors for mortality of
adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort
study. Lancet. 2020;395:10229. 34. Chu X, Ilyas IF, Krishnan S, Wang J. Data cleaning: Overview and emerging
challenges, in Proc. Int. Conf. Manage. Data SIGMOD Conf., San Francisco,
CA, USA, Jun./Jul; 2016. p. 2201–6. 10. Wang D, Hu B, Hu C, Zhu F, et al. Clinical characteristics of 138 hospital-
ized patients with 2019 novel coronavirus–infected pneumonia in
Wuhan, China. JAMA. 2020;323(11):1061. 35. Baytas I M, Xiao C, Zhang X, et al. Patient Subtyping via Time-Aware LSTM
Networks. the 23rd ACM SIGKDD International Conference. ACM, 2017. 11. Yang X, Yu Y, Xu J, Shu H, Xia J, Liu H, et al. Clinical course and outcomes
of critically Ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a
single-centered, retrospective, observational study. Lancet Respir Med. 2020;8(5):1–7. 36. Corduneanu C. Integral Equations and Applications; 1991. https://doi. org/10.1017/CBO9780511569395. 36. Corduneanu C. Integral Equations and A
org/10.1017/CBO9780511569395. 37. Laurens VDM, Hinton G. Visualizing Data using t-SNE. J Mach Learn Res. 2008;9(2605):2579–605. 12. Spadon G, Hong S, Brandoli B, Matwin S, Rodrigues-Jr JF, Sun J. Pay Atten-
tion to Evolution: Time Series Forecasting with Deep Graph-Evolution
Learning. arXiv preprint arXiv. 2020;2008:12833. 38. Ester M, Kriegel H-P, Sander J, Xiaowei X. A density-based algorithm
for discovering clusters in large spatial databases with noise. KDD. 1996:226–31. 13. Sun C, Hong S, Song M, Li H. A review of deep learning methods for
irregularly sampled medical time series data. arXiv. 2020;2010:12493. 39. Wang S, Wang S, Zhang S, Fan F, He G. Research on recognition of
medical image detection based on neural network. IEEE Access. 2020;8:94947–55. 14. Wang C, Deng R, Gou L, Fu Z, Zhang X, Shao F, et al. Preliminary study to
identify severe from moderate cases of COVID-19 using NLR&RDW-SD
combination parameter. 2020. medRxiv 2020.04.09.20058594. 40. References 24. Babukarthik RG, Adiga VAK, Sambasivam G, Chandramohan D, Amud-
havel J. Prediction of COVID-19 Using Genetic Deep Learning Convolu-
tional Neural Network (GDCNN). IEEE Access. 2020;8:177647–66. 1. World Health Organization. Coronavirus Disease 2019 (COVID-19) Situa-
tion Report 68, 28 March 2020. https://www.who.int/docs/default-sourc
e/coronaviruse/situation-reports/20200328-sitrep-68-covid-19.pdf. 1. World Health Organization. Coronavirus Disease 2019 (COVID-19) Situa-
tion Report 68, 28 March 2020. https://www.who.int/docs/default-sourc
e/coronaviruse/situation-reports/20200328-sitrep-68-covid-19.pdf. 25. Wang L, Wong A. COVID-Net: A tailored deep convolutional neural
network design for detection of COVID-19 cases from chest radiography
images. arXiv. 2020;2003:09871. 2. World Health Organization. Coronavirus Disease 2019 (COVID-19) Situa-
tion Report 147, 15 June 2020. https://www.who.int/docs/default-sourc
e/coronaviruse/situation-reports/20200615-covid-19-sitrep-147.pdf?sfvrs
n=2497a605_2 26. Li L, Qin L, Xu Z, Yin Y, Wang X, Kong B, et al. Using artificial intelligence
to detect COVID-19 and community-acquired pneumonia based
on pulmonary CT: evaluation of the diagnostic accuracy. Radiology. 2020;296(2):E65–71. 3. Emily Czachor. WHO Director Warns COVID-19 Pandemic is ‘Speeding Up,’ Here
for ‘Long Haul’. Newsweek, News. 6/29/2020. https://www.newsweek.com/
who-director-warns-covid-19-pandemic-speeding-here-long-haul-1514169. 3. Emily Czachor. WHO Director Warns COVID-19 Pandemic is ‘Speeding Up,’ Here
for ‘Long Haul’. Newsweek, News. 6/29/2020. https://www.newsweek.com/
who-director-warns-covid-19-pandemic-speeding-here-long-haul-1514169. 27. Radanliev P, Roure DD, Walton R. Data mining and analysis of scientific
research data records on covid 19 mortality, immunity, and vaccine
development - in the first wave of the Covid-19 pandemic. Diabetes
Metab Syndr. 2020;14(5):1121. 4. Sébastien Farcis. Coronavirus: worries and worries about bed shortage
in New Delhi. Liberation, Reportage. 6/15/2020. https://www.liberation
.fr/planete/2020/06/15/coronavirus-a-new-delhi-inquietude-et-desar
roi-face-a-la-penurie-de-lits_1791300. 4. Sébastien Farcis. Coronavirus: worries and worries about bed shortage
in New Delhi. Liberation, Reportage. 6/15/2020. https://www.liberation
.fr/planete/2020/06/15/coronavirus-a-new-delhi-inquietude-et-desar
roi-face-a-la-penurie-de-lits_1791300. 28. Adam G, Rampášek L, Safikhani Z, et al. Machine learning approaches to
drug response prediction: challenges and recent progress. Precis Onc. 2020;4:19. 5. Katherine Fung. Arizona Hits Record-High Hospital Capacity as Coronavirus
Cases Climb. Newsweek, News. 6/29/2020. https://www.newsweek.com/
arizona-hits-record-high-hospital-capacity-coronavirus-cases-climb-1511578. 29. Jalali A, Lonsdale H, Do N, et al. Deep learning for improved risk predic-
tion in surgical outcomes. Sci Rep. 2020;10:9289. y
6. Huang C, et al. Clinical features of patients infected with 2019 novel
coronavirus in Wuhan, China. Lancet. 2020;395:497–506. 6. Huang C, et al. Clinical features of patients infected with 2019 novel
coronavirus in Wuhan, China. Lancet. 2020;395:497–506. 30. Siuly S, Zhang Y. Medical big data: neurological diseases diagnosis
through medical data analysis. Data Sci Eng. 2016;1:54–64. 7. Chen N, et al. Epidemiological and clinical characteristics of 99 cases of
2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395:507–13. 31. References Contextual sentiment neural network for
document sentiment analysis. Data Sci. Eng. 2020;5:180–92. 48. Gibney HMJ. Analysis of meal patterns with the use of supervised data
mining techniques—artificial neural networks and decision trees. Am J
Clin Nutr. 2008;88(6):1632–42. 22. Panwar H, Gupta PK, Siddiqui MK, et al. Application of deep learning
for fast detection of COVID-19 in X-rays using nCOVnet. Chaos, Solitons
Fractals. 2020;138:109944. 23. Harsh P, Gupta PK, Siddiqui MK, Morales-Menendez R, Bhardwaj P, Singh
V. A deep learning and grad-CAM based color visualization approach for
fast detection of COVID-19 cases using chest X-ray and CT-Scan images. Chaos, Solitons Fractals. 2020;140:110190. Author details 1 School of Electronics Engineering and Computer Science, Peking University,
Beijing, People’s Republic of China. 2 Key Laboratory of Machine Perception
(Ministry of Education), Peking University, Beijing, People’s Republic of China. 3 National Institute of Health Data Science, Peking University, Beijing, People’s
Republic of China. 4 Institute of Medical Technology, Health Science Center
of Peking University, Beijing, People’s Republic of China. 5 Institute of Popula-
tion Research, Peking University, No.5 Yiheyuan Road, Beijing 100871, People’s
Republic of China. Received: 17 July 2020 Accepted: 30 November 2020 Received: 17 July 2020 Accepted: 30 November 2020 Sun et al. BMC Med Inform Decis Mak (2021) 21:45 Page 16 of 16 Page 16 of 16 References Shang J, Xiao C, Ma T, Li H, Sun J. GAMENet: graph augmented
memory networks for recommending medication combination. AAAI. 2019:1126–33. 15. Farid AA, Selim GI, Khater HAA. A novel approach of CT images feature
analysis and prediction to screen for corona virus disease (COVID-19). Int
J Sci Eng Res. 2020;11(3):1–9. 41. Tang Z, et al. Severity assessment of coronavirus disease 2019 (COVID-19)
using quantitative features from chest CT images. 2020. arXiv:2003:11988. 42. Mohamadou Y, Halidou A, Kapen PT. A review of mathematical modeling,
artificial intelligence and datasets used in the study, prediction and
management of COVID-19. Appl Intell. 2020;50(11):3913–25. 16. Kumar R, Arora R, Bansal V, Sahayasheela VJ, Buckchash H, et al. Accurate
prediction of COVID-19 using chest X-ray images through deep feature
learning model with SMOTE and machine learning classifiers. 2020. medRxiv 2020.04.13.20063461. 43. Wang Z, He Z, Shah M, Zhang T, Fan D, Zhang W. Network-based multi-
task learning models for biomarker selection and cancer outcome predic-
tion. Bioinform. 2020;36(6):1814–22. 17. Batista AFM, Miraglia JL, Donato THR, Chiavegatto Filho ADP. COVID-19
diagnosis prediction in emergency care patients: a machine learning
approach. 2020. medRxiv 2020.04.04.20052092. 44. Liu L, Li H, Hu Z, Shi H, Wang Z, Tang J, Zhang M. Learning hierarchical
representations of electronic health records for clinical outcome predic-
tion. AMIA Annu Symp Proc. 2020;2019:597–606. 18. Li K, et al. The clinical and chest CT features associated with severe and
critical COVID-19 pneumonia. Investig Radiol. 2020;55(6):327. 45. Wynants L, Calster BV, Bonten MMJ, et al. Prediction models for diagnosis
and prognosis of covid-19 infection: systematic review and critical
appraisal. BMJ (online). 2020;369:m1328. 19. Liang W, Yao J, Chen A, et al. Early triage of critically ill COVID-19 patients
using deep learning. Nat Commun. 2020;11:3543. 20. Sujath R, Chatterjee JM, Hassanien AE. A machine learning forecast-
ing model for COVID-19 pandemic in India. Stoch Env Res Risk Assess. 2020;34(7):959–72. 46. Molnar C. Interpretable machine learning: a guide for making black box
models explainable; 2019. 46. Molnar C. Interpretable machine learning: a guide for making black box
models explainable; 2019. 21. Dhamodharavadhani S, Rathipriya R, Chatterjee JM. COVID-19 mortality
rate prediction for India using statistical neural network models. Front
Public Health. 2020;8:441. 47. Ito T, Tsubouchi K, Sakaji H, et al. Contextual sentiment neural network for
document sentiment analysis. Data Sci. Eng. 2020;5:180–92. 47. Ito T, Tsubouchi K, Sakaji H, et al. Publisher’s Note
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p15PAF binding to PCNA modulates the DNA sliding surface
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Nucleic acids research
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cc-by
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ABSTRACT Sliding clamps are ring-shaped proteins that tether poly-
merases and other factors of the replisome to the ge-
nomic template, enabling DNA replication and repair. The
molecular architecture of sliding clamps is conserved in
all domains of life. Proliferating Cell Nuclear Antigen
(PCNA)––the eukaryotic sliding clamp––is an 86-kDa ho-
motrimeric ring with a six-fold pseudosymmetric rotation
axis running through the centre of the clamp and a cen-
tral channel lined with lysine and arginine-rich -helices
through which DNA is threaded (1–6). Experimental and
computational analyses of the human PCNA–DNA com-
plex showed that the DNA in the channel is tilted and its
phosphates transiently interact with a set of basic residues
forming a right-hand spiral that matches the DNA pitch
(5,7). This dynamic interaction may allow the clamp to slide
by rotationally tracking the DNA helix, or by a linear mo-
tion uncoupled from the helical pitch, or by a combina-
tion of the two modes (8). A recent report based on coarse-
grained MD simulations (9) supports that the coupling be-
tween rotation and translation in PCNA sliding is weak,
and that the translational motion is much faster than the
rotational one, suggesting that PCNA slides on the dou-
ble helix like a washer on a screw, rather than a nut on a
screw. Importantly, growing evidence confirms the earlier
observation that the PCNA–DNA interaction is critical for
the function of the polymerase bound to the clamp (10). A
recent report showed that acetylation of conserved lysine
residues at the sliding surface of yeast PCNA is induced by
DNA lesions and stimulates repair by homologous recom-
bination (11). Acetylation of K20 negatively affects the pro-
cessivity of the replicative polymerase (pol ), but not that
of the translesion synthesis (TLS) polymerase (pol ), spe- p15PAF is an oncogenic intrinsically disordered pro-
tein that regulates DNA replication and lesion bypass
by interacting with the human sliding clamp PCNA. In
the absence of DNA, p15PAF traverses the PCNA ring
via an extended PIP-box that contacts the sliding sur-
face. Here, we probed the atomic-scale structure of
p15PAF–PCNA–DNA ternary complexes. Crystallogra-
phy and MD simulations show that, when p15PAF oc-
cupies two subunits of the PCNA homotrimer, DNA
within the ring channel binds the unoccupied sub-
unit. C⃝The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Matteo De March1,†, Susana Barrera-Vilarmau2,†, Emmanuele Crespan3,†, Elisa Mentegari3,
Nekane Merino4, Amaia Gonzalez-Maga˜na4, Miguel Romano-Moreno4, Giovanni Maga3,
Ramon Crehuet2, Silvia Onesti1, Francisco J. Blanco4,5 and Alfredo De Biasio
1,6,* 1Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy, 2Institute of Advanced
Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18–26, 08034, Barcelona, Spain, 3Institute of Molecular Genetics,
IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy, 4CIC bioGUNE, Parque Tecnol´ogico de Bizkaia Edificio 800,
48160 Derio, Spain, 5IKERBASQUE, Basque Foundation for Science, Bilbao, Spain and 6Leicester Institute of
Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd,
Leicester LE1 7HB, UK Received October 31, 2017; Revised July 26, 2018; Editorial Decision July 27, 2018; Accepted July 31, 2018 Received October 31, 2017; Revised July 26, 2018; Editorial Decision July 27, 2018; Accepted July 31, 2018 9816–9828
Nucleic Acids Research, 2018, Vol. 46, No. 18
doi: 10.1093/nar/gky723 9816–9828
Nucleic Acids Research, 2018, Vol. 46, No. 18
doi: 10.1093/nar/gky723 Published online 8 August 2018 To whom correspondence should be addressed. Tel: +44 116 252 5391; Email: adb43@leicester.ac.uk
The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors. p15PAF binding to PCNA modulates the DNA sliding
surface Matteo De March1,†, Susana Barrera-Vilarmau2,†, Emmanuele Crespan3,†, Elisa Mentegari3,
Nekane Merino4, Amaia Gonzalez-Maga˜na4, Miguel Romano-Moreno4, Giovanni Maga3,
Ramon Crehuet2, Silvia Onesti1, Francisco J. Blanco4,5 and Alfredo De Biasio
1,6,* Received October 31, 2017; Revised July 26, 2018; Editorial Decision July 27, 2018; Accepted July 31, 2018 Protein expression and DNA duplexes Human PCNA (UniProt: P12004) was produced in Es-
cherichia coli BL21(DE3) cells grown in appropriate cul-
ture media to obtain protein with natural isotopic abun-
dance or uniform enrichment using a clone with N-terminal
His6-tag and PreScission protease cleavage site in a pET-
derived plasmid. For NMR samples the protein was purified
from the soluble fraction by Co2+-affinity chromatography,
cleaved by PreScission protease and polished by gel filtra-
tion chromatography (22). All columns and chromatogra-
phy systems used where from GE Healthcare. Protein elu-
tion was monitored by absorbance at 280 nm and confirmed
by SDS-PAGE. The purified protein contained the extra
sequence GPH- at the N-terminus. The PCNA sample for
crystallization was obtained by introducing two additional
purification steps (4). The sample cleaved with PreScission
protease was dialyzed against 50 mM sodium acetate pH
5.5, 100 mM NaCl. After separation of some precipitated
material, the solution was loaded on a HiTrap Heparin HP
column equilibrated with the same buffer. After column
washing, the protein was eluted with a 0–100% gradient of
50 mM sodium acetate pH 5.5, 2 M NaCl in 20 column vol-
umes (CV). The protein containing fractions of the major
peak were dialyzed against 20 mM Tris–HCl buffer pH 7.6,
150 mM NaCl and injected into a HiTrap Chelating HP col-
umn loaded with Co2+ cations to remove uncleaved PCNA. The flowthrough was loaded on a HiTrap Q Sepharose col-
umn and eluted with a 0–60% gradient of 20 mM Tris–HCl
pH 7.6, 1 M NaCl in 5 CV. The protein containing fractions
were concentrated and polished using a Superdex 200 26/60
column equilibrated with PBS, pH 7.0, and then exchanged
into the crystallization buffer (20 mM Tris–HCl, pH 7.5,
10% glycerol, 2 mM DTT) using a PD10 column. Stock so-
lutions in PBS or crystallization buffer were flash-frozen in
liquid nitrogen and stored at −80◦C. The protein concen-
trations were measured by absorbance at 280 nm using the
extinction coefficient calculated from the amino acid com-
position (15 930 M−1 cm−1). All indicated concentrations of
PCNA samples refer to protomer concentrations. dsDNA
and pDNA duplexes were obtained by mixing equimolar
amounts of the appropriate oligonucleotides, at 93◦C for
2 min with subsequent annealing by slow cooling at room
temperature. ABSTRACT The structure of PCNA-bound p15PAF in the ab-
sence and presence of DNA is invariant, and solution
NMR confirms that DNA does not displace p15PAF
from the ring wall. Thus, p15PAF reduces the avail-
able sliding surfaces of PCNA, and may function as
a belt that fastens the DNA to the clamp during syn-
thesis by the replicative polymerase (pol ). This con-
straint, however, may need to be released for effi-
cient DNA lesion bypass by the translesion synthe-
sis polymerase (pol ). Accordingly, our biochemical
data show that p15PAF impairs primer synthesis by
pol –PCNA holoenzyme against both damaged and
normal DNA templates. In light of our findings, we
discuss the possible mechanistic roles of p15PAF in
DNA replication and suppression of DNA lesion by-
pass. Nucleic Acids Research, 2018, Vol. 46, No. 18 9817 etry of binding dictates the available sliding surfaces. Given
the inhibitory activity of p15 in TLS (18), we hypothesized
that the constraint imposed by p15 to DNA may need to be
released for efficient DNA lesion bypass by the TLS poly-
merase pol . This agrees with our data showing that p15
downregulates the activity of pol –PCNA holoenzyme in
bypassing a cisplatin-induced DNA lesion and in extend-
ing the corresponding undamaged template. Based on our
findings, we discuss the possible mechanistic roles of p15 in
DNA replication and lesion bypass. cialized in traversing DNA lesions such as thymine dimers
or cisplatin adducts, suggesting that the modulation of the
PCNA–DNA interaction can regulate the function of poly-
merases. The front face of the PCNA ring contains the site of
interaction of polymerases and other proteins, named the
PIP-box binding site (3,12). The back face contains the
sites of ubiquitylation and sumoylation (13,14). PIP-box
interacting partners bind PCNA through a short consen-
sus sequence with the pattern QXXhXXaa, where h is an
aliphatic-hydrophobic residue, a aromatic-hydrophobic and
X any residue (3,12). A Protein expression and DNA duplexes We have previously shown that, in absence of DNA, up
to three p15 molecules bind the human trimeric PCNA ring
at a site that extends from the PIP-box binding pocket to
the clamp inner channel (4), and that the disordered p15 N-
termini exit the clamp from the back face and directly inter-
act with DNA (4,21). Negative stain electron microscopy of
a p15–PCNA–DNA ternary complex showed particles with
DNA in the clamp channel (4), but the molecular details of
this assembly remained undefined. yi
In this work, we characterized the structure of ternary
complexes composed of PCNA, DNA and the PCNA-
interacting region of p15, by combining experimental and
computational approaches. The co-crystal structure of
PCNA in complex with two p15 molecules and a 10 bp
primed DNA substrate, solved at 3.2 ˚A resolution, shows
the duplex portion of DNA in the PCNA channel leaning
towards the subunit not occupied by p15. The p15 residues
N-terminal to the PIP-box contact four helices on the ring
inner wall, partly shielding the DNA binding site of two
subunits. This molecular arrangement is recapitulated by
MD simulations of PCNA in complex with two p15 frag-
ments with longer N-termini and a 40 bp DNA duplex. So-
lution NMR experiments show that DNA does not displace
p15 from the inner rim of a PCNA ring in which the three
subunits are occupied by p15. Accordingly, when PCNA is
co-crystallized with three p15 peptides and DNA, the elec-
tron density map does not show features of DNA in the
clamp channel. Thus, p15 outcompetes DNA for a com-
mon binding site in the clamp channel, and the stoichiom- PCNA complexes crystallization and structure determination
p1550–77–PCNA–pDNA
complex. Stocks
of
PCNA,
p1550–77 and pDNA solutions were mixed to final con- MATERIALS AND METHODS y
( ,
)
The PCNA–associated factor p15PAF (hereafter named
p15) is an oncogenic, 11 kDa intrinsically disordered pro-
tein that regulates DNA replication and lesion bypass via a
PIP-box interaction with PCNA (4,15–18). p15 co-localizes
with PCNA in the nucleus of proliferating cells mainly in
the S phase of the cell cycle (18–20). Depletion of p15 sig-
nificantly decreases DNA synthesis (17–20), suggesting that
p15 modulates the function of PCNA as a processivity fac-
tor. Co-immunoprecipitation from pancreatic cancer cell
lines suggests that p15 is part of a DNA-replication complex
with PCNA, pol and the endonuclease Fen-1 in replication
foci (18). During unperturbed DNA replication, PCNA-
bound p15 is mono-ubiquitylated at two N-terminal lysines
(18) (K14 and K25). UV-induced replication stalling trig-
gers the recruitment of pol to the damaged site and the
degradation of ubiquitylated p15 (18), and Povlsen and co-
workers proposed that p15 may compete with pol for
binding to PCNA. However, the molecular mechanisms un-
derlying the function of p15 in DNA replication and DNA
lesion bypass remain unclear. Protein expression and DNA duplexes MD simulations centrations of 0.4, 0.5 and 1.1 mM, respectively (1:1.2:2.7
protein monomer:peptide:pDNA molar ratio), and incu-
bated at room temperature for 30 min before screening
crystallization conditions using the hanging drop vapour
diffusion method. Best diffracting co-crystals grew within
2 days at 4◦C in droplets obtained by mixing 1 l of the
complex solution and 1 l of a solution containing 10%
polyethylene glycol 3350 in 0.1 M sodium acetate buffer,
pH 4.5. The best crystals from the p1550–77–PCNA–DNA
complex diffracted at 3.2 ˚A resolution on the ESRF-ID29
beamline, and belonged to P21 space group. XDS (23) and
the CCP4i suite (24) were used for data processing. Molec-
ular replacement was used to place one hPCNA trimer
(PDB ID: 4D2G) in the asymmetric unit after removing
p1550–77 molecule and solvent. Several cycles of refinement
using REFMAC5 (25) and model building using COOT
(26) were carried out before placing the two p1550–77 chains
into the Fo – Fc electron density map. NCS and TLS
restraints were used. Inspection of the resulting unbiased
difference Fourier’s map inside the PCNA ring showed
some electron density for one DNA strand of the double
helix. Due to the disorder and/or partial occupancy the
second DNA strand was only partially visible. However,
modeling and refining the DNA in the same position as in
the PCNA–DNA binary complex (5) gave rise to reasonable
crystallographic parameters (i.e. model statistics, B-factor
values and quality of the 2Fo – Fc map) and was consistent
with the result from the MD simulations (see text for
further details). Data collection and refinement statistics
are listed in Supplementary Table ST2. Stereo view of
2Fo – Fc electron density map around the p1550–77 peptide
with higher occupancy is displayed in Supplementary
Figure S1. All figures with molecular models were prepared
using PyMOL (www.pymol.org). Atomic coordinates and
structure factors of p1550–77–PCNA–DNA complex have
been deposited with PDB ID: 6EHT. Two 300 ns MD simulation replicas were performed for the
same system. The system is a ternary complex composed of
PCNA, two p15 peptides spanning residues 47–70 and a 40
bp DNA. The initial MD model was built by combining two
different crystal structures: the p1550–77–PCNA complex (4)
and the PCNA–dsDNA complex (5). The p15 peptide was
designed based on the p1550–77–PCNA complex structure
(4). MD simulations The seven C-terminal residues are flexible and do not
interact with PCNA and were thus excluded, while five ex-
tra residues at the flexible N-terminus were added as they
are located in the clamp channel, and may transiently in-
teract with DNA, resulting in a final segment p1547–70. The
DNA segment, with 10 bp in the crystallographic structure,
was also extended by 15 bp in each direction of the heli-
cal axis. Extension of all fragments was performed using
COOT (26). The system was completed by adding TIP3P
water molecules in a truncated dodecahedron box at least
1.5 nm away from the DNA or protein atoms. Cl- and Na+
ions were added for charge neutralization and to mimic ex-
perimental conditions of 100 mM salt concentration. The
system was minimized and equilibrated for 0.1 ns in the
NVT ensemble and then for 0.1 ns in the NPT ensemble. All calculations were performed using Gromacs 5.1 (27) and
parmBSC1 force field (28), the trajectories were analyzed
using MDTraj package (29) and plots were generated using
Matplotlib Python Library (30). The stability of the simu-
lations was checked by visual inspection of the trajectories
and the RMSD with respect to the starting structure as plot-
ted in Supplementary Figure S2. To track the evolution of
the DNA position inside the PCNA ring (Figure 2B), we
have followed this procedure: First, the PCNA chains are
superimposed for all frames, to eliminate global rotation
and translation. Second the centre of each PCNA chain is
calculated for all trajectory frames. Third, DNA base-pairs
17–21 for chain F and 20–24 for chain G are selected as
those being inside the PCNA ring. Its centre is also calcu-
lated for each frame. Fourth, to project into a 2D space, a
Principal Component Analysis is performed for the PCNA
chain centres, and DNA centres are projected into the first
two components of this subspace. Downloaded from https://academic.oup.com/nar/article/46/18/9816/5068262 by gue p1541–72–PCNA complex. Crystals of p1541–72–PCNA
complex were obtained by hanging-drop vapor diffusion
method at 4◦C. Cubic crystals were grown on precipitant
solution containing 28% polyethylene glycol 400, 0.2 M
CaCl2 in 0.1 M Hepes pH 7.0 buffer. Stocks of PCNA,
p1541–72 and DNA solutions were mixed to final con-
centrations of 0.5, 0.5 and 0.5 mM, respectively (1:1:1
protein monomer: peptide: DNA duplex molar ratio),
and incubated at room temperature for 30 min before
crystallization. MD simulations Best diffracting co-crystals grew within 1
day and were flash-frozen directly, and diffracted to 2.9 ˚A
resolution on the Elettra XRD1 beamline, and belonged
to P21 space group (Supplementary Table ST2). XDS (23)
and the CCP4i suite (24) were used for data processing. Molecular replacement was used to place one hPCNA
trimer (PDB ID: 1VYM) in the asymmetric unit. Several
cycles of refinement using REFMAC5 (25) and model
building using COOT (26) were carried out before placing
the three p1541–72 chains into the Fo – Fc electron density
map. Jelly-Body restraints were used. Inspection of the
resulting unbiased difference Fourier’s showed no electron
density attributable to DNA inside the PCNA ring. PCNA complexes crystallization and structure determination p1550–77–PCNA–pDNA
complex. Stocks
of
PCNA,
p1550–77 and pDNA solutions were mixed to final con- 9818 Nucleic Acids Research, 2018, Vol. 46, No. 18 9818 centrations of 0.4, 0.5 and 1.1 mM, respectively (1:1.2:2.7
protein monomer:peptide:pDNA molar ratio), and incu-
bated at room temperature for 30 min before screening
crystallization conditions using the hanging drop vapour
diffusion method. Best diffracting co-crystals grew within
2 days at 4◦C in droplets obtained by mixing 1 l of the
complex solution and 1 l of a solution containing 10%
polyethylene glycol 3350 in 0.1 M sodium acetate buffer,
pH 4.5. The best crystals from the p1550–77–PCNA–DNA
complex diffracted at 3.2 ˚A resolution on the ESRF-ID29
beamline, and belonged to P21 space group. XDS (23) and
the CCP4i suite (24) were used for data processing. Molec-
ular replacement was used to place one hPCNA trimer
(PDB ID: 4D2G) in the asymmetric unit after removing
p1550–77 molecule and solvent. Several cycles of refinement
using REFMAC5 (25) and model building using COOT
(26) were carried out before placing the two p1550–77 chains
into the Fo – Fc electron density map. NCS and TLS
restraints were used. Inspection of the resulting unbiased
difference Fourier’s map inside the PCNA ring showed
some electron density for one DNA strand of the double
helix. Due to the disorder and/or partial occupancy the
second DNA strand was only partially visible. However,
modeling and refining the DNA in the same position as in
the PCNA–DNA binary complex (5) gave rise to reasonable
crystallographic parameters (i.e. model statistics, B-factor
values and quality of the 2Fo – Fc map) and was consistent
with the result from the MD simulations (see text for
further details). Data collection and refinement statistics
are listed in Supplementary Table ST2. Stereo view of
2Fo – Fc electron density map around the p1550–77 peptide
with higher occupancy is displayed in Supplementary
Figure S1. All figures with molecular models were prepared
using PyMOL (www.pymol.org). Atomic coordinates and
structure factors of p1550–77–PCNA–DNA complex have
been deposited with PDB ID: 6EHT. NMR spectroscopy There-
fore, the small measured shifts are not caused by differences
in pH. The titration with the peptide allowed for an ex-
tensive transfer of NMR signal assignments from the free
PCNA to the p1550–77-bound PCNA spectra (with a cover-
age of 72% of non proline residues). For the p1550–77-DNA-
bound PCNA the assignment transfer covered 69% of the
PCNA signals. The CSP caused by the peptide or the ds-
DNA were computed as the weighted average distance be-
tween the backbone amide 1H and 15N chemical shifts in
the free and bound states (31,32). (MACHEREY-NAGEL, D¨uren, Germany) was digested to
confirm the presence of the gene expressing pol . Trans-
formed E. coli cells were used to inoculate a 50 ml starter
culture. After overnight growth at 37◦C, 12 ml of the
starter culture were put into 1 l of LB medium (containing
30 mg/ml kanamycin). After 6 h growth at 37◦C, cells were
harvested by centrifugation and pellet frozen at –80◦C. The
pellet was resuspended in 40ml of lysis buffer (50mM Tris–
HCl pH 7.5, 0.3 M NaCl, 20 mM imidazole, 10% glycerol,
10 mM b-mercaptoethanol [BME], 1× lysozime (Eurobio,
Courtaboeuf, France), 1× ethylenediaminetetraacetic acid
[EDTA]-free protease inhibitor (SIGMAFAST™Protease
Inhibitor Cocktail Tablets, Sigma-Aldrich), 1 mM phenyl-
methane sulfonyl fluoride [PMSF] and lysed through son-
ication. After ultracentrifugation at 98 000g at 4◦C for 1.5
h, the supernatant was loaded onto a 1-ml Ni-NTA column
(HisTrap™HP, GE Healthcare). Column washing was per-
formed with 3 ml of W1 buffer (20 ml Tris–HCl pH 7.5,
1 M NaCl, 20 mM imidazole, 10% glycerol, 10 mM BME)
followed by 3 ml of W2 buffer (10 mM Na-phosphate pH
7.7, 0.3 M NaCl, 20 mM imidazole, 10% glycerol, 10 mM
BME). Elution of target protein was obtained using buffer
H (10 mM Na-phosphate pH 7.7, 0.3 M NaCl, 200 mM
imidazole, 10% glycerol, 10 mM BME). The pol positive
fractions (0.5 ml each) were pooled and overnight dialyzed
with buffer M (20 mM Na-phosphate pH 7.3, 0.1 M NaCl,
10% glycerol, 10 mM BME), in dialysis cassette (Slide-A-
Lyzer™Dialysis Cassettes, 3.5K MWCO, Thermo Scien-
tific). Pool was then loaded onto a 1-ml cation exchanger
column (HiTrap SP, Pharmacia Biotech). Buffer N (20 mM
Na-phosphate pH 7.3, 0.5 M NaCl, 10% glycerol, 10 mM
BME) was used to elute pol with a linear gradient. NMR spectroscopy The pol
positive fractions (0.5 ml each) were aliquoted and stored
at –80◦C in 20% final glycerol. i
Recombinant ScRF-C was obtained as a kind gift from
the laboratory of Alessandro Costa (Francis Crick Insti-
tute), and was prepared following the procedure described
in (34). NMR spectroscopy 1H–15N TROSY spectra were recorded at 35◦C on a Bruker
Avance III 800 MHz (18.8 T) spectrometer equipped with
a cryogenically cooled triple resonance z-gradient probe. A
400 ul sample of 100 M U-[2H,13C, 15N,] PCNA in 20
mM sodium phosphate buffer, 50 mM NaCl, pH 7.0, 20
M 2,2-dimethyl-2-silapentane-5-sulfonate, 0.01% NaN3,
1 mM DTT and 5% 2H2O was placed in a 5 mm Shigemi
NMR tube (without plunger) and increasing volumes of
p1550–77 or dsDNA stock solutions were added and mixed
(by capping and inverting the tube). The peptide and the
DNA stocks solutions were prepared in the same buffer as
the PCNA samples (except that no NaN3, DSS or 2H2O
was added). For that purpose, and to remove unwanted salts
from the synthetic peptide and oligonucleotides, they were
dissolved in 20 mM sodium phosphate buffer, 50 mM NaCl,
pH 7.0 and desalted on a PD-10 Minitrap G25 column. For Nucleic Acids Research, 2018, Vol. 46, No. 18 9819 duplex formation, equimolar amounts were mixed and an-
nealed (2 min at 95◦C in a thermoblock followed by slow
cooling down to room temperature). The duplex and the
peptide were concentrated by ultrafiltration up to 20.84 mM
(dsDNA) or 9.52 mM (p1550–77) and concentrated DTT
was added up to 1 mM. Small volumes of the stock pep-
tide solution were added stepwise to the PCNA samples,
causing a 7% PCNA dilution. TROSY spectra were mea-
sured with 144 or 256 indirect points (alternating between
8 and 14 h total duration). The PCNA–p1550–77 sample re-
mained clear during the 6-day long titration. When the pep-
tide was present at an excess molar ratio of 6.4, the observed
changes in the PCNA spectrum were judged to be within
the experimental error with respect to the previous addi-
tion, and PCNA was considered to be saturated with the
peptide. Then a volume of dsDNA stock was added to a
1:3 molar ratio (PCNA trimer:DNA duplex). Further addi-
tions of DNA did not cause further changes in the PCNA
signals. The structural integrity of the DNA duplex was as-
sessed from the imino signals observed in one-dimensional
proton spectra, whose intensities increased upon duplex ad-
dition. The pH of the PCNA samples was measured at the
beginning and at the end of the titrations inside the NMR
tubes and found to deviate by less than 0.1 units. Crystallographic evidence for p15–PCNA–DNA interactions We co-crystallized human PCNA with a 10-bp primed
DNA duplex (pDNA, as seen in published crystallographic
analysis with both bacterial clamp (35) and Saccharomyces
cerevisiae PCNA (2) and either the p15 fragment that was
previously co-crystallized with PCNA alone (p1550–77, com-
prising the extended PIP-box) (4), or a longer fragment that
includes nine additional N-terminal residues (p1541–72). In
both crystals, incorporation of DNA is confirmed by their
blue color, due to the presence of a Cy5 probe attached to
the DNA (Figure 1A). Crystals including the p1550–77 peptide diffracted to 3.2 ˚A
resolution, and the Fourier difference map calculated after
placing and refining the PCNA ring alone in the asymmetric
unit showed two PIP-box sites occupied by the p1550–77 pep-
tide and electron density features in the channel that may be
attributed to one strand of the DNA duplex. However, elec-
tron density from the second strand is weak and the 4-base
single stranded overhang invisible (Figure 1B). This sug-
gests partial disorder and/or low occupancy of DNA. We
then aligned the previously determined structure of PCNA
bound to a 10 bp dsDNA (5) onto the current model and
found that the DNA duplex fits reasonably well the residual
electron density in the ring channel (Figure 1B). This DNA
position, which leans towards the PCNA subunit not oc-
cupied by p1550–77, also results in the best model statistics,
lowest B-factors of DNA and best quality of the 2Fo – Fc
electron density map (Figure 1C, and Supplementary Ta-
ble ST2) and, importantly, agrees with the results from MD
simulations (see below). The electron density for the DNA
is still weak, indicating low occupancy and/or the presence
of multiple conformations, but allows to propose a model,
which shows the duplex portion of the DNA substrate in
a similar position to that seen in the PCNA–dsDNA bi-
nary model, in the presence of two p15 peptides (Figure
1C). As in the p1550–77–PCNA binary structure (4), the sto-
ichiometry of p1550–77 binding to PCNA is defined by the
crystal packing, where a symmetry-related PCNA molecule
occludes the peptide binding site on one subunit. The two
p1550–77 peptides show different occupancies. MD simulation of PCNA in complex with two p15 PIP-boxes
and a 40 bp DNA Two replicas of a 300 ns MD simulation of a ternary
complex composed of PCNA, two p15 peptides spanning
residues 47–70 and a 40 bp DNA (Supplementary Table
ST1) were performed. The initial MD model was built by
combining features of two different crystal structures: the
p1550–77–PCNA complex (4) and the PCNA–dsDNA com-
plex (5) by extending the DNA segment by 15 bp in each
direction of the helical axis. The p15 peptide for this model
was designed based on the p1550–77–PCNA complex struc-
ture, by deleting the seven p15 C-terminal residues that are
flexible and do not interact with PCNA and adding three
extra residues at the flexible N-terminus, as they are lo-
cated inside the clamp channel, and may transiently inter-
act with DNA. Before starting the simulation, the DNA
was moved away from its binding site on the inner wall of
the clamp channel to a central position with minimal con-
tacts with PCNA. Along the trajectory, the p15 peptides
stay anchored to their binding sites on two PCNA subunits,
while DNA rotates and tilts towards the wall of the sub-
unit that is not occupied by p15 (Figure 2A and B, Supple-
mentary Movie S1 and Supplementary Figure S2). At the
end of the simulation, the DNA segment within the chan-
nel has a position similar to that observed in a previous
250 ns simulation of PCNA bound to a 30 bp DNA in ab-
sence of p15, where DNA simultaneously interacts with two
adjacent sets of DNA-helix matching residues located on
two PCNA subunits, as well as with residues on the clamp
back face (5) (Figure 2A). Importantly, the topology of po-
lar interactions between DNA and the PCNA subunit not
occupied by p15 coincides with that observed in the crys-
tal structure of the PCNA–dsDNA complex (Figure 2C). These results are consistent with the crystal structure of the
p1550–77–PCNA–DNA complex presented in this work and
the proposed position for the partially disordered and/or
incompletely occupied DNA. Altogether, these data suggest
that, in the presence of two p15 molecules, a DNA duplex
longer than 10 bp may still bind one of the three PCNA
sliding surfaces. Crystallographic evidence for p15–PCNA–DNA interactions The peptide
with higher occupancy has its PIP-box (Q62-F69) sitting
on at the PCNA front face forming a 310 helical turn, with
a type-I -turn at its N-terminus (P59-Q62) that positions
residues P52-T58 to contact PCNA helices A2 and B2 on
the clamp inner wall (Figure 1C and Supplementary Figure
S1). Features of the peptide with lower occupancy are com-
parable yet weaker, and the peptide N-terminus could be
modelled up to V53. Because of the partial disorder of DNA
and the presence of a symmetry related loop that plugs the
top of the PCNA channel (and may potentially affect both
DNA positioning and occupancy, Figure 1B), we resorted
to MD simulations to corroborate the crystallographic re-
sults and gain further structural insights on the ternary as-
sembly. Co-crystals of PCNA with p1541–72 and pDNA were also MD simulation of PCNA in complex with two p15 PIP-boxes
and a 40 bp DNA DNA synthesis assays Chemicals. Deoxynucleotides were purchased from Gene-
Spin (Milan, Italy). Chemicals. Deoxynucleotides were purchased from Gene-
Spin (Milan, Italy). Oligonucleotides. The 24-mer template oligonucleotide
containing the cis-PtGG adduct was a kind gift from S.J. Sturla (ETH, Z¨urich) and was prepared and purified as de-
scribed previously (Nilforoushan, 2015). All other DNA
oligonucleotides, all HPLC purified, were synthesized by
Biomers.net (Germany). The 18mer primer oligonucleotide
was 5′-labeled with carboxyfluorescin (FAM) group. The
labeled primer was mixed to the complementary template
oligonucleotide at 1:1 (M/M) ratio in the presence of
150 mM Hepes–KOH pH 7.4, 500 mM KCl, 10 mM MgCl2,
250 mM NH4Ac, heated at 95◦C for 5 min and then slowly
cooled at room temperature. Enzymatic assays. All reactions were performed in a 10
l final volume using the following conditions: 40 mM Tris
pH 8, 1 mM dithiotreitol (DTT), 0.25 mg/ml bovine serum
albumin (BSA), 10 mM Mg2+ (unless otherwise stated in
the figures or figure legends). Enzymes and DNA sub-
strates concentrations are indicated in figure legends. Re-
actions were incubated at 37◦C for 15 min, unless otherwise
stated. Reaction mixtures were stopped by addition of stan-
dard denaturing gel loading buffer (95% formamide, 10 m
methylenediaminetetraacetic acid, xylene cyanol and bro-
mophenol blue), heated at 95◦C for 5 min and loaded on a
7-M urea 12% polyacrylamide (PA) gel. Human recombinant pol η. pJM879 (33), expressing N-
terminal His-tagged human pol , was a kind gift from
R. Woodgate (NIH, USA). Human recombinant pol
was expressed and purified with a modified protocol:
BL21 DE3 competent E. coli cells were transformed with
pJM879. Plates containing 30 mg/ml kanamycin were used
to identify kanamycin-resistant colonies that were picked
and grown overnight at 37◦C. DNA purified from bac-
terial cultures using NucleoSpin® Plasmid (NoLid) kit Electronic image manipulation. Linear transformations
have been applied in some instance to the whole images
using the exposure/brightness filters of Adobe Photoshop
CS6 with the sole purpose of reducing excessive back-
ground. No masking/enhancement was applied to any spe-
cific feature of the images. 9820 Nucleic Acids Research, 2018, Vol. 46, No. 18 RESULTS ure 1D), suggesting that, although incorporated in the crys-
tal, the DNA is not sufficiently ordered to generate a struc-
tured signal. The electron density map showed three p15
fragments spanning residues 50–72 in the corresponding
PIP-box sites, with a conformation analogous to that ob-
served in the co-structure with the p1550–77 peptide (Figure
1E and Supplementary Figure S1). Notably, due to steric
hindrance, the location of the p1541–72 peptides would in-
terfere with DNA binding to PCNA in the orientation ob-
served in the PCNA–dsDNA binary structure (Figure 1E),
suggesting that p15 may outcompete DNA for binding to
the PCNA inner rim. MD simulation of PCNA in complex with two p15 PIP-boxes
and a 40 bp DNA (E) Top view of p1541–72–PCNA complex structure, color-coded as in (C). The DNA shown as a grey transparent ribbon in the same position as in
(C) would cause a steric clash with the N-terminus of the p15 peptide on the third PCNA subunit. ture by isothermal calorimetry (4). For some residues of the
latter group, new signals appearing at saturation could be
tentatively assigned to the bound form (Figure 3A). When
projected onto the PCNA surface (Figure 3C), the residues
whose signals disappear at substoichiometric peptide con-
centration strongly overlap with those at the interface in
the p1550–77–PCNA–DNA crystal structure (Figure 1C), in-
dicating that they interact tightly with PCNA, while the
residues whose persisting signals significantly shift are lo-
cated next to the main binding site (Supplementary Figure
S5). Signals of K77, K80 and H153 disappear, while sig-
nal of K217 persists but is significantly perturbed (Figure
3B, C and Supplementary Figure S5). These are four of the
five residues at the PCNA–DNA interface in the p1550–77–
PCNA–DNA crystal structure (Figure 1B). This is consis-
tent with the partial overlap between the p15 and DNA
binding sites seen in the crystal structure, and suggests that,
in solution, p15 may compete with DNA binding. DNA. In particular, polar contacts between peptide Y47
and G49 and DNA phosphates are detected. Conversely,
DNA shows extensive interactions with the clamp (Figure
2A), and the side chains of many basic residues at the in-
terface can randomly switch between adjacent DNA phos-
phates on a sub-nanosecond time scale (Supplementary
Figure S4), as was observed in the MD simulation of the
binary complex (5). DNA. In particular, polar contacts between peptide Y47
and G49 and DNA phosphates are detected. Conversely,
DNA shows extensive interactions with the clamp (Figure
2A), and the side chains of many basic residues at the in-
terface can randomly switch between adjacent DNA phos-
phates on a sub-nanosecond time scale (Supplementary
Figure S4), as was observed in the MD simulation of the
binary complex (5). MD simulation of PCNA in complex with two p15 PIP-boxes
and a 40 bp DNA The cartoon below shows the sequence of
the DNA substrate. (B) Side view of the 2Fo – Fc omit map of the p1550–77–PCNA–DNA complex refined without DNA in the model, contoured at 0.7
, showing the PCNA central channel. PCNA subunits (green and wheat) and p1550–77 peptide in the background (blue) are in stick representation. The
loop of a symmetry related PCNA molecule is shown in grey. The DNA, modeled as in the PCNA–dsDNA binary structure (5), is shown in orange. (C)
Side- and top views of the refined p1550–77–PCNA–DNA complex structure. PCNA and p1550–77 are shown in ribbon representation, and the protein and
peptide chains colored differently. The DNA, shown in orange, is modeled as in the PCNA–dsDNA binary structure. The 2Fo – Fc map around DNA is
shown contoured at 0.7. (D) Side view of the 2Fo – Fc map of the p1541–72–PCNA complex contoured at 0.7, showing the PCNA central channel as in
(B). (E) Top view of p1541–72–PCNA complex structure, color-coded as in (C). The DNA shown as a grey transparent ribbon in the same position as in
(C) would cause a steric clash with the N-terminus of the p15 peptide on the third PCNA subunit. Figure 1. Crystal structures of human PCNA bound to p15 fragments and DNA. (A) Blue crystals of p1550–77–PCNA–DNA complex. Co-crystals of
PCNA mixed with p1541–72 and DNA were also blue, confirming incorporation of DNA in the crystal lattice. The cartoon below shows the sequence of
the DNA substrate. (B) Side view of the 2Fo – Fc omit map of the p1550–77–PCNA–DNA complex refined without DNA in the model, contoured at 0.7
, showing the PCNA central channel. PCNA subunits (green and wheat) and p1550–77 peptide in the background (blue) are in stick representation. The
loop of a symmetry related PCNA molecule is shown in grey. The DNA, modeled as in the PCNA–dsDNA binary structure (5), is shown in orange. (C)
Side- and top views of the refined p1550–77–PCNA–DNA complex structure. PCNA and p1550–77 are shown in ribbon representation, and the protein and
peptide chains colored differently. The DNA, shown in orange, is modeled as in the PCNA–dsDNA binary structure. The 2Fo – Fc map around DNA is
shown contoured at 0.7. (D) Side view of the 2Fo – Fc map of the p1541–72–PCNA complex contoured at 0.7, showing the PCNA central channel as in
(B). MD simulation of PCNA in complex with two p15 PIP-boxes
and a 40 bp DNA Distance analysis of the intermolecular contacts along
the MD trajectory shows that p15 residues N-terminal to
the PIP-box (residues 52–61) are stably anchored to the in-
ner wall of the PCNA ring, while the extreme N-termini
(residues 47–51) remain flexible and thread the channel
(Supplementary Figure S3 and Supplementary Movie S1). Overall, the p15 peptides establish limited contacts with y
Co-crystals of PCNA with p1541–72 and pDNA were also
obtained and diffracted to 2.9 ˚A resolution (Supplementary
Table ST2). In the electron density map, however, no signif-
icant density was observed that may arise from DNA (Fig- Nucleic Acids Research, 2018, Vol. 46, No. 18 9821 Figure 1. Crystal structures of human PCNA bound to p15 fragments and DNA. (A) Blue crystals of p1550–77–PCNA–DNA complex. Co-crystals of
PCNA mixed with p1541–72 and DNA were also blue, confirming incorporation of DNA in the crystal lattice. The cartoon below shows the sequence of
the DNA substrate. (B) Side view of the 2Fo – Fc omit map of the p1550–77–PCNA–DNA complex refined without DNA in the model, contoured at 0.7
, showing the PCNA central channel. PCNA subunits (green and wheat) and p1550–77 peptide in the background (blue) are in stick representation. The
loop of a symmetry related PCNA molecule is shown in grey. The DNA, modeled as in the PCNA–dsDNA binary structure (5), is shown in orange. (C)
Side- and top views of the refined p1550–77–PCNA–DNA complex structure. PCNA and p1550–77 are shown in ribbon representation, and the protein and
peptide chains colored differently. The DNA, shown in orange, is modeled as in the PCNA–dsDNA binary structure. The 2Fo – Fc map around DNA is
shown contoured at 0.7. (D) Side view of the 2Fo – Fc map of the p1541–72–PCNA complex contoured at 0.7, showing the PCNA central channel as in
(B). (E) Top view of p1541–72–PCNA complex structure, color-coded as in (C). The DNA shown as a grey transparent ribbon in the same position as in
(C) would cause a steric clash with the N-terminus of the p15 peptide on the third PCNA subunit. Downloaded from https://academic.oup.com/nar/article/46/18/9816/5068262 by guest on Downloaded from https://academic.oup.com/nar/article/46/18/9816/5068262 by guest on 24 October 2024 Figure 1. Crystal structures of human PCNA bound to p15 fragments and DNA. (A) Blue crystals of p1550–77–PCNA–DNA complex. Co-crystals of
PCNA mixed with p1541–72 and DNA were also blue, confirming incorporation of DNA in the crystal lattice. NMR analysis of PCNA binding to the p15 PIP-box and a
10 bp DNA In the initial frame, DNA is close to (0,0), the centre of the three PCNA chains, and it quickly translates to a non-
centered position. The final position is retained due to the stabilizing interactions reported in Supplementary Figure S4. (C) Close-up of the equilibrium
state of the MD trajectory showing the PCNA–DNA interface. Interacting PCNA side chains and DNA phosphates (interatomic side chain nitrogen –
DNA phosphorus distance < 4 ˚A) are shown as sticks and black spheres, respectively. DNA in yellow corresponds to the position in the crystallographic
PCNA–dsDNA binary structure (5), with interfacial phosphates shown as spheres. Downloaded from https://academic.oup.com/nar/article/46/18/9816/5068262 by guest on 24 October 2024 Figure 2. MD simulation of PCNA bound to two p1547–70 peptides and a 40 bp DNA (A) Superposition of the initial and equilibrium states of the MD
trajectory. PCNA is shown as a gray surface and DNA as a ribbon. The DNA in magenta (with transparency), and black correspond to the initial and
equilibrium states of the simulation, respectively. PCNA residues whose side chains are engaged in polar contacts with DNA phosphates are labeled. Residues of different PCNA subunits are colored in green, yellow and wheat. (B) Principal Component Analysis of the evolution of the DNA position
inside the PCNA ring (see Methods section for details). The centre of DNA in each trajectory frame was projected onto the first 2 components of the
subspace composed of the centres of the 3 PCNA subunits. Each frame is coloured using the viridis colormap, which goes from dark purple for the first
frames to yellow for the last ones. In the initial frame, DNA is close to (0,0), the centre of the three PCNA chains, and it quickly translates to a non-
centered position. The final position is retained due to the stabilizing interactions reported in Supplementary Figure S4. (C) Close-up of the equilibrium
state of the MD trajectory showing the PCNA–DNA interface. Interacting PCNA side chains and DNA phosphates (interatomic side chain nitrogen –
DNA phosphorus distance < 4 ˚A) are shown as sticks and black spheres, respectively. DNA in yellow corresponds to the position in the crystallographic
PCNA–dsDNA binary structure (5), with interfacial phosphates shown as spheres. ever, we cannot discard the possibility that DNA only par-
tially penetrates the PCNA channel saturated with p1550–77,
either from the front or back face. NMR analysis of PCNA binding to the p15 PIP-box and a
10 bp DNA We characterized the interaction of PCNA with p1550–77
and a 10 bp dsDNA (Supplementary Table ST1) by solution
NMR. 2H–15N-labeled PCNA was firstly titrated with un-
labeled p1550–77 and chemical shift perturbations of PCNA
backbone amide signals analyzed. Two groups of interact-
ing residues were identified: residues whose signals gradu-
ally shift along the titration (Figure 3A and Supplementary
Figure S5), implying a fast exchange regime on the NMR
time scale, and residues whose signals broaden and disap-
pear (due to signal attenuation below the noise level or un-
traceable shifting) at substoichiometric concentrations of
peptide (Figure 3A and B), indicating an intermediate ex-
change regime. For the residues of the first group, a dissoci-
ation constant of ∼35 M at 35◦C was derived (Supplemen-
tary Figure S6), at the same order of magnitude as the 12.5
M constant previously measured at the same tempera- In order to map the interaction site of DNA onto p15-
bound PCNA, a labeled PCNA sample saturated with un-
labeled p1550–77 was used for a second titration with ds-
DNA. Signal shift saturation with dsDNA was achieved at
1:3 molar ratio (PCNA trimer:DNA duplex) (Figure 3A). The fact that, in an analogous titration of PCNA with ds-
DNA in the absence of p1550–77, only ∼10% of complex was
formed at this molar ratio (5) indicates that the presence
of p1550–77 increases the apparent DNA affinity for PCNA. 9822 Nucleic Acids Research, 2018, Vol. 46, No. 18 Figure 2. MD simulation of PCNA bound to two p1547–70 peptides and a 40 bp DNA (A) Superposition of the initial and equilibrium states of the MD
trajectory. PCNA is shown as a gray surface and DNA as a ribbon. The DNA in magenta (with transparency), and black correspond to the initial and
equilibrium states of the simulation, respectively. PCNA residues whose side chains are engaged in polar contacts with DNA phosphates are labeled. Residues of different PCNA subunits are colored in green, yellow and wheat. (B) Principal Component Analysis of the evolution of the DNA position
inside the PCNA ring (see Methods section for details). The centre of DNA in each trajectory frame was projected onto the first 2 components of the
subspace composed of the centres of the 3 PCNA subunits. Each frame is coloured using the viridis colormap, which goes from dark purple for the first
frames to yellow for the last ones. NMR analysis of PCNA binding to the p15 PIP-box and a
10 bp DNA This result is consistent with the fact that no DNA bind-
ing affinity can be biochemically measured for PCNA alone,
whereas a weak but detectable affinity for DNA has been
previously measured (4) by fluorescence polarization in the
presence of p1550–77. Like in PCNA alone titrated with ds-
DNA or pDNA, backbone amide signal shifts are small
(CSP < 0.06 ppm), suggesting that the interaction involves
amino acids with long side chains (Figure 3B). The DNA-
induced perturbations map to residues within the channel
as well as residues that line the p1550–77 binding site on the
front face of the PCNA ring (Figure 3C). The peptide, how-
ever, remains anchored to its binding site since the signals
of PCNA residues that disappear in the presence of sub-
stoichiometric p1550–77 are not recovered by DNA addition
(Figure 3A and B). Overall, these data suggest that DNA
may thread through the PCNA channel when p1550–77 sat-
urates the three PIP-box sites, but that p1550–77 remains an-
chored to the inner wall of the ring. The perturbations near
the front face of the ring may arise from transient contacts
that the threaded DNA makes with p1550–77, slightly alter-
ing the position of the side chains. Based on this data, how- p15-induced inhibition of pol –PCNA holoenzyme activity Given the importance of p15 in regulating the activity of
pol during TLS shown in cell-based experiments (18), we
performed biochemical studies using purified proteins to
gain further mechanistic insight in light of our new struc-
tural data. Thus, we first probed the effects of p15 on the
activity of pol –PCNA holoenzyme in extending a DNA
primer across a site-specific cisplatin lesion. A time course
of pol bypass in the presence or absence of PCNA and p15
was performed with a DNA template bearing a cisPt(GG)
adduct at positions +1 and +2 (Figure 4A). Data shows that
pol alone (40 nM) was able to complete the bypass, result-
ing in the incorporation of two dCMPs opposite both Gs in
the adduct (lanes 6–7, Figure 4A). At increasing times, the
+1 product was reduced, being converted into +2 product. Further elongation past the lesion was minimal, as expected
from the highly distributive nature of pol , especially in Nucleic Acids Research, 2018, Vol. 46, No. 18 9823 Figure 3. NMR analysis of PCNA binding to p1550–77 and a 10 bp dsDNA. (A) Superposition of 1H-15N TROSY spectra of 95 M PCNA in the absence
(black) and presence (green) of 606 M of p1550–77 and (red) of 92 M dsDNA (left) generated with oligonucleotides 3–4 in Supplementary Table S1. Spectra were acquired at 35◦C on samples in 20 mM sodium phosphate, 50 mM NaCl, pH 7.0. The expansion shows signals of three representative residues. A96 signal is not perturbed by the addition of either p1550–77 or DNA. R149 signal persists upon p1550–77 addition, and shifts significantly by the sequential
addition of DNA. Conversely, K77 signal disappears at substoichiometric concentrations of p1550–77, and is not recovered by DNA addition. The dotted
arrow points to a signal that is tentatively assigned to K77 in the p1550–77-bound form. (B) Chemical shift perturbations (CSP) of backbone amide 1H
and 15N NMR resonances induced by DNA. The dotted line indicates the average plus two standard deviations. The green bars indicate the position of
residues that disappear upon addition of substoichiometric p1550–77, and are not drawn to scale. The residues perturbed by p1550–77 and that also appear
at the interface of the p1550–77–PCNA–DNA crystal structure are labeled. (C) Front- and back-face views of PCNA surface. p15-induced inhibition of pol –PCNA holoenzyme activity PCNA residues whose amide
signals disappear in the presence of substoichiometric p1550–77, or are significantly perturbed by DNA are colored green or red, respectively. p1550–77 at
the three PCNA PIP-box sites is shown in sticks, and DNA in the crystallographic position is shown as and orange ribbon. Downloaded from https://academic.oup.com/nar/article/46/18/9816/5068262 by guest on ded from https://academic.oup.com/nar/article/46/18/9816/5068262 by guest on 24 October 2024 Figure 3. NMR analysis of PCNA binding to p1550–77 and a 10 bp dsDNA. (A) Superposition of 1H-15N TROSY spectra of 95 M PCNA in the absence
(black) and presence (green) of 606 M of p1550–77 and (red) of 92 M dsDNA (left) generated with oligonucleotides 3–4 in Supplementary Table S1. Spectra were acquired at 35◦C on samples in 20 mM sodium phosphate, 50 mM NaCl, pH 7.0. The expansion shows signals of three representative residues. A96 signal is not perturbed by the addition of either p1550–77 or DNA. R149 signal persists upon p1550–77 addition, and shifts significantly by the sequential
addition of DNA. Conversely, K77 signal disappears at substoichiometric concentrations of p1550–77, and is not recovered by DNA addition. The dotted
arrow points to a signal that is tentatively assigned to K77 in the p1550–77-bound form. (B) Chemical shift perturbations (CSP) of backbone amide 1H
and 15N NMR resonances induced by DNA. The dotted line indicates the average plus two standard deviations. The green bars indicate the position of
residues that disappear upon addition of substoichiometric p1550–77, and are not drawn to scale. The residues perturbed by p1550–77 and that also appear
at the interface of the p1550–77–PCNA–DNA crystal structure are labeled. (C) Front- and back-face views of PCNA surface. PCNA residues whose amide
signals disappear in the presence of substoichiometric p1550–77, or are significantly perturbed by DNA are colored green or red, respectively. p1550–77 at
the three PCNA PIP-box sites is shown in sticks, and DNA in the crystallographic position is shown as and orange ribbon. replicating damaged templates (36). Addition of a 10-fold
excess of PCNA (lanes 4–5) did not significantly affect pol
activity. Such effect is not surprising: while PCNA has been
shown to stimulate pol activity on DNA substrates with
blocked ends (36,37) or circular templates (38), this stimu-
lation may not be captured on a DNA substrate with free
ends as the one in our assay, because of the rapid turnover
of PCNA across the substrate. p15-induced inhibition of pol –PCNA holoenzyme activity Addition of a 10-fold
excess of PCNA (lanes 4–5) did not significantly affect pol
activity. Such effect is not surprising: while PCNA has been
shown to stimulate pol activity on DNA substrates with
blocked ends (36,37) or circular templates (38), this stimu-
lation may not be captured on a DNA substrate with free
ends as the one in our assay, because of the rapid turnover
of PCNA across the substrate. In addition, if PCNA stim-
ulation of pol results from an increased affinity for the
incorporated nucleotide (38), the saturating nucleotide con-
centrations used in our experiment would mask the stimu-
lation. On the other hand, addition of equimolar amounts
of PCNA and p15 (lanes 2–3) reduced nucleotide incorpo-
ration at +2 and +3 positions reproducibly also in indepen-
dent experiments (Supplementary Figure S7). To rule out
the possibility that the inhibitory effect of p15 on pol ac-
tivity is due to a defective loading of PCNA onto the primer-
template (P/T) junction of the DNA substrate, the TLS
experiment was repeated in the presence of Saccharomyces
Cerevisiae Replication Factor C (ScRF-C), which is able to
load human PCNA on DNA (39). Our results (Supplemen-
tary Figure S8) show that p15 delays TLS by pol –PCNA
across a cis-Pt lesion even in the presence of RF-C. pol alone (lanes 10–13) or in the presence of PCNA (lanes
6–9) showed equal processivity, the addition of PCNA and
p15 reduced nucleotide incorporation at position +2 at the
initial time point (lane 2), and slowed down the synthesis
of the full-length product (lanes 3–5). To confirm that the
inhibitory effect of p15 is mediated by the interaction with
PCNA and not by a direct interaction with pol , the activ-
ity of pol in replicating the substrate was tested in the ab-
sence or presence of p15 alone, showing that p15 alone does
not affect the activity of the polymerase (Supplementary
Figure S9). To assess whether a p15 fragment spanning the
region interacting with PCNA is sufficient to induce the in-
hibitory effect on pol observed with full length p15, pol
activity was tested on the undamaged DNA substrate (Fig-
ure 4C) in the presence of PCNA and in the absence (lanes
2 and 3) or in the presence of p1541–72 peptide (lanes 4,5)
or full length p15 (lanes 6,7). p15-induced inhibition of pol –PCNA holoenzyme activity In addition, if PCNA stim-
ulation of pol results from an increased affinity for the
incorporated nucleotide (38), the saturating nucleotide con-
centrations used in our experiment would mask the stimu-
lation. On the other hand, addition of equimolar amounts
of PCNA and p15 (lanes 2–3) reduced nucleotide incorpo-
ration at +2 and +3 positions reproducibly also in indepen-
dent experiments (Supplementary Figure S7). To rule out
the possibility that the inhibitory effect of p15 on pol ac-
tivity is due to a defective loading of PCNA onto the primer-
template (P/T) junction of the DNA substrate, the TLS
experiment was repeated in the presence of Saccharomyces
Cerevisiae Replication Factor C (ScRF-C), which is able to
load human PCNA on DNA (39). Our results (Supplemen-
tary Figure S8) show that p15 delays TLS by pol –PCNA
across a cis-Pt lesion even in the presence of RF-C. Th
li
i
i
d
i h h pol alone (lanes 10–13) or in the presence of PCNA (lanes
6–9) showed equal processivity, the addition of PCNA and
p15 reduced nucleotide incorporation at position +2 at the
initial time point (lane 2), and slowed down the synthesis
of the full-length product (lanes 3–5). To confirm that the
inhibitory effect of p15 is mediated by the interaction with
PCNA and not by a direct interaction with pol , the activ-
ity of pol in replicating the substrate was tested in the ab-
sence or presence of p15 alone, showing that p15 alone does
not affect the activity of the polymerase (Supplementary
Figure S9). To assess whether a p15 fragment spanning the
region interacting with PCNA is sufficient to induce the in-
hibitory effect on pol observed with full length p15, pol
activity was tested on the undamaged DNA substrate (Fig-
ure 4C) in the presence of PCNA and in the absence (lanes
2 and 3) or in the presence of p1541–72 peptide (lanes 4,5)
or full length p15 (lanes 6,7). Addition of p1541–72 or p15 in
combination with PCNA caused a reduction of DNA syn-
thesis with respect to pol and PCNA alone, which stopped
at positions +1 and +2, corresponding to incorporation op-
posite the first two Gs of the template. These results indicate
that p15 or p1541–72 in conjunction with PCNA are able to
reduce pol synthesis at comparable levels. replicating damaged templates (36). p15-induced inhibition of pol –PCNA holoenzyme activity (B) Time course of the reaction of pol on the template without the lesion (10 nM), in the presence of PCNA/p15 at equimolar
concentrations (lanes 2–5), in the presence of PCNA (lanes 6–9), or pol alone (lanes 10–13), with all four dNTPs at the indicated concentration. (C)
Reaction of pol replicating the undamaged template in the presence of PCNA and in the absence or presence of p1541–72 peptide or full length p15. Reactants at the indicated concentrations were incubated at 37◦C for 30 s and the reaction was stopped by addition of standard denaturing gel loading
buffer. In all these experiments, PCNA was not ubiquitylated. These experiments show that p15 downregulates the activity of pol –PCNA holoenzyme
in bypassing a cisplatin lesion as well as in replicating a normal DNA substrate. Downloaded from https://academic.oup.com/nar/article/46/18/98 Figure 4. Inhibition of pol holoenzyme by p15 (A) Time course of the reaction of pol in the presence of PCNA/p15 at equimolar concentrations
(Lanes 2 and 3), in the presence of PCNA (Lanes 4 and 5), or with pol alone (lanes 6 and 7) on a cisPt(GG) template (10 nM), with all four dNTPs at the
indicated concentration. (B) Time course of the reaction of pol on the template without the lesion (10 nM), in the presence of PCNA/p15 at equimolar
concentrations (lanes 2–5), in the presence of PCNA (lanes 6–9), or pol alone (lanes 10–13), with all four dNTPs at the indicated concentration. (C)
Reaction of pol replicating the undamaged template in the presence of PCNA and in the absence or presence of p1541–72 peptide or full length p15. Reactants at the indicated concentrations were incubated at 37◦C for 30 s and the reaction was stopped by addition of standard denaturing gel loading
buffer. In all these experiments, PCNA was not ubiquitylated. These experiments show that p15 downregulates the activity of pol –PCNA holoenzyme
in bypassing a cisplatin lesion as well as in replicating a normal DNA substrate. stants for the pol –PCNA (Kd = 0.4 M, measured by sur-
face plasmon resonance at 25◦C) (40) and p15–PCNA (Kd
= 1.1 M, measured by ITC at 25◦C) (4) binding equilibria,
we estimated the relative populations of binary complexes
assuming that binding of pol and p15 to PCNA is mu-
tually exclusive. p15-induced inhibition of pol –PCNA holoenzyme activity The limited number of contacts between p1550–77 and
DNA observed in our computational analysis suggests that
p15 mostly operates as a passive steric obstacle constrain-
ing the DNA in the clamp channel. Critically, p15 shields
key residues at the PCNA sliding surfaces, confining DNA
in discrete positions, which depend on the p15 stoichiome-
try of binding (Figure 5A–D). This mode of binding, with
DNA partially competing with p15 for a single binding site
on the clamp inner ring, is also supported by (i) our NMR
study showing that DNA does not disengage p15 from the
inner wall of PCNA saturated with p15 and (ii) our struc-
ture of PCNA co-crystallized with three p15 peptides and
DNA, showing that DNA does not occupy the central chan-
nel. Because p15 is stably associated with PCNA on chro-
matin during the S phase of the cell cycle (18), it is likely
that during replication polymerases and other DNA-editing
enzymes bind one or two PCNA sites only, so that the free
sites(s) would be available for p15 binding. Indeed, the cat-
alytic subunit of pol (p125) and Fen-1 were co-precipitated
with p15 and PCNA from pancreatic cell lysates (19). While
Fen-1 is a monomeric enzyme that binds PCNA through a p15-induced inhibition of pol –PCNA holoenzyme activity Under this assumption, 42% of pol and
23% of p15 are saturated with PCNA. Thus, each dNTP in-
sertion step is carried out by a combination of pol alone
and pol holoenzyme. However, if p15 did inhibit binding
of pol to PCNA, a drop of pol activity in the presence of
p15 should not be observed, because the latter would favor
the formation of free pol , which shows full activity. Fur-
thermore, the relatively high (30 nM) (36) and low (5 M)
(4) affinity of pol and p15 for DNA, respectively, rules out
that p15 may prevent the access of pol to the DNA P/T
junction. This suggests that inhibition of pol processivity
in the presence of PCNA and p15 is due to the formation
of an impaired ternary p15–PCNA–pol holoenzyme, defi-
cient in primer synthesis against both damaged and normal
templates. the structure of the p15 segment interacting with PCNA is
invariant in the absence or presence of DNA. In our MD
simulations, the disordered N-termini of the p15 fragments
exit the PCNA back face, a topology analogous to that of
full length p15 bound to PCNA in the absence of DNA
(4,21). The limited number of contacts between p1550–77 and
DNA observed in our computational analysis suggests that
p15 mostly operates as a passive steric obstacle constrain-
ing the DNA in the clamp channel. Critically, p15 shields
key residues at the PCNA sliding surfaces, confining DNA
in discrete positions, which depend on the p15 stoichiome-
try of binding (Figure 5A–D). This mode of binding, with
DNA partially competing with p15 for a single binding site
on the clamp inner ring, is also supported by (i) our NMR
study showing that DNA does not disengage p15 from the
inner wall of PCNA saturated with p15 and (ii) our struc-
ture of PCNA co-crystallized with three p15 peptides and
DNA, showing that DNA does not occupy the central chan-
nel. the structure of the p15 segment interacting with PCNA is
invariant in the absence or presence of DNA. In our MD
simulations, the disordered N-termini of the p15 fragments
exit the PCNA back face, a topology analogous to that of
full length p15 bound to PCNA in the absence of DNA
(4,21). p15-induced inhibition of pol –PCNA holoenzyme activity Addition of p1541–72 or p15 in
combination with PCNA caused a reduction of DNA syn-
thesis with respect to pol and PCNA alone, which stopped
at positions +1 and +2, corresponding to incorporation op-
posite the first two Gs of the template. These results indicate
that p15 or p1541–72 in conjunction with PCNA are able to
reduce pol synthesis at comparable levels. Considering the concentrations of pol , PCNA and p15
in the assays in Figure 4A and B, and the dissociation con- The replication experiment was repeated with the same
DNA substrate without the lesion (Figure 4B). Again, while 9824 Nucleic Acids Research, 2018, Vol. 46, No. 18 Figure 4. Inhibition of pol holoenzyme by p15 (A) Time course of the reaction of pol in the presence of PCNA/p15 at equimolar concentrations
(Lanes 2 and 3), in the presence of PCNA (Lanes 4 and 5), or with pol alone (lanes 6 and 7) on a cisPt(GG) template (10 nM), with all four dNTPs at the
indicated concentration. (B) Time course of the reaction of pol on the template without the lesion (10 nM), in the presence of PCNA/p15 at equimolar
concentrations (lanes 2–5), in the presence of PCNA (lanes 6–9), or pol alone (lanes 10–13), with all four dNTPs at the indicated concentration. (C)
Reaction of pol replicating the undamaged template in the presence of PCNA and in the absence or presence of p1541–72 peptide or full length p15. Reactants at the indicated concentrations were incubated at 37◦C for 30 s and the reaction was stopped by addition of standard denaturing gel loading
buffer. In all these experiments, PCNA was not ubiquitylated. These experiments show that p15 downregulates the activity of pol –PCNA holoenzyme
in bypassing a cisplatin lesion as well as in replicating a normal DNA substrate. Figure 4. Inhibition of pol holoenzyme by p15 (A) Time course of the reaction of pol in the presence of PCNA/p15 at equimolar concentrations
(Lanes 2 and 3), in the presence of PCNA (Lanes 4 and 5), or with pol alone (lanes 6 and 7) on a cisPt(GG) template (10 nM), with all four dNTPs at the
indicated concentration. Topology and stoichiometry of p15 binding to PCNA loaded
on DNA The data reported in this study reveals that DNA can thread
through the PCNA ring along with two p15 chains, and that Nucleic Acids Research, 2018, Vol. 46, No. 18 9825 Figure 5. Possible effects of p15 on PCNA sliding (A) PCNA can diffuse
on DNA contacting three equivalent sliding surfaces, each composed of
two homologous sets of basic residues spanning across the interface of two
subunits (the 3 PCNA subunits are colored green, yellow and wheat). (B–
D) The stoichiometry of p15 binding to the PCNA homotrimer defines
the available surfaces for clamp sliding. Whether a configuration where
PCNA simultaneously binds three p15 chains and DNA, can be achieved,
and whether it completely or partially hinders sliding, remains to be deter-
mined. PCNA–DNA interaction is weak and transient (2,4,5,7,9),
and recent evidence showed that human pol maintains
a loose association with PCNA while replicating (49). Be-
cause the polymerase needs to maintain a fixed position rel-
ative to the phosphodiester backbone at the P/T junction, a
constrained orientation of PCNA with respect to the helical
pitch may improve the overall stability of the holoenzyme. Such stabilizing role of p15 would explain the negative ef-
fects of p15 knockdown on DNA synthesis (19,20). PCNA–DNA interaction is weak and transient (2,4,5,7,9),
and recent evidence showed that human pol maintains
a loose association with PCNA while replicating (49). Be-
cause the polymerase needs to maintain a fixed position rel-
ative to the phosphodiester backbone at the P/T junction, a
constrained orientation of PCNA with respect to the helical
pitch may improve the overall stability of the holoenzyme. Such stabilizing role of p15 would explain the negative ef-
fects of p15 knockdown on DNA synthesis (19,20). p
y
(
,
)
While
a
high-resolution
structure
of
a
PCNA–
polymerase–DNA complex is still awaiting, both the
medium resolution EM structure (50) and MD simulations
of Pyrococcus furiosus (Pfu) PCNA bound to PolB and
DNA (51) show that DNA within the clamp is tilted. Particularly, the MD model of the complex in polymer-
izing mode shows features at the clamp–DNA interface
analogous to those observed in the p1550–77–PCNA–DNA
model presented here, where five conserved positively
charged residues, matching the dsDNA B-helix archi-
tecture, interact with five consecutive phosphates of one
DNA strand, suggesting that this key determinant of the
interaction is conserved and may be present in the pol
holoenzyme. Topology and stoichiometry of p15 binding to PCNA loaded
on DNA Single molecule experiments suggested that PCNA may
slide by rotationally tracking the DNA helix or by a less
frequent translational mode uncoupled from the helical
pitch (8), while a recent computational work predicts that
the coupling between rotation and translation is weak (9),
suggesting that the translational mode is prevalent. Thus,
p15 binding to PCNA may increase the rotation-translation
coupling by reducing the available sliding surfaces (Figure
5). This, together with the DNA binding activity of the p15
disordered N-terminus, may result in a slower diffusion of
PCNA on DNA. Therefore, p15 might regulate the sliding
velocity of PCNA, and this function may be required for the
DNA damage response to prevent a rapid drift of PCNA
from stalled forks in between polymerase swapping events. Upon encounter of a DNA lesion, pol dissociates from
PCNA, which becomes ubiquitylated, and is replaced by
pol that replicates DNA past the lesion (54,55). While
the ubiquitin moieties of ubiquitylated-PCNA may interact
with the C-terminal ubiquitin binding motif (UBZ) of pol
, a large body of data argues that ubiquitylation of PCNA
is not strictly necessary for pol recruitment and activity
in TLS (38,56,57). Notably, a recent report unambiguously
demonstrates that the binding of pol to PCNA, and DNA Single molecule experiments suggested that PCNA may
slide by rotationally tracking the DNA helix or by a less
frequent translational mode uncoupled from the helical
pitch (8), while a recent computational work predicts that
the coupling between rotation and translation is weak (9),
suggesting that the translational mode is prevalent. Thus,
p15 binding to PCNA may increase the rotation-translation
coupling by reducing the available sliding surfaces (Figure
5). This, together with the DNA binding activity of the p15
disordered N-terminus, may result in a slower diffusion of
PCNA on DNA. Therefore, p15 might regulate the sliding
velocity of PCNA, and this function may be required for the
DNA damage response to prevent a rapid drift of PCNA
from stalled forks in between polymerase swapping events. The 78-kDa pol is less bulky than pol and binds
PCNA mainly through a single PIP-box located at its flex-
ible C-terminus (40). Considering the comparable PIP-box
affinities for PCNA (4,40), pol and p15 may co-exist on
one PCNA homotrimer. Topology and stoichiometry of p15 binding to PCNA loaded
on DNA The recently determined negative
stain EM structure of ubiquitylated PCNA bound to pol
and DNA (48), where two PIP-box sites would be free for
p15 binding, supports this hypothesis (Figure 6A). p
y
pp
g
Upon encounter of a DNA lesion, pol dissociates from
PCNA, which becomes ubiquitylated, and is replaced by
pol that replicates DNA past the lesion (54,55). While
the ubiquitin moieties of ubiquitylated-PCNA may interact
with the C-terminal ubiquitin binding motif (UBZ) of pol
, a large body of data argues that ubiquitylation of PCNA
is not strictly necessary for pol recruitment and activity
in TLS (38,56,57). Notably, a recent report unambiguously
demonstrates that the binding of pol to PCNA, and DNA Topology and stoichiometry of p15 binding to PCNA loaded
on DNA Indeed, mutation of residues at the PCNA–
DNA interface impairs both initiation of DNA synthesis
(10) and processivity of pol (11), suggesting that the
PCNA–DNA interactions control both clamping and slid-
ing activities of PCNA in processive DNA replication. In
their computational work, Ivanov and co-workers (51) also
showed that the repositioning of the PolB core during the
conformational switch from polymerizing to editing modes
forces the DNA to tilt from one side of the PfuPCNA
channel to the other. A 30◦change in DNA tilt within the
clamp in the catalytic core of the bacterial replisome from
polymerizing to editing modes was also observed in the
recent cryo-EM work by Lamers and colleagues (52,53). Perhaps, in the human pol holoenzyme, p15 plays a role
in guiding DNA through the PCNA inner rim in between
DNA synthesis and editing steps of the polymerase. Figure 5. Possible effects of p15 on PCNA sliding (A) PCNA can diffuse
on DNA contacting three equivalent sliding surfaces, each composed of
two homologous sets of basic residues spanning across the interface of two
subunits (the 3 PCNA subunits are colored green, yellow and wheat). (B–
D) The stoichiometry of p15 binding to the PCNA homotrimer defines
the available surfaces for clamp sliding. Whether a configuration where
PCNA simultaneously binds three p15 chains and DNA, can be achieved,
and whether it completely or partially hinders sliding, remains to be deter-
mined. single PIP-box (41), human pol consists of four subunits
(p125, p66, p50 and p12) and all of them are required for
optimal holoenzyme activity (42). Although all four sub-
units contain potential PIP-box sites, examination of re-
constituted holoenzymes in which the PCNA binding mo-
tifs have been mutated or inactivated have only been tested
for p12 and p66 (43–45), and there may exist multiple sub-
assemblies of pol in vivo (46,47). Thus, considering its
small size and high flexibility, p15 may coexist with pol on
the same PCNA homotrimer in a replicating cell. Likewise,
a comparison of the Fen-1–PCNA (41) (PDB ID: 1UL1)
and p1550–77–PCNA (4) (PDB ID: 4D20) crystal structures
suggests that Fen-1 and p15 may both be accommodated on
a single PCNA ring. DNA synthesis and editing steps of the polymerase. Possible roles of p15 in the holoenzymes with the replicative
and TLS polymerases We propose that p15 is part of the human holoenzyme that
replicates the DNA lagging strand, and may function to fas-
ten the DNA within the clamp channel by reducing the ac-
cessible sliding surfaces. We and others have shown that the 9826 Nucleic Acids Research, 2018, Vol. 46, No. 18 Figure 6. Structural models of pol -PCNA holoenzymes with p15 and DNA. (A) The PCNA trimer of the p1550–77–PCNA crystal structure (PDB ID:
4D2G) was superposed to PCNA of the low-resolution structure of human pol –PCNA–DNA generated from EM data (PDB ID: 3JA9 and 3JAA) (33). DNA is shown in black. The vacant PIP-box site on PCNA (subunit wheat) was occupied by the C-terminal PIP-box of pol using the crystal structure
of human PCNA bound to pol residues 700–710 (chain W of PDB ID 2ZVK) (40). The dashed line indicates the flexible pol C-terminus (residues
433–699). (B) The PCNA trimer of the structure of p1550–77–PCNA–DNA complex (PDB: 6EHT) was superposed to PCNA of the pol –PCNA–DNA
(48) complex (PDB: 3JA9 and and 3JAA). The DNA of the first complex (elongated to 40 bp) is shown as an orange ribbon, that of the latter (elongated
to 25 bp) as a black ribbon. According to these models, it is possible that p15 may co-exist with pol on the same PCNA ring. However, the constraint on
DNA within the clamp channel imposed by p15 may hinder the translocation of pol holoenzyme on DNA. Figure 6. Structural models of pol -PCNA holoenzymes with p15 and DNA. (A) The PCNA trimer of the p1550–77–PCNA crystal structure (PDB ID:
4D2G) was superposed to PCNA of the low-resolution structure of human pol –PCNA–DNA generated from EM data (PDB ID: 3JA9 and 3JAA) (33). DNA is shown in black. The vacant PIP-box site on PCNA (subunit wheat) was occupied by the C-terminal PIP-box of pol using the crystal structure
of human PCNA bound to pol residues 700–710 (chain W of PDB ID 2ZVK) (40). The dashed line indicates the flexible pol C-terminus (residues
433–699). (B) The PCNA trimer of the structure of p1550–77–PCNA–DNA complex (PDB: 6EHT) was superposed to PCNA of the pol –PCNA–DNA
(48) complex (PDB: 3JA9 and and 3JAA). The DNA of the first complex (elongated to 40 bp) is shown as an orange ribbon, that of the latter (elongated
to 25 bp) as a black ribbon. Supplementary Data are available at NAR Online. Supplementary Data are available at NAR Online. Supplementary Data are available at NAR Online. Possible roles of p15 in the holoenzymes with the replicative
and TLS polymerases According to these models, it is possible that p15 may co-exist with pol on the same PCNA ring. However, the constraint on
DNA within the clamp channel imposed by p15 may hinder the translocation of pol holoenzyme on DNA. DNA are deposited in the Biological Magnetic Resonance
database BMRB under accession code 27558. synthesis by a pol holoenzyme are both independent of
PCNA monoubiquitylation (36). DNA are deposited in the Biological Magnetic Resonance
database BMRB under accession code 27558. During
unperturbed
replication,
p15
is
mono-
ubiquitylated at K15 and K24 and is degraded by the
proteasome after UV irradiation or cisplatin treatment
(18). Degradation of ubiquitylated p15 upon DNA damage
is required for the recruitment of pol to the replication
foci and efficient lesion bypass, and the authors suggested
that p15 may prevent the binding of pol to PCNA. In
this work, we showed that p15 has an inhibitory activity on
the pol –PCNA holoenzyme in synthesizing past the 5′dG
of a 1,2-d(GpG) cisplatin DNA adduct and in extending
the undamaged template. Importantly, a p15 fragment
spanning only the region of interaction with PCNA is
sufficient to inhibit pol activity. Rather than preventing
pol from binding to PCNA, our data suggests that p15
inhibits pol activity by associating to the holoenzyme, a
possibility supported by structural considerations (Figure
6A). Although the DNA in the EM map of pol bound
to ubiquitylated PCNA and DNA is not fully defined
(48), the DNA duplex within PCNA lies close to one
of the clamp subunits, in a position different from that
observed in our p15–PCNA–DNA complex structure
(Figure 6B). We propose that the constraint imposed to
DNA by p15 in the central channel of PCNA may hinder
the advancement of DNA in the pol active site required
for the incorporation of the nucleotide opposite to the 5′dG
of the DNA template. Thus, after the insertion of the first
dCMP, the polymerase may become ‘idle’ and dissociate
from PCNA. Further high-resolution structural studies on
pol holoenzyme will shed light on this possibility. FUNDING Italian Association for Cancer Research [iCARE fellow-
ship from AIRC and the European Commission to A.D.B. and AIRC Grant IG14718 to S.O., IG20762 to G.M
and MFAG18811 to E.C.]; Spanish Ministry of Economy
and Competitiveness [CTQ2017-83810-R grant to F.J.B.];
CIC bioGUNE acknowledges MINECO for the Severo
Ochoa Excellence Accreditation [SEV-2016-0644]; S.B-V. and A.G.-M. acknowledge fellowships from MINECO
[BES-2013-063991 and BES-2015-075847]; M.R.-M. is sup-
ported by a pre-doctoral fellowship from the Basque ACKNOWLEDGEMENTS We thank Adriana L. Rojas (CIC bioGUNE) for help with
crystal structure determination, and Pietro Roversi (Univer-
sity of Leicester) for his useful comments. We acknowledge
CERIC-ERIC for the use of the XRD1 beamline at Elettra
Sincrotrone Trieste. The authors thankfully acknowledge
the computer resources, technical expertise and assistance
provided by the Red Espa˜nola de Supercomputaci´on, the
Barcelona Supercomputing Centre, and the Catalan CSUC. Author Contributions: G.M., R.C., S.O., F.J.B. and A.D.B. guided the research experiments. M.D.M., A.G.-M. and
M.R.-M. crystallised the complexes, solved and refined the
crystal structures. S.B.-V. performed and analyzed the MD
data. E.M. and E.C. purified pol and performed the func-
tional assays. N.M. purified PCNA and p15PAF proteins. F.J.B. performed and A.D.B. analyzed the NMR exper-
iments. A.D.B. wrote the manuscript with contributions
from all other authors. REFERENCES Ivani,I., Dans,P.D., Noy,A., Perez,A., Faustino,I., Hospital,A.,
Walther,J., Andrio,P., Goni,R., Balaceanu,A. et al. (2016) Parmbsc1:
a refined force field for DNA simulations. Nat. Methods, 13, 55–58. 9. Daitchman,D., Greenblatt,H.M. and Levy,Y. (2018) Diffusion of
ring-shaped proteins along DNA: case study of sliding clamps. Nucleic Acids Res., 46, 5935–5949. 29. McGibbon,R.T., Beauchamp,K.A., Harrigan,M.P., Klein,C.,
Swails,J.M., Hernandez,C.X., Schwantes,C.R., Wang,L.P., Lane,T.J. and Pande,V.S. (2015) MDTraj: A modern open library for the
analysis of molecular dynamics trajectories. Biophys. J., 109,
1528–1532. 10. Fukuda,K., Morioka,H., Imajou,S., Ikeda,S., Ohtsuka,E. and
Tsurimoto,T. (1995) Structure-function relationship of the eukaryotic
DNA replication factor, proliferating cell nuclear antigen. J. Biol. Chem., 270, 22527–22534. 30. Hunter,J.D. (2007) Matplotlib: A 2D graphics environment. Comput. Sci. Eng., 9, 90–95. 06826 11. Billon,P., Li,J., Lambert,J.P., Chen,Y., Tremblay,V., Brunzelle,J.S.,
Gingras,A.C., Verreault,A., Sugiyama,T., Couture,J.F. et al. (2017)
Acetylation of PCNA sliding surface by Eco1 promotes genome
stability through homologous recombination. Mol. Cell, 65, 78–90. 31. Sanchez,R., Torres,D., Prieto,J., Blanco,F.J. and Campos-Olivas,R. (2007) Backbone assignment of human proliferating cell nuclear
antigen. Biomol. NMR Assigm., 1, 245–247. 12. De Biasio,A. and Blanco,F.J. (2013) Proliferating cell nuclear antigen
structure and interactions: too many partners for one dancer? Adv. Protein Chem. Struct. Biol., 91, 1–36. 32. De Biasio,A., Campos-Olivas,R., Sanchez,R., Lopez-Alonso,J.P.,
Pantoja-Uceda,D., Merino,N., Villate,M., Martin-Garcia,J.M.,
Castillo,F., Luque,I. et al. (2012) Proliferating Cell Nuclear Antigen
(PCNA) interactions in solution studied by NMR. PLoS One, 7,
e48390. 13. Freudenthal,B.D., Gakhar,L., Ramaswamy,S. and Washington,M.T. (2010) Structure of monoubiquitinated PCNA and implications for
translesion synthesis and DNA polymerase exchange. Nat. Struct. Mol. Biol., 17, 479–484. 33. Frank,E.G., McDonald,J.P., Karata,K., Huston,D. and Woodgate,R. (2012) A strategy for the expression of recombinant proteins
traditionally hard to purify. Anal. Biochem., 429, 132–139.l 14. Freudenthal,B.D., Brogie,J.E., Gakhar,L., Kondratick,C.M. and
Washington,M.T. (2011) Crystal structure of SUMO-modified
proliferating cell nuclear antigen. J. Mol. Biol., 406, 9–17. 34. Yeeles,J.T.P., Janska,A., Early,A. and Diffley,J.F.X. (2017) How the
eukaryotic replisome achieves rapid and efficient DNA replication. Mol. Cell, 65, 105–116. 15. De Biasio,A., Ibanez de Opakua,A., Cordeiro,T.N., Villate,M.,
Merino,N., Sibille,N., Lelli,M., Diercks,T., Bernado,P. and
Blanco,F.J. (2014) p15PAF is an intrinsically disordered protein with
nonrandom structural preferences at sites of interaction with other
proteins. Biophys. J., 106, 865–874. 35. Georgescu,R.E., Kim,S.S., Yurieva,O., Kuriyan,J., Kong,X.P. and
O’Donnell,M. (2008) Structure of a sliding clamp on DNA. Cell, 132,
43–54. 36. Hedglin,M., Pandey,B. and Benkovic,S.J. (2016) Characterization of
human translesion DNA synthesis across a UV-induced DNA lesion. Elife, 5, e19788. 16. REFERENCES 1. Krishna,T.S., Kong,X.P., Gary,S., Burgers,P.M. and Kuriyan,J. (1994) Crystal structure of the eukaryotic DNA polymerase
processivity factor PCNA. Cell, 79, 1233–1243. 21. Cordeiro,T.N., Chen,P.C., De Biasio,A., Sibille,N., Blanco,F.J.,
Hub,J.S., Crehuet,R. and Bernado,P. (2017) Disentangling
polydispersity in the PCNA-p15PAF complex, a disordered, transient
and multivalent macromolecular assembly. Nucleic Acids Res., 45,
1501–1515. 2. McNally,R., Bowman,G.D., Goedken,E.R., O’Donnell,M. and
Kuriyan,J. (2010) Analysis of the role of PCNA-DNA contacts
during clamp loading. BMC Struct. Biol., 10, 3. 22. De Biasio,A., Sanchez,R., Prieto,J., Villate,M., Campos-Olivas,R. and Blanco,F.J. (2011) Reduced stability and increased dynamics in
the human proliferating cell nuclear antigen (PCNA) relative to the
yeast homolog. PLoS One, 6, e16600. 3. Mailand,N., Gibbs-Seymour,I. and Bekker-Jensen,S. (2013)
Regulation of PCNA-protein interactions for genome stability. Na
Rev. Mol. Cell Biol., 14, 269–282. 4. De Biasio,A., de Opakua,A.I., Mortuza,G.B., Molina,R.,
Cordeiro,T.N., Castillo,F., Villate,M., Merino,N., Delgado,S.,
Gil-Carton,D. et al. (2015) Structure of p15(PAF)-PCNA complex
and implications for clamp sliding during DNA replication and
repair. Nat. Commun., 6, 6439. y
g
23. Kabsch,W. (2010) Integration, scaling, space-group assignment and
post-refinement. Acta Crystallogr. D. Biol. Crystallogr., 66, 133–144 24. Winn,M.D., Ballard,C.C., Cowtan,K.D., Dodson,E.J., Emsley,P.,
Evans,P.R., Keegan,R.M., Krissinel,E.B., Leslie,A.G., McCoy,A. et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D. Biol. Crystallogr., 67, 235–242. 5. De March,M., Merino,N., Barrera-Vilarmau,S., Crehuet,R.,
Onesti,S., Blanco,F.J. and De Biasio,A. (2017) Structural basis of
human PCNA sliding on DNA. Nat. Commun., 8, 13935. 25. Murshudov,G.N., Skubak,P., Lebedev,A.A., Pannu,N.S.,
Steiner,R.A., Nicholls,R.A., Winn,M.D., Long,F. and Vagin,A.A. (2011) REFMAC5 for the refinement of macromolecular crystal
structures. Acta Crystallogr. D. Biol. Crystallogr., 67, 355–367. 6. De March,M. and De Biasio,A. (2017) The dark side of the ring: role
of the DNA sliding surface of PCNA. Crit. Rev. Biochem. Mol. Biol.,
52, 663–673. i
structures. Acta Crystallogr. D. Biol. Crystallogr., 67, 355–3 26. Emsley,P., Lohkamp,B., Scott,W.G. and Cowtan,K. (2010) Features
and development of Coot. Acta Crystallogr. D. Biol. Crystallogr., 66
486–501. 7. Ivanov,I., Chapados,B.R., McCammon,J.A. and Tainer,J.A. (2006)
Proliferating cell nuclear antigen loaded onto double-stranded DNA:
dynamics, minor groove interactions and functional implications. Nucleic Acids Res., 34, 6023–6033. 27. Abraham,M.J., Murtola,T., Schulz,R., Pail,S., Smith,J.C., Hess,B. and Lindhal,E. (2015) GROMACS: High performance molecular
simulations through multi- level parallelism from laptops to
supercomputers. SoftwareX, 1–2, 19–25 8. Kochaniak,A.B., Habuchi,S., Loparo,J.J., Chang,D.J.,
Cimprich,K.A., Walter,J.C. and van Oijen,A.M. (2009) Proliferating
cell nuclear antigen uses two distinct modes to move along DNA. J. Biol. Chem., 284, 17700–17710. 28. DATA AVAILABILITY Atomic
coordinates
of
p1550–77–PCNA–DNA
and
p1541–72–PCNA complexes have been deposited in the
Protein Databank under the accession codes 6EHT and
6GWS, respectively. Assignments of backbone amide
NMR resonances of human PCNA bound to p1550–77 and Nucleic Acids Research, 2018, Vol. 46, No. 18 9827 Nucleic Acids Research, 2018, Vol. 46, No. 18 9827 Government [PRE 2016 2 0249]. Funding for open access
charge: University of Leicester.l Government [PRE 2016 2 0249]. Funding for open access
charge: University of Leicester.l dynamics reveals a key role for PAF15 ubiquitylation in
DNA-damage bypass. Nat. Cell Biol., 14, 1089–1098. dynamics reveals a key role for PAF15 ubiquitylation in
DNA-damage bypass. Nat. Cell Biol., 14, 1089–1098. 19. Hosokawa,M., Takehara,A., Matsuda,K., Eguchi,H., Ohigashi,H.,
Ishikawa,O., Shinomura,Y., Imai,K., Nakamura,Y. and Nakagawa,H. (2007) Oncogenic role of KIAA0101 interacting with proliferating
cell nuclear antigen in pancreatic cancer. Cancer Res., 67, 2568–2576. Conflict of interest statement. None declared. Conflict of interest statement. None declared. Conflict of interest statement. None declared. 20. Chang,C.N., Feng,M.J., Chen,Y.L., Yuan,R.H. and Jeng,Y.M. (2013)
p15(PAF) is an Rb/E2F-regulated S-phase protein essential for DNA
synthesis and cell cycle progression. PLoS One, 8, e61196. REFERENCES Yu,P., Huang,B., Shen,M., Lau,C., Chan,E., Michel,J., Xiong,Y.,
Payan,D.G. and Luo,Y. (2001) p15(PAF), a novel PCNA associated
factor with increased expression in tumor tissues. Oncogene, 20,
484–489. 37. Haracska,L., Unk,I., Prakash,L. and Prakash,S. (2006)
Ubiquitylation of yeast proliferating cell nuclear antigen and its
implications for translesion DNA synthesis. Proc. Natl. Acad. Sci.,
103, 6477–6482. 17. Emanuele,M.J., Ciccia,A., Elia,A.E. and Elledge,S.J. (2011)
Proliferating cell nuclear antigen (PCNA)-associated
KIAA0101/PAF15 protein is a cell cycle-regulated
anaphase-promoting complex/cyclosome substrate. Proc. Natl. Acad. Sci. U.S.A., 108, 9845–9850. 38. Haracska,L., Johnson,R.E., Unk,I., Phillips,B., Hurwitz,J.,
Prakash,L. and Prakash,S. (2001) Physical and functional
interactions of human DNA polymerase eta with PCNA. Mol. Cell. Biol., 21, 7199–7206. 18. Povlsen,L.K., Beli,P., Wagner,S.A., Poulsen,S.L., Sylvestersen,K.B.,
Poulsen,J.W., Nielsen,M.L., Bekker-Jensen,S., Mailand,N. and
Choudhary,C. (2012) Systems-wide analysis of ubiquitylation 9828 Nucleic Acids Research, 2018, Vol. 46, No. 18 39. Dzantiev,L., Constantin,N., Genschel,J., Iyer,R.R., Burgers,P.M. and
Modrich,P. (2004) Defined human system that supports bidirectional
mismatch-provoked excision. Mol. Cell, 15, 31–41. 48. Lau,W.C., Li,Y., Zhang,Q. and Huen,M.S. (2015) Molecular
architecture of the Ub-PCNA/Pol eta complex bound to DNA. Sci. Rep., 5, 15759. 49. Hedglin,M., Pandey,B. and Benkovic,S.J. (2016) Stability of the
human polymerase delta holoenzyme and its implications in lagging
strand DNA synthesis. Proc. Natl. Acad. Sci., 113, E1777–E1786. 40. Hishiki,A., Hashimoto,H., Hanafusa,T., Kamei,K., Ohashi,E.,
Shimizu,T., Ohmori,H. and Sato,M. (2009) Structural basis for novel
interactions between human translesion synthesis polymerases and
proliferating cell nuclear antigen. J. Biol. Chem., 284, 10552–10560. 50. Mayanagi,K., Kiyonari,S., Saito,M., Shirai,T., Ishino,Y. and
Morikawa,K. (2009) Mechanism of replication machinery assembly
as revealed by the DNA ligase-PCNA-DNA complex architecture. Proc. Natl. Acad. Sci., 106, 4647–4652. 41. Sakurai,S., Kitano,K., Yamaguchi,H., Hamada,K., Okada,K.,
Fukuda,K., Uchida,M., Ohtsuka,E., Morioka,H. and Hakoshima,T. (2005) Structural basis for recruitment of human flap endonuclease 1
to PCNA. EMBO J., 24, 683–693. 51. Xu,X., Yan,C., Kossmann,B.R. and Ivanov,I. (2016) Secondary
interaction interfaces with PCNA control conformational switching
of DNA polymerase PolB from polymerization to editing. J. Phys. Chem. B, 120, 8379–8388. 42. Xie,B., Mazloum,N., Liu,L., Rahmeh,A., Li,H. and Lee,M.Y.W.T. (2002) Reconstitution and characterization of the human DNA
polymerase delta four-subunit holoenzyme. Biochemistry, 41,
13133–13142. 52. Fernandez-Leiro,R., Conrad,J., Yang,J.C., Freund,S.M., Scheres,S.H. and Lamers,M.H. (2017) Self-correcting mismatches during
high-fidelity DNA replication. Nat. Struct. Mol. Biol., 24, 140–143. 43. Li,H., Xie,B., Zhou,Y.J., Rahmeh,A., Trusa,S., Zhang,S.F., Gao,Y.,
Lee,E.Y.C. and Lee,M.Y.W.T. (2006) Functional roles of p12, the
fourth subunit of human DNA polymerase delta. J. Biol. Chem., 281,
14748–14755. 53. Fernandez-Leiro,R., Conrad,J., Scheres,S.H. and Lamers,M.H. REFERENCES (2015) cryo-EM structures of the E. coli replicative DNA polymerase
reveal its dynamic interactions with the DNA sliding clamp,
exonuclease and tau. Elife, 4, e11134. 44. Rahmeh,A.A., Zhou,Y.J., Xie,B., Li,H., Lee,E.Y.C. and
Lee,M.Y.W.T. (2012) Phosphorylation of the p68 subunit of Pol delta
acts as a molecular switch to regulate its interaction with PCNA. Biochemistry, 51, 416–424. 54. Biertumpfel,C., Zhao,Y., Kondo,Y., Ramon-Maiques,S.,
Gregory,M., Lee,J.Y., Masutani,C., Lehmann,A.R., Hanaoka,F. and
Yang,W. (2010) Structure and mechanism of human DNA
polymerase eta. Nature, 465, 1044–1048. 45. Zhang,S.F., Zhou,Y.J., Trusa,S., Meng,X., Lee,E.Y.C. and
Lee,M.Y.W.T. (2007) A novel DNA damage response - rapid
degradation of the p12 subunit of DNA polymerase delta. J. Biol. Chem., 282, 15330–15340. polymerase eta. Nature, 465, 1044–1048. 55. Waters,L.S., Minesinger,B.K., Wiltrout,M.E., D’Souza,S.,
Woodruff,R.V. and Walker,G.C. (2009) Eukaryotic translesion
polymerases and their roles and regulation in DNA damage
tolerance. Microbiol. Mol. Biol. Rev., 73, 134–154. 46. Meng,X., Zhou,Y., Zhang,S., Lee,E.Y., Frick,D.N. and Lee,M.Y. (2009) DNA damage alters DNA polymerase delta to a form that
exhibits increased discrimination against modified template bases and
mismatched primers. Nucleic Acids Res., 37, 647–657. 56. Hoege,C., Pfander,B., Moldovan,G.L., Pyrowolakis,G. and Jentsch,S. (2002) RAD6-dependent DNA repair is linked to modification of
PCNA by ubiquitin and SUMO. Nature, 419, 135–141. mismatched primers. Nucleic Acids Res., 37, 647–657. 47. Meng,X., Zhou,Y.J., Lee,E.Y.C., Lee,M.Y.W.T. and Frick,D.N. (2010) The p12 subunit of human polymerase delta modulates the
rate and fidelity of DNA synthesis. Biochemistry, 49, 3545–3554. 57. O’Donnell,M., Langston,L. and Stillman,B. (2013) Principles and
concepts of DNA replication in bacteria, archaea, and eukarya. Cold
Spring Harb. Perspect. Biol., 5, a010108.
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Measurement of the track reconstruction efficiency at LHCb
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Measurement of the track reconstruction efficiency
at LHCb To cite this article: The LHCb collaboration 2015 JINST 10 P02007 View the article online for updates and enhancements. This content was downloaded from IP address 161.116.168.89 on 17/05/2022 at 17:12 You may also like You may also like
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Kishor et al. - Journal of Instrumentation PUBLISHED BY IOP PUBLISHING FOR SISSA MEDIALAB PUBLISHED BY IOP PUBLISHING FOR SISSA MEDIALAB RECEIVED: August 7, 2014
REVISED: December 6, 2014
ACCEPTED: January 3, 2015
PUBLISHED: February 12, 2015 RECEIVED: August 7, 2014
REVISED: December 6, 2014
ACCEPTED: January 3, 2015
PUBLISHED: February 12, 2015 2015 JINST 10 P020 This content was downloaded from IP address 161.116.168.89 on 17/05/2022 at 17:12 This content was downloaded from IP address 161.116.168.89 on 17/05/2022 at 17:12 PUBLISHED BY IOP PUBLISHING FOR SISSA MEDIALAB c
⃝CERN 2015 for the benefit of the LHCb collaboration, published under the terms
of the Creative Commons Attribution 3.0 License by IOP Publishing Ltd and Sissa
Medialab srl. Any further distribution of this work must maintain attribution to the author(s) and the
published article’s title, journal citation and DOI. doi:10.1088/1748-0221/10/02/P02007 Measurement of the track reconstruction efficiency
at LHCb JINST 10 P02007 The LHCb collaboration doi:10.1088/1748-0221/10/02/P02007 doi:10.1088/1748-0221/10/02/P02007 Contents
1
Introduction
1
2
Detector and software description
2
3
Track reconstruction at LHCb
3
4
Tag-and-probe methods
4
4.1
VELO method
4
4.2
T-station method
5
4.3
Long method
6
5
Trigger and selection requirements
6
5.1
Mass resolution
7
6
Calculation of efficiency
8
7
Efficiency dependencies
9
7.1
Comparison of magnetic field polarities
10
7.2
Dependencies of track reconstruction efficiency
10
7.3
Efficiency ratios
10
8
Systematic uncertainties
15
9
Hadronic interactions
15
10 Conclusion
16
The LHCb collaboration
19 Contents
1
Introduction
2
Detector and software description
3
Track reconstruction at LHCb
4
Tag-and-probe methods
4.1
VELO method
4.2
T-station method
4.3
Long method
5
Trigger and selection requirements
5.1
Mass resolution
6
Calculation of efficiency
7
Efficiency dependencies
7.1
Comparison of magnetic field pola
7.2
Dependencies of track reconstructi
7.3
Efficiency ratios
8
Systematic uncertainties
9
Hadronic interactions
10 Conclusion
The LHCb collaboration Contents
1
Introduction
1
2
Detector and software description
2
3
Track reconstruction at LHCb
3
4
Tag-and-probe methods
4
4.1
VELO method
4
4.2
T-station method
5
4.3
Long method
6
5
Trigger and selection requirements
6
5.1
Mass resolution
7
6
Calculation of efficiency
8
7
Efficiency dependencies
9
7.1
Comparison of magnetic field polarities
10
7.2
Dependencies of track reconstruction efficiency
10
7.3
Efficiency ratios
10
8
Systematic uncertainties
15
9
Hadronic interactions
15
10 Conclusion
16
The LHCb collaboration
19 2015 JINST 10 P020 5 JINST 10 P02007 The LHCb collaboration 19 The LHCb collaboration E-mail: michel.de.cian@cern.ch ABSTRACT: The determination of track reconstruction efficiencies at LHCb using J/ψ →µ+µ−
decays is presented. Efficiencies above 95% are found for the data taking periods in 2010, 2011,
and 2012. The ratio of the track reconstruction efficiency of muons in data and simulation is com-
patible with unity and measured with an uncertainty of 0.8% for data taking in 2010, and at a
precision of 0.4% for data taking in 2011 and 2012. For hadrons an additional 1.4% uncertainty
due to material interactions is assumed. This result is crucial for accurate cross section and branch-
ing fraction measurements in LHCb. KEYWORDS: Large detector-systems performance; Pattern recognition, cluster finding, calibration
and fitting methods; Performance of High Energy Physics Detectors ARXIV EPRINT: 1408.1251 c
⃝CERN 2015 for the benefit of the LHCb collaboration, published under the terms
of the Creative Commons Attribution 3.0 License by IOP Publishing Ltd and Sissa
Medialab srl. Any further distribution of this work must maintain attribution to the author(s) and the
published article’s title, journal citation and DOI. 1
Introduction The track reconstruction efficiency is an important quantity in many physics analyses, especially
those that aim at measuring a production cross section or a branching fraction. The uncertainty on
the track reconstruction efficiency was a source of large systematic uncertainties with early LHCb
data [1]. The method presented in this paper has significantly reduced this uncertainty for recent
measurements [2]. In physics analysis, the track reconstruction efficiency is usually estimated with simulated
events. To take possible differences between simulation and data into account, a data-driven cor-
rection procedure is applied. A clean sample of J/ψ →µ+µ−decays is selected in data with a
tag-and-probe approach. J/ψ →µ+µ−decays are ideal candidates for efficiency measurements as – 1 – they are abundant, clean, and the decay products cover the momentum spectrum needed in most
physics analyses in LHCb. The purity of the sample is enhanced by selecting J/ψ from b-hadron
decays. The tag track is fully reconstructed and is well identified as a muon. The probe track is
only partially reconstructed, not using information from at least one subdetector which is probed. The track reconstruction efficiency is determined by checking for the existence of a fully recon-
structed track corresponding to the probe track as this allows to determine the efficiency of the
subdetector that is not used in the reconstruction of the probe track. It is calculated as a function of
the momentum of the probe track, p, its pseudorapidity, η, and the track multiplicity of the event,
Ntrack. These are chosen because the efficiency is most affected by them. No strong dependence on
the polar angle φ is observed. The main result of this paper is the track reconstruction efficiency
ratio between data and simulation for prompt tracks and tracks from B and D mesons. This ratio
is used in physics analyses to correct the track reconstruction efficiency in simulated events and to
determine its uncertainty. The measurement is performed on several data samples to meet the re-
quirements of the analyses performed at LHCb. 1
Introduction In this paper, the results are presented for the three
data samples from run I, corresponding to different running conditions, proton-proton (pp) centre-
of-mass energies and integrated luminosities: data taken in 2010 at √s = 7 TeV corresponding to
29 pb−1, data taken in 2011 at √s = 7 TeV corresponding to 1 fb−1, and data taken in 2012 at √s =
8 TeV corresponding to 2 fb−1. The 2010 results are valid for the full 2010 data set, corresponding
to a luminosity of 37 pb−1, since the same running conditions and track reconstruction were used
throughout this period. 2015 JINST 10 P02 5 JINST 10 P02007 2
Detector and software description The LHCb detector [3] is a single-arm forward spectrometer covering the pseudorapidity range
2 < η < 5, designed for the study of particles containing b or c quarks. The detector includes a
high-precision tracking system consisting of a silicon-strip vertex detector, VELO [4], surround-
ing the pp interaction region; a large-area silicon-strip detector, TT [5], located upstream of a
dipole magnet with a bending power of about 4Tm; and three stations of silicon-strip detectors
(Inner Tracker) [6] and straw drift tubes (Outer Tracker) [7] placed downstream of the magnet,
called T stations. The tracking system provides a measurement of momentum, p, with a rela-
tive uncertainty that varies from 0.4% at low momentum to 0.6% at 100GeV/c. The minimum
distance of a track to a primary vertex (PV), the impact parameter (IP), is measured with a res-
olution of (15 + 29/pT)µm, where pT is the component of p transverse to the beam, in GeV/c. The polarity of the dipole magnet is reversed periodically throughout data taking. The config-
uration with the magnetic field vertically upwards (downwards), bends positively (negatively)
charged particles in the horizontal plane towards the centre of the LHC. Different types of charged
hadrons are distinguished using information from two ring-imaging Cherenkov detectors, RICH1
and RICH2. Photon, electron, and hadron candidates are identified by a calorimeter system con-
sisting of scintillating-pad and preshower detectors, an electromagnetic calorimeter, and a hadronic
calorimeter. Muons are identified by a system composed of alternating layers of iron and multi-
wire proportional chambers [8]. The trigger [9] consists of a hardware stage, based on informa-
tion from the calorimeter and muon systems, followed by a software stage, which applies a full
event reconstruction. – 2 – Figure 1. Tracking detectors and track types reconstructed by the track finding algorithms at LHCb. 2015 JINST 10 P02 Figure 1. Tracking detectors and track types reconstructed by the track finding algorithms at LHCb. In the simulation, pp collisions are generated using PYTHIA 6.4 [10] with a specific LHCb
configuration [11]. Decays of hadronic particles are described by EVTGEN [12], in which final
state radiation is generated using PHOTOS [13]. The interaction of the generated particles with
the detector and its response are implemented using the GEANT4 toolkit [14, 15] as described in
ref. [16]. Hit inefficiencies, e.g. due to dead channels, are typically in the range 1-2% and are in-
cluded in the simulation. 2
Detector and software description Differences in the positioning of the sensors between data and simulation
are at the level of 0.5mm. Both effects have a negligible impact on the tracking efficiency. The
simulated events used in this study are required to contain at least one J/ψ →µ+µ−decay. 5 JINST 10 P02007 Differences in the response of the detectors in simulation and data could potentially lead to
a different behaviour of the track reconstruction. The hit efficiencies have been measured in data
using tracks. For the different subdetectors, they range from 98-100%. Dead channels are included
in the simulation, using an average over the data taking period. From simulations it is known that
the (high) hit efficiency does not have any impact on the track reconstruction, as the algorithms have
been written to be robust against small hit inefficiencies. The size of the sensitive detector elements
are known very accurately and the positioning of the sensitive elements in the simulation is accurate
at the level of 0.5mm. Compared to the overall size of the tracking system, any inaccuracy at this
level has negligible impact on the acceptance of the detector. 3
Track reconstruction at LHCb Owing to the design of the LHCb detector, which consists of tracking detectors mainly outside the
magnetic field, charged particle tracks are in approximation straight line segments in the upstream
part (VELO and TT) and in the downstream part (T stations). Figure 1 shows an overview of the
different track types defined in the LHCb reconstruction: VELO tracks, which have hits in the
VELO; upstream tracks, which have hits in the two upstream trackers; T tracks, which have hits in
the T stations; downstream tracks, which have hits in TT and the T stations; and long tracks, which
have hits in the VELO and the T stations. The latter tracks can additionally have hits in TT. If a particle is reconstructed more than once, as different track types, only the track best suited
for analysis purposes is kept. Hereby, long tracks are preferred over any other track type, upstream
tracks are preferred over VELO tracks, and downstream tracks are preferred over T tracks. The – 3 – number of unique tracks in an event, Ntrack, is used in this study as a measure for the event multi-
plicity; it is strongly correlated with the number of hits in the tracking detectors. The number of
tracks is chosen over the number of hits in a tracker to give a balanced measure of the upstream
and the downstream occupancy. The reconstruction of long tracks starts with a search for VELO tracks [17, 18]. VELO tracks
are reconstructed exploiting the fact that tracks form straight lines due to the absence of a magnetic
field in the VELO. Two algorithms promote these VELO tracks to long tracks. The first algorithm,
called forward tracking [19], combines VELO tracks with hits in the three T stations. For a given
VELO track and a single hit in one of the T stations the momentum is fixed, enabling the algorithm
to project hits in the T stations along the trajectory. Hits which form clusters in the projection are
used to define the final long track. In the second algorithm, called track matching [20, 21], long
tracks are made combining VELO tracks with T tracks, which are found by a standalone track
finding algorithm [22]. 2015 JINST 10 P02 If hits compatible with the long track trajectory are found in TT, they are added to the track
to improve the momentum resolution and as discrimination against fake tracks. 3
Track reconstruction at LHCb This procedure is
identical for the forward tracking and the track matching. JINST 10 P02007 Most analyses use long tracks because they provide the best momentum and spatial resolution
among all track types. Unless otherwise stated, track reconstruction at LHCb refers to the recon-
struction of long tracks. In a typical signal triggered event in 2011 or 2012, around 60 long tracks
are reconstructed. Other track types, such as downstream tracks [23], are used for the reconstruc-
tion of decay products of long-lived particles such as K0
S mesons, or for internal alignment of the
tracking detectors. They are reconstructed from T tracks, which are propagated back through the
magnetic field to find corresponding hits in the TT stations. The efficiency to reconstruct charged particles as long tracks is determined in two approaches. The first approach measures the track reconstruction efficiency in the VELO and in the T stations
individually and combines these efficiencies to a single measurement. The second approach deter-
mines the efficiency to reconstruct a long track directly. 4
Tag-and-probe methods The tag-and-probe method uses two-prong decays, where one of the decay products, the “tag”, is
fully reconstructed as a long track, while the other particle, the “probe”, is only partially recon-
structed. The probe should carry enough momentum information that the invariant mass of the
parent particle can be reconstructed with a sufficiently high resolution. The invariant mass of the
two-prong decay allows for a discrimination against background. The track reconstruction effi-
ciency for long tracks is then obtained by matching the partially reconstructed probe track to a long
track. If a match is found, the probe track is defined as efficient. The three methods described
below all use J/ψ →µ+µ−decays, as the daughter particles have information in the muon system
which can be exploited in the reconstruction of the probe track. The approaches, however, use
different combinations of tracking detectors for the partial reconstruction of the probe track. 4.1
VELO method The track reconstruction efficiency in the VELO is measured using downstream tracks as probes, as
illustrated in figure 2(a). A downstream track and a long track of the same muon do not necessarily – 4 – (a)
(b)
(c)
Figure 2. Illustration of the three tag-and-probe methods: (a) the VELO method, (b) the T-station method,
and (c) the long method. The VELO (black rectangle), the two TT layers (short bold lines), the magnet coil,
the three T stations (long bold lines), and the five muon stations (thin lines) are shown in all three subfigures. The upper solid blue line indicates the tag track, the lower line indicates the probe with red dots where hits
are required and dashes where a detector is probed. (a)
(b)
(c) (a) 2015 JINST 10 P020 (b) JINST 10 P02007 Figure 2. Illustration of the three tag-and-probe methods: (a) the VELO method, (b) the T-station method,
and (c) the long method. The VELO (black rectangle), the two TT layers (short bold lines), the magnet coil,
the three T stations (long bold lines), and the five muon stations (thin lines) are shown in all three subfigures. The upper solid blue line indicates the tag track, the lower line indicates the probe with red dots where hits
are required and dashes where a detector is probed. share all hits in the T stations. Therefore, a probe track is considered to be found as a long track
if there is a long track with at least 50% common hits in the T stations. In simulated events the
fraction of 50% common hits is found to be an appropriate and stable matching criterion. 4.2
T-station method The measurement of the track reconstruction efficiency in the T stations for particles that have
VELO and muon segments is illustrated in figure 2(b). A dedicated algorithm reconstructs muons
as straight tracks starting from hits in the last muon station, see for example refs. [24, 25]. These
are subsequently matched to VELO tracks. A long track is considered to be matched to a probe track if two requirements are met. Firstly,
the probe track and the long track have to be reconstructed from the same VELO seed. Secondly, at – 5 – Table 1. Settings of the software trigger selection as a function of data taking period. Only the tag muon
required to pass the selection. For more information see refs. [9, 26–28]. Table 1. Settings of the software trigger selection as a function of data taking period. Only the tag muon is
required to pass the selection. For more information see refs. [9, 26–28]. required to pass the selection. For more information see refs. [9, 26 28]. 2010
2011
2012
2012
(first 0.7 fb−1)
(remaining 1.3 fb−1)
IP > 0.11mm
IP > 0.5mm
IP > 0.5mm
IP > 0.5mm
χ2
IP > 16
χ2
IP > 200
χ2
IP > 200
χ2
IP > 200
p > 8.0GeV/c
p > 8.0GeV/c
p > 8.0GeV/c
p > 3.0GeV/c
pT > 1.0GeV/c
pT > 1.3GeV/c
pT > 1.3GeV/c
pT > 1.3GeV/c
χ2/ndf(track) < 2
χ2/ndf(track) < 2
χ2/ndf(track) < 2.5
χ2/ndf(track) < 2.5 2015 JINST 10 P02 least two hits on the probe track in the muon stations have to be compatible with the extrapolation
of the long track into the muon stations. It is found in simulated events that requiring two common
hits in the muon stations is sufficient to ensure compatible trajectories of the long track and the
VELO-muon probe track. JINST 10 P02007 4.3
Long method The long method uses probe tracks that have hits in the TT and in the muon stations as illustrated
in figure 2(c). This method measures the efficiency to reconstruct long tracks because the long-
track-finding algorithms do not require the presence of TT hits. Therefore, the efficiency to find
a long track is, to first order, independent of the efficiency to find such a TT-muon track. These
(TT-muon) tracks are found by a dedicated reconstruction of tracks in the muon stations, which
are subsequently matched to TT hits. A TT-muon track is considered to be reconstructed as a long
track in case more than 70% of the hits in the muon stations are compatible with the extrapolation
of the long track into the muon stations. In case the long track has TT hits, it needs to share at least
60% of the TT hits as well. These fractions have been optimised in simulation and the results are
stable with respect to small differences in data and simulation. 5
Trigger and selection requirements VELO
T-station
Long
method
method
method
Tag
Long track
used in single muon trigger
DLLµπ > 2
DLLµπ > 2
χ2/ndf(track) < 5
χ2/ndf(track) < 3
χ2/ndf(track) < 2
p > 5.0GeV/c
p > 7.0GeV/c
p > 10GeV/c
pT > 0.7GeV/c
pT > 0.5GeV/c
pT > 1.3GeV/c
IP > 0.5mm
Probe
Downstream track
VELO-muon track
TT-muon track
p > 5.0GeV/c
p > 5.0GeV/c
p > 5.0GeV/c
pT > 0.7GeV/c
pT > 0.5GeV/c
pT > 0.1GeV/c
J/ψ
Mµµ ∈[2.9,3.3]GeV/c2
Mµµ ∈[2.7,3.5]GeV/c2
Mµµ ∈[2.6,3.6]GeV/c2
χ2/ndf(vertex) < 5
χ2/ndf(vertex) < 5
χ2/ndf(vertex) < 5
NJ/ψ = 1
NJ/ψ = 1
NJ/ψ = 1
p > 7.0GeV/c
IP < 0.8mm
software trigger in order to avoid any bias on the track reconstruction efficiency, caused by fully
reconstructing the two-prong decay with two long tracks. Table 2. Selection requirements on the tag and probe tracks and on the combination into a J/ψ candidate for
the three different methods. 2015 JINST 10 P02 JINST 10 P02007 software trigger in order to avoid any bias on the track reconstruction efficiency, caused by fully
reconstructing the two-prong decay with two long tracks. Further selection criteria are applied as listed in table 2: the χ2/ndf from the track fit of
the tag tracks must be small to reduce the number of fake tracks. Tag tracks have to fulfil the
standard muon selection, which requires hits in the muon stations in a search window around the
track extrapolation as explained in ref. [29]. Both the tag and probe tracks have minimal p and
pT requirements to remove badly reconstructed tracks and combinatorial background. In order to
remove contamination from hadrons, the particle identification system is used. The differences
between the logarithm of the likelihood of the tag to be a muon and to be a pion, DLLµπ, is
computed and only tag tracks with a high DLLµπ are used. The range of the invariant mass of
the µ+µ−combination, Mµµ, is chosen sufficiently large to estimate the background contribution
from the mass sidebands. Finally, the χ2/ndf from the vertex fit of the tag- and the probe-track
has to be small, in order to remove combinatorial background; and the number of J/ψ decays
per event (NJ/ψ ) must be one, to simplify the association procedure described in the preceding
subsections. 5
Trigger and selection requirements Additionally, the T-station method only considers J/ψ candidates with a momentum
greater than 7GeV/c, and the long method only J/ψ candidates with an IP smaller than 0.8mm, as
both selections are effective in reducing background contamination without biasing the efficiency
determination. After the full selection chain the sample amounts to about 6000 decays for 2010
for the long and the T method, while for the VELO method 12000 decays are selected. The
2011 and 2012 data samples comprise more than 300000 decays in total for all methods and data
taking periods. 5
Trigger and selection requirements The candidate decays are first required to pass a hardware trigger, which selects muons in the muon
system with a transverse momentum, pT > 1.48GeV/c, or dimuons where the product of the two
transverse momenta is greater than pT1 × pT2 > (1.296GeV/c)2. In 2012 these thresholds have
been raised to pT > 1.76GeV/c and pT1 × pT2 > (1.6GeV/c)2, respectively. The reconstruction
of both muons in the hardware trigger does not bias the determination of the track reconstruction
efficiency since it does not use information from the tracking system (VELO, TT, and T stations). The subsequent software stage reconstructs the tag muon in the entire tracking system and in
the muon system. The tag muon is required to have high pT, high p, large IP and χ2
IP with respect
to all PVs in the event, where χ2
IP is defined as the difference in χ2 of a given PV reconstructed
with and without the considered track. Furthermore, a good χ2 per degree of freedom (χ2/ndf) of
the trigger track fit is required. Different selection criteria are used during data taking as listed in
table 1 to fit different data taking conditions. The IP and χ2
IP requirements restrict the sample to
J/ψ originating from b hadron decays. Only the tag muon is required to be reconstructed in the – 6 – Table 2. Selection requirements on the tag and probe tracks and on the combination into a J/ψ candidate for
the three different methods. VELO
T-station
Long
method
method
method
Tag
Long track
used in single muon trigger
DLLµπ > 2
DLLµπ > 2
χ2/ndf(track) < 5
χ2/ndf(track) < 3
χ2/ndf(track) < 2
p > 5.0GeV/c
p > 7.0GeV/c
p > 10GeV/c
pT > 0.7GeV/c
pT > 0.5GeV/c
pT > 1.3GeV/c
IP > 0.5mm
Probe
Downstream track
VELO-muon track
TT-muon track
p > 5.0GeV/c
p > 5.0GeV/c
p > 5.0GeV/c
pT > 0.7GeV/c
pT > 0.5GeV/c
pT > 0.1GeV/c
J/ψ
Mµµ ∈[2.9,3.3]GeV/c2
Mµµ ∈[2.7,3.5]GeV/c2
Mµµ ∈[2.6,3.6]GeV/c2
χ2/ndf(vertex) < 5
χ2/ndf(vertex) < 5
χ2/ndf(vertex) < 5
NJ/ψ = 1
NJ/ψ = 1
NJ/ψ = 1
p > 7.0GeV/c
IP < 0.8mm
software trigger in order to avoid any bias on the track reconstruction efficiency, caused by fully
reconstructing the two-prong decay with two long tracks. Table 2. Selection requirements on the tag and probe tracks and on the combination into a J/ψ candidate for
the three different methods. 5.1
Mass resolution To illustrate the mass resolutions that can be achieved, the dimuon invariant mass distributions
from J/ψ candidates in the three methods are shown in figure 3 using the 2011 data sample. The – 7 – ]
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Figure 3. Invariant mass distributions for reconstructed J/ψ candidates from the 2011 dataset. The solid
line shows the fitted distribution for signal and background, the dotted line is the signal component. The
subfigures are (a) the VELO method, (b) the T-station method, (c) the long method. For comparison of
resolution and signal purity (d) shows the invariant mass distribution of J/ψ candidates obtained with the
standard reconstruction at LHCb. ]
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Long method 5 JINST 10 P02007 Figure 3. Invariant mass distributions for reconstructed J/ψ candidates from the 2011 dataset. The solid
line shows the fitted distribution for signal and background, the dotted line is the signal component. The
subfigures are (a) the VELO method, (b) the T-station method, (c) the long method. 5.1
Mass resolution For comparison of
resolution and signal purity (d) shows the invariant mass distribution of J/ψ candidates obtained with the
standard reconstruction at LHCb. difference in the visible ranges in figure 3(a) compared with the other distributions in figure 3
is a consequence of the different dimuon invariant mass cuts as listed in table 2. The invariant
mass distribution using two long tracks is shown in figure 3(d) for comparison. The signal peak
is fitted with the sum of two Gaussian functions for this illustration. The effective mass resolution
is about 24MeV/c2 for the VELO method, 57MeV/c2 for the T-station method and for the long
method. This is to be compared to the standard reconstruction with two long tracks that achieves a
resolution of 16MeV/c2. 6
Calculation of efficiency The track reconstruction efficiency is calculated as the fraction of reconstructed J/ψ decays where
the probe track can be matched to a long track. To estimate the number of J/ψ decays, an un-
binned extended maximum likelihood fit is performed to the mass distributions. For the VELO and
T-station methods the mass distributions are described by a single Gaussian function for the signal
and an exponential function for the combinatorial background. This model is preferred over the
aforementioned sum of two Gaussian functions to improve the fit stability when measuring the de-
pendence of the track reconstruction efficiency on kinematic variables and other event parameters. For the long method, a Crystal Ball function [30] is used for the signal, to take the tail on the left-
hand side of the mass peak into account. Since the number of decays in the 2010 data is relatively – 8 – low, in this case a simple sideband subtraction is applied for the VELO and T-station methods. All
shape parameters were allowed to vary in the fit for the denominator of the efficiency; they were
constrained to the found values for the numerator of the efficiency. This procedure was performed
to stabilise the fit, as no difference in the shape of the numerator and denominator could be ob-
served. It has been checked that the choice of the model for the mass distribution has a negligible
effect on the efficiency determination. The efficiencies obtained from the VELO and T-station methods are assumed to be uncorre-
lated, aside from effects due to dependencies on the track kinematics and the event multiplicity. The data sample is binned in kinematic variables and Ntrack to combine the VELO and T-station
efficiencies. The efficiencies obtained with the VELO and T-station methods can be multiplied in
each bin to obtain the efficiency for finding long tracks. This combined efficiency can be compared
with the efficiency found by the long method, giving two independent methods to probe the long
track reconstruction efficiency. 2015 JINST 10 P02 There are, however, small differences between these two approaches. The long method mea-
sures the efficiency for tracks that pass through TT. In the combined method, only the VELO
method requires this. Furthermore, both the VELO method and T-station method include the ef-
ficiency that, given that both the VELO and the T-station segment tracks are reconstructed, the
corresponding long track is found. 6
Calculation of efficiency Therefore, in the combined efficiency, this so-called matching
efficiency is counted twice. All these effects can lead to small differences in the measured long-
track efficiency. For this reason, the ratio between the efficiencies in data and simulation is used to
compare the methods, as these uncertainties are common for simulated and real decays and cancel
when the ratio of efficiencies is formed. JINST 10 P02007 On simulated events the track reconstruction efficiency is commonly defined as the fraction of
simulated charged particles with sufficient hits in the VELO and T stations that can be associated
to a track that shares at least 70% of the hits in each participating subdetector with this particle. For
all methods, this so-called hit-based efficiency in simulation agrees within 1% with the efficiency
measured with the tag-and-probe methods. Furthermore the matching efficiency was determined
to be very close to 100%. The very small matching inefficiency does not affect the agreement
between the hit-based efficiency and the tag-and-probe based efficiency in simulation. By taking
the ratio between the efficiencies on data and simulation, these discrepancies are reduced to a
negligible level. 7
Efficiency dependencies Using the momentum spectrum of the J/ψ decay products obtained with the VELO method from
data as a benchmark, the average track reconstruction efficiency for long tracks is measured to
be (95.4 ± 0.7)% for 2010 data, (97.78 ± 0.07)% for 2011 data and (96.99 ± 0.05)% for 2012
data. All results confirm the good performance of the LHCb tracking system. The uncertainties
on these numbers are statistical only; they are binomial errors with additional terms to account
for the statistical uncertainty on the number of background events. Systematic uncertainties are
discussed in section 8. The difference in the efficiencies between the three years is a consequence of
changes in the track reconstruction and the higher centre-of-mass energy, leading to a higher track
multiplicity and hence lower reconstruction efficiency for the 2012 running period. Dependencies – 9 – Table 3. Track reconstruction efficiencies in % for the individual running periods using the long method for
positive and negative muons and different magnetic field polarities (statistical uncertainties only). Magnet up
Magnet down
Data
Positive
Negative
Positive
Negative
2010
94.1±1.3
96.0±1.3
99.3+0.7
−1.8
98.4+1.6
−1.7
2011
97.0±0.3
97.3±0.3
97.2±0.3
97.4±0.3
2012
96.2±0.2
96.2±0.2
96.2±0.2
96.3±0.2 2015 JINST 10 P02 2015 JINST 10 P02007 on the polarity of the dipole magnet, the charge of the muons, and kinematic properties as well as
the agreement with the simulation are investigated in further detail in the following subsections. 7.2
Dependencies of track reconstruction efficiency The efficiency to reconstruct long tracks mainly depends on the particle kinematics and the number
of charged particles in an event. As a parametrisation p, η and Ntrack are chosen, as the track
reconstruction efficiency shows the largest dependence on these three observables. The simulated
events are weighted according to the Ntrack distribution observed in data. The track reconstruction
efficiencies for the combination of the VELO and T-station methods and for the long method are
shown for the different data-taking periods in figures 4–6 as a function of p, η, Ntrack, and as a
function of the number of reconstructed primary vertices, NPV. The efficiency coming from the
combination of the VELO and the T-station method is calculated by multiplying the individual
efficiencies. Overall, a reasonable agreement is found between simulated and real data for all data-
taking periods. As the agreement between the tag-and-probe based track reconstruction efficiency
and the true track reconstruction efficiency (based on hit information) is within 1%, the results
shown in figures 4–6 give an accurate description of the efficiency in simulation. 7.1
Comparison of magnetic field polarities The track reconstruction efficiencies determined from the long method are split up into positively
and negatively charged muons and into the two different magnetic field polarities (named up and
down). The results are summarised in table 3. They show compatible numbers for magnetic field
up and down and for positive and negative muons. JINST 10 P02007 For data from 2011 and 2012 there is no difference between positive and negative muons or be-
tween the different magnet polarities. In 2010 data, a 2.3σ difference between the different magnet
polarities is observed for positive muons. No unambiguous source of the difference is found. 7.3
Efficiency ratios The efficiency ratio is defined as the efficiency measured in data divided by the efficiency measured
in simulation, The efficiency ratio is defined as the efficiency measured in data divided by the efficiency measured
in simulation,
ε ratio = εdata
εsim
. (7.1) ratio = εdata
εsim
. (7.1) The efficiency dependence versus Ntrack and NPV is reasonably well described in the simulation, see
figures 4–6: when fitting a first-order polynomial to the efficiency distributions in simulation and
real data, the slopes agree with each other within 2 standard deviations, except for the efficiency The efficiency dependence versus Ntrack and NPV is reasonably well described in the simulation, see
figures 4–6: when fitting a first-order polynomial to the efficiency distributions in simulation and
real data, the slopes agree with each other within 2 standard deviations, except for the efficiency – 10 – ]c
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Figure 4. Track reconstruction efficiencies for the 2010 data and for weighted simulation. The left-ha
column shows the results of the combined method while the right-hand column shows the results of the lo
method. The efficiency is shown as a function of p (first row), η (second row), Ntrack (third row), and N
(fourth row). The error bars indicate the statistical uncertainties. 7.3
Efficiency ratios ]c
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VELO+T efficiency Figure 4. Track reconstruction efficiencies for the 2010 data and for weighted simulation. The left-hand
column shows the results of the combined method while the right-hand column shows the results of the long
method. The efficiency is shown as a function of p (first row), η (second row), Ntrack (third row), and NPV
(fourth row). The error bars indicate the statistical uncertainties. 7.3
Efficiency ratios – 11 – ]c
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Figure 5. Track reconstruction efficiencies for the 2011 data and for weighted simulation. The left-ha
column shows the results of the combined method while the right-hand column shows the results of the lo
method. The efficiency is shown as a function of p (first row), η (second row), Ntrack (third row), and N
(fourth row). The error bars indicate the statistical uncertainties. 7.3
Efficiency ratios ]c
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column shows the results of the combined method while the right-hand column shows the results of the long
method. The efficiency is shown as a function of p (first row), η (second row), Ntrack (third row), and NPV
(fourth row). The error bars indicate the statistical uncertainties. 7.3
Efficiency ratios – 12 – ]c
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Figure 6. Track reconstruction efficiencies for the 2012 data and for weighted simulation. The left-han
column shows the results of the combined method while the right-hand column shows the results of the lon
method. The efficiency is shown as a function of p (first row), η (second row), Ntrack (third row), and NP
(fourth row). The error bars indicate the statistical uncertainties. 7.3
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VELO+T efficiency Figure 6. Track reconstruction efficiencies for the 2012 data and for weighted simulation. The left-hand
column shows the results of the combined method while the right-hand column shows the results of the long
method. The efficiency is shown as a function of p (first row), η (second row), Ntrack (third row), and NPV
(fourth row). The error bars indicate the statistical uncertainties. – 13 – ]c
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Data/Simulation 2011 Efficiency ratio 5 JINST 10 P02007 10 Figure 7. Track reconstruction efficiency ratios as a function of p between data and simulation for (left)
2010 data, (right) 2011 data, and (bottom) 2012 data. 7.3
Efficiency ratios as a function of the number of tracks in the combination of the VELO and T-station method in
2012. It is therefore sufficient to weight the simulated events to establish agreement in Ntrack while
the efficiency ratio is determined in bins of p and η. The number of bins is chosen to keep the
statistical uncertainty in each bin sufficiently small. For the final result, the weighted average of
the combined and long method is taken in each bin of p and η. Figure 7 shows the efficiency ratio versus p for run I, weighted by the event track multiplicity
observed in data; the data are split into two ranges of η. Overall a good agreement of the track
finding efficiency is found between events in simulation and in data for all data taking periods and
most momenta and pseudorapidity regions. The difference between the track finding efficiencies is
generally smaller than 1% between events from simulation and data and no trend can be observed
for the 2011 and 2012 dataset, with the number of events being too low to draw conclusions from
the 2010 dataset. The agreement is worse for tracks with momentum below 10GeV/c, which might
point to a less accurate modelling of multiple scattering effects in the simulation. The overall efficiency ratio and its uncertainty depend on the particle distribution of the data
in terms of p and η. Using the momentum spectrum of the J/ψ decay products obtained with
the VELO method from data, an average efficiency ratio is found of 0.994 ±0.007 for 2010 data,
0.9983±0.0009 for 2011 data and 1.0053±0.0008 for 2012 data. The uncertainties represent the
statistical uncertainties only. The ratio is close to one in all three cases as different features seen
in the efficiency distributions in simulation and data average out when integrating over the full
momentum spectrum or pseudorapidity range. – 14 – 8
Systematic uncertainties Small differences in the ratio of efficiencies are seen when reweighting the simulated samples in
different parameters such as the number of primary vertices, or the number of hits or tracks in the
different subdetectors. The largest of these differences is taken as a systematic uncertainty and
amounts to 0.4%. No systematic uncertainty is assigned for the agreement of the track reconstruc-
tion efficiency determined by the tag-and-probe method and the hit-based method (which is on the
order of 1%), as the differences cancel when forming the efficiency ratio. Accordingly, no sys-
tematic uncertainties are assigned for the fit model as these cancel when forming the fraction of
reconstructed J/ψ decays where the probe can be matched to a long track. It has been checked
that this is true for a range of fit models, the largest variation being 0.2%. Furthermore, no sys-
tematic uncertainty is assigned to the possible matching of a correctly reconstructed probe track
to a fake long track, as the requirement for a large overlap in the subdetectors ensure that both
reconstructed tracks are either real tracks or fake tracks, where the latter would not peak at the
J/ψ mass. No systematic uncertainty is assigned for the fact that the VELO + T-station method
and the long method show slightly different results in figures 4–6, as both methods probe different
momentum spectra and any residual difference will cancel when forming the ratio with simulation. No systematic uncertainty is assigned for the double-counting of the matching efficiency in the
combined method, as this efficiency is very close to 100%, and any uncertainty would get further
reduced when forming the ratio with simulation. No systematic uncertainty is assigned for the large
difference for the VELO + T efficiency between simulation and data at low momenta in 2011 and
2012, as this is automatically taken into account when forming the ratio of efficiencies. Despite
this difference, the integrated track reconstruction efficiencies between simulation and data are in
agreement due to compensation of this effect for high momenta, where the efficiency is higher in
simulation than in data. 2015 JINST 10 P02 5 JINST 10 P02007 9
Hadronic interactions The methods presented in this paper are based on muons and require that they reach the muon
stations. Thus, these methods are not sensitive to the effects from hadronic interactions and large-
angle scatterings with the detector material. For hadrons, the largest effect is due to hadronic inter-
actions. The cross section depends on the particle type, charge and the momentum. A simulation
of B0 →J/ψ K∗0 decays (where K∗0 →K+π−) shows that about 11% of the kaons (averaged over
positive and negative kaons) and about 14% of the pions cannot be reconstructed due to hadronic
interactions that occur before the last T station. This number depends primarily on the momentum
of the particle. Due to the uncertainty on the material budget and consequently on the interaction
with the detector material, the reconstruction efficiency obtained from simulation has an intrin-
sic uncertainty, which is not accounted for in the track reconstruction efficiencies measured with
muons. When assuming that the total material budget in the simulation has an uncertainty of 10%,
the systematic uncertainty due to hadronic interactions is between 1.1–1.4%. The 10% uncertainty
is used as a conservative upper limit and is composed as follows: for the VELO a calculation in
ref. [4] shows an uncertainty on the material budget of 6%. No direct measurements exist for the
T and TT stations. However, weight measurements for the Inner Tracker for the silicon sensors – 15 – and the detector boxes give an accuracy of 2%, while an agreement of 5% is reached for the ca-
bles and the support structure [31, 32]. The Outer Tracker modules have been weighted and this
measurement is precise to about 1% [33]. Furthermore, the sum of the weights of the individual
components of a module adds up to the total weight of a module within the uncertainties. Taking
into account that some level of detail is missing in the detector description in the simulation, an un-
certainty of 5% is assumed for the outer tracker. Weight measurements for the sensor modules and
the insulation material of TT have been performed. Given the detail of the detector description [34]
an uncertainty of 5% on the material budget is well justified. The beam-pipe was implemented in
the software following the design drawings, where a precision better than 10% for all pieces was
confirmed following measurements after production. 10
Conclusion Track reconstruction efficiencies at LHCb have been measured using a tag-and-probe method with
J/ψ →µ+µ−decays. The average efficiency is better than 95% in the momentum region 5GeV/c <
p < 200GeV/c and in the pseudorapidity region 2 < η < 5, which covers the phase space of LHCb. The uncertainty per track is below 0.5% for muons and below 1.5% for pions and kaons, where
the larger uncertainty takes the uncertainty on hadronic interactions into account. All uncertainties
have been added in quadrature. Furthermore, the ratio of the track reconstruction efficiency of
muons in data and simulation is measured, where an uncertainty of 0.8% for data collected in
2010 and an uncertainty of 0.4% for data collected in 2011 and 2012 is achieved. The integrated
efficiency ratios for all three years of data taking are compatible with unity. This result presents
a significant improvement over the uncertainties determined with previous methods ranging from
3 to 4%. 9
Hadronic interactions The solid radiator (aerogel) and the gas radia-
tor (C4F10) contribute more than two-third of the material budget for the RICH1 detector [35]. The
amount of aerogel is known up to 2% and the differences between 2011 and 2012 are accounted
for in the simulation. The density of the C4F10 was monitored, with the RMS of the distribution
being about 1%. The other components of RICH1 have a smaller contribution to the interaction
length. The overall uncertainty of 10% for the full material budget was then chosen to also take
uncertainties on the GEANT4 cross-sections and additional uncertainties, coming from simplified
descriptions of the detector elements in the simulation, into account. 2015 JINST 10 P02 JINST 10 P02007 Acknowledgments We express our gratitude to our colleagues in the CERN accelerator departments for the excel-
lent performance of the LHC. We thank the technical and administrative staff at the LHCb in-
stitutes. We acknowledge support from CERN and from the national agencies: CAPES, CNPq,
FAPERJ, and FINEP (Brazil); NSFC (China); CNRS/IN2P3 (France); BMBF, DFG, HGF, and
MPG (Germany); SFI (Ireland); INFN (Italy); FOM and NWO (The Netherlands); MNiSW and
NCN (Poland); MEN/IFA (Romania); MinES and FANO (Russia); MinECo (Spain); SNSF and
SER (Switzerland); NASU (Ukraine); STFC (United Kingdom); NSF (U.S.A.). The Tier1 com-
puting centres are supported by IN2P3 (France), KIT and BMBF (Germany), INFN (Italy), NWO
and SURF (The Netherlands), PIC (Spain), GridPP (United Kingdom). We are indebted to the – 16 – communities behind the multiple open source software packages on which we depend. We are
also thankful for the computing resources and the access to software R&D tools provided by Yan-
dex LLC (Russia). Individual groups or members have received support from EPLANET, Marie
Skłodowska-Curie Actions, and ERC (European Union), Conseil g´en´eral de Haute-Savoie, Labex
ENIGMASS, and OCEVU, R´egion Auvergne (France), RFBR (Russia), XuntaGal, and GENCAT
(Spain), Royal Society and Royal Commission for the Exhibition of 1851 (United Kingdom). References [1] LHCb collaboration, Measurement of σ(pp →b¯bX) at √s = 7 TeV in the forward region, Phys. Lett. B 694 (2010) 209 [arXiv:1009.2731]. 2015 JINST 10 P020 [2] LHCb collaboration, Production of J/ψ and ϒ mesons in pp collisions at √s = 8 TeV, JHEP 06
(2013) 064 [arXiv:1304.6977]. [3] LHCb collaboration, The LHCb detector at the LHC, 2008 JINST 3 S08005. 5 JINST 10 P02007 [4] R. Aaij et al., Performance of the LHCb Vertex Locator, 2014 JINST 9 09007 [arXiv:1405.7808] [5] LHCb collaboration, LHCb reoptimized detector design and performance: technical design report,
LHCB-TDR-009 (2003). [6] LHCb collaboration, LHCb inner tracker: technical design report, LHCB-TDR-008 (2002). [7] LHCB OUTER TRACKER GROUP collaboration, R. Arink et al., Performance of the LHCb Outer
Tracker, 2014 JINST 9 P01002 [arXiv:1311.3893]. [8] A.A. Alves Jr. et al., Performance of the LHCb muon system, 2013 JINST 8 P02022
[arXiv:1211.1346]. [9] R. Aaij et al., The LHCb trigger and its performance in 2011, 2013 JINST 8 P04022
[arXiv:1211.3055]. [10] T. Sj¨ostrand, S. Mrenna and P.Z. Skands, PYTHIA 6.4 physics and manual, JHEP 05 (2006) 026
[hep-ph/0603175]. [11] I. Belyaev et al., Handling of the generation of primary events in Gauss, the LHCb simulation
framework, IEEE Nucl. Sci. Symp. Conf. Rec. (NSS/MIC) (2010) 1155. [12] D.J. Lange, The EvtGen particle decay simulation package, Nucl. Instrum. Meth. A 462 (2001) 152 [13] P. Golonka and Z. Was, PHOTOS Monte Carlo: a precision tool for QED corrections in Z and W
decays, Eur. Phys. J. C 45 (2006) 97 [hep-ph/0506026]. [14] GEANT4 collaboration, J. Allison et al., GEANT4 developments and applications, IEEE Trans. Nucl. Sci. 53 (2006) 270. [15] GEANT4 collaboration, S. Agostinelli et al., GEANT4 — A simulation toolkit, Nucl. Instrum. Meth. A 506 (2003) 250. [16] LHCb collaboration, The LHCb simulation application, Gauss: design, evolution and experience, J. Phys. Conf. Ser. 331 (2011) 032023. [17] D. Hutchcroft, VELO pattern recognition, CERN-LHCB-2007-013 (2007). [18] O. Callot, FastVelo, a fast and efficient pattern recognition package for the Velo,
LHCb-PUB-2011-001 (2011). [19] O. Callot and S. Hansmann-Menzemer, The forward tracking, LHCb-2007-015 (2007). – 17 – [20] M. Needham and J. Van Tilburg, Performance of the track matching, LHCb-2007-020 (2007). [21] M. Needham, Performance of the track matching, CERN-LHCB-2007-129 (2007). [22] O. Callot and M. Schiller, PatSeeding: a standalone track reconstruction algorithm,
CERN-LHCB-2008-042 (2008). [23] O. Callot, Downstream pattern recognition, CERN-LHCB-2007-026 (2007). [24] G. Manca, L. Mou and B. References Saitta, Studies of efficiency of the LHCb muon detector using cosmic rays,
LHCb-PUB-2009-017 (2009). [25] G. Passaleva, A recurrent neural network for track reconstruction in the LHCb muon system, IEEE
Nucl. Sci. Symp. Conf. Rec. (2008) 867. 2015 JINST 10 P02007 [26] J. Albrecht et al., Commissioning and performance of the LHCb HLT1 muon trigger,
LHCb-PUB-2011-006 (2011). [27] V.V. Gligorov, A single track HLT1 trigger, LHCb-PUB-2011-003 (2011). [28] LHCB HLT PROJECT collaboration, J. Albrecht et al., Performance of the LHCb high level trigger in
2012, J. Phys. Conf. Ser. 513 (2014) 012001 [arXiv:1310.8544]. JINST 10 P02007 [29] F. Archilli et al., Performance of the muon identification at LHCb, 2013 JINST 8 P10020
[arXiv:1306.0249]. [30] T. Skwarnicki, A study of the radiative cascade transitions between the ϒ′ and ϒ resonances, Ph.D. thesis, Institute of Nuclear Physics, Krakow, Poland (1986), DESY-F31-86-02. [31] V. Fave, Estimation of the material budget of the Inner Tracker, LHCb-2008-054 (2008). [32] V. Fave, Survey of the cables of the inner tracker, LHCb-2008-055 (2008). [33] J. Nardulli and N. Tuning, A study of the material in an outer tracker module, LHCb-2004-114
(2005). [34] C. Salzmann and J. Van Tilburg, TT detector description and implementation of the survey
measurements, LHCb-2008-061 (2008). [35] LHCB RICH collaboration, N. Brook et al., LHCb RICH1 engineering design review report,
LHCb-2004-121 (2005). – 18 – The LHCb collaboration De Silva57, P. De Simone18, Decamp4, M. Deckenhoff9, L. Del Buono8, N. D´el´eage4, D. Derkach55, O. Deschamps5, F. Dettori38, Di Canto38, H. Dijkstra38, S. Donleavy52, F. Dordei11, M. Dorigo39, A. Dosil Su´arez37, D. Dossett48, Dovbnya43, K. Dreimanis52, G. Dujany54, F. Dupertuis39, P. Durante38, R. Dzhelyadin35, A. Dziurda26, Dzyuba30, S. Easo49,38, U. Egede53, V. Egorychev31, S. Eidelman34, S. Eisenhardt50, U. Eitschberger9, Ekelhof9, L. Eklund51, I. El Rifai5, Ch. Elsasser40, S. Ely59, S. Esen11, H.-M. Evans47, T. Evans55, R. Ekelhof9, L. Eklund51, I. El Rifai5, Ch. Elsasser40, S. Ely59, S. Esen11, H.-M. Evans47, T. Evans55, Falabella14, C. F¨arber11, C. Farinelli41, N. Farley45, S. Farry52, RF Fay52, D. Ferguson50, A. Falabella14, C. F¨arber11, C. Farinelli41, N. Farley45, S. Farry52, RF Fay52, D. Ferguson50, V. Fernandez Albor37, F. Ferreira Rodrigues1, M. Ferro-Luzzi38, S. Filippov33, M. Fiore16,f , M. Fiorini1 Fernandez Albor37, F. Ferreira Rodrigues1, M. Ferro-Luzzi38, S. Filippov33, M. Fiore16,f , M. Fiorini16,f , Firlej27, C. Fitzpatrick39, T. Fiutowski27, M. Fontana10, F. Fontanelli19,j, R. Forty38, O. Francisco2, M. Frank38, C. Frei38, M. Frosini17,38,g, J. Fu21,38, E. Furfaro24,l, A. Gallas Torreira37, D. Galli14,d, M. Frank38, C. Frei38, M. Frosini17,38,g, J. Fu21,38, E. Furfaro24,l, A. Gallas Torreira37, D. Galli14,d, J. Garra Tico47, L. Garrido36, C. Gaspar38, R. Gauld55, L. Gavardi9, G. Gavrilov30, E. Gersabeck11, J. Garra Tico47, L. Garrido36, C. Gaspar38, R. Gauld55, L. Gavardi9, G. Gavrilov30, E. Gersabeck11, M. Gersabeck54, T. Gershon48, Ph. Ghez4, A. Gianelle22, S. Giani’39, V. Gibson47, L. Giubega29, Gersabeck54, T. Gershon48, Ph. Ghez4, A. Gianelle22, S. Giani’39, V. Gibson47, L. Giubega29, V. Gligorov38, C. G¨obel60, D. Golubkov31, A. Golutvin53,31,38, A. Gomes1,a, C. Gotti20, V.V. Gligorov38, C. G¨obel60, D. Golubkov31, A. Golutvin53,31,38, A. Gomes1,a, C. Gotti20, Grabalosa G´andara5, R. Graciani Diaz36, L.A. Granado Cardoso38, E. Graug´es36, G. Graziani17, M. Grabalosa G´andara5, R. Graciani Diaz36, L.A. Granado Cardoso38, E. Graug´es36, G. Grazian ,
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A. Grecu29, E. Greening55, S. Gregson47, P. Griffith45, L. Grillo11, O. Gr¨unberg62, B. Gui59, E. Gushchin33 A. Grecu29, E. Greening55, S. Gregson47, P. Griffith45, L. Grillo11, O. Gr¨unberg62, B. Gui59, E. Gushchin33, A. Grecu29, E. Greening55, S. Gregson47, P. Griffith45, L. Grillo11, O. Gr¨unberg62, B. Gui59, E. G Yu. Guz35,38, T. Gys38, C. Hadjivasiliou59, G. Haefeli39, C. Haen38, S.C. Haines47, S. Hall53, . Guz35,38, T. Gys38, C. Hadjivasiliou59, G. Haefeli39, C. Haen38, S.C. Haines47, S. Hall53, Hamilton58, T. Hampson46, X. Han11, S. Hansmann-Menzemer11, N. Harnew55, S.T. Harnew46, B. Hamilton58, T. Hampson46, X. Han11, S. The LHCb collaboration R. Aaij41, B. Adeva37, M. Adinolfi46, A. Affolder52, Z. Ajaltouni5, S. Akar6, J. Albrecht9, F. Alessio38,
M. Alexander51, S. Ali41, G. Alkhazov30, P. Alvarez Cartelle37, A.A. Alves Jr25,38, S. Amato2,
S. Amerio22, Y. Amhis7, L. An3, L. Anderlini17,g, J. Anderson40, R. Andreassen57, M. Andreotti16,f ,
J.E. Andrews58, R.B. Appleby54, O. Aquines Gutierrez10, F. Archilli38, A. Artamonov35, M. Artuso59,
E. Aslanides6, G. Auriemma25,n, M. Baalouch5, S. Bachmann11, J.J. Back48, A. Badalov36, W. Baldini16,
R.J. Barlow54, C. Barschel38, S. Barsuk7, W. Barter47, V. Batozskaya28, V. Battista39, A. Bay39,
L. Beaucourt4, J. Beddow51, F. Bedeschi23, I. Bediaga1, S. Belogurov31, K. Belous35, I. Belyaev31,
E. Ben-Haim8, G. Bencivenni18, S. Benson38, J. Benton46, A. Berezhnoy32, R. Bernet40, M.-O. Bettler47,
M. van Beuzekom41, A. Bien11, S. Bifani45, T. Bird54, A. Bizzeti17,i, P.M. Bjørnstad54, T. Blake48,
F. Blanc39, J. Blouw10, S. Blusk59, V. Bocci25, A. Bondar34, N. Bondar30,38, W. Bonivento15,38,
S. Borghi54, A. Borgia59, M. Borsato7, T.J.V. Bowcock52, E. Bowen40, C. Bozzi16, T. Brambach9,
J. van den Brand42, J. Bressieux39, D. Brett54, M. Britsch10, T. Britton59, J. Brodzicka54, N.H. Brook46,
H. Brown52, A. Bursche40, G. Busetto22,r, J. Buytaert38, S. Cadeddu15, R. Calabrese16,f , M. Calvi20,k,
M. Calvo Gomez36,p, P. Campana18,38, D. Campora Perez38, A. Carbone14,d, G. Carboni24,l,
R. Cardinale19,38,j, A. Cardini15, L. Carson50, K. Carvalho Akiba2, G. Casse52, L. Cassina20,
L. Castillo Garcia38, M. Cattaneo38, Ch. Cauet9, R. Cenci58, M. Charles8, Ph. Charpentier38, S. Chen54,
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k53 2015 JINST 10 P020 M. Calvo Gomez36,p, P. Campana18,38, D. Campora Perez38, A. Carbone14,d, G. Carboni24,l, JINST 10 P02007 L. Castillo Garcia38, M. Cattaneo38, Ch. Cauet9, R. Cenci58, M. Charles8, Ph. Charpentier38, S. Chen54 L. Castillo Garcia38, M. Cattaneo38, Ch. Cauet9, R. Cenci58, M. Charles8, Ph. Charpentier38, S. Chen54, P.E.L. Clarke50, M. Clemencic38, H.V. Cliff47, J. Closier38, V. Coco38, J. Cogan6, E. Cogneras5, P.E.L. Clarke50, M. Clemencic38, H.V. Cliff47, J. Closier38, V. Coco38, J. Cogan6, E. Cogneras5, Collins38, A. Comerma-Montells11, A. Contu15, A. Cook46, M. Coombes46, S. Coquereau8, G. Corti38, Corvo16,f , I. Counts56, B. Couturier38, G.A. Cowan50, D.C. Craik48, M. Cruz Torres60, S. Cunliffe53, Currie50, C. D’Ambrosio38, J. Dalseno46, P. David8, P.N.Y. David41, A. Davis57, K. De Bruyn41, S. De Capua54, M. De Cian11, J.M. De Miranda1, L. De Paula2, W. De Silva57, P. De Simone18, De Capua54, M. De Cian11, J.M. De Miranda1, L. De Paula2, W. The LHCb collaboration Hansmann-Menzemer11, N. Harnew55, S.T. Harnew4 Harrison54, J. He38, T. Head38, V. Heijne41, K. Hennessy52, P. Henrard5, L. Henry8, He38, T. Head38, V. Heijne41, K. Hennessy52, P. Henr J. Harrison54, J. He38, T. Head38, V. Heijne41, K. Hennessy52, P. Henrard5, L. Henry8, A. Hernando Morata37, E. van Herwijnen38, M. Heß62, A. Hicheur1, D. Hill55, M. Hoballah5, J.A. Hernando Morata37, E. van Herwijnen38, M. Heß62, A. Hicheur1, D. Hill55, M. Hoballah5, C. Hombach54, W. Hulsbergen41, P. Hunt55, N. Hussain55, D. Hutchcroft52, D. Hynds51, M. Idzik27, Hombach54, W. Hulsbergen41, P. Hunt55, N. Hussain55, D. Hutchcroft52, D. Hynds51, M. Idzik27, P. Ilten56, R. Jacobsson38, A. Jaeger11, J. Jalocha55, E. Jans41, P. Jaton39, A. Jawahery58, F. Jing3, Ilten56, R. Jacobsson38, A. Jaeger11, J. Jalocha55, E. Jans41, P. Jaton39, A. Jawahery58, F. Jing3, M. John55, D. Johnson55, C.R. Jones47, C. Joram38, B. Jost38, N. Jurik59, M. Kaballo9, S. Kandybei4 M. John55, D. Johnson55, C.R. Jones47, C. Joram38, B. Jost38, N. Jurik59, M. Kaballo9, S. Kandybei4 W. Kanso6, M. Karacson38, T.M. Karbach38, S. Karodia51, M. Kelsey59, I.R. Kenyon45, T. Ketel42, nso6, M. Karacson38, T.M. Karbach38, S. Karodia51, M. Kelsey59, I.R. Kenyon45, T. Ketel42, B. Khanji20, C. Khurewathanakul39, S. Klaver54, K. Klimaszewski28, O. Kochebina7, M. Kolpin11, B. Khanji20, C. Khurewathanakul39, S. Klaver54, K. Klimaszewski28, O. Kochebina7, M. Kolpin11, – 19 – Komarov39, R.F. Koopman42, P. Koppenburg41,38, M. Korolev32, A. Kozlinskiy41, L. Kravchuk33, I. Komarov39, R.F. Koopman42, P. Koppenburg41,38, M. Korolev32, A. Kozlinskiy41, L. Kravchuk3 p
pp
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Kucharczyk20,26,38,k, V. Kudryavtsev34, K. Kurek28, T. Kvaratskheliya31, V.N. La Thi39, D. Lacarrere38, G. Lafferty54, A. Lai15, D. Lambert50, R.W. Lambert42, G. Lanfranchi18, C. Langenbruch48, Lafferty54, A. Lai15, D. Lambert50, R.W. Lambert42, G. Lanfranchi18, C. Langenbruch48, Langhans38, T. Latham48, C. Lazzeroni45, R. Le Gac6, J. van Leerdam41, J.-P. Lees4, R. Lef`evre5, B. Langhans38, T. Latham48, C. Lazzeroni45, R. Le Gac6, J. van Leerdam41, J.-P. Lees4, R. Lef`evr A. Leflat32, J. Lefranc¸ois7, S. Leo23, O. Leroy6, T. Lesiak26, B. Leverington11, Y. Li3, T. Likhomanenko63, Leflat32, J. Lefranc¸ois7, S. Leo23, O. Leroy6, T. Lesiak26, B. Leverington11, Y. Li3, T. Likhomanenko63, M. Liles52, R. Lindner38, C. Linn38, F. Lionetto40, B. Liu15, S. Lohn38, I. Longstaff51, J.H. Lopes Liles52, R. Lindner38, C. The LHCb collaboration Linn38, F. Lionetto40, B. Liu15, S. Lohn38, I. Longstaff51, J.H. Lopes2, N. Lopez-March39, P. Lowdon40, H. Lu3, D. Lucchesi22,r, H. Luo50, A. Lupato22, E. Luppi16,f , N. Lopez-March39, P. Lowdon40, H. Lu3, D. Lucchesi22,r, H. Luo50, A. Lupato22, E. Luppi16,f , G. Mancinelli6, J. Maratas5, J.F. Marchand4, U. Marconi14, C. Marin Benito36, P. Marino23,t, R. G. Mancinelli6, J. Maratas5, J.F. Marchand4, U. Marconi14, C. Marin Benito36, P. Marino23,t, R. M¨arki39, 2015 JINST 10 P020 F. Martinez Vidal64, D. Martins Tostes2, A. Massafferri1, R. Matev38, Z. Mathe38, C. Matteuzzi20, Martinez Vidal64, D. Martins Tostes2, A. Massafferri1, R. Matev38, Z. Mathe38, C. Matteuzzi20, Meier9, M. Meissner11, M. Merk41, D.A. Milanes8, M.-N. Minard4, N. Moggi14, J. Molina Rodriguez60, Monteil5, M. Morandin22, P. Morawski27, A. Mord`a6, M.J. Morello23,t, J. Moron27, A.-B. Morris50, R. Mountain59, F. Muheim50, K. M¨uller40, M. Mussini14, B. Muster39, P. Naik46, T. Nakada39, Mountain59, F. Muheim50, K. M¨uller40, M. Mussini14, B. Muster39, P. Naik46, T. Nakada39, R. Nandakumar49, I. Nasteva2, M. Needham50, N. Neri21, S. Neubert38, N. Neufeld38, M. Neuner Nandakumar49, I. Nasteva2, M. Needham50, N. Neri21, S. Neubert38, N. Neufeld38, M. Neuner11, JINST 10 P02007 A.D. Nguyen39, T.D. Nguyen39, C. Nguyen-Mau39,q, M. Nicol7, V. Niess5, R. Niet9, N. Nikitin32, D. Nguyen39, T.D. Nguyen39, C. Nguyen-Mau39,q, M. Nicol7, V. Niess5, R. Niet9, N. Nikitin32, T. Nikodem11, A. Novoselov35, D.P. O’Hanlon48, A. Oblakowska-Mucha27, V. Obraztsov35, S. Og Nikodem11, A. Novoselov35, D.P. O’Hanlon48, A. Oblakowska-Mucha27, V. Obraztsov35, S. Oggero41, Ogilvy51, O. Okhrimenko44, R. Oldeman15,e, G. Onderwater65, M. Orlandea29, J.M. Otalora Goicochea2, P. Owen53, A. Oyanguren64, B.K. Pal59, A. Palano13,c, F. Palombo21,u, M. Palutan18, J. Panman38, Owen53, A. Oyanguren64, B.K. Pal59, A. Palano13,c, F. Palombo21,u, M. Palutan18, J. Panman38, Papanestis49,38, M. Pappagallo51, L.L. Pappalardo16,f , C. Parkes54, C.J. Parkinson9,45, G. Passaleva17, A. Papanestis49,38, M. Pappagallo51, L.L. Pappalardo16,f , C. Parkes54, C.J. Parkinson9,45, G. Pass G.D. Patel52, M. Patel53, C. Patrignani19,j, A. Pazos Alvarez37, A. Pearce54, A. Pellegrino41, G.D. Patel52, M. Patel53, C. Patrignani19,j, A. Pazos Alvarez37, A. Pearce54, A. Pellegrino4 M. Pepe Altarelli38, S. Perazzini14,d, E. Perez Trigo37, P. Perret5, M. Perrin-Terrin6, L. Pescatore45, Pepe Altarelli38, S. Perazzini14,d, E. Perez Trigo37, P. Perret5, M. Perrin-Terrin6, L. Pescatore45, E. Pesen66, K. Petridis53, A. Petrolini19,j, E. Picatoste Olloqui36, B. Pietrzyk4, T. Pilaˇr48, D. Pinci25, E. Pesen66, K. Petridis53, A. Petrolini19,j, E. Picatoste Olloqui36, B. Pietrzyk4, T. Pilaˇr48, D. Pinci25, D. Popov10, B. Popovici29, C. Potterat2, E. Price46, J. Prisciandaro39, A. Pritchard52, C. Prouve46, D. Popov10, B. The LHCb collaboration Popovici29, C. Potterat2, E. Price46, J. Prisciandaro39, A. Pritchard52, C. Prouve46, Pugatch44, A. Puig Navarro39, G. Punzi23,s, W. Qian4, B. Rachwal26, J.H. Rademacker46, V. Pugatch44, A. Puig Navarro39, G. Punzi23,s, W. Qian4, B. Rachwal26, J.H. Rademacker46, B. Rakotomiaramanana39, M. Rama18, M.S. Rangel2, I. Raniuk43, N. Rauschmayr38, G. Raven4 Rakotomiaramanana39, M. Rama18, M.S. Rangel2, I. Raniuk43, N. Rauschmayr38, G. Raven42, S. Reichert54, M.M. Reid48, A.C. dos Reis1, S. Ricciardi49, S. Richards46, M. Rihl38, K. Rinnert52 Reichert54, M.M. Reid48, A.C. dos Reis1, S. Ricciardi49, S. Richards46, M. Rihl38, K. Rinnert52, Rives Molina36, D.A. Roa Romero5, P. Robbe7, A.B. Rodrigues1, E. Rodrigues54, P. Rodriguez Perez54, Roiser38, V. Romanovsky35, A. Romero Vidal37, M. Rotondo22, J. Rouvinet39, T. Ruf38, F. Ruffini23, H. Ruiz36, P. Ruiz Valls64, J.J. Saborido Silva37, N. Sagidova30, P. Sail51, B. Saitta15,e, Ruiz36, P. Ruiz Valls64, J.J. Saborido Silva37, N. Sagidova30, P. Sail51, B. Saitta15,e, Salustino Guimaraes2, C. Sanchez Mayordomo64, B. Sanmartin Sedes37, R. Santacesaria25, V. Salustino Guimaraes2, C. Sanchez Mayordomo64, B. Sanmartin Sedes37, R. Santacesaria25, C. Santamarina Rios37, E. Santovetti24,l, A. Sarti18,m, C. Satriano25,n, A. Satta24, D.M. Saunders46 Santamarina Rios37, E. Santovetti24,l, A. Sarti18,m, C. Satriano25,n, A. Satta24, D.M. Saunders46, M. Savrie16,f , D. Savrina31,32, M. Schiller42, H. Schindler38, M. Schlupp9, M. Schmelling10, B. Schmidt38 Savrie16,f , D. Savrina31,32, M. Schiller42, H. Schindler38, M. Schlupp9, M. Schmelling10, B. Schmidt38, Schneider39, A. Schopper38, M.-H. Schune7, R. Schwemmer38, B. Sciascia18, A. Sciubba25, M. Seco37, Semennikov31, I. Sepp53, N. Serra40, J. Serrano6, L. Sestini22, P. Seyfert11, M. Shapkin35, Shapoval16,43,f , Y. Shcheglov30, T. Shears52, L. Shekhtman34, V. Shevchenko63, A. Shires9, R. Silva Coutinho48, G. Simi22, M. Sirendi47, N. Skidmore46, T. Skwarnicki59, N.A. Smith52, E. Smith55,49 J. van Tilburg41, V. Tisserand4, M. Tobin39, S. Tolk42, L. Tomassetti16,f , D. Tonelli38, S. Topp-Joergensen55, N. Torr55, E. Tournefier4, S. Tourneur39, M.T. Tran39, M. Tresch40, S. Topp-Joergensen55, N. Torr55, E. Tournefier4, S. Tourneur39, M.T. Tran39, M. Tresch40, – 20 – A. Tsaregorodtsev6, P. Tsopelas41, N. Tuning41, M. Ubeda Garcia38, A. Ukleja28, A. Ustyuzhanin63,
U. Uwer11, V. Vagnoni14, G. Valenti14, A. Vallier7, R. Vazquez Gomez18, P. Vazquez Regueiro37,
C. V´azquez Sierra37, S. Vecchi16, J.J. Velthuis46, M. Veltri17,h, G. Veneziano39, M. Vesterinen11, B. Viaud7,
D. Vieira2, M. Vieites Diaz37, X. Vilasis-Cardona36,p, A. Vollhardt40, D. Volyanskyy10, D. Voong46,
A. Vorobyev30, V. Vorobyev34, C. Voß62, H. Voss10, J.A. de Vries41, R. Waldi62, C. Wallace48,
R. Wallace12, J. Walsh23, S. Wandernoth11, J. Wang59, D.R. Ward47, N.K. Watson45, D. Websdale53,
M. Whitehead48, J. The LHCb collaboration Wicht38, D. Wiedner11, G. Wilkinson55, M.P. Williams45, M. Williams56, F.F. Wilson49,
J. Wimberley58, J. Wishahi9, W. Wislicki28, M. Witek26, G. Wormser7, S.A. Wotton47, S. Wright47, S. Wu3,
K. Wyllie38, Y. Xie61, Z. Xing59, Z. Xu39, Z. Yang3, X. Yuan3, O. Yushchenko35, M. Zangoli14,
M. Zavertyaev10,b, L. Zhang59, W.C. Zhang12, Y. Zhang3, A. Zhelezov11, A. Zhokhov31, L. Zhong3,
A. Zvyagin38 A. Tsaregorodtsev6, P. Tsopelas41, N. Tuning41, M. Ubeda Garcia38, A. Ukleja28, A. Ustyuzhanin63,
U. Uwer11, V. Vagnoni14, G. Valenti14, A. Vallier7, R. Vazquez Gomez18, P. Vazquez Regueiro37,
C. V´azquez Sierra37, S. Vecchi16, J.J. Velthuis46, M. Veltri17,h, G. Veneziano39, M. Vesterinen11, B. Viaud7,
D. Vieira2, M. Vieites Diaz37, X. Vilasis-Cardona36,p, A. Vollhardt40, D. Volyanskyy10, D. Voong46,
A. Vorobyev30, V. Vorobyev34, C. Voß62, H. Voss10, J.A. de Vries41, R. Waldi62, C. Wallace48,
R. Wallace12, J. Walsh23, S. Wandernoth11, J. Wang59, D.R. Ward47, N.K. Watson45, D. Websdale53,
M. Whitehead48, J. Wicht38, D. Wiedner11, G. Wilkinson55, M.P. Williams45, M. Williams56, F.F. Wilson49,
J. Wimberley58, J. Wishahi9, W. Wislicki28, M. Witek26, G. Wormser7, S.A. Wotton47, S. Wright47, S. Wu3,
K. Wyllie38, Y. Xie61, Z. Xing59, Z. Xu39, Z. Yang3, X. Yuan3, O. Yushchenko35, M. Zangoli14,
M. Zavertyaev10,b, L. Zhang59, W.C. Zhang12, Y. Zhang3, A. Zhelezov11, A. Zhokhov31, L. Zhong3,
A. The LHCb collaboration Wills Physics Laboratory, University of Bristol, Bristol, United Kingdom
47 Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
48 Department of Physics, University of Warwick, Coventry, United Kingdom
49 STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
50 School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
51 School of Physics and Astronomy, University of Glasgow, Glasgow, United Kingdom
52 Oliver Lodge Laboratory, University of Liverpool, Liverpool, United Kingdom
53 Imperial College London, London, United Kingdom
54 School of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
55 Department of Physics, University of Oxford, Oxford, United Kingdom
56 Massachusetts Institute of Technology, Cambridge, MA, United States
57 University of Cincinnati, Cincinnati, OH, United States
58 University of Maryland, College Park, MD, United States
59 Syracuse University, Syracuse, NY, United States
60 Pontif´ıcia Universidade Cat´olica do Rio de Janeiro (PUC-Rio), Rio de Janeiro, Brazil, associated to 2
61 Institute of Particle Physics, Central China Normal University, Wuhan, Hubei, China, associated to 3
62 Institut f¨ur Physik, Universit¨at Rostock, Rostock, Germany, associated to 11
63 National Research Centre Kurchatov Institute, Moscow, Russia, associated to 31
64 Instituto de Fisica Corpuscular (IFIC), Universitat de Valencia-CSIC, Valencia, Spain, associated to 36
65 KVI - University of Groningen, Groningen, The Netherlands, associated to 41
66 Celal Bayar University, Manisa, Turkey, associated to 38
a Universidade Federal do Triˆangulo Mineiro (UFTM), Uberaba-MG, Brazil
b P.N. The LHCb collaboration Lebedev Physical Institute, Russian Academy of Science (LPI RAS), Moscow, Russia
c Universit`a di Bari, Bari, Italy
d Universit`a di Bologna, Bologna, Italy
e Universit`a di Cagliari, Cagliari, Italy
f Universit`a di Ferrara, Ferrara, Italy
g Universit`a di Firenze, Firenze, Italy
h Universit`a di Urbino, Urbino, Italy
i Universit`a di Modena e Reggio Emilia, Modena, Italy
j Universit`a di Genova, Genova, Italy
k Universit`a di Milano Bicocca, Milano, Italy
l Universit`a di Roma Tor Vergata, Roma, Italy
m Universit`a di Roma La Sapienza, Roma, Italy
n Universit`a della Basilicata, Potenza, Italy
o AGH - University of Science and Technology, Faculty of Computer Science, Electronics and
Telecommunications, Krak´ow, Poland
p LIFAELS, La Salle, Universitat Ramon Llull, Barcelona, Spain
q Hanoi University of Science, Hanoi, Viet Nam
r Universit`a di Padova, Padova, Italy
s Universit`a di Pisa, Pisa, Italy
t Scuola Normale Superiore, Pisa, Italy
u Universit`a degli Studi di Milano, Milano, Italy 39 Ecole Polytechnique F´ed´erale de Lausanne (EPFL), Lausanne, Switzerland 39 Ecole Polytechnique F´ed´erale de Lausanne (EPFL), Lausanne, Switzerland 40 Physik-Institut, Universit¨at Z¨urich, Z¨urich, Switzerland 41 Nikhef National Institute for Subatomic Physics, Amsterdam, The Netherlands 2015 JINST 10 P020 53 Imperial College London, London, United Kingdom 5 JINST 10 P02007 56 Massachusetts Institute of Technology, Cambridge, MA, United States University of Cincinnati, Cincinnati, OH, United States 58 University of Maryland, College Park, MD, United Sta 59 Syracuse University, Syracuse, NY, United States The LHCb collaboration Zvyagin38 2015 JINST 10 P020 1 Centro Brasileiro de Pesquisas F´ısicas (CBPF), Rio de Janeiro, Brazil
2 Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
3 Center for High Energy Physics, Tsinghua University, Beijing, China
4 LAPP, Universit´e de Savoie, CNRS/IN2P3, Annecy-Le-Vieux, France
5 Clermont Universit´e, Universit´e Blaise Pascal, CNRS/IN2P3, LPC, Clermont-Ferrand, France
6 CPPM, Aix-Marseille Universit´e, CNRS/IN2P3, Marseille, France
7 LAL, Universit´e Paris-Sud, CNRS/IN2P3, Orsay, France
8 LPNHE, Universit´e Pierre et Marie Curie, Universit´e Paris Diderot, CNRS/IN2P3, Paris, France
9 Fakult¨at Physik, Technische Universit¨at Dortmund, Dortmund, Germany
10 Max-Planck-Institut f¨ur Kernphysik (MPIK), Heidelberg, Germany
11 Physikalisches Institut, Ruprecht-Karls-Universit¨at Heidelberg, Heidelberg, Germany
12 School of Physics, University College Dublin, Dublin, Ireland
13 Sezione INFN di Bari, Bari, Italy
14 Sezione INFN di Bologna, Bologna, Italy
15 Sezione INFN di Cagliari, Cagliari, Italy
16 Sezione INFN di Ferrara, Ferrara, Italy
17 Sezione INFN di Firenze, Firenze, Italy
18 Laboratori Nazionali dell’INFN di Frascati, Frascati, Italy
19 Sezione INFN di Genova, Genova, Italy
20 Sezione INFN di Milano Bicocca, Milano, Italy
21 Sezione INFN di Milano, Milano, Italy
22 Sezione INFN di Padova, Padova, Italy
23 Sezione INFN di Pisa, Pisa, Italy
24 Sezione INFN di Roma Tor Vergata, Roma, Italy
25 Sezione INFN di Roma La Sapienza, Roma, Italy
26 Henryk Niewodniczanski Institute of Nuclear Physics Polish Academy of Sciences, Krak´ow, Poland
27 AGH - University of Science and Technology, Faculty of Physics and Applied Computer Science, Krak´ow,
Poland
28 National Center for Nuclear Research (NCBJ), Warsaw, Poland
29 Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest-Magurele, Romania
30 Petersburg Nuclear Physics Institute (PNPI), Gatchina, Russia
31 Institute of Theoretical and Experimental Physics (ITEP), Moscow, Russia
32 Institute of Nuclear Physics, Moscow State University (SINP MSU), Moscow, Russia
33 Institute for Nuclear Research of the Russian Academy of Sciences (INR RAN), Moscow, Russia
34 Budker Institute of Nuclear Physics (SB RAS) and Novosibirsk State University, Novosibirsk, Russia
35 Institute for High Energy Physics (IHEP), Protvino, Russia
36 Universitat de Barcelona, Barcelona, Spain
37 Universidad de Santiago de Compostela, Santiago de Compostela, Spain
38 European Organization for Nuclear Research (CERN), Geneva, Switzerland JINST 10 P02007 13 Sezione INFN di Bari, Bari, Italy 15 Sezione INFN di Cagliari, Cagliari, Italy 16 Sezione INFN di Ferrara, Ferrara, Italy 19 Sezione INFN di Genova, Genova, Italy 20 Sezione INFN di Milano Bicocca, Milano, Italy 21 Sezione INFN di Milano, Milano, Italy 22 Sezione INFN di Padova, Padova, Italy 23 Sezione INFN di Pisa, Pisa, Italy 24 Sezione INFN di Roma Tor Vergata, Roma, Italy 25 Sezione INFN di Roma La Sapienza, Roma, Italy 28 National Center for Nuclear Research (NCBJ), Warsaw, Poland 29 Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest- 30 Petersburg Nuclear Physics Institute (PNPI), Gatchina, Russia 31 Institute of Theoretical and Experimental Physics (ITEP), Moscow, Russia 33 Institute for Nuclear Research of the Russian Academy of Sciences (INR RAN), Moscow, Russ 34 Budker Institute of Nuclear Physics (SB RAS) and Novosibirsk State University, Novosibirsk, Russia 35 Institute for High Energy Physics (IHEP), Protvino, Russia 35 Institute for High Energy Physics (IHEP), Protvino, Russia 36 Universitat de Barcelona, Barcelona, Spain 37 Universidad de Santiago de Compostela, Santiago de Compostela, Spain 37 Universidad de Santiago de Compostela, Santiago de Compostela, Spain 38 European Organization for Nuclear Research (CERN), Geneva, Switzerland – 21 – 39 Ecole Polytechnique F´ed´erale de Lausanne (EPFL), Lausanne, Switzerland
40 Physik-Institut, Universit¨at Z¨urich, Z¨urich, Switzerland
41 Nikhef National Institute for Subatomic Physics, Amsterdam, The Netherlands
42 Nikhef National Institute for Subatomic Physics and VU University Amsterdam, Amsterdam, The Netherlan
43 NSC Kharkiv Institute of Physics and Technology (NSC KIPT), Kharkiv, Ukraine
44 Institute for Nuclear Research of the National Academy of Sciences (KINR), Kyiv, Ukraine
45 University of Birmingham, Birmingham, United Kingdom
46 H.H. a Universidade Federal do Triˆangulo Mineiro (UFTM), Uberaba-MG, Brazil b P.N. Lebedev Physical Institute, Russian Academy of Science (LPI RAS), Moscow, Russia c Universit`a di Bari, Bari, Italy d Universit`a di Bologna, Bologna, Italy e Universit`a di Cagliari, Cagliari, Italy f Universit`a di Ferrara, Ferrara, Italy g Universit`a di Firenze, Firenze, Italy h Universit`a di Urbino, Urbino, Italy i Universit`a di Modena e Reggio Emilia, Modena, Italy i Universit`a di Modena e Reggio Emilia, Modena, Italy j Universit`a di Genova, Genova, Italy k Universit`a di Milano Bicocca, Milano, Italy l Universit`a di Roma Tor Vergata, Roma, Italy m Universit`a di Roma La Sapienza, Roma, Italy m Universit`a di Roma La Sapienza, Roma, Italy n Universit`a della Basilicata, Potenza, Italy o AGH - University of Science and Technology, Faculty of Computer Science, Electronics and
Telecommunications, Krak´ow, Poland p LIFAELS, La Salle, Universitat Ramon Llull, Barcelona, Spain q Hanoi University of Science, Hanoi, Viet Nam r Universit`a di Padova, Padova, Italy s Universit`a di Pisa, Pisa, Italy t Scuola Normale Superiore, Pisa, Italy u Universit`a degli Studi di Milano, Milano, Italy u Universit`a degli Studi di Milano, Milano, Italy – 22 –
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https://openalex.org/W831184870
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https://pubs.lib.uiowa.edu/igsar/article/id/804/download/pdf/
|
English
| null |
The Stratigraphy of the Mississippian Formations of Iowa
|
Annual report for ... with accompanying papers
| 1,923
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public-domain
| 172,942
|
CHAPTER II.
THE KINDERHOOK GROUP Definition ................. _ .................................. _ ...................................... _ .......... _ .... _ ............. 49
Areal distribution ....... _ .................. _ ...................................................... _ .......... __ .... _ ...... 49
Lithologic character ............................. _ .. _ ........................ _ ...................... _ ...... : ................ 50
Thickness ....... _ .......................................................... _ .. _ ........................................ _ ........... 51
Subdivisions ................. _ .......................... _ .......... _ ............................................................... 51
Stratigraphic relations ..................... _ .... __ ...................... _ .. _ ........................................... 52
Area~e~:~c:liPs\i~t~~~ntC~~~~~~~ .. :::::::::::::=::::=::=::::::::::::=::::::::::=::::::::::::::::::::::::::::==::::::: ~~
Kinderhook of southeastern Iowa ........... _ ............ _ ................................ _ .. _ ......... 53
Lee county ................. _ ......................................................................................... 53
Des Moines county ....... _ .............. _ .................... _ ...... __ ..................................... 53
Louisa county ....... _ .............. _ ................ _ .. _ ...... _ .............. _ .. _........................... 63
Correlation of Kinderhook beds of Louisa county ....... _ .......... _..... 70
Muscatine county ....... _ .............. _ ............ _ ............ _ ........................................... 70
Washington county ........... _ ................ _ ...................................... _ .... _ .. _ ............. 71
Poweshiek county ............... _ ...... _ ........................................ _............................. 77
Iowa county ................. _ ........ _ .................. _ ........................................ _ .... _ .. _ ..... 78
Jasper county ....... _ ............ _ ............................................................................... 78
Kinderhook of central Iowa ..................................................... _ .. _ ......................... 78
General statement ......................... _ ................................ _ ........ _.:..................... 78
Marshall county ....................................................................................... _ .. _ ..... 80
Le Grand beds ....................... _ .................. _ .......................... _ .......... _ ....... 80
Marshalltown shales ....... _ .......................... _ .......... _ .......•............ _ .. _ ......... 84
Tama county ....................................................... _ ............................................... 84
Grundy county ........... _ .. _ ........ _ ........ _ .......... _ .... _ .......................................... _ ... 87
Correlation of Kinderhook in central Iowa ............... __ .... _ ....................... 88
Kinderhook of north· central Iowa ......................... _ ............ _ ...... _ .................. _ ..... 90
General stateme·nt ............. _ .................... _ .. _ .. _ .......... _ .. _ ................................. 90
The Sheffield beds ....... _ ........................ _ .. _ .......... ~ .. _ ...................... _ ....... 91
The Chapin beds ... _ .......... _ ........ _ .................. _ ........................................... 91
The Mayne Creek beds ....... _ .................................................... _ ............... 92
The Eagle City beds ... _ .......... _ ........ _ .......... _ ........ _ ................................. 92
The Iowa Falls dolomite .......................................................................... 92
The Alden lim·estone ....... _ .................................. _ ............................ _....... 92
Hardin county ................. _ ................................................ _ ................ _ ............... CHAPTER I.
THE MISSISSIPPIAN SYSTEM IN IowA PAGE
Introduction ........................................ _ ................................................................................. 39
Distribution and importance ....... _ .... _ ........ _ ........................................ _ ......................... 39
Topography ......................................................... _ ................................................................. 40
Drainage ......................................................... _ .................................................. _ .... _ .. _......... 40
Character and general relations ........................................................... _ .... _ ................... 41
Relation to the type section ............................................. _ ...... _ ............................. 41
Subdivisions ..................................... _ .................. _ .................................. _ ................... 41
Thickness and lithologic character ....................... _ ........................................ _ ..... 41
Stratigraphic relations ....................................... _ .... _ ....................................................... 42
Regional structure .............................................................................................................. 45
Previous work ......................................................... _ .................. _ ............................ _ ......... 45 THE STRATIGRAPHY OF THE MISSISSIPPIAN
FORMATIONS OF IOWA BY
FRANCIS M. VAN TUYL THE OSAGE GROUP Definition of Osage _________________________________________________________________________________________ . _____ . _____ 117
Distribution of the group ______________________________________________________________________________________ 117
Lithologic character ________ . __________________________________________________________________________________________ 118
Thickness ________________ ~-------------------------------------___ , ________________ ..: __________________________________ . _____ 118
Stratigraphic rela tions ______________________ . __________________________________________________________________________ 118
The Burlington limestone ______________________ . ____________________________________ . _________________________ . ____ .118
Nomenclature, _________ . ______________________________________________________________________________________________ 118
Areal distribution __________________________________________ . _______________________________________________ 118
Lithologic character _____________________ . ______________________________________________________ . ____________ ~19
Thickness _______________ . ____________________________________________________________________________________________ 121
Areal description by counties ________ . __________________________________________________________________ 121
De,s Moines and Lee counties __________________________________________ . ____________________________ 121
Van Buren county _______ . ____________________ . __________________ . ____________________________________________ 135
Louisa county ____________________________________ . __________________________________ . ____ .. ____ ._. __ : _______ 136
Washington coun ty _______________________________________________________ . ___________________________ 141
The Keokuk limestone _________________________________________________________________________________________________ 142
Nomenclature and character ____ . ______________________________ . __________________________________________ 142
Stratigraphic relations _________________ . _____ ... ___________________ . _______________ .. ________________________ 143
Areal distribution ___ ._. ____________ .. ______ . _________________________________________________ . ____ . ______________ 144
Areal description by counties ________ .. _______ . _____ . ____________________________________ .. __________________ 145
Lee county and adjacent parts of illinois ______ ..... _ ..... _____ . _____ . ___________ ._. ____ .145
D ~ Moines county ______________ . ___________ . __________________________ . ______________ . ______________ ._163
Varn Buren county ______ .... _____ . ______ . _______ ._. ____ . ______ . _____________________________ . ____ . ________ 168
Henry coun ty ________ . ____ ._ ... ___ .. __________ . __________ ... ____________________ . ______ . ____________ . __________ .. 17 4
Louisa coun ty _________ . _______ .. _______________________________________________ . ________ .. ___________________ .176
ICeokuk county ________ . _____ . _________________________________________ . ___________ . ___ . _____ . _________ . ____ 178
CHAPTER IV. THE MERAMEC GROUP
Definition of Meramec ________________________________________________________________________________________________ .182
Distribution of the group ____ . __ ... _. _______ . ___________________ .. _________________ . ____ . _____ . _____ .. ___ .. _______ . __ 183
Lithologic character : _______ . ________ . _______ ._. _________________ . ________________________ . ______ . ____ ._. ____________ . ___ 183
Thickness
_____ . __ ..... _. ________________ . ____ ._. ___________________________ .. ________ . _____ . ________ .. ____ .. __ .... _._. __ .. _. ___ . ____ 184
Stratigraphic relations ________ .. ___ .. _. _____ .. _. _________ . _________ . ___ . _____ . ___________________ . _____ . CHAPTER II.
THE KINDERHOOK GROUP 92
The Eagle City beds ................... _ .................... _ .................... _ ................. 93 36 CON'fEN'I.'S PAGE
The Iowa Falls dolomite _______________ , __________________________________ . ____ . __________ . __ 97
The Alden limestone ________ . _________ ._______________________________________________________________ 99
Franklin county ____________________________________________________________________________________________ 100
The Sheffield beds ____________ . ____________________________________________________________________ 101
The Chapin beds __________________________________________________________________________________ 104
The Mayne Cr,eek beds ___________________________ . ______________________________________ . ________ ~05
Butler county _______ . _________________________________________________________________________________________ 106
The Sheffield beds ______________________________________________________________________________ 107
The Chapin and Mayne Creek beds __________________ . ________________________________ 108
Wright county ____________________________________ . ____________________________ . ______________________________ 109
Humboldt coun ty ____________________________________________________ . ___________________________________ 1 09
Pocahontas county ________________________ : ___________________________________________________ . __ . _________ 113
Cerro Gordo county _________________________________________________________________ . _____________________ 114
Kossuth, Hancock and Winnebago counties ________________________________________ .:. ____ 115
C'orrelation of Kinderhook of north-central Iowa __________ . ____ . _____ . ____________ 115 C orrelation of Kinderhook of north-central THE OSAGE GROUP ______________ ._184
The Warsaw formation . ______ .... ___ . __ .. __ . _____________ .. ____ . __ . __________ .. _______________ .... _. ___ . ___________ . __ 184
Nomenclature and distribution ___ . ____ .. _._. _____________ .. _________________ . __________ .. ___ . ___ . ___ .... _184
The Lower Warsaw beds __ .. _ ... _. __________________________ .. ____ .. ______ . ___ . ______ ._ .. _ .... ____ . _____ . ____ 186
Lithologic character ________ .. ____ .... __ . _______ .. _______ ........ ________________________ . ____ . ____ . ____ . _________ 186
Areal description by counties _ .. _________________ . __________________________________ . ______________ ._ .... _187
Hancock county, Illinois ____ . ____________ . _________ . ________ . ________ . _______________________________ 187
Lee county ________ .. ___ . ____ .. __ . ____ . ___ . ______ . ________ ._. __________________________ ._._ .. ________ . _____ . ________ .192 CONTENTS 37 PAGE
E~a:~~f::st~o!~~o_~~_~ __ :::::::::::::::::=::::::::::::::::::::::::::::=::::::::::::::::::::::=:=::::::~::l~~
Henry county __________________________ . ___ . __ . __ . __ . __________ . _______ .--___ . ____________________________ . _________ 196
_ Van Bure.n. county ____ . ___________________ ~. -,-- , --.,-------.-.. --------. _____ , _____ . ________ ,---:-----------198
The Upper Warsaw beCLs ______ . ____ .. ___________________ . ________________ . ______ . __________________________________ 203
Description of the type section ______________________ • _______________________________________ , ___ ,,-______ 203
The Upper Warsaw in Iowa ___________________ ,--,-----_-------------------------___________ • ___ -'-_. _______ 210
The Spergen formation _________________________________________ ,-------,----____________________
--------~------ -----213
N omenclature __________________________________________________ • __________________________________________________________ 213
Areal distribution __________________________________________________________ . _____ . _______________ . ______________ 2'14
Character and stratigraphic relations ---w---------------------.--.-----.----__________ ... ________ . ____
214
A,eal description by counties _______________________________ .. ~--- ------- ,- --------_______ .. ___________ ,----215
Lee county ___________________ .. ______________ . _________________________________ . __ .. _______ . ______ .. _____________ 215
Hancock county, illinois _____ . _______ .. _______________________ . _________________________________________ 223
Des Moines county ______________________________ : __________ . ______ . _________________ .. _______________________ 226
Van Buren coun ty ________ , ______ . _______________________ . _______________________ . ___________________________ 227
Henry county ____ . _______________________________ ._. ____________ . ____________ . ___________________________________ 229
Jefferson county ... _____ . ______________________________________ . ____________ . ________ . ______________________ ._.230
The St_ Louis limestone _________________________________________ . ____________________ . ___________________________________ 230
Character and general relations _______________________________________________ . ____________________________ 230
Brecciation effects _______________ .. __ . ______________ . _______________ ... _. ___ ._ .... THE OSAGE GROUP __ . _______________________ .,-----.-233>
Areal distribution _______ . __________ . ______________ . __ . ___________________________ .. _________________ . __ .... _. __ 236
Areal description by counties _____ ._. ________________ . ______________ . ___________________ ._. ____________ 237
Lee county ________________________________________________________ . ____ . _____ . __ . _______________ . ________________ 237
Van Buren county ______ .. ____ . _________ . __________ . __________________ .. __ . __ . ________ .. __________________ 247
Des Moines county _. _________________ ________________________________________ . ________ . ____________________ 263
Henry county ____ . _______________________ . _____ . ___ ._ .. _______ . __ .. ____ ._. _____________ . _____ . __ ... ____________ 263
J efferson county ... _. ______________________________________ . __________ ... __ .. ___________________ . ____________ 267
Wapello county . ___________________________ . _____ . __________ .. __ . ___ . __ ..... _______ . __ . ____ ._. __________ . ___ ... 270
Louisa county _________ . __ ._. ___ : ... ____ . ___ .. __ . ____ ., __ .... __ ., __ .. _ ... __ . ____ . __ .. _____________ . __________ 271
Yvashington county _______________________________ . ___ . ________ .. _________ .. _________ :._. ________ . _________ 271
Keokuk county . ______ . _____ .. ____ ._._ ... _ .. ___________________ ..... __ . __ . ____ . ____ ._. __ . ____ . __ .... ______ .. __ 27 4
Mahaska county ..... _ ... _ ... __ . _____ ._ ... ______________ .... :._ .. __ ._. ___ .... _____ ._._._.:_ .. _ .. _____ .. _______ 2.77
Marion county ___ ... ________ . ___________________________ ._. ____ .. _____ .... __ . ____ .... ________ . ________________ 278
Poweshiek coun ty . ___ . ____ . ___________________ . ________ . ___ .. _ .. __ . _____ .... ___ .... ____ . ___ ._. ______ . ___ .. _27 8
Marshall county ... ___________ ._. ____ .. _______________________ .. ____________________________________________ 279
Story county ____ .... ___________________ . __________ . ___________________________ . _________ . ____________________ .. _____ 280
Webster county _______________ .. _______________ . ___ . ___________ . ___ ... ____________ .. _________ . _________________ 282
Humboldt county _______________________ .. _._L __________________________ . _._. __ •• ___________________ .284
The Ste. Genevieve formation .. ______________ .. ________ .. ______ .. ______ .. ___ ........ _______________ .. __ .. ___ .... _287
N omenclature .. __ : __________ .... THE OSAGE GROUP _ .. __ .. __ ...... ____ ... _________________ .. ___________ .. _ .. __ .. ___ .. __ ... ___ .. ________ 287
Areal distribution _ .... __________________________ .. _____ .. ________________ .. __________________________ ___ .. _______ .. _288
Lithologic character and thickness -.. -----.. -----... ------..... ___ ........ __ ....... __ .. _ .. _____ .... _288
Stratigraphic relations ..... ______________________________ .. _ .. __ ...... ___ .. _____ .. ________ .. ____ .... ___ .. _ ..... _ .. _B88
Changes at close of Ste. Gene·vieve time __ .. __ .... __ .. _________ .. __ .. _________________________ 289
Areal description by counties _ .. _____ .. __ .. __ .. ___ .. __________ .. __ .. ____ .. _ .. _ .. __ ....... _____ .. ______ .... _289
Lee county .... __ . _____ .. __ .. ___ ..... ____ ........ __ .... ______ .. __ .. _____ .. __ .. ____ .. _____ .. ___ .. _____________________ 289
Van Buren county .... _ .. _. ___ .. _________ . ___ .. ____ ...... _____ .. ______ ... ______________ .... __ ... __ .. ____ . .290
Davis county . ___ .. ____________ .. ___ .. __ . _________ .. _____ .. _ .. _____ ..... _ .. _ ..... _______ .... ________ .. _._ .. _.293
Henry county .. __ .. _______ .. __ .... __ .. _______________ .... _________ . _____ .. _________ .. ______________ .. ____ . ______ 293
Jefferson county .. __________ .... _______ .. ____________ .... _ .... _____ .... ____ .. __ .. ______________________________ 294
Wapello county .... ______ .... _______________ .. ________ .. _. __ .. _ ...... __ .. ____ .. __ .. ______ .. _______ ...... _____ 296
Washington county ___ . ____ .. ______ .. ___ .... ____ .. ____ .. _______________ .. ____________ .. : ___ .. ___ .. _________ 298
Keokuk county ___ .... ____________________ .. __ . __________ .. ______________ .. ___ .. _______________ .. ___________ 299
Mahaska county .. ____________________________________________ .. ____ .. ____________________ : ___ .. ______ .. _299
Poweshiek county ........ ___________ .. _______ .. ___ .. _ .. _______________________________ .... __ ... ___ . ____ .. 300
Marion county .. __ .... ____ .... _____________________________ . ___ .. ________ .. ___ .. ___ . ___________________ .. ___ .... _300
Webster coun ty ...... ___ .. _ .... THE OSAGE GROUP _.340
Origin of the geodes .......... _ ........... _ ............................. _ .................... _ ................ _ ......... 341
CHAPTER \"'1. GEOLOGIC HISTORY
Conditions at the close of the Devonian .................................... _ ................................ 347
The Kinderhook transgression ........................................... _ ........................................... 347
Conditions during Osage time ............. _ ........................................................ _ ................. 347
Oscillations during 1-Ieramec time ................. _ ........ _ ................. __ ........................ _ ..... 348
Warping at dose of Meramec time ................. _ ............................................................... 348 PAGE
Definition of geode .............................................................................................................. 304
Other occurrence,s of geodes .... , .................................................................................. _ .. .306
Geodes of the Keokuk beds ........................................... _ ............ _ .................... _ ........... 306
Geodes of the Lower Warsaw beds .......................................... _ ................................. 308
Occurrence and size ............. _ ............. _ ..................... ~_ ...... _ .................................... 308
Mineralogical character ............................................... _ .................... _ ..... _ ............. 311
Relation to the containing rock ............................................ _._ .......................... 312
Important localities .. _ .. _._ ..... _ .. _._ .... _ ........ _ ............... __ .... _ .. _ .............. _ ......... 317
Description of typical geodes _ ............................. _ ..... _ ..... _ ....... _ .... _ ............ 327
Minerals of the geodes and the inclosing rocks ........... _ .... _ ..... _ .... _._ ...... _ ............ 335
Paragenesis of the minerals .... _ ........................................... __ ..................... _.340
Origin of the geodes .......... _ ........... _ ............................. _ .................... _ ................ _ ......... 341 Conditions at the close of the Devonian .................................... _ ................................ 347
The Kinderhook transgression ........................................... _ ........................................... 347
Conditions during Osage time ............. _ ........................................................ _ ................. 347
Oscillations during 1-Ieramec time ................. _ ........ _ ................. __ ........................ _ ..... 348
Warping at dose of Meramec time ................. _ ............................................................... 348 Warping at dose of Meramec time FiGURE GURE
PAGE
1. Columnar section of Mississippian system in southeastern Iowa .................. 43 1. Columnar section of Mississippian system in southeastern Iowa .................. 43
2
S
i
hi
l
i
f
Mi
i
i
i
f
i
l
f S 2. Stratigraphic relations of Mississippian formations at close of Ste. Genevieve time ................. _ ................................................. _.............................. 44
3
K
k k li
h
f S
k
K
k k
145 3. Keokuk limestone, mouth of Soap creek, Keokuk ............................................ 145
4
G
d
b d
L
W
Mi
i
i
i
i
bl ff
K
k k
192 Keokuk limestone, mouth of Soap creek, Ke
G
d
b d
L
W
Mi
i
i
i
i 4. Geode bed or Lower Warsaw, Mississippi river bluff, Keokuk. ........ _ ........... 192
5
L
W
b d
l
S
k
t K
k k
193 5. Lower Warsaw bed along Soap creek at Keokuk. .................................... _ ..... 193
6
St
L
i
li
t
U
W
h l
K
k k
212 s limestone on Upper Warsa,w shale, Keokuk
d
i t d f
ti
W
Illi 7. Spergen and associated formations near Warsaw, Illinois .............................. 224
8
B
i t d L
St L
i
li
t
l i
l
l
b dd d S 8. Brecciated Lower St. Louis limestone overlying regularly bedded Spergen
limestone. Near Colchester, lllinois ................. _ .............. _ ........................... 232
9
R
f
i
L
S
L
i
li
M
239 9. Reef·structure in Lower St. Louis limestone near Montrose ................... _ ..... 239
10
I
l
t
t b t
L
d U
St
L
i
li
t 10. Irregular contact between Lower and Upper St. Louis limestone near
Belfast ........................................................... , ........................................................ 243
11
P
d
di
f
it
i
St
L
i
li
t
ki
b
d
b t 11. Pseudo·disconformity in St. Louis limestone marking boundary between
dolomitic portion below and unaltered portion above. Indian creek,
near Farmington .................................................................................................. 250
12
B
i
d L
S
L
i
li
R
d
k
B
253 12. Brecciated Lower St. Louis limestone. Reed creek, near Bonaparte ........ 253
13
B
i
d S
L
i
li
R
d
k
B
253 13. Brecciated St. Louis limestone. Reed creek, near Bonaparte ...................... 253
14
S
ll
d f
lt i
L
St
L
i
li
t
R
d
k 14. LIST OF ILLUSTRATIONS FiGURE
PAGE
1. Columnar section of Mississippian system in southeastern Iowa .................. 43
2. Stratigraphic relations of Mississippian formations at close of Ste. Genevieve time ................. _ ................................................. _.............................. 44
3. Keokuk limestone, mouth of Soap creek, Keokuk ............................................ 145
4. Geode bed or Lower Warsaw, Mississippi river bluff, Keokuk. ........ _ ........... 192
5. Lower Warsaw bed along Soap creek at Keokuk. .................................... _ ..... 193
6. St. Louis limestone on Upper Warsa,w shale, Keokuk ........... _ ....................... 212
7. Spergen and associated formations near Warsaw, Illinois .............................. 224
8. Brecciated Lower St. Louis limestone overlying regularly bedded Spergen
limestone. Near Colchester, lllinois ................. _ .............. _ ........................... 232
9. Reef·structure in Lower St. Louis limestone near Montrose ................... _ ..... 239
10. Irregular contact between Lower and Upper St. Louis limestone near
Belfast ........................................................... , ........................................................ 243
11. Pseudo·disconformity in St. Louis limestone marking boundary between
dolomitic portion below and unaltered portion above. Indian creek,
near Farmington .................................................................................................. 250
12. Brecciated Lower St. Louis limestone. Reed creek, near Bonaparte ........ 253
13. Brecciated St. Louis limestone. Reed creek, near Bonaparte ...................... 253
14. Small reversed fault in Lower St. Louis limestone. Reed cree,k, near
Bonaparte .............................................................................................................. 255
15. Undisturbed dolomitic phase of Lower St. Louis limestone. Rock creek,
near Bentonsport .................................................................................................. 259
16. GeQdes in place in Geode bed along creek northeast of Warsaw, Illinois .. 319
PLATE
PAGE
I. Geological map of Iowa, to face ..... _ .............................................................. _ .. .360
II. A group of geodes frOllIll Dower W3i!'SlJ)W beds ..... _ .... _ .. _ ............ _ ...... _ .. _ ....... 309
In. Characteristic fossils from the Klnderhook group ............. _ _ . __ ............. __ ..... 353
IV. Characteristic fossils from the Burlington beds .............. _ ............... _ .. _ .......... .355
v. Characteristic fossils from the Warsaw and Spergen beds ..................... _ ..... 357
VI. Characteristic fossils from the St. Louis and Ste. Genevieve beds ... _ .. _ ....... 359 THE OSAGE GROUP _______ .. _ .. _____ .. __ .. _._. ____ ... ______ ....... __ ... ___ .... __ .. _ ........ _ .. .301
CHAPTER V. THE GEODES OF THE KEoKUK AND L OWER WARSAW BEDS
Introduction
:
304 __ 304 38 ILLUSTRATIONS PAGE
Definition of geode .............................................................................................................. 304
Other occurrence,s of geodes .... , .................................................................................. _ .. .306
Geodes of the Keokuk beds ........................................... _ ............ _ .................... _ ........... 306
Geodes of the Lower Warsaw beds .......................................... _ ................................. 308
Occurrence and size ............. _ ............. _ ..................... ~_ ...... _ .................................... 308
Mineralogical character ............................................... _ .................... _ ..... _ ............. 311
Relation to the containing rock ............................................ _._ .......................... 312
Important localities .. _ .. _._ ..... _ .. _._ .... _ ........ _ ............... __ .... _ .. _ .............. _ ......... 317
Description of typical geodes _ ............................. _ ..... _ ..... _ ....... _ .... _ ............ 327
Minerals of the geodes and the inclosing rocks ........... _ .... _ ..... _ .... _._ ...... _ ............ 335
Paragenesis of the minerals .... _ ........................................... __ ..................... _.340
Origin of the geodes .......... _ ........... _ ............................. _ .................... _ ................ _ ......... 341
CHAPTER \"'1. GEOLOGIC HISTORY
Conditions at the close of the Devonian .................................... _ ................................ 347
The Kinderhook transgression ........................................... _ ........................................... 347
Conditions during Osage time ............. _ ........................................................ _ ................. 347
Oscillations during 1-Ieramec time ................. _ ........ _ ................. __ ........................ _ ..... 348
Warping at dose of Meramec time ................. _ ............................................................... 348 PAGE
Definition of geode .............................................................................................................. 304
Other occurrence,s of geodes .... , .................................................................................. _ .. .306
Geodes of the Keokuk beds ........................................... _ ............ _ .................... _ ........... 306
Geodes of the Lower Warsaw beds .......................................... _ ................................. 308
Occurrence and size ............. _ ............. _ ..................... ~_ ...... _ .................................... 308
Mineralogical character ............................................... _ .................... _ ..... _ ............. 311
Relation to the containing rock ............................................ _._ .......................... 312
Important localities .. _ .. _._ ..... _ .. _._ .... _ ........ _ ............... __ .... _ .. _ .............. _ ......... 317
Description of typical geodes _ ............................. _ ..... _ ..... _ ....... _ .... _ ............ 327
Minerals of the geodes and the inclosing rocks ........... _ .... _ ..... _ .... _._ ...... _ ............ 335
Paragenesis of the minerals .... _ ........................................... __ ..................... FiGURE Small reversed fault in Lower St. Louis limestone. Reed cree,k, near
Bonaparte .............................................................................................................. 255
15
U di t
b d d l
iti
h
f L
St
L
i
li
t
R
k
k 15. Undisturbed dolomitic phase of Lower St. Louis limestone. Rock creek,
near Bentonsport .................................................................................................. 259
16
G Qd
i
l
i
G
d
b d
l
k
th
t
f W
Illi
i
319 16. GeQdes in place in Geode bed along creek northeast of Warsaw, Illinois .. 319
PLATE
PAGE
I
G
l
i
l
f I
f
360 I. Geological map of Iowa, to face ..... _
II
A group of geodes frOllIll Dower W3i!'Sl I. Geological map of Iowa, to face ..... _ .............................................................. _ .. .360
II
A group of geodes frOllIll Dower W3i!'SlJ)W beds
309 II. A group of geodes frOllIll Dower W3i!'SlJ)W beds ..... _ .... _ .. _ ............ _ ...... _ .. _ ....... 309
I
Ch
t
i ti
f
il
f
th
Kl d
h
k
353 A group of geodes frOllIll Dower W3i!'SlJ)W beds
Characteristic fossils from the Klnderhook gr II. A group of geodes frOllIll Dower W3i!'SlJ)W beds ..... _ .... _ .. _ ............ _ ...... _ .. _ ....... 309
In
Characteristic fossils from the Klnderhook group
353 In. Characteristic fossils from the Klnderhook group ............. _ _ . __ ............. __ ..... 353
IV
Ch
t
i ti
f
il
f
th
B
li
t
b d
355 IV. Characteristic fossils from the Burlington beds .............. _ ............... _ .. _ .......... .355
v
Ch
t
i ti
f
il
f
th
W
d S
b d
357 v. Characteristic fossils from the Warsaw and Spergen beds ..................... _ ..... 357
VI
Ch
t
i ti
f
il
f
th
St
L
i
d St
G
i
b d
359 istic fossils from the Warsaw and Spergen bed
ristic fossils from the St
Louis and Ste
Genev VI. Characteristic fossils from the St. Louis and Ste. Genevieve beds ... _ .. _ ....... 359 Introduction
l
f As a result of the development of a cooperative plan of study
and correlation of the Mississippian formations of the Mississ-
ippi Valley by the several' state geological surveys of the area
and the U. S. Geological Survey in 1913, the writer ·was re-
quested by Doctor Kay of·the Iowa Geological Survey to under-
take a stratigraphic study and revision of these formations in
Iowa under the direction of Professor Stuart Weller of the
University of Chicago. Field work was carried on during the summers of 1913, 1914,
1915 and 1917. In addition the months of October to June,
1914-1915, were spent at ,Valker Museum, The University of
Chicago, in a st.udy and identification of fossil collections made
during the progress of the field inyestigations. F
d h l f l
i
h
i
i
i For encouragement and helpful suggestions the writer is in-
debted to both Doctor .Kay and Professor '\Veller. Doctor A. O. Thomas of the State University of Iowa has kindly assem-
bled and prepared the material for the plates illustrating
typical Mississippian fossils. Topography The state of Iowa lies entirely in the Prairie Plains physio-
graphic province. The elevation of the surface of the area in
which the ,Mississippian formations are the highest consolidated
rock ranges from a little more than 500 feet in the valley of
Mississippi river .below Keokuk in southeastern Iowa· to about
1300 feet in the north-central part. The Mississippian belt lies in the path of the continental
glaciers and partakes of the characteristics of a glaciated re-
gion. In the southeastern and central parts of the state where
the glacial deposits are of early Pleistocene age the topography
is of the mature type. However, the relief is not great except
adjacent to Mississippi river. Exposures of the consolidated
rocks are numerous along the larger streams and their tributar-
ies. In northern Iowa, on the other hand, the surface is under-
lain by glacial deposits belonging to the late Pleistocene. The
topography is youthful and the relief slight. The drift if>
thicker and rock exposures are less comInon . Distribution and Importance
i
f
ti
tit t
th The Mississippian formations constitute the bed rock in a
diagonal belt twenty to sixty mile;;; wide extending from the
southeastern corner of the state northwestward through the
central and north-central parts into southern Minnesota. There
are also a number of small patches and linear areas of these
rocks to the west and southwest of this belt as a result of the
erosion of the Pennsylvanian rocks by the larger streams. Drill
records indicate their presence beneath younger deposits over
the entire southern and southwestern parts of the state. There
is evidence that they likewise formerly extended 'some distance
northeast of the present belt of exposures as will be brought
out on a later page. 40 MISSISSIPPIAN STRATA OF IOWA Occasional small outliers of ~ennsylvanjan strata appear ill
the main Mississippian area. The system is of considerable economic as well as scientific
importance. It contains valuable deposits of clay, building
stone, road material and cement rock. In addition it involves
the type sections of several formations of the lower portion or
the standard Mississippian column which are known the world
over for their profusion of excellently p;reserved fossil remains. . Drainage The area in Iowa in which the Mississippian rocks are ex-
posed lies entirely within the drainage basin of Mississippi
river, which crosses the belt along the southeastern boundary of
the state. The runoff is through four southeasterly trending
tributaries of the "Father of Waters", namely: Cedar river,
which parallels the Mississippian belt on the northeast; IOvYa
river, which crosses the belt in central Iowa; Skunk river, which
crosses it in southeastern Iowa; and finally Des Moines river,
which parallels the belt on the southwest. The postglacial DIVISIONS OF MISSISSIPPIAN 41 drainage lines do not conform to the preglacial ones at many
points along the stream courses. For this reason the distribu-
tion of outcrops along the valleys is often erratic. . The more
typical exposures are usually at those points where the streams
have been diverted from their preglacial courses and have been
compelIed to cut new valleys through the drift and the indur-
ated rocks below. 1 Illinois State Geo!. Survey, Bull. "1, p . 80; 1920.
2 J
G
!
l
XXVIII
281
1920 2 Jour. Geo!., vol. XXVIII, p. 281; 1920. 2 Jour. Geo!., vol. XXVIII, p. 281; 1920. Character and General Rela.tions Relation to' the Type Section.-The Mississippian succession
was formerly regarded as a subdivision of the C.arboniferous
system, which was made to include the Mississippian at the
base, the Pennsylvanian in the middle and the ~ermian at the
top. At the present time there is a tendency to elevate each of
these to the status of a distinct system. . Th
d
d
i
f
h
Mi
i
i
i
i
i
h The standard section of the Mississippian system is in the
Mis~issippi valley, extending from southeastern Iowa into
southern Illinois and sout~eastern Missouri. S bdi i i
Th
f ll
i
l
ifi
i
f h
Mi
i
i Subdivisions.-The following classification of the Mississipp-
ian formations of the standard section, after 'Veller, incorpor-
ates several revisions necessitated by recent work and may be
regarded as representing the latest word on the subject.1 ;2
A
f h
f()
i
l
i
f h
I
S
i An of the f()rmational units of the Iowa Series are represent-
ed in Iowa. ' ·The type sections of the Burlington and Keokuk
formations are ~t the cities of thes~ names in southeastern
Iowa, while the Warsaw beds derive their n~me from the town
of Warsaw, Illinois, on the east bank of Mississippi river,' near-
ly opposite Keokuk, Iowa. The Spergen, St. Louis and Ste. Genevieve formations are represented iIi Iowa by marginal de-
posits only. f h
Ch
f
i
i
d i
h N one of the Chester formations is represented in the state,
and it is probable that the Chester seas never extended this far
north. Thickness and Lithological Character.-The thickness and
lithologic character of the formational · units 'in southeastern
Iowa, where the system attains its most complete development
in the state, are indicated in the accompanying generalized MISSISSIPPIAN STRATA OF IOWA 42 CLASSIFICATION OF THE MISSISSIPPIAN FORMATIONS OF THE MISSSISSIPPI VALLEY
(AFTER WELLER)
Kinkaid
Degonia
Clore
Upper
Palestine
Chester
:Menard
Waltersburg
ttl
Vienna
.~
.... Tar Springs
'"
rn
.... Glen Dean
jl
.,
Middle
Hardinsburg
'"
.r:
0
Chester
Golconda
Cypress
Mississippian
Paint Creek
Lower
Yankeetown
Chester
Renault
Aux Vases
--
Ste. Genevieve
Meramec
St. Louis
Spergen
'"
W~rsaw
'"
.~
~
Keokuk
'"
Osage
Burlington
I!:
0
~
Various local
Kinderhook
formations in
Mississippi Valley
columnar section (fig. 1). Character and General Rela.tions In central and north-central Iowa the
character and succession of the formations is somewhat differ-
ent as ~ill be pointed out in later pages. CLASSIFICATION OF THE MISSISSIPPIAN FORMATIONS OF THE MISSSISSIPPI VALLEY
(AFTER WELLER) columnar section (fig. 1). In central and north-central Iowa the
character and succession of the formations is somewhat differ-
ent as ~ill be pointed out in later pages. Stratigraphic R,elations The Mississippian system succeeds the Devonian in Iowa. Along the northeastern boundary of the belt of outcrops of
Mississippian strata the Kinderhook is in contact with the
Cedar Valley limestone except in western Butler, northeastern
Franklin, southwestern Cerro Gordo, northeastern Hancock and
southeastern Winnebago counties, where it rests upon the over-
lying Lime Creek shales. However, exposures showing the con-
tact of the two systems are very rare, owing to the drift cover- RELATIONS OF MISSISSIPPIAN 43 ing and to the tendency of the basal Kinderhook shales to
weather in such a way as to conceal the tmderlying strata. h
l
i
f
h
i
i
i
i
h
l i The relation of the Mississippian system to the overlying ~YHEM GROUP
FORMATION
x:
o o
:c
a:
LU
a <
~
S!rE. GENEVIEVE
(PELLA)
ST. LOUIS
SPERGEN
(BELFAST)
WARSAW
KEOKUK
BURLINGTON
KIIiD~RHOOX
,sECTION
::' ~:.;';/;"';'"
THICI(-
NE,sS
55
40-60
LITHOL06-/C CHARACTER
Fine-grained bluish sand-
stone at base suoceeded by
bluish shale. Pine-grained
gray limestone above. Fine-grained gray limest one
ohiefly. ~wer division
looally brownish and dolo-
mitio. In plaoes brecciatsd. -=
\ 0-35
Crinoidal limest one grading
\~ __ +-_in_t_o __
a_r_e_n_a~o_e_ou __
s_d_o_l_o_m_i_t_e~. __ ~
20-65
63
71
"
: ... .. . 300:1:
Interbedded shales and gray
fossiliferous limestone. Geodes in lower part. Gray to bluish gray orinoid-
al limestone interbedded
with shale in upper part. Cherty in lower part. Gray. orino~dal. oherty lime-
stone interbedded with
brownish fine-grained
oherty magnesian limestone. A thiok body of shale in
lower part suooeeded by
interbedded limestone and
sandstone. A bed of
oolitio limestone appears
near the top. FIG. l.-Generahzed columnar sectIOn of the MISSISSIppian system III south.astern Iowa. 71 MISSISSIPPIAN STRATA OF IOWA 44 rocks is much more diversified, owing (1) to variation in the
original distribution of the Mississippian formations, (2) to
the profound erosion which followed the retreat of the Mississ-
ippian seas and preceded the Pennsylvanian transgression and
(3) to the erosion which ensued between Pennsylvanian and
Cretaceous time. In southeastern Iowa and in \Vebster county the border of
the main body of Pennsylvanian' strata rests on the St. Louis
and Pella formations but occasional outliers of the" Coal Meas-
ures" to the northeast rest on older beds ranging down to the
Kinderhook. Regio-nal Structure The diagonal belt in which the Mississippian formations are
the highest consolidated rocks is on the flank of a large gently
dipping geosyncline the axis of which plunges to the southwest
through southwestern Iowa into northwestern Missouri and
northeastern Kansas. The reader is referred to Norton's maps
showing the elevation of the Saint Peter sandstone in Iowa, and
to Van Tuyl's structure contour map4 of the Western Interior
geosyncline for details regarding the character and extent of
this basin and its influence upon the distribution of the outcrops
of the Paleozoic systems. The probable age of this basin and
its influence on the present distribution of the Mississippian
deposits .is discuss,ed on page 349 of this report. Stratigraphic R,elations In central and north-central Iowa the Pennsylvan-
ian beds are in contact with the Kinderhook almost everywhere
along the boundary of the two systems except in Webster coun-
ty as noted above, and in western Humboldt and western Kos-
suth counties, where the Cretaceous sediments succeed the
Kinderhook. \
' I ~ I ,4 The stratigraphic relations of the Mississippian formations
among themselves are somewhat complex as a result of the os-
cillation of the strand line during deposition. The Burlington,
Keokuk, Warsaw and Spergen formations are confined to the
southeastern part of the state. The St. Louis limestone over-
laps these deposits and rests directly upon the Kinderhook in
north-Central Iowa
Southeastern Iowa north-Central Iowa PELLA
ST. :WUIS
. FIG. 2.~Showing stratigraphic relations of Mississippian formations in Iowa at the close of
Ste. Genevieve time. The dip of the pre·St. Louis formations is exaggerated. . FIG. 2.~Showing stratigraphic relations of Mississippian formations in Iowa at the close of
Ste. Genevieve time. The dip of the pre·St. Louis formations is exaggerated. WORK OF JAMES HALL 45 north-central Iowa. The Ste. Genevieve deposits extend' to this
section of the state also. In the Fort Dodge area they are found
above the St. Louis rocks. The accompanying diagram (fig. 2)
expresses the approximate stratigraphic relations of the forma-
tional units of the Mississippian of Iowa as they appeared at
the close of Ste. Genevieve time. north-central Iowa. The Ste. Genevieve deposits extend' to this
section of the state also. In the Fort Dodge area they are found
above the St. Louis rocks. The accompanying diagram (fig. 2)
expresses the approximate stratigraphic relations of the forma-
tional units of the Mississippian of Iowa as they appeared at
the close of Ste. Genevieve time. :5 Rept. Geol. Survey Wisconsin , Iowa and Minnesota, p. 92; 1852.
f 4 Jour. Geology. vol. XXV, p. 152; 1917.
R
G
l
S
Wi
i
I
d CRept. Geol. Survey State of Iowa, vol. I, part I, pp. 46 lind 92 ff. 3 Iowa Geol. Survey, vol. XXI (pocket); 1912. 4 Jour. Geology. vol. XXV, p. 152; 1917.
R
G
l
S
Wi
i
I
d Mi
92
1852 PrevioUSI Work Owen5 was among the first geologists to study the forma-
tions in Iowa which are now referred to the Mississippian sys'-
tern. He grouped the beds into ten units chiefly upon the basis
of their lithologic character. Severa] of these units correspond
to formations recognized in the modern classification. He
placed them in the Subcarboniferous period. . The foundation for all later work on the Mississippian of
Iowa was laid by Hall,6 whose classification and nomenclature
of the formations, published in 1858, paved the way for succeed-
ing investigations. The formations recognized by him in as-
cending order were as follows : Burlington limestone, Cherty
limestone of Keokuk rapids, Keokuk limestone, Geode bed, War-
saw formation and the St. Louis limestone. The strata directly MISSISSIPPIAN STRATA OF IOWA 46 below the Burlington limestone were regarded by him as
Chemung in age. The Carboniferous age of these was later
demonstrated by Meek and W orthen7 who named them the
Kinderhook beds because of their typical development near the
town of that name in illinois. WhiteS later recognized the beds
below the Burlington limestone at Burlington as Kinderhool\:
and described other exposures of' this group in central and
northern Iowa. He also further enhanced our knowledge of the
overlying formations. His classification differs from that of
I-iall in that he grouped the cherty limestone, Keokuk limestone
and Geode bed all as Keokuk and the Warsaw formation and
St. Louis limestone inclusive as St. Louis. Keyes' classification
of 18939 recognizes three major divisions of the Mississippian
in Iowa, namely: the Kinderhook, the Augusta and the St. Louis. The Augusta is made to include the Lower and Upper
Burlington limestone, the Keokuk limestone, the Geode bed and
the Warsaw shales and limestone. The same author in the reports on the geology of Lee and Des
Moines counties1o contributed several new points on the strati-
graphy of the formations in the southeastern part of the state. He designated the cherty limestones of Hall the Montrose 'cherts
and again included all formations from the Burlington lime-
stone to the base of the St. Louis in his Augusta series. The
ad~sability of ,the use of this term, however, is questioned by
~E:lper,l1 who po~nts out th~t the name Osage as proposed by
Wil:liams12 for deposits of the same age along Osage river in
M;i.ssouri has priority. 7 Am. Jour. Sci., 2d series, vol. 32, p. 288; 1861.
S GeoL of Iowa, vol. I, p. 192; 1870.
9 Iowa GeoL Survey, vol. I, p. 50.
10 Iowa GeoL Survey, vol. III, pp. 305·492; 1895.
11 Am. Geologist, vol. XXII, p. 12; 1898.
12 U.S. GeoL Survey Bull. 80, p, 169 ; 1891.
13 Iowa GeoL Survey, vol. IV, p. 206; 1895. 7 Am. Jour. Sci., 2d series, vol. 32, p. 288; 1861.
G
L
f I
l
I
192
1870 15 Iowa Geol. Survey, vol. V, PI>. 113·173; 1896. 14 Iowa Geol. Survey, vol. IV, pp. 257·311 ; 1895.
G
l
S
l PrevioUSI Work In Gordon's report on tl].e Geology of Van Buren county13 the
Montrose cherts of Keyes are referred to. the Burlington, and
the Keokuk limestone, Geode shales and Warsaw shales and. l~estones collectively to the K.eokuk groul{. The overlying St. Louis is subdivided into arenaceo-m~gnesian beds at the base. brecciated limestone in the middl~ and compact and granular
limestone at the top. CLASSIFICATIONS OF MISSISSIPPIAN FORMATIONS OF low A CLASSIFICATIONS OF MISSISSIPPIAN FORMATIONS OF low A HALL 1858
St. Louis
Warsaw
Geode bed
Keokuk
Cherty
limestone
Burlington
Chemung
WroTE 1870
St. Louis
Keokuk
Burlinlgton
Kinderhook
KEYES 1895
GORDON 1895
oj
...,
~
~
St. Louis
Sonora
Warsaw
~
Geodebed I~
Keokuk
Montrose
chert
Burlington
Kinderhook
St. Louis
Warsaw
Geode
shales
Keokuk
Burlington
Kinderhook
B,AIN 1896
Pella
St. Louis I
Verdi
I~ringvale
Aug"Usta
Kinderhook
PRESENT REPORT
Ste. Oenevieve (Pella)
St. Louis
Upper
(Verdi)
Lower
(Crolxm)
Spergen (Belfast)
Upper
Warsaw
Lower
Keokuk
Burlington
Kinderhook
~
Ul
Ul
H
~
~
~
~
o
bj
Ul
>-3
~
~
,;.. ... MISSISSIPPIAN STRATA OF IOWA 48 H. F. Bain, in his description of the geology of Keokuk14 and
Washington15 counties adopted the Augusta series of Keyes for
the Burlington and Keokuk limestones, which he believed to be
incapable of differentiation in that part of the state. He sub-
divided the ·St. Louis of earlier workers into three units which
he designated the Springvale at the base, the Verdi in the mid-
dIe and the Pella at the top. Additional data regarding the
Mississippian deposits of Iowa have appeared in numerous
other county reports and in scientific articles published in many
journals and proceedings of learned societies. Reference is
made to the more important of these elsewhere in this volume. IS On the accompanying chart an attempt IS made to show the
evolqtion of the present classification of the Iformatlons in Iowa. I Definition The name Kinderhook group was applied by Meek apd
yVorthen'6 in 1861 to the strata between the black slate and the
base of the BUrlington limestone at Kinderhook, Pike county,
Illinois. Similar, beds at Burlington w~re referred to the same
group. They, regarded the KinderhoQk as basal 9ar,bonjferou:-;
in age. . Five iYears later Worthen 17 further .·defined the group
and point~q. out that the so-called ,"Chunlung group" a~ de-
scribed by Hall' s at Burlington, Io"va, ~>{as of Kinderhook age. In northeastern Missouri the group is ;represented by the fol-
lowing sectipn, ·according to Weller :'9 Osag~ group
. ) ,
4. Burlington limestone '
Jrinderhook group
3. Fine-graiI1ed, compa.ct, buff limestone . ____ .... __ .. .-__ .. ______ ....... _ .. ____ . ____ 10-15
2. "'Vermicular sandstone and shale" (Hannibal sandstone)_______
70
1. COmpact
blue-gray
limestone
with
lithographic
texture
(Louisiana limestone) _____________________________________________________________
60 He s'tates20 that" in central MissoUri the entire Kinderhook is
represented in the' Chouteau limestone, about 100 feet in thick-
ness ". In southwestern Missouri and in Jefferson county, twenty-
five miles south of St. Louis, it exhibits still other variations. 'Weller remarks that "in no case can any formational unit be
traced continuously throughout the entire basin". 16 Am. Jour. Sci., 2d series, vol. 32, p. 288.
17 Geol. Survey of Illinois, vol. I, pp. 108 ff. ; 1866.
10 Rept. Geol. Survey Iowa, vol. I, part I, p. 90; 1858.
19 Monograph I, Illinois State Geol. Survey, p. 14; 1914.
20 Idem, p. 14. 19 Monograph I, Illinois State Geol. Survey, p. 14; 1914.
20 Idem, p. 14. Rept. Geol. Survey Iowa, vol. I, part I, p. 90; 1858. 17 Geol. Survey of Illinois, vol. I, pp. 108 ff. ; 1866. Areal Distribution The Kinderhook group is the bed rock over a larger area MISSISSIPPIAN STRATA OF IOWA 50 than any other division of the Mississippian of Iowa. With the
exception of a small outlier of shale in Muscatine county which
may possibly be of this age the group forms the highest con-
solidated rock over a continuous belt extending from Lee coun-
ty in the extreme southeastern corner of the state northeast-
ward and thence northward along the valley of Mississippi river
to Louisa county, from which area it runs northwestward in the
form of a broad irregular band to the north-central part of the
state and doubtless continues across the boundary into Minne-
sota. However, no outcrops of the formation appear north of
Humboldt county, owing to the heavy drift cover in that direc-
tion. This Kinderhook area is bordered on the northeast by Middle
and Upper Devonian limestones and shales. On the southwest,
however, the boundary is much more complicated, owing to the
disconformable relationship of the Kinderhook with several
younger formations. In southeastern Iowa it is bordered by
the Burlington limestone, presumably as far northwest as
Poweshiek county, although the exact extent of the latter forma-
tion to the northwest beneath the drift is unknown. From this
point to Humboldt county the Pennsylvanian rocks form the
southwest boundary. In Hardin and Grundy counties the Kind-
erhook belt is scarcely half its normal width, owing toa tongue-
like extension of .Pennsylvanian deposits to the northeast. Be-
ginning in Humboldt county, Cretaceous deposits form the west
boundary, the trend of which shifts from northwest to nearly
due north and thence to northeast in .Kossuth county near the
north boundary of the state. 21 Iowa Geol. Survey, vol. XXI, p. 683; 1912.
22 Idem, p. 647.
23 Idem, pp. 970 and 893. Lithologic Character In southeastern Iowa the Kinderhook gTOUp is represented
chiefly by clastic deposits with shale predominating over sand-
stone.. Near and at the top of the group several limestone beds,
one of which is oolitjc, are ' present. The proportion of lime-
stone in the upper part gradually increases to the northwest. In central Iowa there is a continuous bed of limestone more
than sixty feet thick at the top of the se:r:ies. In north-central
Iowa there js an even greater development of limestone in the DIVISIONS OF KINDERHOOB.. 51 upper part of the formation with a corresponding reduction in
thickness of the underlying clastic strata. upper part of the formation with a corresponding reduction in
thickness of the underlying clastic strata. Thickness The thickness of the Kinderhook in Iowa has been determined
only by the study of deep well logs. The individual exposures
are all of limited vertical and lateral extent and the strata are
so gently tilted that traverses from contact to contact are 'not
practicable. At the cjty of Keokuk wh.ere the group is ent~rely bene:;tth
the surface its thickness is given by Norton21 as 270 feet: In
a deep well drilled at Burlingtpn the upper ,limit of the group
was not definitely determined but the full thickness is probably
between 300 and' 350 feet. A deep well at. M;ui1t Ple~sant, in
Henry county, passed through 360 feet of Kind~rhook, accord-
in 0' to N orton.22
. b
. ,
. . A prospect hole at Marf:lhalltown, in central Iowa, whjch
started at the 'top of the Kinderhook, encountered the Devonian
lime'stone at 320 feet. In the vicinity of Iowa Falls, in Hardin
county; the total thickness, as determined by the study of sur-
face ~xposures in conjunction With the log of a well, is about
300 feet. There is some evidence of a thinning of th~ group to
the southwest of the outcrop belt. For example, N orton23 gives
its' t:l).ic~ness as 125 feet at Pella, in Marion county, and as 16Q
feet at Des 'Moines, in Polk county. Subdivisions Owing to ,the lithologic and faunal variations in the Kinder-
hook beds in passing from southeastern· Iowa to the' north-cen-
tral part of the state it is n0t possible to subdivide the group
into formational units of more than local application. In Lee, Des Moines and Louisa counties no formation names
have been applied. The Washington county succession has been
subdivided by Bain into the Maple Mill shale at the base, the
English River grits tone in the middle and the Wasson'Ville lim~
stone at the top. Still farther northwest in Marshall county,
. , MISSISSIPPIAN STRATA OF IOWA 52 Beyer used the names LeGrand beds and Marshalltown shales
for the upper exposed part of the group. D
i
h
i
i
i
i
f
d
d i
bl During the present investigation it was found advisable to
subdivide the Kinderhook group of north-central Iowa into six
distinct formations "which, from the bas(~ upward, are designatpd
the Sheffield shale, the Chapin beds, the Mayne Creek formation,
the Eagle City beds, the Iowa Falls dolomite and the ~A..ldell
limestone. Stratigraphic Relations The stratigraphic relations of the Kinderhook beds with the
underlying "Devonian deposits are not well understood since the
contact is everywhere concealed except possibly in Muscatine
county where dark shales o~ questionable age rest upon Cedar
Valley limestone. However, the evidence points to the presence
of a dis conformity between the Devonian and Mjssissippian
systems in Iowa. III tlle southeastern and central parts of the
state the relation of basal Kinderhook and Cedar Valley out-
crops is such as to indicate that these groups are in contact
while in north-central Iowa the Kinderhook is known to rest
upon the younger Lime Creek formations of the Devonian. h
f
i
i
i h h
i d
h
k
b
f The formations in contact with the Kinderhook above are of
variable age. In southeastern Iowa there appears to be a
transition into the Burlington limestone but to the northwest
where there is a pinching out of the Burlington, Keokuk, WaJ'-
saw and Spergen formations the Kinderhook is succeeded di-
rectly by the St. Louis limestone. As a result of the erosion of
the overlying Mississippian deposits prior to the advance of the
Lower Pennsylvanian seas deposits of Pennsylvanian age rest
upon the Kinderhook in the form of occasional outliers in
northeastern Washington county while for a considerable dis-
tance along the southwestern boundary of the Kinderhook in
central and north-central Iowa the main body of the P enns~1-
vanian overlies the basal Mississippian deposits. At the north-
western extremity of the Mississippian belt the Dakota member
of the Cretaceous system rests upon the Kinderhook beds. Areal Deseri ption by Counties
GENERAL STATEMENT
Previous to the present investigation the Kinderhook beds Areal Deseri ption by Counties
GENERAL STATEMENT
Previous to the present investigation the Kinderhook beds KINDERHOOK AT BURLINGTON 53 have received careful study only in the southeastern part of the
state, especially, near the city of Burlington in Des Moines
county. The character of the group to the northwest has been
discussed in a general way in several county reports, but no
detailed examination of the succession of beds has been made. It is now known that the Kinderhook strata of north-central
Iowa, central Iowa and southeastern Iowa are very different
both lithologically and faunally. For this reason the areas are
described separately. 24 Iowa Geol. Survey, vol. III, pp. 339.
25 Iowa Geol. Survey, vol. X, pp. 63-79; 1900. Section of Kinderhook beds at Burlington (After W eller)
~: ~Ulb~~li~~tik!:oe:!O~~ .. :::::::::::::::::::::::::::::::::::=:::::::::::::::::::::::::::::::
24 Iowa Geol. Survey, vol. III, pp. 339.
25 Iowa Geol. Survey, vol. X, pp. 63-79; 1900.
FEET
3·5
2·4 ~: ~Ulb~~li~~tik!:oe:!O~~ .. Section of Kinderhook beds at Burlington (After W eller) KINDERHOOK OF SOUTHEASTERN IOWA Soft friable argillaceous srundstone, in some places harder and
bluish in col<>r, filled with fossils in the upper part, the most
abundant of which is Chonopectus jisoheri ........................... _......... 25 '
1. Soft blue argillaceous shale (exposed) .................. _......................... 60 1. Soft blue argillaceous shale (exposed) .................. _......................... 60 In the present investigation, Weller's subdivisions have been
adopted 'without modification. A mor~ detailed description of
the beds at Prospect Hill than has hitherto been given follows: Seotion of Kinderhook beds at Prospeot Hill, Bllrlington
7. Limestone, soft, buff to browmsh, d<>lomitic; with casts of fossils;
grading up into the Lower Burlington limestone .........................•
6. Limestone, white, oolitic, scaling off obliquely on weathered
surfaces ..................................... _ .... _ ...................................................... . 5. Sandstone, soft, :fine· grained, drab weathering buff; shaly in
upper part; some seams filled with casts of fossil shells; bear·
ing occasional plant remains ............................................................... . 4. Limestone, upper one to two feet brownish and dolomitic. Lower
layers consisting of dense gray lithographic·like limestone mottled
w~th small patches of ·bro,wuish
do~omite which in some in·
stances follow small fractures. Small calcite geodes occur in
the dolomitic lareas, and occasional small pockets of sphalerite
appear in both the limestone and dolOlnite ....................... _ ............ . 3. Limestone. Lo,wer half coarse·grained and filled with Chonetes. Upper half oolitic. Upper sl,lrface very undulating, although
there is a transition from the oolite into the limestone above. Contact witli bed below :im: places irregular ............ : ...................... . 2. Sandstone, :fine·grained, soft, drab weathering buff, massive;
with occasional thin intercalated layers of shale; upper two
foot filled with casts of fossils, most abundant of which is
CMnopectus jisoheri ......... ,. ..... _ .................... _ .......... _ .............. _ .......... . 1. Shale, bluish, argillaceous, locally calcareous,
drab, sparsely
fossiliferous, grading into the bed above. The greatest thick·
ness of this bed is in the old clay pit, where nineteen feet is
shown. Between ,the bed of the pit and the level of Mississippi
river, about fourteen feet more is concealed. The total thick·
ness of this member at Burlington, as indicated by deep borings,
is probably not less than three hundred feet. Exposed ........... . FEET
5
3
6
10
2/ 3
22%
19 2. Sandstone, :fine·grained, soft, drab weathering buff, massive;
with occasional thin intercalated layers of shale; upper two
foot filled with casts of fossils, most abundant of which is
CMnopectus jisoheri ......... Seotion of Kinderhook beds at Prospeot Hill, Bllrlington KINDERHOOK OF SOUTHEASTERN IOWA L ee County.-Regarding the Kinderhook . of Lee county,
Keyes24 has this to say : "Although this member of the Lower Carboniferous is such
an important formation in Des Moines county, immediately to
the north, and in northeastern Missouri to the south, it lies al-
most entirely belo'w the river level in Lee. It has only been
recognized in a single place on the Skunk river near the Chi-
cago, Burlington and Kansas City railroad bridge over that
stream." Des Moines County.-The area over which the Kinderhook
beds form the surface rock in Des Moines county is confined to
the valley of :Mississippi river and the lower courses of' its
larger tributaries in the eastern part of the county. h
i
d
l
i
f h
i d The most representative and complete section of the Kinder-
hook in this county as well as in the ",rhole of southeastern Iowa
is in the Mississippi river bluff at Burlington. The Prospect
Hill exposure is especially favorable for field study. A review
of the literature on the Kinderhook of this area is given by
W eller25 in .his report on "The Succession of Fossil Faup,as in
the Kinderhook Beds at Burlington, Iowa."
After a discussion
of the descriptions of the strata by earlier investigators he
adopted the following classification based , upon the lithology
and fossil content of the beds: Section of Kinderhook beds at Burlington (After W eller)
~: ~Ulb~~li~~tik!:oe:!O~~ .. :::::::::::::::::::::::::::::::::::=:::::::::::::::::::::::::::::::
24 Iowa Geol. Survey, vol. III, pp. 339. 25 Iowa Geol. Survey, vol. X, pp. 63-79; 1900. FEET
3·5
2·4 MISSISSIPPIAN STRATA OF IOWA 54 5. Fine·grained yellow sandstone ... _ ..... ~ .... _ .. _ .. _ .. _ .... _ ...................... _. 6·7
4. Fine·grained, compact, fragmental gray limestone ............... _..... 12·18
3. Thin band of hard impure limestone filled with Chont7tes; in
some places associated with a thin oolite band ................. _............. lA,.%,
2. Soft friable argillaceous srundstone, in some places harder and
bluish in col<>r, filled with fossils in the upper part, the most
abundant of which is Chonopectus jisoheri ........................... _......... 25 '
1. Soft blue argillaceous shale (exposed) .................. _......................... 60 5. Fine·grained yellow sandstone
4
Fine grained
compact
fragme g
,
p
,
g
g
y
3. Thin band of hard impure limestone filled with Chont7tes; in
some places associated with a thin oolite band ................. _............. lA,.%,
2. KINDERHOOK OF SOUTHEASTERN IOWA ,. ..... _ .................... _ .......... _ .............. _ .......... . 1
Sh l
bl i h
ill
l
ll
l
d
b
l
22% 1. Shale, bluish, argillaceous, locally calcareous,
drab, sparsely
fossiliferous, grading into the bed above. The greatest thick·
ness of this bed is in the old clay pit, where nineteen feet is
shown. Between ,the bed of the pit and the level of Mississippi
river, about fourteen feet more is concealed. The total thick·
ness of this member at Burlington, as indicated by deep borings,
is probably not less than three hundred feet. Exposed ........... . 19 19 " Almost cOI).tin~ous exposures of the Kinderhook beds appear
i~ the Mississippi river bluff for more than two miles to the
southwest of. the above s,ection, but owing to the fact that the dip
of the beds is slightly greater than the gradient of the stream,
only the uppermost beds are exposed. In the Albert Kirschner
quarries at Picnic Point, two miles southwest of Prospect
Hill, beds 6 and 7 outcrop in the lower part of the openings. Bed 7 is only three feet in thickness and is represented almost
entirely by brownish crinoidal·limestone. h
b d
d
h
b
f h
i
i
h The same beds are exposed at the base of the section in the FAUNA OF KINDERHOOK BEDS 55 Kemper quarries one mile south of the last named locali.ty
(NW.1/4 sec. 29, T. 69 N., R. 2 W.). Kemper quarries one mile south of the last named locali.ty
(NW.1/4 sec. 29, T. 69 N., R. 2 W.). Other outcrops of the Kinderhook occur north of Prospect
Hill. In the Main Street cut at North Hill, in Burlington, the
succession involves the same beds as at Prospect HilL Similar exposures appear along Flint river at Starr Cave
(NW.1/4 sec. 19, T. 70 N., R. 2 W.) two miles northwest of
Burlington. The section here involves all the beds from the
lower sandstone (bed 2) to the lower part of the Upper Burl-
ington limestone. Fau,na of the Kinderhook Beds at Bu·rlington. Our knowledge of the faunas of the individual beds of the
Kinderhook at Burlington has been greatly. enhanced through
the efforts of Weller26 to assign the species, which had been
described from the group at this locality, to their respective
stratigraphic horizons. 27 Iowa Geol. Survey, vol. X, pp. 73, 74; 1900. KINDERHOOK OF SOUTHEASTERN IOWA The following faunal lists are his with
occasional changes in nomenclature and with additions necessi-
tated by the writer's studies. The additions are indicated by
asterisks. List of Fosstils from bed 1 of the Kilnderho07c Group at Burlington
SPONGIAE-
Dictophyton sp. undet. CRINOIDEA-
Crinoid stems
BRAcmoPoDA-
Lingula sp. undet. Ol'biculoidea sp. undet. Schizophoria sp. undet. Rhipidomella sp. cf. R. burlingtonensis
(Hall)
"
Productella sp. undet. Productus ovatus Hall
Productus sp. undet. Eumetria altirostris (White)
PELECYPODA-
A viculopecten sp. undet. GASTROPODA-
Platyschisma sp. undet. Porcellia sp. undet. Conularia sp. undet. CEPHALOPODA-
Gomphoceras sp. undet. CRUSTACEA-
PalaeopalaemOII1 newberryi Whitf. ,
VERTEBR.ATA-
Coelacanihus welleri Eastman
PLANTS-
Fragments of stems and leaves
List of Fossils from bed 2 of the Kinderhook Gro'up at Bu·rlington
CRINOIDEA-
Joints of crinoid stems
I
VERMES-
Worm burrows
26 Idem, pp. 69 to 78. BRACHIOPoDA-
Lingula membranacea Win. Orbiculoidea capax (White)
Schellwienella inaequalis (Hall)
Chonetes illinoisensis Worthen List of Fosstils from bed 1 of the Kilnderho07c Group at Burlington
SPONGIAE-
Dictophyton sp. undet. CRINOIDEA-
Crinoid stems
BRAcmoPoDA-
Lingula sp. undet. Ol'biculoidea sp. undet. Schizophoria sp. undet. Rhipidomella sp. cf. R. burlingtonensis
(Hall)
"
Productella sp. undet. Productus ovatus Hall
Productus sp. undet. Eumetria altirostris (White)
PELECYPODA-
A viculopecten sp. undet. GASTROPODA-
Platyschisma sp. undet. Porcellia sp. undet. Conularia sp. undet. CEPHALOPODA-
Gomphoceras sp. undet. CRUSTACEA-
PalaeopalaemOII1 newberryi Whitf. ,
VERTEBR.ATA-
Coelacanihus welleri Eastman
PLANTS-
Fragments of stems and leaves List of Fosstils from bed 1 of the Kilnderho07c Group at Burlington SPONGIAE-
Dictophyton sp. undet. CRINOIDEA-
Crinoid stems Productus sp. undet. E
i
l i
i
( Eumetria altirostris (White) List of Fossils from bed 2 of the Kinderhook Gro'up at Bu·rlington BRACHIOPoDA- BRACHIOPoDA-
Lingula membranacea Win. Orbiculoidea capax (White)
Schellwienella inaequalis (Hall)
Chonetes illinoisensis Worthen 26 Idem, pp. 69 to 78. MISSISSIPPIAN STRATA OF IOWA Chonetes sp. cf. C. geniculatus White
Chonetes sp. undet. Chonopectus fischeri (N. and P.)
Produetus curtirostris Win. Produetus mesicostalis Weller
Produetus oooperensis Swallow
Productus ovatus Hall
Productella nummularis (Win.)
Schizophoria sp. P f1.ryphol'hynchus transversum 'Weller
Rhynchonella sp. undet. Eumetria altirostris (White)
Composita , corpulenta (W'in.)
Spirifer subrotundus Hall
"Spirifer platynotus Weller
Spirifer biplicatus Hall
Syringothyris extenuatus (Hall)
Reticularia eooperensis (Swallow)
BRYOZOA-
FelWstella sp. undet. PELECYPODA-
. AvicuJopeeten tenuicostus Win. Aviculopecten caroli Win. * Avieulopeeten sp. Pterinopeeten ef. P. laetus Hall
*P ernopecten cf. P. eooperensis (Shuro.)
Per1lJOIp<'lcten f sp. undet. . Leiopteria spinalata (Will.)
Avicula strigosa (White)
Pteronites whitei (Win.)
MytiJarca occidentalis (W. KINDERHOOK OF SOUTHEASTERN IOWA and W.)
MytiJarca fibristriata (W. and W.)
Goniophora jennae (Win.)
Parallelodon oochlearis (Win.)
Parallelodon modesta (Win.)
Grammysia plena Hall
Grammysia amygdalinus (Win.)
Edmondia burlingtOilL€'l1sis (W. and W.)
Edmondia quadrata (W. and W.)
Edmondia a.equimarginalis Win. Edmondia nitida Win. Edmondia jejunus (Win.)
Sphenotus rigiduB (W. and W.)
Sphenotus bicarinatus (Win.)
Sphenotus iowensis (Win ) Chonetes sp. cf. C. geniculatus White
Chonetes sp. undet. Chonopectus fischeri (N. and P.)
Produetus curtirostris Win. Produetus mesicostalis Weller
Produetus oooperensis Swallow
Productus ovatus Hall
Productella nummularis (Win.)
Schizophoria sp. P f1.ryphol'hynchus transversum 'Weller
Rhynchonella sp. undet. Eumetria altirostris (White)
Composita , corpulenta (W'in.)
Spirifer subrotundus Hall
"Spirifer platynotus Weller
Spirifer biplicatus Hall
Syringothyris extenuatus (Hall)
Reticularia eooperensis (Swallow) Spherootus bicostatus Weller
Spathella ventricosa (W. and W.)
*Nucula iowensis W. and W. Cardiopsis megambonata Win. Schizodus iowensis Weller
Schizodus burlingtonensis Weller
Cyprical'dinia sulcifera (Win.)
Glossites elliptica (Win.)
Glossitesf burlingtonensis Weller
Promacrus euneatus Hall
Posidonomya f ambigua Win. Promacrus euneatus Hall
P
id
f
bi
Wi Posidonomya f ambigua Win. GASTROPODA-
Loxonema shumardana (Win.)
Loxonema oligospira Win. Loxonema sp. undet. Mu rchisonia quadricineta Win. Strophostylus bivolve (W. and W
Sphaerodoma pinguis (Win.)
N aticopsis depressa Win. Stl'aparoUus maeromphalus Win. Straparollus ammon (W. ll!nd W.)
Straparollus angularis Weller
Platysehisma barrisi (Win.)
Platyschisma depressa Weller
Ph~~rotinus parllldoxus Win. Bellerophon bilabiatus W. and W . Bellerophon vinculatus W. and W;
Bellerophon panneus White'
Bucanopsis defieetus Weller
P atellostium scriptiferus (White)
Poreellia crassinoda W. amd W. Porcellia obliquinoda White
Porcellia rectinoda Win. Conularia byblis White GASTROPODA-
Loxonema shumardana (Win.)
Loxonema oligospira Win. Loxonema sp. undet. Mu rchisonia quadricineta Win. Strophostylus bivolve (W. and W. Sphaerodoma pinguis (Win.)
N aticopsis depressa Win. Stl'aparoUus maeromphalus Win. Straparollus ammon (W. ll!nd W.)
Straparollus angularis Weller
Platysehisma barrisi (Win.)
Platyschisma depressa Weller
Ph~~rotinus parllldoxus Win. Bellerophon bilabiatus W. and W . Bellerophon vinculatus W. and W;
Bellerophon panneus White'
Bucanopsis defieetus Weller
P atellostium scriptiferus (White)
Poreellia crassinoda W. amd W. Porcellia obliquinoda White
Porcellia rectinoda Win. Conularia byblis White GASTROPODA-
Loxonema shumardana (Win.)
Loxonema oligospira Win. Loxonema sp. undet. Mu rchisonia quadricineta Win. Strophostylus bivolve (W. and W.)
Sphaerodoma pinguis (Win.)
N aticopsis depressa Win. Stl'aparoUus maeromphalus Win. Straparollus ammon (W. ll!nd W.)
Straparollus angularis Weller
Platysehisma barrisi (Win.)
Platyschisma depressa Weller
Ph~~rotinus parllldoxus Win. Bellerophon bilabiatus W. and W . . Bellerophon vinculatus W. and W;
Bellerophon panneus White'
Bucanopsis defieetus Weller
P atellostium scriptiferus (White)
Poreellia crassinoda W. amd W. KINDERHOOK OF SOUTHEASTERN IOWA FOSSILS FROM KINDERHOOK BEDS 57 FOSSILS FROM KINDERHOOK BEDS
57
List of Fossils from bed 9 of the Kilnderhoo1c Group at B1wlington
BRACHIOPODA-
*Schellwienella sp. ·Chonetes gregarius Weller
Ohonetes cf. C. geniculata White
Chonopectus fischeri (N. and P.)
*Rhipidomella sp. *Rhynchonella sp. *Paryphorhynchus sp. *Spirifer platynotus Weller
*Spirifer biplicatus Hall'
*Spirifer subrotundus RaIl
PELECYPODA-
A viculopecten iowensis Miller
*Per!L(}pecten sp. ParaJlelodon leptogaster (Win.)
*Schizodus sp. GASTROPODA-
*BellerophoIIJ sp. *Straparollus sp. Holopea subconica Win. Holopella Iilira Win. List of Fossils from bed ./, of the Kilnderhoo1c Group at Burlington
BRACHIOPODA-
*Chonetes sp. *Chonetes sp. Chonopectus fischeri (N. and P.)
Rhynchonella unica Win. Rhynchopora pustulosa (White)
Paryphorhynchus striaticosliaJtum
(M. and W.)
Allorhynchus heteropsis (Win.)
* Allorhynchus sp. Syringothyris halli Win. PELECYPODA-
* Allorisma sp. "Schizodus sp. List of Fossils from bed 5 of the Kilnderhoo1c Group at Burlington
BRYOZOA-
*Ptilopora sp. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella inaequalis (Hall)
*Chonetes sp. Productus arcuatus Hall
Productus parvulus Win. "Productus blairi Miller
Pustula morbilliana (Win.)
Camarophorella lenticularis (W.andW.)
Cranaena , allei (Win.)
Spirifer biplicoides Weller
*Spirifer platynotus Weller
Brochythyris JlCculiaris (Shum.)
*Syringothyris sp. Reticularia cooperensis (Swallow)
Cyrtina acutirostris (Shum.) ,
PELECYPODA-
Pterinopecten nodocostus (W. and W.)
Pernopecten cooperensis (Shum.)
*Lithophaga d. L. minuta Weller
Parallelodon parvus CW. and W.)
Edmondia nuptialis Win. 'Edmondia strigillata Win. Spherootus cylindricus (Win.)
Spathella phaselia Win. Nucula iowensis W. and W. Palaeone1lo microdonrta (Win.)
Palaeoneilo barrisi (W. and W.)
Leda saccata (Win.)
Dexiobia ovata (Hall)
Dexiobia haIli Win. Schizod'us trigonalis (Win.)
"Cypricardinia sulcifera (Win.)
GASTROPODA-
Straparollus angularis Weller
Straparollus sp. undet. Bellerophon sp. undet. Bucanopsis perelegans (W. and W.)
SCAPHOPODA-
Dentalium grandaevum Win. VERTEBRATA-
"Fish t eeth. List of 'Fossils from bed 6 of the Kinderhoo1c Gr01!p at B1!rlington
ANTHOZOA-
Zaphrentis sp. undet. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella infiata (W. and W.)
''Schellwienella planumbona Weller
*Schellwienella 'inaequalis (Hall)
"Schellwienella crenulicostata Weller
Chonetes logani N. and P. "Chonetes burlingtonensis Weller
Chonetes illinoisensis Worthen
"Chonetes sp. Productus arcuatus Hall
"Productus ovatus Hall
Productella concentrica (Hall) List of Fossils from bed 5 of the Kilnderhoo1c Group at Burlingto BRYOZOA-
*Ptilopora sp. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella inaequalis (Hall)
*Chonetes sp. Productus arcuatus Hall
Productus parvulus Win. "Productus blairi Miller
Pustula morbilliana (Win.)
Camarophorella lenticularis (W.andW.)
Cranaena , allei (Win.)
Spirifer biplicoides Weller
*Spirifer platynotus Weller
Brochythyris JlCculiaris (Shum.)
*Syringothyris sp. Reticularia cooperensis (Swallow)
Cyrtina acutirostris (Shum.) ,
PELECYPODA-
Pterinopecten nodocostus (W. and W.)
Pernopecten cooperensis (Shum.)
*Lithophaga d. L. minuta Weller
List of 'Fossils from bed 6 of the
ANTHOZOA-
Zaphrentis sp. undet. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella infiata (W. and W.)
''Schellwienella planumbona Weller
*Schellwienella 'inaequalis (Hall) BRYOZOA-
*Ptilopora sp. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella inaequalis (Hall)
*Chonetes sp. Productus arcuatus Hall
Productus parvulus Win. "Productus blairi Miller
Pustula morbilliana (Win.)
Camarophorella lenticularis (W.andW.)
Cranaena , allei (Win.)
Spirifer biplicoides Weller
*Spirifer platynotus Weller
Brochythyris JlCculiaris (Shum.)
*Syringothyris sp. Reticularia cooperensis (Swallow)
Cyrtina acutirostris (Shum.) , BRACHIOPODA-
Leptaena convexa Weller
Schellwienella inaequalis (Hall)
*Chonetes sp. Productus arcuatus Hall
Productus parvulus Win. "Productus blairi Miller
Pustula morbilliana (Win.)
Camarophorella lenticularis (W.andW.)
Cranaena , allei (Win.)
Spirifer biplicoides Weller
*Spirifer platynotus Weller
Brochythyris JlCculiaris (Shum.)
*Syringothyris sp. Reticularia cooperensis (Swallow)
Cyrtina acutirostris (Shum.) , GASTROPODA-
Straparollus angularis Weller
Straparollus sp. undet. Bellerophon sp. undet. Bucanopsis perelegans (W. and W.) SCAPHOPODA-
Dentalium grandaevum Win. VERTEBRATA-
"Fish t eeth. VERTEBRATA-
"Fi h
h "Fish t eeth. KINDERHOOK OF SOUTHEASTERN IOWA Porcellia obliquinoda White
Porcellia rectinoda Win. Conularia byblis White BRYOZOA-
FelWstella sp. undet. PELECYPODA-
. AvicuJopeeten tenuicostus Win. Aviculopecten caroli Win. * Avieulopeeten sp. Pterinopeeten ef. P. laetus Hall
*P ernopecten cf. P. eooperensis (Shuro.)
Per1lJOIp<'lcten f sp. undet. . Leiopteria spinalata (Will.)
Avicula strigosa (White)
Pteronites whitei (Win.)
MytiJarca occidentalis (W. and W.)
MytiJarca fibristriata (W. and W.)
Goniophora jennae (Win.)
Parallelodon oochlearis (Win.)
Parallelodon modesta (Win.)
Grammysia plena Hall
Grammysia amygdalinus (Win.)
Edmondia burlingtOilL€'l1sis (W. and W.)
Edmondia quadrata (W. and W.)
Edmondia a.equimarginalis Win. Edmondia nitida Win. Edmondia jejunus (Win.)
Sphenotus rigiduB (W. and W.)
Sphenotus bicarinatus (Win.)
Sphenotus iowensis (Win.) FelWstella sp. undet. PELECYPODA-
. AvicuJopeeten tenuicostus Win. Aviculopecten caroli Win. * Avieulopeeten sp. Pterinopeeten ef. P. laetus Hall
*P ernopecten cf. P. eooperensis (Shuro.)
Per1lJOIp<'lcten f sp. undet. . Leiopteria spinalata (Will.)
Avicula strigosa (White)
Pteronites whitei (Win.)
MytiJarca occidentalis (W. and W.)
MytiJarca fibristriata (W. and W.)
Goniophora jennae (Win.)
Parallelodon oochlearis (Win.)
Parallelodon modesta (Win.)
Grammysia plena Hall
Grammysia amygdalinus (Win.)
Edmondia burlingtOilL€'l1sis (W. and W.)
Edmondia quadrata (W. and W.)
Edmondia a.equimarginalis Win. Edmondia nitida Win. Edmondia jejunus (Win.)
Sphenotus rigiduB (W. and W.)
Sphenotus bicarinatus (Win.)
Sphenotus iowensis (Win.) AvicuJopeeten tenuicostus Win. A i
l
t
li Wi Goniophora jennae (Win.)
P
ll l d
hl
i
(W Parallelodon oochlearis (Win.)
P
ll l d
d
t
(Wi
) Parallelodon modesta (Win.)
G
i
l
H ll SCAPHOPODA-
Dentalium grandaevum Win . . Grammysia plena Hall
Gramm sia am gdalin SCAPHOPODA-
Dentalium grandaevum Win . . Grammysia amygdalinus (Win.)
Edmondia b rlingtOilL€'l1sis (W and W ) Edmondia burlingtOilL€'l1sis (W. and W.)
Edmondia q adrata (W and W ) CEPHALOPODA-
Orthoceras whitei Win. Orthoceras heterocinctum Win. Orthoceras indianense Hall
Phragmoeeras expansum Win:
Cyrtoceras unicorne Win. Agoniatites opimus (W. and W.) The strongly Devonian aspect of this assemblage is com-
mented upon by Weller.27
All the genera of the pelecypods,
for example, except two are represented in the Devonian faunas
of eastern New York. The cephalopods also have Devonian
affinities. The brachiopods, on the other hand, are chiefly
Carboniferous types. Weller states that" the strongly Carbon-
iferous element among the brachiopods in the Chonopectus
sandstone, is to be considered as a weightier evidence than the
holdover pelecypods and cephalopods." 27 Iowa Geol. Survey, vol. X, pp. 73, 74; 1900. List of Fossils from bed 9 of the Kilnderhoo1c Group at B1wlington BRACHIOPODA-
*Schellwienella sp. ·Chonetes gregarius Weller
Ohonetes cf. C. geniculata White
Chonopectus fischeri (N. and P.)
*Rhipidomella sp. *Rhynchonella sp. *Paryphorhynchus sp. *Spirifer platynotus Weller
*Spirifer biplicatus Hall'
*Spirifer subrotundus RaIl
PELECYPODA-
A viculopecten iowensis Miller
*Per!L(}pecten sp. ParaJlelodon leptogaster (Win.)
*Schizodus sp. GASTROPODA-
*BellerophoIIJ sp. *Straparollus sp. Holopea subconica Win. Holopella Iilira Win. List of Fossils from bed ./, of the Kilnderhoo1c Group at Burlington
BRACHIOPODA-
*Chonetes sp. *Chonetes sp. Chonopectus fischeri (N. and P.)
Rhynchonella unica Win. Rhynchopora pustulosa (White)
Paryphorhynchus striaticosliaJtum
(M. and W.)
Allorhynchus heteropsis (Win.)
* Allorhynchus sp. Syringothyris halli Win. PELECYPODA-
* Allorisma sp. "Schizodus sp. List of Fossils from bed 5 of the Kilnderhoo1c Group at Burlington
BRYOZOA-
*Ptilopora sp. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella inaequalis (Hall)
*Chonetes sp. Productus arcuatus Hall
Productus parvulus Win. "Productus blairi Miller
Pustula morbilliana (Win.)
Camarophorella lenticularis (W.andW.)
Cranaena , allei (Win.)
Spirifer biplicoides Weller
*Spirifer platynotus Weller
Brochythyris JlCculiaris (Shum.)
*Syringothyris sp. Reticularia cooperensis (Swallow)
Cyrtina acutirostris (Shum.) ,
Parallelodon parvus CW. and W.)
Edmondia nuptialis Win. 'Edmondia strigillata Win. Spherootus cylindricus (Win.)
Spathella phaselia Win. Nucula iowensis W. and W. Palaeone1lo microdonrta (Win.)
Palaeoneilo barrisi (W. and W.)
Leda saccata (Win.)
Dexiobia ovata (Hall)
Dexiobia haIli Win. Schizod'us trigonalis (Win.)
"Cypricardinia sulcifera (Win.)
GASTROPODA-
Straparollus angularis Weller
Straparollus sp. undet. Bellerophon sp. undet. Bucanopsis perelegans (W. and W.) List of Fossils from bed ./, of the Kilnderhoo1c Group at Burlington BRACHIOPODA-
*Chonetes sp. *Chonetes sp. Chonopectus fischeri (N. and P.)
Rhynchonella unica Win. Rhynchopora pustulosa (White)
Paryphorhynchus striaticosliaJtum
(M
and W )
Allorhynchus heteropsis (Win.)
* Allorhynchus sp. Syringothyris halli Win. PELECYPODA-
* Allorisma sp. "Schizodus sp BRACHIOPODA-
*Chonetes sp. *Chonetes sp. Chonopectus fischeri (N. and P.)
Rhynchonella unica Win. Rhynchopora pustulosa (White)
Paryphorhynchus striaticosliaJtum
(M. and W.)
Allorhynchus heteropsis (Win.)
* Allorhynchus sp. Syringothyris halli Win. PELECYPODA-
* Allorisma sp. "Schizodus sp. y
p
Syringothyris halli Win. PELECYPODA-
* * Allorisma sp. p
"Schizodus sp. List of Fossils from bed 5 of the Kilnderhoo1c Group at Burlington List of 'Fossils from bed 6 of the Kinderhoo1c Gr01!p at B1!rlington ANTHOZOA-
Zaphrentis sp. undet. BRACHIOPODA-
Leptaena convexa Weller
Schellwienella infiata (W. and W.)
''Schellwienella planumbona Weller
*Schellwienella 'inaequalis (Hall) "Schellwienella crenulicostata Weller
Ch
t
l
i N
d P "Schellwienella crenulicostata Weller
Chonetes logani N. and P. "Chonetes burlingtonensis Weller
Chonetes illinoisensis Worthen
"Chonetes sp. Productus arcuatus Hall
"Productus ovatus Hall
Productella concentrica (Hall) ANTHOZOA-
Zaphrentis sp. undet. Chonetes logani N. and P. "Ch
t
b
li
t
i
W ll MISSISSIPPIAN S'l'RATA OF IOWA 58 *Rhipidomella thiemei (White)
*Schizophoria subelliptica (W. and W.)
Cranaena , allei (Win. )
Spirifer platynotus Weller
'-Spirifer biplicoides Weller
*Cliothyridina hirsuta (Hall) ,
Athyris crassicardinalis White *Rhipidomella thiemei (White)
*Schizophoria subelliptica (W. and W.)
Cranaena , allei (Win. )
Spirifer platynotus Weller
'-Spirifer biplicoides Weller
*Cliothyridina hirsuta (Hall) ,
Athyris crassicardinalis White GASTROPODA-
StraparoUus StraparoUus obtusus (Hall)
Pleurotomaria quinquesulcata W Pleurotomaria quinquesulcata Win
Lo~onema sp
undet Lo~onema sp. undet
Capulus sp
undet Capulus sp. undet. CEPHALOPODA-
Orthoceras indianensis HaU
Gyroceras burlingtonensis Owen Orthoceras indianensis HaU
Gyroceras burlingtonensis Owen Orthoceras indianensis HaU
Gyroceras burlingtonensis Owe Gyroceras burlingtonensis Owen PELECYPODA-
*Pernopecten cooperensis (Shum.)
Pernopecten circulus. (Hall)
Conocardium pulchellum W. and W. PELECYPODA-
*Pernopecten CRUSTACEA-
*G iffithid Pernopecten circulus. (Hall)
Conocardium pulchellum W *Griffithides 7 sp. Conocardium pulchellum W. and W. List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng List of Fossils from bed 7 of the Kinder:hook Group at B~trlVngton ANTHOZOA-
*Zaphrentis sp. *Syringopora sp. Leptopora typa Win. CRINOIDEA-
*Seve.ral undetermined species '
BRYOZOA-
*Cystodictya sp. *Fenestel1a sp. *Ptilopora sp. BRAcmoPoDA-
*Leptaena convexa Weller
Sch.el.lwienella in:fiata (W. and W.) ,
Schelhyienella inaequalis (Hall)
*Schellwienella sp. *Chonetes multicosta Win. *Chonetes logani N. and P . *Chonetes illinoisensis Worthen
"Chonetes sp. . Productella concentrica (Hall)
*Productus sampsoni Weller
*Productus sp. *Rhipidomella thiemei (White)
*Rhynchotetra caput-testudinis (White)
Rhynchopora persinuata (Win.)
*Dielasm~ burlingtonensis (White) f
Spiriferina solidirostris White
*Spirifer cf. S. mundulus Rowley
*Spirifer grimesi HaUl
*Spirifer forbesi N. and P. "Spirifer platynotus Weller
*Syringothyris sp. *ReticUlaria cooperensis (Swallow)
Nucleospira barrisi Wlhite
*Cliothyridina glenparkensis Weller ,
GASTROPODA-
Pleurotomaria mississippiensis W.andW. "Strophostylus bivolve (W. and W.)
Bellemphon panneus White
Igoeeras undata (Win,)
Crupulus paralius W. and W. Capulus vomerium (Win.) ANTHOZOA-
*Zaphrentis sp. *Syringopora sp. Leptopora typa Win. *Productus sampsoni Weller
*Productus sp *Productus sp. *Rhipidomella *Rhipidomella thiemei (White
*Rhynchotetra caput testudinis *Rhynchotetra caput-testudinis (White)
Rhynchopora persinuata (Win ) CRINOIDEA-
*Seve.ral undetermined species CRINOIDEA-
*Seve.ral undetermined species Spiriferina solidirostris White
*Spirifer cf
S
mundulus Rowley *Spirifer cf. S. mundulus Rowley
*Spirifer grimesi HaUl BRYOZOA-
*Cystodictya sp. *Fenestel1a sp *Spirifer grimesi HaUl
*Spirifer forbesi N
a *Spirifer forbesi N. and P
"Spirifer platynotus Weller Spirifer platynotus Weller
*Syringothyris sp *Ptilopora sp. BRAcmoPoDA-
*Leptaena convexa Weller
Sch.el.lwienella in:fiata (W. and W.) ,
Schelhyienella inaequalis (Hall)
*Schellwienella sp. *Chonetes multicosta Win. *Chonetes logani N. and P . *Chonetes illinoisensis Worthen
"Chonetes sp. . Productella concentrica (Hall) *Ptilopora sp. *Syringothyris sp. *ReticUlaria coope *ReticUlaria cooperensis (Swallow)
Nucleospira barrisi Wlhite The vertical range of the Kinderhook species at 'Burlington
is indicated in the following table: Table Showing Range of Species in Kinderhook Beds at Burlington
I
Horizons
\~-\
3 1--'-4
1-'------5
1 6-'-1
7 I
SPONGIAE
I
Dictophyton sp. undet. _______________ : __ ;: ________________ . _______ ._
x
______________________________ . _____ .. ____ _
ANTHOZOA
Zaphrentis sp. undet. _______________________________________ . _____ ._ _______ _______ _______ _______ _______
x
______ _
~~~i~a:~~::~~;::::::::::::::::::::::=::::::::::::::::::::~~: :::::::: :::=::: ::::::: :::=::f::::: :::=::: ~ Table Showing Range of Species in Kinderhook Beds at Burlington
I KINDERHOOK FOSSILS AT BURLINGTON 59 Table Showing Range of Species 1m, Kim,derlwo7c B eds at Burlitrogton-C01!,tinued. 1
Horizous
I
lll2lsl415j6j7j
BRYOZOA
Feuestella sp. undet ............ _ .. _. __ ... _ .. _................ ........ x
... _ ...... _ ...... _ ...... _ ...... _ .. . List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng Fenestella sp .......................................... _ ........... _ .............. _ ...... _ .............. _ ...... _... x
Ptilopo,ra sp .... _ ........................................................... _ .... _ ... _._ ........... _... x
... _ ..• ... _ .. . Ptilopora sp .... _ .......... _ ............................................................... ... _ ...... _ ...... _ ...... __ • x
Cystodictya sp ..................... __ ... _ ........ _ .... _ .................. _ ...... _ ...... _ ...... _ ...... _ ...... _... x
B R.A.cmoPoDA
Lingula membr3lI1acea Win .... _ .. _ .. _ ............................ _... x
... _ .............. _ ...... _ ...... _ .. . Lingula sp. undet ................................................ _..... x
........... _ ...................... _ ........... . Orbiculoidea capax (wnite) ........................... _....... ........ x
... _._ ... _ .............. _ ... ... _ .. . Orbiculoidea sp. undet ........ _ .............. _._ .... _..... x
........... _ ...... _ ...... _ ...... -., .... -.. . Leptaeua couvexa Weller ... _ ................... _ ... _ ......... _ ... _ ... ... _ ...... _ ... ... _... x
x
x
Schellwienella inaequalis (Hall).............................. ........ x
... _ ... ... _... x
x
x
Schellwienella infiat8J (W. and W.) ... _ .... _ ................................ _... ........ ........ x x,
Schellwienella planumbona Weller ... _ ........................ _ ..•... _ ...... _ ...... _ .. , ... _... x
Sch.ellwienella crenulicostata Weller ........................ "._ ..•... _ ...... _ ... ........... _... x
Schellwienell3i sp .... _ .... _ .... _ .... _ ...................... _ ............ _ ...... _... x
... _ ...... _ ... ... _ .......... . Schellwienella sp ...... _ ........ _ ....................................... ... _ ...... _ ...... _ ... ... _ ...... _ ... ... _... x
Chonetes illinoisensis W orthen................................ ........ x
... _ ........... ... _... x
x
g~~:;: ~;~~~ri;e:~~~~ .. ~~.~~::::::::::::::~::::=::: :::=::: ... ~... ~ :::=::: :::=::: ::::::: :::::::\
Chonetes burliIl:gtonensis Weller ................................. _ ........... ... _ ........... ... _... x
........ ,
Chonetes loganl N. and P ............................ _ .... _ .............. _ ...... _ ... ... _ ...... _... x
x
Chonetes multicosta Win .... _ ............................ _ .......... _ ...... _ ... ... _ ... ... _ ... ... _ ...... _... x
Chonetes sp. undet ........................................................ _... x
........ ................... _ ...... _ .. . Chonetes sp ........ _ .................. _ ........ _ ........................... ... _ ...... _ ...... _ ...... _... x
........... _ .. . List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng Chonetes sp .... _ ........ _ .. _ .... :. .. _ .... _ .. _ .............. _ ...... _ ... ... _ ...... _ ... ... _ .............. _ ...... _... x
Chonetes sp .................. _ ........ _ ........ _ ................. _ .......... _ .............. _... x
... _ ...... _ ...... _ .. . Chonetes sp ........ _ ........ _ .................. _ .............................. _ ... ........... _... x
... _ ...... _ ...... _ .. . Chonetes sP .... _ ............ _ ................................................ "'-'" "'r'" ••• _ ................... , x
....... . Chonopeetus fischeri (N. and P.) ............................. _... x
x
x , ... _ .............. _ .. . Productella nu=ularis (Win.) ......... _.................. ........ x
........ ... _ ...... _ ... ... _ .......... . Productella concentrica (Hall) ........................... _ .............. _ ...... _ ........... 1 ... _... x
x
~~~~~~i~~a c;;ti:!~!~··w~::=::::::::::::::::::=::=::::=::: ... ~ ... ... ; ... :::=::: I:::~::: :::=::: :::=::: :::=:::
~~~~~~i~: ~~~1~~e~:Il~::~~~~::::::::::::::::::::::=::::::::: ... ~... ~ :::=::: :::=::: :::::::: ... ; ... :::=:::
Productus mesicostalis Weller ................................ ... _... x
... _ ...... _ ... ................ ... _ .. . Productus arcuatus HaJj.......................................... ........ ........ ........ ........ x
x
Productus blairi Miller ............................................................ ... _... ........ x
... _ .......... . Productus parvulus Win .... _ ................................ _ ... ... _ ...... _ ... ... _... ........ x
... _ ... ....... . Productus sampsoni Weller ................................................. _ ... , ... _ ... , ... _ ... , ... _ ...... -... x 1
Productus sp .................................. _ ................................... ... -...... _ ... ... -...... -...... _... x I
ProductllS sp .......................... · ....... _ ............... ·· .......... 1 x 1 ... _ ...................... _ ...... _ ...... _ .. . Pustula morbilliana (Win.) ...................................... .... ····1· .. ····· ... _ ... .. · .... ·1 x , ... _ ........... ,
Rhipidomella thiemei (White) ........................................ , ... _ ... ... _ ...... _ ... \ ... _... x
x
Rhipidomella cf. R. burlingtonensis HalL......... x
... _ .............................. _ ......... .. Rhipidomella sp .................................................................... _... x
... _ ... 1 ... _ ...... _ ........... \
Schizophoria subelliptica (W. and W.) ........................... _ ................... , ... _... x ... _ ... Schizophoria sp................................................... ....... ........ x
........ ... _ .............. _ ...... _ ... 1
Schizophoria sp. undet ........................................ _..... x
... _ ................... , ... _ ...... - ... ........ List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng __
x
........................................ I
Spathella vent1'icosa W. and W ____ ...... _ .... __ .... · ....... I __ . ___ .I x
... _ ........................ --. ........ I
~~:::;;~i!~=a ~f.:::::::::::::::::::::::::::::::::::::::::::::I:::~:::1 .. ·;-·1:::~:::1::::::::1 ... ~ ... 1::::::::1::::::::1
Grammysia. amygdalinus (Win.)............................ ........ x
................ --...... ...... -- __ ...... 1 Tabl~ Showitng Eam,ge of Species itn Kitnderhoo1c Beds at Burlington---Continued • Tabl~ Showitng Eam,ge of Species itn Kitnderhoo1c Beds at Burlington
Continued
./::£orizons
1
I. \1!2!3!4!51
6 17 ! ParypllQrhynchus striatocostatum (M. BlllJd W.) ..•. I==== ........ ,----x-== ...... __ ........ ~~~J:~~~{I~C~~iC~Pwi~::::::::::~::::::::::::::~::::::~::::::: :::~::: :::=::: ... ~ ...... ; ... :::=::: :::~::: ::::::::
Rhynchonella sp ...................... _ ............................ _ ...... _ ...... _... x
................... _ ......... .. Rhynchonella sp. ~et
..... ~ .......... _ ......... _ ..... _ .. __ .. , .. _... x ... _ ...... _ ...................... _ ... Allorhynchus heteropsis (Win.) ...................................... "._". ........ x ........... _ ... ...... .. Allorhynchus sp.' ................. _ .... _ .................. _ ........ _ ............. __ .... ........ x
........... _ .......... . Rhynchotetra caput·testudinis (White) ............................ _ ...... _ ...... _ ...... _ ...... _... x
Rhynchopora pel'sinuata (Win.) .............................. __ ....... _ ...... ___ .... ___ .... ___ . __ ._.__
x
Rhynchopora pustulosa (White) .... __ .L_ .................... _... ........ ........ x .......... --.......... .. Dielasma burlingtonensis (White) L ............................. _ ...... _ ...... _ ...... _ .. ' ... _... x
Crana.elll.a f allei (Win.) .. , .. __ ..... · ...... _.: ....................... _ ...... _ .............. _... x
x
... _ .. . Cyrtina acu tirostris (Shum. ) L._ ................ _ .......... _ ...... _ ...... _... ........ x
... ___ ........ . Spiriferina solidirostris White ... ___ ....................... __ ... _ ...... _ ...... _ ...... ___ . __ ._ ...... _... x
Spirifer platyno.tus Weller...................................... ........ ·x
x
........ x
x
x
Spirifer subr6tundus Hall ......................... ___ .... __ . ____ ... _... x
x ... _ ...... _ ... J _____ •• _____ •
Spirifer biplicatus HaIL ____ ...... __ .. __ ... _ ........ __ .. _______ . __ .. ____
x
xt ... _., .... ___ . __ ... __ .... -.--
Spi1'ifer grimesi HalI .......... __ ..... __ ........ :.. .. __ .................. _ .............. ___ .. ,._ ...... _ ...... ___ . x
Spirifer biplicoides Weller ............ __ ................................... _ ...... _... ........ x
x
... - .. List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng . Spirifer forbesi N. and P ............................ _ ..................... _ ...... _ .............. _ ...... _... x
Spirifer cf. S. mundulus R()wley ................................. __ .... _ ........... ... _ ... ... _ ...... _... x
Brachythyl'is peculiaris (Shum.) ............................ ........... -...... _ ... 1 ........ 1 x ...... -- ....... . Syrin:gothyris haJ.li Win .......... _ ................. ________ .... __ ........ --...... __ ._ ... 1 x 1"'-'" --.---...... --. ~~:~::;;f: :~~~~~~ ... ~~~.~ .. :~.::~.::~ .... ~~~.: ... ~~ ...... ~ .. :: :::~::: --.~--. :::=::: :::::::: ... ~--. :::::::: ::::::::
Syringothyris sp. __ .. ________ .. __ . ___ ... ________ ..... _ ..... __ .. ____ .... ' __ . ___ . ________ .... ____ .. __ .... ______ .... ____ .. x
Reticularia cooperensis (Swallow) ... _ ............ ______ . ________
x ... ___ . ____ .... x ........ x
Eumetria altirostris (White) __ .. __ .. __________ ... _ .. __ .... __ . x
x
... _ ... __ " __ " ...... ______ ......... __ . Nueleospira b8Jl'risi White ______ ._ .. ____ .. _ ...... __ .... ___ ........ _ ...... _ ... __ ................. _ ...... _... x
Cama.rophorella lenticularis (W. and W.) ....... _ ...... _ ... __ ._ ...... _ ... __ ...... x
--......... - ... Athyris crassicardinalis White ... _ .. __ ..................... __ .. __ .............. : ................ _... x
... _ .. . Cliothyridina glenparkensis Weller L .......... __ ........... __ ........... _ ...... _ ...... _ ...... _... x
Cliothyridina hiI'suta (Haill)
~ .......................... ____ .................................. " __ "__
x
...... .. Composita (f) corpulenta (Win.) ................ __ .... : .......... x
...................................... .. PELECYPODA
Promacrus cuneatus HalL ........................ ,............. ........ x
...................................... .. Glossites elliptica (Win.) ... _................................... ........ x
...................................... .. Glossites , burlingtou'ensis Weller ... _ .... _.: .... _ .. _. ........ x
........ __ ...... .............. __ ...... .. E·dmondia burliugtonensis 'iV. and W................... ........ x
...................................... .. Edmondia quadrata (W. and W.)........................ ........ x
........ .............................. .. Edmondia aequimal'ginalis W:in .... _......................... ........ x
.... __ ................................ .. Edmondia nitida W:in ...... __ ................ __ ........ _ .............. _... x
.................. __ .... __ ............ .. Edmondia jejunus (W:in.) ...................................... ........ x
........................ .. __ ........... . ~:~~~~l; n~~~~t~!~:r~;~~:~::::::::::=::::::::::::::::::::: :::=::: ::::::: :::::::: :::::::: ~ ::::::::1::::::::
Sphenotus bicostatus Welle1' ........ ____ ... _................... ........ x
.......... __ .... ...................... List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng 1
Paryphorhynchus transversum Weller.................... ........ x
... _ ........................... 1 ... ·· .. ·1 Table Showing Range of Species 1m, Kim,derlwo7c B eds at Burlitrogton-C01!,tinued. MISSISSIPPIAN STR:AT.A, OF IOWA 60. Tabl~ Showitng Eam,ge of Species itn Kitnderhoo1c Beds at Burlington---Continued •
./::£orizons
1
I. \1!2!3!4!51
6 17 ! ParypllQrhynchus striatocostatum (M. BlllJd W.) ..•. I==== ........ ,----x-== ...... __ ........ ~~~J:~~~{I~C~~iC~Pwi~::::::::::~::::::::::::::~::::::~::::::: :::~::: :::=::: ... ~ ...... ; ... :::=::: :::~::: ::::::::
Rhynchonella sp ...................... _ ............................ _ ...... _ ...... _... x
................... _ ......... .. Rhynchonella sp. ~et
..... ~ .......... _ ......... _ ..... _ .. __ .. , .. _... x ... _ ...... _ ...................... _ ... Allorhynchus heteropsis (Win.) ...................................... "._". ........ x ........... _ ... ...... .. Allorhynchus sp.' ................. _ .... _ .................. _ ........ _ ............. __ .... ........ x
........... _ .......... . Rhynchotetra caput·testudinis (White) ............................ _ ...... _ ...... _ ...... _ ...... _... x
Rhynchopora pel'sinuata (Win.) .............................. __ ....... _ ...... ___ .... ___ .... ___ . __ ._.__
x
Rhynchopora pustulosa (White) .... __ .L_ .................... _... ........ ........ x .......... --.......... .. Dielasma burlingtonensis (White) L ............................. _ ...... _ ...... _ ...... _ .. ' ... _... x
Crana.elll.a f allei (Win.) .. , .. __ ..... · ...... _.: ....................... _ ...... _ .............. _... x
x
... _ .. . Cyrtina acu tirostris (Shum. ) L._ ................ _ .......... _ ...... _ ...... _... ........ x
... ___ ........ . Spiriferina solidirostris White ... ___ ....................... __ ... _ ...... _ ...... _ ...... ___ . __ ._ ...... _... x
Spirifer platyno.tus Weller...................................... ........ ·x
x
........ x
x
x
Spirifer subr6tundus Hall ......................... ___ .... __ . ____ ... _... x
x ... _ ...... _ ... J _____ •• _____ •
Spirifer biplicatus HaIL ____ ...... __ .. __ ... _ ........ __ .. _______ . __ .. ____
x
xt ... _., .... ___ . __ ... __ .... -.--
Spi1'ifer grimesi HalI .......... __ ..... __ ........ :.. .. __ .................. _ .............. ___ .. ,._ ...... _ ...... ___ . x
Spirifer biplicoides Weller ............ __ ................................... _ ...... _... ........ x
x
... - .. . Spirifer forbesi N. and P ............................ _ ..................... _ ...... _ .............. _ ...... _... x
Spirifer cf. S. mundulus R()wley ................................. __ .... _ ........... ... _ ... List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng ... _ ...... _... x
Brachythyl'is peculiaris (Shum.) ............................ ........... -...... _ ... 1 ........ 1 x ...... -- ....... . Syrin:gothyris haJ.li Win .......... _ ................. ________ .... __ ........ --...... __ ._ ... 1 x 1"'-'" --.---...... --. ~~:~::;;f: :~~~~~~ ... ~~~.~ .. :~.::~.::~ .... ~~~.: ... ~~ ...... ~ .. :: :::~::: --.~--. :::=::: :::::::: ... ~--. :::::::: ::::::::
Syringothyris sp. __ .. ________ .. __ . ___ ... ________ ..... _ ..... __ .. ____ .... ' __ . ___ . ________ .... ____ .. __ .... ______ .... ____ .. x
Reticularia cooperensis (Swallow) ... _ ............ ______ . ________
x ... ___ . ____ .... x ........ x
Eumetria altirostris (White) __ .. __ .. __________ ... _ .. __ .... __ . x
x
... _ ... __ " __ " ...... ______ ......... __ . Nueleospira b8Jl'risi White ______ ._ .. ____ .. _ ...... __ .... ___ ........ _ ...... _ ... __ ................. _ ...... _... x
Cama.rophorella lenticularis (W. and W.) ....... _ ...... _ ... __ ._ ...... _ ... __ ...... x
--......... - ... Athyris crassicardinalis White ... _ .. __ ..................... __ .. __ .............. : ................ _... x
... _ .. . Cliothyridina glenparkensis Weller L .......... __ ........... __ ........... _ ...... _ ...... _ ...... _... x
Cliothyridina hiI'suta (Haill)
~ .......................... ____ .................................. " __ "__
x
...... .. Composita (f) corpulenta (Win.) ................ __ .... : .......... x
...................................... .. PELECYPODA
Promacrus cuneatus HalL ........................ ,............. ........ x
...................................... .. Glossites elliptica (Win.) ... _................................... ........ x
...................................... .. Glossites , burlingtou'ensis Weller ... _ .... _.: .... _ .. _. ........ x
........ __ ...... .............. __ ...... .. E·dmondia burliugtonensis 'iV. and W................... ........ x
...................................... .. Edmondia quadrata (W. and W.)........................ ........ x
........ .............................. .. Edmondia aequimal'ginalis W:in .... _......................... ........ x
.... __ ................................ .. Edmondia nitida W:in ...... __ ................ __ ........ _ .............. _... x
.................. __ .... __ ............ .. Edmondia jejunus (W:in.) ...................................... ........ x
........................ .. __ ........... . ~:~~~~l; n~~~~t~!~:r~;~~:~::::::::::=::::::::::::::::::::: :::=::: ::::::: :::::::: :::::::: ~ ::::::::1::::::::
Sphenotus bicostatus Welle1' ........ ____ ... _................... ........ x
.......... __ .... ...................... .. Sphenotus ventricosa (W. and W.)........................ ........ x
........................................ I
~~~:~,~~~: r~~~~a\:· (:i:)!.:::::::::::::::::::::::::~::: :::::::: ~ :::::::: :::::::: :::::::: :::::::: ::::::::1
Spheootus iowensis (Win.) .......... __ ...................... __ ........ List of Fossils from bed 7 of the Kinder:hook Group at B~trlVng .. Sphenotus ventricosa (W. and W.)........................ ........ x
........................................ I
~~~:~,~~~: r~~~~a\:· (:i:)!.:::::::::::::::::::::::::~::: :::::::: ~ :::::::: :::::::: :::::::: :::::::: ::::::::1
Spheootus iowensis (Win.) .......... __ ...................... __ ........ __
x
........................................ I
Spathella vent1'icosa W. and W ____ ...... _ .... __ .... · ....... I __ . ___ .I x
... _ ........................ --. ........ I
~~:::;;~i!~=a ~f.:::::::::::::::::::::::::::::::::::::::::::::I:::~:::1 .. ·;-·1:::~:::1::::::::1 ... ~ ... 1::::::::1::::::::1
Grammysia. amygdalinus (Win.)............................ ........ x
................ --...... ...... -- __ ...... 1 PELECYPODA KINDERHOOK FOSSILS AT BURLINGTON 61 Table Showing'Rangd of Species in Kittderhoo"k Beds at Burlington-Continued. I
Horizo'liJS
1
1
1112/3/4/5/6/71
Cardiopsis megambonata Win .. __ . ___________________________ === -x-====== == === ________ 1
Nucula iowensis W. and W. ____ .. ______________________________ _______
x
_______ ________
x
_______________ _
Palaeoneilo microdonta (Win.) ___ .__________________________ ________ _______ _______ ________ x
_______________ _
Palaeoneilo barrisi (W. and W_)_________________________ ________ _______ _______ _______
x
_______________ _
Leda saccata (Win.) _____ . ____ . _____________________ . ______________ ._ ________ _______ _______ _______
x
_______________ _
Dexiobia halli Win. ___________ . _____ . _____________________________________________________ . ________
x
_____________ . Dexiobia ovata (Hall) ______________________________________ .____ ________ _______ _______ _______
x
________ _______ _
Pal'allelodon cochleal'is (W i!lI, ) ____ . ___ . _______ . ____________________ :
x
_______________________ _______________ _
Pal'allelodon modesta (Win.) ___ .______________________________ _______ x
__________________________________ . ___ _
Parallelodon leptogastel' (Win.)_ .... _. ________ .-.---------- _______ _______
x
_____________________ _______ _
ParaJlelodon pa,rvus ('V. and W.). ___ ... __ . _______ . _____ . _______________________ .. _____
x
______________ __
Mytilarca occidentalis (W_ and W.}___________________ ________
x
___________________________________ __
Mytilarca fibristl'iata (W. and W.)______________________ ________
x
_______________________ _______________ _
Conocardium pulchellum W. and W______________________ _______ ________ ________ ________ ________
x
Avicula strigosa (White)________________________________________ ________
x
__________________________ . __________ __
Pteronites whitei (Win..)___________________________________ ________
x
______________________________________ __
Leiopteria spinalata (Win.) __________________________________ _______
x
______________________________________ __
Posidonomy~ f ambigua Win ______________________________ .. _______
x
______________________________________ __
Schizodus iowerisis Weller ________________________________________ \ _______ \ . x \-------- ------- ------- ________ \ _______ 1
Schizodus burlingtonensis Weller __________________________ -------
x
------- -------- -------- -------- ________ I
E8~H~: :i~~:~~~~:::~:~L::::=::::::::::::=::::::::::::::: :::=::~ :::~::: :::~::: :::~::: :::~::: :::=::: :::~:::I
Aviculopecten tenuicostus Win .. ____________________________ _______
x
______________________________________ __
Aviculopecten caroli Win .. ______________________________________ ________
x
_____________________________________ __
Aviculopecten iowensis Miller _______________________________ .. _ _______ _______
x
____________________________ __
Aviculopecten sp. undet___________________________________________ _ x
_______ _____________________________________ _
Aviculopecten sp______________________________________________________ _ ________
x
_____________________________________ __
Pter~no'Pecten cf. P. laetus H.all.. ______________ .. _______ .. _ _______
x
_______________________________________ \
Ptermopecten nodocostus (W. and W.) ______________ _ ________ _______ _______ ________
x
______________ __
Pernopecten cf. P. coopercnsis (Shum.)____________ ________
x
_____________________________________ __
Pernopecten cooperensis (Shum.) ____________________ .. _______ :_ ________ ________ ________
x
x
Pernclpecten circulus (Hall)___________________________________ ________ ________ ________ ________ ________
x
Pernopecten f sp. PELECYPODA undet.._______________________________________ ________
x
______________________________________ __
PernopectellJ sp_____________________________________________________________ ________ _______
x
_____________________________ __
Goniophora jennae (Win.) ______________________________________ ________
x
________ ________ ______________________ __
Lithophaga cf. L. minuta Weller__________________________ ________ _______ _______ ________
x
______________ __
Allorisma sp .. _______________________________________________________________ ________ ________ ________
x
______________________ _
Cypricardinia sulcifera (Win. ) ______________________________ ________ x
________ ________
x
______________ __
SCAPHOPODA
Dentalium grandaevum Win .. _________________________________ _______
x
x
GASTROPODA
1
Pleurotomaria quinquesulcata Win. _________________________ ------- ------- ________ 1 __ __ ____ ________ I x
Pleurotomaria mississippiensis W_ and W .. ______ ... ------- ------- --------1-------- -------- --------I x I
Porccllia crassinoda W. and W .. _____________________________ ________
x
______________________________________ __
Porcellia obliquinoda White. ________________________________ .. _ .. --.. --
x
-------- -------- -------- -------- ________ 1
Porcellia rectinoda Win ___________________________________________ --------
x
________ 1 ________ ------:- ________ 1 ______ __
i1o:::~i~~n~i· q~:~~1~~~t;:--wi~::::::::::::::::::::::::::::::::: ---~--- ---;---:::=::: ::::::::, ::::::::, :::=::: 1 :::=:::,
Bellerophon bilabiatus W. and W _________________________ --------
x
-------- ______ :_1 ________ 1 ________ 1 ________ 1
Bellerophon vinculatus W. and W ________________________ -------
x
-------- -------- -------- -------- ________ 1 MISSISSIPPIAN STRATA OF IOWA 62 Table Showmg Ban.ge of Species m Kinderhook Beds at Burlmgton-Oontinued. I
Horizons
\
( 1 ( 2 ( 3 ( 4 ( 5 I 6 I 7 I
Bellerophon panneus White L ......................... _ ...... _... x ... _ ...... _ ...... _... ........ x \
~:ii:~~~~~! ~~:··;;;;·d;;t::::::::::=::::::::::::::::::=::::::::::::::: :::=::: :::::::: ... ~ ... :::=::: ... ~ ... :::::::: ::~=:::I
Bucanopsis deflectus Weller ..................... _ ............. ... _... x
................................... _ .. . Bucanopsis perelegans (W. and W.) ... _ .................. _ .............. _ ...... _... x
........... _ .. . Patellostium scriptiferus (White) .......................... ........ x
... _ .............................. _ .. . Straparollus macromphalus Win............................. ........ x
................................... _ .. . Straparollus ammon (W. and W.) ........................ ... _... x
... -... ........... -...... _ .......... . Straparollus angularis Weller.................................. ........ x
... _ ...... _... x
........ ... _ .. . Straparollus obtusus (Hall)_ .......................... _ ....... _ ................................... _... x
....... . Straparollus sp. undet ........................ _ ........ _ .... _ ........... _ ....... _. ........ ........ x
... __ ........ . Straparollus sp ........ _ ............................................ _' ............. ,.... x .................... _ .......... . Platychisma barrisi (Win.) ......... _ ......................... ... _... x
... _ .............. _ ...... _ .......... . ~l~E1::;s s~e:~~~~;.~::::=::::::::::=::::::::::=::::: :::~::: ... ~ ... PELECYPODA :::::::: :::::::: ::::::: ::~=::t::::::
N aticopsis depressa Win ......... _ .... __ .. _ .................... _ ... _... x
... _ ........... .. __ ...... _._ ........ . Loxonema shumardana (Win!.) ................................. _... x
....•.............. _ ...... _ .. ....... . Loxonema oligo spira Win ................ _ .......... _ .... _ ...... _... x
... _ .............. _ .................. . Loxonema sp. undet ................ _ ...................... _ .......... _... x
................... _ ...... _ .......... . Loxonema sp. undet ........................................ _ ....... ................................... _... x
... _ .. . Holopea subconica Win ........................................ ,.. ........ ........ x
........ ... _ ...... _ .......... . Holopella miJ:a Win................................................... ........ ........ x
........ ........... _ ... ........ \
Igoceras undata (Win.) ....................................................... _... ........ ........ ........ ........ x
Capulus paralius W. and W ................................ _ ............................................ _... x
Capulus vomerium (Win.) ........................... _......... ........ ........ ........ ........ ........ ........ x
Capulus sp. undet .......................................................................................... _... x
Strophostylus bivolve (W. and W.) ............... _ ........ _... x' .. ", .. , ........ ........ ........ x
Sphaerodoma pinguis (Win.) ... _ .... _ .......................... _... x
........................... _ .......... . Conularia byblis White ........................................... _ ... _... x
................... _ .................. . Conularia sp. undet .............................. _ .. _............... x
... _ ...... _ ...................... _ .. _ ....... . 1
Orthocems w:::A::~:~ ................................. _ ............. ) x \ ... _ ... , ... _ ........... ', ........ , ....... .1
Orthoceras heterocinetum Win .... _ .............. _ ......... \ ........ \ x
........... _ ... \ ................... _ ... \
Orthoceras indianense HalL ......................... _ ......... I ... _ ... ) x , ... _ ... \ ........ \ ........ \ x , ........ \
Gomphoceras sp·········· .. ··· .. ····:··· .. · .. ·.······ .. · .... ··· ... · ..... ··1 x
... - ...... - ... \ ................ 1 ... _ ...... _···1
Phragmoceras exp,ansum Will ................................. _. ........ x \ ........ \ ................ , ........ \ ........ \
Cyrtoceras unicorne Win ................................................. 1 'x \ ........ \ ........................ , ........ 1
Gyroceras burlingtonensis Owen ...................................... ) ........ ) ........ \ ................ , x
........ 1
Agoniatites opimus (W. and W.) ............... _ .... _... ........ x
........ / ................ \ ................ /
CRUSTACEA
1
\
1
1
\
1
\
/
\
Griffithides , sp ...................... _ .......................... _ ..... \ ................ , ........ ........ \........ x
....... . PELECYPODA Palaeopalaemon newberryi Whitf. L ·· .. ··· .. ····· .. ····I x
... -...... _ ... 1 ........ 1 ... _ .............. _ .. . Coffi_th" ::::::""~~__I x IIL.I.I.I
,
,
1
1
,
1 I
1
PLANTS
1
1 'I
,
'
1
1
1
1
1
,
Fragments of stems and leaves ............... _ ............. , x , x \ ........ \ x \ ........ \ ... _ ... \ ........ \ Table Showmg Ban.ge of Species m Kinderhook Beds at Burlmgton-Oontinued. I KINDERHOOK OF LOUISA COUNTY 63 It "will be observed that the Upper Kinderhook beds carry Ii
typical Mississippian fauna, the Devonian aspect which charac-
terizes the collections from the lower beds being entirely lost. The appearance of such forms as Spirifer grimesi and Spirife1'
forb esi in the topmost bed of the IGnderhook together' with the
lithologic character of this member at Burlington suggests a
transition into the limestone of the Lower Burlington. Such a
relationship is indicated also by the field relations of the two
formations. Attention is called to the Chouteau affinities of the
fossils of beds 6 and 7 of the Kinderhook beds at Burlington. Louisa CO'Ltnty.-In this county the Kinderhook succession is
much the same as at Burlington, but some of the individual
members of the series are more attenuated. The best and most complete section exposed in the county is
described by J. A. Udden28 in his report on the geology of the
county. This appears "in and near Anderson's Quarry on the
east bank of Smith creek, west of the center of the SW. 1/4 of
sec. 29, Tp. 73 N., R. 2 'V." The succession there as revised by
the writer is as follows: S·Q.ction at Anderson qUa1"ry. FEET
INCHES
8. Drift ......... _ ........... _ .......................... _ .......................... _ .......... _ .... _..... 5
BURLINGTON. 7. Limestone, brownish and dolomitic below, but gray and cri·
noidal above ......... _............................................................................... 28
6
KINDERHOOK. 6. Limestone, yellowish to brownish, dolQmitic; with geodic
cavities lined with calcite ... _ .............. _............................................. 6
5. Limestone, light gray, oolitic ............. _........................................... 3
4. Sandstone, ash· colored, :fine·grained _ ..................... _ ................... __
3
3. Limestone, irregularly bedded, bro·wnish, dolomitic ......... _......... 3
6
2. Sandstone, ash·gray, :fine· grained ....... _ .......................... _................. 9
6
1. PELECYPODA Shale, bluish, argillaeoous; progressively more calcareous be-
lQw; with a carbonaceous seam about eight inches thick near
the middle. Exposed in the east bank of the creek about
forty rods north of the quarry ... _ ................ _ ...................... _ ......... 20
The fauna of the Kinderhook beds at this locality is listed be- q
y
FEET
INCHES
8. Drift ......... _ ........... _ .......................... _ .......................... _ .......... _ .... _..... 5
BURLINGTON. 7. Limestone, brownish and dolomitic below, but gray and cri·
noidal above ......... _............................................................................... 28
6
KINDERHOOK. 6. Limestone, yellowish to brownish, dolQmitic; with geodic
cavities lined with calcite ... _ .............. _............................................. 6
5. Limestone, light gray, oolitic ............. _........................................... 3
4. Sandstone, ash· colored, :fine·grained _ ..................... _ ................... __
3
3. Limestone, irregularly bedded, bro·wnish, dolomitic ......... _......... 3
6
2. Sandstone, ash·gray, :fine· grained ....... _ .......................... _................. 9
6
1. Shale, bluish, argillaeoous; progressively more calcareous be-
lQw; with a carbonaceous seam about eight inches thick near
the middle. Exposed in the east bank of the creek about
forty rods north of the quarry ... _ ................ _ ...................... _ ......... 20
The fauna of the Kinderhook beds at this locality is listed be-
low:
FQ/UOO of the Kinderhook Beds, Anderson Quarry Seotion. BRACHIOPODA
Lingula sp .......................................................... _ .... _............ x
........ ................... _ ......... . 28 Iowa Geol. Survey, vol. XI, p. 74; 1901. The fauna of the Kinderhook beds at this locality is listed be-
low: FQ/UOO of the Kinderhook Beds, Anderson Quarry Seotion. BRACHIOPODA
Lingula sp .......................................................... _ .... _............ x
........ ................... _ ......... . 28 Iowa Geol. Survey, vol. XI, p. 74; 1901. FQ/UOO of the Kinderhook Beds, Anderson Quarry Seotion. MISSISSIPPIAN STRATA OF IOWA 64 FUII.IIfW, of the Kinderhook Beds, Anderson,' Quarry Sectionr---Continued. Horizons
,
g~~~~~s g!nr~~;:t~;"Whl;~~~~~~~~::~=~::::::=::~~:::=~~~ ::::::~::::: :::::::: ~ :::=::: ~:~::::: ::::::::\::::::~:
Chonetes sp .................................. ¥....................................... ........ x
............................... . Chonetes sp .................................................... _......... ........... ........ x
........ x
x
....... . Ohonetes sp.......................................................................... ........ ........ ........ ........ x
....... . Chonopectus fischeri (N. 3J1d P.)..................................... ........ x
........ ........................ . Productella sp....................................................................... ........ x
............................... . Prod ctus cf. P. curtirostris Win ............ _.................... .......• x
... _ ...... _ .................. . Productus ovatus Hall ............. _........................................ ........ x
... _ .................. _ .. _. Productus arcuatus Hall. .. _ .... _ ... _ ......... _....................... ........ ........ ........ x
............... . PELECYPODA Productus blairi Miller ............ _ .. _.................................. ........ ........ ........ x
... _ .......... . Productus sp ............................ _ .... _ ... _ ....... _ ..... __ ............ x
....................................... . Productus sp .......................................................... _............ ........ ........ ........ x
............... . Rhipidomella thiemci (White) ....• ____ ...... __ ........... ........ ........ ........ x
x
...... .. Schizophoria sp .......................... _ .... _................................. ........ x
... _... x
............... . Rhynchonella sp ...................... _ .... _ ....... _ .... _._......... ........... x
x
.............................. .. Paryphorhynchus transversum Weller ... _......................... ........ x
............................... . Spirifer biplicatus Hall... ........................... __ ............... ........ x
............................... . Spirifer biplicoides Weller ......... _ ................ _.................... ........ ........ ........ x
............... . Spirifer platynotus Weller .......................................................................... _... x
...... .. Spirifer subrotundus Hall ......... _...................................... ........ x
............................... . Spirifer sp .... _ .. _ ....... -r ........................ _................... ........... ........ ........ ........ x
............... . Brachythyris burlingtJonensis Weller ............................... \........ ........ ........ x
... _ ......... .. Reticularia cooperensis (Swallow)................................. ........ ........ ........ x
............... . Ambocoelia. parva Weller ....................... _ .. _ ..... _.. ........... ........ ........ ........ x
_ ............ .. Nucleospira barrisi White................................................. ........ ........ ........ x
........ ...... .. . Composita , corpulenta (Winchell).................... ........... ........ x
................ ............... . PELECYPODA
~g:~~g~~ ~~ti:~ ;.!~~~~~ ... ~.~~:::::~=::::::::::===:=::::~::::::I::~::::: :~:::::: ~:::::~: ~ ~::=::: ::::~:::
Sphenotus iowensis (Win.) ............... _ ......................... _... ........ x
................................ . Sphenotus sp............................................................. ........... ........ ........ ........ x
............... . Grammysia plena Hall ............................... ,........................ ........ x
.............................. .. Nucula iowensis W. 3J1d W................................... ........... ........ ........ ........ x
............... . r..e<1a saooata (Win.) ... _ ........................................ _............ ........ ........ ........ x
............... . Parallelodon parvus Wand W .......................... _. ........... ........ ........ ........ x
............... . Schizodus trigonalis (Win.) ........................................................ _... ........ x
... _ .......... . Pernopecten cooperensis (Shum.)................................... ........ x
........ x
... _ .......... . Dentalium gr::;a::
A
Win ....................................................... -.. ./.. ...... 1 x
GASTROPODA
\
\
,
)'
Bellerophon sp .......... _ ......................................... , ........................ / ........ / ........ ,
g~~~~~Ht\~~;~~::::::::::::::::::::::::::::::::::::::::::::::::::~::: .::::::::::: ::::::::\ ::::::::1::::::::
, , ,
VERTEBRATA
, ,
,
,
,
,
1
. . . 1
,
1
1
Fish teeth .................... : ................ _ ....................................... 1 ........ 1 ... _ ... 1 . ....... ,
,
~ 1"';'''1::::::::\
x
................ 1
x , ... _ ... , ........ \
\ I I
1
,
1
x 1 ........ 1 ........ KINDERHOOK FOSSILS IN LOUISA COUNTY 65 In the Anderson quarry section, bed 1 is equivalent to the
shale member (bed 1) at Burlington. Bed 2 is the attenuated
equivalent of the Chonopectus sandstone (bed 2) and bed 3 is a
thin dolomitic facies of bed 4. The thin limestone (bed 3) at
Burlington is absent in Louisa county. The oolitic limestone
(bed 6) and the overlying buff limestone (bed 7) at Burlington
are equivalent to beels 5 and 6 in the above section. The higher beds of the Kinderhook are again well exposed
in the east bank of Smith creek near the bridge in the NW. 1/4
of sec. 31, T. 73 N., R. 2 W. The section given below is slightly
modified after U dden.2 9 Section of K inderhoo7c beds, Smith creek. B URLINGTON. FEET
9. LimestQne, brQwnish, crinQidal, bearing L obocrim/.S pyriformis, a
Pentremit-es and P1'od~ictus burlingt<mensis __________________ .. ___________________ 8
8. Chert .... __ .. _ .. ____________________________________ ___________________________________________________________ 1
7. LimestQne, buff, (lQlQmitic, irregularly bedded; with casts oil' crinoid
stems _________________ .. ____ .. ____________________ .. ______ .. _____________ ________________________________________
5
6. Limestone, SQft, gray weathering yellQwish; with fragments Qf
crinQid stems ____ .. ____________________________ .. __________________________________________________________
3
5. LimestQne, gray, crinQidal ; with seams Qf brQwnish dQlQmitic
limestQne ; mQTe irregularly bedded and cherty bellOw ____________________ 10
KINDERHOOK_
4. LimestQne, blxHvnish, SQft, dQlQmitic, in tWQ ledges, each three
f eet in thickness ________________ .. __________ .. _______________________ ________________________________
6
3. Limestone, light gTay, oolitic ______ .. ________________________________________________________
2%
2. Sandstone, bluish, fine-grained, with a thin seam Qf shale near
'the middLe ____ .. _______________________________________________ ____ .. ______________________________________
3lh
1. LimestQne, dark gray, fine-grained, imperfectly dQlQmitizecl, ex-
posed _____ .. __________ .. __________ .. ____ .. ______________________ .. ______________________________ ________________
11h
The fauna of the Kinderhook beds in this section follows : The fauna of the Kinderhook beds in this section follows FiIlUna of Kinderhook Beds, in Bank of Smith Creek. FiIlUna of Kinderhook Beds, in Bank of Smith Creek. Horizons
I
II! 2 I 3 141
ANTHOZOA
I i
I
I
~;;:;~~~~:p~p:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::1 :::::::: 1 :::::::: I ~ I::::::::
B RACHIOPODA
I I
II
Leptaena convexa Weller ---------------------------------------------------------------------- ________ I x
1 _______ --------
Schellwienella planumbona Weller L ________________________________________________ --------\--------1
X ' --------
~~~~::::~: !~~~~~---~~:--~~~--~-.-~---~---~--~~~~----~~~~--~~--:::::::::::::::::::::::::::::: :::::::: I ---~--- l ---~--- ::::::::
29 I owa Geol. Survey, vol. XI , p. 74; 19 101. 29 I owa Geol. Survey, vol. PELECYPODA 1 FUII.IIfW, of the Kinderhook Beds, Anderson,' Quarry Sectionr---Continued. KINDERHOOK FOSSILS IN LOUISA COUNTY Section of K inderhoo7c beds, Smith creek. KINDERHOOK FOSSILS IN LOUISA COUNTY XI , p. 74; 19 101. MISSISSIPPIAN STRATA OF IOWA 66 Fauna of Kinderhoo·"k Beds, Smith C7'ee"k, Lo·wisa Co·unty-Continued Fauna of Kinderhoo·"k Beds, Smith C7'ee"k, Lo·wisa Co·unty-Continued
Horizons
1
I 1 I 2 I 3 141
g~l~~~~C~:~··~:·~~::~::::::::::::::=::::::::=::::::::=::::::::::::::=:::::::::::::::I···~···II:::::::: :::~::: :::~:::
Chonetes burlingtonensis Weller .......................................................... 1........ ........ ........ x
Chonetes multicosta WiIn ...................................................................... 1........ ........ ........ x
Chonetes sp............................................................................................. ........ ........ x
..... , .. g~b~:~:: :~::::::::=::::::::::::::::::::::::::::::::::=::::::::::::::::::::::::::::::::::::::::::::::: ... ~ ... :::::::: :::=::: ... ~ .. . Productus parvulus Win....................................................................... ........ x
............... . Productus arcuatus Hall...................................................................... ........ ........ ........ x
Productus sp........................................................................................... ........ ........ ........ x
Productus sp ........................... :............................................................... ........ x
............... . Rhipidomell.a thiemei (White)............................................................ ........ ........ x
....... . i~~~~1~~ ~~~~i~i;::~~i;~:.:j~~~~~~~~~~::~:::::::::~:~~:~::::::::::::::::::::::::::::::\:::~::: ... ~ ... :::~::: ::::::::
Rhynchotetra caput·testudinis (White) ............................................ ........ ........ ........ x
Rhynchopora pustulosa (White) ................................................. : ....... 1 x
.............. _ ....... . Spiriferina solidirostris (White)........................................................ ........ ........ ........ x
Spirifer platynotus Weller.................................................................. ........ x
x
....... . Spirifer biplicoides Weller.................................................................... ........ x
........ x
Brachythyris sp ............................................................. ,......................... ........ x
............... . Athyris crassicardinalis White............................................................ ........ ........ x
....... . Nucleospira barrisi White .................................................................... \........ x
........ ........ \
PELECYPODA
1
Cypricar?inia. s~l~ife:a ~Win.).......................................................... ........ x
................................ \
Worthema mlsslsslpplensls W. and W............................................... ........ x
Palaeoneilo barrisi (W. Ihlld W.)..................................................... ........ x
........ 1 ........ 1
Nucula iowensis W. and W ............. __ ............................................... ........ x
................ I
Edmoodi. ":::.0: w~-------·----------r--
x 1--"1--1
Dentalium grandaevum Win .. ·· .. ········ ................................................. I........ x \ ... _ ... \ ........ \
GASTROPODA
1
I
I
Bucanopsis perelegans (W. and W.) ........................................ _ ...... I ........ ' x
........... _. Bellerophon sp ....................................................................................... 1........ x
........... __ . Murchisonia quadricincta Win ........ · .......... ·· .. ·· .. · .. · .... · .. ··· .. · ................ ·I· ...... ·1 x I I
Straparollus obtusus (Hall) .. · .. · ........ · .. · .............................................. I ........ 1 x
... ~ ... :::=:::
Straparollus sP ...................... · .................. · .. · .... · .... · .............. · ..... · .. · .. · .... ·I ........ I x
................ 1
1
1
1
I
' 1
I I I \ I
Orthoceras indianense Hall .... · .... · .......... · ........ · .. · .. ·· ........ · .................... I ........ 1 x 1 x 1 ........ 1
CEPHALOPODA
Orthoceros sp ...... · .......... · ...... · .... · .... · ............ · .... · ................. 30 Geology of Louisa County, I owa Geol. Survey, vol. XI, pp. 72-82 ; 1901. KINDERHOOK FOSSILS IN LOUISA COUNTY · .................... 1 ........ I x 1 x 1 .. · .... ·1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
Phillipsia f sp ........................................ _ ....... _ ...................................... J ........ 1 ........ 1 ........ 1 x 1
TRILOBITA
Several other exposures of the Kinderhook in Louisa county x
x
x
x
x Several other exposures of the Kinderhook in Louisa county KINDERHOOK NEAR MORNING SUN 67 have been described by J. A. Udden.30
The location and de-
scription of these are taken from his report. Sections in the Bluffs and Creeks North and East of Morning
Sun Section 011J the first c'reek in the Mississippi blruffs north of the county line S01!thwest
of Oakville, t,n the SW. 1,4 of seo. 35, T. 73 N., R. 2 W . (.After Udden.)
BURLINGTON. FEET Section 011J the first c'reek in the Mississippi blruffs north of the county line S01!thwes
of Oakville, t,n the SW. 1,4 of seo. 35, T. 73 N., R. 2 W . (.After Udden.)
BURLINGTON. FEET of Oakville, t,n the SW. 1,4 of seo. 35, T. 73 N., R. 2 W . (.After Udden.)
URLINGTON. FEET
11. Disintegrated crinoidal limestone .................................................... 6
10. Chert ............. _........................................................................................... 1
9. Disintegrat ed crinoidal limestone ............... _................................... 3
8. Blue shale ................................................................................................ 1
7. Hard white crinoidal limestone with chert in upper layers ... _
8
6. Beds grading from a disintegrated yellow shaly residue below
t o a somewhat crumbling crinoidal limestone with much chert
above ......... _............................................................................................... 20
INDERHOOK. 5. Yellow magnesian limestone with irregular bedding above and
occasional quartzose Iloncretions ...................................................... 7
4. Oolitic yellow or brown fossiliferous disintegrated limestone .... 2
3. Fine sandstone, like number 1 ................................................... _ .... _. 1112
2. Compact dark gray limestone, somewhat weathered, showing
small cavities and veins filled with calcite ................................ 3
1. Bluish white fine sandstone, weathering yellow, with casts of
gastropods and lamellibranchs .......................................................... 8 11. Disintegrated crinoidal limestone
h 11. Disintegrated crinoidal limestone .................................................... 6 10. Chert ............. _........................................................................................... 1 9. Disintegrat ed crinoidal limestone ............... _................................... 3
8
Bl
h l
1 9. Disintegrat ed crinoidal limestone ............... _................................... 3
8
Bl
h l
1 9. Disintegrat ed crinoidal limestone
l
h l g
8. Blue shale ................................................................................................ 1 7. Hard white crinoidal limestone with chert in upper layers ... _
8 5. Yellow magnesian limestone with irregular bedding above and
occasional quartzose Iloncretions ...................................................... 7 q
4. Oolitic yellow or brown fossiliferous disintegrated limestone .... 2. Compact dark gray limestone, somewhat weathered, showing
small cavities and veins filled with calcite ................................ 3 1. Bluish white fine sandstone, weathering yellow, with casts of
gastropods and lamellibranchs .......................................................... 8 Seotio7IJ on the Mississippi river bluffs 0711 the second creek north of the c01!nty line
in the east half of seo. 34, T. 73 N ., R. 2 W . (.AfPer Udden). BURLINGTON. FEET Seotio7IJ on the Mississippi river bluffs 0711 the second creek north of the c01!nty lin
in the east half of seo. Sections in the Bluffs and Creeks North and East of Morning
Sun 34, T. 73 N ., R. 2 W . (.AfPer Udden). BURLINGTON. 15. Blue shaly beds, weathering yellow, with some calcareous and
cherty bands above ........................................................................... . 14. Goncealed
...... ~ .......................... _ ............................................................ _
13. Chert ....................................................................................................... . 12. Brown limestone and chert ........................................................... _
11. Brown limestone, disintegrated ......................................................... . 10. Bluish shaly material, with quart z geodes below ......... _ ............ . 9. White crinoidal limestone, with quartz geodes in a shaly seam
8. 7. 6. 5. near base ................................................................................................. . Concealed ................................................................................................. . White crinoidal limestone ................................................................... . Concealed ................................................................................................. . Hard white and yellow crinoidal limestone, moderately f ine·
grained, with layers of chert ............................................................. . KINDERHOOK. 4. Yellow rather fine·grained dolomitic crinoidal limestone, broken
with many joints in upper part ................................. _ ................... _ .. _
3. Oolitic limestone with Spirifer 'IIuM·ionensis, Productella oonoen·
trioa, Spirifro1' (undescr. sp.), .Athyris sp., Zaphrentis sp., and
Orthoceras sp. . .................... _ .. _ ........................................................ _ .... . 2. Yellow or rusty brownish weathered compact limeston:e, with
arenaceous 110ck a,bove ............ _ .............. _ ............................... -- ............ . 1. Bluish fine sandstone, weathering yellow, with teeth of H elo&u81
and casts of brachiopods in upper part. Syringothyris extenuatus
occurs near the top of the lo·west member j also Spirifo1' bipli·
ootus and ProW!wt1!S sp . ................................................................... _ .... . 30
FEET
15' ,
1
21h
1
2
8 ,
4 ,
10
10
3
5
9 Seotio7IJ on the Mississippi river bluffs 0711 the second creek north of the c01!nty line
in the east half of seo. 34, T. 73 N ., R. 2 W . (.AfPer Udden). BURLINGTON. 15. Blue shaly beds, weathering yellow, with some calcareous and
cherty bands above ........................................................................... . 14. Goncealed
...... ~ .......................... _ ............................................................ _
13. Chert ....................................................................................................... . 12. Brown limestone and chert ........................................................... _
11. Brown limestone, disintegrated ......................................................... . 10. Bluish shaly material, with quart z geodes below ......... _ ............ . 9. White crinoidal limestone, with quartz geodes in a shaly seam
8. 7. 6. 5. near base ................................................................................................. . Concealed ................................................................................................. . White crinoidal limestone ................................................................... . Concealed ................................................................................................. . Hard white and yellow crinoidal limestone, moderately f ine·
grained, with layers of chert ............................................................. . KINDERHOOK. 4. Yellow rather fine·grained dolomitic crinoidal limestone, broken
with many joints in upper part ................................. _ ................... _ .. _
3. KINDERHOOK.
5
Y ll NDERHOOK. 5. Yellow limestone, exhibiting oOlitic structure below _________________ . _____ _
4
Blue evenly bedded argillaceous sandstone
FEET
10 4. Blue evenly bedded argillaceous sandstone _________ . ___________________________ _
3
Fi
i
d
ti
ll
b
li
t
di i
2 3. Fine-grained, concretiona.ry yellow or brown limestone, disin-
tegrated
____ . ____________________________________________________________ . ______________________________ _
4 2. Soft fine-grained sandstone, with H eloOOs teeth at base ___ .......... . 1
Bl
f
d
i l
i h
ll
i
d b
d
2 1. Blue soft sandy material, with wavy yellow stained bands con-
taining Chonopectus fischeri, above ................................................... . 6 Section on the east ban7c of a mi,lroad cut at the edge of the ~bpland, t717"ee mile
north of Morning S~m (.After Udden). Section on the east ban7c of a mi,lroad cut at the edge of the ~bpland, t717"ee miles
north of Morning S~m (.After Udden). KINDERHOOK. FEET
5
Di i
d b
i h
i
li
i h A h
i
i 5. Disintegrated brownish magnesian limestone with Athyris in·
crassaPus and Chonetes illinoisensis .................................................... 3
4
Y ll
h
d fi
d
i h Ed
di
b
li
i 4. Yellow weathered fine sandstone, with Edmondia burlingtonensis,
Spirifer b iplioart~ts, Chonopect~ls jischeri, Pwryphm·hync7t,W; stl-iato·
costatum (var), Orthotetes Mweqll,alis ?, Chonll3tes sp., Fenestella
sp. . .. ... ............................................... ............... ................. ,.................... 3 3. Fine blue sandstone, with few fossils .............................................. 10
2
Fi
i
d
bl
d
i h
f
P d1b
l
i 3. Fine blue sandstone, with few fossils ................... 2
Fi
i
d
bl
d
i h
f
P 2. Fine·grained blue sandstone, with casts of Prod1bctus laevi·
costat~ls, Pl·od~LCt~I'S cooperensis, AthYl·is corzyu,lenta, Orthotete8
inaequaUs< i, and other lameJ.libranchs in abundance .................... 2
1
Blue shale
1 Section on a small tributary of Long ereeTc, slTtlth of the U'nter of the SE. 14 of
seo. 13, T. 74 N., R. 5 W.
(After Udden). 2.
Blue soft :fine sandstOll1e, with Orthotetes inaequlJJlis, Chmwpectus
fischeri, AviCYulopecten ca:oli, Produot~ts levicostus, Rhipidmnella 4. Brownish gray compact siliceous rock, possibly chrulrged locally
from a dolomitic limestone by infiltration _.........................................
8
3
Not exposed
2 Kinderhook Sections in Long Creek Basin "Following Long creek west we find bed rock for the first
time near the east line of sec. 13, Tp. 74 N., R. 5 W. From this
point the exposures are almost continuous along the south fork
for two miles, but have a limited vertical range. The Kinder-
hook beds gradually disappear under the overlying limestones. The Buffington fork is rocky a mile from its mouth, and has a
few scattered exposures farther west. The north or main
branch runs through a valley in which the Burlington limestone
is frequently exposed in the bluffs or on the · small tributaries. But with few exceptions these rocky cliffs are less than twenty
feet in height. " ection on a small tributary of Long ereeTc, slTtlth of the U'nter of the SE. 14 of
seo. 13, T. 74 N., R. 5 W. (After Udden). KINDERHOOK. FEET
4. Brownish gray compact siliceous rock, possibly chrulrged locally
from a dolomitic limestone by infiltration _......................................... 8
3. Not exposed ........ _______ . ___ .. _ .. ___ ._. _______ . __ .... _______________________ . __ . ___ . _________ .. ________
2
2. Blue soft :fine sandstOll1e, with Orthotetes inaequlJJlis, Chmwpectus
fischeri, AviCYulopecten ca:oli, Produot~ts levicostus, Rhipidmnella Sections in the Bluffs and Creeks North and East of Morning
Sun Oolitic limestone with Spirifer 'IIuM·ionensis, Productella oonoen·
trioa, Spirifro1' (undescr. sp.), .Athyris sp., Zaphrentis sp., and
Orthoceras sp. . .................... _ .. _ ........................................................ _ .... . 2. Yellow or rusty brownish weathered compact limeston:e, with
arenaceous 110ck a,bove ............ _ .............. _ ............................... -- ............ . 1. Bluish fine sandstone, weathering yellow, with teeth of H elo&u81
and casts of brachiopods in upper part. Syringothyris extenuatus
occurs near the top of the lo·west member j also Spirifo1' bipli·
ootus and ProW!wt1!S sp . ................................................................... _ .... . FEET
15' ,
1
21h
1
2
8 ,
4 ,
10
10
3
5
9 15. Blue shaly beds, weathering yellow, with some calcareous and
cherty bands above ........................................................................... . l d
15' 5. Hard white and yellow crinoidal limestone, moderately f ine·
grained, with layers of chert ............................................................. . DERHOOK. 10 4. Yellow rather fine·grained dolomitic crinoidal limestone, broken
with many joints in upper part ................................. _ ................... _ .. _
li i
li
i h S
f
'
d
ll
10 p
2. Yellow or rusty brownish weathered compact limeston:e, with
arenaceous 110ck a,bove ............ _ .............. _ ............................... -- ............ . 1
5 1. Bluish fine sandstone, weathering yellow, with teeth of H elo&u81
and casts of brachiopods in upper part. Syringothyris extenuatus
occurs near the top of the lo·west member j also Spirifo1' bipli·
ootus and ProW!wt1!S sp . ................................................................... _ .... . 9 MISSISSIPPIAN STRATA OF IOWA 68 Beds 1, 2, 3, and the lower portion of 4 of this section are to
be referred to the Kinderhook. All above belong to the Lower
Burlington. Section in a creeTc one mile sootheast of ElricTc J~mctiolfl. in the sooth part of sec. 29, T. 73 N., R. 2 W. (After Udden) . Section in a creeTc one mile sootheast of ElricTc J~mctiolfl. in the sooth part of sec. 29, T. 73 N., R. 2 W. (After Udden) . KINDERHOOK
FEET 29, T. 73 N., R. 2 W. (After Udden) . KINDERHOOK. 5. Yellow limestone, exhibiting oOlitic structure below _________________ . _____ _
4. Blue evenly bedded argillaceous sandstone _________ . ___________________________ _
3. Fine-grained, concretiona.ry yellow or brown limestone, disin-
tegrated
____ . ____________________________________________________________ . ______________________________ _
2. Soft fine-grained sandstone, with H eloOOs teeth at base ___ .......... . 1. Blue soft sandy material, with wavy yellow stained bands con-
taining Chonopectus fischeri, above ................................................... . Section on a small tributary of Long ereeTc, slTtlth of the U'nter of the SE. 14 of
seo. 13, T. 74 N., R. 5 W.
(After Udden).
KINDERHOOK.
FEET
4. Brownish gray compact siliceous rock, possibly chrulrged locally
from a dolomitic limestone by infiltration _.........................................
8
3. Not exposed ........ _______ . ___ .. _ .. ___ ._. _______ . __ .... _______________________ . __ . ___ . _________ .. ________
2
2.
Blue soft :fine sandstOll1e, with Orthotetes inaequlJJlis, Chmwpectus
fischeri, AviCYulopecten ca:oli, Produot~ts levicostus, Rhipidmnella 3. Not exposed ........ _______ . ___ .. _ .. ___ ._. _______ . __ .... _______________________ . __ . ___ . _________ .. ________
2
Bl
ft fi
d tOll1
ith O th t t
i
lJJli
Ch
t Sections in the Bluffs and Creeks North and East of Morning
Sun FEET
10
2
4
23h
6 KINDERHOOK.
FEET
4. Brownish gray compact siliceous rock, possibly chrulrged locally
from a dolomitic limestone by infiltration _.........................................
8
3. Not exposed ........ _______ . ___ .. _ .. ___ ._. _______ . __ .... _______________________ . __ . ___ . _________ .. ________
2
2.
Blue soft :fine sandstOll1e, with Orthotetes inaequlJJlis, Chmwpectus
fischeri, AviCYulopecten ca:oli, Produot~ts levicostus, Rhipidmnella KINDERHOOK.
5
G KINDERHOOK. 5
G 5. Gray compact limestone
4
C
l d 5. Gray compact limestone
4
C
l d 4. Concealed ............................ 3
B
i h
itt
k 4. Concealed .................................................................................................. 13
3
B
i h
itt
k
3 3. Brownish gray gritty rock
2
Bl
ft fi
d t 2. Blue soft fine sandstone, with casts of Bellerophon bilabiatus,
Straparollus macromphalus, Spirifer s'tlbrot1mdatus, Orthooeras
whitei, Glossites elliptica, Straparoll1ts sp., ]J[odiomorpha i sp.,
B ellerophon (two species) ..................................................... _............. 3
1
Bl
f
k
i h
h l
b l
12 1. Blue arenaceous soft rock, with shale below.................................... 12 Seotian in a tributary of Clifton oreek in the NE. 1,4 of the NE. 1,4 of seo. 27,
T. 75 N., R. 5 W.
(Afterr Udden).
FEET ~NDERHOOK.
5 5. Irregularly bedded, compact brown or gray dolomite; some bra·
chiopods with a few crinoid fragments ............................................ 10
4
R
h
h
d
h
h
b l
b
h
2 4. Rather harder than that below, brown earth
3
S ft
th
if
bl i h
li ht 2. Alternating layers of fine loose s~dston
1
Green clayey shale Seotia'7/; om the west bamk of Long oreele one-fourth mile s011th of the mouth o
Johnny creele, near the center of the south line of sec. 12, T. 74, R. 5 W. (After Udden). KINDERHOOK
FEET eotian in a tributary of Clifton oreek in the NE. 1,4 of the NE. 1,4 of seo. 27,
T. 75 N., R. 5 W.
(Afterr Udden).
FEET
7.
Crinoida:I fossiliferous limestone, with chert seams (exposed far·
ther up in the creek) ..............................................................................
10
6.
Concealed ................................................... _.............................................
4 ,
5.
Chert of oolitic aspect, and with fragments of fossils ..................
14
4. Yellow decayed limestone, with sparse crinoid joints ............... _...
2
3. Chert of oolitic appearance, and containing small fragments of
fossils ... _...................................................................................................
lh
2.
Yellow disintegrated limestone, with scattered joints of crinoids,
a Productus, and various gastropods ......... -.....................................
lh
1. Bluish gray arenaceous rock, with fish teeth near the top and KINDERHOOK ON IOWA RIVER KINDERHOOK ON IOWA RIVER 69 burlingtonensis, Macrodon eochlearris, Orthoeeras whitei, CO'YIllllaria
(mioronema f), Edmo7liPia sp .............................................................. . 1. Soft shale (seen farther east) ............................. _ ............................ . 4
T
Section in the wes·t bluff of Long oreek, south of t1/i{;} center of the NW. 14 of sec. 13, T. 74 N., R. 5 W. (After Udden). ~NDERHOOK. FEET
5. Irregularly bedded, compact brown or gray dolomite; some bra·
chiopods with a few crinoid fragments ............................................ 10
4. Rather harder than that below, brown earthy stone ........................ 2
3. Soft rather uniform bluish gray, light colored fine sandstone,
with lamellibranchs and teeth of Helodus near top ............. _....... 5
2. Alternating layers of fine loose s~dstone ................................. :...... 5
1. Green clayey shale ........................................................... _..................... 3
Seotia'7/; om the west bamk of Long oreele one-fourth mile s011th of the mouth of
Johnny creele, near the center of the south line of sec. 12, T. 74, R. 5 W. (After Udden). KINDERHOOK. FEET
5. Gray compact limestone ............... _ ................ _ .............................. _..... 8
4. Concealed .................................................................................................. 13
3. Brownish gray gritty rock ................... :................................................ 3
2. Blue soft fine sandstone, with casts of Bellerophon bilabiatus,
Straparollus macromphalus, Spirifer s'tlbrot1mdatus, Orthooeras
whitei, Glossites elliptica, Straparoll1ts sp., ]J[odiomorpha i sp.,
B ellerophon (two species) ..................................................... _............. 3
1. Blue arenaceous soft rock, with shale below.................................... 12 burlingtonensis, Macrodon eochlearris, Orthoeeras whitei, CO'YIllllaria burlingtonensis, Macrodon eochlearris, Orthoeeras whitei, CO'YIllllaria
(mioronema f), Edmo7liPia sp .............................................................. . 1
4
T g
,
,
,
(mioronema f), Edmo7liPia sp .............................................................. . 1
S f
h l
(
f
h
)
4
T g
(mioronema f), Edmo7liPia sp .............................................................. . 1
S f
h l
(
f
h
)
4
T (mioronema f), Edmo7liPia sp ... 1
S f
h l
(
f
h
) 1. Soft shale (seen farther east) ............................. _ ............................ . T 1. Soft shale (seen farther east) Section in the wes·t bluff of Long oreek, south of t1/i{;} center of the NW. 14 of sec. 13, T. 74 N., R. 5 W. (After Udden). Sections on Clifton Creek and Iowa River "N orth of Long creek basin the drift rapidly increases in
thjclmess and the bed rock js rarely exposed. It has been ob-
served only in sections 22 and 27, Tp. 75 N., R. V. 'l-l., and in
.and near the bluffs of the Iowa river in sections 16 and 17, Tp. 76 N., R. V. W. At th~ s latter place the blue Kinderhook shale
is exposed in the bank of the river, rising some five · or SL,{ feet
above the water for a distance of a few rods. It is covered by
the shale and sandstone of the coal measures. Over most of
this northern territory the Burlington limestone has been re-
moved and the unprotected Kinderhook beds have been deeply
eroded." Seotian in a tributary of Clifton oreek in the NE. 1,4 of the NE. 1,4 of seo. 27,
T. 75 N., R. 5 W. (Afterr Udden). FEET
7. Crinoida:I fossiliferous limestone, with chert seams (exposed far·
ther up in the creek) .............................................................................. 10
6. Concealed ................................................... _............................................. 4 ,
5. Chert of oolitic aspect, and with fragments of fossils .................. 14
4. Yellow decayed limestone, with sparse crinoid joints ............... _... 2
3. Chert of oolitic appearance, and containing small fragments of
fossils ... _................................................................................................... lh
2. Yellow disintegrated limestone, with scattered joints of crinoids,
a Productus, and various gastropods ......... -..................................... lh
1. Bluish gray arenaceous rock, with fish teeth near the top and 70 MISSISSIPPIAN STRATA OF IOWA various gastropods; also A. thyris corpulenta, ProducPus
I1UTti-
rostra, Productella nwmmularis, Orthoceras iIooequalis, EdmQ11,dia
burlingtQ11,en&i&,
Eumetria
altirostris,
Porcellia. obliqwinoda,
Grammy&ia plena, Bellerophon (undescr 7) and a Platyschisrma
4 Correlation of the Kinderhook Beds of Lowisa Oownty Only the upper portion of the basal shale is exposed in this
county though the lower beds have been penetrated by the drill
at several localities. Its total thickness is reported to be as
much as 180 feet. The sandstone bed above, which is correlated
with the Ohonopectus . sandstone of the Kinderhook beds at
Burlington, is very similar in character to the equivalent bed at
Burlington and bears essentially the same fossils, though its
thickness is less than half as great. Bed 3 of the Burlington section has not been recognized in
any of the Kinderhook exposures of Louisa county. This is not
surprising since it has a thickness of only eight inches at Bur-
lington. 82 Jour. Geol., vol. XVII, pp_ 273, 274; 1909. 31 Iowa Geol. SUl'vey, vol. IX, pp. 289-303; 1898. liS Iowa Geol. Survey, vol. IX, p. 302; 1898. FEET
4.
Limestone, ferruginous, arenaceous in places, fine'grained,
red, containing numerous casts of fossils, and with thin
chert layers two to eight inches thick, also
fossiliferou~..... .
10
3.
Sandstone. or gritstone,. very fine'grained, white to buff,
very fossiliferous ................................................. _...........................
18
2.
Limestone, fine·grained, non·fossiliferous ........................... _....... 1/6
1. Shale, argillaceous, dark blue to drab, almost black in places 12 S4 Jour. Geol.. vol. XVII. pp. 273, 274; 1909.
35 Geololrr of Washington County. Iowa. Geol. Survey. vol. V. p. 127; 1896. S4 Jour. Geol.. vol. XVII. pp. 273, 274; 1909. Sections on Clifton Creek and Iowa River Beds 4 and 5 of the Kinderhook at Burlington are present in
Louisa county but are more attenuated and less typically de-
veloped. For example, the lithographic limestone (bed 4)"
which is ten feet thick at Burlington, is represented in this area
by only three and one-half feet of brownish dolomitic limestone. The oOlitic limestone and the overlying brownish dolomitic
limestone of the Louisa county sections are easily identified as
beds 6 and 7 of the Burlington section. They have essentially
the same development in the two areas. • Muscatine Oounty.-No strata of Kinderhook age are known
positively to exist jn Muscatine county. However, the Sweet-
land Creek beds of Udden31 which were referred by him to the
Upper Devonian may possibly be an outlier of the basal Kinder-
hook as suggested by Weller. 32 This deposit consists of interbed-
ded dark shale, green shale and argillaceous magnesian lime-
stone with a maximum thickness of about forty-eight feet. It is
disconformable with Cedar Valley limestone of Devonian age
below and with Pennsylvanian sandstone above. Udden38 lists the following fossils from the Sweetland Creek
beds: 71 2.
Limestone, fine·grained, non·fossiliferous ...
Sh l
ill
d
k bl
d
b
l Section of Kinderhook beds at Maple Mill (After Bain). Revised section of Kilnderhook beds at Maple Mill. 7. 6. 5. 4. 3. 2. 1. Revised section of Kilnderhook beds at Maple Mill. FEET
INCHES
Drift ... _ .................................................................................. _ .... _....... 2
Limestone, yellowish, dolomitic; speckled with darker patches
in lower part; massive; with occasional bands of darker
chert ............................................................................................ _ ........ 16
Limestone, brownish, speckled, tough, dolomitic; of a ' darker
color than bed above; in some places showing indications of
obscure oolitic texture ... _ ...................... _ .......... _ .... _....................... 2
4
Sandstone, ash·colored, fine· grained, shaly in middle part;
grading gradually upward into the bed above ........................ 2
Limestone, brownish to reddish; dense and tough when
fresh but weathering to soft thin layers. No recognizable
fossils found ....................... _............................................................... 1
8
Sandstone, ash· colored, :fine-grained, soft, with molds and
casts of fossils .................................................................................... 13
Concealed to level of river .......................................................... 13
6 1. Concealed to level of river It will be noted that beds 1 and 2 of Bain's section are novv
concealed and that his bed number 3 is divided into three mem-
bers (bed!s 2, 3, and 4) in the writer's section. The shale ex-
posed at the time of Bain's visit was correlated by him with the
basal shale (bed 1) of the Kinderhook section at Burlington, al-
though he was not able to secure fossils to substantiate this cor-
relation. This division of the Kinderhook has been designated by
Bain the Maple Mill shale from the fact that it is well developed
at this locality. He reports36 that the same shale outcrops along
the bank of English river southeast of Kalona (Tp. 77 N., R. 7
W., sec. 16) where it has an exposed thickness of twelve feet. The sandstone member of Bain's section (bed 3) was named
by him, the English River gritstone, and was regarded as the
equivalent of the Chonopect~ts sandstone which occupies a simi-
lar position above the basal shale at Burlington. The fauna of
this member has been studied by Weller.37
In correlating it
with the beds at Burlington he says: "This fauna of the English River Grit is essentially that of
the Chonopectus bed at Burlington, but with certain modifica-
tions. 36 Op. cit., p. 133.
37 Jour. Geo!., vo!. 13, pp. 617 ff.; 1905. KINDERHOOK AT MAPLE HILL KINDERHOOK AT MAPLE HILL Solenocaris strigata Meek ~
Ptyctqdus calceolus M. and W. Rhynchodus cf. ·excayatus Newb. Synthetodus
Impressions of plants. Lingula cf. melie Hall
Lingula cf. nuda Hall
Lingula subspatulata M. and W. Lingula sp. undet. Gastropod
Spathiocaris emersoni Clarke Spathiocaris emersoni Clarke Weller34 calls attention to the fact that Ptyctodus calceolus
occurs in beds known to be basal Kinderhook at several locali-
ties in Missouri and that a Spathiocaris is represented both in
the Upper Devonian black shale of southern Illinois and in a
basal Kinderhook shale in southwestern Missouri. Further
study of the Sweetland Creek beds by Dr. A. O. Thoma~ and
the writer failed to bring to light additional species sufficiently
diagnostic to fix thE' age of the formation more definit<~]y. ~rhe
problem is the more difficult because there are no known expos-
ures of the basal Kinderhook in southeastern Iowa which can
be compared with the Sweetland Creek beds. Washington County.-The area underlain by the Kinderhook
in Washington county is confined to its northeastern and ex-
treme northern parts. The best exposures appear in the valley
of English river, though occasional small outcrops occur along
the tributaries of this stream and on Goose creek and Whiskey
run. Probably the most compl~te section of the Kinderhook in this
county is the exposure at Maple Mill on the south bank of Eng-
lish river, a short distance south of the center of section 8 of
Lime Creek township. This has been described by Bain35 as
follows: Section of Kinderhook beds at Maple Mill (After Bain). FEET
4. Limestone, ferruginous, arenaceous in places, fine'grained,
red, containing numerous casts of fossils, and with thin
chert layers two to eight inches thick, also
fossiliferou~..... . 10
3. Sandstone. or gritstone,. very fine'grained, white to buff,
very fossiliferous ................................................. _........................... 18
2. Limestone, fine·grained, non·fossiliferous ........................... _....... 1/6
1. Shale, argillaceous, dark blue to drab, almost black in places 12 The "vriter's section of the Kinderhook at Maple Mill differs
only in detail from that of Bain. MISSISSIPPIAN STRATA OF IOWA 72 Revised section of Kilnderhook beds at Maple Mill. Chonopect~ts fischeri, although present in the fauna, is
not one of the most abundant species; in fact, although most of
the species at Maple Mill can be identified with Burlington
forms, many of those that are common at Burlington are rare
on English river, and vice versa, rare species at Burlington are
in several instances more common on English river." . The writer has little to add to the above correlations further FOSSILS FROM MAPLE MILL 73 than to suggest that the Chonopectu8 sandstone of Burlington
is represented only by the lower thirteen feet of Bain's bed 3,
corresponding to bed 2 of the revised section. Following this
interpretation, the thin dolomitic limestone member (bed 3)
and the sandstone above (bed 4), represent the attenuated rep-
resentatives of the "Lithographic limestone" (bed 4) and the
upper sandstone (bed 5) of the Burlington section. The marked
thinning of these beds in Louisa county is in conformity with
this view. It must be admitted, however, that the faunas of the
uppermost beds are not sufficient to ,make this correlation cer·
tain. The fauna of bed 2 of the revised section at Maple Mill is as
follows: IMt of fossils from bed e, Maple Mill section, Washington county,
VERMES-
Scalarituba missouri6Ilsis Weller
BRAcmoPoDA-
Schellwienella , sp. Chonetes sp. Mytilarea oceidentalis (W. and W.)
Ptcronites whitei (Win.)
Leiopterla spinalata (Win.)
Leiopteria sp. A viculopecten (two species)
Pernopectcn cooperensis (Shum.)
Goniophora jennae (Win.)
OhI:mopootus :fi.seheri (N, and P.)
Productella JlJu=ulal'is (Win.)
Productella conc6Iltriea (Hall)
Productus mesicostalis Weller
Productus ovatus Hall
SCAPHOPODA-
Dentalium grandaevum Win. GASTROPODA-
Productus arcuatus Hall
Productus curtirostris Win. Schizophoria sp. . Pal'yphorhynchus transversum Weller
Allorhynchus heteropsis (Win.) 7
Spirifer biplicatus Hall
Spirifer maplelhSis Weller
Syringothyris extenuatus
(Hall)
Eumetria altirostris (White)
Composita 7 corpulenta (Win.)
PELECYPODA-
Poreellia obliquinoda White
Murchisonia sp. Bellerophon bilabiatus W. and W. Bellerophon vinculatus W. and W. Bellerophon sp. Euphemus sp. Straparollllil a=o.n (W. and W.)
Straparollus sp. Edmondia jejunis (Win.)
Sphenotus iowensis (Win.)
Sphenotus sp. Platyschisma barrisi (Win.)
Naticopsis depressus Win. Strophostylus bivolve (W. and W.)
CEPHALOPODA-
Gra=ysia plena Hall
Grammysia amygdalinus (Win.)
Palaeoneilo microdonta (Win.)
ParallelodoJll cochlearis (Win.)
Orthoceras whitei Win. Orthoceras heterocinctum Win. Phragmoeeras expansum Win. TRILOBITA-
Phillip.sia , sp.' IMt of fossils from bed e, Maple Mill section, Washington county,
ES-
alarituba missouri6Ilsis Weller
oPoDA-
hellwienella , sp. onetes sp. Mytilarea oceidentalis (W. and W.)
Ptcronites whitei (Win.)
Leiopterla spinalata (Win.)
Leiopteria sp. Revised section of Kilnderhook beds at Maple Mill. A viculopecten (two species)
Pernopectcn cooperensis (Shum.)
Goniophora jennae (Win.)
I:mopootus :fi.seheri (N, and P.)
oductella JlJu=ulal'is (Win.)
oductella conc6Iltriea (Hall)
oductus mesicostalis Weller
oductus ovatus Hall
SCAPHOPODA-
Dentalium grandaevum Win. GASTROPODA-
oductus arcuatus Hall
oductus curtirostris Win. hizophoria sp. . 'yphorhynchus transversum Weller
orhynchus heteropsis (Win.) 7
irifer biplicatus Hall
irifer maplelhSis Weller
ringothyris extenuatus
(Hall)
metria altirostris (White)
mposita 7 corpulenta (Win.)
PODA-
Poreellia obliquinoda White
Murchisonia sp. Bellerophon bilabiatus W. and W. Bellerophon vinculatus W. and W. Bellerophon sp. Euphemus sp. Straparollllil a=o.n (W. and W.)
Straparollus sp. mondia jejunis (Win.)
henotus iowensis (Win.)
henotus sp. Platyschisma barrisi (Win.)
Naticopsis depressus Win. Strophostylus bivolve (W. and W.)
CEPHALOPODA-
a=ysia plena Hall
ammysia amygdalinus (Win.)
aeoneilo microdonta (Win.)
allelodoJll cochlearis (Win.)
Orthoceras whitei Win. Orthoceras heterocinctum Win. Phragmoeeras expansum Win. TRILOBITA-
Phillip.sia , sp.' IMt of fossils from bed e, Maple
VERMES-
Scalarituba missouri6Ilsis Weller
BRAcmoPoDA-
Schellwienella , sp. Chonetes sp. OhI:mopootus :fi.seheri (N, and P.)
Productella JlJu=ulal'is (Win.)
Productella conc6Iltriea (Hall)
Productus mesicostalis Weller
Productus ovatus Hall
Productus arcuatus Hall
Productus curtirostris Win. Schizophoria sp. . Pal'yphorhynchus transversum Weller
Allorhynchus heteropsis (Win.) 7
Spirifer biplicatus Hall
Spirifer maplelhSis Weller
Syringothyris extenuatus
(Hall)
Eumetria altirostris (White)
Composita 7 corpulenta (Win.)
PELECYPODA-
Edmondia jejunis (Win.)
Sphenotus iowensis (Win.)
Sphenotus sp. Gra=ysia plena Hall
Grammysia amygdalinus (Win.)
Palaeoneilo microdonta (Win.)
ParallelodoJll cochlearis (Win.) Phillip.sia , sp.' The brownish dolomitic limestone (bed 3) has not yielded
fossils sufficiently well preserved to be specifically identified, but
a few species have been collected from the fine sandstone of bed
4 above. T.hese are listed below. MISSISSIPPIAN STRATA OF IOWA 74 List of fossils from bed 4, Maple Mill section, Washington county. List of fossils from bed 4, Maple Mill section, Washington county. BRAomOPODA-
Schellwienella ~ sp. Chonetes. Syringothyris , sp. ReticuIaria cooperensis (Swallow)
Nucleospira 'barrisi White
Schizophoria chouteauensis Weller ~
Spirifer platynotus Weller
PELEOYPODA-
Pernopecten cooperensis (Shum.) BRAomOPODA-
Schellwienella ~ sp. Chonetes. Syringothyris , sp. ReticuIaria cooperensis (Swallow)
Nucleospira 'barrisi White
Schizophoria chouteauensis Weller ~
Spirifer platynotus Weller
PELEOYPODA-
Pernopecten cooperensis (Shum.) Syringothyris , sp. R
i
I
i The brownish dolomitic limestone capping the section at
Maple Mill represented by bed 4 of Bain's section and bed 6 of
the reVised one is the topmost member of the Kinderhook in
Washington county. List of fossils from beds 8 and 10 of Wassonville Mill section, Washington co'unty.
BRAOHIOPODA-
Spiriferina solidirostris White
Schellwienella crenulicostata
Chonetes logani N. and P.
Chonetes multicosta Win.
Weller
Spirifer platy notus Weller
P roductus arcuatus H all
Camarotoechia chouteauensis We·ller f
38 I owa Geol. Survey, vol. V, p. 134; 1896.
PELEOYPODA-
Sphenotus cylindricus (W:iu.) ,
Lcda sp.
Parallelodon parvus (W. and W.) Revised section of Kilnderhook beds at Maple Mill. This member attains its typical develop-
ment at the old vVassonville mill one and one-half miles west () E
the above described exposure. Hence the name Wassonville
limestone as applied by Bain. 38 38 I owa Geol. Survey, vol. V, p. 134; 1896. 390p. cit., p. 133.
40 Op. cit., p. 133. WASSONVILLE LIMESTONE WASSONVILLE LIMESTONE 75 A viculopecten sp. P elecypods
(several
undetermined
species)
Bucanopsis sp. Straparollus sp. Gastropods
(several
undetermined
SCAPHOPODA-
Dentalium gram.daevum Wm. GASTROPODA-
Bellerophon sp. species)
CEPHALOPODA-
Orthoceras sp. Another excellent exposure of the Wassonville limestone is
shown in an abandoned quarry on the opposite side of the river
at the head of the big bend (Tp. 77 N., R. 8 W., sec. 6, SE.1/4). The succession of beds at this place is indicated below. Section of Wassonville limestone at the head of the big bend. Section of Wassonville limestone at the head of the big bend. FEET
INCHES
8. Drift ------__________ . ________________________________________________________________ .. _. ________ ... __ 3 . 7_
Limestone, brownish, dolomitic, soft ______ . __________________ .... _____________ .. 9
6
.6_ Chert, in the form of a band of nodules . __ . ___________ .. _. _________ ... ___
4
5. Limestone, brownish yellow, dolomitic, massive ___ . ____ . ___________ . 7
4. Chert, in the form of a band of nodules _____________________ . __________ . 3
3. Limestone, yellowish, massive, dolomitic _______________ . ___________ ._________
5
6
2. Chert, in the form of a discontinuous band, slightly coarser-
grained than that in the bedS above ______________________________________
2
1. . Limestone, yellowish to brownish, m'<l.SSive, soft, dolomitic;
bearing a few poorly preserved fossils similar to those in the
chert just above. Exposed _________________________________________ .____________________
2 The Wassonville limestone is again ,veIl exposed in an aband-
oned railway quarry three miles northeast of Wellman. BainslI
describes this section as follows: "In the old Burlington, Cedar Rapids andN orthern railway
quarry (Tp. 77 N., R. 8 W. Sec. 16) the limestone layers are ex-
posed twenty feet thick, with the base twenty feet above the
bridge on Smith creek. 'l'he stone is of the usual earthy mag-
nesian character, and runs in ledges two to four feet thick, sep-
arated by thin layers of chert. The Augusta (BUrlington) is
reported to occur immediately above the top .' of the quarry,
though it is not now exposed". The contact relations of the W assonville limestone with the
overlying Burlington limestone are not certainly known, since
no section showing the actual contact of the two formations is
now exposed in the region. Section at Wassonville Mill. Section at Wassonville Mill. FEET
INCHES
15. Drift ..................... ____________________________ _____ . _______________________ ..... _ .. ____ . _____ .... __
1
14. Shale, brownish, dolomitic, much weathered _____ .. ____________ . ___ . __ . 2
13. Limestone, soit, yellowish,
dolomitic.;
showing fine,
close
stratification on weathered surface; bearing a few silicified
fragments of crinoid stems _____ ___________ . _______________ .. _____________ . _______ ._._
5
6
12. Chert, white, nonfossiliferous; in the form of
lense~ and
nodules
________________ . _____ . __ . ___ . _____ _____________________ ._ .. _. _______ . ____ ... ____________ . __ ._.. 3
11. Limestone, buff, dolomitic, thin-bedded ______ . ____ . __ .. ____ .. ___ . _____ .____
6
10. Band of soft white fossiliferous chert nodules ........ _._. _____ ..... 3
9. Limestone, massive, yellowish, dolomitic __________ . _____________ ._ ... _____
3
6
8. Band of soft white fossiliferous chert nodules __________ .___________
3
7. Limestone, massive, yellowish, dolomitic .... _____________________ . ____ ._._.. 7
6
6. Band of white fossiliferous chert nodules ______________ . ___________________ . 3
5. Limestone, soft, massive, yellowish, dolomitic _____ ... _ .... _ ...... ____ . 5
2 . 4. Limestone, soft, massive, brownish, dolomitic _________ . _____ ._ .. ___ . ___ .... 2
6
3. Limestone, tough, brownish, dolomitic, weathering int.o thin,
nodular layers . __ .. __ .. ____________________________ . __ .... __ .... __ ... ___ .. ____ ..... _____ ._. __ . __ .___
2
2. Sandstone, ash-colored, fine·grained; ·exposed ... _ .. _____ . _____ . _________ . 4
8
1. Concea~ed to level of water in river . _____________ ._. _____ ._. ___ . __ . ____ .___
5
3 Beds 5 to 15 of the above section are exposed in a quarry
back of the mill, while beds 1 to 4 are shown in the river bank
just below. The dolomitic limestone layers are nearly barren of
identifiable fossils, but certain of the nodular chert bands, espe-
cially beds 8 and 10,. contain many excellently preserved speci-
mens. The following fossils were collected from the cherts: WASSONVILLE LIMESTONE Bain40 refers to a possible contact
section on Smith creek as follows: "Southeast of W elhnan the creek soon cuts through the
Augusta into the Kinderhook.- In section 19 (Tp. 77 N., R. 8 MISSISSIPPIAN STRATA OF IOWA 76 W.) the latter was encountered in the base of a quarry on a
level with the stream". W.) the latter was encountered in the base of a quarry on a
level with the stream". At the time of the writer's visit in the summer of 1915, this
section was no longer exposed. Th
l ti
f th
V
ill li
t
ith th
Ki d The correlation of the vVassonville limestone with the Kinder-
hook at Burlington is attended with some difficulty, owing in
part to lack of lithologic similarity and in part to faunal differ-
ences. Thus, we hav~ at least thirty-five feet of yellowish
cherty dolomite at the top of the Kinderhook in this region,
while at Burlington the only bed which resembles this lithologic-
ally is a zone five feet in thickness at the very top of the section
(bed 7) . Again, there are many undescribed species of pelecy-
pods and· gastropods in the Wassonville limestone which have
not been found in the uppermost Kinderhook beds at Burling-
ton. Upon the basis of the brachiopod faunas of the two re-
gions, however, it is possible to say with a reasonable degree of
certainty that the Wassonville represents beds 6 and 7, and pos-
sibly part of bed 5, of the Burlington section. All of the brach-
iopods of the Wassonville, with the exception of Spiriter platy-
notus, which ranges from bed 2 to bed 7, at Burlington, are
confined -to the three uppermost beds at the latter locality. Th
k d thi
i
f th
l
b
f th
Ki d
h
k The marked thinning of the lower members of the Kinderhook
is continued from Louisa county into Washington. The extent
of the attenuation of the basal shale in this region is not known,
but evidently it is considerable, for a deep boring at Sigourney
in Keokuk county, which borders Washington on the west,
shows this member to be only 198 feet thick as compared to a
thickness of 300 feet at Burlington. n Iowa. Geol. Survey, TOI. XX, pp. 254, 255. WASSONVILLE LIMESTONE The sandstone above this
(English River gritstone) is only a little more than one-half as
thick as at Burlington, and the limestone and s;:tndstone beds
directly above are much less than one-half as thick as their
probable equivalents in the latter region. Th
hi h
b
f th
Ki d
h
k
th
th
h
d The higher members of the Kinderhook, on the other hand,
are dii:ltinctly thicker in vVashington county than the beds of the
same horizon both in Louisa county and at Burlington. It is
safe to say that the Wassonville limestone is represented by not
'more than ten to twelve feet of strata at Burlington. A thicken-
ing of the higher limestone beds, which carry a Chouteau fauna,
and a thinning of the lower clastic ones is a persistent feature KINDERHOOK OF POWESHIEK COUNTY 77 of the Kinderhook as it is traced from southeastern Iowa north-
westward to the northern part of the state. The belt of Kinderhook rocks extending northwest from
Washington county does not appear again at the surface, ex-
cept for a small exposure in Iowa county, until Marshall and
Tama counties are reached. Poweshiek County.-"\Vith reference to the Kinderhook of
Poweshiek county Stookey41 says: "N 0 rocks of this stage appear at the surface in Poweshiek
county. All that area where they form the country rock is cov-
ered to a depth of from two hundred to four hundred feet with
glacial deposits, through which the streams have nowhere cut. All that is positively known of rocks of this age in this county
is obtained from the meager records of wells that have been
sunk here and there into the rocks. h
i
ll
ll
h
b d
f li
d
h l The Grinnell wells show a body of limestone and shale more
than three hundred fifty feet in thickness next below the drift
that is regarded as chiefly representing this stage. Wells in the
vicinity of Brooklyn penetrate similar deposits. In the north-
west quarter of section 12, Bear Creek township, the Talbott
and Thompson well shows the following as reported by W. W. Shannon of Brooklyn: FEET
Pleistocene deposits ............................................................................... ....... 355
Shale .................................................................................................................. 175
Limestone and shale (water) ...................................................................... 76 Pleistocene deposits
Shale In section 16, Bear Creek township, on the Newkirk farm the
well is reported as follows : FEET
Yellow and blue clay ................................................................... "'.'.'.'.' ... WASSONVILLE LIMESTONE '.'
350
'Soapstone' ........................................................................................................ 75
Limestone, honeycombed .............................................................................. 125 FEET
Yellow and blue clay ................................................................... "'.'.'.'.' ... '.'
350
'Soapstone' ........................................................................................................ 75
Limestone, honeycombed .............................................................................. 125 Yellow and blue clay
'Soapstone' Yellow and blue clay
'Soapstone' The nearest surface exposure of Kinderhook rocks to the east
is at Amana in Iowa county, near the Iowa river. Along the
same river in Marshall and Tama counties to the north 'expos-
ures are found that have been described in detail in the reports
by Beyer and Savage. It is not possible to map accurately the
limits of this terrane in Poweshiek county, but it is safe to say
that the area to the north and east of the divide between the
Iowa river basin and that of the North Skunk has as its country
rock the Kinderhook deposits." 78 MISSISSIPPIAN STRATA OF IOWA Iowa County.-The Kinderhook of Iowa county is described
by Stookey42 as follows: "At Amana in the bank of Price creek is an exposure of lime-
stone, the only one within the limits of the county. The area
of exposure is limited to one or two square rods. The rock is
brown to buff in . color, irregularly and thinly bedded, and
cherty. Both the chert anrllimestone are fossiliferous. Spirifer
biplicatus and two or three species of Productus are among the
fossils. This is the only exposure of Kinderhook rocks in Iowa
county. The discovery of rocks of this age so far to the east-
ward is a matter of surprise, and carries the margin of the
Kinderhook terrane much farther to the northeastward than
was believed to be the case. It is a general law of outerop in
Iowa that the margins of the terranes run in a northwest-south-
east direction. It seems a proper inference that the rocks un-
rlerlying the drift to the west and south belong to the Kinder-
hook stage. h
i
h
l
d
h
f
h Everywhere in the central and northwestern parts of the
county the glacial deposits overlie a dark shale' of considerable
thiclmess, evidently the upper member of the Kinderhook stage. This deposit is referred to by well drillers as 'soapstone',
and is dreaded by them as it is barren of water, and often, ac-
cording to their reports, as much as three hundred feet in
thiclmess. WASSONVILLE LIMESTONE In the southwest part of Benton county the drill
strikes the same shale, though its thickness is not so great in
that county." Jasper County.-Referring to the Kinderhook beds in this
county, Williams43 says: "In Jasper county the area underlain by the Kinderhook
rocks cannot be definitely outlined as these materials are deeply
buried beneath the glacial deposits. The area outlined as
Kinderhook on the map is determined by projecting the line of
the strilre from outcrops in Marshall county." &2 Iowa Geol. Survey. vol. XX. p. 167.
&3 Iowa Geol. Survey, vol. XV, p . 809. &3 Iowa Geol. Survey, vol. XV, p . 809. &2 Iowa Geol. Survey. vol. XX. p. 167.
&3 I
G
l
S
l
XV
809 KINDERHOOK OF C:ENTRAL row A General statement.-The area underlain by the Kinderhook
in this section of the state comprises roughly the eastern half
of Marshall county, the whole of Tama county, with the excep-
tion of a small triangular area in the extreme northeast corner
which is underlain by the Devonian and the southwestern two- WELL AT MA..RSH.ALLTOWN 79 thirds of Grundy county, excepting a small area of Pennsylvan-
ian in the western part. thirds of Grundy county, excepting a small area of Pennsylvan-
ian in the western part. The KinderhoC?k of this area shows a marked variation both
lithologically' and faunally from the series as it is developed
elsewhere in the state, and this has rendered difficult the exact
correlation of the beds. Owen,44 as a result of his study of the
formations, referred the beds in question to the Subcarbonifer~
ous. Still later vVhitney45 described the deposits in this part of
the state and referred them to the Carboniferous upon the b~sis
of their fauna. In his Geology of Iowa, Volume II, page 312;
1870, vVhite describes the exposures near LeGrand and refers
the beds to the Kinderhook formation. Wachsmuth and
Springer46 later devoted some space to the strata in this area
in connection with their description of the munerous species of
crinoids and blastoids from LeGrand, Iowa. More recent reports on the area are Beyer's Geology of Mar-
shall county47 and Savage's Geology of Tama county.48 The lower beds of the Kinderhook formation are not exposed
in central Iowa, though we have some knowledge of their char-
acter as a result of Norton's description of the cuttings of a
deep well at Marshalltown which was published by Beyer.49 The upper portion of the record is as follows: FEET
Limestone, light gray, in fine sand, with many angular frauments
of limpid quartz at 68 feet _________________________________________ .. _ .. ___ .. ___ .. _______
70
Limestone, light yellow, compact, earthy lustre, three samples ________
45
Limestone, brown, crystalline, cherty at 115 feet ____________________ .________
30
Shale, soft, light green, calcareous ________________________________________________________
175
Limestone , no samples (Devonian) ________________________________________ .. __ .. ______
145 It will be observed that the beds' above the iimestone identi-
fied as Devonian are composed of 175 feet of shale, overlain by
145 feet of limestone. The shale beds were referred provision-
ally by Beyer to the basal Kinderhook and the writer has no
reason to question this correlation. 44 Geological Survey Wisconsin, Iowa and Minnesota, pp. 98-102; 1852.
45 Geology of Iowa, vol. I, pt. I, pp. 267, 268; 1858.
~6 Geol. Survey Illinois, vol. VIII, pp. 155-20S; lSg0.
47 Iowa Geol. Survey, vol. VII, pp. 197-262; 1897.
48 Iowa Geol. Survey, vol. XIII, p. 213 ff.; 1903.
49 Iowa Geol. Survey, vol. VII, pp. 211, 212; lS97. 48 Iowa Geol. Survey, vol. XIII, p. 213 ff.; 1903.
l
l 47 Iowa Geol. Survey, vol. VII, pp. 197-262; 1897. 44 Geological Survey Wisconsin, Iowa and Minnesota, pp. 98-102; 1852.
45 Geology of Iowa
vol
I
pt
I
pp
267
268; 1858 49 Iowa Geol. Survey, vol. VII, pp. 211, 212; lS97. 45 Geology of Iowa, vol. I, pt. I, pp. 267, 268; 1858. FEET
Limestone, light gray, in fine sand, with many angular frauments
of limpid quartz at 68 feet _________________________________________ .. _ .. ___ .. ___ .. _______
70
Limestone, light yellow, compact, earthy lustre, three samples ________
45
Limestone, brown, crystalline, cherty at 115 feet ____________________ .________
30
Shale, soft, light green, calcareous ________________________________________________________
175
Limestone , no samples (Devonian) ________________________________________ .. __ .. ______
145 Geol. Survey Illinois, vol. VIII, pp. 155-20S; lSg0. 44 Geological Survey Wisconsin, Iowa and Minnesota, pp
45 Geology of Iowa, vol. I, pt. I, pp. 267, 268; 1858.
~6 Geol
Survey Illinois
vol
VIII
pp
155 20S; lSg0 KINDERHOOK OF C:ENTRAL row A The overlying limestones
belong to the formations designated as the LeGrand beds by
Beyer because of their exposure in the quarries near the town MISSISSIPPIAN STRATA OF IOWA 80 of this name. It IS possible also that the Marshalltown shales
of Beyer are represented in the upper part of the section. of this name. It IS possible also that the Marshalltown shales
of Beyer are represented in the upper part of the section. h ll C
h
i d
h
k
f
h ll Marshall County.--The Kinderhook area of Marshall county
occupies approximately its eastern half, the western part being
underlain by the" Coal Measures." The most important exposures of the series in this county are
in the quarries near LeGrand inthe northern part of LeGrand
t0W11ship, though outcrops of lesser importance appear at Rock-
ton in Marion township, and near Marshalltown in Linn town-
ship. LEGRAND BEDS.-A number of years ago several quarries
were worked a short distance north and northwest of LeGrand
by the LeGrand Quarry Company. The sections are somewhat
similar in all of these, but the succession is most complete and
can be most satisfactorily studied in the two east quarries. Low-
er beds are exposed in these than in any other outcrops in the
county. Th
i
i
h
h
f I
i
i
h The succession in the east quarry, north of Iowa river, in the
extreme northwest corner of section 1 of LeGrand township, IS
as follo"ys: ~O 10 ...... Geol. Survey, TO!. VII, p. 214; 1697. FOSSILS FROM LEGRAND BEDS FOSSILS FROM LEGRAND BEDS 81' lIist of fossils from bed 1 of east quarry. ANTHOZOA·-
Zaphrentis sp.
BR.ACHIOPODA-
Productus sp.
Productus sp.
Orthotetes
~ sp.
Rhipidomella sp.
Composita sp. Section in the east qUMry. Section in the east qUMry. FEET
INCHES
Drift ..................................................................................................... . 6. Limestone, soft, buff, magnesian, much weathered; somewhat
nodular; no fossils noted .............................................................. 2
5. Limestone, brownish, sub crystalline to crinoidal; some layers
in upper half slightly oolitic ........................................................ 12
5
4. Limestone. gray, magnesian, weathering buff; upper part
thin bedded; lower half more massive when fresh but weath·
ering into thin layers; with a rather pm'sistent three inch
chert band six and one·half feet below the top; interbedd,ed
with a few seams and layers of brownish, crinoidal limestone
ranging from oua inch to twelve inches in thickness; thin
seams of oolitic limestone appear in the lower part of the
upper four feet of the bed. With .some thin fossilj£erous
seams ...................................................................................................... 9
8
3. Limestooo, ash· colored to buff, magnesia!Il; subcrystaUine;
cleaving into thin layers'; locally grading in part into brown·
ish, crinoidal limestone; the main crinoid zone ; surface of
layers in places showing faint ripple marks; with styJolytic
seams
................................. _ ........................................................ _..... 5
2. Limestone, buff to yellowish, magnesian; with nodular len·
tils and discontinuous seams of dense gray chert weather·
ing whitish; in upper part are two discontinuous seams of
brownish crinoidal limestone which have a maximum thick·
ness of one foot. The uppermost of these bears pebbles
and angular fragments of limestone similar in charac.ter to
that in the lay,er just below, but no certain evidence of
a disconformity at this level is to be found ... _ ....................... 25
6
1. Limestone, light gray, oolitic, very fossiliferous. Exposed...... 7
6 lIist of fossils from bed 1 of east quarry. ANTHOZOA-
Zaphrentis sp. Dielasma sp. Camarotoechia sp. BR.ACHIOPODA-
Chonetes logani N. and P. Chonetes sp. Spirifer platynotus Weller
Spirifer d. S. platynotus Weller
Spirifer sp. Schellwienella inflata (W. and W.)
Schellwienella pla.numbona
Weller
Schellwienella sp. Productus sp. Productella sp. Productella sp. RhipiiLomella sp. Syringothyris sp. Cliothyridina tenuilineata (Rowley)
Composita opposita (W. and W.)
GASTROPODA-
Straparollus obtusus (Hall)
CEPHALOPODA-
Ortho,ceras sp. List of fossils fro7l1 bed 2 of east quarry List of fossils fro7l1 bed 2 of east quarry. MISSISSIPPIAN STRATA OF IOWA MISSISSIPPIAN STRATA OF IOWA 82 List of fossils from quarries south Of Iowa rilVer. ANTHOZOA-
Zaphrentis sp. Delthyris clarksvillensis (Winchell)
Spirifer platynotus Weller
Spirifer sp. CRINOIDEA-
Platycrinus sp. BRACHIOPODA-
Orthotetes . ~ sp. Productus sp. Rhipidomella cf. R. dubia
Camarotoechia sp. Spiriferina solidirostris White
Spiriferina sp. Spirifer sp. Spirifer sp. Spirifer sp. Spirifer sp. (Hall)
Spirifer , sp. Eumetria sp. Composita sp. GASTROPODA-
Spiriferina sp. Straparollus (two species) Spirifer sp. S i if At the point where the Minneapolis and St. Louis railway
crosses Timber creek, three and three-fourths miles west of Le-
Grand, beds corresponding in age to those at the , top of ' the
above described east quarry section are well exposed in an
abandoned quarry. However, certain of the layers are much
more oolitic here. Timber CI'eek section. FEET
INCHES
8. Drift
.................................................................................................. .. 7. Limestone, compact, gray, magnesian, weathering yellowish,
thin bedded, nonfossiliferous; cherty in middle part .................. 6
6
6. Limestone, brownish, medium·grained, slightly crinoid aI,
thin bedded; with a median layer of compact gray m'<l,gne·
sian limestone three inches thick ................................................ 2
0
5. Limestone, brownish, rather coarse·grained, crinoidal, fossili·
ferous; locally grading laterally into oolite ............................ 0
6
4. Limestone, gray, oolitic, weathering to thin layers ................ 5
0
3. Limestone, medium· grained, bluish when fresh but weather·
ing brownish ........................................................................................ 0
6
2. Limestone, bluish, compact, magnesian, weathering buff; with
occasional seams of bluish unaltered limestone; rather. mas·
sive ........................................................................................................ 7
0
1. Limest0:':l~ '. bluish when fresh but weathering to a gray
color, oohtIe ........................................................................................ 4
0
Collections were made from beds 1, 5, and 6. List of fos,~ils from bed 1 of Timber creek section. Camarotoechia
~ sp. Rhipidomella sp. Eumetria sp. Spirifer sp. Spirifer sp. List of fossils from beds 5 and 6 of Timber cTflek section. Camarotoechia sp. Rhipidomella sp. Streptorhynchus sp. Spirifer sp . Cliothyridina sp. Composita sp:
DC'ntalium grandaevum Win. . The latter beds are believed to represent a portion of bed 5
f the east quarry section. Timber CIeek section. FEET
INCHES
8. Drift
.................................................................................................. .. 7. Limestone, compact, gray, magnesian, weathering yellowish,
thin bedded, nonfossiliferous; cherty in middle part .................. 6
6
6. Limestone, brownish, medium·grained, slightly crinoid aI,
thin bedded; with a median layer of compact gray m'<l,gne·
sian limestone three inches thick ................................................ 2
0
5. Limestone, brownish, rather coarse·grained, crinoidal, fossili·
ferous; locally grading laterally into oolite ............................ 0
6
4. Limestone, gray, oolitic, weathering to thin layers ................ 5
0
3. List of fossils fro7l1 bed 2 of east quarry. BR.ACHrOPODA-
Leptaena cf. L. analoga (Phillips)
Chonetes multicosta Win. . Productella sp. Prodllctus ovatllS Hall
Productus arcuatus Hall ~
Orthotetes ~ sp. Schuchertella
~ sp. Camarotoe,chia sp. Dielasma sp. Spirifer platy notus Weller
Spirifer sp. Eumetria sp. Composita sp. List of fossils from bed 3 of east q~barry. Schuchertella
~ sp. Eumetria sp. Composita sp. List of fossils from bed 3 of east q~barry. BR.ACHIOPODA--
Orthotetes 1 sp. Productella i sp. Chonetes nmlticosta Win. Leptaena analoga (Phillips)
Camarotoechia sp. Spirifer legraniLen~is Weller
Spirifer calvini Weller
Spirifer sp. Syringothyris ~ sp. Reticularia cf. R. cooperensis
(Swallow)
Composita sp. BRYOZOA-
Chaetetes . ~ sp. Rhombopora sp. GASTROPODA-
Platyceras sp. Lisrt of fossils from bed 5 of east quar·ry. BR.ACHIOPODA--
Orthotetes 1 sp. Productella i sp. Chonetes nmlticosta Win. Leptaena analoga (Phillips)
Camarotoechia sp. Spirifer legraniLen~is Weller
Spirifer calvini Weller
Spirifer sp. Platyceras sp. Lisrt of fossils from bed 5 of east quar·ry. SpirifeTina solidirostris White
S i if
l
W ll ANTHOZOA·-
Zaphrentis sp. BR.ACHIOPODA-
Productus sp. Productus sp. Orthotetes
~ sp. Rhipidomella sp. Composita sp. SpirifeTina solidirostris White
Spirifer platynotus Weller p
Spirifer platynotus Weller
S i if Spirifer platy
S i if Spirifer sp. i if Spirifer sp. BRYOZOA- Fenestella sp. Orthotetes
~ sp. Rhi id
ll CEPHALOPODA- Rhipidomella sp. C
it Orthoceras sp. Composita sp. Lower layers were formerly exposed in this section. Thus
Beyer50 reports a thickness of fifteen feet for the oolite beel
(bed 1 of above section) and describes an underlying fine-
grained bluish sandstone with an exposed thickness of ten feet. Collections were' made in the quarries south of the river from
the same horizon as bed 5 of the preceding section. The forms
have heen identified as follows: ' 8.
Drift
7
Li
t List of fossils from quarries south Of Iowa rilVer. Limestone, medium· grained, bluish when fresh but weather·
ing brownish ........................................................................................ 0
6
2. Limestone, bluish, compact, magnesian, weathering buff; with
occasional seams of bluish unaltered limestone; rather. mas·
sive ........................................................................................................ 7
0
1. Limest0:':l~ '. bluish when fresh but weathering to a gray
color, oohtIe ........................................................................................ 4
0
Collections were made from beds 1, 5, and 6. 1. Limest0:':l~ '. bluish when fresh but weathering to a gray
color, oohtIe ........................................................................................ 4
0 Collections were made from beds 1, 5, and 6. Collections were made from beds 1, 5, and 6. List of fos,~ils from bed 1 of Timber creek section. Camarotoechia
~ sp. Rhipidomella sp. Eumetria sp. Spirifer sp. Spirifer sp. List of fossils from beds 5 and 6 of Timber cTflek section. Camarotoechia sp. Rhipidomella sp. Streptorhynchus sp. Spirifer sp . Cliothyridina sp. Composita sp:
DC'ntalium grandaevum Win. . The latter beds are believed to represent a portion of bed 5
of the east quarry section. EOIDNODERMS FROM LEGRAND BEDS 83 Beyer51 reports that the topmost beds at LeGrand are again
exposed in the old quarries at Rockton near the central part of
Marion township. The section there is described by him as
follows: Seotion of L eGrand bed8 at Eaoleton (After B eyer) . FEET
6. L oess
and
soil
....................... _ .... __ ............................................. 1·3
5. Till, yellow (I owan) ............................................................... _......... 2·4
4. Till, reddish brown, sometimes blue below (Kansan)............ 0·3
3. Limestone, brown, subcrystalline, rubbly .................................... 3·5
2. Limestone, oolitic, heavy bedded ... _ .......... _ .... _ ................ _............. 5
1. Limestone, gray·brown, beds thinner · and slightly argilla·
ceous ... _ .................................. _ ................ _............................................. 2 The strata of the above described sections have been designat-
ed the LeGrand beds by Beyer. 52 The limestone above the basal
oolite has yielded many species of Echinodermata in the Le-
Grand area. These have been described by Wachsmuth and
Springer, by Miller and Gurley and by Worthen . . The list fol-
lows: List of eohinoderms desori.bed from the LeGra;nd beds. CYSTOIDEA-
Agelacrinus legrandensis Miller
a.nd Gurley
BLASTOIDEA-
Orophocrinus conicus W. ancl Sp. Orophocrinus fusiformis W. and Sp. ORrNOIDEA-
Rhodocrinus kirbyi W . and Sp. Rhodocrinus nanus M . and W . Rhodocrinus · watersianus W. and Sp. Me;gistocrinus nobilis W. and Sp. Batocrinus macbridei W. and Sp. Batocrinus
poculum
Miller
and
Gurley
Aorocrinus i=aturus W. and Sp. Aorocrinus parvibasis W. and Sp. 510p. cit., p. 216.
52 Idem, p. 221 ' ff. List of eohinoderms desori.bed from the LeGra;nd beds. List of fossils from quarries south Of Iowa rilVer. Cactocrinus
ornatissimus yrr. and
~. . Cactocrinus nodobrachiatus W . and
Sp. Eutaxocrinus fletcheri Worthen
Taxocrinus intermedius W. and Sp. Gamocrinus
sculptilis
Miller
and
Gurley
Cyathocrinus marshallensis Worthen
Poteriocrinus
gcnista
Miller
and
Gurley
Poteriocrinus hammondi Miller and
Gurley
Poteriocrinus legrandensis Miller and
Gurley
Poteriocrinus maccabei Miller and
Gurley
P oteriocrinus maccabei var. deerep·
itus Miller and Gurley
. Poteriocrinus
soopae
Miller
and
Gurley
Scaphiocrinus elegantulus W. and
Sp. Scaphiocrinus globosus W. and Sp. Scaphiocrinus notatus Miller
and
Gurley
Graphiocrinus longicirrifer W . and
Sp. Cactocrinus . probo!<~.idialis (Hall)
Cactocrinus amoldi W. and Sp. Platyc.rinus symmetricus W. and Sp. Platycrinus agassizi W. and Sp. Dichocrinus inornat.us W. and Sp. Dichocrinus delicatus W. and Sp. Dichocrinus
cinctus
Miller
and
ECHINOIDEA-
Gurley
Archaeocidaris
legrandensis
Miller
and Gurley Cyathocrinus marshallensis Worthen
P t
i
i
i t
Mill
d Poteriocrinus
gcnista
Miller
and
Gurley
P
i
i
h
di Mill
d Poteriocrinus
gcnista
Miller
and
Gurley
P
i
i
h
di Mill
d Poteriocrinus hammondi Miller and
Gurley Poteriocrinus hammondi Miller and
Gurley Poteriocrinus legrandensis Miller and
Gurley Poteriocrinus legrandensis Miller and
Gurley Poteriocrinus legrandensis Miller and
Gurley Poteriocrinus maccabei Miller and
Gurley Poteriocrinus maccabei Miller and
Gurley
i
i
b i
d Poteriocrinus maccabei Miller and
Gurley P oteriocrinus maccabei var. deerep·
itus Miller and Gurley
P
i
i
Mill
d Aorocrinus parvibasis W. and Sp. C
t
i
ti
i
rr
d Poteriocrinus
soopae
Miller
and
Gurley
S
hi
i
l
l
W
d Poteriocrinus
soopae
Miller
and
Gurley
S
hi
i
l
l
W
d Scaphiocrinus elegantulus W. and
Sp. Scaphiocrinus elegantulus W. and
Sp. Scaphiocrinus globosus W. and Sp. Scaphiocrinus
notatus
Miller
and p
g
p
Scaphiocrinus notatus Miller
and
Gurley
G
hi
i
l
i i
if
d Cactocrinus . probo!<~.idialis (Hall)
C
i
ldi W
d S Scaphiocrinus notatus Miller
and
Gurley
G
hi
i
l
i i
if
d Scaphiocrinus notatus Miller
and
Gurley
G
hi
i
l
i i
if
W
d Graphiocrinus longicirrifer W . and
Sp. Archaeocidaris
legrandensis
Miller
and Gurley Archaeocidaris
legrandensis
Miller
and Gurley Dichocrinus delicatus W. and Sp. Di h
i
i
t
Mill
d Dichocrinus
cinctus
Miller
and
Gurley 510p. cit., p. 216. 52 Idem, p. 221 ' ff. Section of Kindel'hook beds, section 17, Indian Village township (After Savag~).
FEET
INCHES
14.
Yellowish brown loess ......................................................................
2
13. Brown cl'1Y containing numerou~ crystalline pebbles ..............
6
12. Bed of grayish brown, impure limestone which breaks up
"3 Op. cit., pp. 214, 215 , 226.
54 Iowa Geol. Survey, vol. XIII, p. 213 ff.; 1903 . 54 Iowa Geol. Survey, vol. XIII, p. 213 ff.; 1903 . 13. Brown cl'1Y containing numerou~ crystalline pebbles ..............
6
12
Bed of grayish brown
impure limestone which breaks up 12. Bed of grayish brown, impure limestone which breaks up 14.
Yellowish brown loess ......................................................................
2
13
Brown cl'1Y containing
numerou~ crystalline pebbles
6 "3 Op. cit., pp. 214, 215 , 226.
I
G
l
S
l
XI "3 Op. cit., pp. 214, 215 , 226.
54 Iowa Geol. Survey, vol. XIII, p. 213 ff.;
1903 . "3 Op. cit., pp. 214, 215 , 226.
54 Iowa Geol. Survey, vol. XIII, p. 213 ff.; 1903 . List of fossils from quarries south Of Iowa rilVer. MISSISSIPPIAN STRATA OF IOWA 84 MARSHALLTOWN SHALEs.-Beyer53 reports the occurrence of
about fifteen feet of argillo-calcareous beds, named by him the
Marshalltown shales, above the LeGrand beds in an exposure
near the flouring mills at Marshalltown. He describes them as
follows : "They consist of ash blue to deep blue shales interbedded
with argillaceous limestones. Chert nodules are present in the
upper calcareous layers. .After diligent search no trace of or-
ganic remains could be found." .At the time of the writer's visit these beds were largely con-
c:ealed. Only three feet of soft browish dolomitic limestone
0verlain by three feet of residual soil was exposed. Tama County.-Savage54 describes the Kinderhook of Tama
county as follows : ".As these rocks are exposed in Tama county they present
three different facies. The lowest phase is a yello"v, fine-
grained sandstone which bears but few fossils and which is
seen in but a few of the outcrops in the area. Overlying this
sandstone is a stratum of light colored, oolitic limestone which
occurs in thick, massive layers. 'l'his phase is very fossilifer-
ous throughout and is quite lmiformly developed and constantly
present wherever in the county the rocks of this horizon are ex-
posed. The upper phase is a brown magnesian limestone
which in some layers changes to a yellowish brown, fine-grained
sandstone. The layers of this upper phase carry quite a num-
ber of fossils, usually in the form of casts or moulds. Near
the upper part the magne.sian character gives way to thinly
bedded limestone which, in the uppermost layers exposed, car-
ries a ~arge quantity of the comminuted fragments of the stems
of crinoids." These beds are the equivalent of the LeGrand beds of Mar-
shall county. .A typical exposure of them a'Ppears in an old
quarry near the east side of section 17, Indian Village township. The following description is after Savage. KINDERHOOK IN TAMA COUNTY 85 into narrow layers and irregular pieces when exposed to the
action of the weather. F ossils rare ................................................ 3
11. Band composed largely of nodules of chert ....... _....................... 3
10. Impure limestOlD.e, bmwn in color, with few fossils; species of
Chonetes, Rhynchonella, and Spirifer were found ......... _............. 1
9. Band of chert nodules ...................................................................... 3
8. 'fhick, heavy layer of brown magnesian limestone containin.g
casts of Chonetes and Rhynclwnella ... _......................................... 21
6
7. List of fossils from quarries south Of Iowa rilVer. Layer composed mostly of nodules of chert .................. _.......... 4
6. Layer of brown magnesian limestone with casts of Zaphren··
tis, Chonetes a11d Rhy'TIJChonella ..................................... _............... 10
5. Brown limestone with numerous chert nodules intermingled,
containing casts of a species of P1'od1;ctUS ... _ ........ __ .......... 10
4. Massive layers of brown magnesian limestone in which there
is a considerable quantity of sand .. _...................................... 4
8
3. H eavy layer of oolite which weathers into small irregular
blocks and bits, containing in abundance' Orthotctes C1"6nc
istria, a species of Rhynchonella, Spirifer extenuatus, Spvrifer
biplioatus and Stmpal/"ollus latus .................................................... 5
8
2. Massive beds of oolite in two layers similar to number 3
above and carrying similar fossils, the lower part somewhat
talus covered ...................................................................................... 8
6
1. Yellowish sandstone with some clay, containing f ew fossils;
not well exposed. 'fo level of road .............................................. 8 Band composed largely of nodules of chert . 1. Yellowish sandstone with some clay, containing f ew fossils;
not well exposed. 'fo level of road .............................................. 8 Numerous crinoids and fish remains are reported to have
been found by the quarrymen in the seams separating the layers
of magnesian limestone. At the time C. A. vVhite visited this
quarry in 1869 a greater thiclrness of yellow sandstone was ex-
posed below the oolite bed. At present none of the sandstone
outcrops. In another quarry situated near the southwest corner of sec-
tion 8 of the same township a greater thickness of strata is pre-
served above the oolite. Savage's description of this exposure
is given below: Exposure in section 8, Indiarn, Village township (A fter Savage). FEET
INCHES
15. Gray, crinoidal limestone which weathers into thin pieces.... 1
14, Crinoidal limestone., gray in color, with numerous fossil
fragments ............................................................................................ 8
13. Fissile limestone in thin layers, few f ossils .............................. 4
12. Brown magnesian limestone with layer of chert nodules two
inches in thickness at top ....................... _ .............................. "'.'
9
11. Bed of rather soft, friable sandstone, much water seamed
and corutaining numerous chert nodules; fossils few................ 7
10. Arenaceo·magnesian limestone, fine·grained and quite hard,
brown in color, layers 8 to 12 inches in thickness, containing
Clasts of a species of Chonetes, Productus, Rhynchonella and
Spirife1' ............... _ .... _ .............. _ .......... _ ............................ _................. 4
9. Bed of incoherent brown fine· grained sand ........................ 1
2
8. Exposure in section 8, Indiarn, Village township (A fter Savage). List of fossils from quarries south Of Iowa rilVer. Band made up of chert nodules ................................................ 4
7. Impure arenaceo·magnesian limestone, few fossils .................. 1
1
6. Bed composed largely of nodules of. chert carrying a layer
of sand 3 inches in thickness ...................................................... 1 MISSISSIPPIAN STRATA OF IOWA 86 5. Magnesian limestone containing some fine· grained yellow
sand ....... _ ...................... _..................................................................... 1
8
4. Bed similar to number 5 above .................................................... 1
6
3. Layer of massive oolite w,eathering into small bits and bear·
ing numer()us fossils, among which appear Orthotetes oreni--
.!'tria, Spirifer biplicatus, Spvl'·ifer cf. exte'TIIUatus, and Stmparol·
Ius lat1b8 ... _ .................................. _....................................................... 7
2. Layer similar to number 3 above in lithological characters
and fossils contents ............................................................. _ .... _...... 4
6
1. Layer of light gray oolite similar to numbers 2 and 3 above 3 4. Bed similar to number 5 above
3
Layer of massive oolite weatherin 3. Layer of massive oolite w,eathering into small bits and bear·
ing numer()us fossils, among which appear Orthotetes oreni--
.!'tria, Spirifer biplicatus, Spvl'·ifer cf. exte'TIIUatus, and Stmparol·
Ius lat1b8 ... _ .................................. _....................................................... 7
2
L
i
il
t
b
3
b
i
lith l
i
l
h
t 2. Layer similar to number 3 above in lithological characters
and fossils contents
4 and fossils contents
1
Layer of light gray At the "Devils Anvil", near the southeast corner of section
7, Indian Village township, Savage measured the following sec-
tion on the east side of the hill. Section at "Devils Anvil" (After Savage). Section at Devils Anvil (After Savage). FEET
9. Reddish brown clay, containing numerous small pebbl€s
3
8. Bed of crinoidal limestone which weathers into thin layers
1 to 4 inches in thickness .......................................................... ""
7
7. Layer of crinoidal limestone bearing a band of chert nodules
near the middle ... _ .......................... _ ............................ _ .... _................. 2
6. Bed made up of irregular layers of brown colored magnesian
limestone 1 to 4 inches in thickness, and containing numerous
nodules of chert 6 to 12 inches in long diameter and 3 to 6
inches in
the short direction. Casts of fossils
not rare;
among them appear species of Rhynchon;ella, Zaphrentis, Chonetes
and Productus ............... _ .................... _ ............................ _................... 10
5. Impure magnesian limestone, brown in color, containing but
few fossils, and showing numerous cavities which appear to
have been formed by the dissolving action of percolating
waters ... _ ...................... _ .............. _ .. _ ................ _ ...................... _ .......... _. 4
4. Bed of fine·grained brown colored sandstone in layers 9 to
18 inches in thickness, a part of the lay'ers containing some
magnesian limestone, and all of them bearing numerous chert
nodules ..................................................... _............................................... 8
3. Band of chert nodules on the surface of which appear casts
of fossils, among them Orthotetes and Pro ductus .................. 1/3
2. Bed of impure sandstoDe which appears massive in places and
at other places weathers into irregular layers 2 to 4 inches
in thickness ............................... _........................................................... ~
1. ' Bed of light gray oolite containing numerous fossil fragments
among which are Orthotetes
crcnistria, Spirit-err
biplicatus,
and Straparollus latus ... _ ...................... _ .......... _ .... _ .............. _ ........ _. 6 The oolite bed at the base of the exposure is the same as that
of the two preceding sections. The overlying layers have a
greater thickness than elsewhere in the county. At the north
end of the exposure there are several small bryozoan reefs in
the upper four feet of bed 8. These reefs consist of compact
gray limestone filled with bryozoans and flanked on the sides by
brownish crinoidal limestone. I The reef limestone is structureless but weathers to irregular
flakes. ~5 Iowa Geol. Survey. vol. XX. p. 77 ; 1910.
5e Iowa Geol
Survey
vol
X
pp
270 271 5e Iowa Geol. Survey. vol. X. pp. 270·271. Section at "Devils Anvil" (After Savage). The reefs are roughly lenticular in shape and range in
size from masses two to three feet long and one foot high to KINDERHOOK IN GRUNDY COUNTY 87 others as milch as six feet long and two to three feet high. In
some places there is a slight interfingering of the reef material
with the limestone on the sides. The fauna of the reef zone is as follows: BLASTOIDEA-
Orophocrinus conicus w. and Sp. BRACHIOPODA-
BRYOZOA-
Leioclema. wachsmuthi Ulrich
Rhombopora sp. Streblotrypa sp. Leptaena analoga (Phillips)
Camarotoechia sp. Spirifer calvini Weller
'l'aeniodictya cf. T. mmulosa var. burLingtonensis Ulrich
Fenestella sp. Spirifer legrandf',tlsis Weller f
Reticularia cooperensis (Swallow)
U nc1eterminec1
(several species) Spirifer calvini Weller
Spirifer
legrandf'tlsis Spirifer legrandf ,tlsis Weller f
Reticularia cooperensis
(Swallow) Reticularia cooperensis (Swallow) Numerous other exposures of the oolite bed and the overlying
layers of magnesian limestone appear along the sOilth bank of
Iowa river northeast of LeGrand station and at several points
along the bluffs of Sugar creek, a tributary from the north. Grundy County.-Regarding the Kinderhook of Grundy coun-
ty, Arey55 says: "While there is little superficial demonstration of the fact
within the limits of the county, there is no doubt that by far the
greater portion of the eounty is underlain with rock of the
Kinderhook series. As has been stated elsewhere already, the
only actual rock exposures are on Wolf creek near Beaman and
Conrad. At the latter place, an abandoned quarry gives the
only opportunity for an examination of rock in place where a
section can be secured." A section of the quarry at Conrad given by Beyer56 in his
Hardin county report is as follows: Section of Kitnderhook beds at Conrad. f
FEET
5. Drift (modified Kansan probably) ............................................ 5
4. Limestone, residual, consists chiefly of cherty concretions imbed·
ded in a matrix of greenish clay streaked and mQ.ttled with
f erruginous ano marly material .......................................................... 3
3. Limestone, slightly oolitic, composed essentially of a shelly
breccia a.lIoost identical with No. 1 in the Eagle City section,
2. Limestone, hard, subcrystalline, containing numerous brachiopod
casts ... _____ . ______________________________ , _____ ... _____ .. _.0 ____________ ____________________ ··___________ ____
2
1. Limestone. typical oolite in heavy b eds; a Straparollus and
a turreted form of gastropod were noted, also numerous
brachiopod casts .................................................................................. 5
A number of species \vere collected from this exposure by the
author, viz: 5. Drift (modified Kansan probably) ............................................ 5
4
Limestone
residual
consists chiefly of cherty concretions imbed 4. Limestone, residual, consists chiefly of cherty concretions imbed·
ded in a matrix of greenish clay streaked and mQ.ttled with
f erruginous ano marly material .......................................................... 3
3
Limestone
slightly oolitic
composed essentially of a
shelly 1. Limestone. typical oolite in heavy b eds; a Straparollus and
a turreted form of gastropod were noted, also numerous
brachiopod casts .................................................................................. 5 A number of species \vere collected from this exposure by the
author, viz: MISSISSIprPIAN STRATA OF IOWA 88 Zaphrentis sp. Schellmenella inflata (W. and W.)
Camarotoechia sp. Rhipidomella thiemei (White) ,
Dielasma ~ sp. Spirifer platy notus Weller
Conocardium sp. Straparollus obtusus (Hall)
Loxonema , 59 Iowa Geol. Survey, vol. VII, p . 221 ; 1897.
60 Iowa Geol
Survey
vol
XIII
p
225 ff 58 Geol. Surv. IlJinois, vol. VIII, pp. 55.
59 Iowa Geol
Survey
vol VII
p
221 ; 1 60 Iowa Geol. Survey, vol. XIII, p. 225 ff. 57 Geology of Iowa, vol. I, pp. 19.5 197; 187
58 Geol. Surv. IlJinois, vol. VIII, pp. 55.
59 Iowa Geol
Survey
vol VII
p
221 ; 189 57 Geology of Iowa, vol. I, pp. 19.5-197; 1870.
58 Geol
Surv
IlJinois
vol VIII
pp
55 57 Geology of Iowa, vol. I, pp. 19.5-197; 1870.
58 Geol. Surv. IlJinois, vol. VIII, pp. 55.
59 Iowa Geol. Survey, vol. VII, p . 221 ; 1897.
60 Iowa Geol. Survey, vol. XIII, p. 225 ff.
' Correlation of Kinderhook of Central Iowa
f
h
h l
l i
h
D
i
li A
h
i
B
i
d h
b d h
b
i
d
i
f At the time Beyer examined the beds he submitted a series of
fossils, some of which were taken from the uppermost strata, to
Professor Calvin, who found them all to be distinctly Kinder-
hook in character.fi9
S
di
th
l ti
f th
b d
i
hi
t Savage discusses the correlation of the beds in his report on
the geology of Tama county.60 He points out the marked differ- OHARAOTE'RI OF LEGRAND BEDS 89 ence between the faunas of beds 6 and 7 at Burlington and
those of the beds correlated with them by White but states that
a larger proportion of the fossils of the oolite layers is similar
to those found in bed 6 than to those of any other member of
the Burlington section. - Numerous collections were made from the LeGrand beds dur-
ing the writer's field studies. The identification of these has
strengthened the correlation of the formation with the upper-
most beds of the Kinderhook at Burlington, though the presence
of a large number of species, many of which are undescribed,
in the northern section, which are absent from the beds at Bur-
lington makes exact correlation difficult. Most of the brachio-
pods specifically identified from the LeGrand beds, which are
common to the two localities, are confined to beds 6 and 7 at
Burlington though a few species range do,Vll into lower beds
and an occasional one occurs in the Lower Burlington of the
type section. . The crinoid element of the fauna is remarkable in that none
of the species has been found in the Kinderhook elsewhere in
Iowa. However, Cactocrinus proboscidialis occurs in the Low-
er Burlington limestone_ Wachsmuth and Springer have de-
scribed another species, Dichocrimts delicat~t8, as common to
the Lower Burlington limestone at Burlington and the Kinder-
hook beds of Marshall county. The exact horizon of the
latter is not given but probably it came from the upper part of
the LeGrand. The LeGrand beds are tentatively correlated with the Upper
Kinderhook of southeastern Iowa. The uppermost layers at
LeGrand very probably represent a transition, into the Lower
Burlington limestone. The marked difference in thickness of the LeGrand beds as . compared to the Upper Kinderhook at Burlington is worthy of
note. Correlation of Kinderhook of Central Iowa
f
h
h l
l i
h
D
i
li The age of the shales overlying the Devonian limestone in
central Iowa is not definitely known but they are believed to be-
long to the Kinderhook. If they are Kinderhook they undoubt-
edly belong to the middle or lower or both middle and lower
portions of this formation as developed farther south as sug-
gested by the fauna of the overlying LeGrand beds. . Th
t
t
k
th
L G
d b d
i
T
d The strata now known as the LeGrand beds in Tama and
Marshall counties were correlated with the Kinderhook beds at
Burlington, Iowa, by White.57
However, he believed that the
middle part of the Burlington Kinderhook was not represented
in this part of the state. The oolite bed (bed 6) at Burlington
was regarded as the equivalent of the oolite bed near or at the
base of the exposures in Tama county, while the underlying
sandstone in this county was believed to be the equivalent of
the basal shales (bed 1) in the southern section. He noted the
similarity of the crinoidal limestones in the upper part of the
LeGrand beds to the Burlington limestone in the type section
but correlated them neyertheless with the topmost bed of the
Kinderhook (bed 7) at Burlington. Wachsmuth and Springer
in their report on the echinoderms Wachsmuth and Springer58 in their report on the echinoderms
from LeGrand agree that the lower part of the series belongs to
the Kinderhook but remark that the occurrence of Cactocrinus
proboscidialis, a characteristic lower Burlington fossil, in the
topmost beds renders their correlation with that formation
probable. Correlation of Kinderhook of Central Iowa
f
h
h l
l i
h
D
i
li If we assume their equivalence we must explain this
great, discrepancy in thickness as due either to more favorable
conditions for the deposition of limestone in the northern area
or to the presence of a dis conformity between the Kinderhook
and Lower Burlington formations in southeastern Iowa_ Inas-
much as a study of this contact over wide areas in Des Moines
and Louisa counties has revealed no evidence of a break in sedi- MISSISSIPPIAN STRATA OF IOWA 90 mentation, the theory of original differences in deposition is
favored. The continued thickening of the Kinderhook lime-
stones north,vard fl'om 1'I~arshall county as indicated by the ex-
posures in Hardin cOlmty also lends weight to this view. The age of the Marshalltown shales is not definitely known
owing to the fact that their contact ,vith the LeGrand beds is
not exposed and that no diagnostic fossils have as yet been col-
lected fDom these strata. If the uppermost limestones of the
LeGrand beds are regarded as transition layers between the
Kinderhook and Lower Burlington formatioJ;ls then these shales
may represent the near shore facies of the basal beds of the
Lower Burlington. KINDERHOOK OF NORTH-OENTRAL IOWA General statement.-The Kinderhook has a much more wide-
spread distribution in north-central Iowa than .in any other
part of the state, but the beds are effectually concealed over a
large part of the area by a thick mantle of glacial drift. Be-
ginning at the southern part of this province we find that, to
the best of our knowledge, the Kinderhook constitutes the sur-
face rock in Hardin county in its extreme southeastern corner,
- in its central part and in the northern part. It underlies small
areas in the north-central part of Hamilton county and in the
southwestern part of Butler county; the whole of Franklin
county, with the exception of a small area occupied by the Lime
Creek beds in the northeast corner; all of Wright county except
small areas in the southeastern and southwestern parts; the
northern half of Humboldt county; a very narrow linear area
in the extreme eastern part of Pocahontas county; all of
Kossuth county except the area occupied by the Cretaceous in
the western and northwestern parts; the whole of Hancock
eounty barring a . small area of Lime Creek in the northeast
~~orner; and the greater part of Winnebago county. Prior to the present investigation the Kinderhook beds of
this part of the state were imperfectly understood and it must
be admitted that the exact character and extent of several of
the formations is even now not definitely known, owing to the
fact that the drift mantle is thick and the outcrops are few and
usually small. CHARAOTER OF CHAPIN BEDS 91 The Kinderhook of northern Iowa is somewhat related to that
of the central part of the state but possesses little in common
with that of southeastern Iowa. The thickness is approximately
the same (350 feet), but lithologically and faunally the series is
very different. The group is divided into six distinct forma-
tions, upon the basis of individual exposures and the log of a
well at Iowa Falls. The Alden limestone
Th
I
F ll
d l The Iowa Falls dolomite
Th
E
l
Cit
b d The Eagle City beds
Th
M
C
k b d The Mayne Creek beds
Th
Ch
i
b d The Chapin beds
Th
Sh ffi ld b d 6 The Sheffield beds60> THE SHEFFIELD BEDs.-This basal member of the Kinderhook
has a thickness, of about sixty feet. 60- See footnote 76, page 116. KINDERHOOK OF NORTH-OENTRAL IOWA The main mass of the
formation, representing approximately the lower two-thirds,
consists of bluish plastic shale intercalated with which are thin
layers of fine-grained sandstone and brownish impure lime-
stone, but the upper third is more calcareous. It is brownjsh
and dolomitic and locally bears a lenticular bed of gray ooljtic
limestone which, at those localities where it is typically de-
veloped, is a.bout six feet in thickness. Fossils are scarce and
poorly preserved except in the upper part of the 'formation,
where a few species with Chouteau affinities occur. It is possible that the lower shaly portion of the Sheffield
beds will ultimately be referred to a distinct formation of either
I(jnderhook or Upper Devonian age. The paucity of recogniz-
able fossils in the lower shales and intercalated sandy layers
renders their exact correlation impossible at present. However,
the absence of any evidence of a disconformity between the:-;e
strata and the fossiliferous layers above favors the reference of
the entire succession to one formation. The formation takes its name from the town of Sheffield in
northern Franklin county in the vicinity of which it is well ex-
posed. TH}<; CHAPIN BEDs.-These have a thickness of perhaps twenty
to thirty feet and consist of a massive limestone, the lower part
of which is altered to dolomite at some localities, followed by
fine-grained yellow sandstone. They are best exposed in a
small quarry near the town of Chapin in Franklin county. At MISSISSIPPIAN STRATA OF IOWA 92 this locality the beds are very fossiliferous, having yielded
about thirty-five species. THE MAYNE CREEK BEDS.-This formation consists chiefly of
soft brownish dolomitic limestone, which at several horizons IS
arenaceous. It has a thickness of about sixty-eight feet. Occa-
sional chert nodules in the formation yield well preserved fos-
sils. It is best exposed at a locality on Mayne creek in Geneva
township of Franklin county. THE EAGLE CITY BEDS.-This division is made up of alternat-
ing beds of brownish dolomite and gray limestone. Some of the
linlestone beds are oolitic. It is best exposed in the banks of
Iowa river at Eagle City in Hardin county and in the lower part
of the gorge at Iowa Falls. The limestone horizons contain
brachiopods of Upper Kinderhook age. Its thickness is seventy-
~fu~
. KINDERHOOK OF NORTH-OENTRAL IOWA THE IOWA FALLS DOLOMITE.-This member is typically de-
veloped in the gorge of Iowa river at Iowa Falls in Hardin
county where it has a maximum thiclmess of not less than fifty
feet. Its contact with the lmderlying formation is very undu-
lating, but this is believed to have resulted from uneven dolomi-
tization rather than from disconformity. The formation is
heavily bedded, except at the very top where the layers are
comparatively thin. It is brownish in color, and contains but
few fossils. . THE ALDEN LIMESTONE.-This is a light gray thin-bedded
slightly oolitic limestone which is well exposed at the town of
Alden in Hardin county. It has a maximum exposed thickness
of about thirty-two feet. The contained fossils are very poorly
preserved and the exact age of the formation is open to ques-
tion: It is referred tentatively to the Kinderhook. The contact
of this formation w:ith the underlyihg dolomite has been ob-
served at only one locality. This is at the old Ivanhoe quarries
along Iowa river midway between Alden and Iowa Falls. It is
there very irregular, and there is evidence of a distinct discon-
formity between the two formations. Hardin County.-The greater part of the surface of Hardin
county is underlain by Pennsylvanian strata, but the erosion of STRATA IN WELL AT IOWA FALLS 93 these overlying deposits has brought the Kinderhook to the
surface over small areas in the southeastern and central parts
of the county, and over a broad area in its northern part. The most important exposures, by far, are along Iowa river
between Alden and Eagle City. Indeed, the exposures between
these two points furnish the most complete and representative
section of the Kinderhook in the northern part of the state. So far as the writer is aware no strata older than the Eagle
City formation are exposed within the limits of Hardin county. Our knowledge of the character and thickness of the lower beds
of the Kinderhook in this region has been considerably en-
hanced by the record of the city well at Iowa Falls. This well
is located near the head of Rock Run gorge. The log of the
strata passed through as given by Beyer61 is as follows: Log of well at Iowa Falls (After Beyer). THICKNESS
FEET
1. 61 Iowa Geol. Survey, vol. X, p. 265. KINDERHOOK OF NORTH-OENTRAL IOWA List of fossils from bed 1 of the bridge section at Eagle City. BBAcmoPoDA-
Eumetria cf. E. verneuiliana (Hall)
Leptaena analoga (Phillips)
BRYOZOA-
Orthotetes
( ~) several species
Chaetetes , sp. Schellwienella inflata (W. and W.) ,
Rhombopom ' sp. Productus sp. :E1enestella sp. Dielasma f sp. GASTROPODA-
Spirifer cf. S. legrandensis Weller
Orthonychia sp. Reticularia cooperensis (Swallow)
Straparollus
~ sp. The following species were collected from bed 3: The following species were collected from bed 3: List of fossils from bed 9 of the bridge section. at Eagle City. Productus ovatus Hall
Orthotetes ~ sp. Camarotoechia chouteauensis
Weller
Spirifer cf. S. legrandensis Weller List of fossils from bed 9 of the bridge section. at Eagle City. List of fossils from bed 9 of the bridge section. at Eagle City. Productus ovatus Hall
Orthotetes ~ sp. Camarotoechia chouteauensis
Weller
Spirifer cf. S. legrandensis Weller Bed 4 yielded the fossils listed below: Bed 4 yielded the fossils listed below: List of fossils f1'om bed 4 of the bridge seotion at Eagle City. KINDERHOOK OF NORTH-OENTRAL IOWA Drift and weathered ma.terial ___________________________________________________
50
2_ Limestone, light gray; compact ______________________________________________
15
3_
Limestone, brown, dolomitic, sub crystalline ______________________
29
4_
Limestone, gray-blue, magnesian, cleavage fragments of
calcite not tmcommon; compact; grading downwal'd into
a light colored and less magnesian limestone ______________________
16
5_
Limestone, gray, semi-oolitic in texture ______________ ____ ____________
5
6_ Limestone, gray-brown, dolomitic and porous; drillings of
a gray compact limestone abundant ___________________________________ 11
7_
Limestone, brown, dolomitic, with considerable light-
colored chert
______________________________________________________________________________
37
8_
Dolomite, gray-brown ________________________________________________________________
7
9. Dolomite, yellowish brown, sugary __________________________________ ____
7
10_ Sandstone, gray-blue, shaly ________________________________ ____________________
7
11_
Sandstone, white, friable and very fine-grained ______________
10
12_ Sandstone, gray,' fine-grained and compact; slightly
argillaceous and noncalc:lreous ______________________________________________ 14
13_ Limestone, blut'-gray to yellowish gray, compact; slightly
argillaceous and exhibits an almost 'earthy fracture ________
6
14_
Shale, plastic, even-textured, light gray-blue, and slightly
calcareous above ___________ _______________________________________________________________ 62
15. Limestone, hard, compact (penetrated) __________________________________
2
DEPTH
FEET
50
65
94
110
115
126
163
170
177
184
194
208
214
276
278 Log of well at Iowa Falls (After Beyer). Bed 15 of this section is believed to represent Devonian lime-
stone; bed 14, the Sheffield shale; beds 13 and 12, the Chapin
formation; beds 11 to 7, the Mayne Creek formation; and beds
6 to 2, the Eagle City formation. THE EAGLE CITY BEDs.-The outcrops of this formation
in Hardin country are confined to the valley of Iowa river, the MISSISSIPPIAN STRATA OF IOWA 94 most complete exposure of the formation being at Eagle City in
the extreme southwestern corner of Aetna township. At the
east end of the bridge over Iowa river at this place, the follow-
ing section is shown in an abandoned quarry: Section of Eagle City formaticm at Eagle City. FEET
INCHES
5. Drift ......................................................................... _........................... 5
4. Dolomite, thin·bedded at top but more massive below, brown-
ish, soft ............................................................... _ ......... ___ .... _ .......... _. 25
3. Limestone, gray, oolitic, compact ................... _............................. 1
4
2. Dolomite, yellow to brownish, thin-bedded, soft .................... 2
10
1. Limestone, gray, oolitic ......................................................... _ ...... 4 All of these beds are distinctly lower than any observed at
Iowa Falls. The fossils collected from bed 1 are as follows: List of fossils from bed 1 of the bridge section at Eagle City. FEET
Limestone ( No. 1 of above section) ... _...............................................
2 'h
Dolomite, soft, yelJowish ......................................................................
12
Limestone, dense, lithographic, th:i:nJJy and irregularly bedded.
Exposed. above wa tel' ........................................... ~......... ..................
1 63 In the writer's opinion tJJ.ese beds are probably older than the upper beds at Iowa Falls.
They may be correlated tentatively with the Eagle City. List of fossils f1'om bed 4 of the bridge seotion at Eagle City. Leptaena analoga
(Phillips)
Schellwienella (several species)
Camal'otoechia sp. Schizophoria sp. Spirifel'in,a subtexta, White
~
Spirifer cf, S, legrandensis Weller
Spirifer sp. Reticularia
cooperensis
(Swallow)
Bryozoan sp, Leptaena analoga
(Phillips)
Schellwienella (several species)
Camal'otoechia sp. Schizophoria sp. Spirifel'in,a subtexta, White
~ Schizophoria sp. S i if l'i
b Spirifel'in,a subtexta, White
~ A few rods upstream from the above described quarry, iowel'
beds are exposed in the river bank, viz: FEET
Limestone ( No. 1 of above section) ... _............................................... 2 'h
Dolomite, soft, yelJowish ...................................................................... 12
Limestone, dense, lithographic, th:i:nJJy and irregularly bedded. Exposed. above wa tel' ........................................... ~......... .................. 1 Limestone ( No. 1 of above section)
D l
i
f
lJ
i h Dolomite, soft, yelJowish
i
d
li h EAGLE CITY BEDS ON IOWA RIVER 95 . Regarding the Kinderhook exposures along Iowa river below
Eagle City, Beyer62 has this to say: "Beyond Eagle City the beds disappear rapidly, and the sur-
face outcrops ~f the I~inderhook beds are almost entirely ob-
scured by glaCIal debns and coal measure talus. At Hardin
City, Steamboat Rock, and at one or two points betweelJ. num-
!Jer 4 of the Eagle City section is visible and rises some' SL'l: or
eight feet above the water level. In all cases it is greatly
weathered and shattered, making its identity difficult to estab-
lish. Between Steamboat Rock and Eldora, the Lower Carbon-
iferous passes entirely below the stream channel, but rises again
immediately south of the wagon road bridge at Eldora. Going
down stream from the Eldora bridge, a weathered dolomite ap-
pears in the stream bed and also in the right bank about sixty
rods below the road crossing. The ledges rise eight feet above
the water and appear to be identical, both lithologically and
faunally, with the upper member at Iowa Falls.63 Straparollus
casts and a cystophylloid coral were found. These beds appear
more or less interruptedly from this 'Point to Union, forming-
low benches on one or both sides of the river. At Xenia and
agajn between Gifford and Union, the white limestone member
is visible. The maximum eX'Posure is south of Gifford, near a
small stream which enters the Iowa from the west. The beds
exposed to view are: Seotion o{ KVnderhook beds south of Gifford (.4tter B eyer). Seotion o{ KVnderhook beds south of Gifford (.4tter B eyer). 62 Iowa Geol. Survey, vol. X, p. 269·270.
63 In the writer's opinion tJJ ese beds are p 63 In the writer s opinion tJJ.ese beds are probably
They may be correlated tentatively with the Eagle Ci Seotion o{ KVnderhook beds south of Gifford (.4tter B eyer). 4. Drift and wash
3
Limeston:e
light FEET
6. Drift ..................... _ .... _.........................................................................
2- 3
low A FALLS DOLOMITE.
5
D l
i
f
b
i h
hi
b dd d
b
b
i List of fossils f1'om bed 4 of the bridge seotion at Eagle City. Probably
formed by the alteration of a medium·grained
lime~tone. 'l'hin shaly scams occur in the basal part ................................... 20
EAGLE CITY B"tDS. 4. Limestone, gray, oolitic, more compact and in thicker layers
than in bluff at Iowa Falls. The upper part is locally dolo·
mitizec1 allddJiscolorec1 yel10wish .................................................... 3- 5
3. Limestone, light gray, lithographic, the upper three and
one·half feet interbedded with layers anc1 discontinuous
seams of coarser dark gray c1olo,mite .... :......................................... 12
2. Dolomite, fine· grained, soft, gray weathering yellowish,
rather thinly bedded. With many small pockets and seams
of calcite. In some places parts of the bed are filled with
masses and streaks of pyrite, which in some instances is asso·
ciated with the calcite ____ ..... _._ ....... _ ........................ __ ........ "'_"'_'_'"
6
1. Dolomite, clark gray when fresh, cdnse, massive. :r~xposed .. __
7 FEET
6. Drift ..................... _ .... _......................................................................... 2- 3
low A FALLS DOLOMITE. 5. Dolomite, soft, brownish, thin-bedded above but massive
below. Resting on the irregular surface of the bed bp.low. A two foot zone five feet below the top is rich in ~i.mple
comJs, and bears numerous specimens, of Straparollus obt~ £sus. The dolomite is granular and slightly vesicular. Probably
formed by the alteration of a medium·grained
lime~tone. 'l'hin shaly scams occur in the basal part ................................... 20
EAGLE CITY B"tDS. 4. Limestone, gray, oolitic, more compact and in thicker layers
than in bluff at Iowa Falls. The upper part is locally dolo·
mitizec1 allddJiscolorec1 yel10wish .................................................... 3- 5
3. Limestone, light gray, lithographic, the upper three and
one·half feet interbedded with layers anc1 discontinuous
seams of coarser dark gray c1olo,mite .... :......................................... 12
2. Dolomite, fine· grained, soft, gray weathering yellowish,
rather thinly bedded. With many small pockets and seams
of calcite. In some places parts of the bed are filled with
masses and streaks of pyrite, which in some instances is asso·
ciated with the calcite ____ ..... _._ ....... _ ........................ __ ........ "'_"'_'_'"
6
1. Dolomite, clark gray when fresh, cdnse, massive. :r~xposed .. __
7 4. Limestone, gray, oolitic, more compact and in thicker layers
than in bluff at Iowa Falls. The upper part is locally dolo·
mitizec1 allddJiscolorec1 yel10wish .................................................... 3
Li
li h
li h
hi
h
h
d 3. List of fossils f1'om bed 4 of the bridge seotion at Eagle City. Seotion o{ KVnderhook beds south of Gifford (.4tter B eyer). FEET
4. Drift and wash ............. _ .... _ .................. _ ...................... _ .... _................. 0-3
3. Limeston:e, light gray; white when weathered ... _ ............ : ....... _..... 0-3
2. Dolomite, yellowish brown, much shattered and unevenly bedded 6-8
1. Dolomite, red·brown, heavy, but unevenly bedded, exposed............ 4-6 FEET
4. Drift and wash ............. _ .... _ .................. _ ...................... _ .... _................. 0-3
3. Limeston:e, light gray; white when weathered ... _ ............ : ....... _..... 0-3
2. Dolomite, yellowish brown, much shattered and unevenly bedded 6-8
1. Dolomite, red·brown, heavy, but unevenly bedded, exposed............ 4-6 Numbers 1 and 2 are, in a sense, complementary. Where one
thins the other thickens, and the two aggregate twelve feet ex-
posed. Not the slightest trace of organic remains could be
found. Southward and southeastward the beds are cut out with-
in one hundred yards by the coal measure shales, only to come
into view again a quarter of a mile down the branch on the
terrace of the Iowa." Other exposures of brownish dolomitic limestone of Eagle
City age appear at intervals in the banks of Iowa river above
Eagle City all the way to Iowa F'alls. N ear the east line of the northwest quarter of section 20, MISSISSIPPIAN STRATA OF iOWA' 96 Hardin township, at the mouth of a small creek in the north
bank and near the point where the river turns south, twenty-two
feet of thinly and irregularly bedded yellowish dolomite out-
crops. The rock evidently was once an oolitic limestone, in part
at least, as indicated by the fact that small remnants of imper-
fectly dolomitized gray oolite were observed in the dolomite. No fossils were noted here. One-half mile above this point in the southeast orie-fourth of
the southeast quarter of section 18, Hardin township, another
good exposure of these beds is afforded in the quarry of the
Ells'worth Stone Company. Seotion in the quarry of the Ellsworth Stone Company. FEET
6. Drift ..................... _ .... _......................................................................... 2- 3
low A FALLS DOLOMITE. 5. Dolomite, soft, brownish, thin-bedded above but massive
below. Resting on the irregular surface of the bed bp.low. A two foot zone five feet below the top is rich in ~i.mple
comJs, and bears numerous specimens, of Straparollus obt~ £sus. The dolomite is granular and slightly vesicular. Seotion in the quarry of the Ellsworth Stone Company. 5.
Dolomite, soft, brownish, thin-bedded above but massive
below.
Resting on the irregular surface of the bed bp.low.
A two foot zone five feet below the top is rich in ~i.mple
comJs, and bears numerous specimens, of Straparollus obt~ £sus.
The dolomite is granular and slightly vesicular. Probably
formed by the alteration of a medium·grained
lime~tone.
'l'hin shaly scams occur in the basal part ................................... List of fossils f1'om bed 4 of the bridge seotion at Eagle City. Limestone, light gray, lithographic, the upper three and
one·half feet interbedded with layers anc1 discontinuous
seams of coarser dark gray c1olo,mite .... :......................................... 2
D l
i
fi
i
d
f
h
i
ll
i h 2. Dolomite, fine· grained, soft, gray weathering yellowish,
rather thinly bedded. With many small pockets and seams
of calcite. In some places parts of the bed are filled with
masses and streaks of pyrite, which in some instances is asso·
ciated with the calcite ____ ..... _._ ....... _ ........................ __ ........ "'_"'_'_'" 1. Dolomite, clark gray when fresh, cdnse, massive. :r~xposed .. __ Beds 1 to 4 of this section are referred to 'the Eagle City, but
probably they represent a higher horizon of that formation
than is represented at the type locality described above. Bed!) ~
on the other hand, belongs to the lower part of the Iowa Falls
dolomite. The contact of this formation with the limestone be-
low is undulating in such a way as to suggest a dis conformity
at this level, but the phenomenon probably is due to uneven
dolomitization, in which case it should be classed as a pseudo-
disconformity. Another excellent opportunity for. studying the Kinderhook is
furnished in the gorge of Iowa river below the dam at Iowa IOWA FALLS DOLOMITE 97 ]'alls, two miles above the Ellsworth quarry. The river has cut
through an anticlinal flexure here, exposing in the' west bank
about seventy feet of strata, the lower twenty-five feet of which
belongs to the Eagle City. The section is as -follows: IOWA FALLS DOLOMITE.
6
D l
it
ll Section in gorge at Iowa Falls Section in gorge at Iowa Falls
IOWA FALLS DOLOMITE. FEET
6. Dolomite, yellowish to brownish, massive below but thin-bedded
at the top; slightly vesicular. The lower beds tendin.g to
recede in the cliff. Contact with bed below very undulating,
as a result of uneven dolomitization ____ .... ______________ .. _________________
44
EAGLE CITY FORMATION. 5_
Limestone, gray, lithographic, contact with bed above wavy
owing
to dolomitization
along an irregular
line; bearing
Camal-o-toechia sl!bglobosa _____________________________________________________________________
21h
4. Limestone, dark gray, dolomitic, in a single layer with regular
contacts ____________________________________________________________ ____________________________ ._____________
1
3. Limestone, gray, compact, faintly oolitic below but distinctly
so -above. Flaking off parallel to surface of bluff. This and
bed above receding
_____ .______________________ ______________________________________________
6
2_
~estone, gray, lithographic, in thin layers but in places
assuming a
massive appearance. No
fossils no-ted. With
layers of darker gray dolomitic limestone interbedded at the
top. Weathering whitish _: _______________ ._______________________________________________
10
1. Limestone, dark gray, dolomitic, dense, brittle; in laye
of
medium thiclmess. Exposed _____________________________________________________________
21h 4. Limestone, dark gray, dolomitic, in a single layer with regular
contacts ____________________________________________________________ ____________________________ ._____________
1
3
Li
t
t
f i tl
liti
b l
b t di ti
tl 1. Limestone, dark gray, dolomitic, dense, brittle; in laye
of
medium thiclmess. Exposed _____________________________________________________________
21h At the dam, bed 5 is seven feet thick and is not dolomitized. Further down stream it thins abruptly and is dolomitized local-
ly. Bed 3 of the above section contains occasional fossils, several
of which are undescribed. A list of those collected is given be-
low: List of fossils from Eagle City formation at Iowa Falls. Syringopol'a
~ sp. Camarotoechia subglobosa Weller
Camarotoechia sp. Eumetria
sp_
Conocardium sp. Schizodus (sevel1al species)
Pelecypods
(several
undetermined
species)
Stl'a,parollus obtusus (Hall) Eumetria
sp_
C
di Conocardium sp. THE IOWA FALLS DOLOMITE.-This division of the Kinderhook
attains its typical development only in the vicinity of Iowa
Falls where it caps the section in the west bank of the gorge of
Iowa river at the point where it cuts through the anticline. The
character of the formation in this exposure has been considered
in the above-described section. In general it consists of yellow-
ish to brownish slightly vesicular beds of dolomite, massive in
the lower part, but thin-bedded at the top. The lower beds at
many places recede slightly in the cliff. Section in gorge at Iowa Falls :MISSISSIPPIAN STRATA OF IOWA 98 At a point in the west bank about one hundred yards below
the axis of the anticline, this dolomite may be seen in irregular
contact with the Eagle City formation. It has her(3 a thickness
of forty-four feet, but higher beds undoubtedly have been erod-
ed. The upper six feet is thin-bedded. A
d
f thi
b
l
h
t di A good exposure of this member also appears a short dis-
tance upstream in the cliff at the west end of the Washington
street bridge. It has an exposed thickness of forty-four feet
six inches at this point, the contact with the lower beds being
situated two or three feet below the water level. The upper
five feet is thin-bedded. I
Wild C
Gl
h
id
f h
i
f
f In Wild Cat Glen, on the west side of the river, not far from
the last mentioned exposure, the thin-bedded member at the top
of the Iowa Falls is eight feet six inches thick, and bears a
number of fossils in the form of molds. These are listed below: • IMt of fossils from Iowa Falls dolomite at Wild Cat Glen. ANTHOZOA-
Zaphrentis sp. Spirifer sp. Ambocoelia sp. BR.ACmOPODA-
Orthotetes
~ sp. Centron.elloidea rowleyi (WQrthen)
Athvris crassicardinalis White f
Dielasma sp. GASTROPODA-:-
(Miller)
Orthonychia 81"
Camarotoechia: d . O. tuta
Camarotoechia f sp. Spiriferina solidirostris White
Ho~opea subc.onica Win. f
A
i
l
d
h lf
il
f h Camarotoechia f sp. Spiriferina solidirost Spiriferina solidirostris White Approxiroately one and one-half miles west of the gorge sec-
tions, the Iowa Falls dolomite is again well exposed in a high
cliff on the solith side of Iowa river in the northwest quarter of
section 14, Hardin township. The following succession was
measured: Sectio'TIJ of Iowa Falls dolomite in Hardin township. FEET
4. Drift
............. _ ............................................... ______ ... __________ . ____ . __ .. _. ____ . __ . __
3. Dolomite, thi.n-bedded, brownish . _________ .... _________________________ .. ___ .. ______ .. 9
2. Dolomite, brownish,
massive, soft,
showing
concretionary
structure _______ .. _________ . ___ .. _ .. _____ .. _ ... _. ___ ... ___ .... __ .... ____________________ . ___________ . __ .. _
26
1. Dolomite, soft, brownish, thin· bedded with thin disCOO1t:inJuOUS
bands of chert. Exposed . ___ .. ____ .. _______ ... ____ .. _ .... 3.
Dolomite, thi.n bedded, brownish
2
Dolomite
brownish
massive • IMt of fossils from Iowa Falls dolomite at Wild Cat Glen.
ANTHOZOA-
Zaphrentis sp.
Spirifer sp.
Ambocoelia sp.
BR.ACmOPODA-
Orthotetes
~ sp.
Centron.elloidea rowleyi (WQrthen)
Athvris crassicardinalis White f
Dielasma sp.
GASTROPODA-:-
(Miller)
Orthonychia 81"
Camarotoechia: d . O. tuta
Camarotoechia f sp.
Spiriferina solidirostris White
Ho~opea subc.onica Win. f
A
i
t l
d
h lf
il
t
f th Section in gorge at Iowa Falls _______ .. _ ... _ ... __ ...... _..... 10 Sectio'TIJ of Iowa Falls dolomite in Hardin township. 4. Drift
3. Dolom 3. Dolomite, thi.n bedded, brownish
2
Dolomite
brownish
massive 1. Dolomite, soft, brownish, thin· bedded with thin disCOO1t:inJuOUS
bands of chert. Exposed . ___ .. ____ .. _______ ... ____ .. _ .... _______ .. _ ... _ ... __ ...... _..... 10 Three hundred yards up stream, in the opposite bank, Des
Moines shales and sandstones ' replace these beds of dolomite
They appear to rest on the irregular surface of bed 1 of tho
preceding section and to extend down almost to the water level
in places. They doubtless fill an old channel cut into the dolo-
mite in pre-Pennsylvanian time. ALDEN LIMESTONE NEAR ALDEN 99 One-half mile southwest of this point a small exposure of the
Iowa Falls dolomite appears at the east end of the railroad
bridge, a short distance . south of the center of section 15 of
Hardin township. It consists of fifteen feet of brownish dolo-
mite in the form of thin even layers in the basal part, massive
beds in the middle, and thin, nodular layers at the top. No
fossils were found. Sixty rods above the railroad bridge in the southwest quarter
of section 15, the Iowa Falls dolomite may be seen . in discon-
formable relation with the Alden limestone. The contact line is
very uneven and: undulating. At the south end of the exposure
it is at places below the level of the water of the river and at
other places is above that level. Toward the north end it rises. The maximum exposed thickness of the dolomite is SL,{ feet. It
is thin-bedded and nodular in places, and tends to recede in the
low bluff. The overlying gray slightly otlitic .A1den limestone
has a maximum exposed thickness of eighteen feet. Lenticular
masses of shale, some of which are of large size, appear here
and there along the contact. Another excellent contact section of the Iowa Falls dolomite
with the Alden limestone is shown a short distance upstream ill
the old Ivanhoe quarries. This exposure is described under the
discussion of the Alden limestone. THE ALDEN LIMESTONE.-This member of the Kinderhook is
typically exposed in the south bank of Iowa river just below the
wagon bridge at the town of Alden in Alden township. Section in gorge at Iowa Falls It con-
sists of light gray, slightly oolitic, subcrystalline limestone in
thin layers which locally are cross-bedded. Many of the layers
are less than one inch in thickness, and layers exceeding three
inches are rare. The total thickness of beds exposed in this sec-
tion is about seventeen feet. Careful search was made for
fossils, but no identifiable specimens were found. A second exposure of the Alden limestone of considerable in-
terest is found in the quarry of the Hale Roberts Stone Com-
pany, just northeast of Alden between the wagon road and the
Chicago and North Western railway in the southeast quarter of
section 18, Alden township. This shows lower layers than are
exposed in the river bank at Alden. About thirty-two feet of
limestone is exposed, of which the upper half is like that ex- MISSISSIPPIAN STRATA OF IOWA 100 posed along the river. It is light gray in color, thin-bedded aml
slightly oolitic. The lower part is a darker gray when fresh
and some is slightly bluish. It is in thicker layers and is less
oolitic than that above and evidence of cross-bedding is shown
at several horizons. Some of the layers near the bottom are as
much as a foot in thickness. Occasional fissures, widened by
solution, have been filled with clay. One set of these trends
nearly north-south and another set nearly east-west. The drift
at the top. is thin, usually being only a foot or two in thickness. At the old Ivanhoe quarries in the southeast quarter of sec-
tion 16 of Alden township, this formation is shown in contact
with the Iowa Falls dolomite. The section at that place is as
follows: 64 Geology of Franklin County, Iowa Gaol. Survey, vol. XVI, p. 478 _ Section in Ivanhoe quarries. 2. Limestone, light gray, faintly oolitic, some layers slightly
crinoidal, especially in the lower part. The upper half weath·
ers to thin layers, but the lower part is more massive and
tends to show a darker tint when fresh. Locally slightly
mashed and showing slickensided structure along small irregu·
lar fract.ures ............................................................................................ 18 1. Dolomite, brownish, cavernous and vesicular; in places concre·
tionary; contact with bed above very irregular and undulating,
locally marked by lenses of fine sandstone and shale one foot
or more in thickness. Some of these beal' small fragml'.nts of
carbonized wood. Exposed ................................................................ 6 Bed 1 of this section represents the Iowa Falls dolomite. Bed
2 is the Alden limestone which was formerly quarried. No
fossils sufficiently well preserved to be identified were found. In the northwest quarter of section 2, Tipton township, a
limestone similar to the Alden in lithologic character outcrops
on the west bank of the South Fork of Iowa river just below the
wagon bridge. Four feet of slightly mashed gray medium-
grained limestone, some layers of which are finely crinoidal, is
exposed here. No fossils were found. Franklin County.-·With the exception of a small area in its
extreme northeastern part where the Upper Devonian forms the
surface rock, the Kinderhook underlies the whole of Franklin
county. In the western part of the county it is buried by Wis-
consin drift, but to the east, beyond the border of this drift
sheet, it is exposed at many localities in the banks of the larger
streams. SHEFFIELD BEDS NEAR SHEFFIELD Orthotetes , sp.
Camarotoechia ch Seotwn of Sheffield beds in Ross township (After Willia'T/.s).
3.
Shale, buff to yellow, slightly magnesian, containing irregular
concretions of lime carbonate and thin bands of lime!ttone at
FEET
top; nonfossiliferous ._________________________________________________________________________
3
2.
Shale, yellow, pink to :red, plastic____________________________________________________
6
1.
Shale, nonfossiliferous, phlstic, blue, with some carbonaceous
matter and occasional thin seams of selenite ________________________________
6 Spirifer sp.
CliOithyridina prouti (Swallow) Seotwn of Sheffield beds in Ross township (After Willia'T/.s). SHEFFIELD BEDS NEAR SHEFFIELD 101 The Kinderhook of this area comprises the three basal forma-
tions : the Sheffield beds, the Chapin beds and the Mayne Creek
formation. THE SHEFFIELD BEDs.--The lower part of this member is well
exposed in a clay pit at the brick plant one-half mile south of
the town of Sheffield, near the center of section 9, Ross town-
ship. The section at this point as described by Williams64 is as
follows : . Seotwn of Sheffield beds in Ross township (After Willia'T/.s). 3. Shale, buff to yellow, slightly magnesian, containing irregular
concretions of lime carbonate and thin bands of lime!ttone at
FEET
top; nonfossiliferous ._________________________________________________________________________
3
2. Shale, yellow, pink to :red, plastic____________________________________________________
6
1. Shale, nonfossiliferous, phlstic, blue, with some carbonaceous
matter and occasional thin seams of selenite ________________________________
6 2. Shale, yellow, pink to :red, plastic_______
1
Sh l
f
ilif
hl ti
bl 1. Shale, nonfossiliferous, phlstic, blue, with some carbonaceous
matter and occasional thin seams of selenite ________________________________
6 A well drilled at the plant encountered firm limestone (Upper
Devonian ~ ) about twenty feet below the bottom of the pit. Williams refers the shale in this exposure to the Hackberry
shale member of the Upper Devonian, and it is so represented
on his geological map of Franklin county. But its correlation
with similar bodies of shale exposed in the eastern part of the
county and referred to the Kinderhook appears to the writer to
be the more reasonable one. Unfortunately the shaly character
of the basal Kinderhook in this region has caused its contact
relations with the Upper Devonian to be obscured. . The greatest exposed thickness of the Sheffield shale observed
in Franldin county is shown about three-fourths mile southeast
of the clay pit mentioned above, in the south bank of Bailey
creek just east of the road along the west side of section 10,
Ross township, and in a road cut above. Forty-four feet of argillaceous shale, gray when dry but blu-
ish when wet and containing thin bands and flakes of brownish
dolomitic limestone in the lower part, is present in the bluff. In
the road cut near the top of the bluff this is overlain conform-
ably by twelve feet of soft brownish dolomitic shale which bears
the following fossils: Spirifer sp. SHEFFIELD BEDS NEAR SHEFFIELD CliOithyridina prouti (Swallow) 102
MISSISSIPPIAN ST 102 MISSISSIPPIAN STRATA OF IOWA This assemblage of fossils is characteristic of the topmost
member of the Sheffeld shale wherever it outcrop~ in northern
Iowa. The work of Prof. A. O. Thomas has shown the presence of
an outlier of the Sheffield formation in sections 7, 8, 17, and 18
of West ]fork township which had been mapped previously by
Williams as Upper Devonian. The total thickness of the forma-
tion in this region, according to Thomas, who has studied cer-
tain well records, is sixty feet. Along the north-south ro'ad near
the northeast corner of section 17 , West Fork township, a good
opportunity is afforded for studying these beds. Section of Sheffield beils, section 17, West Fork township. FEET
3. Drift ........................................................... _............................................. 11
2. Shale, brownish and dolomitic in upper part, but ,gray and
slightly gritty below. A thin seam of chert eleven f eet below
the top bears Cliothyridina, prouti, Praductus bl/lli,ri, Co.ma7·otoe·
chio. chouteauensis, and a Spirifer resembling Spirifer whitneyi
16 '1
1. Shale, bluish, argillaceous, no fossils noted ..................... :................ 2,2 3. Drift ........................................................... _............................................. 11
2. Shale, brownish and dolomitic in upper part, but ,gray and
slightly gritty below. A thin seam of chert eleven f eet below
the top bears Cliothyridina, prouti, Praductus bl/lli,ri, Co.ma7·otoe·
chio. chouteauensis, and a Spirifer resembling Spirifer whitneyi
16 '1
1. Shale, bluish, argillaceous, no fossils noted ..................... :................ 2,2 The fossils of bed 2 are characteristic of the upper fossilifer-
ous part of the Sheffield. In an abandoned quarry in the southeast quarter of section 7,
higher beds of the Sheffield are exposed. The section here is as
follows: Section of Sheffield beds, section 7, w,est Fork township. Section of Sheffield beds, section 7, w,est Fork township. FEET
3. Drift ............................................................................................... _......... Ilh
2. Shale, dolomitic, yellowish, thin· bedded ; bearing thin flakes of
chert .......................................................................................................... 2
1. Limestone, gray, in thim: layers filled with fragments of
brachiopods, crinoids, and other fossils,
Locally cross·bedded
on a small scale. Many fragments of fossils are silicified and
stand in relief on weathered surfaces. Exposed .......................... 4 1. Limestone, gray, in thim: layers filled with fragments of
brachiopods, crinoids, and other fossils,
Locally cross·bedded
on a small scale. Many fragments of fossils are silicified and
stand in relief on weathered surfaces. Exposed .......................... Section of Sheffield beils, section 17, West Fork township. Section of Sheffield beils, section 17, West Fork township.
FEET
3. Drift ........................................................... _.............................................
11
2.
Shale, brownish and dolomitic in upper part, but ,gray and
slightly gritty below. A thin seam of chert eleven f eet below
the top bears Cliothyridina, prouti, Praductus bl/lli,ri, Co.ma7·otoe·
chio. chouteauensis, and a Spirifer resembling Spirifer whitneyi
16 '1
1. Shale, bluish, argillaceous, no fossils noted ..................... :................
2,2 SHEFFIELD BEDS NEAR SHEFFIELD 4 The following fossils were collected from beds 1 and 2 : Productus blairi Miller ,
Camarotoechia sp. Spirifer sp. (similar to S. whitneyi)
Cliothyridina prouti (Swallow)
Eumetria 'I sp. About twenty rods south of this quarry along the east-west
road on the north line of the northeast quarter of section 18, a
small outcrop shows several feet of bluish argillaceou~ shale
overlain by one foot of thin-bedded limestone rich in fragments
of crinoids. This limestone bed is at a level twenty-seven feet FOSSILS IN SHEFFIELD BEDS 103 below the quarry described above. collected from it:
'
The following fossils were below the quarry described above.
collected from it:
'
The following fossils were below the quarry described above. collected from it:
'
The following fossils were Camarotoechia
~ sp,
Spirifer sp. (resembles S. whitneyi) Camarotoechia
~ sp,
Spirifer sp. (resembles S. whitneyi) Productus sp. Camarotoechia ,sp. Productus sp. Camarotoechia ,sp. Camarotoechia
~ sp,
Spirifer sp. (resembles S. whitneyi) The upper fossiliferous beds of the Sheffield, including the
oolitic limestone member, are again well exposed in an aband-
oned quarry located near the middle of the north line of sec-
tion 14 of Geneva township. The section is described below. Seotion of Sheffield beds, ,section 14, Geneva township. Seotion of Sheffield beds, ,section 14, Geneva township. FEET
4, So'il ........................................................................... _ ....... :......................... 1-2
3. Dolomite, yellowish, soft, thin·bedded, much w,eathered, earthy,
stratification very imperfect ................................................................ 5
2,
Dolomite,
yello~vish brown, massive when fI'esh but weathering
to thin layers. Lower part filled with silicified fossils ................ 2%
1. Limestone, gray to pinkish, oolitic, massive when fre~h;
' cut
by very even vertical joints with remarkably flat surfaces............ 61h On the opposite side of a· small valley at this place there is a
change in profile at a level about one foot below the hottom of
thfl quarry. A shale bed is believed to underlie the oolite. LiS't 01 fossils from above exposure. Spirifer sp. Schellwienella sp. Productus blairi Miller
Productus arcuatUf< Hall 'I
Productus sp. Camarotoechia sp. Spirifer sp. (resembles S. whitneyi)
Cliothyridina prouti (Swallow)
Fish spine. LiS't 01 fossils from above exposure. LiS't 01 fossils from above exposure. Productus blairi Miller
P
d
t
tUf< H l Productus arcuatUf< Hall 'I
P
d
t Productus sp. C
hi Camarotoechia sp. One mile slightly north of west of the preceding expo::ml'e, in
the southwest one-fourth ,of the southeast quarter of section 10,
Geneva township, strata of a similar horizon appear in an
abandoned quarry situated just east of the bridge over Mayne
creek. The sucession of beds here is indicated below: Section of Sheffield beds in section 10, Geneva township.' Section of Sheffield beds in section 10, Geneva township. FEET
3. Soil
.......................................................................................................... '
1
2. Shale, brownish, dolomitic, with a band of chert nodules near
the middle ............................................................................................ _
11
1. Dolomite, yellowish brown, in one massive ledge. Soft and
vesicular. Exposed ... _........................................................................... 10 Silicified fossils are common. The beds are rent by rather
widely spaced vertical joints. Fragments of oolitic limestone
were noted in the rubble and doubtless came from a lower bed MISSISSIPPIAN STRATA OF IOWA 104 now concealed. A line of springs appears about ten feet below
the base of bed 1. now concealed. A line of springs appears about ten feet below
the base of bed 1. List of fossi-ls from bed 1 of the Chapin beds, near the southwest corner of
section 29, Ross township. ANTHOZOA-
Zaphrentis calceola (W. and W.)
Zaphrentis sp.
Amplexus sp. FEET
6.
Drift ................................................................................................. _.......
12
5.
Dolomite, yellowish brown, soft, thin· bedded, with occasional
t hin lenses of chert ..............................................................................
10
4.
Dolomite, yellowish brown, soft, in rather heavy, irregular
layers, becoming soft,
pulverulent and saccharoidal where
weathered; with thin discontinuous seams and nodules of fos·
siliferous chert which weathers chalky................................................
16
3.
Dolomite, yellowish, compact and tough; more resistant than
the bed below......................................................................................
1
2.
Dolomite, very soft, much weathered, brownish, flaking off
obliquely; with occasional thin discontinuous ~eams of chert
some of which are fossiliferous ..........................................................
10
1.
Dolomite, compact, brownish, tough, with occasional
~mall
nodules of chert. A few imperfect casts and impressions
of fossils were noted ..................................... ,....................................
4 CHARACTER OF MAYNE CREEK BEDS CHARACTER OF MAYNE CREEK BEDS 105 BRACHIOPODA-
Spirifer platyno,tus Weller ,
Spirifer sp. Spirifer sp. Syringothyris sp. Leptaena analog'd. (Phillips)
Chonetes
multico~ta Win. Chonetes logani N. and P. Productus arcuatus Hall
Productus ovatus Hall
Schizophoria chouteauensis Weller'
Rhipidomella tenuicostata Weller
Spiriferina solidirostl'is White
Spirifer forbesi N. GJ1d P. Athyris crassicardinalis White ,
Nucleospira barrisi White. '
BRYOZOA-
,
Fenestella sp. GASTROPODA-
Straparollus obtusus (Hall)
Spirifer legrandensis Weller BRACHIOPODA-
Spirifer platyno,tus Weller ,
Spirifer sp. Spirifer sp. Syringothyris sp. Leptaena analog'd. (Phillips)
Chonetes
multico~ta Win. Chonetes logani N. and P. Productus arcuatus Hall
Productus ovatus Hall
Schizophoria chouteauensis Weller'
Rhipidomella tenuicostata Weller
Spiriferina solidirostl'is White
Spirifer forbesi N. GJ1d P. Athyris crassicardinalis White ,
Nucleospira barrisi White. '
BRYOZOA-
,
Fenestella sp. GASTROPODA-
Straparollus obtusus (Hall)
Spirifer legrandensis Weller Spirifer platyno,tus Weller ,
S i if Spirifer sp. S i if Productus arcuatus Hall
P
d
H ll Rhipidomella tenuicostata Weller
i if
i
lidi
l'i
Whi
,
Feneste Spirifer forbesi N. GJ1d P. S i if
l
d
i
W ll Spirifer legrandensis Weller List of fossils from bed 2 of the Chap1in, beds, necw the southwest oorner of seotion
29, Boss township. ANTHOZOA-
Zaphrentis I>p. L ANTHOZOA-
Zaphrentis I>p. Leptopora typa Win. Spiriferina solidirostris White
Spirifer legrandensis Weller
Spirifer , sp. BRACHIOPODA-
Spirifer sp. Leptaena analoga (Phillips)
Chonetes multicosta Win. Chonetes sp. Syringothyris cf. S. halli Win. Syringothyris sp. Productus arcuatus Hall
Productus ovatus Hall
Productus sp. Schizophoriu. chouteauensis
Caruarotoechia sp. Dielasma sp. Cliothyridina sp. Nucleospira barrisi White
BRY;OZOA-
Cystodictya sp. Welled
Fenestella sp. PELECYPODA-
Conocardium sp. Spiriferina cf. S. subtexta White Type seotion of the MC1!JJne Creek formation. List of fossils from abo1J6 exposure. Chonetes sp. Streptorhynchus sp. Productus blairi Miller
Oamaroooechia chouteaunsis Weller Cliothyridina pro uti (Swallow)
Spirifer sp. (resembles S. whitneyi)
Fish plate. Streptorhynchus sp. Productus blairi Miller Oamaroooechia chouteaunsis Weller THE CHAPIN BEDS.-Following the Sheffield shale conformably
appear the Chapin beds. These differ in character from place
to place, but consist typically of shale at the base followed
above by cross-bedded crinoidal and slightly oolitic limestone
which is in turn overlain by brownish soft fine-grained sand~
stone. The two uppermost beds, however, in places pass later-
ally into soft brownish dolomitic limestone. All the beds are
highly fossiliferous. The thickness of the Chapin is twenty to
thirty feet. The most representative exposure of these beds in Franklin
county is at the type section, "which is shown in an abandoned
quarry one mile west of the town of Chapin in the southwest
corner of the southwest quarter of section 29, Ross township. The succession of beds there is as follows: Section of Chapin beds near Chapin. Section of Chapin beds near Chapin. Section of Chapin beds near Chapin. FEET
3. Drift ....................................................................................................... 2-3
2. Sandstone, very fiEe',grained, soft, gray when fresh but
weathering yellowish; lower two feet massive, but upper four
and one·half feet thin·bedded; filled' with casts of fossils......... 6%
1. Limestone" gray, sub crystalline, faintly oolitic, with inter .. bedded layers of crinoidal limestone which weather brownish. In rather heavy, even layers when fresh but weathering into
thinner layers. Exposed ..................................................................... 6% Section of Chapin beds near Chapin. FEET
3. Drift ....................................................................................................... 2-3
2. Sandstone, very fiEe',grained, soft, gray when fresh but
weathering yellowish; lower two feet massive, but upper four
and one·half feet thin·bedded; filled' with casts of fossils......... 6%
1. Limestone" gray, sub crystalline, faintly oolitic, with inter .. bedded layers of crinoidal limestone which weather brownish. In rather heavy, even layers when fresh but weathering into
thinner layers. Exposed ..................................................................... 6% 6% In a smaller opening only a few rods away in the northeast
corner of section 31, number 1 has an exposed thickness of
seven feet. Beds-1 and 2 are highly fossiliferous. The species collected _
are listed below. List of fossi-ls from bed 1 of the Chapin beds, near the southwest corner of
section 29, Ross township. ANTHOZOA-
Zaphrentis I>p.
L
t
t Leptopora typa Win. Leptopora typa Win. BRACHIOPODA- Leptaena analoga (Phillips)
Ch
t
lti
t
Wi Chonetes multicosta Win. Chonetes sp Chonetes sp. P
d
t Productus arcuatus Hall
P
d
t
t
H ll Productus ovatus Hall
P
d
t Spiriferina cf. S. subtexta White THE MAYNE CREEK BEDS.-This formation is typically de-
veloped along Mayne creek in Franklin county, hence its name. The type section is located in the north bluff of this creek in
the northeast quarter of section 21, Reeve township. .A. revised
description of the succession at this place is given below: Type seotion of the MC1!JJne Creek formation. FEET
6. Drift ................................................................................................. _....... 12
5. Dolomite, yellowish brown, soft, thin· bedded, with occasional
t hin lenses of chert .............................................................................. 10
4. Dolomite, yellowish brown, soft, in rather heavy, irregular
layers, becoming soft,
pulverulent and saccharoidal where
weathered; with thin discontinuous seams and nodules of fos·
siliferous chert which weathers chalky................................................ 16
3. Dolomite, yellowish, compact and tough; more resistant than
the bed below...................................................................................... 1
2. Dolomite, very soft, much weathered, brownish, flaking off
obliquely; with occasional thin discontinuous ~eams of chert
some of which are fossiliferous .......................................................... 10
1. Dolomite, compact, brownish, tough, with occasional
~mall
nodules of chert. A few imperfect casts and impressions
of fossils were noted ..................................... ,.................................... 4 .A. number of species of brachiopods, pelecypods and gastro-
pods, several of which are undescribed, were collected from the
chert seams of bed 2. These have been identified as follows: MISSISSIPPIAN STRATA OF IOWA 106 List of fossils from the Mayne Creek forl1?'ation in the northeast quarter of seotion
21, Reeve township. AN'.PHOZOA-
. Zaphrentis f sp. BRYOZOA-
Cystodictya sp. BRACHIOPODA-
Chonetes multicosta Win. Orthotetes ~ sp. Camarotoechia sp. Spiriferina solidirostris White
Spirifer legranclensis Weller'
~
PELECYPODA-
Leda saccata Win. Myalina sp. GASTROPODA-
Bellerophon sp. Bucanopsis sp. Meekospira
~ sp. Orthonychia sp. CRUSTACEA-
Phillipsia
~ sp. PELECYPODA-
Leda saccata Win. Myalina sp. GASTROPODA-
Bellerophon sp. Bucanopsis sp. Meekospira
~ sp. Orthonychia sp. CRUSTACEA-
Phillipsia
~ sp. PELECYPODA- Leda saccata Win. M
li Myalina sp. Camarotoechia sp. Spiriferina solidirostris White
S i if
l
l
i
W ll
'
~ Spirifer legranclensis Weller'
~ Two miles northeast of the above described bluff section, near
the northwest corner of the northeast quarter of section 23,
Reeve township, a part of the Mayne Creek beds is exposed in
an abandoned quarry on the ,property of Mr. Butler County.-The Kinderhook beds constitute the highest Reticulal'ia cooperensis (Swallow)
Composita
~ sp. ANTHOZOA-
Zaphrentis I>p.
L
t
t Bert Jones. At
the present time ten feet of thin-bedded, shelly brownish dolo-
mitic limestone is shown in the quarry face. The upper half
contains thin discontinuous bands of chert, and becomes cavern-
oU's where long exposed to weathering. Several specimens of a
Productus and an Orthotetes? were collected from the chert. A
few small cavities lined with calcite were noted at one point in
the middle part of the ledge. East of the road, near the middle of the west side of section
18, Geneva township, there is a conspicuous outlier of ' Mayne
Creek limestone. About twelve feet of brownish, dolomitic lime-
stone is exposed at the top of the hill. The lower half is mas-
sive, cavernous and cherty, and weathers to a brownish pulver-
ulent mass. The upper half is thin-bedded, and contains fossil-
iferous chert seams. The fossils collected from these seams
are: Leptaena analoga (Phillips)
Schizophoria chout.eauensis Weller
Reticulal'ia cooperensis (Swallow)
Composita
~ sp. Reticulal'ia cooperensis (Swallow)
Composita
~ sp. The Mayne Creek formation appears again in a small aband-
oned quarry in the north bank of a small creek about fifty yards
west of the road in the southeast one-fourth of the southeast
quarter of section 9, Reeve township. Ten feet of soft, brown-
ish, thin-bedded dolomite, with occasional bands and lenses of
light gray chert are shown. Numerous poorly preserved fossils
occur in the chert. Butler County.-The Kinderhook beds constitute the highest SEJE:E'FIELD BEDS IN BUTLER COUNTY 107 consolidated rock over a small area in the southwestern part of
Butler county. The distribution of the formation' as indicated
in Arey's geological map of the county65 is only approximately
correct. For example, the narrow area of Kinderhook repre-
sented in the northwestern part of Madison township and ex-
tending into the southwestern part of Pittsford township prob-
ably does not exist. Apparently the fact that Williams66 erron-
ously referred to the Kinderhook the Owen limestone which
outcrops near the middle of the north-south line between section
18, Madison township, Butler cOlmty, and section 13, Geneva
township, Franklin county, iSI responsible for the confusion. Again the occurrence of Sheffield shale three-fourths mile north
of the town of Aplington in Monroe township as described be-
low necessitates a shifting of the Kinderhook border in that
region some distance to the northeast. 65 Iowa Geol. Survey, vol. XX, opposite page 58.
66 Williams
I
A
Iowa Geol
Survey
vol
XVI
p y,
,
pp
p g
66 Williams, I. A., Iowa Geol. Survey, vol. XVI, p. 487. 65 Iowa Geol. Survey, vol. XX, opposite page 58.
66 Williams, I. A., Iowa Geol. Survey, vol. XVI, p. 487 66 Williams, I. A., Iowa Geol. Survey, vol. XVI, p. 48 ANTHOZOA-
Zaphrentis I>p.
L
t
t The Kinderhook formations represented in Butler county are
the Sheffield, the Chapin and the Mayne Creek. The Sheffield
covers by far the largest area. THE SHEFFIELD BliDs.-The basal member of the Kinderhook
series of this part of the state outcrops at a number of localities
in Washington and Monroe townships. \
h
i h b
k
f
k
f h
f
i In the right bank of Beaver creek east of the center of section
31, Washington township, there appears eight feet of bluish,
plastic shale with thin intercalated layers of brownish dolomite. It is believed that these beds should be correlated with the low-
er shaly division of the Sheffield. N ear the middle of the north line of section 18, Washington
to'wnship, .about six feet of soft thin-bedded cherty dolomitic
shale outcrops in ' a roadside gully. Silicified specinlens of the
following forms were collected at this locality: Schellwienella ~ sp. Productus blairi Miller
Camarotoechia chouteauensis Weller
Spirifer
sp. (resembling S. whit-
neyi)
Cliothyridina pro uti (Swallow)
Th
i
i di
h
di i i
f h
Sh ffi ld Spirifer
sp. (resembling S. whit-
neyi)
Cliothyridina
prouti
(Swallow) Spirifer
sp. (resembling S. whit-
neyi)
Cli th
idi
ti
(S
ll
) Schellwienella ~ sp. Productus blairi M Productus blairi Miller
Camarotoechia chouteaue Cliothyridina pro uti (Swallow) Camarotoechia chouteauensis Weller These species indicate the topmost division of the Sheffield. B d
i
h
f
d i
b
d Beds carrying the same fauna are exposed in an abandoned
quarry in section 28, Washington township, a few rods west of
the railway bridge over Beaver creek. Five feet of brownish MISSISSIPPIAN STRATA OF IOWA 108 arenaceous and dolomitic shale is shown here at the present
time. arenaceous and dolomitic shale is shown here at the present
time. In Monroe township, this fossiliferous zone of the Sheffield
may be studied to good advantage in the gullies along the north-
south road in the northwest quarter of section 20, three-fourths
of a mile north of the town of Aplington. Seven feet of soft
brownish dolomite with a few imperfect casts and impressions
of fossils is here overlain by four feet of soft brownish dolo··
mitic shale which bears silicified specimens of the same species
as listed above. Arey67 reports the occurrence of Lime Creek beds in this
vicinity but no trace of such beds could be found by the writer. FEET
3.
Dolomite, soft, yellowish, thin·bedded; with occasional sma11
lenses of chert.
No identifiable fossils noted ......................... -.
n~
2.
Sandstone, very fine, soft, yellowish, with occasional thin
layers of brownish dolomite. A zone in lower part filled
with casts of fossils ................................................................. ,..........
7
1. Dolomite, tough, brownish. :E'ossils scarce ...............................
4
67 Iowa Geol. Survey, vol. XX, p. 36.
Id
39 67 Iowa Geol. Survey, vol. XX, p. 36.
68 Idem, p. 39. 67 Iowa Geol. Survey, vol. XX, p. 36.
Id
39 ANTHOZOA-
Zaphrentis I>p.
L
t
t THE CHAPIN AND MAYNE CREEK BEDS.-At two points in Wash-
ington'township these formations appear in contact. The most
complete exposure is found in an old quarry near the center of
the west half of sectie>n 31, between Beaver creek and the Illi-
nois Central railroad. This has been described by Arey68 and
the following description is copied in part from his: Section in section 31, Washington township. FEET
INCHES
5. Limestone, thin·bedded, yellow to drab, with bands and
nodules of chert .............................................................................. 3
4. Limestone, brown, sugary, dolomitic; with a five inch band
of chert in the lower half ............................................................ 1
10
3. ' Chert, in the form of a series of lenses ..... _ ............... __ ............ 3
2. Dolomite,' massive, yeUowish, finely
aren~ceous, fossiliferous 6
6
1. Dolomite, brownish, massive, tough ; bearing casts and im·
pressions of fossils. Exposed ..................... _ .... _............................. 5
6 Section in section 31, Washington township. Beds 1 and 2 of the above section bear a Chapin fauna and
they are referred to that formation. The overlying cherty beds
are correlated with the Mayne Creek. Near the southwest cor-
ner of the southwest quarter of section 28 there is an east-west
ridge just north of Beaver creek. On the south side of this the
following composite section is exposed: FEET
3. Dolomite, soft, yellowish, thin·bedded; with occasional sma11
lenses of chert. No identifiable fossils noted ......................... -. n~
2. Sandstone, very fine, soft, yellowish, with occasional thin
layers of brownish dolomite. A zone in lower part filled
with casts of fossils ................................................................. ,.......... 7
1. Dolomite, tough, brownish. :E'ossils scarce ............................... 4
67 Iowa Geol. Survey, vol. XX, p. 36. 68 Idem, p. 39. KINDERHOOK IN HUMBOLDT COUNTY 109 The fauna of beds 1 and 2 suggests their Chapin age. Bed 3
is referred to the Mayne Creek. The species collected! from bed
2 are listed below: Spirifer legranclensis Weller
Spirifer platynotus Weller ,
Syringothyris sp. Cliothyridina tenuilineata (Rowley)'
Conocardium sp. Spirifer legranclensis Weller
Spirifer platynotus Weller ,
Syringothyris sp. Cliothyridina tenuilineata (Rowley)'
Conocardium sp. Schizoblastus roemerl Shumard
F
ll Fenestella sp. P
l Procluctus sp. P
l Procluctus sp. Procluctus sp Procluctus sp. Procluctus sp Procluctus sp. h ll
i
ll Schellwicnella , stl. 69 Iowa Geol. Survey, vol. XX, pp. 100-149; 1910.
70 Iowa Geol. Survey, vol. IX, p . 123. ANTHOZOA-
Zaphrentis I>p.
L
t
t Another section-in which appear beds believed to be of Mayne
Creek age is in an old quarry in the southeast one-fourth of the
northeast quarter of section 32 of Washington township. Eigh-
teen feet of fine gray massive sandstone with several discontin-
uous seams of chert is exposed. Fragments of fossils occur in
the cherts. Wright County.-The Kinderhook formation is believed to
form the bed rock over the greater part of 'Wright county
though no exposures of rocks of this age are described by Mac-
bride69 in his report on the geology of Hamilton and 'Wright
counties. Humboldt County.-The Kinderhook is nearly everywhere
covered by glacial drift in Humboldt county. But in the vicin-
ity of the towns of Humboldt and. Rutland, oolitic limestones of
this age appear at the surface over small areas. The largest
of these appears in the east bank of the West Fork of Des
Moines river in the southwest part of the town of Humboldt. At an abandoned lime kiln in this area, the limestone has an
exposed thickness of twelve feet. The rock is gray in color,
and the texture is typically oolitic. In the lower part of the
section, the oolite grains are small and the matrix lithographic,
but in the upper part the grains are coarser and the texture is
more crystalline. Macbride70 lists the following gastropods from the oolites of
the Humboldt area: . Strapa.rollus planispira. Hail ,
Straparollus sprin:gvalensis (White)
Bellerophon sublaevis Hall. . Strapa.rollus planispira. Hail ,
Straparollus sprin:gvalensis (White)
Bellerophon sublaevis Hall. Loxonema yanclellana Hall ,
Straparollus macromphalus Winchell
Straparollus obtusus (Hall) Loxonema yanclellana Hall ,
St
ll
h l
Wi Loxonema yanclellana Hall ,
Straparollus macromphalus Winchell
St
ll
bt
(H ll) Straparollus macromphalus Winchell
S
ll
b
(
ll) Straparollus obtusus (Hall) The following additional forms have been collected and de- 110 MISSISSIPPIAN STRATA OF IOWA scribed from this locality by Sardeson71 who remarks that "fos-
sils are readily found in certain strata at Humboldt along the
river's bank from 'Bicknell's Park to the dam .... " scribed from this locality by Sardeson71 who remarks that "fos-
sils are readily found in certain strata at Humboldt along the
river's bank from 'Bicknell's Park to the dam .... 71 Am. Geologist, vol. XXX, p. 300 ff.; 1902. Cyathophyllum glabrum Keyes
Macrodon cf. co~hlearis Win. Louis limestone in contact with the Kinderhook. The succession
is as follows: SelJtion near the orea;mery at Rutlamd. SelJtion near the orea;mery at Rutlamd. FEET
4. Drift ... _ ................ _ .... __ ....................... _ .. _ .... _ ...... _ ............... _................... 2
ST. LOUIS
3_ Limestone, brecciated, dense, gray, imperfectly -dolomitized;
lower surface irregular and undulating ............... _._ .. _ ............. _........ 3
2_
Limestone, dense, gray, tough, in the form of one u!l1dulatu1g
layer which fills irregular depressions in the limestone be·
neath ......... _ ......... _ ......... _ ..... _ ............ _ ......... _ ..... _._ .. _ ............. _ ... _ ........ _ ... __ Ih to 1
KINDERHOOK
1. Limestone, light gray; stratification very imperfect; finely
oolitic except in middle part where there is a thin seam of
coa-rse oolite ........... ___ ... _ ........ _ .... _ ....... _ .... __ ...................... _ ............ _ ......... _2
to 3lh 4. Drift ... _ ................ _ .... __ ....................... _ .. _ .... _ ...... _ ............... _................... 2
ST. LOUIS 3_ Limestone, brecciated, dense, gray, imperfectly -dolomitized;
lower surface irregular and undulating ............... _._ .. _ ............. _........ 3
2
Limestone
dense
gra
to gh
in the form of one
!l1d lat 1g 2_
Limestone, dense, gray, tough, in the form of one u!l1dulatu1g
layer which fills irregular depressions in the limestone be·
neath ......... _ ......... _ ......... _ ..... _ ............ _ ......... _ ..... _._ .. _ ............. _ ... _ ........ _ ... __ Ih to 1
NDERHOOK 1. Limestone, light gray; stratification very imperfect; finely
oolitic except in middle part where there is a thin seam of
coa-rse oolite ........... ___ ... _ ........ _ .... _ ....... _ .... __ ...................... _ ............ _ ......... _2
to 3lh At the mouth of this creek, in the southeast quarter of the
northwest quarter of section 29, Rutland township, the contact
of the Kinderhook and the St. IJouis is again shown. At this
point about four feet of the oolite is exposed above the bed of
the creek. This is overlain by three feet of gray tough St. Louis dolomite which weathers ;yellowish. At one point in the
exp~sure this dolomite grades laterally, in part, into unaltered
gray brecciated limestone. About seventy-five yards below this exposure the contact is
shown in the river bank. ANTHOZOA-
Zaphrentis I>p.
L
t
t " Myalina ~ abstemia &rdeson
Cyathophyllum glabrum 'Keyes Euomphalus lu.'(us White
Loxonema difficile Sardeson Euomphalus lu.'(us White
Loxonema difficile Sardeson On the east side of the river just below the dam at Humboldt
fifteen feet of oolite is exposed in the river bank. The texture
of some of the upper layers is very finely oolitic and approaches
that of a lithographic limestone, but elsewhere the grains are
large except for occasional thin seams. Stratification is very
imperfectly dev:eloped, and the rock shows many fractures. Slickensided structure is abundantly shown along the fissures. I
h
h
f
i
33 R
l
d
hi
j In the northeast quarter of section 33, Rutland township, just
east of the Humboldt cemetery, the oolite is well exposed in a
small drainage ditch about four feet 'in depth. The upper one-
third of the outcrop consists of coarse oolite, but in the lower
two-thirds the grains are very fine and the rock is dense and
rather brittle. Large pisolitic masses ranging from the size of
a pea to three or four inches in diameter are common through-
out. Many of these consist of a nodule of oolitic limestone
coated with concentric layers, but a few show concentric struc-
ture throughout. No fossils weFe noted. At the town of Rutland the oolite is exposed on the south side
of the river both above and below the bridge. On the north
side there are good exposures farther west, in the vicinity of
the dam. ,The maximum thiclmess exposed 'On this side is ten
feet and the rock is rather brittle. The lower half is not well
stratified, and weathers to irregular polyhedrons. The oolite
grains are small in this part. The upper half is evenly bedded,
and the oolite g~ains are large. Sardeson regards these beds as identical 'with those at Hum-
boldt. He lists the following species from this locality: Cyathophyllum glabrum Keyes
Macrodon cf. co~hlearis Win. Murchisonia sp. undet. In the south bank of a small creek southwest of the creamery
at Rutland, there is a very interesting section showing the St. 71 Am. Geologist, vol. XXX, p. 300 ff.; 1902. KINDERHOOK AT RUTLAND 111 Louis limestone in contact with the Kinderhook. The succession
is as follows: Louis limestone in contact with the Kinderhook. The succession
is as follows: Three feet of Kinderhook oolite i~
~ucceeded by a two to three foot layer of yellowish undulating
limestone, and this again by four feet of dense gray thin-bedded
unaltered limestone which locally is mashed into mounds of
breccia. The Kinderhook at this locality also shows consider-
able fracturing and slight brecciation. Several other exposures
between this point and the bridge show similar contact relation-
ships. The gray limestone of the St. Louis js five and one-half
feet thick at one point. The relation of the Humboldt oolite to the Kinderhook forma-
tions of Hardin and Franklin counties has not been determined
definitely owino- to the absence of exposures of underlying
formations in Humboldt and adjacent counties. The fauna and -
the lithologic character of the oolite are of little aid in correlat-
ing it with other Kinderhook formations. The fact that it is
overlain by the St. Louis limestone at several localities indi-
cates that it represents the topmost member of the Kinderhook
group m this part of the state. It may be younger than the MISSISSIPPIAN STRATA OF IOWA 112 Alden limestone of Hardin county, which has not been found in
contact with the St. Louis, but the possibility of greater erosion
of the Kinderhook in the Humboldt area than in the Iowa Falls
area in pre-St. Louis time must be borne in mind. Inasmuch as
the Humboldt oolite bears no resemblance, either lithologically
or faunally, to the Iowa Falls or older formations, it is believed
to represent either a more oolitic and more fossiliferous facies
of the Alden lime ~tone or a younger formation not prese'rved
in Hardin county. In the southwestern part of Hmnboldt county a limestone
formation which is referred provisionally to the Kinderhook
group outcrops at several localities. This was formerly corre-
lated with the St. Louis limestone by Macbride
72 who describes
the exposures as follows: "At various points in Weaver ~ownship, as in the northeast·
quarter of section 9, there are 'exposures of limestone rock
which must be considered here. These are mostly in the form
of quarries, originally sink-holes, which have been developed to
meet the local demand for rubble stone. From the exposure in
section 9, just mentioned, a large amount of rock has been
taken. The quality seems to be excellent, and the bedding is
such as to make comparatively light the labor of the quarrymen. 72 Iowa Geol. Survey, vol. IX, p . 132. Louis limestone in contact with the Kinderhook. The succession
is as follows: The rock is a rather coarse-grained, crystalline, encrinital lime-
stone, reminding one of rocks elsewhere referred to the Augusta
stage, unlike any seen anywhe-re in the river exposures. Open
sink-holes in this neighborhood show almost everywhere rock
of the same character, so that it is probable that all the south-
western part of the county is underlain by similar strata, except
where removed by pre-glacial erosion. In the town of Gilmore,
for instance, a similar rock in the northeast part of the village
comes to the surface of the ground, while a few rods west, the
town well goes down SL"{ty feet before encountering rock at all. Nevertheless, we may consider this peculiar encrinitallimestone
as the surface rock for all that part of Humboldt county lying
south of the west fork, except the flood plains immediately ad-
jacent to the stream. The same rock extends far into Poca-
hontas county, and is there exposed in precisely the sa~e way. Thus in Clinton township, in Pocahontas county, one TIllIe west
of Gilmore, and one and one-half miles north, is a sink-hole
quarry, which for years has been very extensively worked". FossHs were collected from this limestone in the outcrops
across the county line in Pocahontas county. The age of the 72 Iowa Geol. Survey, vol. IX, p . 132. KINDERHOOK FOSSILS NEAR GILMORE 113 formation is discussed in connection with the description of
these exposures. formation is discussed in connection with the description of
these exposures. Pocahontas Oounty.-The same limestone formation which
outcrops in ,Veaver township, Hmnboldt county, forms the bed
rock along a narrow belt in the extreme eastern parts of Gar-
field and Lake to"wnships in Pocahontas county. To the west jt
passes under Cretaceous deposits. rrhe Pocahontas county ex-
tension of this form'ation was also formerly referred to the St. Louis upon the basis of a few poorly preserved fossils.73
h
f h
Gil
l
d C
C In the quarry of the Gilmore Portland Cement Company, one
and one-half miles northwest of Gilmore City, the following
beds are exposed : Section. in. Gilmore Portland Cement Company's q~w,rry. p
y
FEET
5,
Limestone, light gray, fine· grained, thin·bedded, rather soft:
Exposed at the south ·end of the qualTy ............. _ ........ _................... 4%
4. Li~eston.~,. ~ompact~ gray, dense, fine'grained, brittle, very
famtly oohtlc, m:1SSJ,ve ............................ _......................................... 10
3. 7.3 Iowa Goal. Survey, vol, IX, p . 132, and vol. XV, p. 255, Louis limestone in contact with the Kinderhook. The succession
is as follows: Limestone, as in bed 2 .but filled with cylindrical corals ... _ .... _
21f.l
2. Limestone, gmy, oolitic, compact, brittle .................................... 4
1. Limestone, gray, massive, slightly crinoidal, oolitic. Exposed
6 2. Limestone, gmy, oolitic, compact, brittle
1
Limestone
gray
massive
slightly crinoid The beds dip gently in a southeasterly direction in the quarry
face, the axis of a low anticline being shown in the northwest
end of the quarry. One-half mile northwest of the preceding section similar
beds are shown in two adjoining sink-hole quarries: Section iIn sink hole quarries. Section iIn sink hole quarries. q
FEET
3. Limestone, gray, compact, brittle, slightly oolitic ...................... 7
2. Limestou.e, gray, crinoidal, massive, the matrL-;: oolitic, crinoid
fragments less pronounced and oolitic character more char·
teristic in lower half. Showing tendency towards cross
bedding
........................... __ .... _ ............... __ ................................ __ .... 8
1. Limestone, gray; compact, fine· grained, slightly oolitic, thim.-
bedded and somewhat shaly below. EA."posed ... _____ .... __ ........ _..... 4 1h 3. Limestone, gray, compact, brittle, slightly oolitic ...................... 7
2
Limestoue
gray
crinoidal
massive
the matrL ;: oolitic
crinoid 3. Limestone, gray, compact, brittle, slightly oolitic ...................... 7
2. Limestou.e, gray, crinoidal, massive, the matrL-;: oolitic, crinoid
fragments less pronounced and oolitic character more char·
teristic in lower half. Showing tendency towards cross
bedding
........................... __ .... _ ............... __ ................................ __ .... 8
1. Limestone, gray; compact, fine· grained, slightly oolitic, thim.-
bedded and somewhat shaly below. EA."posed ... _____ .... __ ........ _..... 4 1h 2. Limestou.e, gray, crinoidal, massive, the matrL-;: oolitic, crinoid
fragments less pronounced and oolitic character more char·
teristic in lower half. Showing tendency towards cross
bedding
........................... __ .... _ ............... __ ................................ __ .... 8
1
Limestone
gray; compact
fine·grained
slightly oolitic
thim 1. Limestone, gray; compact, fine· grained, slightly oolitic, thim.-
bedded and somewhat shaly below. EA."posed ... _____ .... __ ........ _..... 4 1h The following fossils were collected from these exposures: List of fossils from simk hole q~rries two miles Mrthwest of Gilmore City. NTHOZOA
Spirifer
f
gp Spirifer f ,gp. S i if Spirifer
sp
SyringothYl'is f SyringothYl'is f sp. Eumetria sp Monotrypa sp. A
OPODA Eumetria sp. Eumetria
sp Eumetria sp. Cliothyridina Camarotoechia sp. Camarotoechia sp Camarotoechia sp. Spiriferina sp Spiriferina sp. Spirifer
sp Spirifer sp. -- 7.3 Iowa Goal. Survey, vol, IX, p . 132, and vol. XV, p. 74 Iowa Geol. Sury., v,ol. VII, p. 170. Louis limestone in contact with the Kinderhook. The succession
is as follows: 255, MISSISSIPPIAN STRATA OF IOWA 114 All of the beds in these exposures belong to a horizon below
the coral zone (bed 3) of the cement quarry. The total exposed
thickness of the formation, therefore, is not less than thirty-six
and one-half feet. A well record at the cement plant is reported
to have shown a thiclmess of forty-one feet of this type of lime-
stone, succeeded below by a brownish dolomitic limestone. The lack of diagnostic fossils in the fauna listed above, most
of the species being undescribed, together with the absence of
exposures of associated formations of known age renders the
exact correlation of the Gilmore City limestone impossible at
present. Lithologically it resembles the Alden limestone of
Hardin cOlmty more closely than any other formation in north-
central Iowa, but unfortunately no identifiable fossils were
found in the Alden limestone which could be compared with
those collected near Gilmore City. The occurrence of brownish
dolomitic limestone below the Gilmore City oolitic limestone as
reported in the boring at the cement.quarry reminds one of the
similar succession in Hardin county where the bro'wnish Iowa
Falls dolomite underlies the oolitic Alden lin1estone. However,
exact correlation must await the discovery of better preserved
fossil remains in the Alden limestone than have hitherto been
found. The relation of the Gilmore City limestone to the Humboldt
oolite could not be determined by field study since no exposure
showing them in contact has been found. The inference is that
the Humboldt oolite is the younger of the two formations. Cerro Gordo Co~£nty.-The Kinderhook series extends into
the southwestern part of Cerro Gordo county. Calvin74 wrote
as follows regarding the beds : "Strata of the Kinderhook stage of the Lower Carboniferous
series are exposed along Beaver Dam creek in section 36 of
Pleasant Valley township. Where the county line road, on the
Routh side of the section, crosses the creek, the Kinderhook beds
are composed of soft, shaly, magnesian limestone; but in Frank-
lin county, 'a short distance south of the road, beds that occupy
a higher position are exposed in the sides of the vallev, and
these are firm enough to afford quarry stone suitable for bridge
piers, foundations, and other rough masonry. An Athyri.s re- KiNDERHOOK OF NORTH-CENTRAL IOWA 115 sembling Athyris proutii Swallow, a Productus related to P. pwnctatu.s, and Orthothetes sp. are the characteristic fossils. Louis limestone in contact with the Kinderhook. The succession
is as follows: The next exposures east of the Kinderhook outcrops are the
Devonian beds already noted on· Beaver creek. The contact of
the Carboniferous with the pevonian was not observed, but the
line of overlap ljes between the two localities last named." ](os8'uth, Hancock and Winnebago C01unties.-The Kinder-
hook apparently extends over this area but it is deeply buried
by drift. No exposures are referred to in the literature on these
counties. The Cretaceous deposits of western Kossuth county
are bebeved to rest upon the Kinderhook beds_ 76 In connection with the term S heffield attention should be called to the fact that in a
paper by C. L. Fenton on the Upper Devonian of Iowa in The American Journal of Science,
volume xlviii, pages 355-376, 1919, the name Sheffield wa.s applied to the plastic blue shale
which underlies the mal'ly fossiliferous wnes of the Cerro Gordo sub-sta)!e at Rockford,
Juniper Hill, Hackberry Grove, Mason City and elsewhere l1(}rth and east of
Sheffield.
Fenton was doubtl"ss under the impression that the shales at Sheffield were identical with
those of Devonian age at Mason City and Rockford, being apparently misled by Williams'
error in describing and mapping 1he shales at Sheffield as Upper Devonian in the · Franklin
county report.
(Iowa Geological Survey, volume xvi, pages 477-481, 502 and ma.p opposite
page 506.)
However, the beds at Sheffield are Kinderhook according to Van Tuyl's evidence
and the name as employed by him seems appropriate.
Since the name Sheffield for obviouR
reasons is unavailable for the Upper Devonian shales, the name Juniper Hill is here offered
for that formation.
Juniper Hill, located about one mile northwest of the Rockford Brick
and Tile Plant,
i~ in the midst of numerous gooll exposures of the form ation and where its
relation to the beds above and below may be readily observed.-A_ O. Thomas_ Correlation of the Kinderhook of North-central Iowa The Kinderhook of north-central Iowa attains its most typical
development in 'Franklin, Butler and Hardin counties. From a
study of indiV'idual exposures and the log of a deep well at
Iowa Falls in Hardin county the series has been subdivided into
six distinct formations as follows: The Alden limestone
·I'he Iowa Falls dolomite
The EI3,gle City beds
The Mayne Creek beds
'1'he Chapin beds
The Sheffield beds The Alden limestone
I'he Iowa Falls dolom ·I he Iowa Falls dolomite
The EI3gle City beds The EI3,gle City beds
The Mayne Creek bed The Mayne Creek beds
'1'he Chapin beds 1he Chapin beds
The Sheffield beds The Sheffield beds 'rhe pancity of fossils in the lower shaly strata of the Shef-
field beds renders their age uncertain. Further study may indi-
cate their Upper Devonian affinities. The collection~ obtained
from the limestone and dolomitic shale directly above the shales
of doubtful age contain a few species of brachiopods and an oc-
casional fish remain. With the exception of a Spirifer which
resembles Spirifer whitneyi of the Upper Devonian the brachio-
pods are Kinderhook types and are for the most part species
characteristic of the Chouteau formation. Th
f
f h
Ch
i
M
C
k E
l
Ci
d I The faunas of the Chapin, Mayne Creek, Eagle City and Iowa
Falls formations contain many undescribed species but the as-
semblages are all distinctly Kinderhook in aspect. Occasional
species of Burlington brachiopods occur in the higher forma-
tions of the series. Th
f
h
i
i
Ch
i
i
h The appearance of characteristic Chouteau species in the up-
per portion of the Sheffield formation and in the Chapin beds is
worthy of note. The latter formation has yielded thirty-five MISSISSIPPIAN STRATA OF IOWA 116 species. Twenty of these have been identified specifically. Nearly all of the twenty are characteristic Chouteau forms and
twelve of them occur in beds 6 and 7 of. the Kinderhook at Burl-
ington. In this connection, Weller's conclusions regarding the age of
the Chouteau fauna in Missouri are of interest. 75 "From the outline of the faunal history here given, it is evi-
dent that the arrangement of the Kinderhook formations into
three successi ve divisions, the Louisiana, Hannibal, and
Chouteau, as has usually been done, does not express the proper
relationships of the faunas. 75 Jour. Geol., vol. 17, pp. 274, 2 75 ; 1909. Definition of Osage The term Osage group was proposed by H. S. Williams' in
1.891. to include the Burlington and Keokuk formations. In later
reports several authors have included the Warsaw beds in the
Osage also, but Weller2 now refers the Warsaw to the overlying
Meramec group. Keyes 3 has used the term Augusta series to include the Burl-
ington, Keokuk and vVarsaw formations but as vVeller4 has
pointed out the term Osage clearly has priority. Correlation of the Kinderhook of North-central Iowa The Chouteau fauna, in some of its
expressions, is without doubt as old as the Louisiana fauna, and
it is as impracticable to make one continuous section to contain
all of the Kinderhook formations, as it would be to make a
standard Devonian section to include the formations of New
York and Iowa." From the above statement it is apparent that while the faunas
of the upper 'Sheffield 76 and Chapin beds have Chouteau affinities
and are more closely related to the faMules of beds 6 and 7 at
Burlington than to those of the underlying Kinderhook beds,
this does not necessarily indicate the exact equivalency of these
beds. The evidence supports the view that the Chouteau fauna ap-
peared earlier in Kinderhook time in the northern area, as it
did in central Missouri, than in the Burlington area. The
Chonopectus fauna of the lower beds in the Burlington area
may have existed simultaneously with the Chouteau fauna to
the north. 1 u. s. GeoI: Survey Bull. 80. p. 169. 2 Illinois Geol. Survey. Bull. 41, p. 80; 1920. 1 u. s. GeoI: Survey Bull. 80. p. 169.
2 Illinois Geol. Survey. Bull. 41, p. 80; 1920.
3 Iowa Geol. Survey, vol. I, p. 50; 1893.
4 Am. Geologist, vol. XXII, p. 12 If; 1898. 1 u. s. GeoI: Survey Bull. 80. p. 169.
2 Illinois Geol. Survey. Bull. 41, p. 80; 1920. 3 Iowa Geol. Survey, vol. I, p. 50; 1893.
4 Am. Geologist, vol. XXII, p. 12 If; 1898. 3 Iowa Geol. Survey, vol. I, p. 50; 1893. 3 Iowa Geol. Survey, vol. I, p. 50; 1893.
4 Am. Geologist, vol. XXII, p. 12 If; 1898. Distribution of the Group Exposures of the Osage group are confined to the southeast-
ern part of Iowa. For the most part they appear in a sinuous
northwest-southeast trending belt of irregular width extending
from southern Lee county on the south to Keokuk county on the
north. It is probable that rocks of this age are present beneath
the glacial deposits in southwestern Iowa and south-central
Poweshiek counties also. The belt is bounded by the Kinder-
hook group on the northeast and by the Meramec group on the
southwest. As a result of the study of deep well records the
group is known to be present beneath Meramec and younger
formations in south-central Iowa. The Osage attains its full development in Iowa in Des Moines,
Lee and Van Buren counties only. To the northwest there is a
thinning of the group from above downwards probably due jn
part to nondeposition and in part to post-Osage erosion. In
the vicinity of Keokuk both members of the group are present,
though the Burlington limestone is below the surface. In south- MISSISSIPPIAN STRATA OF IOWA 118 ern Des Moines county the Burlington and Keokuk formations
are fully developed and both are well exposed. Still farther
northwest, in Keokuk and Washington counties, the Keokuk is
reduced in thickness. Stratigraphic ReI.3.tions, The Osage group apparently is conformable with the Kinder-
hook beds below. It is succeeded by the Meramec beds without
a break in the extreme southeastern part of the state but to the
northwest, where the St. Louis limestone member of the Mera-
mec overlaps successively older formations, a well marked dis-
conformity exists at the top of the group. LithoLogic Character The Osage group is composed of interstratified gray to bluish
gray crinoidal limestone, gray to brownish dolomitic limestone
and ash-colored to bluish shales,. The bluish gray crinoidal
limestones are characteristic of the Keokuk while the gray ones
appear in the Burlington. Shale beds increase in number and
thickness towards the top of the group, presumably as a result
of a gradual recession of the sea from the area during Osage
time . Thickness Where both formational members of the Osage are fully de-
veloped, it has a thickness of 134 feet. In Washington and
Keokuk counties it is, probably not much more than one hundred
feet thiclr. . . NOMENCLATURE The Burlington limestone was so namedi by HaW because of
its typical development in the exposures in and near the city of
this name in Des Moines county, Iowa. AREAL DISTRIBUTION
The distribution of the Burlington limestone as an individual AREAL DISTRIBUTION
The distribution of the Burlington limestone as an individual 5 Rept. GeoI. Survey. State of Iowa, vol. I, Part i, p. 92; 1858. AREAL DISTRIBUTION 5 Rept. GeoI. Survey. State of Iowa, vol. I, Part i, p. 92; 1858. CHARACTER OF BURLINGTON BEDS 119 unit is not definitely indicated on the geological map of Iowa,
since this member is included with the Keokuk in the Osage
group, the smallest division which has been mapped. The area
over which the Burlington constitutes the surface rock repre-
sents only a small part of the area indicated as Osage, owing to
the fact that a large proportion of this area is underlain by the
Keokuk beds. Previous studies have shown that the exposures
of Burlington limestone are confined to a restricted area in the
southeastern part of the state, including parts of Van Buren,
Lee, Des Moines, Louisa, vVashington, and possibly Keokuk
counties. In Van Buren county it forms the surface rock over a small
area in the bed of Des Moines river at Bentonsport. It under-
lies a larger area in the . eastern part of Lee county, but
its outcrops are confined to a few isolated localities. Thus,
there. are small exposures in the bed and banks of Lost creek
southeast of Denmark; in a number of small quarry openings
west of vVever; and in the bed and banks of Skunk river and
along its tributaries at and near South Augusta. It doubtless constitutes the surface rock over the greater part
of the eastern half of Des Moines county, but its outcrops are
limited, the more important ones being along the ravines about
Augusta, in the bluffs of Mississippi river, and numerous other
natural exposures, quarries and street cuts in and near the city
of Burlington. The area underlain by the Burlington in Louisa county is con-
fined to its southwestern and southern parts, the more jmport-
ant exposures being located in Morning Sun township. Northwestward from Louisa county actual exposures of the
Burlington have been found by the writer only in Washington
county, although there is a strong prob~bility thaf it underlies
the drift over small areas in northeastern Keokuk and southern
Iowa counties. In vVashington county, it follows a broad, ir-
regular band extending across the central part of the county
from southeast to northwest. The most satisfactory exposures
are located on and near Crooked creek, northwest of Washing-
ton. LITHOLOGIC CHARAOTER The Burlington limestone succeeds the Kinderhook in vertical MIS>SISSIPPIAN STRATA OF IOWA 120 ,succession with no indications of a stratigraphic break. Litho-
logically, the formation is a unit, but it is desirable to subdivide
it into the Lower and Upper BUrlington upon the' basis of its
crinoid fauna, as was pointed out long ago by Niles and Wachs-
muth. 6 The Montrose cherts, which were referred by Keyes
7 to the
Upper Burlington, have been demonstrated by the present study
to represent the basal member of the Keokuk limestone (see
page 142). '
Th
B
li
li
h
10
b
d f
i
f The Burlington limestone has 10ng been noted for its profu-
sion of crinoid remains. Probably at no other time in the
earth's history have crinoids flourished so prolifically. More
than four hundred species of crinoids have been described from
this formation alone. At several horizons in the limestone the
beds are made up almost completely of the disconnected plates
of the calyces and fragments of the stems and arms of crinoids. When they are pure these crinoidal beds are light gray to whit-
ish in color; when impure, they are discolored brownish. N or-
mally they contain occasional discontinuous bands and nodules
of chert. Stylotytic seams also are abundantly developed. Alternating with these crinoidal beds and comprising a large
part of the formation are beds of fine-grained brownish magne-
sian, cherty limestone. In the vicinity of Burlington, Iowa,
there is a seam of bluish shale averaging about one foot in
thickness, in the lower part of the Upper Burlington, but this
has not been observed at any other locality in Iowa. Th
b
d
f th
B
li
t
i
k d b
fi h b d The upper boundary of the Burlington is marked by a fish bed
of widespread extent. Regarding this, Wachsmuth and Spring-
erS say: . "The close of the Upper Burlington limestone was marked by
an extraordinary destruction of fishes whose remains, in the
form of teeth and spines, are found in the greatest profusion in
a stratum two to ten inches in thickness, which occurs at the
very top of the regular limestone beds. 6 Am. Jour. Science, 2d ser., vol 42, pp. 95-99; 1866.
7 Iowa Gool. Survey, vol. III, p. 341; 1893.
8 Proc. Acad. Nat. Sciences, Philadelphia. 1878. Part II. p. 2 7 Iowa Gool. Survey, vol. III, p. 341; 1893.
8 P
A
d
N t
S i
Phil d l hi
187 8 Proc. Acad. Nat. Sciences, Philadelphia. 1878. Part II. p. 227 7 Iowa Gool. Survey, vol. III, p. 341; 1893.
8 P
A
d
N t
S i
Phil d l hi
18 6 Am. Jour. Science, 2d ser., vol 42, pp. 95-9
7 Iowa Gool. Survey, vol. III, p. 341; 1893.
P
A
d
N
S i
Phil d l hi
1878 6 Am. Jour. Science, 2d ser., vol 42, pp. 95-99; 18
7 Iowa Gool
Survey
vol
III
p
341; 1893 6 Am. Jour. Science, 2d ser., vol 42, pp. 95-99; 1866.
7 Iowa Gool. Survey, vol. III, p. 341; 1893. AREAL DESCRIPTION BY OOUNTIES Des Moines and Lee Counties.-The type section of the Burl-
ington limestone is at Burlington, Iowa, where numerous ex-
posures of the formatioI). in and near the city make it possible
to work out th/il complete succession of beds and collect their
fossils. The following generalized section will illustrate the
character of the formation at this locality: General seotion of Burlmoton lime$tone at Burlinoton. General seotion of Burlmoton lime$tone at Burlinoton. General seotion of Burlmoton lime$tone at Burlinoton. General seotion of Burlmoton lime$tone at Burlinoton. UPPER BURLINGTON. FEET
. 6. Limestone, brownish to whitish, crinoidal; with occasional
chert bands; middle part sometimes magnesian; a thin zone
of fish teeth near the top ....................... _....................................... 10·12
5. Shale, bluish, ar.gillaceous, not everywhere present ....... _...... 114
4. Limestone, light gray, crinoidal, very fossiliferous .................... 5·8
3. Limestone, brownish, crinoidal ........................................ :................. 6·8
LOWER BURLINGTON. 2. Limestone,
brownish,
fine· grained,
magnesian,
irregularly
bedded; cherty, especially near the base; in places bears a
layer of crinoidal limestone near the middle ............................ 34-39
1. Limestone,
brownish,
crinoidal, massive,
locally magnesian
in part ....................................................... c............................................ 8-11
KINDERHOOK p
_
5. Shale, bluish, ar.gillaceous, not everywhere present ....... _...... 114
i
li h
i
id l
f
ilif
5 8 4. Limestone, light gray, crinoidal, very fossiliferous .................... 5·8
3
Li
t
b
i h
i
id l
6 8 3. Limestone, brownish, crinoidal ........................................ :................. 6·8
LOWER BURLINGTON. 2. Limestone,
brownish,
fine· grained,
magnesian,
irregularly
bedded; cherty, especially near the base; in places bears a
layer of crinoidal limestone near the middle ............................ 34-39
1
Li
b
i h
i
id l
i
l
ll
i 1. Limestone,
brownish,
crinoidal, massive,
locally magnesian
in part ....................................................... c............................................ 8-11
KINDERHOOK Beds 1 and 2 represent the Lower Burlington. They are well
exposed in the old quarry back of the high school, in the quar-
ries at Picnic Point and in the Mississippi river bluff at several
points in and near Burlington. Bed 3 outcrops in the bluff at the Cascade and on the slope
below the Miller quarry above the Cascade. Beds 4 and 6 are excellently exposed in the Miller quarry I
above the Cascade. Overlying bed 6 at this point, there appears
fifteen feet of brownish magnesian limestone, crinoidal in the
middle part, which yielded no identifiable fossils but which is
referred to the basal Keokuk. TmCKNESS TmCKNESS
The thickness of the Burlington limestone in the type section
where it is fully developed is approximately seventy-one feet, of
which twenty-seven feet is referred to the Upper Burlington and
the remainder to the Lower. In Louisa county the lower mem-
ber is only one-half as thick as at Burlington, while the upper
member is seventeen feet in thickness. LITHOLOGIC CHARAOTER It is one of the best
stratigraphic landmarks that we know in this formation, as it is
found over a wide area in localities over a hundred miles apart
and always in the same position relative to the heavy limestone
beds." BURLINGTON BEDS AT BURLINGTON BURLINGTON BEDS AT BURLINGTON 121 TmCKNESS
The thickness of the Burlington limestone in the type section
where it is fully developed is approximately seventy-one feet, of
which twenty-seven feet is referred to the Upper Burlington and
the remainder to the Lower. In Louisa county the lower mem-
ber is only one-half as thick as at Burlington, while the upper
member is seventeen feet in thickness. List of fOS'8ils from bed 1 of the Burlington lim·estone at Burlington. List of fOS'8ils from bed 1 of the Burlington lim·estone at Burlington. Burlington lim·estone at Burlington
Spirifer forbesi N. and P. Spirifer grimesi Hall
. Spirifer imbrex Hall ,
Spirifer louisianensis Rowley
Brachythyris sp. Syringothyris , sp. ,
)
)
Athyris lamellosa (Leveille)
PELECYPODA-
A viculopecten , sp. GASTROPODA-
Orthonychia sp. TRILOBITA-
Phillipsia , sp. VERTEBRATA-
Fish teeth CRINOIDEA-
Platycrinus ol'tlwgranulus McChesney ,
Platycrinus sculptus Hall
~
Platycrinus sp. Cactocrinus . multibrachiatu's (Hall)
Cactocrinus proboscidialis (Hall) ¥
Batocrinus subaequalis (McChesney)
Batocrinus sp. Dorycrinus unicornis (0. and Sh.)
BLASTOIDEA-
CryptoblaSitus melo O. and Sh. BRYOZOA-
Fenestella serratula Ulr. ¥
BRACHIOPODA-
Diclasma osceolensis Weller
Rhipidomella burlingtonensis (Hall) Spirifer forbesi N. and P. S i if
i
i H ll CRINOIDEA-
Platycrinus ol'tlwgranulus McChesney ,
Platycrinus sculptus Hall
~
Platycrinus sp. Cactocrinus . multibrachiatu's (Hall)
Cactocrinus proboscidialis (Hall) ¥
Batocrinus subaequalis (McChesney)
Batocrinus sp. Dorycrinus unicornis (0. and Sh.)
BLASTOIDEA-
CryptoblaSitus melo O. and Sh. BRYOZOA-
Fenestella serratula Ulr. ¥
BRACHIOPODA-
Diclasma osceolensis Weller
Rhipidomella burlingtonensis (Hall) CRINOIDEA
Platycrinus ol'tlwgranulus McChesney ,
Platycrinus sculptus Hall
~
Platycrinus sp. Cactocrinus . multibrachiatu's (Hall)
Cactocrinus proboscidialis (Hall) ¥
Batocrinus subaequalis (McChesney)
Batocrinus sp. Dorycrinus unicornis (0. and Sh.)
BLASTOIDEA-
CryptoblaSitus melo O. and Sh. BRYOZOA-
Fenestella serratula Ulr. ¥
BRACHIOPODA-
Diclasma osceolensis Weller
Rhipidomella burlingtonensis (Hall) Platycrinus ol'tlwgranulus McChesney ,
Pl t
i
l t
H ll
~ Spirifer grimesi Hall
S i if
i
b
H ll Spirifer imbrex Hall ,
S i if
l
i i
i
R Platycrinus sculptus Hall
~
Pl
i Platycrinus sp. C
t
i Spirifer louisianensis Rowley
B
h th
i Brachythyris sp. S
i
th
i Athyris lamellosa (Leveille)
PELECYPODA Phillipsia , sp. VERTEBRATA VERTEBRATA
Fi h Fish teeth Rhipidomella burlingtonensis (Hall) List of fossils from bed 2 of the B~rlington limestone at B~lrlington. AREAL DESCRIPTION BY OOUNTIES The fossils collected by the writer from the successive hori-
zons of the Burlington limestone are listed below: MISSISSIPPIAN STRATA OF IOWA 122 BRACHIOPODA-
)
Ch
t
i ANTHOZOA-
BRACHIOPODA-
Triplophyllum dalei (M.-E. Zaphtentis sp. CRINOIDEA-
Platycrinus sp. and H.)
Chonetes illinoisensis Worthen
Pustula alternata (N. and P.)
Spirifer grimesi Hall
Brachythyris suborbicularis (Hal
Cliothyridina in.crossata (Hall) Triplophyllum dalei (M.-E. Zaphtentis sp
and H.)
Chonetes illinoisensis Worthen
Pustula alternata (N and P ) .)
Chonetes illinoisensis Worthen
P
t l
lt
t
(N
d P ) Pustula alternata (N. and P.)
S i if
i
i H ll Spirifer grimesi Hall
B
h th
i
b
bi Brachythyris suborbicularis (Hall)
Cli th
idi
i
t
(H ll) Cliothyridina in.crossata (Hall) List of fossils from bed 3 of the Burlington limestone at B~lrlington. ANTHOZOA-
Eucladocrinus praenuntius W. and
Had,ophyllum glans White
Sp . . ~
Triplophyllum dalei (M.-E. and H.) mLASTOIDEA-
Monilopora sp. Orbitremites norwoodi (0. and Sh. CRINOIDEA-
BRACHIOPODA-
Periechocrinus sp. Chonetes sp. Megistocrinus cf. M. evansi (0. Rhipidomella burlingtonensis (Hall
and Sh.)
. Schi.7.ophoria swallovi (Hall)
Eutrochocrinus christyi
(Shum.)
Spirifer grimesi Hall
Uperocrinus pyriformis (Shum.)
Syringothyris typus Winchell
Physetocrim{s ventricosus (Hall)
Spiriferella plena (Hall)
Strotocrinus regalis (Hall)
Reticularia pseudolineata (Hall)
Platycrinus planus O. and Sh. ,
Reticularia sp. Platycrinus sp. Cliothyridina incrassata (Hall)
Platycrinus sp . ANTHOZOA-
Eucladocrinus praenuntius W. and
Had,ophyllum glans White
Sp . . ~
Triplophyllum dalei (M.-E. and H.) mLASTOIDEA-
Monilopora sp. Orbitremites norwoodi (0. and Sh.)
CRINOIDEA-
BRACHIOPODA-
Periechocrinus sp. Chonetes sp. Megistocrinus cf. M. evansi (0. Rhipidomella burlingtonensis (Hall)
and Sh.)
. Schi.7.ophoria swallovi (Hall)
Eutrochocrinus christyi
(Shum.)
Spirifer grimesi Hall
Uperocrinus pyriformis (Shum.)
Syringothyris typus Winchell
Physetocrim{s ventricosus (Hall)
Spiriferella plena (Hall)
Strotocrinus regalis (Hall)
Reticularia pseudolineata (Hall)
Platycrinus planus O. and Sh. ,
Reticularia sp. Platycrinus sp. Cliothyridina incrassata (Hall)
Platycrinus sp . ANTHOZOA-
Eucladocrinus praenuntius W. and
Had,ophyllum glans White
Sp . . ~
Triplophyllum dalei (M.-E. and H.) mLASTOIDEA-
Monilopora sp. Orbitremites norwoodi (0. and Sh.)
CRINOIDEA-
BRACHIOPODA-
Periechocrinus sp. Chonetes sp. Megistocrinus cf. M. evansi (0. Rhipidomella burlingtonensis (Hall)
and Sh.)
. Schi.7.ophoria swallovi (Hall)
Eutrochocrinus christyi
(Shum.)
Spirifer grimesi Hall
Uperocrinus pyriformis (Shum.)
Syringothyris typus Winchell
Physetocrim{s ventricosus (Hall)
Spiriferella plena (Hall)
Strotocrinus regalis (Hall)
Reticularia pseudolineata (Hall)
Platycrinus planus O. and Sh. ,
Reticularia sp. Platycrinus sp. Cliothyridina incrassata (Hall)
Platycrinus sp . Eucladocrinus praenuntius W. and
Sp . . IMt of fossils from bed 6 of the Burlington limestone a>t Burlington, ANTHOZOA-
Cosinium latum Ulrich
Zaphrentis calceola
Zaphrentis sp. (W. and W.)
BRACHIOPODA.-. Schellwienella
~ sp. Triplophyllum dalei (M.·E. and H.)
Amplexus fragilis White and St. John
CRrNOIDEA-
Eretmocrinus calyculoides (Hall)
Macrocrinus konincki (Shum.)
Macrocrinus verneuilianus (Shum. )
Dizygocrinus rotundus (Shum.)
Dizygocrinus andrewsianus (McChes·
ney)
Eutrochocrinus christyi (Shum.)
Eutrochocrinus lovei (W. and Sp.)
~
Uperocrinus
~ sp. Aorocrinus parvus (Shum.)
Dorycrinus quinquelobus (Hall)
Dorycrinus sp. Agaricocrinus OrJlotrema Hall
Teleiocrinus umbrosus (Hall)
Physetocrinus ventricosus (Hall)
Physetocrinus , sp. Strotocrinus glyptus (Hall)
~
Platy-crinus halli Shum. Platycrinus sp. BLASTOIDEA-
Chonetes illinoisensis Worthen f
Chonetes sp. Productus burlingtonensis Hall
Productus sp. Pustula alternata (N. and P.)
Rhipidomella burlingtonensis (Hall)
Rhipidomella dubia (Hall)
Rhynchopora sp. Dielasma sp. Dielasma sp. Spirifer grimesi Hall
Spirifer incertus Hall
Spirifer sp. Spirifer sp. Brachythyris sub orbicularis (Hall)
Brachythyris sp. Syringothyris typus Win. ~
Spiriferella plena (Hall)
Reticularia pseudolineata (Hall)
Eumetria sp. Athyris lamellosa (Leveille)
Cliothyridina tenuilineata (Rowley)'
Cliothyridina obma:rima(McChesney) ~
Cliothyridina incrassata (Hall)
GASTROPODA-
P entl'emites elong-atus Shum. Orbitremites norwoodi (0. and Sh.)
Lepetopsis capulus (Hall)
BRYOZOA-
Batostomella
~ sp. Fenestella burlingtonensis Ulrich
Rhombopora sp. Rhombopora sp. Rhombopora sp. Cystodictya ~ sp. Orthonychia
pabulocrinus
(Owen)
Platyceras obliquum Keyes ,
Platyceras latum Keyes
Platyceras paralium W. and W. Platyceras &p. VERTEBRATA.-
Fish teeth Table Showing Range of Species in Burlington Lilmestone at Burlington. Table Showing Range of Species in Burlington Lilmestone at Burlington. Horizons ~
1 121 3 I 4 I 6 I
ANTHOZOA
Zaphrentis calceola (W. and W.).............................................. ........ ........ ........ x
x
Zaphrentis sp ...................................................... _ ......... "'''''''''''','''''''' ........ ........ ........ x
Zaphrentis sp. .. ............................. _............................................. ........ ........ ........ x
....... . Zaphrentis sp. .............................................................................. ........ x
....................... . Triplophyllnm dalei (M.'E. and H.)...................................... ........ x
x
x
x
Amplexus fragilis White and St. John ... _ ............................ ,.,,,., ........... _... ........ x
Hadrophyllum glans (White)..................................................... ........ ........ x
x
...... .. Monilopora sp. .............................................................................. ........ ........ x
............... . CRINOIDEA
I
Periechocrinus sp ......................................................................... 1........ ........ x
.............. .. Table Showing Range of Species in Burlington Lilmestone at Burlington. Horizons ~
1 121 3 I 4 I 6 I
ANTHOZOA
Zaphrentis calceola (W. and W.).............................................. ........ ........ ........ x
x
Zaphrentis sp ...................................................... _ ......... "'''''''''''','''''''' ........ ........ ........ x
Zaphrentis sp. .. ............................. _............................................. ........ ........ ........ x
....... . Zaphrentis sp. .............................................................................. ........ x
....................... . Triplophyllnm dalei (M.'E. and H.)...................................... ........ x
x
x
x
Amplexus fragilis White and St. John ... BRACHIOPODA-
)
Ch
t
i ~
ASTOIDEA Uperocrinus pyriformis (Shum.)
Ph
t
i
{
t i
(H l Physetocrim{s ventricosus (Hall)
St
t
i
li
(H ll) Strotocrinus regalis (Hall)
Pl t
i
l
O
d Reticularia pseudolineata (Hall)
R ti
l
i Platycrinus planus O. and Sh. ,
Pl t
i Reticularia sp. Cli th
idi
i Cliothyridina incrassata (Hall) Platycrinus sp. Pl t
i Platycrinus sp . . List of fos~ls from bed 4, of the Burlington lwnestone at Burlington. ANTHOZOA-
Zaphrentis calceola (W. and W.)
Zaphrentis sp. . Triplophyllum dalei C~L-E. and H.)
Hadrophyllum glaJ1S (White)
CRINOIDEA-
Platycrinrus sp. Uperocrinus pyTiformis , (Shum.)
BRYOZOA-
Fenestella burlingtonensis Ulrich
Rhombopora gracilis Ulrich
Cystodictya sp. BRACHIOPODA-
Chonetes illinoisensis W ortlien
Productus burlingtonensis Hall
Productus sp. Rhipidomella dubia (Hall)
Dielasma sp. Spirifer grimesi Hall
Spirifer incertus H all
Syringothyris typus Win. Athyris lamellosa (Leveille)
GASTROPODA-
Straparollus sp. Lepetopsi~ capulus (Hall)
Platyceras sp. Orthonychia sp. TRILOBITA-
Phillipsia
~ sp. ANTHOZOA-
Zaphrentis calceola (W. and W.)
Zaphrentis sp. . Triplophyllum dalei C~L-E. and H.)
Hadrophyllum glaJ1S (White)
CRINOIDEA CRINOIDEA-
Platycrinrus sp. Uperocrinus pyTiformis , (Shum.)
BRYOZOA BRYOZOA-
Fenestella burlingtonensis Ulrich
Rhombopora gracilis Ulrich
Cystodictya sp. BRACHIOPODA BRACHIOPODA-
Chonetes illinoisensis W ortlien
Productus burlingtonensis Hall FOSSILS FROM'BURLINGTON BEDS 123 IMt of fossils from bed 6 of the Burlington limestone a>t Burlington, _ ............................ ,.,,,., ........... _... ........ x
Hadrophyllum glans (White)..................................................... ........ ........ x
x
...... .. Monilopora sp. .............................................................................. ........ ........ x
............... . CRINOIDEA
I
Periechocrinus sp ......................................................................... 1........ ........ x
.............. .. Table Showing Range of Species in Burlington Lilmestone at Burlington. MISSISSIPPIAN STltATA OF IOWA 124 Table Showing Bange of Species in Burlington Lfmtesto?1Je at Burlington--Continued. Table Showing Bange of Species in Burlington Lfmtesto?1Je at Burlington--Continued. I
Horizons
11121314161
Megistocrinus cf. M. evansi (0. and Sh.) ............................. _ ... 1 ... _... x
............... . Batocrinus subaequalis (McChesney) .................................... x
................... _ ...... _ .. . Batocrinus sp. . ................ _........................................................... x
........... _ .................. . Eretmocrinus calyculoides (Hall) ............................................... _ ...................... _ .. _ x
Macrocrinus konineki (Shuro. ) ................. _ ........................ _. ........ ........ ........ ........ x
MacI'ocrinus verneuilianus (Shuro.) ................. _ .............................. _... ........ ........ x
Dizygocrinus rotundus (Shuro.) ................. _ ................... : .......... _... ........ ........ ........ x
Dizygocrinus andrewsianus (McChesney) ............................ ........................... _... x
Eutrochocrinus christyi (Shuro.) ....... _ .............................................. _... x
x
Eutrochocrinus lovei (W. and Sp.) .............•............................................... _ ... ... _ .. _ x
Aorocrinus parvus (Shum. ) ....... _ ........ _ .... _ ...................... _..... ........ ........ ........ ........ x
Uperocrinus pyriforrois (Shum.) ....................................................... _... x
x
Uperocrinus sp ........ _ .................. _ ........................................ _ ........ _... ........ ........ ........ x
Dorycrinus unicornis (0. and Sh.) ... _....................................... x
........................... _ .. . Dorycrinnls quinquelobus (Hall) ........... _................................. ........ ........ ........ ........ x
Dorycrinus sp .............. _ .................................................. _........... ........ ........ ........ ........ x
Agaricocrinus Olnotrema HaIL .............. _ ............................................ ........... _... ........ x
Cactocrinus proboscidialis (Hall) ......... _ ................. _............... x
........................ ... _ .. . Cactocrinus roultibrachiatus (Hall) ...................................... x
........ ........... _ ... ... _ .. . Teleioerin'lls urobrosus (Hall) .......... _ ....................................... ........................... _... x
Phy"setocrinus ventricosus (Hall) ............................................ ........ ........ x
x
Physetocrinus 7 sp. . .. _ ................................ _ .... _ ..•....................... _... ........ ........ ........ x
Strotocrinus regalis (Hall) ......................................... _ ........ _ .... _... ........ x
........... _ .. . Strotocrinus glyptus (Hall) f ................................................ ........ ........ ........ ........ x
PlJatycrinus oTnogranulus McChesney ... _ ................................ _. x
................ ........... _ .. . Platycrinus sculptus Hall 'I ................. _ ...................... _ ........ _. x
................... _ ... ....... . Platycrinus planus O. and Sh. 7 ............................................ ........ ........ x
........... _ .. . Platycrin,us halli Shuro . ................. _ ........ IMt of fossils from bed 6 of the Burlington limestone a>t Burlington, _ .................................... _ .......... _ ........... _... x
Platycrinus sp. . ........................................................................... """" ........ x
............... . Plrutycrinus sp. . ................................ _ ......................................... ... _... ........ x
............... . Platycrinus sp ........ _ ...................................... _ ........................ _... ........ ........ ........ x
Platycri.nlus sp. . .. _ ............ _ ............................................................................ _ ...... _... x
Platycrinus sp. . ............................... _ ........... :............................... x
................... _ .......... . Eucladocrinus praenuntius W. and Sp. , ....................................... _... x
............... _
Eucladocrinus sp. . ................ _ ........................................................................ _... ........ X
BLASTOIDEA
Cryptob1astus melo (0. and Sh.) .......................................... x
........ ....................... . Orbitremites norwoodi (0. and Sh.) ......................................... _... ........ x
x
Pentreroites elongatus Shuro. . ........................................................ _ ................... _... x
BRYOZOA
Batostomella 7 sp . ....... _ ................................................ _........... ........ ........ ........ ........ x
Fenestella serratula Ulrich ........................................................ x
........................... _ .. . Fenestella burlingtonensls Ulrich ....... _ ................................................ _ ........ x
x
Rhombopom gracilis Ulrich ................................................... _ ................ _ ........ x
Rhombopora sp ................................................................................ _... ........ ........ ........ x
Rhombopora sp .............. _ .............................. _ ................................ _... ........ ........ ........ x
Rhombopora sp .............. _ .............................. _ ................................ _... ........ ........ ........ x
g~:~:Yfat;~ ·Ui;i~h··:::~::::::::::=::::::::::::::::::::::::::~::::::~::=::::: ::::::::1 :::::::: :::~::: ... ~... x BURLINGTON FOSSILS AT BURLINGTON 125 Table Showing Bange of Species in Burlington Limestorue at Burlingt011r-Continued. Horizons
1 I 2 I 3 141 6
BRACHIOPODA
Schellwienella 1 sp. _ .......... __ ... _ .... __ .. __ ..... ___ . __ .... _ ... _ ... _ ... ____ .... __ ... _ .... _ .... ____ .... __ ._. ___ ._. ___ . x
Chonetes illinoisensis W olthen __ .. _. __ .. _ .... _._. ___ ....... _._ ... __ ... _ ..... ___ .. _.__
x
__ .. ___ .. x
x
Chonetes sp. ____ ... ___ .. ____ ....... _ .. _. ___ ...... _. __ ...... _._ .......... __ .. _____________ . _. ______ . __ .. _._
x
. ___________ ... . Chonetes sp. ____ ._. __________ .. _________ . __ . ____ . ____ . ____ .. _. ______________ .. __ ... __ . __ ._. _________ ____________ . _____ . ___ . x
Productus burlingtonensis Hall _________ . ___ .. ___ ._. ______ ... _______ .. _ .. __ .. ________ .... ____ . ___ .__
x
x
Productus sp. ________ .... __ : ___ . _______ .. ____ . ___ . ___ . ___ ... IMt of fossils from bed 6 of the Burlington limestone a>t Burlington, ____ . ____ ._. ___ . ___ . ___ ... _. __ . _____ ._. __ ._ . __ ._ ... ____ .. _. x
Productus sp. _ ......... ____ . __ . _____ . __ .. ___________ .... ____ . __ . __________ . _____ .. _ .. _. __________________ .. ____ .. x
_ .. ____ _
Pustula alternata (N. and P.) . __ .. ___________ . ___ . __ ..... _ .. _._. __ . __ .___ ________
x
. ____ ._. ___ ... _. x
Rhipidiomella burlingtonensis (Hall) ___ .. ____________ ...... _____ :...____
x
________
x
________
x
Rhipidomella dubia (Hall) . _______ .. _________ . ______________ ... ___________________ . ______ . ____ ... __ ... x
x
Schizophoria swallovi (Hall) _______ ... _________________ . ______ ... _. ___________ . ____ .... __ ... .x
_______ . _ ... ___ _
. Rhynchopora sp. ______________________ . _______ . _______________ . ___ ... _______ . __________ ____________ . ____________ .______
x
Dielasma osceolensis Weller --------.--..... -.-.---.-----------.. ---------------
x 1'_' __ '" ---.-.-. --.-.-. -.. --.--
~~::~ :~: :::=::::::::::::::::::::::::::::::::=:::::::::::::::::::::::::::~::::::::::::: :::::::: :::=::: :::::::: :::=::: ~
Dielasma sp. . ________ . ______ . __ . ______ __ . ______________________ ~.-. __ ... __ . _________________ . __ . __ .. ___ .. _______
x
Spirifer grimesi Hall ___________ ._ ... ____ .. ______ . _________________ . _______ .________
x
x
x
x
x
Spirifer incertus Hall .... ___________ . ____________________________ ._ .. __ .. _______ ._. __ ____ . ______ .___ ________ x
x
Spirifer forbesi N. and P. _________________________ . __ : _______ ._._. __ .... ___ .____
x
_____________________________ .. Spirifer imbrex Hall _____________ . ________ . ____ .. __________________ .. _ .. __________ . x
_____ ._. ________________ . ___ ._ .. Spirifer louisianellsis Rowley _________________________________ . _____ ._._._.____
x
________ ____ ._ .. __ . ___________ _
Spirifer sp. . ... _ ..... __ .. ______________ . _________ . _______ .. _____ . __ .. _____ ._ ... _ ... _____ ._ .. __________ .. _____________ .... ____
x
Spirifer sp. .. __ ._ .... __ . ___________ . ___ .. ____ .. _____ . ____ . ___ . __ ._. _____ .. ______________ . _____________________ . _____ ._. __ . x
Brachythyris sub orbicularis (Hall) . _______ .. _________ ___ .. ___ .. ________ ________
x
_______ ________
x
Brachythyris sp. _ .. IMt of fossils from bed 6 of the Burlington limestone a>t Burlington, _._._ .. _._ .. __________________ ...... __ .. _______ . ___ ... ____ . ______ .__
x
_______ . ______________________ _
Brachythyris sp. _. ________ . _______ . _____ .. _ ... ______ .. ____________ . ________ .. ___ .. __ .. ___ ... __ .. ____ .. _________________ .. x
Syringothyris typus Win. ____ ._._ .. ______ ._._. _____ . __ . ____________________________________ . __ . x
x
xi
Syringothyris , sp. ____ ._ .. _______ . ____ . _____ ... _____ . _____ . ___ ... _ .. ____ .... __ .______ x
. ___________________ ... ____ . __ _
Spiriferella plena (Hall) _______________________ . ________ . ___ .. ____ . _____ ._. ____ .. ___ .... __ ..... x
_______ . 'x
Reticularia pseudolineata (Hall) _______ ._. _________ . ____ ._._ .. __ ._. ___________________ . ____ . x
________
x
Eumetria sp. ______________ . ___ . ________________ ._. _______ ._._. _________ .. _____________ . __ . _ ... __ .. ____ .... _______ ________
x
Athyris lamellosa (Leveille) ________ .. ____ ... _____________ . ____________ ._______ x
______ ._ .. ______
x
x
Cliothyridilla tenuilineata (Rowley) 1 _. _______________ . ______ ._ .. ____ ... _._ . ... __ . _______ . _________ . x
Cliothyridina obmaxima (McChesney) , ___________ ... ____ . _________ . ____ . ___ .... _____ ._____ _______
x
Cliothyridina incrassata (Hall) __ . _____ . ___ . __________ . ___________ . ____________ .. __
x
x
x
P ELECYPODA
I
GASTROPODA
x
-.---..... -.-.-- .-------1--------
Aviculopecten , sp. _._. _________ . ____ . _____ . _______ .. ____ . _______ ... _____ .. ---_ .. _. ___ _
Lepetopsis capulus (Hall) _____________ ._. __ ... ____ ... _. ________ . __ .. ______ .. ____ .. ____________ . __ . _______
x
x
Strapru-ollus sp. ____ ...... _____ . __________ ... ___ ._ ... __ ... _____________ ..... ________ ... ____ . _______ . ______ ._____ x
Orthonychia pabulocrinus (Owen) __ ...... ____ .. ____ ... _______ .. __ ... __ . ______ .. _ ... _. __ .__ _______ ________ x
Orthonychia sp . .. __ ._._. ________________________________________________ . __________________ . __ . __ .... __ .. ___ .____ x
_. __ ._. ~r:~~~~!iar~t~~;;~:~;~~~~~:~~~:-:~~~~~~~:~-:~~:~-:~~::::::::::::::::::=::~::: I
:::~::: :::=::: :::=::: :::~::: I'--~---
Platyceras paralium W. and W. ___ . ______ .. ___ .. ____ . ___ ...... ___ .. 9 "The North American Crinoidea Camerata", Mem. Harvard Coil, Mus. Compo Zool., vol.
XXI; 1897. MISSISSIPPIAN STRATA OF IOWA 126 Table Showing Range of Species in Burlington Limtestone at Bllrlingto1lr-Continued. I
Horizons
I
11', 2 , °3 I 4 I 6 I
Platyceras sp. . ........................................................................................ _... ........ ........ x
TRILOBITA
Phillipsia , sp. ............................................................................ x........ ........ x
....... . VERTEBRATA
Fish teeth
x ........................ x Table Showing Range of Species in Burlington Limtestone at Bllrlingto1lr-Continued. I
Horizons
I
11', 2 , °3 I 4 I 6 I
Platyceras sp. . ........................................................................................ _... ........ ........ x
TRILOBITA
Phillipsia , sp. ............................................................................ x........ ........ x
....... . VERTEBRATA
Fish teeth
x ........................ x Wachsmuth and Springer9 and other investigators have col-
lected and described a large number of other invertebrates,
chiefly crinoids, from the Lower. and Upper Burlington lime-
stones at this locality in addition to the forms listed above. Unfortunately, neither the time available during the present in-
vestigation nor the opportunities for collecting at Burlington
rendered it possible for the writer to determine the exact hori-
zon in the section from which each of these came. In addition to the exposures in the Burlington area, there are
other outcrops showing the various phases of the formation in
their typical development in outlying districts in Des Moines
county. For example, the Lower Burlington is excellently ex-
posed in the Kemper quarries located in the Mississippi river
bluff between the city of Burlington and the station of Spring
Grove (T. 69 N., R. 2 W., sec. 29, ~rw. 1,4, SvV. 14). The sec-
tion there is as follows: 5.
Limestone, light gl'ay to brown, crinoidal .................................... 7%
4
Limestone
brownish
soft
magnesian
cherty
18 4.
Limestone-, brownish, soft, magnesian, cherty ........................ 18 .
3
Limestone
light gray or whitish where fresh
but in some 1. Limestone, oolitic,
Exposed IMt of fossils from bed 6 of the Burlington limestone a>t Burlington, _________ \ ___ .. __ .\_ ... _ ... \ .. ___ ... \ _______ \ x \
Platyceras sp. .._. ____ .. _. ____ . __ . ____ .. __ .... ______ . __ ._ .... ____________ .. _ ... ____ ., ... _________ ._ . __ .. ___ x
___ . ____ _______ . Table Showing Bange of Species in Burlington Limestorue at Burlingt011r-Continued. 3.
Limestone, light gray or whitish where fresh, but in some
places brownish
8% to South .&ugus,ta section.
UPPER BURLINGTON.
FEET
8_
Limestone,
~oft, huff, not everywhere present ______________ _______
0-1
7.
Limestone, light gray, crinoidal; with occasional small nodules
and thin, irregular, discontinuous seams of chert; some layers
very crinoidal; stylolytic ____________________________________________________________________
17
6.
Limestone, compact, .lense, browni h, nodular, cherty, magne-
sian; 'no fossils noted ________________________ ________________________________________ _______
8
5.
Chert, in the form of a solid band, replacing a layer of crin-
oidal limestone;
some
unreplaced
crinoid fragments
pre-
servpd _______ _______ ________________________________________________________________________________________
1
4_
Limestone soft, buff, magnesia,n _____________________________________________________ -" ____ 1-11h
3_
Limestone, gray to whitish, crinoid aI, cherty, with occasional
thin layers of soft buff limestone. The main crinoid zone __________ 71h-8 1h Section at Kemper quarries. Section at Kemper quarries. FEET
5. Limestone, light gl'ay to brown, crinoidal .................................... 7%
4. Limestone-, brownish, soft, magnesian, cherty ........................ 18 . 3. Limestone, light gray or whitish where fresh, but in some
pla.ces brownish .................................................................................. 8% to 9 1h
2,
Limestone, buff to brownish, soft, magnesian; with occa·
sional seams of brownish crinoidal limestone; grading into
the limestone above ............................................................................ 41j2 to 5
1. Limestone, oolitic,
Exposed ..................................................... _ ..... 2 All the beds except munbers 1 and 2, which represent the
Kinderhook, are of Lower Burlington age. South .&ugus,ta section. BURLINGTON BEDS AT AUGUSTA BURLINGTON BEDS AT AUGUSTA 127 In the banks of Flint creek in the vicinity of Starr's cave two
miles northwest of Burlington, the Lower Burlington is again
typically exposed in contact with the Kinderhook below and the
lowermost beds of the Upper Burlington above. The ·Upper Burlington is very satisfactorily exposed in the
quarry of the Burlington Quarry Company located one-half
mile north of the Chicago, Burlington, and Quincy railroa<l
shops at West Burlington. The succession of layers at this
place is given below: Section near West Burlvnoton. Section near West Burlvnoton. Section near West Burlvnoton. FEET
7. Drift . ______________________________________________________________________________________________________ 13
6. Limestone, soft, buff, thin-bedded, Clherty __________
~ ____ ,, ______ :_________________ 3
5. Limestone, gray to brownish, crinoidal, very cherty in middle
part ____________________________________________________________________________________________________________
31h
4. Limestone, cherty,
thin-bedded,
gray am
crinoidal
below,
but fine-grained, soft and brownish above, ____________________________________
61h
3. Limestone, gray, crinoidal, with stylolytic seams ___________________________
6 to 61h
2. Limestone, gray, crinoidal, finer-grained, with stylQlytic seams. Massive when fresh. Upper one and one-half feet brownish, and
grading locally into fine-grained nodular limestone. Bearing
Spirifer grimesi,
Spiriferella plena, Dizygocrilrl;u$. rotuMus,
Pentremites sp_, Lepetopsis capulus and othor species ___________________
9
1. Limestone, gray, crinoi.dal, with brownish tint_ Locally cherty
in upper portion_
DizygoC1-inus rottmUils, Rhipidomella
bt~r-
lingtone'llsis, Spirifer grimesi and Spiriferella plena. _______________ ,____
51h
Beds 1 to 4 represent the Upper Burlington while bed's 5 and 1. Limestone, gray, crinoi.dal, with brownish tint_ Locally cherty
in upper portion_
DizygoC1-inus rottmUils, Rhipidomella
bt~r-
lingtone'llsis, Spirifer grimesi and Spiriferella plena. _______________ ,____
51h Beds 1 to 4 represent the Upper Burlington, while bed's 5 and
6 are referred to the Keokuk. In the vicinity of the town of Augusta, nine miles southwest
of Burlington, both divisions of the formation are well exposed
and afford an opportunity for collecting from all horizons. The
most complete section is in the bluff of a creek tributary to
Skunk river at South Augusta (NE. 1M, sec. 25, Denmark town-
ship) . MISSISSIPPIAN STRATA OF IOWA 128 LOWER BURLINGTON. 2
Li
t LOWER BURLINGTON. 2. Limestone, fine-grained, soft, bluish gray when fresh but
weathering buff;
exhibiting numerous
concretionary iron
stains;' with occasional layers of brownish impure cherty crin-
oic1al limestone ranging up to two feet in thickness ________________ 12:t,2-13:t,2
1
Li
t
b
t lli
h
t
i
t 1. Limestone, gray, sub crystalline, very cherty in upper part. Exposed. __________________ ________________________ .______________________________________________________
4 Bed 1 is well exposed also at the mouth of the creek less than
one-fourth mile below the bluff, where it causes the rapids in
Skunk river. Bed 3 is excellently exposed farther up the creek on the
Frank Crabtree and Menelie properties. This bed outcrops also
at the south end of the wagon bridge over Skunk river. Excel-
.lent opportunities for collecting crinoids from this bed are af-
forded at the above localities. Beds 7 and 8 were formerly quarried in the face of the bluff. Section near West Burlvnoton. They are overlain at one point by twelve feet of cherty lime-
stone of Keokuk age. 'fhefossils of all the beds from which identifiable speCImens
were collected are listed below: List of fossils from bed 1 in the bluff section at South Augusta. OZOA
S hi
h
i
ll
i
(H l List of fossils from bed 1 in the bluff section at South Augusta. BRYOZOA-
Schi:>:ophoria swallovi (Hall)
Fenestella sp. Spiriferina , .sp. BRACHIOPODA-
Spirifer sp. Productus sp. Pseuc10syrinx ,
sp. Productus sp. Reticularia sp. Leptaena analoga (Phillips)
Composita trinuclea (Hall) ,
Rhynchonella sp. Cliothyric1ina incrassata (Hall)
Camal'ophoria bisinuata (Rowley) Schi:>:ophoria swallovi (Hall)
S i if
i BRYOZOA-
Fenestella sp. BRACHIOPODA Spiriferina , .sp. Spirifer sp Productus sp. Productus
sp Productus sp. Leptaena analo Composita trinuclea (Hall) ,
Cliothyric1ina
incrassata
(Hall) Leptaena analoga (Phillips)
Rhynchonella
sp Cliothyric1ina incrassata (Hall) Rhynchonella sp. C
l'
h
i
bi Camal'ophoria bisinuata (Rowley) List of fossils f~'om bed 1 ill/, the bank of Skunk rwer at South A~bg List of fossils f~'om bed 1 ill/, the bank of Skunk rwer at South A~bgusta. THOZOA
S i if
i
i H ll List of fossils f~'om bed 1 ill/, the ba
THOZOA List of fossils f~'om bed 1 ill/, the bank of Skunk rwer at South A~bgusta. NTHOZOA
S i if
i
i H ll f f
,
f
ANTHOZOA-
Zaphrentis sp. Zaphrentis , sp_
Triplophyllum dalei (M.-E. and H.)
BRACHIOPODA-
Chonetes multicosta Win. Productus sp. Orthotetes , sp. Leptaena analoga (Phillips)
Rhipic10mella dubia (Hall)
Rhipidomella burlingtonensis (Hall)
Schizophol'ia swallovi (Hall)
Dielasma ' osceolensis Weller
Dielasma sp. Spiriferina. d. S. subtexta White
Spirifer grimesi Hall
Spil'ifer carinatus Rowley ,
Spirifer insculptus Rowley
Spirifer sp. Brachythyris sub orbicularis (Hall)
Composita , sp. Cliothyridina parvil'ostris
(M. and
W.)
GASTROPODA-
Strapal'ollus obtusus (Hall)
Platyceras sp. Igoceras sp. TRILOBITA-
Griffithic1es f sp. List of fossils trom bed 2 in the bluff seotion at South Augusta. CRINOIDEA-
Spirifer sp. Platycrinus sp. Spiriferella plena
(Hall)
BRACHWPODA-
A thYl'is lamellosa (Leveille)
Schizophoria swaJlovi (Hall)
Cliothyridina incrassata (Hall)
Spirifer grimesi Hall f f
f
ANTHOZOA-
Zaphrentis sp. Zaphrentis , sp_
Triplophyllum dalei (M.-E. and H.)
BRACHIOPODA-
Chonetes multicosta Win. Productus sp. Orthotetes , sp. Leptaena analoga (Phillips)
Rhipic10mella dubia (Hall)
Rhipidomella burlingtonensis (Hall)
Schizophol'ia swallovi (Hall)
Dielasma ' osceolensis Weller
Dielasma sp. Spiriferina. d. S. subtexta White
Spirifer grimesi Hall
Spil'ifer carinatus Rowley ,
Spirifer insculptus Rowley
Spirifer sp. Brachythyris sub orbicularis (Hall)
Composita , sp. Cliothyridina parvil'ostris
(M. and
W.)
GASTROPODA-
Strapal'ollus obtusus (Hall)
Platyceras sp. Igoceras sp. TRILOBITA-
Griffithic1es f sp. List of fossils trom bed 2 in the bluff seotion at South Augusta. CRINOIDEA-
Spirifer sp. Platycrinus sp. Spiriferella plena
(Hall)
BRACHWPODA-
A thYl'is lamellosa (Leveille)
Schizophoria swaJlovi (Hall)
Cliothyridina incrassata (Hall)
Spirifer grimesi Hall Spirifer grimesi Hall
Spil'ifer carinatus Ro Spil'ifer carinatus Rowley ,
Spirifer insculptus Rowley Spirifer insculptus Rowley
S i if Triplophyllum dalei (M.-E. and H.)
BRACHIOPODA Spirifer sp. Brachythyri Brachythyris sub orbicularis (Hall)
Composita
sp Cliothyridina parvil'ostris
(M. and
W.) Cliothyridina parvil'ostris
(M. and
W.)
GASTROPODA Strapal'ollus obtusus (Hall)
Platyceras sp Platyceras sp. Igoceras sp Igoceras sp. ILOBITA TRILOBITA-
G iffithi Griffithic1es f sp. List of fossils trom bed 2 in the bluff seotion at South Augusta
A
S i if List of fossils trom bed 2 in the bluff seotion at South Augusta. IDEA
S i if CRINOIDEA-
Spirifer sp. Platycrinus sp. Spiriferella plena
(Hall)
BRACHWPODA-
A thYl'is lamellosa (Leveille)
Schizophoria swaJlovi (Hall)
Cliothyridina incrassata (Hall)
Spirifer grimesi Hall Spirifer sp. S i if
ll Spiriferella plena
(Hall
AthYl'is lamellosa
(Levei A thYl'is lamellosa (Leveille)
Cli th
idi
i
t
(H Schizophoria swaJlovi (Hall)
Spirifer grimesi Hall Cliothyridina incrassata (Hall) BURLINGTON FOSSILS NEAR AUGUSTA 129 List of fossils from bed 3 Vn. the bluff section at South A1~gusta. List of fossils from bed 3 Vn. the bluff section at South A1~gusta. ANTHOZOA-
Spirifer sp. TriplophyJlum daIei (M.-E. and H.)
CRINOIDEA-
Brachythyris sub orbicularis
Spiriferella plena (Hall)
Athyris laroellosa (Lev.eille)
(Hall)
Eutro:chocrinus christyi (Shum.)
BR.ACHIOPODA-
Schizophoria swallovi (Hall)
Spirifer griroesi Hall
GASTROPODA-
Platyceras sp. Orthonychia sp. ANTHOZOA-
Spirifer sp. TriplophyJlum daIei (M.-E. and H.)
CRINOIDEA-
Brachythyris sub orbicularis
Spiriferella plena (Hall)
Athyris laroellosa (Lev.eille)
(Hall)
Eutro:chocrinus christyi (Shum.)
BR.ACHIOPODA-
Schizophoria swallovi (Hall)
Spirifer griroesi Hall
GASTROPODA-
Platyceras sp. Orthonychia sp. Schizophoria swallovi (Hall)
S i if
i
i
ll Spirifer griroesi Hall List of fossils collected from exposure~ of bed 3 along creek on Crabtree and
Mtmelie prope·rties. p
p
ANTHOZOA-
Orbitremites norwoodi (0. and Sh.)
Triplophyllum dailli (M.-E. and H.) BRYOZOA-
Zaphrentis sp. Several undetermined species
Zaphrentis ~ sp. BR.ACHIOPODA-
Cyathaxonia sp. Productus burlingtonensis Hall
Amplexus
sp. Pustula alternata (N. and P.)
CRINOIDEA-
Chone·tes sp. Batocrinus grandis W. and Sp. Rhipidomella dubia (Hall)
Batocrinus d. B. laura (Hall)
Rhipidomella burlingtonensis (Hall)
Macrocrinus konincki (Shum.)
Schizophoria swallovi (Hall)
Eutrochocrinus christyi (Shum.)
Spirifer incertus Hall
Upel'ocrinus aequibrachiatus var. as-
Spirifer grimesi Hall
teriscus (M. and W.)
Spirifer sp. Uperocrinus pyriformis (Shum.)
Spiriferella plena (Hall)
Dorycrinus missouriensis (Shum.)
Brachythyris sub orbicularis
(Hall)
Oact.ocrinus glans (Hall)
P seudosyrinx , sp. Cactocrinus longus (M. and W.)
~
Athyris lamellosa (Leveille)
Actinocrinus multiradiatus Shum. Cliothyridina obmaxiroa (McChesney)
Actinocrinus scitulus M. and W. Cliothyridina incrassata (Hall)
Strotocrinus glyptus Hall
PELECYPODA-
Platycrinus burlingtonensis O. and
Cypricardinia '1 sp. Sh. GASTROPODA-
Platycrinus discoideus O. and Sh. Lepetopsis capulus (Hall)
Platycrinus (several species)
Platyceras
(several
undetermined
Eucladocrinus pleurovimenus (White)
species)
Crinoids (several undetermined
Orthonychia (sev.eral undetermined
species)
species) ANTHOZOA-
Orbitremites norwoodi (0. and Sh.)
Triplophyllum dailli (M.-E. and H.) BRYOZOA-
Zaphrentis sp. Several undetermined species
Zaphrentis ~ sp. BR.ACHIOPODA-
Cyathaxonia sp. Productus burlingtonensis Hall
Amplexus
sp. Pustula alternata (N. and P.)
CRINOIDEA-
Chone·tes sp. Batocrinus grandis W. and Sp. Rhipidomella dubia (Hall)
Batocrinus d. B. laura (Hall)
Rhipidomella burlingtonensis (Hall)
Macrocrinus konincki (Shum.)
Schizophoria swallovi (Hall)
Eutrochocrinus christyi (Shum.)
Spirifer incertus Hall
Upel'ocrinus aequibrachiatus var. as-
Spirifer grimesi Hall
teriscus (M. and W.)
Spirifer sp. Uperocrinus pyriformis (Shum.)
Spiriferella plena (Hall)
Dorycrinus missouriensis (Shum.)
Brachythyris sub orbicularis
(Hall)
Oact.ocrinus glans (Hall)
P seudosyrinx , sp. Cactocrinus longus (M. and W.)
~
Athyris lamellosa (Leveille)
Actinocrinus multiradiatus Shum. Cliothyridina obmaxiroa (McChesney)
Actinocrinus scitulus M. and W. Cliothyridina incrassata (Hall)
Strotocrinus glyptus Hall
PELECYPODA-
Platycrinus burlingtonensis O. and
Cypricardinia '1 sp. Sh. GASTROPODA-
Platycrinus discoideus O. and Sh. List of fossils from bed 3 Vn. the bluff section at South A1~gusta. Lepetopsis capulus (Hall)
Platycrinus (several species)
Platyceras
(several
undetermined
Eucladocrinus pleurovimenus (White)
species)
Crinoids (several undetermined
Orthonychia (sev.eral undetermined
species)
species) Zaphrentis sp. Z
h
i
~ Zaphrentis ~ sp. C
th
i Cyathaxonia sp. Amplexus
sp Amplexus
sp. O
A Batocrinus grandis W. and Sp. B t
i
d
B
l
(H ll) Batocrinus d. B. laura (Hall)
M
i
k
i
ki (Sh
) Macrocrinus konincki (Shum.)
E
h
i
h i
i
(Sh
) Eutrochocrinus christyi (Shum.)
U
l'
i
ib
hi t Oact.ocrinus glans (Hall)
C
i
l
(M Actinocrinus multiradiatus Shum. A
i
i
i
l
M
d W Actinocrinus scitulus M. and W. S
i
l
H ll Strotocrinus glyptus Hall
Pl t
i
b
li
t Platycrinus discoideus O. and Sh. Platyceras
(several
undetermined
species) Platycrinus (several species) Eucladocrinus pleurovimenus (White)
C i
id
(
l
d
i
d Orthonychia (sev.eral undetermined
i
) Crinoids (several undetermined
species)
AS O
A y
(
species) species) BLASTOIDEA- BLASTOIDEA-
P entremites
el~ngatus Shum. P entremites
el~ngatus Shum. List of fossils collected from
expo~es of bed 9 at south end of wagon bridgt:
over Skunk'river. List of fossils collected from
expo~es of bed 9 at south end of wagon bridgt:
over Skunk'river. 3. L imeston:c,
coarse· grained,
crinoida~ ;
wi til stylolytic seams;
brownish below but light gray above; upper 1 to llh feet, fine- Section of the Upper B~bTlington limestone at Augusta. Cystodictya sp. Cystodictya sp. ANTHOZOA-
Cystodictya sp. Triplophyllum dalei (M.-E. and
Zaphrentis sp. H.) BR.ACHIOPODA-
CRINOIDEA-
Undetermined (several species)
Dizygocl'inus rotundus (Shuro.)
Physetocrinus ventricosus (Hall)
Upel'ocrillus pyriformis (Shuro.)
Actinocrinus sp. Barycrillus sp. Platyc]'inus (plates of several species)
Eutrochocrinus christyi (Shum.)
BLASTOIDEA-
Orbitremites norwoodi (0. and S.)
BRYOZOA-
Undetermined (several species)
Pllstula alternata (N. and P.)
Chonetes multicosta Win. , Rhipidomella dubia (Hall)
Rhipidomella burlingtonensis Hall
Schizophoria swallovi (Hall)
Spirifer incertus Hall
Spirifer grimesi Hall
Brachythyris suborbicularis
(Hall)
Spiriferella plena (Hall)
Athyris lamellosa (Leveille)
Cliothyridina incrassata (Hall)
GASTROPODA-
Igoceras sp. Platyceras sp. Undetermined (several species)
Di
l'i
d
(Sh
) Dizygocl'inus rotundus (Shuro.)
Ph
i
i
(H Orbitremites norwoodi (0. and S.)
BRYOZOA-
U d
i
d
(
l
i
)
y
GASTROPODA-
Igoceras sp. GASTROPODA- Igoceras sp. Pl Undetermined (several species) Platyceras sp. MISSISSIPPIAN S'l.'RATA OF IOWA 130 List of fossils in bed 7 of the bhbff seotion at Scnbth A~bgusta . List of fossils in bed 7 of the bhbff seotion at Scnbth A~bgusta . ANTHOZOA-
BR.ACHIOPODA-
Triplophyllum dalei (M.-E. and H. )
Productus burlingtonensis Hall
BLASTOIDEA-
Rhipidomella burlingtonensis (Hall,
Orbitremites norwoodi (0. and S.)
Schizophoria swallovi (Hall)
CRINOIDEA-
Spirifer grimesi Hall
Dizygocrinus dodecadactylus (M. and
Spirifor incertus H all
W.)
Spiriforella plena (Hall)
Dizygocrinus rotundus (Shum.)
Cliothyridina incrassata (Hall)
Uperocrin'us pyriformis (Shum. )
GASTROPODA-
Actinocrinus multiradiatus Shum. Platyceras sp. Piatycrinus sp. ANTHOZOA-
BR.ACHIOPODA-
Triplophyllum dalei (M.-E. and H. )
Productus burlingtonensis Hall
BLASTOIDEA-
Rhipidomella burlingtonensis (Hall,
Orbitremites norwoodi (0. and S.)
Schizophoria swallovi (Hall)
CRINOIDEA-
Spirifer grimesi Hall
Dizygocrinus dodecadactylus (M. and
Spirifor incertus H all
W.)
Spiriforella plena (Hall)
Dizygocrinus rotundus (Shum.)
Cliothyridina incrassata (Hall)
Uperocrin'us pyriformis (Shum. )
GASTROPODA-
Actinocrinus multiradiatus Shum. Platyceras sp. Piatycrinus sp. It "vill be noted that the faunule obtained from bed 7 of the
Upper Burlington limestone in the above section is meager. Much better facilities for collecting from this horizon are af-
forded by the exposures along the banks of Barb creek, one mile
northwest of South Augusta, near the center of section 23, Den-
mark township. The follovving species were collected here: List of fossils from bed 7 of B~brlington limestone on Barb creek. ANTHOZOA-
BRYOZOA-
Triplophyllum dalei (M.-E. and H .)
Fenestella sp. Zaphrentis sp. BR.ACHIOPODA-
Amplexus sp. Productus burlingtonensis Hall
CRINOIDEA-
Productus (several species)
Batocrinus laura (Hall)
Pustula alternata (N. and P.) f
Macrocrinus verneuilianus (Shum.)
Camarotoechia sp. Dizygocrinus rotlIDdus (Shum.)
Rhipidomella bul'lingtonensis (Hall)
Dizygocrinus undrewsianus (McChes-
Schizophoria swallovi (Hall)
ney)
Spirifer grimesi Hall
Eutrochocrinus christyi (Shum.)
Spirifer incertus Hall
tJipeI'ocrinus hagetri (McChesney) 1
Brachythyris sub orbicularis (Hall)
Aorocrinus 1 sp. Spiriferella plena (Hall)
Cactocrinus ~ sp. Reticularia pseudolineata (Hall)
Platycrinus (plates of several unde-
Syringothyris
~ sp. termined species)
Athyris lamellosa (Leveille)
Eucladocrimlus pleurovimenus (White)
Cliothyridina incrassata (Hall)
BLASTOIDEA-
GASTROPODA-
Orbitremites norwoodi (0. and S.)
Lepetopsis capulus (Hall)
Pentremites elongatus Shum. Platyceras sp. tJipeI'ocrinus hagetri (McChesney) 1
Aorocrin s 1 sp Aorocrinus 1 sp. C
t
i
~ Cactocrinus ~ sp. Platycrinus (plate BLASTOIDEA-
Orbitremites norwoodi (0. and S.)
Pentremites elongatus Shum. N ear Augusta on the opposite side of Skunk river, there is an
excellent exposure of the Upper Burlington, overlain by the
Keolmk limestone, in the bed and banks of a small creek onc-
half mile north of the Augusta bridge in the eastern part of sec. 23, Augusta township. The following section was measured at
this locality: FOSSILS OF UPPER BURLINGTON 131 grained, soft and weathering buff. List of fossils in bed 7 of the bhbff seotion at Scnbth A~bgusta . Some seams in upper part
filled with crinoid fragments. Zone of fish teeth 22 inches
below top ............. : ................... _............................................................... 16 ·17
2. Limestone, soft, buff, cherty, dolomitic; resting on the irregu·
lar undulating surface of the bed beneath ...................................... llh· 2
1. Limestone, gray, sub crystalline ; with coarser· grained cherty,
crinoidJal layers m upper and lower parts. Exposed ................... _... 3
N'O fossils were collected from bed 2, but beds 1 and 3 'yielded
umerous speCIes. 2. Limestone, soft, buff, cherty, dolomitic; resting on the irregu·
lar undulating surface of the bed beneath
l N'O fossils were collected from bed 2, but beds 1 and 3 'yielded
numerous speCIes. List of fossils from bed 1 of seotion of Upper Burlington limestone at
Augusta. Augusta. ANTHOZOA-
'rriplophyllum dalei (M.·E. and H.)
CRINOIDEA-
Platycrinus
(plates
of
several
species)
BLASTOIDEA-
Orbitremites norwoodi (0. and Sh.)
BRYOZOA-
Evactinopora grandis M. and W. T
Rhombopora sp. Schizophoria swallovi (Hall)
Spirifer grimesi Hall
Spirifer incertus Hall
~
Spirifer sp. Brachythyris sub orbicularis (Hall)
Spiriferella plena (Hall)
Syringothyris , sp. Athyris lamellosa (Leveille)
Cliothyridina incrassata (Hall)
Oliothyridina parvirostris (M. and
BRACHIOPODA-
Chonetes sp. Productus sp. W .)
GASTROPODA-
RhipidomelLa dubia. (Hall)
Rhipidomella burlingtonensis (Hall)
Lepetopsis capulus (Hall)
Platyceras sp. ANTHOZOA-
'rriplophyllum dalei (M.·E. and H.)
C
O ANTHOZOA-
'rriplophyllum dalei (M.·E. and H.)
C
O 'rriplophyllum dalei (M.·E. and H.)
CRINOIDEA- CRINOIDEA-
Platycrinus
(plates
of
several
species) BLASTOIDEA-
Orbitremites norwoodi (0. and Sh.)
BRYOZOA BLASTOIDEA-
Orbitremites norwoodi (0. and Sh.)
BRYOZOA Orbitremites norwoodi (0. and Sh.)
BRYOZOA BRYOZOA-
Evactinopora grandis M. and W. T
Rhombopora sp. Evactinopora grandis M. and W. T
Rh
b BRACHIOPODA-
Ch
t Chonetes sp. Prod ct s sp Productus sp. Rhi id
lL
d Lepetopsis capulus (Hall)
Pl t RhipidomelLa dubia. (Hall)
Rhipidomella burlingtonen Platyceras sp. Rhipidomella burlingtonensis (Hall) List of fossils from bed S of seotion of Upper Burlmgton limestone at Augusta List of fossils from bed S of seotion of Upper Burlmgton limestone at Augusta. ANTHOZOA-
Zaphrentis sp. Triplophyllum dalei (M.·E and H.)
Hadrophyllum glans (White)
Amplexus sp. CRINOIDEA-
Batocrinus laura (Hall)
Macrocrinus verneuilianus (Shum.)
Dizygocrinus andrewsian,us (McChes·
ney) T
Dizygocrinus rotundus (Shum.)
Eutrochocrinus christyi (Shum.)
Agaricocrinus sp. Actinocrinus multiradiatus Shum. Actinocrinus sp. Teleiocrinus umbrosus (Hall)
Platycrinus
(plates
of
several
species)
Eucladocrinus pleurovimenus (White)
BLASTOIDEA-
Pentremites elongatus Shum. Orbitremites norwoodi (0. and Sh.)
BRYOZOA-
Cystodictya sp. BRAcmoPODA-
Chonetes sp. Productus viminalis White
Productus burlingtonensis Hall
Productus sp
Productus sp. Pustula alternata (N. and P .)
Rhipidomella dubia (Hall)
Rhipidomella burlingtonensis (Hall)
Schizophoria sWallovi (Hall)
Dielasma gp. Camarotoechia sp. Spirifer grimesi Hall
Spirifer incertus Hall
Spirifer sp. Spiriferella plena (Hall)
Brachythyris suborbicularis (Hall)
Syringothyris sp. Cliothyridina incrassata (Hall)
Athyris lamellosa (Leveille)
GASTROPODA-
'
Lepetopsis capulus (Hall)
Orthonychia pabulocrinus (Owen)
Orthonychia quincyellJse (McChes·
ney)
Orthonychia sp. Platyceras latum Keyes
Platyceras obliquum Keyes
Platyceras sp. TRILOBITA-
Griffithides , sp. VERTEBRA.TA-
Fish teeth. ANTHOZOA-
Zaphrentis sp. Triplophyllum dalei (M.·E and H.)
Hadrophyllum glans (White)
Amplexus sp. CRINOIDEA-
Batocrinus laura (Hall)
Macrocrinus verneuilianus (Shum.)
Dizygocrinus andrewsian,us (McChes·
ney) T
Dizygocrinus rotundus (Shum.)
Eutrochocrinus christyi (Shum.)
Agaricocrinus sp. Actinocrinus multiradiatus Shum. Actinocrinus sp. Teleiocrinus umbrosus (Hall)
Platycrinus
(plates
of
several
species)
Eucladocrinus pleurovimenus (White)
BLASTOIDEA-
Pentremites elongatus Shum. Orbitremites norwoodi (0. and Sh.)
BRYOZOA-
Cystodictya sp. BRAcmoPODA-
Chonetes sp. Productus viminalis White
Productus burlingtonensis Hall
Productus sp. G
T
V ANTHOZOA-
Zaphrentis sp. Triplophyllum dalei (M.·E and H.)
Hadrophyllum glans (White)
Amplexus sp. CRINOIDEA-
Batocrinus laura (Hall)
Macrocrinus verneuilianus (Shum.)
Dizygocrinus andrewsian,us (McChes·
ney) T
Dizygocrinus rotundus (Shum.)
Eutrochocrinus christyi (Shum.)
Agaricocrinus sp. Actinocrinus multiradiatus Shum. Actinocrinus sp. Teleiocrinus umbrosus (Hall)
Platycrinus
(plates
of
several
species)
Eucladocrinus pleurovimenus (White)
BLASTOIDEA-
Pentremites elongatus Shum. Orbitremites norwoodi (0. and Sh.)
BRYOZOA-
Cystodictya sp. BRAcmoPODA-
Chonetes sp. Productus viminalis White
Productus burlingtonensis Hall
Productus sp. G
T
V Macrocrinus verneuilianus (Shum.)
Dizygocrinus andrewsianus
(McChes 132 MISSISSIPPIAN STRATA OF IOWA From the exposures at and near South Augusta and at
Augusta, the following generalized section of the Burlington
has been constructed. Generalized seotion of Burlington limestone at and near Augusta. Generalized seotion of Burlington limestone at and near Augusta. 7. LimestQne, brQwnish belQw, but light gray abQve, crinQidal,
with stylQlytic seams, bearing QccasiQnal thin, irregular,
discQntinous seams Qf chert .............................................................. 16
to 17
6
Li
tQ
b Q
i h
i
b
t lli
t
fi 6. LimestQne,
brQwnish, magnesian, sub crystalline to fine·
grained, cherty, with occasional se'ams Qf crinQidal lime·
stone ......................................................... _ .................................... _ ....... I>
5
Ch
t
i
th
fQ
f
lid b
d
l
i
l
f 2. Limestone. fine· grained, soft, bluish ,gray when fresh but
. weathering buff and exhibiting numerQUS
concretiQnary
iron stains; with occasional layers of brownish impure cherty
crinQidJal limestQne ranging' up to 2 feet in thickness ................ 12% to 13%
1
Li
t
b
t lli
h
t
i
t 1. Limestone, gray, sub crystalline, very cherty in upper part. Exposed ................................................... _ .............. _ ............................. 4 The range of the more characteristic fossils collected by the
writer from the individual beds of the section is indicated on the
chart which follows: Table Showing Ra;nge of Fossils in the Burlington Beds at and near Augusta. I
HorizQns
I
1112131617\
ANTHOZOA
I
Zaphrentis sp .................................................... _......................... x
x ........ x
Cyathaxonia sp. . .................................... _ .............. __ .................... ........ ........ x
........... _ .. . Hadrophyl1um glaals (Whiti6).................................................... ........ ........ ........ ........ x
Triplophyllum dalei (M.·E. and H.) ............... __ ._ ............... __
x ... _... x
x
x I
.Amplexus sp ...................................... _ ............................................... \ ... _... x 1 ........ 1 ........ 1
BatQcrinus Cf~:~O::a (Hall) ............... _ ............. _ ....................... L .. ...\ x 1
... _ ...... _ .. !~~r?c;~~sfa2~r~~~ills~::~::::::::=::::::::::::::=:::::::::::::::::::::::: :::=::: ::::::J .. ~ ... :::~:= :::~:::
Macrocrinus verneuilianus (Shum.) ............... ---................. _ .... _ ........... I ........... -... x 1
Dizygocrinus rotundns (Shum.) ......................... _ .................................... \ x
........ x
Dizygocrinus dodecadactylu8 (M. and W.) ... _ ..................... _. ........ ........ ........ ........ x able Showing Ra;nge of Fossils in the Burlington Beds at and near Augusta. Table Showing Ra;nge of Fossils in the Burlington Beds at and near Augusta. Table Showing Ra;nge of Fossils in the Burlington Beds at and near August RANGE OF BURLINGTON FOSSILS 133 Table Showing Bange of Fossils irn the B'Ulrlington Beds at amd 'fI!eOlr Augusta--
Continued. Table Showing Bange of Fossils irn the B Ulrlington Beds at amd fI!eOlr Augusta--
Continued. Generalized seotion of Burlington limestone at and near Augusta. 1
Horizons
1
1112131617\
Dizygocrinus andrewsiaalUS (McChesney) ____________________________ : _______ 1 ________ -------- --------
x
Eutrochocrinus christyi (Shum.) __________________________ ~--------------- _______ _______
x ' ________
x
Aorocrin'lls
~ sp. _________________________________________________________________________________ .___ ________ ________
x
Uperocrinus pyriformis (Shum_) _____________________________________________ _______ _______
x
x
Uperocrinus aequibrachiatus, vaJ:. asteriscus (M. and W.) __ _______ ________
x
______________ _
Uperocrinus hageri (McChesney) .f _____________________________________ _______ ________ ________ _______ x
Dory~rinu.s missouriensis (Shum.) _____________________ .____________________ ________ _______
x
________ ._._ .. _
Agancocrmus sp. __________________________ ._. ______________________ ---_________________ _______________ ________ ________
x
Actinocrinus scitulus M. and W. _________ . ____________ .____________________ ________ ________
x
__ , ______ . _____ . Actin-ocr'inus multiradiatus Shum._. ___ . ________ .___________________________ ________ ________
x
x
ActiniOcrinus sp. ______________________________________________________ .___________________ _______ ________ ________ ________ x
Cactocrinus longus (M. and 'lif. )
~ _________ . ____ .____________________________ ________ _______
x
__ . _____ . ___ _
Cactocrinus glans (Hall) __________________________________________________________ ________ _______
x
___________ . __ _
Teleiocrinus umbrosus (Hall) _______________________________________________________________________________ . x
Physetocrinus ventricQsus (Hall) _________________________________________ ________ ________
x
_____________ _
Strotocrinus glyptus (Hall) .. __________________________ ._________________________ ________ ________
x
______________ _
Platycrinus discoideus 0. and Sh. ~ _________________ . ___________________ ,______ ________
x
______________ _
Platycrinus burlirugtonensis O. and Sh. ____ . ______ ._. ___ . _________________________ :__
x
_____________ . Eucladocrinus pl~uovime:nrus ("White) _________________ . _______________ . ____________ \ ________ \ x
x
x
Barycrinus sp. ________________ . _________ . ________ .. ___ . __________________ . _______________________ ____ .___
x
_________ . ___ . BLASTOIDEA
1
Pentremites elongatus Shum. . _____ . _________ . _____________ . __ ._._. ________________ .____ ________
x
Orbitremites norwOiOdi (0. and S.) _______________ . _____ . ___________ . ________________ ._._
X
x
BRYOZOA
Rhombopora sp. _. ____ . _______ . _________ : ____ . ____ .. _ ... ____ . _____ ..... _ ........ _, ... __ ._._ .. __ ________ ________
x-
Evactinopora grandis M. and W. , . _____ .. ____ ... _____ . ___________________________ .. ______ . x
x
x
Cystodictya sp .. _____ .. ____ .. ___ . __ . __ ._. ___ . _______ . ____ .. __ . _____________________________________ .___
x
___ . __ ._ ._._ .. _
Cystodictya sp. -----______ ..... ___ ........ _. _______ .. __________ ... ___ ---.----.--.---.. - ----.-- -------- ... ____ .1 ___ .• __ . x
BRACHIOPODA
Leptaena analoga (Phillips) __________________ . ____________________ . ___________ .__
x
_________________________ .... Generalized seotion of Burlington limestone at and near Augusta. __
Chonetes multicosta Win. ..._. ______ .... ______ . ________ .. ______ .____________
x
x
______________ _
Chonetes sp. ____________________________ . __________ . _____ . __ . _____ . __________ . ____ . ________ ._____ ________ _______
x
x
Productus burlingtonensis Hall .-.------.. -.--.-.---------.-.. ------------ ________ 1 ________ 1 x
-------
x
Productus viminalis White , _________________ .. __________________ . _________________________________________ • x
Pustula alternata. (N. and P.) ______ .. _____________ . _________ ._____________ _______ ________
x
________
x
Rhipidomel1a dubia (Hall) ______________________________ . _____ . ____________ --------
x 1 ________ \ x
x
x 1
Rhipidomella burlingtonensis (Hall) __ . ________________________ .-______ x
________
x
x
x
1
Schimphoria swallovi (Hall) -------------------------------.----------------
x I x
x
x
x 1
Oamarophoria bisinuata (Rowley) .-------.-.-.-------.--------------------
x
________ 1 ________ --------1--------1
g::~~e~~~~l~~i~--w~ii~~--:::::::::=::::::::::=:::::::::::::::::::::::::::::: ---;---\ :::::::: :::::::~I::::::::I _
__ ~_ .. ,
Dielasma SIp. ----------.-------.-----------------------------.---------.-------------------- -------- \ -------- ~ --.------------- ~ x 1
~~~~~:~n~~f·;:.\~~-~~~--~-~--:::::=::::::::=:::::::::::::::::::::::=:
~ I---~---I---;---I---;---I·--;···
Spirifer carinatus Rowley ----------------------------.-------.-------------------I x 1--------1--------· --------1---·----1
Spirifer insculptus Rowley .------------.------------.-----.-------.. --.-------
x 1 ________ 1 __________ • ____ 1 ______ ._
Spirifer in:eertus Hall ----------------------_________________ . _______________________________ 1 ________ 1 x
x
x 1
Brach;vthyris suborhicularis (Hall) ______ _______________ . __________________ 1 x 1"--'---1 x x, x I
Reticularia pseudolineata (Hall) -----------------------.----------.. ---.. ____ ... ____ 1._. __ .. ----.. __ ._._1 x Lis~ of fossils from exposure of Upper Burlitngton limestone on Lost creek.
ANTHOZOA-
Dizygocrinus
dodecadactylus
(M.
'rriplophyllum dalei (M.-E. and H.)
and W. )
Cyathaxonia sp.
Dizygocrinus rotundus (Shum.)
CRlNOIDEA-
Actinocrinus sp.
Batocrinus laura (Hall) ,
Platycrinus (fragments of ·several
Eretmocrinus sp.
species)
Macrocrinus verneuilianus (Shum.) Macrocrinus verneuilianus (Shum.) Eretmocrinus sp.
M
i Batocrinus laura (Hall) ,
E
t
i BLASTOIDEA MISSISSIPPIAN STRATA OF IOWA 134 Table Slwwitng Range of Fossils in the Bu-rlington Beds. at and near Augustar--
Continued. 1
Horizons
1
1.1 I 21 3 I 6 I 7 J
Syringothyris , sp. __________ .. ________________________ .. _________ .• ___________ ________ ______ _______ _______
x
Pseudosyrinx , sp. ____________________ .. _______________ .. __ .__________________ ________ _______
x
___________ • __ _
Spiriferella plena (Hall) _________________________________ .. _____________ ,_____ _______
x
x
x
x
Athyris lamellosa (Leveille) __________________________________________ .. ______ ________
x
x
x
x
. Cliothyridina incrassata (Hall) __________________________________________ x
x
x
x
x
Cliothyridin!l- obmaxima (McChesney) _____________ .__________________ _______ ________
x
___________ . __ •. Oliothyridina parvirostris (M. lIJld W.) ___ ._ ........ _ .. ___ .. _._._. x
__ .. ___ . __ .. ___ . x
__ .. _._. Composita triDJucIea (Hall) ___ .. ____ . _____ .... __ ... ___ . __ ... ______ ._________
x
_. _______________________ •• ___ _
GASTROPODA
Lepetopsis capulus (Hall) ________________________________ . __ ... _ .. __________ _______ ________
x
x
x
Straparollus ohtusus (H:all) ... _ ....... _ .............. _ ..... ___ ._._. ___ .. _ .. _ x
. ____ . _____ . ___________________ _
Orthonychia pabulocrinus (Owen) • ______________________________________________________________ .______
x
Orthonychia quincyense (McChesney) _____________ . __________________________________________ ,______
x
Orthonychia sp. ________________________ . _______ . ___________ .__________________ ________ ________
x
______________ _
Platyceras latum Keyes. .. _ ......... ___ ... _________ . __ . __ . ___ ._ .. ________ ------------ -------- --------1------- -------
x
~i:~::::: ~;.li~~~~---~~:.~:::=::::::::::::::::::::::::~=~::::::::::::::::::: ::::::: ::::::: ::::::: ---;--- ___ ~ __ _
i~:~:=~a~~~:-.::::::::::::::::::::=:::::::=:::=:::=::::::::::::::::::::::::::::::: :::::::: ---;---1::::::: ::::=: --~---
TRILOBITA
I
I
I
I
I
~rif!ithides , sp. ------------.-----------------------
. ... . . .•.. ..... 1 x
1 .. .-1
1 .·-1 x Table Slwwitng Range of Fossils in the Bu-rlington Beds. at and near Augustar--
Continued. Table Slwwitng Range of Fossils in the Bu-rlington Beds. at and near Augustar--
Continued. 'rriplophyllum dalei (M.-E. and H.)
Cyathaxonia sp.
l 2.
Limestone, gray, sub crystalline
Li
li h
b TRILOBITA The mingling of Lower and Upper Burlington types of crin-
oids in bed 3 is worthy of attention_ ·This is of importance in
that it suggests the absence of a stratigraphic break between
these divisions of the Burlington limestone_ : Along Lost creek in vVashington township, Lee county, three
miles south of Augusta, there are several exposures' of the U p-
per Eurlington, both in the banks of the stream and in quarry
openings. One such exposure appears in the south bank of the
creek just back of the Lost Creek church (NE. 14, sec. 10). Eight feet of gray to brownish crinoidal limestone is shown. This corresponds in position to bed 7 of the general section at
Augusta and to bed 6 of the section at Burlington. The follow-
ing species were collected at this locality:
. BURLINGTON BEDS NEAR BENTONSPORT 135 BLASTOIDEA-
Orbitremites norwoodi (0. and Sh.)
BRYOZOA-
]<~enestella sp. Cosinium latum Ulrich
BRACHIOPODA-
Chonetes illinoiserisis Worthen
Productus viminali~ White
Productus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Rh~pidomella bmlingtonensis (Hall)
Schizophoria swallovi (Hall)
Spirifer grimesi Hall
Spirifer incertus Hall
Spirifer sp. Brachythyris suborbicularis (Hall)
Spiriferella plena (Hall)
Cliothyridina incrassata (Hall)
Athyris lamellosa (Leveille)
GASTROPODA-
Orthonychia sp. Platyceras sp. Lepetopsis capulus (Hall) BLASTOIDEA-
Orbitremites norwoodi (0. and Sh.)
BRYOZOA-
]<~enestella sp. Cosinium latum Ulrich
BRACHIOPODA-
Chonetes illinoiserisis Worthen
Productus viminali~ White
Productus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Rh~pidomella bmlingtonensis (Hall)
Schizophoria swallovi (Hall)
Spirifer grimesi Hall
Spirifer incertus Hall
Spirifer sp. Brachythyris suborbicularis (Hall)
Spiriferella plena (Hall)
Cliothyridina incrassata (Hall)
Athyris lamellosa (Leveille)
GASTROPODA-
Orthonychia sp. Platyceras sp. Lepetopsis capulus (Hall) Orbitremites norwoodi (0. and Sh.)
BRYOZOA Productus sp. Pustula alternata (N. and P. Rhi id
ll
d bi
(H ll) Rhipidomella dubia (Hall)
Rh~pidomella Rh~pidomella bmlingtonensis (Hall) On the Beebe property near Lost creek, west of Wever, there
are several small quarry openings in the Upper Burlington, but
the facilities for collecting at this place are not good at the
present time. The forms obtained are: List of fossils from Upper Burlington limestone west of We1ler. List of fossils from Upper Burlington limestone west of We1ler. ANTHOZOA-
BLASTOIDEA-
Zaphrentis sp. Orbitremites llorwoodi (0. and Sh.)
Triplophyllum dalei (M.·E. and
CRINOIDEA-
H.) BRACHIOPODA-
Platycrinus (fragments of .several
species)
. Strotocrin us sp. Dorycrinus cornigerus (Hall)
Agaricocrinus gracilis (M. and W.)
Macrocl'inus verneuilianus (Shum.)
Productus burlingtonensis Hall f
Productus sp. f f
f
f
pp
g
p
ANTHOZOA-
Zaphrentis sp.
Triplophyllum dalei (M.·E. and H.)
BRACHIOPODA-
Productus viminalis White
Productus sp. 10 Iowa Geol. Survey. vol. XI. pp. 71-89; 1901.. TRILOBITA Amplexus sp. Spiriferina , sp. BB.AOmOPODA-
Spirifer grimesi Hall
Chonetes sp. Spirifer sp. Productus burlingtonensis Hall
Brachythyris suborbicularis (Hall)
Pustula alternata (N. and P.)
Syringothyris , sp .. Pustula sp. Reticularia pseudolineata (Hall)
Rhynchooella Bp. Louisa County.-There are a number of important exposures
of the Burlington limestone in Louisa county. These have been
described previously by Udden.10 In the quarries on Honey creek near the north line of the
southwest quarter of section 28, T. 73 N., R. 3 W., a nearly com-
plete section can be worked out. Only the basal portion of the
Lower Burlington fails to outcrop. A generalized section of the Burlington at this locality, and
lists of fossils collected by the writer from the successive beds
are given below. General section of Burlington limestone m. the quarries 01li Honey creek. PPER BURLINGTON. FEET
7. Limestolne, gray, coarse-grained, crinoidal, cherty; lower and '
upper parts often dolomitizedl and represented by brownish
soft fine-grained cavernous dolOIlllitic limestone. A six mch
layer ,lilt the top is in, some places rich in fish teeth. With
stylolytic seams ___________________________________ . ______________________________________________ 10 to 10%
6. Limestone,
gray,
subcrystalline,
locally
crinoidjjl
in part. Tends to be greenish in upper part owing to incluOed. greenish
specks _________________________ . _____________________________________________________________________________ 6 to
7%
OWER BURLINGTON. 5. Limestone, gray, subcrystaIline; some layers crinoidal; filled
with ilTegular nodules __________________________________________________________________________ 1 to 2%
4. Limestone, brownish, soft, fine-grained; dolomitic for the most
part, but locally crinoidal and little altered in upper part;
nodular above but more massive below ______________________________________________ :_ 7
3_ Chert b!l.Thd ___________________________________ ___________________ ______________________________________
Ih
2. Limestone, brownish, crinoi.dal; grading laterally into fine-
grained' soft d()lomitic limeston~ except in basal part. With
nodules, lenses and bands of gray chert in upper part ___________________ 9
1. Limestone, brownish yellow, dolomitic; with a discontinuous
seam of brownish crmoidal limestone in lower part; filled
with irregular nodular seams of gray chert which weathers
whitish. Exposed _____________________________________________ ___________ .. ________________________ 3 6. Limestone,
gray,
subcrystalline,
locally
crinoidjjl
in part. Tends to be greenish in upper part owing to incluOed. greenish
specks _________________________ . _____________________________________________________________________________ 6 to
7% 5. Limestone, gray, subcrystaIline; some layers crinoidal; filled
with ilTegular nodules __________________________________________________________________________ 1 to 2%
4
Li
b
i h
f
fi
i
d
d l
i i
f
h 1. TRILOBITA Rhipidomella burlingtonensis (Hall)
Rhipidomella dubia (Hall)
Schizophoria swallovi (Hall)
Spirifer grimesi Hall
Spiriferella plena (Hall) f f
f
pp
g
f
ANTHOZOA-
BLASTOIDEA-
Zaphrentis sp. Orbitremites llorwoodi (0. and Sh.)
Triplophyllum dalei (M.·E. and
CRINOIDEA-
H.) BRACHIOPODA-
Platycrinus (fragments of .several
species)
. Strotocrin us sp. Dorycrinus cornigerus (Hall)
Agaricocrinus gracilis (M. and W.)
Macrocl'inus verneuilianus (Shum.)
Productus burlingtonensis Hall f
Productus sp. Rhipidomella burlingtonensis (Hall)
Rhipidomella dubia (Hall)
Schizophoria swallovi (Hall)
Spirifer grimesi Hall
Spiriferella plena (Hall) Strotocrin us sp. p
Dorycrinus cornigerus (Hall)
A
i
i
ili
(M
d Agaricocrinus gracilis (M. and W.)
M
l'i
ili
(Sh
) Macrocl'inus verneuilianus (Shum.) Van Buren County.-In Van Buren county, only one exposure
of the Burlington limestone has been found. This is of the Up-
per Burlington and appears in the north bank of Des Moines
river, just above the water level, one-half mile below the rail-
way station at Bentonsport. It is due to the erosion of a· small
anticlinal uplift which almost parallels the river at this point. Keokuk limestone is exposed in the bluff higher up. The sec-
tion is as follows: Section, of Upper BurliThgton, limesto'IWnear Bentonsport. Section, of Upper BurliThgton, limesto'IWnear Bentonsport. Section, of Upper BurliThgton, limesto'IWnear Bentonsport. FEET
INCHES
2. Limestone, gray, sub crystalline .................................................... 3
10
1. Limestone, light gray, sub crystalline, with occasional thin
crinoidal seams. Exposed .............................................................. 2
2
The fossils collected from these beds are listed below:
List of fossils from bed 1 of the Upper Burlington limestone Mar Bentonsport. ANTHOZOA-
Zaphrentis sp. Triplophyllum dalei (M.·E. and H.)
BRACHIOPODA-
Productus viminalis White
Productus sp. The fossils collected from these beds are listed below: MISSISSIPPIAN STRATA OF IOWA 136 Productus sp. Pustula alternata (N. and P.)
Pustula , sp. Spirifer sp. Athyris lamellosa (Leveille)
Cliothyridina incrassata (Hall)
Rhipidomella burlingtonensis
Rhynchopora sp. (Hall) GASTROPODA-
Spirifer rostellatus Hall
Spirifer grimesi Hall
Spirifer sp. Platyceras sp. Orthonychia quincyensis
(McChes-
ney)
Orthonychia sp. Spirifer sp. A h
i
l Athyris lamellosa (Leveille)
Cli th
idi
i
t
(H List of fossils from bed :e of the Upper Burlilngton li1nestone near Bentonsport. ANTHOZOA-
Dielasma sp. Amplexus sp. Spiriferina , sp. BB.AOmOPODA-
Spirifer grimesi Hall
Chonetes sp. Spirifer sp. Productus burlingtonensis Hall
Brachythyris suborbicularis (Hall)
Pustula alternata (N. and P.)
Syringothyris , sp .. Pustula sp. Reticularia pseudolineata (Hall)
Rhynchooella Bp. List of fossils from bed :e of the Upper Burlilngton li1nestone near Bentonsport. ANTHOZOA-
Dielasma sp. General section of Burlington limestone m. the quarries 01li Honey creek. BURL,INGTON FOSSILS IN LOUISA COUNTY 137 Beds 1 to 6 are well exposed in the creek bank just below the
main quarry. Beds 5 to 7 are typically developed in the main
quarry. There is a suggestion of a dis conformity at the. base of bed 5
in the bluff section, the contact of this member with bed 4 being
undulating. It is probable, however, that there is no strati-
graphic break at this horizon, and that the relationship is due
to uneven dolomitization, for the lower bed is partly altered at
this place. On(:'-fifth mile upstream from the main quarry and in the op-
posite bank, there is a fresh quarry opening which shows twelve
feet of basal Keokuk limestone overlying bed 7 of the above
section. A table showing the species collected and their range in the
Burlington limestone on Honey creek follows: Table ShowVn,g Range of Fossils in the Burli-ngtan Limestone, Haney Creek SecUan,
LO'I.bisa Cownty. I
Horizons I
I
2 I
6 I
7 i
ANTHOZOA
Hadrophyllum gla.ns (White) ........................... _ .. _ ................ __ ... _ ... _ .......... ~... x
Triplophyllum dalei (M.·E. and H.) .. _ ............ _. __ .......... _ ..... _ .. _ ... ___ ... x
x
Zaphrentis sp. . ...... _ .... _ .. _ .................. _ ........ _ ...................... _ .......... _ .............. _... x
Zaphrentis sp. . .................. _ ...................... _ .............. _ .. _ .................. _........... ........ ........ X
CRINOIDEA
Actinocrinus multiradiatus Shum .............................. _ ................ _ ...................... _... x
Actinocrinus sp. . ........ _ .......... _ .......... _ ...... _ ...... _ .... _ .... _ .... ____ .................... _ ... _...... x
Platycrinus d. P. glyptus HalL .......................... _ ...... _ .......... __ ........ _..... ........ ........ x
Platycrinus sp ......... , ........ _ ...................... _ ............................ _....................... ........ ........ x
Platycrinus sp ..................... _ ........ _ ... _ ...... ,.. ........ _ ... __ .. _ .... _._ ...... _............ x
_ ............. . Platycrinus sp. . ...... _ ........................................................ _._ .. ___ .............. x
............... . Uperocrinus pyriformis (Shum.) ............. _ .. _ .................. _......................... x
........... _ .. . Ba.tocrinus laura (Hall) ....... _ .......... _ .............. _ ....................... __ ._ ...................... _... x
Batocrinus clypeatus (Hall) , ................................. _ .. _ ..... _.,. __ ... _......... x
... _ ...... _ .. . Macrocrinus konincki (Shum.) ,_ ...... _ ... __ . __ .. TRILOBITA Limestone, brownish yellow, dolomitic; with a discontinuous
seam of brownish crmoidal limestone in lower part; filled
with irregular nodular seams of gray chert which weathers
whitish. Exposed _____________________________________________ ___________ .. ________________________ 3 BURL,INGTON FOSSILS IN LOUISA COUNTY BURL,INGTON FOSSILS IN LOUISA COUNTY __ .. __ ._ .. _ .... _............ x
... _ .......... . Macrocrinus verneuilianus (Shum.) ................................... _ ... _._ ...... _ ...... _... x
x
Dichocrinus , sp ............................................. _ .......... _ ... __ ._................... ........ x
....... . Dorycrinus gp. . ...... _ ........ _ .... _ .. _ ......................... _ .... __ .. _ ....... _ ...... _ .. _ ........... _.. x
Strotocrinus regalis (Hall.) ....................... _ .......... _ ......... _ .......... _ .. _ .. _ .. ........ ........ x
Strotocrinus glyptus (Hall) ............. _ ............................................................ _... ........ x
Physetocrinus ventricosus (Hall) ... _ ........ _ ............ _................................. ........ ........ x
Te1eiocrinus umbrosus (Hall) ....... _ ...... _ .......... _ .................. _ ...... _ .............. _ ...... _... x
Dizygocrinu~ l'otundus (Shum.) ... _ ....................... _ ................ _................... ........ ........ x
Eutrochocrinus christyi (Shum.) ................... _ .......... _ .. _ ................. ~ .................... _... x MISSISSIPPIAN STRATA OF IOWA 138 Table Showing Bange of Fossils in the Burlington Limtestone, Honey Creek Seotion,
Louisa County-Continued. I
Horizons I
I 2 1 6) 71
1;~~~~~~~~::~~s ___ ~~_~_~_~:~_::::::::::::::::::::::::::::::=::::~:::::=::::::::::=::=::=::::::::::: :::=::: :::=:::
~
BLASTOIDEA
Pentremites elongatus Shum. ______________________________________________________________________ ________
x
x
Pentremites sp. ______________________________ .. ______________________________________________________________ _______ ________ x
Metablastus lineatus (Shum.) , ______________________________________ ._________________________ _______ ________
x
Orbitremites norwoodi (0. and Sh.) _______________________________________________________ ________
x
X
BRYOZOA
Fenestella burlingtonensis Ulrich ______________________________________________________________ ________ _______
x
Fenestella serratula Ulrich _____________ . __________________________________________________________ .. ______ . ________
x
Fooestella sp. ____ ... ____ ..... __ ....... ____ .. __ .. ____ . _______________________ ... ________ . __ . ______ . __ ._. _____ ... ____ . __ . __ .. ____
x
Rhombopora gracilis Ulrich , ________________________________ . __________ . ______ . ___ : ____________ ----____ .______
I x
Rhombopora sp. __ . __ . ____ . ______ .. ____ ._ .. ____ ... __________ .. ____________ . __ ... _________ .. __ . ____ . ___ . _____ . __ .. __ .. _____ ... X
BRACHIOPODA
Chonetes sp. ______ . __ ... ___ . ____ . _______ .. _ ... _________________________ . ____________ . __ .. __ -: .. __ .. ___________________ . ___ .____
x
Chonetes sp. . .. __ ._. ____ ... ___ . __ .. ____ ._. _____________ . ___ . ________ . ______ .. ____ ... __ . ____________________ .. ___ .. __ . x
____ . __ . Orthotetes sp. __ .. ____ . BURL,INGTON FOSSILS IN LOUISA COUNTY __ . _______________ .. ______ . __ .. ____________ . __ . __ . __ .. __ ... __ ... ___ . __ ._________________ ________
x
____ .. __
Pustula sp. _____ ; __ .. ____ . ________ .. ___ .. _____________ .. __ .. ___ . __ . ____ ~ ___ . __ , .. ___ . ________ . __ .... ____ . __ .. ______ .. _______ . ___ . x
Pustula sp. ____ . __ . ___ . __ .. ________ . __ .. __ . ______ .. ___ . ___ . ____ ._ .. _________ . ______ . __ . ____ . _____ .. ______ . __ . ____ . ___ . x
Productus burlingtonensis Hall ______________ . ____ . __________________ . _______ . __________ . __ . ______ . ____ . x
--.-.--
Rhipidomella burlingtonensis (Hall) __________ . __ . ____________ . ____ . ________ . ______ . ____________ . __ . x
x
Rhipidomell:t sp. ____ .. __ . __ ..... ______ :_ .. ________ .. ________ ... _________________ .. __ . ______________ . __ . __ .... ___ . x
_ .. ___ .. ~~~~~~rh~~~r~:aa~:A ~~~~~~. __ :::::::::::::::::::=:.::::::::::::::::::::::::=::::::::::::::::::::: ~ ___ ~ ... I ::::::::
Spirifer grimesi Hall . __ . __________ . __________________ . ______ . _________________ . ______________ . __ .____
x
x
x
Spirifer sp. __ . __ . _____ ..... __ . ___ . ______ . ____ ._. __________ . __________ . __ ._. __ . ___________ ._. __ .-------.------ ----.--. x
Brachythyris suborbicularis (Hall) __ . ______________________ . __ . ________________ . __ . ______ . x
x
x
., ~~~~u1~~Y: :;::~Ol~~~ ('iI~i·)--·:::=:::::::::::::::::;::::==::~::::::=::::=::::::=::=: --.~.-- --.~--. ~
Athyris lamellosa (Leveille) __________ . _________ . __ . _________________ . ____ . _________________ . x
x I x
PELECYPODA
. Aviculopecten sp. __ . __ ... ______ .. _____________ . __ ._. ______ . _________ . __ . __ . ______ . __________________ . __________ . x
Myalina sp .. __ . __ . ___ .. ____ .. _____________ . ____ . ___ . __ . __ .. __ . __ . _____ . ______ . ____ . ____ . __ . __ . ______ .. _________ . ----... X
GASTOPODA
~~~:;~~i~a£~l~~--('iI~ii·)·:::::::::::::::::::::::::::::::::=::::::::::::::::::::=::::::::::::::::::: \--.~--. :::::::: 1--';--'\
I
I
Fish teeth ----~-:~.=.:~~------------------------------------------.--.------.--.----.--------.--------. Section in A'lLderscm/s quarry on the east bank of Smith creek west of the oenter
of the SW. 14, seo. 29, Tp. 73 N., R. 2 W.
FEET 11 Iowa Geol. Survey, vol. XI, pp. 7&-81; 1901. "Seotion m a quarry belonging to Jamie8 Elrick near the sooth OO1lnty line on the
left bank of Smith creek (After Ucldern).
FEET "Seotion m a quarry belonging to Jamie8 Elrick near the sooth OO1lnty line on the
left bank of Smith creek (After Ucldern).
FEET
12. Weathered limestone __________ . _____ ,____________________________________________________________
22
11. Chert ______________________________________________________ --------___________ . ___________ . ____ .... _._....
lh
10.
Crinoidal limestone, with fish teeth near top _ .... _ ... __ ._._ ............ _
2 "Seotion m a quarry belonging to Jamie8 Elrick near the sooth OO1lnty line on the
left bank of Smith creek (After Ucldern).
FEET
12. Weathered limestone __________ . _____ ,____________________________________________________________
22
11. Chert ______________________________________________________ --------___________ . ___________ . ____ .... _._....
lh
10.
Crinoidal limestone, with fish teeth near top _ .... _ ... __ ._._ ............ _
2
9.
Soft limestone .. _ ... _ .. _ ... _ ... ___ .............. _ ........ _ .. ___ .. _. ___ .......... _ ....... _ ......... _...
1
11 Iowa Geol. Survey, vol. XI, pp. 7&-81; 1901. 10.
Crinoidal limestone, with fish teeth near top
9
Soft limestone 12. Weathered limestone __________ . _____ ,___________________________________
11. Chert
--------
. BURL,INGTON FOSSILS IN LOUISA COUNTY -------- ----.--.1 x I
The Anderson quarry exposure is of interest in that it show:::
the contact between the Kinderhook and the Lower Burlington. Table Showing Bange of Fossils in the Burlington Limtestone, Honey Creek Seotion,
Louisa County-Continued. x
x
x
I x
X . . The Anderson quarry exposure is of interest in that it show:::
the contact between the Kinderhook and the Lower Burlington. BURLINGTON BEDS IN LOUISA COUNTY 139 The Kinderhook section at this locality has been described on
page 63. The Burlington succession is as follows: The Kinderhook section at this locality has been described on
page 63. The Burlington succession is as follows: Section in A'lLderscm/s quarry on the east bank of Smith creek west of the oente
of the SW. 14, seo. 29, Tp. 73 N., R. 2 W. FEET Section in A'lLderscm/s quarry on the east bank of Smith creek west of the oenter
of the SW. 14, seo. 29, Tp. 73 N., R. 2 W. FEET
7. Drift . _____ .. _______ .... _._. __ ... _. __ ....... _________________________________ ._______________________________
5
UPPER BURLINGTON. 6. Limestone, gray, coarse-grained, crinoidal (bed 7 of the Honey
creek section) ------------------------------------------------------------------_________________
1:lh
5. Limestone, gray, subcrystalline, with crinoidal seams, stylolytic
(bed 6 of the Honey creek section) .__________________________________________
5:lh
LoWER BURLINGTON. 4. Limestone, gray, sub crystalline, cherty (bed 5 of the Honey
cr·eek section) .-____________________________________________________ -----____________________________
1:lh
3. Mostly concealed. Probably consisting of crinoidal lime-
stone and brownish dolomiti.c rock. (Beds 3 and 4 and upper
part of bed 2' of the HoneY' creek section) ___________________________________
12
2. Limestone, soft, dolomitic, brownish; cherty in middle and
less dolo,mitic above ___________________________________________________________________________
7
1. Limestone, buff, dolomitic, ~ ft ________________________________________________________
1
The following species were collected by the writer from bed
5 at this place: 7. Drift . _____ .. _
UPPER BURLINGTON. 6
Li UPPER BURLINGTON. 6
Li
t 5. Limestone, gray, subcrystalline, with crinoidal seams, stylolytic
(bed 6 of the Honey creek section) .__________________________________________
5:lh
oWER BURLINGTON. 4
Li
b
lli
h
(b d 5
f
h
H 4. Limestone, gray, sub crystalline, cherty (bed 5 of the Honey
cr·eek section) .-____________________________________________________ -----____________________________
1:lh
3
Mostl
concealed
Probabl
consisting
of
crinoidal
lime 3. Mostly concealed. Probably consisting of crinoidal lime-
stone and brownish dolomiti.c rock. BURL,INGTON FOSSILS IN LOUISA COUNTY (Beds 3 and 4 and upper
part of bed 2' of the HoneY' creek section) ___________________________________
12
2
Li
t
ft
d l
iti
b
i h
h
t
i
iddl
d 2. Limestone, soft, dolomitic, brownish; cherty in middle and
less dolo,mitic above ___________________________________________________________________________
7
1
Limestone
buff
dolomitic
~ ft
1 2. Limestone, soft, dolomitic, brownish; cherty in middle and
less dolo,mitic above ___________________________________________________________________________
7 1. Limestone, buff, dolomitic, ~ ft ________________________________________________________
1 The following species were collected by the writer from bed
5 at this place: List of fossils from bea 5 of Burlington limestone itn AMerson quarry. A NTHOZOA-
Hadrophyllum glans White
BRYOZOA-
Cystodictya sp. BRACHIOPODA--
Chonetes illinoisensis Worthen
Chonetes sp. Productus burlingtonensis Hall
Rhipidomella dubia (Hall)
Rhipidomella burlingtonensis (Hall)
Spirifer grimesi Hall
Spirifer,ella plena (Hall)
Brachythyris suborbicularis (Hall) Chonetes illinoisensis Worthen
Chonetes sp Chonetes sp. The marked thinning of both divisions of the Burlington in
tracing them from Des Moines county northwestward is empha-
sized by the two preceding sections. Thus the Lower Burling-
ton has decreased in thickness from forty-three feet at Burling-
ton to one-half that amount in Louisa county, while the Upper
Burlington has decreased in the same way from twenty-seven to
seventeen feet. The following sections have been copied from Udden's report
on the Geology of Louisa County.ll 140 M.ISSISSIPPIAN STRATA OF IOWA 8. Blue shale, with some chert below ... _................................................ 2
7. Fine·grained, yellowish limestone, with Productus sen1.ilreticmlartus,
Spilrifer plenus, a Pentremites; in straight even ledges, with fish
teeth above ..................................................................... _....................... 2
6. Blue shale ................................................................ _............................... 14
5. Bluish, rather fine· grained limestone .............................................. 2
4. Chert layers, interrupted ........................... _..................................... 1
3. Coarse·grained, yellowish or white, criIIlioidal limestone.................. 4%
2. Bluish white crinoidal limestone, upper ledges very evenly
bedded, lower ledges somewhat :fine· grained, with Dielasma row lei
8
1. Softer limestone, with some quartz geodes .................................... 1 " 8. Blue shale, with some chert below . 7
Fi
i
d
ll
i h li 5. Bluish, rather fine· grained limestone ......................................... 4
Ch
t
l
i t
t d 2. Bluish white crinoidal limestone, upper ledges
b dd d l
l d
h t fi
i
d
ith Di 1. Softer limestone, with some quartz geodes .................................... .. Section in J. H. Wasson's quarry Vn the s01lth bank of the sooth branch of Long
c1'eek Vn the northwest comer of BOO. e3, Tp. 74 N., R. 5 W. (After Udden). .. Sections Vn a ravine fol101ving the west banlc of the rail1'oad one and a half miles
north of Morruing Stvn., Vn the northeast corner of sec. 19,
T
73 N
R
3 W
(Af
Udd
) 4. Chert layers
3
Whit It Section seen in some quarries on Gospel run, near the north line of sec. e7,
Tp. 73 N ., R. 3 W . (.:lfter Udden).
FEET ' 6.
Disintegrated limestone, with ba'llds of chert ............... _...................
3
5.
Yellow, disintegrated limestone ............... _ ............................ _.............
3
4.
Blue shale ................................................... _...........................................
1
3.
Yellow slightly disintegrated crinoidal limestone, with amaH hoI·
lows filled with calcite crystals (also zinc blende) ......................
4
2. Yellowish, partly disintegrated limestone, with fish teeth, such as 6.
Disintegrated limestone, with ba'llds of chert ............... _...................
3
5
Y ll
di i t
t d li
t
3 . Section in J. H. Wasson's quarry Vn the s01lth bank of the sooth branch of Long
c1'eek Vn the northwest comer of BOO. e3, Tp. 74 N., R. 5 W. (After Udden).
FEET
6.
Disintegrated limestone, with ba'llds of chert ............... _...................
3
5.
Yellow, disintegrated limestone ............... _ ............................ _.............
3
4.
Blue shale ................................................... _...........................................
1
3.
Yellow slightly disintegrated crinoidal limestone, with amaH hoI·
lows filled with calcite crystals (also zinc blende) ......................
4
2. Yellowish, partly disintegrated limestone, with fish teeth, such as Deltodus and Oladod'LIS
2
G
i h
hi
i
id l 12 Iowa Geol. Survey. vol. V. 1'1' 140·143; 1896. BURL,INGTON FOSSILS IN LOUISA COUNTY 1 " Bed 1 and possibly a part of bed 2 doubtless belong to the
Lower Burlington, while those above are referred to the Upper
Burlington, except beds 11 and 12 which represent ·the basal
Keokuk. It Section seen in some quarries on Gospel run, near the north line of sec. e7,
Tp. 73 N ., R. 3 W . (.:lfter Udden). FEET ' 8. Chel·t and disintegrated limestone, with Eut1'ochom'inus lovei ..... . 7. Crinoidal limestone, somewhat thin· bedded, with a Pent1'emites
6. Thin·bedded, crinoidal limestone ... _ .................................................... . 5. Chert ................................. _ ...................................... _ .............................. . 4. Yellow irregularly bedded limestone .................................................. .. 3. Yellow disintegrated crilloidal linrestone ... _ ..................................... .. 2. Coarsely aggregated crinoidal limestone, with Lobocrinus pyri·
formis ....... : ................................................................. _ ............................ . 1. Shaly, disintegr,ated material ................................. _ ............................ ,
FEET '
3
9
2
%
4
3%
2
1" Beds 1 to 5 of this section represent the Lower Burlington,
and the higher beds, the Upper Burlington . north of Morruing Stvn., Vn the northeast corner of sec. 19,
Tp. 73 N., R. 3 W. (After Udden). 'FEET
4. Chert layers ......................... _ ...... ~ ..................... _..................................... 5/6
3. White or yellowish, cl'inoidal limestone, with teeth of Orodus,
Deltodus and Oladod'LIS ......................... _ ........................................ _..... 2%
2. Greenish white crinoidal limestone, with Lobocrinus pyriformis,
Dizygocrinus ro'ttlndtLS, Dorycrinus qt~V!U[llelobu8, EutrocMcrinus
lovei, Pentrernites elongatus, Actinom'inus scitulus ......... _............. 1%
1. White crinoidal limestone, with Rhipidomella burlingtonensis,
and Spi1'ifer plenus .............................................................................. 4"
All of these beds are referable to the Upper Burlington Section in J. H. Wasson's quarry Vn the s01lth bank of the sooth branch of Long
c1'eek Vn the northwest comer of BOO. e3, Tp. 74 N., R. 5 W. (After Udden). FEET
6. Disintegrated limestone, with ba'llds of chert ............... _................... 3
5. Yellow, disintegrated limestone ............... _ ............................ _............. 3
4. Blue shale ................................................... _........................................... 1
3. Yellow slightly disintegrated crinoidal limestone, with amaH hoI·
lows filled with calcite crystals (also zinc blende) ...................... 4
2. Yellowish, partly disintegrated limestone, with fish teeth, such as BURLINGTON IN WASHINGTON COUNTY BURLINGTON IN WASHINGTON COUNTY 141 DeltoiPus spatulat~is, Psamnwdus glyptus, Cladodus sp., H elodlis
d O
d
llh g yp
,
p ,
sp., and Orodus sp .... - ........................................ - .... - .... - .......... -....... llh
1. Crinoidal white limestone in ledges from six to ten inches in
thicknetl$ .. ·with Eut1'oclwcri711U8 lovei, Batocrirllus laura val'. sin·
uosus, B artocrVlws latUra, Dizy gocrill1tUs rotuniJJu,s ............................. 4112 ' , sp., and Orodus sp .... - ....................................... C i
id l
hit
li
t
i
l d
f
i 1. Crinoidal white limestone in ledges from six to ten inches in
thicknetl$ .. ·with Eut1'oclwcri711U8 lovei, Batocrirllus laura val'. sin·
uosus, B artocrVlws latUra, Dizy gocrill1tUs rotuniJJu,s ............................. 4112 ' , Beds 1 ood 2 are of Upper Burlington age ; beds 3 to 6 are
basal Keokuk. Beds 1 ood 2 are of Upper Burlington age ; beds 3 to 6 are
basal Keokuk. "Section m G?'ay's quarry near the no1'th barn7c of the north b1'arnch of Long creek
in the NE.1/4 of the NW.V~, of sec. 3, Tp. 74 N., R. 5 W . (After Udden) . "Section m G?'ay's quarry near the no1'th barn7c of the north b1'arnch of Long creek
in the NE.1/4 of the NW.V~, of sec. 3, Tp. 74 N., R. 5 W . (After Udden) . "Section m G?'ay's quarry near the no1'th barn7c of the north b1'arnch of Long creek
in the NE.1/4 of the NW.V~, of sec. 3, Tp. 74 N., R. 5 W . (After Udden) . 5. Yellow ilisintegrated crinoidal limestone, with fish teeth near
the basl'l, and with Schizophoria s'Wallo';i, E~btroclw ()rin!l/os christyi,
FEET
Batocrill1tUs laura, Dizygocrm~M rotundus, Mld teeth of D e ltod~ts
5
4. Encrinital white limestone ill heavy ledges, ,hth Proal1ict~tS semi·
retimilatus, Prodllctus b~irlingtonensis, Spi?'ifer g?'imesi ... _........... 3
3. Chert ................................................... _ .................................................... ~
5/ 6
2. Brownish yellow porous, disintegrated limestone ... _....................... 3
1. Bluish white crinoidal limestone, with occasional crinoids near
top ............................................................................... _ ........................... _
5"
Thi
i
i
i
l
f U
B
li 1. Bluish white crinoidal limestone, with occasional crinoids near
top ............................................................................... _ ........................... _
5" This succession is entirely of Upper Burlington age "Section in F. J. Moore's quarry on the ea.st bank of Long creek in the SW.1/4 of
the NE.1/4 of sec. 33, Tp. 75 N., R. 5 W. (Afte?' Udden). 6. B~nds of chert ... 1 3 Geo!. of Iowa, vo!. I, part I, p, 94 ; 1858.
14 Idem, p . 193.
15 Iowa Gool. Survey, vol. IH, pp. 341 and ' 445; 1895.
16 Iowa Goo!. Survey, vol. IV, p . 206; 1895.
17 Iowa Goo!. Survey, vol. XII, p. 254; 1902. BURLINGTON IN WASHINGTON COUNTY _ .................................................................................. . 5. Yellowish shaly material or disintegrated limestone .................... .. 4. Yellow partly disintegrated limestone, with chert bands and fish
teeth ill the upper part, containing Deltodopsis
bialveat~i8,
Deltodopsis cowvexus, Deltodus spat1/.1a,tus, Cladodu.s, fragments
of spines ................................................................................................ .. 3. Bluish white crinoidal limestone in ledges from six to ten inches
in thickness, with Productus b~i1'lmgt 01WTl.sis ... _ .............................. . Z. Shelly limestome, with many brachiopods and Igoce1'as oopuills
1. Crinoidal' white limestone ..................................................................... . FEET
1
2
2
2
1
2"
These beds again represent the Upper Burlington. 1. Crinoidal' white limestone These beds again represent the Upper Burlington. Wa.shington Cownty.-In Washington county, the Burlington
and Keokuk limestones have not been differentiated in previous
reports. Thus, Bain1 2 in his Geology of Washington County
describes them under the title of "Augusta formation."
He
says: "The greater number of fossils found belong to the Burling-
ton fauna, though a few Keokuk forms occur. The formation
is, however, as a whole, a distinct, well marked, stratigraphic
unit for the region studied. It is neither advisable nor possible
to divide it into formations which could be separately mapped". In the course of the present study, it has been found that the
Burlington and Keokuk limestones are recognizable as strati· MISSISSIPPIAN STRATA OF IOWA 142 graphic units, although their formational characteristics are not
nearly so pronounced as in the counties to the southeast. Th
b
d
C
k d
k
h The best exposures are on and near Crooked creek, northwest
of the town of WashingtQn. The Eckles quarry section is typi-
cal (S\iV. 1;4, sec. 2, Tp. 75 N., R. 8 \iV.). • Eckles qU47TY section. FEET
5. Drift ........................................................................................................... 12
4. Limestone, gray, medium· grained, with slight bluish tint, thin·
bedded ........................................................................................................ 2%
3. Shaly parting .......................................................................................... 112
2. Limestone, gray, crinoidal, with occasional small lenses of chert
and thin layers of brown dolomitic limestone, with stylolytic
seams .......................................................................................................... 6
1. Limestone, gray, crinlOidal, with greenish tint above; stylolytic
seams. Bears C08invum latum and other Burlington fossils........ 10 1. Limestone, gray, crinlOidal, with greenish tint above; stylolytic
seams. Bears C08invum latum and other Burlington fossils........ 10 The fauna of the above beds indicates their Upper Burlington
age. 17 Iowa Goo!. Survey, vol. XII, p. 254; 1902 16 Iowa Goo!. Survey, vol. IV, p . 206; 1895.
17 I
G
!
S
l
XII
254
1902 15 Iowa Gool. Survey, vol. IH, pp. 341 and 445; 189
16 I
G
!
S
l
IV
206
1895 NOMENCLATURE AND CHARACTER The Keokuk formation as defined by HaItH consists of cherty
limestone at the base, the encrinallimestone or "Lower Archi-
medes Limestone" of Owen directly above, which is well exposed
at Keokuk" and the overlying. geode bearing shales. Worthen 'S14
clas'sification is essentially the same as that of Hall. T
h
h
l
f L
d D
M i
j Tn the reports on the geology of Lee and Des Moines c.ountjes
Keyes15 designated the basal cherty limestone as the Montrose
cherts and referred them to the Upper Burlington. He de-
scribed the Geode bed as a distinct formation. Gordon16 like-
wise referred the Montrose cherts exposed in Van Burel?- county
to the Burlington. He includes the Keokuk limestone, the Geode
shales and the Warsaw shales and limestones in the Keokuk
stage. In his Geology of Henry County, Savage17 includes the
limestone phase and the Geode shales in the Keokuk. Th
d
h
d
d h
K
k k
f h The present study has demonstrated the Keokuk age of the
Montrose cherts. The Geode shales on the other hand are more RELATIONS OF KEOKUK LIME8TONE 143 closely related faunally to the Warsaw formation than to the
Keokuk. As at present defined, therefore, the Keokuk forma-
tion consists of the transition beds known as the Montrose
cherts, which are about thirty feet in thickness, and the Keokuk
limestone, which is about forty feet in thickness. The lower
division consists of alternating layers of gray and bluish
cherty limestone. In this division, several Keokuk types of
brachiopods appear for the first time. Some of these evidently
represent forms intermediate between typical Burlington types
and true Keokuk forms. The crinoid fauna of the beds shows
similar characteristics, as was pointed out by Wachsmuth and
Springer.1s They say: "The transition beds are more or less fossiliferous through-
out, though the occurrence of the fossils is irregular, and their
preservation very variable. 'J~hey exhibit in an irregular man-
ner the lithologic characters' of both formations, while the· crin-
oidal remains which have been obtained from them show such
an intermingling and blending of the Burlington and Keokuk
species, that it is impossible to say where the one begins and
the other ends. The majority of the' crinoids found in them can
neither be called Burlington nor Keokuk series, and may often
be identified as either. NOMENCLATURE AND CHARACTER They constitute a kind of intermediate
type between them, and throw much light upon the growth of
the individual and the development of species in the course of
time." This part of the Keokuk formation is well exposed near
Augusta, Iowa, and in Cedar Glen, between Hamilton and War-
saw, Illinois. The beds above, constituting the Keokuk lime-
stone of earlier writers, consist of layers of gray to bluish
limestone, alternating with beds of shale, which are increasing-
ly prevalent and thicker towards the·top. It appears that there
was a slow contraction of the sea during Keokuk time, as is in-
dicated by this change in the sediments. 18 Proc. Acad. Nat. Sci. Philadelphia. Part II. p. 228; 1878. STRATIGRAPHIC RELATIONS No convincing evidence of · a stratigraphic break has been
found either at the base or at the top of the Keokuk. Indeed
the faunal transition from the Burlington into the ~eokuk be- MISSISSIPPIAN STRATA OF IOWA 144 low and from the Keokuk into the Lower Warsaw (Geode bed)
above is such as to preclude the possibility of an important dis-
conformity at either level. However, the presence of rolled
shells of Spirifer grimesi in the basal 'bed of the Keokuk sug-
gests a shallowing of the sea in the region at the close of Burl-
ington time. 20 Geological map of Des Moines county. Iowa Geol. Survey. vol. III. oPP. p. 492; 1895.
21 Geological map of Henry county. Iowa Geol. Survey. vol. XII. opp. p. 302; 1902. 19 Iowa Geol. Survey. vol. III, opp. p. 408; 1895. 19 Iowa Geol. Survey. vol. III, opp. p. 408; 1895.
20 Geological map of Des Moines county
Iowa Geol
Survey
vol
III
oPP AREAL DISTRIBUTION The Keokuk limestone forms the surface rock over a compar-
atively small area in southeastern Iowa. It has been recognized
in Lee, Van Buren, Des Moines, Henry, Louisa, Washington
and Keokuk 'c0unties, It outcrops also in Hancock county, Illi-
nois, situated directly east of Lee in Iowa, and in Clark county,
Missouri, to the south of Lee. In all of the Iow'a 'counties, how-
eyer, its areal extent is limited. In Van Buren county it comes
to the surface only along the valley of Des Moines river in the
vicinity of Bonaparte and Bentonsport where it has been ex-
posed by the erosion of a small anticlinal uplift. Its distribution in Lee county is shown on the geological map
of this area prepared by Keyes.19
The more important areas
underlain by the Keokuk are (1) along the valley of MissiSSIppi
river and its tributaries at and near the city of Keokuk; (2)
in northern Washington township and (3) over the greater part
of Denmark township. It also forms a northwe~t-southeast belt several miles wide in
the southwestern part of Des Moines county/o to the north of
Lee .. , . The Keokuk of Henry county21 comes to the surface only over
a'small area along the valley of Skunk river in Jackson town-
ship and appears to h~ve been exposed by the erosion of a
gentle anticline .. The Keokuk and Burlil).gton limestones have not bee.n differ-
entiated on the geological map of Louisa county but all known
exposures of the Keokuk are confined to Morning Sun, southern
Wapello and southwestern Elliot townships, in the southern
part of the county. The Keokuk. of vVashington county likewise has not been dif- KEOKUK BEDS AT KEOKUK 145 ferentiated by previous workers in the field nor has there been
found an exposure of typical Keokuk in the area during the
present investigation. It seems probable, however, that this
limestone underlies the drift over a narrow belt extending
through the middle of the county in a northwest-southeast di-
rection, bounded on the northeast by the Burlington beds and
on the southwest by the St. Louis limestone, which succeeds the
Keokuk directly in this part of the state. In Keokuk county, exposures of the Keokuk limestone occur
along Rock creek north of Ollie. Bu't doubtless it forms the sur-
face rock at several other localities, notably along a belt be-
tween the St. AREAL DISTRIBUTION Louis and Burlington areas in the northeastern
part of the county. AREAL DESCRIPTION BY COUNTIES L ee County and adjacent parts of Illinois.-The type section
of Keokuk limestone is at Keokuk, Iowa. Excellent facilities
for studiying the formation at that place are afforded in the ex-
posures along Soap creek and in a quarry in the Mississippi
river bluff, near the mouth of the creek, where an almost com-
plete succession of the beds is shown (fig. 3). FIG. 3.- Keokuk limestone overlain by glacial drift. Qnarry at mouth of Soap creek, Keokuk. FIG. 3.- Keokuk limestone overlain by glacial drift. Qnarry at mouth of Soap creek, Keokuk. MISSISSIPPIAN S'l'RATA OF IOWA 146 Generalwed section of K eokuk lilmestone along Soap oree7c and near its mcJ'Uth,
Keokuk. Generalwed section of K eokuk lilmestone along Soap oree7c and near its mcJ'Uth,
Keokuk. Keokuk. FEET
16. 15. Limestone, gra,y, sub crystalline .............................. _ ................... 1 1/3-3 1/ 2
Shale, bluish, argillaceous; locally grading wholly or in
14. part into' gray subcrystalline limestone ........................... : ...... 2 1/2-3 1/ 2
Limestone, ash· colored, fine· grained, magnesian;
locally
grading in part into, gray more crystalline fossiliferous
13. limestone. The" cotton wood ledge" of quarrymen ... _ .... _ ... 1 1/ 2-2 1/2
Limestone, bluish gray, subcrystalline; Composita globosa
abundant
....................................... _ ............................................... 1 1/ 2-2 1/ 2
12. LiInJelSto!rue, bluish gray, thin·bedded, cherty; with shaly
seams ................................................................................................ 1 5/6-2 1/ 2
11. Limestone, massive, blnish, subcrystalline; with layers and
seams of graly fine· grained magnesian limestone and calca·
reons shale. Fish teeth locally abundant at base ................ ..4 1/2-·6
10. Limestone, bluish,' sub crystalline, Spirifer
ke07c~!k abun·
dant ........................... _ ................................................................... (\
9. Shale, bluish; argillaceous, very fossiliferous; locally with
8. seaJllS of gray sub crystalline limestone .................................. 1
Limestone, gray, compact, most of the layers thin and
lenticular; with thin intercalated shaly seams. Fish teeth
:-1 1/ 2
.,-1 1/ 2 ,
in topmost layer ... _ .............................................. _ .......... _ ........... 2 3/ 4-3
7. Limestone, gray, subcrystalline, the "gTay ledge"
OT
6. 5. "eighteen inch ledge" of quarrymen. Beal'ing a few fish
teeth ......................................................................................... _ ....... 1
Limestone, light gray, massive, cherty; locally grading into
shale in pa.rt. A shaly parting at· the base is rich in crin·
oids. The" white ledge '.' ,of qual'J'ymen ................................ 3
Limestone, gray, impure, massive, fine· grained, magnesian,
cherty; locally with occasiollal seams of gray, subcrystalline
limestone; bearing a few large calcite geodes many of ,
which contain millel'ite:
the" millerite ledge"
of quarry·
men .............................. , .............. _ ........................................ _ ......... 5
-21/ 2
--4
-6
4. Li.me~ton e, light gray, impure, soft; bearing occasional
cnnOlds ................................................... _....................................... 5/6-1
3. Limestone, bluish, medium grained; bearing a few fish
teeth ................................................................................................ 3/4-1 1/3
'2. Limestone, grayish, medium· grained .. : ....... , .. _ ...... _ ............ _ .... 2
-3 "
1. Limestone,
grayi"sh, medium-grained, cherty;
fish
teeth ·
locally abundant. Exposed ... _ ........ __ .................. _ .... _ .... _ ...... __ .. 6
Th
f
il
f th
i
b d
li t d b l FEET
16. 15. Limestone, gra,y, sub crystalline .............................. _ ................... 1 1/3-3 1/ 2
Shale, bluish, argillaceous; locally grading wholly or in
14. Generalwed section of K eokuk lilmestone along Soap oree7c and near its mcJ'Uth,
Keokuk. 2
1
Li
i" h
di
i
d
h
fi h
h 1. Limestone,
grayi"sh, medium-grained, cherty;
fish
teeth ·
locally abundant. Exposed ... _ ........ __ .................. _ .... _ .... _ ...... __ .. 6 The fossils of the successive beds are listed below : Generalwed section of K eokuk lilmestone along Soap oree7c and near its mcJ'Uth,
Keokuk. part into' gray subcrystalline limestone ........................... : ...... 2 1/2-3 1/ 2
Limestone, ash· colored, fine· grained, magnesian;
locally
grading in part into, gray more crystalline fossiliferous
13. limestone. The" cotton wood ledge" of quarrymen ... _ .... _ ... 1 1/ 2-2 1/2
Limestone, bluish gray, subcrystalline; Composita globosa
abundant
....................................... _ ............................................... 1 1/ 2-2 1/ 2
12. LiInJelSto!rue, bluish gray, thin·bedded, cherty; with shaly
seams ................................................................................................ 1 5/6-2 1/ 2
11. Limestone, massive, blnish, subcrystalline; with layers and
seams of graly fine· grained magnesian limestone and calca·
reons shale. Fish teeth locally abundant at base ................ ..4 1/2-·6
10. Limestone, bluish,' sub crystalline, Spirifer
ke07c~!k abun·
dant ........................... _ ................................................................... (\
9. Shale, bluish; argillaceous, very fossiliferous; locally with
8. seaJllS of gray sub crystalline limestone .................................. 1
Limestone, gray, compact, most of the layers thin and
lenticular; with thin intercalated shaly seams. Fish teeth
:-1 1/ 2
.,-1 1/ 2 ,
in topmost layer ... _ .............................................. _ .......... _ ........... 2 3/ 4-3
7. Limestone, gray, subcrystalline, the "gTay ledge"
OT
6. 5. "eighteen inch ledge" of quarrymen. Beal'ing a few fish
teeth ......................................................................................... _ ....... 1
Limestone, light gray, massive, cherty; locally grading into
shale in pa.rt. A shaly parting at· the base is rich in crin·
oids. The" white ledge '.' ,of qual'J'ymen ................................ 3
Limestone, gray, impure, massive, fine· grained, magnesian,
cherty; locally with occasiollal seams of gray, subcrystalline
limestone; bearing a few large calcite geodes many of ,
which contain millel'ite:
the" millerite ledge"
of quarry·
men .............................. , .............. _ ........................................ _ ......... 5
-21/ 2
--4
-6
4. Li.me~ton e, light gray, impure, soft; bearing occasional
cnnOlds ................................................... _....................................... 5/6-1
3. Limestone, bluish, medium grained; bearing a few fish
teeth ................................................................................................ 3/4-1 1/3
'2. Limestone, grayish, medium· grained .. : ....... , .. _ ...... _ ............ _ .... 2
-3 "
1. Limestone,
grayi"sh, medium-grained, cherty;
fish
teeth ·
locally abundant. Exposed ... _ ........ __ .................. _ .... _ .... _ ...... __ .. 6 13. g
q
y
_
_
Limestone, bluish gray, subcrystalline; Composita globosa
abundant
....................................... _ ............................................... 1 1/ 2-2 1/ 2 12. LiInJelSto!rue, bluish gray, thin·bedded, cherty; with shaly
seams ................................................................................................ 1 5/6-2 1/ 2 '2. Limestone, grayish, medium· grained .. : ....... , .. _ ...... _ ............ _ .... The fossils of the successive beds are listed below : List of fossils from bed 1 of the K eoh!k limestone at K eokuk. THOZOA ANTHOZOA-
Triplophyllum dalei (M.-E. anld H.)
Pala.eaeis obtusus (M. and W. )
BRYOZOA-
Fenestella triserialis Ulrich ,
Fenestella species II ,
F enestella limitaris Ulrich
~
F enestella serra.tula. Ulrich
F enestella tenax Ulrich
Polypol'a burlingtonensis Ulrich
Cy'stodictya lineata Ulrich
Worthenopora spinosa Ulrich
Glyptopora sp. BRACHIOPODA-
Orthotetes lreokuk (Hall)
Productus cf. P. gallatinensis Girty
Productus setigerus Hall
Avomia sp. Pustula alternata (N. and P.) ANTHOZOA-
Triplophyllum dalei (M.-E. anld H.)
Pala.eaeis obtusus (M. and W. )
BRYOZOA-
Fenestella triserialis Ulrich ,
Fenestella species II ,
F enestella limitaris Ulrich
~
F enestella serra.tula. Ulrich
F enestella tenax Ulrich
Polypol'a burlingtonensis Ulrich
Cy'stodictya lineata Ulrich
Worthenopora spinosa Ulrich
Glyptopora sp. BRACHIOPODA-
Orthotetes lreokuk (Hall)
Productus cf. P. gallatinensis Girty
Productus setigerus Hall
Avomia sp. Pustula alternata (N. and P.) ANTHOZOA-
Triplophyllum dalei (M.-E. anld H.)
Pala.eaeis obtusus (M. and W. )
BRYOZOA-
Fenestella triserialis Ulrich ,
Fenestella species II ,
F enestella limitaris Ulrich
~
F enestella serra.tula. Ulrich
F enestella tenax Ulrich
Polypol'a burlingtonensis Ulrich
Cy'stodictya lineata Ulrich
Worthenopora spinosa Ulrich
Glyptopora sp. BRACHIOPODA-
Orthotetes lreokuk (Hall)
Productus cf. P. gallatinensis Girty
Productus setigerus Hall
Avomia sp. Pustula alternata (N. and P.) Pustula biseriata (Hall)
Tetracamera sub trigona (M. and W.)
Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Syringothyris subcuspidatus (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hg.]])
Athyris lamellosa (Leveille) f
Composita trinuclea (Hall) I
l'ELlccYPODA-
Aviculopecten sp. Cypricardinia f sp. GASTROPODA-
Platyceras equilateralis Hall
Orthonychia pabulocrinus (Owen)
VERTEBRATA-
Fish teeth (Sandalodus, etc.) Pustula biseriata (Hall)
Tetracamera sub trigona (M. and W.)
Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Syringothyris subcuspidatus (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hg.]])
Athyris lamellosa (Leveille) f
Composita trinuclea (Hall) I
l'ELlccYPODA-
Aviculopecten sp. Cypricardinia f sp. GASTROPODA-
Platyceras equilateralis Hall
Orthonychia pabulocrinus (Owen)
VERTEBRATA-
Fish teeth (Sandalodus, etc.) Pustula biseriata (Hall)
Tetracamera sub trigona (M. and W.)
Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Syringothyris subcuspidatus (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hg.]])
Athyris lamellosa (Leveille) f
Composita trinuclea (Hall) I
l'ELlccYPODA-
Aviculopecten sp. Cypricardinia f sp. GASTROPODA-
Platyceras equilateralis Hall
Orthonychia pabulocrinus (Owen)
VERTEBRATA-
Fish teeth (Sandalodus, etc.) Fenestella species II ,
ll
li
i
i
l i h
~ F enestella limitaris Ulrich
~ F enestella serra.tula. Ulrich Fish teeth (Sandalodus, etc.) Pustula alternata (N. 22 Am. Jour. Sci., 3d ser., vol. 40, p. 296, 1890.
23 OP. cit., p. 29&. The fossils of the successive beds are listed below : and P.) FAUNA OF KEOKUK LlMESTOl'."'E 147 Eutrochocrinus plMlodiscus (Hall)
Platyceras fissu~ella Hall The following additional species are listed from this bed by C.
H. Gordon :22 Eutrochocrinus plMlodiscus (Hall)
Platyceras fissu~ella Hall List of fossils from bed e of Keo1ruk limestone at Keo7c'U7c. List of fossils from bed e of Keo1ruk limestone at Keo7c'U7c. ANTHOZOA-
rrriplophyllum dalei (M.-E. and H .)
VERMES-
Enchostoma sp. CRINOIDEA-
Actinocrinus sp. BRYOZOA-
Ferrestel1a rnuItispinosa Ulrich
BRACHIOPODA-
Productus viminalis White f
Pr<oductus setigerus Rall f
Productus sp. Pustula biseriata (Hall)' ,
Rhipidomella dubia (Hall)
Tetracamera subcuneata (Hall)
Rhynchopora beecheri (Greger)
Dielasma sp. Spirifer cf. S. keokuk Hall
Spirifer lo.gam Hall ,
Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Syringothyris sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria sp. PEL.ECYPODA-
Myalina keokuk Woo·then
GASTROPODA-
Platyceras equilateralis Hall
VERTEBRATA-
Fish teeth Dielasma sp. Spirifer cf. S. keokuk Hall
Spirifer lo.gam Hall ,
Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Syringothyris sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria sp. PEL.ECYPODA-
Myalina keokuk Woo·then
GASTROPODA-
Platyceras equilateralis Hall
VERTEBRATA-
Fish teeth List of fossils from bed 3 of Keokuk lvmestone at Keok~!7c. List of fossils from bed 3 of Keokuk lvmestone at Keok~!7c. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus setigerus Hall f
Pustula biseriata (Ifull)
Rhipidornella dubia (Hall)
~pirifer cf. S. keokuk Hall
Brachythyris suborbicularis (Hall)
Brachythyris sp. Syringothyris sp. Reticularia pseudolineata (Hall)
Cliothyridina parvirostris (M. and W.) ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus setigerus Hall f
Pustula biseriata (Ifull)
Rhipidornella dubia (Hall)
~pirifer cf. S. keokuk Hall
Brachythyris suborbicularis (Hall)
Brachythyris sp. Syringothyris sp. Reticularia pseudolineata (Hall)
Cliothyridina parvirostris (M. and W.) ~pirifer cf. S. keokuk Hall
Brachythyris suborbicularis (Hall)
Brachythyris sp. Syringothyris sp. Reticularia pseudolineata (Hall)
Cliothyridina parvirostris (M. and W.) ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus setigerus Hall f
Pustula biseriata (Ifull)
Rhipidornella dubia (Hall) List of fossils fr01n bed 4 of K eokuk lilmestone a·t Keokuk. List of fossils fr01n bed 4 of K eokuk lilmestone a·t Keokuk. ANTHOZOA--'-
BRACHIOPODA-
Triplophyllum dalei (M.-E. and H.)
'Productus lip. Amplexus sp. Pastula alternata (N. and P .)
CRrNOIDEA-
Spiriferella neglecta (Ifull)
Actinocrinus pernodosus Hall ,
Brachythyris suborbicuIaris (Hall)
Actinocrinus lowei Hall ,
Reticularia pseudolineata (Hall)
Agaricocrinus americanus var. tuber-
Cliothyridina sp. osus Hall
GASTROPODA-
BRYOZOA-
PlatyCJel'as equilateralis Hall f
Fenestella muItispinosa Ulrich' Actinocrinus pernodosus Hall ,
A ti
i
l
i H ll Actinocrinus lowei Hall ,
Agaricocrin s american s
ar Fenestella muItispinosa Ulrich' Gordon2s reports three species of crinoids from this bed which
were not found by the writer, namely: Agaricocrinus amerieanus (Roemer)
M
i
l
l
(H ll) Macrocrinus lagunculus (Hall)
Pl t
i
ff
di H Jl Platycrinus saffordi H:aJl MISSISSIPPIAN STRATA OF IOWA 148 List of fossils from bed 5 of Keokuk linnestone at Ke07l7u1c. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
CRINOIDEA-
Eucladocrinrus sp. Barycrinus sp. BRYOZOA-
Penestella compressa Ulrich ,
Fenestella se1'l'atula Ulrich
Fenestella ten3X Ulrich
Fenestella sp. Archimedes owenanus Hall
Polypora halliana Prout ,
Rholttbopora dichotoma Ulrich ,
Cystodictya lineata Ulrich
Glyptopora sp. BRACHIOPODA-
Ol'thotetes keokuk (Hall)
Productus setigerus Hall
Productus sp. Avonia sp. Pustula alternata (N. and P.)
Pustula hiseriata (Hall)
Pustula sp. Spirifer cf. S. keokuk Hall
Brachythyris suborbicularis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseuilolineata (Hall)
Composita trinucLea (Hall)
List of fossils from bed 6 of Keok~!k linnestone at Keokuk
ANTHOZOA-
. Zaphrentis sp. Amplexus sp. 'rriplophyllum dalei (M.-E. and H .)
Hadrophyllum (species undescribed)
Palaeacis obtusus (M. and W.)
CRINOIDEA-
Cystodictya lineata Ulrich
Worthenopora spinosa Ulric.h
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus setigr:rus Hall
Productus cf. P. gallatinensis Girty
Productus ovatus Hall
Agaricocrinus 3.ITlericanus val'. tuber-
Productus sp. osus Hall
Agaricocrinus sp. Agaricocrinus sp. Actinocrinus lowei Hall
Actinocrinus pernodosus Hall
Uperocrinus nashviUa.e (Hall)
Platycrinus saffordi Hall ,
Platycrinus sp. Platycrinus sp. Barycrinus spurius (Hall)
Barycrinus stellaitus (Hall)
BRYOZOA-
:F1enestella serratula Ulrich
Fenestella tenax Ulrich
Fenestella compressa Ulrich
Fenestella species III
Fenestella species IT
Polypora hailiana Prout
Polypora varsoviensis Prout
Polypora species II
Pustula biseriata (Hall)
Pustnla alternata. (N. and P.)
Pustula , &p. Avonia (species undescribed)
Rhipidomelhv dubia (Hall)
Dielasma sp. Spil'ifer cf. S. keokuk Hall
Spirifel' l'ostellatus Hall
Spirifer tenuicostatus Hall
Spirifer subaequalis Hall ,
Syringothyris (') sp. Spiriferella neglecta' (Hall)
Reticulal'ia pseudoliroeata (Hall)
Cliothyridina obma.xima (McChesney)
Composita trinuclea (Hall)
PELECYPODA-
Conocardium sp. List of fossils fr01n bed 4 of K eokuk lilmestone a·t Keokuk. Myalina keokuk Worthen
GASTROPODA-
Platyceras equilateralis Hall
Gordon24 found the following crinoids in this bed:
Actinocrinus sp. Agaricocrinus americaJtus (Roemer)
Barycl'inus magistel' (Hall)
List of fossils from bed 8 of Ke07~u 7c limestone at K eoh,k,
ANTHOZOA-
Zaphrentis varsoviensis ·Worthen
Zaphrentis sp. Triplophyllum daJei (M.·E. and H.)
Amplexus sp. Palaeacis obtusus (M. and W.)
CRINOIDEA-
Dorycrinus sp. ·Agaricocrinus americarI1us val'. tuber-
osus Hall
BRYOZOA-
Fistulipora spergenensis Rominger , Gordon24 found the following crinoids in this bed: List of fossils from bed 8 of Ke07~u 7c limestone at K eoh,k, List of fossils from bed 8 of Ke07~u 7c limestone at K eoh,k, CRINOIDEA-
Dorycrinus sp. ·Agaricocrinus americarI1us val'. tuber-
osus Hall
BRYOZOA-
Fistulipora spergenensis Rominger , ANTHOZOA-
Zaphrentis varsoviensis ·Worthen
Zaphrentis sp. Triplophyllum daJei (M.·E. and H.)
Amplexus sp. Palaeacis obtusus (M. and W.)
24 OP. cit.. p. 296. CRINOIDEA-
Dorycrinus sp. ·Agaricocrinus americarI1us val'. tuber-
osus Hall
BRYOZOA-
Fistulipora spergenensis Rominger , 24 OP. cit.. p. 296. FAUNA OF KEOKUK BEDS AT KEOKUK FAUNA OF KEOKUK BEDS AT KEOKUK 149 Stenopora sp. Fenestella serratula ' Ulrich
Fenestella multispinosa Ulrich
Fenestella triserialis Ulrich
. Fen estella compressa Ulrich , . Fenestella species I
Fenestella species II i
Hemitrypa perstriata Ulrich
Polypora simulatrix Ulrich
Polypora species I
Polypora sp. Archimedes cf. A. negligens Ulrich
Pinnatopora Slp. Rhombopor3. attenuata Ulrich T
BRACHIOPODA -
Orthotetes keokuk (Hall)
Productus d. P. gallatinensis Girty
Productus setigel'Us Hall
Productus ovatus Hall
Productu9 sp. Productus sp. Productus sp. Pustula biseriata (Hall)
Pustula alternata (N. and P.)
P
T
V Stenopora sp. Fenestella serratula ' Ulrich
Fenestella multispinosa Ulrich
Fenestella triserialis Ulrich
. Fen estella compressa Ulrich , . Fenestella species I
Fenestella species II i
Hemitrypa perstriata Ulrich
Polypora simulatrix Ulrich
Polypora species I
Polypora sp. Archimedes cf. A. negligens Ulrich
Pinnatopora Slp. Rhombopor3. attenuata Ulrich T
BRACHIOPODA -
Orthotetes keokuk (Hall)
Productus d. P. gallatinensis Girty
Productus setigel'Us Hall
Productus ovatus Hall
Productu9 sp. Productus sp. Productus sp. Pustula biseriata (Hall)
Pustula alternata (N. and P.)
P
T
V Pustula (species undescribed)
Avonia sp. Rhipidomella dub!i.a (Hall)
Dielasma sinuata Weller
Dielasma sp. Spiriferina i sp. Spiriferina , sp. Spirifel' keokuk Hall
Spirifor tenuicostatus H all
Spirifer rostellatus Hall
Brachythyris :mborbicularis (Hall)
Syringothyris sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Cliothyric1ina parvirostris (M. & W. )
Composita peutag-oala Weller
Composita trinuclea (Hall)
Composita sp. PELECYPODA-
Lithophagus illinoisensis Worthen
TRILOBITA-
Griffithides (1) 8p. VERTEBRATA-
Fish teeth VERTEBRATA-
Fish teeth Pustula alternata (N. and P.) List of foss·ils fl'om bed 1£ of Keo7c1~k limestone at Keokmk List of foss·ils fl'om bed 1£ of Keo7c1~k limestone at Keokmk. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRYOZOA-
Stenopo.ra sp. Stenopora sp. Archimedes Bp. Fenestella tenax IDrich
Ptilopora sp. Rhombopora sp. BRACHIOPODA-
Pustula alternata (N. and P .)
Spirifer d. S. keokuk Hall
Cliothyridina obmaxima (McChesney) BRYOZOA-
Stenopo.ra sp. Stenopora sp. Archimedes Bp. Fenestella tenax IDrich
BRACHIOPODA-
Pustula alternata (N. and P .)
Spirifer d. S. keokuk Hall
Cliothyridina obmaxima (McChesney) Stenopora sp. A
hi
d
B Archimedes Bp. F
t ll
t Fenestella tenax IDrich List of fossils from bed 19 of Keo7cuk lillnest07i!IJ at Keo7cuk. List of fossils from bed 19 of Keo7cuk lillnest07i!IJ at Keo7cuk. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Zaphrentis d. Z. spinulosa (M.-E. and !II.)
Zaphrentis sp. Monilopma beecheri Grabau
CRINOIDEA-
Agarioocrinus americanus var. tuber·
osus Hall
Actinocrinus pernodosus Hall
Dorycrinns sp. BRYOWA-
Fistulipora spergonensis Rom. Fenestella serratula IDrich ,
Fenestella species II T
Fenestella sp. Fenestella species III
Polypora stri:ruta Cunrin·gs
Polypora varsoviensis Prout
Rhombopora varians Ulrich ,
BRACHIOPODA-
Productus sp. Productus sp. Pustula altern~ta (N. and P.)
Rhipidomella dubia (Hall)
Spirifer keokuk Hall
Brachythyris subcardifonnis (Hall)
Composita globosa Weller
TRILOBITA-
Griffithides f sp. VERTEBRATA-
Cochliodus nobilis N. run.d: W. Fenestella species II T
F
t ll Cochliodus nobilis N. run.d: W. Fenestella sp. List of foss>ils from bed 9 of KeoTcuTc limestone at K eo/"''''Uk. Myalina keokuk Worthen
List of fossils from bed 11 of K eokuk lillnestone at Keokuk. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRYOZOA-
Stenopora sp. BRACHIOPODA--
Orthotetes keokuk (Hall)
Productella sp. Productus setigerus Hall ,
Productus sp. Productus sp. Productus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Dielalsma 8p. Spil'ifer keokuk Hall
Pseudosyrinx keokuk Weller
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
GASTROPODA-
Platyceras sp. Orthonychia sp. Orthonychia sp. Conularia d. C. missouriensis Swallow
TRILOBITA-
Griffithides , sp. VEr~TEBRATA
Fish teeth List of foss>ils from bed 9 of KeoTcuTc limestone at K eo/"''''Uk. List of foss>ils from bed 9 of KeoTcuTc limestone at K eo/"''''Uk. f f
f
f
ANTHOZOA-
ZaphreJitis varsoviensis Worthen
Triplophyllum dalei (M.-E. and H .)
Amplexus sp. Monilopora beecheri Grabau
CruNOIDEA-
Bat.()lcrinus 1 sp. Do'rycrinus mississippiensis Roemer
Dorycrinus sp. Ptilopora valida Ulrich
Rhombopora attenuata Ulrich
Acanthoclema confluens Ulrich
Taenioc1ictya l'amulosa Ulrich
Cystodictya sp. Cystodictya sp. GlyptKlpora keYSieTlingi (Prout)
Cyclopora (several species)
Proutella discoidea (Prout) ,
Agaricocrinus :1mericanus val'. osus Hall
tuber-
Wortheno.pora spinosa Ulrich
BRAcHIOPoDA-
Barycrinus tumidus (Hall)
Barycrinus stellatus (Hall)
BRYOZOA-
Fistulipora sp. Leioclema punctatum (Hall)
FeIJestella serratula Ulrich
F enesteHa tenax Ulrich
. F enestella multispinosa Ulrich
Fenestella triserialis Ulrich ,
Fenestella compressa Ulrich ,
F enestella rudis Ulrich
Fenestella sp. Fenestella sp. Hemitrypa prout ana Ulrich
Hemitrypa perstriata Ulrich'
Polypora varsovie1'lsis Prout
Polypora reb'orsa Ulrich
PoIypora maccoyan'<L Ulrich
Polypora simulatrix Ulrich
Polypora sp. Productus setigerus Hall
Pustula alternata (N. and P.)
Spiriferina sp. Spi.rifer tenuicostatus Hall
Spirifer cf. S. pellaensis Weller
Spirifer keokuk Hall
Syringothyris sp. Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Cliothy'ridina parvirostris (M. and W.)
Composita trinuclea (Hall)
PELECYPODA-
Aviculopecten sp. Aviculop('cten sp. Lithophagus illinoisensis Worthen
C.'llrica,rdinia sp. GASTROPODA-
Platyceras sp. YER'l'EBRATA-
Pleuracanthus
List of fossils from bed 10 of the KeoTcuTc limestone at KeoTcuk. ANTHOZOA-
BRYOZOA-
Triplophyllum dalei (M.-E. and H.)
Fenestella serra tula Ulrich , ANTHOZOA-
ZaphreJitis varsoviensis Worthen
Triplophyllum dalei (M.-E. and H .)
Amplexus sp. Monilopora beecheri Grabau
CruNOIDEA-
Bat.()lcrinus 1 sp. Do'rycrinus mississippiensis Roemer
Dorycrinus sp. Agaricocrinus :1mericanus val'. osus Hall
tuber-
Barycrinus tumidus (Hall)
Barycrinus stellatus (Hall)
BRYOZOA-
Fistulipora sp. Leioclema punctatum (Hall)
FeIJestella serratula Ulrich
F enesteHa tenax Ulrich
. F enestella multispinosa Ulrich
Fenestella triserialis Ulrich ,
Fenestella compressa Ulrich ,
F enestella rudis Ulrich
Fenestella sp. Fenestella sp. Hemitrypa prout ana Ulrich
Hemitrypa perstriata Ulrich'
Polypora varsovie1'lsis Prout
Polypora reb'orsa Ulrich
PoIypora maccoyan'<L Ulrich
Polypora simulatrix Ulrich
Polypora sp. P
Li
f f
il
f
b d 10
f List of fossils from bed 10 of the KeoTcuTc limestone at KeoTcuk. List of fossils from bed 10 of the KeoTcuTc limestone at KeoTcuk. ANTHOZOA-
BRYOZOA-
Triplophyllum dalei (M.-E. and H.)
Fenestella serra tula Ulrich , MISSISSIPPIAN STRATA OF IOWA 150 BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus setigerus Hall
Pustula alternata (N. and P.)
Pustula biseriata (H-aJ.l)
Rhipidomella dubia (Hall)
Dielasma sinuata Weller
Spirifer keokuk Hall
Spirifer tenuicostatus Hall
Syringothyris textus (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall)
Composita globosa Weller
PELECYPODA-
. List of fOSlSils from bed 14 of Keokmk lillnestone at Keokuk List of fOSlSils from bed 14 of Keokmk lillnestone at Keokuk. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Monilopo:ra beecheri Grabau
CRINOIDEA-
Barycrinus lip. BRYOZOA-
Fen estella Bp. Cystodictya lineata IDrich
BRACHIOPODA-
Pustula biseriata (Hall) ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Monilopo:ra beecheri Grabau
CRINOIDEA-
Barycrinus lip. BRYOZOA-
Fen estella Bp. Cystodictya lineata IDrich
BRACHIOPODA-
Pustula biseriata (Hall) BRYOZOA-
Fen estella Bp. Cystodictya lineata IDrich
BRACHIOPODA-
Pustula biseriata (Hall) BRYOZOA-
Fen estella Bp. Cystodictya lineata IDrich
BRACHIOPODA-
Pustula biseriata (Hall) ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Monilopo:ra beecheri Grabau
CRINOIDEA-
Barycrinus lip. FAUNA OF KEOKUK BEDS A'l' KEOKUK 151 Produckus setigerus Hall
Rhyn.chonella sp. Dielasma sp. Cliothyridina parvirostrisa (M. and
W.)
SpLrifer cf. S. keokuk Hail
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Cliothyridina obmaxima (McChesnc.")
PELECYPODA-
Lithopha,gus illinoisell$is Worthon f
Aviculopecten sp. Cliothyridina parvirostrisa (M. and
W.)
li
h
idi
b
i
h Cliothyridina parvirostrisa (M. and
W.)
Cli
h
idi
b
i
(
Ch
") Produckus setigerus Hall
Rh
h
ll Produckus setigerus Hall
Rh
h
ll Rhyn.chonella sp. Di l Cliothyridina obmaxima (McChesnc.")
PELECYPODA- Dielasma sp. S L if
f SpLrifer cf. S. keokuk Hail
S i if
ll
l
(H ll) Lithopha,gus illinoisell$is Worthon f
Aviculopecten sp. Spiriferella neglecta (Hall)
R
i
l
i
d li
(H Reticularia pseudolineata (Hall) Several additional species are reported from this bed by
Gordon25, viz: Agaricocrinus americanus (Roemer)
val'. Barycrinus tumidus (Hall)
Archimedes owenunus H all Uperocrinus llashvillae (Hall)
Di
i
bi
bi
(H Uperocrinus llashvillae (Hall)
Di
i
bi
bi
(H Dizygocrinus biturbinatus (Hall)
D
i
i
i
i
i
i
R Dorycrinus mississippiensis Roemer
A
i
i
th
i H ll Agaricocrinus wortheni Hal 25 Am. Jour. Sei.: 3d ser., vol. 40, p. 296. List of foss-bls from bed 15 of Keo/rule limestone at Keo/,uk. List of foss-bls from bed 15 of Keo/rule limestone at Keo/,uk. ANTHOZOc<\.-
Triplophyllum dalei (M.-E. and H. ) . BRYOZOA-
Stenopora sp. BRACHIOPODA-
Pnstula alterna.ta (N. and P.)
Rhipidomella dubia (Hall)
Spirifer cf. S. keokuk Hall
Bmchythyl'is suboroocularis (Hall)
Brachythyl'is subcardiformis (Hall)
C.omposita globosa Weller ANTHOZOc<\.-
Triplophyllum dalei (M.-E. and H. ) . BRYOZOA-
Stenopora sp. BRACHIOPODA-
Pnstula alterna.ta (N. and P.)
Rhipidomella dubia (Hall)
Spirifer cf. S. keokuk Hall
Bmchythyl'is suboroocularis (Hall)
Brachythyl'is subcardiformis (Hall)
C.omposita globosa Weller ANTHOZOc<\.-
Triplophyllum dalei (M.-E. and H. ) . BRYOZOA-
Stenopora sp. BRACHIOPODA-
Pnstula alterna.ta (N. and P.) ANTHOZOc<\.-
Triplophyllum dalei (M.-E. and H. )
BRYOZOA-
Stenopora sp. BRACHIOPODA-
Pnstula alterna.ta (N. and P.) Rhipidomella dubia (Hall)
Spirifer cf. S. keokuk Hall
Bmchythyl'is suboroocularis (Hall)
Brachythyl'is subcardiformis (Hall)
C.omposita globosa Weller Rhipidomella dubia (Hall)
Spirifer cf. S. keokuk Hall
Bmchythyl'is suboroocularis (Hall)
Brachythyl'is subcardiformis (Hall)
C.omposita globosa Weller Pnstula alterna.ta (N. and P.) List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. ANTHOZOA-
Productus ovatus Hall ,
Triplophyllum dalei (M.-E. and H.)
Productus cf. P. gallatinensis Girty
Monilopora bee cheri Grabau
Productus sp. BRYOZOA-
Pustula biseriata (Hall)
Brutostolmllla sp. Rhipidomella dubia (Hall)
Stenopora sp. Tetracamera subtrigooa (M. and W.)
Stenopora sp. Dielasma sp. . Archimedes owenanus Hall
Spirifer cf. S. keokuk Hall
PoJypora varsoviensis Prout
Spirifer tenuicostatus Hall
Hemitrypa sp. Bmchythyris subcardiformis (Hall)
F enestella serratula Ulrich
Syringothyris textus (Hall) ,
Fenestella compl'essa Ulrich
Reticulaa'ia sp. Fenestella triserialis Ulrich
Cliothyridina (') sp. Fene,stella compressa var. nododorsalis
Composita trinuclea (Hall)
Ulrich
PELECYPODA-
. }'euestel1a multi spinosa ffirich f
Myalina keokuk Worthen
Fenestella species II
Aviculopecten sp. Pinnatopora sp. Aviculopecten sp. Rhombopora s.p. GASTROPODA-
Cystodictya lineata ffirich '
Platyceras equilateralis Hall (f)
Worthenopora spinosa ffirich
Ptychomphalus (f) sp. BRACHIOPODA-
TRILOBITA-
Ol'thotetes keokuk (Hall)
Griffithides (') sp. Chonetes sp. VEltTEBRATA-
Productus setigerus Hall
Fish tooth ANTHOZOA-
Productus ovatus Hall ,
Triplophyllum dalei (M.-E. and H.)
Productus cf. P. gallatinensis Girty
Monilopora bee cheri Grabau
Productus sp. BRYOZOA-
Pustula biseriata (Hall)
Brutostolmllla sp. Rhipidomella dubia (Hall)
Stenopora sp. Tetracamera subtrigooa (M. and W.)
Stenopora sp. Dielasma sp. . Archimedes owenanus Hall
Spirifer cf. S. keokuk Hall
PoJypora varsoviensis Prout
Spirifer tenuicostatus Hall
Hemitrypa sp. Bmchythyris subcardiformis (Hall)
F enestella serratula Ulrich
Syringothyris textus (Hall) ,
Fenestella compl'essa Ulrich
Reticulaa'ia sp. Fenestella triserialis Ulrich
Cliothyridina (') sp. Fene,stella compressa var. nododorsalis
Composita trinuclea (Hall)
Ulrich
PELECYPODA-
. }'euestel1a multi spinosa ffirich f
Myalina keokuk Worthen
Fenestella species II
Aviculopecten sp. Pinnatopora sp. Aviculopecten sp. Rhombopora s.p. GASTROPODA-
Cystodictya lineata ffirich '
Platyceras equilateralis Hall (f)
Worthenopora spinosa ffirich
Ptychomphalus (f) sp. BRACHIOPODA-
TRILOBITA-
Ol'thotetes keokuk (Hall)
Griffithides (') sp. Chonetes sp. VEltTEBRATA-
Productus setigerus Hall
Fish tooth ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Monilopora bee cheri Grabau
BRYOZOA-
Brutostolmllla sp. Stenopora sp. Stenopora sp. Archimedes owenanus Hall
PoJypora varsoviensis Prout
Hemitrypa sp. F enestella serratula Ulrich
Fenestella compl'essa Ulrich
Fenestella triserialis Ulrich
Fene,stella compressa var. nododorsali
Ulrich
}'euestel1a multi spinosa ffirich f
Fenestella species II
Pinnatopora sp. Rhombopora s.p. Cystodictya lineata ffirich '
Worthenopora spinosa ffirich
BRACHIOPODA-
Ol'thotetes keokuk (Hall)
Chonetes sp. Productus setigerus Hall Fish tooth The vertical range of all the more characteristic species listed
above is shown in the following table: MISSISSIPPIAN STRATA OF IOWA 152 Table Showing Ra;nge of Species iIn the Keokuk' Limestone at K e07cuk. List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. I Table Showing Ra;nge of Species iIn the Keokuk Limestone at K e07cuk. I
Horizons
I
~ 1
~ 2l3l4l5(6(7(S(9 110111112113114115116\
HadrOPhYllUmA~~~~~.~.~ ............................ _ ............. _ .......... .... / .... / .... x .... .... .... ........ .... ....... .\....1....\
'l'riplophyllum dalei (M.·E. and H.) ... _ .... _ ......... ···· x x x I x Ix x .... x x x x x x x Ix x
Zaphrentis varsoviensis '\Vorthen ............... _ ......... ,··· .... ........ ................ x x ............ .... .... ....... . Zaphl'entis cf. Z. spinulosa (M.·E. and H.) ........... .... .... ........................................ x ........ .. .. Zaphrentis sp .......................................... _ ................. ·· ...................... x .... x .............................. .. Amplexus sp ............................ _ ........ __ ....................... -...... ........ x .... x .... x x .......................... .. Palaeacis obtusus (M. and W.) ........................... # •• • x ................ x .... x ................ .... ........ ... . Monilopora. beecheri Grabau ................................. _ .................................. x ............ x x .... X
VERMES
EnchostoIr1131 Sp .... _ .................................................... · ...... x ............................ .... .... ........ .......... .. CRINOIDEA
Platycrinus saffordi HalL .............................................. .... .... x .... x ~ ................ ................ .... .. .. Platycrintls sp .......................................................... _ ...................... x .... .................................. .. Eucladocrinus sp ....................................................... _ ...... ............ x ........ ................................ .. .. !~~:~~~~: f;~~d::lL~.~~~::::::::::::::::=::::::::=::: .:: :::: :::: :::: ~ ; :::: ~ :::: :::: :::: :::: :::: :::: .~. :::: :::: ::::
Actinocrinus sp ............. ~ .......................................... # ....... .... . ........... x ............ .......................... .. Actinocrinus sp ........................................................ # .. • .... x ................ .................... ........ ........ .. .. Batocrinus sp .................. _ .................. ___ .. _ ................. · ........ ........ ................ x .......................... .. Macrocrinus lagunculus (Hall) .............................................. x .... ............ ........ .... ................ .. .. Uperocrinus nashvillae (Hall) ... _ .......... __ .......... _. __ ........................ x ............ ................ x ...... .. AgaricocrinJus americanus (Roeri:t~r) ............... _ ... _ .............. x .... x ................ ............ x ...... .. Agaricocrinus americanus V!!Jr. tuberosus HalL.~ ............... x .... x .... x x .... ........ x .......... .. ~~;;i~~~~Ii:::~~~~i;;;;:::::::::::::::=::::=::: :::: :::: :::: :::: :::: :~: :::: :::: :~: :::: :::: :::: :::: .~. :::: ::::
~~£i:=~~i~~:~~!~~~-(f~~d~:::::::=::::::=::=::::: :~: :::: :::: :::: :::: :::: :::: :~: :~: :::: :::: ::::
:~: :~: :::: ::::1
Barycrinus spurius (Hall) ........................... _ .... _ ....................... .... x .... ................................... . BarY(ll'inus magister (Hall) ... _ .... _ .... _ .... _ ................... ............ .... x .... List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. .... .... ........ ............ ...... .. Barycrinus tumidus (Hall) ... _ ...................... _ ........................................... x ............ .... x ...... .. Barycrinus stellatus (Hall) ......... __ .................... _..... .... .... .... ........ x........ x .... .... ........ ........ .. .. Ba,ycriDIUs sp .............. __ .. _ ...................................... _ ................. .... x .... ................ ................ ...... .. Fistulipoo-a s:e~~~~~!SiS Rommger ... _ ......................... .... .... ............ .. A xf .... .... .... .... xf .... ........ 1
f~~~~~~~~~~~~~~=::~~~;: ~-:: ~ ~ ~ ~ .~. ~, ~= ~: ~~.; .;. tl
F enestella serratula Ulrich .... · .......... _ .... __ .......... · ..... 1 x 1 .... 1 .... 1 .... 1 x x I .... x 1 x xf .... .... x, .... /.. .. / x I
F enestella ten ax UlriCh ............... _ .... _ .. _ .......... _ ....... / x / .... / ........ I x x I"" .... I x 1
.... 1· .. ·1 x 1· .. ·1 .... / .... / .... ,
F ellestella multispinosa ~rich ... -.-............................. xf .... x ............ x x .... .... .... ............ xfl
F enestella compressa Ulnch ... _ ................ _ ...... _ ...... .... 1 .... ........ xf x .... x, x, .................... 1 .... 1 x I
F enestella rudis UlriCh ........... _ ........ _ .. :._ .... _: ............ ! .... ! .... ! ........................ x .... .... ........ , ........ ' .... 1
F enestella compressa var. nododorsahs Ulnch ................ .... .... ......................................... .... x
E~: ?~J~~~l:=Il~j¥~g:_ I:~~. ~::=~::: ~ ~'I:: :::: ~ ::,::f~' RANGE OF FOSSILS IN KEOKUK BEDS 153 Table Showilng Range of Species in the Keo1.,"'Uk Iknestollle at Keokuk-Continued. I
Horizons
I
\ 1 (2 (3 ( 4 ( 5 ( 6 j 7 ( 8 (9 (10(11(121131141151161
ArchimJedes owelW,nIIlS Hall ..................... _ ...... _ .. _ ..................... x ............ 1 .................... x :::XI
Archimedes cf. A. negligens Ulrich ...................................................... x .... ........................... . Polypora burlingtonensis Ulrich ... _ .... _ .... _ ............. x, ................................ ................ ........... . Polypora halliana Prout ................................. _ .... _..... .... .... .... .... x x ........................ ............... . Polypora varsoviensis Prout ........................... _ ... _ ........... ..... _ ..... x ........ x ............ x ........ x
Polyp ora simulatrix Ulrich. .................... _ .... _ .... _..... .... .... .... .... .... .... .... x x .... .... ................ ... . Polypora. retrorsa Ulrich. List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. .. _ ...................... _ .•.... _....... .... .... .... .... .... .... .... .... x ........................... . Polypora maccoyana Ulrich ............. _ ................ _ .. _ ................................... x .... .... ........ _ ......... . Polypora striata CUmings ............... _ .... _ .............. _ .................................................... x .... ....... . Polyp ora species II. ...................................... _ .... _ .. ~ ....................... x ............ ............................ 1
~r~~io~!:ir~;i~:::=:::::::::::::::::=:::::::::::::::::::::::: :::: :::: :::: :::: :::: :::: :::: .~. :~: :::: :::: :::: :::: :::: :::: :~:I
RhombOlpora attenuata Ulrich ......... _ ......................... ........ .... ........ ........ xf x .... .................... ... . Rhombopora dichotoma Ulrich .......................................... ........ x ........................ ............ ....... . Rhombopora varians Ulrich ........................... _ .. _ ....... .... ................ ............................ xf ........... . Acanthoclema confluens Ulrich ... _ .... _ ................ _ ...... : ...... ........ .... ........ .... x .................... ....... . Taeniodictya ramulosa Ulrich ........................... _ ....................................... x ........................... . Cystodictya lineata Ulrich ............................... _ ..... _.. x.... .... .... x x .... .... ............ ..... :.. x .... X
gr;;,~~;: ~~y~~~gi··(P;~~t)=:=::::=::::=::::::::::::::: :::: :::: :::: :::: :::: :::: :::: :::: ~ ::::1:::: :::: :::: :::: :::: ::::1
~~J:t~h~adiss~~id~···(·p;~~t)·::::::::::::::::::::::::::::::::::::: .~. :::: :::: :::: .~. :::: :::: ::::~, :::: :::: :::: :::: :::: :::: ::::1
w ortheIlKlpora spinosa Ulrich ......... _ .......... _ ......... _.. x .... .... .... .... x.... .... x .... .... .... .... .... .... x
BRAcmOPODA
Orthotetes keokuk (Hall) .....................................• ... x .... x .... \ x x .... x .... x x, ............ 1 .... x,
~~~~~~~~:P~~tig~~~··Ii~ii:::::::::::::::::::::::::::::::::::::::::::: .~. ~.~ ·~t'-'-'-I·~·I·~· :::: .~. ';'1';' ~'; :::: :::: ·~t:::1 ~
Pro ductus ovatus HaIL ..................................... _ ........................... x j .... x .... , .... .... j ........ j .... j .... j x 1
Productus cf. P. gallatinenSis Girty .................... _ .. x ................ x .... x ................ .... ........ x r
Productus viminali-s White ............................................ xi .... .... ......................... 1 ............ ••••.... •... Pustula biseriata (Hall) ... _ ................ __ ................. x x x .... x x .... x .... 1 x 1····j····I···· x 1 .... 1 x 1
Pustula alternata (N. and P.) ................................ x x .... x x x .... x x x x x x .... x 1 .... 1
Pustu~a sp ...................................... _ ........................... _ .. / .... / ........ 1 .... x I···· .... / x ·:··1····1···· ............ , ....... . AV?Il:la sp ............. : ................................. ~ .......... -........... x ........ .... List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. x : .... x / .... / ........ ! ........ ........ / .... 1
Rhlpidomella dubla (Hall) .................................... •..... x x ........ 1 x .... x .... x x .... x .... x xl
Tetra=era subc~neata (Hall) ............... _ ................... x ····1···· .... / .... ····1···· .... / .... .... ........ ···t···I····1
~~t;~~e::a sb~~~~~r(J;-;g:)~ ... ~
... ?~::~·.-.~::~·.·.~~~·.·.:::: .~ .. ~. :::: :::: ::::I~::: ::::1:::: ::::/:::: :::: :::: :::: :::: :::: I.~. Dielasma sinuata Weller ................................................ .... .... 1 ........ .... .... x .... x ........ ........ ....... . Dielasma sp ................................................ _ ..................... x 1 .... 1 .... .... x .... x .... 1 .... x ........ x .... x
SP~r~fe
. rina sp ............................................................... .... .... 1 .... 1 ........ 1 .... ····Ix' x r···· ........ ····1···· ....... . Spinfer keokuk HalL ................................... _ ................. 1 .... 1 .... 1 .... ····1····1···· x 1 x x x .... x 1····1· ... ····1
Bpirifer d. S. keokuk HalL. ...... _ .................... _ ...... x 1 x 1 x .... x I x 1 .... 1····1···· ····1····1 x .... 1 x I x xl
Sp~r!f er cf. S: pellaensis Weller ... _ ................ _ ............. 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... / .... 1 x 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1
Spmfer tenUlcostatus H:al.L .................. _ ................. x I x 1 .... 1 .... 1 .... 1 x I .... x I x I x 1 .... 1 .... 1 .... 1 .... 1 .... xl
Sp!r!fer logani HaIL .......................................... _ ......... lx'I····I .. ··I.···I····I····I·.·.I····I····I····I· ... 1 .... 1 .... 1 .... 1 .... 1
Sp~r~fe r rostellatu? Hall·····································_· .... I .... I: ... 1 .... 1 .... 1 .... 1 x 1····1 x 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1
Spmfer subaequahs HaIL····································· .. ..! .... I .... 1 .... 1 .... 1 .... 1 x 1····1···· .· .. 1····1····1···· .... / .... 1 .... 1 .... 1
Brachythyris suborbicularis (Hall) .. ······· .. ·.· .. ····· .... 1 x 1 x I x I x I x 1..·-1-···1 x 1····1 .... 1····1····1 .. · ..... 1 x 1····1
Brachythyris subcardiformis (Hall)···················· .... I .... I···.I .... I .... I .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. 1 .... 1 x 1 .... 1 x I x I
Syringothyris subcuspidatus (Hall)························lx'I····I····I····I····I .... 1 .... 1 .... 1 .... / .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1
Syringothyris textus (Hall) ..................... _ ........ _ ..... I .... I .... I .... 1 .... 1 .... 1 .... / .... 1 .... 1 .... x 1 .... 1 .... I .... I .... I .... 1x'l
Pseudo syrinx keokuk Weller·····················_·······_··.···I····I····I····I····I····I····I····I····I····I····!x'I····I····I···.1 .... 1 .... 1 Table Showilng Range of Species in the Keo1.,"'Uk Iknestollle at Keokuk-Continued. I MISSISSIPPIAN STRATA OF IOWA 154 Table Showing Range of Species in the Keokuk Lianesto711e at Keoku7c-Continued. ,
Horizons
,
iIi 2 i 3 1415.16171819110111112113114115116/
Spiriferella neglecta (Hall) ............... _ ..................... x x .... x x x .... x x x x ........ x ....... . Reticularia pseudolineata (Hall) ......................... , ... x x x x x x .... x .... x x ........ x .... _ .. . Reticularia setigera (Hall) ... _ ... _._ ................... __ ............................ : ....... .. __ x .......... _ ...... __ ..... ___ . Eumetria verneuiliana (Hall) ...... __ ._._ .. _ ......... _......... .... .... .... .... .... .... .... .... .... x ................ ....... . Eumetria sp ............................................................... _ ....... x .............. _ .. _ .................. ................... . Athyris lamellosa (Leveille) .................. _ .. _ ............... x'l ................... _._ ...... ............................... . C1iothyridina parvirosiris (M. and W.) ............ _ .... ...... _. x ... _ ............ x x ............ _ ... x _ ... ... . Cliothyridina obmaxima (McChesney) ................................ _ ....... x .... "" ............ x .... x: ... _ .. . Composita trinuclea (Hall) ..... __ ... _ .... _ .......... _ ......... x .... _ ....... x x .... x x ... _ .... ................ x
Oomposita pentagona Weller ............................................... : ...... _ ....... .... x .... .................... ...... _. Composita gl(}bosa \Veller ................................ _ ..... _ ............... _ ....................... x ........ x .... x __ .. PELECYFODA
Conocardium sp .................................................... _ ........ _ .............. . _ .. x ........ .... ..... _ .... _ ... _ ............ . ~;i~~nO~!:~~p~~~~~~:::::::::::::::==::=::==::::=::::::::: .~ .. ~. :::J::: :::: .~. :::: :::: :::: .~. :::: :::: :::: :::: :::: .~. Aviculopecten sp .... _ ..... _ ............... ___ ........... _ ......... _ ............... ........ _ .... ___ ........ ............. _ ............ _. Section of K eo7cu7c limestone at Cedar Glen, Illinois
17. Drift, yellowish, sandy, of variable thickness_
FEET
INCHES
16. Limestone,
grayish,
coarse-grained,
cherty.
Spirifer
keokuk common..
Bed 10 of Keokuk section _____________ .. __
2
4
15. Limestone, grayish, cherty; in thin irregular layers
separated by shaly partings __________________________________________________
2
4 List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. x
~~~~~~:E~: i~1~~~~~:~~~:::~~~~~~~:::::::::::::::::::::::::: :~: :::: :::: :::: :::: :::: :::: :~: ~ :::: :::: :::: :::: ~:~ :::: ::::
GASTROPODA
Ptychomphalus , sp ........................................ _ .... _ ......... .... .... ................ .... ................. _ .......... x
Orthonychia pabulocrinJUs (Owenl) ... _ .. _ ................... x ................ ........ .... ........ .............. _ ........ . Orthonychia sp .................................. -.............. -.......... ................ .... ... _ ............ .... x ........ .. _ ........ . Platyceras fissurella HalL ....... _................................. x ................................ .... ............. _ ......... . Platyceras equilateralis Hall.. ....... _ ............ : ............. x x'l .... xl! ... _ x .................... ... _ ............ xi
Conularia cf. y. miss(}uriensig Swallow ... _ .......... _ ............................ ... t ........... x,"" ............... . TRILOBITA
I
'
I
Griffithides , sp .......... -................ -.... - .... - .. --........... _ ... .. _ ... _ ................. ""j x, ....... x .... x ........ xl
VERTEBRATA
I 1
I
. 1 1 1
1
1
1
PleuracM1thus sp .... -................................................. _ ... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 .... 1 x 1 .... 1 .... 1 .... 1 ................ 1
Cochliodus nobilis (N. !l.nd W.) ....................... _ ... _ ....... 1 .... 1 ........ 1 .... .... 1 .... 1 .... 1 ..... ·.·1···· .... x 1··-· ....... . The lower portion of the Keokuk, comprising the beds called
in earlier reports the Montrose cherts, is not exposed at Keokuk
at the present time, but was formerly opened to observation in
the excavation beneath the bed of Mississippi river for the
Keokuk dam. Table Showing Range of Species in the Keokuk Lianesto711e at Keoku7c-Continued. The lower portion of the Keokuk, comprising the beds called
in earlier reports the Montrose cherts, is not exposed at Keokuk
at the present time, but was formerly opened to observation in
the excavation beneath the bed of Mississippi river for the
Keokuk dam. KEOKUK BEDS AT CEDAR GLEN 155 ction of Montl'ose cherts in excavation below bed of Mis8lissippi river at Keokuk
APPROXIMATE
TmCKNESS
PERCENTAGE
FEET
INCHES
OF CHERT
13. Limestone, dark gray; impreg,nated with
small irregular patches of chert and chal·
cedony, and containing small, imperfect
calcareous geodes ....................................... _. __ .. 12. I~imestone, ash·colol'ed, impure; very fine·
grained. Chert
correspondingly
fine-
grained, :and occurring as discontinuous
SeanIS most of which run parallel to the
bedding _____ ._. __ ....... _ .. Section of K eo7cu7c limestone at Cedar Glen, Illinois 17. Drift, yellowish, sandy, of variable thickness_
FEET
16
Li
i h
i
d
h
S i if MISSISSIPPIAN STRATA OF IOWA MISSISSIPPIAN STRATA OF IOWA 14. Limestone, grayiSih, subcrysoaJline; cherty in lower part. Orthotetes keokuk abund3illJt. Bed 7 of the Keokuk
section .. ~.................... ..... ....................... ......... ............. . ... . . ............ 1
13
Li
li h
i
l
h
h
i 13. Limestone, light gray, in places cherty; weathering to
an inegular chipstone; the "White ledge" of the Keo·
kuk section. Lower part somewhat shaly ........................ 2
12
Li
t
i h
d l
t
b
t l
6 an inegular chipstone; the "White ledge" of the Keo·
kuk section. Lower part somewhat shaly ........................ 2
12
Limestone
grayish; upper and lower parts subcrystal
6 12. Limestone, grayish; upper and lower parts subcrystal·
line, and weathering to thin ine.gular chips; middle palt
consisting of ash·colored magnesian limestone in heavier
layers. The" Millerite ledge" of the K eokuk sectiO'D. .... 5
11
Li
bl i h
i
d
P l
i
b
8 11. Limestone, bluish gray, coarse-.grained, Palaeacis ob·
tusus and fish teeth common ..................... _........................... 1
10
Li
i h
i h
li h
bl i h
i
J'
8 10. Limestone,
grayish with slight
bluish
tint,
coaJ'se-
grained, highly fossiliferous. Bed 2 of Keokuk section 2
9
Li
t
i ti
f
h
t
b
t lli 9. Limestone,
consisting of cherty gray subcrystalline
limestone, with thin cherty seallIs of bluish gray coarse-
grained limestone. Bed 1 of Keokuk section .................... 5
8
i
fi
i
d
h
l
d
i
i h 7. Limestone, bluish gmy, coarse· grained, cherty .................. 4
6
Limestone
fine grained
cherty
ash colored
magnesian
5 6. Limestone, fine· grained, cherty, ash·colored, magnesian. Chert in form of very irregular patches. No fossils
noted ............ J •••••••• _ • ••• • •••• ••••••• _ •••• _.......... • ••••••••••••••••••••••••••• ••• •• ••
6
5
Li
i h
di
i
d
h 5. Limestone, grayish, medium to coarse· grained, cherty;
locally in massive layers but for the most part split into
thinl layers of chert bands ........................... _......................... 8
4
Li
fi
i
d
h
i
i h 4. Limestone, gray, fine· grained, cherty, magnesian; with
discontinuous layers of cherty gray coarse·grained lllOn·
magnesian limestone. Locally the coarse· grained lime·
stone predominates. Grading into the bed bel'OlW through
a layer of fossiliferous limestone about 8 inches to 1
foot thick. List of fossils from bed 16 of Keoleuk limestone at Keo/cuTe. ____ . _____________________ . ____ ._______
3
11. Chert, white, gray and bluish, dense; with
discontinuous bands and irregular pockets
of dark gray crinoidal limestone. A few
geodJic cavities in the chert are lined with
drusy quartz studded with rhombs of cal-
cite _____________________________________ .______________________________
1
10. Limestone,
dark
gray,
crinoidal,
fin;e-
grained; locally almost entirely replaced
by dark gray chert _________________________________________
1
9. Limestone, illlpure, very fine-grained, ash-
colored;
wit.h
pockets BJId
patches of
bluish to whitish chert ______________________________ . 5
8. Limestone, dark gray, crinoidal, cherty _______ _
7. Limestone,
dark
gray;
bearing
small
crinoid stems; with whitish chert band in
middle
__________________________ . ___________________ . ______ .,______
2
6. Limestone, very fine-gra.iJruld, ash-colored;
bearing irregular patches of whitish . chert . 1
5. Che!rt, in the form of a layer about 7
inches thick which locally grades into gray
crinoidal limestone ________________________________________ __
4. . Limesrtone, fine-grained; with SeanIS and
nodules of bluish amd whitish chert ____ .... 1
3. Limestone, gray; bearin'g whitish fossil-
iferous chert as laJl'ge irregular patches
and irregular discontinuous bands .. ________ .. 3
2. Li.mestonc, fine-grained; with nodules of
white :andJ dark colored chert _____ , ______ • ____ . ____ '_
1
1. Limestone, drurk gray, crinoidal, lighter
colored and pu'rer downward; . in layers 6
to 22 inches thick, bearing fossiliferous
chert in the form of bands, lenses and
nodules .. ____________ . __________________________________ .. __________
8
8
8
3
9
9
2
7
5
50
30
75
50-75
33
33
50
25
25
25
50
30
30 The basal cherty beds of the Keolmk may be studied to good
advantage at the present time along Cedar Glen, a small creek
on the Illinois side of Mississippi river, about midway between
the towns of Hamilton and Warsaw. The section of the
Keokuk, which is nearly complete at this place, is as follows: Section of K eo7cu7c limestone at Cedar Glen, Illinois
17. Drift, yellowish, sandy, of variable thickness_
FEET
INCHES
16. Limestone,
grayish,
coarse-grained,
cherty. Spirifer
keokuk common.. Bed 10 of Keokuk section _____________ .. __
2
4
15. Limestone, grayish, cherty; in thin irregular layers
separated by shaly partings __________________________________________________
2
4 156 Spirifer tenuicostatus Han
S i if
l
i H ll Pustula alternata (N. and P.)
S i if
t
i
t t
Han List of fossils frorn bed 2 of Keoku7c limestone at Cedar Glen., Illinois. List of fossils frorn bed 2 of Keoku7c limestone at Cedar Glen., Illinois. List of fossils frorn bed 2 of Keoku7c limestone at Cedar Glen., Illinois. ANTBOZOA-·
. Cyatha..'wnia' sp. 'retracamera subtrigona (M. and W.)
Dielasma sp. Triplophyllum dalei (M.-E. and H .)
Zaphrentis sp. BRYOZOA'-
Cystodictya sp. BRACHIOPODA-
Pl'oductus sp. Productus sp. Spirifer logani Hall
Spirifer cf. S. grimesi Hall
Reticularia pseudolineata (Hall)
Cliothyridina obma..'dma (McChesney)
GASTROPODA-
Orthollychi~ , sp. ANTBOZOA-·
. Cyatha..'wnia' sp. 'retracamera subtrigona (M. and W.)
Dielasma sp. Triplophyllum dalei (M.-E. and H .)
Zaphrentis sp. BRYOZOA'-
Cystodictya sp. BRACHIOPODA-
Pl'oductus sp. Productus sp. Spirifer logani Hall
Spirifer cf. S. grimesi Hall
Reticularia pseudolineata (Hall)
Cliothyridina obma..'dma (McChesney)
GASTROPODA-
Orthollychi~ , sp. ANTBOZOA-·
. Cyatha..'wnia' sp. Triplophyllum dalei (M.-E. and H .)
Zaphrentis sp. BRYOZOA'-
Cystodictya sp. BRACHIOPODA-
Pl'oductus sp. Productus sp. List of fossils from bed 3 of Keoh£7c lirnestone at Cedar Glen, Illinois. BRYOZOA-
Dielasma sp. Cystodictya sp. BRACHIOPODA-
Chonetes sp. Productus sp. Pustula alternata (N. and P.)
Delthyris similis Weller ~
Spirifer tenuicostatus Hall
Reticularia pseudolineata (Hall)
Cliothyridina incrassata (Hall) BRYOZOA-
Cystodictya sp. BRACHIOPODA-
Chonetes sp. Productus sp. Pustula alternata (N. and List of fossils frarm bed 4, of Ee'07cu7c lirnestone at Ced(Jff Glen, Illinois. ANTHOZOA-
Triplo-phyllum dalei (M.-E. and H.)
Amplexus sp. BRYOZOA-
Stenopora , sp. Fenestella multispinosa Ulrich
Fenestella serratula Ulrich
Fenestella sp. Fenestella sp. Taeniodictya ramulosa Ulrich
Cystodictya sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Chonetes sp. Productus sp. Productus sp. Avonia sp. Pustula alternata (N. and P.)
Pustula sp. TetI'acamera subtrigona (M. and W.)
Dielasma sp. Delthyris sp. Spirifer tenuicostatus Hall
Spirifer cf. S. keokuk Hall
Spirifer cf. S. grimesi Hall
Spirifer sp. Bracllythyris suborbicularis (Hall)
8piriferella neglecta (Hall) ,
Reticularia pseudolineata (Hall)
Oliothyridina sp. Oomposita trinuclea (Hall)
GASTROPODA-
Orthonyc.hia sp. Pustula alternata (N. and P.)
Pustula sp. TetI'acamera subtrigona (M. and W.)
Dielasma sp. Delthyris sp. Spirifer tenuicostatus Hall
Spirifer cf. S. keokuk Hall
Spirifer cf. S. grimesi Hall
Spirifer sp. Bracllythyris suborbicularis (Hall)
8piriferella neglecta (Hall) ,
Reticularia pseudolineata (Hall)
Oliothyridina sp. Oomposita trinuclea (Hall)
GASTROPODA-
Orthonyc.hia sp. Pustula alternata (N. and P.)
Pustula sp. TetI'acamera subtrigona (M. and W.)
Dielasma sp. Delthyris sp. Spirifer tenuicostatus Hall
Spirifer cf. S. keokuk Hall
Spirifer cf. S. grimesi Hall
Spirifer sp. Bracllythyris suborbicularis (Hall)
8piriferella neglecta (Hall) ,
Reticularia pseudolineata (Hall)
Oliothyridina sp. Oomposita trinuclea (Hall)
GASTROPODA-
Orthonyc.hia sp. MISSISSIPPIAN STRATA OF IOWA This is bluish and coarse·grained above, but
is gradually a finer and lighter gray ' cherty crinoidal
limestone below ............... _ .......... _ .... _....................................... 9 3. Limestone, light gray to whitish, crinoidal, with occa·
sional bands or lenses of whitish chert; massive where
fresh; weathered surfaces flaking off obliquely .............. 2-4 g
q
y
2. Limestone,
light
gray,
sub crystalline ;
some
layers
crinoidal; bearing irregular chert nodules many of which
exhibit concretionary structme in the form of alternn.ting
bands of lighter and darker colored material. Chert
much shattered where weathered, as' in other layers. Bed receding slightly; tending to scale off obliquely to
weruthered surface ......... _......................................................... 4 1. Limestone, light gray, crinoidal, with occasional large
whitish chert nodules; massive where freSih, but scaling
off obliqu.eJy to weathered surface. Exposed .................. 2 1. Limestone, light gray, crinoidal, with occasional large
whitish chert nodules; massive where freSih, but scaling
ff
bli
J
t
th
d
f
E
d
2 whitish chert nodules; massive where freSih, but scaling
off obliqu.eJy to weathered surface. Exposed .................. 2 Collections were made from the lower members of the section. Collections were made from the lower members of the
The forms identified from each bed are as follows :
' Collections were made from the lower members of the section. The forms identified from each bed are as follows : List of fossils fr01n bed 1 of Keokuk limestone at Cedar Gllm, IlIVnois. ANTHOZOA-
Triplophyllum dalei (M.·E. and H.)
BKYOZOA-
Cystodictya sp. BRACHIOPODA-
Pustula alternata (N. and P.)
Spirifer tenuicostatus Han
Spirifer logani Hall
Spirifer sp. ,
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
Athyris Iannello sa (Leveille)
CliothyriiLina obma.. .. dma (McChesney)
GASTROPODA'-
Platyceras s'll. List of fossils fr01n bed 1 of Keokuk limestone at Cedar Gllm, IlIVnois. Spirifer sp. ,
B
h th
i Reticularia pseudolineata (Hall)
Ath
i
I
ll
(L
ill ) Athyris Iannello sa (Leveille)
Cli
h
iiLi
b
d
(M C CliothyriiLina obma.. .. dma (McChesney) Platyceras s'll. Spirifer logani Hall KEOKUK FOSSILS AT CEDAR GLEN 157 List of fossils frorn bed 2 of Keoku7c limestone at Cedar Glen., Illinois. Li8t of fossils fr01n bed 5 of 'Keo7cuk limestone at Cedar Glen, Illinois. ANTHOZOA-
Delthyris sp. Cyathaxonia , sp. Spirifer logani H!JlI
Triplophyllum dalei (M.-E. and H .)
Spirifer cf. S. grimesi Hall
Amplexus sp. Spirifer keokuk Hall
Palaeacis obtusus (M. and! W.)
Spirifer tenuicostatus Hall
CRrNOIDEA-
Reticularia pseudolineata (Hall)
Platycrinus , sp. Eumetria verneuiliMta (Hall)
BRYOZOA-
Athyris lamellosa (Leveille)
Fenestella serratula Ulrich
Cliothyridina obmaxima (McChesney)
Rhombopora varians Ulrich
Composita trinuclea (Hall)
Cystodictya sp. PEJ,ECYPODA-
BRACHIOPODA-
Conocardium sp. Orthotetes keokuk (Hall)
Myalina keokuk Worthen
Prod.uctus sp. GAS'fROPODA-
Pustula alternata (N. and P.)
Orthonychia' sp. Rhipidomella dubia (Hall)
TRILOBITA-
Tetracamera sub~u.neata (Hall) . Griffithides , sp. Tetracamera subtrigona (M. and W.) VERTEBRATA-
Dielasma sp. Fish teeth
Delthyriil sp. ANTHOZOA-
Delthyris sp. Cyathaxonia , sp. Spirifer logani H!JlI
Triplophyllum dalei (M.-E. and H .)
Spirifer cf. S. grimesi Hall
Amplexus sp. Spirifer keokuk Hall
Palaeacis obtusus (M. and! W.)
Spirifer tenuicostatus Hall
CRrNOIDEA-
Reticularia pseudolineata (Hall)
Platycrinus , sp. Eumetria verneuiliMta (Hall)
BRYOZOA-
Athyris lamellosa (Leveille)
Fenestella serratula Ulrich
Cliothyridina obmaxima (McChesney)
Rhombopora varians Ulrich
Composita trinuclea (Hall)
Cystodictya sp. PEJ,ECYPODA-
BRACHIOPODA-
Conocardium sp. Orthotetes keokuk (Hall)
Myalina keokuk Worthen
Prod.uctus sp. GAS'fROPODA-
Pustula alternata (N. and P.)
Orthonychia' sp. Rhipidomella dubia (Hall)
TRILOBITA-
Tetracamera sub~u.neata (Hall) . Griffithides , sp. Tetracamera subtrigona (M. and W.) VERTEBRATA-
Dielasma sp. Fish teeth
Delthyriil sp. ANTHOZOA-
Delthyris sp. Cyathaxonia , sp. Spirifer logani H!JlI
Triplophyllum dalei (M.-E. and H .)
Spirifer cf. S. grimesi Hall
Amplexus sp. Spirifer keokuk Hall
Palaeacis obtusus (M. and! W.)
Spirifer tenuicostatus Hall
CRrNOIDEA-
Reticularia pseudolineata (Hall)
Platycrinus , sp. Eumetria verneuiliMta (Hall)
BRYOZOA-
Athyris lamellosa (Leveille)
Fenestella serratula Ulrich
Cliothyridina obmaxima (McChesney)
Rhombopora varians Ulrich
Composita trinuclea (Hall)
Cystodictya sp. PEJ,ECYPODA-
BRACHIOPODA-
Conocardium sp. Orthotetes keokuk (Hall)
Myalina keokuk Worthen
Prod.uctus sp. GAS'fROPODA-
Pustula alternata (N. and P.)
Orthonychia' sp. Rhipidomella dubia (Hall)
TRILOBITA-
Tetracamera sub~u.neata (Hall) . Griffithides , sp. Tetracamera subtrigona (M. and W.) VERTEBRATA-
Dielasma sp. Fish teeth
Delthyriil sp. ANTHOZOA-
Delthyris sp. Cyathaxonia , sp. Spirifer logani H!JlI
Triplophyllum dalei (M.-E. and H .)
Spirifer cf. S. grimesi Hall
Amplexus sp. Spirifer keokuk Hall
Palaeacis obtusus (M. and! W.)
Spirifer tenuicostatus Hall
CRrNOIDEA-
Reticularia pseudolineata (Hall)
Platycrinus , sp. Eumetria verneuiliMta (Hall)
BRYOZOA-
Athyris lamellosa (Leveille)
Fenestella serratula Ulrich
Cliothyridina obmaxima (McChesney)
Rhombopora varians Ulrich
Composita trinuclea (Hall)
Cystodictya sp. PEJ,ECYPODA-
BRACHIOPODA-
Conocardium sp. Orthotetes keokuk (Hall)
Myalina keokuk Worthen
Prod.uctus sp. FEET
INCHES
14.
Thin layers of g:ray cherty limestone and bluish shale
interbedded; weathering buff.
Exposed only in quarry
2
13. Limestone, gray, thin-bedded, fine-grained and cherty in
ban.I. of. creek, but more massive, bluish and coarser-
gramed m quarry ............. __ ............................ __ .......................
4
12.
Limestone, bluish, medium-grained, tough; locally pass- Section of K eokuk limestone near Nauvoo, Illinois. List of fossils frorn bed 2 of Keoku7c limestone at Cedar Glen., Illinois. GAS'fROPODA-
Pustula alternata (N. and P.)
Orthonychia' sp. Rhipidomella dubia (Hall)
TRILOBITA-
Tetracamera sub~u.neata (Hall) . Griffithides , sp. Tetracamera subtrigona (M. and W.) VERTEBRATA-
Dielasma sp. Fish teeth
Delthyriil sp. MISSISSIPPIAN S'l'RATA OF IOWA 158 List of fOBsils from bed 7 of Keokuk limestone at Cedar Glen, Illinois. ANTHOZOA-
Tetracamera subcuneata (Hall)
Triplophyllum dalei (M.-E. and H.)
Tetracamera subtrigona (M. and W.)
Amplexus sp. Delthyris sp. Palaeacis obtusus (M. and W.)
Spirifer tenuicostatus Hall
BRYOZOA-
Spirifer l'ostellatus Hall
Meekopo'ra sp. Spirifer cf. S. keokuk Hall
Fen estella multispinosa Ulrich ,
Spirifer logani Hall
F enestella sp. Brachythyris suborbicularis .(Hall)
Hemitrypa sp. Syringothyris sp. Cystodictya sp. Spiriferella neglecta (Hall)
Cyclopora , sp. Reticularia pseudolineata (Hall)
BRACHIOPODA-
Cliothyridina obmaxima (McChesney)
Orthotetes keokuk (Hall)
Olmposita trinuclea (Hall)
Chon.etes sp. PELECYPODA-
Productus sp. Cypricardinia , sp. ProductuSi sp. GASTROPODA-
Pustula alternata (N. and P.)
Orthonychia' sp. Rhipidomella dubia (Hall)
VERTEBRATA-
Schizophoria sp. Fish teeth ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. Palaeacis obtusus (M. and W.)
BRYOZOA-
Meekopo'ra sp. Fen estella multispinosa Ulrich ,
F enestella sp. Hemitrypa sp. Cystodictya sp. Cyclopora , sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Chon.etes sp. Productus sp. ProductuSi sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Schizophoria sp. Tetracamera subcuneata (Hall)
T
b i
(M
d W ) Fen estella multispinosa Ulrich ,
F
t ll F enestella sp. H
it Hemitrypa sp. C
di Cystodictya sp. C
l Reticularia pseudolineata (Hall)
Cli
h
idi
b
i
(M Ch Cyclopora , sp. RACHIOPODA Cliothyridina obmaxima (McChesney)
Ol
it
t i
l
(H ll) Productus sp. P
d
t Si ProductuSi sp. P
t l
lt Pustula alternata (N. and P.)
Rhi id
ll
d bi
(H ll) VERTEBRATA-
Fi h
h Rhipidomella dubia (Hall)
S hi
h
i Fish teeth Schizophoria sp. 12.
Limestone, bluish, medium-grained, tough; locally pass- List of fossils fnnn bed 8 of Keokuk limestone at Cedar Glen, Illinoi Limestone, gray, fine· grained to medium· grained, brittle ;
weathering to thin irregular layers. Triplophyllum dalei;
Fenestella sp.; H emitrypa sp.;
C'!J~todictya p.; Pl'O'
ductus Sip.;
Productus setigerus ;
P1bstula
alternata;
Orthotctcs 7ceoKu7c; Bra.chythYl·is stbbol·bicnlal·is.; Phil·
l~p'sia , sp .......................................................... _ ................ _..... 3
7. Shaly plll:ting with seams und lentils of cherty limestone
6. Limestone, gray, dense, brittle, thinly and . inegularly
bedded, cherty. Some layers passin·g laterally iuto gray
calcareous shale locally. Cystodimya sp. ; Orthotetes
ke07cuk; Dielasma sp.; Spirifer tenuicostattls; Brachy·
thyris sub01·bim.lMis; Retimtlaria pseudolmenta; Hemi·
trypa sp.; Spil/"ifer d. S. 7ceo7c1b7c ............. _......................... 2
5. Limestone, bluish gray. Fossils scarce. Flakes off ob·
liquely on weathel'ed surface. Palaeacis obttbSus; Spiri·
fer keok'u7c .................................................................................. 1
4. Limestone, like No. 1. A bluish layer 3 to 4 inlches thick
in middle part is rich in fish teeth. Palaea:.cis obttis1is;
Ortlwtetes
7ce07~u7c ; Pcst1£la. altern-ata; Dielasma sp. ;
Platyoeras sp. ..._ ............................ _ .................... _................... 7
3. Limestone, bluish gray, medinm·grained, weathering to
-thin
flakes. Pust1bln
altcrnat(ll;
Orthotetes
7ceolc1bk;
Rhipidomella dtbbia; Spirifer tentticostat1tS; Spi1'if er cf. 10
10
2
S. keo7cuk ..................................................... _ .... _ ........ _............. 1
2. Shaly parting ......... _ ................................................................ . 10
10
1. Limestone, gray, fine· grained, irregularly stratified; with
thin layers of medium·grained bluish gray cherty lime·
stone. Ftmestella Sip.; Prod1.ct1is sp.; P1bSt1ila sp.; Orth·
otetes 7ceokuk; Girtyella india1tensis; Retioularia pse1.do·
lineata ... :...................................................................................... 7 . The uppermost part of the exposure is very fossiliferous. Collections were made from beds 9, 10, 11, 13 and 14. The fol-
owing lists were prepared from these:
liist of fossils from bed 9 of the Keokulc limestone at Namloo, Illinois. NTHOZOA-
Zaphrentis varsoviensis WorthEl!l1
Triplophyllum dalei (M.·E. and H.)
Amplexus sp. Monilopora beecheri Grabau
RINOIDEA-
Actino'crinus lowei Hall
Dorycriruus sp. . RYOZOA-
Leioclema punctatum (Hiall)
Fenestella serratula Ulrich
Rhombopora varians Ulrich
Phractopora trifolia (Rominger)
BRACHIOPODA-
Spirifer sp. Reticularia pseudolineata (Hall)
GAS1'ROPODA-
Ptychospira sp. Platyceras sp. List of fossils from bed 10 of Keokl.k limestone at Nauvoo, llliMis. NTHOZOA-
Triplophyllum dalei (l'vL·E. and H.)
Amplexus sp. Monilopora beeeheri Grabau
Palaeacis obtusus (M. and W.) ing into shale. FenestellUi sp.; PusPtbla sp.; Orthotetcs
keokuk; Rhipidomella dubia; Dielasm,a, ? sp.; Spirifer
ko.oku7c; Retiaularia pse1bdolimeata; Phillipsia ? sp............. 12-15
11
Sh l
i h
hi
l
f
bl i h f
ilif 11. Shale, with thin layers of gray to bluish fossiliferous
limestone ... ~ ..... _ .............................................. _ ......................... List of fossils fnnn bed 8 of Keokuk limestone at Cedar Glen, Illinoi 1 1/2-2
10
Li
bl i h
l'
di
i
d
i
h 10. Limestone, bluish gl'ay, medium·grained; massive when
fresh but weathering to thin irregular layers. Contact
with bed above very UIleveu and undulating ... _ ................ .4-4 1/2
9
Sh l
i
i h
hi
f li 9. Shaly parting with thin seams of limestou
8
Li
fi
i
d
di 8. Limestone, gray, fine· grained to medium· grained, brittle ;
weathering to thin irregular layers. Triplophyllum dalei;
Fenestella sp.; H emitrypa sp.;
C'!J~todictya p.; Pl'O'
ductus Sip.;
Productus setigerus ;
P1bstula
alternata;
Orthotctcs 7ceoKu7c; Bra.chythYl·is stbbol·bicnlal·is.; Phil·
l~p'sia , sp .......................................................... _ ................ _..... 3
h l
lll i
i h
d l
il
f
h
li 7. Shaly plll:ting with seams und lentils of cherty limestone
6
Li
t
d
b ittl
thi l
d i
l
l
10 6. Limestone, gray, dense, brittle, thinly and . inegularly
bedded, cherty. Some layers passin·g laterally iuto gray
calcareous shale locally. Cystodimya sp. ; Orthotetes
ke07cuk; Dielasma sp.; Spirifer tenuicostattls; Brachy·
thyris sub01·bim.lMis; Retimtlaria pseudolmenta; Hemi·
trypa sp.; Spil/"ifer d. S. 7ceo7c1b7c ............. _......................... 2
5
Li
t
bl i h
F
il
Fl k
ff
b
2 5. Limestone, bluish gray. Fossils scarce. Flakes off ob·
liquely on weathel'ed surface. Palaeacis obttbSus; Spiri·
fer keok'u7c .................................................................................. 1
4
Li
t
lik
N
1
A bl i h l
3 t
4 i l h
thi k 4. Limestone, like No. 1. A bluish layer 3 to 4 inlches thick
in middle part is rich in fish teeth. Palaea:.cis obttis1is;
Ortlwtetes
7ce07~u7c ; Pcst1£la. altern-ata; Dielasma sp. ;
Platyoeras sp. ..._ ............................ _ .................... _................... 7
3
Li
t
bl i h
di
i
d
th
i
t 1. Limestone, gray, fine· grained, irregularly stratified; with
thin layers of medium·grained bluish gray cherty lime·
stone. Ftmestella Sip.; Prod1.ct1is sp.; P1bSt1ila sp.; Orth·
otetes 7ceokuk; Girtyella india1tensis; Retioularia pse1.do·
lineata ... :...................................................................................... 7 . The uppermost part of the exposure is very fossiliferous. Collections were made from beds 9, 10, 11, 13 and 14. The fol-
lowing lists were prepared from these: liist of fossils from bed 9 of the Keokulc limestone at Namloo, Illinois. liist of fossils from bed 9 of the Keokulc limestone at Namloo, Illinois. f f
f
f
,
ANTHOZOA-
Zaphrentis varsoviensis WorthEl!l1
Triplophyllum dalei (M.·E. and H.)
Amplexus sp. List of fossils fnnn bed 8 of Keokuk limestone at Cedar Glen, Illinoi List of fossils fnnn bed 8 of Keokuk limestone at Cedar Glen, Illinois. List of fossils fnnn bed 8 of Keokuk limestone at Cedar Glen, Illinois. NTHOZOA
BRACHIOPODA ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRYOZOA-
Meekopora , sp. Leioclema punctatum (Hall)
Polypora retrorsa Ulrich ,
Cystodictya sp. Cystodictya sp. Cyclopora , sp. BRACHIOPODA-
Avonia sp. Productus sp. Tet.racamera subcuneata (Hall)
CranaeDa sulcata Weller
Delthyris lIP. Spirifer , sp. Reticularia pseudolineata (Hall)
Athyris lamellosa (Leveille)
Composita trinuclea (Hall) ' ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
BRYOZOA-
Meekopora , sp. Leioclema punctatum (Hall)
Polypora retrorsa Ulrich ,
Cystodictya sp. Cystodictya sp. Cyclopora , sp. BRACHIOPODA-
Avonia sp. Productus sp. Tet.racamera subcuneata (Hall)
CranaeDa sulcata Weller
Delthyris lIP. Spirifer , sp. Reticularia pseudolineata (Hall)
Athyris lamellosa (Leveille)
Composita trinuclea (Hall) ' BRACHIOPODA-
A
i Avonia sp. P
d Productus sp. T t Meekopora , sp. L i
l
t Tet.racamera subcuneata (Hall)
C
D
l
t
W ll Leioclema punctatum (Hall)
P l
t
Ul i h Delthyris lIP. S i if Polypora retrorsa Ulrich ,
C
di Cystodictya sp. C
t di t Cystodictya sp. C
l Cyclopora , sp. Composita trinuclea (Hall) ' List of fOSlSils fro'TIt bed 9 of K eoku,k limestone at Cedar Glen, Illinois. ANTHOZOA-
Triplophyllum dalei (M.-E. aDid H .) '
Padaeacis obtusus (M. IIJlJd W.)
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus sp. Productus sp. Avonia sp. Rhipidomella dubia (Hall)
Tetracamera subtrigona (M:. and W.)
Dielasrna , sp. Spiriferella neglecta (Hall) '
Reticularia pseudolineata (Hall)
VERTEBRATA-
Fish teeth BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus sp. Productus sp. Avonia sp. A fairly complete section of the Keokuk limestone appears
near Nauvoo, Illinois, opposite Montrose, Iowa. The following
section is exposed in the banks of a small creek and in a quarry
near its mouth a short distance south of the city limits of
Nauvoo. 159 KEOKUK FOSSILS AT NAUVOO ing into shale. FenestellUi sp.; PusPtbla sp.; Orthotetcs
keokuk; Rhipidomella dubia; Dielasm,a, ? sp.; Spirifer
ko.oku7c; Retiaularia pse1bdolimeata; Phillipsia ? sp............. 12-15
11. Shale, with thin layers of gray to bluish fossiliferous
limestone ... ~ ..... _ .............................................. _ ......................... 1 1/2-2
10. Limestone, bluish gl'ay, medium·grained; massive when
fresh but weathering to thin irregular layers. Contact
with bed above very UIleveu and undulating ... _ ................ .4-4 1/2
9. Shaly parting with thin seams of limestoue ................... . 8. MISSISSIPPIAN STRATA OF IOWA MISSISSIPPIAN STRATA OF IOWA 160 BRYOZOA-
Cyclopora sp. Fistulipora sp. Bactl'o'Pora simplex Ulrich
Fenestella sp. Polypora sp. Archimpdes negligens Ulrich
Hemitryp31 sp. Leioclema pUl1ctatum (Hall)
Cystodictya !!p. Phl'actopora trifolia (Rominger)
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
CliobhYl'idina parvirostris (M. and W.)
Cliothyridinla obmaxima (McChesney) BRACHIOPODA-
O h
k Orthotetes keokuk (Hall)
P
d List of fossils from bed 11 of K eoku7c limestone at Naut)oo, IllinotS. ,
. Streblotrypa major Ulrich
Cystodictya sp. Phractopora trifolia Ulrich
Worthenopora spinosa Ulrich
Worthenopora sp. BRACHIOPODA-
Productus sp. Orthotetes keokuk (H all)
Pustula alternata (N. and P.)
Camarotoec.hia mutata (Hall)
Rhipidomella dubia (Hall)
Spiriferina sp. Spirifer keokuk Hall
Spirifer tenruicostatus Hall
Reticularia pseudolineata (Hall)
Composita trinuclea (Hall)
Cliothyridina parvirostris (M. and W.)
TRILOBITA-
Griffithides f sp. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.) ,
Mo·ruilopora beec.heri Grabau
Amplexus sp. Zaphrentis varsoviensis Worthen
Palaeacis obtusus (M. and W.)
CRINOIDEA-
Parichthyocrillus meeki (Hall)
BRYOZOA-
Leioclema punctatum (Hall)
Fenestella serratula Ulrich
F enestella multispiIlJOsa Ulrich
Hemitrypa pateriformis Ulrich
Archimedes negligens Ulrich
Polypora simulatrL"{ Ulrich
Polypor,a mnccoyalla Ulrich
Polypora halliana Prout
Bactropora simplex Ulrich
RhombopOl13, attenuata Ulrich
Rhombopora varians Ulrich ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Mo·ruilopora beec.heri Grabau
Amplexus sp. Zaphrentis varsoviensis Worthen
Palaeacis obtusus (M. and W.)
CRINOIDEA-
Parichthyocrillus meeki (Hall)
BRYOZOA-
Leioclema punctatum (Hall)
Fenestella serratula Ulrich
F enestella multispiIlJOsa Ulrich
Hemitrypa pateriformis Ulrich
Archimedes negligens Ulrich
Polypora simulatrL"{ Ulrich
Polypor,a mnccoyalla Ulrich
Polypora halliana Prout
Bactropora simplex Ulrich
RhombopOl13, attenuata Ulrich
Rhombopora varians Ulrich Leioclema punctatum (Hall)
F
t ll
t l
Ul i h Fenestella serratula Ulrich
F
t ll
lti
iIlJO
Ul i h F enestella multispiIlJOsa Ulrich
H
it
t
if
i
Ul i h Griffithides f sp. Rhombopora varians Ulrich List of fossils from bed 13 of Keokuk limestone at Nauvoo, IllinQis. BRYOZOA-
Stenopora sp. Chaetetes f sp. Taeniodictya ramulo a Ulrich
Worthenopora spinosa Ulrich
Archimedes sp. Rhombopora n,ttenuata Ulrich
BRACHIOPODA-
Chonetes illi~oisensis Worthen
Pustula altemata (N. and P.)
Productus mesialis Hall
Productus sp. Spiriferina sp. Spirifer keokuk Hall
Syringothyris sp. Spiriferella neglecta (Hall)
Eumetria verneuiliana (Hall)
List of fossils fl'011l bed 14 of the K eoku7c limestone at Natlvoo, Illinois. ANTHOZOA-
Monilopora beecheri Grab.au
CRINOIDEA-
DOl'Ycrinns sp. Barycrinus sp. BRYOZOA-
Stenopora sp. Leioclema gracillimum Ulrich
Worthenopora spinosa Ulrich
C:vstodictya sp. List of fossils fnnn bed 8 of Keokuk limestone at Cedar Glen, Illinoi Monilopora beecheri Grabau
CRINOIDEA-
Actino'crinus lowei Hall
Dorycriruus sp. . BRYOZOA-
Leioclema punctatum (Hiall)
Fenestella serratula Ulrich
Rhombopora varians Ulrich
Phractopora trifolia (Rominger)
BRACHIOPODA-
Spirifer sp. Reticularia pseudolineata (Hall)
GAS1'ROPODA-
Ptychospira sp. Platyceras sp. List of fossils from bed 10 of Keokl.k limestone at Nauvoo, llliMis. ANTHOZOA-
Triplophyllum dalei (l'vL·E. and H.)
Amplexus sp. Monilopora beeeheri Grabau
Palaeacis obtusus (M. and W.) ANTHOZOA-
Zaphrentis varsoviensis WorthEl!l1
Triplophyllum dalei (M.·E. and H.)
Amplexus sp. Monilopora beecheri Grabau
CRINOIDEA-
Actino'crinus lowei Hall
Dorycriruus sp. . BRYOZOA-
Leioclema punctatum (Hiall)
Fenestella serratula Ulrich
Rhombopora varians Ulrich
Phractopora trifolia (Rominger)
BRACHIOPODA-
Spirifer sp. Reticularia pseudolineata (Hall)
GAS1'ROPODA-
Ptychospira sp. Platyceras sp. BRYOZOA-
Leioclema punctatum (Hiall) List of fossils from bed 10 of Keokl.k limestone at Nauvoo, llliMis. ANTHOZOA-
Triplophyllum dalei (l'vL·E. and H.)
Amplexus sp. Monilopora beeeheri Grabau
Palaeacis obtusus (M. and W.) Se<Jtion of KeoWu,k liflnlMto'IIJe new)" Niota, Illinois. 27. Shale, highly calcareous, grayish blue in oo~or, bearing a few
hollow geodes most of whose shells are stained with bitumen
1 hollo·w geodes most of whose shells are stained with bitumen.... 1
26
Shale
argillo calcareous
bluish
no geodes noted
3 26. Shale, argillo·calcareous, bluish, no geodes note
25
Limestone
light gra
fine gmined
eathering 24. Shale, bluish, argillaceous ............... _............................................... 4
23
Limestone
dark gray
crystalline very fossiliferous
Some of p
p
f
p
22. Shale, bluish ............... _......................................................................... 1
21
Limestone
gray
crystalline
2 21. Limestone, gray, crystalline ..................................................... 20
Limestone
shaly
thinly laminated 21. Limestone, gray, crystalline ......... 20
Limestone
shaly
thinly laminate 20. Limestone, shaly, thinly laminated ................................. _............. 1
10
19
Limestone gray
delllSe crystalline fossiliferous bearing a few 20. Limestone, shaly, thinly laminated
19
Limestone gra
delllSe cr stalline 19. Limestone, gray, delllSe, crystalline, fossiliferous, bearing a few
nodules of chert .................................................................................. 3
18
Sh l
b
i
f
ilif
fl k
f li
t
1 18. Shale, bearing fossiliferous flakes of limestone ............................ 1
17
Limestone
impUl'e
nne grained
cherty
bearing
bands
of 17. Limestone, impUl e, nne· grained, cherty, bearing bands of
coarsely crystalline limestone .......................................................... 3 17. Limestone, impUl e, nne grained, cherty, bearing bands of
coarsely crystalline limestone .......................................................... 3
8
16
Limestone
grayish fine grained
dense no fossils recognized
2
8 coarsely crystalline limestone .......................................................... 3
8
16
Limestone
grayish fine grained
dense no fossils recognized
2
8 16. Limestone, grayish, fine· grained, dense, no fossils recognized,... 2
8
15
Limestone
gray
crystalline bearing Spirifm' keo7cu7c Girtyella 15. Limestone, gray, crystalline, bearing Spirifm keo7cu7c, Girtyella
turgida and othcr fossils .................................................................. 1
2
14
Limestollle
ash colored
very fine grainred
weathering to thin 14. Limestollle, ash· colored, very fine·grainred, weathering to thin
irregular layers .................................................................................... 1
6
13
Li
t
i
id l
O th t t
k
k k
b
d
t
1
8 13. Limestone, gray, criuoidal, Orthotetes keokuk abundant ............ 1
8
12
Limestone
shaly
1
4 11. Limestone, coarse-grained and crinoidal in upper part but fine-
grained and shaly below; bearing two inch chert band near
the top. Some of the fossils collected from this layer are :
Orthotetes keoWu,k, Spirifer keokuk, Spirifer lagcvni, RetWt!laria
psendolineata, Tetraoamera sub trigona, Productt!s sp. ..._....... 2
6
10
Chert
bluish dense fossiliferous
8
8 10. Chert, bluish, dense, fossiliferous .................................................... KEOKUK LIMESTONE NEAR NIOTA 161 Near Niota, Illinois, opposite Port Madison, Iowa, there are
other good exposures of the Keokuk limestone. The following
section was measured two miles southwest of Niota in the banks
of a small creek tributary to Mississippi river. MISSISSIPPIAN STRATA OF IOWA Phractopora trifolia (Rominger )
Rhombopora "aI·jans Ulrich
Rhombopora ~ aspcl'ula Ull'ich
Rhombopora attenruata Ulrich
Stl'eblotl'ypa major Ulrich
Taeniodictya J'amu]osa Ulri ~Jt
Glyptopora keyserlingi (Pl'Out)
Fenesiella cingulata Ulrich
Fellestell a serratula Ulrich
Fenestella l'Udis Ulrich
Polypora biseriata Ulrich
PolypO'ra retrorsa Ulrich •
Hemitrypa sp
Ptilopora sp. Archimedes negligens Ulrich
BRAcmoPoDA-
PI'odnctus sp. Rhipidomella dnbia (Hall)
Cama,rotoechia mutata Hall
SpiI'iferina sp. Spil'ifer keokuk Hall List of fossils fl'011l bed 14 of the K eoku7c limestone at Natlvoo, Illinois. KEOKUK LIMESTONE NEAR NIOTA Beds 1 to 25 inclusive constitute the Keokuk limestone; beds Se<Jtion of KeoWu,k liflnlMto'IIJe new)" Niota, Illinois. ·8
9
Limestone
grayish
blue
crystalline
bearing
disseminated 9. Limestone, grayish blue, crystalline, bearing disseminated
crystals of PYl'ite and a few chert nodules : ... :............................. 8 crystals of PYl'ite and a few chert nodules : ... :............................. 8
Shale
bluish
calcareous
2 crystals of PYl ite and a few chert nodules : ... :............................. 8
8. Shale, bluish, calcareous .................................................................... 2
6
7
Limestone
crystalline
cherty
bearing ' rounded geodic masses 8. Shale, bluish, calcareous
7
Limestone
cr stalline
c 7. Limestone, crystalline, cherty, bearing ' rounded geodic masses
f
l it
ith i
l t
h l
d
i
h ll
2
5 7. Limestone, crystalline, cherty, bearing ' rounded geodic masses
of calcite with incomplete chalcedonic shells ............................ 2
5 7. Limestone, crystalline, cherty, bearing ' rounded geodic masses
of calcite with incomplete chalcedonic shells ............................ 2
5
6
Shale bluish
argillaceous
2 ,
y
,
y,
g
g
of calcite with incomplete chalcedonic shells ............................ 2
5
6. Shale, bluish, argillaceous .................................................................. 2 p
6. Shale, bluish, argillaceous .................................................................. 2
5
Shale
bluish
calcareous
with bands of cherty fossiliferous 5. Shale, bluish, calcareous, with bands of cherty fossiliferous
limestone ................................................ :............................................... 4
Li
t
t lli
ith i t
l t d
h l
b
d b 4
Limestone, gray, crystalline; with intercalated shale band; bear·
ing Spirifer loga'llJi, R eti<Jl!lGll"ial pseudolineata and Spirifer keo·
7cu7c ........................................................................................................ 3
Shaly parting 2. Shale, calcareous, beall ing irr€igU1ar seams and nodules of
chert ...................................................................................................... 1
Li
t
li ht
fi
i
d
h
t
b
i
O th t t 1. Limestone, light gray, fine· grained, cherty; bearing Orthotetes
keoh!k and other Keokuk species. Exposed .............................. 3 Beds 1 to 25 inclusive constitute the Keokuk limestone; bed MISSISSIPPIAN STRATA OF IOWA 162 26 to 28, on the other hand, represent the Geode bBd or Lower
Warsaw. . 26 to 28, on the other hand, represent the Geode bBd or Lower
Warsaw. . In Denmark township, Lee county, Iowa, the Keokuk lime-
stone is well exposed in a bluff two and one-half miles north-
west of the town of Denmark. FEET
4. Residual gool filled with ?JlguIar chert fragments.
To bro,w
of hill ........................... _ .................................... _ .... _...........................
3
3.
Limestone, thin·bedded. gray, sub crystalline, very cherty; a
solid layer of chert twenty inches thick at base at one point.
Bed 3 of Aug'usta section ....................................... _.........................
3%
2.
Limestone, gray, coarse·grained, crinoidal, vel'y cherty, espe·
cially in lower part.
Bed 2 of Augusta section ......................
6
1. Limestone, coarse·grained, "rinoidal, gray below but bluish gray
above, bearing wo,rn shells of Spirifer grimesi.
Bed 1 of
Augusta section ..................................................................................
1112 to 2 FEET
4. Residual gool filled with ?JlguIar chert fragments.
To bro,w
f hill
3 Seotion of Keokuk limestO'llll3 at South Augtlsta. Section of KeoWtlk limestone northwest of Denmark. The following
forms were noted:
Conula?'ia sp., Spirifer keoleu7c, O?'thotetes
keokuk,
Cliothyridi;n.a,
sp.,
Retioularia. 21S17luZolineata
and
Tet?'aoam.era stlbtrigona ............................................................... ,.... 1
6 12. 11
Limestone, argillaceous, buff, lliOill·fossilifel'ous, stratification
obscure, disintegrating into aJlgular blocks .................................. 2
Sh l
ti 11. 10
Shaly parting ..................................................................................... . Li
t
d
h
t
b
1 10. 9
Limestone, dense, gray, cherty above ............................................ 1
Sh l
hi hl
l
i
f
ilif
h
ki
4 10. 9
Limestone, dense, gray, cherty above ..................... Sh l
hi hl
l
i
f
ilif 9. Shale, highly calcareous, massive, unfossiliferous; checking
il'l'egularly and containing irregular bands of chert and a few
imperfect geodes ................................................................................ 5
8
Li
t
i
th
f
f
d
l
6
8 8. Limestone, in the form of a dense gray layer .......................... .. 7
Shaly paJ ting
1 7. Shaly paJ-ting ...................................................................................... 1
6
Limestone massive weathering to thin spalls
1 Shaly paJ-ting ......................................................... Limestone massive weathering to thin spalls 6. Limestone, massive, weathering to thin spalls .......................... 5
Shale
argillaceous
thiruly laminated 5. Shale, argillaceous, thiruly laminated .............................................. 1
4
Li
OOill
i
i
id l
h
t
b l
2 4. LimesOOille, massive, crinoidal, cherty below................................ 2
3
Shale
calcareous; showing no bedding; bands of cherty lime 3. Shale, calcareous; showing no bedding; bands of cherty lime·
stone intercalated ................................................................................ 6
2
Li
i
d
i
id l
b
il)
d l
h 2. Limestone, coarse-grained, crinoidal, bearil).g nodular chert
below. Ptlstula alternata, Produotus setigerus and Retioularia
psoudolineata ..................................................................... _ .... _ .... _..... 1
1
Shale
passin~ laterally into limestone
4 1. Shale, passin~ laterally into limestone In a bluff at South Augusta (NE. 14 sec. 25, Denmark town-
ship) the basal beds of the Keokuk are exposed in contact with
the Upper Burlington limestone. 3.
Limestone, thin·bedded. gray, sub crystalline, very cherty; a
solid layer of chert twenty inches thick at base at one point.
Bed 3 of Aug'usta section ....................................... _.........................
3%
2
Li
i
d
i
id l
l'
h Section of KeoWtlk limestone northwest of Denmark. 19. 18. 17. 16. 15. 14. 13. ,
12. 11. 10. 9. Section of KeoWtlk limestone northwest of Denmark. FEET
Massive, gray limestone bearing numerous broad shells of
O?'thotetes leeoktt7c .............................................................................. 1
Limestone layers with thin intercalated shale bands .................. 2
Shale, calcareous below but more argillaeeous ab6ve ................ 3
Limestone, gray and buff ................................................................ 1
Limestone, cherty, stratification very il'l'egular or lacking;
checking into il'l'egular blocks <illd weathering buff; Spilrife?'
keo7cuk co=on .................................................................................. 2
Shaly parting ..................................................................................... . Limestone, gray and blue, very fossiliferous. The following
forms were noted:
Conula?'ia sp., Spirifer keoleu7c, O?'thotetes
keokuk,
Cliothyridi;n.a,
sp.,
Retioularia. 21S17luZolineata
and
Tet?'aoam.era stlbtrigona ............................................................... ,.... 1
Limestone, argillaceous, buff, lliOill·fossilifel'ous, stratification
obscure, disintegrating into aJlgular blocks .................................. 2
Shaly parting ..................................................................................... . Limestone, dense, gray, cherty above ............................................ 1
Shale, highly calcareous, massive, unfossiliferous; checking
il'l'egularly and containing irregular bands of chert and a few
imperfect geodes ................................................................................ 5
8. Limestone, in the form of a dense gray layer .......................... .. 7. Shaly paJ-ting ...................................................................................... 1
6. Limestone, massive, weathering to thin spalls .............................. 1
5. Shale, argillaceous, thiruly laminated .............................................. 1
4. LimesOOille, massive, crinoidal, cherty below................................ 2
3. Shale, calcareous; showing no bedding; bands of cherty lime·
stone intercalated ................................................................................ 6
2. Limestone, coarse-grained, crinoidal, bearil).g nodular chert
below. Ptlstula alternata, Produotus setigerus and Retioularia
psoudolineata ..................................................................... _ .... _ .... _..... 1
1. Shale, passin~ laterally into limestone ........... _ .... _ .................. _ .. . INCHES
5
6
4
4
4
6
4
6
4
6
8
2
5
3
5
4 19. 18
Massive, gray limestone bearing numerous broad shells of
O?'thotetes leeoktt7c .............................................................................. 1
Li
l
i h
hi
i
l
d
h l
b
d
2
5 18. 17
Limestone layers with thin intercalated shale bands .................. 2
Sh l
l
b l
b t
ill
b6
3 17. 16
Shale, calcareous below but more argillaeeous ab6ve ................ 3
Li
t
d b ff
1 16. 15
Limestone, gray and buff ............................................................ Li
t
h
t
t
tifi
ti
il'l'
l
l
ki 15. 14
Limestone, cherty, stratification very il'l'egular or lacking;
checking into il'l'egular blocks <illd weathering buff; Spilrife?'
keo7cuk co=on .................................................................................. 2
Shaly parting
4
4 14. 13
Shaly parting ..................................................................................... . Limestone
gray and blue
very fossiliferous
The following 13. ,
Limestone, gray and blue, very fossiliferous. 2.
Limestone, gray, coarse·grained, crinoidal, vel'y cherty, espe·
cially in lower part.
Bed 2 of Augusta section ......................
6 Se/)tio?~ of K.eo1c111c limestone neal' A'lI,g1!sta.
FEET
INCHES
13. Drift ............................................................. _ .... _................................. 2
12. Limestone, bluish gray, impure.
Exposed ..................................
1
11.
Concealed, probably soft shaJy limestone; loose blooks on
surface highly fossiliferous ......... _...................................................
3
10. Limestone, bluish gray, medium· grained, dense ... _.....................
2
2
9.
Limesto.ne, consisting of thin layers of bluish gray coarse·
grained limestone altem2ting with layers of thin·bedded grn)'
fine·grairood chert.y limestl)lle which weathers buff .....................
7
6
8.
Limestone, bluish gra.y, medium· grained, bearing Orthotetes
1ceo1c-u,1c and Pustula aJltemata ............................. _ ................ _......... 7
11
7.
Limestone, gray, subcrystalline, thinly and irregula.rly bed·
ded, cherty ............................................................... _ .......... _.............
1
6
6.
Limestone, bluish gray, medium grained, Orthotetes 1ceo1cu7.
and Palaeaois obtusus abundant ................................... _...............
6
5.
Limestone, da.rk gray to bluish gray, thinly and irregularly
bedded, cherty ........................................................... _.......................
2
4.
Limestone, bluish gray, medium· grained, to crinoidal; for the Se/)tio?~ of K.eo1c111c limestone neal' A'lI,g1!sta. Seotion of Keokuk limestO'llll3 at South Augtlsta. Seotion of Keokuk limestO'llll3 at South Augtlsta. Seotion of
eokuk limestOllll
at South
ugtlsta. FEET
4. Residual gool filled with ?JlguIar chert fragments. To bro,w
of hill ........................... _ .................................... _ .... _........................... 3
3. Limestone, thin·bedded. gray, sub crystalline, very cherty; a
solid layer of chert twenty inches thick at base at one point. Bed 3 of Aug'usta section ....................................... _......................... 3%
2. Limestone, gray, coarse·grained, crinoidal, vel'y cherty, espe·
cially in lower part. Bed 2 of Augusta section ...................... 6
1. Limestone, coarse·grained, "rinoidal, gray below but bluish gray
above, bearing wo,rn shells of Spirifer grimesi. Bed 1 of
Augusta section .................................................................................. 1112 to 2 KEOKUK LIMESTONE NEAR AUGUSTA 163 Li.st of fossils from bed. 1 of KeoWu,1c limestone at S01~th Augusta. ANTHOZOA-
Zaplll'entis sp. BRACHIOPODA-
Brachythyris suborbicularis (Hall)
Reticula.ria pseudolineata (Hall)
Clio,thyridina mcrassata (Hall)
Spirifer grimesi Hall
Spirifer tenuicostatus Hall
TmLoBITA-
Griffithides f sp. List of fossils fl'olr/, bed 2 of Keo1cl~1c limestQ7l,e at SmIth Al~!lusta . BRACHIOPODA-
Spirifer grimesi Hall
Spirifer sp. Reticularia pseudolineata (Hall)
VERTEBRA'I.'A-
~
Fish teeth Li.st of fossils from bed. 1 of KeoWu,1c limestone at S01~th Augusta. ANTHOZOA-
Zaplll'entis sp. BRACHIOPODA-
Brachythyris suborbicularis (Hall)
Reticula.ria pseudolineata (Hall)
Clio,thyridina mcrassata (Hall)
Spirifer grimesi Hall
Spirifer tenuicostatus Hall
TmLoBITA-
Griffithides f sp. List of fossils fl'olr/, bed 2 of Keo1cl~1c limestQ7l,e at SmIth Al~!lusta . BRACHIOPODA-
Spirifer grimesi Hall
Spirifer sp. Reticularia pseudolineata (Hall)
VERTEBRA'I.'A-
~
Fish teeth Li.st of fossils from bed. 1 of KeoWu,1c limestone at S01~th Augusta. ANTHOZOA-
Zaplll'entis sp. BRACHIOPODA-
Brachythyris suborbicularis (Hall)
Reticula.ria pseudolineata (Hall)
Clio,thyridina mcrassata (Hall)
Spirifer grimesi Hall
Spirifer tenuicostatus Hall
TmLoBITA-
Griffithides f sp. List of fossils fl'olr/, bed 2 of Keo1cl~1c limestQ7l,e at SmIth Al~!lusta . BRACHIOPODA-
Spirifer grimesi Hall
Spirifer sp. Reticularia pseudolineata (Hall)
VERTEBRA'I.'A-
~
Fish teeth Li.st of fossils from bed. 1 of KeoWu,1c limestone at S01~th Augu ANTHOZOA-
Zaplll'entis sp. BRACHIOPODA-
Spirifer grimesi Hall
Spirifer tenuicostatus Hall List of fossils fl'olr/, bed 2 of Keo1cl~1c limestQ7l,e at SmIth Al~!lusta . ACHIOPODA-
Spirifer grimesi Hall
Spirifer sp. Reticularia pseudolineata (Hall)
VERTEBRA'I.'A-
~
Fish teeth BRACHIOPODA-
Spirifer grimesi Hall
Spirifer sp. List of fossils from bed 3 of Keo1cu7c limestone at SmIth A1Ig1~sta . List of fossils from bed 3 of Keo1cu7c limestone at SmIth A1Ig1~sta . CRINOIDEA-
Spirifm tenuicostatus Hall
Batocrinus sp. Spirifer l'ostellatus Hall
BRYOZOA-
Spiriferella ooglecta (Hall)
Fenestella Bp. Syringothyris sp. Seotion of Keokuk limestO'llll3 at South Augtlsta. Tlaeniodictya l'amulosa Ulrich
Reticularia pseudolineata (Hall)
Proutella f sp. . Athyris lamelLosa (Leveille)
BRACHIOPODA-
Cliothyridina incrassata (Hall)
Productus ovatus Hall
Composita trinuclea (Hall)
Avonia sp. PELECYPODA-
Dielasma Bp. Co.Iliocardium sp. Tetracamera subtrigona (M. and W.) TRILOBITA-
Spiriferina sp. Griffithides , sp. CRINOIDEA-
Spirifm tenuicostatus Hall
Batocrinus sp. Spirifer l'ostellatus Hall
BRYOZOA-
Spiriferella ooglecta (Hall)
Fenestella Bp. Syringothyris sp. Tlaeniodictya l'amulosa Ulrich
Reticularia pseudolineata (Hall)
Proutella f sp. . Athyris lamelLosa (Leveille)
BRACHIOPODA-
Cliothyridina incrassata (Hall)
Productus ovatus Hall
Composita trinuclea (Hall)
Avonia sp. PELECYPODA-
Dielasma Bp. Co.Iliocardium sp. Tetracamera subtrigona (M. and W.) TRILOBITA-
Spiriferina sp. Griffithides , sp. BRYOZOA-
Fenestel Fenestella Bp. Tlaeniodictya l Tlaeniodictya l amulosa Ulrich
Proutella f sp Proutella f sp. ACHIOPODA Avonia sp. Dielasma B Dielasma Bp. Tetracamera Des Moines County.-The Des Moines cQunty exposures .of
the KeQkuk limestQne are cQnfined chiefly tQ the area abQut
Augusta in the sQuthern part .of the cQunty. HQwever, the basal
beds .of this fQrmatiQn have been recQgnized at IQcalities farther
nQrth. One .of the mQst cQmplete sectiQns in the CQunty .occurs alQng
the banks .of a small creek .one-half mile nQrth .of the Augusta
wagQn bridge in' the eastern part .of sectiQn 23, Augusta tQwn-
ship. The successiQn .of beds there is as fQllQws: Se/)tio?~ of K.eo1c111c limestone neal' A'lI,g1!sta. FEET
INCHES
13. Drift ............................................................. _ .... _................................. 2
12. Limestone, bluish gray, impure. Exposed .................................. 1
11. Concealed, probably soft shaJy limestone; loose blooks on
surface highly fossiliferous ......... _................................................... 3
10. Limestone, bluish gray, medium· grained, dense ... _..................... 2
2
9. Limesto.ne, consisting of thin layers of bluish gray coarse·
grained limestone altem2ting with layers of thin·bedded grn)'
fine·grairood chert.y limestl)lle which weathers buff ..................... 7
6
8. Limestone, bluish gra.y, medium· grained, bearing Orthotetes
1ceo1c-u,1c and Pustula aJltemata ............................. _ ................ _......... 7
11
7. Limestone, gray, subcrystalline, thinly and irregula.rly bed·
ded, cherty ............................................................... _ .......... _............. 1
6
6. Limestone, bluish gray, medium grained, Orthotetes 1ceo1cu7. and Palaeaois obtusus abundant ................................... _............... 6
5. Limestone, da.rk gray to bluish gray, thinly and irregularly
bedded, cherty ........................................................... _....................... 2
4. Seotion of Keokuk limestO'llll3 at South Augtlsta. Limestone, bluish gray, medium· grained, to crinoidal; for the MISSISSIPPIAN STRATA OF IOWA 164 most part massive but in places divided into thin layers by
chert bands _____ ____________________________________________________________________________________
1
6 most part massive but in places divided into thin layers by
chert bands _____ ____________________________________________________________________________________
1 3_
Limestone, gray, sub crystalline, thin-bedded, cherty; with a
massive layer od: crinoidal limestone in upper part ____________________ ] 0 L
Limestone, coarse-grained, crinoidal, gray below but bluish
above; the topmost layer, which is 8 inches thick. bears
water-worn specimens of Spirifer grimcsi _________________________________
1 The Keokuk limestone is underlain at this point by t-wenty-
one feet of crinoidal limestone of Upper Burlington age. This
has been described in a previous chapter. The fossils of the
successive beds of the Keokuk limestone near Augusta are listed
below. List of fossils from bed 1 of Ke07cu7e limes'tone neal- Augusta. List of fossils from bed 1 of Ke07cu7e limes tone neal
Augusta. ANTHOZOA-
Triplophyllum dalei (M.-E. and Ho.)
Cyatha.xonia SIp. Amplexus sp. BRYOZOA-
Fenestella ~p . Cystodictya sp. BRAcmoPoDA-
Orthotetes sp. Pustula alternata (N. and Po)
Tetracamera subtl'igo-n!L (Hall)
Spirifer grimesi Hall
Spirifer tenuicostatus Hall
Reticularia pseudolineata (Hall)
Brachythyris suborbiculal'is (Hall)
Athyris lamellosa (Leveille)
Cliothyridina incrassata (Hall)
Cliothyridina pan-virostris (M. amd W.)
PELECYPODA--
Conocardium sp. GASTROPODA-
Platyceras sp. Orthonychia sp. VERTEBRATA--
Fish teeth g
Reticularia pseudolineata (Hall)
Brachythyris suborbiculal'is (Hall)
Athyris lamellosa (Leveille)
Cliothyridina incrassata (Hall)
Cliothyridina pan-virostris (M. amd W.)
PELECYPODA--
Conocardium sp. GASTROPODA-
Platyceras sp. Orthonychia sp. VERTEBRATA--
Fish teeth List of fossils from bed Ie of K eolUltk limcstOM neaj' Aug~tsta. CRINOIDEA---
Actinocrinus sp. BRYOZOA-
Benestella sp. BRACHIOPODA-
Productus sp. Pustula nlternata (N_ and P.)
Spirifer incertus Hall
Spirifer grimesi Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
Cliothyridina incrassata (Hall)
GASTROI?ODA-
Ortho'D~chia sp. Orthonychia sp. TRILOBITA-
Griffithides , sp. List of fossils from bed 7 of K e07cuk limeston.e Mar Aug~.sta. TRILOBITA-
G iffithid List of fossils from bed 9 oj K eokuk limestone near Augusta List of fossils from bed 9 oj K eokuk limestone near Augusta. CRINOIDEA-
Actinocrinus lowei Hall
BRACHIOPODA-
Spiriferella neglecta (Hall) ,
Cliothyridina incrassata (Hall)
GASTROPODA-
Tetracamera subtrigooa. Spirifer logani Hall
(M. and W.)
PlaJtyceras sp. BRACHIOPODA-
GASTROPODA-
Tetracamera subtrigooa. Spirifer logani Hall
(M. and W.)
PlaJtyceras sp. Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. List of fossils fj'om bed S of Keoht7e limestone near Augusta List of fossils fj'om bed S of Keoht7e limestone near Augusta. BRYOZOA-
Fenestella sp. Proutella sp. BRACHIOPODA-
Tetracamera subtrigona
Productus ovatus Hall
Prodiuctus sp. Pustula sp. Dielasma sp. (M. and W.)
Spil'ifer tenuicostatus Hall
Spirifer 1'0stellatus Hall
Reticularia pseudolineata (Hall)
SpiTiferina sp. Athyris lamellosa (Leveille)
Cliothyridina obma.xima (McChesney)
Cliothyridina p31rvirostris (M. am.d W.)
GASTROPODA-
Orthonychia
~ sp. List of fossils from bed 5 of Keokuk limestone neaT Aug~tsta. ANTHozoA-
BRACHIOPODA-
Triplophyllum dalei (M.-E. and H .)
Pl'oductus ovatus Hall BRYOZOA-
Fenestella sp. Proutella sp. BRACHIOPODA-
Tetracamera subtrigona
Productus ovatus Hall
Prodiuctus sp. Pustula sp. Dielasma sp. (M. and W.)
Spil'ifer tenuicostatus Hall
Spirifer 1'0stellatus Hall
Reticularia pseudolineata (Hall)
SpiTiferina sp. Athyris lamellosa (Leveille)
Cliothyridina obma.xima (McChesney)
Cliothyridina p31rvirostris (M. am.d W.)
GASTROPODA-
Orthonychia
~ sp. List of fossils from bed 5 of Keokuk limestone neaT Aug~tsta. ANTHozoA
BRACHIOPODA List of fossils from bed 5 of Keokuk limestone neaT Aug~tsta. ANTHozoA-
BRACHIOPODA-
Triplophyllum dalei (M.-E. and H .)
Pl'oductus ovatus Hall FOSSILS OF KEOKUK NEAR AUGUSTA FOSSILS OF KEOKUK NEAR AUGUSTA 165 ProductuSi sp. Avouia sp. Chonetes sp. Delthyris ~ sp. Spirifer logani Hall
Spil"ifer sp. ~
Brachythyris suborbicularis (Hall)
Rcticularia pseudolineata (Hall)
Composita trinuclea (Hall)
PELECYPODA-
Cypricardinia sp. List of fossils from bed 6 of K e07cuk Umestcme near Augusta. ANTHOZOA-
BrachythYJ'is sub orbicularis (Hall)
Palaeacis obtusus (M. and W. )
Reticularia pseudolineata (Hall)
Triplophyllum dalei (M.·E. and H.)
Syringothyris sp. BRACHIOPODA-
Cliothyridm obmaxima (McChesney)
Pustula altemata (N. and P .)
GAS'l.'ROPODA-
Tetracamera subtrigona (M. and W.)
Platyceras sp. Spiriferina sp. VERTEBRATA-
Spirifer sp. Fish teeth
List of fossils from bed 7 of K e07cuk limeston.e Mar Aug~.sta. ANTHOZOA-
Zaphrentis sp. CRINOIDEA-
Dorycrinus (spine)
Platycrinus sp. BRYOZOA-
Cystodictya sp. Worthenopora spinosa Ulrich ,
BRACHIOPODA-
Pustula alternata (N. and P.)
DieIasma sp. Tetracamera subtrigona (M. and W.)
Spiriferina sp. ~eti culari a pseudoliTheata (Hall)
Athyris lamellosa (Leveille)
Cliothyridina incrassata (Hall) ,
Clio.thyridina obma.'·dma (McChesney)
GASTROPODA-
Platyceras sp. Orthonychia sp. TRILOBITA-
Griffithides f sp. List of fossils from bed 9 oj K eokuk limestone near Augusta. CRINOIDEA-
Actinocrinus lowei Hall
BRACHIOPODA-
Spiriferella neglecta (Hall) ,
Cliothyridina incrassata (Hall)
GASTROPODA-
Tetracamera subtrigooa. Spirifer logani Hall
(M. and W.)
PlaJtyceras sp. Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. B!tYOZOA-
Phractopora trifolia (Rominger)
BRACHIOPODA-
Spirifer keokuk Hall
Spirifer logani Hall
Reticularia pseuGolineata (Hall)
List of fossils f1'om bed 11 of K eokuk lillilestonc near Augusta. ANTHOZOA-
Zaphrentis varsoviensis "Worthen ,
Triplophyllum dalei (M ... E. and H.)
Amplexus sp. MOlllilopora beecheri Grabau
CRINOIDEA-
Actinocrinus sp. Platycrinus sp. SyubathoCl'inus sp. BRYOZOA-
Cyclopora , Sip. Leioclema gracillimum Ulrich
Leioclerna. punctatum (Hall)
. Phractopora trifolia (Rominger)
Taeniodictya ramulosa Ulrich
Glyptopora kcyserlingi (Prout)
Rhombopora varians Ulrich
Rhombopora attenuata Ulrich
Rhombopora transversalis Ulrich
Cystodictya pustulosa Ulrich
Fenestella serratula Ulrich
Fenestella multispinO£a Ulrich ,
Streblotrypa radialis Ulrich
BRACHIOPODA-
Orthotetes , sp. Productus wortheni Hall ,
Pustula sp. 1'Ietracamera subtrigona (M. and W.) ProductuSi sp. Avouia sp. Chonetes sp. Delthyris ~ sp. Spirifer logani Hall
Spil"ifer sp. ~
Brachythyris suborbicularis (Hall)
Rcticularia pseudolineata (Hall)
Composita trinuclea (Hall)
PELECYPODA-
Cypricardinia sp. f f
f
f
g
ANTHOZOA-
BrachythYJ'is sub orbicularis (Hall)
Palaeacis obtusus (M. and W. )
Reticularia pseudolineata (Hall)
Triplophyllum dalei (M.·E. and H.)
Syringothyris sp. BRACHIOPODA-
Cliothyridm obmaxima (McChesney)
Pustula altemata (N. and P .)
GAS'l.'ROPODA-
Tetracamera subtrigona (M. and W.)
Platyceras sp. Spiriferina sp. VERTEBRATA-
Spirifer sp. Fish teeth ANTHOZOA-
BrachythYJ'is sub orbicularis (Hall)
Palaeacis obtusus (M. and W. FOSSILS OF KEOKUK NEAR AUGUSTA )
Reticularia pseudolineata (Hall)
Triplophyllum dalei (M.·E. and H.)
Syringothyris sp. BRACHIOPODA-
Cliothyridm obmaxima (McChesney)
Pustula altemata (N. and P .)
GAS'l.'ROPODA-
Tetracamera subtrigona (M. and W.)
Platyceras sp. Spiriferina sp. VERTEBRATA-
Spirifer sp. Fish teeth Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. B!tYOZOA-
Phractopora trifolia (Rominger)
BRACHIOPODA-
Spirifer keokuk Hall
Spirifer logani Hall
Reticularia pseuGolineata (Hall)
List of fossils f1'om bed 11 of K eokuk lillilestonc near Augusta. ANTHOZOA-
Zaphrentis varsoviensis "Worthen ,
Triplophyllum dalei (M ... E. and H.)
Amplexus sp. MOlllilopora beecheri Grabau
CRINOIDEA-
Actinocrinus sp. Platycrinus sp. SyubathoCl'inus sp. BRYOZOA-
Cyclopora , Sip. Leioclema gracillimum Ulrich
Leioclerna. punctatum (Hall)
. Phractopora trifolia (Rominger)
Taeniodictya ramulosa Ulrich
Glyptopora kcyserlingi (Prout)
Rhombopora varians Ulrich
Rhombopora attenuata Ulrich
Rhombopora transversalis Ulrich
Cystodictya pustulosa Ulrich
Fenestella serratula Ulrich
Fenestella multispinO£a Ulrich ,
Streblotrypa radialis Ulrich
BRACHIOPODA-
Orthotetes , sp. Productus wortheni Hall ,
Pustula sp. 1'Ietracamera subtrigona (M. and W.) B!tYOZOA-
Phractopora trifolia (Rominger)
BRACHIOPODA-
Spirifer keokuk H
Spirifer logani Ha B!tYOZOA-
Phractopora trifolia (Rominger) List of fossils f1'om bed 11 of K eokuk lillilestonc near Augusta. ANTHOZOA-
Zaphrentis varsoviensis "Worthen ,
Triplophyllum dalei (M ... E. and H.)
Amplexus sp. MOlllilopora beecheri Grabau
CRINOIDEA-
Actinocrinus sp. Platycrinus sp. SyubathoCl'inus sp. BRYOZOA-
Cyclopora , Sip. Leioclema gracillimum Ulrich
Leioclerna. punctatum (Hall)
. Phractopora trifolia (Rominger) ANTHOZOA-
Zaphrentis varsoviensis "Worthen ,
Triplophyllum dalei (M ... E. and H.)
Amplexus sp. MOlllilopora beecheri Grabau
CRINOIDEA-
Actinocrinus sp. Platycrinus sp. SyubathoCl'inus sp. BRYOZOA-
Cyclopora , Sip. Leioclema gracillimum Ulrich
Leioclerna. punctatum (Hall)
. Phractopora trifolia (Rominger) ANTHOZOA-
Zaphrentis varsoviensis "Worthen ,
Triplophyllum dalei (M ... E. and H.)
Amplexus sp. MOlllilopora beecheri Grabau
CRINOIDEA-
Actinocrinus sp. Platycrinus sp. SyubathoCl'inus sp. BRYOZOA-
Cyclopora , Sip. Leioclema gracillimum Ulrich
Leioclerna. punctatum (Hall)
. Phractopora trifolia (Rominger) , MISSISSIPPIAN STRATA OF IOWA 166 Tetracamera subcuneata (Hall)
Brachythyris sub orbicularis (Hall)
Rhipidomella dubia (Hall)
Reticularia pseudolineata (Hall)
Spiriferina , gp. Syringothyris sp. Spirifer tlenuicostatus Hall 'I
Cliothyridina incrassata (Hall)
Spirifer logani Hall
PELECYPODA-
Spirifer d . S. keokuk Hall
Conocardium sp. Spirifer rostellatus Hall
GASTROPODA-
Spiriferella neglecta (Hall)
Platyceras sp. The following faunal table includes the more characteristic
species of the collections made at both South Augusta and
Augusta. Table Showin1Jg Bange of Fossils in the K e07cu1c B eds at Augusta and South Augusta. I
Horizons ;
I
11 j2j3j5j 617jsj9jlo \ 11 \
ANTHOZOA
j
Zaphrentis varsoviensis Worthen , ... _ .......... _.. ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Triplophyllum dalei (M.·E. and H.) ................. x ............ x
x ...... .................. x
~!~=~~t~;~·~···(M:~··;.;d··W:):::=::::=:::=:~:::::: .. ~ .. :::::: :::::: :::::: .. ~ .. Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. :::::: :::=: :::::: :::=: :::=:
Monilopora beecheri Grabau ........................... _.. ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Amplexus sp ................................................... ,...... x...... ...... ...... ...... ...... ...... ...... ...... x
CRINOIDEA
Batocrinus sp .......................................................... , ........ _. x .............................. ........... . ~~k:=us (~~=\i·~n:::=::::::::::::::=:::=:::::=:::::: :::::: :::=: :::::: :::::: :::=: .. ~ .. :::::: .. ~ .. :::::: :::::~
Actinocrinus sp ....................................... :: ..... .., ...... ...... .... r ••••.. .••.•. •••... . ...•• ....•. ••••.. .••••. x
~;!~:tt~~u;~p::::==::::::::::::::::::::::=::::=::::=:::::: :::=:
.:~ .. :::::: ::::::
:::~: :::::: :::::: :::::: :::::: .. ~ .. BRYOZOA
t:~~::: ~~~~~=~m (~~;~~~=~~~ .. =~~~~~~:~~~=:: :::::: :::=: :::::: :::::: :::=: ::;::: :::::: :::::: :::::: ~
'l1aeniodictva ramulosa Ulrich............................. ...... ....... x...... ...... ...... ...... ...... ...... x
Cystodietya. pustulosa Ulrich............................... ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Cystodictya sp........................................................ ...... ...... ...... ...... ...... x ...................... .. Cystodictya sp........................................................ x ............ ............ ............................. . Phractopora trifolia (Rominger) ............... _ .......................................... ............ x
x
Glyptopora keyserlingi (Prout) ....................................................... ...... ...... ...... ...... x
Rhombopora attenuata Ulrich........................... ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Rhombopora varians Ulrich ........................................................................... ~..... ...... x
Rhombopora transversalis Ulrich ................................ _ ................... ...... ;..... ...... ...... x
Streblotrypa radialis Ulrich ........................... _.. ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Fenestell~ serratula Ulrich................................. ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Fenestella multispinosa Ulrich. ................................ ...... ...... 1 ...... ... _. ...... ...... ...... ...... x
~~;:!~p~;;:·~pi;~~~··Ui;i~h .. i.::::::::::::::::::==:::: :::::: :::::: .. ~ .. I:::::: :::::: .. ~ .. :::::: :::::: :::::: ::::::
\ '
I
Orthotetes ke:::~:::~)~ .............. _ .......... _ ....... ................... I ...... 1 ...... L... x \... ......... ', ..... . 9rthotetes sp.......................................................... x 1 ...... 1 ...... 1 ...... ...... I ...... ·· .... 1·· .... 1 ...... .... .. RANGE OF FOSSILS OF KiEOKUK BEDS 167 Table Showilng Eange of Fossils iIn the Keokuk Beds at A1bgusta and South Augusta.. Continued. I
I Continued. I
Horizons
I
11 12131516171819110 111 I
Chonetes sp ........ _ .................. _ ........ _ ........ _ ........... · ...... ...... ...... x .................. ................ .. Productus o,vatus H,all.......................................... ...... ...... x
x .............................. .... .. Productus worth~ Hall 7 ................................ --....................................................... x
Pustula altel'llata (N. and P.) ........................... x
x ...... ...... x
x
x ................ .. Pustula sp.............................................................. ...... ...... ...... ...... ...... ...... ...... ...... ...... x . Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. Avonia sp ............................................................ --.............. x
x ................................... . Rhipidomella dubia (Hall) ................................. .............................. ........................ x
Tetracamera subtrigona (M. and W.) ............. x ...... x ...... x
x ...... x ...... x
Tetracamera subcuneata (Hall) ..................................................... ............ ............ x
~~~;=~as~p:~~~~~~::::~=::=~:~::~~::::~:::::~=~::::::::::'.:::::::: :::::: :::::: ~ :::=: .. ~.. ~ :::::: :::::: :::::: ::::::
Spirifer grimesi HalL......................................... x
x .................. ............................. .. Spirifer incertus HalL ................................... -.... ...... x ........................ ...................... .. Spirifer tenuicostatus Hall................................. x ...... x...... ...... ...... ...... ...... ...... x
Spirifer rostellatus Hall ..................... _ .......... _ .. '''''' ...... x ...... ",,,. "'''' ...... ...... ...... x
Spirifer logani HalL ........................................... · ...... ...... ...... x...... ...... ...... x
x
x
Spirifer keokuk HalL ...................................... , .. """ ...... ...... ...... ...... ...... ...... ...... x .... .. S,pirifer cf. S. keokuk HalL._ ........................................................ _. ...... ...... ...... ...... x
Bra.chythyris suborbicularis (Hall) ............... _ .. x
x ... _. x
x .................. ...... x
Spiriferella neglecta (Hall) ........................................... x ........................ xi ...... x
Reticularia pseudiolineata (Hall) ....................... x
x
x
x
x
x ............ x
x
Syringothyris sp .................................. _ ............ _.. ...... ...... ...... ...... ...... ...... ...... ...... ...... x
Athyris· lamellosa (Leveille) ............................... x ...... x ...... ...... x ... _ . ................ .. Cliothyridilrua incrassata (Hall) ......................... x
x
x ... _ . ...... d
...... x "'''' x
Cliothyridina obmaxima (McChesney) ................... ...... x ...... x
x ............ ........... . Cliothyridina parvirostris (M. and W.) ........... x ...... x ........................... __ ........... .. Composita trinuc1ea (Hall) ................. _ .......................... x
x ...... ............................. . PELECYPODA
g=::J=a S;p::::::::=::::::::=::::::::::::==::::::::::::::: .. ~ .. :~~~:: .. ~ ..... ~ .. ~~:~~: ::::~: :::=: :::~:: ::~=: .. ~ . GASTROPODA
i~[?~:~~~-~~:~~~:-~=~--:~~-::j:,~~ ~~. ~-:I~-C~ -:.-:. =~;-: =~:
Orthonychia sP .......... _ .... _ .... · .. · .. · .... · .. · ........ · ........ ·I ...... , x, ............ 1 ...... 1 ............ 1 ................ .. Orthonychia sp .... _.................................................. ...... x ............ 1 ...... \ ............................ .. TRILOBITA
I
'
1 I 1 'I'
. . I
I
I I I I I
G;nffithldes , sp ...................... - .......................... · .. t x 1 x 1 x 1 ...... 1 ...... 1 x 1 ...... 1· ..... 1· ..... 1 ...... Seotion i;n the south bam,"k of Long creek Seotion i;n the south bam,"k of Long creek Seotion i;n the south bam,"k of Long creek
FEET
INCHES
12. Drift, to brow of hill ...................................................................... . 11. Limestone, as in bed 7. Interbedded with layers of soft
shale ...................................................................................................... 5
10. Limestone, bluish gray, slightly crino~daL Orthotetes "keo"ku"k,
Spilrifer "keo"ku"k, Retioularia pseudolvneata" R. dubia, Pust~!la
sp .......... _ .... _ ...................... _ .... _ .... _ ................. ________ . ________ . __________ . _______ . 2
9. Limestone as in bed 7. Spirifer tem!icostatus . __ . __ . __________ .________
4
6
8. Limestone, gray, medium·grained; in thin layers separated by
shaly seams . __ .. _________________________________________ . __________ . ______________________________ . 2
8
7. Limestone, gray to drab, soft, magnesian; flaking off ob·
liquely to surface. No fossils noted __ . _______________________________________ . 5
6
6. Limestone, gray, medium·grained; with seams of fine·grained
soft limestone __________________________ . ______ . __________ . ____ . ____ . __ .. __________________ .________
3
6
5. Shaly seanl ____ . ____________ .. ___ .. __ ... __ .. ______________ ______ ... _______________________ ._____
6
4. Limestone, gray, fure-grained, soft, cherty; with layers :md
seams of gray to bluish coarser· grained slightly crinoidal
fossiliferous limestone. A thin bluish crinoidal layer at the
top bears many fish teeth. Palaeacis
()bt~!Sus, Zaphrentis
IJMsoviensis, Fenestella sp . . _________________ . ____________ . ___________ . __________ . ______ . 5
6
3. Limestol1ie, bluish gray, cherty, slightly crinoidal. Triplo·
phyllum dalei, Brachythyris suborb~!laris, Pl!stula alternata,
Rhipidomella dubia, Conocardium I;!p. Retioularia pseudolineata,
Spirifer tem!ioostatu8 and fragments of fish teeth . __________________ . 10
2. Shaly seam ... ____________ . ____ .. __ . ______________________ . ______________ . ____ .. _______________ .. __ . 3
1. Limesta:ne, drab, fine'gr,ained, magnesian, with segregations of
calcite. To water in creek .. __ . ____ . ____ . ________________ ... __ .. ______ .... ____ . __ .. __ ... 4
6 Drift, to brow of hill ....................................... i
i
b d
b dd d
i h Limestone as in bed 7. Spirifer tem!icostatu
Li
di
i
d
i
hi
l 6. Limestone, gray, medium·grained; with seams of fine·grained
soft limestone __________________________ . ______ . __________ . ____ . ____ . __ .. __________________ .________
3
5
Shaly seanl Thirty rods north of this exposure there is a bluff section on
the opposite bank of the creek. Li.st of fossils from bed 10 of K eokuk limestone 'near A1.gusta. 1
Approximately two miles northeast of Augusta the Keokuk
limestone is again well exposed in the south bank of Long creek
on the Harry Hillgardner property. The following beds are
exposed at this place: Approximately two miles northeast of Augusta the Keokuk
limestone is again well exposed in the south bank of Long creek
on the Harry Hillgardner property. The following beds are
exposed at this place: Approximately two miles northeast of Augusta the Keokuk
limestone is again well exposed in the south bank of Long creek
on the Harry Hillgardner property. The following beds are
exposed at this place: 168 MISSISSIPPIAN STRATA OF IOWA Seotion i;n the south bam,"k of Long creek Bed 10 is overlain at this point
by eighteen feet of bluish shale, calcareous in the lower part,
which is referred to the Lower Warsaw. This member is jn
turn followed above by five feet of Spergen dolomitic limestone. In the region about Burlington only the basal beds of the
Keokuk are preserved. Thus; in the Miller quarry above the
Cascade the ~ollowing beds are seen in contact with the upper
Burlington limestone. Section of Keo"ku"k limestone in Miller quarry. FEET
INCHES
3. Limestone, brOlWIlish, magnesian, very cherty ..... __ ....... ____ ... __ ... ____
7%
2. Limestone, brownish, crmoidal ... _ .... __ ..... __ ...... ______ .......... ____ .. __ ..... __ ... 1
5
1. Limestone, yello,wish, magnesian, 'cherty, especially near the
base __ . _______________________________ . ______________ . __ . __ . __ . ______________ . ____ . _______ . ____________ . __ .. 5
3 No identifiable fossils were found in any of the layers but
their position above the Upper Burlington suggests their
Keokuk age. Van Buren County.-The exposures of the Keokuk limestone
in Van Buren county are confined to a narrow belt along Des
Moines river where the overlying formations have been eroded KEOKUK BEDS AT BENTONSPORT 169 as a result of the uplift of an anticline which nearly parallels
the river. A general section of the Keokuk limestone as ex-
posed at and near the town of Bentonsport is as follows: as a result of the uplift of an anticline which nearly parallels
the river. A general section of the Keokuk limestone as ex-
posed at and near the town of Bentonsport is as follows: Generalized section of the Keo:bu7c linn/3\Stcm:e a,t B entonsport and vicilnity. FEET
20. Limestonel bluish gray, coarse· grained ; in one massive ledge.... 3
19. Shale, blUlsh, argillaceous, highly fossiliferous; with discontin·
uous seams and flakes of gray impure, cherty limestone .......... 1
18. Limestone, gray, medium·grained ... _ ...................... _....................... 1
17. Shale, bluish, argillaceous, slightly fossiliferous ............... _ ...... . 16. Limestone, bluish, rather coarse·grained; sepauated from the
bed belo'w by a shaJy parting 5 to 10 inches thick ......... _......... 2
15. Limestone, gray, subcrystallin:e, with irregular nodules of chert;
massive when fresh but weathering into thin layers; locally
nhaly in lower part ... _....................................................................... 2
14. Limestone, bluish, coarse-grained, cherty; for the most part in
one massive ledge .............................................................................. 2
13. Generalized section of the Keo:bu7c linn/3\Stcm:e a,t B entonsport and vicilnity. List of fossils fTom bed 1 of Keokntk limestone iIn BentonspOTt area List of fossils fTom bed 1 of Keokntk limestone iIn BentonspOTt area. CRINOIDEA-
Spirifer grimesi HaJl
Dorycrinus sp. Spirifer logani Hall
BRYOWA-
Spirifer rostellatus Hall
Leioclema pu]]ctatum (Hall)
Spirifer tenuicostatus Hall
BRACHIOPODA-
Spirifer d. S. keokuk Hall
pi'oductus setigerus Hall
Spiriferella neglecta (Hall)
' Productus sp. Composita trinuclea (Hall)
Pustula biseriata (Hall)
GASTROPODA-
Tetracamera subtrigona (M. and W.)
P latyceras sp. Diela!!Illa sp. •
Platyceras sp. ' Dielasma sp. TRILOBI'l'A-
Spiriferina sp. Griffithicles
~ sp. List of fossils from bed I!! of K eoht7c limestone in B l7Thtonsport area. BRACIflOPODA-
Avonria sp. Dielasma f sp,
Dielasma sp. Tetracamera: subtrigona (M. and W.)
Spirifer sp. Reticularia pseudolineata
GASTROPODA-
Orthonychia sp. (Hall) BRACIflOPODA-
Avonria sp. Dielasma f sp,
Dielasma sp. Tetracamera: subtrigona (M. and W.)
Spirifer sp. Reticularia pseudolineata
GASTROPODA-
Orthonychia sp. (Hall) Seotion i;n the south bam,"k of Long creek Limestone, light gray to whitish, medium·grained, slightly crin·
oidal; grading locally into gray subcrystalline limesto'lle which
weathers to yellowish shaly layers ................................................ 2
12. Limestone, consisting of alternating l:vyers of l'ather coarse·
grained bluish limestoille and gray subcrystalline limestone
which weathers shaly ............................. :.......................................... 6
11. Limestone, bluish gray, r:vther coarse· grained; with shaly p:vrt·
ings between the layers in lower part ........................................ 3
10. Limestone, grayish, subcrystalline; with seams of coarser·
grained bluish cherty limestone in lower part ..... _ ........ ,............ 4
9. Shale, bluish, calcareous, weathering drab and yellowish, un·
fossiliferous .......................................................................................... 6
8. Limestone, bluish gray, SUbCl'ystalline, with a shaly parting
four inches thick near the middle ....................... _........................... 3
7. Limestone, :fine·grained, impure, ash· colored, dolomitic; shaly
towards the top; weathering buff; with a few cherty seams.... 3
6. Limestone, gray, subcrystalline, cherty ............................... _....... 1
5. Limestone, bluish gray and medium·grained in lower part, but
:fine·grained and ash-colored above ................................................ 5
4. Limestone, gray, :fine· grained, structureless, cherty; locally
passing into gray subcrystalline fossiliferous limestone' .......... 3
3. Limestone, bluish gr:vy, medium·grained to coarse· grained,
slightly cri:rooidal; upper one·half locally bearing fish teeth and
pygidia od: trilobites; middle part rich in crinoids ... _................. 3
2,
Limestone, grayish, subcrys1JaJline, very cherty; locally grading
into coarse-grained bluish gray crinoidal limestone ......... _..... 2
1. Limestone, bluish gray, cherty ........................................................ 1
INCHES
6
6
2-12
6
6
5
6
9
6
10
9
9
5
3 2,
Limestone, grayish, subcrys1JaJline, very cherty; locally grading
into coarse grained bluish gray crinoidal limestone
2 into coarse-grained bluish gray crinoidal limestone ......... _..... 1
Limestone
bluish gray
cherty Beds 1 to 4 represent the basal portion of the formation and
are well exposed on Lexington creek, nearly one mile above its
mouth, in section 7, Bonaparte township. Beds 5 to 20, on the
other hand, are exposed in the north- bluff of Des Moines river
about one-fourth mile below the station at Bentonsport. Bed 20
is overlain here by highly fossiliferous shales and shaly lime-
stones of the Lower 'Warsaw (Geode bed). These are described
in ;:t later chapter devoted to this formation. 170 MISSISSIPPIAN STRATA OF IOWA The fossils of the individual beds of the Keokuk limestone in
this area are listed below. List of fossils from bed 3 of K eokuk limestone im B entonsport area. List of fossils from bed 3 of K eokuk limestone im B entonsport area. ANTHOZOA-
,Cyathaxonia sp. Amplexus sp. Z'a,phrentis varsoviensis 'Worthen (~
'Zaphrentis sp. . Triplophyllum dalei (M.-E. and H . Palaeacis obtusus (M. and W.)
CRINOIDEA-
: Actinocrinus' sp. Dorycrinus sp. EHINOIDEA-
' Archaeocidaris sp. BRYOZOA-
Stenopora sp. Cyclopora , sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus setigerus Hall
Productus sp. Pustula alternata (N. and P.)
Pustula ~ sp. Rhipidomella dubia (Hall) Rhipidomella dubia (Hall) List of fossils from bed 4, of K eohtk limestone in B ent011.sport area. BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Fenestella sp. F enestella sp. BRACHIOPODA-
Orthotetcs keokuk (Hall)
Chonetes shumardanus De Koninck
Productus
Avonia sp
Pustula a
Pustula s
Oamaroph
Camaroto
Dielasma
Dielasma Productus sp. A
i Stenopora sp. F
ll p
p
Fenestella serratula Ulrich
F
t ll Fenestella sp. F
t ll Fenestella sp. F enestella sp. F enestella sp. ACHIOPODA Dielasma sp. Di l Dielasma sp. KEOKUK FOSSILS AT BENTONSPORT KEOKUK FOSSILS AT BENTONSPORT List of fossils from bed 6 of Keokuk limestone in Bentonsport area. ANTHOZOA-
Cyathaxonia sp. Triplophyllum dalei (M.-E. and H.)
Palaoo.cis obtusus (M. and W.)
CRINOIDEA-
Platycrinus sp. Agaricocrinus sp. BRYOZOA-
Cystodictya sp. BRACHIOPODA-
Schuchertella , sp. Productus sp. Produc.tus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetracamea.'a subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer rostellatus Hall
Spirifer keokuk Hall
Spirifer logani Hall
. Brachythyris suborbicula~is (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Cliothyridina obmaxima (McChesney)
PELECYPODA-
Lithophagus illinoisensis Worthen'
Cypricardini31 f sp. GASTROPODA-
Platyceras sp. Platyceras sp. Ortho~chia sp. Orthonychia sp. List of fossils from bed 6 of Keokuk limestone in Bentonsport area. ANTHOZOA-
Cyathaxonia sp. Triplophyllum dalei (M.-E. and H.)
Palaoo.cis obtusus (M. and W.)
CRINOIDEA-
Platycrinus sp. Agaricocrinus sp. BRYOZOA-
Cystodictya sp. BRACHIOPODA-
Schuchertella , sp. Productus sp. Produc.tus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetracamea.'a subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer rostellatus Hall
Spirifer keokuk Hall
Spirifer logani Hall
. Brachythyris suborbicula~is (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Cliothyridina obmaxima (McChesney)
PELECYPODA-
Lithophagus illinoisensis Worthen'
Cypricardini31 f sp. GASTROPODA-
Platyceras sp. Platyceras sp. Ortho~chia sp. Orthonychia sp. ANTHOZOA-
Cyathaxonia sp. Triplophyllum dalei (M.-E. and H.)
Palaoo.cis obtusus (M. and W.)
CRINOIDEA-
Platycrinus sp. Agaricocrinus sp. BRYOZOA-
Cystodictya sp. BRACHIOPODA-
Schuchertella , sp. Productus sp. Produc.tus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetracamea.'a subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer rostellatus Hall
Spirifer keokuk Hall
Spirifer logani Hall
. Brachythyris suborbicula~is (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Cliothyridina obmaxima (McChesney)
PELECYPODA-
Lithophagus illinoisensis Worthen'
Cypricardini31 f sp. GASTROPODA-
Platyceras sp. Platyceras sp. Ortho~chia sp. Orthonychia sp. Triplophyllum dalei (M.-E. and H.)
P l
i
bt
(M
d W ) Palaoo.cis obtusus (M. and W.)
RINOIDEA Ortho~chia sp. O th
hi List of fossils from Qed 7 of Keokuk limestone i'Y') Bento~sport area. NTHOZOA
T
b i
(M
d ANTHOZOA-
Triplophyllum dalei (M.-E. amd .H.)
CRINOIDEA-
Dorycrinus Inississippiens'is Roemer
Eutrochocrinus planodiseus Hall
BRACHIOPODA-
Pustula alternata (N. and P.)
Pustula sp:
Pustula sp. Tetracamera subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer koo'kuk Hilll
. Spirifer rostellatus ;Hall
Reticularia pseudolfueata (Hall)
Cliothyridina obma.-a.ma (McChesney)
GASTROPODAt-
Straparollus sp. Platyceras 8p_ ANTHOZOA-
Triplophyllum dalei (M.-E. amd .H.)
CRINOIDEA-
Dorycrinus Inississippiens'is Roemer
Eutrochocrinus planodiseus Hall
BRACHIOPODA-
Pustula alternata (N. and P.)
Pustula sp:
Pustula sp. Tetracamera subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer koo'kuk Hilll
. KEOKUK FOSSILS AT BENTONSPORT 171 KEOKUK FOSSILS AT BENTONSPORT
171
Spiriferilla Sp. PELECYPODA-
Delthyris f sp. AviculopeeteIIJ ct. A. oblongus (M •. Spirifer l100tellrutus Hall
amd W.)
Spirifer cf. S. Jreokuk Hall
Allorisma sp. Pseudosyrinx keokuk Weller
GASTROPODA-
Reticularia pseudolineata (Hall)
Platyceras sp. Cliothyridina obmaxima (McChesney) CEPHALOPODA-
Orthoceras sp. List of fossils from bed 6 of Keokuk limestone in Bentonsport area. ANTHOZOA-
Cyathaxonia sp. Triplophyllum dalei (M.-E. and H.)
Palaoo.cis obtusus (M. and W.)
CRINOIDEA-
Platycrinus sp. Agaricocrinus sp. BRYOZOA-
Cystodictya sp. BRACHIOPODA-
Schuchertella , sp. Productus sp. Produc.tus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetracamea.'a subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer rostellatus Hall
Spirifer keokuk Hall
Spirifer logani Hall
. Brachythyris suborbicula~is (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Cliothyridina obmaxima (McChesney)
PELECYPODA-
Lithophagus illinoisensis Worthen'
Cypricardini31 f sp. GASTROPODA-
Platyceras sp. Platyceras sp. Ortho~chia sp. Orthonychia sp. List of fossils from Qed 7 of Keokuk limestone i'Y') Bento~sport area. '
ANTHOZOA-
Triplophyllum dalei (M.-E. amd .H.)
CRINOIDEA-
Dorycrinus Inississippiens'is Roemer
Eutrochocrinus planodiseus Hall
BRACHIOPODA-
Pustula alternata (N. and P.)
Pustula sp:
Pustula sp. Tetracamera subtrigona (M. and W.)
Spirifer tenuioostatus Hall
Spirifer koo'kuk Hilll
. Spirifer rostellatus ;Hall
Reticularia pseudolfueata (Hall)
Cliothyridina obma.-a.ma (McChesney)
GASTROPODAt-
Straparollus sp. Platyceras 8p_
List of fossils from bed ~ of Keokuk li1nestone in Bentonsport area. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Zaphrelltis varsoviensis . Worthen
Zaphrentis gp. Amplexus sp. Palaeacis obtusus (M. and W_ )
CRINOIDEA-
Dorycrinus sp. Actinocrinus f sp. BRYOZOA-
Meekopora sp. Cystodictya sp. BRACurOPODA-
Orthotetes , sp. Schuchertella ~ sp. Productus wortheni HraJJ. ,
Productus mesialis Hall
Productus sp. Pustula alternata (N. and P.)
Pustula sp. RhipidJomella dnbia (Hall)
Tetracaanera sUbtrigona (M. and W.)
Dielasma sp. Spirifer tenuicostatus Hall
Spirifer logani Hall
. Spirifer keokuk Hall
Spirifer cf. S. keokuk Hall
Spirifer sp. Brachythyris suborbi<lularis (Hall)
Syringothyris subcuspidatus (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliama (Hall)
Cliothyridin,a incrassata (Hall) T
Cliothyridina sp. GASTROPODA-
Platyceras sp. Platycer31s sp. TRILOBITA-
Griffithides f sp. VERTEBRATA-
Fish teeth Spiriferilla Sp. PELECYPODA-
Delthyris f sp. AviculopeeteIIJ ct. A. oblongus (M •. Spirifer l100tellrutus Hall
amd W.)
Spirifer cf. S. Jreokuk Hall
Allorisma sp. Pseudosyrinx keokuk Weller
GASTROPODA-
Reticularia pseudolineata (Hall)
Platyceras sp. Cliothyridina obmaxima (McChesney) CEPHALOPODA-
Orthoceras sp. PELECYPODA-
A i
l Spirifer cf. S. Jreokuk Hall
Allorisma sp. Pseudosyrinx keokuk Weller
GASTROPODA-
Reticularia pseudolineata (Hall)
Platyceras sp. Cliothyridina obmaxima (McChesney) CEPHALOPODA-
Orthoceras sp. KEOKUK FOSSILS AT BENTONSPORT and H.)
Amplexus sp. BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Fenestella cingulata Ulrich
Fenestella sp. Hemitrypa sp. Cystodictya sp. Worthenopora spinosa Ulrich
C
l
'
Productus cf. P . setigerus Hall
Productus sp. Productus sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Pustula sp. RhipidomeUa dubia (Hall)
Tetracamera sp. Dielasma sp. Spirifer rostellatus Hall
Spirifer sp. Brachythyris suborbicularis (Hall)
Spiriferella neglecta (Hall) MISSISSIPPIAN STRATA OF IOWA 172 KEOKUK FOSSILS AT BENTONSPORT Spirifer rostellatus ;Hall
Reticularia pseudolfueata (Hall)
Cliothyridina obma.-a.ma (McChesney)
GASTROPODAt-
Straparollus sp. Platyceras 8p_ Pustula alternata (N. and P.)
P
t l Straparollus sp. Pl t
8 Platyceras 8p_ Pustula sp. List of fossils from bed ~ of Keokuk li1nestone in Bentonsport area. f f
f
f
p
ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Zaphrelltis varsoviensis . Worthen
Zaphrentis gp. Amplexus sp. Palaeacis obtusus (M. and W_ )
CRINOIDEA-
Dorycrinus sp. Actinocrinus f sp. BRYOZOA-
Meekopora sp. Cystodictya sp. BRACurOPODA-
Orthotetes , sp. Schuchertella ~ sp. Productus wortheni HraJJ. ,
Productus mesialis Hall
Productus sp. Pustula alternata (N. and P.)
Pustula sp. RhipidJomella dnbia (Hall)
Tetracaanera sUbtrigona (M. and W.)
Dielasma sp. Spirifer tenuicostatus Hall
Spirifer logani Hall
. Spirifer keokuk Hall
Spirifer cf. S. keokuk Hall
Spirifer sp. Brachythyris suborbi<lularis (Hall)
Syringothyris subcuspidatus (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliama (Hall)
Cliothyridin,a incrassata (Hall) T
Cliothyridina sp. GASTROPODA-
Platyceras sp. Platycer31s sp. TRILOBITA-
Griffithides f sp. VERTEBRATA-
Fish teeth 172
MISSISSIPPIAN STRATA OF IOWA
List of fossils from bed 10 of Keohlk limestone in Bentonsport Mea. ANTHOZOA-
Amplexus sp. BRYOZOA-
Rhombopora varians Ulrich
Cyclopora sp. Worthenopora spinosa Ulrich
. BRACHIOPODA-
Schuchertella f sp. Orthotetes keokuk (Hall)
Productus setigerus Hall
Productus ovatus Hall
Productus sp. Productus sp. Pustula alternata (N. and P .)
Pustula sp. Pustula sp. Rhipidoroolla dubia (Hall)
Tetracamera subtrigona (M. and W.)
Cranaena sulcata Weller ,
Dielasma sinua,ta Weller
Dielasma sp. Spirifer tenuicosta.tus Hall
Spirifer rostellatus Hall
Spirifer sp. Spirifer sp. Spirifer sp . Spirifer sp. Brachythyris ~uborbicularis (Hall)
Syringothyris , sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall) ,
Clio.thyridina parvirostris (M. and W.)
Composita , sp. PELECYPODA-
Aviculopecten sp. A~iculopecten sp. GASTROPODA-
Orthonychia sp. List of fossils from bed 11 of K e07cuk IVmeston~ iIro Bentonsp01·t area. ANTHOZOA.,..... Palaeacis obtmms (M. and W.)
CRINOIDF..A-
Dorycrinus sp. BRYOZOA-
Stenopora sp. Hemitrypa sp. Cystodictya sp. BRACHIOPODA-
Schuchertella sp. Productus setigerus Hall
Productus wortheni Hall
Productus ovatus Hall
Productus sp. Avonia sp. Avonia sp. Pustula biseriata (Hall)
Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetracamera subtrigona (M. and W.)
Rhynchopora sp. DieJasma sp. Dielasma sp. Spiriferina , sp. Spirifer keokuk Hall
Spirifer sp. Spirifer sp. Spirifer sp. Spirifer sp. Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall)
GASTROPODA-
Orthonychia sp. VERTEBRATA-
Fish teeth
List of fossils from bed 12 of Keokuk limestone in Bentonsport area. ANTHOZOA-
Zaphrentis illinoisensis Worthen ,
Triplophyllum dalei (M.-E. List of fossils from bed 10 of Keohlk limestone in Bentonsport Mea.
i l List of fossils from bed 10 of Keohlk limestone in Bentonsport Mea. ANTHOZOA-
Amplexus sp. BRYOZOA-
Rhombopora varians Ulrich
Cyclopora sp. Worthenopora spinosa Ulrich
. BRACHIOPODA-
Schuchertella f sp. Orthotetes keokuk (Hall)
Productus setigerus Hall
Productus ovatus Hall
Productus sp. Productus sp. Pustula alternata (N. and P .)
Pustula sp. Pustula sp. Rhipidoroolla dubia (Hall)
Tetracamera subtrigona (M. and W.)
Cranaena sulcata Weller ,
Dielasma sinua,ta Weller
Dielasma sp. Spirifer tenuicosta.tus Hall
Spirifer rostellatus Hall
Spirifer sp. Spirifer sp. Spirifer sp . Spirifer sp. Brachythyris ~uborbicularis (Hall)
Syringothyris , sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall) ,
Clio.thyridina parvirostris (M. and W.)
Composita , sp. PELECYPODA-
Aviculopecten sp. A~iculopecten sp. GASTROPODA-
Orthonychia sp. List of fossils from bed 10 of Keohlk limestone in Bentonsport Mea. ANTHOZOA-
Amplexus sp. BRYOZOA-
Rhombopora varians Ulrich
Cyclopora sp. Worthenopora spinosa Ulrich
. BRACHIOPODA-
Schuchertella f sp. Orthotetes keokuk (Hall)
Productus setigerus Hall
Productus ovatus Hall
Productus sp. Productus sp. Pustula alternata (N. and P .)
Pustula sp. Pustula sp. Rhipidoroolla dubia (Hall)
Tetracamera subtrigona (M. and W.)
Cranaena sulcata Weller ,
Dielasma sinua,ta Weller
Dielasma sp. Spirifer tenuicosta.tus Hall
Spirifer rostellatus Hall
Spirifer sp. Spirifer sp. Spirifer sp . Spirifer sp. Brachythyris ~uborbicularis (Hall)
Syringothyris , sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall) ,
Clio.thyridina parvirostris (M. and W.)
Composita , sp. PELECYPODA-
Aviculopecten sp. A~iculopecten sp. GASTROPODA-
Orthonychia sp. Dielasma sp. S i if
i List of fossils from bed 11 of K e07cuk IVmeston~ iIro Bentonsp01·t area. Rhipidomella dubia (Hall)
Tetracamera subtrigona (M. and W. Rhynchopora sp. DieJasma sp. Dielasma sp. Spiriferina , sp. Spirifer keokuk Hall
Spirifer sp. Spirifer sp. Spirifer sp. Spirifer sp. Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall)
GASTROPODA-
Orthonychia sp. VERTEBRATA-
Fish teeth ANTHOZOA.,..... Palaeacis obtmms (M. and W.)
CRINOIDF..A-
Dorycrinus sp. BRYOZOA-
Stenopora sp. Hemitrypa sp. Cystodictya sp. BRACHIOPODA-
Schuchertella sp. Productus setigerus Hall
Productus wortheni Hall
Productus ovatus Hall
Productus sp. Avonia sp. Avonia sp. Pustula biseriata (Hall)
Pustula alternata (N. and P.) Pustula alternata (N. and P.) List of fossils from bed 12 of Keokuk limestone in Bentonsport area. List of fossils from bed 12 of Keokuk limestone in Bentonsport area. ANTHOZOA-
Zaphrentis illinoisensis Worthen ,
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Fenestella cingulata Ulrich
Fenestella sp. Hemitrypa sp. Cystodictya sp. Worthenopora spinosa Ulrich
Cyclopora ' . sp. List of fossils from bed 10 of Keohlk limestone in Bentonsport Mea.
i l BRACHIOPODA-
SchucherteJla , sp.·
Schuchertella , sp. Productus setigerus Hall
Productus cf. P . setigerus Hall
Productus sp. Productus sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Pustula sp. RhipidomeUa dubia (Hall)
Tetracamera sp. Dielasma sp. Spirifer rostellatus Hall
Spirifer sp. Brachythyris suborbicularis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria sp. Cliothyridina parvirostris (M.lIJThd W.) limestone in Bentonsport area. Productus cf. P . setigerus Hall
Productus sp. Productus sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Pustula sp. RhipidomeUa dubia (Hall)
Tetracamera sp. Dielasma sp. Spirifer rostellatus Hall
Spirifer sp. Brachythyris suborbicularis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria sp. Cliothyridina parvirostris (M.lIJThd W.) limestone in Bentonsport area. Productus cf. P . setigerus Hall
Productus sp. Productus sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Pustula sp. RhipidomeUa dubia (Hall)
Tetracamera sp. Dielasma sp. Spirifer rostellatus Hall
Spirifer sp. Brachythyris suborbicularis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria sp. Cliothyridina parvirostris (M.lIJThd W.) ANTHOZOA-
Zaphrentis illinoisensis Worthen ,
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Fenestella cingulata Ulrich
Fenestella sp. Hemitrypa sp. Cystodictya sp. Worthenopora spinosa Ulrich
Cyclopora ' . sp. BRACHIOPODA-
SchucherteJla , sp.·
Schuchertella , sp. Productus setigerus Hall ANTHOZOA-
Zaphrentis illinoisensis Worthen ,
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Fenestella cingulata Ulrich
Fenestella sp. Hemitrypa sp. Cystodictya sp. Worthenopora spinosa Ulrich
Cyclopora ' . sp. BRACHIOPODA-
SchucherteJla , sp.·
Schuchertella , sp. Productus setigerus Hall 173 FAUNA OF KEOKUK BEDS List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. Orthotetes keokuk (Hall)
Productus setigerus Hall
Productus ovatus Hall
Productus cf. P. altonensis Welle
Productus sp. Productus sp. Pustula altemata (N. and P.)
Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Spirifer toouicostatus Hall
Spirifer keokuk Hall
Spirifer sp. Spirifer sp. Reticularia pseudolinea ta (Hall)
EUDletria verneuiliana
(Hall)
Eumetria f sp. Composita trinuclea (Hall)
PELECYPODA-
Conocardium sp. Mvalina keokuk Worthen
TRILOBITA-
Griffithides f sp. eokuk limestone in Bentonsport area. Productus cf. P. altonensis Welle
Productus sp. Productus sp. Pustula altemata (N. and P.)
Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Spirifer toouicostatus Hall
Spirifer keokuk Hall
Spirifer sp. Spirifer sp. Reticularia pseudolinea ta (Hall)
EUDletria verneuiliana
(Hall)
Eumetria f sp. Composita trinuclea (Hall)
PELECYPODA-
Conocardium sp. Mvalina keokuk Worthen
TRILOBITA-
Griffithides f sp. ANTHOZOA-
Palaea.cis obtusus
(~r. and W.)
Zaphrentis varsoviensis 'Worthen f
Triplophyllum dalei (M.·E. and H.)
Monilopora beecheri Grabau
BRYOZOA-
Meekopora sp. Stenopora sp. Leioclema punctatum (Rall)
Fooestella serratula Ulrich
Hemitrypa sp. Uystodictya sp. Cyclopora ~ sp. Cyclopora , sp. vVortheno'pora spinosa Ulrich
BRACHIOPODA-
Chonetes illinoisensis
Schuchertella sp. Orthotetes keokuk (Hall)
Productus setigerus Hall
Productus ovatus Hall Orthotetes keokuk (Hall)
Productus setigerus Hall Productus setigerus Hal
Productus ovatus Hall Productus ovatus Hal Ltst of fossils from bed 20 of Keokuk limestone in Bentonsport area. )
Camarotoechia mutata (Hall)
Rhy:nchopora beecheri Greger
Dielasma f sp. Dielasma f Ap. Girtyella indianensis (Girty)
Spirifer keokuk Hall
Spirifer cf. S. keokuk Hall
Spirifer teuuicostatus Hall
Reticularia pseudolineata (Hall)
Composita trinuclea (Hall)
GASTROPODA-
Orthonychia Ep_ ANTHOZOA-
Zaphrentis varsoviensis Worthen
Triplophyllum dalei (M.-E. and H .)
BRYOZOA-
Stenopora sp. Taeniodictya ramulosa Ulrich
BRACHIOPODA-
. Orthotetes keokuk (Hall)
Productus setigerus Hall
Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Rhy:nchopora beecheri Greger
Dielasma f sp. Dielasma f Ap. Girtyella indianensis (Girty)
Spirifer keokuk Hall
Spirifer cf. S. keokuk Hall
Spirifer teuuicostatus Hall
Reticularia pseudolineata (Hall)
Composita trinuclea (Hall)
GASTROPODA-
Orthonychia Ep_ Zaphrentis varsoviensis Worthen
Triplophyllum dalei (M E
and Triplophyllum dalei (M.-E. and H .)
BRYOZOA-
Stenopora sp Taeniodictya ramulosa Ulrich
BRACHIOPODA Orthotetes keokuk (Hall)
Productus setigerus Hall Productus setigerus Hall
Pustula alternata (N an Pustula alternata (N. and P.)
Pustula biseriata (Hall) Pustula biseriata (Hall
Rhipidomella dubia (Ha Rhipidomella dubia (Hall Henry County . 26 Iowa Gool. Survey. vol. XII, PI). 256-258; 1902. Seotion of ,K,eo7ctlk limestone near Webster s mill.
FEET
INCHES
19. Limestone, bluish ' gray, medium-grained, upper part gra,y,
very cherty; filled with bryozoans _______________________________________________
8
18. Limestone, as above, with fish teeth ________________ . ____ . ___________ .__________
3
17. Shale, soft, bluish, argillaceous _________________ . __ . ____ ._________________ ________
10
16. Limestone, bluish gray ____ . _________________________________________ . _______________ ._
4
26 I
G
l
S
l
XII
PI)
256 258
1902 FEET
INCHES
19. Limestone, bluish ' gray, medium-grained, upper part gra,y,
very cherty; filled with bryozoans _______________________________________________
8
18. Limestone, as above, with fish teeth ________________ . ____ . ___________ .__________
3
17. Shale, soft, bluish, argillaceous _________________ . __ . ____ ._________________ ________
10
16. Limestone, bluish gray ____ . _________________________________________ . _______________ ._
4 Seotion of ,K,eo7ctlk limestone near Webster's mill. List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. ANTHOZOA-
Amplexus
~ sp. CRINOIDEA-
Agaricocrinus EIp. Platycrinus , sp. BRYOZOA-
Meekopora , sp. Leioclema punctla.tum (Hall)
F ellestell a serratula Ulrich
F€:IIestella (several species)
Cystodictya (several species)
Worthenopora spinosa Ulrich
BRACHIOPODA-
Schuchertella , sp. Productus setigerus Hall f
Productus sp. Avonia sp. Pustula biseria.ta (Hall)
Pustula sp. Pustula biseria.ta (Hall)
P
l Pustula sp. List of fossils from bed 14 of Keokuk limestone iIn Bentonsport arM. BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Cystodictya sp. B'RACHIOPODA-
Pl'ocluctus setigerus Hall
Productus sp. Pustula sp. Rhipidomella clubia (Hall)
Dielasma , sp. Spirifer tenuicostatus Hall
Spirifer sp. Reticularia pseudolineata (Hall)
Cliothyriclina panirostl'is (M. and W
GAS'l'ROPODA-
Orthonychia sp. Platyceras sp. TRILOBITA-
Griffithides f sp. VER'.rEDRATA-
F ish teeth BRYOZOA-
Stenopora sp. Fenestella serratula Ulrich
Cystodictya sp. B'RACHIOPODA-
Pl'ocluctus setigerus Hall
Productus sp. Pustula sp. Rhipidomella clubia (Hall)
Dielasma , sp. Spirifer tenuicostatus Hall Spirifer sp. Reticularia pseudolineata (Hall)
Cliothyriclina panirostl'is (M. and W.)
GAS'l'ROPODA-
Orthonychia sp. Platyceras sp. TRILOBITA-
Griffithides f sp. VER'.rEDRATA-
F ish teeth Fenestella serratula Ulrich
C
t di t List of fossils from bed 15 of Keoku7c limestone in B C'TIJtonsport area. ANTHOZOA-
Molliilopora beecheri Grabau
Palaeacis obtnsus (M. and W.)
BRACruOPODA-
,~chuchertella sp. Proclnctus setigerus Hall
Productus ovatns Hall
Procluctus sp. Productns sp. Prodnctus sp. Productus sp. Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Rhynchopora beecheri Greger
Spirifer tenuicostatus Hall
Spirifer keokuk Hall
Reticularia pseudolineata (Hall)
PELECYPODA-
Myalina keokuk Worthen
Lithophagus illinoisensis Worthen
TRILOBITA-
Griffithides f sp. List of fossils from bed 16 of KeoHn£k lillnestone in B ento'TlJ8port area. List of fossils from bed 16 of KeoHn£k lillnestone in B ento'TlJ8port area. ANTHOZOA-
Palaeacis obtnsns r.M. and W. ~
Triplophyllum clalei (M.-E. and H.)
BRYOZOA-
Sten<lpora , sp. Fenestella serratula Ulrich
BRACHIOPODA-
Orthotetes keokuk (Hall)
Productus sp. Rhipidomella dubia (Hall)
Dielasma sp. Spirifer cf_ S. keokuk Hall
Spirifer tenuicostatus Hall
Composita trinuclea (Hall)
GASTROPODA-
Orthonychia sp. MISSISSIPPIAN STRATA OF row A 174 List of fossils from bed 18 of Keokuk limestone in Bentonsport area. List of fossils from bed 18 of Keokuk limestone in Bentonsport area. ANTHOZOA-
Palaea.cis obtusus
(~r. and W.)
Zaphrentis varsoviensis 'Worthen f
Triplophyllum dalei (M.·E. and H.)
Monilopora beecheri Grabau
BRYOZOA-
Meekopora sp. Stenopora sp. Leioclema punctatum (Rall)
Fooestella serratula Ulrich
Hemitrypa sp. Uystodictya sp. Cyclopora ~ sp. Cyclopora , sp. vVortheno'pora spinosa Ulrich
BRACHIOPODA-
Chonetes illinoisensis
Schuchertella sp. ,
g
y
___ 18. Limestone, as above, with fish teeth ________________ . ____ . ___________ .__
17.
Shale, soft, bluish, argillaceous
. .
. BRACHIOPODA-
Pustula biseriata (Hall)
Spirifer keokuk Hall List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. 1
175
4
2
6
10
6
2
6
Collections made from the various beds were identified as
ollows :
List of fossils fr01n bed 1 of K eokuk limest01!!e near Webster's mill. RACHIOPODA-
Spirifer keokuk Hall
Pustula alternata (N. an'd P.)
Reticularia pseudolineata (Hall)
Spirifer logani Hall
List of fossils from bed 3 of
NTHOZOA-
Amplexus sp. RACHIOPODA-
Ke07cu7c lilln.est01te near Webster's mill. Pustula nlternata (N. and P.)
Orthotetes keokuk (Hall) ,
Tetracamera sp 15. Sha:1e, soft, bluish, argillaceous ..................... _ .................... _......... 1
14. Limestone, bluish gray, medium· grained, weathering into thin
la;yers ....... _ .................................... _ ... _................................................. 4
13. Shale, bluish, argillaceous ... _ .... _ ........ _ ............................ _............. 1
12. Limestone,. dark gray, medium· grained ... _ .................................... . 11. Shale, and gray sub crystalline limestone in alternating layers. The limestone is filled with bryozoans ......... _ .... _ .... _ .... _ .... _ .... _. 7
10. Limestone, gray, subcrystalline, with wavy boundaries .... _ .. _._... 1
9. Shale, bluish, argillaceous above . but calcareous below. No
fossils noted ............... _ .... _ ................ _............................................... 4
8. Limestone, gray, subcrystalline and cherty above; bluish gray
and medium· grained below ............................................... _............. 3
7. Shale, bluish, argillaceous ............... _.................................................. 1
6. Lim€stone, gray and 'subcrystalline above but bluish and
coarse· grained below; shaly in middle part; with a band of
fine·grained, chert.y limestone 3 to 10 inches thick in lower part 4
5. Shale, bluish, argillaceous ................................................................ 1
4. Limestone, ash· colored, soft, impure, dolomitic, nonfossiliferous
7
3. Limestone, bluish gray, medium· grained, contact with bed
above not Been .......................................................................... 2 to
3
2. Shale, bluish, argillaceous ..................... _ .... _ ........ _ .. _....................... 8
1. Limestone, gray, medium·grained, with a band of chert at the
top ................................................... _ ........... _ ...................... _................. 1
4
2
6
10
6
2
6
Collections made from the various beds were identified as
ollows : 15. Sha:1e, soft, bluish, argillaceous
14
Li
bl i h
di 13. Shale, bluish, argillaceous . 12
Li
t
d
k
di 1. Limestone, gray, medium·grained, with a band of chert at the
top ................................................... _ ........... _ ...................... _................. 1 Collections made from the various beds were identified as
follows : Collections made from the various beds were identified as
follows : List of fossils fr01n bed 1 of K eokuk limest01!!e near Webster's mill. List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. ..-The only exposures of the Keokuk limestone
of importance in Henry county appear along a creek emptying
into Skunk river from the south, a short distanc.e west of Web-
ster's mill in the western part of section 4 of Jackson township. This section has been described previously by Savage26 in his
Geology of Henry County. Fifty-two feet of Keokuk "limestone
overlain by impure limestones and shales of the Lower Warsaw
(Geode bed) is exposed along this creek. The section is given
below. Seotion of ,K,eo7ctlk limestone near Webster's mill. FEET
INCHES
19. Limestone, bluish ' gray, medium-grained, upper part gra,y,
very cherty; filled with bryozoans _______________________________________________
8
18. Limestone, as above, with fish teeth ________________ . ____ . ___________ .__________
3
17. Shale, soft, bluish, argillaceous _________________ . __ . ____ ._________________ ________
10
16. Limestone, bluish gray ____ . _________________________________________ . _______________ ._
4
26 Iowa Gool. Survey. vol. XII, PI). 256-258; 1902. KEOKUK FOSSILS AT WEBSTER'S MILL 175 KEOKUK FOSSILS AT WEBSTER'S MILL
15. Sha:1e, soft, bluish, argillaceous ..................... _ .................... _......... 1
14. Limestone, bluish gray, medium· grained, weathering into thin
la;yers ....... _ .................................... _ ... _................................................. 4
13. Shale, bluish, argillaceous ... _ .... _ ........ _ ............................ _............. 1
12. Limestone,. dark gray, medium· grained ... _ .................................... . 11. Shale, and gray sub crystalline limestone in alternating layers. The limestone is filled with bryozoans ......... _ .... _ .... _ .... _ .... _ .... _. 7
10. Limestone, gray, subcrystalline, with wavy boundaries .... _ .. _._... 1
9. Shale, bluish, argillaceous above . but calcareous below. No
fossils noted ............... _ .... _ ................ _............................................... 4
8. Limestone, gray, subcrystalline and cherty above; bluish gray
and medium· grained below ............................................... _............. 3
7. Shale, bluish, argillaceous ............... _.................................................. 1
6. Lim€stone, gray and 'subcrystalline above but bluish and
coarse· grained below; shaly in middle part; with a band of
fine·grained, chert.y limestone 3 to 10 inches thick in lower part 4
5. Shale, bluish, argillaceous ................................................................ 1
4. Limestone, ash· colored, soft, impure, dolomitic, nonfossiliferous
7
3. Limestone, bluish gray, medium· grained, contact with bed
above not Been .......................................................................... 2 to
3
2. Shale, bluish, argillaceous ..................... _ .... _ ........ _ .. _....................... 8
1. Limestone, gray, medium·grained, with a band of chert at the
top ................................................... _ ........... _ ...................... _................. BRACHIOPODA-
Productus sp.
Ortho-tetes keokuk (Hall )
Rhipidomella dubia (Hall)
Dielasma sp. 27 Iowa Geol. Survey. vol. XI, pp. 72-89; 1901. List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. Leioclema punctatum (Hall)
Cystodictya pustulosa Ulrich
Cystodictya lineata Ulrich
Phractopora trifolia (Rominger)
Bactropora simplex Ulrich
Rhombopora attenuata Ulrich
Rhombopora transversalis Ulrich
Streblotrypa major Ulrich
Streblo.trypa radialis Ulrich
Fenestella tenax Ulrich
F enestella multi spinosa Ulrich
F enestella rudis Ulrich
F enestella limitaris Ulrich
Fenestella serratula Ulrich
Hemitrypa sp. PolypOIw simulatrix Ulrich
Polypora radialis Ulrich
Worthenopora spinosa Ulrich
BRACHIOPODA---'
Productus setigerus Hall
Camarotoechia mutata (Hall)
Spiriferina sp. Spirifer tenuicostatus Hall
Cliothyridina parvirostris (M. ana W.)
TRILOBITA-
Griffithidcs portlocki (M. and W.) , List of fossils frorn bed 11 of Keokuk limestone near Webster's mill. ANTHOZOA-
Zaphrentis varsoviensis Worthen
Triplophyllum dalei (M.-E. and H .)
Amplexus sp. Monilopora bee cheri Grabau
BRYOZOA-
Stenopora sp. Leioclema punctatum (Hall)
Cystodictya pustulosa Ulrich
Cystodictya lineata Ulrich
Phractopora trifolia (Rominger)
Bactropora simplex Ulrich
Rhombopora attenuata Ulrich
Rhombopora transversalis Ulrich
Streblotrypa major Ulrich
Streblo.trypa radialis Ulrich
Fenestella tenax Ulrich
F enestella multi spinosa Ulrich
F enestella rudis Ulrich
F enestella limitaris Ulrich
Fenestella serratula Ulrich
Hemitrypa sp. PolypOIw simulatrix Ulrich
Polypora radialis Ulrich
Worthenopora spinosa Ulrich
BRACHIOPODA---'
Productus setigerus Hall
Camarotoechia mutata (Hall)
Spiriferina sp. Spirifer tenuicostatus Hall
Cliothyridina parvirostris (M. ana W.)
TRILOBITA-
Griffithidcs portlocki (M. and W.) , ANTHOZOA-
Zaphrentis varsoviensis Worthen
Triplophyllum dalei (M.-E. and H .)
Amplexus sp. Monilopora bee cheri Grabau
BRYOZOA-
Stenopora sp. Leioclema punctatum (Hall)
Cystodictya pustulosa Ulrich
Cystodictya lineata Ulrich
Phractopora trifolia (Rominger)
Bactropora simplex Ulrich
Rhombopora attenuata Ulrich
Rhombopora transversalis Ulrich
Streblotrypa major Ulrich
Streblo.trypa radialis Ulrich
Fenestella tenax Ulrich F enestella multi spinosa Ulrich p
F enestella rudis Ulrich y
p
(
)
TRILOBITA-
Griffithidcs portlocki (M. and W.) , Griffithidcs portlocki (M. and W.) , List of fossils from bed 12 of Keokuk limestone neal' Webster's mill. List of fossils from bed 12 of Keokuk limestone neal' Webster's mill. Camarotoechia mutata (Hall)
Rhipidomella dubia (Hall)
Dielasma sp. Spirifcr keokuk Hall
Reticu!.aria pseudolineata (Hall) Camarotoechia mutata (Hall)
Rhipidomella dubia (Hall)
Dielasma sp. Spirifcr keokuk Hall
Reticu!.aria pseudolineata (Hall) Palaeacis obtusus (M. and W.) Zaphrentis varsoviensis Worthen BRACHIOPODA- Productus sp. List of fossils frCYm bed 14 of Keok'u7c limestone near Webster's mill. List of fossils frCYm bed 14 of Keok'u7c limestone near Webster's mill. ANTJIOZOA-
Zaphrentis sp. BRYOZOA-
LeiQdema punctatum (Hall)
Fenestella. ten ax Ulrich
Fenestella serratula Ulrich
Cystodictya lineata Ulrich
BRACHIOPODA--
Orthotetes keokuk (Hall)
Pustula a.lternata (N. a
Rhipidomella dubia (Ha
Dielasma f sp. Dielasma sp. Spirifer tenuicostatus
Eumetria verneuiliana
Cliothyridin:a incrassata
Composita trinuclea (H ANTJIOZOA-
Zaphrentis sp. BRYOZOA-
LeiQdema punctatum (Hal
Fenestella. ten ax Ulrich
Fenestella serratula Ulrich
Cystodictya lineata Ulrich
BRACHIOPODA--
Orthotetes keokuk (Hall) Pustula a.lternata (N. and P.)
Rhipidomella dubia (Hall)
Dielasma f sp. Dielasma sp. Spirifer tenuicostatus Hall
Eumetria verneuiliana (Hall)
Cliothyridin:a incrassata (Hall)
Composita trinuclea (Hall) , LeiQdema punctatum (Hall)
F
ll
Ul i h Fenestella. ten ax Ulrich
ll
l
l Fenestella serratula Ulrich
C
di
li
Ul i h Cystodictya lineata Ulrich
BRACHIOPODA-- Cystodictya lineata Ulrich BRACHIOPODA-- BRACHIOPODA--
Orthotetes keokuk (Hall) Orthotetes keokuk (Hall) List of fossils from bed 19 of Keo'Hntk limewtone near Webster's mill. Rhombopora attenuata Ulrich
Stenopora sp. BRAcmoPoDA-
Productus setigerus Hall
Produetus sp. Pustula alterna.ta (N. and P.)
Dielasma sp. Spiriferina sp. Spirifer keokuk Hall ANTHOZOA-
Monilopora beeched Grabau Rhombopora attenuata Ulrich
Stenopora sp. BRAcmoPoDA-
Productus setigerus Hall
Produetus sp. Pustula alterna.ta (N. and P.)
Dielasma sp. Spiriferina sp. Spirifer keokuk Hall List of fossils from bed 19 of Keokuk lillnestone iIn BentlJ'lWport area. BRACHIOPODA-
Spirifer keokuk Hall
Pustula alternata (N. an'd P.)
Reticularia pseudolineata (Hall)
Spirifer logani Hall
List of fossils from bed 3 of
ANTHOZOA-
Amplexus sp. BRACHIOPODA-
Productus mesialis Hall
List of fossils from bed 6 of
ANTHozOA-
Zaphrentis varsoviensis 'Worthen
Palae.aeis obtusu (M. and W.)
C!UNOIDEA-
Batocrinus sp. Dorycrinus sp. BRACHIOPODA-
Productus sp. Ke07cu7c lilln.est01te near Webster's mill. Pustula nlternata (N. and P.)
Orthotetes keokuk (Hall) ,
Tetracamera sp. Spirifer keokuk Hall
K eokuk limestone near Webster'~ mill. Pustula alternata (N. and P .)
Tetracamera sub trigona (M. and W.)
Rhipidomella dubia (Hall)
Brachythyris
cf. B. suborbicularis
(Hall)
Reticular-ia pseudolineata (Hall)
VEItTEBRATA-
Fish teeth
List of fossils fl·Q1n. bed 8 of Keokuk limestone near Webster'.7 mill. BRACHIOPODA-
Productus sp. Ortho-tetes keokuk (Hall )
Rhipidomella dubia (Hall)
Dielasma sp. Spiriferina sp. Spirifer rostellatus Hall
Spirifer cf. S. keokuk Hall
Cliothyridina parvirostris (M. & W.)'
List of f08sils from bed 10 of K eoklbk limestone near Webster's mill. BRACHIOPODA-
Pustula biseriata (Hall)
Spirifer keokuk Hall
Spirifer tenuicostatus Hall
Composita trinuclea (Hall) List of fossils fr01n bed 1 of K eokuk limest01!!e near Webster's mill. BRACHIOPODA-
Spirifer keokuk Hall
Pustula alternata (N. an'd P.)
Reticularia pseudolineata (Hall)
Spirifer logani Hall List of fossils from bed 3 of
ANTHOZOA-
Amplexus sp. BRACHIOPODA-
Productus mesialis Hall
Ke07cu7c lilln.est01te near Webster's mill. Pustula nlternata (N. and P.)
Orthotetes keokuk (Hall) ,
Tetracamera sp. Spirifer keokuk Hall Productus mesialis Hall List of fossils from bed 6 of
ANTHozOA-
Zaphrentis varsoviensis 'Worthen
Palae.aeis obtusu (M. and W.)
C!UNOIDEA-
Batocrinus sp. Dorycrinus sp. BRACHIOPODA-
Productus sp. K eokuk limestone near Webster'~ mill. Pustula alternata (N. and P .)
Tetracamera sub trigona (M. and W.)
Rhipidomella dubia (Hall)
Brachythyris
cf. B. suborbicularis
(Hall)
Reticular-ia pseudolineata (Hall)
VEItTEBRATA-
Fish teeth List of fossils fl·Q1n. bed 8 of Keokuk limestone near Webster'.7 mill. BRACHIOPODA-
Productus sp. Ortho-tetes keokuk (Hall )
Rhipidomella dubia (Hall)
Dielasma sp. List of f08sils from bed 10 of K eoklbk limestone near Webster's mill. BRACHIOPODA-
Pustula biseriata (Hall)
Spirifer keokuk Hall BRACHIOPODA-
Pustula biseriata (Hall)
Spirifer keokuk Hall MISSISSIPPIAN STRATA OF IOWA 176 List of fossils frorn bed 11 of Keokuk limestone near Webster's mill. ANTHOZOA-
Zaphrentis varsoviensis Worthen
Triplophyllum dalei (M.-E. and H .)
Amplexus sp. Monilopora bee cheri Grabau
BRYOZOA-
Stenopora sp. ANTHOZOA-
Monilopora beeched Grabau BRYOZOA- Leioclema punctatum (Hall)
F
ll
di
Ul i h Fenestella rudis Ulrich
F
ll
l
Ul i Fenestella serratula Ulrich
H
i Dielasma sp. i if
i Hemitrypa sp. Hemitrypa sp. Spiriferina sp. S i if
k
k Cystodictya lineata Ulrich
Rh
b
i
Ul i h Spirifer keokuk Hall Rhombopora varians Ulrich Louisa Co~~lnty.-Only the lowermost beds of the Keokuk
limestone, corresponding to the Montrose chert horizon, are
known to occur in Louisa county. These have been recognized
by Udden27 in a number of exposures. A section in a Honey creek quarry opening one-fifth mile up- 27 Iowa Geol. Survey. vol. XI, pp. 72-89; 1901. KEOKUK BEDS IN LOUISA COUNTY 177 stream from the main quarry, which is located near the north
line of the southwest quarter of section 28, Morning Sun town-
ship, has been measured and redescribed by the writer. Section of K eokuk limestone on Honey cTeek. Section of K eokuk limestone on Honey cTeek. FEET
INCHES
8. Drift ..................... _............................................................................... 1
7. Limestone, brownish yellow, soft, dolomitic, cherty; with oc·
casional layers and lenses of gray sub crystalline, nlondolomitic
fossiliferous limestone ............... _ ...................... _............................... 3
6
6. Limestone, gray, tough, crinoidal; with small irregular chert
nodules .................................................................................................. 10
5. Limestone, brownish yellow, so,ft, dolomitic, fine· grained, with
a chert band in the lower part ......... _........................................... 1
4
4. Limestone, gray, compact, tough, crinoidal .................................. 1
4
3. Limestone, soft, brownish, dolomitic, crinoidal in upper part 1
8
2. Shale, bluish, argillaceous ......... _ ............................ _....................... 10
1. Limestone, crinoidal, bluish with greenish specks below but
brownish and with soft fine· grained dolomitic seams above; a
chert band 2 to 8 inches thick in upper part ............................ 3 A few identifiable fossils collected from beds 1 and 7 are
listed below: List .of fossils fTom bed 1 of Keoku7c limestone on Honey creek. List .of fossils fTom bed 1 of Keoku7c limestone on Honey creek. ANTHOZOA-
Zaphl'entis sp. BRACHIOPODA-
Chonetes sp. Rhipidomella sp. Schizophoria sp. Spirifer tenuicostatus Hall
Spil'ifer gl'imesi Hall
Brachythyris sub orbicularis (Hall)
Cliothyridina sp. List of fossils tro'Yn bed 7 of K eokuk limestone on Honey creek. HRACHIOPODA-
Pl'oductus sp. Dielasma sp. Spirifer rostellatus HaJl
Spirifer sp. Reticula,ria pseudolineata (Hall)
Composita globosa Weller
Composita trinuclea (Hall) List .of fossils fTom bed 1 of Keoku7c limestone on Honey creek. ANTHOZOA-
Zaphl'entis sp. BRACHIOPODA-
Chonetes sp. Rhipidomella sp. Schizophoria sp. 28 Iowa Geol. Survey, vol. XI, p. 75; 1901.
29 Idem, p. 81. ANTHOZOA-
Monilopora beeched Grabau Spirifer tenuicostatus Hall
Spil'ifer gl'imesi Hall
Brachythyris sub orbicularis (Hall)
Cliothyridina sp. ANTHOZOA-
Zaphl'entis sp. BRACHIOPODA-
Chonetes sp. Rhipidomella sp. List of fossils tro'Yn bed 7 of K eokuk limestone on Honey cree List of fossils tro'Yn bed 7 of K eokuk limestone on Honey creek. HRACHIOPODA-
Pl'oductus sp. Dielasma sp. Spirifer rostellatus HaJl
Spirifer sp. Reticula,ria pseudolineata (Hall)
Composita globosa Weller
Composita trinuclea (Hall) Spirifer sp. Reticula,ria pseudolineata (Hall)
Composita globosa Weller
Composita trinuclea (Hall) HRACHIOPODA-
Pl'oductus sp. Dielasma sp. Spirifer rostellatus HaJl
Spirifer sp. Reticula,ria pseudolineata (Hall)
Composita globosa Weller
Composita trinuclea (Hall) HRACHIOPODA-
Pl'oductus sp. Dielasma sp. Spirifer rostellatus HaJl Spirifer sp. Reticula,ria pseudolineata (Hall)
Composita globosa Weller
Composita trinuclea (Hall) In the Elrick quarry located near the south county line on the
left bank of Smith. creek, Udden28 found twenty-two feet of
weathered limestone overlying the Upper Burlington. How-
ever, no fossils are listed by him from this exposure. Again
Udden29 reports fifteen feet of "weathered sh-aly limestone and
shale with cherty layers" of this horizon in an exposure along
Long creek in the southeast corner of section 33 of Columbus
tovvnship. . Th~ following section from Udden2"9, located in the south
bank of Long creek near the -West line in the northwest quarter MISSISSIPPIAN STRA'rA OF IOWA 178 of' section 32, Columbus township, also represents the basal
Keokuk. Section of Ke07ctbk limestone in section S!3, Colwmbus township (.AfPer Ydden). FEET
3. Shaly limestone .................................................................................. 5
2. Blue shale ............................................................................................ 1 Section of Ke07ctbk limestone in section S!3, Colwmbus township (.AfPer Ydden). FEET 3. Shaly limestone
2
Blue shale 2. Blue shale
1
Yellow lime 1. Yellow limestone, somewhat fin.e·gramed ........................................ K eokuk County.-Several exposures of the Keokuk limestone
have been reported from Keokuk county. The more important
ones appear along Rock creek northwest of Ollie. One of the
more typical of these, is shown in the "Granite" quarry in the
southwest quarter of the southeast quarter of section 10, J ack-
son township. Section of Keokuk limestone in "Grwnite" IJ:I.barry
FEET
lNCHES
8. Concealed. With chips of soft brownish dolomitic lln1estone on
slope. Indications of bluish argillaceous shale in upper part. PrOibably consists of shale with interbedded layers of hI·own·
ish dolomitic limestone ...................................................................... 8
7. Limestone, brownish, soft, dolomitic, cherty.............................. 1
10
6. ConceaJed, chips 'of soft brownish dolomitic limestone on slope 7
10
5. List of fossils from bed 8 of
BRYOZOA-
Ke07cuk
li1?~estone in "Granite"
Stl'eblotrypa sp.
quarry.
Leioclema punctatum (Hall)
Rhombopora va:riaJIs Ulrich
Fenesteila sp.
F enestella 8p
BRACHIOPODA-
Orthotetes f sp.
Spirife:r sp. Section of Keokuk limestone in "Grwnite" IJ:I.barry 3. Shaly limestone
2
Blue shale ANTHOZOA-
Monilopora beeched Grabau Limestone, soft, brownish, dolomitic, with irreg1!lar bands of
compact gray chert ............................................................................ 3
6
4. Shale, bluish, argillaceous ................................................................ 3
6
3. Limestone, bluish gray, coarse-grained .......................................... 2
7
2. Shale, bluish, argillaceous ................................................................ 2
1. Limestone, bluish gray, coarse'grained, crinoidal; in rather
heavy layers. Top layer weathering into thin shaly sooms ........ 5 3. Limestone, bluish gray, coarse-grained ................................. 2
Shale
bluish
argillaceous 2. Shale, bluish, argillaceous ................................................................ 1
Limestone
bluish gray
coarse'grained
crinoidal;
in
rather 1. Limestone, bluish gray, coarse'grained, crinoidal; in rather
heavy layers
Top layer weathering into thin shaly sooms
5 Collections were made from beds 1 and 8. These have been
identified as follows : List of fossils from bed 1 of Keok1~k lwnestone in "Granite" .qua?·ry. ANTHOZOA-
Triplophyllum dalei (M.·E. and H.)
Zaphrentis vJ)..rsoviensis Worthen
Palaoocis obtusus (M. and W.)
CRINOIDEA-
Platycrinus sp. B RACHIOPODA-
Orthotetes keokuk (Hall)
Productus sp. Pustula alternata (N. and P.)
Rhipiclomella dubia (Hall)
Girt yell a indianensis (Girty)
Spirifer keokuk Hall
Spil'ifer rostellatus Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
Clio,thyric1ina parvil'ostris (11. 2.nd W.)
Cliothyridina incrassata (Hall)
PELECYPODA-
Conoca:rdium sp. GASTItOPODA-
Platyceras sp. Platyceras sp. TRILOBITA-
Griffi thides f sp. List of fossils from bed 1 of Keok1~k lwnestone in "Granite" .qua?·ry. ANTHOZOA-
Triplophyllum dalei (M.·E. and H.)
Zaphrentis vJ)..rsoviensis Worthen
Palaoocis obtusus (M. and W.)
CRINOIDEA-
Platycrinus sp. B RACHIOPODA-
Orthotetes keokuk (Hall)
Productus sp. Pustula alternata (N. and P.)
Rhipiclomella dubia (Hall)
Girt yell a indianensis (Girty)
Spirifer keokuk Hall
Spil'ifer rostellatus Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
Clio,thyric1ina parvil'ostris (11. 2.nd W.)
Cliothyridina incrassata (Hall)
PELECYPODA-
Conoca:rdium sp. GASTItOPODA-
Platyceras sp. Platyceras sp. TRILOBITA-
Griffi thides f sp. List of fossils from bed 8 of
BRYOZOA-
Ke07cuk
li1?~estone in "Granite"
Stl'eblotrypa sp. quarry. Leioclema punctatum (Hall)
Rhombopora va:riaJIs Ulrich
Fenesteila sp. F enestella 8p. BRACHIOPODA-
Orthotetes f sp. Spirife:r sp. Triplophyllum dalei (M.·E. and H.)
Zaphrentis vJ) rsoviensis Worthen Pustula alternata (N. and P.)
Rhipiclomella dubia (Hall) Rhipiclomella dubia (Hall
Girtyella indianensis (Gir Girt yell a indianensis (Girty
Spirifer keokuk Hall Spirifer keokuk Hall List of fossils from bed 8 of
BRYOZOA-
Ke07cuk
li1?~estone in "Granite"
Stl'eblotrypa sp. quarry. Leioclema punctatum (Hall)
Rhombopora va:riaJIs Ulrich
Fenesteila sp. F enestella 8p. BRACHIOPODA-
Orthotetes f sp. Spirife:r sp. Leioclema punctatum (Hall)
Rhombopora va:riaJIs Ulrich Rhombopora va:riaJIs Ulrich
Fenesteila sp Fenesteila sp. F enestella 8p F enestella 8p. Seotion (}f Keokuk beds in secti<m 10, Jaokson lIownship. ANTHOZOA-
Monilopora beeched Grabau KEOKUK FOSSILS IN KEOKUK COUNTY 179 Three hundred yards south of the above section a small
abandoned quarry opening shows several beds of the Upper St. Louis. The hasal bed of the section lies about twenty-two feet
above the level of the top of bed 8 of the" Granite" quarry. It
is believed that the Lower St. Louis limestone occupies the con-
cealed interval between the two beds and that the latter forma-
tion succeeds the Keokuk formation directly, the Warsaw beds
and the Spergen limestone being absent in this area. Less than half a mile north of the" Granite" quarry a good
exposure of the Keokuk beds appears in the north bank of Rock
creek, just west of the wagon bridge, in the northeast qua:rter
of the southwest quarter of section 10, Jackson township. Seotion (}f Keokuk beds in secti<m 10, Jaokson lIownship. FEET
INCHES
11. Drift ..................... _ ................ _ ...................... _ ...................... _............. 1
10. Limestone, buff, dolomitic, soft, rotten, with chert bands. Bed 5 'of "granite" quarry section ......... _ .... __ .. _ ....... _. __ ._........... 3
9. Shale, bluish, argillaceous. Bed 4 of "granite" quarry seCJtiOOl
2
6
8. Limestone, bluish gray, coarse-grained except in middle part,
which. is dolomitic, buff and. fine-grained. Bed 3 of "gran-
ite" quarry section _ .. _.: ...... _ ...... __ ... _ .. _ .... _. ____ ........ __ ... __ ... _____ .. _ .. ,. __ . 2
8
7. Concealed. Shale. Bed 2 of "granite" quany section _ ...... ___
3
6. Limestone, bluish gray, coarse-grained, with intercalated layers
of gray subcrystalline limestone. A layer at top filled with
Spiriler keokuk. ' Bed 1 of "granite" quarry section _._......... 5
5. LimestoT).e, ash-colored, fine-grained, doloriritic, impure, soft,
weathering yellowish _ .... _._ ...... _ .. ___ ._ .. _ .......................................... _. 2
6
4. Limestone, gray, subcrystalline, cherty; interbedded with lay-
ers of s<Y.ft buff cherty dolomitic limestone ..................... _ ...... _..... 6
3. Shale, calcareous, ash·gray in color, weathering slightly yel-
lowish ........................... _ ........................ _ .......... _ .... :.. .............. _ ..... _._..... 2
6
2. Limestone, gray, dense, brittle, subcrystalline, cherty ... _ .......... _ 2
1. Limestone, gray, crinoidal, with occasional chert bands. Lower
part poorly exposed ... _ .............. _ .......... _ .... _ .... _ .......... _................... 5
9 1. Limestone, gray, crinoidal, with occasional chert bands. 30 Iowa Geo!. Survey. vol. IV. p. 273; 1894. ANTHOZOA-
Monilopora beeched Grabau Lower
part poorly exposed ... _ .............. _ .......... _ .... _ .... _ .......... _................... 5 The following species were identified from the various beds:
,
t r List of fossils from bed 1 (}f Keo7cu7c limestonJe in section 10, Jac7cson township ANTHOZOA-
,
Z:lJphrentis varsoviensis Worthen'
Triplophyllum dalei (M.-E. and H.)
CRINOIDEA-
Macrocrinus verneuilianus (Shumard)
Actinocrinus sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Orthotetes
~ sp. Productus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetra.camera subtrigona (M. :llld W.)
Dielasma 8p. . Spirifer grimesi Hall
Spirifer Bp. Brachythyris suborbicularis (Hall)
Syringothyris sp. Reticularia pseudolineata (Hall)
O1iothyridina incrassata (Hall)
GASTROPODA-
Platyceras Bp. Platyceras Bp. Platyceras 8p. OrthO'Ilychia Bp. TRILOBITA-
Phillipsia , sp. ANTHOZOA-
,
Z:lJphrentis varsoviensis Worthen'
Triplophyllum dalei (M.-E. and H.)
CRINOIDEA-
Macrocrinus verneuilianus (Shumard)
Actinocrinus sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Orthotetes
~ sp. Productus sp. Pustula alternata (N. and P.)
Rhipidomella dubia (Hall)
Tetra.camera subtrigona (M. :llld W.)
Dielasma 8p. . Spirifer grimesi Hall
Spirifer Bp. Brachythyris suborbicularis (Hall)
Syringothyris sp. Reticularia pseudolineata (Hall)
O1iothyridina incrassata (Hall)
GASTROPODA-
Platyceras Bp. Platyceras Bp. Platyceras 8p. OrthO'Ilychia Bp. TRILOBITA-
Phillipsia , sp. Phillipsia , sp. MISSISSIPPIAN STRATA OF IOWA. 180 List of fossils front bed 2 of Keok;uk linlestone in s.eotion 10, Jackson township. BRYOZOA-
Fenestella sena,tula Ulrich
Fenestella multispinosa Ulrich
Fenestella sp. Cystodictya sp. BRACHIOPODA-
Productus setigerus Hall f
Pustula sp. Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
GASTROPODA--
Platyceras sp. Pustula sp. Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
GASTROPODA--
Platyceras sp. BRYOZOA-
Fenestella sena,tula Ulrich
Fenestella multispinosa Ulrich
Fenestella sp. Cystodictya sp. BRACHIOPODA-
Productus setigerus Hall f
Pustula sp. Spirifer tenuicostatus Hall
Brachythyris suborbicularis (Hall)
Reticularia pseudolineata (Hall)
GASTROPODA--
Platyceras sp. Pustula sp. S i if
t BRYOZOA-
F Fenestella sena,tula Ulrich
Fenestella multispinosa Ul List of fossils from bed 4 of Keok~lk limestone in section 10, Jackson township.' ANTHOZOA-
Amplexus sp. BRYOZOA--
Stenopora T sp. BRACHIOPODA-
Chonetes sp. Productus sp. Pustula sp. Avonia sp. Camarophoria bisinuata (Rowley)
Cranaena globosa Weller
Dielasma sp. Spirifer keokuk Hall
Spirifer tenuicostatus Hall
Spirifer ro~tellatus Hall
Syringothyris sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Athyris lamellosa (Leveille)
Cliothyridiua obmaxima (McChesney)
Composita trinuclea (Hall)
GASTROPODA-
Phanerotinus f sp. Orthonychia , sp. ANTHOZOA-
Amplexus sp. BRYOZOA--
Stenopora T sp. BRACHIOPODA-
Chonetes sp. Productus sp. Pustula sp. Avonia sp. Camarophoria bisinuata (Rowley)
Cranaena globosa Weller
Dielasma sp. Spirifer keokuk Hall
Spirifer tenuicostatus Hall
Spirifer ro~tellatus Hall
Syringothyris sp. Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Athyris lamellosa (Leveille)
Cliothyridiua obmaxima (McChesney)
Composita trinuclea (Hall)
GASTROPODA-
Phanerotinus f sp. Orthonychia , sp. Phanerotinus f sp. O th
hi Orthonychia , sp. List of fossils from bed 6 of K eo7cuk limestone in secti01~ 10, Jackson township List of fossils from bed 6 of K eo7cuk limestone in secti01~ 10, Jackson township. ANTHOZOA-
Zaphrentis varsovienMs Worthen
Monilopora sp. Palaeacis obtusus (M. and W.)
CRlNOIDEA-
Eucladocrinu8 sp. BRYOZOA-
Stenopora sp. Leioclema gra.cillimum Ulrich
Fenestella multi spinosa Ulrich
Hemitrypa sp. Polypora sp. Rhombopora varians Ulrich
Rhombopora attenuata Ulrich
Cystodictya sp. Glyptopora keyserlingi (Prout) BRACJTIOPODA-
Orthotetes keokuk (Hall)
Productus setig,erus Hall
Pustula sp. Rhipidomella dubia (Hall)
Tetracamera subtrigoua (M. and W.)
Spirifer keokuk Hall
Spirifer tenuicostatus Hall
Syringothyris textus (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall)
PELECYODA-
Schizodus sp. GASTROPODA-
Orthonychia sp. ANTHOZOA-
Zaphrentis varsovienMs Worthen
Monilopora sp. Palaeacis obtusus (M. and W.)
CRlNOIDEA-
Eucladocrinu8 sp. BRYOZOA-
Stenopora sp. Leioclema gra.cillimum Ulrich
Fenestella multi spinosa Ulrich
Hemitrypa sp. Polypora sp. Rhombopora varians Ulrich
Rhombopora attenuata Ulrich
Cystodictya sp. Glyptopora keyserlingi (Prout) Fenestella multi spinosa Ulrich
H
it PELECYODA
S hi
d Rhombopora varians Ulrich
Rhombopora attenuata Ulric Rhombopora attenuata Ulrich
C
t di t Schizodus sp. STROPODA GASTROPODA-
O th
hi Cystodictya sp. Glyptopora keyserlingi (Prout) Cystodictya sp. Glyptopora keys Orthonychia sp. Glyptopora keyserlingi (Prout) List of fossils from bed 8 of Keokuk limestone in section 10, Jackson ,township. BRACHIOPODA-
GASTROPODA- List of fossils from bed 8 of Keokuk limestone in section 10, Jackson ,township List of fossils from bed 8 of Keokuk limestone in section 10, Jackson ,township. BRACHIOPODA-
GASTROPODA-
Spirifer keokuk Hall
Bulimorpha f keokuk (Worthen) 31 Idem, p. 273.
82 Idem, pp. 277·279; 1894. BRACHIOPODA-
Spirifer keokuk Hall GASTROPODA-
B li
h BRACHIOPODA-
Spirifer keokuk Hall Bulimorpha f keokuk (Worthen) Bulimorpha f keokuk (Worthen) Bulimorpha f keokuk (Worthen One-half mile north of the preceding section is located the
Weber quarry now owned by Elbert Davis (NW. % NE. %. sec. 10, Jackson township). Sixteen feet of gmy coarse-grained
cherty crinoidal limestone, interbedded with gray subcrystalline
cherty limestone and soft buff cherty dolomitic limestone is ex-
posed. The outcrop is believed to represent beds 1 to 5 of the
preceding bluff section. Bain30 describes the Keokuk ("Augusta") limestone in Con·· 30 Iowa Geo!. Survey. vol. IV. p. 273; 1894. KEOKUK A'r SPRINGVALE MILL 181 nor's quarry, in the southwest quarter of the southeast quarter
of section 15, Sigourney township, as being in contact with the
St. Louis limestone. His section is as follows : nor's quarry, in the southwest quarter of the southeast quarter
of section 15, Sigourney township, as being in contact with the
St. Louis limestone. His section is as follows : Seotion
~n Con'IWr'lI quarrry (afte1' Bwitn). Seotion
~n Con'IWr'lI quarrry (afte1' Bwitn). rEET
~. Limestone, yellow, soft, magnesian; apparently arenaceous in
part, massive. Exposed ............................................... _ .... _ .... _ ..... 10
1. Limestone, coarse, sub crystalline. Exposed at water's edge.... 4 1. Limestone, coarse, sub crystalline. Exposed at water's edge.... 4 He refers bed 1 to the" Augusta" and bed 2 to the St. Louis. Bed 1 is concealed at the present time. Bain31 further makes
the following statement : "About two and one-half miles west of Conner's quarry (Tp. 75 N., R. 12 W., sec. 18, SE. qr., SE.14) the Augusta lime-
stone having the usual characteristics rises above the water four
feet. Both above and below this point the St. Louis is well
developed. ' , At the Springvale mill :five miles south of the town of Delta
in Warren township an exposure of bluish calcareous shales ap-
pears in a low bluff of Skunk river. In the Keokuk county re-
port Bain32 designates these shales the Springvale beds and cor-
relates them provisionally with the lower division of the St. Louis limestone. These shales possess all the characteristics of
those present in the upper part of the Keokuk limestone else-
where in Keokuk county and although they have not been found
to contain fossils sufficiently well preserved to make this corre-
lation positive they are referred to this formation on lithologic
grounds. The term Springvale as applied to the lower division
of the St. Louis limestone in this part of Iowa is therefore be-
lieved to be a misnomer. 1 U. S. GeoI. Survey Prof. Paper 24, table opp. p. 9
2 Illinois Geo!. Survey, Bull. 41, pp. 96, 97; 1920. CHAPTER IV '
THE MERAMEC GROUP Definition of Meramec Definition of Meramec Definition of Meramec Ulrich1 proposed the name Meramec in 1904 to include the
Warsaw, Spergen Hill and St. Louis formations which outcrop
along Meramec river in Missouri. Several later authors have
restricted the group to include only the St. Louis and Spergen,
the underlying Warsaw being referred to the Osage. W ll 2 i
hi
h
l
f H
di
Illi Weller2 in his report on the geology of Hardin county, Illi-
nois, includes the Warsaw in this group as well as the Ste. Genevieve formation. The following quotation from his report
will make his position in the matter clear: "As originally defined, the Meramec group included in as-
cending order, the Warsaw limestone, the Spergen (Salem)
limestone, and the St. Louis limestone. In the present report
the Ste. Genevieve limestone is also included as a fourth forma-
tion in the group, above the St. Louis limestone. For many
years after the original definition of the Ste. Genevieve lime-
stone by Shumard in 1859, the formation was scarcely or not at
all recognized, the beds representing it being commoruy includ-
ed with the St. Louis limestone. Ulrich revived the name of the
formation in 1905, but excluded it ' from the Meramec group,
making it the lowest formation of the Chester group, an inter-
pretation that he still holds to at this time. All the evidence,
however, that has been gathered during a period of a ,dozen
years, shows the much closer relationship of the Ste. Genevieve
to ' the St. Louis limestone than to any of the Chester forma-
tions. In a number of pUblications durinK r~cent years; as a
compromise measure, the Ste. Genevieve has been treated as a
separate unit in the Mississippian system, being united with
neither the Meramec group below, nor the Chester group above,
but the time has now come when it is desirable to place the Ste. Genevieve limestone where it properly belongs, with the St. Louis limestone. In order to accomplish this result it is neces-
sary either to modify the original definiti?n of. the Meramec
group so that it shall include the Ste. GeneVIeve lImestone, or to CHARAQTER OF MERAMEC BEDS 183 propose a new group name for the four formations. Distribution of the Group The ,Varsaw and Spergen members of the Meramec group
are restricted to the southeastern part of the state, but the St. Louis and Ste. Genevieve formations extend far beyond to the
north-central part. On the geologic map of Iowa, the V\T arsaw
deposits are included in the Osage areas while the Spergen, St. Louis and Ste. Genevieve, all of which were formerly identified
as St. Louis limestone, are mapped under that heading. The
group forms the highest consolidated rock over a much larger
area in southeastern Iowa than farther northwest. It appears
in the southern and northwestern parts of Lee county, over al-
most the entire area of Henry county, the southwestern parts of
Louisa and Washington counties, and the greater part of Keo-
kuk county. It has been mapped also along the valleys of
Skunk and Des Moines rivers and some of their larger tributar-
ies in Van Buren, Jefferson, 'vVapello, Mahaska, Marion and
southern Poweshiek counties·. In west-central Story county, the' St. Louis member of the
group has been exposed as a result of the erosion of the overly-
ing Pennsylvanian rocks over a low dome. Small inliers of the
Ste. Genevieve and St. Louis also appear in ,Vebster county,
while farther north in central and western Humboldt county
there are restricted outliers of the St. Louis in the Kinderhook
area. The extent of the group to the southwest beneath the
Pennsylvanian is not definitely known, but evidently is consider-
able. Definition of Meramec As it seems
more desirable to retain the name already in use with a slightly
modified definition, than to add confusion to the nomenclature
by introducing a totally new name, such a procedure is conse-
quently followed here." The revised usage of the term Meramec as recommended by
Weller is adopted in this report. Lithologic Character The Meramec group is made up of a l~lrger proportion of
clastic material and is much more diversified in character than
is true of the preceding Osage deposits. It is represented in MISSISSIPPIAN STRATA OF IOWA 184 Iowa by marginal facies of formations which are thickff, more
typically developed and more uniform in character farther
south in the Mississippi valley. The Warsaw formation consists of bluish argillaceous shales
with thin intercalated layers of gray fine-grained fossiliferous
limestone. The Spergen is represented typically by brownish
arenaceous magnesian limestone but locally some layers pass
into shales or cross-bedded crinoidal limestone. The St. Louis
consists for the most part of limestone which in the unaltered
condition is thin-bedded, gray, fine-grained. and dense. Locally
it grades laterally in part into brownish massive dolomite or
into sandstone. In some of its exposures it is brecciated. The
Ste. Genevieve is normally made up of a fine-grained bluish
gray basal sandstone, followed above by shale and then lime-
stone, but in north-central Iowa it is nearly all shale. Thickness The Meramec group attains its maximum thickness in Iowa
only in the southeastern part of the state where all its members
are present. The aggregate thickness there is approximately
two hundred feet. However, this value is subject to consider-
able variation from place to place owing to the thickening and
thinning of the individual formations. 3 Geol. of Iowa, vol. I, pt. I, p. 97; 1858. StratigTaphic Relations In Lee, Henry, Van Buren and Des Moines counties, where
the Warsaw beds are present, there appears to be a transition
from the Osage into the Meramec group but farther northwest
the Spergen and St. Louis formations overlap the ·Warsaw and
there a disconformity is present. Disconformities appear with-
in the group between the Spergen and St. Louis and between
the St. Louis and Ste. Genevieve. However, these represent
erosion intervals of limited duration. Between the Meramec
and basal Pennsylvanian deposits there exists a profound strat-
igraphic break. The Warsaw Formation
NOMENCLATURE AND DISTRIBUTION
The Warsaw formation as defined by HalP and described by The Warsaw Formation NOMENCLATURE AND DISTRIBUTION The Warsaw formation as defined by HalP and described by DISTRIBUTION OF WARSAW BEDS 185 later writers, consists of approximately forty feet of inter-
bedded shale and limestone, typically developed near the town
of Warsaw, in Hancock county, western Illinois. The present
investigation, however, has demonstrated the advisability of in-
cluding the underlying Geode bed with this formation. This
division, as has been pointed out, was included with the Keokuk
limestone by Hall and his successors. But a study of its fauna
indicates a stronger relationship to the Warsaw. In the present
report it is designated the Lower Warsaw, while the Warsaw
of Hall is referred to the Upper Warsaw. Altogether one hun-
dred and twelve fossils have been specifically identified from
this member by the writer. According to all the evidence at
hand, about forty-fiVie of these (chiefly crinoids and bryozoans)
appear for the first time. Eighteen of this number occur either
in the Warsaw of Hall or in the overlying Spergen formation. y
g
p
g
The fauna of the Warsaw of Hall, or the Upper Warsaw as
revised, is noted for its profusion of bryozoans and other fos-
sils. Many of these fossils are of a distinctly Spergen aspect,
in spite of the fact that in Iowa a dis conformity separates the
two members. Both divisions of the Warsaw pinch out to the north and
northwest, probably due in part to the proximity of the old
shore line in that direction, and in part to pre-Spergen erosion. The upper division pinches out much more abruptly than the
lower. At Keokuk, Iowa, about four miles northwest of War-
saw, this member is less than two-thirds as thick as at the type
locality, and a few miles beyond, it evidently wedges out com-
pletely. It has been found nowhere north of the limits of Lee
county. The northernmost exposures of beds known certainly
to represent the Lower Warsaw occur along Mud creek near
Lowell in southern Henry cOlmty and in the banks of Long
creek about two miles northwest of the town of Augusta in
southern Des Moines cOlmty. To the northwest it has been ob-
served as far as Van Buren COlmty. In the marginal areas this
member is usually succeeded above by the Spergen due to the
overlap of that formation beyond the Upper Warsaw but at
some localities the Lower St. NOMENCLATURE AND DISTRIBUTION Louis limestone appears above as
a result of the disconformity between this formation and the
Spergen. 186 MISSISSIPPIANI STRATA OF IOWA LITHOLOGIC CHARkCTER This division is approximately thirty-six feet in thickness in
the vicinity of Warsaw, Illinois, which is the type locality. Near
,Varsa,v" and at Keokuk, Iowa, it is divisible into three portions. The lower one-third is usually represented by a fine-grained
soft ash-colored massive, impure, geode-beaJ:ing magnesian
limestone which upon exposed surfaces scales off obliquely to
the surface of the bluff. At some localities this is interbedded
with thin layers of grayish blue fossiliferous limestone similar
to that of the underlying Keokuk formation. A layer of gray
thin-bedded cherty limestone overlies this bed. It is locally
brownish and dolomitized and is two to four feet thiclc The'upper portion of the Lower -Warsaw is a tough argillace-
ous or slightly calcareous shale which breaks down readily to a
gritty clay on exposure: ' It is laminated in many exposures, a
character which is in contrast to the massive beds below. At
some localities geodes are more numerous in ' this than in the
lower portion, but they are generally much smaller and more
poorly developed. The Lower Warsaw is represented by geodiferous and non-
geodiferous phases. In places these pass into each other later-
ally within short distances. The only apparent physical differ-
ence between the two phases is the usual presence of fossils in
that phase which bears no geodes, and their paucity in the
geodiferous portions. The Lower Warsaw at some localities
contains calcareous nodules, whose relationship to the contain-
ing rock is the same as that of the geodes. The composition of the lower portion of the Lower Warsaw
at a point along Soap creek at Keolmk, where it contains large
well developed geodes, is shown by the following analysis: PER CENT
Insoluble matter (largely free silica) _______________________________________________________
33.80
Fe,O.+Al,O, ___________________________________________________________________________________________________
2.80
CaCO,
__________________________________________________________________________________________________________
39_99
MgCO. _______________________________________________________________________________________________________________
12.50
Moisture rund carbonaceous matter ___________________________________________________________
7.70
Undetermined _____________________________________________________________________________________________________
3.21
100.00 PER CENT
Insoluble matter (largely free silica) _______________________________________________________
33.80
Fe,O.+Al,O, ___________________________________________________________________________________________________
2.80
CaCO,
__________________________________________________________________________________________________________
39_99
MgCO. _______________________________________________________________________________________________________________
12.50
Moisture rund carbonaceous matter ___________________________________________________________
7.70
Undetermined _____________________________________________________________________________________________________
3.21
100.00 Satisfactory outcrops of the Lower Warsaw are riot often
found where the formation is not capped by more resistant lay- LOWER WARSAW BEDS NEAR WARSAW 187 ers, because of the tendency of the shaly parts to weather back
in the form of gentle slopes which become covered by 'vegeta-
tion. Slumping of the shale, which likewise is common, also has
obscured many exposures. LITHOLOGIC CHARkCTER Well defined outcrops of this divi-
sion of the Warsaw occur locally along the banks of the larger
streams and their tributaries in southern and eastern Lee coun-
ty, southeastern Van Buren county, and southern Henry and
Des Moines counties. Good exposures appear also in Hancock
county, Illinois, and Clark county, Missouri. AREAL DESCRIPTION BY COUNTIES Limestone, in thin shaly, cherty layers filled with bryozoa ____ _
2. Shale, ash-colored, calcareous; weathering to very irregular
flakes with a few poorly prese,rved fossils . ________________________ . ___ _
1. Limestone, shaly; with thin interbedded cherty layers of gray
subcrystalline limestone,
which
is
increasingly
prevalent
towards the base. The shaly limestone layers bear a rich
bryozo,an fauna, while the sub crystalline limestone bears a
fauna nearly identical with the middle member of the Lower
Warsaw, which it resembles very closely physically. This
division outcrops along the bed of the creek only and its thick-
ness could not be determined accurately. It is believed to be
about ten feet _____ . ________ c _______________________________ ____________________________ • ____ • __
FEET
2
lh-l
3
2
10:1: Section of 'upper member of Lower Warsaw beds in Soap Factory Hollow. 6. Shale, bluish, argillaceous, overlain by Utin-bedded, no=ag-
nesian fossiliferous limestone of the basa~ Upper Warsaw _____ _
5. Geode bed, with many siliceous geodes ____ . ___________________________ . __
4. Shale, argillaceous, bluish ___________________________________ ____________________________ _
3. Limestone, in thin shaly, cherty layers filled with bryozoa ____ _
2. Shale, ash-colored, calcareous; weathering to very irregular
flakes with a few poorly prese,rved fossils . ________________________ . ___ _
1. Limestone, shaly; with thin interbedded cherty layers of gray
subcrystalline limestone,
which
is
increasingly
prevalent
towards the base. The shaly limestone layers bear a rich
bryozo,an fauna, while the sub crystalline limestone bears a
fauna nearly identical with the middle member of the Lower
Warsaw, which it resembles very closely physically. This
division outcrops along the bed of the creek only and its thick-
ness could not be determined accurately. It is believed to be
about ten feet _____ . ________ c _______________________________ ____________________________ • ____ • __
FEET
2
lh-l
3
2
10:1: The geodes of bed 5 range in diameter from a few inGhes
to over two feet. Locally they are so closely crowded as to
form a continuous layer for several yards. In such cases of
crowding the geodes are ' very irregular in shape, and in some
instances several specimens are grown closely together. Many
of them are imperfectly developed. Quartz and dolomite ap-
pear to be the common minerals lining their interiors. Pockets
of kaolin appear in the chalcedonic shells and in the interiors
of imperfect specimens. Section of 'upper member of Lower Warsaw beds in Soap Factory Hollow. AREAL DESCRIPTION BY COUNTIES Hancock Oounty, Illinois.-The most typical exposure,of the
fossiliferous facies of the Lower Warsaw known to the Iwriter
is that along the creek known as Soap Factory Hollow, which
joins the Mississippi from the east about one-half mile south of
Lower Warsaw, Illinois. The section begins with the city quar-
ry. From this point the exposures continue along the creek bed
and in its banks for nearly one-half mile up stream. In the upper part of the quarry there is exposed a few feet
of shales, with thin layers of. limeshme interbedded, followed
below by three and op.e-half feet of gI;ay thin-bedded cherty
limestone, representing the middle member of the Lower 'Wal'-
'saw. Under this comes el~ven and one-half feet of ' fine-grained
bluish magnesian, cherty limestone with interbedded seams and
layers of grayish to bluish coarse-grained fossiliferous lime-
stone which is correI'ated with the lower member. Geodes are
wanting except for an occasional imperfectly developed one. About three feet of bluish fossiliferous Keokuk limestone , is
shown in the quarry face below this member. Still lower layers
of the Keokuk limestone are shown in the creek bed nearby. ex~ The lower member of the, Lower Warsaw is excellently ex~
posed along the bed of the creek above the quarry. Some of
the limestone layers of this member bear sinuous pipelike fucoid
markings on their surfaces. A few of these are selectively re-
placed by chert. They range from a fraction of an inch to an
inch or more in greatest diameter. They are somewhat com-
pressed vertically. Excellent opportunities are afforded for
collecting from this member at this locality. At no other known
place is the Lower Warsaw so highly fossiliferous. MISSISSIPPIAN STRATA OF IOWA 188 The middle limestone member of the Lower Warsaw is well
exposed in the creek bed a short distance farther up stream
around the first bend. It grades gradually upward into the up-
per member of the Lower Warsaw. The upper member of the Lower Warsaw is represented far-
ther up the creek by the following beds listed in descending
order: Section of 'upper member of Lower Warsaw beds in Soap Factory Hollow. 6. Shale, bluish, argillaceous, overlain by Utin-bedded, no=ag-
nesian fossiliferous limestone of the basa~ Upper Warsaw _____ _
5. Geode bed, with many siliceous geodes ____ . ___________________________ . __
4. Shale, argillaceous, bluish ___________________________________ ____________________________ _
3. AREAL DESCRIPTION BY COUNTIES and W.)
Composita trinuclea (Hall)
GASTROPODA-
Platyceras equilateralis Hall f Orthotetes keokuk (Hall) f List of fossils from the middle member of the Lower Warsaw boos List of fossils from the middle member of the Lower Warsaw boos. Dielasma sp. Cranaena Bulcata Weller
Cranaena Bp. Spirifer bifurcatus Hall
Spirifer tenuicostatus Hall
Spirifer cf. S. keo,kuk Hall
Brnchythyris subcardiformis (Hall)
Brachythyris suborbicularis (Hall)
Reticularia setigera (Hall)
Eumetria verneuiliana (Hall)
Oliothyridina parvirostris (M. and W.)
Compoaita trinillclea (Hall)
Composita globosa Weller
PELECYPODA-
Allorisma gp. Aviculopecten sp. Aviculopecten sp. SCAPHOPODA-
Laevidentalium sp. GASTROPODA-
Holopea proutana Hall
Strophostylus 'f carleyaJIlJa (Hall) , Dielasma sp. Cranaena Bulcata Weller
Cranaena Bp. Spirifer bifurcatus Hall
Spirifer tenuicostatus Hall
Spirifer cf. S. keo,kuk Hall
Brnchythyris subcardiformis (Hall)
Brachythyris suborbicularis (Hall)
Reticularia setigera (Hall)
Eumetria verneuiliana (Hall)
Oliothyridina parvirostris (M. and W.)
Compoaita trinillclea (Hall)
Composita globosa Weller
PELECYPODA-
Allorisma gp. Aviculopecten sp. Aviculopecten sp. SCAPHOPODA-
Laevidentalium sp. GASTROPODA-
Holopea proutana Hall
Strophostylus 'f carleyaJIlJa (Hall) , ANTHOZOA-
Triplophyllum dalei (M.·E. and H
Zaphrentis (f) sp. Amplexus Bp. VERMES-
Spirorbis (') sp. BRYOZOA-
Fenestella tenax ffirich
Fenestella serratula ffirich
Fenestella multispinoaa ffirich
Penestella triserialis ffirich
Hemitrypa pateriformis Ulrich ,
Hemitrypa sp. Polypora retrorsa Ulrich
Rhombopora attenuata ffirich ,
Cystodictya pustulosa Ulrich 'f
W orthenopora spinosa ffirich
Cyclopora sp. BRACHIOPODA-
Productus setigerus Hall 'f
Pustula alternata (N. and P .)
Pustula biseriata (Hall)
Camarotoechia mutata (Hall) Camarotoechia mutata (Hall) AREAL DESCRIPTION BY COUNTIES The faunules of the three members of the Lower Warsaw at
Soap Factory Holloware listed below: List of fossils from the basal member of the Lower Warrsaw beds. ANTHOZOA.-
Triplophyllum dalei (M.-E. and H .)
Amplexus sp. Monilopora beecheri Grabau
CRINOIDEA.-
Barycrinus Bp. Uperocrinus nashvillae (Hall)
Agaricocrinus wortheni Hall
BLA.STOIDEA.-
Schizoblastus granulosus (M. and W.)
ECHINOIDEA.-
Archaeocidaris keokuk Hall
BRYOZOA.-
Stenopora sp. Fenestella serratull!. Ulrich
Fenestella limitaris Ulrich
Fenestella triserialis Ulrich
Fen.estella tenax Ulrich
Fenestella multispinosa Ulrich
FenestelLa funicula Ulrich Stenopora sp. F
ll Fenestella serratull!. Ulrich
F
ll
li
i
i
Ul i h Schizoblastus granulosus (M. and W.) FOSSILS OF LOWER WARSAW BEDS IS!) Fenestella compressa ffirich
Fenestella sp. Fenestella sp. Hemitrypa pateriformis ffirich
Archimedes owenanus Hall
Polypora gracilis Prout
Polypora varsoviensis Prout
Ptilopora sp. Ptilopora sp. Pinnatopora conferta Ulrich
Rhombopora varians ffirich
Rhombopora attenuata Ulrich
Cystodictya pustulosa ffirich
Cystodictya lineata ffirich
Worthenopora spinosa Ulrich
RACHIOPODA-
Orthotetes keokuk (Hall) f Fenestella compressa ffirich
Fenestella sp. Fenestella sp. Hemitrypa pateriformis ffirich
Archimedes owenanus Hall
Polypora gracilis Prout
Polypora varsoviensis Prout
Ptilopora sp. Ptilopora sp. Pinnatopora conferta Ulrich
Rhombopora varians ffirich
Rhombopora attenuata Ulrich
Cystodictya pustulosa ffirich
Cystodictya lineata ffirich
Worthenopora spinosa Ulrich
BRACHIOPODA-
Orthotetes keokuk (Hall) f
Productus ovatus Hall
Productus sctigerus Hall
Pustula alternata (N. and P.)
Camarotoech1a mutata (Hall)
Dielasma Bp. Spirifer rostellatus Hall 'f
Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Brachythyris sub orbicularis (Hall)
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Cliothyridina parvirostris (M. and W.)
Composita trinuclea (Hall)
GASTROPODA-
Platyceras equilateralis Hall f Fenestella compressa ffirich
Fenestella sp. Fenestella sp. Hemitrypa pateriformis ffirich
Archimedes owenanus Hall
Polypora gracilis Prout
Polypora varsoviensis Prout
Ptilopora sp. Ptilopora sp. Pinnatopora conferta Ulrich
Rhombopora varians ffirich
Rhombopora attenuata Ulrich
Cystodictya pustulosa ffirich
Cystodictya lineata ffirich
Worthenopora spinosa Ulrich
BRACHIOPODA-
Orthotetes keokuk (Hall) f Productus ovatus Hall
Productus sctigerus Hall
Pustula alternata (N. and P.)
Camarotoech1a mutata (Hall)
Dielasma Bp. Spirifer rostellatus Hall 'f
Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Brachythyris sub orbicularis (Hall)
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Cliothyridina parvirostris (M. and W.)
Composita trinuclea (Hall)
GASTROPODA-
Platyceras equilateralis Hall f Productus ovatus Hall
Productus sctigerus Hall
Pustula alternata (N. and P.)
Camarotoech1a mutata (Hall)
Dielasma Bp. Spirifer rostellatus Hall 'f
Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Brachythyris sub orbicularis (Hall)
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Cliothyridina parvirostris (M. SecUon of Lower Warsaw beds northeast of Warsaw. List of fossils from the upper member of the' Lower Warsaw beds. List of fossils from the upper member of the' Lower Warsaw beds. Fenestella ten ax Ulrich
Fenestella rudis ffirich
Fenestella triserialis Ulrich
Fenestella exigua Ulrich
Fenestella multispinosa , ffirich
F enestella compress a ffirich
Fenestella sp. Archimedes owenanus Hall
Archimedes wortheni Hall
Hemitrypa pateriformis ffirich
Hemitrypa sp. Polypora biseriata ffirich
Polypora v,arsoviensis Prout
Polyp ora gracilis Prout
Polyp ora retrorsa ffirich
Ptilopora valida UJrich
Ptilopora sp. ANTHOZOA-
Zaphrentis Bpergenensis 'Worthen
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. Monilopora bee cheri Grabau
Monilopora ~ sp. VERMES-
Spi ror bis sp. CRINOIDEA-
Barycrinus sp. BRYOZOA-
Fistulipora , sp. Meekopora sp. Ba tostomella (') sp. Stenopora sp. Leioclema punctatum (Hall)
Feucstella serratula Ulrich ANTHOZOA-
Zaphrentis Bpergenensis 'Worthen
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. Monilopora bee cheri Grabau
Monilopora ~ sp. VERMES-
Spi ror bis sp. CRINOIDEA-
Barycrinus sp. BRYOZOA-
Fistulipora , sp. Meekopora sp. Ba tostomella (') sp. Stenopora sp. Leioclema punctatum (Hall)
Feucstella serratula Ulrich MISSISSIPPIAN STRATA OF IOWA 190 Spil'ifer d. S. keokuk Hall
Spil'ifer bifurcatus Hall
Spil'ifel' tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Eumetria verneuiliana (Hall)
Cliothyridina parvirostris (M. and W.)
Composita trinuclea (Hall)
Composita globosa Weller ,
P ELECYPODA-
Schizodus cf. S. circulus Worthen
Schizodus sp. Edmondia voafsoviensis Wo'rthen
Edmondia illinoisensis Worthen
Aviculopecten sp. Lithophagus illiuoisensis Worthen
GASTROPODA-
Platyceras , sp. Straparollus sp. Ptilopora sp. Rhombopora attenuata Ulrich
Rhombopora varians Ulrich
Rhombopora sp. Cystodictya pustulosa Ulrich
Glyptopora keysel'lingi (PJ'out)
WOl'thenopora spinosa Ulrich
Cyclo'pol'a sp. Spil'ifer d. S. keokuk Hall
Spil'ifer bifurcatus Hall
Spil'ifel' tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Eumetria verneuiliana (Hall)
Cliothyridina parvirostris (M. and W.)
Composita trinuclea (Hall)
BRACHIOPODA-
Composita globosa Weller ,
Ol'biculoidea sp. Productus se6g.erus Hall
Pl'OductllS indianensis Hall ,
Pl'OductllS sp. Pustula bisel'iata (Hall) ,
Pustllia altel'na,ta ( . and P.)
Pustula sp. Avonia sp. Camarotoechia mutata (Hall) ,
Dielasma sp. Spirifel'ina sp. P ELECYPODA-
Schizodus cf. S. circulus Worthen
Schizodus sp. Edmondia voafsoviensis Wo'rthen
Edmondia illinoisensis Worthen
Aviculopecten sp. Lithophagus illiuoisensis Worthen
GASTROPODA-
Platyceras , sp. Straparollus sp. Spil'ifer d. S. keokuk Hall
Spil'ifer bifurcatus Hall
Spil'ifel' tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Eumetria verneuiliana (Hall)
Cliothyridina parvirostris (M. and W.)
Composita trinuclea (Hall)
Composita globosa Weller ,
P ELECYPODA-
Schizodus cf. S. circulus Worthen
Schizodus sp. Edmondia voafsoviensis Wo'rthen
Edmondia illinoisensis Worthen
Aviculopecten sp. Lithophagus illiuoisensis Worthen
GASTROPODA-
Platyceras , sp. Straparollus sp. Ptilopora sp. Rhombopora attenuata Ulrich
Rhombopora varians Ulrich
Rhombopora sp. List of fossils from the upper member of the' Lower Warsaw beds. Cystodictya pustulosa Ulrich
Glyptopora keysel'lingi (PJ'out)
WOl'thenopora spinosa Ulrich
Cyclo'pol'a sp. BRACHIOPODA-
Ol'biculoidea sp. Productus se6g.erus Hall
Pl'OductllS indianensis Hall ,
Pl'OductllS sp. Pustula bisel'iata (Hall) ,
Pustllia altel'na,ta ( . and P.)
Pustula sp. Avonia sp. Camarotoechia mutata (Hall) ,
Dielasma sp. Spirifel'ina sp. Good exposures of the Lower Warsaw in contact with the
Upper Warsaw are Present in the bluffs of a small creek tribu-
tary to the Mississippi, a short distance northeast of the town
of Warsaw. The Lower Warsaw is geode-bearing at this local-
ity and is alniost barren of recognizable fossils: The section is
as follows: SecUon of Lower Warsaw beds northeast of Warsaw. . FEET
lNCHES
4. Upper Warsaw shales and limestone .............................................. 18
6
3. Shale, argillafleous, weathering into thin laminre; , more reo
sistant layers
slig~tly projecling; bearing numerous small
geodes arl'aIJged in bands ... _ ........................................................... 23
2. Limestone, impure, buff, magnef\ian, containing discontinuous
bands and' nodules of chert ............................................. _............... 3
3
1. Limestone, drab, fine· grained, impure. magnesian, massive;
scalin'g off obliquely to the face of the ' bluff; geodes few anel
scattered in upper part but more abundant below; many of
them broken because of the fragile condition of their shells. Exposed .................... : .................. : .................................... ,................... 6 1. Limestone, drab, fine· grained, impure. magnesian, massive;
scalin'g off obliquely to the face of the ' bluff; geodes few anel
scattered in upper part but more abundant below; many of
them broken because of the fragile condition of their shells. Exposed .................... : .................. : .................................... ,................... 6 The Lower Warsaw in its typical development comprises
numbers 1 to 3 of this section. Attention is called to the fact
that the middle member is here dolomitic. ' The Lower Warsaw is exposed also near Hamilton, Illinois,
four mjles north of Warsaw, in the clay pits of the Hamilton
Clay Company. The blue calcareous shale of the upper member
is here, used in the manufacture of brick and tile and large num-
bers of geodes which have been picked from the clay are avail·
able for study. I
h
i i i
f Ni
i
H
k co~ty, h
L
W In the vicinity of Niota, in Hancock co~ty, the Lower War- LOWER WARSAW BEDS NEAR NIOTA 191 saw is exposed at several localities. Section of Lower W arsaw beds SO'!bth of Niota.
FEET
11. Till, yellow, beaTing bowlders of St. Louis limestone ................ 9
10. Shale, argillaceous, bluish gray when fresh but weathering
yellow; some layers more calcareous a:nd bearing geodes ........ 4
9. Shale, calcareous, geodiferous .......................................................... 1
8. Shale, bluish when f resh; few or no geodes ... _ ...................... _... 1
7. Shale, highly calcareous, gray, bearing many geodes studded
with dolomite .... _ ........................................ __ .............. _....................... 2
INCHES
6
6
3 List of fossils from the upper member of the' Lower Warsaw beds. The following beds out-
crop on the west bluff of a small creek one-half mile east of the
town. FEET
lNCHES
.. 5. Drift ......... _ ................ _ ................ _ .... _ .................................... _ .......... .
4. Shale, argillaceous, bluish, with thin layers of limestone inter·
calated near the top ....................................... _ ............................ _..... 5
3. Shale, calcareous, ash·colored; upper part bea.ring small geodes
whose shells are fragile and uSJIally stained with bitumen ;
lower part with a bituminous band which bears broken geodes 3
G
2. Shale, argillaceous ..................................................... _ .... _.................. 1
8
1. Limestone, in bed of creek .................. _ .......................................... . 8. Shale, bluish when f resh; few or no geodes
7
Sh l
hi hl
l
b
i Section ' of Lower . WarS1aw beds east of Niota. FEET
2. Shale, argillo·calca.reous, with flakes of impure non fossiliferous
limestone; bearill'g a few geodes ranging up to four inches FEET
2. Shale, argillo·calca.reous, with flakes of impure non fossiliferous
limestone; bearill'g a few geodes ranging up to four inches 1. Limestone, impure,
fine· grained, ma,gnesian;
intel'stratified
near the middle with ban(l,g of bluish fossiliferous lim stone 6
to 8 inches thick ; a few gllodes in the more impure parts ... _. 15 At the Fort Madison-Appanoose quarries, which are located
i;n the Mississippi river bluff two miles above Niota, twenty-
two and one-half feet of dolomitic Spergen limestone rests dis-
conformably upon the bluish calcareous geodiferous shale ' or
Lower Warsaw ao'e. 'l'he Upper 'Warsaw, if ever present at
this place, was completely. eroded before the deposition of the
Spergen. Many of the geodes which are found to the south of Niota
bear asphaltic material and the rocks in which they occur are
locally also bituminous. About one-half mile south of the toWn
the Lower Warsaw may be studied along a small creek. A sec-
tion of the strata at this place follows : Section of 'Lower WarsoAv beds south of Niota. FEET
lNCHES
.. 5. Drift ......... _ ................ _ ................ _ .... _ .................................... _ .......... . 4. Shale, argillaceous, bluish, with thin layers of limestone inter·
calated near the top ....................................... _ ............................ _..... 5
3. Shale, calcareous, ash·colored; upper part bea.ring small geodes
whose shells are fragile and uSJIally stained with bitumen ;
lower part with a bituminous band which bears broken geodes 3
G
2. Shale, argillaceous ..................................................... _ .... _.................. 1
8
1. Limestone, in bed of creek .................. _ .......................................... . 1. Limestone, in bed of creek .. Another section of interest is located two miles south of Niota
on the north branch of the first main creek below that town. Section of Lower W arsaw beds SO'!bth of Niota. FEET
11. Till, yellow, beaTing bowlders of St. Louis limestone ................ 9
10. Shale, argillaceous, bluish gray when fresh but weathering
yellow; some layers more calcareous a:nd bearing geodes ........ 4
9. Shale, calcareous, geodiferous .......................................................... 1
8. Shale, bluish when f resh; few or no geodes ... _ ...................... _... 1
7. Shale, highly calcareous, gray, bearing many geodes studded
with dolomite .... _ ........................................ __ .............. _....................... 2
INCHES
6
6
3 MISSISSIPPIAN STRATA OF IOWA 192 6. 5. Section ' of Lower . WarS1aw beds east of Niota. '4. 3. 2. 1. Limestone, impure, buff, magnesian; bearing fronds of a
fenestelloid bryozoan; small masses of sphalerite common_______
6
Shale, argillaceous; breaking down to ash-colored clay; no
geodes noted ____________________________________________________________________________________
3
10
Shale, arg'illaceous, grayish blue; bituminous geodes scattered
throughout, although shale is not appreciably stained with
this material ________________________________________________________________________________________
2
Shale, highly calcareous, ash-colored, bearing a few geodes,
none of which was found to contain bitumen __________________________
1
7
Shale, argillaceous, grayish blue in color, no geodes noted ______
2
10
Limestone, gray, crinoidal ______________________________________________________________ . 1
10 5. '4
Shale, argillaceous; breaking down to ash-colored clay; no
geodes noted ____________________________________________________________________________________
3
10
Sh l
'ill
i h bl
bi
i
d
d 3. 2
Shale, highly calcareous, ash colored, bearing a few geodes,
none of which was found to contain bitumen __________________________
1
7
Sh l
ill
i h bl
i
l
d
t d
2
10 2. 1
Shale, argillaceous, grayish blue in color, no geodes noted ______
2
10
Limestone
gray
crinoidal
1
10 1. Limestone, gray, crinoidal ______________________________________________________________ . 1
10 1. Limestone, gray, crinoidal All of the members of this section except 1 and 11, which
resent the Keokuk and Pleistocene respectively, belong t
Lower Warsaw. L
C
t
I
N
ll
h
i
th
L All of the members of this section except 1 and 11, which rep-
resent the Keokuk and Pleistocene respectively, belong to the
Lower Warsaw. Lee Cownty, Iowa.-Numerolls exposures showing the Lower
Warsaw in contact with both the Keokuk limestone and the
Upper Warsaw may be seen in and near the city of Keokuk~
Iowa, in the extreme southern part of Lee county. These occur
in the bluffs of Soap creek, and in the north bluff of Mississippi
river, at intervals from the Union Station to the Taber lumber
mills, two miles do·wn stream (fig. 4). Fro. 4.-The "Geode bed," or Lower Warsaw. Mississippi river bluff back of Taber lumber
mills, Keokuk. Fro. 4.-The "Geode bed," or Lower Warsaw. Mississippi river bluff back of Taber lumber
mills, Keokuk. The section on Soap creek near the end of Fourteenth Street
is typical (fig. 5). The section on Soap creek near the end of Fourteenth Street
is typical (fig. 5). LOWER WARSAW FOSSILS AT KEOKUK 193 FIG. 5.-View of Lower 'Warsaw bed ' along Soap creek at Keokuk. Section of Lower Warsaw beds on Soap <Yf'ee7c FIG. Section ' of Lower . WarS1aw beds east of Niota. 5.-View of Lower 'Warsaw bed ' along Soap creek at Keokuk. Section of Lower Warsaw beds on Soa,p <Yf'ee7c. FEET
3. Shale, bluish, argillaceous, geodiferous, with occasional thin
layers 'of magnesian limestone near the to]:>
20 2. Limestone, light gray, fine-grained, cherty ______________ ... _________ .______
1
Limestone
ash colored
impure
siliceous
magnesian
geodifer 1. Limestone, ash-colored, impure, siliceous, magnesian, geodifer-
ous; with occasional seams and layers of grayish or bluish
fossiliferous limestone ____ . ______ . _________________ . ____ . ____________ . ____ . ___________ .. ______
7112 The following faunal lists were prepared from collections
made by the writer along Soap creek and in the Missjssippi
rIver bluff sections. List of fossils front bed 1 of the Lowe)' Warsaw beds a,t Keokuk. AN'l'HOZOA-
Zaphrentis sp. Triplophyllum dalei (M.-E. and H.)
Monilopora bee cheri Grabau
CRINOIDEA-
Dizygocrinus f sp. Uperocrinus nashvillae (Hall)
Dorycrinus mississippiensis Roemer
Dol'ycrinus sp. Agal'icocl'inus americanus val'. tuber-
osus Hall
Barycrinus spmius (Hall)
Barycrinus sp. ECHINOIDEA-
Archaeocidaris sp. BRYOZO.>l.-
Fistulipora , sp. Fenestella cormpressa Ulrich
Fenestella multispinosa Ulrich
:B'enestella exigua Ulrich
Fenestella tena..'( Ulrich
Fenestel1a serratula Ulrich
Fencstella sp. Hemitl'ypa sp. Archimedes owenMl'llS Hall
Polypora gracilis Prout
Polypora varsoviensis Prout
Pinnatopora conferta Ulrich
Rhombopora dichotoma Ulrich
Rhombopora sp. Dorycrinus mississippiensis Roemer
Dol'ycrinus sp Barycrinus spmius (Hall)
Barycrinus sp Archaeocidaris sp. MISSISSIPPIAN STRATA OF IOWA 194 Spirifer tenuicostatus Hall
Spirifer keokuk Hall
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineaJta (Hall)
Eumetria verneuiliana (Hall)
Composita sp. Cliothyridina parvirostris (M. and W.)
P]<;LECYPODA-
Pinna subspatulata Worthen
Aviculopecten sp. GASTROPODA-
Platyceras equilateralis Hall Spirifer tenuicostatus Hall
Spirifer keokuk Hall
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineaJta (Hall)
Eumetria verneuiliana (Hall)
Composita sp. Cliothyridina parvirostris (M. and W.)
P]<;LECYPODA-
Pinna subspatulata Worthen
Aviculopecten sp. GASTROPODA-
Platyceras equilateralis Hall Cystodictya lineata Ulrich
Wo.rthenopora spinosa Ulrich
BRACHIOPODA-
Productus ovatus Hall
Productus setigerus Hall
Productus sp. Avonia sp. Pustula aJterna.ta (N. and P .)
Pustula biseriata (HaJI)
Orthotetes keokuk (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Dielasma sp. Cystodictya lineata Ulrich
Wo.rthenopora spinosa Ulrich
BRACHIOPODA-
Productus ovatus Hall
Productus setigerus Hall
Productus sp. Avonia sp. Pustula aJterna.ta (N. and P .)
Pustula biseriata (HaJI)
Orthotetes keokuk (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Dielasma sp. In the Mississippian crinoid collection at the Walker Museum,
University of Chicago, the following species of crinoids listed
from Keokuk, Iowa, are believed to have been collected from
this bed as suggested by the character of their. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Zaphrentis spel'genensis Worthen
Zaphrentis sp.
Amplexus sp.
Moniloporn beecheri Grabau Section of Lower WMsaw beds in north bluff of Fox river near Fox City.
FEET
INCHES
8. Drift ........... _ .................................... _... ................................................
1
7.
Shale, argillo·calcal'eous, pyritiferous, bluish when fresh but
brea,king down readily to a gray friable clay and releasing a
few smaH geodes .................................................................................. 17
6.
Limestone, gray, cl'inoi-dal; shaly in places; cherty near the
base ........... _ .... _ ............................ _....................................................... 5 6.
Limestone, gray, cl'inoi-dal; shaly in places; cherty near the
base ........... _ .... _ ............................ _....................................................... 5 8. Drift ........... _ .................................... _... ................................................
1
7.
Shale, argillo·calcal'eous, pyritiferous, bluish when fresh but
brea,king down readily to a gray friable clay and releasing a
few smaH geodes .................................................................................. 17
6.
Limestone, gray, cl'inoi-dal; shaly in places; cherty near the
base ........... _ .... _ ............................ _....................................................... 5 Section ' of Lower . WarS1aw beds east of Niota. Polypora cf, p, biseriata lnrich
Polyp ora retrorsa IDrich T
Polyp ora spininodata Ulrich
Polypora sp,
Hemitrypa aspera IDrich
Hemitrypa proutana Ulrich
Hemitrypa perstriatru IDrich
Hemitl'ypa plumosa Prout 1
Hernitrypa sp,
Ptilopora prouti Hall
Rhombopora sp,
Rhombopora attenuata Ulrich Fen€,stella serratula IDrich
Fenestella multispinosa Ulrich
Fenestolla wnax IDrich
Fenestella compressa IDrich ,
Fenestella triserialis IDrich ,
Polypora varsoviensis PI'out
. Polypora cf, p, biseriata lnrich
Polyp ora retrorsa IDrich T
Polyp ora spininodata Ulrich
Polypora sp,
Hemitrypa aspera IDrich
Hemitrypa proutana Ulrich
Hemitrypa perstriatru IDrich
Hemitl'ypa plumosa Prout 1
Hernitrypa sp,
Ptilopora prouti Hall
Rhombopora sp,
Rhombopora attenuata Ulrich Cystodictya lineata Ulrich
Cystodictya pustulosa IDrich
Glyptopora elegans (Prout)
Glyptopora keyserlingi (Prout)
G'lyptopora sp,
W orthenopora spinosa Ulrich
Cyclopora fungia IDrich
BRACHIOPODA-
Pustula biseriata (Hall)
Orthotews keokuk (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Dielasma sp,
Spiriferina sp,
Spirifer of, S, keokuk Hall
Spirifer tenuicostatus Hall
Reticularia setigera (Hall)
Cliothyridina parvirostris (M, and W.) Fen€,stella serratula IDrich
Fenestella multispinosa Ulrich
Fenestolla wnax IDrich
Fenestella compressa IDrich ,
Fenestella triserialis IDrich ,
Polypora varsoviensis PI'out
. Polypora cf, p, biseriata lnrich
Polyp ora retrorsa IDrich T
Polyp ora spininodata Ulrich
Polypora sp,
Hemitrypa aspera IDrich
Hemitrypa proutana Ulrich
Hemitrypa perstriatru IDrich
Hemitl'ypa plumosa Prout 1
Hernitrypa sp,
Ptilopora prouti Hall
Rhombopora sp,
Rhombopora attenuata Ulrich
Cystodictya lineata Ulrich
Cystodictya pustulosa IDrich
Glyptopora elegans (Prout)
Glyptopora keyserlingi (Prout)
G'lyptopora sp,
W orthenopora spinosa Ulrich
Cyclopora fungia IDrich
BRACHIOPODA-
Pustula biseriata (Hall)
Orthotews keokuk (Hall)
Rhipidomella dubia (Hall)
Camarotoechia mutata (Hall)
Dielasma sp,
Spiriferina sp,
Spirifer of, S, keokuk Hall
Spirifer tenuicostatus Hall
Reticularia setigera (Hall)
Cliothyridina parvirostris (M, and W.) Rhombopora sp,
Rhombopora atte Rhombopora attenuata Ulrich Worthen has described several species of crinoids from the
upper shales of the Geode bed one mile below Keokuk in Volume
VII of the Geological Survey of Illinois. Inasmuch as these un-
doubtedly came from bed 3 of the writer's section'they are list-
ed here, the revised J;lomenclature being used. Rhod>oerinlUs coxanus Worthen
Scaphiocrinus briaerius (Worthen)
Sea,phiocrinus extensus W. and S,
Scaphiocrinus iowensis (Worthen)
Scaphiocrinus obscurus W, and S. 8. Drift
7
Shale Section ' of Lower . WarS1aw beds east of Niota. matrix. Gilbertsocrinus s-p. Batocrinus sp. Dizygocrinus biturbinatus (Hall)
Eutroc.hocrinus planodiscus (Hall)
Agaricocrinus wortheni Hall
AgaricocriIJlllS nodulosus val'. maca-
damsi Worthen
Agaricocrinus nodulosus 'Worthen
Actinocrinus pernodosus Hall
Platycrinus saffordi Hall
Platycrinus sp. Fo-rbesiocrinuB worthenri. Hall
Synbathocrinus Bwallowi Hall
HalysiooriIJllls tunicatus (Hall)
Barycrinus spurius (Hall)
Barycrinus magister (Hall)
BarycriIJllls tumidus (HaJI)
Barycrinus stellatus (Hall)
Barycrinus bullatus (Hall)
Pachylocrinus Bp. Scylatocrinus sp. Fo-rbesiocrinuB worthenri. Hall
Synbathocrinus Bwallowi Hall
HalysiooriIJllls tunicatus (Hall)
Barycrinus spurius (Hall)
Barycrinus magister (Hall)
BarycriIJllls tumidus (HaJI)
Barycrinus stellatus (Hall)
Barycrinus bullatus (Hall)
Pachylocrinus Bp. Scylatocrinus sp. Dizygocrinus biturbinatus (Hall)
Eutroc hocrinus planodiscus (Hall) Eutroc.hocrinus planodiscus (Hall)
Agaricocrinus wortheni Hall Agaricocrinus wortheni Hall
AgaricocriIJlllS
nodulosus
va AgaricocriIJlllS nodulosus val . maca-
damsi Worthen
A
i
i
d l
'W
th Agaricocrinus nodulosus 'Worthen
Actinocrinus pernodosus Hall Pachylocrinus Bp. S
l t
i Actinocrinus pernodosus Hall
Plat crin s saffordi Hall Scylatocrinus sp. Platycrinus saffordi Hall
Platycrinus sp Platycrinus sp. List of fossils fro'l'/, bed e of the Lower Warsaw beds at Keokuk. ANTHOZOA-
Amplexus Bp. Zaphrentis sp. BRYOZOA-
Stenopora Bp. Fenestella serroitula Ulric.h
Fenestella tenax Ulrich ,
Hemitrypa proutana Ulrich
Polypora sp. Cystodictya lineata Ulrich
Worthenopora, spinosa Ulrich
BRACHIOPODA-
Productus sp. Productus sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Camarotoechia mutata (Hall)
Cranaena sulcata Weller
Dielasma , lip. Dielasma sp. Dielasma sp. Spiriferina norwoodana (Hall)
Spiriferina sp. Spirifer tenuicostatus Hall
Spirifer keokuk hall
Brachythyris suborbicularis (Hall)
Pseudosyrinx keoh.-uk Weller 1
Reticularia setigera (Hall)
Eumetria verneuilialla (HaJI)
Cliothyridina parvirostris (M. and W.)
PELECYPODA-
A viculopecten sp. GASTROPODA-
H olopea cf. H. proutana Hall
VERTEBRATA-
Fish teeth
List of fossils from bed 3 of t he Lower Warsaw beds at Keokuk. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Zaphrentis spel'genensis Worthen
Zaphrentis sp. Amplexus sp. Moniloporn beecheri Grabau
CRINOID EA'-
DOI'YCl'inus sp. BRYOZOA-
Fistulipora sp. Stellopora sp. Leioclema punctatuml (Hall)
Archimedes d. A. owenanus Hall Dielasma , lip. Di l Fenestella serroitula Ulric.h
Fenestella tenax Ulrich Fenestella tenax Ulrich ,
Hemitrypa proutana Ulrich Camarotoechia mutata (Hall)
Cranaena sulcata Weller Cranaena sulcata Weller List of fossils from bed 3 of t he Lower Warsaw beds at Keokuk. ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Zaphrentis spel'genensis Worthen
Zaphrentis sp. Amplexus sp. Moniloporn beecheri Grabau Moniloporn beecheri Grabau LOWER WARSAW NEAR FOX CITY 195 Fen€,stella serratula IDrich
Fenestella multispinosa Ulrich
Fenestolla wnax IDrich
Fenestella compressa IDrich ,
Fenestella triserialis IDrich ,
Polypora varsoviensis PI'out
. 7.
Shale, argillo·calcal'eous, pyritiferous, bluish when fresh but
brea,king down readily to a gray friable clay and releasing a
few smaH geodes .................................................................................. 17
6
Li
t
l'i
i d l
h l
i
l
h
t
th Section ' of Lower . WarS1aw beds east of Niota. Scaphiocrinus ol'e&tes (Worthen)
Zoocrinus 'keokuk Worthen
Woodocrinus asperatus (Worthen)
Woodocrinus tentaculatus (W.orthen) Scaphiocrinus ol'e&tes (Worthen)
Zoocrinus 'keokuk Worthen
Woodocrinus asperatus (Worthen)
Woodocrinus tentaculatus (W.orthen) Scaphiocrinus ol'e&tes (Worthen)
Zoocrinus 'keokuk Worthen
Woodocrinus asperatus (Worthen)
Woodocrinus tentaculatus (W.orthen) Rhod>oerinlUs coxanus Worthen
Scaphiocrinus briaerius (Worth Rhod>oerinlUs coxanus Worthen
Scaphiocrinus briaerius (Wort Scaphiocrinus briaerius (Worthen)
Sea phiocrinus extensus W and S Sea,phiocrinus extensus W. and S,
Scaphiocrinus iowensis (Worthen) Scaphiocrinus iowensis (Worthen)
Scaphiocrinus obscurus W
and S Scaphiocrinus obscurus W, and S. The Lower Warsaw outcrops seven and one-half miles north
of Keokuk in the banks of a small creek just south of the town
of Montrose. This member is thirty feet in thickness at this
locality and is succeeded directly by the Spergen formation, the
Upper Warsaw being absent. Olark Oownty, Missotwi.-The Lower Warsaw is well exposed
in Clark county, Missouri, along the north bluff of Fox river
four miles northwest of \Vayland and one-fourth mile northwest
of Fox City. The geodes and their relation to the containing
rock may be very satisfactorily studied at this place. The sec-
tion is given below: MISSISSIPPIAN STRATA OF IOWA 196 5. Limestone, impure, magnesian, fine·grained, drab; scaling off
obliquely in large slabs ............................................. _._ .... _. __ .............. 3 5. Limestone, impure, magnesian, fine·grained, drab; scaling off
obliquely in large slabs ............................................. _._ .... _. __ .............. 3
8
4. Shale, highly calcareous, bluish; locally more argillaceous and
exhibiting I-aminated structures. Geodes present, some exceed·
ing 15 inches in diamet~r; arranged roughly in bands; many
closely arranged .... __ ................. _ .... __ .... __ ............. _ ..... _._ ..... _ ...... _ .. _ ... ___ .. 6
3. Limestone, gray, crinoidal; cherty near the base ........... _............ 7
2. Limestqne, impu1'e, shaly, fine· grained ; bearing a few scattered obliquely in large slabs ............................................. _._ .... _. __ .............. 3
8
4. Shale, highly calcareous, bluish; locally more argillaceous and
exhibiting I-aminated structures. Geodes present, some exceed·
ing 15 inches in diamet~r; arranged roughly in bands; many
closely arranged .... __ ................. _ .... __ .... __ ............. _ ..... _._ ..... _ ...... _ .. _ ... ___ .. 6
3
Li
t
i
id l
h
t
th
b
7 y
g
3. Limestone, gray, crinoidal; cherty near the base ........... _............ 7 g
y
y
2. Seotion of Lower W(krSaW beds on Mud oreek. Seotion of Lower W(krSaW beds on Mud oreek. Seotion of Lower W(krSaW beds on Mud oreek. Seotion of Lower W(krSaW beds on Mud oreek. FEIDT
INCHES
6. Drift ...................................................................................................... 1
6
5. Shale, argillaceous, bluish, breaking down to a gritty drab·
colored clay; containing a few scattered irregular uiliceous
nodules which contain geodic cavities ............................................ 10
6
4. Limestone, impure, buff, magnesian; checking into irregular
blocks antl boacr-ing the impressions of fronds of fenestelloid
bryozoans; lenticular siliceous masses near the base inclose
material identical with that of the surrounding rock ................ 2
3. ShaIe, bluish when fresh; thickly set with geodes less than 6
inches in diameter, which are not confined to bands .................. 2
8
2. Shale, highly calcareous, gray aud buff in color; geodes scarce 1
6
1. SOOJe, calcareous, bluish. Some of thE fossils collected from
this layer a,re:
O'rthotetes
7ceo].,"1.~7c, SpiJrifer 7.e07'1!7, 1, Retio·
ularia sp., imperfectly preserved bryozoa, and nlUmerous small
fish teeth. Exposed ........... ................................................................. 8 Seotion of Lower W(krSaW beds on Mud oreek. FEIDT
INCHES
6. Drift ...................................................................................................... 1
6
5. Shale, argillaceous, bluish, breaking down to a gritty drab·
colored clay; containing a few scattered irregular uiliceous
nodules which contain geodic cavities ............................................ 10
6
4. Limestone, impure, buff, magnesian; checking into irregular
blocks antl boacr-ing the impressions of fronds of fenestelloid
bryozoans; lenticular siliceous masses near the base inclose
material identical with that of the surrounding rock ................ 2
3. ShaIe, bluish when fresh; thickly set with geodes less than 6
inches in diameter, which are not confined to bands .................. 2
8
2. Shale, highly calcareous, gray aud buff in color; geodes scarce 1
6
1. SOOJe, calcareous, bluish. Some of thE fossils collected from
this layer a,re:
O'rthotetes
7ceo].,"1.~7c, SpiJrifer 7.e07'1!7, 1, Retio·
ularia sp., imperfectly preserved bryozoa, and nlUmerous small
fish teeth. Exposed ........... ................................................................. 8 An ' outcrop a short distance up the creek at a point just west
of the second bridge over Mud creek exposes number 1 of the
previous section to a height of about three feet. The upper part
of this member at this place bears many rounded concretionary
nodules of material which appears to be more calcareous than
the containing rock. These nodules range from less than an
inch to more than six inches in diameter. Seotion of Lower Warsaw beds in seotio~ 22, Balt·imore township.
FEET
INCHES
5. Limestone, massive, magnesian, yello·wish, no- geodes nor fos·
sils noted .............................................................................................. 4
4.
Shale, bluish, calcareous; grading upward into limestone ........
2
3.
Limestone, impure, buff, magnesian .............................................. 1
8
2.
Shale, calcareous, bearing several large geodes ........................ 2
1. Shale, bluish, argillaceous; bearing rounded caJcareous nodules
near the top.
Exposed ...................................................................... 4 Section ' of Lower . WarS1aw beds east of Niota. Limestqne, impu1'e, shaly, fine· grained ; bearing a few scattered
b t l
d
1
6 but large geodes ........... _ .... _. ____ ._ .... _ ...... _ . 1. Limestone, gray, crinoidal; exposed ... _ 1. Limestone, gray, crinoidal; exposed Bed 1 of this section evidently represents the uppermost mem-
ber of the Keokuk limestone. All of the succeeding layers are
referable to the Lower vVarsaw except bed 8. Des Moines County, Iowa.-The Lower Warsaw is consider-
ably thinner in Des Moines county than in Lee and adjacent
counties to the south. 'fhe only important exposures in this
county which are known to the writer occur along Long creek
in the eastern part of Augusta township. At a small quarry opening on the vVm. Madlener property, in
the southwest one-fourth of the southeast quarter of section 12,
twelve feet of bluish argillaceous shale with occasional siliceous
nodules is exposed. This .shale is ovedain by thirty ' feet of
buff, dolomitic Spergen limestone. Lower Warsaw shale of
similar character outcrops a short distance down the creek. The
bed is eighteen feet thick and is underlain by nine feet of Keo-
kuk limestone and overlain by five feet of brownish massive
dolomitic Spergen limestone. -Henry COttnty.-The Lower Warsaw is exposed along Mud
creek, a stream emptying into Skunk river about one mile east
of Lowell in Henry county. Outcrops of. this subdivision occur
at intervals along the banks of the creek for a distance of one
mile north of the iron bridge which crosses the stream in the
southern part of section 27, Baltimore township. Farther up
the creek outcrops of the Keokuk limestone appear, a fact which
suggests an upward flexure of the strata at this place. Complete sections of the Lower Warsaw are wanting at this
locality as a result of erosion and slumping. But for the abund-
anc'e and perfection of its geodes this place is unexcelled. The
section here given was measured a few rods north of the iron
bridge mentioned above, at a low bluff on the east side of the
creek. A section along the bed and banks of a creek emptying into LOWER WARSAW IN HENRY COUNTY LOWER WARSAW IN HENRY COUNTY 197 Seotion of Lower Warsaw beds in seotio~ 22, Balt·imore township. Seotion of Lower W(krSaW beds on Mud oreek. _..................... 1
6. Shale, bluish, argillaceous, soft ................. _ ................ _................. 2
3
5. Limestone, ash·colored, soft, impure, shaly, arenaceous in the
upper part ........... _ .......... _ ................ _ .... _ .... _ .................................. _. 1
3
4. Shllle, bluish, argillaceous ... _ .......... _ ...................... _ .. _ .. _ ...... _....... 1
6
3. Concealed, probably soft shale ......... _ .......... _ .... _........................... 6
2. Limestoue, soft, gray, shaly, with bands of irregular siliceous
segregations; exposed iDi a little gully near the main strearn.... 2
1. Limestone, brownish, dolomitic, medium· grained in middle part
but fine· grained above and below. Shaly in lower .part. Con·
tact with Keokuk limestone below concealed ... _ ................ _......... 3 Seotion in western part of J alC7cs011i town.ship. LoWER S'.r. LOUIS. FEE(r
INCHES
11. Limestone, buff, do·lomitic, massive, exposed along the bed of
the creek ... _ ...... _ .................................................. _ .......... _..... 5-6
10. Limestone, dark gray, compact, dense, fine·grained, much
brecciated and mashed; forming low moUil1ds alO'I\g the bed of
the creek a Sihort distance above ... _ .......... _ ................................... 1¥.l-21h
LOWER WARSAW. 9. Limestone, brownish, dolomitic, thin·beddied, locally arenaceous
in part ......... _ ............................ _ .... _ .......... _......................................... 1
1
8. Sandstone, soft, fin&-grained, bluish ... _ ............ _ ........................ _... 3
8
7. Sandstone, bluish, fine'gro.ined, filled with large angular frag·
ments of white chert ... _ .............................................. _..................... 1
6. Shale, bluish, argillaceous, soft ................. _ ................ _................. 2
3
5. Limestone, ash·colored, soft, impure, shaly, arenaceous in the
upper part ........... _ .......... _ ................ _ .... _ .... _ .................................. _. 1
3
4. Shllle, bluish, argillaceous ... _ .......... _ ...................... _ .. _ .. _ ...... _....... 1
6
3. Concealed, probably soft shale ......... _ .......... _ .... _........................... 6
2. Limestoue, soft, gray, shaly, with bands of irregular siliceous
segregations; exposed iDi a little gully near the main strearn.... 2
1. Limestone, brownish, dolomitic, medium· grained in middle part
but fine· grained above and below. Shaly in lower .part. Con·
tact with Keokuk limestone below concealed ... _ ................ _......... 3 1. Limestone, brownish, dolomitic, medium· grained in middle part
but fine· grained above and below. Shaly in lower .part. Con·
tact with Keokuk limestone below concealed ... _ ................ _......... Seotion of Lower W(krSaW beds on Mud oreek. Bl ff
f h
L
W
b d
b
hi
f
i
h i h Bluffs of the Lower Warsaw beds about thirty feet in height
are present about three-fourths of a mile north of the last men-
tioned point, in the extreme northern part of section 27 and the
southernmost part of section 22, on the east bank of the stream. The natur.e of the beds at this point, howeVier, is largely ob-
scured on account of slumping and the encroachment of vegeta-
tion upon the weathered slopes of the material. Many geodes
occur in the beds and the weathered slopes of the deposit are
strewn with specimens. Some of these have a diameter as great
as eighteen inches. The following section of the Lower Warsaw
was measured in a ravine which opens into Mud creek from the
east about one-fourth mile north of these bluffs: Seotion of Lower Warsaw beds in seotio~ 22, Balt·imore township. FEET
INCHES
5. Limestone, massive, magnesian, yello·wish, no- geodes nor fos·
sils noted .............................................................................................. 4
4. Shale, bluish, calcareous; grading upward into limestone ........ 2
3. Limestone, impure, buff, magnesian .............................................. 1
8
2. Shale, calcareous, bearing several large geodes ........................ 2
1. Shale, bluish, argillaceous; bearing rounded caJcareous nodules
near the top. Exposed ...................................................................... 4 A section along the bed and banks of a creek emptying into MISSISSIPPIAN STRATA IN IOWA 198 Skunk river from the south a short distance west of Webster's
mill in the western part of section 4 of Jackson township, shows
the Lower Warsaw in contact with the overlying St. Louis and
the underlying Keokuk limestone. The section of the Keokuk
at this point is described on pages 174 and 175 of this report. Seotion in western part of J alC7cs011i town.ship. LoWER S'.r. LOUIS. FEE(r
INCHES
11. Limestone, buff, do·lomitic, massive, exposed along the bed of
the creek ... _ ...... _ .................................................. _ .......... _..... 5-6
10. Limestone, dark gray, compact, dense, fine·grained, much
brecciated and mashed; forming low moUil1ds alO'I\g the bed of
the creek a Sihort distance above ... _ .......... _ ................................... 1¥.l-21h
LOWER WARSAW. 9. Limestone, brownish, dolomitic, thin·beddied, locally arenaceous
in part ......... _ ............................ _ .... _ .......... _......................................... 1
1
8. Sandstone, soft, fin&-grained, bluish ... _ ............ _ ........................ _... 3
8
7. Sandstone, bluish, fine'gro.ined, filled with large angular frag·
ments of white chert ... _ .............................................. Seotion in western part of J alC7cs011i town.ship. Seotion of Lower W(krSaW beds on Mud oreek. 3 The following species · were collected from bed 1: Pustula
biseriata (Hall), Spirifer tenuicostatus Hall, and Composita
trinuclea (Hall). Beds 7, 8 and 9 possibly represent the Sper-
gen formation in an attenuated condition. Van Buren County.-The Lower Warsaw is present in Van
Buren county though it is somewhat thinner and less typically
developed than at Warsaw, Illinois, the type locality. The beds may be studied to good advantage in this county
along Indian creek near Farmington, on Bear creek at Vernon,
on Copperas creek above Bentonsport, in the north bluff of Des
Moines river just below Bentonsport and on Potters branch
near Bonaparte. The Lower Warsaw is well expoS'ed in the north bluff of Des
Moines river one-fourth mile below the railroad station at Ben-
tonsport. It yields numerous fossils throughout its exposure. A section of the underlying Keokuk beds at this locality has
been described in a preceding chapter. LOWER WARBA W FOSSILS AT BENTONSPORT LOWER WARBA W FOSSILS AT BENTONSPORT 199 Seotion of L ower Warsaw beds one-fourth mile below Bentonsport_ Seotion of L ower Warsaw beds one-fourth mile below Bentonsport_ rsaw beds one-fourth mile below Bentonsport_ Seotion of L ower Warsaw beds one-fourth mile below Bentonsport_
8_
Concealed (to bro~ of bluff)
FEET
INCHES
DES MOINES
7. Sandstone, gray to whitish, weathering yellowish, bearing a
few plant remains. Exposed _________________________________________________________
1
5
6. Concealed _____________________________________________________________________________________________
4
LOWER ST_ LoUIS
. ,
5. Limestone, broW'Illish, dolomitic _____________________________________________________
4
4. Concealed _____________________________________________________________________ ________________________ 27
10
LOWER WARSAW
3. Shale, bluish, argillaceous, with oecasional layers of brownish
impure limestone, containing a few imperfect siliceous geod.es. Poorly exposed on slope of bluff ________ .. ___________________________________________ 20
2. Limestone, gray, fine-grained, brittle, fucoidal, with occasional
thin layers of coarse-grained bluish gray limestone in middle
part and in the basal parts a few fine-grained impure layers
which weather yellowish __________________________________________________________________
4
1. Limestone, shaly, grayish weathering yellowish, filled with
bryozo3JILS ___________________________________________________________________________________________
3 8_
Concealed (to bro~ of bluff)
DES MOINES
7
Sandstone
gray to whitish
w 8_
Concealed (to bro~ of bluff)
DES MOINES
7
S
d t
t
hiti h ________________________________________
LOWER ST_ LoUIS
5
Limestone
broW'Illish
dolomitic 5. Limestone, broWIllish, dolomitic
4. Concealed _____________________________________ ______________________________________
LOWER WARSAW
3
Sh l
bl i h
ill
i h 3. Shale, bluish, argillaceous, with oecasional layers of brownish
impure limestone, containing a few imperfect siliceous geod.es. Poorly exposed on slope of bluff ________ .. ___________________________________________ 20
2
Limestone gray
fine grained
brittle
fucoidal
with occasional 1. Limestone, shaly, grayish weathering yellowish, filled with
bryozo3JILS ___________________________________________________________________________________________
3 The fossils identified from beds 1, 2 and 3 of the Lower War-
saw are as follows : List of fossils from bed 1 of Lower Warsaw beds near BentonspO'1't. f f
f
f
p
ANTHOZOA-
Triplophyllum dalei (M.-E. and H.)
Amplexus sp. Monilopora sp. BLASTOIDEA.-
Metablastus wortheni (Hall)
CRINOIDEA.-
Dorycrinus sp. Barycrinus 8p. Barycrinus 8p. ECHINOIDEA-
Archaeocidaris sp. BRYOZOA-
Meekopora sp. Meekopora. sp. Fistulipora , sp. Stenoporlli 8p. Leioclmna punctatum (Hall)
Leioclema foliatum IDrich
Fenestella serratula IDrich
Fooestella multispinosa IDrich
Fenestella l'udis IDrich
Fenestella triserialis Ulrich
Fenestella tena;x IDrich
Fenestella exigua IDrich
Fenestella sp. Fenestella sp. Fenestella sp. Fenestella sp. Hemitrypa proutana IDrich
Hemitrypa nodosa IDrich
Hemitrypa aspera Ulrich
Hemitrypa perstriata IDrich
Hemitrypa cf_ H. beedei Cumings
Hemitrypa Bp. Archimedes owenanus Hall ~
Archimedes negligens IDrich
Archimedes sp. Archimedes sp. Archimedes Bp. LOWER WARBA W FOSSILS AT BENTONSPORT Polypora retrorsa IDrich
Polypora halliana Prout
Polypora spi:n.i.nodata. IDrich
Polypora Bp. Polypora sp. Pinnatopol'a sp. Rhombopora attenuata IDrich
Rhombopora varians Ulrich
Bactropora simplex IDrich
Streblotrypa cf. S. radialis Ulrich
Streblotrypa major IDrich
Cystodictya nitida IDrich
Cystodictya americana Ulrich
Cystodictya. sp. Phractopora trifoJia (Rominger)
Glyptopora sageneHa (Prout)
Glyptopol1a keyserlingi (Prout)
Glyptopora eleg!lJ1lS (Prout)
G>lyptopora sp. Glyptopora Bp_
Cyclopora sp . . Worthenopora spinosa IDrich
BRACHIOPODA-
Schuchertella
~ sp. Camarotoechi·a mutata (Hall)
Dielasma. sp. Spiriferina sp. Spirifer cf. S_ pellaensis Weller
Spirifer tenuicostatus Hall
Brachythyris subcardiformis (Hall)
Syringothyris subcuspidatus (Hall)
Reticl1laria pseudolineata (Hall) ANTHOZOA-
Triplophyllum dalei (M.-E. and H
Amplexus sp. Monilopora sp. BLASTOIDEA.-
Metablastus wortheni (Hall)
CRINOIDEA.-
Dorycrinus sp. Barycrinus 8p. Barycrinus 8p. ECHINOIDEA-
Archaeocidaris sp. BRYOZOA-
Meekopora sp. Meekopora. sp. Fistulipora , sp. Stenoporlli 8p. Leioclmna punctatum (Hall)
Leioclema foliatum IDrich
Fenestella serratula IDrich
Fooestella multispinosa IDrich
Fenestella l'udis IDrich
Fenestella triserialis Ulrich
Fenestella tena;x IDrich
Fenestella exigua IDrich
Fenestella sp. Fenestella sp. Fenestella sp. Fenestella sp. Hemitrypa proutana IDrich
Hemitrypa nodosa IDrich
Hemitrypa aspera Ulrich
Hemitrypa perstriata IDrich
Hemitrypa cf_ H. beedei Cumings
Hemitrypa Bp. Archimedes owenanus Hall ~ Dorycrinus sp. Barycrinus 8p Barycrinus 8p. Barycrinus 8p MISSISSIPPIAN STRATA OF IOWA 200 CHOithyridina parvirostris (M. and W.)
Orthonychia sp. GASTROPODA-
TRILOBITA-
Platyceras sp. Griffithides f sp. Orthonychia ci. O. acutirostra Hall CHOithyridina parvirostris (M. and W.)
Orthonychia sp. GASTROPODA-
TRILOBITA-
Platyceras sp. Griffithides f sp. Orthonychia ci. O. acutirostra Hall List of fossils from bed 2 of Lower Warsaw beds near Bentonsport. f f
f
f
p
ANTHOZOA-
Zaphrentis sp. Triplophyllum pellaellsis (Worthen)
Amplexus sp .. Syringopora sp. Monilopora sp. CRINOIDEA-
Actinocrinus sp. ECHINOIDEA-
Archaeocidaris keokuk Hall
Pholidocidaris irregularis (M. and W.)
BRYOZOA-'
Stenopora sp. Leio,clema punctatum (Hall)
Fenestella serratula Ulrich
Fenestella multispinosa Ulrich
F ellestella exigua Ulrich
Fellestella sp. Fenestella sp. Fenestella sp. Hemitrypa sp. Archimedes sp. Polyp ora cf. P. va,rso·viensis Prout
Polypora varsoviensis Prout
Polyp ora sp. . Polypora sp. Ptilopora f sp. Rhombopora varians 1nrich
Rhombopora transversalis Ulrich
Rhombopora , sp. Bactropol'a simplelX 1nricil
Taeniodictya ramulosa 1nrich
Cystodictya ilp. Phractopom trifolia (Rominger)
Glyptopora sageoolla var. ,
Glyptoporra sp. CycIopora , sp. BRACHIOPODA-
Schuchertella ~ ' sp . Productus ovatus Hall
Productus setigerus Hall
Productus sp. Productus sp. Productus sp. Avonia ~ sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Pustula sp. Rhipidomolla dubia (Hall)
Oamarotoechia IDuta1Ja (Hall)
Dielasma inftata Weller f
Dielasma sp. Girtyella indiaIlJensis (Girty)
Spiriferina sp. Spirifer rostell:'1Jtus HalL ,
Spirifer tenuicostatus Hall
Spirifer sp. Ikachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Reticu laria setigel'a (Hall)
;Eumetria verneuiliana (Han)
,
Cliothyridina obmaxima (McChesney)
Clilothyridina parvirostris (M: and W.)
PELECYPOD A-
ConcardiUlll sp. Schizodus sp. Schizodus sp. Schizodus sp. Schizodus sp. Aviculopecten , sp. Aviculopecten sp. Aviculopecten sp. Aviculopecten sp. Lithophagus illinoisensis Worthen
Cypricardinia sp. SCAPHOPODA-
Laevidenltalium sp. GASTROPODA-
Orthonychia sp. TRILOBITA--
Griffithides
~ sp. ANTHOZOA-
Zaphrentis sp. Triplophyllum pellaellsis (Worthen)
Amplexus sp .. Syringopora sp. Monilopora sp. CRINOIDEA-
Actinocrinus sp. ECHINOIDEA-
Archaeocidaris keokuk Hall
Pholidocidaris irregularis (M. and W.)
BRYOZOA-'
Stenopora sp. Leio,clema punctatum (Hall)
Fenestella serratula Ulrich
Fenestella multispinosa Ulrich
F ellestella exigua Ulrich
Fellestella sp. Fenestella sp. Fenestella sp. Hemitrypa sp. Archimedes sp. Polyp ora cf. P. va,rso·viensis Prout
Polypora varsoviensis Prout
Polyp ora sp. . Polypora sp. Ptilopora f sp. Rhombopora varians 1nrich
Rhombopora transversalis Ulrich
Rhombopora , sp. Bactropol'a simplelX 1nricil
Taeniodictya ramulosa 1nrich
Cystodictya ilp. Phractopom trifolia (Rominger)
Glyptopora sageoolla var. ,
Glyptoporra sp. CycIopora , sp. BRACHIOPODA-
Schuchertella ~ ' sp . Productus ovatus Hall
Productus setigerus Hall
Productus sp. Productus sp. Productus sp. Avonia ~ sp. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
Pustula sp. Rhipidomolla dubia (Hall)
Oamarotoechia IDuta1Ja (Hall)
Dielasma inftata Weller f
Dielasma sp. Girtyella indiaIlJensis (Girty)
Spiriferina sp. Spirifer rostell:'1Jtus HalL ,
Spirifer tenuicostatus Hall
Spirifer sp. List of fossils from bed 2 of Lower Warsaw beds near Bentonsport. Ikachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia pseudolineata (Hall)
Reticu laria setigel'a (Hall)
;Eumetria verneuiliana (Han)
,
Cliothyridina obmaxima (McChesney)
Clilothyridina parvirostris (M: and W.)
PELECYPOD A-
ConcardiUlll sp. Schizodus sp. Schizodus sp. Schizodus sp. Schizodus sp. Aviculopecten , sp. Aviculopecten sp. Aviculopecten sp. Aviculopecten sp. Lithophagus illinoisensis Worthen
Cypricardinia sp. SCAPHOPODA-
Laevidenltalium sp. GASTROPODA-
Orthonychia sp. TRILOBITA--
Griffithides
~ sp. p
p
Lithophagus illinoisensis Worthen List of fossils fr01n bed 3 of Lo,wer Warsaw beds near Bentonsport. BRYOZOA-
Stenopora sp. Leioclema punetatum (Hall)
F enestella serratula Ulrich
Fenestella tenax 1nrich
Fenestella multi spinosa Ulrich
Archimedes negligens 1nrich
Archimedes owenanus Hall
Polypora varsoviJensis Prout
Ptilopora. sp. -
Rhombopora attenuata 1nrich
Rhombopora
~ asperula 1nrich
Cystodictya linea,ta 1nrich
PhractoplO~'a tl'ifoJia (Rominger)
Glyptopora sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Rhipidomella dubia (Hall)
Spirifer keokuk Hall
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Composita globosa Weller BRYOZOA-
Stenopora sp. Leioclema punetatum (Hall)
F enestella serratula Ulrich
Fenestella tenax 1nrich
Fenestella multi spinosa Ulrich
Archimedes negligens 1nrich
Archimedes owenanus Hall
Polypora varsoviJensis Prout
Ptilopora. sp. -
Rhombopora attenuata 1nrich
Rhombop
Cystodict
PhractoplO
Glyptopo
BRACHIOPODA
Orthotete
Rhipidom
Spirifer
Spirifere
Reticular
Composit Rhombopora
~ asperula 1nrich
Cystodictya linea,ta 1nrich
PhractoplO~'a tl'ifoJia (Rominger)
Glyptopora sp. BRACHIOPODA-
Orthotetes keokuk (Hall)
Rhipidomella dubia (Hall)
Spirifer keokuk Hall
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Composita globosa Weller BRYOZOA-
Stenopora sp. Leioclema punetatum (Hall)
F enestella serratula Ulrich
Fenestella tenax 1nrich
Fenestella multi spinosa Ulrich
Archimedes negligens 1nrich
Archimedes owenanus Hall
Polypora varsoviJensis Prout
Ptilopora. sp. -
Rhombopora attenuata 1nrich LOWER WARSAW FOSSILS NEAR FARMINGTON 201 The following section is exposed along Indian creek a short
distance back from its mouth, near Farmington: Section on lndiam creek nC(1l1" Farmington. FEET
INCHES
7. Loess ............... _..................................................................................... 2
6. Till, yellowish, arenaceous; passing locally into an incoherent
stratified sand ... _ .... _ ................ _ ................ _ .... _ .......... _ .. _ .... _ .......... _ 19
5. Shale, bluish, argillaceous, laminated; no geodes oor calcar-
eous nodules ... _ .... _ .......... _ .... _ .......... _ .......... _ .... _ .. _ .. _ ................ _..... 4
10
4. Limestone, bluish, fine· grained, magnesian; pinching out later-
ally ... __ .............. _ .... _ .......... _ .......... _ ...... _ .. _ .......... _ ....•... _ .... _........... 1
10
3. Shale, bluish, argillaceous, no geodes ... _ .... _ .... _ .................... _..... 2
2. List of fossils from bed 2 of Lower Warsaw beds near Bentonsport. Limestone, bluish, fine· grained, magnesian; passing latera.lly
into shale ................................................... _ .... __ .. __ .. _ .... _ .... _ .... _..... 1
1. Shale, bluish, laminated, argillaceous; bearing geodes and
calcareous nodules in lower part ............... _ .... _ ................ _........... 4 Beds 1 to 5 represent the Lower Warsaw. A similar section may be studied along Bear creek in the
northeast quarter of section 11 of Henry township, about six
miles northwest of the Indian creek locality. Section of Lower War8C/W beds on Bear creek. Section of Lower War8C/W beds on Bear creek. FEET
INCHES
3. Shale, bluish, argillaceous; with occasional impure fossiliferous
limestone flakes; more calcareous amd bearing siliceous geodes
in basal part ......... _ ............................ _ .......... _ .... _ .... _ .... _ .... _ ...... _... 15
2. Limestone, grayish, medium·grained, fossiliferous ................... _. 2--19
1. Shale,. bluish, argillaceous; with thin seams of impure fossili·
ferous limestone. Exposed to bed of creek ._ .. _ .................... _... 11
,6 The species collected from the various beds are as follows: List of fossils fro'TIt bed 1 of above section. List of fossils fro'TIt bed 1 of above section. List of fossils fro'TIt bed 1 of above section. List of fossils fro'TIt bed 1 of above section. ANTHOZOA-
Triplophyllum dalei (M.·E. and H.)
Monilopora beecheri Grabau
BRYOZOA-
Stenopora sp. Leioclema. punctatum (Hall)
Fenestella rudis Ulrich
Fenestella serratula Ulrich
Fenestella multispinosa Ulrich
Fenestella sp. Hemitrypa. sp. Archimedes negligens Ulrich
Rhombopora attenuata Ulrich
Rhombopora varians Ulrich
Bactropora simplex Ulrich
Cystodictya lineata Ulrich
W.orthenopora spinosa Ulrich
List of fossils from b~d t of above seotion. BRYOZOA-
Stenopora sp. Fenestella multispinJOsa Ulrich
Archimedes sp. Bactropora simplex Ulrich
Glyptopora m'icheli..n!i.a (Prout)
W orthenopora spinosa Ulrich
DRACHIOPODA-
Rhipidomella dubia (Hall)
Spiriferina sp List of fossils froTIt bed 1 of above section. ANTHOZOA-
Triplophyllum dalei (M.·E. and H.)
Monilopora beecheri Grabau
BRYOZOA-
Stenopora sp. Leioclema. punctatum (Hall)
Fenestella rudis Ulrich
Fenestella serratula Ulrich
Fenestella multispinosa Ulrich
Fenestella sp. Hemitrypa. sp. Archimedes negligens Ulrich
Rhombopora attenuata Ulrich
Rhombopora varians Ulrich
Bactropora simplex Ulrich
Cystodictya lineata Ulrich
W.orthenopora spinosa Ulrich
Li t
f f
il
f
b~d t
f
b
ti BRYOZOA-
Stenopora sp. Fenestella multispinJOsa Ulrich
Archimedes sp. Bactropora simplex Ulrich
Cystodictya linea.ta Ulrich 202 MISSISSIPPIAN STRATA OF IOWA List of fossils from bed :1 of above section. BRYOZOA-
Stenopora sp. Rhombopora attenuata Ulrich
Pluactopora trifo,lia (Rominger)
Glyptopoo-a michelinri.a (Prout)
Glyptopora sp. W orthenopora spinosa Ulrich
BRACHIOPODA-
Leioclema punctatum (Hall)
Fenestella erigua Ulrich
Fenestella serratula Ulrich
Fenestella tenax Ulrich
Hemitrypa sp. Polypora retrorsa Ulrich
Polypora varsoviensis Prout
Rhipidoonella dubia (Hall)
Spiriferina (species undescribed)'
Spirifer tenuicostatus Hall Hemitrypa sp. P l Polypora retrorsa Ulrich
P l
i
i
P Polypora varsoviensis Prout Geodes do not occur at this place but they are common in the
shale farther up the creek. The following section of the Lower \Varsaw is ' exposed along
Copperas creek two miles northwest of Bentonsport. Seotion of Lower Warrsaw beds along Coppetras creek. FEET
4. Drift ...... _ ..... _ .............. _ ....................... _ ...... _ ..................... _ .................. _
Ill.! 3. Shale, bluish, weathering drab ................... _ .. _ .................. _........... 4
2. Limestone, fine·grained, impure, shaly in middle ...................... 2
1. Shale, bluish, nonfossilife rous; bearing imperfect geodes and
discontinuous bands of siliceous material in lowe-r part ........ 11 Seotion of Lower Warrsaw beds along Coppetras creek. At an exposure on Potter's branch in the southeast one-fourth
of the southeast quarter of section 9, Bonaparte township,
eleven feet of Lower Warsaw shale, argillaceous above but cal-
careous below, is overlain by thirty-three feet of Spergen shales
~nd limestones. The following section is shown a few rods farther down in the
north bank: Section on Potters branch. Section on Potters branch. LOWER WARSAW
FEET
8. Slope strewn with imperfect siliceous geodes .............................. 21
7. Limestone. buff, massive, dolomitic, shaly in lower part ...... 13
KEOKUK
6. Limestone, bluish gray, subcrystalline, unaltered, fossiliferous · 2
5. Limestone, yellowish, dolomitic, vesicular, tough, massive.... 2
4. Shaly. parting ... _ ................................................................................... . 3. Limestone, bluish, compact, massive, dolomiJtic, with molds of
fossils ... _ .... _ .... _ .................................. _ .............. _~ .......... _ ................ _ 2
2. Shale, bluish, argillaceous ... _ ................ _ .. _ ...... _............................... 1
1. Limestone, bluish gray, unaltered, with shaly seams in . upper and lower part. Exposed to bed of creek .................... 4
INCHES
6
10
8
1
9 An outcrop of bluish Lower Warsaw shale appears in the east
bank of Rock creek about one hundred yards above the railway
bridge in the northwest quarter of section 21, Washington town-
ship, Van Buren county. 4 Geol. of Iowa, TOI. I, part 1, p. 97; 1858, List of fossils from bed :1 of above section. It is nine feet in thickness and con- UP.PER WARSAW NEAR WARSAW 203 tains thin intercalated flakes of limestone. Both the shale and
the limestone are fossiliferous. A thin bed of fine-grained
cream-colored limestone is exposed at the top of the section. The follo'wing species were collected from the shale: LiJst of fossils fr01'Y! Lower Warsa'w shale on Rock cree7c. LiJst of fossils fr01'Y! Lower Warsa'w shale on Rock cree7c. BRYOZOA-
Stenopora sp. Leioclema punctatum (Hall)
. Fenestella serratula Ulrich
Hemitrypa sp.'
Archimedes sp. Rhom bopora attenuata Ulrich
Rhombopora , asperula Ulrich
Cystodictya lineata Ulrich
Worthenopora spinosa Ulrich
BRACHIOPODA-
Pustula biseriata (Hall) ,
Rhipidomella dubia (Hall)
Spiriferina sp. Spirifer tenuicostatus Hall
PELECYPODA~
Cypricardinia indianensis Hall Rhom bopora attenuata Ulrich
Rhombopora
asperula Ulrich Rhombopora , asperula Ulrich
C
t di t
li
t
Ul i h Cystodictya lineata Ulrich About ten feet of bluish calcareous shale of a slightly lower
horizon outcrops in the west bank near the mouth of the creek. Reddish siliceous segregations appear in this member. DESCRIPTION OF THE TYPE SECTION 4 to 8 DESCRIPTION OF THE TYPE SECTION The Upper member of the Warsaw formation is typically de-
veloped near the town of Warsaw in Hancock county, illinois,
where it was examined and described by Hall~ under the head-
ing of "\Varsaw, or Second Archlmedes limestone." The most
satisfactory exposures appear along a small tributary of Mis-
sissippi river a short distance northeast of the town. The up-
per layers of the Keokuk limestone, the entire section of the
Lower and Upper Warsaw, the Spergen limestone, and the
basal part of the St. Louis limestone are ~cellently exposed
along this creek. The upper layers of the Keokuk limestone ap-
pear at the north of the creek, and along its bed for a short dis-
tance up str~am. The Warsaw beds outcrop thence in the bed
of the creek and along its bank continuously as far as a small
waterfall beyond the first stone arch bridge. The basal lime-
stone of the Upper 'Warsaw caps the ledge at the falL Above
this point the Upper Warsaw beds are exposed in the bed of the
stream and along its banks for a considerable distance, finally
giving way to the Spergen and St. Louis limestones. Th
i
f h
U
W
hi h
f ll The section of the Upper Warsaw, which was carefully meas-
ured in the bluffs below the first stone bridge, and along the 4 Geol. of Iowa, TOI. I, part 1, p. 97; 1858, MISSISSIPPIAN STRATA OF IOWA 204 stream above the small waterfall, is given below, the succession
being from above downwards: Section of Upper Warsaw beds northeast of Warsaw. 5. Limestone, bluish, magnesian, locally arenaceous or shaly in
part;
the
"arenaceo·magnesian
limestone"
of
authors. FEET
Fossils scarce except in lower part .............................................. 3 to 7%
4. Shale, bluish, argillaceous; with interbedded layers and
flakes of gray sub crystalline limestone, some layers of which
are shaly'. A fine· grained bluish fossiliferous sandstone near
the midcUe
............ _ ....................................................................... ,.... 18%
3. Limestone, bluish gray, lenticular, sub crystalline" locally
dolomitic in part. Massive where fresh but weathering to
thin layers ............................. _ ...................................................... _... 0 to 3
2. Shale, bluish, argillaceous, with occasional thin layers of
shaly, fossiliferous limestone ....... _._ .......... , .... __ .............................. 7
1. Limestone, bluish, magnesian; layers thin and undulating in
creek bed, but thicker and morc even in blaiIlk od' creek further
down .......... _ ................................... ' ...................... _ ................................. Section of Upper Warsaw beds northeast of Warsaw. 2. Shale, bluish, argillaceous, with occasional thin layers of
shaly, fossiliferous limestone ....... _._ .......... , .... __ .............................. 7 1. Limestone, bluish, magnesian; layers thin and undulating in
creek bed, but thicker and morc even in blaiIlk od' creek further
down .......... _ ................................... ' ...................... _ ................................. 4 to 8 Bed 1 represents the basal member of the Upper Warsaw. At Keokuk, and in the Soap Factory Hollow section, two mjles
below Warsaw, this member is represented by an unaltered
thin-bedded fossiliferous limestone. Evidently dolomitization
has affected this ' bed locally and incompletely. Occasional
seams in the dolomitjc limestone are filled with the molds of
fossils, mainly of, bryozoans. It also bears a few small irregu-
lar and imperfect siliceous geodes lined with quartz or calclte,
or both. Surfaces of the layers are pitted locally due to the
weathering and removal of small pyrite nodules. The contact
of this bed with the topmost shale member of the Lower War-
saw is gradational. The uppermost part of bed 2 furnishes a clay product valued
for molding purposes. It has been worked in a desultory man-
ner just west of the first stone bridge. This bed bears few well
preserved fossils except in the interbedded limestone layers. Bed 3 may aptly be called the lenticular limestone .member. The thickening and thinning appears to take place from the
lower side only. In places it pinches and swells very abruptly
and at one point in the bank of the creek it disappears complete·
ly for a distance of several yards. It is there replaced by shale. It is usually in the form of a massive ledge when fresh but
weathers into thin layers. It is divided locally into two parts
by a shaly parting. The surfaces of the layers are pitted and
are blotched here and there with limonite, a condition which is FOSSILS OF UPPER WARSAW BEDS 205 caused by the oxidation and 'weathering of pyrite nodules which
nre common in the fresh rock. This bed of limestone is locally dolomitic in part, but the
dolomite occurs at no definite level. At one point it is in the
upper part, at another it is in the lower. Evidently the altera-
tion 'was very local and imperfect. 'Where it is dolomitized the
limestone carries molds of fossils only. Section of Upper Warsaw beds northeast of Warsaw. In bed 4 a conspicuous ten-inch layer of bluish fossiliferous
sandstone with fucoidal markings appears seven feet ten inches
below the top. Ten and one-half feet below the top there occurs
an eight inch layer of limestone which thickens abruptly in the
bed of the creek below Main ,street bridge. It attains a thickness
of four feet at one point. It bears many spiral axes of Archi-
medes wortheni and may be designated the Archimedes lime-
stone. The following detailed section will show the nature of
the individual layers of this member: Layers of B ed 4. FEET
INCHES
Shale, with thin layers of fossiliferous limestone interbedded. Well exposed along creek between the bend and the falls of
the north fm'k ___ ...... _ .................................. _ .............. __ ... _ ........ _ .. ___ ...... _ 7
10
Sandstone, fine-grained, bluish, fucoidal ______________ ._. ________ . ____ . _____ .. ___
10
Shale, blu~sh, argillaceous _ ................... __ .. _ ..... _. ___ ~ ...... ____ . __ .... _ ...... ___ .. ____
1
10
Limestone, gray, filled with Archvmedes and other fossils. ______ . ______ ._
8
Shale
____ ... ___ .. ___ ._. ____ .. _._ .... ___ . _____ .. __________ . ____ . _______ . ____ . ___ ._._ .. ____________ . ___ .. :_._.____
1
6
Limestone, shaly _. ___ . ____ . ___ . ____ . __ ... ___________ . ________ . __ . _________ . ______ ..... ____ . ____ ._____
1
3
Shale ___________ . ____ .. ____ .. ____ . _____ . __ .. __ .. ____ . _________ . _____ ....... __ .. ________ ... _____________________
10
Limestone
_________________________ .. ___________________ ....... ____ . ____ . ___ . __ . ____ . ______ . _________ .__
7
Shale ____ .. ____ .. ______ ._. _____ . ______ ._. ___ . ______ . __ . __ . __________ .. ____ ._ .... _. __________ .. _ .. ______________
3
3 Bed 5 is typically represented by massive layers of arenace-
ous magnesian limestone, but in a ravine east of the high school
it is shaly. The shaly facies is bluish and weathers into irregu-
lar chips. The arenaceo-magnesian facies becomes brownish
when weathered. Section of Upper Warsaw beds northeast of Warsaw. Leioclema punctatum (Hall)
Leioclema foliatum Ulrich
Fenestella tenax Ulrich
Fenestella serratula Ulrich
:E'e·nestella rudis Ulrich
F enestella exigua Ulrich
FenesteUa multispinosa Ulrich
Fenestella sp. Fenestella sp. Hemitrypa proutana Ulrich
Hemitrypa noc1osa Ulrich
H~mitryp a sp. Archimedes wortheni Hall
Archimede,s negli.gens Ulrich
Archimedes sp. Fenestralia sancti-Iudovici Prout
Polypora biseriata Ulrich
Polypora varsoviensis Prout
Polyp ora spininodata Ulrich
Polypora sp. Ptilopora prouti Hall
Ptilopora sp. Ptilopora sp. MISSISSIPPIAN STRATA OF lOW A 206 Bl'achythyris subcardiformis (Hall)
Reticularia setigera (Hall)
Eumetl'ia verneuiliana (Hall)
Composita sp. ,
Lithophagus illinoisensis Worthen
GASTROPODA-
Orthonychia sp. TRILOBITA-
PELECYPODA-
Philli psia
~ sp. Cypricardinia indi'anensis Hall
List of fossils from bed 2 of the Upper Warsaw near . Warsaw
ANTHozoA-
Rhombopora varians Ulrich
Tl'iplophyllum dalei (M.-E. and H.)
Cystodictya lineata Ulrich
BRYOZOA-
Cystodictya pustulosa Ulrich ,
Stenopora sp. Glyptopora sp. Leioclema punctatum (Hall)
Cyclopora sp. Archimedes owenanus Hall
Cyclopol'ella
(~) sp. Archimedes wOl'theni Hall
BRACHIOPODA-
Fenestella multispinosa l,"'lrich f
Lingula varsoviensis Worthen
Penestella tenax Ulrich
Productus ovatus Hall
Fenestella sel'ratula Ulrich
Spirifer pellaen.sis Weller
Fene.stella exigua Ulrich
~
Brachythyris subcardiformis (Hall)
Fenestella triserialis Ulrich ,
Reticularia setigera (Hall)
Fenestella sp. Eumetria verneuiliana (Hall)
Hemitrypa proutana Ulrich
PELECYPODA-
Hemitrypa proutana var. nododors-
Lithophagus illinoisensis Worthen
alis Cumings
Cypricardinia indianensis Hall ,
Hemitrypa sp. Aviculopecten sp. Polypora varsoviensis Prout
GASTROPODA-
Polypora biseriata Ulrich
Orthonychia sp. Ptilopora sp. VERTEBRATA-
Rhombopora attenuata Ulrich
Fish teeth Fish teeth Section of Upper Warsaw beds northeast of Warsaw. The fossils collected from the individual members of the Up-
per vVarsaw at this locality are listed below: Li.st of fossils fr01n bed 1 of the Upper Warsaw neal/' Warsaw. Pustula alternata (N. and P.)
Pustula biseriata (Hall)
~
Carnarotoechia mutata (Hall)
Dielasma sp. Girtyella inclianensis (Girty)
Spiriferina sp. Spirifer pellaensis Welle·l'
Spirifer tenuicostatus Hall Pustula alternata (N. and P.)
Pustula biseriata (Hall)
~
Carnarotoechia mutata (Hall)
Dielasma sp. Girtyella inclianensis (Girty)
Spiriferina sp. Spirifer pellaensis Welle·l'
Spirifer tenuicostatus Hall BRYOZOA-
Stenopora sp. FenesteUa serratula Ulrich
Polypora val' ovieusis Prout
Worthenop0Ta spinosa Ulrich
BRACIIIOPODA-
/
Procluctus sp. Procluctus setigerus Hall BRYOZOA-
Stenopora sp. FenesteUa serratula Ulrich
Polypora val' ovieusis Prout
Worthenop0Ta spinosa Ulrich
BRACIIIOPODA-
/
Procluctus sp. Procluctus setigerus Hall 206
MISSISSIPPIAN STRATA OF lOW A
Bl'achythyris subcardiformis (Hall)
Reticularia setigera (Hall)
Eumetl'ia verneuiliana (Hall)
Composita sp. ,
Lithophagus illinoisensis Worthen
GASTROPODA-
Orthonychia sp. TRILOBITA-
PELECYPODA-
Philli psia
~ sp. Cypricardinia indi'anensis Hall
List of fossils from bed 2 of the Upper Warsaw near . Warsaw
ANTHozoA-
Rhombopora varians Ulrich
Tl'iplophyllum dalei (M.-E. and H.)
Cystodictya lineata Ulrich
BRYOZOA-
Cystodictya pustulosa Ulrich ,
Stenopora sp. Glyptopora sp. Leioclema punctatum (Hall)
Cyclopora sp. Archimedes owenanus Hall
Cyclopol'ella
(~) sp. Archimedes wOl'theni Hall
BRACHIOPODA-
Fenestella multispinosa l,"'lrich f
Lingula varsoviensis Worthen
Penestella tenax Ulrich
Productus ovatus Hall
Fenestella sel'ratula Ulrich
Spirifer pellaen.sis Weller
Fene.stella exigua Ulrich
~
Brachythyris subcardiformis (Hall)
Fenestella triserialis Ulrich ,
Reticularia setigera (Hall)
Fenestella sp. Eumetria verneuiliana (Hall)
Hemitrypa proutana Ulrich
PELECYPODA-
Hemitrypa proutana var. nododors-
Lithophagus illinoisensis Worthen
alis Cumings
Cypricardinia indianensis Hall ,
Hemitrypa sp. Aviculopecten sp. Polypora varsoviensis Prout
GASTROPODA-
Polypora biseriata Ulrich
Orthonychia sp. Ptilopora sp. VERTEBRATA-
Rhombopora attenuata Ulrich
Fish teeth
List of fossils from bed 3 of the Upper Warsaw near Warsaw . . BRYOZOA-
Stenopora .sp. Archimedes sp. Glyptopora ele·gans (P·rout) ,
W orthenopora spinosa Ulrich
BRACHIOPODA-
Lingula varsoviensis Worthen
Proc1uctus setigerus Hall
Productus ovatus Hall
Productus sp. ,
Pustula biseriata (Hall)
Tetracamera subcuneata (Hall)
Dielasma sp. Spirifer pellaensis Weller
Brachythyris subcardiformis (Hall)
SpirifereUa neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall)
List of fossils from bed 4 of the Upper Warsaw near Warsaw. AN'fHOZOA-
Zaphrentis spinulifera Hall
Zaphrentis cassedyi M.-E . and H. Aulopora sp. Monilopora beecheri Grabau ,
Monilopora sp. VERMES-
Spirorbis sp. BLASTOIDEA-
P entremites conoide·us Hall
ECHINOIDEA-
Archaeocidaris sp. BRYOZOA-
Fistulipora sp. Stenopora sp. 3.
Shale, bluish, argillaceous; geodiferous and nearly banen
of fossils at the town of War,saw but richly fossiliferous in
the Soap Factory Hollow section two miles south ................. . List of fossils from bed 3 of the Upper Warsaw near Warsaw List of fossils from bed 3 of the Upper Warsaw near Warsaw . . BRYOZOA-
Stenopora .sp. Archimedes sp. Glyptopora ele·gans (P·rout) ,
W orthenopora spinosa Ulrich
BRACHIOPODA-
Lingula varsoviensis Worthen
Proc1uctus setigerus Hall
Productus ovatus Hall
Productus sp. ,
Pustula biseriata (Hall)
Tetracamera subcuneata (Hall)
Dielasma sp. Spirifer pellaensis Weller
Brachythyris subcardiformis (Hall)
SpirifereUa neglecta (Hall)
Reticularia pseudolineata (Hall)
Eumetria verneuiliana (Hall)
List of fossils from bed 4 of the Upper Warsaw near Warsaw. AN'fHOZOA-
Zaphrentis spinulifera Hall
Zaphrentis cassedyi M.-E . and H. Aulopora sp. Monilopora beecheri Grabau ,
Monilopora sp. VERMES-
Spirorbis sp. BLASTOIDEA-
P entremites conoide·us Hall
ECHINOIDEA-
Archaeocidaris sp. BRYOZOA-
Fistulipora sp. Stenopora sp. Leioclema punctatum (Hall)
Leioclema foliatum Ulrich
Fenestella tenax Ulrich
Fenestella serratula Ulrich
:E'e·nestella rudis Ulrich
F enestella exigua Ulrich
FenesteUa multispinosa Ulrich
Fenestella sp. Fenestella sp. Hemitrypa proutana Ulrich
Hemitrypa noc1osa Ulrich
H~mitryp a sp. Archimedes wortheni Hall
Archimede,s negli.gens Ulrich
Archimedes sp. Fenestralia sancti-Iudovici Prout
Polypora biseriata Ulrich
Polypora varsoviensis Prout
Polyp ora spininodata Ulrich
Polypora sp. Ptilopora prouti Hall
Ptilopora sp. Ptilopora sp. AN'fHOZOA-
Zaphrentis spinulifera Hall
Zaphrentis cassedyi M.-E . and H
Aulopora sp. Monilopora beecheri Grabau ,
Monilopora sp. VERMES-
Spirorbis sp. BLASTOIDEA-
P entremites conoide·us Hall
ECHINOIDEA-
Archaeocidaris sp. BRYOZOA-
Fistulipora sp. Stenopora sp. Leioclema punctatum (Hall)
Leioclema foliatum Ulrich
Fenestella tenax Ulrich
Fenestella serratula Ulrich CHARACTER OF WARSAW BEDS 207 Uhombopora varians Ulrich
Uhombopora attenuata Ulrich
Rhombopora sp. f
Bactropora simplex Ulrich
~
Cystodictya sp. Cystodictya sp. GIyptopora elegans (p)'out)
Glyptopol'a michelinia (Prout)
Glyptop()ra sagenella (Prout)
Glyptopora sagen ella var. caliculosa
Ulrich '
GIyptopora plumosa (Prout)
Cyclopora sp. Worthenopora spinosa Ulrich
"\Vol'thenopora spatulata (Prout)
Worthenopora sp. BRACHIOPODA-
Lingula varsoviensis Worthen '1
Orthotetes '1 sp. Productus aItonensis N. and P. Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
'l'etracamera subcuneata (Hall)
Dic.]asma sp. Girtyella turgida (Hall) Spiriferina sp. Spirifer tenuicostatus H all
Spirifer indianensis Weller
Spirifer pellaensis Weller
a
Spirifc'r bifurcatus Hall
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Eume,tria verneuiliana (Hall) ,
Cl.iJOIthyridina parvirostris (1£. and W.)
C'omposita trinuclea (Hall)
P ELECYPODA-
Schizodus sp. Aviculopecten sp. Aviculopecten sp. Cypricardinia indiancnsis Hall
Cypricardinia sp. G ASTROPODA-
Platyceras sp. Orthonychia sp. TRILOBITA-
Phillip.sia '1 sp. V ERTEBRATA-
Fish teeth Uhombopora varians Ulrich
Uhombopora attenuata Ulrich
Rhombopora sp. f
Bactropora simplex Ulrich
~
Cystodictya sp. Cystodictya sp. GIyptopora elegans (p)'out)
Glyptopol'a michelinia (Prout)
Glyptop()ra sagenella (Prout)
Glyptopora sagen ella var. caliculos
Ulrich '
GIyptopora plumosa (Prout)
Cyclopora sp. List of fossils from bed 3 of the Upper Warsaw near Warsaw Worthenopora spinosa Ulrich
"\Vol'thenopora spatulata (Prout)
Worthenopora sp. BRACHIOPODA-
Lingula varsoviensis Worthen '1
Orthotetes '1 sp. Productus aItonensis N. and P. Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
'l'etracamera subcuneata (Hall)
Dic.]asma sp. Girtyella turgida (Hall) Uhombopora varians Ulrich
Uhombopora attenuata Ulrich
Rhombopora sp. f
Spiriferina sp. Spirifer tenuicostatus H all
Spirifer indianensis Weller
Spirifer pellaensis Weller
Bactropora simplex Ulrich
~
Cystodictya sp. Cystodictya sp. GIyptopora elegans (p)'out)
Glyptopol'a michelinia (Prout)
Glyptop()ra sagenella (Prout)
Glyptopora sagen ella var. caliculosa
Spirifc'r bifurcatus Hall
Brachythyris subcardiformis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall)
Ulrich '
GIyptopora plumosa (Prout)
Cyclopora sp. Worthenopora spinosa Ulrich
"\Vol'thenopora spatulata (Prout)
Worthenopora sp. BRACHIOPODA-
Lingula varsoviensis Worthen '1
Orthotetes '1 sp. Productus aItonensis N. and P. Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
'l'etracamera subcuneata (Hall)
Dic.]asma sp. Girtyella turgida (Hall)
Eume,tria verneuiliana (Hall) ,
Cl.iJOIthyridina parvirostris (1£. and W.)
C'omposita trinuclea (Hall)
P ELECYPODA-
Schizodus sp. Aviculopecten sp. Aviculopecten sp. Cypricardinia indiancnsis Hall
Cypricardinia sp. G ASTROPODA-
Platyceras sp. Orthonychia sp. TRILOBITA-
Phillip.sia '1 sp. V ERTEBRATA-
Fish teeth Fish teeth Girtyella turgida (Hall) UPPER WARSAW
8. Limestone, bluish, magnesia.n ................... _ ...................................... .
7.
Shale, bluish, argillaceous, with interbedded layers of gray
fossiliferous limestone and fine bluish sandstone ..................... .
6.
Limestone, bluish gray, lenticular ............................ _ ................. .
5.
Shale, bluish, argillaceous, with thin flakes of fo.ssiliferous
limestone .............................................................................................. ..
4.
Limestone, bluish, maguesian ............. _ .................... _ ...................... .
OWER WARSAW
,
3.
Shale, bluish, argillaceous; geodiferous and nearly banen
of fossils at the town of War,saw but richly fossiliferous in
the Soap Factory Hollow section two miles south ................. .
FEET
3-7 11.2
18%
0-3
7
4-8 BRYOZOA-
St Rhombopora attenuata Ulrich
C
l Cyclopora sp. Worthc'nopora Worthc'nopora spinosa Ulrich
Wmthen()pora spatulata (Prou Wmthen()pora spatulata (Prout) The composite section of the Lower and Upper members of
the Warsaw formation as they are developed at the type local-
ities is given below: , Geneml seotion of Warsaw B eds at Warsaiw and Soap Factory Hollow. UPPER WARSAW
8. Limestone, bluish, magnesia.n ................... _ ...................................... . 7. Shale, bluish, argillaceous, with interbedded layers of gray
fossiliferous limestone and fine bluish sandstone ..................... . 6. Limestone, bluish gray, lenticular ............................ _ ................. . 5. Shale, bluish, argillaceous, with thin flakes of fo.ssiliferous
limestone .............................................................................................. .. 4. Limestone, bluish, maguesian ............. _ .................... _ ...................... . LOWER WARSAW
,
3. Shale, bluish, argillaceous; geodiferous and nearly banen
of fossils at the town of War,saw but richly fossiliferous in
the Soap Factory Hollow section two miles south ................. . FEET
3-7 11.2
18%
0-3
7
4-8 8. Limestone, bluish, magnesia.n
7
Sh l
bl i h
ill 4.
Limestone, bluish, maguesian
LOWER WARSAW
, 4.
Limestone, bluish, maguesian List of fossils from bed 5 of :he Upper Wa?'saw n,ear Warsl1!w. List of fossils from bed 5 of :he Upper Wa?'saw n,ear Warsl1!w. BRYOZOA-
Stenopora sp. BRACHIOPODA-
Lingula sp. Archimedes wortheni Hall
Fenestella rudis Ulrich
Fenestella serratula Ulrich
Fenestella multispinosa Ulrich
H emitrypa proutana Ulrich
Polypora biseriata Ulrich
Polypora varsoviensi.s Prout
Rhombopora attenuata Ulrich
Cyclopora sp. Streptorhynchus ruginosum (Hall
and Clarke)
Pustula biseriata (Hall)
Tetracamera subcuneata (Hall)
Dielasma sp. Cyclopora sp. ,
Worthc'nopora spinosa Ulrich
Wmthen()pora spatulata (Prout)
Spirifer pellaensis Weller
Spirifer tenuicostatus Hall
Spiriferella ne-glecta (Hall)
Reticularia setigera (Hall)
P ELECYPODA-
Avicul()pecten sp. GASTROPODA-
Platyceras sp. BRACHIOPODA-
Lingula sp. Streptorhynchus ruginosum (Hall
and Clarke)
Pustula biseriata (Hall)
Tetracamera subcuneata (Hall)
Dielasma sp. Spirifer pellaensis Weller
Spirifer tenuicostatus Hall
Spiriferella ne-glecta (Hall)
Reticularia setigera (Hall)
P ELECYPODA-
Avicul()pecten sp. GASTROPODA-
Platyceras sp. BRYOZOA-
Stenopora sp. Archimedes wortheni Hall
Fenestella rudis Ulrich
Fenestella serratula Ulrich
Fenestella multispinosa Ulrich
H emitrypa proutana Ulrich
Polypora biseriata Ulrich
Polypora varsoviensi.s Prout
Rhombopora attenuata Ulrich
Cyclopora sp. Cyclopora sp. ,
Worthc'nopora spinosa Ulrich
Wmthen()pora spatulata (Prout) UPPER WARSAW
8
Li
t 5. Shale, bluish, argillaceous, with thin flakes of fo.ssiliferous
limestone .............................................................................................. .. 4
Li
t
bl i h
i
7
4 8 208 MISSISSIPPIAN STRATA OF IOWA 2. Limestone, cherty; impure, buff-colored and magnesian at
Warsaw; thin-bedded, gray and nonmagnesian at Soap Fact-
ory Hoilow ... -.-.-_. ___ ... _ ... _ ................. _ ... __ .. __ ............ ___ ..... _ ......... _....... 314
1. Limestone, drab, fine-grained, impure, magnesian. Fos.sils
scarce in geodiferous phase at Warsaw but common in Soap
Factory Hollow section .... __ ... __ ... _._ ....... __ ............ __ ... __ ... __ . __ .. __ .... __ .. _
lllh 2. Limestone, cherty; impure, buff-colored and magnesian at
Warsaw; thin-bedded, gray and nonmagnesian at Soap Fact-
ory Hoilow
...-.-.- . ... ... ................. ... .. ............ ..... ......... ....... 314 y
1. Limestone, drab, fine-grained, impure, magnesian. Fos.sils
scarce in geodiferous phase at Warsaw but common in Soap
Factory Hollow section .... __ ... __ ... _._ ....... __ ............ __ ... __ ... __ . __ .. __ .... __ .. _
lllh The accompanying chart indicates the vertical distribution of
the more characteristic species of the Warsaw fauna through
the several members of the formation as developed at Warsaw
and Soap Factory Hollow. Table showing Range of Species in the Warsaw Formation at Warsaw and Soap
Factory Hollow. Lowe'r I
Upper
I
Warsaw
W'arsaw
I 1 I 2 I 3 I 4 151 6 I 7 i 8 I
z~~~:eO:t~ spergenensis Worthen ________________________________ ______ ______
:x: __________ J
_____ ------ ---J
Zaphrerutis cassedyi M.-E. and H. _____ . _________ . _____________________ . _____ . _____ . ___________ . ______
:x: • ___ ._
Zaphrentis spinulifera Hall _______________________ . ____ ~ __ .__________ ______ ______ ______ ______ ______ ______
x ___ . __
Triplophyllum dalei (M.-E. and H.) ___ . _____ . __ .. ____________ . x
x
x ______
x _________ . _____ . __
Amplexus sp. ---------.--------.-------.----------------------.-----------.-----.. x I x
x --.--. ----. ----.. ----.. ----.. ~~~~~~~~~ ~;.e~~~~-~---~-~~~-~-~--:::::::::::::::::::::::::=::::=::::::: ___ ~_ :::::: ___ ~_ ~~~~:: :::::: :::::: x; ::::::
Aulopora sp. ________ .. __________________ . _____ . _________ .. ____ . ___________ . __________________ . __________ .. ____ .. ______
x . __ ... CRINOIDEA
x -----. ------ ----~- ------ ------ -.--------..I
Agaricocrms wortheni Hall __ .. ___________________ . ____ . _____ . ________ _
Uperocrinus nashvillae (Hall) ____________ .. UPPER WARSAW
8
Li
t ____________________ _ :x: ___________ • ____________________________ . Barycrinus IIp. __________________________ . ________ .. _________________ -----------
x ______ _______________________ . _____ . _____ . BLASTOIDEA
Pentremites conoideus Hall ____ . ___ . _____________________________ . _________ -'-___ . _____ . _________ .__ ______
x __ .. __
Schizoblastus granulosus (M. and W.) _____________________
:x: 1 _______ __ .. __ ___________ _____ ... ___ . _____ . ECHINOIDEA
I
Archaeocidaris keokuk Hall _____ . ____ . __________ . ____________ .. ______
x _____________________________ . _____ . ___ ._. VERMES
Spirorbis sp. _____ . ___________ . _________________________________________________________
x~
x __________ ._ ______
x _____ _
BRYOZOA
~¥~E;E~~~;~~-::~~:~~::~~~~~~~:;: •• ~. ~-:~ :~.§:I
Cystodictya pustulosa Ulrich ____________________________________ .. :x:
x
x ______
x ___________ . _____ _
g~~:~~~~ ~f:gs:~~inf~r~~:)~~~-:::::~=::~=::=:::::::::::::::::::: :::::: :::~: ---~- ::::::r:::::: -~,- ---~- ::::::
Glyptopo'ra michelinia (Prout) ____________ . _________ ... ____________ ______ ______ ______ ______ ______ ______
x _____ _
Glyptopora sagenella (Prout) ---------------------.-.-------.----------------- ----J----- ---__ --____ ______
x ------ Table showing Range of Species in the Warsaw Formation at Warsaw and Soap
Factory Hollow. RANGE OF FOSSILS IN WARSAW BEDS 2Of) Table showing Range of Species in the Warsaw Formation at Wwrsaw and Soap
Fact01'Y Hollow.-Contimmed. I
Lower]
Upper
1
WarsaJW I
Warsaw
! 1 ! 2 ! 3 ! 4 ! 5 ! 6 ! 7 I 8 I
Glyptopora sageneUa var. caliculosa Ulrich L .............. 1 ... _. -..... ...... ...... ...... x
Glyptopora p~umosa .<Pr?ut)_ ................. _ ........ _._ ... _.......... ...... ...... ...... ...... ...... ...... x
Bactropora sImplex Ulnch L ................................... _ ......... ...... ... _. ...... ...... ...... x
Rhombopora varians Ulrich ........................... _............. x ...... x ...... x _...... x
Rhombopora attenuata Ulrich ........................... _ .... _.... x
x
x ...... x ... _. x xf
Fenestella serratula Ulrich ............. _ ... _ .... _................... x
x
x
x
x ...... x
x
Fcnestella limitaris Ulrich .................... _ .... _ .............. _.. x ............ ............... _ ........ ..... . Fenestella triseriallis Ulricj:J. _ ..................... _ .. _ ........ _.... x
x
x _..... x ............ ... _. Fenestella tenax Ulrich ....... _ .......... _ .. _....................... x
x
x ...... x ...... x .... :. Fenestella IDultispinosa Ulrich .... _ ................... _ .. _ ..... _.. x
x
x ...... x ...... x
x
Fenestella funicula Ulrich ............. _ .. _ ................ _........ x _ ........... ......... _ .... _ .. _ ........ _. UPPER WARSAW
8
Li
t Fenestella compressa Ulrich ....... _ ................ _ .. _........... x ...... x ..................... _ ...... . Fenestella exigua Ulrich ................................................ ...... ...... x ...... x ... _. x
Fenestella rudis Ulrich ............. _ .................. _............... ...... ...... x ... _. ...... ...... x
x
Archimedes negligens Ulrich ................. _ .................. _. _ ..... _ .. _ ........... _ .... _. ...... x
Archimedes owen anus Hall ... _ .. _ .... _ ............... _............. x ...... x ...... :x ...... ... _ ...... . Archimedes worthe·ni Hall ................................ _ ... _...... ...... ...... x ...... x ... _. x
x
Hemitrypa pateriformis Ulrich ................. _.................. x
x
x ......... _ ............. " .. ' .. Hemitrypa proutana Ulrich ................................. _ ........... _ ........... _ .. _..... x ...... x
x
Hemitrypa proutana var. lllOdodorsalis CUmings .... _ ........ _ ..... _. ...... ...... x ................. . Hemitrypa nodosa Ulrich ..... _ ............ _ ............... _ ............................. ............... _.. x .... :. Fenestralia sancti·ludovici Prout _ .. _ .. _ .............. _ ........................................ _. x .... :. Polypora gracilis Prout .................................................. x ...... x ......... _ .................. . Polyp ora varsoviensis Prout ........................... _ ... __ .. _. x ...... x
x
x ... _. x x
Poly-pora retrorsa Ulrich ............... _ ..... _ .. _..................... ...... x
x ......... _ ................. _. Polypora biseriata Ulrich ....... _ ........ _ .... _ ............. _..... ...... ...... x ...... x .:.... x
x
Polypora spininodata Ulrich ............................ _ .. _ ..... _..... ...... ...... ...... ...... ...... ...... x ..... . Ptilopora valida Ulrich ....................................... _ ............ _ .... _.. x ... _ ......... _ ......... ..... . Ptilopora prouti Hall ....... _ .. _ ........ _ ......... __ .. _ .... _ .. _ .... _ ...... ...... ...... ...... ...... ...... x ..... . Pinnatopora conf.erta Ulrich ............. _......................... x ... _ .......... _ ... _ ...... _ ............ . W orthenopora spinosa Ulrich ... _ ........ _ .......... _ ... _.......... x
x
x
x ... _. x
x
x
Worthenopora spatulata (Prout) ......................... - .............. - . ............... -. ······1 x I x I
BRACHIOPODA-
Lingula varsoviensis Worthen ....... _ ........ _ .... _ ... _ .... _. ...... ...... ...... ...... x
x xi ..... . Orbiculoidea sp ... __ .................. _ .. _ ....... _ .......... _ ............ _. ...... ...... x ... _ ....... ............ UPPER WARSAW
8
Li
t ..... . Streptorhynchus ruginosum (Hall and Clarlre)_ ..... _ ............ _ .......... _ .... _ .......... _. x
Orthotetes keokuk (Hall) ....... _ .... _ .............. _ ........ _..... x ............ ............................. . Productus setigerus Hall ... _........................................... x
x
x
x ...... x ...... ..... . Productus ovatus Hall ....... _ ...................................... _... x...... ...... .....• x
x ............ . Productus altonensis N. and P. f ... _ ..................................................... _. ...... ...... x ..... . Productus indianensis Hall f ....................... _ .. _ .... _ ............ _. x ..................... _ .... _. Pustula alternata (N. and P.) ................... _ ........ _..... x
x
x
x ......... _ ............ . Pustula biseriata (Hall) ................. _ .... _ ................ _..... ...... x
x
x ... '"
x
x
x
Rhipidomella dubia (Hall) ....... _ ........ _ ........ _ ...... _ .. _ ... ...... ...... , ... _ .... _ .... _. ...... x ..... . Camarotoechia IDutata (Hall) ....... _ ........ _ ................ _. x
x
x
x ......... _ ....... ..... . Tetracame-ra subcuneata (Hall) ....... _ .... _ ............ _ .............. _. ...... ...... ...... x
x
X
Cranaena sulcata Weller .............................. _ ..... _......... ...... x ... _ .. .............................. . Dielasma sp. . ...... _ .... _ .. _ ........ _ ...................................... _. x
x
x
x ... _. x
x
x
Girt yell a turgida (Hall) ................... _ ...... _ ...... _ ...................................... _. ...... x ..... . ~~~;.rfee~~~n~~~~.~.~~.~ .. ~.~~.~~L.~~~~~~~~~~~~~~~::::;~~~~:::~::~:::~: :::~:: ::~::: .. ~ .. ... ~. ::~~~~ ~~~~~~ .. ~ .. ::::~~
Spirifer rostellatus Hall , ......... - .... -.................... -....... x j"'-' x ... - .... -.1 ............ ······1
Sph:ifer cf. S. keokuk Hall ................. - .................. - ... x
x
x ... - ................... " .. "1
Spirifer te·nuicostatus Hall .......................................... x
x
x
x...... ...... x I x Lingula varsoviensis Worthen ....... _ ........ _ .... _ ... _ .... _. ...... ...... ...... ...... x
x xi ..... . Orbiculoidea sp ... __ .................. _ .. _ ....... _ .......... _ ............ _. ...... ...... x ... _ ....... ............ ..... . Streptorhynchus ruginosum (Hall and Clarlre)_ ..... _ ............ _ .......... _ .... _ .......... _. x
Orthotetes keokuk (Hall) ....... _ .... _ .............. _ ........ _..... x ............ ............................. . Productus setigerus Hall ... _........................................... x
x
x
x ...... x ...... ..... . UPPER WARSAW
8
Li
t Productus ovatus Hall ....... _ ...................................... _... x...... ...... .....• x
x ............ . Productus altonensis N. and P. f ... _ ..................................................... _. ...... ...... x ..... . Productus indianensis Hall f ....................... _ .. _ .... _ ............ _. x ..................... _ .... _. Pustula alternata (N. and P.) ................... _ ........ _..... x
x
x
x ......... _ ............ . Pustula biseriata (Hall) ................. _ .... _ ................ _..... ...... x
x
x ... '"
x
x
x
Rhipidomella dubia (Hall) ....... _ ........ _ ........ _ ...... _ .. _ ... ...... ...... , ... _ .... _ .... _. ...... x ..... . Camarotoechia IDutata (Hall) ....... _ ........ _ ................ _. x
x
x
x ......... _ ....... ..... . Tetracame-ra subcuneata (Hall) ....... _ .... _ ............ _ .............. _. ...... ...... ...... x
x
X
Cranaena sulcata Weller .............................. _ ..... _......... ...... x ... _ .. .............................. . Dielasma sp. . ...... _ .... _ .. _ ........ _ ...................................... _. x
x
x
x ... _. x
x
x
Girt yell a turgida (Hall) ................... _ ...... _ ...... _ ...................................... _. ...... x ..... . ~~~;.rfee~~~n~~~~.~.~~.~ .. ~.~~.~~L.~~~~~~~~~~~~~~~::::;~~~~:::~::~:::~: :::~:: ::~::: .. ~ .. ... ~. ::~~~~ ~~~~~~ .. ~ .. ::::~~
Spirifer rostellatus Hall , ......... - .... -.................... -....... x j"'-' x ... - .... -.1 ............ ······1
Sph:ifer cf. S. keokuk Hall ................. - .................. - ... x
x
x ... - ................... " .. "1
Spirifer te·nuicostatus Hall .......................................... x
x
x
x...... ...... x I x MISSISSIPPIAN S'fRATA OF IOWA 210 Table showing Range of Species in the Warsaw Formation at Warsaw am.d Soap
Factory Hollow.-Contirlllbed. Table showing Range of Species in the Warsaw Formation at Warsaw am.d Soap
Factory Hollow.-Contirlllbed. I
Lower
II
Upper
Warsaw
Wai'saw
! 1 I 2 I 3 I 4 I 5 I 6 I 7 1
8 I
Spirifer bifurcatus Hall ................................................ ...... x
x ... _ .. ... __ .... __
x " __ '_
Spirifer indianensis Weller
~ ........ _ ............ _._ .. __ ... _ ............... __ .... _ .... __ ...... .. __ .. x ..... . Spirifer pellaensis Weller ......... _ ............. _ .............................. _ ..... _. x
x
x
x
x
Brachythyris suborbicularis (Hall) .............. _ .. _ .......... . x
x .... _ ............ _ ._ ... _ .... ___ .. UPPER WARSAW
8
Li
t _ .. Brachythyris subcardiformis (Hall) .............. ···_ .... ····1 x
x .... _-
x
x
x
x _ .... -
Spi~iferel.la ne~lee:a (Hall) ......................................... _ x ... _.. x ...... .. _ .. _ x
x
x
RetlCulana setlgem (Hall) ....... _._ ............... _ .... _ .. _..... x
x
x
x
x ...... x
x
Reticularia pseudolineata (Hall) ._ ....................... _ ....... _ ..... _ .... __ ................. _ x ........... _
Eumetria verneuiliana (Hall) ... _ ................ _ ................ ... _ .. x
x
x
x
x
x ..... . Cliothyridina parvirostris (M. IIlllJd W.) ..................... _._
x
x
x ... _ ..... _, ...... x ..... . Composita trinuclea (Hall) ._ .................. ___ .............. _.... x
x
x . __ ........ __ ..... x .... __
Composita globosa Weller ................................... _ .. _ ...... _ ... _ x
x ...... .... __ .... ~ ...... _ .... __
PELECYPODA
Edmondia varsoviensis Worthen ............................. _ .............. _. x ......... _ .............. ... _. Edmondia illinoise·nsis Worthen .................. _ ............ __ .... __ ... _.. x .... _ .... _ .. ......... _ ..... _ .. Schizodus cf. S. circulus Worthen ............. _ .............. _ ..... _ . ..... _ x _ ... _ ......... __ .. ...... .... __
Schizodus sp .. __ .... _ ......... _ .... _ ... _ .... _ .. _._ ....... __ ........... _ ....... _ ... _._ ... __ . x ......... _ ............. ___ .. _
Schizodus sp. . ................ __ ........ _ .................... _ ......... _ ........... _ .... _ ........ ............... __ ...... x
A viculopecten sp .......................... ___ ...... _ ... _ .............. _ ... _ ..... _. x ......... _ . ............. ___ ._ .... _. A viculopecten sp ................ _ ......... __ ............ _ .............. _ .. _. __ .. __
.x ...... _ .. _ ....... _ ........... _ ..... _
A viculopecten ........ __ ........................... _ ....................................... __
x ...... _ .. _ .... ___ . ...... ..... _
A viculopecten sp ........ _ ........ ___ ..................... _ ... _ ......... _ .. __ ... _. ...... x ...... ... _ .. .. _ .. _ ..... __ .... . Lithophagus illinoisensis Worthen .............................. ...... ...... x
x
x _ ........... ___ .. _
Cypricardinia indianensis Hall ................. __ ............... _ ............... _._
x
x .... __
x ..... _
. Allorisma sp . UPPER WARSAW
8
Li
t ........ _ ........ _ .... _ ............ _ ........... _ ........................ _ .... _. x ... _ .................. __ ..... _
SCAPHOPODA
Laevidentalium sp. GASTROPODA
x ...... ..... _ ..... _ ............ ..... . Holopea proutana Hall ......... _ ........ _ .......... - ................... _. ...... x ... _.- ..... - ... -- .... _ ..... _ ... __ .. 1
Strophostylus ~ earleyana H:all , ... _ ........ _ .......... _ ... _..... x ...... . _ ... _ .... _ . ......... _ ....... . Platyceras equilate·ralis Hall , ....... _ ...................... _.... x .... __ ........ __ ........ _ .... _ ... ___ .... __
Straparollus sp. . ................. _ .......... _ ... _ ............. _ ................... _ ..... __
x ... _ ... _._ .. .... __ .... _ ..... __
TRILOBITA
Phillipsia , sp. ....... _ ........... _ ................... _ ..... _ .. _ .......... _ ...... 1 .... -.1. .. _._ . __ . __ .... _ ..... _ ....... 1 x ... _ .. 1 The following species were collected from the Upper Warsaw
a t this place : The following species were collected from the Upper Warsaw
a t this place : List of fossils from bed 1 of Upper Wa.rsaw in above section. D-RYOZOA-
Leioclema punct&tum (Hall)
Archimedes owenanus Hall ~
Archimedes cf. A. owen anus Hall
Fenestella serratula Ulrich
Fe,nestella tenax Ulrich
Hemitrypa plumosa Prout ,
Polypora retr~rsa Ulrich
Rhombopora attenuata Ulrich
Cystodictya lineata Ulrich
Cystodictya pustulo,sa Ulrich
Cyclopora sp. W orthenopora spinosa Ulrich
BRACHIOPODA-
Pustula biseriata (Hall)
Rhipidomella dubia (Hall)
Spiriferina sp. Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setigera' (Hall)
Cliothyridina parvirostris (M. and W.)
PELECYPODA-
Pinna subspatulata Worthen 1
GASTROPODA-
Orthonychia cf. O. acutirostre Hall Section two miles below Keokuk Uwion Station. THE UPPER WARSAW IN row A The Upper Warsaw thins abruptly to the north from the type
section and is absent from the exposures within a distance not
exceeding fifteen miles. ' h
i
i
h
Mi
i
i
i
i
bl ff b
k
f h
h i 'rhe section in the Mississippi river bluff back of the whoie-
sale office of the Taber Lumber Company situated two miles
below the Union station at Keokuk, Iowa, involves the upper
part of the Keokuk limestone, which is exposed at the foot of UPPER WARSAW AT KEOKUK 211 the bluff, the whole of the Lower and Upper Warsaw, the
Spergen limestone and the lower and upper divisions of the
St. Louis limestone. The Upper Warsaw is considerably thin-
ner at this point than at Warsaw and has a total thickness of
only twenty-two feeL The beds are described below: the bluff, the whole of the Lower and Upper Warsaw, the
Spergen limestone and the lower and upper divisions of the
St. Louis limestone. The Upper Warsaw is considerably thin-
ner at this point than at Warsaw and has a total thickness of
only twenty-two feeL The beds are described below: Section two miles below Keokuk Uwion Station. ST. LOUIS
FEET
SPERGEN
3. Limestone, brownish, dolomitic ....................... _............................... 2%
UPPER WARSAW
2: Shale, bluish, argillaceous ......•......................................................... 18
1. Limestone, .gray, with interbedded shale ................... _ .. __ ........... 4
LOWER WARSAW 2: Shale, bluish, argillaceous
1
Limestone
gray
with inte D-RYOZOA-
Leiocl Orthonychia cf. O. acutirostre Hall W orthenopora spinosa Ulrich List of fossils from bed e of Upper Warsaw in llIbove section Glyptopora sp. Cystodictya pustulosa Ulrich
Cystodictya lineata Ulrich
Worthenopora spinosa Ulrich
BRACHIOPODA-
Productus ovatus Hall
Rhipidomella dubia (Hall)
Tetraea.mera subcuneata (Hall)
Dielasma sp. Spiriferina sp. Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setige'ra (Hall)
PELEC'YPODA-
A viculopecten sp. Aviculopecten sp. Glyptopora sp. Cystodictya pustulosa Ulrich
Cystodictya lineata Ulrich
Worthenopora spinosa Ulrich
BRACHIOPODA-
Productus ovatus Hall
Rhipidomella dubia (Hall)
Tetraea.mera subcuneata (Hall)
Dielasma sp. Spiriferina sp. Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setige'ra (Hall)
PELEC'YPODA-
A viculopecten sp. Aviculopecten sp. ANTHOZOA-
Zaphrentis sp. l3'RYOZOA-
Fistulipora (') Bp. Stenopora (') sp. Leioclema punctatum (Hall)
Archimedes wortheni Hall
Archimedes owenanus Hall
Archimedes sp. Fenestella tenax Ulrich
Fene,stella serratula Ulrich
Fenestella exigua Ulrich
Fenestella triserialis Ulrich
Hemitrypa sp. Polyp ora varsoviensis Prout
Rhombopora attenuata Ulrich
Glyptopor31 keyserlingi (Prout) Glyptopora sp. Cystodictya pustulosa Ulrich
Cystodictya lineata Ulrich
Worthenopora spinosa Ulrich
BRACHIOPODA-
Productus ovatus Hall
Rhipidomella dubia (Hall)
Tetraea.mera subcuneata (Hall)
Dielasma sp. Spiriferina sp. Spirifer cf. S. keokuk Hall
Spirifer tenuicostatus Hall
Spiriferella neglecta (Hall)
Reticularia setige'ra (Hall)
PELEC'YPODA-
A viculopecten sp. Aviculopecten sp. A low bluff on B street near its intersection with Reid street,
West Keokuk, shows seven feet of interbedded limestone and MISSISSIPPIAN STRATA OF IOWA 212 shale containing Archimedes wortheni and other characteristic
Upper Warsaw fossils. It is overlain directly by the brecciated
nondolomitic basal bed of the St. Louis limestone which is here
three and one-half feet thick (fig. 6). As a result of the discon-
formity at the base of the St. Louis the Spergen limestone is FIG. 6.-St Louis limestone resting upon Upper Warsaw shale on B street near its inter
. section with Reid street, Keokuk. FIG. 6.-St Louis limestone resting upon Upper Warsaw shale on B street near its inter·
. section with Reid street, Keokuk. not present in this section. Inasmuch as the base of the Upper
vVarsaw is not exposed at this locality its total thickness could
not be determined. I
h
i i i
f B lli
Sidi
fi
d
h lf
il In the vicinity of Ballinger Siding, five and one-half miles
north of Keokuk, the Spergen limestone rests upon shales which
are believed to represent the Lower Warsaw. Section in DCOIlnude quarries. SPERGEN LLMESTONE
UPPER WARSAW Bl:DS SPERGEN LLMESTONE
UPPER WARSAW Bl:DS
•
FEET
3. Concealed, probably shale; LI.?·chimedes wo?·theni found on
weathered slope .................................................................................. 614
2. Limestone,
blu~sh, lenticular, arenace'o·magnesian; weather·
imlg to thin layers ......... _ ........................................ _ ....................... :. 0-41h
1. Shale, bluish, argillaceous, bearin.g a few calcareous nodules. Exposed ........... _ .............. _ .......... _ .... _ .............................................. _......... 4
Bed 2 contains the following Ispecies: UPPER WARSAW Bl:DS
3
C
l d 1. Shale, bluish, argillaceous, bearin.g a few calcareous nodules. Exposed
4 Bed 2 contains the following Ispecies: BRYOZOA-
Streblotrypa sp. BRACHIOPODA-
Lingula varsoviensis Worthen
Productus sp. Girtyella indianensis (Girty) ,
Spil'ife'rella neglecta (Hall)
Reticularia setigera (Hall)
PELECYPODA-
Aviculopecten sp. GASTROPODA-
Conulal'ia sp. Spil'ife'rella neglecta (Hall)
Reticularia setigera (Hall)
PELECYPODA-
Aviculopecten sp. GASTROPODA-
Conulal'ia sp. Productus sp. Girtyella indi Girtyella indianensis (Girty) , The presence of Lingula varsoviensis and Archimedes worth-
eni in this exposure suggests the Upper Warsaw age' 6f the
beds. In his report on Van Buren county5 Gordon reports fifty-five
feet of shales above the Keokuk limestone and refers the upper
part of these to the Warsaw of Hall. In the present report
these are referred to the Lower Warsaw because of the lack in
them of fossils indicative of their Upper Warsaw age. How-
ever, t.he possibilit.y of their upper part representing the Upper
"T arsaw must be granted. 5 Iowa Geol. Survey, vol. IV, pp. 213-214; 1895.
6 U . S. Goo!. Survey Prof. Paper 24, table opp. p. 90. D-RYOZOA-
Leiocl The outcrops
along a small creek near the centre of section 25, Township 66
North, Range !) vVest, show about twenty-five feet of bluish
argillaceous shale underlying the Spergen limestone. The con-
tact of the Spergen with the shales appears to be even and reg-
ular although a disconformity undoubtedly exists. Exposures
along the banks of a small creek seven and one-half miles north
of the city of Keokuk and just south of the town of Montrose
show Spergen dolomitic limestone in contact with the Lower
vVarsaw iIi its typical deV1elopment. A
i
il
h
h
l
l
b
hi
i
f h A similar though apparently less abrupt thinning of the Up- THE SPERGEN FORMATION 213 per Warsaw beds takes place westward from Warsaw, Illinois. F]xposures along Des Moines river and its tributaries show the
Spergen limestone underlain by shales which probably repre-
sent an attenuated equivalent of the Upper Warsaw. The following layers are exposed below the Spergen beds in
the Deamude quarries located near the center of section 13 of
Des Moines township, Lee county: 6 U . S. Goo!. Survey Prof. Paper 24, table opp. p. 90. NOMENCLATURE The term Spergen was applied first as a formation name by
Ulrich6 in 1904 although several authors in publications dating
back to 1860 referred to the highly fossiliferous strata of this
age at Spergen Hill, Indiana, as "Spurgen 's Hill beds", "Sper- MISSISSIPPIAN STRATA OF IOWA 214 gen Hill limestone", etc. The name Salem limestone as pro-
posed for this formation by Cumings7 in 1901 has appeared in
the literature on Mississippian geology many times, but the U. S. Geological Survey now favors the use of Spergen. This formation was recognized by the writerS as a distinct
unit in the Mississippian column of Iowa several years ago. AREAL DISTRIBUTION The Spergen formation has a very restricted areal distribu-
tion in Iowa. In earlier reports it has usually been mapped as
St. Louis limestone. Exposures of rocks of this age appear
<;mly in the southeastern part of the state, the most conspicuous
ones being in Des Moines river valley in Lee and Van Buren
counties. Small isolated outcrops appear at a few other local-
ities in Lee. D~s Moines, Henry and Jefferson counties. S Iowa Acad. Sci. Proc., vol. 19, pp. 167, 168; 1912. 7 Jour. Geol., vol. IX, pp. 232-233.
S I
A
d
S i
P
l
19 CHARACTER AND STRATIGRAPHIC RELATIONS The Spergen is represented in southeastern Iowa by an at-
tenuated, near-shore facies, to which the name Belfast beds is
given, because of the excellent exposures of the formation near
the town of Belfast in Lee county. Until recent years the Spergen has not been recognized in
Iowa owing to the fact that it was confused in some places with
the Warsaw formation and in others with the basal member of
the St. Louis limestone. This confusion was due in large part
to the failure of earlier workers to recognize the disconformi-
ties at the base and at the top of this formation. The apparent
tendency of the Spergen to grade laterally into the Warsaw or
the Lower St. Louis evidently is ue to this relationship. The
Spergen as developed in the area in question has a wide range
in character, owing in part to original conditions of sedimenta-
tion and in part to differences in the degree of dolomitization. It is not uncommon to find a cross-bedded crinoidal limestone
passing laterally into a massive brown dolomitic limestone, and
this again into a brownish arenaceous dolomite, which may in
turn give way to a fine-grained bluish sandstone. In Van Buren
county the formation contains a large proportion of shale. Such SPERGEN BEDS NEAR BELFAST 215 differences clearly suggest near-shore conditions of deposition. This also is suggested by the limited areal extent of the forma-
tion in Iowa, and by its thinning to the northwest. It has not
been found north of Jefferson county. As a result of the dis-
conformity below the Spergen it may rest upon either the Upper
or the Lower Warsaw. Owing to the hiatus above, it is in some
places entirely cut out by the St. Louis limestone. The thick-
ness of the formation thus ranges from almost nothing to thirty-
five feet. BRYOZOA-
FenestelllL serratula Ulrich
Hemitrypa sp.
BRACHIOPODA-
Productus altonensis N. and P.
Pustula biseriata (Hall)
Tetracamera arctirostrata (Swallow)
Dielasma sp.
Girtyella indianensis (Gil-ty)
Spirifel' tenuicostatus Hall
Bl'ac.hythyris subcardif(}rmis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall ~
Eumetria ve1'l1euiliana (Hall)
GASTROPODA-
Ortho.n.ychia sp.
C{)uularia sp.
At th
th
f
i
f
t
d
th
t
f th
d AREAL DESCRIPTION BY COUNTIES Lee County, Iowa.-The most representative sec~ions of the
Spergen formation in Iowa are those in the quarries in the east
bluff of Des Moines river south of the town of Belfast in Lee
county. Several different exposures are d~scribed in this area
in order to emphasize the vaTiability of the beds. The forma-
tion is well. exposed in the old Deamude quarry, located near
the middle of section 13, Des Moines township. At the north-
east end of the quarry opening the following section of the
Spergen was measured: Section of Spergen fO?"l1t(htion in Deam~b('l e quarry. FEET
INCHES
4. Limestone, gray, crinoidal, cross·bedded, overlain disconform·
ably by conglomeratic St. Louis limestone .................................. 2
9
3. Limestone, bluish, massive, arenaceo'magnesian, with occa·
.sional highly fossiliferous seams ............................. _ .. _............. 4
6
2. Shale, drab, arenaceous ................................... , ... _ .......... _ ........... _ ..... 1-2
6
1. Limestone·, bluish, massive, magnesian, very arenaceous. Exposed ... _................................................................................... ........ 4
6 Pustula biseriata (Hall)
Tetracamera arctirostrata Tetracamera arctirostrata (Swallow)
Dielasma sp Seotion in (!J ravine at the Dewmude quarry. Seotion in (!J ravine at the Dewmude quarry. SPERGEN
FEET
INCHES
8. Limestone, gray, crinoidal, cross·bedded, overlain by conglom·
eratic St . . Louis limestone ................................. _ ................ _ .. _....... 2
3
7. Shale, drab, arenaceous with thin layers of arenaceous mag·
nesian limestone; containing mica flakes ............. _ .... __ ........ _..... 5
9
6. Limestone, al'enaceo'magnesian, weathering yellowish, in layers
about 6 inches thick ......... _ .............................................. _ .. _........... 3
5. Shale, blu~sh,arenaceous; containing mica flakes ............... _ .... _. 2
7
4. Limestone, bluish, arenaceo·magoosian, in layers 2 to 9 inches
thick ......... _ .............................................. _........................................... 3
UPPER WARSAW
. 3. Concealed, probably shale in large part. Arohitmedes wortheni
found on weathered slope ......... _ ...................... _ ................ _........... 6
3
2. Limestone, bluish, lenticular, arenaceo·magnesian, weathering
to thin layws, thickening and thinning abruptly on lower sur·
face. Bearing a few fossils. Passing into shales at one
point ......... _ ...... _ ............................... , .............. _ .... _ .... _ .... _ ........... 0 to 4
6
1. Shale, bluish, argillaceous, bearing a few calcareous nodules. Exposed · ....................................... _ ........................ _ .. _ .............. _........... 4 p
2. Limestone, bluish, lenticular, arenaceo·magnesian, weathering
to thin layws, thickening and thinning abruptly on lower sur·
face. Bearing a few fossils. Passing into shales at one
point ......... _ ...... _ ............................... , .............. _ .... _ .... _ .... _ ........... 0 to 4
6
1
Sh l
bl i h
ill
b
i
f
l
d l A comparison of this section with the preceding one will illus-
trate the range in character of the Spergen in this region. Bed
8 of the last section correspqnds to number 4 of the former. The lower beds of the Spergen in the two sections possess little
in common. Other excellent sections of the Spergen appear in the Des
Moines river bluff along the Chicago, Rock Island & Pacific rail-
way a short distance below Belfast. The most satisfactory ex-
posures are in the old' Fox quarry openings, and in the ravines
which cut through the bluff at intervals between these, in the
western part of section 12, Des Moines township. A detailed
study of these sections brings to light some very puzzling feat-
ures in the' way of lithologic differences of the formation. Section of Spergen fO?"l1t(htion in Deam~b('l e quarry Section of Spergen fO?"l1t(htion in Deam~b('l e quarry. 3. Limestone, bluish, massive, arenaceo'magnesian, with occa·
.sional highly fossiliferous seams ............................. _ .. _............. 4
6
2
Sh l
d
b
1 2
6 2. Shale, drab, arenaceous ................................... , ... _ .......... _ ........... _ ..... 1-2
6
1
Limestone
bluish
massive
magnesian
very
arenaceous 1. Limestone·, bluish, massive, magnesian, very arenaceous. Exposed ... _................................................................................... ........ 4 Beds 1, 2 and 4 contain only fragmentary fossils but bed 3
yields molds of numerous species which are listed below: Ligt of fossils from bed fj of Spergen fonnation in Deam1bde qUQI/'ry. Ligt of fossils from bed fj of Spergen fonnation in Deam1bde qUQI/ry. BRYOZOA-
FenestelllL serratula Ulrich
Hemitrypa sp. BRACHIOPODA-
Productus altonensis N. and P. Pustula biseriata (Hall)
Tetracamera arctirostrata (Swallow)
Dielasma sp. Girtyella indianensis (Gil-ty)
Spirifel' tenuicostatus Hall
Bl'ac.hythyris subcardif(}rmis (Hall)
Spiriferella neglecta (Hall)
Reticularia setigera (Hall ~
Eumetria ve1'l1euiliana (Hall)
GASTROPODA-
Ortho.n.ychia sp. C{)uularia sp. A
h
h
f
i
f
d
h
f h
d Ortho.n.ychia sp
C{)uularia sp C{)uularia sp. Dielasma sp. Girtyella ind Girtyella indianensis (Gil-ty) At the mouth of a ravine forty yards southeast of the preced-
ing section lower layers, which are believed to represent the
Upper 'Vol arsa:w, outcrop below the Spergen. 216 MISSISSIPPIAN STRATA OF IOWA Seotion of Spergen formation in upper Fw; qUMry.
Drift.
FEET
SPERGEN
4. Limestone, brownish, magnesian, with molds of bryozoans.... 2
3.
Shale, bluish,arena.ceous ... _ .. _ ................ _ ...... _ ........ _ .... _ .......... _1 to 2
2. Limestone, dolomitic, bluish to brownish, arenaceous ............ 5 ~o 7
1. Limestone, gray, fossiliferous, cross·bedded in upper paa:t.
Exposed ................................. _ ...................... _ ............................ _ .... _.
6 3.
Shale, bluish,arena.ceous Seotion in (!J ravine at the Dewmude quarry. The first quarry opening, three-fourths of a mile below Bel·
fast, presents the following section: Seotion of Spergen formation in upper Fw; qUMry. Drift. FEET
SPERGEN
4. Limestone, brownish, magnesian, with molds of bryozoans.... 2
3. Shale, bluish,arena.ceous ... _ .. _ ................ _ ...... _ ........ _ .... _ .......... _1 to 2
2. Limestone, dolomitic, bluish to brownish, arenaceous ............ 5 ~o 7
1. Limestone, gray, fossiliferous, cross·bedded in upper paa:t. Exposed ................................. _ ...................... _ ............................ _ .... _. 6 An irregular lens of unaltered gray fossUiferous cross-bedded
limestone four inches to one foot thick and about ten feet long
occurs at one point in bed 2. A few yards south of the above exposure the following suc-
cession appears at the mouth of a ravine: SPERGEN FOSSILS NEAR BELFAST Seotion at mouth of ravilne below Belfast. Seotion at mouth of ravilne below Belfast. Seotion at mouth of ravilne below Belfast. ST. Loms
FEET
4. Limestone, conglomeratic ... _ ................ _ ................ _ ................ _ .... : 8 to 10
SPERGEN
3. Limestone, brownish, dolomitic, somewhat arenaceous, bearing
small angular whitish chert fragments ... _ ................ _ .... _........... 2
2. Sh;.W.e, bluish, argillaceous ......... _ ................ _................................... 3% to 4
1. Limestone, heavy bedded, consisting of bluish dolomitic lime-
stone, locally arenaceous, with interbedded seams and layers of
grayish nondolomitic, fossiliferous limestone. Exposed ............ 11112
Twenty-five yards up the same ravine at a small waterfall tho
f ll
i
i
d ST. Loms
4
Li ST. Loms
4
Li g
1. Limestone, heavy bedded, consisting of bluish dolomitic lime-
stone, locally arenaceous, with interbedded seams and layers of
grayish nondolomitic, fossiliferous limestone. Exposed ............ 11112 Twenty-five yards up the same ravine at a small waterfall tho
following section was measured: Section 01 Sperrgen forrn,a,tion in!. rOJVine below B elfast. Section 01 Sperrgen forrn,a,tion in!. rOJVine below B elfast. 4. Drift. SPERGEN SPERGEN
3 3. Limestone, bro·wnish, dolomitic, massive ; with molds of fenes·
telloid bryozoans; thickening abruptly locally at the expense
of the thin·bedded limestone beneath owing to uneven dolomiti·
ZJation .............................................................................................. 1 to 4 ZJation .............................................................................................. 1 to 4
4
2. Limestone, gray, in the form of thin cross' bedded highly
fossiliferous layers. The slope of the cross·bedding ranges
from about 9 degrees to 20 degrees. Direction of slope, west,
southwest, and southeast. At one point the lower one and
one·half feet of this limestone bed passes abruptly into a mas·
sive dolomitic layer, which continues ten to fifteen feet, and
thence grades gradually back into thin·bedded unaltered lime·
stone
:
:
2 to 6
6 1. Limestone, bluish, arenaceo·magnesian, in heavy la.yers when
fresh but weathering into thinner layers ...................................... 5
6 The species listed below were collected from bed 2 of this sec-
tion: ANTHOZOA-
M
il The lens of dolomite has a rounded
surface in the outcrop. It is seven and one-half feet long and
has a maximum thickness of ten inches. It is of about the same
texture as the limestone, and bears the same types of fossils,
but it is bluish to brownish in color while the limestone is gray. The contact of the upper cross-bedded limestone member
(bed 2 of preceding section) with the dolomitic beds above and
below is irregular owing to uneven dolomitization. It appears
that the dolomitization of the Spergen must have taken place
after all of, the beds were deposited. The arenaceous limestones
'of the Spergen are believed to have been more susceptible to
alteration than the purer limestones for they are dolomitic in
nearly every exposure in which they appea;r. Th
f ll
i
i
i
h
i
i
b The following succession is shown in a quarry opening about
ninety yards below the last section: ANTHOZOA-
M
il Worthenopora spinosa Ulrich
BRACHIOPODA-
Productus indianensis Hall
Productus altonoosis N. and P. Pustula biseri3Jta (Hall)
Rhip~domella dubia (Hall)
Tetracamera subcuneata (Hall)
Tettracamera arctirostl'ata (Swallow)
Girtyella turgida (Hiall)
Girt yell a indianensis (Girty)
Spirifer tenuicostatus Hall
Spirifer bifurcatus Hall
Bl'achytJl)'l1.s subcardiformis (Hall)
Reticulal'ia setigera (Hall)
Eumetria verneuiliana Hall
Cliothyridina parvirostl'is (M. amid W.)
Composita tl'inuclea (Hall)
GASTROPODA-
Orthonychia acutirostre (Hall)
TRILClBITA-
Griffithides , sp. ANTHOZOA-
Worthenopora spinosa Ulrich
Monilopora beecheri Grabau
BRACHIOPODA-
Zaphrentis sp. Productus indianensis Hall
BLASTOIDEA.-
Productus altonoosis N. and P. P entremites sp. Pustula biseri3Jta (Hall)
Metablastus sp. Rhip~domella dubia (Hall)
BRYOZOA-
Tetracamera subcuneata (Hall)
Fistulipora sp. Tettracamera arctirostl'ata (Swallow)
Stemopora sp. Girtyella turgida (Hiall)
Leioclema gracillimum Ulrich
Girt yell a indianensis (Girty)
Fenestella serratula Ulrich
Spirifer tenuicostatus Hall
Fenestella multispinosa Ulrieh
Spirifer bifurcatus Hall
Hemitrypa sp. Bl'achytJl)'l1.s subcardiformis (Hall)
Polyp ora biseriata Ulrich
Reticulal'ia setigera (Hall)
Rhombopora bedfordensis Cumings
Eumetria verneuiliana Hall
Rhombopora varians Ulrich
Cliothyridina parvirostl'is (M. amid W.)
Rhombopora attenuata Ulrich
Composita tl'inuclea (Hall)
Bactropora simplex Ulrich
GASTROPODA-
Cystodictya lineata Ulrich
Orthonychia acutirostre (Hall)
Glyptopora sagenella (Pront)
TRILClBITA-
Glyptopora sp. Griffithides , sp. ANTHOZOA-
Monilopora beecheri Grabau
Zaphrentis sp. BLASTOIDEA.-
P entremites sp. Metablastus sp. BRYOZOA-
Fistulipora sp. Stemopora sp. Leioclema gracillimum Ulrich
Fenestella serratula Ulrich
Fenestella multispinosa Ulrieh
Hemitrypa sp. Polyp ora biseriata Ulrich
Rhombopora bedfordensis Cumings
Rhombopora varians Ulrich
Rhombopora attenuata Ulrich
Bactropora simplex Ulrich
Cystodictya lineata Ulrich
Glyptopora sagenella (Pront)
Glyptopora sp. Some interesting relationships of limestone and dolomite are
shown in a quarry face in the bluff just south of the ravine men- MISSISSIPPIAN STRATA OF IOWA 218 tioned above. In addition to layers of dolomite, which grade
laterally into limestone, there occurs a lens of dolomite in a
limestone bed. Two bowlder-like masses of dolomite appear in
the same limestone nearby. The lens of dolomite has a rounded
surface in the outcrop. It is seven and one-half feet long and
has a maximum thickness of ten inches. It is of about the same
texture as the limestone, and bears the same types of fossils,
but it is bluish to brownish in color while the limestone is gray. Th
t
t
f th
b dd d li
t
b tioned above. In addition to layers of dolomite, which grade
laterally into limestone, there occurs a lens of dolomite in a
limestone bed. Two bowlder-like masses of dolomite appear in
the same limestone nearby. Section in a quarry below Belfast. ST. LOUIS
FEET
4. Limestone, conglomeratic, in the form of a mound with less
disturbed layers of brownish dolomitic limestone lapping up
on its flanks ..... _ .............. __ ... _........................................................... 12 to 15
SPEMEN
3. Limestone, brownish, dolomitic w:ij;h smaH scattered subangular
quartz grains and occasional smalI angular fragments of whit·
ish chert ............................... _ ............ _ ................................... _ .. _.......... 1
2. Limestone, gray, crinoidal, filled with bryozoans; massive when
fresh but weathered surfaces show thin cross·bedded layers. The lower part passes locally into dolomite indistinguisha.ble
from the dolomite below. At the north end of the opeming
the lower 3 feet of this bed is represented entirely by dolo·
mite. This is very massive where it is dolomitic, although it
was thin-bedded originally. At the south end of this opening there is a large lenticular
layer of bluish dolomitic limestone near the middle of this
member. It attains a maximum thickness of about 2 feet and
is 25 to 30 feet long. Large irregular bo·wlders of dolomite
and a smaller lens of dolomite also were noted in the upper
part of this member ................................................ :........................... 14lh
1. Limestone, al'enaceo·magnesian, bluish when fresh but weather-
ing brownish, bearing thin discontinuous seams of compact blu·
ish dolomitic limestone. The arenaceous material is very fine-
grained. Exposed ....................... _ .................... _ .............. _ ............ _ .. _ 11
About ninety yards farther down stream there is another ST. LOUIS
FEET
4. Limestone, conglomeratic, in the form of a mound with less
disturbed layers of brownish dolomitic limestone lapping up
on its flanks ..... _ .............. __ ... _........................................................... 12 to 15
SPEMEN
3. Limestone, brownish, dolomitic w:ij;h smaH scattered subangular
quartz grains and occasional smalI angular fragments of whit·
ish chert ............................... _ ............ _ ................................... _ .. _.......... 1
2. Limestone, gray, crinoidal, filled with bryozoans; massive when
fresh but weathered surfaces show thin cross·bedded layers. The lower part passes locally into dolomite indistinguisha.ble
from the dolomite below. At the north end of the opeming
the lower 3 feet of this bed is represented entirely by dolo·
mite. This is very massive where it is dolomitic, although it
was thin-bedded originally. At the south end of this opening there is a large lenticular
layer of bluish dolomitic limestone near the middle of this
member. It attains a maximum thickness of about 2 feet and
is 25 to 30 feet long. Seotion in a q1wrry newr the preoeding one. Seotion in a q1wrry newr the preoeding one. ST. Loms
FEET
INCHES
3. Limestone, conglomeratic, marly in lower part ................•............. 15
SPERGEN
2. Limestone, bluish, arenaceo·magnesian, massive when fresh
but weathering to thin layers . and sC3Jling off obliquely. Locally with shaly streaks ........................... ~ ................................ _.. 9
10
1. Limestone, massive, bluish when fresh but weathering brown·
ish ; bearing molds of bryozoans. Exposed ... _ .............. _............. 8
6 ST. Loms
FEET
INCHES
3. Limestone, conglomeratic, marly in lower part ................•............. 15
SPERGEN 2. Limestone, bluish, arenaceo·magnesian, massive when fresh
but weathering to thin layers . and sC3Jling off obliquely. Locally with shaly streaks ........................... ~ ................................ _.. 9 y
y
_
1. Limestone, massive, bluish when fresh but weathering brown·
ish ; bearing molds of bryozoans. Exposed ... _ .............. _............. 8 1. Limestone, massive, bluish when fresh but weathering brown·
ish ; bearing molds of bryozoans. Exposed ... .............. ............. 8
6 Bed 2 is correlated with bed 2 of the preceding section, in
part at least. The upper parts of the beds were traced into
each other but the transition of the lower beds is concealed by
talus. The transition observed was abrupt. The limestone first
graded into arenaceous material and thence became dolomitic. Fossils are scarce and poorly preserved in the dolomitic facies
but are abundant in the cross-bedded limestone facies. Two hundred and sixty yards farther down the following beds
appear in the bluff: Section t1t the Des Moines "iver bl'U,jf below Belfast . . ST. LOUIS
,
FEET
4. Limestone, much disturbed, some blocks dolomitic ... _............... 15
SPERGEN
3. Limestone, bro'wnish, arenaceous, with chert fragments ............ 1
2. Limestone, gray, thin·bedded, crinoidal, shaly in lower part;
resting on the irregular surface of bed beneath ... _ ................ _ 0 to 5
1. Limestome, dolomitic, slightly arenaceous; bluish when fresh. but weathering brownish;. in heavy layers which in lower part
are separated by layers of bluish arenaceous shale. Exposed
18lh 1. Limestome, dolomitic, slightly arenaceous; bluish when fresh. but weathering brownish;. in heavy layers which in lower part
are separated by layers of bluish arenaceous shale. Exposed
18lh At one point in this exposure bed 2 is cut out completely by
the local thickening of bed 1. This relationship is believed to
be due to uneven dolomitization. Section in a quarry below Belfast. Large irregular bo·wlders of dolomite
and a smaller lens of dolomite also were noted in the upper
part of this member ................................................ :........................... 14lh
1. Limestone, al'enaceo·magnesian, bluish when fresh but weather-
ing brownish, bearing thin discontinuous seams of compact blu·
ish dolomitic limestone. The arenaceous material is very fine-
grained. Exposed ....................... _ .................... _ .............. _ ............ _ .. _ 11
About ninety yards farther down stream there is another
good exposure in a quarry opening. 3. Limestone, brownish, dolomitic w:ij;h smaH scattered subangular
quartz grains and occasional smalI angular fragments of whit·
ish chert ............................... _ ............ _ ................................... _ .. _.......... 2
Limestone gray
crinoidal filled with bryozoans; massive when 2. Limestone, gray, crinoidal, filled with bryozoans; massive when
fresh but weathered surfaces show thin cross·bedded layers. The lower part passes locally into dolomite indistinguisha.ble
from the dolomite below. At the north end of the opeming
the lower 3 feet of this bed is represented entirely by dolo·
mite. This is very massive where it is dolomitic, although it
was thin-bedded originally. At the south end of this opening there is a large lenticular At the south end of this opening there is a large lenticular
layer of bluish dolomitic limestone near the middle of this
member. It attains a maximum thickness of about 2 feet and
is 25 to 30 feet long. Large irregular bo·wlders of dolomite
and a smaller lens of dolomite also were noted in the upper
part of this member ................................................ :.......................... 1
Li
t
l'
i
bl i h
h
f
h b t
th _ 11 About ninety yards farther down stream there is another
good exposure in a quarry opening. SPERGEN BEDS BELOW BELFAST 219 Seotion in a q1wrry newr the preoeding one. A few yards farther downstream the following section ap-
pears III a quarry: Section near tho preceding. ST. LOUIS
7. Limestone, conglomeratic, dolomitic and nondolomitic blocks
indiscriminately mixed, marly toward the base ......... _ ......... _ ..... . SPERGEN
6. Limestone, gray, criooidal, thin·bedded, slightly cross· bedded
5. Limestone, brownish, dolomitic, slightly arenaceous ............... _ .. 4. Shale, calcareous aJIlJd aronaceous ... _ ............................ _ .......... _._ .. . 3. Limestollle, bluish, dolomitic, arenaceous ...................................... _. 2. Linrestone, gray, crinoidal ... __ ........ _ .............. _ .. _ .......... _ ..... _ .......... . 1. Limestone, brownish, arenaceo·magnesian, in one massive ledge. FEET
11
4
4 1/3
2
1 to 2
4
Exposed ............... _ ................................................................... _.............. 10 2. Linrestone, gray, crinoidal ... __ ........ _ .............. _ .. _ .......... _ ..... _ .......... . 1
Li
t
b
i h
i
i
i
l d Bed 3 differs greatly in thickness and lies upon the irregular
surface of bed 2. Bed 2 passes laterally into dolomite at one
point in the quarry face. 220 MISSISSIPPIAN STRATA OF IOWA The quarries end at a ravine one mile below the station at
Belfast. Beyond this point a few good natural exposures may
be seen in the bluff. One such exposure occurs sixty rods below
this ravine. SeCJtion iIn bl14J of Dcs Moines river one 7wile below B ~lfast. ST. LOUIS
FEET
INCHES
10. Limesto,ne, congLomeratic, p'oorly exposed. SPERGEN
9. Limestone, bluish. to brownish, with large rounded quartz
grains and occasional angular chert fr:a.gments .......................... 2
4
8. Sandstone, fine· grained, bluish, shaly ... _ .... _ ..... _ ............ _. ___ . _____ .. 2
3
7. Limestone, bluish, arenaceo-magnesian _________ . __ .. __ ._ .. _ .. _________________
5
9
6. Shale, bluish, arenaceous, bearing small mica flakes ________________ 1
4
5. Limestone, arenaceo-magnesian, shaly in upper part _________________
3
1
4. Limestone, arenaceo·magnesian, shaly in upper part _________ . _______ . 3
8
3. Shale, bluish, arenaceous, with mica flakes __ ._ .. _____ . __ .. _ ... ___ ._ .. ________
6
6
2. Limestone, bluish, arenaceous . _____ . _____ . ________ . ____________ . _______ . _________ . ___ . 6
10
1. Shale, bluish, argillaceous. Exposed at foot of bluff ________ .. ___
6 Some very interesting sections occur on Mumm creek two and
one-half miles west of Belfast. SeCJtion iIn bl14J of Dcs Moines river one 7wile below B ~lfast. Section in small bTlJY/l;ch of Mtt71l11lt creek neM preceding section. Seotion in a q1wrry newr the preoeding one. A short distance above_ the
mouth of the creek, the following succession is shown in an east
branch (SE.14 sec. 33, T. 67 N., R. 7 W.). Section in the east branch of Mumm creek. SPERGEN
FEET
Limestone, arenaceo-magnesian, bluish weathering yello,wish to
brownish; with thin discontinuous seams of bluish magnesian
limestone which weather in relief. Massive when fresh, but
weathering to thin layers. ",'Veathered surface of a massive
ledge in lower part shows indications of cross-bedoing. Bearing
molds of fenestelloid bryozoans . _____ ... _________________ . ______ ... _________ ... ___ .... _
19
WARSAW
Shale, bluish to black, argillaceous, more calcareous in upper part
and grading into the beds above. No fossils found, but occa·
sional banos of small imperfect siliceons geodes were noted. Exposed .... _ ....... __ .. __ ......... _ ... ___ ............. _._ .. _ ....... _. __ .............. ____ ..... _._______
14% Section in the east branch of Mumm creek. ;
f
p
g
LOWER ST. LoUIS
FEET
INCHES
5.
Limestone, compact, buff, magnesian ______ . ___ .. ___ .. _ .. ________ ..... _______ .___
1
4. Limestone, buff, magnesian in the nodular layers ... _____ . ______ ... __ . 1
6
3.
Limestone, yellowish, conglomeratic, magnesian; the structure
partly obliterated by dolomitization; resting on the irregular
surface of the bed beneath . ___ ._ ... ___ ._. __ . __ . ___ . ____ ._._. ___ ._ ... ___ .______________ 2
6
SPERGEN
2.
Shale, drab, arenaceous, bearing small mica flakes .___________________
6
1. Limest()ne,
arenaceous and magnesian, massive; a
, small
amonnt of buff cherty magnesian J limestone in upper part.
Exposed
_______________________ . ______ ......... __ . ____ ._._. _______ . __ . _____ ... __ ... ______________ ._ .. 17
6 LOWER ST. LoUIS
5
Limestone SPERGEN
Li WARSAW
Shale, bluish to black, argillaceous, more calcareous in upper part
and grading into the beds above. No fossils found, but occa·
sional banos of small imperfect siliceons geodes were noted. Exposed .... _ ....... __ .. __ ......... _ ... ___ ............. _._ .. _ ....... _. __ .............. ____ ..... _._______
14% About two hundred and thirty-five yards up the creek the sec-
tion given below was measured in a small ravine in the east
bank. Section in small bTlJY/l;ch of Mtt71l11lt creek neM preceding section. LOWER ST. LoUIS
FEET
INCHES
5. Limestone, compact, buff, magnesian ______ . ___ .. ___ .. _ .. ________ ..... _______ .___
1
4. Limestone, buff, magnesian in the nodular layers ... _____ . ______ ... __ . 1
6
3. Limestone, yellowish, conglomeratic, magnesian; the structure
partly obliterated by dolomitization; resting on the irregular
surface of the bed beneath . ___ ._ ... ___ ._. __ . __ . ___ . ____ ._._. ___ ._ ... ___ .______________ 2
6
SPERGEN
2. Shale, drab, arenaceous, bearing small mica flakes .___________________
6
1. Limest()ne,
arenaceous and magnesian, massive; a
, small
amonnt of buff cherty magnesian J limestone in upper part. Exposed
_______________________ . ______ ......... __ . ____ ._._. _______ . __ . _____ ... __ ... ______________ ._ .. 17
6 SPERG'RN BEDS ABOVE BELFAST 221 In a small branch about eighty yards north of the above de·
scribed section, the conglomeratic and dolomitic basal limestone
layer of the St. Louis succeeds twenty and one-half feet or
arenaceo-magnesian Spergen limestone. A.bout one foot of
shale is exposed at the mouth of the branch beneath the Sper-
gen. The weathering out of the shale undermines the massive
limestone ledge for many feet, and several huge blocks of the
latter have tumbled down into the bed of the cre~k. Some seams
in the Spergen at this place are less arenaceous and are highly
fossiliferous. These tend to weather out in relief and in many
cases indicate the existence of cross-bedding in the original Trwk. T
h
d
d
d
f
h
i
i
h
k Two hundred yards farther upstream a section in the creek
bank extends from the top of the ,Varsaw shale to the Upper
St. Louis limeRtone. The Spergen is very much attenuated
her e, averaging only about one foot in thickness in the face of
the bluff. Seotion in the east book of Monk creek northwest of Belfast
LowER. ST. LoUIS
'
'
FEET
INCHES
4.
Limestone, c<}llIglomeratic, matrix calcareous above but shaly
below ............... _ ........................................ _ .................... : ...................... 13
SPERGEN
3.
Limestone, brownish, magnesian, sort, thin·bedded, bearing
molds of fenestelloid bryozoans .................... _ .......................... _..... 2
6
2. Limestone, brownish, arenaceo·magnesian, in one massive ledge
which shows faint indications of cross·bedding at one point,
but composed of thin rotten layers a few yards downstream,
where it is much weathered ............... _ ...................... _ ..................... 11
3
VVARSAW
1.
Shale, argillaceous, dark blue . to black where fresh but
weathering drab; bearing effloresence of a mineral which
appears to be gypsum; containing a few small crushed impel"
f ect siliceous geodes; somewhat calcareous in upper part and
gr1J.ding into the bed above. A few poorly preserved fossils in
the upper part. Exposed __ .... __ ................... __ ..... __ ... _ ....................... 24
5 Seotion in the east book of Monk creek northwest of Belfast
LowER. ST. LoUIS
'
'
FEET
4
Limestone
c<}llIglomeratic
matrix calcareous above but shaly SPERGEN
Li The abrupt thinning of the Spergen in passIng from
the previously described Mumm creek sections to this point is
undoubtedly due to pre-St. Louis erosion. Th
S
li
h
hi k
f hi
f The Spergen limestone has a thickness of thirteen to fourteen
feet in the east bank of Monk creek just northwest of Belfast. It is underlain by shales provisionally' referred to the Warsaw
and is overlain by the Lower St. Louis limestone. There is a
possibility that the shales belong, in part at least, to the Spel'-
gen. In the absence of well preserved fossils their age cannot
be determined definitely. Seotion in the east book of Monk creek northwest of Belfast
LowER. ST. LoUIS
'
'
FEET
INCHES
4. Limestone, c<}llIglomeratic, matrix calcareous above but shaly
below ............... _ ........................................ _ .................... : ...................... 13
SPERGEN
3. Limestone, brownish, magnesian, sort, thin·bedded, bearing
molds of fenestelloid bryozoans .................... _ .......................... _..... 2
6
2. Limestone, brownish, arenaceo·magnesian, in one massive ledge
which shows faint indications of cross·bedding at one point,
but composed of thin rotten layers a few yards downstream,
where it is much weathered ............... _ ...................... _ ..................... 11
3
VVARSAW
1. Shale, argillaceous, dark blue . to black where fresh but
weathering drab; bearing effloresence of a mineral which
appears to be gypsum; containing a few small crushed impel"
f ect siliceous geodes; somewhat calcareous in upper part and
gr1J.ding into the bed above. A few poorly preserved fossils in
the upper part. Exposed __ .... __ ................... __ ..... __ ... _ ....................... 24
5
A
d i
h
i i i
f
h
i
f K
k k
h
S 1. Shale, argillaceous, dark blue . to black where fresh but
weathering drab; bearing effloresence of a mineral which
appears to be gypsum; containing a few small crushed impel"
f ect siliceous geodes; somewhat calcareous in upper part and
gr1J.ding into the bed above. A few poorly preserved fossils in
the upper part. Exposed __ .... __ ................... __ ..... __ ... _ ....................... 24 At and in the vicinity of the city of Keokuk the Spergen
ranges from practically nothing to a little more than eight feet MISSISSIPPIAN STRATA OF IOWA 222 in thickness. The St. SPERGEN
Li Louis limestone lies directly upon the
Upper Warsaw shale at an exposure in B street near its inter-
section with Reid street, but in the Mississippi river bluff back
of the Taber lumber mill, two miles below the Union Station, the
Spergen is represented by a layer of bluish gray sandy lime-
stone which weathers brownish and is two and one-half to SL,{
feet thick. Upper Warsaw shales underlie the limestone while
conglomeratic St. Louis limestone outcrops above it. G
d
f h
S
d
i
d b d
b Good exposures of the Spergen and associated beds may be
seen along a small creek in the northeast quarter of section 24
of Jackson township, about three-fourths of a mile northwest of
Rand Park at Keokuk. The following section was measured at
this locality. Seotion ne/llr Rand Park, Keokuk Seotion ne/llr Rand Park, Keokuk FEk:T LoWER ST. LOUIS
3. Limestocne, for the most part conglomeratic; cocnsisting chiefly
of irregularly disposed blocks and sub angular bowlders of
compact gray limestone; matrix shaly below but more cal-
careous above;
bearing silicified corona of Lith.ostrotion
canadensis. Upper two to three feet more evenly-bedded. A
more regular layer of compact gray limestone ranging m
thickness from a few inches up to 2 feet or more appears at
the base. It rests upon !len irregular and eroded surface of
the Spergen .. _ ............ _ ............. _ .... ___ ... __ .. __ .. ___ ....... _ ... ____ ._ ....... __ .. ______
SPERGEN 16 2. Sandstone, grayish blue, fine· grained, with scattered subangular
quartz grains ranging up t.o 1 mm. or more in diameter. This
bed becomes somewhat yellowish on weathered surfaces. The
upper half exhibits a tendency towards cross·bedding of the
torrential type ano' the uppermost two feet is weathered into
thin layers. Locally some O'f the arenaceous layers pass into
a bluish compact magn.esiilll limestone. The fronds of fenes-
telloid bryozoans so commonly observed in the Spergen are
seldom SCilll here. The lower two feet of the formation is
somewhat sh3.ly and appea~s to pass graoually downward into
the Warsaw shales below _. __ .. ___ .. __ ........... __ .. _._ ...... __ .. ___ .. __ ....... __ ._._... WARSAW
1
Shale
bluish
argillaceous 81,4 12 Several outcrops of Spergen limestone appear along the north
and south forks of a small creek near the center of section 25,
Montrose township, five miles north of Keokuk. The greatest
exposed thickness of the formation is ten feet. In some of the
exposures the limestone is brownish, arenaceous and dolomitic. In others it consists chiefly of gray subcrystalline slightly al-
tered limestone. The formation is shown at several points in
contact with the disturbed facies of the St. Louis limestone. At
a small fall in the creek a short distance below the confluence of SPERGEN BEDS NEAR WARSAW 223 the two branches the Spergen is nine and one-half feet in thick-
ness. The upper half consists of shale and the lower half of
bluish to brownish arenaceo-magnesian limestone with abundant
molds of fenestelloid bryozoans. The formation is here overlain
by the basal disturbed layer of the St. Seotion near the High Sohool at Warsaw. ST. LOUIS
FEET
INCHES
Limestone, gray, compact; the disturbed basal layer of the St.
Louis _ .. _________________________ . _________________________________ . ____ .___________________________
2 Limestone, gray, compact; the disturbed basal layer of the St.
Louis _ .. _________________________ . _________________________________ . ____ .___________________________
2 Seotion ne/llr Rand Park, Keokuk Louis limestone one and
one-half feet in thickness, and is underlain by the Lower War-
saw shale with an exposed thickness of four feet. Farther down
.the creek lower beds of the Lower Warsaw appear. . Th
S
li
t
t
i
j
t
th
f th
t The Spergen limestone outcrops again just south of the town
of Montrose along a small tributary of the Mississippi. It is
ash-colored to brownish in color and arenaceous and dolomitic
in character. Poorly preserved molds of fenestelloid bryozoans
are the only important fossils. The formation here has a thick-
ness of twenty-one feet. Thirty feet of geodiferous Lower
Warsa.w shales is exposed below it along the banks of the creek
while conglomeratic St. Louis limestone of variable thickness
appears above. Th
S
i
h
f ll
i
bl ff
i
i
h The Spergen appears in the following bluff section in the
northern part of section 13 of Pleasant Ridge township: Seotion in PleasOfn,t 'Ridge township. SPERGEN
6. Limestone, magnesian, brownish; cross-bedded and laminated;
impure and arenaceous tOWJaJ"d the base. Impressions of
fenestelloid bryozoans abundan t ____ ._. __ . ________________________________________ _
5. Shale, argillaeeous, with intercalated layers of sandstone rund
magnesian limestone near the top __________ . ___________________________________ _
4. Limestone, magnesian, in a massive ledge _____ . _______________ . _______ ~ _______ _
WARSAW
3. Shale, bluish, argillaceous ______________________ . ____ . _______________________ . ____ . ____ _
2_
Oo.n.cealed ____________________________________________ . ____________ . _____ . ______________________ _
1. Shale, calcareous, in bed of creek_
FEE'r
2
10 SPERGEN
6 ,
,
g
______
2_
Oo.n.cealed ___________________________________ 1
Shale
cal 1. Shale, calcareous, in bed of creek_ Hancock Cownty, Illinois.-The Spergen formation outcrops
at a number of localities in this county. In the vicinity of War-
saw it is very thin, owing no doubt to the erosion interval
which followed its deposition and preceded the incursion of the
St. Louis sea (fig. 7). I
ll
i
ib
h
l
k
h
di In a small ravine tributary to the large creek a short distance
east of the High School, the following section was measured: MISSISSIPPIAN STRATA OF IOWA 224 SPERGEN
i Limestone, yellowish, magnesian, with ocoosional rounded sand
grains
1 Limestone, gray, fossiliferous, thin-bedded _______________________________________
1
7
WARSAW
Li
t
i
f
t
b
i h
d
i Limestone, magnesian; upper one foot brownish and massive;
lower five feet bluish and shaly ______________________________________________
6 The following succession may be seen in an old quarry face
in the south bank of the creek, about thirty yards northeast of
the ravine section : Section itn quarry near the precedilng 8ection. Section itn quarry near the precedilng 8ection. PERGEN
FEET
INCHES
Limestone, brownisll, magnesian, 'with scattered ~ounded quartz
grains about 1 mID. in diametel' __ . _________ . _____ . _______________ . __ ...... __________
G
Li
t
i h f
ilif
i
th
f
f thi
b dd d Limestone, grayish, fossiliferous, in the form of thin cross-bedded
!:ayers; resting on the wavy surface o'f the bed beneath ________ :_ 1
6
WARSAW
Limestone
brownish
in two massive ledges
Exposed
5 Limestone, grayish, fossiliferous, in the form of thin cross-bedded
!:ayers; resting on the wavy surface o'f the bed beneath ________ :_ 1
6
WARSAW
Limestone
brownish
in two massive ledges
Exposed
5 Limestone, brownish, in two massive ledges. Exposed __________ .______
5 Limestone, brownish, in two massive ledges. Exposed __________ .______
5 FIG. 7.-View of the Spergen and associated formations near Warsaw, Illinois.. The cross-
bedded member is the Spergen, the underlying- shale is 'Varsaw and the overlying
limestone ledge is St. Louis. Notice the disconformab:e relations of the Spergen and
Warsaw. FIG. 7.-View of the Spergen and associated formations near Warsaw, Illinois.. The cross-
bedded member is the Spergen, the underlying- shale is 'Varsaw and the overlying
limestone ledge is St. Louis. Notice the disconformab:e relations of the Spergen and
Warsaw. The follo'wing section is exposed at the bend of the creek a
short distance above the Main Street bridge: SPERGEN BEDS NEAR NIOTA 225 SeotiO'n ab01!e MaNn Street bridge. SeotiOn ab01!e MaNn Street bridge. ST. LOUIS
Limestone, gray, compact, brecciated ............................. _ .................. . SPERGEN
Limestarue, gray, fossilifeJ;ous, cross·bedded ................. _ .... _ .... _ .... _. WARSA.W
Limestone, bluish, arenaceo·magnesian, weathers brownish ... _ ...... . FEET
2%
1
7% ST. LOUIS
Limest The Spergen was formerly quarried extensively in the Missis-
sippi river bluff one mile south of Sonora, Illinois. The forma-
tion consists of arenaceo-magnesian limestone and is twenty
feet thick in the southernmost of the quarry openings, where it
overlies bluish argillaceous shale presumably of Lower Warsaw
age. It is succeeded above by six to twelve feet of conglomer-
atic St. Louis limestone. The latter pinches out a few rods
north of this exposure and the Sper,gen is succeeded dirf,ctly by
::;anc1stones and shales of Pennsylvanian age, which contain
characteristic plant remains. The Sonora sandstone of Keyes9
represents t4e Spergen of the aboV'€ described section. 9 Iowa Goo!. Survey, vo!' III, p. 348; 1893. 2. Shale, bluish, argilla.oeous
1
Limestone
massi e
dolom SlMtion one-half mile rwrtlwast of Niota. FEET
INCHES
10. Drift, yellowish, with blocks of lim estOOle. ST. LOUIS
9. Limestone, gray, dense, fine-grained, brecciated ___ ......... ____ ... __ .__
4
SPERGEN
8. Limestone, bluish, areuaceo·magnesia.n, lower half bearing
angular fragments of white chert ... _ .. ___ . ____ ................ ___ . ____ ._ .... __ .. _ 1
1
7. Sandstone, fine-grained, bluish, incoherent __ ._ ....... _. __ ._. ____ .... _....... 2
6. Limesto.ne, impure, buff, magnesian, passing dowDiward into
sandstone ........... _____ .. __ ._._. ___ . ____ .... _ ......... _._ ....... _ .... _. ___ ._. __ .. _ ........ ___ .. ___
1
3
5. Sandstone, fine-gl'ained, bluish, calcareous, grading downward
into bed below _._ .............. _ ... _ ... _ ... ___________ ......... __ .. ____ ._ ............ _____ ._.____
3
4. Limestone, arenaceo-magnesian, weathering yellowish brown ____
2
2
3. Shale, bluish, arenaceous, locally more calcareous and massive. Bearing impressions of feneswlluid bryozoans ... _ ... ___ .......... __ . __ ... 14
2. Limestone, brownish on weathered surface, magnesian .......... _ ... 1-2
1. Shale, blue, argillaceous, weathering to a grayish blue plastic
clay. Upper part grading laterally into a fossiliferous mag-
nesian limestone .............. __ ... __ ... __ ._ .... _ .......... __ ._ ...... _._ .. __ ._ ..... _. ____ . ___ . 3 10. Drift, yellowish, with blocks of lim estOOle. ST. LOUIS 4. Limestone, arenaceo-magnesian, weathering yellowish brown
3
Sh l
bl i h
l
ll
l
d
i 4. Limestone, arenaceo-magnesian, weather
3
Sh l
bl i h
l
ll 2. Limestone, brownish on weathered surface,
1
Sh l
bl
ill
h
i Des Moines County, Iowa.-The only exposures of the Sper-
gen which are known to occur in Des Moines county appear on
Long creek in section 12 of Augusta township. In an abandoned
quarry on the property of vVm. Madlener, in the north bluff of
the creek (S\iV. ~~ of SK14 sec. 12), it has an exposed thickness
of thirty-four and one-half feet. The beds are described in the
accompanying section: Section of Madlener q1,arry
5. Drift ... _ .......... _ ... __ ....... ____ . ____ .. ___ . ____ ... ____ .. _____ . ______ . ___ . ____ .. ______ . _____ . ___ .. _
SPERGEN
4. Limestone, buff, dolomitic ._._ .. _____ .. _ ........... _ .... ____ . ___ ... Section itn quarry near the precedilng 8ection. The following section appears in the Fort Madison-Appa-
noose Stone Company quarry about two miles northeast of
Niota, Illinois. Section in Fort Maillison·Appanwosc Stone Company quarry. ST. LOUIS
FEET
3. Limestone, gray, compact, fine'grained, brecciated and dis·
turbed . ____ • __ . __ ._. __ .... __ . ____ ... __ . _____ ... ___ .... ___ ... _______ .... __ ._ .. _ ... _._ .... _.......... 25
SPERGEN
,
2. Shale, bluish, argilla.oeous . ___ .. _______ .. ______ ... ______ .... _._. __ . ___ .. ___ .. __ .. _. 3 to 6
1. Limestone, massive, dolomitic, vesicular, boo.ring many im·
pressions of fenestelloid bryozoans; bmwnish and buff above
but dJ:81b below and containing disseminated pyrite ._ ...... __ ...... 22%
The contact of bed 1 with the Lower Warsaw may be studied
i
i
b 1. Limestone, massive, dolomitic, vesicular, boo.ring many im·
pressions of fenestelloid bryozoans; bmwnish and buff above
but dJ:81b below and containing disseminated pyrite ._ ...... __ ...... 22% The contact of bed 1 with the Lower Warsaw may be studied
in a ravine near by. h
S
i
hi k
f
l
h
fi The Spergen attains a thickness of not less than twenty-five
feet along a creek skirting the Pontusac road, about two lIilles
east of Niota. All but the upper _three feet of the formation at
this place is a massive magnesian limestone.. The upper three
feet is made up of thinly laminated and cross-bedded gray lime-
stone which bears brachiopods and numerous bryozoans. The
contact with the Lower Warsaw is shown here also. The Spergen outcrops in a somewhat different facies about
one-half mile east of Niota on the west bank of a creek. MISSISSIPPIAN STRATA OF IOWA 226 5. Drift.
SPFIWEN
4
Li 5. Drift. SPFIWEN
4
Li 2. Shale, bhtish, argillaceous, more calcareous in lower part; a
few small imperfect siliceous. geodes on slope ................... _......... 18
KEOKUK
1
Limestone
bluish
medium to co'arse'grained
OTthotetes keo 1. Limestone, bluish, medium to coarse grained, OTthotetes keo·
kuk abundant. Exposed above level of water in creek ... _....... 11 Van Buren County.-The Spergen is exposed at several local-
ities along Des Moines river and its tributaries in Van Buren
county. In the northeast quarter of section 3 of Farmington
township it outcrops in the banks of Indian creek. An exposure
of limestone five and one-half feet high which yields many char-
acteristic Spergen fossils appears one hundred yards below the
railroad bridge across the stream. The limestone is gray in
color, slightly crinoidal and thinly bedded. Locally, parts of the
bed grade laterally into heavier bedded bluish dolomitic lime-
stone. Three feet of dolomitized conglomeratic St. Louis lime-
stone overlies the Spergen. The following beds of the Spergen are
bank one-fourth mile below this exposure. appears above. shown in the creek
St. Louis limestone Section in bluff below pTecedvng exposuTe. Section in bluff below pTecedvng exposuTe. FEET
5. Drift. SPFIWEN
4. Limestone, soft, buff, dolomitic, filled with the molds of
fenestelloid bryozoans and other foSSlils ... _ ...................... _......... 6
LoWER WARSAW
3. Concealed ............... _ ................................................ _........................... 71h
2. Shale, bhtish, argillaceous, more calcareous in lower part; a
few small imperfect siliceous. geodes on slope ................... _......... 18
KEOKUK
1. Limestone, bluish, medium to co'arse'grained, OTthotetes keo·
kuk abundant. Exposed above level of water in creek ... _....... 11 SlMtion one-half mile rwrtlwast of Niota. ____ ._._ ... ___ ... _. __
3. Shale, bluish, argillaceous ____ . __ ._ .. __ .. _._. __ ... ____ ... __ ....... __ ... _ .. _ ... __ .. _ .. 2. Limestone, buff, dolomitic, massive, filled with the molds of
fenestelloid bryozoans and other fossils;
with occasional
streaks and patches of denser bluish dolomitic limestone ._ ... __ _
LOWER W ARSA W
1. Shale, bluish, argillaceous, with occasiJo·naJ siliceous segrega·
tions. Exposed ____ . ___ .... ____ ._ ...... ___ ... _. __ ... __ .... _ ............................ _ ... _ .... . FEET
1
1
3
12 Section of Madlener q1,arry The fossils identified from bed 2 of this section are as follows : List of fossils from Spergen formation in Madlaner q~WJrrry. List of fossils from Spergen formation in Madlaner q~WJrrry. Fenestelloid bryozoa (impressions)
Pl'oditlctus altonensis N. and P. Pustula biseriata (Hall)
Dielasma sp. Spiriferina salemensis Weller
SpiTifer bifU1'catus Hall
Spirifer tenuicostatus Hall
Reticu laria setigera (HJaJl)
Brachythyris subcardifol'lnis (Hall)
Orthonychia acutirostre (Hall) Dielasma sp. S i if
i Spiriferina salemensis Weller A bluff on the same bank of . the creek three hlmdred yards
farther down stream shows the following succession. SPERGEN BEDS 1'."'EAR FARMINGTON 227 SPERGEN
5 5. Limestone, bluish gray when fresh, weathering brownish; a
few 'small angular chert fragments present at one point; filled
with mold·s of bryozoans and other fossils. This bed is over·
lain disconformably by the St. Louis limestone except at the
west end of the section where the Pennsylvanian sandstone
rests upon the Spergen ................................. _ .......... _ ....................... 0 to Ilh
4
Li
t
i
bl i h
ith
ld
f f 4. Limestone, arenaceo·magnesian, bluish; with molds of fenes·
telloid bryozoans and other fossils. Consists typically of a
bluish dolomitic sandstone with irregular, discontinuous seams
·of fine·grained bluish dolomitic limestone. Locally this memo
bel' passes completely into a fine· grained bluish sandsto'ne,
nearly barren of fossils. One large fish' tooth was found in
the sandstone. This facies tends to flake off obliquely to the
weathered surface. The shaly portion at the top bears mica
flakes ......... _ .......... _ .......... _ .............................................. _ ................ _. 4 to 51f1,
3
Shale
bluish
argillaceous
slightly arenaceous in
the basal 2. Shale, calcareous, arenaceous in upper part; approaching an
impure limestone below; ash-colored, grading into the bed
above, bearing Spirifer sp., ConulaTia sp. and bryozoans ............ 1 to 2
LoWER WARSAW 1. Shale, bluish, argillaceous. No fossils noted. Contact with
the bed above mostly conooaled. Exposed .................................... 7 228 MISSISSIPPIAN STRA'l'A. OF IOWA Other important exposures of the Spergen are shown along
Reed creek in the northeast quarter of section 15, Bonaparte
township. The following section is .exposed in an abandoned
quarry about half a mile above the mouth of the stream: Section in aband01wd q'Ua;rry on Reea C7·ee7c. ST. LOUIS
5. Limestone, brownish, dolomitic, mashed and broken in lower
part ....................................................................................................... . SPERGEN
4. Limestone, brownish, arenaceo'magnesian ..................................... . 3. Sandstone, fine'gTai:rued, soft, bluish ............................................. . 2. Concealed ........................................................ , ................................... .. WARSAW
1. Shale, bluish, argillaceous. Exposed to bed of Cl'eek ................ .. FEET
15
5 to 8
1
6 Another ' outcrop of the Spergen, twelve feet high, appears
about two hundred yards farther upstream and is capped by
drift. The formation as here exposed consists of fine-grained
bluish sandstone the upper two-thirds of which is massive when
fresh but weathers into thin layers. The lower third is thinly
and irregularly bedded and locally is shl;lly. ~rhe same beds appear again in the banks ,of the creek one
hundred and twenty-five ' yards east of the abo-ve section. Section of Spergen formation on Bear CT(!e7c.
j,'EET
!NCHES
7.
Sandstone, bluish, fine·grained; blocks of St. Louis limestone
on slo.pe above ....................................................................................
3
6.
Shale, bluish, argillaceous ................. _............................................. 4 WARSAW
Shales SPERGEN
5 At
.this point the Spergen is represented dominantly by shale. Six-
teen feet of bluish argillaceous shale with thin layers and dis- . continuous seams of bluish sandstone is overlain by drift. A small exposure on Potters branch in the southeast quarter
of section 9, Bonaparte township, shows the Spergen in contact
with the vVarsaw shales. 6.
Shale, bluish, argillaceous ................. _............................................. 4 Secti01~ on Potters bTanch. Secti01~ on Potters bTanch. SPERGEN
FEET
Shale, argillaceous, bearing a few imperfect siliceous geodes ........ 12
Limestone, brownish, dolomitic ................................................................. 16
Shale, arenaceous and calcareous, with a band of siliceous nodules
near the middJe; bearing fenestelloid bryoZOlans. Resting un·
evenly on the bed beneath ..................... :......................................... 514
WARSAW
. Shales .................................................. :......................................................... 11 The following section of the Spergen is exposed in the south
bank of 'Bear creek, in the northeast quarter of section 10,
Henry township. Section of Spergen formation on Bear CT(!e7c. j,'EET
!NCHES
7. Sandstone, bluish, fine·grained; blocks of St. Louis limestone
on slo.pe above .................................................................................... 3
6. Shale, bluish, argillaceous ................. _............................................. 4 ,229 SPERGEN IN HENRlY COUNTY 5. Sandstone, :fine-grained, yellowish; resting unevenly on the
bed beneath; with angular white chert fragments in basal
part _______________________________________________________________________________________________ 1 to 2
4. Limestone, cream-colored, with irregular seams and nodules
of whitish chert; weathering to polyhedral blocks ______________________
2
6
3_ Shale, bluish, ::tJ'gillaceous ____________________________________________________________
2
2. Sandsto·ne, fine-grained, bluish, calcareous, massive when fresh
- but weathering to shaly layers ___________________________________________________
2
3
1. Shale, bluish, argillaceous. To bed of creek ______________________________
6
6 3_ Shale, bluish, ::tJ gillaceous
2
S
d t
fi
i
d
bl - but weathering to shaly layers ___
1
Shale bluish
argillaceous
To b - but weathering to shaly layers ______________________
1
Shale bluish
argillaceous
To bed of creek 1. Shale, bluish, argillaceous. To bed of creek __________________ A second exposure in the creek bank a little more than one-
fourth mile east of the above section shows a considerable dif-
ference in the character of the above beds. Section of Spergen fO'l"mation on Turkey creek. Section of Spergen fO'l"mation on Turkey creek. 2. Sandstone, soft, weathering bmwnish, probably gray when
fresh; less massive than bed below; bearing minute mica. FEET
flakes; dolomitic below ...................................................................... 4%
1. Sandstone, gray with bluish tint when fresh, micaceous; in one
great massive ledge; lower half dolomitic and showing oblique
stratification lines on weathered surface. This also has small
lenses and streaks of bluish dolomitic limestone free from
sandstone; sand grains coarser in lower half. Bearing Worth·
enopora spi1lJosa and other bryozoans. Exposed ........................ 11 2. Sandstone, soft, weathering bmwnish, probably gray when
fresh; less massive than bed below; bearing minute mica. FEET
flakes; dolomitic below ...................................................................... 4%
1
S
d t
ith bl i h ti t
h
f
h
i
i 1. Sandstone, gray with bluish tint when fresh, micaceous; in one
great massive ledge; lower half dolomitic and showing oblique
stratification lines on weathered surface. This also has small
lenses and streaks of bluish dolomitic limestone free from
sandstone; sand grains coarser in lower half. Bearing Worth·
enopora spi1lJosa and other bryozoans. Exposed ........................ 11 10 GeoL of Keokuk County. Iowa GooL Survey. vol. IV. pp 277·282; 1895. Section of Spergen fm'motion in Cedar Bl~!ff . Section of Spergen fm'motion in Cedar Bl~!ff . FEET
INCHES
4. Sandstone, gray with slight greenish tint, fine· grained, weath·
ering yellowish, soft, incoherent ... c................................................ 7
8
3. Sandstone, as above, thin·bedded, weathering yellowish ............ 2
2. Sandstone, as above, with greenish tint, massive, soft ............ 8
4
1. Sandstone, fine-grained, gray with greenish tint, with numer·
ous small greenish patches and occasional thin buff dolomitic
seams. Worthenopora spinosa, Stenopora sp., Polypora sp. .... 3 Section of Spergen fm'motion in Cedar Bl~!ff . Fifteen and one-half feet of Spergen sandstone is exposed be·
low the St. Louis limestone in an abandoned quarry in the
north bank of Turkey creek, near the center of the northeast
quarter of section 11, Lockridge township. Seotion of Spergen fOTrnation east of p1'ecedilng section. Seotion of Spergen fOTrnation east of p1'ecedilng section. FEET
INCHES
6. Sandstone, fine-grained- ____________________________________________________________________
1
5. Limestone, cream-colored, bed 4 of preceding seeti:oill ____ .________
2
6
4. Shale, bluish, argillaceous ___________________________________________________________ ______
6
6
3. Limestone, brownish, dolomitic ______________________________________________________
1
. 2
2'. Shale, bluish, argillaceous ______________________________________________________________ 10
10
1. Limestone, bluish when fresh but wea,thering yello·wish; dolo-
mitic; be;u-ing fenestelloid bryozoans. Exposed above bed of
creek
___________ __________ __________________________________________________________________________ • 4 3. Limestone, brownish, dolomit
2'
Shale
bluish
argillaceous 2. Shale, bluish, argillaceous
1
Li
t
bl i h
h
f Considerable arenaceous limestone has been removed from
the Spergen in the old Bear creek quarries which were located
in the northwest quarter of section 11, Henry township. At
present about three feet of arenaceous dolomite with impres-
sions of fenestelloid bryozoans is exposed in the ·floor .of the
quarry. This is overlain .by five feet of arenaceous shale: which
in turn is capped by drift. The limestone ledge which appears
in the quarry has an exposed thiclmess of eight feet in the bank
of the creek near by. . , H enry County.-The only exposure of the Spergen formation
observed by the writer in Henry county appears in the bed of a
small branch of Mud creek about one and one-half miles north~
east of the town of Lowell in Baltimore township. At this
locality it is represented by a wedge-shaped bed of brownish to
buff massive dolomitic limestone between the St. Louis lime-
stone and the vVarsaw· shale. It is 'filled with molds of Pro-
duct~£s altone1'bSis and impressions of fenestelloid bryozoans. The maximum exposed thickness of the limestone is about four
feet. It thins abruptly from this point downstream and within
a few yards disa]>pears completely, thus permitting the basal
bed of the St. Louis limestone to succeed the Lower Warsaw
shale directly. MISSISSIPPIAN STRATA OF IOWA 230 Jefferson County.-The northernmost exposures of the Sper-
gen formation observed by the writer in Iowa occur in Lock-
ridge township of J efferson county. Twenty-one feet of Sper-
gen sandstone underlies an unusually complete exposure of the
St. Louis limestone in the Cedar Bluff section on Skunk river,
one-fourth mile east of the southwest corner of section 12. The
base of the Spergen is not exposed. The section is as follows: Section of Spergen fm'motion in Cedar Bl~!ff . CHARACTER AND· GENERAL ' RELATIONS The St. Louis limestone is named from the city of St. Louis. This formation, like the Spergen, has been poorly understood
in Iowa, owing to the great lateral range in its character, a
range which is due to original differences in sedimentation,
to d.ifferences in the degree of dolomitization, to the presence
of a disconformity at the base and to extensive brecciation
at some localitjtes. According to the old definition the St. Louis in Iowa includes three distinct subdivisions, designat-
ed by Bainlo the Springvale, or basal member, the Verdi, and CHARACTER OF CROTON LIMESTONE 231 the Pella. It is now known that the Pella member is formation-
. ally distinct. This bears a Ste. Genevieve fauna, and is separ-
ated from the true St. Louis beneath by a disconformity. Again
it is now recognized that the arenaceo-magnesian limestone local-
ly exposed above the vVarsaw, and formerly included with the
St. Louis, is a distinct formation and belongs to the Spergen
limestone. Furthermore the type section of the Springvale as
defined by Bain is believed to be of Keokuk age (see page 181)
rather than St. Louis. Consequently this te'rm should be aband-
oned. In its place the name Croton is substituted, since the
lower division of the St. Louis is typically developed in the vi-
cinity of that town in Lee county. The terms Croton and Lower
St. Louis are used synonymously in 'this report. The Croton
limestone is by far the more extensive of the two divisions of
the St. Louis, for it extends far to the north, overlapping all the
earlier divisions of the Mississippian except the Kinderhook,
upon which it rests in Humboldt county (fig. 2, page 44). This
relationship is believed to be due in part to greater uplift and
. erosion in the northern region prior to the Croton submergence
and to nondeposition of the Warsaw and Spergen formations in
the northern area. This division consi!Sts for the most part of
massive, compact buff to brovvnish dolomitic limestone, but fre-
quently these beds are found to grade laterally in short distances
into dense, fine-grained gray nondolomitic limestone. Again,
the two phases may have an interbedded relationship. Further-
more the Croton limestone is brecciated at many localities. At
the close of Croton time, the sea retreated to the southward as
a result of an elevation of the northern area. CHARACTER AND· GENERAL ' RELATIONS An intraforma-
tional disconformity between this division and the Verdi has
been traced as far south as Alton, Illinois, but there is no evi-
dence of it in the St. Louis section in Ste. Genevieve county,
Missouri, where the formation has a greater thickness than in
Iowa. The Croton limestone is about thirty feet in thickness. F ll
i
h
i
l
f
i
h
l
' f C the Pella. It is now known that the Pella member is formation-
. ally distinct. This bears a Ste. Genevieve fauna, and is separ-
ated from the true St. Louis beneath by a disconformity. Again
it is now recognized that the arenaceo-magnesian limestone local-
ly exposed above the vVarsaw, and formerly included with the
St. Louis, is a distinct formation and belongs to the Spergen
limestone. Furthermore the type section of the Springvale as
defined by Bain is believed to be of Keokuk age (see page 181)
rather than St. Louis. Consequently this te'rm should be aband-
oned. In its place the name Croton is substituted, since the
lower division of the St. Louis is typically developed in the vi-
cinity of that town in Lee county. The terms Croton and Lower
St. Louis are used synonymously in 'this report. The Croton
limestone is by far the more extensive of the two divisions of
the St. Louis, for it extends far to the north, overlapping all the
earlier divisions of the Mississippian except the Kinderhook,
upon which it rests in Humboldt county (fig. 2, page 44). This
relationship is believed to be due in part to greater uplift and
. erosion in the northern region prior to the Croton submergence
and to nondeposition of the Warsaw and Spergen formations in
the northern area. This division consi!Sts for the most part of
massive, compact buff to brovvnish dolomitic limestone, but fre-
quently these beds are found to grade laterally in short distances
into dense, fine-grained gray nondolomitic limestone. Again,
the two phases may have an interbedded relationship. Further-
more the Croton limestone is brecciated at many localities. At
the close of Croton time, the sea retreated to the southward as
a result of an elevation of the northern area. An intraforma-
tional disconformity between this division and the Verdi has
been traced as far south as Alton, Illinois, but there is no evi-
dence of it in the St. HRECCIATION OF S,T. LOUIS BEDS 233 11 Jour. Geology. vol. III, pp. 307. 308 ; 1895.
12 Iowa Goo!. Survey. vol. V. p. 150; 1896. BRECcIATION EFFECTS The brecciated and disturbed f~cies of the St. Louis limestone
received considerable attention from the writer in the course of
field work in southeastern Iowa. The brecciation is confined al-
most entirely to the St. Louis limestone as revised, although
locally the succeeding Pella beds are slightly affected. The un-
derlying Spergen beds nowhere share in the fracturing. The
disturbance may involve beds only a few feet in thickness at any
horizon, or it may affect the whole formation from top to bot-
tom. Where it is confined to beds only a few feet in thickness
it is usually very local and the disturbed facies passes laterally
into undisturbed layers within short distances. Where it is
more general, however, the beds are affected over a much larger
area, but even there the signs of disturbance- eventually die out
and give place to evenly lying beds show:ing no signs whatever
of brecciation. The tendency of the beds to grade laterally into
material of an entirely different character within shott dis-
tances is very confusing and this coupled with the puzzling
features produced by variations in the intensity of dolomitiza-
tion at different localities complicates the situation considerably. By previous workers it has usually been assumed that the
brecciated character of the St. Louis limestone is an original
feature which was produced by disturbed conditions during de-
position . . Thus, C. H. Gordonll offers the following possible
explanations: (1)
Wave action upon a rock-bound coast. (1)
Wave action upon a rock-bound coast. (2)
Sytematic alternation of vigorous and quiet action
of wind waves in connection with tidal oscillation in regions
where the sea bottom is subjected! to wave action at low
tide. (3)
Wave action especially facilitated by the develop-
ment of coral reefs . (2)
Sytematic alternation of vigorous and quiet action
of wind waves in connection with tidal oscillation in regions
where the sea bottom is subjected! to wave action at low
tide. (3)
Wave action especially facilitated by the develop-
ment of coral reefs . . The second of these, according to Gordon, best suits the facts. . The second of these, according to Gordon, best suits the facts. Again
Bain12 in his discussion of the Verdi limestone of Again, Bain12 in his discussion of the Verdi limestone of
Washington county expresses himself as follows: "The Verdi contains the record of a time of considerable dis-
turbance. CHARACTER AND· GENERAL ' RELATIONS Louis section in Ste. Genevieve county,
Missouri, where the formation has a greater thickness than in
Iowa. The Croton limestone is about thirty feet in thickness. F ll
i
h
i
l
f
i
h
l
' f C Following a short interval of erosion at the close 'of Croton
time the sea returned and deposition of limestone in the :region
began again. The returning seas, however, probably did not
extend so far north at this time ~s during the Croton. The
Verdi or Upper St. Louis limestones, which were formed at this
time, are, for the most part, light gray in color and fine-grained MISSISSIPPIAN STRATA OF IOWA 232 and compact in texture. But interbedded layers of granular to
oolitic limestone occur at a few localities. This member is dolo-
mitic at only a few places but locally the beds pass laterally in
whole or in part into sandstone. Its thickness is nowhere more
than thirty-five feet. The type section is in the old railroad
quarries near Verdi in Washington county. q
g
y
The fauna of both divisions of the St. Louis is meagre. The
coral, Lithostrotion canadensis, which normally occurs in a zone
at the very top of the Croton, is the most important horizon
marker of that member. The fauna of the Verdi is more var-
ied, consisting of several species of Pt'oductus, a few other
brachiopods and occasional gastropods and pelecypods. The unstable conditions of the St. Louis were terminated by
a greater and more widespread uplift than that which occurred
in this region during preceding Mississippian time. However,
the duration of the erosion interval which followed the uplift
could not have been great, for the deposits of the returning Ste. Genevieve sea, which must have rivalled that of the early St. Louis in size, have not been found in Iowa to rest upon forma-
tions older than the Croton. FIG. S.-Brecciated Lower St. Louis limestone overlying regularly bedded Spergen limestone. Near Colchester. Illinois. . FIG. S.-Brecciated Lower St. Louis limestone overlying regularly bedded Spergen limestone. Near Colchester. Illinois. . HRECCIATION OF S,T. LOUIS BEDS BRECcIATION EFFECTS Shore formations and open sea deposits succeed each "The Verdi contains the record of a time of considerable dis-
turbance. Shore formations and open sea deposits succeed each MISSISSIPPIAN STRATA OF IOWA 234 other in rapid alternation. Huge blocks of the previously
formed limestone were torn from their beds and buried in the
sands, apparently at the foot of a series of cliffs; or they were
beaten upon each other and reduced, in part, to fragments of
varying degrees of coarseness, and in part to finest powder that
eventually cemented the fragments together. Considering the
turbulent conditions under which the beds were formed, it is
not strange that fossils are rare." In his report on the geology of Henry county, Savage inter-
prets the disturbed St. Louis in much the same way. Quoting
from him:1s "The second or middle division is recognized by the extreme
variableness of its beds and its generally disturbed condition. It consists of irregular layers of sandstones and shales with an
occasional bed of brecciated limestone near the upper portion. It is a record of a time of great disturbance and of rapidly
changing conditions. It is for the most part a deposit near the
margin of some troubled sea. The presence of local layers
which thin out rapidly in a short distance, the pockets of sand
and shale, the numerous lenticular beds, and the general irreg-
ular appearance of the strata indicate a vigorous wave action. The ripple marks which are beautifully preserved in the sand-
stone at numerous points, and the local development of oolitic
limestone testify to the close proximity of an old shore line." The most important outcrops of the St. Louis from the stand-
point of brecciation are located at Montrose in Lee county and
along the .creeks tributary to Des Moines river in Van Buren
county. The brecciation effects in the formation may be grouped into
three main types. In the first the disturbed portions assume
the form of small mounds or reefs of limestone blocks, usually
in a calcareous or sandy matrL'X:, with undisturbed layers lap-
ping up on the flanks and filling in the depressions. These ap-
pear at all horizons in the formation, but are most characteris-
tic of the basal Croton and basal Verdi. In the second type the
brecciation is developed along one bed of the Lower St. Louis
owing to differential movements. 13 Iowa Geol. Survey. ·vol. XII. p. 263 ;1902. BRECcIATION EFFECTS The latter type is accom-
panied in a few cases by tongue-like extensions of broken lime-
stones which are forced into the beds below, especially where
the underlying layers are soft shales. The third type embraces TYPES OF BRECCIATION 235 the major part if not the entire formation over an area of dif-
fering but usually limited extent. In this type the disturbance
has been produced by mashing on a large scale and the breccia-
tion is in many places associated with small overthrust fault::;
and folds. The Pella beds also, are involved to a slight extent
in this disturbance but in no instances have the underlying for-
mations been found to exhibit signs of brecciation. Regarding the origin of the brecciation, at.least three periods
of disturbance are believed to have been involved in its produc-
tion. The mounds or reef-like masses of the first type are be-
lieved to have been formed under conditions of violent wave
action possibly induced by local shallowing of the sea during
deposition. The presence in the formation of local disconform-
ties, of stratified breccia, and of cross-bedded limestone sands
supposedly formed by the grinding up of layers already depos-
ited is in favor of this view. Other features which suggest
wave action at the time of deposition are contemporaneous
erosion phenomena, wave-marks and cross-bedding. The brecciation of the second type was formed as a result of
deformation. The importance of this cannot be definitely eval-
uated since its effects are in many cases overshadowed by the
disturbance of the third type. That this disturbance is distinct
from the third is suggested by the fact that there is evidence
of dolomitization having intervened between the two. Thus, the
reefs produced by the first disturbance and the shattered areas
and fracture lines produced by the second are in numerous in-
stances either wholly undolomitized or are very imperfectly
altered while the undisturbed limestone about them is uniform-
ly dolomitized. This relationship supports the theory that dolo-
mitization succeeded the first and second periods of disturbance
and that the brecciated areas were more resistant to alteration. But a later disturbance involves both the poorly dolomitized
areas and the uniformly dolomitized ones and a later series of
fractures cuts the earlier ones. The latter relationship is shown
by the displacement of calcite veinlets which occupy the older
fractures. BRECcIATION EFFECTS (See page 257.) - Furthermore, the fact that dolomitization apparently nowhere
affects the topmost limestone layers of the ' St. Louis nor any
layers of the Pella indicates that the alteration took place prior MISSISSIPPIAN STRATA. OF IOWA 236' to the close of the St. Louis. Now since the brecciation of the
second type is known to have taken place still earlier and ap-
pears to be confined to the Lower St. Louis it seems probable
that this shattering may be related to the uplift which brought
this division to a close. The third period of disturbance was by far the most import-
ant. To this is ascribed the extensive mashing -and shearing
effects and the overthrust faulting and folding on a small scale
so common in the formation. These were influenced to a large
extent by the effects of the preceding disturbances,. and at the
same time they obscured to a large degree the evidence of these
earlier activities. That the deformation which produced the
later disturbances is post-Pella but pre-Pennsylvanian in age is
indicated by the fact that blocks of Pella limestone have been
found sheared down into basal Pella shales and sandstones and
thus preserved at a locality where Pennsylvanian sandstone
rests directly upon these basal beds. (See page 292.) The general parallelism of the strike of the faults and of thH
tilted layers formed at this time with certain folds in the region,
notably the Bentonsport anticline, which trends approximately
N. 68°VV., suggests a common mode of origin of these two types
of deformation. Moreover, it seems probable that both the last period of brec-
ciation and the folds are closely related to the extensive uplift
and tilting to the southwest which affected the region in late
Mississippian time. It is ·well known that the Mississippian
formations were profoundly eroded prior to the deposition of the
Pennsylvanian beds. The belted arrangement of the Mississip-
pian areas in southeastern Iowa was brought about largely by
this period of erosion as is shown by the fact that Pennsylvan-
ian beds are now found resting upon truncated Mississippian
formations of all ages. That the present boundaries of the for-
mations do not represent old shore lines seems certain. The
strata at many localities consist of limestone up to the very
margins and exhibit no shore facies. AREAL DISTRIBUTION The areal distribution of the St. Louis limestone is greatest
in southeastern Iowa, where it forms a broad belt, ,vith occa- ST. LOUIS BEDS AT KEOKUK 237 sional Pennsylvanian outliers, extending from , central Lee
county northward through Henry county and into northeastern
Jefferson and southern vVashington cOlmties, thence northwest-
ward through Keokuk county and into southwestern Iowa and
southeastern Poweshiek counties. Southwest o"f this belt there
are long, linear southeasterly trending areas of St. Louis lime-
stone along the larger streams, notably Skunk and Des Moines
rivers and their larger tributaries, which have cut do"\Vll through
the Coal Measures. The Des Moines river exposures appear in
southwestern Lee, Van Buren, Wapello, southwestern Mahaska
and eastern Marion counties while those related to the Skunk
are chiefly in the northern half of Mahaska county. In south-
ern Lee county there is an imperfect outlier, elliptical in outline,
extending from Keokuk northward to Montrose. In west-cen-
tral Story county there is an irregular inlier of St. Louis lime-,
sto"ne surrounded on all sides by Pennsylvanian strata. The most northerly exposures of the St. Louis in Iowa are in
,Vebster and Humboldt counties where there are several small
isolated exposures chiefly along Des Moines river and its tribu-
taries. ,+he St. Louis · limestone has a widespread distribution in
southern Iowa beneath the Coal Measures as is indicated by
artesian well r~cords . FEET
INCHES
4. Drift.
LOWER ST. LOUIS
3.
Limestone, conglomeratic; mOTe regularly stratified above.
A
layer near the middle bears small irregular quartz grains ______
6
6 AREAL DESCRIPTION BY COUNTIES Lee County.-A section exposed in the Mississippi river bluff
two miles below the K('okuk Union Station ranges from Keo~
limestone up to the base of the Des Moines sandstone. The St. Louis limestone is well exposed at several points near· the brow
of the bluff. One of the most typical sections appears a short di~
tance below the planing mm of the Taber Lumber Compan}f. The"
formation is about thirty-two feet thick at this point and there is
evidence of an intraformational disconformity in" the upper part. The lower or Croton division here is eighteen to twenty-three
feet thick and consists for the most part of massive disturbed
layers of dark gray magnesian limestone "which weathers brown-
ish. The lower part is somewhat conglomeratic and some of the
limestone pebbles in this part are compact, white and unaltered. The matrix and many of the pebbles, on the other hand, are mag- MISSISSIPPIAN STRATA OF IOWA 238 nesian and weather brownish. About one foot of drab sandstone
of Spergen age is exposed at the base at one point. nesian and weather brownish. About one foot of drab sandstone
of Spergen age is exposed at the base at one point. p
g
g
p
p
The contact of the Verdi member with the Croton is very ir-
regular. The Verdi is greatly disturbed and consists ess.entially
of conglomeratic, compact, dense whitish limestone with a cal-
careous matrix. The maximum thickness is fourteen feet. In a ravine back of the wholesale office of the Taber Lumber
Company the St. Louis limestone is overlain disconformably by
ten feet of Des Moine ~ sandstone. The St. Louis is conglomer-
atic throughout its thickness of thirty feet. A very irregular
contact line separates the conglomeratic, compact white Verdi
limestone above from a conglomeratic gray limestone, with
blocks and layers of brownish magnesian limestone, below. Near
the base of the St. Louis there is a bed composed of cemented
grains and pebbles of limestone. The basal Pennsylvanian sandstones are in disconformable
contact with the Croton member of the St. Louis in a bluff sec-
tion a short distance northwest of Rand Park at Keokuk as in-
dicated in the following section : Section in a bluff. northwest of Rand Pa1'k, Keokl.k. DES MOINES
I"EElT
Sandstone, whitish and with carbonaceous seams below, but yellow-
ish abov:e; cross-bedded and irregularly stratified. Weathered
surfaces pitted and cavernous. Section in a bluff. northwest of Rand Pa1'k, Keokl.k. Seotion Vn the s01.th part of Montrose. Section in a bluff. northwest of Rand Pa1'k, Keokl.k.
DES MOINES
I"EElT
Sandstone, whitish and with carbonaceous seams below, but yellow-
ish abov:e; cross-bedded and irregularly stratified. Weathered
surfaces pitted and cavernous. A few eroded eorals and quartz
pebbles in basal part; resting on a very uneven and irregular
surf'a.ce of the Lower St. Louis ..... _ ... __ . ____ .... __ ... _ .. _ .. __ .. __ .. _ ....... __ 11 to 12
LOWER ST. LOUIS
Limestone, compact, gray, conglomeratic, with calcareous matrix;
reef-like and structureless.
One block measures 4 by 8 feet.
;Maximum thickness ___________________________________________________________ : ________ 18 to 19 Seotion Vn the s01.th part of Montrose.
FEET
I Seotion Vn the s01.th part of Montrose.
FEET
INCHES AREAL DESCRIPTION BY COUNTIES A few eroded eorals and quartz
pebbles in basal part; resting on a very uneven and irregular
surf'a.ce of the Lower St. Louis ..... _ ... __ . ____ .... __ ... _ .. _ .. __ .. __ .. _ ....... __ 11 to 12
LOWER ST. LOUIS
Limestone, compact, gray, conglomeratic, with calcareous matrix;
reef-like and structureless. One block measures 4 by 8 feet. ;Maximum thickness ___________________________________________________________ : ________ 18 to 19 _ __ ____
__
_ _ __ __ _
__
LOWER ST. LOUIS
Limestone, compact, gray, conglomeratic, with calcareous matrix;
reef-like and structureless. One block measures 4 by 8 feet. ;Maximum thickness ___________________________________________________________ : ________ 18 to 19 The Upper Warsaw shale, with intercalated layers of bluish
and gray fossiliferous limestone underlies the St. Louis at thi8
place, but the total thickness could not be ascertained owing to
poor exposure. Several exposures of Lower St. Louis limestone appear in the
south part of the town of Montrose along a small creek which
flows into Mississippi river. The following bluff section was
measured a short distance below the wagon bridge. FEET
INCHES 239 ST. LOUIS BEDS NEAR MONTROSE 2. Irregular blocks ailld layers of limestone in a shaly matrix. The blocks in the lower part are brownish and magnesian but
the limestone in the upper part is whitish or ash·colored ........ 6
8
ERGEN
1. Sandstone, gra;y, calcareous, with a few irregular and discon-
tinuous seams of compact gray limestone. Close inspection
l
h
f f
ll id b
d
h
f
il 2. Irregular blocks ailld layers of limestone in a shaly matrix. The blocks in the lower part are brownish and magnesian but
the limestone in the upper part is whitish or ash·colored ........ 6
8
ERGEN 1. Sandstone, gra;y, calcareous, with a few irregular and discon-
tinuous seams of compact gray limestone. Close inspection
reveals the presence of fenestelloid bryozoans and other fossils
in this member. Exposed ............ _................................................... 6 A few rods north of the bluff section described above there is
another good exposure of the Lower St. Louis in a quarry face. At the base of the section is the Spergen formation, consisting
of four feet seven inches of fine-grained bluish sandstone over-
lain by two feet four inches of arenaceous shale. H Iowa Geol. Survey. vol. III, pp. 334-337; 1895. AREAL DESCRIPTION BY COUNTIES In the middle
of the quarry face there is a mound of conglomeratic and dis-
turbed limestone and on the flanks of this are more regularly
bedded layers of limestone (fig. 9). FlO. g.-Reef·structure in Lower St. Louis limestone near Montrose. FlO. g.-Reef·structure in Lower St. Louis limestone near Montrose. The mound evidently represents a reef built up by vigorous
wave action in Lower St. Louis time. The disturpance probab-
ly took place after the basal limestones had been deposited and
consolidated. Several exposures of the St. Louis limestone in the interior of
Lee county have been described by Keyes. H
The more import- MISSISSIPPIAN STRATA OF roWlA 240 ant of these are on the east branch of Sugar creek. The follow-
ing description from Keyes is of an outcrop on this stream in
the northeast quarter of section 20, T. 68 N., R. 5 W. 8ectio"" of St. LO'Uis lil1ne8'tOM on east branch of Sugar creelc (After Keyes). FEET 8ectio"" of St. LO'Uis lil1ne8'tOM on east branch of Sugar creelc (After Keyes). 6. Concealed ............. _ ............. _ .............................. _ ........ _ .................. _ .... . 5. Limestone, hard, bluish white; breaking with conchoidal frac·
ture ............................................................................... _ .................... _ .. . 4. Sandstone, light browJlJ, soft, saccharoidal ....... _ .. __ ... ______ . ___ .. ____ . 3. Limestonc, fine, white, chel'tlike __ .. __ ..... : __ ... _________ . ______________________ __
2. Limestone, soft, or calcareous sandstone grading iloWIllwal'd
into next .. ________________________ . ___________ .. ______ . ______ . _______ ... ______ . __ .. __ .. __________ . 1. Limestone, brecciated, roughly stl'atifiled ____ .. ________ ... ____ .. __ .. ______ . __ __
,FEET
5
3
10
1
10
10 6. Concealed ............. _ ............. _ .............................. _ ........ _ .................. _ .... . 5
Limestone
hard
bluish white; breaking with conchoidal frac
5 It will be observed that the formation as exposed here con-
tains considerable sandstone. E
ll
f h
S
L
i
i
h
h Excellent exposures of the St . . Louis appear in the southwest-
ern part of the cOlmty near Belfast. In the Deamude quarries,
located near the center of section 13, Des Moines township, the
formation is typically developed. The occurrence of the Sper,
gen and Upper Warsaw beds at this locality has been described
on a previous page. AREAL DESCRIPTION BY COUNTIES (See pages 213 and 215.)
. Th
i
f b d
i
h
S
L
i
h
h
d The succession of beds in the St. Louis at the northeast end
of the quarry is given below: UPPER ST. LOUIS
FEE'll
3. Limestone, conglomeratic, light gray, consisting of sub angular
,
blocks rudely stratmed. The matri.'{ is Q,f a lighter gray color.
Rests irregularly on the surface of the bed beneath __ . _____ . __ ._.
9%
LOWER ST. Lours
2. Limestone, compact, massive, brownish on weathered surface,
mUJgnesiMl; locally passing laterally into unaltered limestone__
61h
1.
Limestone, conglomeratic.
Cross·bedded Spergen limestone
below . __________________ .. ___________ .. ____________ .... __ ... __ ... ____________________ ...... __ .. ____ . 10 to 141h
At
i
i t i
thi
t
f th
ll
tli
f Section of St. L01bis limestone in Deamude. quarry. UPPER ST. LOUIS
3
Limestone Section of St. L01bis limestone in Deamude. quarry. UPPER ST. LOUIS
FEE'll
3. Limestone, conglomeratic, light gray, consisting of sub angular
,
blocks rudely stratmed. The matri.'{ is Q,f a lighter gray color. Rests irregularly on the surface of the bed beneath __ . _____ . __ ._. 9%
LOWER ST. Lours
2. Limestone, compact, massive, brownish on weathered surface,
mUJgnesiMl; locally passing laterally into unaltered limestone__
61h
1. Limestone, conglomeratic. Cross·bedded Spergen limestone
below . __________________ .. ___________ .. ____________ .... __ ... __ ... ____________________ ...... __ .. ____ . 10 to 141h
A At cine point in this part of the quarry a small outlier of
Pennsylvanian sandstone occurs. This appears to occupy a
small valley cut into the St. 'Louis. The contact is concealed. B d 1 h
l
i
hi h i
l
i
h
l Bed 1 has a marly matrix which is more prevalent in the low-
er part. Some of the blocks have a fine contorted stratification
and many show stylolytic structure on their surfaces. The con-
glomerate consists of confusedly mingled angular and subangu-
lar blocks of compact dark gray limestone; gray somewhat shaly
fossiliferous limestone; gray subcrystalline limestone filled with
worm castings; compact brownish magnesian limestone; and
drab fine-grained soft impure limestone. Where the blocks are ST. LOUIS BEDS. NEAR BELFAST 241 not greatly disturbed they are rudely stratified. This bed thick-
ens abruptly at one point and bed 2 arches up OYer it. B d
i
bl i h
h
f
h b
h
b
i h
A Bed 2 is bluish gray when fresh but weathers brownish. At
one point it passes abruptly into a thin-bedded gray limestone. To the southwest in the quarry face this bed shares in the gen-
eral disturbance. At this point it is only imperfectly changed
to dolomite, and contains a few chert nodules. No fossils were
found. Bed 3 is composed of blocks of a rather soft gray subcrystal-
line limestone and of compact gr'ay Ihnestone. These , block:,:,
vary from a fraction of an inch to several feet in diameter. At
one point this bed forms a tongue-like extension down through
bed 2 apparently as a result of shearing. Th
S
L
i li
b
f '
i
i
h The St. Louis limestones outcrop at a number of 'points in the
Des Moines river bluff just below Belfast. Section of St. L01bis limestone in Deamude. quarry. Reference has been
made to several of these in the description of the Spergen as
developed there. The following section of the Lower St. Louis
appears in the bluff about one and one-third miles south of Bel-
fast. . Section of L01ver St. Louis lAmi.estone below Belfast. LoWER ST. LoUIS
FEET
INCHES
9. Limestone, gray, compact; in thin nodular layers ...................... 4
8. Limestone, dark gray, compact ; showing no stratification
planes and weathering to irregular chips and polyhedral
blocks; receding ; slightly oolitic .................................................... 2
9
7. Limestone, compact, buff, dolomitic; in. layers ranging from
a few inches to a foot or more in thickness ................................ 4
3
6. Limestone, compact, gray, regularly bedded ......................... _..... 1
4
5. Limestone, yellowish to bl'ownish, dolomitic, massive, e,venly
bedded .................................................................................................. 4
4. Limestone, gray, compact, indefinitely stratified and weather·
ing to irregular chips ........................................................................ 2
3. Shale, bluish, calcareous, receding from bluff about s1.'( feet;
resting on the undul:tting surface of the bed below................. 2
G
2. Limestone, gray, dense and compact; undulating and showing
disturbed stratification ....................................................................... 1
SPERGEN
1. Sandstone, fine'grained, bluish; upper surface slightly undulat·
ing ........ : ..................................................... : ........................................... . The disturbed facies of the St. Louis is seen at the same hori·
zon only a few yards beyond. An excellent section may be seen on Mumm creek in the
southern middle part of section 33, Van Buren township, two
and one-half miles west of Belfast and a little north of that vil-
lage. This section includes the W' arsiw, an attenuated equiva-
lent of the Spergen and both members of the St. Louis. LoWER ST. LoUIS
FEET
INCHES
9. Limestone, gray, compact; in thin nodular layers ...................... 4
8. Limestone, dark gray, compact ; showing no stratification
planes and weathering to irregular chips and polyhedral
blocks; receding ; slightly oolitic .................................................... 2
9
7. Limestone, compact, buff, dolomitic; in. layers ranging from
a few inches to a foot or more in thickness ................................ 4
3
6. Limestone, compact, gray, regularly bedded ......................... _..... 1
4
5. Limestone, yellowish to bl'ownish, dolomitic, massive, e,venly
bedded .................................................................................................. 4
4. Limestone, gray, compact, indefinitely stratified and weather·
ing to irregular chips ........................................................................ 2
3. Shale, bluish, calcareous, receding from bluff about s1.'( feet;
resting on the undul:tting surface of the bed below................. 2
G
2. Limestone, gray, dense and compact; undulating and showing
disturbed stratification ....................................................................... Section of L01ver St. Louis lAmi.estone below Belfast. Section on Mwmm creelc above the preceding seotion.
DES MOINES
S.
Concealed to brow of hill; surface strewn with blockS of
brownish GaDdstone.
UPPER ST. Lours
7.
~!l!l ~stone, light gray, compact; some Jayers granular to
oolItIC ............................. _ ...................................................................... .
6.
Concealed, probably brecciated limestone with 8haly matrix .. ..
5,
Limestone, gray, compact, conglomeratic, rudely stratified .. ..
LOWER ST. Lours
4. Limestone, massive, magnesian, weathm'ing brownish; bearing
a few silicified corolla of Lithost1'otion canadensis,
Very un·
dulating n.nd uneven .......................................................................... ..
3,
Limesto'ne, buff, magnesian. massive, structul'eless; little trace
of bedding; flaking off obliquely; slightly receding,
At one
~EET
12
' 4
1214
3 Se'ction on Mjllmm ureek. Limestone, buff, magnesian, brittle, tending to scale off
obliquely; bears a few rounded chert concretions ...................... 5
2
8. Limestone, gray, compact, dense, unaltered here, but dolomitic
at the bend farther up the creek .................................................. 1
5
7. Limestone, bluish, magnesian, soft, weathering yellowish .......... 3
1
6. Limestone, buff, magnesian, in two layers of about equal
thickness ................................................................................................. 2
9
:J. Limestone, yellowiRh to brownish, dolomitic; distnrbed and
cong'lomeratic, especially in lower part; more evenly bedded
above; passing gradually downward into the bed below; bear·
ing pebbles and irregular p.atches of unaltered compact gray
limesto'Ile. Lower surface extl'emely irregular ...................... 3 to 5
40. Shale, bluish, calOOJ'eous, with imbedded pebbles of compact
gray limestone; of very v3ifiable thickness; resting on the un·
eVlfm snrface of the bed below, and followed unevenly by the
bed above ............................................................ .. .......................... 1 to 3
3. Limestone, gray to buff or y:ellowish, magnesian; conglom·
eratic and disturbed. Some pebbles of unaltered gray com·
pact limestone ................. _ ............................................................. 2 to 311.2
SPERGEN
2,
Limestone, bluish, arenaceo·magn€siaJl ................................ 2/3 to 1
4
WARSAW
•
1. Shale, bluish, argillaceous, more calcareous towards the top
where it carries fish remains, Gonula1'ia sp, and Orbiculoidia
sp. Argillaceous part bears a f ew small imperfect siliceous
geodes. Exposed ................................................................................ S
10
Concealed to bed of creek .................................................................. 3 11. Limestone, gray, compact, con'glomeratic, rudely stratified; with
occasional pockets of carbonaceous shale wnd irregular lines
of fine· grained whitish sandstone at the very base. Resting
on the irregular snrface of the bed beneath. Three 3pecimens
of Lithostrotion canadensis were obtai.ned from a seam of
carbonaceous shale at the base. These were angular, and
showed no evidence of 3Jbrasion ........................................................ 6 8. Limestone, gray, compact, dense, unaltered here, but dolomitic
at the bend farther up the creek .................................................. 7
Li
bl i h
i
f
h
i
ll
i h 7. Limestone, bluish, magnesian, soft, weathering yellowish .......... 3
6
Li
t
b ff
i
i
t
l
f
b
t
l 6. Limestone, buff, magnesian, in two layers of about equal
thickness ................................................................................................. 2 1. Shale, bluish, argillaceous, more calcareous towards the top
where it carries fish remains, Gonula1'ia sp, and Orbiculoidia
sp. Argillaceous part bears a f ew small imperfect siliceous
geodes. Exposed ................................................................................ S
10
Concealed to bed of creek .................................................................. MISSISSIPPIAN STRATA OF IOWA MISSISSIPPIAN STRATA OF IOWA Section of St. L01bis limestone in Deamude. quarry. 1
SPERGEN
1. Sandstone, fine'grained, bluish; upper surface slightly undulat·
ing ........ : ..................................................... : ........................................... . The disturbed facies of the St. Louis is seen at the same hori·
l
f
d
b
d 1. Sandstone, fine'grained, bluish; upper surface slightly undulat·
ing ........ : ..................................................... : ........................................... . The disturbed facies of the St. Louis is seen at the same hori·
zon only a few yards beyond. A
ll
t
ti
b
M
k i
th An excellent section may be seen on Mumm creek in the
southern middle part of section 33, Van Buren township, two
and one-half miles west of Belfast and a little north of that vil-
lage. This section includes the W' arsiw, an attenuated equiva-
lent of the Spergen and both members of the St. Louis. 242 Section on Mwmm creelc above the preceding seotion. Se'ction on Mjllmm ureek. UPPER ST. Loms
FEET
lNCHES
11. Limestone, gray, compact, con'glomeratic, rudely stratified; with
occasional pockets of carbonaceous shale wnd irregular lines
of fine· grained whitish sandstone at the very base. Resting
on the irregular snrface of the bed beneath. Three 3pecimens
of Lithostrotion canadensis were obtai.ned from a seam of
carbonaceous shale at the base. These were angular, and
showed no evidence of 3Jbrasion ........................................................ 6
LOWER S'l'. LOUIS
10. Limestone, brownish, tough, magnesian, bearing the silicified
coralla of Lithwt1'otion canadensis ...................................... 5/ 6 to 1
5
9. Limestone, buff, magnesian, brittle, tending to scale off
obliquely; bears a few rounded chert concretions ...................... 5
2
8. Limestone, gray, compact, dense, unaltered here, but dolomitic
at the bend farther up the creek .................................................. 1
5
7. Limestone, bluish, magnesian, soft, weathering yellowish .......... 3
1
6. Limestone, buff, magnesian, in two layers of about equal
thickness ................................................................................................. 2
9
:J. Limestone, yellowiRh to brownish, dolomitic; distnrbed and
cong'lomeratic, especially in lower part; more evenly bedded
above; passing gradually downward into the bed below; bear·
ing pebbles and irregular p.atches of unaltered compact gray
limesto'Ile. Lower surface extl'emely irregular ...................... 3 to 5
40. Shale, bluish, calOOJ'eous, with imbedded pebbles of compact
gray limestone; of very v3ifiable thickness; resting on the un·
eVlfm snrface of the bed below, and followed unevenly by the
bed above ............................................................ .. .......................... 1 to 3
3. Limestone, gray to buff or y:ellowish, magnesian; conglom·
eratic and disturbed. Some pebbles of unaltered gray com·
pact limestone ................. _ ............................................................. 2 to 311.2
SPERGEN
2,
Limestone, bluish, arenaceo·magn€siaJl ................................ 2/3 to 1
4
WARSAW
•
1. Shale, bluish, argillaceous, more calcareous towards the top
where it carries fish remains, Gonula1'ia sp, and Orbiculoidia
sp. Argillaceous part bears a f ew small imperfect siliceous
geodes. Exposed ................................................................................ S
10
Concealed to bed of creek .................................................................. 3 UPPER ST. Loms
FEET
lNCHES
11. Limestone, gray, compact, con'glomeratic, rudely stratified; with
occasional pockets of carbonaceous shale wnd irregular lines
of fine· grained whitish sandstone at the very base. Resting
on the irregular snrface of the bed beneath. Three 3pecimens
of Lithostrotion canadensis were obtai.ned from a seam of
carbonaceous shale at the base. These were angular, and
showed no evidence of 3Jbrasion ........................................................ 6
LOWER S'l'. LOUIS
10. Limestone, brownish, tough, magnesian, bearing the silicified
coralla of Lithwt1'otion canadensis ...................................... 5/ 6 to 1
5
9. Seotio"" two lvundredJ yards east of precediJno one.
UPPER ST. LoUIS
6.
Limestone, gray, dense, compact, unevenly stratified; exposed
5. Limestone, gray, compact ................................... _ ........................ _ .. .
4.
Limestone, compact, gray, with small white kaolinic patches:
in thin lwyers separated by lamin'<Lted calcareous shale, which
weathers yellowish ............... _ ............................................................ .
3.
Limestone, gray, compact, with seams of gray granular lime·
FEET
714
52/,3
2 Se'ction on Mjllmm ureek. 3 About seven hundred yards farther up, the stream bends
abruptly from the north to an easterly direction. A fine ex-
posure is afforded here in the west bank immediately below the
bend. ST. LOUIS BEDS NEAR BELFAST ST. LOUIS BEDS NEAR BELFAST 243 point a small cave extends back ten to fifteen feet. Highly
fossiliferous in basaJ. part ......................... _ ..................................... 4% to 5 1,-2
2. Limestone, yellowish to brownish, magnesian; in one massive
ledge; resting on the undulating and hummocky surface of
bed below; usually projecting ......... _ ........ _ ............................ _ ....... 2
to 2 %
1. Limestone, bluish, magnesian, in thin, undulating layers;
arching up over mounds in creek bed. Exposed to bed of
creek ........................................................................................................ 2 5/6 2. Limestone, yellowish to brownish, magnesian; in one massive
ledge; resting on the undulating and hummocky surface of
bed below; usually projecting ......... _ ........ _ ............................ _ ....... 2
to 2 %
1. Limestone, bluish, magnesian, in thin, undulating layers;
arching up over mounds in creek bed. Exposed to bed of
creek ........................................................................................................ 2 5/6 The following forms occur as molds in bed 3: Seotio"" two lvundredJ yards east of precediJno one. 14.
Limestone, gray, compact, lo,wer part aronaceous .. , .................. .
13.
Sandstone, fine· grained, y,ellowish ......... _ ........................................ .
9
4% Section along a creek at CI·oton. The following forms occur as molds in bed 3: Girtyella indianensis (Gil'ty)
Spirif'61' (species undescribed)
Bl'llchythyris altonensis Weller
Myalina sp. Myalina sp. Myalina sp. A viculopecten sp. A viculopecten sp. A viculopecten sp. Modiomorpha sp. Conocardium sp. Bellerophon sp. Another excellent exposure of the St. Louis occurs two hun- FIG. lO.-Showing irregular contact between Lower and Upper St. I,ouis limestones on
Mumm creek, near Belfast. FIG. lO.-Showing irregular contact between Lower and Upper St. I,ouis limestones on
Mumm creek, near Belfast. dred yards east of the above mentioned bend in Mumm creek
(fig. 10). The description of this exposure foUows : dred yards east of the above mentioned bend in Mumm creek
(fig. 10). The description of this exposure foUows : dred yards east of the above mentioned bend in Mumm creek
(fig. 10). The description of this exposure foUows : Seotio"" two lvundredJ yards east of precediJno one. UPPER ST. LoUIS
6. Limestone, gray, dense, compact, unevenly stratified; exposed
5. Limestone, gray, compact ................................... _ ........................ _ .. . 4. Limestone, compact, gray, with small white kaolinic patches:
in thin lwyers separated by lamin'<Lted calcareous shale, which
weathers yellowish ............... _ ............................................................ . 3. Limestone, gray, compact, with seams of gray granular lime·
FEET
714
52/,3
2 UPPER ST. LoUIS
6
Li
t 244 MISSISSIPPIAN STRATA. OF IOWA stone; locally oolitic in part; disturbed and structureless at one
point
but passing laterally into eve:nly bedded limestone
1 stone; locally oolitic in part; disturbed and structureless at one
i
b
i
l
ll
i
l
b dd d li point, but passing laterally into eve:nly bedded limestone ... _... 12
2. Limestone, gray, oompact, conglomel1ll,tic, mdcly stratined;
lower portion with calcaTcous matri.-,:: ; upper portion with
shaly matrix; imperfectly dolomitized locally. At one point a
tonguelike mass about Jifteen feet wide appears in the lower
part. 'l'his is nlled with angular blocks of limestone many of
which differ physically fwm those in the adjacent ,_lIs. They
consist of compact light gray limestonc, of light gmy oolitic
limestone, and of bluish Jine·gmined shaly limestonc. The
matrix i shaly and the brcccia has weathcred back slightly,
thus emphasizing the outline of the mass ................... _ .... _....... 12 1. Limestone, doiomitic, bluish gray when fresh but weathering
hrownish, massive; beariJlg a few rounded chert concretions;
beddin.g very uneven and disturbed. Section along a creek at CI·oton.
PELLA
14.
Limestone, gray, compact, lo,wer part aronaceous .. , .................. .
13.
Sandstone, fine· grained, y,ellowish ......... _ ........................................ .
FEET
9
4% ST. LOUIS STRATA AT CROTON ST. LOUIS STRATA AT CROTON UPPER ST. LOUIS
12. Limestone, gray, granular, ill some places slightly oolitic; mid·
dIe p3Jrt cross· bedded. At the very base there is Locally a
conglomeratic layer severoJ inches thick. The lower part of
the granular' limestone passes laterally into gray compact,
subcrystallino evenly bedded limestone which bears small
pelecypods. The upper surface of this layer shows sym·
metrical wave ripples, which have a generaJ. north·south trend. 'l'hey measure three to five' and one·half inches f rom crest to
crest and are one· half inch to one aJld one· half illches deep. This member forms a series of mounds of disturbed limestone
at one point in the creek bled ... __ ........ _ .... __ ........ _ .... _ ................. UPPER ST. LOUIS
12. Limestone, gray, granular, ill some places slightly oolitic; mid·
dIe p3Jrt cross· bedded. At the very base there is Locally a
conglomeratic layer severoJ inches thick. The lower part of
the granular' limestone passes laterally into gray compact,
subcrystallino evenly bedded limestone which bears small
pelecypods. The upper surface of this layer shows sym·
metrical wave ripples, which have a generaJ. north·south trend. 'l'hey measure three to five' and one·half inches f rom crest to
crest and are one· half inch to one aJld one· half illches deep. This member forms a series of mounds of disturbed limestone
at one point in the creek bled ... __ ........ _ .... __ ........ _ .... _ ................. 11
Li i
bl i h
i
hi l
b dd
L
h
h l 11. Liniestone, bluish, magnesian, thinly beddecL; somewhat shaly;
slightly fossiliferous; resting on uneven undulating surface of
bed beneath ........................................................... _ ................ _ ........... 2 10. Limestone, conglomeratic, gradually less disturbed :md more
eV'enIy bedued towards the top. More evenly bedded La.yers
:trching-
up over mounds of conglomeratic iimestone which
consists of pebbles and, blocks of compact gray limestone ;
gray subcrystalline, brittle limootone ; light gray slightly
oolitic limestone and a few small blocks of fine·grained sand·
stone. The matri.., is for the most paa't calcareolls but locally
it is sandy. Some blocks show stylolytic structure. Some of
the matri.., is of a lighter gray color than the blocks. Occa·
sional blocks bear worm castings and some have small irreg·
ular patches of kaolin. Locally cherty in upper vart. The following forms occur as molds in bed 3: At one point a distinct
depression about six feet deep and si.., feet \vide extends into
this member [lJld is fill ed with the cOllg\omeratic limcstone of
the bed above. A few yards to the southeast two other such
tongues appear. These . are bro'ader but less (leop ...................... 2 to 10 Bed 5 of the above section yields the following species: Bed 5 of the above section yields the following species: Girt yell a indiancnsis (Girty)
Spirifer d. S. pellaensis Weller
Compositlt trinuclea (Hall)
Streblopteria f sp. Strap:nollu,s sp. Streptorhynchus ruginosum (Hall and
Cl
k ) f Girt yell a indiancnsis (Girty)
Spirifer d. S. pellaensis Weller
Compositlt trinuclea (Hall)
Streblopteria f sp. Strap:nollu,s sp. Streptorhynchus ruginosum (Hall and
Clarke) f Olthotetes f sp. Pl' d
t
t Pl'oductus ovatu Hall
P
d
i Streblopteria f sp. S
ll Strap:nollu,s sp. Productus tenuioo tatus Hall Good exposures of the upper St. Louis limestone may be seen
along the east branch of Monk creek in the southeast quarter of
section 36, T. 67 N., R. 7 'V., one and one-fourth miles north-
east of Belfast. The relation of conglomeratic mounds to the
evenly-bedded facies is shown her.e on a small scale. 'Well up
in the section a single large partly silicified corallum of Litho-
strotion canadensis was found,. Imperfect ripple marks were
noted on the surface of a lime tone layer a short distance far-
ther up the branch. The mounds of limestone appear to be hut
little altered to dolomite, while the evenly bedded layers on the
flanks are nearly everywhere uniformly altered. ,One of the most complete and representative exposures of the
St. Louis limestone in southeastern Iowa a-ppears along the bed
and banks of a small creek emptyino· into Des Moines river in
the lower edge of the town of Croton (T. 67 N., R. 7 W.) . The
section described below begins up the creek nearly one mile
from its mouth but the more important outcrops of the St. Louis
are in section 20 near the to·wn. FEET
9
4% 2411 2411 3.
Limestone, disturbed, conglomeratic; co))sisting of blocks,
pebbles and subangular bowlders of compact gTa)' limestone;
gray sub crystalline limestone; brow:nish dolomitic limestone
and rather soft bluish, impure limestone, in a calcareous to
shaly matri..,.
Locally evenly bedded la,yors ::t.ppear for a
few yards, but these abut abruptly against conglome)'atic lime·
stone on either side. In one mound the matri.., is sandy. I n
places the conglomeratic limestone assumes the form of
mounds and hummocks, with the c,enly bedded limestone
above lapping up over the elevations ancl filling in the de·
pressions.
Locally the conglomeratic limestone is imperfectly
dolomitized and discolored yellowish.
The calc::t.reous matrix
seems to be the' first to be affected. Occasional blocks in the 2/3 to
3 ST. LOUIS STRATA AT CROTON The
more evenly bedded material towauds the top consists of dense,
compact gray limestone, and of gray subcrystalline limestone. This pm is slightly fossiliferous ... _ ................ _ ... , ........................ _.13 9. Limestone, m-assive, compact, dolomitic, gray when fresh but
weathering yellowish. Locally bearing l'emnants of compact
unaltered gray limestone. The Lithostrotion canadensis zone 0
to 2
8. Limestone, dolomitic, buff, ma,ssive, tough; flaking off ob·
liqnely. Basal part fossiliferous ............... _ .......... _ ...... _ ............... 4lh to 5 7. Limestone, grayish weatheJ'ing buff, dolomitic; locally passing
wholy or in parl into dark gray conglomeratic limestoUie .......... 11/3 to 1 2/3
6. Limestone, bluish, dolomitic, weathers soft and buff, filled with
structures resembling worm castings ..................... _ ....................... 3
to 4
5
Li
b
i h
d l
i i
h
i h
di
i 4. Limestone, drab, subcrystalline, rather compact, brittle; bearing
small, irregnlar patches of kaolin and numerous small chert
concretions with nuclei of greenish clay. Somewhat fossil·
iferous. Lithost:rotiQru p1'o,life1'urn and Syritngopom sp. most
common fossils. Differing in thickness on account of hum·
mocky and ineguJar surface of the bed beneath. This bed
arches up over the mounds below, and fills some of the de,
pressions, thus levelling up the irregular surface. Contains
worm castings.' Locally passes laterally into dolomitic lime·
stone ... __ . ____ .. ____ . _____________________ . ____ . __________ . __ .. __ . __ . __ .. ____ .. __ . __ . __ . __ . __ . __ . __ ..... 4. Limestone, drab, subcrystalline, rather compact, brittle; bearing
small, irregnlar patches of kaolin and numerous small chert
concretions with nuclei of greenish clay. Somewhat fossil·
iferous. Lithost:rotiQru p1'o,life1'urn and Syritngopom sp. most
common fossils. Differing in thickness on account of hum·
mocky and ineguJar surface of the bed beneath. This bed
arches up over the mounds below, and fills some of the de,
pressions, thus levelling up the irregular surface. Contains
worm castings.' Locally passes laterally into dolomitic lime·
stone ... __ . ____ .. ____ . _____________________ . ____ . __________ . __ .. __ . __ . __ .. ____ .. __ . __ . __ . __ . __ . __ . __ ..... 3. 5.
Limestone, brownish.
dolomitic, tough; with discontinuous
seams of unaltered limestone in upper part ... _ .... _ ........ _........... 2/3 to 1
4
Li
d
b
b
lli
h
b i l
b
i ST. LOUIS STRATA AT CROTON Limestone, disturbed, conglomeratic; co))sisting of blocks,
pebbles and subangular bowlders of compact gTa)' limestone;
gray sub crystalline limestone; brow:nish dolomitic limestone
and rather soft bluish, impure limestone, in a calcareous to
shaly matri..,. Locally evenly bedded la,yors ::t.ppear for a
few yards, but these abut abruptly against conglome)'atic lime·
stone on either side. In one mound the matri.., is sandy. I n
places the conglomeratic limestone assumes the form of
mounds and hummocks, with the c,enly bedded limestone
above lapping up over the elevations ancl filling in the de·
pressions. Locally the conglomeratic limestone is imperfectly
dolomitized and discolored yellowish. The calc::t.reous matrix
seems to be the' first to be affected. Occasional blocks in the MISSISSIPPIAN STRATA OF IOWA 246 conglomemte are slightly fossiliferous. Blocks show stylolytic
structure
Exposed
12 to 13 2. Limestone, compact dense, gray; dolomitic in basal part. Upper part with thin wavy concretionary strrutification, the
wavy layers of which conform to the irregular surface of the
limestO'lle below .................................................................................. 1 to 1 2/ 3
RSAW ARSAW
1. Shale, bluish, argillace(}Us; exposed ......•.............. _ .... _................. 5 5/ 6 The Spergen formation apparently was removed by erosion
prior to the deposition of the St. Louis. Fossils collected from beds 3, 4, 10 and 11 were identified as
follows: List of fossils from bed 9 of the St. Louis at Croto,n. Syringopora sp. Eumetria verneuiliana (Hall)
Modiomorpha, f sp. Leperditia carbonaria Hall Modiomorpha, f sp. L
diti
b List of fossils from bed 4, of the St. Louis a·t Croton . Dichotrypa elegans Ulrich ,
Spirifer pellaensis Weller T
Composita trinuclea (Hall)
Phillipsia , sp. Calcareous algae Dichotrypa elegans Ulrich ,
Spirifer pellaensis Weller T
Composita trinuclea (Hall)
Phillipsia , sp. Calcareous algae Zaphrentis sp. •
Lithostrotion proliferum Han
Syringopora sp. Fenestella serratula Ulrich
Fenestella sp. Cystodictya sp. List of fossil~ from bed 10 of th8 St. Louis at· Croton. Lithostrotion proliferum Hall
Spirifer cf. S. pellaeusis Weller
Straparollus sp. List of fossil~ from bed 10 of th8 St. Louis at· Croton. List of fossil~ from bed 10 of th8 St. Louis at· Croton. Lithostrotion proliferum Hall
S i if
f
S
ll
i
W ll List of fossil~ from bed 10 of th8 St. Louis at· Croton. Lithostrotion proliferum Hall
Spirifer cf. S. pellaeusis Weller
Straparollus sp. List of fossils from bed 11 of the St. Lo'lllis at Croton. Productus ovatus Hall
Spirifer cf. S. ST. LOUIS STRATA AT CROTON Shows slight tendency toward
oolitic structure
4
4 oolitic structure ... _ .......... _ ................ _ .......... _................................... 4
4
7. Shale, bluish, argillaceous, weathering yellowish; with thin
interbedded layers of compact bluish gray magnesian lime·
stone which weathers soft and buff
3 6. Limestone, conglomeratic, compact, gray, rudely stratified ... _. 10
1
LOWER ST. LoUIS
5
Li
t
i
i
l d
d l
iti
th
i
b 5. Limestone, in one massive ledge, dolomitic, weathering brown·
ish; middle part locally bears irregular patches of U11altered
limestone ........................... _ ................................ _ .... _ ............. 1 1h to
3% 4. Limestone, dolomitic, bluish when fresh but weathering buff,
brittle, structureless; flaking off obliquely. Slightly fossilifer·
ous; bearing worm burrows ......... , ... _ .... _.: ........ _ ....................... 8 to 9 ;
g
,
_
_
_
3·. Limestone, fine·grained, gmy, compact; locally passing into
dolomitic limestone which. weathers buff in part. At one
point the weathered rock is shaly in middle pa~·t . Upper part
bears occasional sand grains. Shaly part slightly fossiliferous. Bears worm castings. Contact with bed above undulating and
irregular. At olDe point there is a pocket of oarbonaceous
shale at the con,tact. A few yards to the north this bed is
brecciated and sheared down into the beds below .......... 2/3 to 2
magll~ian, 2. Limestone,
bluish,
magll~ian,
rather
soft,
weathering
buff ................................. _ .......... _ .................................. _....... 1 1/ 3 to 2
1
Limestone
b ff
magnesian
massi e
compact
gra ish
hen 1. Limestone, buff, magnesian, massive, compact, grayish when
fresh; locally even·bedded, but generally disturbed and more
or less structureless. Exposed ..................... _ .................... _........... 7 One hundred and forty yards below the above described sec-
tion, twenty feet of massive soft sandstone, whitish when fresh
but weathering yellowish, rests directly upon bed 6 of the pre-
ceding section. This sandstone doubtless is of Pennsylvanian
age, although no plant remains were found in it. Massive beds
of sandstone here bend up over a thick dome of the same ma-
terial to give the appearance of a massive arch. Van Bu,ren County.-Exposures of the St Louis limestone jn
Van Buren county are confined to the valley of Des Moines
river and its tributaries. Along Indian creek west of Farming-
ton it outcrops at a number of points. ST. LOUIS STRATA AT CROTON pellaensis Weller List of fossils from bed 11 of the St. Lo'lllis at Croton. The conglomeratic mounds in beds 3 and 10, representing the
basal parts of the Lower and Upper St. Louis, respectively, are
believed to be due to disturbed conditions during deposition,
although later fracturing undoubtedly has modified the original
relationship somewhat. A section of the St. Louis limestone in the bluff of Des Moines
river .a little more than one mile below Croton, in section 29 of
the same to'wIlship, shows some variations from the one at Cro-
ton. The succession is as follows: Seotion one mile below Croton. D ES MOINES
. . . '
. FEET {, meRES
13. Sandstone, yelloWIsh,l soft, ~ppmg the hill ................. _......... 1 to 2
P ELLA
12. Concealed. Loose blocks of limestone on the slope of the con· 247 ST. LOUIS NEAR FARMING'DON cealed part seem to come from the bed which appears just
above the basal sandstone in the Croton creek section ......... _... 7
4
11
S
d
fi
i
d
di
l
i
d
h3! l cealed part seem to come from the bed which appears just
above the basal sandstone in the Croton creek section ......... _... 7
4
11
S
d
fi
i
d
di
l
i
d
h3! l 11. Sandstone, fine·grained to medium·gl·ained;
somewh3!t cal·
careous; weathering yellowish in lower part; with some iron·
stained patches. Upper part whitish and calcareous. Thinly
and evenly bedded ... _ .... _ .......... _ ................ _ .... _ ...... _ .... _ .......... _..... 5
2
UPPER ST. LOUIS 11. Sandstone, fine·grained to medium·gl·ained;
somewh3!t cal·
careous; weathering yellowish in lower part; with some iron·
stained patches. Upper part whitish and calcareous. Thinly
and evenly bedded
5
2 10. Limestone, gray, compact, with thin, irregular streaks and
pockets of sandstone. Upper surface slightly irregulM' ...... 2 to 3
9
Li
t
li ht
liti
i
t
W
th
d 9. Limestone, light gray, oolitic in upper part. Weathered sur·
faces flaking off obliquely. Contains Conoca-rdVu71t sp., a
Spiri/er resembling S. pellalmsis and a few other fossils .... 5 to 8
8
Li
t
l
i
iddl
b t
t i p
g
p
8. Limestone, gray; gmnular in middle but compact in upper
and lower parts; weathm'ing into thin layers; bearing a few
discontinuous seams of chert. ST. LOUIS STRATA AT CROTON Limestone, gray, granular to compact, locally cross-bedded in
part; a layer 1 foot 6 inches thick near top consists of dense
compa;ct gray limestone. Rolled calcareous algre on surface of
bed. The lower 4 feet consists of compact gray limestone _______ 12
6 Pella. Contains numerous shells of a large Belleroplwn 2% to 4%
6. Limestone, dark gray, sub crystalline and compact; rather
brittle when fresh but becoming tough when weathered; local·
ly filled with small sinuous tubular branching fucoids which
resemble worm castings; bearing l:a.rge calcareous algre some
of which have a maximum diameter of over 5 inches. Upper
surface bearing a few large vertically compressed sinuous pipes
which represent large fucoids. Separated from the bed above
by a shaly parting 1 inch thick .. __________ .... ________ _____ ..... ____________ ..... 2 to
5
Sh l
fi il
h
bl i h
h
f
h
h
i
d
b 5. Shale, fissile, rather bluish when fresh, weathering drrub; up-
per part more calcareous and passing into an impure fissile
limestone. No fossils noted __ ._ .. _____________________________ ... _ .... ___ . __ .. ____ .____
1
5
4
Li
l
h
i
li h
l above. Bears a few small pelecypods ___ .. _. ___ ._._ .... _______ .______________
5 to 6
2
Li
t
t
th
i
t
li ht
l
2 1. Limestone, gray, granular to compact, locally cross-bedded in
part; a layer 1 foot 6 inches thick near top consists of dense
compa;ct gray limestone. Rolled calcareous algre on surface of
bed. The lower 4 feet consists of compact gray limestone _______ 12
6 In the northwest quarter of section 4 of the same township a
small reef appears in the Upper St. Louis limestone. This is
shown in a small quarry opening in the east bank of Indian
creek a short distance south of the Chicago, Burlington and
Quincy railway bridge. The reef is fifteen feet wide and six
and one-half feet high. The lower three feet of the reef consists
of sub angular blocks of granular limestone in a calcareous
matrix. The upper three feet consists of angular and sub-
angular blocks of granular to oolitic limestone and of compact
gray limestone filled with a branching bryozoan. ST. LOUIS STRATA AT CROTON Beginning three and one-
half miles west of Farmington, a series of sections were studied
along the banks of the creek, conti:iming almost to its mouth. Below the Van Aucken quarry in the northwest one-fourth of MISSISSIPPIAN STIM..TA OF IOWA 248 the northeast quarter of section 5, T. 67 N., R. 8 W. there is a
good exposure of the Upper St. Louis. the northeast quarter of section 5, T. 67 N., R. 8 W. there is a
good exposure of the Upper St. Louis. SeoPicn o{ Upper St. Lowis limestone im amd near Van Auc7cen quarry. UPPER ST. Lours
FEET
INCHES
7. Limestone, gray, sub crystalline and compact; in rather heavy
ledges; cherty in upper part; upper surface undulating Il.lld
irregular. Overlain disconformably by basal san<1stone of the
Pella. Contains numerous shells of a large Belleroplwn 2% to 4% irregular. Overlain disconformably by basal san 1stone of the
Pella. Contains numerous shells of a large Belleroplwn 2% to 4%
6. Limestone, dark gray, sub crystalline and compact; rather
brittle when fresh but becoming tough when weathered; local·
ly filled with small sinuous tubular branching fucoids which
resemble worm castings; bearing l:a.rge calcareous algre some
of which have a maximum diameter of over 5 inches. Upper
surface bearing a few large vertically compressed sinuous pipes
which represent large fucoids. Separated from the bed above
by a shaly parting 1 inch thick .. __________ .... ________ _____ ..... ____________ ..... 2 to 6
5. Shale, fissile, rather bluish when fresh, weathering drrub; up-
per part more calcareous and passing into an impure fissile
limestone. No fossils noted __ ._ .. _____________________________ ... _ .... ___ . __ .. ____ .____
1
5
4. Limestone, grlty, compact, weathering to a lighter gray, cleav-
ing easily into thin layers; bell-ring seams of fissile shale
towa,rds the top _____ . ___________________________________ ....... ___ . ___ . ______ .. ____________ . 1
10
3. Limestone, gray, compact; consisting of a single layer showing
thin irregular stratification, the irregular surface of the in-
dividual lamellre being imparted to the layers immediately
above. Bears a few small pelecypods ___ .. _. ___ ._._ .... _______ .______________
5 to 6
2. Limestone, gray, compact; weatheri.ng to light gray layers 2
to 10 inches in thickness; with shaly partings in upper part. No fossils noted . __ . _______________________________________________ ... ____ . ____ ._. __________ .__
1
7
1. 2.
Limestone, dolomitic, bluish gray when fresh but weathering
brownish; bearing silicified corolla of Litho<!trotion oanadensis. 7.
Drift, yellowish, sandy.
UPPEl~ ST. LoUIS
6
Li
dJ k Semwn of St. Louis UI/I/,estone on Indiam (Yfeek. ST. LOUIS STRATA AT CROTON The matrix of
the upper part is in some places a conglomeratic limestone con-
sisting of small limestone pebbles in a calcareous matrix and in
others a gray limestone with the same species of branching
bryozoan as above. On the flanks of this reef-like structure is
granular cross-bedded limestone. The layers of Hils abut
abruptly into the reef and were not found to contain the bry- ST. LOUIS STRATA ON INDIAN CREEK 249 ozoan SO common in the reef. No beds are exposed abov:e the
reef with the exception of one thin layer which extends part
way over it on the north sIde. AssDciated with the bryozoan in the reef are occasional speci-
mens of a small Conularia. Some of the blocks of granular
oolitic limestone in the upper part of the reef contain calcareous
algre. These were not noted in the adjacent evenly bedded lime-
stone. This reef structure doubtless is original in large part. Some of the disturbance, however, may be due to later
mashing. There is a good exposure of the Upper St. Louis and the
topmost members of the Lower St. Louis on the White farm' in
the southeast quarter of section 33, T. 68 N., R. 8 W. This ap-
pears in the north bank of Indian creek two hundred and
twenty-five yards above an abrupt bend of the creek to the
north, and two and one-half miles west of Farmington. FEET p
g
4. Limestone, dark gray, brecciated, consisting of anlgular and
suba:ngular pebbles and blocks of compact gray limestone, and
gray sub crystalline limestone in a calcareous ma,trix. Upper
part less disturbed and more evenly stratified. In some places
filled with fucoid·like markings resembling worm castings. II'·
regular lenses of buff dolomitic limestone were noted at two
points in this bed and at one place a rOlmded bowlder of dolo·
mite 8 inches in diameter occurs. This bed rests on the very
irregular surface of the bed below as a result of uneven dolo·
mitization. The pseudo·disconformity at the base of this bed
is very striking (fig. 11) ......... _....................................................... 2 to 6 4. Limestone, dark gray, brecciated, consisting of anlgular and
suba:ngular pebbles and blocks of compact gray limestone, and
gray sub crystalline limestone in a calcareous ma,trix. Upper
part less disturbed and more evenly stratified. In some places
filled with fucoid·like markings resembling worm castings. 3lh to 81h ST. LOUIS STRATA AT CROTON II'·
regular lenses of buff dolomitic limestone were noted at two
points in this bed and at one place a rOlmded bowlder of dolo·
mite 8 inches in diameter occurs. This bed rests on the very
irregular surface of the bed below as a result of uneven dolo·
mitization. The pseudo·disconformity at the base of this bed
is very striking (fig. 11) ......... _....................................................... 2 to 6 2 to 6 3. Limestone, drab, dolomitic, cQoIl.glomcratic, matrix constituting
a large :part of rock. Pebbles roun(l.ed and subangulal'. A few
flinty masses occur. Lower part more massive and seemulg
to, grade do·wnward into the bOO. beneath. Upper p:nt showing
no stratification and flaking off obliquely to sudace. The
upper surface is very irregular 3Jld undulating. A few blocks
with worm burrows were noted in the upper part. At one
point two irregular lenses of unaltered compact gray limestone
appear in this bed 2 f eet am 3 feet 6 inches respectively be-
low the top ............... _ .......... _ ............................ _ ............................... 3. Limestone, drab, dolomitic, cQoIl.glomcratic, matrix constituting
a large :part of rock. Pebbles roun(l.ed and subangulal'. A few
flinty masses occur. Lower part more massive and seemulg
to, grade do·wnward into the bOO. beneath. Upper p:nt showing
no stratification and flaking off obliquely to sudace. The
upper surface is very irregular 3Jld undulating. A few blocks
with worm burrows were noted in the upper part. At one
point two irregular lenses of unaltered compact gray limestone
appear in this bed 2 f eet am 3 feet 6 inches respectively be-
low the top ............... .......... ............................ ............................... 250 :MISSISSIPPIAN STRA'fA OF IOWA 1. Limestone, bluish gray when ~resh but weathering brownish,
dolomitic, the topmost part of the fossiliferous bed. Ex·
posed in bed of creek ........................................................................ 1 A very instructive exposure appears in the east bank at the
point where the creek bends abruptly to the north, two hundred
and twenty-five yards below the preceding section. Both mem-
bers of the St. Louis are considerably disturbed here, owing to
shearing, mashing and overthrust faulting on a small scale. The
'Upper St. Louis attains a thickness of elev:en and one-half feet FIG. ll.-Pseudo·disconformity in St. Louis limestone marking boundary between dolomitic
portion below and unaltered pol·tion above. Indian creek, near Farmington. FIG. ll.-Pseudo·disconformity in St. Louis limestone marking boundary between dolomitic
portion below and unaltered pol·tion above. Indian creek, near Farmington. Seotion ·on Indian creek in section 9. ST. LOUIS STRATA AT CROTON and is gray, brecciated and nondolomitic. The Lower St. Louis
has an exposed thickness of fourteen and one-half feet and is
brownish and dolomitic. Th
f
l i
i
b
d
l
d i
i
b The reverse faulting is best developed in a massive member
four feet thick at the top of the Lower St. Louis. The overly-
ing and underlying softer limestones appear to have accommo-
dated themselves to the compressive stresses chiefly by mash-
ing. In the largest fault the massive limestone on the north
side of the break appears to have been raised almost vertieally
about four feet, then as a result of compression the upthrown ST. LOUIS IN VAN BUREN COUNTY 25-1 side was made to overlap the downthrown side about ten feet
while the softer beds above and below yielded by mashing. The
strike of the fault is approximately N. 80° E. Several other
small faults and shear zones with nearly vertical displacement
appear in the bluff nearby. side was made to overlap the downthrown side about ten feet
while the softer beds above and below yielded by mashing. The
strike of the fault is approximately N. 80° E. Several other
small faults and shear zones with nearly vertical displacement
appear in the bluff nearby. Other interesting exposures of the Lower St. Louis in contact
with the Upper St. Louis arB shown a short distance farther
down the creek in the southeast one-fourth of the southeast
quarter of section 33 where the valley bends again to the east-
ward. The Lower St. Louis is for the most part evenly bedded
and undisturbed, but at one point a large lenslike mass of
brownish structureless limestone is enclosed within a blue mag-
nesian limestone bed, which at this point thickens greatly. rrhe
limestone of the lens seems to grade into the blue magnesian
limestone on the flanks. The lens has a maximum thiclmlSss of
five feet and is thirty feet wide. It is believed to have been
formed during the deposition of the formation. A bluff section in the south bank of Indian creek just below
the bridge of the Chicago, BUrlington and Quincy Railroad, in
the northeast quarter of section 3, T. 67 N., R. 8 W., shows the
Des Moines sand,stone in contact with the St. Louis. Sandstone, gray, carbonaceous, soft; resting on the oxidized and
decomposed surface of the bed beneath; receding slightly be-
neath the bed above.
Imperfectly stratified ________________________________
2 ST. LOUIS STRATA AT CROTON FEET DES MOINES
Sandstone, grayish, carbonaceous; bearing many plant remains;
imperfectly stratified; locally passing in part into carboIlJ3JCeous
shale. Exposed . __ . ____ -'________________________________________________________________________
7
Sandstone, gray, carbonaceous, soft; resting on the oxidized and
decomposed surface of the bed beneath; receding slightly be-
neath the bed above. Imperfectly stratified ________________________________
2
LowER. Srr. LoUIS
Limestone, disturbed; layers undulating. Stratification oblitel'a,ted
in some plac.es by broociatioIJ;. Some layers dolomitic and
buff. Other layers and blocks which are interstratified anli
mingled with the dolomitic limestone consist of compact gray
lim€Stoue. Dolomitization 3!ppears to have been very impel'-
fect. Tho lower 1 to 3 feet is shaly, and grades downwa.r:l
into the bed beneath. Locally very much discolored. by iron
stains, and decomposed in places, es.pecially in upper part., due
to reacti.on with sulphate solutio·us fl10m the bedabovc_
At points where the limestone is decomposed and iron-stalnccl
it bears small crystals of gypsum, probrubly formed by the
reaction o·f limestone with iron sulphate solutions from the
sandstones a.bove. At points where the limestone is decomposed and iron-stalnccl
it bears small crystals of gypsum, probrubly formed by the
reaction o·f limestone with iron sulphate solutions from the
sandstones a.bove. h l
bl i h
l
h
i
i
i
l
hi
di At points where the limestone is decomposed and iron-stalnccl
it bears small crystals of gypsum, probrubly formed by the
reaction o·f limestone with iron sulphate solutions from the
sandstones a.bove. Shale, bluish, calcareous, weatherin'g into irregular chips; gradiug
gradually upwards into the beds above and resting on the
undulating surface of the bed beneath __________________________________________ Limesto·ne, dense, bluish gray, dolomitic, showing faint stratifica-
tion . _____ . ___________ ._. ______________ . ____________ ,_______________________________________________________ 252 MISSISSIPPIAN S'],RATA OF IOWA Limestone, bluish, arenaceous and dolomitic, tough, porous; fos-
sils poorly preS>eil'Ved; concealed at this point, but with an
exposed thickness of 7 feet beneath the east end of the rail-
road bridge near by _______________________________________________________________________ An exposure on the north bank of the creek just north of the
railway, two hundred yards belo'w the preceding section, again
shows the Des Moines sandstone and Lower St. Louis in contact. The Des Moines is represented by thirteen feet of light gray
medium to coarse-grained sandstone locally discolored yellow-
ish or reddish. It is massive below but thin-bedded above. A
slight development of basal conglomerate appears at the base,
where pebbles of chert were observed. ST. LOUIS STRATA AT CROTON Locally at the contact
there are thin films and small crystals of gypsum. The Lower St. Louis has an exposed thickness of fifteen feet. It is greatly disturbed and imperfectly dolomitized. At several
places in the bluff limestone blocks of certain horizons were
found 'sheared down several feet into lower layers with a differ-
ent physical character. The dip of some of the deformed lay-
ers is as great as thirty-five degrees. At several point~ pockets
of Des Moines sandstone were found in the li~estone several
feet below the con~act. . These evidently represe,nt. the fillings of
solution cavities formed prior to Des Moines sedimentation. That the disturbance of the St. Louis limestone took place prior
to Des Moines time is indicated by the lack of deformation in
the sandstone of this age. In another exposure in the south hank of the creek, two hun-
dred and fifty yards down stream, the basal Des Mojnes sand-
stone, which is here five and one-half feet thick, rests directly
upon the Spergen formation. However, farther along the bluff
to the east the lowermost beds of the St. Louis appear between
the other formations. The exposures of St. Louis limestone along Reed creek in
Bonaparte township are very important in that they illustrate
some of the remarkable lateral variations in the formation due
to the variable conditions of deposition and to differences in the
degree of deformation. Near the middle of the north ljne of section 14, T. 68 N., R. 8
W., a bluff on the south side of the creek is seventy-five feet
high and about two hundred yards long. In this bluff are ex-
posed complete sections of the Pella and St. Louis formations. The Lower St. Louis is much more brecciated and mashed than S'L LOUIS NEAR BONAPARTE 253 the overlying beds (figs. 12 and 13). It is probable that the
presence of a shaly bed in the lower part of this member IS the overlying beds (figs. 12 and 13). It is probable that the
presence of a shaly bed in the lower part of this member IS FIG. 12.-Brecciated Lower St. Louis limestone. Reed creek, near Bonaparte. FIG. 12.-Brecciated Lower St. Louis limestone. Reed creek, near Bonaparte. FIG. 13.-Brecciated Lower St. Louis limestone. Reed creek, near Bonaparte. FIG. 13.-Brecciated Lower St. Louis limestone. Reed creek, near Bonaparte. Seotion on Reed creek. Seotion on Reed creek. UPPER ST. LoUIS
FEET
4. Limestone, buff, dolomitic, with small scattered s3IDJd grains .... 6
3. Limestone, buff, dolomitic, massive ................................................ 2%. 2. Limestone, compact; originally gray, but now altered to buff
dolomite with irreguLa,r remnlants of limestone. Slightly dis·
turbed but not conglomeratic .............................. _......................... 9
LOWER ST. LOUIS
1. Limestone, browni5h, dolomitic, mashed and deformed, shaly
in lower part ........ :............................................................................... 28 ST. LOUIS STRATA AT CROTON largely responsible for this relationship since the limestone lay-
ers above appear to have been mashed and sheared down into
this less resistant bed. However, deformation and mashing MISSISSIPPIAN STRATA OF IOWA 254 have gone on locally in the Upper St. Louis and Pella. In these
beds the disturbance tends to follow shear zones. have gone on locally in the Upper St. Louis and Pella. In these
beds the disturbance tends to follow shear zones. The Pella limestone, with a maximum thickness of twenty-one
and one-half feet, caps the bluff. Below this comes fourteen
feet of basal Pella sandstone with intercalated beds of shale
and limestone and under it lies the St. Louis. The section of
the Pella at this locality is described in a later chapter of this
report (p. 291). The Pella limestone forms a sharp cliff while
the underlying basal Pella sandstone and the conglomeratic Up-
per St. Louis below weather to a more gentle slope which term-
inates below in a sharp escarpment produced by the erosion of
the more resistant Lower St. Louis limestone. N ear the middle of the bluff the following members appear in
the St. Louis: Seotion on Reed creek. UPPER ST. LoUIS
FEET
4. Limestone, buff, dolomitic, with small scattered s3IDJd grains .... 6
3. Limestone, buff, dolomitic, massive ................................................ 2%. 2. Limestone, compact; originally gray, but now altered to buff
dolomite with irreguLa,r remnlants of limestone. Slightly dis·
turbed but not conglomeratic .............................. _......................... 9
LOWER ST. LOUIS
1. Limestone, browni5h, dolomitic, mashed and deformed, shaly
in lower part ........ :............................................................................... 28 Seotion on Reed creek. bout 200 yards farther up the ci'eek a second bluff section UPPER ST. LoUIS
4
Limestone Several remarkable shear zones appear near the east end of
the bluff. The Pella limestone is considerably less disturbed
along these zones than are the underlying strata. Along tlie
most pronounced line of movement blocks of Pella limestone are
sheared downward for at least ten feet into the soft shales and
sandstones below. This tongue-like extension 'of mashed lime-
stone weathers in relief, thus forming a prominent feature in
the face of the bluff. On the east side of the tongue the sand-
stone is but little disturbed but on the west side the layers are
bent down as much as three feet. At points where all members
of the Lower St. Louis are involved in the crushing the shaly
bed in the lower part is locally greatly reduced in thickness and
numerous tongues of mashed limestone extend down through it-
At seV1eral points angular blocks of limestone several feet in
length are kneaded far down into the shaly material belo"v. Some of these shale-enclosed blocks and broken layers are high-
ly tilted. About 200 yards farther up the ci'eek a second bluff section ST. LOUIS NEAR BONAPARTE 255 appears on the opposite bank. The succession of strata here is
essentially the same as in the preceding section except that the
basal Pella sandstone is much thicker and the lowermost bed of
the Lower St. Louis is not exposed. At the south end of the
bluff this member attains a maximum exposed thickness of
twenty-nine feet. A few pockets of bluish shale were noted in
the basal part. appears on the opposite bank. The succession of strata here is
essentially the same as in the preceding section except that the
basal Pella sandstone is much thicker and the lowermost bed of
the Lower St. Louis is not exposed. At the south end of the
bluff this member attains a maximum exposed thickness of
twenty-nine feet. A few pockets of bluish shale were noted in
the basal part. The Lower St. Louis is greatly disturbed here on account of FIG. 14.-Small reversed fault in Lower St. Louis limestone. Reed creek, near Bonaparte. FIG. 14.-Small reversed fault in Lower St. Louis limestone. Reed creek, near Bonaparte. faulting, crushing and shearing. Shear zones and small over-
thrust faults appear at several points in the bluff. . Seotion on R eed oreelc two ]z1tndred yards above pTecediing one.
PELLA
6.
Limestone, gray, :fine· grained .......................................................... .
5.
Shale ... _ ............ _ ........ _ .................................. _ ............................ _ ..... ..
4.
Sandstone, fine-grained, soft, bluish, massive below but thin.
bedded and shaly above; lower part containing pebbles of lime·
stone and chert.
Resting on the uneven surface of the
bed below ......... _ .... _ .............................................. _ ......................... ..
UPPER ST. L OUIS
3.
Limestone, consisting typically of angular to rounded blocks
FEET
18
3lh
24 to 35 UPPER ST. L OUIS
3
Limestone PELLA
5 1. Lim€Soone, brownish, disturbed, imperfectly dolomitized "."". ]4 The St. Louis is again exposed on Slaughters branch in the
northwest quarter of section 23, about one-fourth mile above the
point where the railway crosses the creek. Approximately
twenty feet of Pella limestone and sandstone caps the section
while the Spergen and vYarsaw beds appear below the St. Loui~. Section on Slaughters bra(l'!ch. Section on Slaughters bra(l'!ch. PELLA
11. 10. 9. Section on Slaughters bra(l'!ch. FEET
Limestone capping brow of hill ""."""""""""""""""""""""",,. 2
Concealed ".""""".""""""""""""."""""".,,,,"",,.,,."""""""""""""" 10
Limestone, compact, gray, somewhat speckled; passing wholly
or in part into sandstone """"""""."."""."""""""""."""" .. ",,.,,,,. 1
8. Limestone, c1ense, compact, gl'ay, showing fine lamination ,,",,"
2
7. Sandstone, light gray, tine·grained, bem'ing angular cllert frog·
ments. Lo,wer pa,rt grac1ing in part into compact gray lime·
stone; locally shaly "" .... """."""""""""."."""".,,",, .... ,, .. ,, .. ,, 2 % to 3
UPPER ST. LOUIS
6. Limestone, gray, granular to compact; upper part showing fine
laminations on m'la,thered surfaces ".""""""""""""",,.,,"",,.,, ... ,,.. 9
5. Concealed, slope covered by yellowish Ehales """ ... " .. ".""."""",,. 2
4. Limestone, lower portion compact, gray and disturbed; upper
pOl-tion more evenly bedc1ec1 and consisting of massive buff
imperfectly c1olomitizec1 limestone ... """ .. """".""""",,,,.,,""""",,. 10
LOWER ST. LOUIS
3. Limestone, bl'ownish, dolomitic, with bluish shale bec1 three
feet thick in basal part """""""""" .. """".""."""".,,,,.,,"""",,.,,",,. 24
INCHES
6
4
6
6
4
6
5
3 PELLA
11. 10. 9. Section on Slaughters bra(l'!ch. FEET
Limestone capping brow of hill ""."""""""""""""""""""""",,. 2
Concealed ".""""".""""""""""""."""""".,,,,"",,.,,."""""""""""""" 10
Limestone, compact, gray, somewhat speckled; passing wholly
or in part into sandstone """"""""."."""."""""""""."""" .. ",,.,,,,. 1
8. Limestone, c1ense, compact, gl'ay, showing fine lamination ,,",,"
2
7. Sandstone, light gray, tine·grained, bem'ing angular cllert frog·
ments. Lo,wer pa,rt grac1ing in part into compact gray lime·
stone; locally shaly "" .... """."""""""""."."""".,,",, .... ,, .. ,, .. ,, 2 % to 3
UPPER ST. LOUIS
6. Limestone, gray, granular to compact; upper part showing fine
laminations on m'la,thered surfaces ".""""""""""""",,.,,"",,.,, ... ,,.. 9
5. Concealed, slope covered by yellowish Ehales """ ... " .. ".""."""",,. 2
4. Limestone, lower portion compact, gray and disturbed; upper
pOl-tion more evenly bedc1ec1 and consisting of massive buff
imperfectly c1olomitizec1 limestone ... """ .. """".""""",,,,.,,""""",,. 10
LOWER ST. LOUIS
3. Limestone, bl'ownish, dolomitic, with bluish shale bec1 three
feet thick in basal part """""""""" .. """".""."""".,,,,.,,"""",,.,,",,. 24
INCHES
6
4
6
6
4
6
5
3 LOWER ST. LOUIS
3
Limestone UPPER ST. LoUIS
4
Limestone Most of
these have a steep dip and the displacement is slight, the max-
imum being not more than five feet. Their strike js approxi-
mately N. 55° W. and the upthrow side is on the north. (Sep. fig. 14.) The following section was measured in this bluff: . Seotion on R eed oreelc two ]z1tndred yards above pTecediing one. . Seotion on R eed oreelc two ]z1tndred yards above pTecediing one. PELLA
6. Limestone, gray, :fine· grained .......................................................... . 5. Shale ... _ ............ _ ........ _ .................................. _ ............................ _ ..... .. 4. Sandstone, fine-grained, soft, bluish, massive below but thin. bedded and shaly above; lower part containing pebbles of lime·
stone and chert. Resting on the uneven surface of the
bed below ......... _ .... _ .............................................. _ ......................... .. UPPER ST. L OUIS
3. Limestone, consisting typically of angular to rounded blocks
FEET
18
3lh
24 to 35 256 MISSISSIPPIAN STRATA O~ IOWA of gray to buff dolGmitic limestone 'in a gray impure sandy
matrix. The limestone bears lliIIlall patches of kaolin and
small nodules of chert. M.any of the blocks contain sinuous
tubes resembling worm burrows. Occasional specimens of
Lithostl'otion prolifenilln were noted ..... "" .... '' ... " ..................... "... 10
LOWER ST. LOUIS
2. Limest<>n.e, massive, brownish, dolomitic "."""""""",, .. """""",,. 3
1. Limestoille, brownish, dolomitic; much disturbed and mashed
26 2. Limest<>n.e, massive, brownish, dolomitic
1
Li
t ill
b
i h
d l
iti
h d The Lower St. Louis appears in its normal development in a
cut along the Chicago, Hock Island and Pacific railway in the
western part of section 23, T. 68 N., R 7 VY., a short distance
below the mouth of Slaughters branch. A considerable thick·
ness of sandstone appears in the slope above. The lower por-
tion of this sandstone is believed to represent the Upper St. Louis while the upper portion probably belongs to the base of
the Pella. The section follows: Section below the mo1tth of Sla1tghters branch. PELLA
FEET
INCHES
5. Limestone, gray, brecciated; capping brow of hill ".""."".",,. 3
4
4. Concealed '"'''''''''''''''''''''''''''''''''''' __ ''''''''''''''''''''''''''''''''''''''''''''''''''''' 31
3. Sandstone, light gray, thin·bedded ".""""""""""""",,,,",,"""",,. 5
6
UPPER ST. LOUIS
2. Sandstone, soft, yellowish, bearing occasional rounded and
subangular blocks of compact gray dolomitic limestone "''''" 21
4
LOWER ST. LOUIS
1. Lim€Soone, brownish, disturbed, imperfectly dolomitized "."". ]4
8 PELLA
11 ST. LOUIS BELOW BONAPARTE 257 SPERGEN
2. LimestQne, bluish, massive, arenaceQ·magnesian ... _ .......... _......... 5
WARSAW
1. Shale, bluish, argillaceQus. EXPQsed ..................... _ .... __ ...... _....... 1 A disturbed phase of the lower beds of the Lower St. Loui::;
member appears along Potters branch, one and one-fourth miles
northeast of Bonaparte, in the NW.l,4 sec. 10, T. 68 N., R. 8 W. At several points the upper limestone layers appear to have
been forced down into the lower shaly beds. Locally small
mounds of limestone are exposed. The limestone was mu~h
fractured during at least two periods of disturbance and the
fracture lines are sealed with veinlets of calcite. In several in-
stances bands of limestone immediately adjacent to the frac-
tures of earlier age are gray and unaltered although the rock
elsewhere is brow'nish and dolomitic. It appears that the first
disturbance here took place prior to dolomitization and that the
limestone adjacent to the fractures was less susceptible to alter-
ation, owing to its more crystalline condition or some other
cause, than the surrounding rock. The fractures of later age in
many instances cut across the earlier ones and their associated
limestone bands, which are in such cases usually slightly dis-
placed. The limestone is uniformly dolomitized adjacent to
these younger breaks, a relationship which suggests that they
were formed subsequent to dolomitization. The first period of
fracturing is believed to have occurred at the close of Croton
time, while the second probably occurred at the close of the
P ella. A short distance farther up the creek the following bluff sec-
tion is shown in the south bank. Section in Potters branch. Section in Potters branch. Section in Potters branch. PELLA
FEET
8. SandstQne, 8Qft, yellowish, incQherent. EXPQsed ............... _ ....... 11
UPPER ST. LOUIS
7. Limestone massive,
gray,
subcrystalline,
stylQlytic,
badly
fractured; shaly parting at CQntact with bed below.................. 3
6. Limestone, buff, magnesian, 8Qft, grades into. bed beneath ...... 11
LOWER ST. LoUIS
5. Limestone, buff, magnesian; in Qne massive ledge .............. 2 to. 3
4. Limestone, buff, magnesian, brittle; tending to. flake Qff
Qbliquely ... _ .... _ ................ _ .......... _ .......... _........................................... 4
3. Limestone, buff, magnesian; in one heavy ledge; bearing
small chert nQdules ... _....................................................................... 1
2. Limestone, dense, dark gray; blotched with patches of lighter
gray magnesian limestone; bears irregular seams and nQdules
Qf chert .................................................................................................. Section in Potters branch.
PELLA
FEET
8. SandstQne, 8Qft, yellowish, incQherent.
EXPQsed ............... _ ....... 11
UPPER ST. LOUIS
7.
Limestone massive,
gray,
subcrystalline,
stylQlytic,
badly
fractured; shaly parting at CQntact with bed below..................
3
6. Limestone, buff, magnesian, 8Qft, grades into. bed beneath ...... 11
LOWER ST. LoUIS
5. Limestone, buff, magnesian; in Qne massive ledge .............. 2 to. 3
4. Limestone, buff, magnesian, brittle; tending to.
flake Qff
Qbliquely ... _ .... _ ................ _ .......... _ .......... _........................................... 4
3. Limestone, buff, magnesian; in one heavy ledge; bearing
small chert nQdules ... _....................................................................... 1
2.
Limestone, dense, dark gray; blotched with patches of lighter
gray magnesian limestone; bears irregular seams and nQdules
Qf chert ..................................................................................................
4
1. LimestQne, buff, magnesian, :in rather thin layers. EXPQsed to.
bed Qf creek ..................... _ ........................ _ ........ _ .......... _ .............. _.
2
INCHES
6
6
4
6
4
to. 6
6 f
FEET
I NCHES
12. Drift to brow of hill ............................................. _ ....................... 12
UPPER S'l'. LOUIS
11.
Limestone, gray, compact, dense, brecciated ..............................
3
LOWER ST. Lol.'IS
10. Limestone, buff, dolomitic, tough, massive, overhanging, upper
surface ilTegular ...... : .......................... _ .... _ ...................... _.....
1 to 21h
9. Limestone, buff, dolomitie; tough ..................................................
1
6
8. Limestone, buff, dolomitic; brittle, flaking off parallel to the
face of the bluff; bearing small chert nodules in upper parL.. 7
7.
Limestone, soft, bluish, dolomitic, fucoid markings in middle
part ...................................................... ~ ... .... ............................ .. ............
3
3 PELLA
11 4
1. LimestQne, buff, magnesian, :in rather thin layers. EXPQsed to. bed Qf creek ..................... _ ........................ _ ........ _ .......... _ .............. _. 2
INCHES
6
6
4
6
4
to. 6
6 1. LimestQne, buff, magnesian, :in rather thin layers. EXPQsed to. bed Qf creek ..................... _ ........................ _ ........ _ .......... _ .............. _. 2 lIITSSISSIPPIAN STRATA OF IOWA 258 The following species were collected from bed 7 of the above
section: Spirifer sp. Eumetria verneuiliana Hall
Straparollus sp. Bellerophon sp. Lithostrotion prolifel1lm Hall
Syringopora sp. Productus ovatus Hall
Girt yell a indianensis (Girty) , Spirifer sp. Eumetria verneuiliana Hall
Straparollus sp. Bellerophon sp. Lithostrotion prolifel1lm Hall
S
i Syringopora sp. Productus ovatus Hall Girt yell a indianensis (Girty) , There is a~ excellent exposure of the undisturbed facies of
the Lower St. Louis limestone in an abandoned quarry at the
mouth of Rock creek in the northwest quarter . of section 21,
Washington township, and in the Des Moines river bluff a short
distance above. This phase is followed above by disturbed Up-
per St. Louis limestone which in turn is overlain by the Pella
formation. The section follows: Seotion at the mouth of Rock creek. Seotion in the bank of Roole creek. 7.
Limestone, soft, bluish, dolomitic, fucoid markings in middle
part ...................................................... ~ ... .... ............................ .. ............
3 15 Jour. Geol. TOJ. III. 1>. 304; 1~95. Seotion at the mouth of Rock creek. Seotion at the mouth of Rock creek. PELLA
12. 11. FEET
INCHES
Limestone, gray, fine-grained ... _ .......... _ ...................... _ ................ _. 7
9
Sandst()n.e, fine·grained, massive, more calcareous and approach·
ing brecciated limestone locally in upper part ......... _................. 11
UPPER ST. L OUIS
10. Limestone, gray, compact, fine·grained, brecciated ......... _ ..... 5 to 8
9. Sandstone, soft, fine-grained, bluish, locally with pebbles of
limestone in lower part. Lower six inches in some places
consists o,f arenaceous limestone ... _............................................... 2
8. Limestone, buff, dolomitic; brecciated ........................... _ ....... 8 to 12
LOWER ST. LOUIS
7. Limestone, buff, dolomitic, the LithosfirotiIYn camadensis zone 0 to 1%
6. Limestone, buff, dolomitic, in two massive ledges, with fucoid
markings resembling worm burrows in two thin zones ............ 7
5. Limestone, compact, gray, with shaly seams ................................ 2
4. Limestone, compact, bluish, dolomitic, weathering yellowish ...... 4
3. Limestone, buff, dolomitic, tough ..... _ .................................. _....... 2
2. Limestone, dense, with slight bluish tint, checking into ir·
regular blocks ..................... _ .............................................. _............... 2
1. Sandstone, fine·grained, bluish, calcareous; receding. Exposed 5
8
4
4
4 1. Sandstone, fine·grained, bluish, calcareous; receding. Exposed 5 An even more typical exposure of the undisturbed Lower St. Louis limestone appears in the bank of Rock creek approxi-
mately one-third of a mile north of the quarry just described
(fig. 15). Seotion in the bank of Roole creek. FEET
I NCHES
12. Drift to brow of hill ............................................. _ ....................... 12
UPPER S'l'. LOUIS
11. Limestone, gray, compact, dense, brecciated .............................. 3
LOWER ST. Lol.'IS
10. Limestone, buff, dolomitic, tough, massive, overhanging, upper
surface ilTegular ...... : .......................... _ .... _ ...................... _..... 1 to 21h
9. Limestone, buff, dolomitie; tough .................................................. 1
6
8. Limestone, buff, dolomitic; brittle, flaking off parallel to the
face of the bluff; bearing small chert nodules in upper parL.. 7
7. Limestone, soft, bluish, dolomitic, fucoid markings in middle
part ...................................................... ~ ... .... ............................ .. ............ 3
3 259 ST. LOUIS NEAR KEOSAUQUA At the top it beal's fucoid markings . 2
S
d
bl i h
l
li
' 2. Sandstone,
bluish,
calcareous, line'grained, with
scattered
grains of coarse sand and angular chert fragments included.... 2
WARSAW f 1. Limes,tone, soft, cream· colored, cherty. Expo-sed ...................... 2 FIG. I5.-Undisturhed dolomitic phase of Lowrr
St. Louis limestone. R ock creek,
near
Bentonsport. G. Seotion at the mouth of Rock creek. I5.-Undisturhed dolomitic phase of Lowrr
St. Louis limestone. R ock creek,
near
Bentonsport. A bed of sandstone is exposed in the south bank of Des
Moines river approximately two and one-half miles below the
town of Keosauqua. This has been referred to by C. H. Gor-
don15 as the Keosauqua sandstone, which he regarded as a
phasal development of the limestone designated in this report as
the Verdi or Upper St. Louis. The present study makes the reference of these beds in part
to the basal Pella and in part to the upper portion of the Verdi
appear more plausible. In the above mentioned bluff we have
three to four feet of brecciated Pella limestone which is under-
lain by five to twenty-one and one-half feet of fine-grained mas-
sive yellowish sandstone. This in turn is followed below by
rudely stratified conglomeratic limestone with a bluish sandy MISSISSIPPIAN STRATA OF IOWA 260 matrix. Locally this limestone is represented by sandstone con-
taining blocks and pebbles of limestone. This bed ranges to
more than fourteen feet in thickness. At the base is a brown-
is~ conglomeratic limestone ten feet thIck which is believed to
represent the basal beds of the Verdi. The massive sandstone
of variable thickness below the Pella limestone is referred to
the basal Pella while the underlying sandy conglomeratic lime-
stone very probably belongs to the Upper St. Louis. The Upper St. Louis is exposed on the west fork of Thatcher
creek, about one hundred and fifty yards above its junction with
the east fork near the middle of the west line of section 1, T. 68 N., R. 10 W. The formation at this locality contains a bed
of sandstone. SeCJtion 0'1'1 Th4tche-r creek. PELLA
FEET
4. Sandstone, soft, light gray when fresh but weathering yellow·
ish; fine· grained, massive. Locally structureless but else·
where exhibiting cross· bedding. Slightly overhanging. Ex-
posed ... _ ............. _ .................. , .... _ .......... _ .... _ ................ _ .... _................. 10 to 12
UPPER ST. LOUIS
3. Limestone, compact, gray, rather brittle; in heavy . layers
when fresh but weathering to thin layers and flakes. Bears
Leperditia sp. and shells of a small pelecypod. Apparently
lenticular ... _ ................ _ .......... _ .................... _ .... _ ..... _ ......... _............... 2 to 4
2. Sandstone, fine· grained, soft, bluish, calcareous. Seotion at the mouth of Rock creek. Thinnest
where limestone above is thickest and vice versa ...... _ .. _........... 1 to 4
1. Limestone, light gray, sofh massive, structul'eless, flaking off
parallel to face of bluff; with occasional stylolytic 'seams and
a few patches of greenish mnterial. Exposed ... _ .. _ ............ _..... 6 SeCJtion 0'1'1 Th4tche-r creek. 3. Limestone, compact, gray, rather brittle; in heavy . layers
when fresh but weathering to thin layers and flakes. Bears
Leperditia sp. and shells of a small pelecypod. Apparently
lenticular ... _ ................ _ .......... _ .................... _ .... _ ..... _ ......... _............... 2 to 4 where limestone above is thickest and vice versa ...... _ .. _........... 1 to 4
i
li h
fh
i
l l
fl ki
ff 1. Limestone, light gray, sofh massive, structul'eless, flaking off
parallel to face of bluff; with occasional stylolytic 'seams and
a few patches of greenish mnterial. Exposed ... _ .. _ ............ _..... 6 At the north end of this bluff section all of the above beds are
involved in a disturbance which was accompanied by consider-
able shearing and brecciation. The movement appears to have
been due ' to compression which caused the converging of two
blocks over a wedge-shaped mass. A tongue of mashed and
brecciated Pella limestone about twenty-five feet broad is
sheared down into the disturbed area although this member has
been removed by erosion elsewhere in the bluff. There is a second exposure of the same strata on the east
fork of Thatcher creek just below the wagon bridge and a short
distance above the junction with the west fork. Beds 1 and 2
of the preceding section are represented here by a continuous
bed of sandstone with an exposed thickness of twelve and one-
half feet. At the Price quarry on Price creek in the southwest quarter ST. LOUIS IN VAN BUREN COUNTY 261 of section 20, T. 69 N., R. 10 W., the Lower St. Louis shows evi-
dence of its shallow water origin in the form of strongly de-
veloped cross-bedding and contemporaneous erosion phenomena. Section in qualiTy alt mouth of Price creek. 8.
Drift.
PELLA
7
Limesto 5. Lim€5tone, gray, rather soft, in two massive ledges, fractured,
stylolytic; with thin shaly seams near the middle which beM
a few fossils such as Syringopora sp., OrtM'tetes sp., Zaph-
I'entis sp. .. ______________________________________________________________________________________ 1 7.
Limestone, gray, fractured
6
S
d
f
fi
i S eaion iIn the Price quarry. FEET
INCHES
6. Drift, yellowish, sandy, oxidized. Maximum thickness ... ________ 10
PPER ST. L OUIS
5
Li
t
b ff
d l
iti
i
th
thill l
2 4. Limestone, buff, dolomitic, compact, disturbed, brecciated and
conglomeratic. At one point this member bears at the top a
bed of medium-grained gray sandstone one foot thick. Resting
irregulaa-Iy on bed below _____________________________________________________________
5
8
OWER ST
L UIS 3. Limestone, compact, gray, tough, unaltered. Preserved as a
small lens at one point only _______________________________________________________
0 to 10 2. Limestone, fossiliferous; ill places cherty; imperfectly dolo-
mitized. Represented at some points by compact gray lime-
stone with molds of fossils and at others by dense bluish
mag'nesian limestone weathering buff. Locally this bed ap-
pears to fill smaU channels in the bed below. One such channel
is three feet deep and about twenty-four feet wide_ This mem-
ber is evenly bedded while the member below is cross-bedded 0 to 2lh y
1. Limestone, in the form of one massive ledge in quarry faoo,
arenaceous, magnesian; filled with rather coarse Band grains;
bluish when fresh but weathering buff, cross-bedded; locally
exhibiting a tendency towards thin lamin.a.tion .. ________ :________________
7 The cross-bedding in bed 1 is on a large scale. The heavy
sloping massive layers are truncated by the bed above. A short
distance down the creek, in the south bank, twelve feet of cross-
bedded limestone is shown at the horizon of bed 1. It is over-'
lain by drift. The upper two feet is fossiliferous and more thin-
ly laminated. Below these inclined' layers is a blue soft lime-
stone with fucoid markings resembling worm castings. It has
an exposed thickness of two feet. In the quarry at the mouth of P,rice creek, in the eastern part
of section 20, the Upper St. Louis is thicker than usual and is
somewhat different lithologically' from other exposures in this
part of the state. Section in qualiTy alt mouth of Price creek. FEET
INCHES
8. Drift. PELLA
7. Limestone, gray, fractured ________________________________ :_______________________________ 6
6. Sandsto·n.e, soft, :fine-grained; resting upon the irregular sur-
face of the bed below ______________________________________________________________ . 6
8
UPPER ST_ LOUIS
5. Lim€5tone, gray, rather soft, in two massive ledges, fractured,
stylolytic; with thin shaly seams near the middle which beM
a few fossils such as Syringopora sp., OrtM'tetes sp., Zaph-
I'entis sp. .. 6.
Sandsto·n.e, soft, :fine-grained; resting upon the irregular sur-
face of the bed below ______________________________________________________________ . 6
UPPER ST_ LOUIS
i
€5
h
f
i
i
l d
f
d Section in qualiTy alt mouth of Price creek.
FEET
INCHES
8.
Drift.
PELLA
7.
Limestone, gray, fractured ________________________________ :_______________________________ 6
6.
Sandsto·n.e, soft, :fine-grained; resting upon the irregular sur-
face of the bed below ______________________________________________________________ . 6
8
UPPER ST_ LOUIS
5. Lim€5tone, gray, rather soft, in two massive ledges, fractured,
stylolytic; with thin shaly seams near the middle which beM
a few fossils such as Syringopora sp., OrtM'tetes sp., Zaph-
I'entis sp. .. ______________________________________________________________________________________ 11
9 S eaion iIn the Price quarry. ______________________________________________________________________________________ 11
9 FEET
INCHES 11 262 MISSISSIPPIAN STRATA OF IOWA 4. Limestone, buff, magnesian, dense and massive above but softer
and thin-bed:ded below ________ __________________________________________________ 3% to 5
3
Li
i i
f i
b dd d l
f
d 4. Limestone, buff, magnesian, dense and massive above but softer
d thi
b d d d b l
3% t
5 3. Limestone, consisting of interbedded layers of compact and
granular gray limestone _________________ __________________________ _________ .4 1/3 to· 5 1/3 2. Limestone, brecciated, buff, magnesian; shiaily in upper part;
poorly exposed ___________________________________________________________________________________ 8
WER ST. LOUIS 2. Limestone, brecciated, buff, magnesian; shiaily in upper part;
poorly exposed ___________________________________________________________________________________ 8 1. Limestone, buff, magnesian, bluish when fresh; fucoid mark-
ings in a zone about six inches below the top_
Lower three
feet arenaceou.s and cross-bedded. Upper . part massive. To
bed of creek ____________________________________________ .. ____________________________ .____________
8
6 The Upper St. Loujs is exposed in the south bank of Chequest
creek at the bend. about one-half mile above its mouth (NE.14
of SW.14 sec. 27, T. 69 N., R. 10 W.). It is here represented in
part by sandstone as in the Thatcher creek section. FEET
7. Drift.
D ES MOINES
6. Shale, drab in basal part amd carbonaceous above ___________________ . 28
PELLA
5. ' SLope, strewn with blocks of lim~one __________________________________________
5
4_ Limestone, gray, resting on the uneven surface of the bed.
below ________________________________ .. ____________ .____________________________________ ______ ___________
3
UPPER ST. LOUIS
3.
Limestone, grfUlular to compact, thin-bedded, much fra,cturcd;
contact with bed: below irregular ___________________________________________________
6
to 81Al
2_ Limestone, dense, compact, gr·ay, brecciated, no semblan,ce 0'£
original structure preserved. Resting on the irregular surface
of the bed beneath ________________________________ . _____________________________________ ____ . 3% to 8Y2
LOWER ST. LOUIS
1. Limestone, buff, magnesian, massive.
Exposed ________________________ 1614 6. Shale, drab in basal part amd carbonaceous above ___________________ . 28
PELLA
5 ' SL
t
ith bl
k
f
5 FEET
INCHES
___
7
6
h 6. Limestone; gray, . slightly brecciated ______
5
S
d t
i
fi
i
d
bl i h 5. Sandstone, massive, fine-grained; bluish when fresh but weath-
ering yello·wish; with occalsional angular and sub an gular . blocks of compact gray limestone which bear pelecypods re-
sembling Pella types _________________________________________________________________ 6 to 'Ph
PPER ST. LOUIS ' 4. Limestone, . compact, gray, with a tendency to cleave; locally
mashed _____________________________________________________________________________________________ 1 to 31Al
3
S
d t
i
bl i h
i
l
fill d
ith
d d
d g
p
p
g
y
__________________
2. Limestone, Jl,ne-grainec1, gtfLY, rather soft, massive, stl'uctureless,
stylolytic; with occ.asiomil small dark c.olored rounded chert
concretions; tendillg ' to flake ' off parallel to face of bluff. Total
t~ckness exposed
0I!~Y at onc point where a small
anticline brings- it above 'the level of the creek. Locally
slightly brecciated __________ : _______ ! ____ _____________________________ __ .-;-____ ______ ___________
• 8 . 6 1. Sandstone, fine-grained, bluish, 'soft, some layers calcareous;
exposed in a small anticlinal flexure ___________________________ .... _._ .. _ ...... _ 2 B~ds ranging from the Lower St. Louis limestone to the Des
M~ines sandstone are exposed in the Kilbourne bluff, in the
east bank of Lick creek near its mouth, in the southwest quarter
of section 1, T. 69 N., R. 10 W. The section is as follows: Section in KilbO'llrne bluff. Section in KilbO'llrne bluff. FEET
7. Drift. D ES MOINES
6. Shale, drab in basal part amd carbonaceous above ___________________ . 28
PELLA
5. ' SLope, strewn with blocks of lim~one __________________________________________
5
4_ Limestone, gray, resting on the uneven surface of the bed. below ________________________________ .. ____________ .____________________________________ ______ ___________
3
UPPER ST. LOUIS
3. Limestone, grfUlular to compact, thin-bedded, much fra,cturcd;
contact with bed: below irregular ___________________________________________________
6
to 81Al
2_ Limestone, dense, compact, gr·ay, brecciated, no semblan,ce 0'£
original structure preserved. Resting on the irregular surface
of the bed beneath ________________________________ . _____________________________________ ____ . 3% to 8Y2
LOWER ST. LOUIS
1. Limestone, buff, magnesian, massive. Exposed ________________________ 1614 ST. LOUIS IN HENRY OOUNTY 263 The upper surface of bed 2 is very irregular. Mounds of con-
glomerate . limestone locally extend several feet up into bed 3. Inasmuch as bed 3 does not arch up over these mounds but
tends to fill in the depressions between them and is not itself
conglomeratic it is believed that the disturbed character of bed
2 is original. A bed resembling closely bed 3 of the preceding section is ex-
posed in the east bluff of Des Moines river one and one-half
miles southeast of Kilbourne. This bed rests directly upon the
Lower St. Louis. It is possible that bed 2 of the Kilbourne
bluff section is absent here, but this cannot be proven definitely. See the following section: Section sQutheast of Kilbo1wne. FEET
5. Concealed to brow of hill. PELLA f
4. Sandstone, fine· grained ..................... _ ................ _............................. 2 to 3
3. Concealed ................................................... _ .......... _ .... _ .... _................. 1
UPPER. ST. LOUIS
2. Limestone, gray, granular to compact. Lower portion consist·
ing of thin·bedded, granulaJ" and compact limestone which is
somewhat cross·bedded where it is undisturbed. Upper portion
consisting of a breccia of compact gray limestone in a calcar·
eous matrix. Maximum measured thickness ............. __ ............... 14 2/3
LOWER. ST. L OUIS
1. Limestone, buff, magnesian. Exposed ........... :.............................. 20 FEET 4. Sandstone, fine· grained . 3
C
l d LOWER. ST. L OUIS
1. Limestone, buff, magnesian. Exposed ........... :.............................. 20 Des Moines COtl!nty.-In the report on the geology of Des
Moines cou~ty Keyes16 describes the distribution and character
of the St. la Iowa Goo!. Survey; vol. In p. 447; 1895. 5.
Concealed to brow of hill.
PELLA f
d
fi
i
d Section sQutheast of Kilbo1wne. 4.
Sandstone, fine· grained
3
Concealed Section in KilbO'llrne bluff. Louis as follows : "The chief exposures of this formation are in the extreme
southwestern corner of the county where it underlies an area
of perhaps thirty square miles. It covers most of the uplands
of Augusta township and probably nearly one-half of Danville
township. A small area also occurs in the western part of Un-
ion township. The outcrops are principally on Long and Cedar
creeks and on the Skunk river." The exposures are small and the formation is similar in de-
velopment in all respects to that in the adjacent counties of Lee
and V an Buren. Henry County.-The St. Louis limestone constitutes the bed
rock over a much larger area in Henry than in any other county
in Iowa. In the extreme western and southern borders there
are narrow, irregular strips of Des Moines sandstones with oc- MISSISSIPPIAN STRATA OF lOW A 264 casional small adjacent outliers. Small outliers of this forma-
tion occur also in Center township near the middle of the county
and in the extreme southeastern part. The Keokuk limestone
and Lower Warsaw shale outcrop along Skunk river in the
south-central part of the county ~nd along Mud creek, a tribu-
tary of this stream in the southwestern part. These are the
only important known exceptions to the universal extent of the
St. Louis as the surface rock of Henry county. N early all of the important exposures of the formation are in
the southern part of the county, the more typical outcrops being
along Big Cedar, Little Cedar, Brush and Big creeks. The most complete section observed by the writer in Henry
county occurs along Big creek in section 7 of Baltimore town-
ship. Both divisions of the St. Louis appear in a high bluff just
above the wagon bridge in the southwest quarter of this section. The Croton member is very much mashed and breccia ted and
is imperfectly dolomitized. It has a thickness of about thirtv-
five feet. The lower part is shaly and at the base of the secti~n
there are carbonaceous searrns. At both the east and west ends of
the bluff there appears more evenly bedded and less disturbed
brownish dolomitic limestone, which abuts into the disturbed
phase. Near the east end of the bluff the Upper St. Louis is
exposed in the form of two beds of gray limestone. 4.
Limestone, granular to compact, no fossils noted ........................
71Al Sectio'll on Big uree"k.
P&iliA
rUT
7.
Concealed; slope to top of hill overspread with blocks (}f
Pella limestone ......... __ .......................................................... _...........
3
6. Limestone, ;exposed ......... _ .................................. _ ................ _...........
1/3
5. Concealed; upper part of slope strewn with blocks of P ella.
limestone; lower part wjth blocks of fine·grajned sandstone ....
9lh
UPPER ST. LOUIS
4.
Limestone, granular to compact, no fossils noted ........................
71Al Section in KilbO'llrne bluff. The lower
bed is three to four feet thick and consists of fine-grained, dense
much brecciated and partly dolomitized limestone. It has a
rough upper surface and rests on the irregular surface of a
soft brownish dolomitic limestone layer of Croton age contain-
ing silicified specimens of Libhostrotion canadensis. The upper
bed consists of granular to compact thin-bedded slightly frac-
tured limestone seven feet in thickness. A few rods upstream from the abov;e described bluff section
the following succession is shown near the mouth of a small
ravine: Sectio'll on Big uree"k. P&iliA
rUT
7. Concealed; slope to top of hill overspread with blocks (}f
Pella limestone ......... __ .......................................................... _........... 3
6. Limestone, ;exposed ......... _ .................................. _ ................ _........... 1/3
5. Concealed; upper part of slope strewn with blocks of P ella. limestone; lower part wjth blocks of fine·grajned sandstone .... 9lh
UPPER ST. LOUIS
4. Limestone, granular to compact, no fossils noted ........................ 71Al Sectio'll on Big uree"k. limestone; lower part wjth blocks of fine·grajned sandstone ....
9l
UPPER ST. LOUIS
4
Li
t
l
t
t
f
il
t d
71 4.
Limestone, granular to compact, no fossils noted Section of St. Louis limestone in m e Winter q~larry.
FEET
9. Drift ----.-...... ________ ._._ .... _ .. ___ ... __ . ____ .. _. _____ . ___ ._ .. ___ ..... __ .. _______ .. _._ ... __ . __ ... ____
4
UPPER ST. LOUIS
8. Limestone, soft, shaly; mostly concealed at presoot _ .. __ ._ .. _. ____ ._
6
7.
Limestone, fine-grained, compact, gray; breaking with sub-
conchoidal fmcture; slightly brecciated . ____ . _______ .. _ .. __ ._ .. ___ .. ____ .... __
10
6.
Sandstone, fine-grruned, bluish, shaly ____ ... __ . __________ ... ___ ... ____ .. _________
4 to 5
5.
Limestone, fine-grained, dense, gray; in some places aren:ace- Section of St. Louis limestone in m e Winter q~larry. 6.
Sandstone, fine-grruned, bluish, shaly 5.
Limestone, fine-grained, dense, gray; in some places aren:ace- y
y
p
7.
Limestone, fine-grained, compact, gray; breaking
conchoidal fmcture; slightly brecciated 9. Drift ----.
UPPER ST. LOUIS
8
i P&iliA
7 265 ST. LOUIS IN HENRY COUNTY 3. Limesrtone, fine-grained, compact, gray to buff; imperfectly
dolomitized; little disturbed; co,nItacts above and below poorly
shown ... _. _________________________________________________ ----------.. --------------------------------
OWER ST. LoUIS
2. Limestone, buff, massive, dolomitic, probably the. Lithostrotion
oamadensis zone
__ . ___________________________________________________ ---------------------. 1. Limestone, buff, massive, dolomitic -----------------------------------------------
3
4
5 A third important exposure is shown above the bend of the
creek near the center of section 7. The Lower St. Louis has an
exposed thickness of thirty-five feet at one point. The lower
part is mashed and deformed but the higher layers are only
slightly brecciated. The Upper St. Louis is twelve feet thick
and consists of two members very similar in character to those
in the above described bluff section farther down stream. A good exposure of the St. Louis is present in a meander
scarp of Big creek, near the center of section 6 of Center town-
ship. Section of St. LO'U,is li1pestone on Big creek. FEET
INCHES
8. Drift, yellowish brown clay containiD.g gravel ________________ .__________
2
UPPER ST. LOUIS
7 _ Limestone, com pact, gray, slightly brecciated; massive b ~low
but thin-bedded and nodular above; with rounded limestone
pebbles in upper part ______________________________________________________ . __ .____________
4
6
6. Sandston~, gr,ay, fine-grained, soft _______________________________________________
8
5. Limestone, light gray, granular, bearing Lithcstrotion pro-
li/erum, Compo.sita tr'inuclea, Spirifer sp. and Girtyella indian-. ensis ________________________________ . _________________________________________ ._________________________
l '
8
4. Limestone, buff, dolomitic, soft, rather thin-bedded; weather-
ing to thin irregular chips. A layer near the top is filled with
worm castings ' _____________________ . _________ . ___ .. ________ . _____________ ... _______ ._______
7
6
LOWER ST. LOUIS
3. Limestone, dolomitic, buff, in one massive ledge. The Litho-
strotion canadensis zone .. _____ ... _._. _________ ... _ .. _ .. _______ .. __ .. _._.________________ 3
6
2. Limeston.e, buff, dolomitic.. in rather thin layers; ·resting on
the irregular hummocky surface of the bed beneath ____ . ___ .. __
3
1. Limeston'e, gray, brecci3lted. The lower part is locally evenly
bedded, buff and dolomitic _ .. ___ ....... ____________ ._ .. ___ . _____ . __ .. _ ...... _____ ._ 15 2. Limeston.e, buff, dolomitic.. in rather thin layers; ·resting on
the irregular hummocky surface of the bed beneath ____ . ___ .. MISSISSIPPIAN STRATA OF IOWA MISSISSIPPIAN STRATA OF IOWA vUS; with nodules and bands of dark flint
d
i
fi
i
d 4_
Sandstone; in part fine-grained, gray, calcareous, massive;
with irregular stratification lines; in part shaJy and lamin-
ated; resting 011 the uneven, eroded surface of the bed below Ph to, 2lh ated;
est
g
0
t e u eve , e oded su
ace o
t e bed be ow
h to,
3_
Limestone, light gray, compact, fine-grained, dense; usually
badly mashed and brecciated but ill places little disturbed;
wi th occasiollal reddish chert Ilodules; resting on the uneven
surface of the bell beneath ____________________________________________________________ 3
to 3lh
ST _
2_
Limestolle, buff, dolomitic; weathering illto ra,ther thin irreg-
ular layers; with small irregular patches of unaltered gray
limestone and an occasional non silicified specimen of Litho-
strotio1~ canadensis ________________________________________________________________________ ____ 21f2 L
Limestolle, buff, dolomitic, in rather thiu layers; obscure
worm t,;bes noted at one point in upper pal't.; beM'iug occasion-
al rounded chert nodules:
containing Brachythyris altcmensis,
Avicnblopectm sp_ and other fossils_
Exposed ____________________________ 5 Another excellent exposure of the Croton limestone is located. approximately one mile east of the town of Lowell, in the west
bluff of Mud creek, near the wagon bridge. This division is less
disturbed at this locality than usual and consists of massive buff
to brownish dolomitic limestone 'about thirty-five feet in thick-
ness. It is underlain by shales of Lower Warsaw age. The character of the St. Louis limestone in the northeastern
part of Henry county is well brought out by the following de-
scription by Savage17 of a quarry exposure in Scott township. "Twenty miles directly north of the Lowell exposure and sep-
arated from it by almost the length of the county, there is an
interesting quarry in the Se.1,4 of section 4, of Scott township,
about one mile northeast of the town of Winfield. At this place
an exposure just north of the road on land owned by Mr. G. W. Wilson shows the following succession of layers: 17 Iowa Geol. Survey, vol. XII, pp. 277, 2'18; 1902. P&iliA
7 __
3
1
Li
'
b
i3l d
Th
l
i
l
ll
l 1. Limeston'e, gray, brecci3lted. The lower part is locally evenly
bedded, buff and dolomitic _ .. ___ ....... ____________ ._ .. ___ . _____ . __ .. _ ...... _____ ._ 15 The following beds of the St. Louis are exposed in the Win-
ter quarry, located near the railway bridge over a branch of
Big creek, in the southeast quarter of section 17, Center town-
ship: 266 SectiQn. SectiQn. FEET
5. Clay of a reddish brown color contairuing gravel _______________________
5
4. Bed of fine-grained, fissile limestone, light gray in color, the
layers 'pne to three inches in thickness, and containing but
few fossils ___________________________________ __ :_. ____ . __ . _________ ._____________________________
4
3. Bed of rather soft, fiue-gI1ained standstoue_________________________________
61h
2, Bed of bluish grflly limestone, the layers three to eight inches
in thJi.ckness neal' the top, but in.creasing to as much as twelve
inches nea~' the base, The layers are separated by shaly part-
ings which contain numerous fossils _____ . ____ .___________________________________
10
1. Yellowish brown magnesian limestone p€'l.'fOl'ated with irreg-
ularly shapell cavities ; to the ba e of the exposure _________________
2 Number 1 in the above section is of a stronger yellow color
than the magnesian limestone u ually met with over the COlmty. It is less compact and contains a greater number of cavities
which resemble water worn passages. No traces of fossils were 17 Iowa Geol. Survey, vol. XII, pp. 277, 2'18; 1902. ST. LOUIS ON SKUNK RIVER 267 found in the rocks of this member. Number 2 is a bed of gray
limestone.· The narrower layers are somewhat shaly and weath-
er easily into thin fragments, but the thicker portions are com-
pact and durable. The shaly bands are very fossiliferous and
among them the following forms are abundant: found in the rocks of this member. Number 2 is a bed of gray
limestone.· The narrower layers are somewhat shaly and weath-
er easily into thin fragments, but the thicker portions are com-
pact and durable. The shaly bands are very fossiliferous and
among them the following forms are abundant: Zaphrentis spinulosa E. and H. Lithostrotion canadensis var. proli-
ferum RaIl
Syringopol'a; sp. undet. Archaeocidaris sp. spines and plates
F enestella sp. Dielasma fonnosa f Hall
Spirifer keokuk Hall
Eumetria marcyi Shumard
Athyris subqua.dcr-ata , RaIl" F enestella sp. Dielasma fonnosa f Hall
Spirifer keokuk Hall
Eumetria marcyi Shumard
Athyris subqua.dcr-ata , RaIl" F enestella sp. Dielasma fonnosa f Hall
Spirifer keokuk Hall
Eumetria marcyi Shumard
Athyris subqua.dcr-ata , RaIl" Zaphrentis spinulosa E. and H. Lithostrotion canadensis var. proli-
ferum RaIl
Syringopol'a; sp. undet. Archaeocidaris sp. spines and plates y
g p
;
p
Archaeocidaris sp. 19 Iowa Geol. Survey, vol. XII, pp. 355-437; 1901. 18 Idem, p. 2 76_
19 Iowa Geol. Survey, vol. XII, pp. 355-437; 1901. 18 Idem, p. 2 76_ Zaphrentis spinulosa E. and H.
Lithostrotion canadensis var. proli-
ferum RaIl
Syringopol'a; sp. undet.
Archaeocidaris sp. spines and plates Seotion of Low'er St. Lo'uis lvmestone on T~!T7cey cree7c.
UPPER ST. LOUIS
FEET
9.
Slope, covered with loose blocks of gray nondolomitic lime-
stone.
LOWER ST. LOUIS
8. Limestone,
gray"
, dolomitic, ! weathering
brown.ish,
poorly
exposed ........ __ ...... _ ........ __ ................ _ .... ____ ................ _ ...... _____ .. __ ............
3
7.
Limestone, gra.y weathering buff, soft, dolomitie, much rotted,
structul'eless .......... _ .. ____ ........ __ ...... __________ .... __ ...... _ .... _ ........ __ .... _ ........ _ .. _ 4
6.
Limestone, dark gray weathering buff; tough; massive below
but thin-bedded above; projecting _ ......... __ .............. _ ........ _____ .... _ 2:14
5.
Shale, bluish, weathering buff; arenaceous and dolomitic
above but calcareous below .. __ .... __ .... __ ........ ____ .. __ .............. _ .......... __
4 1/ 6
4.
Limestone, compact, dense, dove-colored, brittle; with fine SectiQn. spines and plates Beds 1 and 2 of the above section probably represent the Cro-
ton while the overlying beds are believed to be of Verdi age. Another section of interest, located in the northwestern part
of the county, two miles west of Wayland, also is described by
Savage.IS Section of St. Louis limestone ~vest of WayZwnd (after Sarvage). Section of St. Louis limestone ~vest of WayZwnd (after Sarvage). FEET
INCHES
6. Bed of browIlJ sandstone, rather hard ILlld coarsely granular 4
5. Layer of white fine-grained nonfossiliferous limestone ____________
1
2
4. Soft fine-grained sandstone ____ . _____________________________________________________ 12
3. Layers of light colored limest.one, eight to ten inches in
thickness, containing no fossils ____ . ___________________________ . _____ .___________
1
6
2. Band of clay- or marl containing very numerous casts of a
fossil which somewhat resembles a species of Athyris ___________
4
1. Layers of light gray n0l!fossiliferous limestone down to the
level of the stream _________________________________ . _______ . ____________ . __ ... _____ .__________
2 4. Soft fine-grained sandstone level of the stream _ Jefferson County.-The mantle rock is underlain over the
greater part of Jefferson county by the Des Moines formation. The St. Louis as mapped by Udden/9 appears in the northeast-
ern part of the county where it has been uncovered by Skunk
river and its tributaries; over a small area in the extreme north-
western part of the county; as small inliers in the eastern,
south-central, and southwestern parts; and as ribbon-like areas
along Cedar creek and its tributaries in the southeastern part. One of the most complete sections in the entire county may be
studied in the Cedar Bluff of Skunk river just southeast of the
mouth of Rattlesnake creek and one-fourth mile east of the
southeast corner of section 12, Lockridge township. The St. Louis is underlain here by fine-grained, bluish sandstone of
Spergen age with an exposed thickness of twenty-one feet. 268 MISSISSIPPIAN STRATA OF IOWA, Section of St. Louis limestone on S7cun7c river. Section of St. Louis limestone on S7cun7c river. FEET
INCHES
14. Drift .----........ -----__ .. _ .................................... _ ........................................ _ 1
PPER ST. LOUIS
13. Limestone, gray to light gray, less brittle and dense than the
bed below, containing Productus ova,tus, Composita tritnruclea,
d lloris-ma. si71lnata .... ---.. --........ ~ .. ___ ................ ___ .. __ ........ _ .. ___ .. _ .. __ .... __ .. _ 2
6
12. Sandstone, soft, fine-grained, bluish, incoherent _ ............ __ .. __ .... _ 2
11. Sandstone, gray, calcareous, fine-grained, in a single lruyer...... 6
10. Limestone, gray, compact, fine-grained, brittle, middle a.nd
upper parts with ribbon-like stratification .. __ ........ __ ...... _ .... __ ...... 3
6
9. Shaly parting ................................ _ ................ __ .. _ ...... ______ ........ __ .... __ .. _
4
8. Limestone, oompact, dark gray, fine-gra.ined; rather heavily
bedded; slightly disturbed in upper part __ .. _ .... __ ........................ ___
1
6
7. Limestone, compact, gray, nodular; in the form of rounded
pellets, ranging from size of pea up to size of walnut, in a
shaly matrix. Filled with Composita trinuclea .... ___ ................. 6
6. Limestone, gray, compact, fine-grained, brittle; weathering
into thin ftal,es; 10caUy brecciated and mashed down into the
bed below; with stylolytic seams. Lower contact poorly p.x-
posed but appears to be irregular where mashini:;- has not taken
place. Spirifer cf. S. pellaensis and Composita trim!clea .. __ 5 to G
OWER ST_ LOUIS
5. Limestone, yellowish to brownish, dolomitic, much decayed;
shale in lower and upper parts; of differing- thickness due to
mashing down of limestone above .................... --...... -........... 41h to 71h
<4,. Limestone, brownish, tough, massive, dolomitic; wit;ll small
fragments and nodules of chert; indistinctly stratified; con-
tact with bed below is an irregular wavy line; slightly vesicu-
lar; in one massive layer .............. __ .... __ .. __ ...................... _ .......... _ 3
6
3. Limestone, gray, tough, dolomitiC, hard; weathering buff and
soft; in layers 2 to 18 inches thick; receding slightly beneath
bed above. Upper surface irregular_
Top layer thickens
and thins from above; shaly and arenaceous in lower part
and grading down into the bed below ..... _ ...... __ ................. __ ........ _ 4
6
2. Shale, bluish, argilLaceous, with seams of light gray more
calcareous shale _ .. _____ .. _ .......... ____ .................. _ ........................... _ .. __ .... Section of St. Louis limestone on S7cun7c river. _ 3
1. Limestone, oompact, buff, dolomitic; in a single layer. Prob-
ably the base of the Lower St. Louis _ ............ _ .... _ ...... __ .... ___ .... _ .. _
8 FEET
INCHES
14. Drift .----........ -----__ .. _ .................................... _ ........................................ _ 1
UPPER ST. LOUIS
13
Li
li h
l
b i l
d d
h
h 13. Limestone, gray to light gray, less brittle and dense than the
bed below, containing Productus ova,tus, Composita tritnruclea,
d lloris-ma. si71lnata .... ---.. --........ ~ .. ___ ................ ___ .. __ ........ _ .. ___ .. _ .. __ .... __ .. _ 2
6 12. Sandstone, soft, fine-grained, bluish, incoherent _ ............ __ .. __ .... _ 2
11
S
d t
l
fi
i
d
i
i
l
l 11. Sandstone, gray, calcareous, fine-grained, in a sing
10
Li
t
t
fi
i
d
b ittl 11. Sandstone, gray, calcareous, fine-grained, in a single lruyer...... 6
10
Li
t
t
fi
i
d
b ittl
iddl
d 10. Limestone, gray, compact, fine-grained, brittle, middle a.nd
upper parts with ribbon-like stratification .. __ ........ __ ...... _ .... __ ...... 3
6
9
Shaly parting
4 9. Shaly parting ................................ _ ................ __ .. _ ...... ______ ........ __ .... __ .. _
8
Li
t
t
d
k
fi
i
d
th
h
il 8. Limestone, oompact, dark gray, fine-gra.ined; rather heavily
bedded; slightly disturbed in upper part __ .. _ .... __ ........................ ___
1
7
Li
d l
i
h
f
f
d d 7. Limestone, compact, gray, nodular; in the form of rounded
pellets, ranging from size of pea up to size of walnut, in a
shaly matrix. Filled with Composita trinuclea .... ___ ................. 6
6
Li
fi
i
d
b i l
h
i 5. Limestone, yellowish to brownish, dolomitic, much decayed;
shale in lower and upper parts; of differing- thickness due to
mashing down of limestone above .................... --...... -........... 41h to 71h
Li
b
i h
h
i
d l
i i
i ll
ll <4,. Limestone, brownish, tough, massive, dolomitic; wit;ll small
fragments and nodules of chert; indistinctly stratified; con-
tact with bed below is an irregular wavy line; slightly vesicu-
lar; in one massive layer .............. __ .... __ .. __ ...................... _ .......... _ 3
6 3. Seotion of Low'er St. Lo'uis lvmestone on T~!T7cey cree7c. Section of St. Louis limestone ()'11; Cedar creek.
FEET
iNCHES
10. Drift, to brow of hill ... _ ................................................. _ .. _..............
6
UPPER ST. LOUIS
9.
Limestone, gray, fine·grained, compact ..........................................
1
6
8.
Concealed ... _ ................... ____ ................... _ ................................. _........... 1
3
7.
Sandstone, gray weathering buff; massive in middle but thin·
bedded above and belo·w ... _ .................................................. _...........
7
6.
Shale, soft, buff, dolomitic ................................................. _............. 8
8
LOWER ST. LOUIS
15.
Limestone, gray, fine·grained, compact, brittle, non dolomitic ; Section of St. Lo'uis liflnestonc in section 3, Loo7cridge township. Section of St. Louis limestone on S7cun7c river. Limestone, gray, tough, dolomitiC, hard; weathering buff and
soft; in layers 2 to 18 inches thick; receding slightly beneath
bed above. Upper surface irregular_
Top layer thickens
and thins from above; shaly and arenaceous in lower part
and grading down into the bed below ..... _ ...... __ ................. __ ........ _ 4
6 8 An excellent section of the Lower St. Louis occurs in an old
quarry opening in the north bank of Turkey creek near the cen-
ter of the northeast quarter of. section 11, Lockridge township. It is here underlain by fifteen and one-half feet of Spergen
sandstone. Seotion of Low'er St. Lo'uis lvmestone on T~!T7cey cree7c. UPPER ST. LOUIS
FEET
9. Slope, covered with loose blocks of gray nondolomitic lime-
stone. LOWER ST. LOUIS
8. Limestone,
gray"
, dolomitic, ! weathering
brown.ish,
poorly
exposed ........ __ ...... _ ........ __ ................ _ .... ____ ................ _ ...... _____ .. __ ............ 3
7. Limestone, gra.y weathering buff, soft, dolomitie, much rotted,
structul'eless .......... _ .. ____ ........ __ ...... __________ .... __ ...... _ .... _ ........ __ .... _ ........ _ .. _ 4
6. Limestone, dark gray weathering buff; tough; massive below
but thin-bedded above; projecting _ ......... __ .............. _ ........ _____ .... _ 2:14
5. Shale, bluish, weathering buff; arenaceous and dolomitic
above but calcareous below .. __ .... __ .... __ ........ ____ .. __ .............. _ .......... __
4 1/ 6
4. Limestone, compact, dense, dove-colored, brittle; with fine 269 ST. LOUIS IN JEFFERSON COUNTY 1. Limestone, gray, subcrystalline; mottled with yellowish dolo·
mitic patches above, but shaly, buff and dolomitic below;
resting on the slightly undulating surfa.ce of the Spergen
sandstone .............................................................................................. 1 The following section is exposed in a quarry and in the ravine
nearby in the southwest one-fourth of the southeast quarter or
section 3, Lockridge township. Section of St. Lo'uis liflnestonc in section 3, Loo7cridge township. Exposed to
level of water in creek ....................................................................... 1
6 containing Lithostrotio1l, p?'olifemm, !::Jpirifer sp., and other
fossils ... - ............................................................................................... 1
7 to
2
• 4. Limestone, gray weathering buff, dolomitic, with occasional
rounded chert nodules; rather soft above. Bears the follow·
ing fossils :
Girtyella indiarnensis, Spirifer sp., S. pellaensis,
Composita t?'inuclea and Straparollus sp. ...................................... 4 2
• 4. Limestone, gray weathering buff, dolomitic, with occasional
rounded chert nodules; rather soft above. Bears the follow·
ing fossils :
Girtyella indiarnensis, Spirifer sp., S. pellaensis,
Composita t?'inuclea and Straparollus sp. ...................................... 4 bearing Lithostrotion prolifemm ............. 1. Limestone, gmy, subcrystalline, non dolomitic. Exposed to
level of water in creek ....................................................................... 1
6 A good exposure of the 1St. Louis occurs in the north bank of
Cedar creek a short distance
E;l~st of the southwest corner of
section 34 of the same township. Section of St. Louis limestone on Cedar creek in section 34. UPPER ST. Lours
,
FEET
INCHES
5. Limestone and sandstone interbedded, the sandstone predomi·
natin.g belo·w and the limestone above. Sandstone soft, fine·
grained and gray; limestone gray, compact, dense and slightly
brecciated. At the top no sandstone appears and the lime·
stone is filled with small sinuous tubes of calcite. Some of
the limestone layers exhibit a tendency towards lamination .... 23 Section of St. Louis limestone on Cedar creek in section 34. PPER ST. Lours
,
FEET
INCHES
5. Limestone and sandstone interbedded, the sandstone predomi·
natin.g belo·w and the limestone above. Sandstone soft, fine·
grained and gray; limestone gray, compact, dense and slightly
brecciated. At the top no sandstone appears and the lime·
stone is filled with small sinuous tubes of calcite. Some of
the limestone layers exhibit a tendency towards lamination .... 23
4. Limestone, gray, fine·grained ; filled with clark brecciated chert 1
6
3. Sandstone, gray, calcareous, weathering yellowish, very iregu·
larly bedded. Locally filled Witll small angular fragments of
whitish chert ......... _ ...................... _..................................................... 4
oWER ST. LOUIS
. 2. Limestone, light gray, fine·grained; weathering to irregular
angular blocks. Bears Lithostrotion oanadensi.f in calcareoU5
form. This ' and the bed below are undulating and much
disturbed
... _ .... _ .... _ ........... _................................................................. 1
9
1. Limestone, dark gray, dense, compact, tough, brecciated. Exposed to water level ... _ .......... _ ..... _ .................... _ ....... ,-................. 4
6 Section of St. 20 Iowa Gool. Survey, vol. XII, pp. 368-386: 1901. 21 Iowa Geo!. Survey, vol. XII, pp. 439-499; 1901. Section of St. Lo'uis liflnestonc in section 3, Loo7cridge township. Section of St. Lo'uis liflnestonc in section 3, Loo7cridge townshi Section of St. Louis liflnestonc in section 3, Loo7cridge township. UPPER ST. LOUIS
FEET
INCHES
12. Sandstone, gray, calcareous ... _......................................................... 1
6
11. Sandstone, fine·grailled, soft, shaly .... c........................................... 3
10. Limestone, gray, compaet .......................................................... 1 to 2%
9. Limestone, compact," gray, nodular; ·filled with a Composita.... 6
8. Limestone, gray, compact, brecciated ......... _ ........ _ ........ _ ....... 3 to 5-%
7. Shale, bluish, calcareous; of variable thickness owing :to
mashing ................................................................................. _ ........... 1 to< 3
6. Limestone,
brownish,
dolomitic,
tough;
with
reddish,
quartzose masses ......... _ .................................. _ .......... _....................... . 6
LOWER ST. LOUIS
5. Limestone, gray, compact, containing Lithostrotion pmlifer·
um, Syringopora sp. and. Compositn trinuclea ............................ 2
6
4. Limestone, gray, dolomitic, slightly vesicular, massive; worm
burrows in 6· inch zone at top ... _ .................................. _............... 5
6
3. Shaly pa.rting ................................. _ ........................................ _........... 8
2.. Limestone, gray weathering yellowish, dolomitic, tough, mas·
sive; irregularly bedded owing to mashing and deformation .... 7
6
1. 'Shale, bluish, dolomitic, weathering buff. Exposed .................. 4 Other characteristic exposures appear in Round Prairie town-
ship. The accompanying section is exposed in the bluff at the
south end of the bridge over Cedar creek, near the middle of the
south line of section 33. Section of St. Louis limestone ()'11; Cedar creek. FEET
iNCHES
10. Drift, to brow of hill ... _ ................................................. _ .. _.............. 6
UPPER ST. LOUIS
9. Limestone, gray, fine·grained, compact .......................................... 1
6
8. Concealed ... _ ................... ____ ................... _ ................................. _........... 1
3
7. Sandstone, gray weathering buff; massive in middle but thin·
bedded above and belo·w ... _ .................................................. _........... 7
6. Shale, soft, buff, dolomitic ................................................. _............. 8
8
LOWER ST. LOUIS
15. Limestone, gray, fine·grained, compact, brittle, non dolomitic ; MISSISSIPPIAN S'l'RATA OF IOWA 270 containing Lithostrotio1l, p?'olifemm, !::Jpirifer sp., and other
fossils ... - ............................................................................................... 1
7 to
2
• 4. Limestone, gray weathering buff, dolomitic, with occasional
rounded chert nodules; rather soft above. Bears the follow·
ing fossils :
Girtyella indiarnensis, Spirifer sp., S. pellaensis,
Composita t?'inuclea and Straparollus sp. ...................................... 4
3. Limestone, gray, dolomitic, weathering buff; in two heavy
layers ...................................................................................................... 2
8
2. Limestone, gray, aren~ceo us, thin· bedded ; cross· bedded below;
bearing Lithostrotion prolifemm .................................................... 4
2
1. Limestone, gmy, subcrystalline, non dolomitic. Section of St. Lo'uis liflnestonc in section 3, Loo7cridge township. Louis limestone on Cedar creek in section 34. UPPER ST. Lours
,
FEET
INCHES
5. Limestone and sandstone interbedded, the sandstone predomi·
natin.g belo·w and the limestone above. Sandstone soft, fine·
grained and gray; limestone gray, compact, dense and slightly
brecciated. At the top no sandstone appears and the lime·
stone is filled with small sinuous tubes of calcite. Some of
the limestone layers exhibit a tendency towards lamination .... 23 4. Limestone, gray, fine grained ; filled with clark brecciated chert 1
6
3. Sandstone, gray, calcareous, weathering yellowish, very iregu·
larly bedded. Locally filled Witll small angular fragments of
whitish chert ......... _ ...................... _..................................................... 4
LoWER ST
LOUIS 2. Limestone, light gray, fine·grained; weathering to irregular
angular blocks. Bears Lithostrotion oanadensi.f in calcareoU5
form. This ' and the bed below are undulating and much
disturbed
... _ .... _ .... _ ........... _................................................................. 1
9 1. Limestone, dark gray, dense, compact, tough, brecciated. Exposed to water level ... _ .......... _ ..... _ .................... _ ....... ,-................. 4
6 At the meander scarp of the large meander, a short distance
east of this point, in the northeast quarter of the southwest
quarter of section 34, the Pella limestone, with a basal sand-
stone three to four feet in thickness, ' rests upon bed 5 of the
preceding section. Numerous other outcrops of the St. Louis limestone in J ef-
ferson county have been described by U dden20 but inasmuch as
the general character of the formation is much the same as jn
the exposures described above further space will not be given to
them here. Wapello County.-The beds in 'Wapello county 'which were
mapped and described as St. Louis by Leonard21 are believed VERDI IN WASHINGTON COUNTY 271 to be everywhere of Pella age. They were so identified by him
with the exception of a layer of soft sandstone, which was seen
below the limestones at two localities, and which he referred to
the Verdi. According to the observations of the writer this
sandstone is more probably of basal P ella age and it is so re-
garded in this report. Louisa County.- In the report on Louisa county submitted by
Udden
22 reference is made to only one locaiity where rocks be-
lieved to be of St. Louis age outcrop. I quote from his descrip-
tion : . 22 Iowa Geol. Survey, vol. XI, pp. 55-12G; 1901. Section of St. Lo'uis liflnestonc in section 3, Loo7cridge township. Filled with stylolytic structure along
fractures,
Small pelecypods and L ep.erditia abundant in
laminated layer at very top ___________________________________________________________ 91h
2_
Sandstone, gray, fine-grained, soft, incoheren.t, shaly; thickens
and thins owing to mashing down of limestone ab{)ve ____________ 1
to· 2lh
1. Sandstone, massive, fine-grained, gray, soft, weathering yellow-
ish; with mashed' irregular lentils of compact gray limestone. ExpOsed _________________ . ___________________________________________________ . _______________________ 7 Section of St. Lo'uis liflnestonc in section 3, Loo7cridge township. "On the left bank of Honey creek in the Se.14 of the Sw.14 of
Sec. 32, Tp. 73 N., R. 3 W., some twenty rods north of the
boundary of the county, there is a limestone breccia of greenish
gray color composed of fragments of varying sizes, interbedded
in a calcareous matrix of the same color. Some of the limestone
blocks contain fragments of crinoid stems and other unrecog-
nizable fossils. There are also seen in them some small cavities
filled with a bright green clay. The breccia is only three or
four feet.high in the bank and rests on an uneven surface of the
lower formation, which is yellow and weathered. An uncon-
formity is here indicated. The rock extends only a few rods
along the stream. A little farther down some reddish shaly
beds appear on the same side of the creek. These are appar-
ently continuous with the geode-bearing horizon of the Augusta
(Osage), exposed nearby. The limestone breccia on this creek
is entirely unlike anything else seen in the county. Doctor Bain,
who visited the locality in company with the author, inclines to
the opinion that it r epresents the St. Louis. stage. If such is the
case there are possibly some more outliers of the same forma-
tion under the drift in the southwest part of the county, where
the bed rock occurs in wells at a considerably higher level than
that of the Burlington limestone in the nearest outcrops". Washington County.-·Beds of St. Louis age cover the south-
ern part .of the county with the exception of small areas in the
southwestern part which are buried by the Des Moines forma-
tion. The type section of the Verdi member is located in this coun-
ty at an abandoned quarry one-half mile south of Verdi station,
in the eastern part of section 9 of Brighton township. The suc-
cession of beds there is as follows : MISSISSIPPIAN STRATA OF IOWA 272 Section one-ha~f 'mile south of Verdi,
}'EET
6,
Drift, reddish, with decayed granite bowlders ____________________________ 41h to 11
DES MOINES
5_
Sandstone, coarse-grained, yellowish, soft ___________________________________ 0
to 6lh
VERDI 4, Limestone, compact, gray, finely brecciated ____________________________
1/3
3. Limestone, ash-gray, fine-grruned, rather soft, brecciated;
thin-bedded and laminated above; locally little disturbed and
heavily bedded below. FEET
7_
Drift to brow of hill ________________________________________________________________ ,____
3
UPPER ST_ LOUIS
6.
Limestone, gl'ay, compact, brecciated; !!lot well exposed _________ ~___
8
5.
Sandstone, gray, fine-grained, massive, calcaJ:eous ______________________
5
4.
Sandstone, yellowish, soft, incoherent; filled with small an.gular
fraglllents of whitish chert __________________________________________________________ .
2 to 3 5.
Sandstone, gray, fine-grained, massive, calcaJ:eous ______________________
5
4
Sandstone yellowish soft incoherent; filled with small angular 6.
Limestone, gl ay, compact, brecciated; !!lot well exposed _________ ~___
8
5
Sandstone
gray
fine-grained
massive
calcaJ:eous
5 7_
Drift to brow of hill ________________________________________________________________ ,____
3
UPPER ST_ LOUIS
6
Limestone gl'ay compact brecciated; !!lot well exposed
~___
8 Semion at and neM Brighton mill.
f hill fraglllents of whitish chert 7_
Drift to brow of hill
UPPER ST_ LOUIS
6
Limestone gl'ay compa Section one-ha~f 'mile south of Verdi, Section one-ha~f 'mile south of Verdi, 5_
Sandstone, coarse-grained, yellowish, soft __
VERDI 4
Li
t
t
fi
l
b
i t d 1. Sandstone, massive, fine-grained, gray, soft, weathering yellow-
ish; with mashed' irregular lentils of compact gray limestone. ExpOsed _________________ . ___________________________________________________ . _______________________ 7 In an exposure two hundred yards north of the preceding sec-
tion in the west bluff of a small creek which parallels the rail-
road the Lower St. Louis appears. ' It consists of twenty feet
of sandstone, dolomitic and shaly below, with a large lentil of
compact gray limestone, about five feet thick in the middle and
fifty feet long, in the upper part. A thin seam of finely brec-
ciated lim~stone near the top of the lens is filled' with a s~all
brachiopod resembling Girtyella. Below the dolomitic shales
comes four feet of thin-bedded, laminated buff dolomitic lime-
stone with thin light gray to whitish chert bands. The following fossils were collected from bed 3 of the above
described quarry section. Orthoootes , sp. A viculopec;.ten sp. A viculopeeten sp. Pustula alternata (N. and P.)
Girtyella indianensis (Girty)
Spirifer cf. S_ pella.ensis Weller
Composita trinuclea (Hall)
Edmondia , sp. Allorisma sinuata McChesney ,
Laevidentalium , sp. Bellemphon sp_
Leperditia carbonmia Hall A viculopec;.ten sp. A viculopeeten sp. Allorisma sinuata McChesney ,
Laevidentalium , sp. Bellemphon sp_
Leperditia carbonmia Hall Orthoootes , sp. Pustula alternata (N. and P.)
Girtyella indianensis (Girty)
Spirifer cf. S_ pella.ensis Weller
Composita trinuclea (Hall)
Edmondia , sp. The Lower St. Louis is exposed in the vicinity of Brighton
mill, one mile slightly east of north of the town of Brighton, in
the southwest quarter of section 20, Brighton township. The
following section appears in the Skunk river bluff at the mill
and in the banks of a small creek just south of the mill. 23 Iowa Geol. Suney, vol. V, p. 148 ft; 1896. Semion at and neM Brighton mill.
f hill ST. LOUIS BEDS NEAR COPPOCK 273 LOWER ST. LOUIS
3. Concealed LOWER ST. LOUIS
3
C
l d OWER ST. LOUIS
3. Concealed ......... _ .... _ .... _ .... _ .......... _ .... _ .... _......................................... 3
2. Shale and limestone; thin layers of dark gray compact, dense
limestone weathering buff, intercalated with layers of shale ... _
1 %,
1. ShaJe, bluish, argillaceous, with thin sandy seams ...................... 14 3. Concealed ......... _ .... _ .... _ .... _ .......... _ .... _ .... _......................................... 3
2. Shale and limestone; thin layers of dark gray compact, dense
limestone weathering buff, intercalated with layers of shale ... _
1 %,
1. ShaJe, bluish, argillaceous, with thin sandy seams ...................... 14 3. Concealed _
_
_
_
_
_
_
2. Shale and limestone; thin layers of dark gray compact, dense
limestone weathering buff, intercalated with layers of shale ... _
1 %,
1. ShaJe, bluish, argillaceous, with thin sandy seams ...................... 14 In a quarry one-half mile south of the Brighton mill a bed
believed to represent an upward continuation of number 6 of the
preceding section is overlain unevenly by sandstone and shale,
viz. : Section one-half mile south of Brighton I1Vill. Section one-half mile south of Brighton I1Vill. FEET
4. Drift ......... _ ...................... _ .................................. _ .......... _................... 4
3. Shale, bluish, argillaceous ....................... _ .... _ ..... _ ................ _........... 1
2. Sandstone, gray, fine· grained, thin· bedded, calcareous; weath·
ering yellowish on surface; slightly cross·hedded; with thin
seams and lenses of compact gray limestone in lower part. Resting on the uneven surface of the bed beneath .................... . 5
1. Limestone, gray, nne-grained, compact, dense, brittle; breaking
with subconchoidal to splintery fracture; in heavy, massive
layers. Lower part slightly brecciated locally; with occasional
small nodules of chert. Leperditia zone at top 4 to 6 inches
thick. Bed 6 of pl'eceding S(lction. Exposed ............................ 5
Th
f
il
li t d b l
f
b d 1 The fossils listed below are from bed 1: Zaphrentis sp. Syringopora sp. Orthotetes , sp. Productus ovatus Hall ,
Girtyella indianensis (Girty)
Spirifer sp. Composita trinuclea (Hall)
Allorisma sp. Sphenotus sp. Myalin,a , sp. Straparollus sp. Leperditia carbonaria Hall' Composita trinuclea (Hall)
Allorisma sp. Sphenotus sp. Myalin,a , sp. Straparollus sp. Leperditia carbonaria Hall' Composita trinuclea (Hall)
Allorisma sp. Sphenotus sp. Myalin,a , sp. Straparollus sp. Semion at and neM Brighton mill.
f hill Leperditia carbonaria Hall' Girtyella indianensis (Girty)
S i if Spirifer sp. An exposure in a ravine one hundred yards south of the quar-
ry section shows the shale bed, number 3, to be overlain by five
and one-half feet of interbedded shales and limestones filled
with characteristic Pella fossils. It is probable therefore that
the sandstone bed, number 2, of the· quarry section represents
the basal member of the Pella formation. Bed f undoubtedly
represents bed 3 of the Verdi section. An exposure in an abandoned quarry along the Chicago,
Burlington and Quincy railway one-half mile northeast of Cop-
pock probably represents a shaly facies of the Lower St. Louis. No fossils were found. Seotion northeast of Coppoc/.;. FEET
3. Limestone, brownish, dolo:m.itic, with shaly and sandy seams;
much decayed and Totted, and with solution cavities ..... _....... 8
' 2. Shale, dolomitic and arenaceous, buff, poorly Ejxposed _. __ .... __ .. 12
1. Sandstone, fine-grained, gray weathering yellowish. Exposed
3
Bain23 has described other exposures of the St. Louis alo~g ' 2. Shale, dolomitic and arenaceous, buff, poorly Ejxposed _. __ .... __ ..
12
1
Sandstone
fine grained
gray weathering yellowish
Exposed
3 Bain23 has described other exposures of the St. Louis alo~g Section one-half mile south of Brighton I1Vill. Seotion northeast of Coppoc/.;.
FEET
3.
Limestone, brownish, dolo:m.itic, with shaly and sandy seams;
much decayed and Totted, and with solution cavities ..... _.......
8
' 2. Shale, dolomitic and arenaceous, buff, poorly Ejxposed _. __ .... __ ..
12
1. Sandstone, fine-grained, gray weathering yellowish.
Exposed
3
Bain23 has described other exposures of the St. Louis alo~g
23 I
G
l
S
l
V
148 ft
1896 Seotion of Upper St. Louis lime.stone west of Ollie.
}'EET
INC lIES
8.
Drift, reddish ........................................................................................
6
7.
Limestone, gray, compact, with subconchoidal fmcture, lamin·
ated; in the form of large lenses in the upper part of the
sandstone member below ..................................................................
2
6
6.
Sandstone, fine·g)'ained, yellowish, of differing thickness due
to limestone lenses in upper part.
'With )'oullded blocks of
Jimestone in lower part .......................................................... :'l1h to G .
5.
Limestone, compact, g)'ay, not everywhere present ....................
8
4.
Limestone, brecciated, with shaly ::md sandy matrix ................
6
3.
Limestonet
~ray, fine·grained ..........................................................
4
2.
Limestone, gray, compact,
finely brecciated;
upper part
locally undisturbed ............................................................................
2
1.
Limestone, gray, compac.t; locally slightly brecciated. Exposed 6 24 Iowa Geol. Survey, vol. IV. p . 277 ff; 1895.
2" Idemf p. 281. Seotion of Upper St. Louis lime.stone west of Ollie. 1.
Limestone, gray, compac.t; locally slightly brecciated. Exposed 6 Seotion northeast of Coppoc/.;. Bain23 has described other exposures of the St. Louis alo~g MJ:SSISSIP'PIAN STRATA OF IOWA 2074 Crooked creek in the southeastern part of the county and on
Skunk river between the Brighton mill and the west county line. /( eokuk Co'unty.-The St. Louis limestone underlies the great-
er part of Keokuk county. Osage formations · appear in the
northeastern p~rt and as isolated inliers in. the St. Louis in the
southern half of the county. Areas of P ennsylvanian project
into the county on the west and southeast and there are small
scattered outliers in the interior. Elsewhere the St. Louis is
the bed rock. The St. Louis as developed in Keokuk county has been sub-
divided by Bain24 into three members designated as the Spring-
vale, the Verdi, and the Pella. He reports the Pella beds as
being sparingly present. His type sectio\l of the Spril1gvale is at the old Springvale
mill on South Skunk river in section 34, Warren township. The
writer has pointed out on an earlier p.age (p. 181) that the shaly
beds exposed here are more probably of Keokuk age, as are the
shaly beds in the" granite" quarry northwest of Ollie, which
were referred by him to the Springvale. It is apparent, how-
ever, that in a few instances, the beds elsewhere in the county
designated by him as Springvale are of true Lower St. Louis
age. One of the most typical sections of the Upper St. Louis ap-
pears in a cut of the Minneapolis and Saint Louis railway one
and one-half miles west of Ollie, in Jackson township. The fol-
lowing description of this is modified after Bain.25 Seotion of Upper St. Louis lime.stone west of Ollie. }'EET
INC lIES
8. Drift, reddish ........................................................................................ 6
7. Limestone, gray, compact, with subconchoidal fmcture, lamin·
ated; in the form of large lenses in the upper part of the
sandstone member below .................................................................. 2
6
6. Sandstone, fine·g)'ained, yellowish, of differing thickness due
to limestone lenses in upper part. 'With )'oullded blocks of
Jimestone in lower part .......................................................... :'l1h to G . 5. Limestone, compact, g)'ay, not everywhere present .................... 8
4. Limestone, brecciated, with shaly ::md sandy matrix ................ 6
3. Limestonet
~ray, fine·grained .......................................................... 4
2. Limestone, gray, compact,
finely brecciated;
upper part
locally undisturbed ............................................................................ 2
1. Limestone, gray, compac.t; locally slightly brecciated. Exposed 6 ST. Seotion in m'eek bed west of Ollie.
FEET
INCHES
9;
Drift, with loose blocks of gray limestone .................................. 2
UPPER ST. LoUIS
8.
Limestone, gray, compact, nne· grained, brecciated. Bed 1 of
railway cut l!ection ... _ .... _ .... _ .......... _ ............ ,.................................. 7 List of fossils f7·om bed 1 of above section. List of fossils f7·om bed 1 of above section. Laevidentalium Bp. Bellerophon sp. Bellerophon sp. Bucanopsis sp. Straparollus sp. Leperditia d. L. carbonaria Hall. Laevidentalium Bp. Bellerophon sp. Bellerophon sp. Bucanopsis sp. Straparollus sp. Leperditia d. L. carbonaria Hall. Stellopora sp. Productus ovatus Hall
Spirifer cf. S. pellaensis Weller
Schizodus sp. Modiomorpha sp. Allorisma sp. Allorisma sp. List of fossils from bed 7 of above &ection. rthotetes kaskaskiensis Weller
pirifer pellaensis Weller
omposita trinuclea (Hall) Seotion northeast of Coppoc/.;. LOUIS BEDS NEAR OLLIE 275 A layer of limestone at the very top of bed 1 is filled with a
small species of a Pelecypod and a small L r:-perditia. The fos-
sils of this bed and of bed 7 are as follows: List of fossils from bed 7 of above &ection. List of fossils from bed 7 of above &ection. Orthotetes kaskaskiensis Weller
Spirifer pellaensis Weller
Composita trinuclea (Hall) Orthotetes kaskaskiensis Weller
Spirifer pellaensis Weller
Composita trinuclea (Hall) Orthotetes kaskaskiensis Weller
Spirifer pellaensis Weller
Composita trinuclea (Hall) Ninety yards east of the above section, twenty-one feet of
Lower St. Louis limestone is exposed in the bluff of a small
creek which parallels the railway on the north. Section 7Wnety yards east of the precedvno section. MISSISSIPPIAN STRATA OF IOWA MISSISSIPPIAN STRATA OF IOWA 7. Sandstone, very soft, incoherent, shaly ......... _ ................ _........... 2
6. Sandstone, gr,ay weathering buff, in one massive ledge; cal·
careous and irregularly stratified in lower part .......................... 5
LOWER ST. LOUIS
5. Limestone, buff, dolomitic; with occasional seams and lenses
of gray compact limestone. Contact with bed above irregular
and undulating ......... _ .......... _ ................ _............................... 1/3 to 1
4. Limestone, buff, fine·grained, dolomitic; soft and shaly in mid·
dIe part; flaking off obliquely; with wne of worm borings
four inches thick in lower part ..... _............................................. 2
3. Limestone, gray, shaly, laminated ....... ___________________ . ______________________ _
2. Limestone, dark gray, fine-g:rained, dense . ____ . _____ . _______________ : _____ . 1. Limestone, soft, buff, dolomitic. Exposed ____________________________________
1
6
3 to 5
8 to 12
3 7. Sandstone, very soft, incoherent, shaly 7. Sandstone, very soft, incoherent, shaly ......... _ ................ _........... 2 6. Sandstone, gr,ay weathering buff, in one massive ledge; cal·
careous and irregularly stratified in lower part .......................... 5
LOWER ST. LOUIS 5. Limestone, buff, dolomitic; with occasional seams and lenses
of gray compact limestone. Contact with bed above irregular
and undulating ......... _ .......... _ ................ _............................... 1/3 to 1 g
4. Limestone, buff, fine·grained, dolomitic; soft and shaly in mid·
dIe part; flaking off obliquely; with wne of worm borings
four inches thick in lower part ..... _............................................. 2
3
Li
t
h l
l
i
t d 3. Limestone, gray, shaly, laminated ....... ________
2
Li
t
d
k
fi
i
d
d , g
y,
y,
___________________ _______________________
2. Limestone, dark gray, fine-g:rained, dense . ____ . _____ . _______________ : _____ . 1
Li
t
ft b ff
d l
iti
E
d
1
3 to
8 to 2. Limestone, dark gray, fine-g:rained, dense . ___
1
Limestone
soft buff
dolomitic
Exposed 1. Limestone, soft, buff, dolomitic. Exposed ____________________________________
1
3 1. Limestone, soft, buff, dolomitic. Exposed Additional exposures in which the Verdi member of the St-
Louis appears prominently are described by Bain (1) in a Additional exposures in which the Verdi member of the St- Additional exposures in which the Verdi member of the St-
Louis appears prominently are described by Bain (1) in a
quarry located in the northeast quarter of section 12, T. 74 N.,
R. 2S Iowa Geol. Survey, vol. IV, p. 278; 1894.
21 Idem, p. 273. Section 7Wnety yards east of the precedvno section. Section 7Wnety yards east of the precedvno section. 4. Drift. LOWER ST. LOUIS
3
Li
t 4. Drift. LOWER ST. LOUIS
3
Li LOWER ST. LOUIS
3
Li
t 3. Limestone, brownish, soft, dolomitic, a thin·bedded chipstone;
with occasional chert nodules and II. few poorly preserved
fossils ......... _ ................ _ .... _ ........................................ _ ........ __ ........ _. 12
2
Li
t
b
i h
d l
iti
i
b
b t thi 2. Limestone, brownish, dolomitic; massive above, but thinner
bedded and rotted below
4 1. Limestone, shaly and arenaceous, bluish to buff; massive in
lower part. Exposed ..................... _ .... _ ................ _......................... 5 About one hundred yards east of this point another bluff on
this branch shows Lower St. Louis in contact with the Upper. Twenty and one-half feet of dolomitic limestone, which is poor-
ly exposed in its upper part, is succeeded by six feet of massive
basal Verdi sandstone. This is overlain by two and one-half
feet of shaly sandstone which is succeeded in turn by three feet
of gray limestone. Another interesting section appears one-fourth mile farther
east in the north bank of the branch a short distance north of
the railroad and about one ana one-fourth miles west of Ollie. 276 28 Iowa Geol. Survey, vol. IV, p. 273.
29 Idem, p. 333 if.
30 Idem, p . 326. MISSISSIPPIAN STRATA OF IOWA At the time of the writer's visit bed 1 was not ex-
posed. Bed 2 is partly concealed but it resembles the Lower St. Louis limestone. Bain28 says further: "About two and one-half miles west of Connor's quarry (Tp. 75 N., R. 12 W., sec. 18, Se.1,4 Se.1,4), the Augusta limestone,
having its usual characteristics, rises above the water four feet. Both above and below this point the St. Louis limestone is well
developed. "
. Mahaska Coun.ty.-According to Bain
2P the Verdi member of
the St. Louis and the Pella beds a~e the only Mississippiall
formations exposed in Mahaska county. They outcrop at ip.ter-
vals alon'g the valleys' of North Skunk, South Skunk and De:;;
Moines rivers, which flow in a southeasteriy direction across the
county in the northeastern, middle and southwestern parts reo
spectively. Both the Verdi and the Pella members were mapper! by Bain as St. Louis without differentiation. The Verdi in this
area contains a large proportion of sandstone. Mahaska Coun.ty.-According to Bain
2P the Verdi member of
the St. Louis and the Pella beds a~e the only Mississippiall
formations exposed in Mahaska county. They outcrop at ip.ter-
vals alon'g the valleys' of North Skunk, South Skunk and De:;;
Moines rivers, which flow in a southeasteriy direction across the
county in the northeastern, middle and southwestern parts reo
spectively. Both the Verdi and the Pella members were mapper! by Bain as St. Louis without differentiation. The Verdi in this
area contains a large proportion of sandstone. Mahaska Coun.ty.-According to Bain
2P the Verdi member of
the St. Louis and the Pella beds a~e the only Mississippiall
formations exposed in Mahaska county. They outcrop at ip.ter-
vals alon'g the valleys' of North Skunk, South Skunk and De:;;
Moines rivers, which flow in a southeasteriy direction across the
county in the northeastern, middle and southwestern parts reo
spectively. Both the Verdi and the Pella members were mapper! by Bain as St. Louis without differentiation. The Verdi in this
area contains a large proportion of sandstone. At Roberts mill, on North Skunk river, (T. 76 N., R. 14 W.,
sec. 4, Nw.1,4 Ne.1,4) Bain30 found twelve feet of poorly exposed
interbedded sandstone and limestone of Verdi age. He also re-
ports six feet of interbedded Verdi limestone and sandstone as
heing exposed at McBride's mill in the southwest quarter of
section 15 of the ~'ame township. MISSISSIPPIAN STRATA OF IOWA 12 W.; (2) in the bank of Cedar creek south of Sigourney
(T. 75 N., R. 12 V.,T., sec. 10, Se.1,4 Sw.1,4); (3) in a railway cut
north of Hedrick and near Showman station; and (4) in the
Atwood quarry (T. 75 N., R. 13 VV., sec. 8, Ne.1,4) . R. 12 W.; (2) in the bank of Cedar creek south of Sigourney
(T. 75 N., R. 12 V.,T., sec. 10, Se.1,4 Sw.1,4); (3) in a railway cut
north of Hedrick and near Showman station; and (4) in the
Atwood quarry (T. 75 N., R. 13 VV., sec. 8, Ne.1,4) . The best evidence at hand supports the view that the Lower ·
St. Louis limestone rests upon shaly beds of Keokuk age in this
part of the state although the writer has not observed any di-
rect contacts. In the "granite" quarry, which is located in the southeast
quarter of section 10, Jackson township, typical Keokuk lime-
stone is overlain by cherty dolomitic shale ten feet in thickness. The fauna of this shaly member jndicates that it also js of
Keokuk age, although Bain~6 referred it to the St. Louis. The
following beds of Verdi limestone are exposed three hundred
yards south of this quarry. Section of Verdi lilmestone near the" grawite"
quan·y. FEET
INCHES
5. Drift ___________________________________________________ . ________________________ .. ________________________
1
UPPER S'l'. LOUIS
4. Sandstone, fine-grained, gray, massive _______________________ .__________________
3
3. Limestone, gray, compact, in single layer ___________ .______________ __________
6
2. Limestone, gray, fine-grained, finely brecciated _________________________
10
1. Limestone, gray, compact. Exposed ______________________________________________
7 Barometric measurements indicate that bed 1 of this section
lies about twenty-two feet above the top of the highest member
of the Keokuk in the" granite" quarry. It is believed that this
interval is occupied by the Lower St. Louis limestone. Bain21 reports the occurrence of St. Louis limestone in con- VERDI IN MAHASKA COUNTY 277 tact with the Augusta limestone (presumably Keokuk) in the
Connor quarry, in the southeast quarter of section 15, Sigour-
ney township. His section is given below: Section in the Connor q~w,rry (After B wiIn). Section in the Connor q~w,rry (After B wiIn). 2. Limestone, yellow, soft, magnesian; apparently arenaceous in
part. Exposed ......................................... _ .......... _............................. 10
1. Limestone, coarse, sub crystalline. Exposed at water's edge.... 4 Bed 2 was referred by Bain to the St. Louis and bed 1 to the
Augusta. 32 Iowa Geol. Survey, vol. XX, pp. 237·270; 1910. . Section of Verdi beds on, TlIIUri>der uree1c.
FEET
INCHES
5. Drift ......................................................................................................
3
4.
Shale, marly; with thin irregular layers of fine·gro.i.ned gray
limestone. Exposed ............................................................................ 4
3.
Limestone, gray; with included rounded pebbles and grains of
compact gray limestone and dark flint .......................................... 1
6
2.
Shale, bluish, 31rgillaceous, weathering buff ................................ 4
6
1. Sandstone, yellowish, malSsive; with thin inte.Tbedded layers of
compact gray limestone which weather in relief ........................ 27
6
•
P
hi k
Coun~y .-The
l
i
l
hi h
i 31 Iowa Geol. Survey, vol. IV, p. 330.
32 Iowa Geol
Survey
vol
XX
pp
237 MISSISSIPPIAN STRATA OF IOWA These beds are overlain by
fossiliferous marls and limel:':tnJlPS of Pella age. The Verdi beds as shown in the valley of Des Moines river in
the southwest quarter of section 14, T. 75 N'1 R 14 W"' 1 have an MISSISSIPPIAN STRATA OF IOWA. 278 exposed thickness of thirty-five feet and consist of soft yellow
cross-bedded sandstones which are capped locally by limestone. An exposure showing the Verdi limestone and sandstone over-
lain by the Pella beds appears in the valley of Spring creek and
in the Des Moines river bluff nearby in the northwest quarter
of section 4, T. 75 N., R. 15 W. Oth
i t
ti
f th
V
di
l
D
M i exposed thickness of thirty-five feet and consist of soft yellow
cross-bedded sandstones which are capped locally by limestone. An exposure showing the Verdi limestone and sandstone over-
lain by the Pella beds appears in the valley of Spring creek and
in the Des Moines river bluff nearby in the northwest quarter
of section 4, T. 75 N., R. 15 W. Oth
i t
ti
f th
V
di
l
D
M i Other interesting exposures of the Verdi along Des Moines
river are described by Bain31 as being present at and above
Bellefountaine in the western part of Scott township. In sec-
tion 18 he found eight feet of white calcareous sandstone over-
lain by twelve feet of fine-grained bluish sandstone. Southward,
in section 19, fifteen feet of limestone with irregular, cross-
bedded sandstone layers of Verdi age is overlain by more than
one hundred feet of Des Moines sandstones and shales. M
i
C
Th
V
di b d
th
l
t
b
f Marion County.-The Verdi beds are the lowest member of
the St. Louis exposed in ,Marion county. So far as the writer is
aware outcrops of these beds are confined to the valleys of
South Skunk river and its tributary, Thunder creek, in the
northeastern part of the county. Th
f ll
i
i
i
i
l
f
h
Th
d
k The following section is typieal of the Thunder creek ex-
posures. It is located in the east bluff of an old meander in the
creek which is now abandoned as a result of an artificial cut-off
in the northeast quarter of section 26, T. 77 N., R. 18 W . . Section of Verdi beds on, TlIIU'ri>der uree1c. . Section of Verdi beds on, TlIIU'ri>der uree1c. . Section of Verdi beds on, TlIIU'ri>der uree1c. FEET
INCHES
5. Drift ...................................................................................................... 3
4. Shale, marly; with thin irregular layers of fine·gro.i.ned gray
limestone. Exposed ............................................................................ 4
3. Limestone, gray; with included rounded pebbles and grains of
compact gray limestone and dark flint .......................................... 1
6
2. Shale, bluish, 31rgillaceous, weathering buff ................................ 4
6
1. Sandstone, yellowish, malSsive; with thin inte.Tbedded layers of
compact gray limestone which weather in relief ........................ 27
6
•
P
hi k
Coun~y .-The
l
i
l
hi h
i Poweshiek Coun~y .-The geological map which accompanies
Stookey's32 report on the geology of Poweshiek county shows an
area of St. Louis linlestone in the southeastern part of the coun-
ty. Inasmuch as no descriptions of outcrops in this area an~
given it is not known whether this represents the true St. Louis
or the P ella since both 'were mapped as St. Louis in the reports
issued at that time. ST. LOUIS IN MARSHALL COUNTY 379 Descriptions are given of exposures of both Pella and Verdi
limestones in Sugar Creek township in the southwestern part of
the county. S.tookey's statements regarding the Verdi are as
follows: "In the northwest quarter of the southwest quarter of section
36, Sugar Creek township, in the east bank of the river near the
Stil,well bridge, eight feet of rather heavily bedded, compact
limestone is exposed. It represents the middle phase of the
Saint Louis stage, known from the typical exposures at Verdi
in Washington county, as the Verdi beds. No fossils were no-
ticed. Above the limestone exposure the drift is intermingled
with fragments of limestone, indicating the extension of these
beds upwards. Elsewhere, as in Washington county, the Verdi
beds are characteristically brecciated, and in Keokuk county
they alternate with beds of sandstone. The phase represented
here is the compact cherty form of the limestone which to the
southeast is found associated with sandstone." The stratigraphic relations of the St. Louis in this county are
not entirely clear, owing apparently to the lack of outcrops
showing this formation in contact with lmderlying deposits. It
is possible that it rests upon the Kinderhook locally as indicated
by Stookey's geological map of the county. However, Norton33
identifies strata below the St. Louis as Osage in his records of
deep wells at Grinnell. Marshall County.-With the exceptio~ of one small ~xposure
in Bangor township, provisionally referred to the St. 33 Iowa Geo!. Survey. va!. XXI. p. 580 II.; 1912.
84 Iowa Grol. Survey. yol. VII. P. 227. . Section of Verdi beds on, TlIIU'ri>der uree1c. Louis by
Beyer,s4 the bed rock over Marshall county is of Des Moines
and Kinderhook age. Beyer's description of the doubtful beds
follows : "In Bangor township in the SW.l,4 SW .~ of sec. 16, a heav-
ily bedded, close-textured limestone is quarried in the bottom of
Honey creek. The rock is of a dark, ash-gray color and con-
tains some small, cherty concretions. Iron pyrites occur in
bands and sheets in certain layers. The rock breaks with f'tn
uneven or hackley fracture, and some blocks give a metaWc
chink when struck 'with a hammer, No fossils conld be found. Lithologically, these beds have a very close resemblance to the
lithographic facies of the Saint Louis limestone as exhibited
at the quarries north of Ames on the Skunk river, and at Web- MISSISSIPPIAN STRATA OF IOWA 280 ster Cit:y: on the Boone river. The area is mapped as Kinder-
hook, but probably should be referred to the Saint Louis. Coal
Measures overlie these beds at this point." Story Cottnty.-The highest consolidated rocks in Story
county are everywhere of Des Moines age except for an irregu-
lar inlier in the vicinity of .L\.roes, in the western part. Thjs
owes its development to a local doming of the rocks and subse-
quent erosion. In the report on the Geology of Story county, Beyer35 says: "The chief outcrops occur along the Skunk and its immediate
tributaries between Ames and Soper's mill, and along Onion
creek, in Franklin township. The beds exposed consist, in the
J;llain, of impure limestone, but arenaceous layers and calcar-
eous shales are usually also present." One of the most typical exposures of the St. Louis in this
area is in the southwest quarter of section 25, Franklin town-
shIp. Beyer's description of this follows : Seotion of St. L~ li?nestone on S7cwnk river (After Beyer) . FEET
5. Drift ............................. _ .......... _ ............ _ .............. _ ...... _ .. _ .. "_."._" .. '
5-10
4. Limestone, earthy, yellow; very much disintegrated and rubbly;
bedding planes almost eliminated ............... _ .... _............................. 4
3. Limestone, fossiliferous ............... _ .... _ .......................... _ .......... _..... 1
2. Limestone, similar to 4; bedding planes a.pparent, but showing
tendency to become marly and assume a. fissile structure in
places ........................... _ .... _ ........................................ _ .... _................. 3
1. 35 Iowa Gool. Survey. vol. IX. pp. 155·245:' 1899. Seotion of St. L~ li?nestone on S7cwnk river (After Beyer) . 6.
Limestone, brownish, dolomitic, impure .
5 Seotion on' Skunk rwer art Soper's mill (After Beyer) . Section of St. Louis lim&tone near the mO'Uth of Onion creek.
FF.Wl'
6.
Limestone, brownish, dolomitic, impure ... _ ...................... _...........
6
5.
Limestone, brownish, heavy bedded; formiIlJJg a pmjecting ledge
llh
4.
Lim~to.ne, shaly, containing Productus ovatus and Fenestella
mult1.-Sptnosa
.................................................................•............... _.....
1
3. Sandstone, yellowish, buff to gray buff; close textured, and
bedding planes not appa.rent; the upper 15 inch layer more
indurated than the lower part; nonfossiliferous ......................
7
2. Sandstone, bluish gray to yellowish gray; irregularly bedded;
containing Modiomorpha sp. ............................................................
4
1. Sandstone intermixed with shale, thinly and evenly bedded;
exposed ......................................... _ ............... _.......................................
2 Section of St. Louis lim&tone near the mO'Uth of Onion creek. . Section of Verdi beds on, TlIIU'ri>der uree1c. Limestone, buff to gray·buff when unweathered and massive;
layers from ten to twenty inches in thickness; compact, litho·
graphic in texture, fracture conchoidal to uneven; and earthy
when weathered (exposed) ... _ ................ _ ................ _ ........ _ .... _....... 6 He reports that a fenestelloid bryozoan and a syringoporjd
coral occur in the upper half of the exposure. From the fossil-
iferous bed he jdentifie'd a cyathophylloid coral and several
brachiopods. . Additional exposures of the St. Louis are to be found in the
banks of Skunk river at Hannom's mill in the southwest quarter
of section 23, Franklin township. The following sect jon of an
escarpment in the south bank was described by Beyer: 35 Iowa Gool. Survey. vol. IX. pp. 155·245:' 1899. ST. LOUIS IN STORY COUNTY 281 Section on "Skunk river at! H=m's mill (After B eyer) . Section on "Skunk river at! H=m's mill (After B eyer) . 6. SQil anld bowldery wash ......... _ .... _ .... _ .... _ .................................... _. 5. Limestone, residual and copcr.etionary · ... _ .... _ .............................. . 4. Limestone, arenaceous, yellowish gr·ay to blue· gray,
thin~y·
bedded and much fractured; in places argillaceous, while in
others tends towards the massive; and nssility is apparently
a function of weathering; small cherty concretions pres'ent ... _. 3. Sanillstone, grayish blue, friable; shaly below ........................... . 2. Limestone, impure, grayish buff; uneven to earthy fracture;
compact and heavy·bedded ............... _ ................ _. ____ ......... _ ............. . 1. Limestone, gr,ay·buff, compact, almost lithographic in char·
FEET
3
lh
6
2
4
acter ............... _ .................................................................. _ .... _........... 5 Section on "Skunk river at! H=m's mill (After B eyer) . 6. SQil anld bowldery wash ......... _ . 5
Li
id
l
d 5. Limestone, residual and copcr.etionary · ... _ .... 4
Li
ll
i h 1. Limestone, gr,ay·buff, compact, almost lithographic in char·
acter ............... _ .................................................................. _ .... _........... 5 The fossiliferous zone of the preceding section occurs in bed
1 at this locality and is at an elevation nearly twenty-five feet
lower. The latter relationship probably is due to the arch which
exists in the Ames area. Beyer states that north of Hannom's mill the St. Louis is
concealed by Pleistocene depos,its as far as Soper's mill, in the
southeast quarter of section 6, Milford township, where he
found the following section: Seotion on' Skunk rwer art Soper's mill (After Beyer) . 4. Drift, pale yellow, bluish below, unoxidized amd UILlooched ..... . 3. Limestone, rubbly, with occasional heavy ledges ....................... . 2. Limestone, cherty, concretionary, cavernous;
some of the
larger caverns coated with calcite crystals, which consist of
complicated combinations of the scalenohedron and rhombo·
hedron; also smaller quartz·decor.ated caverns ........................... . 1. Limestone, gray· buff, compact; heavy, but irregularly bedded;
FEET
10
10
5
some of the layers two· feet in thickness .................................... 10 No fossils were found in these exposures but the strata were
regarded as representing the St. Louis. No fossils were found in these exposures but the strata were
regarded as representing the St. Louis. The following beds are exposed near the mouth of Onion
creek. The section is revised from Beyer's by the writer. Section of St. Louis lim&tone near the mO'Uth of Onion creek. FF.Wl'
6. Limestone, brownish, dolomitic, impure ... _ ...................... _........... 6
5. Limestone, brownish, heavy bedded; formiIlJJg a pmjecting ledge
llh
4. Lim~to.ne, shaly, containing Productus ovatus and Fenestella
mult1.-Sptnosa
.................................................................•............... _..... 1
3. Sandstone, yellowish, buff to gray buff; close textured, and
bedding planes not appa.rent; the upper 15 inch layer more
indurated than the lower part; nonfossiliferous ...................... 7
2. Sandstone, bluish gray to yellowish gray; irregularly bedded;
containing Modiomorpha sp. ............................................................ 4
1. Sandstone intermixed with shale, thinly and evenly bedded;
exposed ......................................... _ ............... _....................................... 2 A similar exposure showing the same layers appears a shor.t
distance farther up the creek. MISSISSIPPIAN STRATA OF IOWA 282 W ebste'r County.-The P ella beds were included with the St. 36 Wilder, F. A. , Iowa Geol. Survey, vol. XII, pp. 63·235; 1902.
37 Idem, p. 78.
See also vol. XXVIII, m ap in pocket and pp. 139·147, 163, 164; 1918.
38 Idem, p. 79. 37 Idem, p. 78.
See also vol. XXVIII, m ap in pocket and pp. 139·147, 163, 164; 1918.
38 Idem, p. 79. 36 Wilder, F. A. , Iowa Geol. Survey, vol. XII, pp. 63·235; 1902.
37 Id
78
S
l
l
XXVIII
i
k t
d
139 14 Section on "Skunk river at! H=m's mill (After B eyer) . Louis in the geological report on Webster county,36 therefore
the areal distribution of the St. Louis as now delimited cannot
be definitely determined without additional field work. The
areas mapped as St. Louis by Wilder are small isolated patches
chiefly along Des Moines river and its tributaries and in the
valleys of Soldier creek and Lizard creek, in the central and
north-central parts of the county. A small inlier in the east-
central part also is indicated on the map. Elsewhere the coun-
try rock is of Pennsylvanian and Permian age. The more important exposures in which St. Louis beds appear
are located in the abandoned Miller quarry on Soldier creek;
in the east bluff of Des Moines river in the southeast quarter of
section 7 and across section 18, Cooper township; and along
Lizard creek west of Fort Dodge. All of these sections have
been described by Wilder37 but they were revisited and exam-
ined by the writer. The Miller quarry is located just below the stone bridge over
Soldier creek in Fort Dodge. The revised section follows: Seotion in the Miller quarry. FEET
lNCHES
7. Drift ...................................................................................................... 1
UPPER ST. LOUIS
6. Limestone, lenticular, gray, compact, brecciated, fossils scarce
and poorly preserved .................................................................... 0 to 1
6
5. Sandstone, :fine· grained ................................................................ 3 to 6
4. Sandstone, fine, calcareous, in a sblgle layer ................................ 1
6
L OWER ST. L OUIS
3. Limestone, massive, dolomitic in lower part; less disturbed
than the beds betl.ow ......... _ .... _ .... _ ................ _ .... _ .. _....................... 3
6
2. Ooncealed ............................................. _ ............... " .................. _._ .. _...... 7
6
1. Limestone, yellowish, tough, d'olomitic, in mashed undulating
layers. Exposed in bed and bank of creek near by.................. 4 1. Limestone, yellowish, tough, d'olomitic, in mashed undulating
layers. Exposed in bed and bank of creek near by.................. 4 The beds are arched up in the quarry. The contact of beds
3 and 4 is irregular, indicating a dis conformity. The exposure
gives evidence of small cavities in the limestone which are filled
with sandstone. 38 Wilder38 states that" a little above Miller's quarry, on Soldier
creek, the St. Louis limestone gives place to Coal Measure
shales. One-half mile farther up Soldier creek in Cooper town- . ST. 39 Idem. p. 82. . Section on Des Moines river in section 7, Cooper township.
UPPER ST. LOUIS
FEET
INCHES
4.
Sandstone, fme'grained, soft, incoherent, marly above .............. 10
3.
Sandstone, fme·grained) gray, calcareous, in one heavy layer....
1
2
LOWER ST. LOUIS
2. Limestone, gray weathering buff, massive, zone o·f
worm
burro.ws ill lower and middle parts. A thin' flint layer near the
top ..........•.......... _ ..... ______ ._.______________________________________________________________________
8
1.
Concealed to level of water in the river ___ . _________ . __ . ___ ._________________
3
(j . Section on Des Moines river in section 7, Cooper township. Section on "Skunk river at! H=m's mill (After B eyer) . LQUIS NEAR FORT DODGE 283 ship, section 19, NE.~~, the limestone again comes to the surface
and appears for 200 feet in the creek bed". Still farther up Soldier creek in the southwest quarter of sec-
tion 17, the St. Louis is overlain by gypsum beds which are be-
lieved to be of Permian age . . At one point seven feet of massive gypsum overlain by thirty
feet of red sandy shale appears in the bank of the creek. The
gypsum comes down to the water's edge. "One hundred yards
farther down stream, at the water level and for three feet aqove
it, the St. Louis limestoIl(~ is exposed" . Within another hun-
dred yards the limestone gives way to Coal Measure shale .. The east bluff of Des Moines riv8r in section 7 Of Cooper
township shows the following beds: . Section on Des Moines river in section 7, Cooper township. UPPER ST. LOUIS
FEET
INCHES
4. Sandstone, fme'grained, soft, incoherent, marly above .............. 10
3. Sandstone, fme·grained) gray, calcareous, in one heavy layer.... 1
2
LOWER ST. LOUIS
2. Limestone, gray weathering buff, massive, zone o·f
worm
burro.ws ill lower and middle parts. A thin' flint layer near the
top ..........•.......... _ ..... ______ ._.______________________________________________________________________
8
1. Concealed to level of water in the river ___ . _________ . __ . ___ ._________________
3
(j A few yards down stream a massive layer of finely brecciated
compact gray limestone three feet thick comes above the level
of bed 4. Drift overlies the limestone. Farther up the river,
around the bend Wilder found Coal Measure shales resting up-
on ten feet of St. Louis limestone. Several other exposures or
limestone along the river between this point and ' the north
boundary of the county are described by the same writer.39 He
says: "The striking peculiarity of the limestone in the north-
ern part of the county is the great amount of drusy quartz and
flint that it . carries, most of it in the upper brecciated layers. Frequently the masses weigh 200 pounds. Calcite is also
abundant. ' , Small exposures of the St. Louis along Des Moines river
below Fort Dodge are described byWildet from sections 5, 8
and 16 of Pleasant Valley township. Elsewhere the Coal Meas-
ures appear along the valley. The Lizard creek sections are most important from the stand- 39 Idem. p. 82. Section on "Skunk river at! H=m's mill (After B eyer) . MISSISSIPPIAN STRATA OF IOWA 284 point of Pella stratigraphy but the St. Louis beds outcrop at a
few points at the base of the exposures. point of Pella stratigraphy but the St. Louis beds outcrop at a
few points at the base of the exposures. In a bluff section near the center of section 24, Douglas town-
ship, approximately thirteen feet of limestone, sandstone and
shale of this age is overlain by more than fifty feet of strata
referred to the Pella. A description of the individual beds is
given below: Section on Ikard creek. PELLA
FEET
9. Marl. Like bed below but free from red areas _________________________
6
8.. Gray marl blotched with red. Bears Sp1;rifer pellaemsis, Pug-
noides ottwmU}{t, Composita trinuclea and other fossils ____________ 34
UPPER ST. LOUIS
7. Limestone, drab, compact, shaly and laminated ________ . ___ .______________
3
6. Shale, drab, argillaceous __________________________________________________________________ 0
3
5. Sandstone .____________________________________________________________________________________________
2
LOWER ST. LOUIS
4. Limestone GiS in bed 2 ____________________________________________________________________
0
to 2/3
3. Shaly partinlg -----____________________________________________ 0_______________________________
lh
2. Limestone, gray, dolomitic, tough; undulating owing to mash-
ing. Bearing impressions of Sigillaria _______________________________________
2/ 3
1. Sandstone, fine-grained, gray, thin-bedded. Exposed
0 __ ___ ______ . ___
3 40 Iowa Acad. Sci., vol. XXV. ll. 602; 1918. Section sfYUthwest of the crea1nery at R1!tland. Section sfYUthwest of the crea1nery at R1!tland. FEET
4. Drift ... _ ...................... _ .... _ .......................................................... _....... 2
ST. LoUIS
3. Limestone, brecciated, dense, gray, imperfectly dolomitized;
1000ver surface irregular and undulating ........................... _........... 3
2. Limestone, dense, gray, tough, in the form of one undulating
layer which fills irregular depressions in the limestone beneath
lh to 1
KINDERHOOK
1. Limestone, light gray; stratification very imperfect; finely
oolitic except in middle part where there is a thin seam of
coarse oolite ......................................................... _ .......... _................. 2
to 3lh 000ve su
ace
egu a
a d u du at
g ..........................._........... 3
2. Limestone, dense, gray, tough, in the form of one undulating
layer which fills irregular depressions in the limestone beneath
lh to 1
KINDERHOOK 1. Limestone, light gray; stratification very imperfect; finely
oolitic except in middle part where there is a thin seam of
coarse oolite ......................................................... _ .......... _................. 2
to 3lh The contact of the Kinderhook and St. Louis is again shown
at the point where this small creek joins the west fork of Des
Moines river, just above the dam at the old mill site. At this
point about four feet of the Kinderhook oolite is exposed
above the bed of the creek. This is overlain by three feet of
gray tough St. Louis dolomite which weathers yellowish. At
one point in the exposure this dolomite grades laterally, in part
at least, into unaltered gray brecciated limestone. This contact is again shown in the river bank about seventy-
five yards below the dam. Three feet of Kinderhook oolite is
succeeded by two feet of yellowish St. Louis limestone in undu-
lating layers, and this again by four feet of dense gray thin-
bedded unaltered' limestone of the same formation, which locally
is mashed into mounds of breccia. Where the St. Louis is disturbed the Kinderhook also shows
considerable fracturing and slight brecciation. Several other expo surfs between this point and the bridge
show a similar relationship. The upper light gray limestone is
five and one-half feet thick at one point. Where it is only
slightly brecciated it tends to assume a ma~sive appearance and
in places is almost lithographic in fineness. In the abandoned quarry and in the bank of a creek twenty
yards west of the creamery at Rutland eight feet of St. Louis
limestone is exposed. Section on Ikard creek. Section on Ikard creek. PELLA
FEET
9. Marl. Like bed below but free from red areas _________________________
6
8.. Gray marl blotched with red. Bears Sp1;rifer pellaemsis, Pug-
noides ottwmU}{t, Composita trinuclea and other fossils ____________ 34
UPPER ST. LOUIS
7. Limestone, drab, compact, shaly and laminated ________ . ___ .______________
3
6. Shale, drab, argillaceous __________________________________________________________________ 0
3
5. Sandstone .____________________________________________________________________________________________
2
LOWER ST. LOUIS
4. Limestone GiS in bed 2 ____________________________________________________________________
0
to 2/3
3. Shaly partinlg -----____________________________________________ 0_______________________________
lh
2. Limestone, gray, dolomitic, tough; undulating owing to mash-
ing. Bearing impressions of Sigillaria _______________________________________
2/ 3
1. Sandstone, fine-grained, gray, thin-bedded. Exposed
0 __ ___ ______ . ___
3 3. Shaly partinlg
_
2
Limestone
gra
d Lees and Thomas40 found thirty feet of St. Louis limestone
exposed in the bluff of South Lizard creek jusf above the junc-
tion of the two branches of the Lizard, one mile west of the
above section. The beds dip eastward, that is, downstream. One hundred feet upstream ten feet of green sandy marl grading
up into gray sandstone underlies the limestone. Below a gap of
six feet they found a two foot bed of limestone. Humboldt Cownty.-So far as the writer is aware only the
Lower St. Louis is represented in these northernmost exposures
of the formation in Iowa. It apparently rests everywhere on
the Kinderhook formation, all of the pre-St. Louis Mississippian
formations except the basal deposits having wedged out to the
south of this area. The exposures are all in the form of small
isolated patches along Des Moines river and its east and west
forks. An excellent opportunity of observing the contact of the St. Louis and Kinderhook limestones is afforded in the banks of a
small creek a short distance southwest of the creamery at Rut-
land, in section 29, Rutland township. 40 Iowa Acad. Sci., vol. XXV. ll. 602; 1918. ST. LOUIS BEDS NEAR RUTLAND 285 41 Iowa Gwl. Survey. vol. IX. pp. 131, 132; 1898. Section sfYUthwest of the crea1nery at R1!tland. The lower two feet consists of disturbed,
hummocky limestone but the upper SL",{ feet is made up of
mashed layers of yellowish dolomitic limestone with seams and
patches of gray dense unaltered limestone. A small isolated exposure occurs along the West Fork of Des
Moines river near the center of section 23, Avery township. Here the St. Louis is represented by undulating, slightly brec-
ciated layers of gray dense limestone. A moundlike mass of MISSISSIPPIAN STRATA OF IOWA 286 structureless brownish dolomite which occupies the middle part
of the outcrop contains small remnants of gray limestone. Macbride shows on his geological map of Humboldt county a
small area of St. Louis in the valley of the Des Moines in the
northern part of section 17, Avery township. The limestone in
the vicinity of Gilmore City in western Humboldt and eastern
Pocahontas counties which was referred to the St. Louis by
:Macbride41 is believed to be of Kinderhook age. A small exposure of the St. Louis appears south of the town
of Humboldt in the east bank of the West Fork of Des Moines
river. In an abandoned quarry back of the slaughter house,
south of the center of section 12, Corinth township, two feet of
yellowish dolomitic limestone is succeeded above by two' feet of
gray to drab calcareous shale and this in turn by two feet of
dimse gray slightly brecciated limestone. A short distance far-
ther downstream massive yellowish dolomitic St. Louis lime~
stone rises ten feet above the water's edge. . . ',. The most complete section of the St. Louis in the county ap-
pears at the ' mill in the east bluff of the East Fo~i{ of Des
Moines ri ver at Dakota City. The section is as follows:
4;~ Section at Dakota City. FEET
5. Drift ...................................................................................................... 1
4. Limestone, soft, brownish, dolomitic; massive and structure·
less and showing evidences of brecciation .................................. 8
3. Limestone, brownish, soft, dolomitic; in layers 2. inches to 1
foot in thickness ... _ .... _ ................ _ .... _............................................. 314
2. Thin interbedded layers of fine·grained gray sandstone and
limesto·ne ........................... __ ................................................................. 2
1. Limestone, dolomitic, dense; gray when fresh but wea.thering
yellowish or bmWD·ish;
Exposed above level of water ............ 2 No fossils were noted in any of the beds. h
fl
i
h
i
h No fossils were noted in any of the beds. Seotion in and near the Welch qua7·ry. 4. Limestone, gray and medium·grained .................................. ~.. ....... ·8
3
S
d t
ft
i
h
t
fi
i
d
d
b
th
i 4. Limestone, gray and medium·grained .......... 3
S
d t
ft
i
h
t
fi
i
d The following section is modified after Macbride's descrip-
tion of an outcrop of St. Louis which appears in the east bank
of Des Moines river, near the south line of the county. Seotion in east bank of Des Moines river. Seotion in east bank of Des Moines river. 8. Limestone, soft, buff, dolomitic ..................................................... . 7. Limestone, yello.wish, dolomitic, brecciated ................................. . 6. Shale seam ,yith pockets of clay ............................................... . 5. Limestone, compact, gray ......... _ ................ _ .... _ .......... _ .. : ............. . 4. Limestone, gmy, dolomitic, weathering yellowish ......... _ ............ . 3. LimestJo<ne, gray, fi:ne-grained ............................................. _ .......... . 2. Concealed ................................. _ .................................. _ ...................... . 1. Limestone, gray, weatheriug yellowish, in bed of river ....... . FEET
6 to 10
5 to
7
4
2
2
4 8. Limestone, soft, buff, dolomitic
7
Li
ll
i h
d l
i i 7. Limestone, yello.wish, dolomitic, brecciated
6
Sh l
ith
k t
f
l 6. Shale seam ,yith pockets of clay
5
Li
t
t 5. Limestone, compact, gray ........ 4
Li
d l
i i 1. Limestone, gray, weatheriug yellowish, in bed of river ....... . The quarry section in the city of Humboldt which Macbride
describes as showing the St. Louis overlying the Kinderhook is
concealed at present. But mounds of gray St. Louis limestone
are exposed along the streets in the northwest part of the town. A particularly good outcrop may be studied three blocks north
of Main street and one block west of the high school. 42 Trans. St. Louis Acad. Sci., vol. I, p. 406 ;1859.
43 Iowa Geol Survey, vol. IV, p. 282; 1894. 42 Trans. St. Louis Acad. Sci., vol. I, p. 406 ;1859.
43 I
G
l S
l
IV
282
1894 44 U. S. Geol. Survey Bull. 173, pp. 166 and 180. Section sfYUthwest of the crea1nery at R1!tland. A
h
fl
i
h
i
h
h
iddl A very sharp flexure is shown in the strata near the middle
of the exposure. The beds are bent down three feet in the
space of six feet although they are essentially horizontal on
each side. The axis of the flexure trends approximately north-
west-southeast. Similar beds are exposed in the Welch quarry
and in the river bank near by in the west bluff of the same
stream in the southeast quarter of section 31, Grove township. 41 Iowa Gwl. Survey. vol. IX. pp. 131, 132; 1898. STE GENEVIEVE FORMATION 287 Seotion in and near the Welch qua7·ry. FEET
INCHES
4. Limestone, gray and medium·grained .................................. ~.. ....... ·8
3. Sandstone, soft,
incoherent,
fine· grained, drab weathering
yellowish
.............................................................................................. 2
2. Limestone, buff, dolomitic; thin·bedded and arenaceous below,
but more calcareous and massi,e ·above ... _................................. 5
1. Shale, drab when fresh but weathering yellowish, with thin
layers of fine· grained drab sandstone also weathering yellow·
ish. Exposed above water ........................................ :....................... 3
6 42 Trans. St. Louis Acad. Sci., vol. I, p. 406 ;1859.
43 Iowa Geol Survey, vol. IV, p. 282; 1894.
44 U. S. Geol. Survey Bull. 173, pp. 166 and 180. LITHOLOGIC CHARACTER AND TRICKNESS The Pella formation is most typically developed in southeast-
ern Iowa where it normally consists of a thin basal sandstone
followed by a bed of shale about five feet in thickness, and this
again by approximately twenty-five feet of compact thinly bed-
ded limestone. To the northwest the limestones give way to
shale. In Webster county, in north-central Iowa, the formation
is represented almost entirely by shale, which is there about
fifty feet in thickness. NOMENCLATURE The name Ste. Genevieve was given by Shumard42 to a lime-
stone formation typically developed in the Mississippi river
bluffs near Ste. Genevieve, Missouri. This formation is repre-
sented in Iowa py the Pella beds of earlier reports. The Pella
formation, so named by Bain4 3 because of its exposure near the
town of Pella in Marion county, was formerly regarded as the
topmost member of the St. Louis limestone. In the year 1900,
however, Nickles and Bassler44 correlated the Pella beds with
the Ste. Genevieve formation upon the basis of the bryozoan
element of their fauna. The Ste. Genevieve affinities of the MISSISSIPPIAN STRATA OF IOWA 288 fauna were later pointed out by Weller/s and the correlation
was definitely established by Weller and Van Tuyl/6 as a result
of further field and faunal studies. AREAL DISTRIBUTION The formation has a limited areal distribution due in part to
erosion in late Mississippian time prior to the deposition of the
Pennsylvanian beds and in part to post-Pennsylvanian denuda-
tion. The most representative sections are along the tributar··
ies of Des Moines river in Lee, Van Buren, ,Vapello, Mahaska
and Marion counties. These deposits have also been recognized
locally in southeastern Iowa in Henry, Jefferson, Washington,
Keokuk and Poweshiek counties. To the northwest of the last
named county the Pella beds, if present, are concealed by Des
Moines sandstone as far as Webster county where several ex-
posures of the formation appear. On the areal geology map of the state of Iowa the Pella
formation is grouped with the St. Louis limestone and the
Spergen formation under the name of "St. Louis limestone." 46 Proc. Iowa Acad. Sci., voL XXII, p. 241 II.; 1915. 45 Journal of Geology, voL XVII, p. 278; 1909.
46 P
I
A
d
S i
L XXII
241 II
19 45 Journal of Geology, voL XVII, p. 278; 1909.
46 Proc. Iowa Acad. Sci., voL XXII, p. 241 II.; 1915. STRATIGRAPHIC RELATIONS The Pella beds rest disconformably upon the St. lJou~s lime-
stone wherever their contact has been observed in Iowa. In
most of the exposures where the contact is shown the basal
sandstone of the formation succeeds the Verdi limestone mem-
ber but at a few localities it overlies the C:roton, or Lower St. Louis limestone. The formation is overlain disconformably by
either Des Moines sandstone or Pleistocene deposits. PELLA BEDS NEAR CROTON 289 CHANGES AT CLOSE OF STE. GENEVIEVE TIME At the close of Pella time the sea withdrew from the Upper
Mississippi Valley again and this region remained a land area
until the close of the Mississippian period. A great waJ;'ping
began to the north at the time of this emergence and continued
probably to the end of the Mississippian. This resulted in a
tilting of the Mississippian and earlier formations to the south-
west and was accompanied by the development of small north-
west-southeast anticlines and synclines ·and by extensive brec-
ciation of the hard, brittle St. Louis limestone. Consequent upon this uplift erosion proce('ded rapidly during
the remainder of Mississippian time and the tilted beds were
partly truncated, thus giving rise to a series of northwest-
southeast belts of formational outcrops in Iowa, some of which
were later buried by the Coal Measures. hi
h
d il i
f h
b d i
l
d This southwestward tilting of the beds in Iowa was related to
a widespread late Mississippian deformation which involved
also eastern Nebraska, eastern Kansas and Missouri, and out-
lined a great southwestwardly pitching geosyncline which was
later occupied by the early Pennsylvanian sea as it advanced
along a narrow trough from the southwest and gradually
spread to the margin of the basin. Section along creek near Croton. PENNSYLVANIAN
3. Sandstone, yellowish, soft.
PELLA S.ection of Pella beds on Indiwn (yreek. AREAL DESORIPTION BY COUNTIES Lee County.-The Pella formation is exposed at few locali-
ties in this county, although the underlying St. Louis limestone
outcrops over large areas. h
i
i
h
b
k
f
ll
k
i
i The section in the banks of a small creek emptying into Des
Moines river in the lower part of the town of Croton is typical. Section along creek near Croton. PENNSYLVANIAN
FEET
3. Sandstone, yellowish, soft. PELLA
2. Limestone, compact, light gray above but dark gray below;
near the middle is ,a bed of calcareous shale 21h feet thick.... 9
1. Sandstone, yellowish, fine· grained; in some places soft and
shaly in lower part; contact with bed below uneven; bearing
large fucoid·lilre markings on surface of layers .......................... 414
UPPER ST. LOUIS
The limestone member yields the following species: FEET 2. Limestone, compact, light gray above but dark gray below;
near the middle is ,a bed of calcareous shale 21h feet thick.... 9
1
Sandstone
yellowish
fine·grained; in some places soft and 1. Sandstone, yellowish, fine· grained; in some places soft and
shaly in lower part; contact with bed below uneven; bearing
large fucoid·lilre markings on surface of layers .......................... 414
PPER ST. LOUIS 1. Sandstone, yellowish, fine· grained; in some places soft and
shaly in lower part; contact with bed below uneven; bearing
large fucoid·lilre markings on surface of layers .......................... 4
PPER ST
LOUIS The limestone member yields the following species: The limestone member yields the following species: MISSISSIPPIAN STRATA OF IOWA 290 BRACHIOPODA-
PELECYPODA-
Edmondia sp. Schizodus sp. Schizodus sp. Allorisma sp. Productus ovatus Hall
Pugnoides ottumwa (White)
Girtyella indianensis (Girty)
Spirifer pellaensis Weller
Composita trinuclea (Hall) f
TRILOBITA-
Phillipsia f sp. PELECYPODA-
Edmondia sp. S hi
d BRACHIOPODA-
Productus ovatus Hall
Pugnoides ottumwa (White)
Girtyella indianensis (Girty)
Spirifer pellaensis Weller
Composita trinuclea (Hall) f Schizodus sp. Van Buren County.-The most important exposures of the
Pella beds in Van Buren county appear along Des Moines river
and its tributaries, especially on Indian and Reed creeks. The following section was measured in an abandoned quarry
on the south bank of Indian creek (NE.% of N\iV.1,4, sec. 5, T. 67 N., R. 8 VV.). S.ection of Pella beds on Indiwn (yreek. S.ection of Pella beds on Indiwn (yreek. FEET
INCHES
5. Drift, yellowish, sandy ...................... ." ................. :............................. 0-8
PELT,A
4. AREAL DESORIPTION BY COUNTIES Limestone, light gray, dense, breaking with conchoidal frac·
ture; coarser·grained and slightly crinoidal in the upper part;
in rather heavy layers separated by thin prurtings of shaly
limestone;
locally seamed with calcitfiJ
veinlets following
fractures ; some layers exhibiting stylolytic structure ................ 8
6
3. Shale, bluish, argillaceous, bearing many pelecypods in cal·
careous seams near top ____________________________________________ .. ________________________
3
5
2. Limestone, gray, sub crystalline, with discontin.uous seams of
fine·grained sandstone in thin undulating layers; bearing a few
small pelecypods ____ .. ________________ .. ____ .. ______________________ . ____________ .. __ .... ________ . 9
1. Sandstone, fine· grained, rather soft; light gray when fresh but
weathering yellowish; in some places with ' angular chert
fragments in basal part __________________________________________________________________ 0-2
UPPER S 'r. LOUIS 5. Drift, yellowish, sandy
PELT,A 4. Limestone, light gray, dense, breaking with conchoidal frac·
ture; coarser·grained and slightly crinoidal in the upper part;
in rather heavy layers separated by thin prurtings of shaly
limestone;
locally seamed with calcitfiJ
veinlets following
fractures ; some layers exhibiting stylolytic structure ................ 8
6 ;
y
g
y
y
3. Shale, bluish, argillaceous, bearing many pelecypods in cal·
careous seams near top ____________________________________________ .. ________________________
3 2. Limestone, gray, sub crystalline, with discontin.uous seams of
fine·grained sandstone in thin undulating layers; bearing a few
small pelecypods ____ .. ________________ .. ____ .. ______________________ . ____________ .. __ .... ________ . 1. Sandstone, fine· grained, rather soft; light gray when fresh but
weathering yellowish; in some places with ' angular chert
fragments in basal part __________________________________________________________________ 0-2 fragments in basal part __________________________________________________________________ 0 2
UPPER S 'r. LOUIS UPPER S 'r. LOUIS The shale bed (bed 3) and the overlying limestone (bed 4)
contain numerous fossils, as is shown by the following lists: List of fossils from bed 3 of (~bove section. List of fossils from bed 3 of (~bove section. List of fossils from bed 3 of (~bove section. BRACHIOPODA-
Pugnoides ottumwa (White)
PELECYPODA-
. Sphenotus (several species)
Nucula illinoisensis
Leda curta M. and W. ,
MyaJina sp. Schizodus (several species)
Aviculopecten sp. Modiola sp. Allorisma sp. GASTROPODA-
Solenospira sp. CRus'rAcEA-
Leperditia sp. List of fossils f1"01n bed 4 of above 8Iection. BRYOZOA-
Rhombopora ;sp. Composita trinuclea (Hall) ,
PELECYPODA-
All
i BRACHIOPODA-
Pugnoides ottumwa (White)
PELECYPODA-
. Sphenotus (several species)
Nucula illinoisensis
Leda curta M. and W. ,
MyaJina sp. Schizodus (several species)
Aviculopecten sp. BRYOZOA-
Rhombopora ;sp.
BRACHIOPODA-
Productus ovatus Hall
Pugnoides ottumwa (White)
Girtyella indianensis (Girty)
Spirifer peHaensis Weller AREAL DESORIPTION BY COUNTIES Modiola sp. Allorisma sp. GASTROPODA-
Solenospira sp. CRus'rAcEA-
Leperditia sp. BRACHIOPODA-
Pugnoides ottumwa (White)
PELECYPODA-
. Sphenotus (several species)
Nucula illinoisensis
Leda curta M. and W. ,
MyaJina sp. Schizodus (several species)
G
C Aviculopecten sp. p
Modiola sp. All
i Allorisma sp. List of fossils f1"01n bed 4 of above 8Iection. List of fossils f1"01n bed 4 of above 8Iection. sp. vatus Hall
tumwa (White)
ianensis (Girty)
aensis Weller
Composita trinuclea (Hall) ,
PELECYPODA-
Allorisma sp. G.\STIWPODA-
Bellerophon sp. TRILOBITA-
Phlllipsia , up. BRYOZOA-
Rhombopora ;sp. BRACHIOPODA-
Productus ovatus Hall
Pugnoides ottumwa (White)
Girtyella indianensis (Girty)
Spirifer peHaensis Weller FOSSILS FROM PELLA BEDS 291 A remarkable section exhibiting both the Pella and the whole
of the St. Louis appears in the south bluff of Reed creek about
three-fourths of a mile above its mouth (near middle of north
line, sec. 14, T. 68 N., R. 8 W.). The succession, as measured
near the middle of the bluff, is as follows: BRACHIOPODA-
Productus ovatus Hall
Girt yell a indianensis (Girty)
Pugnoides ottumwa (White) Sectwn of Pella beds on R eed creek. Sectwn of
ella beds on
eed c eek. FEET
I NCHES
11. Drift. PELLA
10. Limestone, light gray, compact to subcrystaJline; some layers
lithographic·like and breaking with conchoidal fracture; layers
1 inch to 11)2 feet thick, separated by shaly partings some
of which are highly fossiliferous; exhibiting mnch stylolytic
structure; increasingly shaly in lower part 'll1d gruding down·
wards inte- the beel below; locally brecciaLeel in part .............. 21
6
(I. Shale, bluish, argillaceous to calca,reous, of variable thielmess
owing to mashing' ... _ ........................................ _ ........................... 3 to 6
8. Limestone, light gray, compact, in thin irregular layers with
shaly partings ....................................... _............................................. !)
7. Sandstone, bluish, fine· grained, rather soft, bearin'g rounded
and subangular pebbles, of compact gray limestone .................... 6
6. Limestone, gray, compact in middle but subcrystalline a.bove
and below .............................................................................................. 4
5. Sandstone, bluish, fine·grai·ned, calcareous, massive, bearing
rolled chert fragments ...................................................................... 3
UPPER ST. LoUIS
4. Limestone, buff, magnesian, arenaceous ........................................ 6
3. Limestone, buff, dolomitic., massive ................................................ 2
9
2. Limest'one, buff, dolomitic with small irregular remnants and
blocks of compact gmy limesto;ne; slightly brecciated ............ 9
LOWER ST. LoUIS
1. Limestone, buff, dolomitic, mashed and brecciated, shaly in
lower part .......................... __ ................................... __ ................. __ .... __ .... 28
B d
9
d 10
f thi
ti
hi h
t
b
l t d
ith FEET
I NCHES Sectwn of Pella beds on R eed creek. FEET
I NCHES BRACHIOPODA-
Productus ovatus Hall
Girt yell a indianensis (Girty)
Pugnoides ottumwa (White) 292 MISSISSIPPIAN STRATA OF IOWA Other sections measured nearby in the same bluff showed
considerable variation from that given, owing to differential
erosion of the St. Louis prior to the deposition of the Pella and
to the variable character of the basal beds of the Pella itself. The section presented, however, may be regarded as typicaL In another bluff on the opposite side of Reed creek about two
hundred yards above the location of the preceding section the
Pella beds are seen to rest upon somewhat lower beds of the
Upper St. Louis. At this point, bed 10 of the foregoing section
is represented by eighteen feet of limestone; bed 9 by three and
one-half feet of shale; and beds 5, 6, 7 and 8 collectively by a
continuous bed: of sandstone ranging from twenty-four to thirty-
four feet il}. thickness. The underlying St. Louis limestone is
mashed here for the most part, and towards the top the matrix
of the brecciated limestone is filled with sand grains pr.obably
derived from the overlying formation. .The basal sandstone of
the Pella attains a similar development in the vicinity of Keo-
sauqua, whence the name Keosauqua sandstone as applied by
Gordon.;l7 A very interesting and instructive exposure appears along a
small branch of Des Moines river one and one-half miles north
of Farmington, near the middle of the north line of the north-
east quarter of section 26, T. 68 N., R. 8 W. Near the Yargus
coal' bank about fifteen feet of Pella beds is overlain by Des
Moines sandstone. At the base of the exposure there is shown
throe to four feet of fine-grained Pella limestone. OVf'l'lying this
member is eleven feet of fine-grained thin-bedded shaly sand-
stone also of Pella age. Des Moines sandstone caps the section. At one point in the bluft a shear zone appears in the Pella beds
but does not traverse the Des Moines formation, which shows
'no disturbance whatever. Where this shear zone crosses the
Pella sandstone there are numerous angular blocks of limestone
resembling in every way the limestone which normally comes at
the top of the Pella formation in this region. It is believed that
the shearing took place directly after the deposition of the Pella
and before erosion stripped off the limestone member which
normally comes above the sandstone. FEET
I NCHES 4. Limestone, buff, magnesian, arenaceous
3
Limestone buff
dolomitic
massive 3. Limestone, buff, dolomitic., massive
2
Limest'one
buff
dolomitic with sm 2. Limest one, buff, dolomitic with small irregular remnants and
blocks of compact gmy limesto;ne; slightly brecciated ............ 9 blocks of compact gmy limesto;ne; slightly brecciated ............ 9
LOWER ST. LoUIS
1
Limestone
buff
dolomitic
mashed
and
brecciated
shaly
in 1. Limestone, buff, dolomitic, mashed and brecciated, shaly in
lower part .......................... __ ................................... __ ................. __ .... __ .... 28 1. Limestone, buff, dolomitic, mashed and brecciated, shaly in
lower part .......................... __ ................................... __ ................. __ .... __ .... 28 Beds 9 and 10 of this section, which are to be correlated with
beds 3 and 4 of the preceding Indian creek section, are fossil-
iferous. List of fossils fro'ln bed 9 of above section. BRACHIOPODA-
Pugnoides ottumwa (White)
PEL]<;CYPODA-
Solen.omya ~ iowensis Worthen
Sphenotus (several undescribed
species)
Glossites (species undescribed)
Edmondia (species undescribed)
Nucula , sp. Leda curta M. and W. ,
Piima (species undetermined)
Myalina , sp. Myalina (species undetermined)
Schizodus (several undescribed
species)
Aviculopecten (species undetermined
Allorisma (species undescribed)
CRUSTACEA-
Leperditia (species undetermined) List of fossils fro'ln bed 9 of above section. BRACHIOPODA-
Pugnoides ottumwa (White)
PEL]<;CYPODA-
Solen.omya ~ iowensis Worthen
Sphenotus (several undescribed
species)
Glossites (species undescribed)
Edmondia (species undescribed)
Nucula , sp. Leda curta M. and W. ,
Piima (species undetermined)
Myalina , sp. Myalina (species undetermined)
Schizodus (several undescribed
species)
Aviculopecten (species undetermined)
Allorisma (species undescribed)
CRUSTACEA-
Leperditia (species undetermined)
List of fossils from bed 10 of ab01Je section. BRACHIOPODA-
Productus ovatus Hall
Girt yell a indianensis (Girty)
Pugnoides ottumwa (White)
Spirifer pellaensis Weller
Composita trinuclea (Hall) t
PELECYPODA-
Schizodus sp. List of fossils fro'ln bed 9 of above section BRACHIOPODA-
Pugnoides ottumwa (White)
PEL]<;CYPODA-
Solen.omya ~ iowensis Worthen
Sphenotus (several undescribed
species)
Glossites (species undescribed)
Edmondia (species undescribed)
Nucula , sp. Leda curta M. and W. , Piima (species undetermined)
Myalina , sp. Myalina (species undetermined)
Schizodus (several undescribed
species)
Aviculopecten (species undetermined)
Allorisma (species undescribed)
CRUSTACEA-
Leperditia (species undetermined) List of fossils from bed 10 of ab01Je section. vatus Hall
dianensis (Girty)
ttumwa (White)
Spirifer pellaensis Weller
Composita trinuclea (Hall) t
PELECYPODA-
Schizodus sp. List of fossils from bed 10 of ab01Je section. Spirifer pellaensis Weller
Composita trinuclea (Hall) t
PELECYPODA-
Schizodus sp. 41 Jour, Geol., vol. III, p , 304; 1895 . 48 Iowa Gee!. Survey, vol. XX, p . 501 If. Section of Pella b-eds along Brush C'reek. Section of Pella b-eds along Brush C'reek. PELLA
FEET
3. Limestone, gray, :fine-grained, thinr-bedded;
shaly partings
between the layers filled with fossils _______ . ___________________ . __________ .. ____
8%
2. Sandstone, fine-grained, gray, massive, weathering yello.wish____
21
LOWER ST. LoUIS
. . 1. Limestone, buff, dolomitic, massive; Lithostrotion zone at the
top _______________ . _____________________________ . _______________ . ________ .. ___ .___________________________
2 2. Sandstone, fine-grained, gray, massive, weathering yello.wish____
21
LOWER ST. LoUIS
. . 1
Li
t
b ff
d l
iti
i
Lith
t
ti
t th 1. Limestone, buff, dolomitic, massive; Lithostrotion zone at the
top _______________ . _____________________________ . _______________ . ________ .. ___ .___________________________
2 2 A well defined synclinal flexure is developed in the beds of
this locality. In a quarry in the opposite bank of the creek,
directly west of'this exposure, bed 3 has an exposed thickness
of six and one-half feet and is followed by the same thickness
of highly fossiliferous calcareous shale with intercalated lime-
stone layers. The shale is gray when fresh but weathers yel-
lowish. About SL,{ feet of drift comes above. of six and one-half feet and is followed by the same thickness
of highly fossiliferous calcareous shale with intercalated lime-
stone layers. The shale is gray when fresh but weathers yel-
lowish. About SL,{ feet of drift comes above. The following species characterize the limestone (bed 3) : BRYOZOA-
F enestella sp. BRACHIOPODA-
Girt yell a indianensis (Girty)
Spirifer pellaensis Weller
Composita trinuclea (Hall)
Productus ovatus Hall
Pugnoides ottumwa (White)
PELECYPODA-
Allorisma marionensis White BRYOZOA-
F enestella sp. BRACHIOPODA-
Productus ovatus Hall
Pugnoides ottumwa (White) Productus ovatus Hall
Pugnoides ottumwa (W PELECYPODA-
All
i Allorisma marionensis White Pugnoides ottumwa (White) The overlying shale contains a somewhat more diversified
faunule, as the following list shows: ANTHOZOA-
Productus ovatus Hall
Zaphrentis pellaensis Worthen
Productus parvus M. and W. CruNOIDEA-
Pugnoides ottumwa (White)
Stems and fragments
Spirifer pellaensis Weller
BRYOZOA-
Composita trinuclea (Hall)
Anisotrypa :fistulosa Ulrich
Cliothyridina sp. Anisotrypa ramulosa Ulrich
PELECYPODA-
Fenestella sp. . Allorisma sp. BRAcmoPoDA-
VERTEBRATA-
Orthotetes kaskaskienJSis (McChesney)
Fish teeth Zaphrentis pellaensis Worthen
C
NOIDEA Stems and fragments
BRYOZOA Cliothyridina sp
LECYPODA Anisotrypa :fistulosa Ulrich
Anisotrypa ramulosa Ulrich PELECYPODA
All
i Anisotrypa ramulosa Ulrich
Fenestella sp Allorisma sp. RTEBRATA Fenestella sp. FEET
I NCHES After the shearing of
fragments of this bed down into the sandstone a period of PELLA BEDS IN HENRY COUNTY 293 erosion, representing the disconformity between the Mississip-
pian and Pennsylvanian systems, followed. It is believed that
the shearing was contemporaneous, in part at least, with the
local brecciation of the St. Louis limestone and that it was re-
lated to the regional uplift which caused a retreat of the Missis-
sippian sea to the southward at the close of Pella time. An exposure of the Pella beds appears approximately mid-
way between the towns of Farmington and Bonaparte, on
Slaughters branch (NW.1,4 sec. 23, T. 68N., R. 8 W.). S eoUo'T/) of P ellal beds 0'l1i Slaughters brCJ/Mh. S eoUo'T/) of P ellal beds 0'l1i Slaughters brCJ/Mh. S eoUo'T/) of P ellal beds 0'l1i Slaughters brCJ/Mh. FEET
INCHES
4. Limestone, fo·rmerly quarried ODi a small scale . ______________ .. ______
13
6
3. Shale ______________________________________________________________________________________________________
4
2. Limestone, compact, gray, dense ________________________________ ____________________
9
1. Sandstone, fine-grained, light gray, soft and shaly in upper
part. Exposed ______________________________________________________________________________________ 2
10 1. Sandstone, fine-grained, light gray, soft and shaly in upper
part. Exposed ______________________________________________________________________________________ 2
10 The capping limestone contains several typical Pella brach-
iopods, viz.: Pugnoides ottumwa (White)
Spirifer pellaensis Weller Pugnoides ottumwa (White)
Spirifer pellaensis Weller Productns ovatuB Hall
Girtyella indianensis (Girty) At the southeast end of the bridge over Des Moines river at
Keosauqua an exposure shows three to four feet of Pella lime-
stone underlain by thirteen feet of sandstone. Blocks of the
Pella limestone are mashed down several feet into the sand-
stone at one point. Davis COttnty.-In the report on the geology of Davis county,
M. F'. Arey48 describes exposures of limestone along Des Moines
river and its tributaries in the extreme northeastern part of the
county. He refers these to the Pella but in the absence of lists
of diagnostic fossils it is possible that they represent the St. Louis. Henry County.-The most representative sections of the
Pella formation in Henry county occur along Brush creek in
the eastern part of section 6 of Baltimore township. The fol-
lowing beds appear in the east bank of the stream just north
of the wagon road at the point where it crosses the creek. MISSISSIPPIAN STRATA OF IOWA 294 49 Iowa Geol. Survey. vol. XII, pp. 373-386 ;1902. Section of Pella b-eds along Brush C'reek. 71,~ Section in tlw 80'Uth bank of Rock creek (A.fter Udden). 10. Gray marl ................................................................................... _ ...... . 9. Limestone ............................................................................................. . 8. Gray marl ................................................. _ ........................................ . 7. Limestone ... _ .............................................. _ ...... _ ................................ . 6. Marl ........................................................... _ .......................................... . 5. Limestone ........................... _ .... _ .......... _ .............................................. . 4. Yello,w marl containing Product1bs O'Vatus, PrOd1tCt~tS ?!UlJrgini-
Cilnct11S, P~bgnoii.&es otm!?l{~/Ja, Spirifer keokuk, SemilllU/,a trintUolea,
(f) Fenestella serratula, A.nisotrypa fist1tlata, cyathophylloids
FEET
1/3
1/ 2
1 /2
1 1/3
1/ 8
1
and stems of crin.o;ids ......................................... _............................... 5
3. Limestone ............ _ .. _ ........ _._................................................................. 1
2. Marl with some of the same fossils as those above ................ 1/ 8
1
Q it
l
b dd d l d
f bl i h
li
t
71,~ Section in tlw 80'Uth bank of Rock creek (A.fter Udden). 3. Limestone
2
Marl with 2. Marl with some of the same fossils as those above ................ 1/
1
Quite evenly bedded ledges of bluish gray limestone
71,~ The thickness of the formation in this county is given by him
as seventeen feet. The above section therefore contains all the
members of the Pella represented in this part of the state. Th
f
f th
f
ti
i
thi
t
li t d b
lTdd The fauna of the formation in this county as listed by lTdden,
hut now subject to some revision in the light of more recent
paleontological studies, is as follows: List of fossils from the P ella beds in J efferson cmmty (after Udden). PROTOZOA-
BRACHIOPODA-
Endothyra bail('yi (Hall)
Other rhizopods not identified
ANTHOZOA-
ZaphTentis pellaensis Worthen
ECIIINODERMATA-
PentTemites koninckiana Hall
Archaeoci<1aris (spin.es and separate
plates, small) . Crin oids (stems)
VERMES-
Spirorbis ,
BRYOZOA-
Anisotrypa. fistulosa Ulrich
Fenestella' serratula Ulrich
Cleiothyris roissyi (Leveille)
Derbya keokuk (Hall)
DiJelasma formo a (Hall)
Dielasma turgida Hall
Eumetrla marcyi (Shumard)
Productus ma.1'ginicinctus Prout
Productus ovatus Hall
Camarotoechia grosvenori (Hall)
Pugnoides ottumwa (White)
Seminula trinuclea (H&.ll)
Seminda sp. unclt. Spirifer keohuk Hall
P ELECYPODA-
Allorisma marionensis White List of fossils from the P ella beds in J efferson cmmty (after Udden). Section of Pella b-eds along Brush C'reek. A
P DA VERTEBRATA-
)
Fi h t
th Orthotetes kaskaskienJSis (McChesney) Fish teeth Jeffe1-son County.-A number of exposures of the Pella beds
in Jefferson county have been carefully described by J. A. Vdden49•
These occur on the north and middle branches of
Walnut creek in sections 21 and 23 of Penn township; in the
south bank of Brush creek, near the northeast corner of section
3G, Lockridge township; in the bed of Wolf creek, south of the
center of section 5, Round Prairie township; in the' banks of
Cedar Cl'eek in the southwe'3t one·-fourth of the southeast quar-
ter of section 34. Round Prairie township; in the south bank of
Rod\. creek in th€ northeast one-fourth of the northeast quarter
of section 32, Round Prairie township; in a ravine about one- PELLA FOSSILS IN JEFFERSON COUNTY 295 sL"Xth mile southwest of the center of section 23, Round Prairie
town~hip; in the south bank of Cedar creek in the n;)rtheast
quarter of section 34, Cedar iownship; in an old quarry in the
east banJc of Cedar creek, northeast of the center of section 10,
Liherty township; near thc· Chicago,. Rock Island amI Pacific
rail way in the northwest one·fourth of the sOllth~~st quarter of
section 9, Lillprty townshir, and in the bed of Lidr creek neal'
the center of section 25, Des Moines township. l'h
ti
i
th
th b
k
f R
k
k i hi h
i l'he section in the south bank of Rock creek, ivhieh was vis-
ited by the 'writer, is typical for the entire area. lJdden's de-
scription is copied without change. Section in tlw 80'Uth bank of Rock creek (A.fter Udden). 10. Gray marl ................................................................................... _ ...... . 9. Limestone ............................................................................................. . 8. Gray marl ................................................. _ ........................................ . 7. Limestone ... _ .............................................. _ ...... _ ................................ . 6. Marl ........................................................... _ .......................................... . 5. Limestone ........................... _ .... _ .......... _ .............................................. . 4. Yello,w marl containing Product1bs O'Vatus, PrOd1tCt~tS ?!UlJrgini-
Cilnct11S, P~bgnoii.&es otm!?l{~/Ja, Spirifer keokuk, SemilllU/,a trintUolea,
(f) Fenestella serratula, A.nisotrypa fist1tlata, cyathophylloids
FEET
1/3
1/ 2
1 /2
1 1/3
1/ 8
1
and stems of crin.o;ids ......................................... _............................... 5
3. Limestone ............ _ .. _ ........ _._................................................................. 1
2. Marl with some of the same fossils as those above ................ 1/ 8
1
Quite evenly bedded ledges of bluish gray limestone .............-.. 2.
Marl with some of the same fossils as those above ................
1
1
Quite evenly bedded ledges of bluish gray limestone
71, List of fossils from the P ella beds in J efferson cmmty (after Udden). PROTOZOA-
Endothyra bail('yi (Hall)
Other rhizopods not identified
ANTHOZOA-
ZaphTentis pellaensis Worthen
ECIIINODERMATA-
PentTemites koninckiana Hall
Archaeoci<1aris (spin.es and separate
plates, small) . Crin oids (stems)
VERMES-
Spirorbis ,
BRYOZOA-
Anisotrypa. fistulosa Ulrich
Fenestella' serratula Ulrich BRACHIOPODA-
ate
Cleiothyris roissyi (Leveille)
Derbya keokuk (Hall)
DiJelasma formo a (Hall)
Dielasma turgida Hall
Eumetrla marcyi (Shumard)
Productus ma.1'ginicinctus Prout
Productus ovatus Hall
Camarotoechia grosvenori (Hall)
Pugnoides ottumwa (White)
Seminula trinuclea (H&.ll)
Seminda sp. unclt. Spirifer keohuk Hall
P ELECYPODA-
Allorisma marionensis White BRACHIOPODA-
ate
Cleiothyris roissyi (Leveille)
Derbya keokuk (Hall)
DiJelasma formo a (Hall)
Dielasma turgida Hall
Eumetrla marcyi (Shumard)
Productus ma.1'ginicinctus Prout
Productus ovatus Hall
Camarotoechia grosvenori (Hall)
Pugnoides ottumwa (White)
Seminula trinuclea (H&.ll)
Seminda sp. unclt. Spirifer keohuk Hall
P ELECYPODA-
Allorisma marionensis White Endothyra bail( yi (Hall)
Other rhizopods not ident PentTemites koninckiana Hall
Archaeoci<1aris
(spines
and Archaeoci<1aris (spin.es and separat
plates
small) Anisotrypa. fistulosa Ulrich
Fenestella' serratula Ulrich Allorisma marionensis White Fenestella serratula Ulrich MISSISSIPPIAN STRATA OF IOWA 296 Aatartella sp. Lithophaga pertenuis M~ and W. (~)
Pinna , (fragment)
. Leperditia
carbonaria Hall
Phillipsia , (pygidium)
VERTEBRATA-
ARTHROPODA-
Deltodopsis stludovici .St. J. and W. Cytherellina glandella Whitfield . Leperditia
carbonaria Hall
Phillipsia , (pygidium)
VERTEBRATA-
Deltodopsis stludovici .St. J. and W. Aatartella sp. Lithophaga pertenuis M~ and W. (~)
Pinna , (fragment)
ARTHROPODA-
Cytherellina glandella Whitfield Wapello Cottnty.-Exposures of the Pella formation in Wa-
pello county are confined to the valleys of Des Moines river and
its larger tributaries in the central and northwestern parts. But rocks of this age are believed to underlie the mantle rock
over small areas in the northeastern and southeastern corners
of the county also. It is probable that all the rocks in this county mapped and
described by Leonard50 as St. Louis are of Pella age. The sand-
stone below the Pella limestone which he referred to the Verdi
is believed to be a basal sandstone of Pella age. One of the most instructive and complete exposures of the
formation in this county is in an abandoned quarry on Har-
rows branch, one-fourth mile above Second street, in the north-
west part of the city of Ottumwa. The succession is as follows: Section on Harrows branch. Section on Harrows branch. FEET
INCHES
8. Drift, yellowish ......... _ .... _ ...................... _ .... _ .... _............................. 5
DES MOINES
7. Shale, dark, carbonaecous, contact with shale below obscure.... 4
PELLA
6. ~O Iowa Geol. Survey, yol. XII, pp. 439-499; 1901. List of fossils from the P ella beds in J efferson cmmty (after Udden). Shale, drab, marly, with harder calcareous seams in lower
part; blotched and streaked with reddish patches .................... 9
5. Limestone,
drab,
fine· grained;
massive when
fresh
but
weathering shaly; grading into shale above and below ... _ .. _... 2
4. Shale, like bed 6 but free from reddish patches; locally
grading laterally into limestone ... _ ................ _ ...................... _....... 1
9
3. Limestone, like bed 5 ......... _ .......... _ ........................................ _....... 6
2. Shale, like bed 4 ..................... _ .... _ .......... _....................................... 3
2
1. Limestone, drab, fine·grained. Exposed ......................... _........... 2
6· Section on Harrows branch. 1. Limestone, drab, fine·grained. Exposed . The following fossils were collected from the Pella beds at
this locality: ANTHOZOA-
Zaphrentis pellaensis Worthen
CRINOIDEA-
Crinoid stems
BRYOZOA-
Anisotrypa ramulosa Ulrich
Amisotrypa fistulosa Ulrich
Fenestella sp. Bp..ACHIOPODA-
Orthotetes kaskaskiensis (McChesney)
Productus parvus M. and W. Productus ovatus Hall
Pugnoides ottumwa (White)
Gir,tyel1a indianensis (Girty)
Spirifer . pellaensis Weller
Composita trinuelea (Hall)
Cliothyridina hirsuta (Hall)
PELECYPODA-
Allorisma marionensis White
~O Iowa Geol. Survey, yol. XII, pp. 439-499; 1901. Anisotrypa ramulosa Ulrich
A
i
fi
l
Ul i h Amisotrypa fistulosa Ulrich Fenestella sp. Bp..ACHIOPODA- Orthotetes kaskaskiensis (McChesney) PELLA BEDS AT DUDLEY 297 Other important exposures appear in the vicinity of the town
of Dudley. The accompanying section is shown in a quarry
opening on South Avery creek (SW.1,4 of SE.14, sec. 35, T. 73
N., R. 15 "V.). Section of Pella beds on SO'Uth AVIJry creek. Section of Pella beds on SO'Uth AVIJry creek. 4. Drift ..................................................................................................... . 3. Limestone, shaly. Exposed ... _ .......... _ .. _ .... _ .... _ ...................... _ .... . 2. Shale, marly, with (l six inch layer of shaly limestone in
middle ..................... _ ........ __ .............. _ ........................ _ .................... _ .. 1. Limestone, gray, massive when fresh but weathering to thin
:w,yers, :fine·grained. Exposed _._ .... _ ........ _._ ........ __ .... _ .. _ ......... _
FEET
1 to 2
1 Bed 1 yields only a few species, namely: Prod16c'tus ovatus
Hall, Pugnoides ottumwa (White), Spirifer pellaensis Weller,
Composita trinuclea (Hall) and Allorisma sp. The fossils of
bed 2 are much more varied. List of fossils from bed 2 of Pella formc,tion on South Avery creek. List of fossils from bed 2 of Pella formc,tion on South Avery creek. ANTHOZOA-
Productus ovatus Hall
Zaphrentis pellaensis Worthen
Productus parvus M. and W. 3.
Limestone like bed 5
2
Sh l
lik
b d 4 3.
Limestone, shaly.
Exposed
2
Sh l
l
i h
i 2.
Shale like bed 4
1
Lime~tone, d 51 Iowa Geol. Survey. vol. V. p. 150; 1896. List of fossils from the P ella beds in J efferson cmmty (after Udden). CRINOIDEA-
Pugnoides ottumwa (White)
Crinoid stems
Girtyella indianensis (Girty)
BRYOZOA-
Spirifer pellaensis Weller
Anisotrypa ramulosa Ulrich
Composita trinuclea (Hall)
Anisotrypa fistulo-sa Ulrich
PELECYPODA-
Fenestella sp. Allorisma marionensis 'White
BRACHIOPODA-
GASTROPODA-
Orthotetes kaskaskiensis (McOhesney)
Gastropod sp. Anisotrypa ramulosa Ulrich
A i
fi
l
Ul i h Anisotrypa fistulo-sa Ulrich
F
t ll Fenestella sp. BRACHIOPODA BRACHIOPODA- Two hundred yards south of the above exposure the following
layers are exposed in the opposite bank of the creek. Section of Pella beds two hundred yards sO'Uth of the preceding one. 4. Drift ............... _ ........................ _ ........ _ ........... _ .......... _ .......... _ .... __ .... . 3. Limestone, gray, fine·grained, thin·bedded ... _ .................... _ ........ . 2. Concealed ............................................. _ .... _ ............ -........... _ .............. . 1. Sandstone, fine· grained, gr,ay to buff, massive below but in
thin cl"lOOS·beded layers above. Exposed' ....... _ ...... : ...... __ ............. . FEET
10
5%
21,i
10 4. Drift ............... _ ........................ _ ........ _ ........... _ .......... _ .......... _ .... __ .... . 3. Limestone, gray, fine·grained, thin·bedded ... _ .................... _ ........ . 2. Concealed ............................................. _ .... _ ............ -........... _ .............. . 1. Sandstone, fine· grained, gr,ay to buff, massive below but in
thin cl"lOOS·beded layers above. Exposed' ....... _ ...... : ...... __ ............. . FEET
10
5%
21,i
10 4. Drift
3
Li Several feet of the Pella are exposed in an abandoned~ quarry
just west of the Chicago, Burlington and Quincy railway sta-
tion at Dudley. Section of Pella beds i;n, quarry at Dudley. 6. Drift ........... ___ ._ ............... __ . ___ .............. _ ... -.-............. -................. -.... -... . 5. Limestone, gray, fine· grained, shaly .. --........................................ . 4. Shale, gray, marly ..................... _ ......... __ ...... _ ............................. - ... -. 3. Limestone like bed 5 ........................... -.-...... - .... -....... --... -............ . 2. Shale like bed 4 ._._ ............... _ ..... _ ....... _. __ ._ ................... -............... --... . 1. Lime~tone, dove·colored, very compact, thin· bedded ; coarser·
grained and crim,oidal in lower part. Exposed ........................... . FEET
10
1%
2
1h
3
6 Section of Pella beds i;n, quarry at Dudley. MISSISSIPPIAN STRATA OF IOWA 298 The fauna of the formation at this place IS very similar to
that of the foregoing exposures. Fa'una of the Pella beds fin quarry at Dudley. Fa'una of the Pella beds fin quarry at Dudley. S i if
ll
i Fa'una of the Pella beds fin quarry at Dudley. ANTHI!>WA-
Spirifer pellaensis Weller
Zaphrentis pellaensis Worthen
Oomposita trinuclea (Hall)
~NOIDEA-
PELECYPODA-
. Crinoid stems
Schizodus sp. BRYOZOA-
Allorisma marionensis White
Anisotrypa fistulosa Ulrich
Allorisma sp. Anisotrypa l',amulosa Ulrich
GASTROPODA-
BRACHIOPODA-
Bellerophon sp. Orthotetes kaskaskiensis (McChesney) TRILOBITA-
Produetus ovatus Hall
Phillipsia Bp
Productus parvus M. and W. OSTRACODA-
Pugnoides ottumwa (White)
Leperditia sp. Girtyella indianensis (Girty) Spirifer pellaensis Weller
O
i
i
l
(H ll) Oomposita trinuclea (Hall)
LECYPODA Produetus ovatus Hall
P
d
t
M Productus parvus M. and W. P
id
tt
(Whit ) Pugnoides ottumwa (White)
Gi t
ll
i di
i
(Gi t ) Girtyella indianensis (Girty) An excellent exposure of the Pella beds in disconformable
contact with the Des Moines formation may be seen half a mile
east of Dudley where an artificial channel for N orth Avery
creek has been cut in order to shorten its course. The following
section was measured near the west end of the cut: Section east of DU,dley. tEET 7. Drift. 6. Limestone, light gray, compact, fine·grained, thin·bedded above
but in heavier layers below; with a coarser· grained c.rinoidal
layer 20 inches thick in lower P3Jrt ..................... _....................... 7
5. Sandstone, fine· grained, soft, bluish, resting on the irregular
tEET
surface of the bed beneath .............................................................. 1/6-%
4. Limestone, dark gl'ay, fine'gl'ained, compact, locally coarser·
grained and criuoidal in part, very irregular owing to ex·
treme brecciation and mashing; lower boundary irregular owing
to mashmg down into soft sandstone below ......... _....................... 3
3. Sandstone, fine· grained, bluish, soft ................................................ 1 to Ph
2. Limestone, compact, dark gmy, brecciated, with a sandy
matrix ........................................................... _ ........................ _............. 1 to 2
1. Sandstone, gTaY, fine·grained, soft, irregulal'ly and imperfectly
stl'atified. Exposed ... _ ........ _ .. _ ................ _ ............ _......................... 41j~ . Sandstone, fine· grained, bluish, soft .............. 2
Li
t
t
d
k
b
i t A short distance east of this point a black carbonaceous
laminated shale of Des Moines age occupies a broad shallow
valley cut into the Pella formation. On N orth Avery creek, nearby, a bed of sandstone with
an exposed thickness of ten feet is followed above by Pella lime-
stone like bed 6 of the above section, a concealed interval of
two and one-half feet intervening. Washington County.-The Pella beds extend northward from
J effers.on county a short distance into southern Washingtol1
county. BainS1 says: PELLA BEDS IN MAHASKA COUNTY 299 "They have only been preserved from erosion in the immed-
iate neighborhood of Brighton, in the bottom of what is probab-
ly a broad, shallow syncline." The most representative exposures are in the western part of
section 29 of Brighton township. The following succession is
shown in the bank of a small ravine half a mile south of the
Brighton mill. Seotion of P~lla beds near Brighton mill. FEET
INCHES
4. Drift ............. _ .... _ .... _........................................................................... 3
3. Limestone, gray, :fine· grained, in one heavy layer, containing
Spilrifer pella'ensis, Pugnoides ottumwa and Straparollus sp .... _ 1
6
2. Limestone, drab, fine·grained, in layers 2 to 3 inches thick,
separated by shaly layers 1 to 8 inches thick. Pugnoides
ottumwa abundant ... _.......................................................................... 4
2
1. Shale, bluish, arenaceous, with lenses and seams of compact
gray brecciated limestone. Exposed ....................... _ ................ _. 52 Iowa Geol. Survey, vol. IV, p. 305; 1895.
53 Idem, p. 324. if. Seotion of P~lla beds near Brighton mill. Section east of DU,dley. 3
6 Bed 1 of the preceding section has a thicl{ness of one foot in
a quarry opening one hundred yards north of the ravine. It is
underlain by five feet of gray fine-grained thin-bedded basal
Pella sandstone which rests unevenly on the St. Louis limestone. Keokuk County.-Exposures of the Pella beds in Keokuk
county apparently are confined to its western half. Bain52 re-
fers to several quarries east and south of 'What Cheer in Wash-
ington township which derive stone from this formation. The
more important of these are in the southeast quarter of section
11 and the northwest quarter of section 24. At the last locality
Pugnoides ottwmwa and other characteristic fossils were col-
lected by him. Bain states that the quarrie,s north of. Sigour-
ney, the county seat, are in bot~ the Verdi and Pella limestones. Mahaska County.-The distribution of the Pella beds in Ma-
haska comity is similar to that of the St. Louis limestone, al-
though they are not so extensive. Bain5 3 describes scattered
outcrops of the formation .along the north and south forks of
Skunk river and in theV!alley of Des Moines river. O
h
h f
k
f Sk
k i
(1) i
h On the north fork of Skunk river exposures appear (1) in the
Meyer's section (T. 77 N., R. 16 W., sec. 1, NW.1.4 SE.1.4)
where six feet of limestone is overlain by Des Moines shales and
sandstones; (2) in the Union mills sections 'in the east half of MISSISSIPPIAN STRATA OF IOWA 300 section 23 (T. 77 N., R. 15 W.) ; and (3) in the McBride mill
section (T. 76 N., R. 14 W., sec. 15, SW.%). At the last named
locality Bain measured the following section: 54 Iowa Geol. Survey, vol. XX, p. 255 ; 1909. Section at the McBride mill. FEET
6. Limestone, gray, subcrystalline, with interbedded fossiliferous
marl layers ................................................... _ ........ _ .. _ ............ _........... l(l
5. Unexposed ......... _ ...... _ ........ _ .......... _ .. _ ...................................... _....... 11
4. Limestone, ash· gray, compact .......................................................... 1
3. Sandstone, soft, yellow ....................................... _ ........................ _... 1
2. Limestone, as above .................................................. .......................... 2
1. Sandstone, as abo've ..................... _..................................................... 2 3. Sandstone, soft, yellow
2
Li
b 2. Limestone, as above
1
S
d t
b ' 1. Sandstone, as abo've Beds 1 to 4, which he refers to the Verdi, outcrop under the
east pier of the bridge. Bed 6, the Pella, appears in a small
quarry opening about two hundred yards west of the milL Bain identified the Pella on South Skunk river in (1) the Bal-
linger branch section (T. 76 N., R. 17 W., sec. 11, NW.l,4), (2)
in the waterworks section (T. 76 N., R. 16 W., sec. 25, SW.1,4
SE.1,4), and (3) in the Spring creek section (T. 75 N., R. 15 W.,
sec. 4, NW.%). He also reports the presence of the Pella along
Des Moines river in the Given (T. 74 N., R. 16 W., sec. 10,
SW.1,4) and Bluff creek (T. 74 N., R. 16 W., sec. 23, NW.%)
sections. P01Vesh·iek County.-The only exposure of the Pella beds -re-
corded by Stookey54 in his report on the geology of Poweshiek
county is located in the southeast one-fou:rth of the northwest
quarter of section 35, Sugar Creek township, where seven feet
of interbedded shale and limestone of this age is overlai.n by
Des Moines sandstone. The fauna listed by Stookey is very
similar to that of the Pella in adjoining counties. Marion County.-The type section of the Pella formation is
near the town of Pella in Marion county. The nearest exposure
of the beds to the town is in an abandoned quarry one-half mile
southwest of the city limits (T. 76 N., R. 18 W., sec. 9, SE.1,4). 'Other quarry openings are located a short distance south in the
northeast quarter of section 16. The limestone which was
formerly quarried no longer outcrops, but the overlying fossil-
iferous shales have an exposed thickness of eight feet. The
following species were collected from these shales: 301 PELLA BEDS IN WEBSTER COUNTY List of fossils from Pella shales near, Pella'. ANTHOZOA-
Zaphrentis pellaensis 'Vorthen
llLAST()IDEA-
Pentremites conoideus Shumard
CRINOIDEA-
Crinoid stems
BRYOZOA-
Anisotrypa fistulosa Ulrich
Anisotrypa ramulosa Ulrich
Fenestella sp. Polypora sp. BRACFIIOPODA-
Orthotetes kaskaskiensis (McChesney)
Productus ovatus Hall
Productus parvus M. and W. Pugnoides ottumwa (White)
GirtyeHa indianensis (Girty)
Sphifer pellaensis 'Weller
Composita trinuclea (Hall)
Cliothyridina hirsuta (Hall)
PELECYPODA-
Allorisma marionensis White
Schizodus sp. TRILOBITA-
Phillipsia sp. )
Productus ovatus Hall
Productus parvus M. and W. Pugnoides ottumwa (White)
GirtyeHa indianensis (Girty)
Sphifer pellaensis 'Weller
Composita trinuclea (Hall)
Cliothyridina hirsuta (Hall)
PELECYPODA-
Allorisma marionensis White
Schizodus sp. TRILOBITA-
Phillipsia sp. Zaphrentis pellaensis 'Vorthen
LAST()IDEA Crinoid stems
BRYOZOA Anisotrypa fistulosa Ulrich
A i
t
l
Ul i h Anisotrypa ramulosa Ulrich
F
t ll Fenestella sp. P l Polypora sp. CFIIOPODA BRACFIIOPODA-
h
k Orthotetes kaskaskiensis (McChesney) The limestone member of the Pella is exposed below the fos-
siliferous marls in the quarriet; southwest of the town of Tracy
(T. 75 N., R. 18 W., sec. 35, NE.% lof SE.l,4). Near the middle
of the quarry face the succession is as follows: 4. Shale, fossiliferous
3
Li
t
fi Section southwest of Tra01J. Section southwest of Tra01J. DES MOINES
rEET
5. Shale, dark, impregnated with carbonaceous material, arenace·
ous above ............................................. _............................................... 8
PELLA
4. Shale, fossiliferous ................................. _........................................... 4%
3. Limestone, gray, fine· grained, in a single }ruyer ................. _..... 1
2. Limestone, gray, fine·grained, thin·bedded, rather soft ond
shaly ...................................................................................................... 5
1. Limestone, similar to bed 3 .......................................................... 2 5. Shale, dark, impregnated with carbonaceous material, arenace·
ous above ............................................. _............................................... 8
LLA LLA
4. Shale, fossiliferous ................................. _........................................... 4%
3. Limestone, gray, fine· grained, in a single }ruyer ................. _..... 1
2. Limestone, gray, fine·grained, thin·bedded, rather soft ond
shaly ...................................................................................................... 5
1. Limestone, similar to bed 3 .......................................................... 2 4. Shale, fossiliferous
3
Li
t
fi 3. Limestone, gray, fine· grained, in a single }ruyer ................. _..... 1
2. Limestone, gray, fine·grained, thin·bedded, rather soft ond
shaly ...................................................................................................... 5
1. Limestone, similar to bed 3 .......................................................... 2 1. Limestone, similar to bed 3 The . characteristic fossils of the limestone members are:
Pttgnoides ottumwa, Spirifer pellaensis, Composita t1'inuclea
and All07-isma sp. The assemblage in the shale js considerably more diversified,
VIZ.: List of fossils from shale bed at top of Pella in above section. List of fossils from shale bed at top of Pella in above section. ANTHOZOA-
Pugnoides ottumwa (White)
Zaphrentis pellaensis Worthen
Girtyella indianensis ' (Girty)
CRINOIDEA-
Spirifer pellaensis Weller
Crinoid stems
Composita trinuclea (Hall)
BRYOZOA-
PELECYPODA-
Anisotrypa fistulosa Ulrich
Schizodus sp. Anisotrypa ramulosa Ulrich
Schizodus sp. Fenestella cf. F. multi spinosa Ulrich
Allorisma sp. BRACHIOPODA-
. GASTROPODA-
Orthotetes kaskaskiensis (McOhesney)
Bellerophon sp. Productus ovatus Hall
YERTEDRATA-
Productus parvus M. and W. Fish teeth Anisotrypa fistulosa Ulrich
A i
t
l
Ul i h Orthotetes kaskaskiensis (McOhesney)
Be
P
d
t
t
H ll
YERTED YERTEDRATA-
Fi h
h Productus ovatus Hall
Productus parvus M
a Fish teeth Productus parvus M. and W. Webster County.-No exposures of the Pella formation ar~
known northwestward from southwestern Poweshiek county
until Webster county is reached. E~cept for a small inlier of MISSISSIPPIAN STRATA OF IOWA 302 St. Louis limestone in Story county the intervening area is cov-
ered everywhere by the Des Moines formation. Fossils now known as characteristic Pella species were re-
ported from the St. Louis limestone of this area by White55 as
early as 1870. 5r, Report on the Geol. Survey, Iowa, vol. I, p. 221 ff.
56 Iowa Geol. Survey, vol. XII, p. 78; 1901.
See also Wilder's statements in vol. XXVIII,
pp. 146, 154, 1'64; 1918.
.
57 Proc. Iowa Acad. Sci. •. vol. XXII, p. 241 If.
58 Proc. Iowa Acad. Sci, vol. XXV, p. 599 ff.
59 Idem, p. 600 ff. 56 Iowa Geol. Survey, vol. XII, p. 78; 1901.
See also Wilder's statements in vol. XXVIII,
pp. 146, 154, 1'64; 1918.
.
57 Proc
Iowa
Acad
Sci • vol
XXII
p
241
If Section southwest of Tra01J. Many years later Wilder56 described fossilifer-
ous marls on Lizard creek, one mile west of Fort Dodge~ which
he also referred to the St. Louis. Upon the basis of the ·fossils
listed by Wilder, the beds were asigned to the Pella by 'Weller
and Van Tuyl in 1915.57
MOl'e recent studies by Lees and
Thomas5s have demonstrated the presence of a typical Pella
fauna in the marls. Lees and Thomas state that all the known exposures of the
formation in Webster county are, with two exceptions, located
in the valley of Lizard creek west of Fort Dodge. One of these
exceptional localities "is in a ravine which opens into Des
Moines valley from the northwest opposite the dam and about
one-third ;mile above the railroad and wagon bridges over the
river at the mouth of Lizard creek."
Twenty to twenty-five
feet of fossiliferous Pella shales is overlain here by the Coal
Measures. The other locality is in the northwest quarter
of section 6, Cooper township, in a small ravine on the
east side of Des Moines river, about five miles above Fort
Dodge'. Two small outcrops here show a few
in~hes of
sandy shale at water level, above which is two feet of marl. Over this is a foot of clay shale in which were found a few
specimens of Spi'rifer pellaensis and Pugnoi.des ottwrnwa. A
bluff section on Lizard creek near the center of section 24,
Douglas township, shows forty feet of Pella shales underlain by
thirteen feet of interbedded sandstone and li:rnestone of St. Louis age. The lower thirty-four feet of the Pella shale ~s mot-
tled with red areas and contains Spirifer pellaensis, Pugnoides
ottumwa, Compos~ta trinuclea and other fossils. (See also page
284.) Several other exposures of Pella shales on Lizard creek are
described by Lees and Thomas.59 In an exposure about one-
fourth mile U'P the valley from the above mentioned section
they found three feet of nodular gray limestone overlain by PELLA FOSSILS AT FORT DODGE 303 thirty or mpre feet of fossiliferous gray-green shale which is
followed in turn by fi ve feet of red clay shale barren of life
forms. Regarding other outcrops they say: "About four hundred yartls above the junction of North and
South Lizard creeks, on the east bank of North Lizard there is
an exposure of the gray-green shale which rises twenty-five or
thirty feet above the stream. 600p. cit., p. 605 If. Section southwest of Tra01J. Over this shale lies fifteen to
twenty feet of red shale. At several horizons in the gray-green
shale there are harder limy bands which contain large numbers
of fossil brachiopods. The contact of the red shale with the
g-ray is quite sharp and lies just above a layer of fossiliferous
yellow limestone. . The next exposures on this fork, and so far as known to the
writers the last ones, are a group five miles up the valley and
in the southeast quarter of section 8, Douglas township, about
one-fourth mile below the Minneapolis and Saint Louis railroad
bridge on the north bank of the stream. Here a small tributary
ravjne has been cut through six feet of yellow and green shale~
below this through five feet of red and green shale, beneath
which is exposed two feet of gray sandstone or sandy limestone,
then five feet of shaly material beneath which in turn two feet
of green shale is seen above the stream leveL" N one of the beds at this locality yielded any fossils. Regarding the exposures on South Lizard creek Lees and
Thomas have the following to say : "In the lower one-half mile of South Lizard valley there are
several exposures of the red and green shales. Only one of
these, the southernmost, need be described. here. This one shows
beneath twenty or thirty feet of till a body of red clay shale
twelve feet thick. Under it is eight feet of gray sandstone and
below this bed a green and red shale extends fifteen feet to
water level. Some of the shale near the base of this exposure
is finely sandy. All the other outcrops are similar in the char-
acter of the beds exposed and it is noteworthy that none of the
beds carry aIfY fossils." The fauna of the Pella beds of Webster county as reported
by Lees and Thomas
6o js as follows : Batostomella (species undescribed)
Anisotrypa fistu]'osa Ulrich
BRACHIOPODA-
Orthotetes kaskaskiensis (McChesney)
Pugnoides ottumwa (White)
Ghtyella indianensis (Girty)
Spi"ifer pellaensis Weller
Composita trinuclea (Hall)
TRILOBITA-
Phillipsia sp. Batostomella (species undescribed)
Anisotrypa fistu]'osa Ulrich
BRACHIOPODA-
Orthotetes kaskaskiensis (McChesney)
Pugnoides ottumwa (White)
Ghtyella indianensis (Girty)
Spi"ifer pellaensis Weller
Composita trinuclea (Hall)
TRILOBITA-
Phillipsia sp. SPONGIAE-. Section southwest of Tra01J. ClinoJithes lizardensis Lees and
Thomas
VERMES-
Spi rorhis fortdodgensis Lees and
Thomas
CRINOIDEA-
Crinoid stems
BRYOZOA-
Batostomella interstincta ffirich
Batostomella (species undescribed)
Anisotrypa fistu]'osa Ulrich
BRACHIOPODA-
Orthotetes kaskaskiensis (McChesney)
Pugnoides ottumwa (White)
Ghtyella indianensis (Girty)
Spi"ifer pellaensis Weller
Composita trinuclea (Hall)
TRILOBITA-
Phillipsia sp. SPONGIAE-. ClinoJithes lizardensis Lees and
Thomas
VERMES-
Spi rorhis fortdodgensis Lees and
Thomas
CRINOIDEA-
Crinoid stems
BRYOZOA-
Batostomella interstincta ffirich Phillipsia sp. 600p. cit., p. 605 If. .Introduction In no other area in North America do geodes attain such an
exceptional development as in the Keokuk and Lower Warsaw
beds of the central Mississippi Valley. Representative speci-
mens of geodes from this region are now found in the mineral
cabinets of many of the museums of the world. Apart from
Professor Brush'sl preliminary examination and description of
a few select specimens submitted to him in 1865 by A. H. Worthen, then director of the Geological Survey of Illinois, no
study of these remarkable geodes has ever been made, in spite
of the fact that they bear a variety of metallic sulphides and
promise to throw soine light upon the origin of more important
deposits of these materials in sedimentary rocks which show no
signs of igneous influence. The following report on their char-
acteristics is therefore considered justified. 1 Geol. Survey Illinois, vol. I , pp. 90-96 ; 1866_
~ Geology, vol. I, pp_ 416, 417; 1904_
.,. CHAPTER V
THE GEODES OF THE KEOKUK AND LOWER WARSA. W
BEDS .Introduction Definition of Geode The term geode is derived from the Greek word meaning
earthlike. The following definition of geode is given in Web-
ster's International Dictionary : a "A nodule of stone containing a cavity lined with
crystals or mineral matter:" crystals or mineral matter:"
b
"The cavity in such a nodule " crystals or mineral matter:
b "The cavity in such a nodule." b "The cavity in such a nodule." Geodes are described in Dana's Manual of Geology as
"Spheres or irregular spheroids, or balls in rock, hollow within
and lined with crystals."
Ch
b
li
d S li b
i
h i
b
k
G
l Chamberlin and Salisbury2 in their text books on Geology
state that geodes are formed by the partial filling of cavities by
the inward growth of crytsals. DEFINITION OF GEODE 305 Bassler,3 who has recently made a study of geodes, defines
them thus: "Spheroidal or irregular spheroidal, concretion-like masses,
hollow and lined with crystals pointing inwardly are known to
geologists as geodes." The following definition is given by 0 'Hara in Bulletin 9 of
the South Dakota School of Mines: "Geodes are spheroidal masses of mineral matter formed by
deposition of crystals froin mineral solution on the walls of a
rock cavity. The growth is constantly inwa:r:d toward the center. If the process of deposition has continued sufficiently long, the
crystals reach across the ,depositional space, interlock with each
other and the geodes become solid. Often the cr'ystals project
only part way, leaving a considerable cavity and then the geodes
when broken present a crystal lining of much -beauty and inter-
est. " In all but the last of these definitions the impression is given
that geodes are always hollow and that they are formed by the
partial filling of pre-existing cavities by the inward growth of
crystals. Such a view, however, is incorrect, for the growth of
crystals toward the interior has in many cases proceeded suf-
ficiently for them to meet and coalesce, thus giving rise to solid
geodes. Furthermore geodes are not always spheroidal. Some of them
do not even distantly approach the spheroidal form. Many are
very irregular and nodular in shape. A more comprehensive
definition is as follows : Geodes are rounded or nodular masses
formed by the inward growth of mineral matter upon the walls
of pre-existing cavities. 3 u. S. Nat. Museum Proe, vol. 35, p, 133 ff; 1908, Definition of Geode They may be either solid or hollow,
depending upon whether or not the process of filling has been
carried to completion. The origin of the cavities need not enter into the definition. They may be either original, as in amygdaloidal lava, or they
may be due to solution. Solution cavities are characteristic
of sedimentary rocks. In their most typical development,
geodes possess siliceous or calcareous shells and in this respect
they should be distinguished from geodic cavities which are in-
separable from the enclpsing rock. MISSISSIPPIAN STRATA OF IOWA 306 Agates have a method of development analogous to that of
geodes but they always consist of banded chalcedonic quartz. Also they are normally limited to igneous rocks while geodes
are typically confined to shales and limestones. d l
d
i
diff
i
h i
i i
f
d Nodules and concretions differ in their origin from geodes
and agates in that they · grow from a nucleus outward by the
segregation of like material originally disseminated through
thf> surrounding rocks. Other Occurrences of Geodes Some of the more important occurrences of geodes in thi~
country are as follows : (1) In the Keokuk limestone and the
Lower -Warsaw beds of the Central Mississippi Valley; (2) in
the Little Falls dolomite of New York;
(3) in the Lockport
limestone at Lockport and Rochester, New York;
(4) in the
Knobstone shales of Indiana and Kentucky;
(5) in the Ter-
tiary beds of the Big Bad Lands of South Dakota; and (6) in
Tertiary shales at Yaquima Bay on the coast of Oregon. I
E
l
d
d
i
h
l
d d l
i i
l In England geodes occur in the marls and dolomitic conglom-
erate of the Keuper formation and in a basalt at Tortworth. Geodes of the Keokuk Beds Geodes attain their most typical development in the Lower
Warsaw beds. But geodes and calcareo-siliceous masses are
locally found in the Keokuk. These will be considered briefly
before passing to a more detailed discussion of the geodes of
the Lower Warsaw. In this subdivision the masses are confined invariably to un-
fossiliferous calcareous shale beds and impure magnesian lime-
stone layers which are interstratified with the bluish fossilifer-
ous crystalline limestone. They are present at only a few local-
ities in the area. Tlle best known of these are (1) along the
bed of a small intermittent stream two miles northwest of Den-
mark in Lee county; (2) in a quarry along Long creek in the
northern part of section 18 of lJnion township, Des Moines
county ; and (3) at the mouth of Soap creekin the city of K eo-
kuk. The occurrence near Denmark is typical. Imperfect calcar-
",uus geodes and calcareo-siliceous masses appear in several GEODES OF KEOKUK BEDS 307 layers separated from each other by bluish fossiliferous lime-
stone. The most productive layer, however, is an impure buff
magnesian limestone about two and one-half feet in thickness. Rounded and lenticular masses, some of which exceed two feet
in greatest diameter, are common at this level. The relation of
such masses to the surrounding rock is not such as to indicate
appreciable expansion during their growth. The maximum
arching of the overlying layers noted was less than two inches
for a mass two feet in diameter. The majority of these masses
are solid, and although they possess chalcedonic shells, in part
at least, as do the typical geodes of the area, and may have a
similar method of origin, many of them cannot be regarded
strictly as geodes. Rather they should be described as segre-
gations. The interiors of such masses are characterized by no
definite structural arrangement and many of them contain lay-
ers or smaller inclusions of material resembling the surround-
ing rock. They are usually occupied in large part, however, by
crystalline calcite and fine-grained quartzose material. The cal-
cite and massi ve quartz may be indiscriminately mixed but
usually the calcite either occupies the entire interior or is limited
to isolated pockrts in the included limestone. Geodes of the Keokuk Beds In the latter case
the calcite of some masses contains small inclusions of buff cal-
careous material ann in some others is associated with masses
of sphalerite, some of which are as large as a man's fist. In
still other cases it hrars many fibrous inclusions of pyrite or
small sphenoids of chalcopyrite. All three sulphides may occur
in the same mass but not more than two have been found i1) any
one calcite pocket. The chalcopyrite found in some masses has
a zonal arrangement, the small sphenoids generally bein'g most
abundant about the periphery of the calcite clusters. Such segregations are usually surrounded, either wholly or in
large part, by a ~hell of chalcedony which may differ in thick-
ness from a thin film to several centimeters. The outer surfaces
of most shells are marked by numerous ridges, protuberances
and rounded depressions, and in some cases they show ,a blis-
tered appearance. An impure soft magnesian limestone layer which is exposerl
i1). the quarry in ~e('~ion 18, Union township, Des Moines county,
and which belongs in the upper part of the Keokuk limestone, is MISSISSIPPIAN STRATA OF IOWA 308 geode-bearing. Wen formed hollow calcareous geodes are com-
mon at this place. Their shells consist commonly of buff cal-
careous material which is more indurated than the surrounding
rock. But in some cases incomplete siliceous shells envelop a
portion of the, masses. Besides the rhombohedrons of calcite
which line the interiors of these masses, crystals of sphalerite
are abundant. In several instances this mineral was found to
be associated with smithsonite, one of its decomposition pro-
ducts. Well formed caJcareous geodes occur in an impure limestone
bed near the middle of the Keokuk at the mouth of Soap creek
in the city of Keokuk. This geodiferous layer is six feet in
thickness. It bears hollow calcareous geodes ranging up to ten
or twelve inches in diameter. The interiors of these are lined
with transparent rhombohedrons of calcite to which are at-
tached numerous hairlike tufts and fibers of millerite, the sul-
phide of nickeL
These tufts and fibers are intergrown
"\vith the calcite and in some cases they are entirely included
by it. SmaJI geodic cavities have like:wise been noted in the cherty
limestone layers of the Montrose chert which was exposed in the
excavation for the Mississippi river dam at Keokuk. Geodes of the Keokuk Beds These
have no true shells and usually occur in compact chert bands. They are almost all lined with quartz crystals, but upon these
are frequently superimposed rhombohedrons of calcite. Some of
these rhombohedrons carry fibrous inclusions or needle-like pro-
jections of millerite. The nickel mineral, however, is not always
confined to ·calcite, for in one instance its filaments were found
implanted upon the crystals of a pure quartz geode. OCCURRENCE .AND ::nZE The geodes of the Lower vVarsaw are remarkable for their
abundance as well as for their beauty. Geodes occur in great
profusion in the geodiferous phases of this horizon and many
of the outcrops are thickly set with these rounded masses. The
weathering of such outcrops releases large numbers of speci-
mens and the stream beds at some localities are strewn with
many geodes. (See Plate II.) PLATE I IOWA GEOLOGICAL SURVEY PLATE I IOWA GEOLOGICAL SURVEY
PLATE I
Group of !l'eodes from the Lower Warsaw beds. Group of !l'eodes from the Lower Warsaw beds. 311 CHARACTER OF GEODES The geodes from this horizon range in size from about 0.2
centimeter up to 75 centimeters in diameter. Well developed
geodes, however, of either extreme are very rarely found. Many
of the smallest specimens consists of solid chalcedony, but well
formed geodes no larger than a pea occur. The greater num-
ber of the largest examples, on the other hand, are either lentic-
ular and poorly developed, or compound, in which case they
consist of several individuals intergrown. Well formed geodes,
however, ranging up to 60 centimeters in diameter are found,
but most of these are chambered in their interiors. Large and small geodes are not found intimately associated
in any given layer, but there may be considerable range in size
at different levels in . the same exposure. Moreover, there may
be marked differences in their dimensions at the same level at
different localities. In abundance the geodes of the geodiferous phase of the
Lower Warsaw have a wide range both laterally and vertically. In places they are so numerous in a given layer that their free-
dom of growth has been interfered with and they are thus of
very irregular shape. In other places, geodes are very sparing-
ly distributed throughout the rock and none are present in an
outcrop embracing an area of several square feet. In the non-
geodiferous phase no trace of geodes may be found. The proportion of well-developed geodes in the beds differs
greatly at different localities. At some places well formed
geodes do not constitute more than ten per cent of the total, but
at others the great majority of those broken may be of typical
character. The same relationship holds for different levels in
the Lower Warsaw at the same locality. . MlNERALOGIOAL CHARACTER Mineralogically the geodes are almost all siliceous but a few
calcareous geodes and geodic calcareous nodules have been
found. The siliceous types are without exception characterized
by an outer shell of chalcedony. In most geodes this is followed
by crystalline quarts, but calcite occas,ionally succeeds the chal-
cedony. In some instances, however, the interior is lined with
botryoidal chalcedony and no crystalline quartz nor calcite ap-
pears. Many of these chalcedonic types· bear cubes of pyrite, MISSISSIPPIAN STRATA OF IOW.4.- 312 and one. speci,rnen was found which contained sphalerite, partly
decomposed to smithsonite. This geode bore also a slight in-
crustation and a few minute crystals of gypsum, but the same
mineral has been found in normal quartz geodes. Some of the
quartz geodes are solid. In many of those which are hollow the
quartz crystals of the interior are studded with crystals of cal-
cite, dolomite, ankerite, sphalerite, or pyrite. More rarely
elongated crystals of magnetite or the red powder of hematite
are found. Some of these quartz types, on account of their im-
perviousness, contain water, although the surrounding rocks
may be dry. Many hollow siliceous geodes in the vicinity of Niota, Illi-
nois, are filled with a black viscous bitumen, and those from the
upper argillaceous half of the Lower Warsaw, particularly at
Keokuk and Warsaw, commonly contain kaolin in the form of a
flocculent white powder. C l i
d
d
di
l
d l
i h
i h Calcite geodes and geodic calcareous nodules with or without
siliceous shells are much .less common than the quartz variety. A few calcite geodes from the Denmark locality bear small
sphenoids of chalcopyrite. The geodic calcareous nodules, how-
ever, are characterized in general by calcite of two periods of
growth and many of them contain elongated crystals of pyrite. Calcareous nodules without geodic cavities and inclosed by
siliceous shells identical with those of perfect geodes have been
found at several localities. RELATION TO THE CONTAINING ROCK It has been stated previously that the Lower Warsaw is rep-
resented by geodiferous and nongeodiferous phases which may
grade into each other laterally within short distances. The only
apparent physical difference betwken the two phases is that the
member where it bears no geodes is in most cases, although
not in all, fossiliferous, while the geodiferous phase is, except
for occasional limited seams of limestone, nearly destitute of
fossil remains. The Lower Warsaw, in its typical development, is roughly
di visible. intq two halves. The lower of these is massive and
has the composition of an impure magnesian limestone. Bands
or seams of fossiliferous nonmagnesian limestone are sometimes RELATION OF GEODES TO ROCK 313 found interbedded with this type. Where it is geodiferous this
limestone tends to bear large and well developed geodes which
are distributed irrregularly throughout the rock mass. The
upper part, however, is much more argillaceous and in some ex-
posures is laminated. The geodes in this part are much more
numerous than in the lower part but they are much smaller and
more imperfectly developed. In general, it may be said that the
degree of development of the geodes varies directly with the
amount of calcareous matter in the rocks. In this part of the
Lower Warsaw most of the geodes are found in productive lay-
ers or bands parallel to the stratification and ranging from a
few inches to several feet in thickness. These bands are as a
rule separated from each other by layers of barren shales of
differing thickness. Such bands, interbedded with unproductive
shale, and in some localities thickly set with geodes, are in many
cases traceable along the entire width of an outcrop. The relationship of the geodes of the Lower Warsaw to the
. containing rock, as in the case of the masses in the Keokuk
limestone, does not suggest appreciable expansion during their
formation. At no place was the inclosing rock found to be un-
der any strain at the contact, nor was 'there any evidence of
flexing consequent upon lat!'lral pressure. Some thin seams of
limestone, however, which overlie the geodes are slightly arched
upward. But such archings are no greater than would result if
masses analogous in size to the geodes were imbedded in the
sediment at the time of its accumulation, and this seems to be
the true condition. RELATION TO THE CONTAINING ROCK This idea is further strengthened by the oc-
currence of a few limestone layers which exhibit a thinning
where-they pass over the upper surface of the geodes. This is
the usual relationship. An excellent example of such thinning is
found in the lower part of the Lower Warsaw at the outcrop
along Fox river, near Fox City, Missouri. A close study of geodes in place in the rocks reveals. the fact
that their greatest diameter invariably lies in a horizontal
plane, provided their development has not been interfered with. Calcareous nodules when found exhibit a similar relationship. Many of the geodes have been deformed and crushed in place
by the pressure of the superincumbent strata. The imperfect
development of such geodes indicates that the crushing must MISSISSIPPIAN STRATA OF IOWA 314 have taken place while the process of geodization was yet in
progress. Additional evidence of the settling of the rocks is
found in the slickensided structure which characterizes much of
the shaly material adhering to the siliceous shells of the geodes,
and which, in some instances is even impressed upon the sur-
face of the chalcedonic shells. The extent of the geodes in the roek back from the outcrops
is 'worthy of some consideration. Bassler4 in his discussion of
the geodes of the Knobstone shales of Kentucky and Indiana
calls attention to the impervious nature of shale and inclines to
the view that the geodes of that formation, which are of fossil
origin, are confined to the ilmnediate neighborhood of joint
planes or rifts in the strata through which "vater had easy ac-
cess. In speaking of their occurrence he says : , 'U sually the geodes were lying on the surface itself, free or
partially covered with soil, and digging in the compact shale
immediately beneath would reveal no trace of other specimens. In other eases they were apparently buried in the shale, but, in
every instance of this kind, closer examination showed these ex-
amples to lie on the edge or very neal' to joint planes or rifts
in the strata through which the 'water had easy access."
. Such a relationship does llot appear to hold for the geodes of
the Lower Warsaw beds. They do accumulate along ravines as
residual material, but they are found also in appreciable num-
bers in the unweathered shale. 'U. S. Nat. Museum Proc. vol. 35, p.
1~3 ff. RELATION TO THE CONTAINING ROCK Blasting many feet into the
bluff of the Lower Warsaw at Keokuk, Iowa, did not reveal any
discontinuity of its geodiferous character. Geodes occur in a
clay pit in the beds at Hamilton, and the sinking of a well into
this division neal' Bentonsport revealed the presence of perfect
geodes well down within the formation. The mineralogical relationships of the geodes to the contain-
ing rock received some atte!ltion in this study. The O'eneral COll-
clusion drawn from this investigation is that at any given local-
. jty each geodiferous layer or band, as a rule, bears geodes which
are closely related among themselves but which may be mineral-
ogically unlike those from other bands. Such differences, how-
ever, may be trivial, and one series may possess only a greater
and more constant amount of one mineral than the other. Also
the geodes from the same level may differ in general character TYPES OF GEODES 315 at different localities. In this respect it has been found that
there are characteristic geode provinces. at different localities. In this respect it has been found that
there are characteristic geode provinces. To illustrate the diversity of character of the geodes from
different bands, specimens from several levels in the Lower
Warsaw, at Warsaw, Illinois, were studied· and classified upon
the basis of their development and mineral content. The fol-
lowing tables represent the types found in three productive
bands in the lower ten feet of the upper argillaceous half of the
formation at that place. The bands are designated as band A,
band B, and band C, respectively, A being the highest band. BAND A. BAND A. Geodes dominantly of the quartz type. I. Geodes having well developed chalcedonic shells. A. Hollow geodes. NUMBER
1. Interior lined in part with drusy quartz and in part with
granular quartz coated with chalcedony...................................... HI
2. Geodes similar to those of I A 1. but contain:ing kaolin ... _... 25
3. Geodes like I A 1, but with fine crystals of quartz occurring
upon the chalcedonized grains. (a)
Without fl.akes of pyrite ............... _....................................... 12
(b)
With flakes of pyrite ................................. _........................... 2
B. Geo.lllis solid or nearly so. (a)
Like I A 3a but irolll stained! ......... _ .... _ .... _........... ........... 2
II. Geodes with imperfect shells. A. Otherwise like I A 2 ................................. _........................................... 2
B. Otherwise like I A 3 ................................................................................ 3
BAND B. Geodes dominantly of calcite type. I. Geodes with well developed shells. NUMBER
A. Hollow geodes. 1. Interior of chalcedonic shells lined with rhombs of calcite. (a)
Without kaolin .......................................................................... 9
(b)
Bearing ~aolin .......................................................................... 10
B. Solid geodes ( quartzose) ......... _ .... _ ............................ _....................... 1
II. Geodes with imperfect shells. A. Hollow specimens. 1. Bearing calcite, kaolin, clay and sphalerite ................................ 1
B. Geodes solid or nearly so. 1. Otherwise like II A 1 ...................................................................... 1
2. Otherwise like II B 1 but containing no sphalerite ................ 3
BAND C. Geodes dominantly of calcite type. I. Geodes \vith well deve10ped shells. NUMBER
A. Hollow geodes. 1. Interior of shell studded with transparent crystals of calcite
9
2. Like I A 1 but bearing kaolin ........................................................ 1
3. Like I A 1 but bearing a few flakes of pyrite .......................... 1
B. Solid geodes. 1. Interior filled with impure calcite ................................................ 8
2. Like I B 1 but containing kaolin .................................................. 7
3. Like I B 1 but containing blende and kaolin ............................ 1
4. Like I B 1 but containing only blende ......... _............................. 1 Geodes dominantly of the quartz type. ll d
l
d
h l
d
i
h ll Geodes dominantly of the quartz type. I. Geodes having well developed chalcedonic shells. A. Hollow geodes. NUMBER
1. Interior lined in part with drusy quartz and in part with
granular quartz coated with chalcedony...................................... HI
2. Geodes similar to those of I A 1. but contain:ing kaolin ... _... 25
3. BAND B. I. Geodes with well developed shells. NUMBER
A. Hollow geodes. 1. Interior of chalcedonic shells lined with rhombs of calcite. (a)
Without kaolin .......................................................................... 9
(b)
Bearing ~aolin .......................................................................... 10
B. Solid geodes ( quartzose) ......... _ .... _ ............................ _....................... 1
II. Geodes with imperfect shells. A. Hollow specimens. 1. Bearing calcite, kaolin, clay and sphalerite ................................ 1
B. Geodes solid or nearly so. 1. Otherwise like II A 1 ...................................................................... 1
2. Otherwise like II B 1 but containing no sphalerite ................ 3
BAND C. Geodes dominantly of calcite type. I. Geodes \vith well deve10ped shells. NUMBER
A. Hollow geodes. 1. Interior of shell studded with transparent crystals of calcite
9
2. Like I A 1 but bearing kaolin ........................................................ 1
3. Like I A 1 but bearing a few flakes of pyrite .......................... 1
B. Solid geodes. 1. Interior filled with impure calcite ................................................ 8
2. Like I B 1 but containing kaolin .................................................. 7
3. Like I B 1 but containing blende and kaolin ............................ 1
4. Like I B 1 but containing only blende ......... _............................. 1 BAND A. Geodes like I A 1, but with fine crystals of quartz occurring
upon the chalcedonized grains. (a)
Without fl.akes of pyrite ............... _....................................... 12
(b)
With flakes of pyrite ................................. _........................... 2
B. Geo.lllis solid or nearly so. (a)
Like I A 3a but irolll stained! ......... _ .... _ .... _........... ........... 2
II. Geodes with imperfect shells. A. Otherwise like I A 2 ................................. _........................................... 2
B. Otherwise like I A 3 ................................................................................ 3 I. Geodes having well developed chalcedonic shells. A. Hollow geodes. BAND C. I. Geodes \vith well deve10ped shells. NUMBER
A. Hollow geodes. 1. Interior of shell studded with transparent crystals of calcite
9
2. Like I A 1 but bearing kaolin ........................................................ 1
3. Like I A 1 but bearing a few flakes of pyrite .......................... 1
B. Solid geodes. 1. Interior filled with impure calcite ................................................ 8
2. Like I B 1 but containing kaolin .................................................. 7
3. Like I B 1 but containing blende and kaolin ............................ 1
4. Like I B 1 but containing only blende ......... _............................. 1 316
MISSISSIPPIAN S MISSISSIPPIAN STRATA OF IOWA 316 .1\.nother band a few feet above A yielded very imperfectly
developed and nodular geodes. Many specimens from this level
have only incomplete chalcedonic shells· while their interiors are
occupied by clay intermixed with kaolin. The greatest diameter
of these nodular geodes is about three inches. Th
l
f
h
L
W
hi
l
b The lower part of the Lower Warsaw at this place bears
much larger but less 'numerous geodes than does the upper
division. The lower four and one-half feet is by far the most
productive part of the seven and one-half feet of this division
which is exposed. The geodes taken at this level from an area
four and one-half feet high and ten feet wide were studied. ~J..lhe
results .of this study are given in the following table: I. Well formed geodes with chalcedonic shells. NUMBER
A. Solid quartz geodes ..................... _ ...................................... _................... 9
B. Hollow quartz geodes. 1. Interior lined with pure quartz crystals. (a)
Crystals not bearing flakes of pyrite ................................ 3
(b)
Crystals bearing' flakes of pyrite ................... _................. 6
2. Interior lined with quartz crystals which :l,re coated with
chalcedony. (a)
Without flakes of pyrite ..................... _............................... 2
(b)
With flakes of pyrite .............................................................. 5
II. Imperfect geodes; either broken or possessing brittle defective shells;
interiors hollow but occupied by panular and finely crystalline quartz. A. Already broken ... _..................................................................................... 29
B. Broken with hammer ............................................. _............................... 9
63 At this locality the geodes from anyone layer were not found
to differ greatly in their mineralogical character, and this is
the general rule. Instances have been found, however, in which
there is considerable range in the mineral content of the geodes
from the same level. I. Well formed geodes with chalcedonic shells.
NUMBER
A.
Hollow geodes.
1. Interior lined with crystalline quartz ............................................
2
2.
Like I A 1 but quartz crystals bearing elongated crystals of
magnetite upon their surfaces ... _ ...................... _ ......................... ,.
1
3. Like I A 2 but containing calcite also ......... _...............................
1
4. Like I ·A 1 but with quartz bearing flakes and crystals of
pyrite ............................................................................. _.....................
3
5.
Like I A 4 but containing calcite ................................................
7
II. Solid and imperfectly developed geodes;
A. Interior partly filled with shaly material............................................
8 BAND C. This feature is illustrated by the follow-
ing table prepared from the study of geodes taken from a band
in the upper part of the Lower 'lvarsaw, which is exposed along
a small stream on the east side of Mud creek, about one mile
above its mouth, in Henry county, Iowa. I. Well formed geodes with chalcedonic shells. NUMBER
A. Hollow geodes. 1. Interior lined with crystalline quartz ............................................ 2
2. Like I A 1 but quartz crystals bearing elongated crystals of
magnetite upon their surfaces ... _ ...................... _ ......................... ,. 1
3. Like I A 2 but containing calcite also ......... _............................... 1
4. Like I ·A 1 but with quartz bearing flakes and crystals of
pyrite ............................................................................. _..................... 3
5. Like I A 4 but containing calcite ................................................ 7
II. Solid and imperfectly developed geodes;
A. Interior partly filled with shaly material............................................ 8 TYPICAL LOCALITIES FOR GEODES 317 The same feature is illustrated even more forcibly by the
mineralogical nature of the geodes which occur in a band along
a ravine which cuts into the Lower Warsaw in the vicinity of
the Fort Madison and Appanoose Stone Company's quarry near
Niota, Illinois. The. geodes obtained from this band were as
follows : 1. Well formed geodes 'with siliceous shells. N UMBER
A. Hollow geodes. 1. Interior lined with mammillated chalcedony. (a)
Metallic sulphides wanting ........ ___ . ____ . _____________________________ .____
6
(b)
Chalcedony bearing pyrite_
1. Without calcite ________________________________________ . __________________ ._____
3
2. With calcite
__________________________________ . _______ .. _________________________
1
( c)
Chalcedony bearing sphaleri te ______________________________________________
1
2. Interior lined with quartz crystals. (a)
With pyrite ____________________________________________________________________________
1
(b)
Without pyrite _______________________________________________________________________
1
3. Interior lined with crystals of calcite. (a)
With pyrite __ .. __________________ . _________________ . _________________ . ____ ._____________
2
(b)
Without pyrite _____________________ . _________________________ . ___ . _____________ .______
2
B. Solid geodes. 1. Solid chalcedony _________ ._. ______________________________ .... ___ . ___ ........ 1
2_
Solid calcite _______________________________________________________ . __ .____________________________
3
II. Imperfectly developed geodes; containing shaly matter. A. Without kaolin ____________ ___________________________________________________ . ________ ._._._ ....... _ .. ___ . 3
B. With kaolin . ______________________ .. _____ .. ___ ........ _ .. _ .. _________ ... __ . _____ ..... _ ... _______
1 A. Without kaolin
B. With kaolin . B. BAND C. With kaolin The formations overlying the Lower Warsaw do not appear
to_have influenced geode development, for geodes occur at local-
ities where the overlying strata are still preserved, as well as
at localities where they have been completely eroded. Thus, at
Warsaw the geodiferous beds are succeeded above by the Upper
,\Varsaw formation,' but at Lowell the beds are overlain at the
most productive point only by dr~ft. h
b
f
f
i i
b
h The presence or absence of unconformities between the Lower
Warsaw and the overlying formations, however, may have had
some influence, but it is believed that the effect, if there was
any, had to .do with the time of origin rather than with the
mode of development. IMPORTANT LOCALITIES Some of the most typical localities for studying the Lower
,\Varsaw and its geodes have already been mentioned in connec-
tion with the discussion of the stratigraphy of the beds. But
reference is again made to these localities with greater emphasis
Th
b
k
l
li i
i h
d
b
K
k k I The best known localities, without a doubt, are Keokuk, Iowa,
placed on the geodes. MISSISSIPPIAN STRATA OF IOWA 318 and Warsaw, Illinois. It was from these places that A. H. Worthen collected many specimens to distribute among the
museums of the world. The same localitites have, in more re-
cent years, afforded most of the geodes taken from the region
for museum and ornamental purposes. . The Lower \!ItT arsaw is most typically developed at Keokuk
along Soap creek near the end of Fourteenth Street, but it is
exposed also along the west bluff of Mississippi river from the
Union station southward for a distance of at least two miles. The Soap creek exposure is most satisfactory for the study of
. geodes. A section of the beds at this locality has been recorded
earlier in this report. (See page 193.)
h
h
i
i
d
hi
l
li
h
hi The most characteristic geodes at this locality are the thin-
shelled siliceous types which bear crystals of dolomite and
ankerite. These are best developed in the lower part of the
formation but on account of the fragile nature of th~ir siliceous
shells they have been broken in most instances by the scaling off
of large flakes of the containing rock which adheres tightly to
the geodes. . The geodes of the upper part of the beds are much smaller
than those from the lower part, and like those from Warsaw at
this horizon, many of them contain the white powder of kaolin. The subjoined table will indicate the general character of the
geodes occurring in a persistent band near the middle of the
upper part of the beds. 1. Geodes well developed and hollow. N UMBER
A. Interior lined with drusy quartz .......................................................... 1
B. Interior lined with drusy quartz which bears small crystals 0'£
pyrite ............................................................................................................ 2
C. Interior occupied by drusy quartz, pyrite, dolomite and calcite.... 1
D. Interior lined with drusy quartz studded with dolomite ................ 3
E. Interior lined with drusy quartz, dolomite and pyrite .................... 1
F . IMPORTANT LOCALITIES The geodes occur both in the lime- MISSISSIPPIAN STRATA OF IOWA 320 stone and in the shale. They are dominantly of the quartz,
calcite and quartz-calcite varieties. Metallic sulphides are rare. At Hamilton geodes are common along Railroad creek but
conditions are the most favorable for studying them at the clay
pits of the Hamilton Clay Company, situated about one-half
mile southeast of town. The bluish nonfossiliferous shales of
the upper part of the Lower Warsaw are here used for the
manufacture of brick and tile and have been exposed to a max-
imum thickness of about eight feet. Many geodes which have
been picked from the shale in the process of excavation are now
scattered over the floors of the pits. More than one hundred of
these were broken. Of this number about one-fourth were of
the solid quartz variety and the remainder consisted chiefly of
hollow quartz geodes whose interiors were in most cases stud-
ded with rhombs of calcite or crystals of dolomite or ankerite. A few, however, were found to contain pyrite and an occasional
one contained sphalerite. The anke-rite is in many cases partly
decomposed to limonite. The interior linings of nearly all of the
geodes at this place are incrusted, in part at least, with lime
carbonate. Many of the hollow geodes have been fractured transversely
and recemented by calcareous material. These are for the most
part much discolored in their interiors. The rupture of these
is believed to have been caused by the freezing of included
water when they were not far below the surface. A few de-
formed geodes also were observed. Most of these contained
kaolin and included clay but a few were found to contain dolo-
mite or ankerite. h
f h
Ci
i
i i The exposure of the Lower ,Varsaw at Fox City, Missouri, is
very interesting from many standpoints. ~eference has already
been made to the excellent opportunities at this place for study-
ing the relation of the geodes to the containing rock. Many
geodes have been collected at this locality and considerable
blasting has been done along the face of the bluff to f3ccilitate
their removal from the rock. The upper part of the formation
at this place furnishes the greatest number of specimens, but
they are small and most of them are poorly developed. IMPORTANT LOCALITIES Interior occupied by drusy quartz, dolomite and k.aolin ................ 1
G. Interior lined 'with coarse crystals of quartz . ___ ._ .... ___________ .. __________ ... 2
H. Coarse crystals of quartz and pyrite ..... _ .. _ .. _ .. _ .................... _....... 1
2. Geodes well developed but solid ..................... _............................................. 2
3. Geodes imperfectly developed'; interior nearly filled. A. Lined with drusy quartz and dolomite and bearing kaolin ............ 7
B. Interior consisting of drusy quartz, dolomite, kaolin and blende.... 1 1. Geodes well developed and hollow. A
Interior lined with drusy quar 3. Geodes imperfectly developed'; interior nearly filled
A
Lined with drusy quartz and dolomite and bea A. Lined with drusy quartz and dolomite and bearing kaolin ........... B. Interior consisting of drusy quartz, dolomite, kaolin and blende... Another excellent place for studying geodes is along the east
bluff of a creek just northeast of the town of Warsaw (fig. 16),
where the Lower Warsaw is well exposed. A detailed section
of the rocks at this point has been given on page 190. The na-
ture of the geodes at this place is indicated by the tables pre- GEODES IN CRYSTAL GLE N 319 sented under the discussion of the mineralogical relationship of
the geodes to the containing rock. (See pages 315 to 317.) One
of the most striking features in connection ,"lith the geodes at
this locality is that although they are otherwise quite similar to
the Keokuk specimens, they were not found to bear dolomite,
which is a very characteristic mineral in the geodes at Keokuk. FIG. lB.-Geodes in place in Geode bed along creek just northeast of Warsaw, Illinois. FIG. lB.-Geodes in place in Geode bed along creek just northeast of Warsaw, Illinois. Geodes occur also at Soap Factory Hollow, a creek two
miles south of Warsaw, and along the beds of creeks tributary
to the Mississippi between Warsaw and Hamilton. Of these
creeks. Crystal Glen, whose mouth is about two miles above War-
saw, is the most important. Many geodes are strewn along the
bed of this stream and about a mile up the valley an outcrop of
the lower part of the geodiferous phase of the Lower Warsaw
maybe seen. The exposure at this point is about eight feet
high and is made up of highly calcareous shale interstratified
with layers of limestone. IMPORTANT LOCALITIES In size
they range from about 0.2 centimeter to 20 centimeters in diam-
eter. Many of the smallest geodes consists of solid chalcedony. BITUMINOUS GEODES OF J\TIOTA 321 But the larger geodes are usually of the quartz type and many
are nearly or quite solid. Other varieties of subordinate im-
portance are the quartz-pyrite, quartz-calcite, quartz-calcite-
pyrite and the kaolinitic types. The geodes from the lower part of the shale are of far great-
er importance than those from the upper part. A t no other
known locality in the area can such large and well developed
geodes be so satisfactorily studied in place in the rocks. Num-
erous well formed quartz geodes ranging up to 45 centimeters
in greatest diameter may be seen dotting the face of the bluff. They reach their maximum development, however, in a layer six
feet in thickness near the base of the exposure. The geodes
from this layer may be classified as follows: A. Geodes exceeding six inches in diameter. NUMBER
1. Interior hollow. (a)
Intel'ior lined with qumtz crystals which bear small
flakes of pyrite upon their surfaces ...................................... 2
2. Solid geodes. (a)
Interior filled with crystalline quartz .............................. 1
B. Geodes less than sLx inches in diameter. 1. Interior hollow. (a)
Pure quartz type .................................................................... 4
(b)
Interior lined with quartz crystals bearing flakes of
pyrite .......................................................................................... 26
2. Solid or almost solid geodes. (a)
Pure quartz filling the interior .................. :........................... 2
(b)
Interior filled with quartz which bears pyrite .................. 2 The widespread occurrence of pyrite and the paucity of cal-
cite are the most characteristic features of the geodes at this
place. Another Missouri locality for collecting geodes is near Way-
land. A few feet of the Lower "\Varsaw are exposed about one-
half mile southwest of this place" in the east bank of Fox river. Here many of the geodes contain calcite. St. Francisville, Mis-
souri, also is said to be a good locality for quartz geodes. The geodes from the lower part of the Lower Warsaw at sev-
eral localities near Niota, Illinois, are strikingly contrasted to
those in other occurrences in that many of them are partly or
completely filled with a black viscous bitumen. IMPORTANT LOCALITIES The fact that
such bituminous geodes occur in a non-bituminous shale and
may be found in close proximity to ordinary O'eodes which show
no trace of bitumen, lends to this feature still greater interest. As a general rule, however, the regular hollow geodes which MISSISSIPPIAN STRATA OF IOW:A 322 occur in the same layers with bituminous types show at least a
black stain in their chalcedonic shells. Such bituminous geodes occur along a small creek in thfl
southern limIts of Niota. But the most satisfactory place to
study them is two miles south of Niota along the north and
south forks of a small creek a short distance back from their
confluence. At the more northerly of these places bituminous
geodes occur only in a layer a few feet in thickness near the
base of the Lower Warsaw. Above this layer occur thin-shelled
geodes lined with drusy quartz studded with ankerite. These
show no traces of petroleum. The geodes which bear oil are, so far as could be ascertained,
no different from the geodes 'which normally occur at this hor-
izon. Most of them are of either the calcite or the quartz types
but some geodes lined with botryoidal chalcedony also contain
bitumen. Furthermore, the thickness of the wall seems to have
had no great influence, for almost solid quartz geodes have been
found to contain a small amount of the crude oil in their cen-
ters. No bitumen or carbonaceous material has ever been found
included in the quartz. The bitumen, then, must have been in-
troduced at some tin1e subsequent to the development of the
geodes. It certainly has not interfered with their development. The soUrce of the oil is not positively known. It may have
migrated into the basal part of the Lower Warsaw from the
underlying formations. When it penetrated the geodes it must
have been in a much more fluid condition than it now is. Other outcrops of the Lower Warsaw occur along a small
creek which empties into the Mississippi about three miles be-
low Niota. J ear the sources of this creek many rounded cal-
careous nodules occur in a layer of shale exposed along the
bed of the stream. One of these masses was found when broken
to bear a geodic cavity lined with calcite. IMPORTANT LOCALITIES Toward the mouth of the same stream, however, the :<seodifer-
ous shales al;e exposed in their usual facies. They are capped
with drift at this point and are underlain by the upper ledges
of the Keokuk limestone. The maximum exposure of the Lower
Warsaw is about thirty feet. The geodes at this place have
nearly all been deformed by the weight of the overlying sedi-
ments and in consequence of such deformation the upper or 323 GEODES NEAR LOWELL lower sides of many of the geodes were crushed inward before
geodization was complete. Their interiors are now occupied by
impure clay and kaolin. No bitumen was found in any of the
geodes at thi; locality, although conditions were favorable for
its retention. A similar condition prevails ,at the outcrops
above Niota. Thus in the ravine near the Fort Madison and
Appanoose Stone Company's quarry, no trace of oil was found,
although well developed geodes occur at that place. The most famous, and in fact the only known, locality for col-
lecting geodes in Henry county, Iowa, is east of Lowell, in Balti-
more township, along Mud creek, a tributary of Skunk river. Many geodes occur along the bed of this stream and several out-
crops of the Lower Warsaw appear. The first outcrop of
the Lower Warsaw to be seen in following up this creek
from its mouth is one in the southern part of section 27
at the west end of the iron bridge on the Lowell road. The beds
are succeeded above by St. Louis limestone. The exposure of
the Lower Warsaw at this place, however, is largely concealed
and cannot be satisfactorily studied. But a few rods farther
upstream a low bluff capped ·with drift on the east side of the
stream furnishes a section sixteen feet in thickness. The upper
ten feet of the beds at this place is v~ry argillaceous, but the
lower six feet is calcareous and some of the layers approach in
composition an impure magnesian limestone. The geodes of the more shaly part are small, imperfectly de-
veloped and nodular. The siliceous shells of these are of a red-
dish color and in some specimens the red tint shows through the
transparent druses of quartz which line the interior. The lower
part, 'on the other hand, bears more perfectly developed geodes
which are dominantly of the quartz type. IMPORTANT LOCALITIES These have a max-
imUlR diameter of more than ten inches. Flakes of pyrite or
single crystals of sphalerite occur in the interiors of some · of
these geodes while a few were found which were filled with
water. A short distance above this point and just west of the
second wagon bridge which spans Mud creek appears a third
outcrop of the beds. At the base of this section appears a layer
which was not exposed at the above described section. At the
top of the basal layer there occurs a band which is thickly MISSISSIPPIAN STRA'rA OF IOWA 324 set with rounded nodules which appear to be more calcareous
than the containing rock. Still farther up the creek the uppermost ledges of the Keokuk
beds appear in the bed of the stream, a fact which suggests
that an anticlinal arch exists at this place. No other exposures
of the Lower ,Varsaw appear until the northern limit of section
27 is reached. Here on the east bank of 'the stream is a bluff
of shale thirty feet in height, without a\l.y indurated rocks
above the shale beds. Parts of the formation are exposed also
a few rods north of this point in the southeTll part of sectioll
22 in an extension of the same bluff and along the ravines
emptying into Mud creek above this place on the same side of
the stream. These are the most northerly outcrops of the
Lower Warsaw. Beyond this point only the limestones of the
Keokuk appear. The upper part of the Lower Warsaw which is exposed at the
bluff in the northern part of section 27 consists of argillaceous
shale. The lower part is made up of calcareous shale inter-
stratified with bands of impure magnesian limestone. The up-
per argillaceous portion is twelve feet in thiclmess and bears
many geodes, but most of them are very small. In character
they are dominantly of the quartz type. The surfaces of many
of the specimens from this level are partly coated with mamil-
lary pyrites and many of their shells are of the red variety of
chalcedony. These geodes differ from those from other locali-
ties at the same level in that they do not bear kaolin. Many of
the imperfect specimens, however, contain impure clay. IMPORTANT LOCALITIES Just below the argillaceous member there occurs a band of
soft impure buff magnesian limestone which bears large quartz
geodes. A few of these have a maximum diameter of two ·feet. They are usually somewhat lenticular in shape and are cham-
bered within. The walls of some of the geodes from this level
are. quite thin but others possess very strong shells and can bo
broken only with great difficulty. In some of the geodes from
this layer characteristic twinned crystals of calcite are found. The formation is poorly exposed at the bluff in the southern
part of section 22 but many geodes similar in character to those
in the magnesian layer of the above exposure are strewn over
the surface of the slope. In addition to the types described 825 GEODES NEAR DENMARK from the foregoing locality there are found at this place a few
geodes whose interiors are partly or completely occupied by a
soft white gritty variety of silica which in some cases is inter-
sected by a network of veins of transparent quartz. In some
chambered specimens this material is limited to one of several
chambers but in simple geodes it may occupy the entire interior. In some instances cavities lined with small transparent crystals
of quartz appear in the interior of masses of this materiaL One small quartz geode from this exposure was found to bear
small slender crystals of magnetite and the red powder of
hematite. Along the bed of one of the ravines a few rods north
of this point there appear many large quartz geodes whose in-
teriors are stained with limonite as the result of the decomposi-
tion of small flakes of pyrite which they formerly contained. Several of these geodes have a maximum diameter of two feet,
but specimens of such size were invariably found to be of the
compound type. N one of these large geodes was found in place
but judging from the material adhering to their shells they were
derived from a layer of impure magnesian limestone. A short distance farther up the creek many geodes are to be
fOlmd in the drift on the west side of the creek. Beyond this
point a few appear along the bed of the creek as far north as
the bridge crossing the stream in the northern part of section
22. IMPORTANT LOCALITIES Satisfactory outcrops of the Lower Warsaw in Des Moines
county are rare and apparently the typica~ geodiferous phase of
the subdivision is lacking, for well developed geodes were not
found. N ear Denmark in Lee county an interesting exposure of the
Lower Warsaw is to be found along a small stream flowing
through the old Leverett estate, two miles northwest of the
town. In the bed of this creek there appears at one point a
layer of calcareous shale which bears many siliceous ·and cal-
careous nodules some of which are geodic. Some of the calcar-
eous nodules are inclosed by chalcedonic shells and the resem-
blance of these to the siliceous masses strongly suggests that
the latter have been formed by the replacement of their cal-
careous content by silica. Furthermore the similarity of the
geodes to such calcareous and siliceous nodules is striking. The MISSISSIPPIAN STRAT:A. OF IOWA 326 surfaces of many of the nodules and geodes at this place are
partly encrusted with pyrite. Well developed geodes are not
common and the majority of those found are of the calcite or
chalcedony types. Of the calcite geodes some are lined with
rhombohedral calcite but others bear dog tooth spar. Some of
the latter variety bear sphenoids of chalcopyrite. :Many of the
chalcedony geodes, on the other. hand, lack characteristic mamil-
lary structure. Some of the hollow specimens bear perfect
cubes of unaltered pyrite in their interiors. Other interesting localities for studying geodes occur in Van
Buren county. The most important of these are: along Indian
creek across the river from the town of Farmington; along Bear
creek one-half mile south of Vernon; and along Copperas creek
about two miles northwest of Bentonsport. At the Farmington
and Vernon localities rounded calcareous nodules, some with
and some without inclosing shells of chalcedony, are common in
the shale. Some of these are hollow and lined with crystals. Exteriorly most of such masses are indistinguishable from the
typical geodes with which they are occasionally associated, but
when they are broken their true character is revealed. :Many of
those which are hollow bear a brownish variety of calcite upon
which in some cases there are superimposed bright transparent
rhombohedrons of the .same mineral of a later period of
growth. ~ The dimensions given are the greatest in each of the three directions.
Statements made
regarding the thickness of the wall or of the chalcedonic shell are based only upon the
section obtained in breaking the geodes. IMPORTANT LOCALITIES Elongated crystals of pyrite are frequently found in
association with this last variety of calcite; In many of the solid nodules there is considerable evidence of
the partial replacement of original calcareous nlaterial by silica. This replacement product commonly assumes the form of irreg-
ular patches of reddish chalcedony but in some specimens
rounded masses of bluish chalcedony occupy part of the inter-
ior. In addition some specimens bear many radiating groups of
small quartz crystals imbedded in the mass. The Copperas creek locality is noted mainly for the deformed
condition and the irregular surfaces of the geodes. But the oc-
currence of bands and lenticular masses of reddish siliceous ma-
terial intermixed with calcite also is of considerable interest. The upper and lower surfaces of such bands and masses are
tliickly set with small nodular elevations which generally are
blended together and many of which are geodic. DESCRIPTION OF GEODES 327 Over seventy-five per cent of the geodes ' at this place are
either crushed or of a very irregular shape, and only a frac-
tion of the well rounded specimens attain a normal state of de-
velopment. Among the few well formed specimens one geode
of the quartz type was found to bear slender elongated crystals
of magnetite partly decomposed to limonite. DESCRIPTION OF TYPICAL GEODES r:rhe mineralogical variations of the geodes are such that it
is impossible to give a general description of their characters
which is satisfactory. In order that the many mineralogical re-
lationships may be fully presented a number of typical geodes
are described below. Geode No . .1.-Shape roughly oblong. Surface bearing minute
concretionary masses of chalcedony and in places exhibiting
faint slickensided structure. Dimensions5 23.1 by 18.2 by 15.6
cms. Interior hollow; wall 0.5 cm. to 5. cms. thiclc Chalcedonic
shell 0.1 to 0.7 cm. in thickness. Cavity lined with transparent
terminations of quartz crystals. When it was broken this geode
was partly filled with water. Position and locality: In place in an exposure of the Lower
Warsaw along the east bank of Mud creek, just above the iron
bridge east of Lowell, Henry county. Geod'e No. 2.-Shape lenticular; surface fairly smooth but
showing minute concretionary protuberances. Dimensions 15.1
by 14.1 by 8.8 cms. Interio.r hollow; wall 0.85 cm. to 2.8 ems. in thickness; chalcedonic shell not distinctly marked off; outer
part consisting in large part of fine-grained calcareous material
partly replaced by concretionary silica; inner part occupied by
an irregular band of bluish chalcedony. Upon this band there
occurs a perfect .lining of small transparent quartz crystals to-
which the underlying chalcedony imparts a bluish tint. Position and locality:
Basal part of Lower Warsaw two
miles northwest of Denmark, Lee county. Geode No. 3.-Shape approximately spheroidal with slight
compression at one point. Surface exhibiting many small MISSISSIPPIAN STRAT:A OF IOWA 328 rounded elevations of chalcedony. Adhering shale showing
slight slickensided structure in direction of greatest diameter. Dimensions 18.6 by 17.3 by 15.8 cms. Interior hollow; separated
by a perforated partition into two almost equal chambers. Outer
wall 2.2 to 3.75 cms. in thickness, outer shell of chalcedony av-
eraging 0.35 cm. in thickness. Inner part of wall occupied by
crystalline quartz. Chambers lined with pointed quartz crys-
tals. In one chamber there is superimposed upon this quartz a
thin layer of bluish chalcedony. No trace of this mineral is to
be found in the other chamber. Both chambers slightly iron
stained. Close study of this geode shows that it is compound
in character, having resulted from the union of two individuals. The presence of the chalcedony in only one chamber, however,
when the intervening wall offers no resistance to passage of so-
lutions, is difficult to explain. DESCRIPTION OF TYPICAL GEODES Position and locality: Along the bed of Mud creek in section
27 of Baltimore township, Henry county. Geode No. 4.-Shape lenticular, with lower side compressed,
upper surface corraded in places, bearing the usual concretion-
ary elevations and marked with several gougelike depressions;
lower surface smooth but irregular. Dimensions 29 by 28.2 by
17.25 cms. Interior nearly solid. Outer shell of chalcedony
ranging from practically nothing to 0.8 cm. in thickness; bear-
ing a single minute crystal of sphalerite. Succeeding this shell
inwardly there is a band of unequal thickness of solid crystal-
line· quartz analogous to that which lines ordinary quartz geodes. Resting upon this and coating the quartz crystals there appears
a layer of banded chalcedony averaging 0.8 cm. in thickness. Following this there occurs a second layer of quartz more finely
crystalline than the first. In a part of the cavity there is a
thin coating of chalcedony on the terminations of the crystals
of this layer. Implanted on this coating are a few cubes of
pyrite, and in the lower part of the cavity there is a slight in-
crustation of calcium carbonate. A large part of the cavity js
occupied by a mass of crystalline calcite, which bears included
flakes of pyrite. About 'the periphery of this mass are crystals
consisting of a combination of hexagonal prisms of the first or-
der with the negative rhombohedon. Position and locality: Along the bed of a ravine tributary TYPICAL GEODES 329 to Mud creek in the southern part of section 22, Baltimore town-
ship', Henry county. Geode NO.5-Shape globular. Surface fairly smooth and
regular. Dimensions 16.5 by 14.8 by 13.9 cms. Interior hollow,
lined with botryoidal chalcedony. Width of lining 0.35 cm. to
2.7 cms. Outer chalcedonic shell 0.2 cm. to 1.3 cms. thick; bear-
ing a trace of calcareous materiaL Line of contact with inner
layer of chalcedony in general very irregular. Lining of botry-
oidal chalcedony showing faint evidence of banding and markt'd
by numerous rounded pits which extend out to the crust. One
such pit of irregular shape is filled with crystalline sphalerite
which js decomposing to smithsonite. The latter mineral forms
an incomplete crust over the unaltered sulphide. A slight de-
posit of the same mineral forms a coating in the bottom of -the
cavity of the geode. In addition there are a few flakes of
gypsum. DESCRIPTION OF TYPICAL GEODES Position and locality: In place in the Lower Warsaw along
a ravine near the Fort Madison-Appanoose stone quarry, near
Niota, Illinois. Geode No. 6.-Shape subglobose. Surface with many small
rounded concretionary protuberances of chalcedony. Dimen-
sions 8.3 by 8.1 by 7.1 cms. Interior hollow; wall siliceous;
thickness 0.4 cm. to 2.1 cms. Outer shell of chalcedony 0.3 to
0.5 cm. thick. Cavity lined with terminations of small quartz
crystals bearing slender prismatic crystals of magnetite, and
stained with the reddish powder of hematite. The hematite is
later than the magnetite for it forms a coating on some of the
crystals of ·that miner-al. Position and locality: F:rom an exposure in the east bank of
Mud creek in the southern part of section 22, Baltimore town-
ship, Henry county. Geode No. 7.-Shape roughly spheroidaL Outer surface with
irregular elevations. Dimensions 17 by 14 by 13.5 cms. Interior
hollow; walls chalcedonic, 1.2 to 3 cms. thick, showing no trace
of banding. Shell not distinct. Cavity lined with drusy quartz
which possesses a sufficient coating of chalcedony to give it a
milky white appearance. Thickly implanted upon this material
are small, slightly tarnished cubes of pyrite . . In one part of the MISSISSIPPIAN STRATA OF IOWA 330 cavity thel;e also are one large and several small crystals of
calcite. The large crystal is of the same form as that found in
geode No.4. It envelops pyritiferous drusy quartz and is clear-
ly younger than that mineral. In one part of the wall there
occurs a pocket of calcite which bears inclusions of pyrite. Position and locality: In place in lower part of Lower War-
saw two miles northwest of Denmark. Geode No. 8.- Vertical section subcircular, horizontal section
subquadrangular. Surface with minute elevations. Dimensions
9.15 by 8 by 6.6 cms. Interior hollow; wall siliceous, averaging
about 1.6 cms. in thickness. Chalcedonic sltell 0.25 to 0.5 ' oJm. thick, bearing small pockets of kaolin. Succeeding the shell
there is a 'band of crystalline quartz, which is again followed by
a coating of chalcedony of differing thickness. Many small
bright cubes of pyrite occur on this coating and a few minute
crystals and a thin incrustation of gypsum occur in a part of
the cavity. A few stains of limonite were observed on the
chalcedonic lining. DESCRIPTION OF TYPICAL GEODES Position and locality:
In place in Lower Vvarsaw bed along Position and locality: In place in Lower Vvarsaw bed along
Soap creek, Keokuk. Geode No . 9.-Geode large, sub-ovate; longer and wider than
high. Surface smpoth but marked by irregular elevations and
depressions. Dimensions 39 by 37 by 25.3 ems. Interior occu-
pied for the most part by a large rounded mass of cryptocrys-
talline silica coated with crystalline quartz. Several quartz-lined
cavities intervene between this mass and the wall of the geode. Position and locality: In Lower \V" arsaw beds along Mud
creek, so.uth part of section 22, near Lowell. Geode No. 10.-Shape spheroidal; surface with small irregu-
lar protuberances and minute rounded elevations. Dimensions
13.8 by 12.3 by 10.7 ems. Wall siliceous; interior hollow, lined
with quartz crystals, and. almost completely filled with black
viscous bitumen. Position and locality: Along bed of creek south of Niota,
Illinois. Geode No. 11.-Shape, nodular; flattened upon one side by
contact with another specimen; surface smooth. Dimensions CHARACTERISTICS OF GEODES 331 9.8 by 7.8 by 6.6 cms. Interior hollow; wall about 1.1 cms. in
thickness; outer part consisting of a thin shell of chalcedony;
inner part made up of fine-grained impure calcareous material. Lining this wall are small scalenohedrons of calcite on which
are numerous flakes and sphenoids of chalcopyrite. Position and locality: In place in lower part of Lower War-
saw, two miles northwest of Denmark. Geode No. l2.-Shape nodular; surface irregular. Dimen-
sions 12.5 by 11.2 by 8 cms. Interior hollow; wall 0.55 cm. to
1.5 cms. thick, consisting of finely crystalline calcareous mater-
ial; no trace of a chalcedonic shelL Brownish rhombs of calcite,
some which are much elongated, line the wall, and implant-
ed on them are small tarnished crystals of pyrite which exhibit
the fares of the pyritohedron. Superimpo~etl upon both miner-
als are many clear, transparent rhombs of Iceland spar with
which are associated acicular crystals of unaltered pyrite either
as inclusions or as freely projecting needles which upon super-
ficial examination might be mistaken for millerite. Two periods
of mineralization are indicated by this geode. Position and locality: In place in the upper part of the Low-
er Warsaw beds along Indian creek near Farmington, Van
Buren county. Geode No. l3.-Shape lenticular. Surface rough and irreg-
ular, partly coated with mammillary pyrites. Dimensions 21 by
19.1 by 11.4 cms. Interior hollow; wall siliceous, 0.8 cm. DESCRIPTION OF TYPICAL GEODES to 3
cms. thick. Outer shell of chalcedony distinct; showing concre-
tionary structure; partly replaced by pyrite 0.2 cm. to 1.1 cms. in thickness. Cavity lined with quartz and occupied in part by
a large mass and smaller aggregates of calcite which are thick-
ly set with included flakes of pyrite. Small crystals of pyrite
are implanted upon the quartz also and the latter mineral is
partly coated with an incrustation of calcium carbonate. Position and locality: Along bed of ravine emptying into
Mud creek near Lowell. Geode 'No. l4.-Shape irregular and nodular, surface with
concretionary elevations of chalcedony. Dimension 8.5 by 7 by
6.5 cms. Wall siliceous, averaging about 0.6 cm. in thickness. Outer shell of chalcedony 0.1 to 0.5 cm. thick; concretionary; MISSISSIPPIAN STRATA OF IOWA 332 bearing a few small cavities filled with kaolin. Interior of wall
thickly set with small pointed quartz crystals beyond which
occur aggregates of dolomite crystals, which possess character-
istic curved surfaces. Remainder of cavity almost filled with
white fluffy powder of kaolin. Solution of several dolomite
crystals from different places in the cavity showed that some
contained inclusions of kaolin, for a cloudy liquid resulted in
a few instances. lYIlcroscopic examination of the quartz, how-
ever, did not reveal any inclusions of the powder in it. Position and locality: In place in bluff back of Harrison
lumber mills two miles below the Union Station at Keokuk. Geode No. 15.-Shape subglobose; surface rough and irregu-
lar. Dimensions 11.3 by 9.9 by 9.3 ems. Interior hollow; wall
1.8 to 5.1 ems. in thickness ; outer part siliceous ; inner part
dolomite. Chalcedonlc shell concretionary, 0.5 cm. to 2 ems. thick, containing small cavities and irregular pockets of limon-
ite and kaolin. Inner lining of dolomite continuous. Shell suc-
ceeded by massive dolomite in lower part on which are super-
imposed crystals of the same mineral. But in the upper part
crystals of dolomite succeed the siliceous shell directly. The
crystals are rhombohedrons with characteristi~ curved surfaces. Position and locality: In upper part of fossiliferous phase
of the Lower ,Varsaw, two miles below the Union Station at
Keokuk. Position and locality: In upper part of fossiliferous phase
of the Lower ,Varsaw, two miles below the Union Station at
Keokuk. Geode No. l6.-Geode small, globular; surface bearing min-
ute rounded elevations of chalcedony. Dimensions 7 by 7 by
6.3 cms. DESCRIPTION OF TYPICAL GEODES Interior hollow; wall thin, consisting of a shell of
chalcedony, averaging 0.5 cm. in thickness, succeeded in all but
what ·seems to be the lower part, by a thin layer of drusy quartz. In the part excepted, a layer of the massive quartz containing
one large and several small pockets of limonite intervenes be-
tween the shell and the drusy coating. Superimposed upon the
quartz lining are a few rhombs of calcite, the largest of which
measures 1.3 ems. in diameter, and several aggregates of anker-
ite crystals. A whitish efflorescent-like coating of calcium car-
bonate is present as an incrustation on these minerals and on
the drusy quartz. DESCRIPTION OF GEODES 333 Position and locality: From the Lower vVarsaw in the clay
pit of the Hamilton Clay Company, Hamilton; Illinois. Geode No. 17.-Geode small, nodular; surface rough. Dimen-
sions 6.0 by 5.5 by 38.0 ems. Wall thin, averaging 0.5 em., con-
sisting of an outer shell of chalcedony lined with a thin layer of
whitish granular calcite upon which appear numerous minute
crystals of pyrite. Interior almost completely filled with flaky
kaolin. The calcite crystals contain minute flakes of this min-
eral. Geode No. 17.-Geode small, nodular; surface rough. Dimen-
sions 6.0 by 5.5 by 38.0 ems. Wall thin, averaging 0.5 em., con-
sisting of an outer shell of chalcedony lined with a thin layer of
whitish granular calcite upon which appear numerous minute
crystals of pyrite. Interior almost completely filled with flaky
kaolin. The calcite crystals contain minute flakes of this min-
eral. Position and locality : Lower Warsaw along bluff back of
Harrison lumber mills two miles below Keokuk Union Station. Geode No. lB.-Geode large; shape very irregular; surface
rough and uneven. Dimensions 37.3 by 29.0 by 28.5 ems. En-
tirely siliceous. vVall averaging about two centimeters in thick-
ness; lined with crystals; chalcedonic shell distinct. Interior
occupied by a large mass of chalcedonic silica which is covere(:
by a coating of crystalline quartz, some of the crystals of which
are united with those of the wall. The whole interior is strong-
ly stained with limonite, and locally it is incrusted with calcium
carbonate. Geode No. lB.-Geode large; shape very irregular; surface
rough and uneven. Dimensions 37.3 by 29.0 by 28.5 ems. En-
tirely siliceous. vVall averaging about two centimeters in thick-
ness; lined with crystals; chalcedonic shell distinct. DESCRIPTION OF TYPICAL GEODES Interior
occupied by a large mass of chalcedonic silica which is covere(:
by a coating of crystalline quartz, some of the crystals of which
are united with those of the wall. The whole interior is strong-
ly stained with limonite, and locally it is incrusted with calcium
carbonate. Position and locality: Along bed of a ravine in southern part
of section 22 of Baltimore township, Henry county. Geode No. 19.-Geode of medium size, subglobose; surface
rough, irregularly pitted. Dimensions 11.5 by 10.8 by 8.5 ems. Interior hollow; wall averaging about 2.5 ems. in thickness;
chalcedonic shell distinct, bearing minute cavities, some or
which are filled with kaolin. Following this is a layer of crYS7
talline quartz, the interstices of which are filled with chalcedony. Superimposed upon the quartz layer and lining the interior of
the geode is a band 'of chalcedony about three-tenths centimeter
thick which bears botryoidal prominences. A few bright un-
tarnished flakes of pyrite rest upon the surface of the chalce-
dony. In the lower part of the cavity there is a yello\vish stain
of limonite. Position and locality:
In place in Lower vVarsaw, along
Soap creek, Keokuk. Geode No. 20.-Shape nodular and very irregular; surface
bearing many rounded elevations, as if formed by the coal- MISSISSIPPIAN STRATA OF IOWA 334 escence of many small nodules. Dimensions 14.8 by 13.1 by 9.1
cms. Interior hollow; wall siliceous, averaging about 2.4 cms. in
thickness. Outer shell of calcedony exhibiting faint traces of
banding; about 0.4 cm. thiclc Inner part of wall consisting of
massive crystalline quartz. Cavity lined with closely inter-
grown crystals of quartz. In one part of the cavity there oc-
curs a small mass of crystalline calcite about two centimeters
long and one centimeter wide, and implanted upon both the
quartz and . calcite are slender prismatic 'crystals of magnetite. There is a slight incrustation of calcium carbonate in "vhat
seems to be the lower part of the cavity. Position and locality: In Lower Warsaw, along Copperas
creek two miles northwest of Bentonsport, Van Buren county. escence of many small nodules. Dimensions 14.8 by 13.1 by 9.1
cms. Interior hollow; wall siliceous, averaging about 2.4 cms. in
thickness. Outer shell of calcedony exhibiting faint traces of
banding; about 0.4 cm. thiclc Inner part of wall consisting of
massive crystalline quartz. Cavity lined with closely inter-
grown crystals of quartz. DESCRIPTION OF TYPICAL GEODES In one part of the cavity there oc-
curs a small mass of crystalline calcite about two centimeters
long and one centimeter wide, and implanted upon both the
quartz and . calcite are slender prismatic 'crystals of magnetite. There is a slight incrustation of calcium carbonate in "vhat
seems to be the lower part of the cavity. Position and locality: In Lower Warsaw, along Copperas
creek two miles northwest of Bentonsport, Van Buren county. escence of many small nodules. Dimensions 14.8 by 13.1 by 9.1
cms. Interior hollow; wall siliceous, averaging about 2.4 cms. in
thickness. Outer shell of calcedony exhibiting faint traces of
banding; about 0.4 cm. thiclc Inner part of wall consisting of
massive crystalline quartz. Cavity lined with closely inter-
grown crystals of quartz. In one part of the cavity there oc-
curs a small mass of crystalline calcite about two centimeters
long and one centimeter wide, and implanted upon both the
quartz and . calcite are slender prismatic 'crystals of magnetite. There is a slight incrustation of calcium carbonate in "vhat
seems to be the lower part of the cavity. Position and locality: In Lower Warsaw, along Copperas
creek two miles northwest of Bentonsport, Van Buren county. Geode No . . 21.-Size small; bun-shaped; surface fairly
smooth. Dimensions 9.4 by 8.4 by 4.7 cms. Interior hollow;
wall about 0.7 cm. thick; outer half consisting of reddish chal-
cedony which has a concretionary structure; inner part consist-
ing of discolored crystalline calcite. Cavity lined with imper-
fect scalenohedrons of brownish discolored calcite. P
i i
d l
li
I
l
i
L
TV
l Position and locality:
In place in Lower ,TV arsaw, along
Bear creek near V ern on, Van Buren county. Geode No. 22.-Shape approaching lenticular but laterally
compressed. Surface with minute elevations of chalcedony. Dimensions 11.0 by 10.8 by 8.3 cms. Interior hollow; wall
siliceous; outer shell distinct, showing a reddish tint. Interior
of wall lined with drusy quartz which, for the most part, is iron
stained. Implanted upon this quartz occur many small cubes of
pyrite which are decomposing to limonite. Superimposed in-
discriminately upon quartz and pyrite there are, in some parts
of the cavity, small twinned rhombohedrons of calcite. Related
to all three minerals and obviously subsequent to them are a
few slender projecting crystals of gypsum of the usual form. DESCRIPTION OF TYPICAL GEODES One elongated crystal has a length of 1.5 cms., its greatest width
being not more than 0.1 cm. Position and locality: In place in Lower Warsaw beds along
bluff of Mud creek in southern part of section 22 of Baltimore
township, Henry county. Geode No. 22.-Shape approaching lenticular but laterally
compressed. Surface with minute elevations of chalcedony. Dimensions 11.0 by 10.8 by 8.3 cms. Interior hollow; wall
siliceous; outer shell distinct, showing a reddish tint. Interior
of wall lined with drusy quartz which, for the most part, is iron
stained. Implanted upon this quartz occur many small cubes of
pyrite which are decomposing to limonite. Superimposed in-
discriminately upon quartz and pyrite there are, in some parts
of the cavity, small twinned rhombohedrons of calcite. Related
to all three minerals and obviously subsequent to them are a
few slender projecting crystals of gypsum of the usual form. One elongated crystal has a length of 1.5 cms., its greatest width
being not more than 0.1 cm. Position and locality: In place in Lower Warsaw beds along
bluff of Mud creek in southern part of section 22 of Baltimore
township, Henry county. CALCITE IN GEODES 335 Minerals of the Geodes and the Inclosing Rocks Quartz (Rock Crystal), Si02.-This is the most common min-
eral found in the geodes. The majority of specimens are either
lined or completely filled with crystalline quartz. The crystal::;
almost without exception consist of the first order hexagonal
prism terminated with positive and negative rhombohedrons. Usually only the pyramidal terminations line the cavities of the
quartz geodes, but doubly terminated crys~al s are found loose
in the interiors of some specimens. Ched, Si02.-Discontinuous bands and irregular nodules of
chert occur in the Keokuk limestone and in the limestone layer:::;
of the Lower Warsaw. The relation of the material to the lime-
stone suggests that it has resulted from the replacement of that
rock. Ched, Si02.-Discontinuous bands and irregular nodules of
chert occur in the Keokuk limestone and in the limestone layer:::;
of the Lower Warsaw. The relation of the material to the lime-
stone suggests that it has resulted from the replacement of that
rock. Chalcedony, Si0 2.- 'rhe outer siliceous shell which covers al-
most all geodes is of the variety of quartz known as chalcedony. the same mineral also .occurs as a bluish lininO' with botryoidal
prominences in the interior 'of some geodes and it appears com-
monly as a coating on the surfaces of the quartz crystals which
line the cavities. In the first mode of occurrence the chalcedony
in most cases has a concretionary structure, but in the last two
l'nodes it may show only faint evidence of banding. Calcite, CaC03.-This is a common constituent of the geodes
and its relationships are such as to indicate at least two periods-
of formation. This mineral is most commonly found as isolated
crystals or crystal aggregates on the quartz of quartz geodes. But calcite in some instances succeeds the siliceous shell direct-
ly. In all geodes not characterized by chalcedonic shells and in
the geodic calcareous nodules this mineral lines the ' interior. The calcite of the Keokuk limestone in some cases includes crys-
tals of metallic sulphides such as hairlike tufts of millerite,
sphenoids .of chalcopyrite and slender elongated crystals of
pyrite. In the Lower Vvarsaw, on the other hand, some of the
crystals include the white powder of kaolin and a few of them
contain flakes of pyrite. But in many of the geodes from this
horizon the calcite was depos'ited subsequently to the pyrite. Minerals of the Geodes and the Inclosing Rocks The crystals of the earlier period of formation exhibit a variety MISSISSIPrpIAN STRATA OF IOWA 336 of forms and some of them show a brownish discoloration. The
most common forms of the calcite of this age are the rhomb-
ohedron, the scalenohedron, and the scalenohedron modified by
the rhombohedron. Much of the calcite of later growth consists of bright, irans-
parent rhombohedrons of Iceland spar, some of which rest on
calcite of earlier growth. Other forms assumed by the calcite
of this age are the rhombohedron, the hexagonal prism of the
first order in combination with the rhombohedron, and ' a
twinned rhombohedron. Dolom.ite, CaCOs. MgCOa.- Rhombohedrons of this mineral ex-
hibiting characteristic curved surfaces are commonly found in
the geodes at Keokuk, Iowa, and N iota, Illinois. The dolomite
appears as aggregates of crystals resting on the quartz of the
geodes, or it follows the siliceous shell directly. Ankerite, (Ca.Mg.Fe)COs.-Some, of the crystals outwardly
resembling dolomite possess a high iron content and undoubted-
ly they are to be classed as ankerite. The decomposition of tkese
crystals generates a considerable amount of limonite. Th(~
limonite thus formed is in many instances a more or less perfect
pseudomorph after the ankerite. Magnetite, Fes0 4.-Slender elongated crystals of magnetite
appear in the interiors of some of the geodes from the Lower
Warsaw. In most cases the crystals of this substance are im-
planfed on quartz, but in one instance they occur on both quartz
and calcite. Microscopic examination shows that some of the
magnetite crystals have been partly altered to limonite. This
mineral has not been reported previously from the geodes. Hematite, Fe20 a.-In a few of the geodes from the Mud creek
locality the reddish powder of hematite is found staining the
interior lining of quartz. Geode No. 6 exhibits such a relation-
ship. Pyrite, FeS2.-Pyrite is by far the most abundant metallic
mineral associated with tbe geodes. It occurs both in the
geodes 'from the Keokuk limestone and in those from the Lower
Warsaw. It is found also as free crystal aggregates in the CHALCOPYRITE IN G'EODES 337 shale and as a mammillary coating on the surface of some
geodes of the Lower Warsaw. Within the geodes, pyrite of at least two periods of growth
appears. Geode No. 12 illustrates this feature excellently. This
mineral favors no particular associations for its crystals. Minerals of the Geodes and the Inclosing Rocks They
.occur implanted indiscriminately upon quartz, chalcedony, or
calcite. In some specimens it is also. included in calcite. The
pyrite of such inclusions is almost invariably in a fibrous or
flaky condition. This is especially true of the geodes of the
Keokuk limestone. Geode No. 13 from the Lower 'Warsaw ex-
hibits such a relationship. The majority of the uninclosed crys-
tals of pyrite assume more or less well developed forms, but in
a few geodes, of which No. 12 is the type, there are slender
elongated crystals which might easily be mistaken for millerite. The hexahedron is the most common of the crystal forms which
are normally found. Others which have been rioted are the
pyritohedron and the cube with octahedral modifications. De-
composition of the pyrite has taken place in many of the geodes
and bright unaltered crystals are not often found. The altera-
tion has been accompanied by the formation of limonite in each
case and the interiors of many of the geodes are, as a conse-
quence, strongly iron stained. Milleri.te, NiS.-Millerite has been found in the geodes 'of the
Keokuk limestone at Keokuk and in the geodic cavities of the
Montrose chert exposed in the excavation for the dam at the
same city. In both of these occurrenc(':; the mil1erite is closely
associated with calcite. In but a single instance was it found on
quartz. Many of the slender needles of this mineral are includ-
ed in the calcite, but some freely projecting tufts are found. The inclusions resemble very much the flakes of pyrite found in
the calcite of the geodes of the Lower Warsaw. Chalcopyrite, CuFeS 2.-Small sphenoids of this mineral have
been found in the geodes both from the Keokuk limestone and
from the Lower Warsaw at the locality northwest of Denmark. At no other place in the area was this mineral found in these
beds. The crystals of this substance are always associated with
calcite. N one has ever been found on quartz. In the Keokuk
limestone the small sphenoids are entirely included by the cal- MISSISSIPPIAN STRATA OF IOWA 338 cite, but in the geodes of the Lower Warsaw crystals of chal-
copyrite are implanted on the surface (If rllOIllbolleciron::: and
scalenohedrons of this mineral. cite, but in the geodes of the Lower Warsaw crystals of chal-
copyrite are implanted on the surface (If rllOIllbolleciron::: and
scalenohedrons of this mineral. Minerals of the Geodes and the Inclosing Rocks Sphalerite, ZnS.-Sphalerite is commonly found in the geodes
both from the Keokuk limestone and from the Lower Warsaw. It occurs as irregular , crystalline masses which range in size
-from very small particles to those having a diameter of four
inches. It is usually associated with calcite and the two min-
erals are in many instances so inter grown as to indicate a con·
temporaneous deposition. In some geodes, however, sphalerite
is found with quartz. Limonite, 2Fe20 a+3H20.-Limonite is the most common alter-
ation product of the geodes and the interiors of a large percent-
age of the specimens are discolored by ' this mineral. The hy-
drate of iron has two common modes of origin, namely, by the
alteration of pyrite and by the decomposition of ankerite. It
occurs either as a rusty stain or as small ocherous mass.es III
the interiors or in the shells of the geodes. Limonite, 2Fe20 a+3H20.-Limonite is the most common alter-
ation product of the geodes and the interiors of a large percent-
age of the specimens are discolored by ' this mineral. The hy-
drate of iron has two common modes of origin, namely, by the
alteration of pyrite and by the decomposition of ankerite. It
occurs either as a rusty stain or as small ocherous mass.es III
the interiors or in the shells of the geodes. Smithsonite, ZnCOa.-The carbonate of zinc occurs in some
geodes as an alteration product of sphalerite, with which it is
closely related. ' It usually appears as an encrl1sting film over
the unaltered sulphide. Malachite, CuCOa+Cu(OH)2.-The green basic carbonate of
copper is associated with the small sphenoids of chalcopyrite in
some of the geodes which occur in the Keokul{ and Lower War-
saw beds northwest of Denmark. Kaolin, AI20 a, 2Si0 2+2H20.-In some of the geodes there oc-
curs the flocculent white powder of kaolin. This mine:ral is
commo,nly found in the specimens from the upper argill&ceous
part of the Lower Warsaw at Keokuk, Iowa, and Warsaw, Illi- Kaolin, AI20 a, 2Si0 2+2H20.-In some of the geodes there oc-
curs the flocculent white powder of kaolin. This mine:ral is
commo,nly found in the specimens from the upper argill&ceous
part of the Lower Warsaw at Keokuk, Iowa, and Warsaw, Illi- BITUMEN IN GEODES 339 nois, but it also occurs in imperfectly developed geodes at
other localities. Minerals of the Geodes and the Inclosing Rocks Examination of the powder under the micro-
scope shows it to be in the form of fine scales. The relation of
this mineral to. the argillaceous material in some of the speci-
mens suggests that it may have been formed by a leaching pro-
cess. Most of the geodes in which' it occurs are poorly de-
veloped and the calcite found in some kaolinitic specimens in-
cludes the white powder of this mineral. In such cases the
kaolin evidently was formed early in the history of the geodes. Gyps'/,~rn, CaS04+ 2H20.-Gypsum occurs in the shales of the
Lower Warsaw as irregular flakes and in a few of the geodes
from the same horizon as incrusting films and tabular mono-
clinic crystals. Water, H 20.-Some of the geodes, as has been stated, contain
water. No analysis of this water was undertaken by the writer
for it was thought that little emphasis could be placed upon the
result, since circulation and diffusion must have continued long
after the geodes were formed. Professor Brush, however, has
made a chemical examination of the water contained in a geode
from this region. His report follows: "A portion of this water weighing 16.327 grammes, gave, on
evaporation, a crystalline residue weighing .094 grammes, which
on analysis, proves to consist of sulphate of lime and sulphate
of magnsia, with minute traces of silica. Another sample was
examined for carbonic acid with a negative result". The character of this sample suggests that the water was in··
troduced after the geode was formed. Bitumen.-A hydrocarbon. In the vicinity of Niota, Illinois,
many of the geodes from the Lower Warsaw are partly or com-
pletely filled with a black, viscous asphaltic bitumen. In a few
specimens from this place a black solid hydrocarbon was found. This has resulted undoubtedly from the natural distillation of
lighter hydrocarbon from the liquid bitu;men commonly ob-
served. In many cases the rocks containing bituminous geodes show
no evidence of bitumen but the shells of some of the geodes are
strongly discolored with this material. MISSISSIPPIAN STRATA OF IOWA 340 1.
Chalcedony, quartz.
2
Ch l
d
t P ARAG'ENESIS OF THE MINERALS In the discussion of the order of deposition of the minerals
only the primary ones are considered. With reference to these
minerals, no constant order of succession holds for all geodes,
and the same order of formation may not obtain in two adja-
cent specimens. For the purpose of illustrating the variations in the succes-
sion of the minerals in the geodes the order of their deposition
in a number of typical specimens is given. The chalcedony of
the shells of the geodes is listed first for it must be concedecl
that this was formed prior to the deposition of the minerals now
found in the interior of the geodes. 1. Chalcedony, quartz. 2. Chalcedony, quartz, chalcedony. 3. Chalcedony, chalcedony, quartz. 4. Chalcedony, quartz, chalcedony, pyrite. 5. Chalcedony, chalcedony, sphalerite. 6. Chalcedony, quartz, chalcedony, quartz, c
included pYl·ite. 7. Chalcedony, quartz, chalcedony, pyrite, calc
8. Chalcedony, qualtz, calcite with included
9. Chalcedony, quartz, pyrite, calcite. 10. Chalcedony, quartz, pyrite, calcite with in
11. Chalcedony, quartz, chalcedony, pyrite, sp
12. Chalcedony, quartz, dolomite, calcite. 13. Chalcedony, quartz, calcite, calcite. 14. Ohalccdony, quartz, magnetite, hematite. 15. Chalcedony, quartz, pyrite, magnetite. 16. Chalcedony, quartz, pyrite, dolomite. 17. Chalcedony, quartz, dolomite. 18. Chalcedony, quartz, bitumen. 19.- Chalcedony, quartz, calcite, bitumen. 20. Chalcedony, quartz, ankerite, calcite. 21. Chalcedony, qu'artz, pyrite, calcite. 22. Chalcedony, calcite, chalcopyrite. 23. Chalcedony, calcite, calcite and chalcopyri
24. Chalcedony, calcite, calcite. 25. Chalcedony, calcite. 26. Chalcedony, calcite, millerHe. 27. Calcite and millerite. 28. Qmutz, millerite. 4. Chalcedony, quartz, chalcedony, pyrite. 5
Ch l
d
h l
d
h l
it 5. Chalcedony, chalcedony, sphalerite. 6
Ch l
d
t
h l
d 6. Chalcedony, quartz, chalcedony, quartz, chalcedony, pyrite, calcite with
included pYl·ite. 7
Ch l
d
t
h l
d
it
l it 7. Chalcedony, quartz, chalcedony, pyrite, calcit
8
Ch l
d
lt
l it
ith i
l d d 8. Chalcedony, qualtz, calcite with included pyrite. 9
Ch l
d
t
it
l it 9. Chalcedony, quartz, pyrite, calcite. 10
Ch l
d
t
it
l it 11. Chalcedony, quartz, chalcedony, pyrite, sphalerite. 12
Ch l
d
t
d l
it
l it 12. Chalcedony, quartz, dolomite, calcite. 13
Ch l
d
t
l it
l it 13. Chalcedony, quartz, calcite, calcite. 14
Oh l
d
t
tit
h 14. Ohalccdony, quartz, magnetite, hematite
15
Ch l
d
t
it
tit 15. Chalcedony, quartz, pyrite, magnetite. P ARAG'ENESIS OF THE MINERALS 16
Ch l
d
t
it
d l
it 15. Chalcedony, quartz, pyrite, magnetite. 16
Ch l
d
t
it
d l
it 16. Chalcedony, quartz, pyrite, dolomite. 17
Ch l
d
t
d l
it 17. Chalcedony, quartz, dolomite. 18
Ch l
d
t
bit 18. Chalcedony, quartz, bitumen. 19
Ch l
d
t
l it
b 19.- Chalcedony, quartz, calcite, bitumen. 20
Chalcedony
quartz
ankerite
calcite 20. Chalcedony, quartz, ankerite, calcite. 21
Ch l
d
' t
it
l it 21. Chalcedony, qu'artz, pyrite, calcite. 22
Chalcedon
calcite
chalcop rite 22. Chalcedony, calcite, chalcopyrite. 23
Ch l
d
l it
l it
d 22. Chalcedony, calcite, chalcopyrite. 23
Chalcedony
calcite
calcite and chalcopyrite 23. Chalcedony, calcite, calcite and chalcopyrit
24
Ch l
d
l it
l it 24. Chalcedony, calcite, calcite. 25
Chalcedon
calcite 25. Chalcedony, calcite. 26
Ch l
d
l it 26. Chalcedony, calcite, millerHe. 27
C l it
d
ill
it 27. Calcite and millerite. 28
Q
t
ill
it 28. Qmutz, millerite. First in the process of development of the siliceous geodes
there was formed in nearly every case a thin chalcedonic shell. Upon thjs is superposed quartz, in either the crystalline or chal-
cedonic condition, or calcite. ' But where quartz is present in the
specimens studied it always rests on the siliceous shell or on an
inner layer of chalcedony. h
f h
l
i
f
lli
d
h l Upon thjs is superposed quartz, in either the crystalline or chal-
cedonic condition, or calcite. ' But where quartz is present in the
specimens studied it always rests on the siliceous shell or on an
inner layer of chalcedony. The cause of the alternation of crystalline quartz and chalce-
dony in some of the geodes is not known. If the layers were all ORIGIN OF GEODES 341 formed during one period of growth, as seems probable, change~
in the condition and amount of silicia supplied may have given
rise to the phenomenon. Changes in temperature or pressure
cannot be appealed to because in many cases adjacent quartz
geodes in the strata show no such alternations. The position of ,calcite in the geodes is subject to even more
variations. In some instances it succeeds the chalcedonic shell
directly, but in more cases it rests upon a lining of quartz or
chalcedony. Two distinct periods of growth of this mineral arc
,indicated. P ARAG'ENESIS OF THE MINERALS In some of the geodes calcite of both generations
appears. Geode number 12 illustrates this feature excellently. In some specimens the earlier calcite is discolored and in many
cases it is contemporaneous with, or directly followed by sphal-
erite, millerite, chalcopyrite, or pyrite. Crystals of dolomite or
ankerite are sometimes found intervening between the earlier
calcite and that of later age. These crystals rest directly upon
calcite or quartz or in some instances upon the pyrite which suc-
ceeds them. Much of the calcite of later formation is clear and
transparent, and so~e of the crystals are characteristically
twinned. Pyrite is commonly assoGiated with this variety of
calcite, either as included flakes or as implanted crystals. The
occurrence of crystals of magnetite on calcite of this age in
geode number 20 suggests that deposition of this mineral di-
rectly folowed. The kaolin which occurs in some of the geodes has no con-
stant relationship. In some instances it occupies the interior
of well-formed geodes (see geode number 14) but in most cases
it appears in imperfect specimens. In the latter condition the
kaolin evidently is residual for it has interfered with the normal
geode development. In the more perfectly formed kaolinitic
types, however, the material may possibly have been introduced
after the geodes were formed. But the evidellce is in favor of
the view that it is an original constituent. 6 Am. Jour. Sci.. 4th ser .• vol. XLII, p. 38 ff. ; 1916. Origin of the Geodes The following discussion of the origin of the geodes is taken
from an earlier paper by the writer :6
h
i i
f h
d
f h
k k
d The origin of the geodes of the Keokuk and Lower Warsaw 6 Am. Jour. Sci.. 4th ser .• vol. XLII, p. 38 ff. ; 1916. MISSISSIPPIAN STRATA OF IOWA 242 beds has long been a disputed questio:r;t, and, altHough there has
been considerable speculation upon the subject, no one theory or
their development has, as yet, been widely held. The existence of perfectly developed geodes in strata often
very impervious to underground circulation furnishes a · prob-
lem 'which is exceedingly difficult to solve. The containing rock
is in many cases highly argillaceous and no structures whidl
might serve as passage ways for mineralizing solutions are to
be seen. It was formerly believed that the geodes were formed by the
deposition of mineral matter on the walls of cavities formed by
the solution of sponges imbedded in the rocks. Thus, Dana
states :7 "They have been supposed to occupy the centers of sponges
that were at some time hollowed out by siliceous solutions, like
the hollowed corals of Florida, and then lined with crystals by
deposition from the same or some other mineral solution." This theory has had many followers and S. J. Wallace has
even gone so far as to coin a generic name for the sponge whose
solution is supposed to have afforded the cavities in which the
geodes were developed. 8
To this genus, called Biopalla, eight
species were referred upon the basis of difference in size, shape,
and surface ma~kings of the geodes. The sponge hypothesis,
however, is not now widely held. No evidence of sponges capa-
ble of giving rise to geodes has ever been found in the Keokuk
or Warsaw beds. Moreover, the geodes vary widely in size and
shape, a fact which argues strongly against any theory which
presupposes such an origin. Many specimens are nodular and
irregularities of the greatest variety characterize their exterior
form. It may safely be said that no two of them assume exact-
ly the same proportions. 7 Manual of Geology, 4th ed., pp. 97, 98; 1895.
oS Am. Jour. Sci. (3), vol. XV, P. 366 If.; 1878.
9 Bull. Geol. Soc. Am., vol X, p . 253 If. ; 1899. Origin of the Geodes entitle~ Professor Shaler, in a paper entitle~ "Formation of Dikes
and Veins,' '9 also devotes some space to the development of
geodes and, although his studies were based upon geodes known
to be of fossil origin which occur in the Knobstone shales of
Kentucky, his conclusions may well be considered at this point: · BASSLER'S THEORY OF ORIGIN '343 "N ormal geodes are hollow spheroids and are generally found
in s~~lles. ~hey clear~y represent, in most cases, a segregation
Qf SIlIca, whIch has eVIdently taken place under conditions of no
very great heat, brought about by deep burial beneath sediments
or other sources of temperature. It is difficult in all cases to
observe the circumstances of their origin, but in certain instruc-
tive instances this can be traced. It is there as follows: Where
in a bed in which the conditions have permitted the formation of
geodes the calyx of a crinoid occurs, the planes of junction of
the several plates of which it is composed may become the seat
of vein-building. As the process advances these plates are
pushed apart and in course of time enwrapped by the silica un-
til the original sphere may attain many times its original
diameter and all trace of its origin lost to view, though it may
be more or less clearly revealed by 1;>reaking the mass. I
h
f
l
hi h h
d
d
h In the process of enlargement which the geodes undergo they
evidently provide the space for their storage by compressing
the rock in which they are formed. In the rare instances where
I have been able to clearly observe them in their original posi-
tion they were evidently cramped against the country rock, the
layers of which they had condensed and more or less deformed. Although ' when found upon the talus slopes or the soil these
spheres usually contain no water in their central cavities, these
spaces are filled with the fluid while they are forming and so
long as they are deeply buried. There can be no doubt that this
water is under a considerable though variable pressure. 10 Proc. U. S. Nat. Mus., vol. XXXV, p .
~33 fr.; 1908. Origin of the Geodes h
di i
f f
i
f
h
id l
i
d The conditions of formation of spheroidal veins or geodes
clearly 'indicate that an apparently solid mass of crystalline
structure may ' be in effect easily permeated by vein-building
waters, and this when the temperature and pressure could not
have been great. It is readily seen that the walls of these hol.-
low spheres grow interstitially while at the same time the crys-
tals projecting from the inner llide of the shell grow toward the
center. We, therefore, have to recognize the fact that the silex-
bearing water penetrated through the dense wall. In many of
these spherical veins we maY' note that the process of growth in
the interior of the spheres has been from time to time inter-
rupted and again resumed. These changes may be due to the
variations in pressure to which the water in the cavities hi
necessarilv subjected as the conditions of its passage through
the geode~bearing zone ' are altered."
' More recently Bassler has written10 on the formation of the
.Knobstone geodes .. He says : "The majority of geodes in the Knobstone group may be MISSISSIPPIAN STRATA OF IOWA 344 traced directly or indirectly to a crinoidal origin for the simple
reas~n that these stra;ta ave often crowded with the fragments
of thIS class of orgamsms. Probably next in order as a geode
maker is the common brachiopod Athyris lamellosa, but no clas£
of fossil is exempt from replacement by silica when the proper
conditions obtain." Bassler is of the opinion that the Keokuk and Lower Warsaw
geodes may have the same mode of origin as those of the Knob-
stone. But he disagrees with Shaler as to the details of geode
development. Thus: "Retur~ing to the suggestion in Dana's Manual of Geology
that the h .. eokuk geodes are hollowed out sponges lined with
crys,tals it seems more reasonable; in 'View of the absence of such
sponges in that formation and the pres(~nce of numerous speci-
mens indicating the origin described above, that the latter is
nearer the truth. Prof. Shaler's idea that this class of geodes
is formed when deeply buried is not in accord with the facts,
nor does there appear to be any necessity for the wah'r of
formation to be under a considerable though variable pressure. Origin of the Geodes Ordinary surface waters charged with silica seem to he suffi- '
cient. " This generalIzation in so far as it relat~s to the geodes of the
region studied, would seem to be too broad. Out of several
thousand geodes examined only one, which had plainly been
formed by the enlargement of a specimen of the crinoid Bary-
crinu8, showed evidence of this method of geodization. The origin of the geodes in the region studied is believed by
the writer to be related to the calcareous concretionr:; which
originally must have been very abundant in the beds and which
are still preserved at some localities. These nodules, being
more soluble than the inclosing rocks, have been in large part
removed, thus affording cavities in which the geodes could be
formed. Where they are still preserved, the concretions have
exactly the same relationship to the containing rock as the
geodes and possess analogous shapes. They were obviously
formed on the s.ea-bottom while the strata were being deposited,
since lines of stratification do not pass through them and. no
evidence of expansion is encountered about their borders. The
process of solution seems to have started in the interior and
proceedf\d outwards. That this was the method of removal is
indicated by the occurrence in the beds of some geodic nodules PERIODS OF MINERALIZATION 345 whose interiors were only partly hollowed out when deposition
began. Carbonic acid and sulphuric acid, the latter · of which
must have been generated by the decomposition of the pyrite so
common in the beds, probably were the most active solvents. The white powder of kaolin found in some of the geodes is
thought to represent, at least in part, a residual product result-
ing from the leaching of the original argillaceous content of the
nodules. That kaolin can be so formed is clearly indicated by
the presence of this mineral so related to impurities in some of
the nodules that its ·derivation cannot be questioned. The more
common occurrence of kaolin in the geodes from the more
argillaceous part of the beds is .significant in this connection. Moreover, the great majority of the geodes which contain kaolin
are imperfectly developed and the calcite of such specimens in-
variably includes the white powder of this mineral. These facts
strongly support the idea that the kaolin must be a residual pro-
duct. Origin of the Geodes Concerning the time of formation of the geodes, little is defin-
itely known. The removal of the calcareous nodules which, it
is assumed, preceded the geodes, implies an interval of solvent
action during which the Keokuk and Lower Warsaw beds were
above ground-water level. The growth of geodes, on the other
hand, undoubtedly took place below ground-water level. In the development .of the geodes at least two periods of min-
eralization are involved. The first period of development was
by far the most important. During this period of growth the
quartz, chalcedony, dolomite, and a considerable amount of the
calcite together with almost all of the metallic sulphides were
deposited. Of the minerals of the second period of growth, transparent
crystals of calcite and slender untarnished flakes of pyrite are
by far the most important. The minerals of this class are doubt-
less much younger than those of· the former as suggested by th~~
fact that in many instances the pyrite associated with the newer
calcite is perfectly fresh while in the same geode the earlier
pyrite is badly decomposed. The secondary minerals of the geodes such as limonite, gyp-
sum, smithsonite, and malachite are for the most part of much
more recent origin. They have resulted from the alteration of 346 MISSISSIPPIAN STRATA OF IOWA the primary sulphides as is shown by their association with the
partly decomposed members of this group. The bitumen which occurs in some of the geodes must have
been introduced sometime after their formation, since it has not
interfered with the normal geode development. The process of geodization evidently consisted of the inward
growth of crystals upon the walls of cavities left by the solution
of the imbedded concretions. The growth was necessarily ac-
complished by deposition from a solution which filled the inter-
ior completely. As this solution became depleted in its mineral
content, more was introduced by some process of diffusion and
a continuous deposition resulted. In some instances a very im-
pervious wall was developed and growth must have been ex-
tremely slow. But in the majority of geodes numerous feeding
channels in the walls afforded ready passage to -the solutions
after they penetrated t4e siliceous shells. The mineralogical differences of geodes which occur in close
proximity to each other are difficult to account for. The Kinderhook Transgression With the opening of Mississippian time an interior sea occu-
pied a considerable area in the Mississippi Valley region. The
greater proportion of limestone in the group in central and
north-central Iowa suggests that clearer and deeper seas pre-
vailed in those areas than to the S'outheast. The deposits
formed at this time undoubtedly once extended a considerable
distance northeast of their present belt of exposure. Origin of the Geodes It must be
assumed either that the process of geodizatioh was a very local
one and that each individual geode possessed only a small
sphere of attraction, or that a peculiar localization of conditions
favored in some instances the deposition of mineral matter
more widely diffused through the mineralizing solutions. Conditions at the Close of the Devonian The character and distribution of the Upper Devonian depos-
its. in Iowa are such as to suggest that they extended over a
larger area in pre-Kinderhook time and it is believed that an
erosion interval preceded the incursion of the' first Mississip-
pian sea. However, the data bearing on the stratigraphic rela-
tions of the Kinderhook and underlying Devonian deposits in
Iowa are meagre, owing to the fact that no contact of these
older strata with layers definitely known to represent the basal
Kinderhook has been observed. Conditions During Osage Time The exent of the changes at the close of Kinderhook time is
not definitely known. The next succeeding Burlington lime-
stones, exposures of which are now confined to the southeastern
part of Iowa, appear to follow the Kinderhook group conform-
ably. Inasmuch as they exhibit a marked thinning in passing
from the city of Burlington to southern Louisa county, it is
probable that they did not extend far to the northwest. The Keokuk formation succeeds the Burlington without a
stratigraphic break and has essentially the same geographic
distribution in Iowa. It thins to the northwest and is shaly in
its upper part, the argillaceous horizon gradually descending in MISSISSIPPIAN STRATA OF IOWA 348 the formation towards the northwest. This suggests a gradual
recession of the sea to the south during Keokuk time. the formation towards the northwest. This suggests a gradual
recession of the sea to the south during Keokuk time. Oscillations During Meramec Time The contraction of the seas during Keokuk time was appar-
ently continued through the Warsaw. The deposits of this age
consist predominantly of shales. Both divisions of this forma-
tion are confined to the southeastern part of the state, the Up-
per vVarsaw being even more restricted than the Lower. A
h
l
f h
W
i
h
i
i
d At the close of the Warsaw time the interior sea retreated
more rapidly to the south, apparently as a result of an uplift of
the Wisconsin positive element to the north, and the· Warsaw
and earlier Mississippian formations were subjected to erosion. Th
i
f S
i
b bl
b
li l The returning sea of Spergen time probably was but little
more extensive than that of the vVarsaw, since the deposits of
Spergen age in Iowa are of the near-shore type and ~re like-
wise confined to the southeastern part of the state. Th
l
f h
S
k d b
h
d The close of the Spergen was marked by a southward retreat
similar to that at the close of the Warsaw. The readvancing
Lower St. Louis sea extended far to the north, overlapping all
the earlier divisions of the Mississippian except the Kinder-
hook, upon which it rests in Humboldt county. Early in St. Louis time, however, another elevation of the northern area
took place and the strand line retreated rapidly to a point some-
where between Alton, Illinois, and Ste. Genevieve, Missouri. The disconformity resulting from this retreat has been found as
far south as Alton, but no trace of it is shown in the section at
Ste. Genevieve. Following a slight interval of erosion the St. Louis sea returned as rapidly as it ha;d receded and the deposi-
tion of Upper St. Louis limestone in Iowa resulted. Th
t bl
diti
f th
St L
i
t
i
t d b The unstable conditions of the St. Louis were terminated by
still another uplift. The duration of the erosion interval which
followed could not have been great, for the deposits of the re-
turning Ste. Genevieve sea, which must have rivaled that of the
early St. Louis in size, have not been found to rest upon forma-
tions older than the Lower St. Louis. 1 Jour. G<!ol.. vol. x~v. pp. 150-156; 1917. Warping at Close of Meramec Time Warping at Close of Meramec Time Warping at Close of Meramec Time
At the close of Ste. Genevieve time the sea withdrew from the At the close of Ste. Genevieve time the sea withdrew from the At the close of Ste. Genevieve time the sea withdrew from the MISSISSIPPIAN GEOSYNCLINE 349 upper Mississippi Valley again, and the entire region remained
a land area until the close of the Mississippian period. A great
warping took place during and following this emergence, which
resulted in a tilting of the Mississippian and earlier formation~
to the southwest and is known to have been accompanied by the
development of small northwest-southeast trending anticlines
and synclines and by extensive brecciation of the hard, brittle
St. Louis limestone. (See page 236.) Consequent upon this up-
lift erosion proceeded rapidly during the remainder of the Mis-
sissippian and the tilted beds were partly truncated, thus giving
rise to a series of northwest-southeast belts of formational out-
crops in Iowa, many of which were later buried by the Coal
Measures. This southwestward tilting of the beds in Iowa was related to
a widespread late Mississippian deformation involving also
eastern Nebraska, eastern Kansas and Missouri, which outlined
a great southwestwardly pitching geosyncline later occupied by
the early Pennsylvanian sea advancing along a narrow trough
from the southwest and gradually spreading to the margins of
the basin by overlap. A structure contour ' map of the geo-
syncline and a discussion of its influence on Pennsylvanian sedi-
mentation have been published previously by the writer.1 The geosyncline was shallow in early Pennsylvanian time as
is indicated by the fact that the maximum known thickness of
the Cherokee stage, which doubtless repr~sents the time of
greatest sea extension in the province during the period, is only
712 feet. However, it must be remembered that the rim of the
basin had been lowered considerably by pre~Pennsylvanian
erosion. At the present time, the basin is considerably deeper
as a result of subsidence during Pennsylvanian time. 1 Jour. G<!ol.. vol. x~v. pp. 150-156; 1917. PLATES ILLUSTRATING MISSISSIPPIAN
FOSSILS On the follJo'wing plates the illustrations are all natUl13l size. Some of the type
fossils suggested by Doctor Van; Tuyl had to be omitted due to lack of space. This
is especially true of the large Keokuk brachiopods to include which another plate
would have been necessary. Most of the brachiopod Iillustrations were furnished
by Doctor Stuart Weller from the origillal plates of his Monog!1aph 1, Illinois
Geological Survey. Some of the 'crinoids are copied from W·achsmuth and
Springer's Crinoidea Camerata. All others are illustrations of specimens in the
paleontological collections at the State University of Iowa. -A. O. Thomas. TYPE KINDERHOOK FOSSILS Fig. 1. Lep~oPQq'a typa Winchell. Calycinal view of an inx;omplete colony. In railway cut three miles northeast of Morning S Fig. 1. Lep~oPQq'a typa Winchell. Calycinal view of an inx;omplete colony. In railway cut three miles northeast of Morn Fig. 2. L eptaen,al convcxa Weller. Impression of the external surface of a brachial valve. Bed NIDI. 5, Burlin.gton. After Weller, Monog. 1, Ill. Geol. Sm·v. Figs. 3, 4. ScheUwienlg-Uol iq~f la.ta (Wllite and Whitfield). Brachial and lateral views of an internal cast. Bedl No.7, BurlingtolJ], After Weller. Fig. 5. Chonet6s lo·gani Norwood and Pratten. Pedicile view. Bed No·. 6, Burlington. After Weller. Fig. 6. C7wnopeat'!!s fi,scherri Norwood a:J.d Pratten. View of a very perfect pedicle valve sho-wing the spines ~long the
cardinal mm·gin. Bed No. 3, Burliugto1JJ. After Weller. Figs. 7, 8. PTodlttJtus al'ln!atus Hall. 7. Pedicle view of a shell frOml Chouteau Springs, Missouri. 8. Lateral view of a pedicle valve from Bed No.6, Burlington. After
Weller. 8. Lateral view of a pedicle valve from Bed No.6, Burlington. After
Weller. Figs. 9, '10. Parl'ph01'hynchus transverrSltm Weller. 9. Pec1ricle view of a cast from Kinderhook, Illinois. 10. Anterior view orf a cast from Chonopectus sandstone, Burlington. After Weller. Figs. 11, 12. SpiTife?'ina solidirostris Wihite. Pedicle and brachial views of the cotypes. Bed No.7, Burlington. After Weller. Fig. 13. Spirifer platynotttS Weller. View of a brachial v;aJve of one of the cotypes. Bed No.6, Burlington. After Weller. Figs. 14, 15. SpiTifel' biplioa.tus Hall. Pedicle and brachial views. Chonopectus sandstone, Burlington. After Weller. Figs. 16-18. Spil-ifm' subrottmdtts Weller. Pedicle, brachial and lateoo.l views. ClllOlJlopectus sandstone, Burlington,. After Weller. Figs. 19, 20. .Retiln!101-i-a oooperensis (Swallo-w). Pedicle and bnwhial views of 3J specimen from P ettis county, Missouri. It is common. at Burlington and elsewhere m I owa. After Weller. Fig. 21. Edmondia j ejt!'I1Qts (Winchell). View of right valve of an internal mold. IVnssonville. Figs. 2.2, 23. Nt/ln!la iotvensis White and Whitfield. = N. hOltghtJom Stevens. Internal and external views of left aJld right valves, respectively. Wassonville cherts, IVassonville. Fig. 24. DentalM!7n gTol/tdaevt!m Winchell. A typical specimen from the Wassonville . cherts. Fig. 24. DentalM!7n gTol/tdaevt!m Winchell. A typical specimen from the Wassonville . cherts. Fig. 25. Straparoll1t8 obtusus (Hall) . Apical view. Oolitic beds, Humboldt. IOWA GEOJ.O()JCAI, SURVEY
PI,ATE III
2
1
J
5
6
7
4
12
10
14
15
13
16 . 17
18
20
22
. TYPE KINDERHOOK FOSSILS 23 PI,ATE III
J IOWA GEOJ.O()JCAI, SURVEY PI,ATE III 2 2 2 1 J J 6 4 7 4 5 7 6 10 12 12 12 10 13
16 . 14 15 14 15 17 18 16 18 6 17 20 20 20 . 23 . 23 22 22 23 F ig. 22.
L epetopsis capq~lu s (Rnll) .
Sitle vicll' of a mo,]d.
Bec1 No.6, Burlington. TYPE BURLINGTON If'OSSILS F i g~ . I, 2. Z((pli?"entil; Oftlccola, (White amI Whitfield ). '1'11'0 specimens showing size an L1 curvature. Bcd No. 4, Burlington . F i g~ . I, 2. Z((pli?"entil; Oftlccola, (White amI Whitfield ). '1'11'0 specimens showing size an L1 curvature. Bcd No. 4, Burlington . Pig:;. 3, 4. Or bitj' mites nonvoodi (011'011. a nd Shuma rd). Basal an.d intelTadial "ie,vs of a nearl y perfect specim.en sho\\"iu g' the
clevated am bu lacm. Uppcr Du rI ington. I imcstone ; Burlington. Figs. 5, 6. Cj''!f1JtoNastu8 1I/elo (Owen and Shumad ) . Inte;")":1(1ial a.nel apical "ien's showing the sunken a,mbulacm. Burlington P igs. 7, S. jll a01'(lcri'll1tS venumili 01ws (Shumard ) . Right postcrior Ylews of two typica.l calyces of one of t he conunoncst
BuJ"l ington crinoids,
Burlington . Fig. 9. Dizy,gocrinus j'ot'undus (Shumard) . Left postcrior yicw of a. typical calyx. Bu rlingto'll. Fig. 10. Upej'ocrinlls PYj'ifonllis (Shumal·d ) . A nterior vic\\" of a typical caJyx. Bmlingbo,n. Fig. 11. T el&iocrVnlllS mil bj'osus (Ha 11 ) . Postcrior view of a typical but rathe r small calyx. Bu r1in gbO~1. Figs. 12-14. Ch01~e t cs iUinoisensis 'Worthen. Pedicle a,nd bro,chial views of typi(laJ shells from Burlington limestone
at Sp ri~l lgflckl l, Mo. 14 is a view of the intCl'ior of a brachial valve I I"om
tho K eokuk limestone of the same 10caJity. After Weller. Figs. 12-14. Ch01~e t cs iUinoisensis 'Worthen. Pedicle a,nd bro,chial views of typi(laJ shells from Burlington limestone
at Sp ri~l lgflckl l, Mo. 14 is a view of the intCl'ior of a brachial valve I I"om
tho K eokuk limestone of the same 10caJity. After Weller. Figs. 15, IG. Pro(lj/()t~ls blwlin,gtonensis Hall. 1.5. Ped icle view of a. shell hom Bmli ngton . ] 6. Brachial view of a
spccimen from Quincy, Illinois. After Weller. 1.5. Ped icle view of a. shell hom Bmli ngton . ] 6. Brachial view of a
spccimen from Quincy, Illinois. After Weller. Fig. 17. Rhil'id01l1f'lh bl(j'Zing'lon ensil! ( H~1 11 )
. Pecl icle " icw of a typical shell. Bmlington . A ftc I' "Weller. Fig. 17. Rhil'id01l1f'lh bl(j'Zing'lon ensil! ( H~1 11 )
. Pecl icle " icw of a typical shell. Bmlington . A ftc I' "Weller. Fig"3. ] 8, In. , '/Jvrif cj' l]1'imesi Hnll. TYPE BURLINGTON If'OSSILS Vi r w of I:W
in ~llInpll't{) pl'lliclE' ,,:th'c shuwing' th p markings antI the in-
terior of wnoth('l' ped icle yah I' show ill g' t he muscle scar. i::lprillgfielLl
Mo
After
Vclley Fig"3. ] 8, In. , '/Jvrif cj' l]1'imesi Hnll. Vi r w of I:W
in ~llInpll't{) pl'lliclE' ,,:th'c shuwing' th p markings antI the in-
terior of wnoth('l' ped icle yah I' show ill g' t he muscle scar. i::lprillgfielLl, Mo. After , Vclley. Fig. 2U. Spirifer ella
l'~ena (Hall) . Int-c rior of a.picnl part of a pedicle vahe shuwin g t he L1ental la lllellro. B-ul'lingtoll . After , Veller. Fig. 2U. Spirifer ella
l'~ena (Hall) . Int-c rior of a.picnl part of a pedicle vahe shuwin g t he L1ental la lllellro. B-ul'lingtoll . After , Veller. Fig. 2]. A thy1'is la1t( ellosa (L(lI'cillc). Pcd icle view of ::t llearl y perfect Hpccilllen. F rom the Keokuk limes tonlc ; , Va l'saw, Illillui~ It is Hlsu COIllUlOl[ ill t he
Burlington lim esto~lC " Fig. 2]. A thy1'is la1t( ellosa (L(lI'cillc). Pcd icle view of ::t llearl y perfect Hpccilllen. F rom the Keokuk limes tonlc ; , Va l'saw, Illillui~ It is Hlsu COIllUlOl[ ill t he
Burlington lim esto~lC " F ig. 22. L epetopsis capq~lu s (Rnll) . Sitle vicll' of a mo,]d. Bec1 No.6, Burlington. Pr.ATE IV Pr.ATE IV IOWA GEOr,OGICAL SURVEY 2
5
6
7
8
9
11
13
10 2 6 5 2 2
8 9 10 7 9 8 13 13 10 11 11 E'ig. 13.
]llya~in(b keoiC1I./'; WOl·then.
Beel No.6, K eokuk. TY PE KEOKUK AND WARSAW FOSSILS :Figs. 1, 2. Pa./;aea·lJIis Obt1IS11S Meek and Worthen. Calycinal aJld latm'al views of two colonies. Keokuk. Fig. 3. jlI[a c1'0C1'imIS ktg1£1lC1£hls (Hall). Postom-latcnll view of a typical 031yx f rom Keokuk. After Wachsmuth and Spring-m·. Fig. 4. D07'YC1'i1l11S m-ississippiensis RKlemer. Anal "iew of ft vel")' tine e.,'\.lyx. Keokuk. ~~i g . G. A1'clli11ledes 01l1e1U11WS Hall. Part of . pi mJ axis. Keokuk. Fig. G. 0 1'thotct es ke o7nt7~ (Hall) . Pedicle view of ft large and il C!uly complete specimen. Keokuk. After ·Weller. Fig. 7. P1'od1ICtUS setige1'1ls Hall. P ed icle illu tration of a somewhat distorted shell. Hamilton, Illinois. After WellN. Fig. 8. Trtmca111era 8ubt1'ioona (Meek an,l ·Worthen) . Peclicle viel"l of a 1aJ'ge specimen. Warsa.w, Illinois. After Weller. F igs. 9, 10. SpiTifeT 7ceo/.;1£7c Hall. B rachi al ancl lateral views of a nearly perfect specimen. Keokuk. After \'Veller. F igs. ll, 12. Spi1'ife1' 1'ostellaMIS Hall. Pedicle and bmchiaJ views of the holotype. Specimen f rom War ~11W, Illinois. After Weller. E'ig. 13. ]llya~in(b keoiC1I./'; WOl·then. Beel No.6, K eokuk. IOWA GEOLOGICAL SURVEY
PLATE V IOWA GEOLOGICAL SURVEY PLATE V PLATE V PLATE V PLATE V 1'YPE S1'. LOUI S AND PELLA FOSSILS F ig. 1. 1'1'ip lop 7l yll~w1 dalei (Milne-Ec1warc1s an.c1 Haime) . Calycinal viow of a fi.ne specimen f rom St. Louis limestone. H enry county, IQ~va. Figs. 2-4. 'l'l'iplop7l ylhl,1l1 pella,e!1sis (Worthen ) . Lateral views anc1 a calyci'1181 views of t hree typical specimens. Note
tho spine bases. P ella bec1s; P eUa. Lateral views anc1 a calyci'1181 views of t hree typical specimens. Note
tho spine bases. P ella bec1s; P eUa F ig. 5. L ithost!'otiAm oanadense Castelnau. Part of a perfect colony fl'Om. St. Louis limestone. Mt. PleaSaJlt. Fig. 6. A I'cil'i/lI1 edes WOI·t!I &nri, H all. Port ion of t he screw- hapcll ax i. of thi: 1)coI11i:11' fcnestellid bryozo.:l11. Upper Warsaw l ime tone. Keokuk. F ig. 7. Lin,gllla V(/1'soviensis Worthcn . V icw of the holotype. 'Warsaw bec1s; "Varsww, Ill inois. After Weller. F ig. 7. Lin,gllla V(/1'soviensis Worthcn . V icw of the holotype. 'Warsaw bec1s; "Varsww, Ill inois. After Weller. F igs. 8, 9. Ol·tho·tetes 7casicasi.;iensis (McChesney) . B I'achi al aOla pec1icle views of somewhflt hl'ol<cn specimens. P en a, beels ; Fort Doelge. F igs. 8, 9. Ol·tho·tetes 7casicasi.;iensis (McChesney) . B I'achi al aOla pec1icle views of somewhflt hl'ol<cn specimens. P en a, beels ; Fort Doelge. F igs. 10-12. 1'e,t!'(lcannem arotil'ostrata, (Swallow) . P ed icle, brachial anel l,ft,teral views of a specimen f rom Salem limestone. Booneville, Missomi. After Wcller. 12. 1'e,t!'(lcannem arotil'ostrata, (Swallow) . P d i l
b
hi l
l lftt
l
i
f F igs. 10-12. 1'e,t!'(lcannem arotil'ostrata, (Swallow) . P ed icle, brachial anel l,ft,teral views of a specimen f rom Salem limestone. Booneville, Missomi. After Wcller. Fi gs. 1:\-16. P1t,g!l{)ides OttltlllWCL (Wl'Lite). Brachial, pedicle, <111terior anel lateral vicws of spccimClls f rom t he P elln
heels at Fort Dodge. E'igs. 17-19. Gil·tyella indi(/1 !e!lsi.~ (Girty). BraclLial, pedicle lmd lateral views. P ella beels; P ella. After Weller. E'igs. 17-19. Gil·tyella indi(/1 !e!lsi.~ (Girty). BraclLial, pedicle lmd lateral views. P ella beels; P ella. After Weller. Figs. 21, ~2. ..4 1101·islnu InOJl'ionense White. Cast of two specimens "iewcd f rom tho hinge :111c1 f rom the left siele,
respectively. PolI n, heds; Ottumwa. 1'YPE S1'. LOUI S AND PELLA FOSSILS IOWA GEOLOGICAL SURVEY
PLA~'E YJ
5
7
8
6
13
14
11
12
IS PLA~'E YJ PLA~'E YJ IOWA GEOLOGICAL SURVEY IOWA GEOLOGICAL SURVEY 5 5 5 5
6 7 7 8 6 8 6
13
IS 11 11 12 13 13 12 19 19 22 19 19 22 PLATE I
GEOLOGICAL MAP OF IOWA PLATE I
GEOLOGICAL MAP OF IOWA IOWA GEOLOGICAL SURVEY IOWA GEOLOGICAL SURVEY
A
GEOLOGICAL
MAP OF
~A
1922
GEORGE F. KAY,
STATE GEOLOGIST
MISSOURI
DES MOINES
MERAMEC
OSAGE
KINDERHOOK :=====:
DEVONIAN
SILURIAN
OHDOVICIAN
CAMBRIAN
PROTEROZOIC
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https://openalex.org/W2030450814
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https://europepmc.org/articles/pmc4106264?pdf=render
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English
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The importance of waiting
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eLife
| 2,014
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cc-by
| 2,062
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Copyright Sanders and Biron. This
article is distributed under the terms of
the Creative Commons Attribution
License, which permits unrestricted use
and redistribution provided that the
original author and source are credited. elifesciences.org elifesciences.org INSIGHT elifesciences.org MALE MATING BEHAVIOUR The importance of waiting Neural circuits that prevent a male C. elegans worm from copulating
for several minutes after ejaculation have been identified. JARRED SANDERS AND DAVID BIRON time, as they are most sexually potent before
the third day of adulthood (Guo et al., 2012). Given this time pressure, the drive to mate is
likely one of the strongest motivators of a young
adult male. Yet, despite the strength of this
drive, males exhibit a period of sexual disin
terest following ejaculation. While other species
undergo a similar refractory period in response
to sperm release, not much is known about the
molecular and cellular mechanisms that control
the downtime between mating events (Levin,
2009). Related research article LeBoeuf B, Correa P,
Jee C, García LR. 2014. Caenorhabditis
elegans male sensory-motor neurons and
dopaminergic support cells couple
ejaculation and post-ejaculatory behaviors. eLife 3:e02938. doi: 10.7554/eLife.02938
Image The ability of a male C. elegans to
ejaculate is linked to the activity of cells
(shown in white) in the spicules used to
penetrate the vulva of a hermaphrodite Related research article Le This is the first study to identify a role for dopa
mine from neuronal support cells in the regula
tion of mating, and it also supports the idea that
dopamine has an evolutionarily conserved role in
promoting ejaculation (Peeters and Giuliano,
2008). But why have a refractory period in the first
place? One explanation is that this time is required
for the neural circuitry to reset: for example, to
remove the copious amounts of signalling mol
ecules that flood the nervous system, or to
desensitize receptors. Another—not mutually
exclusive—possibility is that the refractory period
could indirectly improve the fitness of the species
by increasing the probability that the male will
mate with multiple partners. Figure 1. After C. elegans males ejaculate, sensory-
motor neurons are inhibited, resulting in a period of
reduced activity and mating ability. The spicules of a
male C. elegans contain the sensory-motor neurons
SPD and SPV. LeBoeuf et al. found that these SPD and
SPV neurons stimulate cholinergic neurons to release
acetylcholine (ACh) when the spicule is inserted into the
hermaphrodite vulva. This begins the sperm initiation
process (that is, sperm are moved from storage in the
seminal vesicle to the vas deferens, ready for release). Figure 1. After C. elegans males ejaculate, sensory-
motor neurons are inhibited, resulting in a period of
reduced activity and mating ability. The spicules of a
male C. elegans contain the sensory-motor neurons
SPD and SPV. LeBoeuf et al. found that these SPD and
SPV neurons stimulate cholinergic neurons to release
acetylcholine (ACh) when the spicule is inserted into the
hermaphrodite vulva. This begins the sperm initiation
process (that is, sperm are moved from storage in the
seminal vesicle to the vas deferens, ready for release). The sensory-motor neurons also stimulate a pair of
glutamateric neurons called PCA to release glutamate
(Glu), which triggers ejaculation. The release of sperm
inhibits the activity of the sensory-motor neurons for
several minutes after ejaculation; during this refractory
period the male cannot copulate. LeBoeuf et al. also
found that glia-like socket cells must also be present if
proper ejaculation is to occur. These cells produce
dopamine (DA), which controls sperm release and affects
the length of the refractory period—more dopamine
means a longer wait before ejaculation is possible again. Uncovering the mechanisms that regulate the
male mating drive, and how it might compete
with other behavioural drives, is a developing story. Related research article Le DOI: 10.7554/eLife.03754 1 of 3 Insight Male mating behaviour | The importance of waiting also had trouble ejaculating, LeBoeuf et al. won
dered whether additional cells that regulate
sperm transfer might control the time between
matings. Since the neural circuit that controls
sperm movement and release has been largely
unexplored, they imaged the physiological activity
of a group of male neurons and identified cells
belonging to two categories: those involved in
moving sperm to the vas deferens, and those
that control sperm release (Figure 1). This cir
cuit was also found to regulate the refractory
period. which light is used to control neurons—to stimulate
ejaculation required activating many neurons that
were not directly associated with the sex organs. Combining optogenetics with cell ablation—
where cells are selectively destroyed—revealed
one pair of glutamatergic sensory neurons (called
PCA) with a particular role in sperm release. This is a classic example of circuit breaking in
neuroscience. In an unexpected and exciting twist, it was found
that dopamine released from non-neuronal support
cells called socket cells—which form a sheath
around the sensory neurons—promotes ejaculation
and increases the length of the refractory period. Cutting off the spicule tips removed both the spic
ule-associated sensory neurons and the socket cells,
so damage to the socket cells could conceivably
have impacted male mating. Destroying the socket
cells reduced the males' ability to ejaculate and
dopamine synthesis in these non-neuronal cells was
necessary for sperm release. So does dopamine
released from the socket cells also regulate the
refractory period? Indeed, it does! Preventing the
socket cells from synthesizing dopamine resulted in
shorter refractory periods, and adding more dopa
mine extended them. As expected, LeBoeuf et al. found that the SPD
and SPV neurons were activated when the spicules
entered the uterus. However, activity in these cells
decreased only once sperm was released, sug
gesting that sensory cues from the hermaphrodite
uterus affect this circuit. Additional experiments
revealed that the SPD and SPV neurons relay
information to the neurons that control the flow of
sperm from the gonad and affect the ability of these
neurons to prime the gonad for sperm movement. Moreover, the use of optogenetics—a technique in Understanding how small neural circuits under
lie behaviour increasingly contributes to our
thinking about more complex neural networks. Related research article Le Mating is an intricate process in C. elegans. Most of the worms are hermaphrodites that can
fertilize their own eggs, but there are also a small
number of males that can fertilize the eggs in the
hermaphrodites. The male responds to contact
with a hermaphrodite by placing the copulatory
apparatus in his tail flush with her body. He subse
quently moves backwards—around her head or
tail if necessary—until his tail contacts the vulva. The male then inserts two structures called spic
ules into the vulva that serve as mechanical
anchors and also facilitate sperm transfer (Liu and
Sternberg, 1995). Following penetration, sperm
flows from where it is stored (the seminal vesicle)
to a duct called the vas deferens in preparation
for release, and after a few seconds it is ejacu
lated (Schindelman et al., 2006). I
n his short story ‘Funes the Memorious’ Jorge
Luis Borges tells of a young boy called Ireneo
Funes who, after he was thrown off a wild horse,
developed the ability to perceive everything and
forget nothing. As a consequence, ‘he was not
very capable of thought. To think is to forget a
difference, to generalize, to abstract. In the overly
replete world of Funes there were nothing but
details, almost contiguous details’. I The ability to draw analogies between phe
nomena that are not identical, to identify imper
fect patterns, is key to analytical thought and
scientific discovery. Correspondingly, simple inver
tebrate model organisms have yielded some
of the best insights into the cellular and molec
ular basis of behaviour in more complex organ
isms, including humans. Now, in eLife, René
García and colleagues at Texas A&M University,
including Brigitte LeBoeuf as first author, have
closely examined one of the most complex behav
iours exhibited by the roundworm Caenorhabditis
elegans—male mating (LeBoeuf et al., 2014). To identify a neural circuit that, as it turned
out, coupled ejaculation to the refractory period,
LeBoeuf et al. experimentally manipulated the
refractory period. Cutting off the spicule tips
reduced the time between subsequent matings. The spicules contain two sensory neurons, called
the SPD and SPV neurons, with endings that are
exposed inside the hermaphrodite uterus during
copulation. Because males with severed spicules It may be surprising given their humble size,
but male worms have a lot to do in very little Sanders and Biron. eLife 2014;3:e03754. Related research article Le The detailed understanding emerging about the
roles of neuromodulation in shaping circuits and
behaviour will be interesting to follow (Bargmann,
2012; Marder, 2012). The sensory-motor neurons also stimulate a pair of
glutamateric neurons called PCA to release glutamate
(Glu), which triggers ejaculation. The release of sperm
inhibits the activity of the sensory-motor neurons for
several minutes after ejaculation; during this refractory
period the male cannot copulate. LeBoeuf et al. also
found that glia-like socket cells must also be present if
proper ejaculation is to occur. These cells produce
dopamine (DA), which controls sperm release and affects
the length of the refractory period—more dopamine
means a longer wait before ejaculation is possible again. Jarred Sanders is in the Committee on Genetics,
Genomics, and Systems Biology, The University of
Chicago, Chicago, United States Sanders and Biron. eLife 2014;3:e03754. DOI: 10.7554/eLife.03754 2 of 3 Insight Insight Male mating behaviour | The importance of waiting David Biron is in the Department of Physics, the
James Franck Institute, and the Institute for Biophysical
Dynamics, The University of Chicago, Chicago,
United States David Biron is in the Department of Physics, the
James Franck Institute, and the Institute for Biophysical
Dynamics, The University of Chicago, Chicago,
United States
david.biron@gmail.com
Competing interests: The authors declare that no
competing interests exist. Published 22 July 2014 and post-ejaculatory behaviors. eLife 3:e02938. doi: 10.7554/eLife.02938. Levin RJ. 2009. Revisiting post-ejaculation refractory
time-what we know and what we do not know in
males and in females. The Journal of Sexual Medicine
6:2376–2389. doi: 10.1111/j.1743-6109.2009. 01350.x. david.biron@gmail.com 6:2376–2389. doi: 10.1111/j.1743-6109.2009. 01350.x. Liu KS, Sternberg PW. 1995. Sensory regulation of male
mating behavior in Caenorhabditis elegans. Neuron
14:79–89. doi: 10.1016/0896-6273(95)90242-2. Marder E. 2012. Neuromodulation of neuronal circuits:
back to the future. Neuron 76:1–11. doi: 10.1016/j. neuron.2012.09.010. Peeters M, Giuliano F. 2008. Central neurophysiology
and dopaminergic control of ejaculation. Neuroscience
and Biobehavioral Reviews 32:438–453. doi: 10.1016/j. neubiorev.2007.07.013. Schindelman G, Whittaker AJ, Thum JY, Gharib S,
Sternberg PW. 2006. Initiation of male sperm-transfer
behavior in Caenorhabditis elegans requires input
from the ventral nerve cord. BMC Biology 4:26. doi: 10.1186/1741-7007-4-26. Competing interests: The authors declare that no
competing interests exist. Published 22 July 2014 Liu KS, Sternberg PW. 1995. Sensory regulation of male
mating behavior in Caenorhabditis elegans. Neuron
14:79–89. doi: 10.1016/0896-6273(95)90242-2. Marder E. 2012. Neuromodulation of neuronal circuits:
back to the future. Neuron 76:1–11. doi: 10.1016/j. neuron.2012.09.010. Sanders and Biron. eLife 2014;3:e03754. DOI: 10.7554/eLife.03754 References Bargmann CI. 2012. Beyond the connectome: how
neuromodulators shape neural circuits. Bioessays
34:458–465. doi: 10.1002/bies.201100185. Guo X, Navetta A, Gualberto DG, Garcia LR. 2012. Behavioral decay in aging male C. elegans correlates
with increased cell excitability. Neurobiology of Aging
33:e1485–1423. doi: 10.1016/j.neurobiolaging. 2011 12 016 Bargmann CI. 2012. Beyond the connectome: how
neuromodulators shape neural circuits. Bioessays
34:458–465. doi: 10.1002/bies.201100185. Bargmann CI. 2012. Beyond the connectome: how
neuromodulators shape neural circuits. Bioessays
34:458–465. doi: 10.1002/bies.201100185. Bargmann CI. 2012. Beyond the connectome: how
neuromodulators shape neural circuits. Bioessays
34:458–465. doi: 10.1002/bies.201100185. Guo X, Navetta A, Gualberto DG, Garcia LR. 2012. Behavioral decay in aging male C. elegans correlates
with increased cell excitability. Neurobiology of Aging
33:e1485–1423. doi: 10.1016/j.neurobiolaging. 2011 12 016 Peeters M, Giuliano F. 2008. Central neurophysiology
and dopaminergic control of ejaculation. Neuroscience
and Biobehavioral Reviews 32:438–453. doi: 10.1016/j. neubiorev.2007.07.013. Guo X, Navetta A, Gualberto DG, Garcia LR. 2012. Behavioral decay in aging male C. elegans correlates
with increased cell excitability. Neurobiology of Aging
33:e1485–1423. doi: 10.1016/j.neurobiolaging. 2011.12.016. Guo X, Navetta A, Gualberto DG, Garcia LR. 2012. Behavioral decay in aging male C. elegans correlates
with increased cell excitability. Neurobiology of Aging
33:e1485–1423. doi: 10.1016/j.neurobiolaging. 2011.12.016. Schindelman G, Whittaker AJ, Thum JY, Gharib S,
Sternberg PW. 2006. Initiation of male sperm-transfer
behavior in Caenorhabditis elegans requires input
from the ventral nerve cord. BMC Biology 4:26. doi: 10 1186/1741-7007-4-26 LeBoeuf B, Correa P, Jee C, García LR. 2014. C. elegans male sensory-motor neurons and
dopaminergic support cells couple ejaculation LeBoeuf B, Correa P, Jee C, García LR. 2014. C. elegans male sensory-motor neurons and
dopaminergic support cells couple ejaculation 3 of 3
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https://masujournal.org/store_file/archive/69-10-10-676-680.pdf
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Maltese
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Effect of Synthetic Pyrethroids on Bollworm Control, Crop Maturity and Seed Cotton Yield in Summer Cotton
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Madras Agricultural Journal
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cc-by
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https://doi.org/10.29321/MAJ.10.A02772 https://doi.org/10.29321/MAJ.10.A02772
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https://openalex.org/W4286899676
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https://zenodo.org/records/5939331/files/O%20Papel%20da%20Log%C3%ADstica%20na%20Distribui%C3%A7%C3%A3o%20e%20Transporte%20de%20Mercadoria.pdf
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Portuguese
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O Papel da Logística na Distribuição e Transporte de Mercadoria
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Zenodo (CERN European Organization for Nuclear Research)
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cc-by
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Journal of Technology & Information Marcos de Oliveira Morais
Universidade de Santo Amaro (UNISA) / Universidade Estácio de Sá
http://orcid.org/0000-0002-5981-4725
marcostecnologia2001@gmail.com Marcos de Oliveira Morais
Universidade de Santo Amaro (UNISA) / Universidade Estácio de Sá
http://orcid.org/0000-0002-5981-4725
marcostecnologia2001@gmail.com Palavras - chave: Logístico, Distribuição, Administração, Transporte e Tempo. Abstract This study seeks to generate knowledge for practical application and solve specific problems, such as on-
time delivery is important for the company and the advantages that the distribution and transport of goods
can offer. Check the prepared questions and understand the objectives are: To analyze the impact that the
delay in delivery can lead to the company and reduce transportation costs and inputs, increase commitment
to customers and consequently retain the same. The study was conducted through case study, qualitative
and exploratory interviews, and data collection conducted through a questionnaire for employees. When
conducting the interview, the result was that the logistics sector operates properly, however an increase in
the vehicle fleet would be an option to be studied according to the customers, but yet does not lack. It can
be concluded that the priority to be changed in the logistics management sector was the same happened and
consequently come to the improvements, some other immediate and progressive. Keywords: Logistics, Distribution, Administration, Transport and Time. Resumo O presente trabalho busca gerar conhecimentos para a aplicação prática e solucionar problemas específicos,
como a pontualidade na entrega é importante para a empresa e quais as vantagens que a distribuição e o
transporte de mercadoria podem oferecer. Verificar pelas questões elaboradas e compreender os objetivos
são eles: Analisar o impacto que o atraso na entrega pode ocasionar para a empresa e reduzir os custos com
transporte e insumos, aumentar o comprometimento com os clientes e consequentemente a fidelizar os
mesmos. O trabalho foi realizado através do estudo de caso, entrevistas de natureza qualitativa e
exploratória, sendo a coleta de dados realizada através de um questionário destinado aos colaboradores. Ao
realizar a entrevista o resultado foi, que o setor logístico opera de maneira correta, entretanto um aumento
na frota de veículos seria uma opção a ser estudada de acordo com os clientes, porém até o momento não
deixa a desejar. Pode-se concluir que a prioridade a ser mudada no setor logístico era gestão, a mesma
aconteceu e por consequência veio às melhorias, algumas imediatas e outras progressivas. 1 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br J 1. Introdução Ballou (2010) e Flores (1994) vêm analisando o tema, conforme apontado na
revisão de literatura, em seus diferentes níveis de entendimento e aplicação ao contexto
organizacional. Pode-se encontrar na literatura definições para o papel da logística na
distribuição e transporte de mercadoria e pontualidade na entrega, o que demanda a
construção de um modelo teórico/gerencial que explicite como esses diferentes conceitos
se articulam e podem contribuir para o entendimento de propostas de desenvolvimento
organizacional. A logística existe desde quando a civilização começou, as guerras requeriam uma
organização primordial e expansiva por parte de quem a comandava, devido à maioria
das guerras serem longas e distantes, era preciso planejar, organizar e executar as tarefas
logísticas para transportar armamentos, tropas, mantimentos e carros de guerra. Da
mesma forma acontece dentro de uma empresa, pois o setor logistico é fundamental, ter
um funcioamento de forma efetiva por ser o responsável em regularizar recursos,
equipamentos e informações e por realizar todas as atividades dentro da mesma. A
logística estuda como a administração pode melhorar o nível de rentabilidade nos serviços
de distribuição aos clientes e consumidores através de planejamento, organização e
controle das atividades de movimentação e armazenagem, visando simplificar o fluxo de
produtos. 2 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information De acordo com Carvalho (2009) levar a quantidade de produtos certos ao lugar
certo na hora certa não é um trabalho simples, nem barato. Pelo contrário, os mercados
de massa, com sua grande diversidade de segmentos, de clientes espalhados por vastas
áreas geográficas, podem tornar cara e dispendiosa à tarefa logística; portanto fazer o
transporte não é algo tão simples assim, como colocar o produto no veículo e encaminhar
até o destino final, tem todo um processo por trás, como o tipo de veículo, a melhor rota,
o prazo de entrega levando em conta trânsito, entre outros fatores. Na literatura acadêmica sobre o papel da logística na distribuição e transporte de
mercadoria e pontualidade na entrega relacionados com o setor transporte existe poucos
estudos sobre o tema Burgess et. al (2005). Os trabalhos identificados na literatura foram
Ballou (2010) e Flores (1994) que mais vezes apareceram na literatura. A logística apesar de ser considerada uma das atividades mais antigas é um
dos conceitos de gerência mais moderno, devido à economia e a tecnologia, com a
globalização houve um aumento nas incertezas econômicas tendo maiores exigências do
cliente em relação aos serviços, mudanças tecnológicas, menores ciclos de vida dos
produtos entre outros, o que tornou possível um gerenciamento logístico mais eficiente e
eficaz. Uma das perguntas chave esta em como a distribuição e o transporte podem
influenciar na empresa? Analisar o impacto que o atraso na entrega pode ocasionar para a empresa; reduzir
os custos com transporte e insumos; aumentar o comprometimento com os clientes e
consequentemente a fidelizar os mesmos; identificar quais são as opiniões dos
funcionários/colaboradores; elaborar ações baseadas nas percepções das situações
vivenciadas pelos funcionários/colaboradores para produção de ações que possibilitem
atingir estes objetivos. O presente estudo visa a contribuir para a elucidação de questões relacionadas aos
dois temas: O papel da logística na distribuição e transporte de mercadoria e pontualidade 3 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information transporte de mercadoria e Pontualidade na entrega. A seguir são detalhados os aspectos
metodológicos; estudo de caso, pesquisa bibliográfica, pesquisa exploratória, entrevistas
entre outros; na terceira seção, é apresentada a organização; na quarta seção os resultados
e discussões e na última seção, são expostas as considerações finais. Journal of Technology & Information na entrega nas empresas. A pontualidade na entrega é um assunto delicado de se tratar,
pois quando ocorre um atraso vêm junto alguns contratempos como não ter alguém para
receber a mercadoria no local acertado, alguns gastos desnecessários, devolução de
mercadoria e até o cancelamento do pedido. Além da perda de confiança na empresa e a
diminuição da credibilidade. O ponto de vista economico é crucial, pois quando essas
adversidades são ajuastadas diminui os custos. na entrega nas empresas. A pontualidade na entrega é um assunto delicado de se tratar,
pois quando ocorre um atraso vêm junto alguns contratempos como não ter alguém para
receber a mercadoria no local acertado, alguns gastos desnecessários, devolução de
mercadoria e até o cancelamento do pedido. Além da perda de confiança na empresa e a
diminuição da credibilidade. O ponto de vista economico é crucial, pois quando essas
adversidades são ajuastadas diminui os custos. Segundo Paura (2012) a distribuição física se preocupa principalmente com a
movimentação de produtos para o cliente; visto que a entega final é um assunto delicado
dentro de uma empresa, é o momento em que todos os outros processos que foram feitos
com excelência e perdem sua importância caso não tenha a entrega feita no prazo
acordado. Almeja-se preencher a lacuna empírica/gerencial identificada na relação entre o
papel da logística na distribuição e transporte de mercadoria e a pontualidade na entrega
nas empresas. O presente estudo constitui uma contribuição para compreender os fatores
competitivos do ramo transporte. Para o desenvolvimento da pesquisa, em termos metodológicos, será adotada a
abordagem qualitativa. Em relação aos procedimentos serão realizadas entrevistas, que
de acordo com as pesquisas deste tipo se caracterizam pela interrogação direta das pessoas
cujo comportamento se deseja conhecerem. Basicamente, procede-se à solicitação de
informações via questionários a um grupo significativo de pessoas acerca do problema
estudado para em seguida, mediante análise, obter as conclusões correspondentes aos
dados coletados. A população entrevistada foi de 25 funcionários/colaboradores de
diferentes hierarquias, as amostras foram analisadas de forma empírica na empresa Unival
Válvulas e Conexões na cidade de Guarulhos. O estudo está estruturado em cinco seções, além desta introdução. Na primeira
seção é discutida a questão da revisão de literatura; O papel da logística na distribuição e 4 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br 2.2. Controle de Pedidos Para Ballou (2010) a distribuição Física aborda a movimentação, estocagem e
processamento de pedidos, costumando-se ser a atividade mais importante em termos de
custo; visto que quando se tem algum problema os prejuízos são consideráveis, pois além
dos custos com insumos pode ocorrer a insatisfação do cliente. De acordo Lambert (1998) o controle de Pedidos engloba as atividades que são:
recebimento e entrada do pedido; processamento do pedido; resgate no estoque e
embalagem; expedição do pedido e entrega e descarregamento no cliente,pois quando o
cliente entra em contato com a empresa e faz seu pedido, o mesmo deseja que a mesma
já tenha ciência dos produtos em estoque informá-lo o prazo de entrega.Como descrito
por Bowersox e Closs (1996), o maior objetivo de se administrar o ciclo de pedido é
reduzir ao máximo o grau de incerteza incorporado a essa atividade; sendo assim a
administração do ciclo de pedido fornece a oportunidade da própria empresa através do
modo que seus clientes, vendo e experimentando a transação da forma que o consumidor
faz. 2.1. Administração do Estoque De acordo com Ballou (2010) não basta melhorar, mas sempre renovar a questão
de gerenciamento, produção, armazenar, manusear e entregar, garantindo assim a
satisfação do cliente; pois quando o cliente faz o pedido ele tem prazos e espera que a
empresa contratada também tenha prazo, afinal quando não se tem a satisfação do cliente
o mesmo não contrata mais os seus serviços. Segundo Paulo (2006) há dois fatores que
influenciam no transporte são eles o tempo e a distância, estão associados, e faz com que
verifiquem o estoque, nível de serviço e custo; porque quando a empresa marca com o
cliente um horário e esse horário não é cumprido afeta a empresa perdendo assim um
pouco de sua credibilidade. De acordo com Martin (2007) o gerenciamento tem o
proposito de remover os obstáculos e os desalinhamentos ocorrido devido ao acumulo de
estoque e maior tempo; pois quando se tem um gerenciamento correto a perca de tempo
é menor, tornando assim o processo logístico mais rápido e eficiente. Como descrito por
Marcio (2014) na distribuição física os pontos de origem da mercadoria são constituídos
pelas fábricas e de depósitos próprios e de terceiros; portanto para se ter um processo
logístico eficiente se faz necessário que a empresa tenha um depósito para que seja
armazenado a mercadoria. 5 Journal of Technology & Information – Volume 1 – Número 2 – 2021 www.jtni.com.br Journal of Technology & Information os caminhos que os produtos devem seguir para melhor adequar as estruturas logísticas;
pois quando se define a rota de transporte economiza tempo e garante que a mercadoria
chegue no horário no seu destino final, deixando assim o cliente satisfeito. De acordo com
Hamifrancy os processos operacionais e de controle permite transferir os produtos desde
a fabricação até a entrega final envolvendo o sistema de distribuição; logo a distribuição
é a parte mais importante do processo logístico, pois é quando se tem contato com o
cliente final vendo a sua satisfação ou não. Segundo Antônio (2007) o objetivo da
distribuição é de conduzir os produtos certos para os lugares certos, no momento certo e
com o nível de serviço estimado e menor custo; porque quando nao se tem esse
planejamento os custos para empresa se tornam maiores e pode ate ocorrer a perca do
cliente. 2.3. Administração de Tráfego De acordo com Angela (1999) o setor logístico envolve desde o processamento
até a entrega final ao cliente, junto com os setores de vendas e marketing, assim que
disponibiliza o produto no tempo; visto que quando uma empresa entra em contato
interessada em seus produtos, ela se preocupa também com o prazo de entrega, um ponto
bastante forte na decisão. Como descrito por Carlos (2000) a importância dos elementos
logísticos com relação ao serviço ao cliente em algumas situações são mais importantes,
pois engloba tempo e preço; uma vez que quando se contrata um serviço a empresa busca
por qualidade e menor preço, no caso do setor logístico a qualidade um dos fatores seria
o prazo de entrega e a pontualidade. Para Philippe (2000) tem como objetivos distinguir 6 Journal of Technology & Information centrada na escolha de aspectos das relações entre sujeitos. (2) A pesquisa empírica lida
com processos de interação e face-a-face, isto é, o pesquisador não pode elaborar a
pesquisa em “laboratório” ou em uma biblioteca, isolada e apenas com livros a sua volta. Nesta modalidade da elaboração do conhecimento, o pesquisador precisa “ir ao campo”. centrada na escolha de aspectos das relações entre sujeitos. (2) A pesquisa empírica lida
com processos de interação e face-a-face, isto é, o pesquisador não pode elaborar a
pesquisa em “laboratório” ou em uma biblioteca, isolada e apenas com livros a sua volta. Nesta modalidade da elaboração do conhecimento, o pesquisador precisa “ir ao campo”. O conhecimento empírico é conceituado por Fachin (2003) como a resposta para
ocorrências baseadas na vivência, experiência de erros e acertos, que não possuem
fundamentação metodológica. Já para Ramos; Ramos; Busnello (2005) acrescenta o
conceito anterior a concepção do autor em que o conhecimento empírico é estabelecido
pela experiência do outro da interação humana e social, na qual são explicitados
conhecimentos implícitos individuais. Dentre as metodologias ao nosso alcance, os
pesquisadores as agrupam em dois níveis: 1. Metodologias Qualitativas e Observação-
participante. 2. Entrevistas não estruturadas e/ou depoimentos. A pesquisa empírica
implica em refletir acerca da relação que se estabelece entre o sujeito e o objeto da
pesquisa. 3. Metodologia O Estudo de Caso como método que apresenta melhor aderência ao objetivo e às
questões norteadoras do trabalho. Tull e Hawkins (1976) afirmam que "um estudo de
caso se refere a uma análise intensiva de uma situação particular". De acordo com Yin
(2005), a preferência pelo uso do estudo de caso deve ser no estudo de eventos
contemporâneos, em situações onde os comportamentos relevantes não podem ser
manipulados, mas onde é possível se fazer observações diretas e entrevistas. Para Quivy e Campenhoudt (1998), no método de observação é importante
ressaltar que este implica um alto grau de subjetividade, uma vez que as pessoas se
manifestam de acordo com sua vivência, histórico de valores e aspectos culturais. Utiliza-
se este tipo de pesquisa empírica quando se quer conseguir informações e conhecimento
referentes a um determinado problema do qual se busca comprová-lo, ou ainda, com a
intenção de descobrir novos fenômenos, percepções ou relações entre eles. O termo
pesquisa empírica, concisamente, se define como: (1) o modo de fazer pesquisa por meio
de um objeto localizado dentro de um recorte do espaço social. A pesquisa empírica está 7 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information e conexões de diversos tamanhos, entregando em todo o território nacional. E de acordo
com Rosa (2011) a logística engloba o transporte, o estoque/armazenagem de produtos e
diversas outras atividades, desde o suprimento para a produção até a entrega do produto
final ao cliente; sendo assim não basta à empresa ter um setor comercial, setor financeiro
entre outros setpres eficiente e o setor logístico não tão eficiente assim, os setores
principalmente o comercial e o logístico devem estar em sintonia, afinal não se pode
cometer erros como vender um produto que não tem no estoque. e conexões de diversos tamanhos, entregando em todo o território nacional. E de acordo
com Rosa (2011) a logística engloba o transporte, o estoque/armazenagem de produtos e
diversas outras atividades, desde o suprimento para a produção até a entrega do produto
final ao cliente; sendo assim não basta à empresa ter um setor comercial, setor financeiro
entre outros setpres eficiente e o setor logístico não tão eficiente assim, os setores
principalmente o comercial e o logístico devem estar em sintonia, afinal não se pode
cometer erros como vender um produto que não tem no estoque. Antes de analisar o setor logístico foi verificado a área de estoque, afinal de acordo
com Ayres (2009) os estoques são elementos cruciais no atendimento a demandas
previstas; alimentam todo o fluxo produtivo, permitem racionalizações nos processos de
compra, garantem homogeneidade em processos produtivos e possibilitam às
organizações a prática de economia de escala em muitas tarefas no processo de obtenção
de insumos, durante as atividades de transformação e ao longo do processo de
distribuição, responsáveis pela colocação de produtos à nossa disposição; uma vez que a
empresa ao receber o pedido e ainda tem que ir no estoque e procurar as peças o setor
logístico se torna ineficiente, pois além de seprar o pedido tem que procurar as peças no
estoque, sendo que a armazenagem tem o papel de deixar os produtos seprados em ordem. Na unival ao receber um pedido o mesmo é passado pelo setor financeiro e fiscal
e entregue ao setor logístico, onde ocorrer o recebimento do pedido, a separação dos
produtos no estoque, a conferência, a embalagem e por fim o carregamento. Entretanto
antes desses produtos serem encaminhados ao (s) veículo (s) de transporte é conferida a
nota e depois o veículo é carregado. 3.1 Análise da Unidade A empresa utilizada para estudo de caso deste artigo, foi a empresa Unival
Válvulas e Conexões fundada em 1986, situada no distrito de Guarulhos estado de São
Paulo – Brasil. Contando as quatro unidades, a matriz em Guarulhos e outras três unidades
sendo no Rio de Janeiro/RJ, Ipatinga/MG e Serra/ES. A Unival Válvulas e Conexões é
composta por 2 sócios e tem uma longa tradição no comercio de seus materiais, suprindo
as principais companhias siderúrgicas, metalúrgicas, químicas, petroquímicas, refinarias
usinas, empresas alimentícias e etc. A empresa comercializa Válvulas Industriais de Aço
Carbono, Aço Inoxidável e Aço Ligado, de 1/2` a 72`. Ao analisar a empresa Unival, foi verificada uma deficiência no setor logístico,
mais precisamente na área de pontualidade na entrega. A empresa trabalha com válvulas 8 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br www.jtni.com.br Journal of Technology & Information Antes de esses produtos saírem a caminho de seu
destino final o setor logístico traça a melhor rota, onde é definido através da qualidade da
estrada, menor tempo, risco de roubo entre outros fatores. Quando estes procedimentos
não são feitos da maneira correta podem ocorrer alguns problemas como gastos
desnecessários com insumos, tempo perdido e a insatisfação do cliente. 9 Journal of Technology & Information – Volume 1 – Número 2 – 2021 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information Os dados foram levantados por meio de revisão de literatura que foi desenvolvida a partir
de material já elaborado, constituído principalmente de livro e artigos científicos, para
dar o devido suporte teórico-acadêmico ao estudo Diehl e Tatim, (2004). Efetuou-se a
pesquisa de campo e entrevistas em profundidade, com questões não estruturadas com 25
entrevistados de nível técnico e gerencial, funcionários da empresa Unival Válvulas e
Conexões, atuantes na cidade de Guarulhos, ligados à área de transporte. Segundo Gephart (2004), um valor importante da pesquisa qualitativa é a
descrição e compreensão das reais interações humanas, percepções, sentidos, e processos
que constituem os cenários da vida organizacional. De acordo com Merriam (1998)
estudos qualitativos interpretativistas podem ser encontrados em disciplinas aplicadas em
contextos da prática. Os dados são coletados por meio de entrevistas, observações e/ou
análise de documentos. O que é perguntado, o que é observado e quais documentos são
relevantes, dependerá da revisão da literatura. A coleta de dados se deu por meio de entrevista semiestruturada. Neste tipo de
trabalho, o pesquisador deve seguir um conjunto de questões previamente definidas, mas
ele o faz em um contexto muito semelhante ao de uma conversa informal, tendo abertura
para incluir novas questões, se necessário, e análise de documentos, por meio das questões
elaboradas buscou-se compreender ao analisar. 3.2 Coleta e Análise de Dados A análise das entrevistas foi feita de maneira empírica e interpretativa, por meio
da utilização da análise de conteúdo. Segundo Gubrium e Holstein (2000) esse tipo de
pesquisa busca apontar os “comos”, e os “por quês” embasados nos discursos oriundos
da análise das entrevistas levando-se em consideração as significações, procurando
identificar as percepções dos funcionários/colaboradores sobre o tema. Um dos
propósitos da utilização das entrevistas como método de coleta de dados na pesquisa
qualitativa, explorar percepções, experiências, crenças e/ou motivações dos
funcionários/colaboradores sobre questões específicas no campo organizacional. A análise foi feita em duas etapas: a) análise e compreensão das pesquisas
bibliográficas e/ou documentais feitas sobre o tema; b) análise e compreensão das
entrevistas realizadas. Sabe-se que, desse modo, a metodologia qualitativa na pesquisa
empírica, ao estabelecer relações face-a-face entre o “sujeito que pesquisa” com o “sujeito
que é pesquisado”, permite vínculos de reflexão entre as partes envolvidas porque estão
todos em presença, isto é, frente-a-frente e em diálogo. Em conformidade com Flores (1994), o roteiro de entrevistas foi elaborado em
função dos objetivos e da questão de pesquisa, e foi guiado pelos principais tópicos
levantados. Sendo uma pesquisa qualitativa, não existe uma rígida delimitação em relação
ao número adequado de sujeitos da entrevista, pois é um dado que pode sofrer alterações
no decorrer do estudo, além disso, pode haver necessidade de complementação de
informações, ou também, em caso de esgotamento, à medida que as respostas se tornam
redundantes. As entrevistas para esse trabalho foram realizadas individualmente no local de
trabalho, com funcionários/colaboradores de diferentes níveis hierárquicos. Estas foram
realizadas entre os dias 04/04 e 15/04 do ano de 2016. Para se atingir os propósitos desse
estudo buscou-se formular um roteiro de entrevistas embasado na teoria descrita. 10 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021 4. Análise e Interpretação dos Resultados Os resultados descritos a seguir foram baseados nas informações colhidas nas
entrevistas, também foram colhidas informações nos sites da organização. Estas
contribuíram para complementar o estudo. Os resultados visaram responder, Como a
distribuição e o transporte podem influenciar na empresa. As discussões apresentadas
buscam traduzir a interpretação do pesquisador, construída a partir da análise das
respostas obtidas pelas entrevistas realizadas, bem como, os dados obtidos a partir da
observação in loco. As informações foram trabalhadas de forma a apresentar as 11 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021 Journal of Technology & Information percepções dos stakeholders com a finalidade de elaborar ações que venham a contribuir
para o Papel da logística na distribuição e transporte de mercadoria. Tabela 1 – Percepções acerca de o papel da logística na distribuição e transporte de mercadoria. Tabela 1 – Percepções acerca de o papel da logística na distribuição e transporte de mercadoria. 12 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021
jt i
b Journal of Technology & Information Após ocorrer a mudança na gestão há dois anos, as reclamações referentes a
problemas básicos e recorrentes foram eliminadas de imediato, onde a principal delas era
a falta de pontualidade nas entregas. Para Couto (2012) mudanças ocorrem constantemente, seja de forma prevista,
desejável ou incontrolável. Sendo assim, se as organizações desejam controlar ou pelo
menos se adaptar às mudanças que estão se processando, é necessário compreender todas
as dimensões de sua própria realidade e assim aproveitar todo o potencial da
transformação. Os clientes entrevistados acreditam que um aumento na frota de veículos no setor
logísticos pode melhorar o prazo de entrega, o tornando menor, pois em algumas entregas
ocorrem atrasos e na maioria das vezes não é por falta de veículo e sim por problemas
climáticos como a chuva, por exemplo, ou o trânsito. Entretanto os funcionários e gestores
não julgam necessário esse aumento de imediato, pois a frota atual atende aos pedidos
com excelência. Outro fator posto em destaque é a falta da elaboração de uma administração de
tráfego, porém na maioria das vezes não é feito devido ao pouco tempo. Segundo Novaes
(2007) o processo de roteirização visa propiciar um serviço de alto nível aos clientes, mas
ao mesmo tempo mantendo os custos operacionais e de capital tão baixo quanto possível. Segundo as pesquisas os colaboradores sugeriram uma administração no estoque,
o que faria com que o setor logístico tivesse um desempenho de maior excelência; para
Arnold (1999) a administração de estoques deve ser responsável pelo planejamento e
controle do estoque, desde a matéria-prima até o produto final. Sendo o estoque resultante da fabricação de produtos acabados ou em processos,
entendendo que os dois devem ser administrados de maneira conjunta; com uma
administração de estoque de excelência os gastos com insumos e armazenagem
diminuirão e o prazo de entrega se torna mais rápido e eficiente. A melhor alternativa 13 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information para a empresa é de administrar o estoque, pois é um dos primeiros passos quando a
empresa recebe um pedido, pois é no estoque que se consegue ver quais produtos tem e a
quantidade de cada um, uma adversidade que pode ocorrer é setor comercial vende um
produto que não tem no estoque, o que passa a imagem da empresa, como uma empresa
má organizada, deixando de ter credibilidade. para a empresa é de administrar o estoque, pois é um dos primeiros passos quando a
empresa recebe um pedido, pois é no estoque que se consegue ver quais produtos tem e a
quantidade de cada um, uma adversidade que pode ocorrer é setor comercial vende um
produto que não tem no estoque, o que passa a imagem da empresa, como uma empresa
má organizada, deixando de ter credibilidade. Para Oliveira (1999) os sistemas de controle de estoque processam dados que
refletem nas mudanças nos artigos em estoque. Os sistemas computadorizados de controle
de estoque auxiliam a empresa a fornecer serviço de alta qualidade para os clientes,
reduzindo ao mesmo tempo o investimento e os custos de manutenção de estoques. Segundo Oliveira (1999) os principais componentes de um sistema são: • A definição dos objetivos, dos usuários quanto aos do sistema, o objetivo é a
finalidade da criação do sistema; • As entradas do sistema, cuja atividade distingue as forças que fornecem ao
sistema o material, a energia e a informação para o processo, gerando com isso as
saídas; • O processo de transformação do sistema, que transformam a entrada em um
resultado; • As saídas do sistema, correspondem aos resultados do processo de transformação
e devem ser coerentes com os objetivos do sistema; • Os controle e as avaliações do sistema, tem como finalidade verificar se as saídas
estão coerentes com os objetivos; • A retroalimentação, é a introdução de uma saída em forma de informação. 14 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information Conforme o resultado das pesquisas os colaboradores abordaram uma mudança
na administração de tráfego, pois ainda ocorrem alguns atrasos que podem ser eliminados,
o que ás vezes ocasiona na perda do cliente; o gerenciamento de tráfego é uma estratégia
muito importante nas políticas, procedimentos e planejamento das cargas concluindo que
quando se tem uma administração de tráfego eficiente o setor logístico trabalha com
excelência por fazer as entregas no prazo por optar pelo caminho mais aconselhável
Caixeta-filho e Martins (2001). Tendo assim clientes satisfeitos. De acordo com as pesquisas com os colaboradores os mesmos propuseram uma
modificação no controle de entrada de pedidos, pois é a primeira etapa do setor logísticos
em relação á entrega. Conforme Ballou (2010) são inúmeros os fatores com peso suficiente para acelerar
ou retardar o tempo de Processamento de Pedidos e Fleury (2006) apresenta fatores
influentes no tempo de processamento de pedidos vistos adiante e complementa com mais
fatores apresentando variabilidades que podem ocorrer no ciclo do pedido; quando se tem
o controle de entrada de pedidos o trabalho no setor logístico funciona de maneira mais
precisa, pois não á gasto de tempo desnecessários e nem custos para a empresa, podendo
assim ter o trabalho final que é a entrega feito com excelência e clientes satisfeitos. A tabela 2 exibe uma confrontação dos fatores citados por Ballou (2010) e Fleury
(2006). 15 Journal of Technology & Information Tabela 2: Fatores que influenciam no tempo do ciclo do pedido. Fonte: Ballou 2010 e Fleuty
2006. Tabela 2: Fatores que influenciam no tempo do ciclo do pedido. Fonte: Ballou 2010 e Fleuty
2006. 16 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information Confrontando os fatores que influem no tempo de Processamento de Pedidos
dados por Ballou (2010) e Fleury (2006), pode-se constatar que estes impasses podem ser
reduzidos ou solucionados através do auxílio de sistemas de informação e estabelecendo
controles e parâmetros elaborados pelo gestor de logística. A empresa tem uma pequena frota de caminhões e tinha somente quatro motoristas
para atender as entregas. Constantemente tínhamos que contratar serviços de terceiros
pois os quatro motoristas não conseguaiam fazer as entregas no prazo. Decidiu-se então
contratar um quinto motorista para reduzir a contratação dos terceiros. Com o tempo, foi
visto que mesmo com cinco motoristas a equipe não estava dando conta das entregas, foi
então que a empresa deciciu colocar rastreador nos veículos e rastrear as rotas. Percebeu-
se então que após a colocação desses rastreadores que os motoristas passaram a fazer as
entregas no prazo. Ocorrerá a eliminação de duas vagas administrativas na Logística. Na atual
situação tem um administrador de carteira para cada segmento. Com o total de quatro
pessoas, porém na maior parte do tempo não se entendem o que atrapalha o trabalho um
do outro ao distribuir as tarefas para o pessoal de operação que atende aos quatro
simultaneamente. Os dois escolhidos para ficar irão administrar juntos as carteiras, sendo
um responsável e o outro auxiliar. Antes dessa mudança cada um queria o seu pedido
atendido prioritariamente, o que na maioria das vezes não era a necessidade da própria
empresa. A eliminação das vagas será realizada no período de 60 dias após a tomada de
decisão, até o treinamento completo das vagas remanescentes. A mesma será feita através
da rescisão contratual de dois colaboradores pelo gerente da área. O que acarretará numa
redução de custo para o departamento na ordem de R$ 60.480,00 anuais a partir de 2016. Foi elevado o grau de treinamento dos colaboradores de separação na logística. Por falta de conhecimento na utilização dos coletores de dados, os funcionários perdiam
muito tempo na separação dos pedidos. Com o treinamento, as operações se tornaram
mais ágeis e assertivas. Esse treinamento será feito no prazo de 30 dias após a contratação 17 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021 www.jtni.com.br Journal of Technology & Information do treinamento. O responsável pelo treinamento será o gerente de TI através da
contratação da empresa fornecedora dos coletores que ministrou o treinamento. Custo do
Treinamento: R$ 3.450,00 no ano de 2016. do treinamento. O responsável pelo treinamento será o gerente de TI através da
contratação da empresa fornecedora dos coletores que ministrou o treinamento. Custo do
Treinamento: R$ 3.450,00 no ano de 2016. O desperdício de insumos irá ser reduzido. Os colaboradores por falta de
orientação subutilizavam as embalagens e demais insumos, como filme strech e paletes. Através do coordenador de logística os colaboradores foram reorientados a utilizar de
forma correta as embalagens para reduzi-la os custos. A orientação irá ser atendida de
imediato e feita nas próprias dependências do setor de expedição. O treinamento será feito
de forma oral e com apresentação de vídeos para redução dos desperdícios. Custo R$
890,00, referentes ás horas dos colaboradores envolvidos. Será criada a função da 2ª conferência na expedição e a implantação do sistema
de armazenagem (WMS) com isso ocorrem muitas reclamações por envio de peças em
quantidades erradas ou de peças trocadas. A 2ª conferência será realizada por pessoas
diferentes. Será implantada assim que ocorrer a contratação de mais um colaborador. A
responsável pela contratação e implantação do novo processo foi o coordenador de
logística. Custo da operação foi de R$ 27.720,00 anuais a partir de 2016. Redução das
reclamações: 86%. Segundo Slack et al (1999) a maioria dos estoques é controlado por
um sistema computadorizado, devido ao grande número de cálculos rotineiros envolvidos
no controle de estoques e as novas tecnologias, como pontos de venda com registro de
transação e leitoras de código de barras. A despeito das limitações da pesquisa, a primeira delas está relacionada à amostra
analisada e seu caráter não probabilístico que impedem que os resultados gerados por essa
pesquisa sejam generalizados para todo o segmento ou para todas as empresas e, a
segunda, por se tratar de um caso único, não possibilita a comparação com outras
empresas, a fim de identificar as semelhanças e diferenças existentes. 18 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information metodológicas que se mostrariam relevantes no sentido de verificar tendências e
oportunidades de pesquisa, para que os profissionais e gestores da área tenham mais
clareza sobre o tema. metodológicas que se mostrariam relevantes no sentido de verificar tendências e
oportunidades de pesquisa, para que os profissionais e gestores da área tenham mais
clareza sobre o tema. A princípio, tinha-se receio de que o questionamento sobre os temas desta
pesquisa não fosse bem compreendido pelos colaboradores durante a entrevista, porém
foi surpreendente o entendimento deles quanto aos assuntos tratados, acreditando-se que
isso se deve pela própria rede de informações que faz parte de seu cotidiano. O presente trabalho resultou em maior clareza de informações sobre como um
setor logístico deve funcionar para obter excelência e como o setor logístico da empresa
estudada (Unival) funciona, expondo suas deficiências e oportunidades. O estudo sobre a
Unival nota-se que no setor logístico o problema de maior importância era a má gestão, e
que depois da mudança problemas básicos e que estavam deixando o setor a desejar foram
solucionados de imediato, tornando assim o setor referência dentro da empresa. 5. Conclusões O objetivo desse trabalho foi analisar o impacto que o atraso na entrega pode
ocasionar para a empresa para tal foi realizado um estudo de caso, com abordagem
qualitativa por meio de entrevistas, na empresa Unival Válvulas e conexões no setor de
logística. A revisão de literatura sugere que existe uma relação entre o papel da logística
na distribuição e transporte de mercadoria e pontualidade na entrega Os principais resultados mostraram que o atraso na entrega causa um impacto
desavorável para a empresa, a Unival se preocupa com o respaldo e a satisfação do cliente. E por se importar com o cliente a mesma tomou decisões que de início o impacto não
seria satisfatório para a empresa, como arriscar numa mudança de gestão, mesmo que a
gestão atual não estava trabalhando com excelência a emnpresa conhecia o trabalho,
entretanto essa mudança não poderia ser mais adiada, até que aconteceu e de acordo com
as pesquisas e entrevistas foi verificado que com a nova gestão as melhorias necessárias
acontecerão conforme previsto e outras melhorias que de momento não se fazia
necessárias também foram feitas, tornando assim um setor mais eficiente e com
colaboradores e clientes satisfeitos. Diante do exposto as implicações mais relevantes são de natureza
empírico/gerencial, pois durante a realização da pesquisa constatou-se a necessidade de
uma mudança na gestão que são eixos empírico e gerenciais mais condizentes com as
necessidades expressas da organização no atual contexto da empresa Fleury (2006). Como sugestão de estudos futuros, é necessário ampliar a amostra para outras
revisões de literatura, ampliar o período de tempo para possibilitar uma visão mais
abrangente do emprego dos métodos de pesquisa, podendo apresentar contribuições
significativas como, por exemplo, permitir novas contribuições metodológicas na área e
ampliar a análise dos resultados e, por fim, a realização de futuras pesquisas ligando o
tema o papel da logística na distribuição e transporte de mercadoria com as escolhas 19 Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Referencial Bibliográfico Arnold, J. T., Rimoli, C., & Esteves, L. R. (1999). Administração de materiais: uma
indrodução. Atlas. Ayres, A. D. P. S. (2009). Gestão de logística e operações. IESDE BRASIL SA. Ballou, R. H. (2010). Gerenciamento da cadeia de suprimentos: planejamento,
organização e logística empresarial. Bookman. Bowersox, D. J., & Closs, D. J. (1996). Logistical management: the integrated supply
chain process. McGraw-Hill College. Carvalho, M. R. (2009). Gestão dos canais de distribuição. Carvalho, M. R. (2009). Gestão dos canais de distribuição. Couto, F. L.; Rossi, D. A mudança organizacional: como um diagnóstico contribui para
um processo de resistência a mudança? Revista de Psicologia. 2012. Disponível
em: http://blog.newtonpaiva.br/psicologia/wp-content/uploads/2012/08/pdf-e2-
64.pdf. Fleury, P. F. (2006). Supply Chain Management: conceitos, oportunidades e desafios da
implementação. Revista Tecnologística, 4(30), 25-32. 20 Journal of Technology & Information – Volume 1 – Número 2 – 2021 www.jtni.com.br Journal of Technology & Information – Volume 1 – Número 2 – 2021
www.jtni.com.br Journal of Technology & Information Flores, J. G. (1994). Análisis de datos cualitativos: aplicaciones a la investigación
educativa (Doctoral dissertation, Universidad de Sevilla, Facultad de Filosofía y
Ciencias de la Educación). Gephart Jr, RP (2004). Pesquisa qualitativa e o Academy of Management Journal. Lambert, DM, Cooper, MC, & Pagh, JD (1998). Gestão da cadeia de suprimentos:
questões de implementação e oportunidades de pesquisa. The International
Journal of Logística Management , 9 (2), 1-20. Martins, E. D. R. (2001). Ética e relações internacionais: elementos de uma agenda
político-cultural. Revista Brasileira de Política Internacional, 44, 5-25. Merriam, S. B. (1998). Qualitative Research and Case Study Applications in Education. Revised and Expanded from" Case Study Research in Education.". Jossey-Bass
Publishers, 350 Sansome St, San Francisco, CA 94104. Novaes, A. G. (2007). Logística e Gerenciamento da Cadeia de Distribuição. 3ª Edição. ed. Rio de Janeiro: Campus Elsevier. Oliveira, D. D. P. R. (1999). Sistemas de informações gerenciais: estratégicas, táticas,
operacionais. Atlas. Paura, SG (2012). O Serviço Social na educação superior. PEREIRA, LD . ROSA, R. D. A. (2011). Gestão de operações e logística I. OSA, R. D. A. (2011). Gestão de operações e logística I. SLACK, N., & CHAMBERS, S. (1999). Administração da produção enxuta. Edição
compactada. São Paulo: Atlas. Tull, D. S., & Hawkins, D. (1976). Marketin Research meaning, measurement and
method. A Text with cases. Estudios de Mercado. medios. Mediciones y Metodos. Texto con ejemplos. Yin, R. K. (2005). Estudo de Caso-: Planejamento e métodos. Bookman editora. 21
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Optimising the identification of causal variants across varying genetic architectures in crops
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Agronomy and Horticulture Department Agronomy and Horticulture Department Introduction Association studies in natural populations have been widely
adopted as a complement to classical gene mapping and gene
knockout approaches in identifying and characterising the func-
tions of specific genes. Association studies identify functionally
variable alleles segregating in target species and these alleles can
guide breeding efforts in crop and livestock species, as well as
provide increasingly accurate predictions of disease risk factors in
humans. Advances in genotyping technology have dramatically
reduced the barriers to conducting association studies with
genome-wide genetic marker datasets across natural popula-
tions. Since becoming feasible in the mid-2000s, genome-wide
association studies (GWAS) have been successfully used to
identify thousands of single nucleotide polymorphisms (SNPs)
associated with diseases in human (Burton et al., 2007) and
complex agricultural traits in plants (Chen et al., 2016; Jia et al.,
2013; Lasky et al., 2015; Romero Navarro et al., 2017). For most
traits analysed, loci identified by GWAS can generally explain only
a subset of total genetically controlled phenotypic variation for
most traits analysed (Maher, 2008; Manolio et al., 2009; Visscher
et al., 2010). Many explanations have been proposed for this
“missing heritability” including epigenetic effects (Gerasimova
et al., 2013), epistasis (Moellers et al., 2017; Visscher et al.,
2008; Zhang et al., 2015), structural variants which are not
detected by conventional SNP genotyping (McCarroll, 2008), rare
alleles with large effects and common alleles with small effect
sizes (Jakobsdottir et al., 2009; Pritchard, 2001). While the first
two proposed explanations for missing heritability are more
difficult to address, both rare alleles with large effect sizes and Many traits of interest to biologists are controlled by complex
genetic architectures (Huang et al., 2012; Lasky et al., 2015;
Romero Navarro et al., 2017) where hundreds, thousands, or the
majority of all genes (Boyle et al., 2017) may control variation in
the target trait. The most straightforward approach to increase
the proportion of causal variants identified is to increase the size
of genotyped and phenotyped populations. However, increases in
population size are expensive and subject to diminishing returns
in terms of the improvement of power to detect both rare alleles
and alleles with small effect sizes. Improved statistical approaches
to isolating a larger proportion of total causal variants controlling
complex traits are therefore highly desirable. Currently, GWAS approaches based on mixed linear models
(MLM) are widely employed in both plant and animal systems. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use,
distribution and reproduction in any medium, provided the original work is properly cited. Summary y
Association studies use statistical links between genetic markers and the phenotype variation
across many individuals to identify genes controlling variation in the target phenotype. However,
this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to
identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor
allele frequency distributions, population structures and linkage disequilibrium patterns. We
demonstrate that different GWAS statistical approaches provide favourable trade-offs between
power and accuracy for traits controlled by different types of genetic architectures. FarmCPU
provides the most favourable outcomes for moderately complex traits while a Bayesian approach
adopted from genomic prediction provides the most favourable outcomes for extremely complex
traits. We assert that by estimating the complexity of genetic architectures for target traits and
selecting an appropriate statistical approach for the degree of complexity detected, researchers
can substantially improve the ability to dissect the genetic factors controlling complex traits such
as flowering time, plant height and yield component. Keywords: genome-wide association
study, polygenic traits, genetic
architecture, quantitative genetics. common alleles with small effect sizes can potentially be
identified through increases in the statistical power of GWAS to
identify causal variants. doi: 10.1111/pbi.13023 doi: 10.1111/pbi.13023 Please cite this article as: Miao, C., Yang, J., Schnable, J.C. (2018). Optimising the identification of causal variants across varying genetic architectures in crops. Plant
Biotechnol. J., https://doi.org/10.1111/pbi.13023 Optimising the identification of causal variants across
varying genetic architectures in crops
Chenyong Miao1,2
, Jinliang Yang1,2 and James C. Schnable1,2,*
1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA Received 28 June 2018;
revised 28 September 2018;
accepted 10 October 2018. *Correspondence (Tel +1 (402)472-3192;
fax +1 (402)472-3139;
email schnable@unl.edu) Optimising the identification of causal variants across varying
Optimising the identification of causal variants across varying
genetic architectures in crops
genetic architectures in crops Follow this and additional works at: https://digitalcommons.unl.edu/agronomyfacpub
Part of the Agricultural Science Commons, Agriculture Commons, Agronomy and Crop Sciences
Commons, Botany Commons, Horticulture Commons, Other Plant Sciences Commons, and the Plant
Biology Commons
Miao, Chenyong; Yang, Jinliang; and Schnable, James C., "Optimising the identification of causal variants
across varying genetic architectures in crops" (2018). Agronomy & Horticulture -- Faculty Publications. 1148. https://digitalcommons.unl.edu/agronomyfacpub/1148
This Article is brought to you for free and open access by the Agronomy and Horticulture Department at
DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Agronomy & Horticulture --
Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Follow this and additional works at: https://digitalcommons.unl.edu/agronomyfacpub Follow this and additional works at: https://digitalcommons.unl.edu/agronomyfacpub Part of the Agricultural Science Commons, Agriculture Commons, Agronomy and Crop Sciences
Commons, Botany Commons, Horticulture Commons, Other Plant Sciences Commons, and the Plant
Biology Commons Part of the Agricultural Science Commons, Agriculture Commons, Agronomy and Crop Sciences
Commons, Botany Commons, Horticulture Commons, Other Plant Sciences Commons, and the Plant
Biology Commons Miao, Chenyong; Yang, Jinliang; and Schnable, James C., "Optimising the identification of causal variants
across varying genetic architectures in crops" (2018). Agronomy & Horticulture -- Faculty Publications. 1148. Miao, Chenyong; Yang, Jinliang; and Schnable, James C., "Optimising the identification of causal variants
across varying genetic architectures in crops" (2018). Agronomy & Horticulture -- Faculty Publications. 1148. https://digitalcommons.unl.edu/agronomyfacpub/1148 This Article is brought to you for free and open access by the Agronomy and Horticulture Department at
DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Agronomy & Horticulture --
Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Plant Biotechnology Journal (2018), pp. 1–13 Characteristics of the four association populations
employed in this study The LD decay curve shown here
for maize is somewhat more rapid than was reported in (Romay
et al., 2013), however, this divergence is likely explained by the
Romay et al. curve being calculated using a subset of ~22 000
SNPs with low missing data and high minor allele frequencies. With the exception of rice, the patterns of LD decay observed
across populations of the remaining three species exhibit a
negative correlation with reported outcrossing frequencies for
each species (Figure S1). This negative correlation suggests that
the difference is the result of biological variation rather than
genotyping strategy (Barnaud et al., 2008; Dje et al., 2004;
Gutierrez and Sprague, 1959; Hufford et al., 2011; Wang et al.,
2010). A second potential approach to accurately identifying causal
variants for traits controlled by complex genetic architectures is
the use of Bayesian multiple-regression methods (Fernando and
Garrick, 2013; Fernando et al., 2017). The Bayesian-based
approaches fit all the available markers simultaneously, which
makes them especially suitable to study highly polygenic traits. Although Bayesian approaches such as BayesA, BayesB, BayesC
and BayesCp have been widely employed in genomic prediction
and selection areas (Bernardo and Yu, 2007; Hayes et al., 2001;
Piepho, 2009; Sun et al., 2011; Verbyla et al., 2009), they are
seldom applied in GWAS, especially in plant GWAS. Several
studies have employed Bayesian-based approaches to identify
putative causal variants in animals (Fan et al., 2011; Peters et al.,
2012); however, the performance of these Bayesian methods
when employed in GWAS have not been extensively evaluated
relative to current non-Bayesian approaches. Here, we systematically compared the performance of MLM,
FarmCPU and Bayesian-based (BayesCp) GWAS approaches
across simulated trait datasets containing 2 to 1024 causal
variants and different levels of heritability ranging from 0.1 to 1. To capture realistic patterns of minor allele frequency distribu-
tions,
population
structure
and
linkage
disequilibrium,
we
employed real-world genotype datasets from four widely studied
crop species: rice (Oryza sativa), foxtail millet (Setaria italica),
sorghum (Sorghum bicolor) and maize (Zea mays) (Jia et al.,
2013; Lasky et al., 2015; McCouch et al., 2016; Romay et al.,
2013). We demonstrate that the power and accuracy of both
FarmCPU and BayesCp to identify causal variants for complex
traits exceed conventional MLM-based approaches. Characteristics of the four association populations
employed in this study of total genetic variance explained by any one locus decreases. Multi-locus mixed-models (MLMM) explicitly identify and con-
trol for the effects of large effect loci as fixed effects as these loci
are identified by the model. Compared to GLM or MLM which
only conduct tests on one marker at a time, the MLMM can test
multiple markers simultaneously by fitting the supposed causal
variants in the process called “forward-backward stepwise linear
mixed-model regression” (Segura et al., 2012). This approach
increases the proportion of the remaining genetic variance
explained by the remaining unidentified variants, and increases
the statistical power of the method to detect a greater number of
causal variants for complex traits. While the high computational
cost of MLMM initially acted as a barrier to widespread adoption,
a modified method, fixed and random model circulating proba-
bility unification (FarmCPU), has dramatically reduced the com-
putational complexity and computing time of this approach (Liu
et al., 2016). Ongoing optimisation and parallelisation efforts
have continued to decrease real-world run times for MLMM-
based approaches (Schnable and Kusmec, 2017). Each of the four populations employed in this study presents a
different combination of linkage disequilibrium, minor allele
frequency
distribution
and
population
structure
(Figure 1,
Table 1). These differences may result from differences in
population demographics, criteria used to assemble the popu-
lations and genotyping technologies employed in each of the
genotype datasets. For example, the comparatively low fre-
quency of rare alleles in rice results from selection loci with
more
frequent
minor
alleles
prior
to
microarray
design
(McCouch et al., 2016), while the low frequency of rare alleles
in foxtail millet results from a post-genotyping, prepublication
filter for loci with relatively more common minor alleles (Jia
et al.,
2013). Marker
selection
for
inclusion
on
the
rice
genotyping
array
incorporated
an
explicit
counter-selection
against
markers
in
high
LD
with
each
other
within
the
resequencing population and the extremely low LD observed
in this set of markers is consistent with the LD analysis in the
original release paper (McCouch et al., 2016). Foxtail millet
population exhibited the slowest LD decay, with the average
correlation coefficient (r2) between genetic markers dropping to
0.25 around 100 kb, consistent with the original description of
this dataset (Jia et al., 2013). Introduction MLM-based approaches are able to control for confounding
effects of both population structure and unequal relatedness
among individuals, which are left uncontrolled in approaches
based on generalised linear models (GLM), at the expense of
greater run times. A wide range of different algorithms have been
proposed and developed to improve the computational efficiency
of MLM, including EMMAX (Kang et al., 2010), Compressed-
MLM (Zhang et al., 2010), FaST-LMM (Lippert et al., 2011) and
GEMMA-MLM (Zhou and Stephens, 2012). However, because
MLM-based methods are ultimately evaluating the relationship
between each genetic marker and the overall variation in a given
trait across a population independently, the statistical power of
these methods rapidly decreases as the total number of variants ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use,
distribution and reproduction in any medium, provided the original work is properly cited. 1 Chenyong Miao et al. 2 2 controlling variation in a given trait increases, and the proportion
of total genetic variance explained by any one locus decreases. Characteristics of the four association populations
employed in this study Of the three
methods, FarmCPU generally provides the most favourable trade-
off between power and low false discovery rates (FDR) for
moderately complex traits controlled by several dozen variants,
while the BayesCp approach provides a more favourable trade-off
for traits controlled by hundreds of more variants. However, the
number of casual variants where the cross-over between the
comparative advantages of these two methods occurred varied
across species. The results presented here, including a set of 4000
simulated phenotypic datasets generated from four real-world
genotype datasets, will provide both a resource for evaluating
future innovations in GWAS software, and information to help
researchers select the most effective experimental design and
statistical approach for their particular research projects. Results Characteristics of the four association populations
employed in this study ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Evaluation of conventional MLM-based GWAS A total of 1000 phenotype datasets were generated per species
with ten independent replicates for each possible combination
of ten different sets of causal variants and ten different levels
of heritability, which represents different levels of genetic
architecture complexity. A causal variant was considered to be
identified if either the causal SNP selected by the simulations,
or one or more markers linked (r2 > 0.6) with the causal SNP
were identified by a given GWAS analysis. As expected, the
power to detect true positives decreased in response to both
increases in the number of simulated causal variants controlling
the trait and decreases in simulated heritability (Figure 2). The
MLM-based approach failed to identify the vast majority of
causal variants for traits controlled by 256 or more loci under
whatever levels of heritability (Figures S2 and S3). Consistent
with previous theory and studies that both rare alleles and
alleles with smaller effect sizes were the least likely to be
identified
in
the
MLM-based
GWAS
analysis
(Figure
S4;
Table
S1). Subsampling
of
each population
was
used
to
evaluate how rapidly the proportion of total causal variants
identified increases with increased population size. The effect
of increasing population size was relatively more pronounced
when
genetic
architecture was
less complex,
and smaller increases were observed with increasing population size for
more complex genetic architectures (Figure 3). Alternative GWAS methods for complex traits
As shown above, MLM-based GWAS identifies only a small
proportion of causal variants for complex traits controlled by over
hundreds of distinct genetic loci. We next evaluated two methods
potentially developed to analyse polygenic traits: FarmCPU (Liu
et al., 2016) and BayesCp (Habier et al., 2011). To avoid
confounding effects from different approaches to scoring the
strength of associations between genetic markers and trait
variation, cross-method comparisons are made based on selecting
equivalent numbers of positive causal variants in each analysis. The proportion of causal variants detected declines in each
species as heritability decreases and as the total number of causal
variants controlling the trait increases. However, FarmCPU and
BayesCp both consistently outperformed MLM-based analysis in
terms of both overall proportion of causal variants identified and
FDR control (Fig res 4 and 5) For moderatel comple traits (32
FarmCPU tends to provide lower false discovery rates than
BayesCp for these genetic architectures (Figures 4 and 5, S5 and
S7). Evaluation of conventional MLM-based GWAS For complex traits with high heritability (128, 256 causal
variants with h2 = 0.9), the BayesCp approach outperforms
FarmCPU on both power and false discovery rate metrics
(Figures 4 and 5, S6, and S8). However, we also observed that
this advantage is less apparent for traits with medium heritability
(h2 = 0.7; Figures S10 and S12). Furthermore, once heritability
decreased to 0.5, the difference between these two methods was
only apparent in the foxtail millet dataset (Figures S9, and S11). The two approaches exhibited similar power to control type I error
for traits controlled by simple genetic architectures while BayesCp
exhibited better performance on false-positive control for traits
controlled by moderately and extremely complex genetic archi-
tectures (Figures S13 and S14). A second analysis was conducted utilising published flowering
time data for 1371 maize inbred lines from the maize association
population utilised in the simulation study above (Romay et al.,
2013) Flo ering time in mai e is an e tremel
comple
trait
Table 1 Statistical summary of each genotype dataset
Species
Genotyping technology
Genome size (Mb)
LD Decay (Kb)
No. of Accessions
No. of Markers
Sorghum bicolor
GBS
732
2
2327
354 940
Setaria italica
Low coverage WGS
406
794
916
663 985
Oryza sativa
Microarray
372
0.004
1568
629 019
Zea mays
GBS
2300
0.063
2503
560 515
Figure 1 Characterisation of the four association
populations and associated genotype datasets
employed in this study. (a) Distribution of minor
allele frequencies across all genotyped markers in
each population. (b) Patterns of linkage
disequilibrium decay in each population based on
average pairwise r2 between genetic markers
(Methods). (c) Cumulative proportion of total
genotypic variance explained up to ten principal
components in each population. (d) PCs
distribution for individuals in each population. Optimising GWAS in crops 3 Optimising GWAS in crops 3 Table 1 Statistical summary of each genotype dataset
Species
Genotyping technology
Genome size (Mb)
LD Decay (Kb)
No. of Accessions
No. of Markers
Sorghum bicolor
GBS
732
2
2327
354 940
Setaria italica
Low coverage WGS
406
794
916
663 985
Oryza sativa
Microarray
372
0.004
1568
629 019
Zea mays
GBS
2300
0.063
2503
560 515 Table 1 Statistical summary of each genotype dataset increases were observed with increasing population size for
more complex genetic architectures (Figure 3). Evaluation of conventional MLM-based GWAS FarmCPU tends to provide lower false discovery rates than
BayesCp for these genetic architectures (Figures 4 and 5, S5 and
S7). For complex traits with high heritability (128, 256 causal
variants with h2 = 0.9), the BayesCp approach outperforms
FarmCPU on both power and false discovery rate metrics
(Figures 4 and 5, S6, and S8). However, we also observed that
this advantage is less apparent for traits with medium heritability
(h2 = 0.7; Figures S10 and S12). Furthermore, once heritability
decreased to 0.5, the difference between these two methods was
only apparent in the foxtail millet dataset (Figures S9, and S11). The two approaches exhibited similar power to control type I error
for traits controlled by simple genetic architectures while BayesCp
exhibited better performance on false-positive control for traits
controlled by moderately and extremely complex genetic archi-
tectures (Figures S13 and S14). ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Alternative GWAS methods for complex traits (b) Change in power to detect true positives as heritability decreases for
traits controlled by simple (N = 8), moderately complex (N = 32) and complex (N = 256) genetic architectures. Positive calls were defined as those above a
Bonferroni corrected P-value cut-off of 0.05. Comprehensive results from all four populations are available in Figures S2 and S3. Figure 3 Changes in the power of conventional MLM-based GWAS to identify causal variants for complex traits in response to increases in population size
in each of the four association populations evaluated. (a) a moderately complex trait controlled by 32 loci; (b) a complex trait controlled by 128; (c) a
complex trait controlled by 256 loci. All analyses used data from traits with heritability of 0.7. Positive calls were defined as those above a Bonferroni
corrected P-value cut-off of 0.05. Figure 3 Changes in the power of conventional MLM-based GWAS to identify causal variants for complex traits in response to increases in population size
in each of the four association populations evaluated. (a) a moderately complex trait controlled by 32 loci; (b) a complex trait controlled by 128; (c) a
complex trait controlled by 256 loci. All analyses used data from traits with heritability of 0.7. Positive calls were defined as those above a Bonferroni
corrected P-value cut-off of 0.05. identified by either only FarmCPU or only BayesCp, and those
missed by both. As shown in Figure 6, causal SNPs identified by
both methods tended to have higher MAFs and larger effect sizes. SNPs identified only by FarmCPU tended to have lower MAFs than
those identified only by BayesCp in all four species (Table S2,
Figure 6). However, we did not observe a statistically significant
difference in effect size distribution (Table S2, Figure 6). Similar
results were obtained in other levels of heritability (Figure S15). Notably, FarmCPU controlled type I error rates equivalently for
SNPs of varying MAFs, while the type I error rate for BayesCp was
higher for common allelic variants and lower for rare allelic
variants (Figure S16). Overall, the two approaches appear to have
complementary strengths for identifying different subsets of
allelic variants missed by conventional MLM-based GWAS meth-
ods. (Buckler et al., 2009; Romero Navarro et al., 2017). MLM,
FarmCPU and BayesCp analyses identified 12, 20 and 32 markers
within this dataset, respectively. Alternative GWAS methods for complex traits To assess accuracy, we employed
a set of candidate flowering time genes identified in an
independent study utilising distinct genotypic and phenotypic
data collected from 4471 maize lines across 22 environments
(Romero Navarro et al., 2017). Of the signals identified by each
algorithm above, 3 (25%), 5 (25%) and 13 (41%) of the markers
identified via MLM, FarmCPU and BayesCp, respectively, were
located within 50KB of a flowering time candidate gene identified
in
the
independent
and
more
highly
powered
study
(Appendix S1). Markers associated with three candidate flowering
time genes were identified by both FarmCPU and BayesCp. No
overlap of identified candidate genes was observed between
candidates identified by MLM and the other two methods. The characteristics of causal variants identified by BayesCp and
FarmCPU were also different. Using data from simulations
conducted with 256 causal variants and heritability of 0.5, causal
variants were classified into four mutually exclusive categories in
each population: those identified by both methods, those Alternative GWAS methods for complex traits As shown above, MLM-based GWAS identifies only a small
proportion of causal variants for complex traits controlled by over
hundreds of distinct genetic loci. We next evaluated two methods
potentially developed to analyse polygenic traits: FarmCPU (Liu
et al., 2016) and BayesCp (Habier et al., 2011). To avoid
confounding effects from different approaches to scoring the
strength of associations between genetic markers and trait
variation, cross-method comparisons are made based on selecting
equivalent numbers of positive causal variants in each analysis. The proportion of causal variants detected declines in each
species as heritability decreases and as the total number of causal
variants controlling the trait increases. However, FarmCPU and
BayesCp both consistently outperformed MLM-based analysis in
terms of both overall proportion of causal variants identified and
FDR control (Figures 4 and 5). For moderately complex traits (32,
64 causal variants), the statistical power of BayesCp and FarmCPU
provided approximately equivalent statistical power, however, A second analysis was conducted utilising published flowering
time data for 1371 maize inbred lines from the maize association
population utilised in the simulation study above (Romay et al.,
2013). Flowering time in maize is an extremely complex trait
controlled by hundreds of genes and most individual loci explain
only extremely small proportions of total phenotypic variance Chenyong Miao et al. 4 Figure 2 Changes in the power of conventional (MLM-based) GWAS to identify causal variants in response to changes in heritability and the complexity of
the genetic architecture controlling the target trait. Data shown are from foxtail millet. (a) Change in power to detect true positives as the number of causal
variants increases under high (0.9), medium (0.5) and low (0.1) levels of heritability. (b) Change in power to detect true positives as heritability decreases for
traits controlled by simple (N = 8), moderately complex (N = 32) and complex (N = 256) genetic architectures. Positive calls were defined as those above a
Bonferroni corrected P-value cut-off of 0.05. Comprehensive results from all four populations are available in Figures S2 and S3. Figure 2 Changes in the power of conventional (MLM-based) GWAS to identify causal variants in response to changes in heritability and the complexity of
the genetic architecture controlling the target trait. Data shown are from foxtail millet. (a) Change in power to detect true positives as the number of causal
variants increases under high (0.9), medium (0.5) and low (0.1) levels of heritability. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Using BayesCp to estimate genetic architecture of
complex traits One key difference between the GWAS presented above and
real-world GWAS is that here the complexity of the genetic Optimising GWAS in crops 5 ure 4 Changes in the power of three GWAS approaches across all four association populations in response to the changes of the statistical
shold employed. To enable comparisons across different methods with different approaches to reporting statistical significance, the x-axis is order
he total number of positive genetic markers accepted at a given statistical threshold. Data shown are for traits with increasingly complex gene
hitectures with near-best-case assumptions for trait heritability (0.9). Results for all other simulated genetic architectures are provided in Figures S
S9 and S10. Figure 4 Changes in the power of three GWAS approaches across all four association populations in response to the changes of the statistical
threshold employed. To enable comparisons across different methods with different approaches to reporting statistical significance, the x-axis is ordered
by the total number of positive genetic markers accepted at a given statistical threshold. Data shown are for traits with increasingly complex genetic
architectures with near-best-case assumptions for trait heritability (0.9). Results for all other simulated genetic architectures are provided in Figures S5,
S6, S9 and S10. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 s. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Chenyong Miao et al. 6 Figure 5 Relationship between power and false discovery rate (FDR) using each GWAS method to analyse simple, medium and complex traits in each
population. Data shown are for traits with increasingly complex genetic architectures with near-best-case assumptions for trait heritability (0.9). Results for
all other simulated genetic architectures are provided in Figures S7, S8, S11 and S12. Figure 5 Relationship between power and false discovery rate (FDR) using each GWAS method to analyse simple, medium and complex traits in each
population. Data shown are for traits with increasingly complex genetic architectures with near-best-case assumptions for trait heritability (0.9). Results for
all other simulated genetic architectures are provided in Figures S7, S8, S11 and S12. ª 2018 The Authors. Using BayesCp to estimate genetic architecture of
complex traits In all four crop species, BayesCp
was able to accurately estimate heritability for traits controlled by
different numbers of causal variants (Figure S17). It also provided
accurate and unbiased estimates of the number of causal variants
when the heritability of the trait was high and/or the total
number of causal variants was small (Figure 7). However, the
number of causal variants was systematically overestimated for
complex traits with lower levels of heritability (Figure 7). Using BayesCp to estimate genetic architecture of
complex traits Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Optimising GWAS in crops 7 erences in the characteristics of causal SNPs identified by BayesCp and FarmCPU in all four species. Distribution of MAF (Left) and abs
ht) for causal variants identified by both BayesCp and FarmCPU, only BayesCp, only FarmCPU, or neither approach. The number of c
h category is indicated as part of the legend of each panel. Data shown are collected from ten replicates with 256 causal variants an
each species. hors Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd
1–13 Figure 6 Differences in the characteristics of causal SNPs identified by BayesCp and FarmCPU in all four species. Distribution of MAF (Left) and absolute
effect size (Right) for causal variants identified by both BayesCp and FarmCPU, only BayesCp, only FarmCPU, or neither approach. The number of causal
variants in each category is indicated as part of the legend of each panel. Data shown are collected from ten replicates with 256 causal variants and 0.5
heritability in each species. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Chenyong Miao et al. 8 8 architecture of each trait is a known variable. However, in real-
world application, the complexity of the genetic architecture
controlling different traits may not be known prior to the start of
analysis. The BayesCp method includes a statistical approach to
estimate the number of causal variants controlling a given trait
prior to fitting a model to the data (Habier et al., 2011). These
estimates serve as a prior for model fitting in BayesCp. As
different GWAS approaches provide the most favourable results
for traits with different complexities, estimation of the number of
genetic loci controlling a trait can also guide which GWAS
approach is best suited to analyse a given dataset. The accuracy
of the estimates of the number of causal variants generated by
the BayesCp approach was evaluated across varying levels of
heritability and trait complexity. Discussion Although ranking enabled com-
parisons of power, type I error, and false discovery rate, the
application of BayesCp-based GWAS in a real-world setting will
require methods to establish such cut-offs. One promising
approach recently discussed in the literature is to estimate
posterior type I error rates (Fernando et al., 2017). Approaches
using machine learning to identify cut-offs, such in NeuralFDR,
also seem a promising avenue of investigation (Xia et al., 2017). In addition, computational resource requirements play a substan-
tial role in which statistical approaches become widely adopted
over time. With the largest of the four genotype datasets
employed here (maize) BayesCp required approximately 4.5 Gb
of RAM and 2 h to analyse one dataset. For comparison, the
MLM implementation in GEMMA required only 1 Gb of RAM and
approximately 40 min to analyse the same dataset and FarmCPU
required approximately 30 min and 5.5 Gb RAM (Figures S19 and
S20). However, optimisation of computational pipelines can
reduce run times dramatically without the need for changes to
statistical models. For example, modifications to the reference
implementation of the FarmCPU algorithm have been shown to
produce the same results while reducing runtime by approxi-
mately two-thirds (Schnable and Kusmec, 2017). (Bernardo, 2016). The identification of common alleles with
moderate effect sizes and rare alleles with large effects would
improve the utility for GWAS for both basic biological and applied
applications. Our results also indicate estimates of the complexity of the
genetic architectures are clearly also needed, given the differ-
ences in the relative strengths of MLM, FarmCPU and Bayesian
approaches. BayesCp can accurately estimate the trait heritability
and the number of causal variants in most situations. However, it
tends to overestimate the number of causal variants for complex
traits with lower levels of heritability. One potential explanation
for this observation is that the model is attempting to explain
residual error – not heritable phenotypic variation – by including
additional, noncausal SNPs in the model. However, with aware-
ness of this limitation, estimation of the number of causal variants
controlling a given trait can aid researchers in determining, which
GWAS method is likely to provide the most informative result for
a given dataset. Evaluations of GWAS approaches can be performed using
either real data or simulated data. Here, simulated phenotypic
dataset was employed, as it provided comprehensive information
for comparison across methods, something unavailable for real-
world phenotype datasets for complex traits. Discussion In this study, we employed four genotype datasets with different
population structures from different crop species. The MLM-
based approach showed substantial reductions in power as the
complexity of the genetic architecture of the trait being analysed
increased. Compared to the MLM-based approach, FarmCPU
approach and BayesCp adopted from genomic prediction show
complementary strengths, higher power and lower false discovery
rates for complex traits. FarmCPU provided a more favourable
trade-off between power and FDR for moderately complex traits
and a greater likelihood of identifying rare causal variants, while
BayesCp approach provided greater power to detect more causal
variants with small effect sizes for extremely complex traits. However, this outperformance is less apparent or nonexistent for
traits
with
lower
levels
of
heritability. Present
statistical
approaches to GWAS have the greatest statistical power to
identify SNPs which are both common, and control a large
proportion of total genetic variation in the target populations. As
a result, few previously unknown loci with utility for plant
breeding have been discovered through GWAS-based analysis Figure 7 Relationship between estimated
complexity of genetic architectures generated by
BayesCp and true genetic architecture complexity
given different levels of heritability in each species. Grey areas indicate 95% confidence bands
around each estimate. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Figure 7 Relationship between estimated
complexity of genetic architectures generated by
BayesCp and true genetic architecture complexity
given different levels of heritability in each species. Grey areas indicate 95% confidence bands
around each estimate. Figure 7 Relationship between estimated
complexity of genetic architectures generated by
BayesCp and true genetic architecture complexity
given different levels of heritability in each species. Grey areas indicate 95% confidence bands
around each estimate. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wile ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Optimising GWAS in crops 9 9 provided a ranking of genetic markers but not the straightfor-
ward method of establishing a cut-off between candidate causal
variants and noncandidate loci. Discussion The use of real-
world genotype datasets captured the patterns of MAFs, LD
decay and population structures are comparable to those
observed in the real world. However, it is also important to
acknowledge the limitations of simulation-based studies. The
simulated phenotype datasets employed here assumed the effect
sizes of minor alleles are drawn from a normal distribution, which
is supported by real-world observations of multiple complex traits
as shown in Figure S18 (Brown et al., 2011; Buckler et al., 2009). Notably, the comparison of MLM and FarmCPU here are similar to
the results described in (Liu et al., 2016), which employed a
geometric distribution of effect sizes. However, not all traits will
exhibit a normal distribution of effect sizes for underlying genetic
loci. For example, traits which have experienced strong and
recent natural or artificial selection are likely to exhibit a non-
normal distribution of effect sizes (Orr, 1998; Wallace et al.,
2014; Xu et al., 2017) and the absolute estimates of power
presented here are likely to be inflated for such traits. More
significantly, the simulation parameters used assumed no corre-
lation between the minor allele frequency of an allele and its
effect size, which does not match predictions from population
genetic theory or observation that rare alleles tend to be
associated with larger molecular phenotypes in maize (Kremling
et al., 2018). These simulations assumed that the true functional
variant was included as one of the genotyped markers within the
dataset. At the moment, in many populations the best case
outcome for researchers is to identify a genetic marker in high LD
with the true causal variant. In the future whole-genome
resequencing or independent genome assemblies may make the
identification of true causal variants more likely, at least in species
such as maize which exhibit rapid LD decay. In addition, the
statistical model used to generate phenotype datasets here did
not incorporate epistatic interactions between causal variants. Conclusion Association studies have been and seem likely to remain an
important tool for investigating how genotype determines
phenotype. Although certain diseases and target traits for
breeding efforts are controlled by a small number of large effect
loci segregating in Mendelian fashion, many traits of interest are
controlled by moderately or extremely complex genetic architec-
tures. Here, we have shown that different approaches to GWAS
have complementary strengths, and the complexity of the genetic
architecture controlling a target trait should be determined prior
to the selection of an appropriate statistical approach for
analysing a given dataset. Further improvements in both statistical
approaches and computational optimisation hold the promise of
dramatically expanding our understanding of the role that both
rare alleles with large consequences and common alleles with
small consequences play in determining how genotype determi-
nes phenotype across species. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Genotype dataset sources and filtering parameters Genotype dataset for foxtail millet (Setaria italica) (Jia et al.,
2013), maize (Zea mays) (Romay et al., 2013), sorghum (Sorghum
bicolor) (Lasky et al., 2015), and rice (Oryza sativa) (McCouch
et al., 2016) were taken from published sources. Foxtail millet
SNPs were discovered and scored using low coverage (0.59)
whole-genome resequencing reads aligned to the Setaria italica
reference genome (v2 from Phytozome v7.0; Bennetzen et al.,
2012). The partially imputed SNP dataset was downloaded from
Millet GWAS Project website (http://202.127.18.221/MilletHap1/
GWAS.php). The downloaded genotype data included 916
diverse varieties and 726 080 SNPs with minor allele frequencies
lower than 5% had been removed prior to the publication of the
dataset. After downloading, SNPs without calls in >10% of
samples were removed from the dataset. The sorghum GBS
dataset which included 404 627 SNPs scored relative to the v1.4 While the results presented here for the use of BayesCp to
identify causal variants are promising, additional work is needed
to further adapt BayesCp for use in GWAS applications. The
model employed here did not yet incorporate any controls for
population structure which may explain a portion of the higher
type one error rates observed for this method. Integrating such a
control might marginally reduce power. The model we employed Chenyong Miao et al. 10 of the sorghum reference genome (Paterson et al., 2009) across a
set of 1943 accessions were downloaded from Data Dryad
website
(http://datadryad.org/resource/doi:10.5061/dryad.jc3ht/
1; Lasky et al., 2015). The maize GBS dataset which included
calls for 681 257 SNPs relative to B73 RefGenV1 (Schnable et al.,
2009) across a set of 2815 accessions was downloaded from
Panzea website (https://www.panzea.org/; Romay et al., 2013). After downloading, both SNPs in sorghum and maize without
genotype calls in >30% of samples and SNPs with heterozygous
calls in >5% of samples were removed from the datasets. After
any filtering parameters described above for individual datasets,
missing data in foxtail millet, sorghum and maize dataset were
imputed using Beagle v4.1 with default parameters (Browning
and Browning, 2016). Data from genotyping 1568 diverse rice
accessions using the 700 000 marker HDRA microarray platform
were downloaded from GEO (ID: GSE71553) (McCouch et al.,
2016). The downloaded SNPs with heterozygous genotype calls in
>5% of samples were removed. Statistics on the final number of
SNP markers and samples in each dataset are provided in Table 1. to 1.0 in steps of 0.1. Methods of Genome-wide association studies All MLM-based GWAS analysis in this study were performed using
GEMMA (version 0.95alpha) with the command “gemma -g
[genotype mean file] -a [genotype annotation file] -p [phenotype
file] -c [PCs file] -k [kinship file] -o [output file]” (Zhou and
Stephens, 2012). Tassel (version 5.0) was used to generate PCs
and the first three PCs from the Tassel analysis were included in
both the MLM and FarmCPU analyses (Bradbury et al., 2007). The
kinship matrix file applied in MLM method was generated using
“gemma -gk 1” command in GEMMA package for each
genotype dataset. Within the MLM, population structure (Q)
and the relationship among individuals (K) were fitted at the same
time, which is also called as Q + K model: y = Q + K + s + e,
where y is an vector of phenotype values for all the individuals in
the population and e is the residue; Q is a matrix known as
covariates/PCs representing the population structure; K is the
kinship matrix representing the relationship among individuals;
and s is the genetic effects. Phenotype simulation Phenotype datasets were simulated using an additive genetic
model (Equation 1)
derived
from
the underlying
genotype
datasets. Yj ¼
X
ai Sij
þ ej
(1) Yj ¼
X
ai Sij
þ ej (1) In the model, Yj is the simulated phenotype for plant j; ai is the
effect of the i-th causal SNP; Sij is the SNP genotype (coded with
0, 1, 2) for the i-th causal SNP of the j-th plant; and ej is the
residual error for j-th plant extracted from a normal distribution
with mean of 0 and standard deviation of Var P
Sijai
ð
Þ
1=h21
, where h2
denotes the heritability. Characteristics and summary statistics of genotype
datasets used in this study The minor allele frequency was calculated for each SNP in each
dataset. Patterns of minor allele frequency distributions for each
dataset were assessed and visualized using kernel density plots
generated using the function ‘kdeplot’ from the Python package
‘seaborn’. For each dataset, the top ten principal components
were calculated using Tassel (version 5.0; Bradbury et al., 2007). The top three principal components from the same analyses were
used to plot population structure using the R package scatter-
plot3d. Plink 1.9 was used to calculated r2 between all pairs of
SNP markers separated by less than 10 million bases (Purcell
et al., 2007). The average r2 values were calculated from 100.1 to
107 using a logarithmic step size of 0.1. A regression curve was fit
to these values using the function ‘regplot’ from the Python
package ‘seaborn.’ FarmCPU was run using the command: FarmCPU (Y = myY,
GD = myGD, GM = myGM, CV = myCV, method.bin = “opti-
mum”) in R. Y, GD and GM represent phenotype, genotype and
genotypic map data respectively. CV represents the principal
components file. The kinship matrix was automatically estimated
in FarmCPU. While kinship matrices were independently gener-
ated by GEMMA and FarmCPU, the correlation between these
two matrices is over 0.9999 (Pearson r2). The parameter
method.bin = “optimum” allows the FarmCPU to selected opti-
mized possible QTN window size and number of possible QTNs in
the model (Liu et al., 2016). The BayesCp approach was adopted from genomic prediction
area to represent Bayesian multiple-regression methods for
GWAS. BayesCp was conducted using GenSel software package
(Version 2.14; Habier et al., 2011). In the Bayesian method, a
two-step procedure was employed to account for the potential
effects of the arbitrary priors (Yang et al., 2018). In the test run,
1000 iterations was used with 100 burn-in iterations of MCMC
simulations using default priors: genetic variance = 1 and residual
variance = 1. In the real run, the priors were replaced using the
posteriors obtained from test run and a longer chain of
simulations was employed (chain length = 11 000, burnin =
1000 and p = 0.9999). All the GWAS jobs were run on HCC’s
(the Holland Computing Center) Crane cluster at University of
Nebraska-Lincoln. Genotype dataset sources and filtering parameters For each combination of heritability and
number of causal variants, 10 independent replicates with
different randomly selected causal variants were generated. Methods of Genome-wide association studies Methods of Genome-wide association studies ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Statistical evaluation of accuracy and power Buckler, E.S., Holland, J.B., Bradbury, P.J., Acharya, C.B., Brown, P.J., Browne,
C
E
E
t
l (2009) Th
ti
hit
t
f
i
fl
i
ti Buckler, E.S., Holland, J.B., Bradbury, P.J., Acharya, C.B., Brown, P.J., Browne,
C., Ersoz, E. et al. (2009) The genetic architecture of maize flowering time. Buckler, E.S., Holland, J.B., Bradbury, P.J., Acharya, C.B., Brown, P.J., Browne,
C., Ersoz, E. et al. (2009) The genetic architecture of maize flowering time. Science, 325, 714–718. C., Ersoz, E. et al. (2009) The genetic architecture of maize flowering time. Science, 325, 714–718. Burton, P.R., Clayton, D.G., Cardon, L.R., Craddock, N., Deloukas, P.,
Duncanson, A., Kwiatkowski, D.P. et al. (2007) Genome-wide association
study of 14 000 cases of seven common diseases and 3000 shared controls. Nature, 447, 661–678. study of 14 000 cases of seven common diseases and 3000 shared controls. Nature, 447, 661–678. Power ¼ No. of true positive SNPs
No. of total causal SNPs
(2) (2) Chen, W., Wang, W., Peng, M., Gong, L., Gao, Y., Wan, J., Wang, S. et al. (2016) Comparative and parallel genome-wide association studies for
metabolic and agronomic traits in cereals. Nat. Commun. 7, 12767. The corresponding FDR and Type I error were defined by
Equation 3 and 4: Dje, Y., Heuertz, M., Ater, M., Lefebvre, C. and Vekemans, X. (2004) In situ
estimation of outcrossing rate in sorghum landraces using microsatellite
markers. Euphytica, 138, 205–212. FDR ¼ No. of flase positive SNPs
No. of positive SNPs
(3) FDR ¼ No. of flase positive SNPs
No. of positive SNPs
(3) (3) Fan, B., Onteru, S.K., Du, Z.Q., Garrick, D.J., Stalder, K.J. and Rothschild, M.F. (2011) Genome-wide association study identifies loci for body composition
and structural soundness traits in pigs. PLoS ONE, 6, e14726. Fernando, R.L. and Garrick, D. (2013) Bayesian methods applied to GWAS. In:
Genome-Wide Association Studies and Genomic Prediction (Gondro, C., The authors have declared that no competing interests exist. The authors have declared that no competing interests exist. Kang, H.M., Sul, J.H., Zaitlen, N.A., Kong, S.Y., Freimer, N.B., Sabatti, C., Eskin,
E. et al. (2010) Variance component model to account for sample structure in
genome-wide association studies. Nat. Genet. 42, 348–354. Type I error ¼ No. of false positive SNPs
No. of noncausal SNPs
(4) Hayes, B. and van der Werf, J. eds), pp 237–274. Totowa, NJ: Humana Press. (4) Fernando, R., Toosi, A., Wolc, A., Garrick, D. and Dekkers, J. (2017) Application
of whole-genome prediction methods for genome-wide association studies: a
Bayesian approach. J. Agric., Biol. Environment. Stat. 22, 172–193. Bayesian approach. J. Agric., Biol. Environment. Stat. 22, 172–19 Gerasimova, A., Chavez, L., Li, B., Seumois, G., Greenbaum, J., Rao, A.,
Vijayanand, P. et al. (2013) Predicting cell types and genetic variations
contributing to disease by combining gwas and epigenetic data. PLoS ONE, 8,
e54359. Acknowledgements This material is based upon work supported by the National Science
Foundation under Grant No. OIA-1557417 to JCS and work
supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture under Award #2016-67013-24613 to
JCS,andstartupfundsandaLaymanseedawardfromtheUniversity
of Nebraska-Lincoln to JY. This work was completed utilising the
Holland Computing Center of the University of Nebraska, which
receives support from the Nebraska Research Initiative. Gutierrez, M.G. and Sprague, G. (1959) Randomness of mating in isolated
polycross plantings of maize. Genetics, 44, 1075–1082. polycross plantings of maize. Genetics, 44, 1075–1082. Habier, D., Fernando, R.L., Kizilkaya, K. and Garrick, D.J. (2011) Extension of
the Bayesian alphabet for genomic selection. BMC Bioinform. 12, 186. Habier, D., Fernando, R.L., Kizilkaya, K. and Garrick, D.J. (2011) Extension of
the Bayesian alphabet for genomic selection. BMC Bioinform. 12, 186. Hayes,
B.,
Goddard,
M.,
Meuwissen,
T.H. (2001)
Prediction
of
total
genetic value using genome-wide dense marker maps. Genetics, 157,
1819–1829. Huang, X., Zhao, Y., Li, C., Wang, A., Zhao, Q., Li, W., Guo, Y. et al. (2012)
Genome-wide association study of flowering time and grain yield traits in a
worldwide collection of rice germplasm. Nat. Genet. 44, 32–39. Author’s contributions Hufford, M.B., Gepts, P. and Ross-Ibarra, J. (2011) Influence of cryptic
population structure on observed mating patterns in the wild progenitor of
maize (Zea mays ssp. parviglumis). Mol. Ecol. 20, 46–55. JS designed the project. JY generated phenotype datasets and
conducted the BayesCp analysis. CM conducted all other analysis. CM, JY and JS generated figures and wrote the manuscript. All
authors have read and approved the final manuscript. Jakobsdottir, J., Gorin, M.B., Conley, Y.P., Ferrell, R.E. and Weeks, D.E. (2009)
Interpretation
of
genetic
association
studies:
markers
with
replicated highly significant odds ratios may be poor classifiers. PLoS
Genet. 5, e1000337. Conflict of interest Jia, G., Huang, X., Zhi, H., Zhao, Y., Zhao, Q., Li, W., Chai, Y. et al. (2013) A
haplotype map of genomic variations and genome-wide association studies
of agronomic traits in foxtail millet (Setaria italica). Nat. Genet. 45, 957–961. Jia, G., Huang, X., Zhi, H., Zhao, Y., Zhao, Q., Li, W., Chai, Y. et al. (2013) A
haplotype map of genomic variations and genome-wide association studies
of agronomic traits in foxtail millet (Setaria italica). Nat. Genet. 45, 957–961. Kang, H.M., Sul, J.H., Zaitlen, N.A., Kong, S.Y., Freimer, N.B., Sabatti, C., Eskin,
E. et al. (2010) Variance component model to account for sample structure in ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Statistical evaluation of accuracy and power For all genetic markers assigned P-values by GEMMA or Farm-
CPU, individual markers were sorted by reported P-values. Within
BayesCp, markers were first sorted by model frequency. When
multiple markers were assigned the same model frequency by
BayesCp, ties were broken by the genetic variance assigned to
each marker by BayesCp. To evaluate FDR, statistical power and
Type I error, an increasing rank method was applied. Each rank
contains the first K markers from the sorted GWAS results as
described above. These K markers were treated as positive
markers and rest of markers were treated as negative markers. A
true positive marker was defined if it was in the causal variants list
or exhibited LD r2 > 0.6 with a causal variant. LD thresholds
between 0.6 and 0.9 did not significantly change observed results An R function ‘simcrop’ was implemented within the open
source ‘g3tools’ R package (https://github.com/jyanglab/g3tools). For the results employed in this study, both the effect sizes of
individual SNPs ai and the error term in measurements of
individual genotypes ej were drawn from normal distributions. However, the software package developed to enable this study
also provides the option to specify other effect size distribution
models. Phenotype datasets were simulated for scenarios where
the number of causal genetic loci ranged from 21 to 210 (2–1024
QTNs) and where the heritability of trait values ranged from 0.1 Optimising GWAS in crops 11 11 (Figure S21), while considering only causal variants as true
positives significantly decreased power for all methods. If there
several positive markers were linked to the same causal variants,
the combined set was counted as only a single true positive and
the number of total positives reduced accordingly. False positives
were defined as positives neither in causal variants list nor in LD
with causal variants. For each scenario, power was defined by
Equation 2: Brown, P.J., Upadyayula, N., Mahone, G.S., Tian, F., Bradbury, P.J., Myles, S.,
Holland, J.B. et al. (2011) Distinct genetic architectures for male and female
inflorescence traits of maize. PLoS Genet. 7, e1002383. inflorescence traits of maize. PLoS Genet. 7, e1002383. Browning, B.L. and Browning, S.R. (2016) Genotype imputation with millions of
reference samples. Am. J. Human Genet. 98, 116–126. Browning, B.L. and Browning, S.R. (2016) Genotype imputa reference samples. Am. J. Human Genet. 98, 116–126. Supporting information Romero Navarro, J.A., Willcox, M., Burgue~no, J., Romay, C., Swarts, K.,
Trachsel, S., Preciado, E. et al. (2017) A study of allelic diversity underlying
flowering-time adaptation in maize landraces. Nat. Genet. 49, 476–480. Figure S6 Relationship between the proportion of causal variants
identified and the number of associated SNPs selected for MLM,
FarmCPU and Bayesian analysis for 128, 512 and 1024 causal
variants. Schnable, P.S. and Kusmec, A. (2017) Farmcpupp: Efficient large-scale GWAS. bioRxiv 238832. Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang,
C. et al. (2009) The b73 maize genome: complexity, diversity, and dynamics. Science, 326, 1112–1115. Figure S7 Relationship between false discovery rate and the
number of associated SNPs selected for MLM, FarmCPU and
Bayesian analysis for 4, 8 and 32 causal variants. Segura, V., Vilhjalmsson, B.J., Platt, A., Korte, A., Seren, €U., Long, Q. and
Nordborg, M. (2012) An efficient multi-locus mixed-model approach for
genome-wide association studies in structured populations. Nat. Genet. 44,
825–830. Bayesian analysis for 4, 8 and 32 causal variants. Figure S8 Relationship between false discovery rate and the
number of associated SNPs selected for MLM, FarmCPU and
Bayesian analysis for 128, 512 and 1024 causal variants. Sun, X., Habier, D., Fernando, R.L., Garrick, D.J. and Dekkers, J.C. (2011)
Genomic breeding value prediction and QTL mapping of qtlmas2010
data using Bayesian methods. In BMC proceedings, vol. 5, S13, BioMed
Central. Figure S9 Relationship between the proportion of causal variants
identified and the number of associated SNPs selected for MLM,
FarmCPU and Bayesian analysis for 16, 64 and 256 causal
variants. Verbyla, K.L., Hayes, B.J., Bowman, P.J. and Goddard, M.E. (2009) Accuracy of
genomic selection using stochastic search variable selection in Australian
Holstein Friesian dairy cattle. Genet. Res. 91, 307–311. Figure S10 Relationship between the proportion of causal
variants identified and the number of associated SNPs selected
for MLM, FarmCPU and Bayesian analysis for 16, 64 and 256
causal variants. Visscher, P.M., Hill, W.G. and Wray, N.R. (2008) Heritability in the genomics era
—concepts and misconceptions. Nat. Rev. Genet. 9, 255. Visscher, P.M., Yang, J. and Goddard, M.E. (2010) A commentary on ‘common
SNPs explain a large proportion of the heritability for human height’ by yang
et al. (2010). Twin Res. Human Genet. 13, 517–524. Supporting information Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J.,
Gundlach, H., Haberer, G. et al. (2009) The sorghum bicolor genome and the
diversification of grasses. Nature, 457, 551–556. Additional supporting information may be found online in the
Supporting Information section at the end of the article. Figure S1 Relationship between LD decay and outcrossing rates
reported from the literature for maize, sorghum and foxtail millet. Peters, S., Kizilkaya, K., Garrick, D., Fernando, R., Reecy, J., Weaber, R., Silver,
G. et al. (2012) Bayesian genome-wide association analysis of growth and
yearling ultrasound measures of carcass traits in brangus heifers. J. Anim. Sci. 90, 3398–3409. Figure S1 Relationship between LD decay and outcrossing rates
reported from the literature for maize, sorghum and foxtail millet. Figure S2 Relationship between the proportion of causal variants
identified and heritability for traits controlled by different
numbers of causal variants (2–1024 causal variants) in each
species in an MLM-based GWAS. Figure S2 Relationship between the proportion of causal variants
identified and heritability for traits controlled by different
numbers of causal variants (2–1024 causal variants) in each
species in an MLM-based GWAS. Piepho, H.P. (2009) Ridge regression and extensions for genomewide selection
in maize. Crop Sci. 49, 1165–1176. Pritchard, J.K. (2001) Are rare variants responsible for susceptibility to complex
diseases? Am. J. Human Genet. 69, 124–137. Figure S3 Relationship between the proportion of causal variants
identified and the number of causal variants controlling a trait
given different levels of heritability (0.1–1) in each species in an
MLM-based GWAS. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D.,
Maller, J. et al. (2007) Plink: a tool set for whole-genome association and
population-based linkage analyses. Am. J. Human Genet. 81, 559–575. Figure S4 Distribution of minor allele frequency and effect size
for true positive and false negative causal variants in each species. Figure S4 Distribution of minor allele frequency and effect size
for true positive and false negative causal variants in each species. Romay,
M.C.,
Millard,
M.J.,
Glaubitz,
J.C.,
Peiffer,
J.A.,
Swarts,
K.L.,
Casstevens, T.M., Elshire, R.J. et al. (2013) Comprehensive genotyping of
the USA national maize inbred seed bank. Genome Biol. 14, R55. Figure S5 Relationship between the proportion of causal variants
identified and the number of associated SNPs selected for MLM,
FarmCPU and Bayesian analysis for 4, 8 and 32 causal variants. References Barnaud, A., Trigueros, G., McKey, D. and Joly, H. (2008) High outcrossing rates
in fields with mixed sorghum landraces: how are landraces maintained? Heredity, 101, 445. Kremling, K.A., Chen, S.Y., Su, M.H., Lepak, N.K., Romay, M.C., Swarts, K.L.,
Lu, F. et al. (2018) Dysregulation of expression correlates with rare-allele
burden and fitness loss in maize. Nature, 555, 520–523. Bennetzen, J.L., Schmutz, J., Wang, H., Percifield, R., Hawkins, J., Pontaroli,
A.C., Estep, M. et al. (2012) Reference genome sequence of the model plant
Setaria. Nat. Biotechnol. 30, 555–561. Lasky, J.R., Upadhyaya, H.D., Ramu, P., Deshpande, S., Hash, C.T., Bonnette, J.,
Juenger, T.E. et al. (2015) Genome-environment associations in sorghum
landraces predict adaptive traits. Sci. Adv. 1, e1400218. Bernardo, R. (2016) Bandwagons I, too, have known. Theoret. Appl. Genet. 129, 2323–2332. Lippert, C., Listgarten, J., Liu, Y., Kadie, C.M., Davidson, R.I. and Heckerman, D. (2011) Fast linear mixed models for genome-wide association studies. Nat. Methods, 8, 833–835. Bernardo, R. and Yu, J. (2007) Prospects for genomewide selection for
quantitative traits in maize. Crop Sci. 47, 1082–1090. Liu, X., Huang, M., Fan, B., Buckler, E.S. and Zhang, Z. (2016) Iterative usage of
fixed and random effect models for powerful and efficient genome-wide
association studies. PLoS Genet. 12, e1005767. Boyle, E.A., Li, Y.I. and Pritchard, J.K. (2017) An expanded view of complex
traits: from polygenic to omnigenic. Cell, 169, 1177–1186. association studies. PLoS Genet. 12, e1005767. Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and
Buckler, E.S. (2007) Tassel: software for association mapping of complex
traits in diverse samples. Bioinformatics, 23, 2633–2635. Maher, B. (2008) Personal genomes: the case of the missing heritability. Nature
News, 456, 18–21. Chenyong Miao et al. 12 12 structured
multi-parent
mapping
populations
of
maize. G3:
Genes,
Genomes, Genet. [Epub ahead of print]. https://doi.org/10.1534/g3.118. 200636. structured
multi-parent
mapping
populations
of
maize. G3:
Genes,
Genomes, Genet. [Epub ahead of print]. https://doi.org/10.1534/g3.118. 200636. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter,
D.J., McCarthy, M.I. et al. (2009) Finding the missing heritability of complex
diseases. Nature, 461, 747–753. McCarroll, S.A. (2008) Extending genome-wide association studies to copy-
number variation. Hum. Mol. Genet. 17, R135–R142. Zhang, Z., Ersoz, E., Lai, C.Q., Todhunter, R.J., Tiwari, H.K., Gore, M.A.,
Bradbury, P.J. et al. (2010) Mixed linear model approach adapted for
genome-wide association studies. Nat. Genet. 42, 355–360. McCouch, S.R., Wright, M.H., Tung, C.W., Maron, L.G., McNally, K.L.,
Fitzgerald, M., Singh, N. References et al. (2016) Open access resources for genome-
wide association mapping in rice. Nat. Commun. 7, 10532. Zhang, J., Singh, A., Mueller, D.S. and Singh, A.K. (2015) Genome-wide
association and epistasis studies unravel the genetic architecture of sudden
death syndrome resistance in soybean. Plant J. 84, 1124–1136. Moellers, T.C., Singh, A., Zhang, J., Brungardt, J., Kabbage, M., Mueller, D.S.,
Grau, C.R. et al. (2017) Main and epistatic loci studies in soybean for
sclerotinia sclerotiorum resistance reveal multiple modes of resistance in
multi-environments. Sci. Rep. 7, 3554. Zhou, X. and Stephens, M. (2012) Genome-wide efficient mixed-model analysis
for association studies. Nat. Genet. 44, 821–824. Orr, H.A. (1998) The population genetics of adaptation: the distribution of
factors fixed during adaptive evolution. Evolution, 52, 935–949. ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 ª 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Supporting information Figure S11 Relationship between false discovery rate and the
number of associated SNPs selected for MLM, FarmCPU and
Bayesian analysis for 16, 64 and 256 causal variants. Wallace, J., Larsson, S. and Buckler, E. (2014) Entering the second century of
maize quantitative genetics. Heredity, 112, 30–38. Figure S12 Relationship between false discovery rate and the
number of associated SNPs selected for MLM, FarmCPU and
Bayesian analysis for 16, 64 and 256 causal variants. Wang, C., Chen, J., Zhi, H., Yang, L., Li, W., Wang, Y., Li, H. et al. (2010)
Population genetics of foxtail millet and its wild ancestor. BMC Genet. 11, 90. Xia, F., Zhang, M.J., Zou, J.Y. and Tse, D. (2017) Neuralfdr: Learning discovery
thresholds from hypothesis features. In Advances in Neural Information
Processing Systems, 1540–1549. y
y
,
Figure S13 Relationship between false-positive rate (Type I error)
and the number of associated SNPs selected for MLM, FarmCPU
and Bayesian analysis for 4, 8 and 32 causal variants. Figure S14 Relationship between false-positive rate (Type I error)
and the number of associated SNPs selected for MLM, FarmCPU
and Bayesian analysis for 16, 64 and 256 causal variants. Figure S15 Differences in the characteristics of causal SNPs Figure S13 Relationship between false-positive rate (Type I error)
and the number of associated SNPs selected for MLM, FarmCPU
and Bayesian analysis for 4, 8 and 32 causal variants. Xu, G., Wang, X., Huang, C., Xu, D., Li, D., Tian, J., Chen, Q. et al. (2017)
Complex genetic architecture underlies maize tassel domestication. New
Phytol. 214, 852–864. Yang, J., Ramamurthy, R.K., Qi, X., Fernando, R.L., Dekkers, J.C., Garrick, D.J.,
Nettleton, D. et al. (2018) Empirical comparisons of different statistical
models to identify and validate kernel row number-associated variants from ors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 1–13 Optimising GWAS in crops 13 Figure S20 Average maximum memory use of a single GWAS
analysis using each of the three methods evaluation in each of the
four populations tested. identified by BayesCp and FarmCPU. Distribution of MAF (Left)
and absolute effect size (Right) for causal variants identified by
both BayesCp and FarmCPU, only BayesCp, only FarmCPU, or
neither approach. identified by BayesCp and FarmCPU. Distribution of MAF (Left)
and absolute effect size (Right) for causal variants identified by
both BayesCp and FarmCPU, only BayesCp, only FarmCPU, or
neither approach. Supporting information identified by BayesCp and FarmCPU. Distribution of MAF (Left)
and absolute effect size (Right) for causal variants identified by
both BayesCp and FarmCPU, only BayesCp, only FarmCPU, or
neither approach. Figure S21 The influence of different LD decay cut-offs on
apparent GWAS power. Data shown are from simulations where
the number of causal variants is 32 and heritability is 0.7. Figure S16 Relationship between minor allele frequency and type
I error rates for markers in the maize, sorghum and rice datasets
for both FarmCPU and BayesCp. Figure S16 Relationship between minor allele frequency and type
I error rates for markers in the maize, sorghum and rice datasets
for both FarmCPU and BayesCp. Table S1. Mann–Whitney U test between SNP groups detected
and undetected by GEMMA. Data shown are from simulations
where the number of causal variants is 64 and heritability is
0.7. Figure S17 Relationship between simulated heritability and
heritability estimates generated by BayesCp for traits controlled
by different numbers of causal variants. Figure S18 Empirically determined effect sizes for loci control
seven different traits in maize. Figure S18 Empirically determined effect sizes for loci control
seven different traits in maize. Table S2. Mann–Whitney U test between SNP groups identified
by FarmCPU, BayesCp, both and neither. Number of causal
SNPs is 256 and heritability is 0.5. Figure S19 Average run time of a single GWAS analysis using
each of the three methods evaluation in each of the four
populations tested. Figure S19 Average run time of a single GWAS analysis using
each of the three methods evaluation in each of the four
populations tested. y
Appendix S1 The significant SNPs identified by MLM, FarmCPU
and BayesCp in real-world maize flowering time dataset.
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Lifestyles of Spanish university students during the 2020 COVID-19 lockdown
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Introduction is arguably one of the dimensions that best predicts a healthy
lifestyle. It has been amply demonstrated that regular exer-
cise significantly decreases the probability of contracting
many diseases and is a powerful indicator of health improve-
ment and life expectancy (Beltrán et al., 2017; Orepic et
al., 2014; Penades et al., 2022; Vagetti et al., 2014; War-
burton and Bredin, 2016). One of the main consequences
of the lockdown ordered from March to June 2020 in Spain
is the significant increase in time spent sitting, without per-
forming any type of physical activity. The repercussions of
immobility can translate into possible health problems, in-
cluding pulmonary thromboembolism (PTE), which ac-
cording to some authors (Franch-Llasat et al., 2020) has in-
creased very significantly during lockdown. On the other
hand, lockdown with low physical activity can have a direct
impact on the respiratory, immune and mental health sys-
tems (García-Tascón et al., 2021; Garzón and Aragón,
2021; Mera et al., 2020). Another fundamental issue to
study in relation to this, is the levels of physical activity of
the population before and during the lockdown. In this
sense, some of the reviewed studies show that there is a
trend towards a decrease in exercise (García-Tascón et al.,
2021; Mercê et al., 2023; Sang et al., 2021; Santos et al.,
2021; Zamarripa et al., 2021). As for eating, one of the The world is facing a pandemic that nobody fully under-
stands, so strategies are needed to mitigate its effects quickly
and efficiently. As Piña-Ferrer (2020) points out, given the
uncertainty caused by the lack of knowledge about the virus,
the only possible vaccine is duly verified scientific infor-
mation about how to protect people from contagion. For
Rodríguez et al. (2020), the best strategy is to prevent the
spread of the virus through self-care, lifestyle changes and
strict compliance with protection measures. One of the strat-
egies implemented in many countries to prevent the spread
of the virus has been to order the population to stay at home. The mandatory lockdown of the population, motivated by
the state of emergency, has led to substantial lifestyle changes
across the general population. In this regard, one of the
groups the lockdown has affected the most is university stu-
dents, who already undergo other significant lifestyle changes
that affect their health condition during this age. Lifestyles of Spanish university students during the 2020 COVID-19 lockdown
Estilos de vida de estudiantes universitarios españoles durante el confinamiento por COVID-19
*Fernando García-Castillo, *Juan Tortosa Martínez, *Irene Ramos-Soler, **Jose A. García del Castillo
*Universidad de Alicante (España), **Universidad Miguel Hernández de Elche (España) Lifestyles of Spanish university students during the 2020 COVID-19 lockdown
Estilos de vida de estudiantes universitarios españoles durante el confinamiento por COVID-19
*Fernando García-Castillo, *Juan Tortosa Martínez, *Irene Ramos-Soler, **Jose A. García del Castillo
*Universidad de Alicante (España), **Universidad Miguel Hernández de Elche (España) Abstract. During the 2020 stay-at-home lockdown ordered as a response to the COVID-19 pandemic, university students had access
to diverse digital technologies, which offered researchers the opportunity to study changes in their lifestyles while they occurred and
to classify them into groups according to such lifestyles. Therefore, the main objective of this research is to establish a typology of
university students according to the lifestyles they followed during the lockdown, based on the study of their daily routines, emotional
state, media consumption habits and use of apps. The study is based on a sample of 913 Spanish university students. Data has been
processed with SPSS 28.0 and SPAD 5.0. The following six groups were identified by using factor analysis and multiple correspondence
analysis: 1) the fearless and adapted (21%); 2) the unhealthy (22.56%); 3) the hardworking and studious (27.93%); 4) the hypercon-
nected (9.09%); 5) the sedentary and withdrawn (13.85%); and 6) the athletic and healthy (6.68%). The use of apps for social relations
is shown as a relevant construct, in relation to other indicators such as emotional state, time spent on studies, leisure, family and
physical activity. The lifestyles observed exhibit differences with respect to sports activity, eating habits and rest routines, as well as
time spent on academic and professional activities. p
p
Key Words: Physical activity, Pandemic, Emotional state, Digital behavior. Resumen. El acceso a la tecnología digital por parte de la población universitaria durante el confinamiento mundial por la COVID-19
ofrece al contexto académico la oportunidad de estudiar los cambios en sus estilos vida en el mismo momento en el que estos se están
produciendo analizando de forma única su posible segmentación. Por ello, el objetivo principal de esta investigación es establecer una
clasificación de estudiantes universitarios en grupos en función del constructo estilo de vida adoptado durante el confinamiento, a partir
del estudio de sus rutinas diarias, actividad física, estado emocional, hábitos de consumo de medios y uso de aplicaciones digitales. Se
ha analizado una muestra de 913 jóvenes universitarios en España. Los datos se han procesado con SPSS 28.0 y SPAD 5.0. Lifestyles of Spanish university students during the 2020 COVID-19 lockdown
Estilos de vida de estudiantes universitarios españoles durante el confinamiento por COVID-19
*Fernando García-Castillo, *Juan Tortosa Martínez, *Irene Ramos-Soler, **Jose A. García del Castillo
*Universidad de Alicante (España), **Universidad Miguel Hernández de Elche (España) A partir de
un análisis factorial y de clasificación se han obtenido seis grupos diferenciados: 1- Sin miedo y adaptados/as (21%), 2-No healthy
(22.56%), 3-Trabajadores/as y estudiantes aplicado/as (27,93%), 4-Hiperconetados/as (9,09%), 5-Sedendarios/as y poco sociables
(13,85%) y 6-Deportistas y sanos/as (6,68%). El uso de aplicaciones digitales y las relaciones sociales online se muestra como un
constructo relevante, en relación a otros indicadores como el estado emocional, el tiempo dedicado a los estudios, al ocio, la familia y
la actividad física. Los estilos de vida observados muestran diferencias respecto a rutinas deportivas, de alimentación y descanso, así
como al tiempo dedicado a tareas académicas y profesionales. p
y p
Palabras clave: Actividad física, Pandemia, Estado emocional, Comportamiento digital. Fecha recepción: 04-09-23. Fecha de aceptación: 19-01-24
Fernando García del Castillo López
fgarciadelcastillo@ua.es 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) 3-342
ón Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) Participants
Th The universe under study is university students living in
Spain. The sampling unit is people over 18 years of age, of
any gender, who were studying a university degree in Spain
when the government declared a state of emergency caused
by COVID19 and mandated stay-at-home lockdown from
March to June 2020. A total of 913 university students have
been studied. Participants’ average age was 21.9, and their
distribution by gender was quite balanced: 51.4% were
women and 48.6% were men. During lockdown, most par-
ticipants lived with their parents (75.1%), 51.3% were not
afraid of being or getting infected by COVID-19, while
46.2% did feared that possibility, which indicates risk per-
ception is quite polarized Leisure time and free time allow young people to
choose ways of enjoying themselves and potentially mean
an increase in their psychological and physical well-being,
provided their activities do not involve health-risk situa-
tions. In this sense, the young population, including univer-
sity students, is more vulnerable to the consumption of sub-
stances such as tobacco, alcohol and other drugs. According
to García del Castillo (2015), psychosocial vulnerability is
directly and indirectly associated with health-risk behaviors
and substance use based on low-risk perception, ineffective
coping strategies, inadequate resilience levels, poor stress
management, inadequate attachment styles, and low emo-
tional intelligence. In Spain, substance consumption de-
creased during lockdown, which could be explained by the
high social component of the consumption habit, which has
been altered by the lockdown (Fernández-Artamendi et al.,
2021; Villanueva-Blasco et al., 2021). Design and procedure The study uses a correlational and ex post facto research
method, with a correlational design, based on the use of
surveys. Data were obtained from a non-random sample,
selected with snowball and sequential techniques, which are
used when it is difficult to access or locate the population,
as in this case. When this sampling method is used, data col-
lection stops when the desired quotas are achieved (Grande
and Abascal, 2007). Data were collected during April and May 2020 using
the online platform Google Forms, due to the extraordinary
circumstances faced nationally and internationally due to
the health emergency caused by the SARS-COV2 virus. Participants
Th Following the ethical principles of the American Psycholog-
ical Association for Research (APA, 2017), the first page of
the online questionnaire informed participants of the objec-
tives and importance of the research, as well as the esti-
mated time to complete it and the way to react to the items. Participants were also informed about their right to not par-
ticipate in the online survey, and about the confidentiality
and anonymization of the data. Before answering the ques-
tionnaire, respondents had to explicitly indicate their agree-
ment to participate in the survey. Research carried out prior to the lockdown found out
that the main leisure activities among young people, in or-
der of importance to them, were going out with friends and
everything related to their social group, followed by listen-
ing to music and, thirdly, using technologies. Going out for
drinks to bars and clubs was in eighth place and sports in
ninth (Aguirre et al., 2019). For university students, inter-
personal relations are, without a doubt, a cornerstone of
their lifestyle and one of the greatest impacts of lockdown
in young people has been an increase in the time spent using
technologies to maintain social relations. However, the ex-
cessive time spent using digital screens has also negatively
impacted young people’s emotional state (Belmonte et al.,
2021; Kanstrup et al., 2020; Sánchez et al., 2021). Introduction Moreover, because sleep quality is im-
perative for overall health, a healthy lifestyle needs to con-
sider the quantity and quality of sleep as a fundamental di-
mension. University students were already especially vul-
nerable to breaking regular sleep patterns prior to the pan-
demic, due to the conditions and demands of their study
programs and campus life (Tsai and Li, 2004; Tsui and
Wing, 2009; Taylor et al., 2011). It is not surprising, there-
fore, that food and rest have played a fundamental role in
university students’ lifestyle and physical and emotional
health during lockdown (Bennett et al., 2021; Cantisano et
al. 2021; Rodríguez Fuentes et al., 2022; Rodríguez-Pérez
et al., 2020). In relation to sleep and its consequences on
lifestyle, we can see its impact on work and academic per-
formance during lockdown (Gálvez, 2021; Hernández,
2020; Valdivieso et al., 2020). COVID-19 lockdown to classify them according to their
emotional state and daily routines. The following three spe-
cific objectives derive from the general research objective: j
g
j
1. Study the main daily activities carried out during
lockdown (in the areas of diet, rest, leisure, sports and ICT
use) and their frequency. y
2. Classify university students into groups, based on
the lifestyles they followed during lockdown. 3. Describe and analyze the different lifestyle-based
groups of university students. Introduction Young peo-
ple, at this stage of development, have more personal auton-
omy, greater independence, and an additional burden of re-
sponsibility. Thus, it is interesting to study the meaning uni-
versity students imprint during this phase of development in
each of the dimensions of healthy lifestyles. Physical activity -333- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) main consequences of the autonomy and independence of
young people lies in the possibility of abusing fast food, in
comparison to a traditional meal, along with other health-
risk behaviors. According to a multicenter study carried out
prior to the pandemic in a sample of 1,418 Chilean univer-
sity students, more than a third presented malnutrition with
high consumption of unhealthy foods, with breakfast con-
sumption below 50% and fruit consumption below 8%
(Durán et al., 2017). Moreover, because sleep quality is im-
perative for overall health, a healthy lifestyle needs to con-
sider the quantity and quality of sleep as a fundamental di-
mension. University students were already especially vul-
nerable to breaking regular sleep patterns prior to the pan-
demic, due to the conditions and demands of their study
programs and campus life (Tsai and Li, 2004; Tsui and
Wing, 2009; Taylor et al., 2011). It is not surprising, there-
fore, that food and rest have played a fundamental role in
university students’ lifestyle and physical and emotional
health during lockdown (Bennett et al., 2021; Cantisano et
al. 2021; Rodríguez Fuentes et al., 2022; Rodríguez-Pérez
et al., 2020). In relation to sleep and its consequences on
lifestyle, we can see its impact on work and academic per-
formance during lockdown (Gálvez, 2021; Hernández,
2020; Valdivieso et al., 2020). main consequences of the autonomy and independence of
young people lies in the possibility of abusing fast food, in
comparison to a traditional meal, along with other health-
risk behaviors. According to a multicenter study carried out
prior to the pandemic in a sample of 1,418 Chilean univer-
sity students, more than a third presented malnutrition with
high consumption of unhealthy foods, with breakfast con-
sumption below 50% and fruit consumption below 8%
(Durán et al., 2017). Retos, número 53, 2024 (abril) Group 1: “The fearless and adapted” This group represents almost 21% of the sample, which
makes it the third largest (187 people). This group is com-
posed mostly of male students (67.38%), with an average
age of 22 years; the majority are in good health (71%) and
are not afraid of contracting COVID-19. In fact, members
of this group affirm that, despite the situation, they remain
hopeful (M=4.55), calm and relaxed. Participants in this
group are in the second and third year of their BA degrees
and spend much of the week, between four and five days,
studying and performing academic tasks related to their
studies. In their day to day, they frequently use email, aca-
demic apps (such as Kahoot, Drive, Office), video-confer-
ence apps (such as Meet, Zoom and Skype), and laptops (be-
tween one and three hours a day). This group has 60% of
all participants who spent the lockdown with friends, class-
mates and/or workmates. Participants in this group do
household chores four to five days a week and shop two or
three times a week, in many cases using shopping apps. a)
Daily activities, physical exercise and consumption
of digital media and apps during lockdown have been used
as active variables. b)
Physical exercise and sports routines before and
during the lockdown, technological devices, opinions, eat-
ing habits, rest and drink consumption during lockdown
and general sociodemographic data were used as illustrative
variables. The nominal variables used in the survey have been
transformed into quantitative data using the data processing
program SPAD (v.5.0). This software produces a hierar-
chical cluster analysis of participants characterized by their
factorial coordinates, using Ward’s clustering method
(Grande and Abascal, 2009), which is the most appropriate
when the variables are the factors, as in this case. The clas-
sification dendrogram is as follows: As for their rest routines, the members of this group are
characterized by sleeping occasionally throughout the day
and staying up at night two or three times a week. Before
the lockdown, sport was an important part of the daily rou-
tine of the members of this group. They used to regularly
perform physical activities, such as bodybuilding, rugby,
and individual sports such as athletics, swimming, cycling
or CrossFit, in some cases with the help of sports-related
apps. Instrument The instrument used in the study combines sections de-
signed ad hoc for this study and sections from other ques-
tionnaires that were adapted to the Spanish population, such
as the lifestyle questionnaire, adapted from Ponce et al. (2016), the physical and sports activities questionnaire, The main objective of this research is to study the life-
styles followed by university students during the 2020 -334- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) adapted from the IPAQ of Craig et al. (2003), and two 7-
point Likert scales on emotional state (anxiety and depres-
sion) during lockdown, adapted from the Hospital Anxiety
and Depression (HAD) Scale developed by Zigmund and
Snaith (1983). The sociodemographic, academic, and ICT-
use sections of the questionnaire were specifically designed
for this research. possible while intergroup inertia is greater. The table below
describes the groups (Table 1). Groups one and three are the most heterogeneous, since
their inertia is the highest, they are also two of the largest
(187 and 255 participants), with group six being the most
homogeneous and the smallest. Data analysis The following sections describe the groups of students
established according to their lifestyles and characteristics. The computer processing of the collected data was car-
ried out using SPSS (Statistical Package for Social Science)
version 28.0 and SPAD (Système Portable pour l’analyse des
donnes) version 5.0. The technique used for data analysis
was the multiple correspondence factor analysis multiple
correspondence factor analysis to achieve the objective of
classifying university students according to the lifestyle
adopted during the lockdown. Retos, número 53, 2024 (abril) Group 2: “The unhealthy” This group represents 22.56% of the sample, with 206
students. Most participants in this group are first-year stu-
dents (42.23%), who perform academic activities between
three and five days a week, for one to three hours a day. They are characterized by using apps such as Drive, Office
and Kahoot on their laptops. The members of this group
affirm that during the COVID19 lockdown they felt tense
and/or wound-up (M=4.73), did not use to buy online;
some of them smoked daily, and performed household
chores one day a week. They like audiovisual content, since
almost 50% of all those who watch TV more than 8 hours a
day are part of this group. Outstandingly, they dedicate be-
tween one and three hours a day to watch these contents,
using platforms such as Netflix, Amazon Prime, HBO, etc. They meet with their friends online at least once a week and
believe that smartphone use has positively influenced their
social relations during this period (M=5.9). Their sleep
habits during lockdown show that they stayed up late prac-
tically every day and spent a lot of time (between one and
three hours a day) playing video games on mobile apps or
consoles. Throughout the day, they listened intensively to
music and radio apps such as Spotify and Shazam. Concerned about their health and physical condition
during the lockdown, they have practiced aerobic exercises,
of different intensities, between two and five days a week. Their weekly sports routine was the same before and during
the lockdown, and centered on group aerobic activities,
such as Zumba, spinning, walking and body pump. They are
also characterized by their use of sports and health-related
apps. All the members of this group have a laptop and a
smartphone, and make very intense use of them, between
six and seven hours a day. They believe that smartphone use
has positively influenced their family relations (M=5.21)
and their physical and sports activity. Regarding their daily
use of social networks and apps, they use WhatsApp be-
tween four and seven hours, and Instagram, between four
and five hours. The frequency with which they use email,
Facebook and news apps is also high (between one and three
hours a day). Their daily use of shopping apps, game apps,
TikTok and Snapchat is less intense, but occurs every week. Group 1: “The fearless and adapted” During lockdown, this group of students continued
with this daily sports routine at home, frequently practiced
strength and aerobic exercises of varying intensity, for one
to one and a half hours, to compensate for the almost five
hours a day they also spent sitting during these months of
isolation. Figure 1. Dendrogram. Source: Authors’ own creation. Table 1. Description of participants into six groups
Inertia Students Weight Distance
Intergroup Inertia
Intragroup Inertia
Group 1/6
Group 2/6
Group 3/6
Group 4/6
Group 5/6
Group 6/6
.2457
.1030
.0818
.1143
.0833
.0690
.0446
187
206
255
83
121
61
187
206
255
83
121
61
.1830
.1301
.0878
.5322
.3567
.8786
Source: Authors’ own creation
17751731173017551743121017571740174816601701174617591770175117631750177317471767174916931724171117641756173917291772176114001760116017541768176211481700168417661765177117531718175817741150171911621776
0%
0%
0%
0%
0%
0%
6 Figure 1. Dendrogram. Source: Authors’ own creation. 17751731173017551743121017571740174816601701174617591770175117631750177317471767174916931724171117641756173917291772176114001760116017541768176211481700168417661765177117531718175817741150171911621776
0%
0%
0%
0%
0%
0%
6 Figure 1. Dendrogram. Source: Authors’ own creation. Regarding their eating habits, this group stands out for
its use of healthy-eating apps and the daily consumption of
protein-rich foods, being fruit, vegetables and natural juices
also common in their diet. Very occasionally, they consume
ice cream, sweets and factory-made pastries and never eat
fatty foods such as butter, fried food, mayonnaise or sauces. Their leisure and entertainment time during the lockdown
is marked by the consumption of movies, series and televi-
sion, between five and three times a week, using streaming
apps, both offline and online. In their leisure time, they also
use apps to virtually enjoy cultural activities, such as listen-
ing to concerts and visiting museums. The intense use of A typology of six groups was established based on the
general principle of classification analysis (minimize internal
variations of clusters and maximize their separation). The
objective is to ensure that the intragroup inertia is as low as Retos, número 53, 2024 (abril) -335- 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) smartphones (between four and five hours a day) also stands
out in this group. They use mobile apps like WhatsApp, In-
stagram, YouTube, Facebook, as well as music, radio, and
gaming apps. to five days a week. They use video conferencing apps such
as Skype, Meet and Zoom; perform household chores daily;
and usually stay up late once a week. Group 1: “The fearless and adapted” Between two and five times a week, they like to enter-
tain themselves with online cultural activities such as listen-
ing to concerts, musicals and visiting museums. They also
have fun with their smartphone and online video games, and
use digital devices to chat online with friends, at least four
or five days a week. These social and leisure activities are
carried out on their smartphones and laptops. The vast ma-
jority do not use video game consoles. Another characteris-
tic of this group is its intense daily use (four to five hours)
of audiovisual content platforms such as Netflix, HBO and
Amazon Prime. Group 2: “The unhealthy” pp
p
y
The members of this group are not very physically ac-
tive, as they did not practice any sport, neither individual
or collective, before or during the 2020 mandatory home
lockdown. Almost 80% spent more than six hours a day sit-
ting and practically never performed strength nor aerobic
exercises nor used sports or health-related apps. They love
to eat between meals. In fact, they only manage to maintain
the daily routine of having breakfast, lunch and dinner at
regular times two or three days a week. They do not eat
fruit regularly (at most once a week) and their diet focuses
mainly on protein-rich foods, fats (fried food, mayonnaise,
sauces, etc.) and vegetables. Two or three times a week,
they also incorporate ice cream, sweets and factory-made
pastries into their diet. They love fizzy and sugary drinks
(such as juices and factory-made teas), yet nearly 98% of
them never drink energy drinks, such as Monster or Red-
Bull. Group 4: “The hyperconnected” This is the second smallest group, with only 83 students,
who represent 9.09% of the sample. They are good stu-
dents, although not especially bright, as their average grade
is “B” (M=7.4). During lockdown, they felt somewhat
tense and/or wound-up (M=5.02). They are fundamen-
tally characterized by being “hooked” to their technological
devices, be it smartphone, computer, tablet or smart
watch. They spend the day connected, especially to their
smartphone, with a daily use of more than eight hours
(77.11%). They use WhatsApp, Instagram and YouTube
most of the day (from six to more than eight hours) and
believe smartphone use has positively influenced their social
relations (M=6.05) and their family (M=5.34) relations. This digital connection also occurs in the academic field,
since they use academic, email, language software and vid-
eoconferencing apps, such as Skype, Meet and Zoom, from
four o more than eight hours a day. They have also used
news apps to stay informed and to meet people during lock-
down. Retos, número 53, 2024 (abril) Group 6: “The athletic and healthy” This is the smallest group of all, with only 61 students,
representing 6.68% of the sample. It is also the most homo-
geneous group, as shown by its inertia. They believe that
their use of smartphones positively influences their physical
and sports activities (M=4.98) as well eating habits
(M=4.8), but also negatively affects their sleep hours
(M=3.2). They use Instagram intensively throughout the
day (for more than 8 hours) as well as gaming apps with
videocall functionality. During lockdown, their diet has been characterized by
being far from what is considered healthy”. They ate be-
tween meals a lot, practically every day, consuming ice
cream, sweets, factory-made pastries and fatty and fried
foods, mayonnaise and sauces. They never ate fruit and fre-
quently consumed sugary drinks, such as prepackaged juices
and teas, soft drinks, energy drinks like RedBull and Mon-
ster, coffee, and tea. Alcohol consumption has also been
sporadically present in this group. Members of this group
say they were sleepy during the day, which may explain
their consumption of tea, coffee and energy drinks. Another
characteristic of the members of this group is that before
lockdown they were not very sporty but stayed active
mainly by practicing gentle physical activities, like walking,
dancing and playing tennis. This has been reflected in the
physical activity performed at home during lockdown,
when they performed low-intensity aerobic exercises with
a moderate weekly frequency of four to five times a week. y
They like to sleep for seven to eight hours a day. They
claim that they get up rested because they sleep well, and
never stay up late. During the lockdown, they enjoyed a
good book, or a good radio or television program (M=5.5),
and used streaming apps like Netflix, Amazon Prime and
HBO many times for more than eight hours a day. They are
characterized for maintaining a constant eating routine
throughout the week: they have breakfast, lunch and dinner
at the same time, and never snacked between meals. Every
day, they eat protein-rich foods, fruits, vegetables and nat-
ural juices. Alcohol and sugary drinks are allowed a few days
a week. They are active and athletic. Group 5: “The sedentary and withdrawn” This group is composed of 121 students, who represent
13.85% of the sample. In this group the weight of the male
gender is high (66.94%). Its members are mainly last-year
students who, during the lockdown, did not work, dedi-
cated most of their time to academic work (72.73%), and
did not use online shopping apps. They are also character-
ized by their intense use of laptops, usually for more than 8
hours a day. They spend a day a week on household chores
and entertain themselves by playing video game consoles,
between one and three hours a day. They do not use gaming
apps on their smartphones. From time to time, they also
watch TV series or movies and use music apps, such as
Spotify and Shazam. Group 3: “The hardworking and studious” This group represent 27.93% of the sample, with 255
students. Their intragroup inertia indicates that it is the
most heterogeneous of all. It is formed mostly by women
(77.65%), who claim to be in good health and do not smoke
(92.16%) but are afraid of being or getting infected by
SARS-COV2. Their daily activities during the lockdown
have been marked mainly by academic work, which they do
for four to five hours every day, even Saturdays and Sun-
days, using apps such as Drive and Office. Members of this
group are also characterized by working remotely, for two Another one of the main daily activities this group car-
ried out during lockdown was watching television series and
movies, which they did intensely from four to eight hours. Retos, número 53, 2024 (abril) -336- 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) Enjoying cultural activities online, such as listening to con-
certs, was another important leisure activity during the pan-
demic. The use of apps to watch movies or series (like Net-
flix, Amazon Prime and HBO) and apps to listen to music
and radio (like Spotify and Shazam) exceeds eight hours a
day in this group. They used online apps intensively to
maintain their social relations with friends, for four to seven
hours a day. They have also used online gaming apps, some
of which include video calls. They shopped at least once a
week, often on smartphone apps. Enjoying cultural activities online, such as listening to con-
certs, was another important leisure activity during the pan-
demic. The use of apps to watch movies or series (like Net-
flix, Amazon Prime and HBO) and apps to listen to music
and radio (like Spotify and Shazam) exceeds eight hours a
day in this group. They used online apps intensively to
maintain their social relations with friends, for four to seven
hours a day. They have also used online gaming apps, some
of which include video calls. They shopped at least once a
week, often on smartphone apps. that during lockdown they never took alcohol, coffee or
tea, and that they usually did not have breakfast. However,
they say they consumed fruit and natural juices from time
to time. Group 6: “The athletic and healthy” Before the lockdown,
they liked walking and strength and bodybuilding exercises
and, during the lockdown, they continued performing
strength and aerobic exercises of different intensities at
home on a daily and intense basis (for one to two hours),
and also participated in physical activities directed by online
professionals. Retos, número 53, 2024 (abril) Discussion Group four,
“the hyperconnected”, is characterized by being composed
of good students, who felt tense and/or anxious during
lockdown and were hooked on their technological devices. Group five, “the sedentary and withdrawn”, is formed
mainly by men who did not work, dedicated most of their
time to their studies, and used their laptop intensively. Fi-
nally, group six, “the athletic and healthy”, is the smallest
cluster and is composed by students who are very active and
athletic, eat a balanced diet and maintain adequate sleep
routines. diseases and to spend leisure time in healthy activities. In
turn, those who stayed more physically active during lock-
down, in addition to being more physically active before it,
have a more active attitude towards exercise, and avoid in-
activity and sedentary lifestyle, which is in line with the re-
sults of recent research works (Camacho et al., 2020; Jimé-
nez et al., 2020; Mera et al., 2020). The subjective incentives to maintain an adequate level
of physical activity during lockdown include the large num-
ber of exercise programs that multiple digital platforms
have promoted (Andreu, 2020) and that have served as an
engine for many users, especially those who had high levels
of physical activity before the lockdown. Therefore, the use
of technology has led, paradoxically, to both an increase in
sedentary time and an increase in physical exercise time. It
should be noted that, although we maintain an adequate
level of physical exercise, if our sedentary time is high dur-
ing the day, we will still be at risk of suffering multiple phys-
ical and psychological health problems, as reflected in some
recent research (Franch-Llasat et al., 2020; García-Tascón
et al., 2021; Garzón and Aragón, 2021; Mera et al., 2020). Physical activity, exercise and sedentary lifestyles have
been determining factors in the configuration of these
groups. During lockdown, sitting hours among the students
in our sample increased compared to the previous period. A large number of participants (more than 300 university
students), the “unhealthy” and “the sedentary and with-
drawn”, spent more than six hours a day sitting and did not
practice any type of aerobic physical exercise before the
lockdown. During the lockdown, 73% of the total sample
exceeded six hours of sitting. Two factors influenced this
result: the mandatory lockdown and the possibility of using
different digital media for interpersonal relations, leisure
consumption, study and remote work. Discussion In fact, the lock-
down has generated a significant increase in the use of tech-
nologies, especially in the areas of communication with
friends and family (more than 80%), study and remote
work (more than 71%), and leisure consumption (more
than 60%) (García del Castillo et al., 2020). As for their diet, most of the students in the sample
maintained healthy habits that include eating three meals a
day and consuming plenty of fruit and vegetables through-
out the week. The “fearless and adapted” and the “athletic
and healthy” are especially healthy in this regard. However,
the “unhealthy” and the “hyperconnected” have unhealthy
eating habits that include the regular consumption of sugary
drinks, ice cream, sweets and factory-made pastries, which
significantly increase the risk of obesity, cholesterol, hyper-
tension, diabetes and emotional problems (Almendra et al.,
2021). In turn, the general trend in the population during the
lockdown period has been a significant decrease in physical
activity (García-Tascón et al., 2021; Sang et al., 2021; San-
tos et al., 2021; Zamarripa, 2021). It is important to keep
in mind that, as the WHO (2020) points out, the state of
lockdown prevents people from carrying out activities that
keep them active, such as work, study, household chores,
transport and leisure. In fact, household chores are the only
activities that can be carried out during lockdown. One of
the issues that prevents people from keeping their pre-lock-
down level of physical exercise during lockdown is the per-
ception that this type of activity must be developed outside
the home. As Irazusta and Ara (2020) point out, the fact of
not being able to go out to the streets to practice exercise
significantly promotes a sedentary lifestyle due to that per-
ception. Regarding rest habits, most students maintain adequate
sleep routines. Despite not being able to leave their home,
the frequency of staying up late is quite high, especially
among the “hyperconnected”, the “unhealthy” and the
“hardworking and studious”. However, hours of sleep are
compensated in many of the cases since students sleep be-
tween seven and eight hours a day. Other studies (Tamayo
et al., 2020) indicate that during lockdown most university
students (85%) suffered from sleep problems associated
with negative emotional feelings (like depression and pessi-
mism) and physical health problems, especially headaches. Likewise Anger et al. Discussion This research has examined the impact of the 2020 lock-
down on the emotional state and behavior of a sample of
Spanish university students, based on the analysis of a series
of lifestyle variables (diet, physical activity, rest, leisure ac-
tivities and digital behavior). The historical lockdown man-
dated after the declaration of state of emergency has al-
lowed us to delve into these variables and to classify univer-
sity students into six types or clusters that reflect different
changes and adaptive responses in their lifestyles during this
exceptional period. They use smartphones between one and three hours a
day, mainly to access Instagram, WhatsApp and YouTube. They believe that the use of smartphones has affected their
sleeping hours (M=2.9). In addition, they are not very so-
ciable, as they talk to their friends online once a week at
most. They are characterized by their sedentary lifestyle
and lack of sports activity. Before the lockdown, they spent
more than six hours a day sitting and did not do practice any
sports or group activities such as Zumba and dancing. This
lack of physical routine continued during lockdown, when
they did not perform any aerobic or strength exercises at
home nor used health or sports apps. Regarding their diet,
they are characterized more by what they did not consume
than by what they did consume. For example, they affirm The sample of students was divided into six groups ac-
cording to their lifestyle profile. Group one, “the fearless
and adapted”, is mostly composed of men wo are in good
health, unafraid of contracting the disease, hopeful and
calm. Group two, “the unhealthy”, is composed of students
who dedicate between three and five days a week to school
activities, make use of laptops, smoke more and recognize
they felt tense and/or wound-up during lockdown. Group
three, “the hardworking and studious”, is the most hetero-
geneous of all and is composed mainly of women who are
in good health, but are afraid of getting infected, and focus -337- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) on studying and working remotely from home. Retos, número 53, 2024 (abril) Discussion (2021) have confirmed that more than
77% of their sample of university students (n=2,619) suf-
fered from sleep problems associated with anxiety, demo-
tivation and sadness. In relation to the Spanish population,
Sandín et al. (2020) concluded, based on a sample of more
than 1000 participants, that there is an association between
sleep problems and negative emotional states. On the other hand, as it has been observed, students
who played sports on a regular basis before lockdown are
also the ones who have played sports at home the most dur-
ing lockdown. This fact is reflected especially in the “ath-
letic and healthy” group but also among the “fearless and
adapted”, the “hardworking and studious” and the “hyper-
connected”. According to Di Renzo (2020), the state of
lockdown can generate maintenance habits on some occa-
sions, such as adherence to physical activity, which may be
linked to the fact that in many students in our sample main-
tained high levels of physical exercise during lockdown. This fact may have been due to health reasons, to combat Therefore, the level of physical activity, diet and rest in-
fluence students’ emotional state (Almendra et al. 2021;
Bennett et al., 2021; Cantisano et al. 2021; García-Tascón
et al., 2021; Ramírez and Zerpa, 2020; Rodríguez-Pérez et
al., 2020). Living in lockdown, especially for as long as peo-
ple did during the Covid-19 pandemic, breaks routines and
forces new ones that can be contradictory: it can improve -338- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) students’ health condition and lifestyle, but can also harm
their physical and emotional state. For example, in our sam-
ple, students in the “unhealthy” group have a lifestyle that
negatively influences their emotional state, the “hypercon-
nected” make an excessive use of technology and have eat-
ing habits that seem to affect their rest and emotional state,
while the “hardworking and studious” are tense and fear
contagion. On the opposite side, the “fearless and adapted”
and the “athletic and healthy” groups lead a healthy lifestyle
that has a positive impact on their physical and emotional
health. American Psychological Association (2017). Ethical princi-
ples
of
psychologist
and
code
of
conduct. www.apa.org/ethics/code/index.aspx g
Andreu, E. (2020). Actividad física y efectos psicológicos
del confinamiento por COVID- 19. Conclusions Students who played sports on a regular basis
before the lockdown are the ones who practiced sports at
home the most during lockdown. Cantisano, L.M., Belando, N., Ballester, A., Blanco, A. y
González, R. (2021). Cambios en el estilo de vida y en
la semociones durante el confinamiento por COVID-
19. International Journal of Developmental and Educational
Psychology,
1(1),
413-424. https://doi.org/10.17060/ijodaep.2021.n1.v1.2078 g
4-
Regarding the existence of differences in the
emotional state of the students during confinement among
the different groups, it is concluded that these are pro-
duced more by gender than by lifestyle segments. Women
score higher in emotional dimensions such as distress, fear,
anxiety and stress, than men. Cocca, A., Liukkonen, J., Mayorga, D. y Viciana, J. (2014). Healthrelated physical activity levels in Spanish
youth and young adults. Perceptual and Motor Skills,
118(1),
247-
260. https://doi.10.2466/10.06.PMS.118k16w1 The main limitations of this research work include the
sample size, so it would be advisable for future studies to
cover larger and heterogeneous populations, to maximize
the generalization of results. Cortés, N. Y., Piñeiro, R. y Vuelvas, C.R. (2020). Psycho-
logical effects and associated factors of Covid-19 in a
Mexican sample. Disaster Medicine and Public Health Pre-
pared-
Ness,
14(3),
413-424. https://doi.org/10.1017/dmp.2020.215 Discussion International Journal
of Developmental and Educational Psychology, 1(2), 209-
220. https://doi.org/10.17060/ijodaep.2020.n1.v2.1828
Á Belmonte, M.L., Álvarez, J.S. y Hernández, M.A. (2021). TIC y ocio familiar durante el confinamiento: agentes
involucrados. Texto Livre, 14(2), e33938. https://doi.org/10.35699/1983-3652.2021.33938 Conclusions Beltrán, V., Sierra, A.C., Jiménez, A., González-Cutre,
D., Martínez, C. y Cervelló, E. (2017). Diferencias se-
gún género en el tiempo empleado por adolescentes en
actividad sedentaria y actividad física en diferentes seg-
mentos horarios del día. Retos. Nuevas tendencias en Edu-
cación
Física,
Deporte
y
Recreación,
31,
3-7. https://www.re-
dalyc.org/pdf/3457/345750049001.pdf According to the objectives set out in this research, it
is concluded that: 1-
The daily routines followed by the university stu-
dents during the 2020 COVID-19 lock-in and their emo-
tional state, allow segmenting the study group into 6 seg-
ments of lifestyles different from each other, and with in-
ternal coherence. y
g
Bennett, G., Young, E., Butler, I., y Coe, S. (2021). The
Impact of Lockdown During the COVID-19 Outbreak
on Dietary Habits in Various Population Groups: A
Scoping Review. Frontiers in Nutrition, 8, 53. https://doi.org/10.3389/fnut.2021.626432 2-
The main activities carried out by the sample of
university students were academic work, followed closely
by use of smartphone apps, video games and online games. Other activities carried out frequently by students are
watching TV (specially series and movies), household
chores and interaction with friends and family through dig-
ital technologies. p
g
Camacho, A., Camacho, M., Merellano, E., Trapé, A. y
Brazo, J. (2020). Influencia de la actividad física reali-
zada durante el confinamiento en la pandemia del CO-
VID-19 sobre el estado psicológico de adultos: un pro-
tocolo de estudio. Revista Española de Salud Pública,
94. https://www.mscbs.gob.es/biblioPublic/publica-
ciones/recursos_propios/resp/re-
vista_cdrom/VOL94/PROTOCO-
LOS/RS94C_202006063.pdf 3-
In the classification of groups obtained based on
lifestyles, physical activity and diet established as habits in
homes during this period have also been decisive. In refer-
ence to eating habits during lockdown, the sample of stu-
dents maintained the routine of eating three meals a day
practically every day of the week, following a quite bal-
anced diet. Students who played sports on a regular basis
before the lockdown are the ones who practiced sports at
home the most during lockdown. 3-
In the classification of groups obtained based on
lifestyles, physical activity and diet established as habits in
homes during this period have also been decisive. In refer-
ence to eating habits during lockdown, the sample of stu-
dents maintained the routine of eating three meals a day
practically every day of the week, following a quite bal-
anced diet. References Craig, C., Marshall, A., Sjostrom, M., Bauman, A.E.,
Booth, M.L., Pratt, M. et al. (2003). International
Physical Activity Questionnaire: 12- country Reliability
and Validity. Medicine & Science in Sports & Exercise, 35,
1381-1395. https://doi.org/10.1249/01.MSS.0000078924.6145
3.FB Aguirre, E., Ballesteros, J.C., Elzo, J., González-Anleo,
J.M, Megías, E., Moreno, A., Rodríguez, E., Rubio,
A.M. y Tudela, P. (2019). Protagonistas y espectadores. Una mirada longitudinal sobre la juventud española. Funda-
ción de Ayuda contra la Drogadicción (FAD). https://oji.fundacion-sm.org/protagonistas-y-especta-
dores-i/ Craig, C., Marshall, A., Sjostrom, M., Bauman, A.E.,
Booth, M.L., Pratt, M. et al. (2003). International
Physical Activity Questionnaire: 12- country Reliability
and Validity. Medicine & Science in Sports & Exercise, 35,
1381-1395. -339- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) Cruz, A., Molerio, O., Llopiz, K., Aguinaga-Villegas, D.,
Gálvez-Suarez, E., Quiroz-Sánchez, T., Alarcón, M.,
Flores, W., Antón de los Santos, P. y Taxa, J. (2020). Percepción de riesgo e incidencia antitabáquica en el
rendimiento académico de estudiantes universitarios de
Ciencias Médicas. Propósitos y Representaciones, 8(1),
e433. http://dx.doi.org/10.20511/pyr2020.v8n1.433 Grande, I. y Abascal, E. (2007). Fundamentos y técnicas de
investigación
comercial. ESIC. https://www.esic.edu/editorial/edito-
rial_producto.php?t=Fundamen-
tos+y+t%E9cnicas+de+investigaci%F3n+comer-
cial&isbn=9788417024406 Giraldo, V.A. (2021). Efectos del confinamiento en estu-
diantes universitarios: un análisis basado en diferencias
de género. Revista Internacional Multidisciplinaria, 2(1),
509-521. https://www.ciidjournal.com/in-
dex.php/abstract/article/view/92/99 Di Renzo, L., Gualtieri, P., Pivari, F., Soldati, L., Attinà,
A., Cinelli, G., Leggeri, C., Caparello, G., Barrea, L.,
Scerbo, F., Esposito, E., & De Lorenzo, A. (2020). Eat-
ing habits and lifestyle changes during COVID-19 lock-
down: an Italian survey. Journal of Translational Medicine,
18(1), 229. https://doi:10.1186/s12967-020-02399-
5 Hernández, G. (2020). Gestión de las emociones en tiem-
pos de pandemia y su impacto en el rendimiento acadé-
mico. Revista de Investigación y Cultura - Universidad César
Vallejo, 9(4), 55-64. https://dialnet.unirioja.es/ser-
vlet/articulo?codigo=7946112 Durán, S., Crovetto, M., Espinoza, V., Mena, F., Oñate,
G., Fernández, M., Coñuecar, S., Guerra, A. y Valla-
dares, M. (2017). Caracterización del estado nutricio-
nal, hábitos alimentarios y estilos de vida de estudiantes
universitarios chilenos: estudio multicéntrico. Revista
Médica
de
Chile,
145(11),
1403-1411. https://scielo.conicyt.cl/pdf/rmc/v145n11/0034-
9887-rmc-145-11-1403.pdf g
Infante, C., Peláez, I. y Giraldo, L. (2021). References Covid-19 y gé-
nero: efectos diferenciales de la pandemia en universita-
rios. Revista Mexicana de Sociología 83, 169-196. http://dx.doi.org/10.22201/iis.01882503p.2021.0.6
0072 Irazusta, J. y Ara, I. (2020). Actividad física en la población
universitaria durante el confinamiento por COVID-19. Con-
sejo Superior de Deportes. http://unizar.es/sites/de-
fault/files/actualidad/adjuntos/0_resumen_pro-
yecto.pdf Fernández-Artamendi, S., Ruiz, M. J. y López-Núñez, C. (2021). Analyzing the Behavior of Cannabis Users dur-
ing the COVID-19 Confinement in Spain. International
Journal of Environmental Research and Public Health,
18(21),
11324. https://doi.org/10.3390/ijerph182111324 y
Jiménez, D., Carbonell, A. y Lavie, C.J. (2020). Physical
exercise as therapy to fight against the mental and phys-
ical consequences of COVID-19 quarantine: Special fo-
cus in older people. Progress in Cardiovascular Diseases. 63(3). https://doi.org/10.1016/j.pcad.2020.03.009 Franch-Llasat, D., Mayor-Vázquez, E., Pedregosa-Díaz,J.,
Herrero-Redondo, M., Ortin-Font, X. y Roche-
Campo, F. (2020). e-Thrombosis en época COVID-19. Efectos colaterales del confinamiento. Medicina Inten-
siva, 45(2), 122-126. https://doi.org/10.1016/j.me-
din.2020.08.003 Jurakić, D., Pedisić, Z. y Andrijasević, M. (2009). Physical
activity of Croatian population: cross-sectional study us-
ing International Physical Activity Questionnaire. Croatian
Medical
Journal,
50(2),
165-173. https://doi.10.3325/CMJ.2009.50.165 Gálvez, M.A. (2021). Pandemia y confinamiento: un des-
orden en los procesos del sueño. Rhombus, 1(2), 50-66. https://www.ulacit.ac.cr/wp-content/uploads/Re-
vistaRhombus-junio-2021.pdf#page=53 Kanstrup, A. M., Bertelsen, P. S., y Knudsen, C. (2020). Changing Health Behavior with Social Technology? A
Pilot Test of a Mobile App Designed for Social Support
of Physical Activity. International journal of Environmental
research
and
Public
health,
17(22),
8383. https://doi.org/10.3390/ijerph17228383 p
p g
García del Castillo, J.A. (2015). Concepto de vulnerabili-
dad psicosocial en el ámbito de la salud y las adicciones. Health and Addictions/Salud y Drogas, 15(1), 5-14. http://dx.doi.org/10.21134/haaj.v15i1.236 Mera, A.Y., Tabares, E., Montoya, S., Muñoz, D. y Mon-
salve, F. (2020). Recomendaciones prácticas para evitar
el desacondicionamiento físico durante el confinamiento
por la pandemia asociada a COVID-19. Universidad y Sa-
lud,
22(2),
166-177. https://doi.org/10.22267/rus.202202.188 García del Castillo, J.A., Ramos, I., López-Sánchez, C. y
Quiles, C. (2020). Information and communication
technologies andquality of life in home confinement:
Developmentand validation of the TICO scale. PLoS
ONE
15(11),
e0241948. https://doi.org/10.1371/journal.pone.0241948 Mercê, C., Cordeiro, J., Romão, C., Branco, M. y Catela,
D. (2023). Niveles de Actividad Física en Niños: Im-
pacto de la Pandemia Covid-19 (Levels of Physical Ac-
tivity in Portuguese Children: the Impact of the Covid-
19
Pandemic). Retos,
47,
174–180. https://doi.org/10.47197/retos.v47.94936 Mercê, C., Cordeiro, J., Romão, C., Branco, M. y Catela,
D. (2023). human-rights-as-key-to-the-covid-19-response Rodríguez-Pérez, C., Molina-Montes, E., Verardo, V., Ar-
tacho, R., García-Villanova, B., Guerra-Hernández, E. J., y Ruíz-López, M. D. (2020). Changes in dietary be-
haviours during the COVID-19 outbreak Confinement
in the Spanish COVIDiet Study. Nutrients, 12, 1730. https://doi.org/10.3390/nu12061730 Orepic, P., Mikulic, P., Soric, M., Ruzic, L. y Markovic,
G. (2014). Acute physiological responses to recrea-
tional inline skating in young adults. European Journal Of
Sport
Science,
14,
25-31. https://doi:10.1080/17461391.2011.638936 Rodríguez, A., Vicente, E., De Mena, J.M. y Pérez, S. (2021). Efecto de la práctica de actividad física gamifi-
cada en el estado de ánimo de jugadoras de baloncesto
en etapa de confinamiento. Retos, 43, 10-16. https://doi.org/10.47197/retos.v43i0.87177 Penaves, G., André, R. Barbosa, L., Almeida, A.M. y
Saravia, J. (2022). Fatores associados com o nível de
atividade física e comportamento sedentário de
professores em tempos de pandemia de COVID-19. Re-
tos, 46, 511-519. https://doi.org/10.47197/re-
tos.v46.93968 Sánchez, A., Flores, I., Veytia, M.G. y Azuara, V. (2021). Tecnoestrés y adicción a las tecnologías de la informa-
ción y las comunicaciones (TIC) en universitarios mexi-
canos: diagnóstico y validación de instrumento. Forma-
ción
Universitaria,
14(4),
123-132. http://dx.doi.org/10.4067/S0718-
50062021000400123 Pinillos, Y. y Herazo, A.Y. (2020). Cambios en la intención
hacia la práctica de la actividad física antes y después de 4
meses del confinamiento obligatorio según variables sociodemo-
gráficas. Universidad Simón Bolívar. http://bonga.uni-
si-
mon.edu.co/bitstream/handle/20.500.12442/6909/
Cambios_Intenci%c3%b3n_Pr%c3%a1ctica_Activi-
dad_F%c3%adsica_AntesDespu%c3%a9s_4Me-
ses_Resumen.pdf?sequence=1&isAllowed=y Sandín, B., Valiente, R.M., García-Escalera, J. y Chorot,
P. (2020). Impacto psicológico de la pandemia de CO-
VID-19: Efectos negativos y positivos en población es-
pañola asociados al periodo de confinamiento nacional. Journal of Psychopathology and Clinical Psychology / Revista
de Psicopatología y Psicología Clínica, 25(1), 1-22. https://doi:10.5944/rppc.27569 Piña-Ferrer, L. (2020). El COVID 19: Impacto psicológico
en los seres humanos. Revista Arbitrada Interdisciplinaria
de Ciencias de la Salud. SALUD Y VIDA, 4(7), 88-199. http://dx.doi.org/10.35381/s.v.v4i7.670 Sang, X., Menhas, R., Saqib, Z. A., Mahmood, S., Weng,
Y., Khurshid, S., Iqbal, W. y Shahzad, B. (2021). The
psychological impacts of covid-19 home confinement
and physical activity: A structural equation model anal-
ysis. Frontier
Psychology,
11,
614-770. https://doi.org/10.3389/fpsyg.2020.614770 p
g
Ponce, N.R., Quispe, L.A., Alfaro, P.R. y Meléndez, C.E. (2016). Creencias y prácticas de la actividad física y es-
tilos de vida saludable en el personal administrativo de
una universidad de Lima, Perú. Revista Herediana de
Rehabilitación,
1(2),
46-58. https://doi.org/10.20453/rhr.v1i2.3205 Santos, E., Rico, J., Carballo, A. y Abelairas, C. (2021). References Niveles de Actividad Física en Niños: Im-
pacto de la Pandemia Covid-19 (Levels of Physical Ac-
tivity in Portuguese Children: the Impact of the Covid- García-Tascón, M., Mendaña-Cuervo, C., Sahelices-Pinto,
C. y Magaz-González, A.M. (2021). Repercusión en la
calidad de vida, salud y práctica de actividad física del
confinamiento por Covid-19 en España. Retos, 42, 684-
695. https://doi.org/10.47197/retos.v42i0.88098 19
Pandemic). Retos,
47,
174–180. https://doi.org/10.47197/retos.v47.94936 Garzón, J. y Aragón, L.F. (2021). Sedentarismo, actividad
física y salud: una revisión narrativa. Retos, 42, 478-499. https://doi.org/10.47197/retos.v42i0.82644 Organización Mundial de la Salud. (2020). Addressing Human
Rights as Key to the COVID-19 Response. April. https://www.who.int/publications-detail/addressing- -340- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) 2024, Retos, 53, 333 342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) human-rights-as-key-to-the-covid-19-response Cambios en hábitos saludables relacionados con activi-
dad física y sedentarismo durante un confinamiento na-
cional
por
covid-19. Retos
43,
415-421. https://doi.org/10.47197/retos.v43i0.89425 Práxedes, A., Sevil, J., Moreno, A., del Villar, F. y García-
González, L. (2016). Niveles de actividad física en estu-
diantes universitarios: diferencias en función del gé-
nero, la edad y los estados de cambio. Revista Iberoameri-
cana de Psicología del Ejercicio y el Deporte, 11(1), 123-132. https://zaguan.unizar.es/record/32795/fi-
les/texto_completo.pdf Swendsen, J. (2020). Covid-19 and mental health: How
one pandemic can reveal another”. Journal of Behavioral
and
Cognitive
Therapy,
30(3),
161-163. https://doi.org/10.1016/j.jbct.2020.08.001 Richardson, A., King, S., Olds, T., Parfitt, G. y Chiera, B. (2018). Study and life: How first year university stu-
dents use their time. Student Success, 9(3). https://pdfs.semanticscho-
lar.org/6234/0e7be5e9c5e76d0fef1a5eb1e7c4e94503
39.pdf Taylor, D.J., Gardner, C.E., Bramoweth, A.D., Williams,
J.M., Roane, B.M., Grieser, E.A. y Tatum, J.I. (2011). Insomnia and mental health in college students. Behavior
Sleep
Medicine,
9(2),
107-16. https://doi.org/10.1016/j.beth.2012.12.001 Tsai, L.L. y Li, S.P. (2004). Sleep patterns in college stu-
dents: gender and grade differences. Journal of Psychoso-
matic
Research,
56(2),
231-7. http://en.smrc-
sa.com/wp-content/uploads/2014/12/Sleep-Pat-
terns-in-College-Students.pdf Rodríguez, T., Fonseca, M., Valladares, A. y López, L. (2020). Protocolo de actuación psicológica ante la CO-
VID-19 en centros asistenciales. Medisur, 18(3), 368-
380. http://medisur.sld.cu/index.php/medisur/arti-
cle/view/4671 Tsui, Y.Y. y Wing, Y.K. (2009). A study on the sleep pat-
terns and problems of university business students in
Hong Kong. Journal of American College Health, 58(2),
167-76. Rodriguez-Fuentes, G., Campo-Prieto, P. y Cancela-Ca-
rral, J. M. (2022). Estilos de vida y hábitos de una Co-
munidad Universitaria Española en tiempos de COVID-
19: un estudio transversal (Lifestyles and habits of a Spa-
nish University Community in times of COVID-19: a
cross-sectional
study). Retos,
46,
283–293. https://doi.org/10.47197/retos.v46.93101 https://doi.org/10.1080/07448480903221418
Vagetti, G.C., Barbosa, V.C., Moreira, N.B., de Oliveira, -341- Retos, número 53, 2024 (abril) 2024, Retos, 53, 333-342 2024, Retos, 53, 333-342
© Copyright: Federación Española de Asociaciones de Docentes de Educación Física (FEADEF) ISSN: Edición impresa: 1579-1726. Edición Web: 1988-2041 (https://recyt.fecyt.es/index.php/retos/index) 18(15),
8028. https://doi.org/10.3390/ijerph18158028 V., Mazzardo, O. y De Campos, W. (2014). Associa-
tion between physical activity and quality of life in the
elderly: a systematic review, 2000-2012. Revista
Brasileira
de
Psiquiatria,
36(1),
76-88. https://doi:10.1590/1516-4446-2012-0895 Warburton, D.E. y Bredin, S.S. (2016). Reflections on
physical activity and health: what should we recom-
mend? Canadian Journal of Cardiology, 32(4), 495-504. https://doi.org/10.1016/j.cjca.2016.01.024 Valdivieso, M.A., Burbano, V.M. y Burbano, A.S. (2020). Datos de los autores: Datos de los autores:
Fernando García del Castillo López
fgarciadelcastillo@ua.es
Autor/a
Juan Tortosa Martínez
Juan.tortosa@ua.es
Autor/a
Irene Ramos Soler
Irene.ramos@ua.es
Autor/a
Jose Antonio García del Castillo Rodríguez
jagr@umh.es
Autor/a
Datos del traductor:
Cruz Alberto Martínez Arcos
cralmarc@gmail.com
Traductor fgarciadelcastillo@ua.es
Autor/a
Juan.tortosa@ua.es
Autor/a
Irene.ramos@ua.es
Autor/a
jagr@umh.es
Autor/a Fernando García del Castillo López
Juan Tortosa Martínez
Irene Ramos Soler
Jose Antonio García del Castillo Rodríguez Retos, número 53, 2024 (abril) human-rights-as-key-to-the-covid-19-response Percepción de estudiantes universitarios colombianos
sobre el efecto del confinamiento por el coronavirus, y
su rendimiento académico. Revista Espacios, 41(42),
269-281. https://doi.org/10.48082/espacios-
a20v41n42p23 Wenham, C., Smith, J., Davies, S.E., Feng, H., Grépin,
K.A., Harman, S., Herten-Crabb, A. y Morgan, R. (2020). Women are most affected by pandemics: Les-
sons from past outbreaks. Nature, 583(7815), 194-198. https://www.nature.com/articles/d41586-020-
02006-z Varela, V., Cancela, J. M., Ayan, C., Martín, V. y Molina,
A. (2012). Lifestyle and health among spanish university
students: differences by gender and academic discipline. International Journal of Environmental Research and Public
Health,
9(8). 2728-
2741. https://doi.10.3390/ijerph9082728 Zamarripa, J., Marroquín-Zepeda, S.D., Ceballos-Gu-
rrola, O., Flores-Allende, G. y Berenice, J. (2021). Ni-
vel de actividad física y conductas sedentarias antes y du-
rante el confinamiento a causa de la COVID-19 en adul-
tos
mexicanos. Retos,
42,
898-905. https://doi.org/10.47197/retos.v42i0.87278 Villanueva-Blasco, V. J., Villanueva Silvestre, V., Isorna,
M., Motos, P., Blay, P. y Vázquez-Martínez, A. (2021). Changes in alcohol consumption pattern based on gen-
der during COVID-19 confinement in Spain. Interna-
tional Journal of Environmental Research and Public Health, Zigmond, A.S. y Snaith, R.P. (1983). The hospital anxiety
and depression scale. Acta Psychiatrica Scandinavica,
67(6), 361-370. https://doi.org/10.1111/j.1600-
0447.1983.tb09716.x Datos de los autores: Datos del traductor: Cruz Alberto Martínez Arcos -342- Retos, número 53, 2024 (abril)
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English
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The Prevalence and Risk Factors for Pneumococcal Colonization of the Nasopharynx among Children in Kilifi District, Kenya
|
PloS one
| 2,012
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cc-by
| 7,007
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Abstract Background: Pneumococcal conjugate vaccines (PCV) reduce nasopharyngeal carriage of vaccine-serotype pneumococci
but increase in the carriage of non-vaccine serotypes. We studied the epidemiology of carriage among children 3–59
months old before vaccine introduction in Kilifi, Kenya. Methods: In a rolling cross-sectional study from October 2006 to December 2008 we approached 3570 healthy children
selected at random from the population register of the Kilifi Health and Demographic Surveillance System and 134 HIV-
infected children registered at a specialist clinic. A single nasopharyngeal swab was transported in STGG and cultured on
gentamicin blood agar. A single colony of pneumococcus was serotyped by Quellung reaction. Results: Families of 2840 children in the population-based sample and 99 in the HIV-infected sample consented to
participate; carriage prevalence was 65.8% (95% CI, 64.0–67.5%) and 76% (95% CI, 66–84%) in the two samples, respectively. Carriage prevalence declined progressively with age from 79% at 6–11 months to 51% at 54–59 months (p,0.0005). Carriage was positively associated with coryza (Odds ratio 2.63, 95%CI 2.12–3.25) and cough (1.55, 95%CI 1.26–1.91) and
negatively associated with recent antibiotic use (0.53 95%CI 0.34–0.81). 53 different serotypes were identified and 42% of
isolates were of serotypes contained in the 10-valent PCV. Common serotypes declined in prevalence with age while less
common serotypes did not. Conclusion: Carriage prevalence in children was high, serotypes were diverse, and the majority of strains were of serotypes
not represented in the 10-valent PCV. Vaccine introduction in Kenya will provide a natural test of virulence for the many
circulating non-vaccine serotypes. ation: Abdullahi O, Karani A, Tigoi CC, Mugo D, Kungu S, et al. (2012) The Prevalence and Risk Factors for Pneumococcal Colonizatio
ong Children in Kilifi District, Kenya. PLoS ONE 7(2): e30787. doi:10.1371/journal.pone.0030787 Editor: Adam J. Ratner, Columbia University, United States of America Editor: Adam J. Ratner, Columbia University, United States of America Editor: Adam J. Ratner, Columbia University, United States of America Received December 22, 2011; Accepted December 29, 2011; Published February 20, 2012 Received December 22, 2011; Accepted December 29, 2011; Published February 20, 2012 Copyright: 2012 Abdullahi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Professor Scott is funded by a research fellowship from the Wellcome Trust (grant 081835). Abstract The KEMRI-Wellcome Trust Research Programme is
supported by core funding from the Wellcome Trust (#092654/Z/10/A). This paper is published with the permission of the Director of the Kenya Medical Research
Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Professor Scott has received grant support from GSK and travel/accommodation support to attend a Merck meeting. Professor Lipsitch
has been paid for consultancy services by Novartis Vaccines & Diagnostics, Pfizer/Wyeth Vaccines, Avian/Pandemic Flu Registry (Outcome Sciences), i3 Innovus
(consulting company that works for pharmas) and AIR (a company developing risk model for pandemic flu). There are no patents, products in development or
marketed products to declare. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials, as detailed online in the
guide for authors. * E-mail: oabdulla@hsph.harvard.edu The Prevalence and Risk Factors for Pneumococcal
Colonization of the Nasopharynx among Children in Kilifi
District, Kenya Osman Abdullahi1,2*, Angela Karani1, Caroline C. Tigoi1, Daisy Mugo1, Stella Kungu1, Eva Wanjiru1,
Jane Jomo1, Robert Musyimi1, Marc Lipsitch2,3, J. Anthony G. Scott1,4 1 Wellcome Trust Research Program, Kenya Medical Research Institute, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya, 2 Department of Immunology and
Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America, 3 Department of Epidemiology, Harvard School of Public Health,
Boston, Massachusetts, United States of America, 4 Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom Pneumococcal Nasopharyngeal Colonization Kenya Pneumococcal Nasopharyngeal Colonization Kenya In 2011, Kenya introduced a 10-valent pneumococcal conju-
gate vaccine (PCV10) into the national childhood immunization
schedule. In Kilifi, prior to vaccine introduction, we established a
system of surveillance for childhood IPD to monitor the impact of
vaccine introduction on disease. To further understand the effect
of vaccine on carriage and transmission we also set up studies to
measure the prevalence, rate of acquisition and the rate of
clearance from the nasopharynx. Here we describe the serotype-
specific prevalence of carriage and the epidemiological risk factors
for prevalent carriage in the pre-vaccine era. pneumococcal growth. Swabs were cultured directly on arrival in
the laboratory. STGG samples were vortexed vigorously for
20 seconds, 10 ml was inoculated onto a blood agar plate
containing 2.5 mcg/ml gentamicin and incubated overnight at
37uC in 5% CO2. Pneumococci were identified by a-hemolysis,
optochin sensitivity and presence of capsule. We serotyped one
colony per plate using Quellung reaction and polyclonal rabbit
antisera (Statens Seruminstitut, Copenhagen, Denmark). Antisera pneumococcal growth. Swabs were cultured directly on arrival in
the laboratory. STGG samples were vortexed vigorously for
20 seconds, 10 ml was inoculated onto a blood agar plate
containing 2.5 mcg/ml gentamicin and incubated overnight at
37uC in 5% CO2. Pneumococci were identified by a-hemolysis,
optochin sensitivity and presence of capsule. We serotyped one
colony per plate using Quellung reaction and polyclonal rabbit
antisera (Statens Seruminstitut, Copenhagen, Denmark). Antisera Table 1. Demographic distribution of the target population
and the study sample. Study design The study was a rolling cross sectional survey conducted over a
period of 26 months and was linked to a study of carriage
clearance [17]. As the objective was to define the characteristics of
carriage at serotype-specific level, we aimed to recruit sufficient
children to observe at least 30 carriers of each serotype that was
responsible for colonizing at least 1% of carriers. Estimating
pneumococcal carriage prevalence in this age group at 75%, the
sample size was 4000 children. Each week we selected a small area
within the KHDSS and applied a random number to each child in
the population register for that area. We then selected the 10% of
children with the highest ranked numbers to study as a population-
based sample. The study moved across contiguous areas to
minimize travel for follow-up swabs [17]. HIV infection is a strong risk factor for IPD and is known to
modulate the epidemiology of carriage. As HIV prevalence among
children in Kilifi is low (,1%), and HIV testing has not been
universally applied across the KHDSS, we selected a group of
HIV-infected children directly from the register of the HIV clinic
at Kilifi District Hospital. At the clinic HIV-infection status was
defined by two rapid tests for HIV antibodies, except for children
,18 months of age, where it was defined by PCR. We approached
families of consecutive children registered at the clinic and resident
in the KHDSS either through home visits or at clinic visits, aiming
to recruit 100 children. Children were excluded from either sample if they were no
longer resident in the KHDSS area, if their parent/guardian
declined consent, or if the child had an illness that prevented us
from taking a nasopharyngeal swab. Study population The study was conducted among children aged 3–59 months
who were registered residents of the Kilifi Health and Demo-
graphic Surveillance System (KHDSS) [16]. This is a longitudinal
surveillance of the population living in a well-defined geographic
area around Kilifi District Hospital (KDH), which is updated
through household visits, monitoring vital events and migration,
every four months. At the planning of the present study (1st July
2006) the KHDSS area had a population of 41,651 aged 3–59
months. Pneumococcal Nasopharyngeal Colonization Kenya Number
selected
Included
in the
study
%
Included
in the
study
x2 p-
value
Sex
Male
2143
1435
67.0
Female
2151
1405
65.3
0.255
Age (months)
3–23
1588
1023
64.4
24–41
1324
886
66.9
42–59
1382
931
67.4
0.184
Location of residence
Banda ra salama
145
99
68.3
Chasimba
275
208
75.6
Gede
168
138
82.1
Jaribuni
71
45
63.4
Junju
470
280
59.6
Kauma
128
102
79.7
Kilifi Township
580
293
50.5
Matsangoni
341
240
70.4
Mtwapa
168
132
78.6
Ngerenya
329
249
75.7
Roka
381
253
66.4
Sokoke
208
136
65.4
Takaungu-Mavueni
380
244
64.2
Tezo
399
245
61.4
Ziani
251
176
70.1
,0.0005
Month of sampling
Jan
308
216
70.1
Feb
409
278
68.0
Mar
392
225
57.4
Apr
347
220
63.4
May
529
278
52.6
Jun
458
283
61.8
Jul
353
271
76.8
Aug
155
118
76.1
Sep
300
178
59.3
Oct
435
326
74.9
Nov
494
337
68.2
Dec
114
110
96.5
,0.0005
Total
4294
2840
66.1
doi:10.1371/journal.pone.0030787.t001 Table 1. Demographic distribution of the target population
and the study sample. PLoS ONE | www.plosone.org Introduction Pneumococcal conjugate vaccines (PCV) have substantially
reduced the incidence of IPD in children in the USA [11] and
have been shown in clinical trials to be effective in African
children, including those infected with HIV [12,13]. In opera-
tional use the effectiveness of these vaccines has been offset by
an increase in the rate of IPD caused by serotypes not included
in the vaccine [14]. In most settings this serotype replace-
ment disease has been small by comparison with the reduction in
disease caused by vaccine serotypes. However, in some popula-
tions, such as Alaska Native children [15], it has been more
substantial. Pneumococcal disease is estimated to cause 826,000 deaths
among young children in developing countries and the majority of
these deaths occur in sub-Saharan Africa [1]. By comparison with
American children, African children have a higher incidence of
invasive pneumococcal disease (IPD) [2], experience disease at an
earlier age [3] and are affected by different serotypes, particularly
types 1 and 5 [4,5]. Nasopharyngeal carriage prevalence in
unvaccinated children is also higher in African ranging from 48%–
90% [6,7,8] compared to 35–52% in the UK/USA [9,10]. PLoS ONE | www.plosone.org February 2012 | Volume 7 | Issue 2 | e30787 1 February 2012 | Volume 7 | Issue 2 | e30787 Pneumococcal Nasopharyngeal Colonization Kenya to differentiate 6C from 6A were not available at the time of this
study. The
Kenya
Medical
Research
Institute/National
Ethical
Review Committee and The Oxford Tropical Research Ethics
Committee approved the study. On behalf of minors/children
participants involved in this study, written informed consent was
obtained from their next of kin, carers or guardians. Analysis The analysis was undertaken in STATA v11.2 (StataCorp,
College Station, TX). To detect bias in the execution of the
sampling methods, we compared the demographic characteristics
of the consenting study participants with the randomly selected
sample of KHDSS using x2. Pneumococcal carriage prevalence
was estimated from the cross-sectional survey and tested against
age and month of study by x2 test for trend. For each population
sample a separate multivariable logistic regression model was
developed
using
backward
stepwise
regression,
sequentially
excluding variables with p.0.05 on likelihood ratio test. Laboratory methods The study followed the guidelines of the WHO working group
on nasopharyngeal studies of Streptococcus pneumoniae [18]. Naso-
pharyngeal specimens were sampled using Dacron-tipped flexible
wire swabs passed via the anterior nares to the posterior
nasopharynx. The swab tips were immersed in skim-milk tryptone
glucose glycerol (STGG) transport medium, separated from its
handle with wire cutters and transported at ambient temperature
to the laboratory. Internal quality control of STGG was conducted
to assure sterility and the ability of the medium to support 2 Pneumococcal Nasopharyngeal Colonization Kenya The only prior use of pneumococcal
conjugate vaccine (7-valent PCV) in the KHDSS area was a study
of 300 children vaccinated as infants [19]; 14 of these were
recruited to the present study at ages varying between 4–34
months. inability of the study to sample children out of hours. Of the 3570
families located and invited to participate, 2840 (80%) consented
to the enrolment of their child into the study. Children who were
recruited to the study differed from those who were originally
selected on the month of sampling and location of residence but
not on age or sex (Table 1). The only prior use of pneumococcal
conjugate vaccine (7-valent PCV) in the KHDSS area was a study
of 300 children vaccinated as infants [19]; 14 of these were
recruited to the present study at ages varying between 4–34
months. y (
g
)
In the HIV-infected sample, 75 (76%, 95%CI 66–84%) of the
99 swab cultures were positive for pneumococcus. Carriage
prevalence did not vary significantly by sex, age, month of
sampling or anti-retroviral treatment (p.0.2 for all, Table 2). By
comparison with the population-based sample, the colonization
prevalence in the HIV-infected group was higher (65.8% vs. 76%, Table 3. Risk factors for prevalent nasopharyngeal carriage of S. pneumoniae. Table 3. Risk factors for prevalent nasopharyngeal carriage of S. pneumoniae. Risk factor
Sample
Carriers
OR
95% CI
aOR
95% CI
Male sex
1435
934
0.94
0.81–1.10
Cough in the last 2 weeks? 1420
1079
2.53
2.15–2.96
1.55
1.26–1.91
Coryza in the last 2 weeks? 1684
1286
3.18
2.71–3.73
2.62
2.12–3.34
Child taken antibiotics in the last 2 weeks? 111
67
0.78
0.53–1.16
0.53
0.34–0.81
Child taken Fansidar in the last 2 weeks? 30
17
0.68
0.33–1.40
Child hospitalized in the last month? 8
5
0.87
0.21–3.63
Child sleeps in the cooking room? 496
344
1.22
0.99–1.50
Cooking fuel
firewood
2761
1814
1.00
gas
10
8
2.09
0.44–9.85
charcoal
60
41
1.13
0.65–1.95
paraffin
9
5
0.65
0.17–2.44
Smoker in the house
517
368
1.36
1.10–1.67
Household member hospitalized in last month
18
12
1.04
0.39–2.78
Study time
(per month)
1.00
0.99–1.01
0.98
0.96–0.99
No. of other children (aged 0–2 y) in the house
(per child)
0.82
0.71–0.95
No. of other children (aged 3–4 y) in the house
(per child)
1.11
0.97–1.28
No. of other children (aged5–9 y) in the house
(per child)
1.05
0.97–1.14
No. Pneumococcal Nasopharyngeal Colonization Kenya Table 2. Carriage prevalence by age, sex and antiretroviral
drug use among HIV-infected children. Variable
Sample Carriers
Prevalence
(%)
95% CI x2 p value
Sex
Male
68
50
74
61–83
Female
31
25
81
63–93
0.44
Age (m)
3–23
33
22
66
48–82
24–41
31
24
77
59–90
42–59
35
29
83
66–93
0.29
Antiretroviral therapy
Yes
40
31
75
62–85
No
59
44
78
62–89
0.74
doi:10.1371/journal.pone.0030787.t002 Children were recruited to the HIV-infected sample between
January 14, 2008 and July 21, 2008. Of 134 parents/guardians
approached, 99 (74%) consented for their children to participate. There were no differences between those who did and did not
consent with respect to age, sex, location or month of sampling (all
p.0.05). The HIV-infected sample did not differ from the
population-based sample on age in years (p = 0.58) but did differ
on sex; the proportion of males was 50.5% (1435/2840) in the
population-based sample and 69% (69/99) in the HIV-infected
sample (p,0.0005). None of the HIV-infected children had
previously received PCV. p
y
Overall, 1868 (65.8%, 95%CI 64.0–67.5%) of the 2840
nasopharyngeal swab cultures from the population-based sample
were positive for Streptococcus pneumoniae. Carriage prevalence
declined markedly with age (x2 test for trend 70.9, p,0.0005)
although it was lower in children aged 3–5 months than those aged
6–11 months (Figure 1, Table S2). Carriage prevalence did not
vary by sex (p = 0.44, Table S2) but did vary by administrative
location across the KHDSS, from 49% to 79% (x2 (14) 84.0,
p,0.0005, Table S2), and by month of sampling, from 51% in
January to 83% in July (x2 (11) 113.7, p,0.005, Figure 1). The
monthly prevalence of carriage was not associated with total
monthly rainfall, nor with monthly medians of daily measurements
of relative humidity, minimum and maximum daily temperature
taken in Kilifi across the 26 months of the study (Figure S1). doi:10.1371/journal.pone.0030787.t002 inability of the study to sample children out of hours. Of the 3570
families located and invited to participate, 2840 (80%) consented
to the enrolment of their child into the study. Children who were
recruited to the study differed from those who were originally
selected on the month of sampling and location of residence but
not on age or sex (Table 1). Results The cross-sectional survey of the population-based sample
began October 23, 2006 and ended December 2, 2008. We
selected 4,294 children at random from the KHDSS population
register and were able to find 3570 (83%) at home. The main
reasons for failing to identify children were the high out-migration
rate in the KHDSS [16], seasonal migration for farming, and the Figure 1. Prevalence (and 95% CI) of nasopharyngeal carriage in children in Kilifi by age and by calendar month within the survey. doi:10.1371/journal.pone.0030787.g001 Figure 1. Prevalence (and 95% CI) of nasopharyngeal carriage in children in Kilifi by age a
doi:10.1371/journal.pone.0030787.g001
PLoS ONE | www.plosone.org
3
F Figure 1. Prevalence (and 95% CI) of nasopharyngeal carriage in children in Kilifi by age and by calendar month within the survey. doi:10.1371/journal.pone.0030787.g001 PLoS ONE | www.plosone.org February 2012 | Volume 7 | Issue 2 | e30787 PLoS ONE | www.plosone.org 3 OR Odds Ratio; aOR adjusted Odds Ratio. Variables included in the final model but not displayed here are age (6 monthly strata), month of sampling and fieldworker
taking the sample (n = 9). The full analysis is displayed in Table S2. The final model fit was tested using Hosmer-Lemeshow x2 in 10 covariate strata (p = 0.95).
doi:10 1371/journal pone 0030787 t003 Pneumococcal Nasopharyngeal Colonization Kenya After accounting for age, month of sampling, and
restricting the analysis to the period when survey of both samples
was concurrent, the odds of colonization were significantly higher
in the HIV-infected sample (OR 2.21, 95% CI 1.35–3.61). Table 4. Serotype carriage prevalence among population-based
and HIV-infected samples. Table 4. Serotype carriage prevalence among population-based
and HIV-infected samples. Population-based sample
HIV-infected sample
Serotype
N
Prevalence (%)
N
Prevalence (%)
19F
283
10.0
14
14
6A
237
8.3
13
13
6B
184
6.5
5
5
23F
117
4.1
9
9
11A
90
3.2
1
1
14
85
3.0
1
1
35B
84
3.0
2
2
23B
70
2.5
1
1
10A
56
2.0
0
0
15B
54
1.9
3
3
19A
53
1.9
1
1
9V
51
1.8
3
3
13
49
1.7
3
3
15A
49
1.7
2
2
15C
43
1.5
2
2
34
38
1.3
0
0
3
34
1.2
4
4
16F
34
1.2
0
0
18C
29
1.0
0
0
19B
25
0.9
2
2
7C
23
0.8
1
1
20
21
0.7
3
3
23A
19
0.7
1
1
21
18
0.6
0
0
35A
15
0.5
0
0
1
13
0.5
0
0
33B
13
0.5
0
0
4
12
0.4
0
0
Other types
69
2.4
4
4
All types
1,868
65.8
75
76
There is no evidence of a difference between the HIV-infected and population-
based samples in the distribution of serotypes (x2 (28) 33.4, p = 0.223). doi:10.1371/journal.pone.0030787.t004 Risk factors that were positively associated with nasopharyngeal
carriage of S. pneumoniae were a history of coryza or cough in the
previous two weeks; children who reported taking antibiotics in the
previous two weeks had lower odds of carriage (Table 3, Table S1). There were no significant interactions between variables in the
final model. The Hosmer-Lemeshow x2 test was non-significant (df
8, p = 0.95) suggesting a good fit of the model to the data. None of
the risk factors were associated with carriage in the HIV-infected
sample. Although the prevalence of carriage varied from month to
month we did not find any evidence of a trend in prevalence over
time in univariate analyses (x2 test for trend by month p = 0.71). However, in the multivariable analysis of carriage, after adjusting
for potential confounders, we observed a 2% decline in carriage
per month of observation (Table 3). Pneumococcal Nasopharyngeal Colonization Kenya Among the population-based sample, we isolated a total of 53
different serotypes from all the swab cultures. The carriage
prevalence of individual serotypes ranged from 10% to 0.03%
(Table 4, Table S2). Among HIV-infected children, we isolated a
total of 23 different serotypes and carriage prevalence of any one
serotype ranged from 14% to 1%. The distribution of serotypes in
the population-based sample and the HIV-infected sample did not
differ (x2 (28) = 33.4, p = 0.22). The ten most common serotypes in
the population-based sample comprised 67.5% of all isolates; in
the
HIV-infected
sample
they
comprised
79%
(p = 0.044)
suggesting that common serotypes dominate more effectively in
HIV-infected children. Variation in serotype prevalence by age is difficult to interpret
because of the large number of strata, in this case 53 serotypes. Confining the analysis to the 20 most frequently observed
serotypes, and collapsing all other types to ‘other’, an association
with age in years was observed (x2 (80) = 109, p = 0.017). We
investigated how changes in serotype distributions with age are
related to the overall prevalence of a serotype. We categorized the
most highly prevalent 20 serotypes into 4 strata of 5 serotypes
based on their prevalence ranking in the whole population-based
survey; all remaining serotypes were categorized as ‘other’. The
distribution of the prevalence of these strata against age in years is
highly significant (x2 (20) 106, p,0.0005, Figure 2). It illustrates a
fall in the prevalence of common serotypes against age that is not
matched by the mixture of less common serotypes. There is no evidence of a difference between the HIV-infected and population-
based samples in the distribution of serotypes (x2 (28) 33.4, p = 0.223). doi:10.1371/journal.pone.0030787.t004 There is no evidence of a difference between the HIV-infected and population-
based samples in the distribution of serotypes (x2 (28) 33.4, p = 0.223). doi:10.1371/journal.pone.0030787.t004 The original formulation of PCV contained antigens for seven
serotypes, 4, 6B, 9V, 14, 18C, 19F and 23F (PCV7). The present
vaccines have extended this formulation to include serotypes
1, 5 and 7F (PCV10) and then, in addition, 3, 6A and 19A
(PCV13). In the population-based sample, the proportions of all
colonizing isolates that were of serotypes represented in PCV7,
PCV10 and PCV13 were 41% (95% CI 38–43%), 42% (39–44%)
and 59% (57–61%), respectively. In the HIV-infected sample they
were 43% (31–55%), 43% (31–55%) and 67% (55–77%),
respectively. Pneumococcal Nasopharyngeal Colonization Kenya though this was inherently linked to season by the rolling cross-
sectional design of the study. We observed 53 different serotypes,
in a well-defined human population of 250 000, maintained at
widely different frequencies - a degree of diversity also observed in
a similar study in The Gambia [21]. Forty-three of these serotypes,
accounting for 58% of all the isolates carried, are not included in
the 10-valent PCV which was introduced into the Kenyan
immunization schedule in 2011. Our estimate of pneumococcal carriage prevalence (66%)
among children aged 3–59 months is similar to prevalence
estimates among children aged ,5 years in Pakistan (62%) [22]
and Uganda (62%) [23] but lower than the prevalence in
Mozambique (87%) [5], The Gambia (.90%) [24] and Malawi
(84%) [25]. Each of these studies sampled sick children presenting
to hospital. Estimates of carriage prevalence among healthy
children were much lower, at 22% in Kenya, [26] and 48% in
Malawi, [8] but even in these studies the children were selected Pneumococcal Nasopharyngeal Colonization Kenya of other children (aged 10–14 y) in the house
(per child)
1.01
0.95–1.07
No. of children (aged #5 y) sharing a bed with child
(per child)
0.95
0.84–1.07
OR Odds Ratio; aOR adjusted Odds Ratio. Variables included in the final model but not displayed here are age (6 monthly strata), month of sampling and fieldworker
taking the sample (n = 9). The full analysis is displayed in Table S2. The final model fit was tested using Hosmer-Lemeshow x2 in 10 covariate strata (p = 0.95). doi:10.1371/journal.pone.0030787.t003 OR Odds Ratio; aOR adjusted Odds Ratio. Variables included in the final model but not displayed here are age (6 monthly strata), month of sampling and fieldworker
taking the sample (n = 9). The full analysis is displayed in Table S2. The final model fit was tested using Hosmer-Lemeshow x2 in 10 covariate strata (p = 0.95). doi:10.1371/journal.pone.0030787.t003 February 2012 | Volume 7 | Issue 2 | e30787 PLoS ONE | www.plosone.org 4 Pneumococcal Nasopharyngeal Colonization Kenya Table 4. Serotype carriage prevalence among population-based
and HIV-infected samples. Population-based sample
HIV-infected sample
Serotype
N
Prevalence (%)
N
Prevalence (%)
19F
283
10.0
14
14
6A
237
8.3
13
13
6B
184
6.5
5
5
23F
117
4.1
9
9
11A
90
3.2
1
1
14
85
3.0
1
1
35B
84
3.0
2
2
23B
70
2.5
1
1
10A
56
2.0
0
0
15B
54
1.9
3
3
19A
53
1.9
1
1
9V
51
1.8
3
3
13
49
1.7
3
3
15A
49
1.7
2
2
15C
43
1.5
2
2
34
38
1.3
0
0
3
34
1.2
4
4
16F
34
1.2
0
0
18C
29
1.0
0
0
19B
25
0.9
2
2
7C
23
0.8
1
1
20
21
0.7
3
3
23A
19
0.7
1
1
21
18
0.6
0
0
35A
15
0.5
0
0
1
13
0.5
0
0
33B
13
0.5
0
0
4
12
0.4
0
0
Other types
69
2.4
4
4
All types
1,868
65.8
75
76
There is no evidence of a difference between the HIV-infected and population-
based samples in the distribution of serotypes (x2 (28) 33.4, p = 0.223). doi:10.1371/journal.pone.0030787.t004 p = 0.04). PLoS ONE | www.plosone.org Discussion The prevalence of pneumococcal carriage in children in Kilifi is
high – despite the insensitivity of sampling and laboratory
detection methods [20], two-thirds of all children aged 3–59
months were found to be carriers. Carriage prevalence decreased
steadily with age and varied significantly by season and HIV-
infection. Carriage prevalence also varied by residential location PLoS ONE | www.plosone.org February 2012 | Volume 7 | Issue 2 | e30787 February 2012 | Volume 7 | Issue 2 | e30787 5 Pneumococcal Nasopharyngeal Colonization Kenya Figure 2. Prevalence of carriage of common and less common pneumococcal serotypes by age. doi:10.1371/journal.pone.0030787.g002 Figure 2. Prevalence of carriage of common and less common pneumococcal serotypes by age. doi:10.1371/journal.pone.0030787.g002 CD4+ Th17 cells, where the action of immune clearance occurs
after a lag interval [31]. because they attended a health facility. More recently, in a study of
villages in The Gambia the prevalence was estimated at over 90%
[27]. The higher prevalence of carriage among healthy children in
The Gambia may be a function of the different climates, sampling
in different seasons, or of differing social organization; life in The
Gambia is based around villages while, in Kilifi, the population
live in more widely dispersed patterns. A history of upper respiratory tract infection (URTI) symptoms,
cough or coryza, during the two weeks prior to nasopharyngeal
sampling was strongly associated with carriage in this study as in
several previous studies [6,32,33]. Unfortunately the cross-
sectional study design does not allow us to differentiate between
several explanations, which include: (1) that coryza physically
enhances the trapping, adherence and growth of pneumococci in
the nasopharynx; (2) that coryza may augment the sensitivity of
swab sampling of the nasopharynx; (3) that pneumococcal
colonization leads directly to the symptoms of an URTI; or (4)
that viral URTIs and pneumococcal carriage are both indepen-
dently associated with seasonal factors, such as cold weather and
crowding, leading to a false association. A key determinant of the prevalence of pneumococcal carriage
in children is age. In our study carriage prevalence reached a peak
of 79% in the children aged 6–11 months and then declined
steadily to 51% among those aged 54–59 months. The rise
between 3–5 and 6–11 months is probably attributable to
cumulative exposure since birth. The subsequent decline in
prevalence is attributable to an age-related increase in clearance
rates. PLoS ONE | www.plosone.org Discussion In the accompanying study [17] we observed a constant rate
of acquisition from 3–59 months of age but a progressive increase
in clearance rates, reducing the mean duration of a colonization
episode from 45 days to 21 days. We have also shown here that the
prevalence of more commonly encountered serotypes declined
markedly with age but the prevalence of less common serotypes
did not. This observation is compatible with acquired serotype-
specific immunity, developed on the basis of prior exposure
[28,29], although to date the impact of serotype-specific immunity
has been documented only for a few serotypes, and only in
reducing acquisition, rather than shortening duration [28,29,30]. As the most common serotypes are also those with the longest
durations, the same epidemiological pattern would also be
predicted by species-specific immunity, such as that mediated by In Kenya, carriage prevalence has been observed to be higher
among HIV-infected than among HIV-uninfected adults [34];
elsewhere pediatric serotypes (e.g. 6B, 14) have been observed
more frequently in HIV-infected adults than HIV-uninfected
adults [35]. Our ability to investigate these associations in children
was constrained by the low prevalence of HIV-infection in Kilifi. HIV-infection is identified in 4–5% of antenatal mothers in Kilifi
[36] but there is an effective program of prevention of mother-to-
child transmission. Therefore, we recruited a separate sample of
children, selected on the basis of known HIV-infection, and did
not test our population-based sample for HIV. Although the
samples were derived from different sources, and there is a small
degree of misclassification in one, the study should be sensitive to PLoS ONE | www.plosone.org February 2012 | Volume 7 | Issue 2 | e30787 February 2012 | Volume 7 | Issue 2 | e30787 6 Pneumococcal Nasopharyngeal Colonization Kenya large variations in epidemiology. We found HIV-infected children
had a two-fold higher odds of carriage than the unselected
population but we did not observe any difference in the serotype
distribution of colonization with HIV prevalence. pneumococcal disease in Africa [4,12] but they are carried by less
than 1% of children in this study. Beyond the PCV10 serotypes we
detected
pneumococcal
strains
from
43
different
serotypes
accounting for 58% of all prevalent carriage episodes. Operational
use of conjugate pneumococcal vaccines in Kenya, justified by
strong evidence of efficacy against invasive pneumococcal disease
[12,13], will provide an interesting natural test of the invasive
potential of the many non-vaccine serotypes circulating in this
population. References 1. O’Brien KL, Wolfson LJ, Watt JP, Henkle E, Deloria-Knoll M, et al. (2009)
Burden of disease caused by Streptococcus pneumoniae in children younger than 5
years: global estimates. Lancet 374: 893–902. 11. MMWR (2008) Invasive pneumococcal disease in children 5 years after
conjugate vaccine introduction–eight states, 1998–2005. MMWR Morb Mortal
Wkly Rep 57: 144–148. 2. Berkley JA, Lowe BS, Mwangi I, Williams T, Bauni E, et al. (2005) Bacteremia
among children admitted to a rural hospital in Kenya. N Engl J Med 352:
39–47. 12. Cutts FT, Zaman SMA, Enwere G, Jaffar S, Levine OS, et al. (2005) Efficacy of
nine-valent pneumococcal conjugate vaccine against pneumonia and invasive
pneumococcal disease in The Gambia: randomised, double-blind, placebo-
controlled trial. Lancet 365: 1139–1146. 3. O’Dempsey TJ, McArdle TF, Lloyd-Evans N, Baldeh I, Lawrence BE, et al. (1996) Pneumococcal disease among children in a rural area of West Africa. Pediatr Infect Dis J 15: 431–437. 13. Klugman KP, Madhi SA, Huebner RE, Kohberger R, Mbelle N, et al. (2003) A
trial of a 9-valent pneumococcal conjugate vaccine in children with and those
without HIV infection. N Engl J Med 349: 1341–1348. 4. Campbell JD, Kotloff KL, Sow SO, Tapia M, Keita MM, et al. (2004) Invasive
pneumococcal infections among hospitalized children in Bamako, Mali. Pediatr
Infect Dis J 23: 642–649. 14. World Health Organization (2010) Changing epidemiology of pneumococcal
serotypes after introduction of conjugate vaccine: July 2010 report. Wkly
Epidemiol Rec 85: 434–436. 5. Valles X, Flannery B, Roca A, Mandomando I, Sigauque B, et al. (2006)
Serotype distribution and antibiotic susceptibility of invasive and nasopharyngeal
isolates of Streptococcus pneumoniae among children in rural Mozambique. Trop
Med Int Health 11: 358–366. 15. Singleton RJ, Hennessy TW, Bulkow LR, Hammitt LL, Zulz T, et al. (2007)
Invasive pneumococcal disease caused by nonvaccine serotypes among alaska
native children with high levels of 7-valent pneumococcal conjugate vaccine
coverage. JAMA 297: 1784–1792. 6. Abdullahi O, Nyiro J, Lewa P, Slack M, Scott JAG (2008) The descriptive
epidemiology of Streptococcus pneumoniae and Haemophilus influenzae nasopharyngeal
carriage in children and adults in Kilifi district, Kenya. Pediatr Infect Dis J 27:
59–64. g
J
16. Scott JA, Bauni E, Moisi J, Ojal J, Nyaga V, et al. (2011) Cohort Profile: The
Kilifi Health and Demographic Surveillance System. Submitted (Int J
Epidemiol). 7. Hill PC, Cheung YB, Akisanya A, Sankareh K, Lahai G, et al. Acknowledgments We thank the families of Kilifi District who took part in the study and the
tremendous work of the field staff. This paper is published with the
permission of the Director of the Kenya Medical Research Institute. Discussion Because of the inherent difficulties and cost of detecting multiple
serotype carriage in the laboratory and the large scale of this field
study, we limited our investigation to studying a single serotype per
swab. This decision has a consequence in estimating the
prevalence. Assuming that, in multiply colonized individuals, the
probability of sampling a strain (by physical swabbing and by
selection of a colony from a culture plate) is proportional to the
frequency of that serotype type in that nasopharynx then the study
is effectively a random sample of strains from a random sample of
human hosts. This will provide an accurate estimate of the relative
prevalence of different serotypes, at an ecological level, but will
underestimate the absolute prevalence of colonization by each
serotype in the population. (PDF) Table S2
Serotype carriage prevalence in population-
based and HIV-infected samples. (PDF) Table S2
Serotype carriage prevalence in population-
based and HIV-infected samples. (PDF) Author Contributions Conceived and designed the experiments: OA JAGS. Performed the
experiments: AK CT DM SK EW JJ RM OA. Analyzed the data: OA
JAGS ML. Wrote the paper: OA JAGS ML. Conceived and designed the experiments: OA JAGS. Performed the
experiments: AK CT DM SK EW JJ RM OA. Analyzed the data: OA
JAGS ML. Wrote the paper: OA JAGS ML. Kenya introduced PCV10 into the routine childhood immuni-
zation program in 2011. The three additional serotypes in this
formulation, 1, 5 and 7F, are important causes of invasive Supporting Information Figure S1
Correlation of monthly pneumococcal car-
riage prevalence with monthly estimates of meteorolog-
ical variables. (PDF) Table S1
Prevalence of carriage by risk factor, with
univariate odds ratios (and 95% CIs) and adjusted odds
ratios (and 95% CIs) in a multivariable logistic regres-
sion model. A current question of public health interest is whether the
benefits of introducing PCV7 into routine childhood immuniza-
tion programs in developing countries will be undermined by an
increase in the incidence of non-vaccine serotype disease. The
potential for ‘serotype replacement disease’ is determined by the
circulation of non-vaccine serotypes and the propensity of those
serotypes
to
cause
disease
once
they
have
colonized
the
nasopharynx [37]. In Kilifi, 59% of carriers harbor serotypes that
are not included in the 7-valent vaccine and this appears to be
consistent over time in this area [6] and across the continent. Similar figures for The Gambia, Mozambique, Malawi and South
Africa are in the range 51–64% [5,7,25,38]. The invasive potential
of these serotypes has not been evaluated in a developing country
but serotypes that have been found to increase invasive disease in
developed countries, e.g. 3, 7F, 15B/C, 19A, 22F, 33F and 38
[39,40,41,42,43,44] are currently carried by 7% of all children in
Kilifi. Pneumococcal Nasopharyngeal Colonization Kenya Pneumococcal Nasopharyngeal Colonization Kenya 20. Abdullahi O, Wanjiru E, Musyimi R, Glass N, Scott JAG (2007) Validation of
nasopharyngeal sampling and culture techniques for detection of Streptococcus
pneumoniae in children in Kenya. J Clin Microbiol 45: 3408–3410. 33. Straker E, Hill AB, Lovell R A study of the nasopharyngeal bacterial flora of
different groups of persons observed in London and south-east England during
the years 1930 to 1937. y
34. Paul J (1997) Royal Society of Tropical Medicine and Hygiene Meeting at
Manson House, London, 12 December 1996. HIV and pneumococcal infection
in Africa. Microbiological aspects. Trans R Soc Trop Med Hyg 91: 632–637. 21. Hill PC, Townend J, Antonio M, Akisanya B, Ebruke C, et al. (2010)
Transmission of Streptococcus pneumoniae in rural Gambian villages: a longitudinal
study. Clin Infect Dis 50: 1468–1476. 35. Nicoletti C, Brandileone MCC, Guerra MLS, Levin AS (2007) Prevalence,
serotypes, and risk factors for pneumococcal carriage among HIV-infected
adults. Diagn Microbiol Infect Dis 57: 259–265. 22. Mastro TD, Nomani NK, Ishaq Z, Ghafoor A, Shaukat NF, et al. (1993) Use of
nasopharyngeal isolates of Streptococcus pneumoniae and Haemophilus influenzae from
children in Pakistan for surveillance for antimicrobial resistance. Pediatr Infect
Dis J 12: 824–830. g
36. Scott JA, Berkley JA, Mwangi I, Ochola L, Uyoga S, et al. (2011) Relation
between falciparum malaria and bacteraemia in Kenyan children: a population-
based, case-control study and a longitudinal study. Lancet epub. 23. Joloba ML, Bajaksouzian S, Palavecino E, Whalen C, Jacobs MR (2001) High
prevalence of carriage of antibiotic-resistant Streptococcus pneumoniae in children in
Kampala Uganda. Int J Antimicrob Agents 17: 395–400. 37. Sleeman KL, Griffiths D, Shackley F, Diggle L, Gupta S, et al. (2006) Capsular
Serotype-Specific Attack Rates and Duration of Carriage of Streptococcus
pneumoniae in a Population of Children. J Infect Dis 194: 682–688. 24. Lloyd-Evans N, O’Dempsey TJ, Baldeh I, Secka O, Demba E, et al. (1996)
Nasopharyngeal carriage of pneumococci in Gambian children and in their
families. Pediatr Infect Dis J 15: 866–871. 38. Mbelle N, Huebner RE, Wasas AD, Kimura A, Chang I, et al. (1999)
Immunogenicity and impact on nasopharyngeal carriage of a nonavalent
pneumococcal conjugate vaccine. J Infect Dis 180: 1171–1176. 25. Feikin DR, Davis M, Nwanyanwu OC, Kazembe PN, Barat LM, et al. (2003)
Antibiotic resistance and serotype distribution of Streptococcus pneumoniae
colonizing rural Malawian children. Pediatr Infect Dis J 22: 564–567. 39. Pneumococcal Nasopharyngeal Colonization Kenya Beall B, McEllistrem MC, Gertz REJ, Wedel S, Boxrud DJ, et al. (2006) Pre-
and postvaccination clonal compositions of invasive pneumococcal serotypes for
isolates collected in the United States in 1999, 2001, and 2002. J Clin Microbiol
44: 999–1017. 26. Rusen ID, Fraser-Roberts L, Slaney L, Ombette J, Lovgren M, et al. (1997)
Nasopharyngeal pneumococcal colonization among Kenyan children: antibiotic
resistance, strain types and associations with human immunodeficiency virus
type 1 infection. Pediatr Infect Dis J 16: 656–662. 40. Byington CL, Samore MH, Stoddard GJ, Barlow S, Daly J, et al. (2005)
Temporal trends of invasive disease due to Streptococcus pneumoniae among
children in the intermountain west: emergence of nonvaccine serogroups.. Clin
Infect Dis 41: 21–29. 27. Hill PC, Akisanya A, Sankareh K, Cheung YB, Saaka M, et al. (2006)
Nasopharyngeal carriage of Streptococcus pneumoniae in Gambian villagers. Clin
Infect Dis 43: 673–679. 41. Gonzalez BE, Hulten KG, Lamberth L, Kaplan SL, Mason EOJ (2006)
Streptococcus pneumoniae serogroups 15 and 33: an increasing cause of
pneumococcal infections in children in the United States after the introduction
of the pneumococcal 7-valent conjugate vaccine. Pediatr Infect Dis J 25:
301–305. 28. Goldblatt D, Hussain M, Andrews N, Ashton L, Virta C, et al. (2005) Antibody
responses to nasopharyngeal carriage of Streptococcus pneumoniae in adults: a
longitudinal household study. J Infect Dis 192: 387–393. 29. Weinberger DM, Dagan R, Givon-Lavi N, Regev-Yochay G, Malley R, et al. (2008) Epidemiologic evidence for serotype-specific acquired immunity to
pneumococcal carriage. J Infect Dis 197: 1511–1518. 42. Kaplan SL, Mason EOJ, Wald ER, Schutze GE, Bradley JS, et al. (2004)
Decrease of invasive pneumococcal infections in children among 8 children’s
hospitals in the United States after the introduction of the 7-valent
pneumococcal conjugate vaccine. Pediatrics 113: 443–449. 30. McCool TL, Weiser JN (2004) Limited role of antibody in clearance of
Streptococcus pneumoniae in a murine model of colonization. Infect Immun 72:
5807–5813. p
j g
43. Miller E, Andrews N, Waight P, Slack M, George R (2011) Herd immunity and
serotype replacement 4 years after seven-valent pneumococcal conjugate
vaccination in England and Wales: an observational cohort study. Lancet Infect
Dis 11: 760–768. 31. Lipsitch M, Abdullahi O, D’Amour A, Xie W, Weinberger D, et al. (2011) Rates
of carriage acquisition and clearance and competitive ability for pneumococcal
serotypes in Kilifi District, Kenya: Application of a Markov transition model
Submitted (Epidemiology). 44. References (2008)
Nasopharyngeal carriage of Streptococcus pneumoniae in Gambian infants: a
longitudinal study. Clin Infect Dis 46: 807–814. 17. Abdullahi O, Karani A, Mugo D, Kung’u S, Wanjiru E, et al. (2011) The
rates of acquisition and clearance of pneumococcal serotypes in the nasopha-
rynges of children in Kilifi District, Kenya. Submitted (Clinical Infectious
Diseases). 8. Yomo A, Subramanyam VR, Fudzulani R, Kamanga H, Graham SM, et al. (1997) Carriage of penicillin-resistant pneumococci in Malawian children. Ann
Trop Paediatr 17: 239–243. 18. O’Brien KL, Nohynek H, The WHO Pneumococcal Vaccine Trials Carriage
Working Group (2003) Report from a WHO working group: standard method
for detecting upper respiratory carriage of Streptococcus pneumoniae. Pediatr Infect
Dis J 22: 133–140. p
9. Hendley JO, Sande MA, Stewart PM, Gwaltney JMJ (1975) Spread of
Streptococcus pneumoniae in families. I. Carriage rates and distribution of types. J Infect Dis 132: 55–61. 19. Scott JAG, Ojal J, Ashton L, Muhoro A, Burbidge P, et al. (2011) Pneumococcal
conjugate vaccine given shortly after birth stimulates effective antibody
concentrations and primes immunological memory for sustained infant
protection. Clin Infect Dis 53: 663–670. 10. Hussain M, Melegaro A, Pebody RG, George R, Edmunds WJ, et al. (2005) A
longitudinal household study of Streptococcus pneumoniae nasopharyngeal carriage
in a UK setting. Epidemiol Infect 133: 891–898. PLoS ONE | www.plosone.org 7 February 2012 | Volume 7 | Issue 2 | e30787 February 2012 | Volume 7 | Issue 2 | e30787 PLoS ONE | www.plosone.org Pneumococcal Nasopharyngeal Colonization Kenya Steenhoff AP, Shah SS, Ratner AJ, Patil SM, McGowan KL (2006) Emergence
of vaccine-related pneumococcal serotypes as a cause of bacteremia. Clin Infect
Dis 42: 907–914. 32. Smillie WG, Caldwell EL (1929) A study of pneumonia in a rural area in
Southern Alabama. J Exp Med 50: 233–244. PLoS ONE | www.plosone.org February 2012 | Volume 7 | Issue 2 | e30787 8
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Efeito de diferentes sistemas de pastejo em atributos físicos do solo
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PUBVET, Publicações em Medicina Veterinária e Zootecnia.
Efeito de diferentes sistemas de pastejo em atributos físicos do
solo1
Karina Ferro Cervelati2, Eurico Lucas de Sousa Neto3, Edson Sadayuki
Eguchi4, Mérik Rocha Silva4 e Maria Aparecida Pereira Pierangeli4
1 Trabalho de Conclusão de Curso do Primeiro Autor.
2 Autora, Zootecnista – UNEMAT, kacervelati@hotmail.com.
3 Professor Orientador, euricolucas@yahoo.com.br.
4 Colaboradores,
edeguchi@yahoo.com, mapp@unemat.br, merikrocha@hotmail.com.
Resumo
Em vista de que é importante a interação solo-clima-planta-animal para PUBVET, Publicações em Medicina Veterinária e Zootecnia. PUBVET, Publicações em Medicina Veterinária e Zootecnia. edeguchi@yahoo.com, mapp@unemat.br, merikrocha@hotmail.com. CERVELATI, K.F. et al. Efeito de diferentes sistemas de pastejo em atributos físicos do
solo. PUBVET, Londrina, V. 5, N. 22, Ed. 169, Art. 1142, 2011. CERVELATI, K.F. et al. Efeito de diferentes sistemas de pastejo em atributos físicos do
solo. PUBVET, Londrina, V. 5, N. 22, Ed. 169, Art. 1142, 2011. CERVELATI, K.F. et al. Efeito de diferentes sistemas de pastejo em atributos físicos do
solo. PUBVET, Londrina, V. 5, N. 22, Ed. 169, Art. 1142, 2011. Resumo Em vista de que é importante a interação solo-clima-planta-animal para
se alcançar boas produtividades nos sistemas de produção, o objetivo
deste estudo foi avaliar as alterações nos atributos físicos do solo
provocado por sistemas de pastejo contínuo e rotacionado. Os sistemas de
uso foram: convencional (CC): Brachiaria brizantha cv. BRS Piatã, sem
adubação anual de reposição, manejado em sistema de lotação contínua;
adubado (AD): Brachiaria brizantha cv. BRS Piatã manejado em sistema
de lotação rotacionado, com a adubação anual de reposição com N-P-K na
proporção de 45-20-20 kg ha-1 ano-1; e consorciado (CS): consórcio de
Brachiaria brizantha cv. BRS Piatã e Stylosanthes Campo Grande,
manejados em sistema de lotação rotacionado, recebendo adubação anual
de reposição com N-P-K de 00-20-20 kg ha-1 ano-1. Para avaliar o efeito do pisoteio animal nos sistemas foram coletados anéis com amostras de
solo com estrutura indeformada nas camadas de 0,00 - 0,06 m e 0,06 -
0,12 m antes e após o pastejo para as determinações de densidade do
solo pelo método do anel volumétrico, macroporosidade, microporosidade
e porosidade total, pelo método da mesa de tensão, foram coletadas
também amostras com estrutura deformada na mesma camada para a
determinação do teor de matéria orgânica. A resistência do solo à
penetração foi determinada antes e após o pastejo nas profundidades de
0,0 -0,1, 0,1 - 0,2, 0,2 - 0,3 e 0,3 - 0,4 m, com o penetrômetro de
impacto. O pisoteio animal alterou somente a microporosidade; a
utilização de diferentes sistemas de cultivo e pastejo não promoveram
diferenças em relação ao teor de matéria orgânica. Os solos do sistema de
pastejo convencional apresentaram maior tendência à compactação do
solo avaliada pela resistência mecânica a penetração de raízes. Palavras-chave: compactação, pisoteio animal, resistência do solo à
penetração Abstract In view of the importance of the interaction soil-climate-plant-animal to
attain good yields in the system, the objective of this study is to evaluate
changes in soil physical properties caused by grazing systems continuous
and rotated. The systems were used: conventional (CC): Brachiaria
brizantha cv. BRS Piatã, unfertilized annual replacement, managed under
continuous stocking; fertilizer (AD): Brachiaria brizantha cv. BRS Piatã
managed under rotational stocking system, with annual replacement
fertilization with NPK at a ratio of 45-20-20 kg ha-1 year-1, and
intercropping (IC): Consortium of Brachiaria brizantha cv. BRS Piatã and
Stylosanthes Campo Grande, managed in a rotational system of stocking,
fertilization receiving annual replacement with 00-20-20 NPK kg ha-1 year-
1. To evaluate the effect of animal trampling on systems with rings were
collected soil samples with undisturbed layers from 0.00 - 0.06 m, 0.06 -
0.12 m before and after grazing for the determination of soil density by the volumetric ring method, macroporosity and total porosity by the
method of the tension table, were also collected samples deformed
structure in the same layer for determining the organic matter content. The resistance to penetration was determined before and after grazing in
the depths of 0.0 - 0.1, 0.1 - 0.2, 0.2 - 0.3 and 0.3 - 0.4 m, with the
impact penetrometer. Animal stepping changed only the microporosity,
the use of different cropping systems and grazing no differences in
relation to organic matter content. The soils of the conventional grazing
system were more tendency to soil compaction measured by penetration
resistance of roots. eywords: compaction, animal trampling, soil resistance to penetratio AGRADECIMENTOS À Deus, porque em todos os lugares e todas as coisas ele sempre está presente para me
proteger e orientar os meus passos. À minha família, por todo o apoio, confiança e dedicação para a conquista desse sonho À Universidade do Estado de Mato Grosso, por ter possibilitado a realização deste
trabalho. Ao Professor Msc. Eurico Lucas de Sousa Neto, a quem sou muito grata por não medir
esforços para me ajudar sempre que precisei, por ter participado da minha formação
acadêmica, orientar e auxiliar no desenvolvimento do meu conhecimento científico e
profissional, e pela confiança e apoio em todos os momentos. Ao Msc. Rodrigo Froede Ruppin por permitir a realização deste trabalho na área de seu
experimento. Ao Departamento de Zootecnia e aos professores do Curso de Zootecnia: Drª. Jocilaine
Garcia; Msc. Giulianna Zilocchi Miguel, Dr. Alexandre Agostinho Mexia; Msc. Edson
Sadayuki Eguchi, Dr. Luiz Juliano Valério Geron, Drª. Maria Aparecida Pereira Pierangeli,
Msc. Marcelo Pinheiro da Silva Meireles, Tatiane Botini, Maurício Arantes Vargas, Msc. Giselde Marques Angreves Silva, Msc. Lourival da Silva Júnior, Osvaldo M. Souza, Drª. Adriana F. B. Mexia e demais professores pela paciência e pelos valiosos ensinamentos. Aos funcionários do Departamento de Zootecnia e do laboratório de Análise de Solos. Ao colega Eurides Ventura Gonçalves e ao amigo Renato Tonhá Alves Júnior que
contribuíram na execução deste trabalho. Aos meus amigos Tatiane Martinhão Pás, Daniely Araújo Freitas, Beatriz Lacerda
Carvalho, Thayná Barcelos Fernandes, Suelen Correa da Silva, e Gheany Roberta Leal por
compartilharem os momentos de luta e lazer. À Danilo Novaes Rodrigues, um homem muito especial em minha vida. “...Hoje me sinto mais forte, mais feliz quem sabe
Só levo a certeza de que muito pouco eu sei
Nada sei... “...Hoje me sinto mais forte, mais feliz quem sabe Só levo a certeza de que muito pouco eu sei
Nada sei... Cada um de nós compõe a sua história
Cada ser em si carrega o dom de ser capaz E ser feliz...”
(Renato Teixeira) E ser feliz...”
(Renato Teixeira) SUMÁRIO 1 INTRODUÇÃO ................................................................................................................. 6
2 REVISÃO BIBLIOGRÁFICA ......................................................................................... 8
2.1 Densidade do solo ......................................................................................................... 14
2.2 Porosidade total ............................................................................................................ 15
2.3 Resistência mecânica do solo à penetração ................................................................. 15
2.4 Matéria orgânica .......................................................................................................... 16
3 MATERIAL E MÉTODOS ............................................................................................ 18
4 RESULTADOS E DISCUSSÃO ..................................................................................... 20
5 CONCLUSÃO ................................................................................................................. 26
REFERÊNCIAS ................................................................................................................. 27 6 6 1 INTRODUÇÃO O bom crescimento e desenvolvimento das plantas, os quais as levam a produzir grãos,
fibras e outros produtos comerciáveis, dependem da harmonia de uma série de fatores
ambientais. A absorção de nutrientes é um dos fatores importantes para que se tenha boas
produções, e pode-se dizer que qualquer obstáculo que restrinja o crescimento radicular reduz
tal absorção (CAMARGO e ALLEONI, 2006). Um dos grandes entraves na obtenção de elevadas produtividades tem sido a
compactação do solo (LIMA et al., 2004). A compactação do solo, dependendo da sua
intensidade, pode causar restrição ao desenvolvimento radicular e afetar a produção das
plantas, e, consequentemente, a produção animal. A redução da produtividade das pastagens tem sido relacionada ao manejo inadequado
da fertilidade do solo, das espécies forrageiras exploradas, da taxa de lotação animal, que
podem comprometer a qualidade física do solo (FIDALSKI et al., 2008), e prejudicar o
desenvolvimento e produtividade das pastagens. O solo suporta a vegetação segundo as suas condições químicas, biológicas e físicas e a
vegetação mantém o gado. O gado modifica a vegetação pelo pisoteio, pelo pastejo
preferencial ou rejeição de plantas, pelo modo de colher as plantas, pela freqüência com que
as procura e por suas excreções (PRIMAVESI, 1999). A qualidade física do solo é importante para a fertilidade do solo, visto que condiciona a
disponibilidade de ar e água para as plantas, assegurando, ainda, o transporte de elementos
nutritivos em solução, além de influenciar a infiltração e distribuição da água dentro do solo
que tem, por sua vez, papel importante no controle da erosão hídrica (TAVARES FILHO et
al., 2005). De acordo com Reichert et al. (2003), a qualidade física do solo está associada ao solo
que: permite a infiltração, retenção e disponibilização de água às plantas; responde ao manejo
e resiste à degradação; permite as trocas de calor e de gases com a atmosfera e raízes de
plantas; e permite o crescimento das raízes. A qualidade física do solo não pode ser medida diretamente, mas é avaliada pelos
atributos físicos do solo, tais como: densidade, porosidade e resistência do solo à penetração
que influenciam no desenvolvimento radicular e consequentemente na produção das plantas. O manejo inadequado do solo, principalmente sob intenso pisoteio animal, pode acarretar
mudanças na estrutura física do solo, reduzindo seu volume e aumentando a densidade do 7 solo, resultando na sua compactação. 1 INTRODUÇÃO Sendo assim, é importante o seu acompanhamento
através dos atributos físicos como parâmetros para identificar problemas de manejo e assim
adequar o sistema para proporcionar boas condições físicas para desenvolvimento e produção
das pastagens e, assim, alcançar boas produtividades animal. Para Freitas (1994) a compactação do solo é considerada a maior limitação à alta
produtividade das culturas em todo o mundo, pois afeta diretamente o crescimento de raízes,
diminui a capacidade de infiltração de água no solo e reduz a translocação de nutrientes,
resultando em uma pequena camada para ser explorada pelas raízes. Em solo compactado o
sistema radicular concentra-se próximo à superfície, tornando a planta mais susceptível a
déficits hídricos e com limitada capacidade de absorver nutrientes em camadas subsuperficiais
(ROSOLEM et al., 1994). A compactação do solo tem sido apontada como um dos principais
problemas evidenciados nas áreas sob pastejo intensivo, pois tem causado a diminuição da
produção de forragem das pastagens cultivadas. O impacto causado pelo pisoteio bovino
sobre o solo e os conseqüentes reflexos sobre alguns atributos físicos, tem sido atribuído ao
fato de seu peso ser distribuído em uma menor área atingida pelo seu casco (RODRIGUES
JUNIOR, 2009). Em vista de que é importante a interação solo-clima-planta-animal para se alcançar boas
produtividades no sistema, o objetivo deste estudo é avaliar as alterações nos atributos físicos
do solo provocado por sistemas de pastejo contínuo e rotacionado. 8 8 2 REVISÃO BIBLIOGRÁFICA 9 A utilização de sistemas de manejo do solo que envolva pastejo animal pode acarretar
mudanças nos atributos físicos, químicos e biológicos do solo, o que pode afetar o
crescimento e desenvolvimento radicular e a produção das culturas implantadas na seqüência
do pastejo (SILVA et al., 2000). A magnitude dessas alterações, principalmente nos atributos
físicos do solo, está na dependência do manejo que é aplicado nas áreas sob pastejo, podendo
variar com a textura, o teor de matéria orgânica, o teor de umidade do solo (TREIN et al.,
1991), a biomassa vegetal sobre o solo (SILVA et al., 2000, 2003), a espécie de planta, a
intensidade e tempo de pastejo e a espécie e categoria animal (CORREA e REICHARDT,
1995). O grau de compactação provocado pelo pisoteio bovino é influenciado pela textura do
solo, sistema de pastejo, altura de manejo da pastagem (CASSOL, 2003) e quantidade de
resíduo vegetal sobre o solo (BRAIDA et al., 2004) e umidade do solo, o que evidencia a
importância do controle das taxas de lotação animal, em relação à quantidade de pastagem
produzida e à manutenção de cobertura vegetal adequada sobre os solos, a fim de mitigar esse
efeito do pisoteio sobre a qualidade física dos solos (SARMENTO et al., 2008). No entanto, o
efeito do pisoteio animal sobre as propriedades físicas do solo é limitado às suas camadas
mais superficiais (TREIN et al., 1991), podendo ser temporário e reversível (CASSOL, 2003). Segundo Muller et al. (2001), a deterioração das condições físicas de solos sob
pastagem foi atribuída ao pisoteio do gado, que causou compactação, expressa pelo aumento
da densidade, da resistência do solo à penetração, e da redução do espaço poroso total, da
macroporosidade e dos valores das propriedades hidráulicas, o que propiciou menor
capacidade de infiltração da água no solo e aumento da susceptibilidade a erosão. Cabe
ressaltar que, quando a carga animal é manejada adequadamente, as alterações nos atributos
físicos são pequenas e não causam qualquer dano à pastagem ou culturas subsequentes
(ALBUQUERQUE et al., 2001a). Para Leão et al. (2003) o impacto dos sistemas de pastejo sobre as propriedades físicas
tem sido subestimado por parte de técnicos e produtores. Leonel et al. 2 REVISÃO BIBLIOGRÁFICA O solo é o principal substrato para produção de alimentos funcionando não somente no
sistema de produção agrícola, mas também na manutenção da qualidade ambiental (DIAS e
MELLO, 1998). O estudo do solo é necessário, pois sua conservação e manutenção são para
garantir seu potencial produtivo em longo prazo. Sendo assim, o uso de indicadores da
qualidade do solo para avaliação da sustentabilidade ambiental é de grande importância
(MENDES et al., 2006). O solo em sua constituição física apresenta as principais propriedades: textura,
estrutura, porosidade, densidade, densidade de partículas, quantidade de água no solo
(umidade gravimétrica) e resistência mecânica à penetração de raízes. Essas propriedades
permitem uma avaliação do estado de conservação do solo (OLIVEIRA NOBRE, 2008),
exceto a textura e densidade de partículas. Os estudos dos atributos físicos podem apontar para uma ação diferenciada dos
processos de manejo, pois são de grande importância na análise do comportamento das
culturas empregadas, já que as características físicas e químicas do solo são diretamente
afetadas pelo tipo de manejo a que ele é submetido (FERNANDES e SOUZA, 2001). Nas últimas décadas as alterações dos atributos que ocasionam a degradação dos solos
têm sido detectadas de forma intensa em áreas agrícolas, em razão de diversos processos que
levam ao depauperamento das características físicas, químicas e biológicas, sendo apontados
como responsáveis o revolvimento excessivo do solo em áreas agrícolas, as práticas agrícolas
inadequadas e o superpastejo. Esses processos são responsáveis por diversos fatores que têm
contribuído para a diminuição do potencial produtivo do solo, o que tem afetado a
sustentabilidade do sistema (AZEVEDO e SVERZUT, 2007). A compactação do solo é uma alteração estrutural, na qual ocorre uma reorganização
das partículas e de seus agregados, resultando no aumento da densidade do solo e redução da
porosidade total e da macroporosidade do solo. A compactação do solo reduz o volume de
macroporos enquanto os microporos permanecem praticamente inalterados, diminuindo as
taxas de infiltração e da condutividade hidráulica do solo (STONE et al., 2002). Isso afeta
negativamente a aeração, a mineralização mais lenta da matéria orgânica, a disponibilidade e
absorção de água e de nutrientes pelas plantas, o fluxo de CO2 e dos nutrientes no solo
(ALVARENGA et al., 1996), e o desenvolvimento do sistema radicular e da parte aérea. 2 REVISÃO BIBLIOGRÁFICA (2003) reforçaram que
a área de pastagem no Brasil necessita de maiores informações de manejo e conservação do
solo, em razão de que a degradação das pastagens e a redução da sua capacidade de suporte
podem estar associadas a vários fatores, dentre eles, as classes de solos e seu manejo, as
espécies forrageiras e as condições climáticas. Desta forma, são necessários estudos que
caracterizem as alterações dos solos sob pastagens, cujo objetivo seja o entendimento das
modificações físicas e químicas que sofrem os solos após a retirada da vegetação original para
o estabelecimento da pastagem (AZEVEDO e SVERZUT, 2007). 10 A avaliação dos efeitos do pisoteio animal sobre as características e propriedades físicas
do solo são geralmente baseadas na mensuração de alguns parâmetros físicos do solo, dentre
os quais se destacam a densidade, a macroporosidade, a microporosidade, a taxa de infiltração
de água e a resistência à penetração de raízes. Adequadas condições de espaço poroso do solo
para o bom desenvolvimento de plantas caracterizam-se por uma boa porosidade e equilibrada
distribuição de diâmetros de poros entre microporos e macroporos. Contudo, é bastante difícil
manter as boas condições físicas do solo, uma vez que a utilização de implementos e
máquinas, assim como o pisoteio animal causam deterioração no espaço poroso através de
pressões que são aplicadas sobre o solo (FLORES, 2007). A pressão do casco dos animais sobre o solo pode comprometer a qualidade física na
camada superficial, em razão do aumento da densidade do solo e da redução da porosidade
(GIAROLA et al., 2007). Um bovino de 400 kg exerce uma pressão de 3,5 kg/cm2
(PRIMAVESI, 1999). O aumento da pressão de pastejo, relação entre o peso animal e a massa de forragem
disponível [kg(animal) kg-1 (massa seca de forragem) dia-1], em conseqüência do aumento da taxa de
lotação animal em pastagens de baixa produtividade, compromete a qualidade física do solo,
pois resulta em maior carga de animais sobre o solo (Silva et al., 2003), independentemente
do sistema de produção (pastejo rotacionado, contínuo e integração lavoura-pecuária),
conforme Lanzanova et al. (2007). Uma excessiva taxa de lotação animal determina a redução na qualidade física e
estrutural do solo sob pastagens. 2 REVISÃO BIBLIOGRÁFICA O descanso da pastagem possibilita a recuperação parcial da
qualidade física do solo, atribuída aos efeitos positivos do crescimento radicular e da micro e
mesofauna do solo em associação com os efeitos de secamento e umedecimento sobre a
estrutura do solo (DA SILVA et al.2002) Um aspecto a ser considerado no estudo de compactação do solo é que os impactos
causados por trafego de máquinas e, principalmente, dos animais pode ser reduzido pela
presença da cobertura do solo (COSTA, 2000). Segundo Dias Filho (1998), pastos formados
com espécies cujo hábito de crescimento não proporciona eficiente cobertura do solo e que
são relativamente exigentes em fertilidade são normalmente mais suscetíveis à degradação
precoce que os pastos formados com gramíneas com hábito de crescimento decumbente e
menos exigentes em fertilidade do solo. Imhoff et al. (2000) defendem que a compactação causada pelo pisoteio dos animais
concorre para a redução da produtividade e longevidade das pastagens. Em geral, a maior
pressão de pastejo resulta em aumento da densidade do solo e redução da porosidade e da 11 estabilidade dos agregados em água na camada superficial, o que causa a degradação da
pastagem. Os animais influem sobre o solo diretamente pelo pisoteio, que é muito mais prejudicial
em épocas muito úmidas e muito secas. Mas influi também indiretamente, através do pastejo
seletivo, desnudando manchas de chão onde se assenta a erosão, e pelo pastejo freqüente que
diminui o tamanho das raízes e contribui para o adensamento do solo. A compactação
depende da umidade do solo, da cobertura vegetal existente (plantas com raízes profundas
sofrem menos) e da vegetação viva ou morta. Nas épocas muito secas o pisoteio é tão
prejudicial que, em épocas muito chuvosas, a compactação pode atingir até 11 cm de
profundidade. Mas como o gado de cria e o gado leiteiro exportam nutrientes, o solo
empobrece, e com ele a vegetação, o que dá margem a uma decadência química e
consequentemente física do solo (PRIMAVESI, 1999). Condições físicas do solo adequadas ao crescimento das plantas resultam de complexas
interações entre resistência do solo à penetração (RP), aeração e disponibilidade de água, as
quais afetam diretamente o crescimento das plantas (TORMENA et al. 2007). A resistência do
solo à penetração é um índice integrado pela densidade do solo, textura, matéria orgânica e
umidade do solo (TORMENA et al., 2004). 2 REVISÃO BIBLIOGRÁFICA Normalmente, as determinações de densidade e de porosidade do solo são as avaliações
mais comuns e difundidas para identificar camadas compactadas no solo, porém a resistência
mecânica deste à penetração também está diretamente relacionada com o estado de
compactação do solo e pode ser uma medida mais sensível para identificar a compactação,
especialmente em camadas pouco espessas (ABREU et al., 2004). O monitoramento
periódico do estado de compactação do solo por meio da resistência à penetração é uma forma
prática de avaliação dos efeitos dos diferentes sistemas de manejo na estrutura do solo e no
crescimento radicular das diferentes culturas, permitindo assim pesquisas e avaliações na
propriedade rural (TAVARES FILHO e RIBON, 2008). Em solos mais argilosos, o aumento da densidade do solo e da resistência do solo à
penetração pode ser mais restritivo às raízes do que em solos arenosos (ALBUQUERQUE et
al. 2001b). A resistência do solo à penetração das raízes está relacionada com a permanência da
continuidade dos poros. Poros formados pela ação das raízes no solo são mais estáveis, pois a
decomposição dessas por microrganismos gera materiais que atuam como cimentantes nas
paredes desses poros, proporcionando maior durabilidade, se comparados com aqueles
formados por implementos mecânicos (ABREU, 2000). 12 A utilização de áreas com pastagens tem assumido destaque em razão da elevada
proporção que tem ocupado em relação ao total das áreas agrícolas, aliado ao fato das
estimativas apontarem que a maioria das áreas degradadas, em nível mundial, esta sob
pastagens (AZEVEDO e SVERZUT, 2007). A degradação das pastagens afeta diretamente a
sustentabilidade da pecuária. Considerando apenas a fase de recria e engorda de bovinos, a
produção animal em uma pastagem degradada pode ser seis vezes inferior à de uma pastagem
recuperada ou em bom estado de manutenção (MACEDO et al., 2000). As pastagens cultivadas destinadas à criação de bovinos, embora em sua maioria
proporcionem boa cobertura de solo, vem sendo utilizadas com lotações inadequadas em
relação a sua capacidade de produção e as características do solo. As propriedades físicas do
solo necessitam ser monitoradas em função da oferta de forragem, pois variando-se os níveis
de oferta de forragem obtêm-se diferentes níveis de pressões de pastejo, em que se avalia a
real capacidade de produção animal das pastagens. Assim, pode-se buscar o ponto ótimo de
oferta de forragem, no qual é possível maximizar os ganhos por animal e por área, e manter
pastagens com boa qualidade. 2 REVISÃO BIBLIOGRÁFICA Sendo assim, é importante detectar o nível crítico de oferta de
forragem, equivalente a uma pressão de pastejo crítica, acima do qual as propriedades físicas
do solo podem sofrer alterações indesejáveis, pois a intensidade de desfolhação das pastagens
e a pressão de pastejo ocasionadas pelo pisoteio dos animais são distintas nos diferentes níveis
de oferta de forragem (BERTOL et al., 2000). Atributos físicos do solo favoráveis ao crescimento do sistema radicular são necessários
para a obtenção e manutenção de elevadas produtividades. Os solos devem possuir suficiente
espaço poroso para o movimento de água e gases e resistência favorável à penetração das
raízes. Neste contexto, a compactação causada pelo pisoteio dos animais concorre para a
redução da produtividade e longevidade das pastagens (SANTANA, 2009). O crescimento do sistema radicular e da parte aérea das plantas é influenciado por
vários atributos físicos do solo, com complexas interações que envolvem o potencial da água
no solo, o teor de oxigênio e a resistência do solo à penetração das raízes (TORMENA et al.,
1998), fatores que dificultam a obtenção de valores críticos ao desenvolvimento e
produtividade das culturas (BEUTLER et al., 2004). Segundo Silva et al. (2006), a densidade
da camada compactada capaz de limitar o crescimento das plantas varia conforme a classe de
solo, condições de umidade, espécie e ou mesmo do cultivar plantado. Segundo Flores (2004) algumas espécies de plantas têm a capacidade de desenvolver
um sistema radicular mais agressivo, capaz de romper camadas compactadas de solo. Entretanto, a maioria das culturas comerciais exploradas apresenta um sistema radicular 13 sensível à compactação. Camargo e Alleoni (1997) denominam “plantas descompactadoras”
aquelas que apresentam raízes com capacidade elevada de penetração em camadas de solo
com alta impedância mecânica. O alongamento radicular só é possível quando a pressão de
crescimento das raízes for maior do que a resistência mecânica do solo à penetração. Geralmente predominam as plantas que melhor suportam o pisoteio e as tosas
freqüentes, e desaparecem as que necessitam de maior tempo para sua recuperação. A maioria
das forrageiras cultivadas exige um solo mais ou menos solto. Em pastagens mistas a
compactação é menor graças aos sistemas radiculares diferentes. Especialmente leguminosas
conseguem manter o solo aberto (PRIMAVESI, 1999). O crescimento das raízes se dá por divisão e expansão das células meristemáticas e, com
isso, a raiz penetra no solo. Desta forma, o crescimento está baseado principalmente no turgor
das células radiculares. 2 REVISÃO BIBLIOGRÁFICA Se a resistência oferecida pelo solo for superior a essa força, o
crescimento radicular é bastante prejudicado, podendo até mesmo cessar. O crescimento
radicular é o parâmetro mais adequado para a avaliação do impedimento ao crescimento de
plantas sobre solos compactados (MELLO, 2002). A rota preferencial de crescimento das raízes é através dos macroporos (CAMARGO E
ALLEONI, 1997). Deste modo, em solos compactados, em que há diminuição dos
macroporos, o desenvolvimento radicular pode ser prejudicado, conforme salientado por Silva
et al. (2000). A redução na macroporosidade, por afetar o movimento de água no solo e a
dinâmica de gases, é considerada por Mello (2002) como o principal efeito danoso do pisoteio
animal sobre o solo. O sistema radicular provoca desarranjos no solo ao penetrar camadas com alta
resistência mecânica e, ao sofrer decomposição, deixa canais (“bioporos”) que contribuem
para a infiltração de água e difusão de gases, melhorando a qualidade física do solo para as
culturas subseqüentes. Além disso, o crescimento radicular pode incrementar a matéria
orgânica ao longo do perfil do solo, a qual promove a estabilização dos agregados, reduzindo
a susceptibilidade do solo à compactação (ROTH et al., 1992). Em solo compactado, o sistema radicular concentra-se próximo à superfície, tornando a
planta mais susceptível a déficits hídricos e limitando sua capacidade de absorver nutrientes
em camadas subsuperficiais (MULLER et al., 2001). Contudo, a influência da compactação sobre as plantas depende da espécie, do tipo de
solo e do teor de água no solo. A compactação do solo, em magnitude moderada, pode
apresentar efeitos benéficos tais como melhoria do contato solo-semente e raiz, favorecendo a 14 absorção de água e de nutrientes pelas plantas, e aumento da disponibilidade de água em anos
secos (DIAS JUNIOR e PIERCE, 1996). Considerando a reciclagem de minerais em um ecossistema da pastagem, a união com o
solo assume importância crucial. Assim, é importante considerar a interação solo-planta-
animal no contexto da ecologia do pasto (NASCIMENTO JR., 1998). As plantas obtêm os
nutrientes que necessitam através da absorção, pelas raízes, dos elementos existentes na
solução do solo. A compactação do solo, afetando o desenvolvimento dos organismos do solo,
pode resultar em um decréscimo na quantidade de nutrientes mineralizados provenientes da
matéria orgânica do solo alterando o processo de reciclagem dos elementos, o que reduziria o
fornecimento às plantas e, conseqüentemente, a produtividade do sistema (COSTA, 2000). 2.2 Porosidade total A porosidade depende, principalmente, da textura e da estrutura dos solos. A porosidade
de um solo pode ser definida como o volume de vazios. Esta é a relação entre a proporção de
espaços que podem ser ocupados por líquidos e ar em relação ao espaço ocupado pela massa
de solo (SANTANA, 2009). Os solos que tem menor porosidade são os arenosos. Como suas partículas são
predominantemente grandes, a tendência é formar a disposição piramidal, que tem menor
espaço vazio. Nas terras de textura fina, as partículas não se arranjam de maneira tão
compactada, além disso, a argila coloidal contribui para formar agregados que aumentam a
porosidade. Considera-se que, em média, a porosidade dos solos arenosos varia de 35 a 50% e
dos argilosos de 40 a 60%, e somente solos ricos em matéria orgânica apresentam porosidade
entre 60 e 80% (RABELO, 2000). O tamanho dos poros do solo pode variar, eles dependem das partículas e dos
agregados. A distribuição dos espaços pode mudar pela atuação de alguma pressão ou
rolamento das partículas. A quantidade, o tamanho, a distribuição e a continuidade são
diferentes de um solo para outro (RESENDE et al., 2002). A porosidade total é dividida em macroporos e microporos, sendo o solo um
emaranhado de capilares de diferentes formas e tamanhos. Estes exercem grande influência na
capacidade do solo em armazenar água. A perda da porosidade total esta relacionada
diretamente com a compactação que reduz o tamanho dos poros (ANDRADE e SANTOS,
2004). 2.1 Densidade do solo A densidade do solo é também chamada de densidade global ou densidade aparente,
sendo bastante afetada pelo manejo do homem sobre o solo (ANDRADE et al., 1998). A densidade do solo pode ser modificada continuamente pelo uso da terra e é
influenciada pelo manejo. A utilização de máquinas e equipamentos pesados e elevada carga
animal, favorece o seu aumento (BERTOL et al., 2006). A densidade do solo depende da natureza, das dimensões e da forma como se acham
dispostas as partículas do solo. Nos solos minerais os valores da densidade do solo oscilam de
1,1 a 1,6 g cm-3 e, no solos orgânicos, a densidade é inferior, achando-se entre 0,6 a 0,8 g cm-3
A amplitude de variação situa-se dentro dos limites médios: solos argilosos, de 1,00 a 1,25 g
cm-3; solos arenosos de 1,25 a 1,40 g cm-3; solos humíferos, de 0,75 a 1,00 g cm-3 e solos
turfosos, de 0,20 a 0,40 g cm-3 (SANTANA, 2009). De maneira geral, pode-se afirmar que, quanto mais elevada for à densidade do solo,
maior será a sua compactação, menor será a sua estruturação, menor a sua porosidade total e,
conseqüentemente, maiores serão as restrições para o crescimento e desenvolvimento das
plantas (RABELO, 2000). 15 2.3 Resistência mecânica do solo à penetração A resistência mecânica do solo à penetração é um parâmetro usado para verificar o grau
de compactação do solo, que pode causar um impedimento físico na superfície e
subsuperfície. Esta propriedade é influenciada pela textura, densidade e conteúdo de água
(CAMARGO e ALLEONI, 1997). A penetrometria consiste num método apropriado para avaliar a resistência mecânica à
penetração das raízes no solo, devido à facilidade, rapidez e à possibilidade de efetuar grande 16 número de repetições na obtenção de dados, embora possam ocorrer dificuldades na
interpretação dos resultados obtidos devido à dependência desses em relação ao conteúdo de
água, matéria orgânica e textura do solo (TAVARES FILHO et al., 1999). O penetrômetro de impacto tem sido amplamente utilizado no campo para caracterizar a
compactação provocada pelo uso e manejo do solo (TORMENA e ROLOFF, 1996), em razão
do baixo custo, da não-necessidade de calibração freqüente e do fato de os resultados
independerem do operador. Os níveis críticos de resistência do solo para o crescimento das plantas variam com o
tipo de solo e com a espécie cultivada (GENRO JUNIOR et al., 2004). Em geral, valores de
resistência do solo à penetração, considerados críticos ao crescimento radicular, variam de 1,5
a 3,0MPa. Valores em torno de 2,5MPa são considerados baixos, ao passo que valores em
torno de 3,5 a 6,5MPa, são considerados como valores capazes de causar problemas para o
desenvolvimento radicular de leguminosas e gramíneas (TORRES e SARAIVA, 1999). Segundo Imhoff et al. (2000) valores de resistência mecânica do solo entre 2 e 3 MPa, são
considerados limitantes ao desenvolvimento radicular. 3 MATERIAL E MÉTODOS O experimento foi conduzido em uma propriedade agrícola, localizada no município de
Vale do São Domingos nas coordenadas S 15° 36’ 329” e W0 59° 06’ 050” e altitude de 489
m, em área caracterizada por relevo plano e solo apresentando características homogêneas. O
clima da região é do tipo Aw segundo a classificação de Köppen, tropical, com chuvas
concentradas no verão (outubro a abril), período seco bem definido durante o inverno (maio a
setembro) e precipitação pluvial média anual de 1.500 mm e temperatura média de 27º C. O
solo do local é classificado como um Argissolo Vermelho (Embrapa, 1999), cujo a
composição granulométrica na camada de 0,20 m é de 345,5 g kg-1 de argila, 98,5 g kg-1 de
silte e 556 g kg-1 de areia. Os tratamentos corresponderam a um fatorial 3 x 2 x 2 num delineamento experimental
inteiramente casualisado com 4 repetições. Os fatores em estudo foram sistemas de pastejo,
época de pastejo e camadas. A área experimental era antes cultivada com Brachiaria brizantha cv. Marandú
pastejada por bovinos em sistema de lotação contínua. Na instalação do experimento a área de
24 ha foi subdividida em três sistemas de produção, cada um com 8 ha. Os sistemas de uso foram: Convencional (CC): formado exclusivamente pelo cultivar
Piatã (Brachiaria brizantha cv. BRS Piatã), sem adubação anual de reposição, manejado em
sistema de lotação contínua, constituído de quatro piquetes de 2 ha cada; Adubado (AD):
constituído de quatro piquetes de 2 ha cada, sendo cada um destes piquetes subdivididos em
quatro sub-piquetes com área de 0,5 ha cada, manejados em sistema de lotação rotacionado,
considerando a altura como critério para a entrada (40 cm) e saída dos animais (20 cm) dos
piquetes formado exclusivamente pelo cultivar Piatã (Brachiaria brizantha cv. BRS Piatã),
com a adubação anual de reposição com N-P-K na proporção de 45-20-20 kg ha-1 ano-1; e
Consorciado (CS): constituído de quatro piquetes de 2 ha cada, sendo cada um destes piquetes
subdivididos em quatro sub-piquetes com área de 0,5 ha cada, manejados em sistema de
lotação rotacionado, considerando a altura como critério para a entrada (40 cm) e saída dos
animais (20 cm) dos piquetes, formado pelo consórcio da gramínea (Brachiaria brizantha cv. BRS Piatã) e leguminosa (Stylosanthes Campo Grande), recebendo adubação anual de
reposição com N-P-K de 00-20-20 kg ha-1 ano-1. 2.4 Matéria orgânica A importância da matéria orgânica nos solos é abrangente. Sua atuação se dá tanto na
melhoria das condições físicas, tais como aeração, maior retenção e armazenamento de água,
quanto nas propriedades químicas e físico-químicas, no fornecimento de nutrientes às plantas
e na maior capacidade de troca catiônica do solo (CTC), além de proporcionar um ambiente
adequado ao estabelecimento e à atividade da microbiota (FIGUEIREDO et al., 2008). Na
Tabela 1 podemos visualizar os níveis de sustentabilidade de matéria orgânica e mais alguns
atributos físicos, como: densidade do solo, porosidade total, resistência mecânica à
penetração, sugerido por Goedert (2005). 17 Tabela 1. Atributos do solo e níveis de sustentabilidade (GOEDERT, 2005). Atributo
Nível de sustentabilidade
Densidade do solo
< 1,0 g cm-3
Porosidade total
> 60 cm³ cm-3
Resistência mecânica à penetração
< 1,0 MPa
Matéria orgânica
Textura argilosa: > 40 g kg-1
Textura média: > 30 g kg-1
Textura arenosa: > 20 g kg-1 Tabela 1. Atributos do solo e níveis de sustentabilidade (GOEDERT, 2005). 18 4 RESULTADOS E DISCUSSÃO A densidade do solo não foi significativamente alterada (Tabela 2). Mas pode-se
observar que pós-pastejo a camada 0,00 – 0,06 m apresentou aumento da densidade do solo
em todos os sistemas e a camada 0,06 – 0,12 m apresentou redução ou não teve mudança na
densidade do solo comparando com o pré-pastejo. Já em relação aos tratamentos o sistema
convencional apresentou em média menores densidades que os outros tratamentos. O fato de
as alterações devido ao pastejo animal na densidade do solo se concentrar na camada de 0,00
– 0,06 m concorda com resultados de outros trabalhos realizados. A pressão exercida sobre o
solo através do pisoteio animal é o agente causador da compactação e há evidências de que a
compactação superficial está relacionada a essa pressão. Esses relatos ajudam a entender o
fato de que a compactação do solo causada pelo pisoteio animal se concentra nas camadas
mais superficiais, até 5,0 cm de profundidade (MORAES e LUSTOSA, 1997). A densidade do solo não foi significativamente alterada (Tabela 2). Mas pode-se
observar que pós-pastejo a camada 0,00 – 0,06 m apresentou aumento da densidade do solo
em todos os sistemas e a camada 0,06 – 0,12 m apresentou redução ou não teve mudança na
densidade do solo comparando com o pré-pastejo. Já em relação aos tratamentos o sistema
convencional apresentou em média menores densidades que os outros tratamentos. O fato de
as alterações devido ao pastejo animal na densidade do solo se concentrar na camada de 0,00 – 0,06 m concorda com resultados de outros trabalhos realizados. A pressão exercida sobre o
solo através do pisoteio animal é o agente causador da compactação e há evidências de que a
compactação superficial está relacionada a essa pressão. Esses relatos ajudam a entender o
fato de que a compactação do solo causada pelo pisoteio animal se concentra nas camadas
mais superficiais, até 5,0 cm de profundidade (MORAES e LUSTOSA, 1997). Tabela 2. Densidade do solo sob diferentes épocas de pastejo, sistemas de uso e camadas (m). 3 MATERIAL E MÉTODOS Na ocasião da instalação do experimento foram realizadas duas gradagens com grade
aradora, seguida de uma gradagem com grade niveladora no início do período chuvoso. Após 19 a realização do preparo do solo a semeadura foi realizada à lanço, na quantidade de 3,5 kg ha-1
de sementes puras viáveis (SPV) de Brachiaria brizantha cv. BRS Piatã nos sistemas CC e
AD e de 3,0 kg ha-1 de SPV de Brachiaria brizantha cv. BRS Piatã misturadas a 2,5 kg ha-1de
SPV de Stylosanthes Campo Grande no sistema CS. A adubação utilizada no sistema AD foi constituída da aplicação de 100 kg ha-1do
formulado 00-20-20 no momento do plantio e 100 kg ha-1 de uréia 90 dias após o plantio e no
sistema CS foi realizada através da aplicação de 100 kg ha-1 do formulado 00-20-20 no
momento do plantio. Todos os tratamentos foram pastejados por 24 animais da raça nelore (Bos taurus
indicus L.), sendo colocados 2 animais por repetição, totalizando 8 animais em cada
tratamento. Em Abril de 2010, para avaliar o efeito do pisoteio animal nos sistemas foram coletados
anéis com amostras de solo com estrutura indeformada nas camadas de 0,00 - 0,06 m e 0,06 -
0,12 m antes e após o pastejo. Estes anéis foram utilizados nas determinações de densidade do
solo pelo método do anel volumétrico (BLAKE e HARTGE, 1986), macroporosidade,
microporosidade e porosidade total, pelo método da mesa de tensão. Foram coletadas também
amostras com estrutura deformada na mesma camada para a determinação do teor de matéria
orgânica (EMBRAPA, 1997). A resistência do solo à penetração foi determinada nas profundidades de 0,0 -0,1, 0,1 -
0,2, 0,2 - 0,3 e 0,3 - 0,4 m, com o penetrômetro de impacto (modelo IAA/ Planalsucar-Stolf),
com ângulo de cone de 30o e os resultados transformados segundo Stolf (1991). Os resultados obtidos foram submetidos à análise de variância e quando significativos
as médias foram comparadas pelo teste de Scott Knott a 0,005 de probabilidade de erro. 20 4 RESULTADOS E DISCUSSÃO Densidade do solo (g cm-3)
Época
Camada (m)
Convencional
Adubado
Consorciado
Pré-Pastejo
0,00 - 0,06
1,39 Aaα
1,40 Aaα
1,37 Aaα
0,06 - 0,12
1,39 Aaα
1,41 Aaα
1,42 Aaα
Pós-Pastejo
0,00 - 0,06
1,43 Aaα
1,45 Aaα
1,43 Aaα
0,06 - 0,12
1,37 Aaα
1,40 Aaα
1,42 Aaα
Letras maiúsculas (AB) entre tratamentos na mesma época e camada;
Letras minúsculas (ab) entre épocas no mesmo tratamento e camada;
Símbolos (αγ) entre camada no mesmo tratamento e época; ela 2. Densidade do solo sob diferentes épocas de pastejo, sistemas de uso e camadas (m) Letras maiúsculas (AB) entre tratamentos na mesma época e camada;
Letras minúsculas (ab) entre épocas no mesmo tratamento e camada;
Símbolos (αγ) entre camada no mesmo tratamento e época; A densidade do solo depende da natureza, das dimensões e da forma como se acham
dispostas as partículas do solo. Nos solos argilosos os valores da densidade do solo oscilam de
1,00 a 1,25 g cm-3 (SANTANA, 2009), e Camargo e Alleoni (1997) consideram crítico o
valor de 1,55 g cm-3 em solos franco-argilosos a argilosos. Considerando esses valores
podemos dizer que solos com densidade entre 1,25 g cm-3 à 1,55 g cm-3 são limitantes e
valores densidade acima de 1,55 g cm-3 são críticos, sendo assim os valores de densidade da
Tabela 1, variando entre 1,37 g cm-3 à 1,45 g cm-3 podem ser limitantes ao desenvolvimento
das raízes das gramíneas e leguminosas no perfil do solo, caracterizando solo compactado. Segundo Rabelo (2000) quanto mais elevada for a densidade do solo, maior será sua
compactação, menor será a sua estruturação, menor a sua porosidade total e, 21 conseqüentemente, maiores serão as restrições para o crescimento e desenvolvimento das
plantas. Azevedo e Sverzut (2007) encontraram que o uso do solo com pastagem propiciou a
alteração dos atributos físicos da camada superficial, evidenciado pela compactação do solo,
pois os valores de densidade do solo, microporosidade e resistência do solo à penetração do
solo sob pastagem foram superiores, e no caso de porosidade total, macroporosidade e
condutividade hidráulica foram inferiores. Em relação aos atributos físicos macroporosidade, microporosidade e porosidade total,
somente foi encontrada diferença significativa na microporosidade (Tabela 3). Tabela 3. Macroporosidade, microporosidade e porosidade total sob diferentes épocas de
pastejo, sistemas de uso e camadas (m). Tabela 3. Macroporosidade, microporosidade e porosidade total sob diferentes épocas de
pastejo, sistemas de uso e camadas (m). 4 RESULTADOS E DISCUSSÃO Macroporosidade (cm3 cm-3)
Época
Camada (m)
Convencional
Adubado
Consorciado
Pré-Pastejo
0,00 - 0,06
0,20 Aaα
0,18 Aaα
0,24 Aaα
0,06 - 0,12
0,23 Aaα
0,20 Aaα
0,21 Aaα
Pós-Pastejo
0,00 - 0,06
0,21 Aaα
0,20 Aaα
0,22 Aaα
0,06 - 0,12
0,25 Aaα
0,26 Aaα
0,27 Aaα
Microporosidade (cm3 cm-3)
Época
Camada (m)
Convencional
Adubado
Consorciado
Pré-Pastejo
0,00 - 0,06
0,27 Aaα
0,28 Aaα
0,24 Baα
0,06 - 0,12
0,24 Aaγ
0,26 Aaα
0,25 Aaα
Pós-Pastejo
0,00 - 0,06
0,24 Abα
0,25 Abα
0,23 Aaα
0,06 - 0,12
0,23 Aaα
0,21 Abγ
0,19 Abγ
Porosidade total (cm3 cm-3)
Época
Camada (m)
Convencional
Adubado
Consorciado
Pré-Pastejo
0,00 - 0,06
0,47 Aaα
0,47 Aaα
0,48 Aaα
0,06 - 0,12
0,47 Aaα
0,46 Aaα
0,46 Aaα
Pós-Pastejo
0,00 - 0,06
0,45 Aaα
0,45 Aaα
0,45 Aaα
0,06 - 0,12
0,48 Aaα
0,47 Aaα
0,46 Aaα
Letras maiúsculas (AB) entre tratamentos na mesma época e camada;
Letras minúsculas (ab) entre épocas no mesmo tratamento e camada;
Símbolos (αγ) entre camada no mesmo tratamento e época; Letras maiúsculas (AB) entre tratamentos na mesma época e camada;
Letras minúsculas (ab) entre épocas no mesmo tratamento e camada;
Símbolos (αγ) entre camada no mesmo tratamento e época; Letras maiúsculas (AB) entre tratamentos na mesma época e camada;
Letras minúsculas (ab) entre épocas no mesmo tratamento e camada;
Símbolos (αγ) entre camada no mesmo tratamento e época; Conforme a Tabela 3 a microporosidade foi significativamente menor no sistema
consorciado, na camada 0,00 – 0,06 m, (CS - 0,24 cm3 cm-3) que nos outros tratamentos na
mesma época e camada (CC - 0,27 cm3 cm-3; AD - 0,28 cm3 cm-3). No mesmo tratamento e
camada, a microporosidade nos sistemas convencional e adubado na camada de 0,00 – 0,06 m
(CC - 0,24 cm3 cm-3; AD - 0,25 cm3 cm-3) e nos sistemas adubado e consorciado na camada
de 0,06 – 0,12 m (AD - 0,21 cm3 cm-3; CS - 0,19 cm3 cm-3) foram significativamente menores 22 no pós-pastejo do que no pré-pastejo. 4 RESULTADOS E DISCUSSÃO Na mesma época e tratamento, no pré-pastejo do
sistema convencional a microporosidade na camada 0,06 – 0,12 m (CC - 0,24 cm3 cm-3) foi
significativamente menor que na camada 0,00 – 0,06 m, enquanto que no pós-pastejo dos
sistemas adubado e consorciado a microporosidade na camada 0,06 – 0,12 m (AD - 0,21 cm3
cm-3; CS - 0,19 cm3 cm-3) foi significativamente menor que na camada 0,00 – 0,06 m. Embora a macroporosidade e a porosidade total não terem apresentado resultados
significativos, seus valores variaram (Tabela 3). Em relação à macroporosidade no pós-
pastejo teve aumento dos valores, exceto na camada 0,00 – 0,06 m do sistema consorciado
que no geral apresentou maior macroporosidade. Já em relação à porosidade total na camada
0,00 – 0,06 m teve redução no pós-pastejo e na camada 0,06 – 0,12 m teve aumento, exceto
no consorciado que não teve alteração. Isso pode ser explicado ao fato de que a pressão
exercida sobre o solo através do pisoteio animal se concentra na camada superficial do solo
(Moraes e Lustosa, 1997), deixando a camada subsuperficial do solo mais solta. Considera-se que, em média, a porosidade dos solos argilosos seja de 40 a 60%
(RABELO, 2000). A porosidade total obtida variando entre 45% a 48% está adequada, tendo
suficiente espaço poroso. Na Tabela 4 estão os valores de matéria orgânica presente nos diferentes sistemas de
uso e camadas do solo, e observa-se que no sistema adubado a quantidade de matéria orgânica
foi significativamente menor na camada 0,06 – 0,12 m (AD - 1,27 dag kg-1) comparando com
a camada 0,00 – 0,06 m (1,62 dag kg-1) do mesmo tratamento. Tabela 4. Teor médio de matéria orgânica sob diferentes sistemas de uso e camadas. abela 4. Teor médio de matéria orgânica sob diferentes sistemas de uso e camadas. Tabela 4. Teor médio de matéria orgânica sob diferentes sistemas de uso e camadas. Matéria orgânica (dag kg-1)
Camada (m)
Convencional
Adubado
Consorciado
0,00 – 0,06
1,40 Aa
1,62 Aa
1,50 Aa
0,06 – 0,12
1,20 Aa
1,27 Ab
1,32 Aa
Letras maiúsculas (AB) entre tratamentos na mesma camada;
Letras minúsculas (ab) entre camadas no mesmo tratamento; Em relação à matéria orgânica (Tabela 4) pode-se observar que os maiores teores
ocorreram na camada de 0,00 – 0,06 m. Justifica-se tal diferença entre as camadas pela
presença de grande quantidade de raízes das gramíneas que se acumulam próximo da
superfície (SALTON et al., 2002). A semelhança no teor de matéria orgânica entre os
sistemas é devido ao comportamento das gramíneas que são excelentes incorporadoras de
matéria orgânica no solo. 23 Estatisticamente não houve diferença significativa na resistência do solo à penetração
entre épocas e tratamentos (Figuras 1 e 2). Estatisticamente não houve diferença significativa na resistência do solo à penetração
entre épocas e tratamentos (Figuras 1 e 2). Segundo Imhoff et al. (2000) valores de resistência mecânica do solo acima de 2 MPa,
são considerados limitantes ao desenvolvimento radicular. Quando a resistência à penetração
é menor do que 1,1 MPa não há limitação ao crescimento radicular, sendo o solo considerado
como de muito baixa resistência, enquanto que para valores entre 1,0 e 2,5 MPa, a resistência
deve ser considerada baixa, ocorrendo pouca limitação ao crescimento radicular (CAMARGO
e ALLEONI, 1997). Tormena et al. (1998) afirmam que a resistência a penetração acima de
2,0 MPa é considerada impeditiva ao crescimento das raízes no solo. Considerando que a resistência do solo à penetração acima de 2 MPa começa a ser
restritiva ao crescimento de raízes no perfil do solo, o sistema consorciado no pré-pastejo foi
o único que não ofereceu resistência à penetração de raízes no perfil do solo, com valores
entre 1,85 MPa a 2,01 MPa (Figura 1), isso é explicado devido ao fato de as raízes de
gramíneas e leguminosas terem diâmetros diferentes, proporcionando maior espaço poroso e
deixando o solo mais solto. Já na Figura 2 observa-se que pós-pastejo na camada superficial
até 5 cm de profundidade ocorreu leve resistência (2,5 cm – 2,28 MPa; 5 cm – 2,18 MPa)
demonstrando que o pisoteio animal provoca alterações nas camadas superficiais do solo. Tabela 4. Teor médio de matéria orgânica sob diferentes sistemas de uso e camadas. 0
10
20
30
40
50
0,00
1,00
2,00
3,00
4,00
5,00
Resistência do solo (MPa)
Camada (cm)
convencional
adubado
consorciado
Figura 1. Resistência do solo à penetração (MPa) pré-pastejo sob diferentes sistemas de uso e
camadas. Figura 1. Resistência do solo à penetração (MPa) pré-pastejo sob diferentes sistemas de uso e
camadas. O sistema adubado no pré-pastejo (Figura 1) ofereceu resistência à penetração nos
primeiros 5 cm do perfil do solo (2,5 cm – 2,8 MPa; 5 cm – 2,74 MPa), sendo limitante ao 24 crescimento de raízes, caracterizando solo compactado, apesar de ser o sistema com maior
quantidade de matéria orgânica nos primeiros 6 cm. Abaixo dos 5 cm a resistência do solo
decaiu mantendo-se próximo de 2 MPa abaixo dos 10 cm. Já no pós-pastejo (Figura 2) a
resistência do solo foi até 15 cm de profundidade (entre 2,45 MPa e 2,98 MPa) e abaixo dos
15 cm se manteve ao redor de 2 MPa, o que é interpretado que o pisoteio animal foi o
causador do aumento da resistência do solo, já que neste sistema não tinha consorcio com
leguminosa, acarretando maior densidade. 0
10
20
30
40
50
0,00
1,00
2,00
3,00
4,00
5,00
Resistência do solo (MPa)
Camada (cm)
convencional
adubado
consorciado
Figura 2. Resistência do solo à penetração (MPa) pós-pastejo sob diferentes sistemas de uso e
camadas Figura 2. Resistência do solo à penetração (MPa) pós-pastejo sob diferentes sistemas de uso e
camadas Os sistemas adubado e consorciado se comportaram relativamente próximos abaixo dos
20 cm de profundidade, sendo próximos de 2 MPa nas duas épocas de amostragem (Figuras 1
e 2). O sistema convencional foi o que ofereceu maior resistência do solo à penetração de
raízes, sendo prejudicial até 20 cm do perfil do solo, tanto no pré-pastejo como no pós-pastejo
(Figuras 1 e 2), pois se manteve acima de 2,2 MPa que é considerado impeditivo ao
crescimento de raízes. Esta resistência é explicada em pastejo contínuo pelo fato dos animais
permanecerem durante todo o tempo no mesmo piquete, não tendo período de descanso e
também pelo crescimento da gramínea ser em touceiras proporciona áreas descobertas de solo
tendo maior impacto da pressão dos cascos dos animais no solo e consequentemente maior
tendência a compactação, sendo confirmada pelo pós-pastejo a resistência à penetração ter
sido maior que no pré-pastejo. Tabela 4. Teor médio de matéria orgânica sob diferentes sistemas de uso e camadas. Abaixo dos 20 cm a resistência do solo decaiu gradativamente 25 até que abaixo dos 25 cm teve menor resistência que os outros dois sistemas. Essa
característica do sistema convencional na camada subsuperficial oferecer menor resistência
que os outros dois sistemas é explicada pelo fato de que o pastejo constante dos animais nesse
piquete exerce maior pressão na camada superficial do solo. De acordo com Alvarenga et al. (1996) à medida que a compactação do solo aumenta,
há uma situação de decréscimo na porosidade total, assim, na medida em que aumenta a
densidade do solo, aumenta a limitação ao crescimento radicular e o armazenamento de água
no solo é reduzido especialmente nas situações de maior compactação. Isso é observado na
camada 0,00 – 0,06 m, que no geral a densidade do solo aumentou e a porosidade total
diminuiu no pós pastejo, e na camada 0,06 – 0,12 m aconteceu o contrário, confirmando o
fato de que a maior pressão exercida pelo pisoteio animal é na camada superficial, exceto para
os valores de resistência do solo à penetração no sistema convencional que tinha lotação
contínua dos animais na pastagem e propiciou camada compactada até próximo dos 25 cm de
profundidade. 26 5 CONCLUSÃO O pisoteio animal alterou somente a microporosidade do solo, ao contrário do que se
tem na literatura, em que o pisoteio animal altera a macroporosidade. Sendo assim, pode-se
concluir que este fato pode ter ocorrido devido que o solo estava muito seco e, neste caso, a
microporosidade é mais facilmente alterada do que a macroporosidade. A utilização de diferentes sistemas de pastejo não promoveu diferenças em relação ao
teor de matéria orgânica. Os solos do sistema de pastejo convencional apresentaram maior tendência à
compactação do solo avaliada pela resistência mecânica a penetração de raízes. 27 BERTOL, I. et al. Propriedades físicas do solo relacionadas a diferentes níveis de ofertas de
forragem de capim-elefante anão cv. Mott. Pesquisa Agropecuária Brasileira, Brasília, v.
35, n. 5, p. 1047-1054, maio 2000. REFERÊNCIAS ABREU, S. L. Propriedades hídricas e mecânicas afetadas por sistemas de manejo e
variabilidade espacial de um Argissolo. 2000. 65p. Dissertação (Mestrado em Agronomia),
Programa de pós-graduação em Agronomia, Universidade Federal de Santa Maria, Santa
Maria, 2000. ABREU, S. L.; REICHERT, J. M.; REINERT, D. J. Escarificação mecânica e biológica para
a redução da compactação em argissolo franco-arenoso sob plantio direto. Revista Brasileira
de Ciência do Solo, v. 28, p. 519-531, 2004. ALBUQUERQUE, J. A.; REINERT, D. J. Densidade radicular do milho considerando os
atributos de um solo com horizonte B textural. Revista Brasileira de Ciência do Solo,
Viçosa, v.25, n.3, p. 539-549, 2001a. ALBUQUERQUE, J. A.; SANGOI, L.; ENDER, M. Efeito da integração lavoura pecuária
nas propriedades físicas do solo e características da cultura do milho. Revista Brasileira de
Ciência do Solo, Lages, v. 25, p. 717-723, 2001b. ALVARENGA, R. C. et al. Crescimento de leguminosas em camadas de solo compactadas
artificialmente. Revista Brasileira de Ciência do Solo, Campinas, v. 20, n. 2, p. 319-326,
maio/ ago. 1996. ANDRADE, C. E. ; SANTOS, M. F. P. Manejo do solo visando maior disponibilidade de
água para a cultura do café. In: ZAMBOLIN, L. Efeitos da irrigação sobre a qualidade e
produtividade do café. Viçosa: UFV, 2004. p. 385-416. ANDRADE, C. L. T. et al. Parâmetros de solo-água para a engenharia de irrigação e
ambiental. In: CONGRESSO BRASILEIRO DE ENGENHARIA AGRÍCOLA, 27, 1998,
Lavras. Anais... Lavras:UFLA/SBEA, 1998. p.1-132. AZEVEDO, E. C. de; SVERZUT, C. B. Alterações dos atributos físicos e químicos do solo
sob pastagem no sudoeste do estado de Mato Grosso. Revista de Agricultura Tropical,
Cuiabá, v. 9, n. 1, 2007. BERTOL, I. et al. Propriedades físicas do solo relacionadas a diferentes níveis de ofertas de
forragem de capim-elefante anão cv. Mott. Pesquisa Agropecuária Brasileira, Brasília, v. 35, n. 5, p. 1047-1054, maio 2000. 28 BERTOL, I.; MAFRA, A. L.; COGO, N. P. Conservação do solo em pastagens. In:
PEDREIRA, C. G. S.; MOURA, J. C.; SILVA, S. C.; FARIA, V. P. As pastagens e o meio
ambiente: Anais do 23º simpósio sobre manejo da pastagem. Piracicaba: FEALQ, 2006. p. 139-163. BEUTLER, A. N.; CENTURION, J. F.; SILVA, A. P. Intervalo hídrico ótimo e a produção de
soja e arroz em dois latossolos. Irriga, Botucatu, v. 9, n. 2, p. 181-192, 2004. BLAKE, G.R.; HARTGE, K. H.Bulk density. IN: KLUTE, A. (Ed). Methods of soil
analysis. 2. ed. DA SILVA, A. P.; et al. Qualidade física de solos sob sistemas intensivos de pastejo
rotacionado. In: SIMPÓSIO SOBRE MANEJO DE PASTAGEM, Inovações tecnológicas no
manejo de pastagens 19, 2002, Piracicaba. Anais... Piracicaba: FEALQ, 2002. p. 79-97. REFERÊNCIAS Madison: American Society of Agronomy/ Soil Science Society of América,
1986. Part. 1, p. 363-375. (Agronomy Monography, 9). BRAIDA, J. A. et al. Relações entre a quantidade de palha existente sobre o solo e a
densidade máxima obtida no ensaio Proctor. In: REUNIÃO BRASILEIRA DE MANEJO E
CONSERVAÇÃO DO SOLO E DA ÁGUA, 15, 2004, Santa Maria, Anais... Santa Maria:
Sociedade Brasileira de Ciência do Solo, 2004. CD-ROM CAMARGO O. A.; ALLEONI, L. R. F. Conceitos gerais de compactação do solo, 2006. Disponível em: <http://www.infobibos.com/Artigos/CompSolo/Comp1.htm>. Acesso em:
05/06/2010. CAMARGO, O. A.; ALLEONI, L. R. F. Compactação do solo e o desenvolvimento das
plantas. Piracicaba, Escola Superior de Agricultura Luiz de Queiroz, 1997. 132p. CASSOL, L. C. Relação solo-planta-animal num sistema de integração lavoura-pecuária
em semeadura direta com calcário na superfície. 2003. 157p. Tese (Doutorado em Ciência
do Solo), Departamento de Agronomia, Universidade Federal do Rio Grande do Sul, Porto
Alegre, 2003. CORREA, J. C.; REICHARDT, K. Efeito do tempo de uso das pastagens sobre as
propriedades de um Latossolo Amarelo da Amazônia Central. Pesquisa Agropecuária
Brasileira, v. 30, p. 107-114, 1995. COSTA, O. V. Impacto animal sobre o componente abiótico do solo: ciclagem de
nutrientes e compactação. (Revisão bibliográfica Forragicultura). UFV, Viçosa, MG, junho
de 2000. DA SILVA, A. P.; et al. Qualidade física de solos sob sistemas intensivos de pastejo
rotacionado. In: SIMPÓSIO SOBRE MANEJO DE PASTAGEM, Inovações tecnológicas no
manejo de pastagens 19, 2002, Piracicaba. Anais... Piracicaba: FEALQ, 2002. p. 79-97. 29 DIAS JÚNIOR, M. S.; PIERCE, F. J. O processo de compactação do solo e a sua modelagem. Revista Brasileira de Ciência do Solo, Viçosa, v. 20, n. 2, p. 175-182, 1996. DIAS JÚNIOR, M. S.; PIERCE, F. J. O processo de compactação do solo e a sua modelagem. Revista Brasileira de Ciência do Solo, Viçosa, v. 20, n. 2, p. 175-182, 1996. FREITAS, P. L. Aspectos físicos e biológicos do solo. In: LANDERS, J. N. Experiências de
plantio direto no Cerrado. Goiânia: APDC, 1994. p. 199-213. DIAS, L. E.; MELLO, J. W. V. de. Recuperação de áreas degradadas. Viçosa: UFV,
Departamento de Solos; SOBRADE, 1998. 251p. GOEDERT, W. Qualidade do solo em sistema de produção agrícola. IN: CONGRESSO
BRASILEIRO DE CIÊNCIA DO SOLO, 2005, Recife. SBCS, v. 1, p. 1-200. MELLO, N. A. Degradação física dos solos sob integração lavoura pecuária. In: ENCONTRO
DE INTEGRAÇÃO LAVOURA-PECUÁRIA NO SUL DO BRASIL, 1, 2002, Pato Branco.
Anais... Pato Branco, 2002. p. 43-60. DIAS, L. E.; MELLO, J. W. V. de. Recuperação de áreas degradadas. Viçosa: UFV,
Departamento de Solos; SOBRADE, 1998. 251p. DIAS, L. E.; MELLO, J. W. V. de. Recuperação de áreas degradadas. Viçosa: UFV,
Departamento de Solos; SOBRADE, 1998. 251p. DIAS-FILHO, M. B.. Pastagens cultivadas na Amazônia Oriental Brasileira: processos e
causas da degradação e estratégias de recuperação. In: DIAS, L. E.; MELLO, J. W. V. (eds.). Recuperação de áreas degradadas. Viçosa, Sociedade Brasileira de Recuperação de Áreas
Degradadas, Universidade Federal de Viçosa, Departamento de Solos, 1998. p.135-147. EMBRAPA. Centro Nacional de Pesquisa de Solos. Sistema brasileiro de classificação de
solos. Brasília: Embrapa Produção de Informação; Rio de Janeiro: Embrapa Solos, 1999. 412
p. EMBRAPA. Centro Nacional de Pesquisa de Solos. Manual e métodos de análise de solo. Rio de Janeiro: Ministério da Agricultura e do Abastecimento, 1997. 212 p. FERNANDES, H. C.; SOUZA, A. P. Compactação dos solos florestais: uma questão de
estudo. Revista Árvore, Viçosa, v. 25, n. 3, p. 387-392, 2001. FIDALSKI, J. et al. Qualidade física do solo em pastagem adubada e sob pastejo contínuo. Pesquisa Agropecuária Brasileira, Brasília, v. 43, n. 11, p. 1583-1590, novembro 2008. FIGUEIREDO, C. C.; RAMOS, M. L. G; TOSTES, R. Propriedades físicas e matéria
orgânica de um latossolo vermelho sob sistemas de manejo e cerrado nativo. Biosci. J.,
Uberlândia, v. 24, n. 3, p. 24-30, jul./set. 2008. FLORES, J. P. C. Atributos de solo e rendimento de soja em um sistema de integração
lavoura-pecuária com diferentes pressões de pastejo em plantio direto com aplicação de
calcário na superfície. 2004. 74p. Dissertação (Mestrado em Ciência do Solo), Departamento
de Agronomia Universidade Federal do Rio Grande do Sul, Porto Alegre , 2004. FLORES, J. P. C. Atributos físicos do solo e rendimento de soja em sistema plantio direto em
integração lavoura pecuária com diferentes pressões de pastejo. Revista Brasileira de
Ciência do Solo, Viçosa, v. 31, n. 4, p. 771-780, jul./ago. 2007. FREITAS, P. L. Aspectos físicos e biológicos do solo. In: LANDERS, J. N. Experiências de
plantio direto no Cerrado. Goiânia: APDC, 1994. p. 199-213. 30 GENRO JÚNIOR, S. A.; REINERT, D. J.; REICHERT, J. M. Variabilidade temporal da
resistência à penetração de um Latossolo argiloso sob semeadura direta com rotação de
culturas. Revista Brasileira de Ciência do Solo, v. 28, p. 477-484, 2004. GIAROLA, N. F. B.; TORMENA, C. A.; DUTRA, A. C. Degradação física de um Latossolo
Vermelho utilizado para produção intensiva de forragem. Revista Brasileira de Ciência do
Solo, Viçosa, v. 31, n. 5, p. 863-873, 2007. GOEDERT, W. Qualidade do solo em sistema de produção agrícola. IN: CONGRESSO
BRASILEIRO DE CIÊNCIA DO SOLO, 2005, Recife. SBCS, v. 1, p. 1-200. IMHOFF, S.; SILVA, A. P. da; TORMENA, C. A. Aplicações da curva de resistência no
controle da qualidade física de um solo sob pastagem. Pesquisa Agropecuária Brasileira,
Brasília, v. 35, n. 7, p. 1493-1500, 2000. LANZANOVA M. E. et al. Atributos físicos do solo em sistema de integração lavoura-
pecuária sob plantio direto. Revista Brasileira de Ciência do Solo, Santa Maria, v. 31, p. 1131-1140, 2007. LEÃO, T. P. et al. Intervalo hídrico ótimo em sistemas de pastejo contínuo e rotacionado. In:
CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 29, 2003, Viçosa. Anais... Viçosa:
Sociedade Brasileira de Ciência do Solo, 2003. 4p. CD-ROM. LEONEL, C. L. et al. Comportamento de forrageiras em diferentes graus de compactação no
Latossolo Vermelho Amarelo Distrófico textura argilosa. In: CONGRESSO BRASILEIRO
DE CIÊNCIA DO SOLO, 29, 2003, Viçosa, Anais... Viçosa: Sociedade Brasileira de Ciência
do Solo. 2003. 4p. CD-ROM. LIMA, C. L. R. et al. Compressibilidade de um solo sob sistemas de pastejo rotacionado
intensivo irrigado e não-irrigado. Revista Brasileira de Ciência do Solo, v. 28, p. 945-951,
2004. MACEDO, M. C. M.; KICHEL, A. N.; ZIMMER, A. H. Degradação e alternativas de
recuperação e renovação de pastagens. Comunicado técnico, Campo Grande: EMBRAPA,
n. 62, novembro 2000. 4p. 31 MENDES, F. G.; MELLONI, E. G. P.; MELLONI, R. Aplicação de atributos físicos do solo
no estudo da qualidade de áreas impactadas em Itajubá-MG. Revista Cerne, Lavras, v. 12, n. 3, p. 211-220, jul./set. 2006. MORAES, A.; LUSTOSA, S. B. C. Efeito do animal sobre as características do solo e a
produção da pastagem. In: SIMPÓSIO SOBRE AVALIAÇÃO DE PASTAGENS COM
ANIMAIS, 1997, Maringá. Anais... Maringá: Universidade Estadual de Maringá, 1997. p. 129-149. MULLER, M. M. L. Degradação de pastagens na Região Amazônica: propriedades físicas do
solo e crescimento de raízes. Pesquisa Agropecuária Brasileira, Brasília, v. 36, n. 11, p. 1409-1418, 2001. NASCIMENTO Jr. Ecossistemas de pastagens cultivadas. In: SIMPÓSIO SOBRE MANEJO
DE PASTAGENS, 15, 1998, Piracicaba. Anais... Piracicaba: FEALQ, 1998. p. 271-296. OLIVEIRA NOBRE, N. A. de. Avaliação dos atributos físicos do solo em três sistemas de
uso e seus impactos na bacia hidrográfica do Rio Carapá em Colíder-MT. 2008. 109 p. Dissertação (Mestrado em Ciências Ambientais), Universidade do Estado de Mato Grosso,
Cáceres, 2008. PRIMAVESI, A. Manejo ecológico de pastagens em regiões tropicais e subtropicais. 5 ed.
São Paulo: Nobel, 1999. p.10-16. PRIMAVESI, A. Manejo ecológico de pastagens em regiões tropicais e subtropicais. 5 ed. São Paulo: Nobel, 1999. p.10-16. RABELO, N. A. Método de Análise (Cadernos Didáticos; 12) Goiânia: Ed. UCG, 2000. 88p. RABELO, N. A. Método de Análise (Cadernos Didáticos; 12) Goiânia: Ed. UCG, 2000. 88p. REICHERT, J. M.; REINERT, D. J.; BRAIDA, J. A. Qualidade do solo e sustentabilidade: de
sistemas agrícolas. Revista Ciência e Ambiente, Ed. 27, p. 29-48, 2003. RESENDE, M. et al. Pedologia: base para distinção de ambientes. 4 ed. Viçosa: NEPUT,
2002. 338p. RODRIGUES JUNIOR; D.J. et al. Compactação do solo e o pisoteio bovino numa
pastagem com e sem irrigação. II Seminário Iniciação Científica – Instituto Federal de
Educação e Tecnologia Triângulo Mineiro, Campus Uberaba, MG. 20 de outubro de 2009. ROSOLEM, C. A. et al. Sistema radicular e nutrição do milho em função da calagem e da
compactação do solo. Revista Brasileira de Ciência do Solo, v. 18, p.491-497, 1994. 32 ROTH, C. H.; CASTRO-FILHO, C.; MEDEIROS, G. B. Análise de fatores físicos e químicos
relacionados com a agregação de um Latossolo Roxo distrófico. Revista Brasileira de
Ciência do Solo, v. 15, p. 241-248, 1992. SALTON, J.C. et al. Pastoreio de aveia e compactação do solo. Revista Plantio Direto, v. 69,
p. 32-34, 2002. SALTON, J.C. et al. Pastoreio de aveia e compactação do solo. Revista Plantio Direto, v. 69,
p. 32-34, 2002. SANTANA, S. C. Indicadores físicos da qualidade de solos no monitoramento de
pastagens degradadas na região sul do Tocantins. 2009. 76 p. Dissertação (Mestrado em
Produção Vegetal), Universidade Federal do Tocantins, Gurupi, 2009. SARMENTO, P. et al. Atributos químicos e físicos de um Argissolo cultivado com Panicum
maximum Jacq. cv. IPR-86 Milênio, sob lotação rotacionada e adubado com nitrogênio. Revista Brasileira de Ciência do Solo, v. 32, p. 183-193, 2008. SILVA, A. J. N. Alterações físicas e químicas de um Argissolo Amarelo Coeso sob
diferentes sistemas de manejo com cana-de-açúcar. 2003. 120p. Tese (Doutorado em
Ciência do Solo). Universidade Federal do Rio Grande do Sul, Porto Alegre, 2003. SILVA, G. J.; MAIA, J. C. S.; BIANCHINI, A. Crescimento da parte aérea de plantas
cultivadas em vaso, submetidas a irrigação subsuperficial e a diferentes graus de compactação
de um Latossolo Vermelho-Escuro distrófico. Revista Brasileira de Ciência do Solo, v. 30,
p. 31-40, 2006. SILVA, V. R.; REINERT, D.; REICHERT, J. M. Densidade do solo, atributos químicos e
sistema radicular do milho afetados pelo pastejo e manejo do solo. Revista Brasileira de
Ciência do Solo, v. 24, p. 191-199, 2000. STOLF, R. Teoria e teste experimental de fórmulas de transformação de dados de
penetrômetro de impacto em resistência do solo. Revista Brasileira de Ciência do Solo,
Campinas, v.15, n.3, p.229-35, 1991. STONE, L. F.; GUIMARÃES, C. M.; MOREIRA, J. A. A. Compactação do solo na cultura
do feijoeiro: I. efeitos nas propriedades físico-hídricas do solo. Revista Brasileira de
Engenharia Agrícola e Ambiental, Campina Grande, v. 6, n. 2, p.207-212, 2002. TAVARES FILHO, J.; EIRA, G. C.; LUDWIG, L. R. F Avaliação da compactação em um
solo cultivado no sistema convencional. Engenharia Agrícola, Jaboticabal, v. 19, p. 219-225,
1999. 33 TAVARES FILHO, J.; RIBON, A. A. Resistência do solo à penetração em resposta ao
número de amostras e tipo de amostragem. Revista Brasileira de Ciência do Solo, v. 32, p. 487-494, 2008. TAVARES FILHO, J.;GRIMALDI, M.; TESSIER, D. Compressibilidade de agregados de
um latossolo amarelo da amazônia em resposta ao potencial da água do solo. Revista
Brasileira de Ciência do Solo, v. 29, p. 489-495, 2005. TORMENA, C. A. et al. Propriedades físicas e taxa de estratificação de carbono orgânico
num Latossolo Vermelho após dez anos sob dois sistemas de manejo. SALTON, J.C. et al. Pastoreio de aveia e compactação do solo. Revista Plantio Direto, v. 69,
p. 32-34, 2002. Revista Brasileira de
Ciência do Solo, Viçosa, v. 28, n. 6, p. 1023-1031, 2004. TORMENA, C. A. et al. Variação temporal do intervalo hídrico ótimo de um latossolo
vermelho distroférrico sob sistemas de plantio direto. Revista Brasileira de Ciência do Solo,
v. 31, p. 211-219, 2007. TORMENA, C. A.; ROLOFF, G. Dinâmica da resistência à penetração de um solo sob
plantio direto. Revista Brasileira de Ciência do Solo, Campinas, v. 20, n. 2, p. 333-339,
1996. TORMENA, C. A.; SILVA, A. P.; LIBARDI, P. Caracterização do intervalo hídrico ótimo de
um Latossolo Roxo sob plantio direto. Revista Brasileira de Ciência do Solo, Viçosa, v. 22,
n. 4, p. 573-581, 1998. TORRES, E.; SARAIVA, O. F. Camadas de impedimento do solo em sistemas agrícolas
com a soja. Circular Técnica, 23. Londrina: Empresa Brasileira de Pesquisa Agropecuária,
1999. 58p. TREIN, C. R.; COGO, N. P.; LEVIEN, R. Métodos de preparo do solo na cultura do milho e
ressemeadura do trevo, na rotação aveia + trevo/milho, após pastejo intensivo. Revista
Brasileira de Ciência do Solo, v. 15, p. 105-111, 1991.
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English
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Multidimensional cerebellar computations for flexible kinematic control of movements
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Nature communications
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cc-by
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Multidimensional cerebellar computations
for flexible kinematic control of movements Akshay Markanday
1,3, Sungho Hong
2,3, Junya Inoue1, Erik De Schutter
2 &
Peter Thier
1 Both the environment and our body keep changing dynamically. Hence,
ensuring movement precision requires adaptation to multiple demands
occurring simultaneously. Here we show that the cerebellum performs the
necessary multi-dimensional computations for the flexible control of different
movement parameters depending on the prevailing context. This conclusion is
based on the identification of a manifold-like activity in both mossy fibers
(MFs, network input) and Purkinje cells (PCs, output), recorded from monkeys
performing a saccade task. Unlike MFs, the PC manifolds developed selective
representations of individual movement parameters. Error feedback-driven
climbing fiber input modulated the PC manifolds to predict specific, error
type-dependent changes in subsequent actions. Furthermore, a feed-forward
network model that simulated MF-to-PC transformations revealed that
amplification and restructuring of the lesser variability in the MF activity is a
pivotal circuit mechanism. Therefore, the flexible control of movements by the
cerebellum crucially depends on its capacity for multi-dimensional
computations. Short-term motor learning is a specific variant of sensorimotor
learning. It provides the ability to rapidly acquire a new control
scheme that allows the motor system to cope with the demands of
often unexpected or sudden changes in the external environment1. Not only external but also internal changes may require fast adjust-
ments. For instance, the motor plant may change due to muscular
fatigue slowing movements. Also, boredom and declining motiva-
tion, i.e., cognitive fatigue will reduce the speed of movements. If not
too extensive, this slowing of movements—the decline of movement
“vigor”—may not necessarily degrade endpoint precision as the
speed reduction can be compensated by cranking up the overall
movement duration, an adjustment of a distinct parameter that
requires the cerebellum2–4. However, behavioral studies indicate
that parametric control by the cerebellum, deployed to swiftly
react to external and internal changes, is not confined to a single
kinematic parameter like movement duration. Rather, work on
goal-directed eye movements as models of cerebellum-based short-
term motor learning has established that adaptation to external and internal changes involves adjustments of several kinematic
parameters2,5–11. How does the cerebellum coordinate the control of multiple
kinematic parameters in order to ensure optimal movements? To
answer this question, we should know at which stage of the cerebellar
neural network the information on the various movement parameters
and necessary adjustments is available and how they are transformed
within the network. Article https://doi.org/10.1038/s41467-023-37981-0 1Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tübingen, Germany. 2Computational Neuroscience Unit, Okinawa Institute of
Science and Technology, Okinawa, Japan. 3These authors contributed equally: Akshay Markanday, Sungho Hong.
e-mail: thier@uni-tuebingen.de Mossy fiber discharge encodes saccade kinematics The saccade-related MFs, all recorded from the oculomotor vermis
(OMV)24,25, could be broadly categorized into three main types —burst-
tonic (BT), short-lead burst (SLB), and long-lead burst (LLB) units
(Fig. 2b, see Methods for details), based on the timing of a burst-
response component and the presence of subsequent tonic discharge. As demonstrated by an exemplary BT unit (Fig. 2a, left panels), a strong
“burst” discharge for saccades made in the preferred leftward hor-
izontal direction was followed by an elevated discharge rate (the tonic
component), that persisted throughout the post-saccadic period and
stopped only when the eyes began to move in the opposite (non-
preferred) direction. Compared to the SLB and BT units that started to
fire vigorously just a few milliseconds before saccade onset (Fig. 2a,
middle; 9 ms in the example), the modulation onset of the LLB units
occurred much earlier (Fig. 2a, right; ~330 ms in the example), reaching
its maximum expression in a ramping manner. Independent of MF unit
type, the discharge rate reached its peak during the saccade and
stopped around the end of saccades, made into a unit´s preferred
direction. The discharge of MFs reflected the trial-to-trial changes in saccade
kinematics. To demonstrate this relationship, we calculated the
population responses for saccades in a unit´s preferred direction,
separately for BT, SLB, and LLB MFs (n = 24, 27, and 60, respectively,
Fig. 2b) and sorted them into bins of PV (bin size = 50 deg/s), ranging
from low to high values (and corresponding changes in saccade
duration). Comparing the MF population responses for the two
extreme bins comprising the lowest and highest velocities, respec-
tively, clearly showed that in all three MF groups (Fig. 2c–e), the peak
firing rate was substantially larger for the high PV bin, associated with
clearly shorter burst duration. Note that in all three classes of MFs, the
peak discharge rate coincided with saccade onset and, moreover, that
not only the saccade profiles but also the associated mean discharge
profiles were clearly less skewed for the high PV bin. This was due to a
shortening of the saccade deceleration phase and a parallel faster
decay of the discharge following the discharge peak. In fact, the peak
discharge rate grew linearly with PV over the full range of PV bins
(Fig. Article lead to conclusions that are biased towards a particular parameter
within a space of multiple encoded movement parameters and, in any
case, it fails to detect information hidden in cell-to-cell variabilities. Unraveling such hidden information in neuronal populations is where
recent studies of the neural dynamics of cortical motor regions have
made remarkable progress17–20. One of the key ideas is that the
apparent
substantial
heterogeneity—high
dimensionality—of
the
responses of individual neurons can be explained by a combination of
a smaller number of underlying patterns, i.e., a low-dimensional latent
structure. This low-dimensional structure, referred to as the “mani-
fold,” captures the essential properties residing inside the population
discharge20–22 concealed by simple averaging across neurons without
the risk of biased conclusions. Markanday et al.23 (Fig. 1d–f). Relative to the early trials, we observed
an overall decrease of 9.9% in the median PV of late centrifugal and
12.1% decrease in late centripetal saccades (Fig. 1d), compensated by
12.2% and 16.5%, respectively, increases in median saccade duration
(Fig. 1e), maintaining the required accuracy (Fig. 1f). On top of these gradual changes, reflecting the consequences of
the development of cognitive fatigue over many trials, we also
observed a within-session, trial-to-trial variability in centrifugal and
centripetal saccade endpoints (“motor noise”), which resulted from
saccades randomly overshooting or undershooting the target (Fig. 1a,
see schematic diagrams with green and yellow-colored arrows). Con-
sequently, both saccade types could result in retinal errors in both
directions that we could resort to when trying to estimate the pre-
ferred error direction of CSs fired by individual PCs as projected on the
left–right axis. Hence, to address if and how the cerebellum accommodates the
multifarious parametric requirements of short-term sensorimotor
learning, here we identify the manifold structure of the activity of key
input and output elements of the cerebellar cortical network, mossy
fibers (MFs) and PCs, of nonhuman primates performing a fatigue-
inducing repetitive saccade task entailing different kinematic changes. We report the multi-dimensional manifolds in the MF and PC-SS
activity that simultaneously encode eye movement velocity and
duration by their geometry and dynamics. We then proceed with
considering the influence of climbing fibers, represented by the PC
complex spike (CS) discharge on the PC manifolds, with a focus on its
function of conveying information on performance error among
others23. Mossy fiber discharge encodes saccade kinematics 2f, h, j), whereas the time of burst offset (see Methods for details)
linearly predicted the time of saccade offset (Fig. 2g, I, k). Even for the
tiniest corrective microsaccades that occurred either during the fixa-
tion period or during the post-saccadic period after under- or over-
shooting saccades, we observed the same linear encoding of these
kinematic parameters by the activity of the three MF types (Supple-
mentary Fig. 1). Article We show that CSs modulate PC manifolds in an error type-
dependent manner that predicts complementary changes in sub-
sequent eye movements by selectively controlling the individual
movement parameters. Finally, we investigate the nature of the inter-
action between the input and output neurons and present evidence
that the underlying network computation amplifies the relatively small
variability in MF responses to transform them into representations of
individual movement parameters, exhibited by PCs in an error-type-
dependent manner. Our results demonstrate an enhanced computa-
tional capacity of PCs that provides the flexible control of more than
one kinematic parameter, ensuring the precision of goal-directed
movements. Velocity-duration adjustments during a fatigue-inducing
repetitive saccade task We trained two monkeys to execute a long series of center-out visually
guided saccades made towards two fixed target locations, left and
right on the horizontal meridian (eccentricity: 15 deg), alternating
between targets, in order to receive a water-based reward at the end of
the movement (Fig. 1a, see Methods for details). As exemplified in Fig. 1b–d, over the course of a session saccades
exhibited a gradual decline in their peak velocity (PV), reflecting a
general loss of motivation (“cognitive fatigue”), arguably due to the
fast and repetitive nature of the task4 (Fig. 1b, up). This gradual drop in
saccade velocities was compensated by a likewise gradual upregula-
tion of saccade duration (Fig. 1b, middle) ensuring that endpoint
accuracy was maintained (Fig. 1b, bottom) within an acceptable range
of error (±2 deg around the target). Since inter-trial intervals were
short (~100 ms), the monkeys had to execute rapid saccades back
towards the fixation point (i.e., centripetal saccades) after every cen-
trifugal saccade to get ready for the subsequent trial. Albeit not
directly rewarded, the kinematic structure and the velocity-duration
adjustments of centripetal saccades were very similar to those of
centrifugal saccades (red and blue traces, Fig. 1b, c). The notion of a
viable velocity-duration tradeoff suggested by the exemplary data
received full support from a behavioral population analysis which was
based on pooled saccades from all sessions in which we had recorded
the responses of 117 MFs and a complementary dataset of saccades
collected while recording from 151 PCs, the latter also the basis of Multidimensional cerebellar computations
for flexible kinematic control of movements Previous studies on saccadic eye movements have
emphasized the control of particular parameters like movement
duration12 or velocity13 by the simple spike (SS) discharge of a popu-
lation of cerebellar Purkinje cells (PCs)—the output currency of cere-
bellar cortex. Although it has been suggested that SS firing rate and
spike time can simultaneously encode the velocity and timing of eye
movement at the individual PC level14, ultimately unifying these
divergent views at the population level is challenged by the large
cell-to-cell variability in the discharge of cerebellar neurons. This
problem is usually addressed by extensive averaging of all or cate-
gorized subsets of neurons in data6,12,13,15,16. However, averaging can Nature Communications| (2023) 14:2548 1 https://doi.org/10.1038/s41467-023-37981-0 Article Simple spikes of Purkinje cells encode saccade kinematics 3d–g and
a
300
500
700
30
50
70
0
5
15
Duration
[ms]
Amplitude
[deg]
Peak velocity
[deg/s]
Right centripetal
100
200
300
100
200
300
Trials
Trials
Left centrifugal
b
c
200 deg/s
20 ms
20 ms
2 deg
400
500
600
700
800
Peak velocity [deg/s]
35
45
55
65
Duration [ms]
14
15
16
Amplitude [deg]
***
***
***
***
ns
ns
d
e
f
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal
OR
left centrifugal
right centripetal
right centrifugal
left centripetal
undershoot
overshoot
undershoot
overshoot
undershoot
overshoot
undershoot
overshoot
centrifugal
centripetal
centrifugal
centripetal
early
late
early
late
Article
https://doi.org/10.1038/s41467-023-37981-0 https://doi.org/10.1038/s41467-023-37981-0 Article a
300
500
700
30
50
70
0
5
15
Duration
[ms]
Amplitude
[deg]
Peak velocity
[deg/s]
Right centripetal
100
200
300
100
200
300
Trials
Trials
Left centrifugal
b
c
OR
left centrifugal
right centripetal
right centrifugal
left centripetal
undershoot
overshoot
undershoot
overshoot
undersh
oversh
centrifugal
centripetal
centrifugal
centripetal
early
late
early
late left centrifugal
right centripetal
undershoot
overshoot
undershoot
overshoot
centrifugal
centripetal a centrifugal c
200 deg/s
20 ms
20 ms
2 deg b c Trials
Trials
400
500
600
700
800
Peak velocity [deg/s]
35
45
55
65
Duration [ms]
14
15
16
Amplitude [deg]
***
***
***
***
ns
d
e
f
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal
Early
centrifugal
Late
centrifugal
Ea
ce Trials
35
45
55
65
Duration [ms]
***
***
e
petal
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal Trials
Trials
400
500
600
700
800
Peak velocity [deg/s]
35
45
55
65
Duration [ms]
***
***
***
***
d
e
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal Trials
400
500
600
700
800
Peak velocity [deg/s]
***
***
d
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal f f 14
15
16
Amplitude [deg]
ns
ns
f
Early
centrifugal
Late
centrifugal
Early
centripetal
Late
centripetal d Amplitude [deg] whereas “burst-pause” and “pause-burst” units exhibited both types of
changes, yet in opposite succession. follow a comparatively simple rule and exhibited a large variability in
their response patterns (see Methods). Simple spikes of Purkinje cells encode saccade kinematics p
p
j
We also recorded 151 OMV PCs and analyzed their SS responses. Whereas MFs exhibited bursting in their preferred saccade direction
and little firing in the non-preferred direction, PC SS patterns for the
two opposite directions—although often clearly different—did not Nature Communications| (2023) 14:2548 2 follow a comparatively simple rule and exhibited a large variability in
their response patterns (see Methods). Therefore, to characterize the
different response patterns and their relation to saccade kinematics we
considered SS responses for centripetal and centrifugal saccades
separately. We classified them into four main categories—burst
(n = 107), pause (n = 99), burst-pause (n = 72) and pause-burst types
(n = 24), using linear discriminant analysis applied to the first two
whereas “burst-pause” and “pause-burst” units exhibited both types o
changes, yet in opposite succession. Pooling the responses of all SS units within each category, sepa
rately for the aforementioned PV bins, we obtained a clear linea
relationship between the firing rate extremes (maximum discharge in
units with burst component, minimal discharge in units with paus
component) and eye velocity for all four SS categories (Fig. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements to unveil multi-dimensional coding of eye movements
However, there is a necessary caveat. Individual units were recorded in
separate sessions. Hence the trial number varied between sessions. Moreover, the behavioral state of a monkey was hardly constant over
sessions. Therefore, we must assume that such differences between
individual sessions might have biased particular velocity bins. For
instance, a session characterized by poor motivation would be
expected to give rise to the emergence of low-velocity bins not found
in sessions of higher motivation and, consequently, confounding
estimates of the influence of PV on neuronal responses at the popu-
lation level. In order to avoid confounded estimates of the kinematic
dependencies of MF and SSs of PC units in our analysis, we resorted to
a computational model that predicted the firing rate of individual MFs
and PC-SSs based on a linear combination of a kinematics-independent
component, namely the mean firing rate of a unit, and a PV- and/or
duration-based modulation as added kinematics-dependent compo-
nents (see Methods, Eq. 1). Finally, by combining the linear models of
individual units, we obtained “pseudo-population” responses of MFs
and PCs to which every unit contributed with an equal number of trials
for any given PV bin as if all units had been recorded simultaneously
during an experimental session22. A step-by-step illustration in Sup-
plementary Fig. 3 shows the reconstruction of neuronal activities
based on Eq. 1, using only PV as the kinematic-dependent parameter to
compute the pseudo-population discharge as an estimate of the true
population response (see also Methods for more details). The population responses estimated by the pseudo-population
model of MFs predicted the actual peak firing rate and duration of the
population burst discharge with high accuracy (Supplementary
Fig. 3e). On the other hand, the pseudo-population model for PC-SSs
also predicted the same quantities significantly, but less well, especially
the burst duration (Supplementary Fig. 3g). Note that the quality of the
prediction did not improve substantially by considering both para-
meters (i.e., PV and duration) or only PV (see Supplementary Fig. 3e, g
and Supplementary Methods). This is expected, since, for the main-
tenance of endpoint precision, a change of one kinematic parameter
must be compensated by a coupled change of the other. Therefore, in
most cases we used the PV-only model to probe the effects of the
compensatory duration change correlated to PV change as in Figs. Simple spikes of Purkinje cells encode saccade kinematics Box plots showing overall reduction of peak velocity (CF: p = 6.51 × 10−18, Z = 8.6; CP:
p = 8.81 × 10−21, Z = 9.3) in late trials (lighter colors) as compared to early (darker
colors) ones which is compensated by the upregulation of saccade duration (CF:
p = 1.31 × 10−20, Z = −9.3; CP: p = 8.81 × 10−21, Z = −9.3) during the late trials to main-
tain amplitude around 15 deg (CF: p = 0.57, Z = 0.6; CP: p = 0.01, Z = 2.5). Each data
point corresponds to the mean value of the early (first 30, dark-colored circles) and
late (last 30, light-colored circles) CF (blue circles) and CP saccades (red circles) of
an individual session (n = 117 sessions). All comparisons based on two-sided Wil-
coxon signed-rank tests. Significant differences are highlighted by asterisks. On
each boxplot, center is median value, lower and upper edges of the box are 25th
and 75th percentiles, respectively, whiskers extend to extreme values and outliers
are marked as “+”. (i.e., last 30 trials, CF: light blue; CP: light red) trials chosen from the experimental
session in b. Data are mean ± SD. d–f Population analysis of 117 behavioral sessions. Box plots showing overall reduction of peak velocity (CF: p = 6.51 × 10−18, Z = 8.6; CP:
p = 8.81 × 10−21, Z = 9.3) in late trials (lighter colors) as compared to early (darker
colors) ones which is compensated by the upregulation of saccade duration (CF:
p = 1.31 × 10−20, Z = −9.3; CP: p = 8.81 × 10−21, Z = −9.3) during the late trials to main-
tain amplitude around 15 deg (CF: p = 0.57, Z = 0.6; CP: p = 0.01, Z = 2.5). Each data
point corresponds to the mean value of the early (first 30, dark-colored circles) and
late (last 30, light-colored circles) CF (blue circles) and CP saccades (red circles) of
an individual session (n = 117 sessions). All comparisons based on two-sided Wil-
coxon signed-rank tests. Significant differences are highlighted by asterisks. On
each boxplot, center is median value, lower and upper edges of the box are 25th
and 75th percentiles, respectively, whiskers extend to extreme values and outliers
are marked as “+”. Fig. 1 | Repetitive saccade task induces a gradual decline in saccade velocity. a Behavioral task. Simple spikes of Purkinje cells encode saccade kinematics However, despite qualitative differences in the CS-ON and OFF direc-
tions obtained by controlling for preferred error directions, the per-
formance of the SS pseudo-population model in predicting the actual
firing rates and burst duration did not improve compared to when
information about CS-ON/-OFF directions was ignored (Supplementary
Fig. 3e), suggesting that large heterogeneity in SS responses still pre-
vailed. To quantify the difference in the kinematics encoding between
MFs and PCs, we performed a PCA on PV-dependent components
(reflecting PV encoding), similar to the PCA on the PV-independent
mean firing rates shown in Fig. 3. We found that many more dimensions
were required in the case of PCs (d = 10), compared to MFs (d = 4), to
explain ~78% of the total variability in the encoding of PV by individual
units (Supplementary Fig. 4e, f), supporting a large discrepancy in the
heterogeneity of PV encoding by MFs and PCs. A possible source of the high unit-to-unit variability could be the mix-
ing of SS responses of individual PCs, each preferring a specific direc-
tion of retinal error. In fact, it has been shown that the conventional
saccade-related SS population averages exhibit higher firing rates if the
saccades considered are made in a direction that is opposite to the
preferred direction of CSs, the latter the direction associated with the
highest probability of observing CSs (CS-ON direction)13. Hence, could
the performance of the PC-SS pseudo-population kinematics predic-
tion be improved by grouping individual PC-SS responses into two
pools that share the preference for error direction, i.e., left and right
error, respectively? Indeed, reorganizing our PC data based on CS
error-tuning, approximated by deciding whether left- or rightward
errors evoked larger CS firing rates, led to a clearer saccade-related
burst around the time of the saccade in the CS-OFF direction, whose
peak clearly modulated with PV (Supplementary Fig. 4a, b), unlike for
saccades made in the CS-ON direction (Supplementary Fig. 4c, d). However, despite qualitative differences in the CS-ON and OFF direc-
tions obtained by controlling for preferred error directions, the per-
formance of the SS pseudo-population model in predicting the actual
firing rates and burst duration did not improve compared to when
information about CS-ON/-OFF directions was ignored (Supplementary
Fig. 3e), suggesting that large heterogeneity in SS responses still pre-
vailed. Simple spikes of Purkinje cells encode saccade kinematics To quantify the difference in the kinematics encoding between
MFs and PCs, we performed a PCA on PV-dependent components
(reflecting PV encoding), similar to the PCA on the PV-independent
mean firing rates shown in Fig. 3. We found that many more dimensions
were required in the case of PCs (d = 10), compared to MFs (d = 4), to
explain ~78% of the total variability in the encoding of PV by individual
units (Supplementary Fig. 4e, f), supporting a large discrepancy in the
heterogeneity of PV encoding by MFs and PCs. Simple spikes of Purkinje cells encode saccade kinematics Therefore, to characterize the
different response patterns and their relation to saccade kinematics we
considered SS responses for centripetal and centrifugal saccades
separately. We classified them into four main categories—burst
(n = 107), pause (n = 99), burst-pause (n = 72) and pause-burst types
(n = 24), using linear discriminant analysis applied to the first two
principal components accrued from a principle component analysis
(PCA) of the discharge patterns (Fig. 3a, c, see Methods). The
responses of typical “burst” and “pause” units were characterized by a
saccade-related increase or decrease in firing rates respectively, Pooling the responses of all SS units within each category, sepa-
rately for the aforementioned PV bins, we obtained a clear linear
relationship between the firing rate extremes (maximum discharge in
units with burst component, minimal discharge in units with pause
component) and eye velocity for all four SS categories (Fig. 3d–g and
Fig. 3h–k). To capture saccade duration-related changes in SS firing, we
relied on the timing of the first discharge rate extreme. As summarized
in Fig. 3l–o, it shifted to later times in burst-pause and pause-burst
units, while showing the same non-significant tendencies in the other Pooling the responses of all SS units within each category, sepa-
rately for the aforementioned PV bins, we obtained a clear linear
relationship between the firing rate extremes (maximum discharge in
units with burst component, minimal discharge in units with pause
component) and eye velocity for all four SS categories (Fig. 3d–g and
Fig. 3h–k). To capture saccade duration-related changes in SS firing, we
relied on the timing of the first discharge rate extreme. As summarized
in Fig. 3l–o, it shifted to later times in burst-pause and pause-burst
units, while showing the same non-significant tendencies in the other Nature Communications| (2023) 14:2548 3 Article https://doi.org/10.1038/s41467-023-37981-0 (i.e., last 30 trials, CF: light blue; CP: light red) trials chosen from the experimental
session in b. Data are mean ± SD. d–f Population analysis of 117 behavioral sessions. Simple spikes of Purkinje cells encode saccade kinematics Saccades were made repetitively, either in left or right directions. All center-out (centrifugal (CF), solid arrows) saccades were rewarded. Centripetal
(CP) saccades (dashed arrows) were not rewarded. Both CF and CP saccades could
lead to errors in leftward (orange arrows) or rightward (green arrows) directions. b Gradual decay of peak velocity (upper panels) in CF (left) and CP (right) saccades
(CF: p = 1.12 × 10−5, Z = 4.4; CP: p = 1.02 × 10−5, Z = 4.4) is paralleled by an increase in
duration (middle panels, CF: p = 1.82 × 10−4, Z = −3.7; CP: p = 1.9 × 10−6, Z = −4.8) to
stabilize amplitudes (lower panels, CF: p = 0.89, Z = −0.1; CP: p = 0.95, Z = 0.1) within
a single session. Comparison based on n = 30 early and late trials, respectively. Each
dot represents data from a single trial. Trends in the data are highlighted by fitting
second-order polynomial fits (dark yellow lines) to the data. All comparisons based
on two-sided Wilcoxon signed-rank tests. c Comparison of horizontal eye position
and velocity profiles of early (i.e., first 30 trials, CF: dark blue; CP: dark red) and late two categories. Hence, one might conclude that the SS discharge of
PCs in our data set encoded both movement velocity13 and duration12,
albeit not as precisely as in the case of MFs. A possible source of the high unit-to-unit variability could be the mix-
ing of SS responses of individual PCs, each preferring a specific direc-
tion of retinal error. In fact, it has been shown that the conventional
saccade-related SS population averages exhibit higher firing rates if the
saccades considered are made in a direction that is opposite to the
preferred direction of CSs, the latter the direction associated with the
highest probability of observing CSs (CS-ON direction)13. Hence, could
the performance of the PC-SS pseudo-population kinematics predic-
tion be improved by grouping individual PC-SS responses into two
pools that share the preference for error direction, i.e., left and right
error, respectively? Indeed, reorganizing our PC data based on CS
error-tuning, approximated by deciding whether left- or rightward
errors evoked larger CS firing rates, led to a clearer saccade-related
burst around the time of the saccade in the CS-OFF direction, whose
peak clearly modulated with PV (Supplementary Fig. 4a, b), unlike for
saccades made in the CS-ON direction (Supplementary Fig. 4c, d). Nature Communications| (2023) 14:2548 Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements f, h, j Average peak firing rate
as a linear function of saccade peak velocity (bin size = 50 deg/s) for each MF category. Linear regression parameters: Burst-tonic (f): p = 0.016, R2 = 0.83; Short- category. Linear regression parameters: Burst-tonic (f): p = 0.016, R2 = 0.83; Short
lead burst (h): p = 0.005, R2 = 0.9; Long-lead burst (j): p = 0.006, R2 = 0.9. Fig. 2 | Encoding of saccade kinematics by mossy fibers (MFs). a Raster plots (up)
and average firing histogram (bottom) of a representative burst-tonic (purple),
short-lead burst (yellow) and long-lead burst (turquoise) MF unit. Solid gray lines
between upper and lower panels are the mean horizontal eye position traces. Data are aligned to saccade onset. b Proportion of MF units in each category. c–e Population response of burst-tonic (purple), short-lead burst (yellow) and long-
lead burst (turquoise) MFs to high and low velocity saccades (see insets for average
velocity profiles), represented by lighter and darker shades, respectively. Solid lines
represent the mean and the shaded regions are ±SEM. f, h, j Average peak firing rate
as a linear function of saccade peak velocity (bin size = 50 deg/s) for each MF g, i, k Average burst offset relative to saccade onset as a function of saccade
duration (calculated from velocity bins) for each MF category. Linear regression
parameters: Burst-tonic (g): p = 0.008, R2 = 0.88; Short-lead burst (i): p = 0.0005,
R2 = 0.96; Long-lead burst (k): p = 0.0005, R2 = 0.97. Solid gray lines represent the
linear regression fits. Light and dark-colored bins correspond to the high and low
peak velocity bins, respectively, for which population responses in c, d and e are
plotted for comparison. Data are mean ± SEM obtained from n = 24 burst-tonic,
n = 60 long-lead burst and n = 27 short-lead burst units, respectively. g
p
g
y
c–e Population response of burst-tonic (purple), short-lead burst (yellow) and long-
lead burst (turquoise) MFs to high and low velocity saccades (see insets for average
velocity profiles), represented by lighter and darker shades, respectively. Solid lines
represent the mean and the shaded regions are ±SEM. f, h, j Average peak firing rate
as a linear function of saccade peak velocity (bin size = 50 deg/s) for each MF (see Methods, Eq. 2). Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements 2
and 3, except for when we investigated the effects of the uncorrelated
changes in PV and duration by the PV and duration-based models, as
discussed later. The relatively poor prediction provided by the pseudo-
population of PC-SSs might be due to a much larger variability of the
kinematics predictions of the individual models, reflected in higher
standard errors of population averages of kinematics-independent and
kinematics-dependent components (Supplementary Fig. 3c, bottom). To mitigate the impact of this apparent large cell-to-cell varia-
bility, we resorted to dimensionality reduced representations of the
pseudo-population responses of MFs and PC-SSs, each given as a linear
combination of components, the first one reflecting the mean
kinematics-independent firing rate and the second, kinematics-
dependent discharge contribution reflecting discharge deviations
due to fluctuations in movement kinematics. To this end, we used the
following approach. First, we ran a PCA on the kinematics-independent
component to identify the number of dimensions explaining a major
chunk of the total cell-to-cell variability of the mean firing rates. However, there is a risk that these dimensions may change due to
spontaneous trial-by-trial changes in PV or duration. Therefore, we
resorted to matrix perturbation theory where we applied minor dis-
turbances in PV or duration resembling trial-to-trial changes in
our data and show that there are no significant changes in these
dimensions as reflected by the eigenvalues of individual dimensions
(Supplementary Fig. 5i). Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements Given that the PCA-derived dimensionality is
stable enough, we finally computed how the result of the first step
would change relative to changes in movement parameters derived
from the same dimensions of the kinematics-dependent component Nature Communications| (2023) 14:2548 4 Long-lead burst
n=60
(51%)
Short-lead
burst
n=27 (23%)
Burst-tonic
n=24
(21%)
b
a
Trials
Firing rate [Hz]
100
200
50
150
250
50
150
250
100
200
100
200
200
400
600
50
150
250
200
400
600
-200
0
100
-100
0
200 -200
0
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-100
200
0
-100
0
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-400
0
100
50
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350
50
150
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350
100
200
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400
50
150
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350
Preferred
Non-preferred
Preferred
Non-preferred
Preferred
Non-preferred
Time from saccade onset [ms]
Time from saccade onset [ms]
Time from saccade onset [ms]
Burst-tonic
Short-lead burst
Long-lead burst
Time from saccade onset [ms]
Firing rate [Hz]
0
100
200
300
50 ms
427 deg/s
689 deg/s
-50
0
50
100
Time from saccade onset [ms]
50 ms
432 deg/s
670 deg/s
-50
0
50
100
0
100
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300
0
50
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200
-50
0
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428 deg/s
669 deg/s
50 ms
Time from saccade onset [ms]
c
d
e
150
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250
Peak firing rate [Hz]
400
500
600 700
Peak velocity
[deg/s]
25
30
35
40
45
Burst offset [ms]
40
50
60
Saccade duration
[ms]
70
Peak firing rate Hz]
150
200
250
300
400
500
600 700
Peak velocity
[deg/s]
25
35
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55
Burst offset [ms]
40 50
60
Saccade duration
[ms]
30
Peak firing rate [Hz]
120
140
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180
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500
600 700
Peak velocity
[deg/s]
Burst offset [ms]
25
30
35
40
20
40
50
60
Saccade duration
[ms]
f
g
h
i
j
k
Misc. n=6
(5%)
Fig. 2 | Encoding of saccade kinematics by mossy fibers (MFs). a Raster plots (up)
and average firing histogram (bottom) of a representative burst-tonic (purple),
short-lead burst (yellow) and long-lead burst (turquoise) MF unit. Solid gray lines
between upper and lower panels are the mean horizontal eye position traces. Data are aligned to saccade onset. b Proportion of MF units in each category. c–e Population response of burst-tonic (purple), short-lead burst (yellow) and long-
lead burst (turquoise) MFs to high and low velocity saccades (see insets for average
velocity profiles), represented by lighter and darker shades, respectively. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements n=6
(5%) a Time from saccade onset [ms]
Firing rate [Hz]
0
100
200
300
50 ms
427 deg/s
689 deg/s
-50
0
50
100
c 0
50
100
150
200
-50
0
50
-100
100
428 deg/s
669 deg/s
50 ms
Time from saccade onset [ms]
e Time from saccade onset [ms]
50 ms
432 deg/s
670 deg/s
-50
0
50
100
0
100
200
300
d
e d c e Time from saccade onset [ms] Time from saccade onset [ms] Peak firing rate Hz]
150
200
250
300
400
500
600 700
Peak velocity
[deg/s]
h [
]
70
Peak firing rate Hz]
150
200
250
300
400
500
600 700
Peak velocity
[deg/s]
25
35
45
55
Burst offset [ms]
40 50
60
Saccade duration
[ms]
30
h
i 150
200
250
Peak firing rate [Hz]
400
500
600 700
Peak velocity
[deg/s]
f [
]
70
25
35
45
55
Burst offset [ms]
40 50
60
Saccade duration
[ms]
30
i [
]
150
200
250
Peak firing rate [Hz]
400
500
600 700
Peak velocity
[deg/s]
25
30
35
40
45
Burst offset [ms]
40
50
60
Saccade duration
[ms]
f
g Peak firing rate [Hz]
120
140
160
180
400
500
600 700
Peak velocity
[deg/s]
Burst offset [ms]
25
30
35
40
20
40
50
60
Saccade duration
[ms]
j
k 25
30
35
40
45
Burst offset [ms]
40
50
60
Saccade duration
[ms]
g 0
Burst offset [ms]
25
30
35
40
20
40
50
60
Saccade duration
[ms]
k h i j f k g Fig. 2 | Encoding of saccade kinematics by mossy fibers (MFs). a Raster plots (up) Fig. 2 | Encoding of saccade kinematics by mossy fibers (MFs). a Raster plots (up)
and average firing histogram (bottom) of a representative burst-tonic (purple),
short-lead burst (yellow) and long-lead burst (turquoise) MF unit. Solid gray lines
between upper and lower panels are the mean horizontal eye position traces. Data are aligned to saccade onset. b Proportion of MF units in each category. c–e Population response of burst-tonic (purple), short-lead burst (yellow) and long-
lead burst (turquoise) MFs to high and low velocity saccades (see insets for average
velocity profiles), represented by lighter and darker shades, respectively. Solid lines
represent the mean and the shaded regions are ±SEM. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements Solid lines
represent the mean and the shaded regions are ±SEM. f, h, j Average peak firing rate
as a linear function of saccade peak velocity (bin size = 50 deg/s) for each MF
category. Linear regression parameters: Burst-tonic (f): p = 0.016, R2 = 0.83; Short-
lead burst (h): p = 0.005, R2 = 0.9; Long-lead burst (j): p = 0.006, R2 = 0.9. g, i, k Average burst offset relative to saccade onset as a function of saccade
duration (calculated from velocity bins) for each MF category. Linear regression
parameters: Burst-tonic (g): p = 0.008, R2 = 0.88; Short-lead burst (i): p = 0.0005,
R2 = 0.96; Long-lead burst (k): p = 0.0005, R2 = 0.97. Solid gray lines represent the
linear regression fits. Light and dark-colored bins correspond to the high and low
peak velocity bins, respectively, for which population responses in c, d and e are
plotted for comparison. Data are mean ± SEM obtained from n = 24 burst-tonic,
n = 60 long-lead burst and n = 27 short-lead burst units, respectively. Article
https://doi.org/10.1038/s41467-023-37981-0 https://doi.org/10.1038/s41467-023-37981-0 Article Long-lead burst
n=60
(51%)
Short-lead
burst
n=27 (23%)
Burst-tonic
n=24
(21%)
b
a
Trials
Firing rate [Hz]
100
200
50
150
250
50
150
250
100
200
100
200
200
400
600
50
150
250
200
400
600
-200
0
100
-100
0
200 -200
0
100
-100
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0
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0
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-400
0
100
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350
50
150
250
350
100
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400
50
150
250
350
Preferred
Non-preferred
Preferred
Non-preferred
Preferred
Non-preferred
Time from saccade onset [ms]
Time from saccade onset [ms]
Time from saccade onset [ms]
Burst-tonic
Short-lead burst
Long-lead burst
Misc. Nature Communications| (2023) 14:2548 Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements This provided a good prediction of the move-
ment parameter-dependent pseudo-population discharge (see Sup-
plementary Methods for mathematical details). For MFs, the first step
found two dimensions that explained 87.6% of the total cell-to-cell
variability (Supplementary Fig. 5b). The second step found that the
first dimension seemed to represent a burst modulation (Supple-
mentary Fig. 5c, top and Fig. 4c, top), similar to the population average
firing whose burst size and duration were modulated by PV. The second dimension (Supplementary Fig. 5c, bottom and Fig. 4c, bot-
tom) represented the sustained responses during the pre- and post-
saccadic period, reminiscent of the long-lead and tonic component of
the LLB and BT MF types, respectively. Here, those components had
opposite signs (rather than being all positive in the average firing
rates), indicating an anti-correlation between the pre- and post-burst
responses. However, in PCs, capturing 92.3% of the total cell-to-cell
variability required four dimensions, where the first two dimensions Nature Communications| (2023) 14:2548 5 Baseline corrected
max firing rate [Hz]
400
500
600
700
Peak velocity [deg/s]
30
35
40
25
60
40
20
Peak timing relative to
saccade onset [ms]
35 40 45 50 55 60
Saccade duration [ms]
d
-40
-20
0
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20 ms
Time from saccade onset [ms]
-100
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Time from saccade onset [ms]
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20 ms
Time from saccade onset [ms]
-100
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e
f
g
Principle component 2 [arb. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements units]
Principle component 1 [arb.units]
-10
-5
0
5
10
-10
-5
0
5
10
Burst-pause
n=72 (23.8%)
Pause
n=99 (32.8%)
Burst
n=107 (35.4%)
Pause-
burst
n=24 (8%)
-300 -200 -100
0
100 200 300
60
120
0
80
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120
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150
Burst
Pause
Burst-pause
Pause-burst
Firing rate [spikes/s]
Time from saccade onset [ms]
Trough timing relative to
saccade onset [ms]
35 40 45 50 55 60
40
35
30
25
20
15
Saccade duration [ms]
-35
-30
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Peak velocity [deg/s]
Baseline corrected
min firing rate [Hz]
15
25
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45
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Peak velocity [deg/s]
Baseline corrected
max firing rate [Hz]
20
15
10
5
0
-5
35 40 45 50 55 60
Saccade duration [ms]
Peak timing relative to
saccade onset [ms]
20
15
10
5
25
Trough timing relative to
saccade onset [ms]
35 40 45 50 55 60
Saccade duration [ms]
-10
-20
-30
-40
Baseline corrected
min firing rate [Hz]
400 500
600
700
Peak velocity [deg/s]
a
b
c
h
i
j
k
l
m
n
o
428 deg/s
427 deg/s
427 deg/s
428 deg/s
670 deg/s
622 deg/s
669 deg/s
670 deg/s
Fig. 3 | Classification of simple spike (SS) responses of Purkinje cells (PCs) into
different categories and their encoding of saccade kinematics. a Scatter plot of
the first two principal components of SS responses. Classification of PCs into four
response categories: burst (blue), pause (orange), burst-pause (green) and pause-
burst (red), separated by decision boundaries (dotted black lines). Each data point
corresponds to a PC’s SS response in one of the two directions. b Saccade onset-
aligned average SS responses of exemplary units taken from each category (large
black circles in a). c The proportion of units in each category. d–g SS population
response (baseline corrected, mean ± SEM) of all four categories to high and low
velocity saccades (see insets for average velocity profiles), represented by lighter
and darker shades, respectively. Data are aligned to saccade onset. h–k Baseline
corrected, average maximum (h, j) and minimum (i, k) firing rates as a function of
saccade peak velocity (bin size = 50 deg/s) for each category. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements Linear regression
parameters: Burst (h): n = 107 units, p = 0.041, R2 = 0.69; Pause (i): n = 99 units,
p = 0.0068, R2 = 0.87; Burst-pause (j): n = 72 units, p = 0.00081 R2 = 0.95; Pause-
burst (k): n = 24 units, p = 0.0059, R2 = 0.88. l–o Average peak (for burst (n = 107)
and burst-pause (n = 72) units; l, n) and trough (for pause (n = 99) and pause-burst
(n = 24) units; m, o) timing relative to saccade onset as a function of saccade
duration (calculated from velocity bins) for each PC category. Linear regression
parameters: Burst (l): p = 0.065, R2 = 0.61; Pause (m): p = 0.087, R2 = 0.56; Burst-
pause (n): p = 0.00015, R2 = 0.98; Pause-burst (o): p = 0.0059, R2 = 0.88. Solid gray
lines represent the linear regression fits. Light and dark-colored bins correspond to
the high and low peak velocity bins, respectively, for which population responses in
d–g are plotted. Data are mean ± SEM. Article
https://doi.org/10.1038/s41467-023-37981-0 Article https://doi.org/10.1038/s41467-023-37981-0 -300 -200 -100
0
100 200 300
60
120
0
80
0
120
0
150
Burst
Pause
Burst-pause
Pause-burst
Firing rate [spikes/s]
Time from saccade onset [ms]
b Principle component 2 [arb. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements units]
Principle component 1 [arb.units]
-10
-5
0
5
10
-10
-5
0
5
10
a Burst-pause
n=72 (23.8%)
Pause
n=99 (32.8%)
Burst
n=107 (35.4%)
Pause-
burst
n=24 (8%)
c a b c a Principle component 1 [arb.units] d
-40
-20
0
20
20 ms
Time from saccade onset [ms]
-100
0
100
200
-20
0
20
40
20 ms
Time from saccade onset [ms]
-100
0
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200
-40
-20
0
20 ms
Time from saccade onset [ms]
-100
0
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Baseline corrected firing rate [Hz]
0
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20 ms
Time from saccade onset [ms]
-100
0
100
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e
f
g
428 deg/s
427 deg/s
427 deg/s
428 deg/s
670 deg/s
622 deg/s
669 deg/s
670 deg/s f d g e 20
15
10
5
25
Trough timing relative to
saccade onset [ms]
35 40 45 50 55 60
Saccade duration [ms]
-10
-20
-30
-40
Baseline corrected
min firing rate [Hz]
400 500
600
700
Peak velocity [deg/s]
k
o Baseline corrected
max firing rate [Hz]
400
500
600
700
Peak velocity [deg/s]
30
35
40
25
h -35
-30
-25
-40
400 500
600
700
Peak velocity [deg/s]
Baseline corrected
min firing rate [Hz]
i -10
-20
-30
-40
Baseline corrected
min firing rate [Hz]
400 500
600
700
Peak velocity [deg/s]
k 15
25
35
45
400 500
600
700
Peak velocity [deg/s]
Baseline corrected
max firing rate [Hz]
j d
j d
i i h k 20
15
10
5
25
Trough timing relative to
saccade onset [ms]
35 40 45 50 55 60
Saccade duration [ms]
y [
g ]
o y
g
20
15
10
5
0
-5
35 40 45 50 55 60
Saccade duration [ms]
Peak timing relative to
saccade onset [ms]
n Trough timing relative to
saccade onset [ms]
35 40 45 50 55 60
40
35
30
25
20
15
Saccade duration [ms]
m 60
40
20
Peak timing relative to
saccade onset [ms]
35 40 45 50 55 60
Saccade duration [ms]
l Fig. 3 | Classification of simple spike (SS) responses of Purkinje cells (PCs) into
different categories and their encoding of saccade kinematics. a Scatter plot of
the first two principal components of SS responses. Classification of PCs into four
response categories: burst (blue), pause (orange), burst-pause (green) and pause-
burst (red), separated by decision boundaries (dotted black lines). Nature Communications| (2023) 14:2548 Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements Each data point
corresponds to a PC’s SS response in one of the two directions. b Saccade onset-
aligned average SS responses of exemplary units taken from each category (large
black circles in a). c The proportion of units in each category. d–g SS population
response (baseline corrected, mean ± SEM) of all four categories to high and low
velocity saccades (see insets for average velocity profiles), represented by lighter
and darker shades, respectively. Data are aligned to saccade onset. h–k Baseline
corrected, average maximum (h, j) and minimum (i, k) firing rates as a function of Fig. 3 | Classification of simple spike (SS) responses of Purkinje cells (PCs) into
different categories and their encoding of saccade kinematics. a Scatter plot of saccade peak velocity (bin size = 50 deg/s) for each category. Linear regression
parameters: Burst (h): n = 107 units, p = 0.041, R2 = 0.69; Pause (i): n = 99 units,
p = 0.0068, R2 = 0.87; Burst-pause (j): n = 72 units, p = 0.00081 R2 = 0.95; Pause-
burst (k): n = 24 units, p = 0.0059, R2 = 0.88. l–o Average peak (for burst (n = 107)
and burst-pause (n = 72) units; l, n) and trough (for pause (n = 99) and pause-burst
(n = 24) units; m, o) timing relative to saccade onset as a function of saccade
duration (calculated from velocity bins) for each PC category. Linear regression
parameters: Burst (l): p = 0.065, R2 = 0.61; Pause (m): p = 0.087, R2 = 0.56; Burst-
pause (n): p = 0.00015, R2 = 0.98; Pause-burst (o): p = 0.0059, R2 = 0.88. Solid gray
lines represent the linear regression fits. Light and dark-colored bins correspond to
the high and low peak velocity bins, respectively, for which population responses in
d–g are plotted. Data are mean ± SEM. the first two principal components of SS responses. Classification of PCs into four
response categories: burst (blue), pause (orange), burst-pause (green) and pause-
burst (red), separated by decision boundaries (dotted black lines). Each data point
corresponds to a PC’s SS response in one of the two directions. b Saccade onset-
aligned average SS responses of exemplary units taken from each category (large
black circles in a). c The proportion of units in each category. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements T-val (Correlated, PV) = 17.97; ***: p = 1.27 × 10−35, T-val (PV, Duration) =
−30.37; ***: p = 2.44 × 10−57, T-val (Correlated vs Duration) = −19.18; ***: p = 4.46 ×
10−38. q Same as p for PCs. T-val (Correlated, PV) = 19.75; p = 5.26 × 10−44, T-val
(PV, Duration) = −47.18; p = 1.36 × 10−92, T-val (Correlated vs Duration) = −48.13;
***: p = 8.24 × 10−94. p Values are from one-sided Student’s t tests. Data are jackknife
mean ± SEM from n = 117 MFs and n = 151 PCs. varying with the correlated (green; a) and independent (orange and blue; f, k)
change of PV and duration. Colors are as the color bars in c, h, m. Right: slope angle
of the lines in left. In computing the angles, the x- and y-coordinates (manifold size
and rotation speed) are normalized by the standard deviation of the correlated
change case. T-val (Correlated, PV) = 17.97; ***: p = 1.27 × 10−35, T-val (PV, Duration) =
−30.37; ***: p = 2.44 × 10−57, T-val (Correlated vs Duration) = −19.18; ***: p = 4.46 ×
10−38. q Same as p for PCs. T-val (Correlated, PV) = 19.75; p = 5.26 × 10−44, T-val
(PV, Duration) = −47.18; p = 1.36 × 10−92, T-val (Correlated vs Duration) = −48.13;
***: p = 8.24 × 10−94. p Values are from one-sided Student’s t tests. Data are jackknife
mean ± SEM from n = 117 MFs and n = 151 PCs. varying with the correlated (green; a) and independent (orange and blue; f, k) Fig. 4 | Manifolds identified in MF and PC-SS activity perform multi- Fig. 4 | Manifolds identified in MF and PC SS activity perform multi
dimensional encoding of eye movements. a Correlated changes in peak velocity
(PV) and duration when PV is used as the only control parameter. b 2D plot of the
first two dimensions in the MF manifold. Triangles and circles mark the saccade
onsets and 250 ms before saccade onsets, respectively. Arrows show the direction
of rotation. c The first two dimensions in b, plotted in time. d, e Same as b, c for PCs. f Isolated changes in saccade PV with the duration kept constant. g, h Isolated PV-
dependent changes in the MF manifold computed from the rate models para-
metrized by PV but with fixed duration. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements d–g SS population
response (baseline corrected, mean ± SEM) of all four categories to high and low
velocity saccades (see insets for average velocity profiles), represented by lighter
and darker shades, respectively. Data are aligned to saccade onset. h–k Baseline
corrected, average maximum (h, j) and minimum (i, k) firing rates as a function of p = 0.0068, R2 = 0.87; Burst-pause (j): n = 72 units, p = 0.00081 R2 = 0.95; Pause-
burst (k): n = 24 units, p = 0.0059, R2 = 0.88. l–o Average peak (for burst (n = 107)
and burst-pause (n = 72) units; l, n) and trough (for pause (n = 99) and pause-burst
(n = 24) units; m, o) timing relative to saccade onset as a function of saccade
duration (calculated from velocity bins) for each PC category. Linear regression
parameters: Burst (l): p = 0.065, R2 = 0.61; Pause (m): p = 0.087, R2 = 0.56; Burst-
pause (n): p = 0.00015, R2 = 0.98; Pause-burst (o): p = 0.0059, R2 = 0.88. Solid gray
lines represent the linear regression fits. Light and dark-colored bins correspond to
the high and low peak velocity bins, respectively, for which population responses in
d–g are plotted. Data are mean ± SEM. manifolds appeared as limit cycle-like rotating trajectories, they
exhibited crucial differences from each other (Supplementary Fig. 5d,
h and Fig. 4b, d). For example, unlike the MF manifolds that were
characterized by an overall PV-related increase in their size almost
symmetrically around the saccade onsets, the PC-SS manifolds based
on the first two dimensions showed no significant changes before
saccade onsets, as depicted by the strong overlapping of the manifolds represented simple monophasic (i.e., bursting or pausing) and bipha-
sic (burst-pause or pause-burst) firing patterns, respectively, whereas
the remaining two dimensions exhibited more complex features
(Supplementary Fig. 5f, g and Fig. 4e). We then plotted the first two of these reduced dimensions as a
function of each other (“2D manifolds”, or in short “manifolds”), both
for MFs and PCs for different values of PV. While both MF and PC Nature Communications| (2023) 14:2548 6 https://doi.org/10.1038/s41467-023-37981-0 Article a
f
l
k
p
Manifold size [arb. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements units]
9
10
11
12
13
Rotation speed
[deg/ms]
3.5
4
4.5
Correlated
PV
Duration
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Change in PV
Change in duration
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c
b
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Dimension 1
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Dimension 2 [arb. units]
j
d
e
i
n
o
Dimension 1
Dimension 2
-0.2
0
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0
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0
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-0.2
0
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Dimension 1
Dimension 2
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100
Time from saccade onset [ms]
0
-0.2
0.2
0
0.2
0.4
0.6
Dimension 1 [arb. units]
Purkinje cells
-0.2
0
0.2
0
0.2
0.4
Dimension 1
Dimension 2
saccade
onset
-0.2
0
0.2
Correlated change
3.8
4
4.2
4.4
Manifold size [arb.units]
0.36 0.38
0.4
0.42
Rotation speed
[deg/ms]
Correlated
PV
Duration
0
45
90
Normalized slope angle [deg]
q
Model parameter: PV
Model parameters:
PV (changed) + Duration (fixed)
Model parameters:
PV (fixed) + Duration (changed)
Dimension 2 [arb. units]
Dimension 2 [arb. units]
Dimension 2 [arb. units]
***
***
***
***
***
***
Fig. 4 | Manifolds identified in MF and PC-SS activity perform multi-
dimensional encoding of eye movements. a Correlated changes in peak velocity
(PV) and duration when PV is used as the only control parameter. b 2D plot of the
first two dimensions in the MF manifold. Triangles and circles mark the saccade
onsets and 250 ms before saccade onsets, respectively. Arrows show the direction
of rotation. c The first two dimensions in b, plotted in time. d, e Same as b, c for PCs. f Isolated changes in saccade PV with the duration kept constant. g, h Isolated PV-
dependent changes in the MF manifold computed from the rate models para-
metrized by PV but with fixed duration. i, j Same as g, h for PCs. k Isolated changes
in saccade duration with constant PV. l–o Same as g, h and i, j but for duration
change. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements i, j Same as g, h for PCs. k Isolated changes
in saccade duration with constant PV. l–o Same as g, h and i, j but for duration
change. p Left: MF manifold size versus rotation speed along the MF manifold of the lines in left. In computing the angles, the x and y coordinates (manifold size
and rotation speed) are normalized by the standard deviation of the correlated
change case. T-val (Correlated, PV) = 17.97; ***: p = 1.27 × 10−35, T-val (PV, Duration) =
−30.37; ***: p = 2.44 × 10−57, T-val (Correlated vs Duration) = −19.18; ***: p = 4.46 ×
10−38. q Same as p for PCs. T-val (Correlated, PV) = 19.75; p = 5.26 × 10−44, T-val
(PV, Duration) = −47.18; p = 1.36 × 10−92, T-val (Correlated vs Duration) = −48.13;
***: p = 8.24 × 10−94. p Values are from one-sided Student’s t tests. Data are jackknife
mean ± SEM from n = 117 MFs and n = 151 PCs. a residual variability, apart from the variability explained by the
velocity-duration tradeoff suggesting complementary changes in PV
and duration. In fact, the natural end-point variability we observed in
saccades is a consequence of these residual variabilities appearing as
slight deviations from the values predicted by the velocity-duration
tradeoff. To capture the residual variability, we independently
manipulated these two kinematic parameters (varying one while
keeping the other fixed) and then tried to identify concomitant
changes in MF manifolds. In fact, a change in PV (Fig. 4f) modulated the
manifold size (i.e., geometry), as well as the time-dependence (i.e.,
rotating neural dynamics). While the manifold size can be interpreted
as the maximal size of firing rate modulation, the rotation speed
represents how rapidly the rate is modulated (Fig. 4g, h, see Methods (Fig. 4a–e). However, the PC manifolds for the third and fourth
dimensions showed clear differences already before saccade onsets
(Supplementary Fig. 5h, bottom). Therefore, PC manifolds based on
different dimensions can selectively encode specific phases of a
movement, preparation and execution, in the same manner as the
“null-space” in cortical manifolds for the preparation of reaching arm
movements18,19, while the MF manifolds lacked this information sui-
table to control specific movement phases. Furthermore, PC manifolds also carried a more disentangled
representation of the two saccade parameters, PV and duration,
compared to MFs. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements p Left: MF manifold size versus rotation speed along the MF manifold
varying with the correlated (green; a) and independent (orange and blue; f, k)
change of PV and duration. Colors are as the color bars in c, h, m. Right: slope angle
of the lines in left. In computing the angles, the x- and y-coordinates (manifold size
and rotation speed) are normalized by the standard deviation of the correlated
change case. T-val (Correlated, PV) = 17.97; ***: p = 1.27 × 10−35, T-val (PV, Duration) =
−30.37; ***: p = 2.44 × 10−57, T-val (Correlated vs Duration) = −19.18; ***: p = 4.46 ×
10−38. q Same as p for PCs. T-val (Correlated, PV) = 19.75; p = 5.26 × 10−44, T-val
(PV, Duration) = −47.18; p = 1.36 × 10−92, T-val (Correlated vs Duration) = −48.13;
***: p = 8.24 × 10−94. p Values are from one-sided Student’s t tests. Data are jackknife
mean ± SEM from n = 117 MFs and n = 151 PCs. Article
https://doi.org/10.1038/s41467-023-37981-0 a
c
b
Dimension 1
Dimension 2
0
1
2
-1
-0.5
0
0.5
500
580
660
PV [deg/s]
Mossy fibers
-1
0
1
Dimension 2 [arb. units]
d
e
Purkinje cells
-0.2
0
0.2
0
0.2
0.4
Dimension 1
Dimension 2
saccade
onset
-0.2
0
0.2
Correlated change
Model parameter: PV
Dimension 2 [arb. units] c
Dimension 1
Dimension 2
0
1
2
-1
-0.5
0
0.5
500
580
660
PV [deg/s]
Mossy fibers
d
e
Purkinje cells
-0.2
0
0.2
0
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0.4
Dimension 1
Dimension 2
saccade
onset
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0
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Dimension 2 [arb. units] Mossy fibers a
f
Change in PV
g
b
h
500
580
660
PV [deg/s]
Dimension 1
0
1
2
-1
0
1
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-1
0
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Dimension 2 [arb. units]
Dimensi
Dimension 2
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500
PV [
-1
0
1
Dimension 2 [arb. units]
j
d
i
Dimension 1
Dimension 2
-0.2
0
0.2
0
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0.4
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Dimensio
Dimension 2
saccade
onset
-0.2
0
0.2
Model parameter: PV
Model parameters:
PV (changed) + Duration (fixed)
Dimension 2 [arb. units]
Dimension 2 [arb. units f
Change in PV
g
h
500
580
660
PV [deg/s]
Dimension 1
0
1
2
-1
0
1
Dimension 2
-1
0
1
Dimension 2 [arb. Nature Communications| (2023) 14:2548 Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements units]
D
-1
j
i
Dimension 1
Dimension 2
-0.2
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0.2
0
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D
Model parameter: PV
Model parameters:
PV (changed) + Duration (fixed)
Dimension 2 [arb. units] j
i
Dimension 1
Dimension 2
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Change in PV
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Dimension 1
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Dimension 2 [arb. units]
i
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-0.2
0.2
Model parameters:
PV (changed) + Duration (fixed)
Dimension 2 [arb. units] j l
k
Change in duration
m
35
45
55
Duration [ms]
Dimension 1
0
1
2
-1
0
1
Dimension 2
Time from saccade onset [ms]
0
100
Dimension 1 [arb. units]
0
1
2
3
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1
Dimension 2 [arb. units]
PV (changed) Duration (fixed)
Model parameters:
PV (fixed) + Duration (changed) n
o
-0.2
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0.2
0
0.2
0.4
Dimension 1
Dimension 2
0
100
Time from saccade onset [ms]
0
-0.2
0.2
0
0.2
0.4
0.6
Dimension 1 [arb. units]
Dimension 2 [arb. units] k 3.8
4
4.2
4.4
Manifold size [arb.units]
0.36 0.38
0.4
0.42
Rotation speed
[deg/ms]
q 3.8
4
4.2
4.4
Manifold size [arb.units]
0.36 0.38
0.4
0.42
Rotation speed
[deg/ms]
Correlated
PV
Duration
0
45
90
Normalized slope angle [deg]
q
***
***
*** arb.units]
4
0.42
Correlated
PV
Duration
0
45
90
Normalized slope angle [deg]
***
***
*** p
Manifold size [arb. units]
9
10
11
12
13
Rotation speed
[deg/ms]
3.5
4
4.5
N
li
d l
l
[d
] p
Manifold size [arb. units]
9
10
11
12
13
Rotation speed
[deg/ms]
3.5
4
4.5
Correlated
PV
Duration
0
45
90
Normalized slope angle [deg]
***
***
*** Correlated
PV
Duration
0
45
90
Normalized slope angle [deg]
***
***
*** Normalized slope angle [deg] Normalized slope angle [deg] p varying with the correlated (green; a) and independent (orange and blue; f, k)
change of PV and duration. Colors are as the color bars in c, h, m. Right: slope angle
of the lines in left. In computing the angles, the x- and y-coordinates (manifold size
and rotation speed) are normalized by the standard deviation of the correlated
change case. PC manifolds reveal the structure of plasticity triggered by
sensorimotor errors Left: An undershooting
eye movement causes an outward error (orange) and CS firing in a population of
PCs with the same CS-ON direction (red) but not in the other, CS-OFF PCs (gray). Right: Same as Left for an overshooting saccade causing an inward error (blue). b Left: PC manifolds reflecting the combined influence of simulated outward error-
encoding CS firing pattern on a particular trial, obtained by combining CS trials of
CS-ON PCs (red circles) and no-CS trials of CS-OFF PCs (gray circles), on subsequent
trials. Note that, in simulated error trials we assume that CS-ON PCs reported an
error by firing a CS during 50–140 ms after saccade offset, whereas CS-OFF PCs
reported the same error by not firing a CS, irrespective of the actual presence of an
error. Right: same as Left, but for the inward error. c Top: manifold size versus
rotation speed after the outward (orange) and inward (blue) error-encoding
CS trials, and after no-CS trials (gray). Color bar gradient represents PV from
500 deg/s (brightest) to 660 deg/s (darkest). Bottom: comparison of normalized
slope angles for each condition. Data are jackknife mean ± SEM from n = 151 PCs. T-val (No-CS, Outward) = 4.11; ***: p = 3.18 × 10−5, T-val (Outward, Inward) =
−20.76; ***: p = 2.20 × 10−46, T-val (No-CS, Inward) = −25.33; ***: p = 1.54 × 10−56. p Values are from one-sided Student’s t tests. d Top: average saccade velocity
profiles in the CS (black) and post-CS trials (colored) for the simulated outward
(left) and inward (right) errors. For highlighting the differences in velocity profiles,
colored lines represent the cumulative effect of five CSs. Bottom: average eye
velocity change from the CS to post-CS trials. Data are mean ± SEM. *p < 0.05 (two-
sided Student’s t test). To understand how the occurrence of CS impacts the multi-
dimensional encoding of eye movements, we investigated how CSs
fired during the post-saccadic period of 50–140 ms in the nth trial (“CS
trial”), reflecting retinal errors arising from natural end-point varia-
bility in saccades23, modulated the PC-SS manifolds of the subsequent,
n + 1th trials (“Post-CS trial”). In our paradigm, errors occurred mainly
when the primary saccade undershot (outward error) or overshot
(inward error) the target location (Fig. 5a). Depending on the direction
of the primary saccade, these inward and outward errors could occur
in both left and right directions (Fig. 1a). Article units]
0
0.2
0.4
0.6
0
0.2
0.4
0.6
b
d
Post-CS trials for
simulated outward error
Post-CS trials for
simulated inward error no-CS
outward
inward
0
45
90
Normalized slope angle [deg]
CS
***
***
Manifold size
[arb. units]
3.6
3.8
4
Rotation speed [deg/ms]
0.35
0.4
0.45
c
no-CS
outward
inward b Eye velocity [deg/s]
Dimension 1 [arb. units]
during CS
post-CS/outward
post-CS/inward
d
0
0.2
0.4
0.6
103
Time from saccade onset [ms]
-20
-10
0
0
20
40
60
Velocity [deg/s]
0
20
40
60
PV increases
Duration
decreases
10 Normalized slope angle [deg] Article for calculating manifold size and rotation-speed). Therefore, in terms
of behavior, an increase in the manifold size can be linked to an
increase in the PV of saccades, whereas a higher rotation speed of the
manifold would suggest shorter saccade duration. Manipulating the
saccade duration (Fig. 4k) also modified the MF manifolds (Fig. 4l, m)
in a manner quite similar to the one resulting from correlated changes
in PV and duration (Fig. 4a) where the perfect velocity-duration tra-
deoff is assumed. In contrast, PV (Fig. 4i, j) and saccade duration
(Fig. 4n, o) varied the PC manifold size and rotating neural dynamics
almost independently. These effects are summarized by the curves
obtained by plotting the average rotation speed as a function of
manifold size and their corresponding slope angles (Fig. 4p, q). Com-
pared to the correlated change case (green in Fig. 4p, q), the curves
with steeper slopes (or larger angles) indicate a bias towards the
rotation speed (related to duration) adjustment, whereas smaller slope
angles suggest stronger changes in the manifold size (related to PV). Therefore, while the slope angles were all comparable in the case of
MFs (Fig. 4p), the PV and duration variation resulted in nearly ortho-
gonal curves in the case of PCs, indicating almost completely dec-
orrelated encoding of the two kinematic parameters (Fig. 4q). vector, leading to CS trials, and in others not, leading to “No-CS” trials. For a given error in the nth trial, we looked at its influence on the entire
population of PCs in our data set and the consequences for the SS
manifolds of the n + 1th trials, rather than restricting our analysis to only
CS-ON units (see Supplementary Fig. 7b), assuming that the behavior is
based on the concerted action of both subpopulations. To this end, we
combined trials following CS-trials from the pool of CS-ON PCs (i.e.,
post-CS trials) and “No-CS” trials from CS-OFF PCs (“Post-no CS trials”),
separately for outward (Fig. 5b, left) and inward errors (Fig. 5b, right). Importantly, we included all “CS trials” from CS-ON PCs (regardless of
whether the actual error occurred or not) assuming that every CS in
the error time window of 50–140 ms after the saccade was fired to
report an error (referred to as simulated error trials in Fig. 5, see
Supplementary Fig. 7a for a detailed illustration). Article Eye velocity [deg/s]
Target
location
-0.2
0
0.2
Dimension 2
[arb. units]
500
580
660
PV [deg/s]
Dimension 1 [arb. units]
0
0.2
0.4
0.6
0
0.2
0.4
0.6
during CS
post-CS/outward
post-CS/inward
a
b
d
no-CS
outward
inward
0
45
90
Normalized slope angle [deg]
outward error
inward error
primary saccade
inward CS-ON PCs
outward CS-ON PCs
no CS
CS
0
0.2
0.4
0.6
103
Time from saccade onset [ms]
-20
-10
0
0
20
40
60
Velocity [deg/s]
0
20
40
60
PV increases
Duration
decreases
(undershoot)
(overshoot)
Post-CS trials for
simulated outward error
Post-CS trials for
simulated inward error
***
***
Manifold size
[arb. units]
3.6
3.8
4
Rotation speed [deg/ms]
0.35
0.4
0.45
c
no-CS
outward
inward
10
Fig. 5 | Complex spike (CS)-driven plasticity of PC manifolds is error-state
dependent and predicts eye movement change. a Two different types of eye
movement errors and CS firing in PCs encoding the errors. Left: An undershooting
eye movement causes an outward error (orange) and CS firing in a population of
PCs with the same CS-ON direction (red) but not in the other, CS-OFF PCs (gray). Right: Same as Left for an overshooting saccade causing an inward error (blue). b Left: PC manifolds reflecting the combined influence of simulated outward error-
encoding CS firing pattern on a particular trial, obtained by combining CS trials of
CS-ON PCs (red circles) and no-CS trials of CS-OFF PCs (gray circles), on subsequent
trials. Note that, in simulated error trials we assume that CS-ON PCs reported an
error by firing a CS during 50–140 ms after saccade offset, whereas CS-OFF PCs
reported the same error by not firing a CS, irrespective of the actual presence of an
error. Right: same as Left, but for the inward error. c Top: manifold size versus
rotation speed after the outward (orange) and inward (blue) error-encoding
CS trials, and after no-CS trials (gray). Color bar gradient represents PV from
500 deg/s (brightest) to 660 deg/s (darkest). Bottom: comparison of normalized
slope angles for each condition. Data are jackknife mean ± SEM from n = 151 PCs. T-val (No-CS, Outward) = 4.11; ***: p = 3.18 × 10−5, T-val (Outward, Inward) =
−20.76; ***: p = 2.20 × 10−46, T-val (No-CS, Inward) = −25.33; ***: p = 1.54 × 10−56. p Values are from one-sided Student’s t tests. Article d Top: average saccade velocity
profiles in the CS (black) and post-CS trials (colored) for the simulated outward
(left) and inward (right) errors. For highlighting the differences in velocity profiles,
colored lines represent the cumulative effect of five CSs. Bottom: average eye
velocity change from the CS to post-CS trials. Data are mean ± SEM. *p < 0.05 (two-
sided Student’s t test). Eye velocity [deg/s]
Target
location
-0.2
0
0.2
Dimension 2
[arb. units]
500
580
660
PV [deg/s]
Dimension 1 [arb. units]
0
0.2
0.4
0.6
0
0.2
0.4
0.6
during CS
post-CS/outward
post-CS/inward
a
b
d
no-CS
outward
inward
0
45
90
Normalized slope angle [deg]
outward error
inward error
primary saccade
inward CS-ON PCs
outward CS-ON PCs
no CS
CS
0
0.2
0.4
0.6
103
Time from saccade onset [ms]
-20
-10
0
0
20
40
60
Velocity [deg/s]
0
20
40
60
PV increases
Duration
decreases
(undershoot)
(overshoot)
Post-CS trials for
simulated outward error
Post-CS trials for
simulated inward error
***
***
Manifold size
[arb. units]
3.6
3.8
4
Rotation speed [deg/ms]
0.35
0.4
0.45
c
no-CS
outward
inward
10
Fig 5 | Complex spike (CS) driven plasticity of PC manifolds is error state Centrifugal saccades could be either leftwards or rightwards, but,
notably, we found that our results did not depend on saccade direc-
tion. To test the potential influence of saccade direction on MF and PC
manifolds, we performed the same analysis on MF and PC data sepa-
rately for leftward and rightward saccades. For MFs, the left and right
groups showed comparable results (Supplementary Fig. 6a, b) as
suggested by high canonical correlations yielded by a canonical cor-
relation analysis (CCA)21,26 (Supplementary Fig. 6c). In the PC case, the
size of the manifold was much larger for saccades in the rightward
direction as compared to leftward saccades (Supplementary Fig. 6d, e). Since around 80% of the recorded PCs had their CS-OFF in the right-
ward direction, the direction-dependent differences in the size of
these manifolds are not surprising and only confirm the gain-field
encoding of SSs13 (Supplementary Fig. 6g–i).Nevertheless, the shape of
these manifolds was highly similar (Supplementary Fig. 6f). Therefore,
MFs and PCs had qualitatively identical manifold structures regardless
of the eye movement direction. -0.2
0
0.2
Dimension 2
[arb. units]
500
580
660
PV [deg/s]
Dimension 1 [arb. PC manifolds reveal the structure of plasticity triggered by
sensorimotor errors Time from saccade onset [ms] In the prevailing theory for cerebellum-dependent sensorimotor
learning, the climbing fiber-driven CSs convey motor error-related
information to prompt parametric adjustments for correcting future
motor behavior, thereby acting as “teacher signals”27–29. Therefore,
motor learning has been attributed to these CSs, serving as a proxy of
sensory feedback on motor errors that, when coincident with the
parallel fiber inputs, modify the PC output by inducing a long-term
depression (LTD) at the parallel fiber-PC synapses30. Fig. 5 | Complex spike (CS)-driven plasticity of PC manifolds is error-state
dependent and predicts eye movement change. a Two different types of eye
movement errors and CS firing in PCs encoding the errors. Left: An undershooting
eye movement causes an outward error (orange) and CS firing in a population of
PCs with the same CS-ON direction (red) but not in the other, CS-OFF PCs (gray). Right: Same as Left for an overshooting saccade causing an inward error (blue). b Left: PC manifolds reflecting the combined influence of simulated outward error-
encoding CS firing pattern on a particular trial, obtained by combining CS trials of
CS-ON PCs (red circles) and no-CS trials of CS-OFF PCs (gray circles), on subsequent
trials. Note that, in simulated error trials we assume that CS-ON PCs reported an
error by firing a CS during 50–140 ms after saccade offset, whereas CS-OFF PCs
reported the same error by not firing a CS, irrespective of the actual presence of an
error. Right: same as Left, but for the inward error. c Top: manifold size versus
rotation speed after the outward (orange) and inward (blue) error-encoding
CS trials, and after no-CS trials (gray). Color bar gradient represents PV from
500 deg/s (brightest) to 660 deg/s (darkest). Bottom: comparison of normalized
slope angles for each condition. Data are jackknife mean ± SEM from n = 151 PCs. T-val (No-CS, Outward) = 4.11; ***: p = 3.18 × 10−5, T-val (Outward, Inward) =
−20.76; ***: p = 2.20 × 10−46, T-val (No-CS, Inward) = −25.33; ***: p = 1.54 × 10−56. p Values are from one-sided Student’s t tests. d Top: average saccade velocity
profiles in the CS (black) and post-CS trials (colored) for the simulated outward
(left) and inward (right) errors. For highlighting the differences in velocity profiles,
colored lines represent the cumulative effect of five CSs. Bottom: average eye
velocity change from the CS to post-CS trials. Identifying manifolds from pseudo-populations of MFs and PCs
to unveil multi-dimensional coding of eye movements To arrive atthisconclusion, we estimated the PV and
duration-based models of MFs and PC-SSs. Since PV and duration in
our data are highly, yet not perfectly correlated, these parameters had 7 Nature Communications| (2023) 14:2548 7 https://doi.org/10.1038/s41467-023-37981-0 Article PC manifolds reveal the structure of plasticity triggered by
sensorimotor errors Data are mean ± SEM. *p < 0.05 (two-
sided Student’s t test). Fig. 5 | Complex spike (CS)-driven plasticity of PC manifolds is error-state Fig. 5 | Complex spike (CS)-driven plasticity of PC manifolds is error-state
dependent and predicts eye movement change. a Two different types of eye
movement errors and CS firing in PCs encoding the errors. Left: An undershooting
eye movement causes an outward error (orange) and CS firing in a population of
PCs with the same CS-ON direction (red) but not in the other, CS-OFF PCs (gray). Right: Same as Left for an overshooting saccade causing an inward error (blue). b Left: PC manifolds reflecting the combined influence of simulated outward error-
encoding CS firing pattern on a particular trial, obtained by combining CS trials of
CS-ON PCs (red circles) and no-CS trials of CS-OFF PCs (gray circles), on subsequent
trials. Note that, in simulated error trials we assume that CS-ON PCs reported an
error by firing a CS during 50–140 ms after saccade offset, whereas CS-OFF PCs
reported the same error by not firing a CS, irrespective of the actual presence of an
error. Right: same as Left, but for the inward error. c Top: manifold size versus
rotation speed after the outward (orange) and inward (blue) error-encoding
CS trials, and after no-CS trials (gray). Color bar gradient represents PV from
500 deg/s (brightest) to 660 deg/s (darkest). Bottom: comparison of normalized
slope angles for each condition. Data are jackknife mean ± SEM from n = 151 PCs. T-val (No-CS, Outward) = 4.11; ***: p = 3.18 × 10−5, T-val (Outward, Inward) =
−20.76; ***: p = 2.20 × 10−46, T-val (No-CS, Inward) = −25.33; ***: p = 1.54 × 10−56. p Values are from one-sided Student’s t tests. d Top: average saccade velocity
profiles in the CS (black) and post-CS trials (colored) for the simulated outward
(left) and inward (right) errors. For highlighting the differences in velocity profiles,
colored lines represent the cumulative effect of five CSs. Bottom: average eye
velocity change from the CS to post-CS trials. Data are mean ± SEM. *p < 0.05 (two-
sided Student’s t test). Fig. 5 | Complex spike (CS)-driven plasticity of PC manifolds is error-state
dependent and predicts eye movement change. a Two different types of eye
movement errors and CS firing in PCs encoding the errors. Linear feed-forward network model shows high-dimensional
transformations by the cerebellar cortex We addressed this question by two approaches, both leading to
the conclusion that the number of dimensions that need to be con-
sidered while trying to account for the properties of MF activity is
definitely much smaller than the maximum number of dimensions,
dMF = 116 (corresponding to the number of MFs used in this analysis), Eye movement error-triggered CS firing is not restricted to our
chosen post-saccadic error period of 50–140 ms15,23. Hence, how would
CSs that fired at other time points influence the SS manifolds? We b
c
0.8
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a
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MF
0
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MF manifold with
d dimensions
d =116
MF
MF
R2
1
10
20
30
PC
MF
d -dimensional
MF manifold
MF
Tij
predicted
PC manifold
reduce
dimensionality
approximate
individual firings
by manifold
Fig. 6 | Linear feed-forward network (LFFN) model from MFs to PCs. a Left:
schematic diagram showing LFFN for MF-to-PC firing rate transformation. Right:
weight matrix computed from the data. Horizontal color bars on the top corre-
spond to the three MF categories (BT burst-tonic, LL long-lead burst, SL short-lead
burst). b Goodness of fit (R2) for individual PCs. The horizontal bar represents the
median and the vertical bar extends from the first to third quantile, respectively. Colored circles correspond to examples shown in c. c Firing rates of example PCs
(black, top and bottom) and LFFN predictions (color). The baselines are subtracted
in the PV-independent component (left). d LFFN prediction of PC manifolds in
Fig. 4d using all dimensions in MF firing. Article Article We found that CS firing associated with inward and outward
errors modified the resulting PC-SS manifolds, based on PV as the
kinematic-dependent parameter, differently (Fig. 5c, top). Relative to
the “Post-no-CS” trials, the normalized slope angle, capturing changes
in PV-dependent manifold size relative to the rotation speed, pro-
foundly increased in the post-inward error trials but decreased, albeit
only slightly, for post-outward error trials (Fig. 5c, bottom). Could it be
that this result may be influenced by the actual error direction, rather
than error type? Our analysis comparing inward and outward errors
made in the same direction revealed that the PC-SS manifolds of
subsequent trials maintained their specificity for inward and outward
errors, even if their vectors pointed in the same direction (Supple-
mentary Fig. 7c–e). Given that the PC manifold size and speed of the
latent dynamics encode PV and saccade duration almost indepen-
dently (Fig. 4q), this result suggested that CSs associated with inward
and outward errors, potentially engaging the same population of PCs,
tuned the population firing more towards duration coding in post-
inward error trials (more compensatory duration change given PV) and
PV coding in post-outward error trials (more compensatory PV change
given duration). tested the influence of relatively late CSs during 140–250 ms from
saccade offset23. We found that those late CSs also modified the SS
manifolds of post-simulated inward and outward error trials, albeit
differently from the earlier ones (Supplementary Fig. 8). These late CSs
modified the PC-SS manifold in a way that prompted adjustments only
in the duration of the subsequent saccades, for both inward and out-
ward errors. Therefore, the CS timing may play an additional role in the
selective control of kinematic parameters. Linear feed-forward network model shows high-dimensional
transformations by the cerebellar cortex We demonstrated that, despite the similar limit-cycle-like properties of
MF and PC manifolds, there were crucial differences in their encoding
of kinematic parameters, especially for PCs which also exhibited a
large heterogeneity in their kinematics-independent and kinematics-
dependent components. The climbing fiber-driven CSs clearly explain
some of the differences between the two (Fig. 5 and Supplementary
Fig. 6). However, additional inputs to PCs arriving from interneurons
may also play a significant role. The role of input from climbing fibers and interneurons not-
withstanding, we found that already a linear feed-forward network
(LFFN) from MFs to PCs33 (Fig. 6a), not considering the aforesaid ele-
ments,
was
able
to
predict
the
kinematics-independent
and
kinematics-dependent activity components of all individual PCs with
high fidelity (R2 = 0.984 ± 0.018, mean ± SD) (Fig. 6b, c), allowing us to
successfully reproduce the PC-SS manifolds from the MF activity
(Fig. 6d; see also Supplementary Fig. 9a–c). But how is it possible that
already a simple linear transformation can explain the many differ-
ences between MF and PC-SS manifolds? This paradox led us to
examine how many dimensions of MF (dMF) firing are necessary to
make good predictions of the PC manifold. Therefore, one would expect to see a reduction in subsequent
saccade’s duration if a CS signal reporting an inward error, caused by
an overshooting saccade in the previous trial, was present. On the
other hand, in case of an outward error (i.e., undershooting saccade),
CSs should trigger an increase in the PV of the next trial to reduce
endpoint error. Indeed, this is what we found. When comparing the
movement velocity of saccades accompanied by a CS to post-CS sac-
cades, we observed that outward errors (undershooting) were cor-
rected mainly through increasing the PV of the subsequent saccade
with a slight increase in the velocity at the end of the saccade (Fig. 5d,
left). In contrast, inward error-encoding CSs prompted a significant
decrease in the duration of the subsequent saccade, reflected by the
narrowing of its velocity profile (Fig. 5d, right). Linear feed-forward network model shows high-dimensional
transformations by the cerebellar cortex e Schematic diagram of the LFFN model
showing steps involved (from bottom to top) in the prediction of PC manifolds
from dMF-dimensional MF manifolds. f Examples of the predicted PC manifold from
e when MF manifold dimension is dMF = 2 (left), 4 (middle), and 20 (right). g Goodness of fit for the predicted PC manifold to the data versus the input MF
manifold dimensions dMF. Dots represent examples in f. Data are mean ± SEM. b
c
0.8
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Firing rate [Hz]
PV-independent
PC
LFFN
PC
LFFN
Time from saccade onset [ms]
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0 b c a
Tij
MFi
PCj
input
output
weight
matrix
Linear feed-forward network
(LFFN) 20
60
100
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LL
SL
weight Tij
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PV-dependent
0
Time from saccade onset [ms]
-200
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0 PC
Linear feed-forward network
(LFFN) Firing rate / PV[Hz/(deg/s)] PV-dependent MFi g
d =2
MF
d =4
MF
d =20
MF
f
Dimension 1 [arb. units]
0
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MF
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MF manifold with
d dimensions
d =1
MF
MF
R2
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d =116
MF
Dimension 1 [arb. units]
-0.2
0
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500
580
660
PV [deg/s]
0
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MF dimensions [d ]
MF
0
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full model,
MF manifold with
d dimensions
d =116
MF
MF
R2
1
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30 f
-
Dimension 2 [arb. units] d
-
Dimension 2 [arb. units] e
i
PC
MF
d -dimensional
MF manifold
MF
Tij
predicted
PC manifold
reduce
dimensionality
approximate
individual firings
by manifold g e d f Dimension 1 [arb. units] in the PV-independent component (left). d LFFN prediction of PC manifolds in in the PV-independent component (left). d LFFN prediction of PC manifolds in
Fig. 4d using all dimensions in MF firing. e Schematic diagram of the LFFN model
showing steps involved (from bottom to top) in the prediction of PC manifolds
from dMF-dimensional MF manifolds. f Examples of the predicted PC manifold from
e when MF manifold dimension is dMF = 2 (left), 4 (middle), and 20 (right). PC manifolds reveal the structure of plasticity triggered by
sensorimotor errors Therefore, depending on the
CS-ON direction of individual PCs, the inward and outward errors will
elicit CSs with high probability in those PCs whose CS-ON directions
are aligned with the error vector (Fig. 5a, red circles), as compared to
those cases in which the CS-ON direction and the error vector do not
match13,15,23,31,32 (Fig. 5a, gray circles, also see Supplementary Fig. 7a). In
other words, for any retinal error in a particular trial, there will always
be a subpopulation of PCs whose CS-ON direction matches the error Nature Communications| (2023) 14:2548 8 8 https://doi.org/10.1038/s41467-023-37981-0 Discussion The present study demonstrates the presence of multi-dimensional
manifolds, latent in the activities of the cerebellar input and output,
MFs and PCs respectively, and how their geometric and dynamic fea-
tures encode key kinematic eye movement parameters (see Supple-
mentary Fig. 10 for summary). Climbing fiber-driven CSs, signaling
error-related information to PCs, modify the PC manifolds, differen-
tially depending not only on the direction of error but also the type of
error, which predicts how the subsequent eye movements are cor-
rected. Finally, we show that the cerebellar cortical circuit amplifies
seemingly insignificant variabilities in the MF activity to generate
highly selective PC outputs. The fast and repetitive nature of our paradigm induced cognitive
fatigue, a gradual decline in the speed of saccades, which was com-
pensated by duration upregulation8. However, on top of fatigue, we
also observed natural trial-to-trial changes in the saccade velocity
requiring rapid duration adjustments in order to guarantee endpoint
precision. Therefore, the same velocity-duration trade-off mechanism
that maintained movement accuracy across hundreds of trials within a
session also ensured reduced endpoint variability (motor noise) on a
trial-to-trial basis. The residual motor noise led to tiny, albeit specific
error types, directed inward and outward respectively, depending on
whether the eye movements were too large or fell short relative to the
target location. What is the nature of this transformation? Notably, a simple LFFN
model33 simulating the MF-to-PC pathway could accurately explain the
MF-to-PC transformation at the firing rate and manifold level, but only
if the high dimensional components in the MF inputs, representing a
tiny fraction (<5%) of the total MF-to-MF variability, were preserved. This result suggests that a disentangled movement encoding at the PC
level emerges through substantial amplification of those seemingly
insignificant variabilities in MF responses by the cerebellar network. Highly correlated activity, resulting in an apparently small dimen-
sionality, has been widely observed in work on the cerebellar input
layer46–48 (but see also ref. 44). We found the same in our MF data, but
our analysis together with the PC data suggests that enhancing small
input variabilities is a fundamental information processing principle of
the cerebellar network. This expansion of variability may allow PCs to
extract as much information as possible during the movement so it can
be used optimally when errors occur. Therefore, the cerebellar circuit
can predict the dynamical, trial-to-trial deviations from the forward
model for the average eye movement. Article Article but significantly higher than two or four, the dimensionalities captur-
ing a major chunk of cell-to-cell variability in MFs and PCs, respectively
(Supplementary Fig. 5a–h). In the first approach, we first created the
dMF-dimensional pseudo-population firing rate model of MFs (Fig. 6e,
gray circles) using the dMF-dimensional MF manifold (red arrow), then
generated the prediction of individual PC-SS firings using the LFFN
(black circles), and finally identified the predicted PC-SS manifold
(green arrow). The PC-SS manifold (in the first two dimensions) was
relatively poorly predicted (R2 < 0.9) when dMF < 9 (Fig. 6f, g). In the
second approach (Supplementary Fig. 9d), we directly tested whether
the prediction of individual PC firings requires high dimensional
components in MF firings by another LFFN model, where MFs and PCs
communicate through a dimensionally reduced submanifold, called
the “communication subspace”34. This model also showed that a good
prediction of individual PC responses requires a high-dimensional
(d > 15) communication subspace (Supplementary Fig. 9d,e). Note that
the dimensions higher than four (i.e., d > 4) explain only 4.3% of the
total MF-to-MF variance together due to rapid decay (∝1/d3.23) in the
explained variance (Supplementary Fig. 5b). Therefore, the properties
of multi-dimensional control of movements by PC-SS manifolds
emerge from transformations by the cerebellar cortical circuit that
amplifies those small variabilities in MF inputs. proportion
of
cell-to-cell
variability22. Moreover,
these
low-
dimensional components exhibited a mixture of different features
observed in the firing patterns of individual MF and PC-SS responses,
thereby capturing specific interactions between individual units to
generate activity patterns relevant for selective kinematic control of
movements. In the MF case, this cell-to-cell variability could be
attributed to different inputs from a variety of premotor nuclei in the
brain stem. For instance, the SLB MFs may represent the activity pat-
tern of paramedian pontine reticular formation (PPRF) short-lead burst
neurons36. The origin of the LLB types seems less clear. Candidate
sources may include as well the PPRF but also the nucleus reticularis
tegmenti pontis (NRTP) and the dorsal pontine nuclei25,36–43. These
various nuclei provide the precise information on the kinematics of
macro- and micro-saccades to MFs needed (Fig. 2 and Supplementary
Fig. 1). And in the case of PCs, it might be the concerted impact of the
granule
cells-parallel
fibers44
together
with
interneurons45
that
accounts for the large heterogeneity in PC responses reflected by their
larger number of low-dimensional components (Supplementary
Fig. Article 4e, f). PC discharge, the output of the cerebellar cortex, is only a few
synapses away from the final stage motor neurons. Therefore, moving
up the cerebellar circuitry, one would expect the PC signals to be far
more refined and informative about the movements than the signals at
earlier stages, e.g., at the level of MF afferents. At first glance, our
results from the population analysis seemed to contradict this
expectation as the MF pseudo-population exhibits a much more pre-
cise encoding of relevant kinematic parameters while the kinematics
description provided by PC-SS pseudo-population responses is com-
paratively sloppy as a consequence of the large heterogeneity of
individual firing patterns. However, a very different perspective is
opened if one resorts to the low-dimensional pseudo-population
manifolds that reveal the hidden dynamics of PC-SS activity for the
flexible control of key movement parameters like velocity and dura-
tion in a movement phase specific manner. Furthermore, the PC
manifolds carried significantly more disentangled representations of
movements than the MF manifolds. Unlike MFs, the PC-SS manifolds
exhibited distinct geometric and dynamical properties related to the
two specific kinematic parameters, velocity, and duration. This con-
spicuous difference between the MF and the PC-SS manifolds indicates
a highly nontrivial transformation by the network. Nature Communications| (2023) 14:2548 Linear feed-forward network model shows high-dimensional
transformations by the cerebellar cortex g Goodness of fit for the predicted PC manifold to the data versus the input MF
manifold dimensions dMF. Dots represent examples in f. Data are mean ± SEM. Fig. 6 | Linear feed-forward network (LFFN) model from MFs to PCs. a Left: Fig. 6 | Linear feed-forward network (LFFN) model from MFs to PCs. a Left:
schematic diagram showing LFFN for MF-to-PC firing rate transformation. Right:
weight matrix computed from the data. Horizontal color bars on the top corre-
spond to the three MF categories (BT burst-tonic, LL long-lead burst, SL short-lead
burst). b Goodness of fit (R2) for individual PCs. The horizontal bar represents the
median and the vertical bar extends from the first to third quantile, respectively. Colored circles correspond to examples shown in c. c Firing rates of example PCs
(black, top and bottom) and LFFN predictions (color). The baselines are subtracted Fig. 6 | Linear feed-forward network (LFFN) model from MFs to PCs. a Left:
schematic diagram showing LFFN for MF-to-PC firing rate transformation. Right:
weight matrix computed from the data. Horizontal color bars on the top corre-
spond to the three MF categories (BT burst-tonic, LL long-lead burst, SL short-lead
burst). b Goodness of fit (R2) for individual PCs. The horizontal bar represents the
median and the vertical bar extends from the first to third quantile, respectively. Colored circles correspond to examples shown in c. c Firing rates of example PCs
(black, top and bottom) and LFFN predictions (color). The baselines are subtracted Nature Communications| (2023) 14:2548 9 9 https://doi.org/10.1038/s41467-023-37981-0 Discussion We found
that CSs that fired relatively earlier during the post-saccadic retinal
error period modified SS manifolds such that they predicted a PV
change in post-outward error trials. However, when CSs fired later, the
same errors were compensated by only a duration change. This result
may seem perplexing as different periods of CS activity suggest dif-
ferent kinematic adjustments and yet, the motor system selects only
one optimal behavior for the next trials. However, given that CSs sig-
nals carry a multiplexed code of behaviorally relevant information23,
the different dimensions in PC firing may utilize these valuable CS
signals, staggered in time, by integrating all the multiplexed informa-
tion to make context-dependent, appropriate behavioral adjustments. Therefore, the multidimensional nature of cerebellar computations is
necessary for the flexible, context-dependent control of movements
and their rapid adaptation. voluntarily enter a customized mobile chair for the first few weeks
following which they were transported to the experimental area where
they were gradually acclimatized to the new environment. To proceed
with experimental training, it was necessary to painlessly immobilize
the head in order to record eye movements reliably. Therefore, once
the animals felt fully comfortable in the experimental setups, the first
major surgical procedure of installing the foundations of cranial
implants was performed. During this procedure, the scalp was cut
open and these foundations, made from titanium, were fixed to the
skull using titanium bone screws. The scalp was then closed with the
help of sutures under which the foundations were allowed to rest and
stabilize for at least 3-4 months to ensure their durability and also full
recovery of the animals. After this period, the second surgical proce-
dure was performed in which the scalp was opened just enough to
allow a titanium-based hexagonal tube-shaped head-post to be
attached to the base of the implanted head-holder. Since this proce-
dure was rather quick, the surgery was also accompanied by implan-
tation of magnetic scleral search coils52,53 to record high-precision eye
movements. After 2–3 weeks of recovery, monkeys were trained fur-
ther on the behavioral task until their performance was accurate
enough to consider neural recordings. To this end, the final surgical
procedure was performed in which the upper part of the cylindrical
titanium recording chamber (tilting backward by an angle of 30° with
respect to the frontal plane, right above the midline of the cerebellum)
was attached to the already implanted chamber foundation. Experimental set-up and behavioral task p
p
All experiments were performed inside a dark room where monkeys,
with their heads fixed, were seated comfortably in a primate chair
placed at 38 cm in front of a CRT monitor such that their body axis was
aligned to the center of the monitor. All neural and behavioral data
presented in this study were collected during a simple to-and-fro
saccade task in which monkeys were asked to rapidly shift their eye
gaze repeatedly in order to follow a jumping target that appeared in
two fixed locations along the horizontal axis on the monitor in an
alternating manner (Fig. 1a). Before the beginning of each trial, the
fixation target (a red dot of diameter 0.2 deg) appeared at the center of
the monitor with an invisible fixation window of size 2 × 2 deg centered
on it. Only if the monkeys moved their gaze within the fixation window
the trial was initiated. This was followed by a short fixation period
ranging from 400 to 600 ms from trial onset after which the fixation
target vanished and, at the same time, another target (with the same
properties as the fixation target) appeared at a new horizontal loca-
tion, giving the impression that the target “jumped” centrifugally
(Fig. 1a, solid arrows), i.e., from the center of the screen to this new
location. The size (=15 deg) and the direction (left or right) of the target
jump were kept constant within a session. Every target jump served as
a “go-cue” which prompted the monkey to execute a saccade towards
the new target location within the 2 x 2 deg fixation window centered
on it, in order to receive an instantaneous reward (water drops)
marking the end of a trial. The peripheral target disappeared
approximately 700–900 ms relative to the go-cue, immediately after
which the central fixation dot reappeared indicating the beginning of
the next centrifugal trial. To proceed with the next trial, the monkey Discussion This property is important for
the cerebellum’s function and role in dynamic, online movement
control. Furthermore, together with the finding that serial single-unit
recordings are sufficient to generate reliable MF and PC manifolds, the
prediction power of the LFFN model implies that MFs should use
asynchronous firing rate coding. Depending on the firing pattern of individual MFs and SSs of PC
units, we could broadly classify them into different categories by using
strict statistical criteria to compute population averages of each
category13,25,35. Yet, in our analysis, these units appeared continuous in
their distribution (Supplementary Fig. 2) rather than forming discrete
clusters, due to a large cell-to-cell variability exceeding between-
category distances. Therefore, one may question the reliability of the
classify-and-average approach in testing the encoding of specific
kinematic parameters as it may be prone to the risk of sampling bias. This problem gets even worse if one additionally considers the large
between-session variability in eye movements also influencing the fir-
ing rates of individual units. To avoid exactly these biases, we esti-
mated the firing rates of all individual units, based on a firing rate
model that varies linearly with key kinematic parameters, to obtain a
“pseudo-population” of MFs and PC-SSs. This new approach allowed us to identify multi-dimensional, limit
cycle-like manifolds of neuronal activity from dimensionality reduc-
tion of the pseudo-population responses capturing a significant PCs are also influenced by the direct climbing fiber pathway,
imparting plastic changes in their activity via CSs. Indeed, we found Nature Communications| (2023) 14:2548 10 Article https://doi.org/10.1038/s41467-023-37981-0 that CSs modulated the geometry and dynamics of the PC-SS mani-
folds on a trial-to-trial basis, in an error-type dependent manner, pre-
dicting selective post-CS parametric adjustments of eye movements. The forced error-based short-term saccadic adaptation is similarly
error-type dependent6, which supports that PCs, by duration coding,
control movements flexibly in response to external and internal
(fatigue) changes8. On the other hand, recent studies have demon-
strated the effects of CS-driven plasticity on the movement velocity,
thereby emphasizing velocity-coding by PCs13,15. We demonstrate that
those two mechanisms coexist and can be interwoven to exhibit
complex forms of population-level plasticity. Notably, other properties
of CS firing, such as the time of occurrence of these spikes may also
govern the selective control of kinematic parameters by PCs. Nature Communications| (2023) 14:2548 Discussion A small
area of the skull within the confines of the chamber was removed to
allow electrode access to our region of interest, the oculomotor vermis
(OMV, lobules VIC/VIIA). The position and orientation of the chamber
were carefully planned and confirmed based on pre-and post-surgical
MRI, respectively. All surgical procedures were performed under
aseptic conditions using general anesthesia in which all vital physio-
logical parameters (blood pressure, body temperature, heart rate, pO2
and pCO2) were closely monitored54. After surgery, analgesics
(buprenorphine) were delivered to ensure painless recovery which was
monitored using regular ethograms under the strict supervision of
animal caretakers and veterinarians. Our findings provide a novel outlook on the existing theories of
cerebellar function in sensorimotor control. Particularly, the so-called
internal model hypothesis proposed that the cerebellum operates as a
predictive circuit, implementing a control-theoretic internal model
that estimates an outcome of a controlled system to an input49,50. With
the pioneering use of the LFFN analysis (Fig. 6), an earlier study sup-
ported this theory by showing that the final output of the cerebellum,
the deep cerebellar nuclei, can predict the external network input
provided by MFs33. Our results significantly advance this concept by
elucidating how the cerebellum can process the efference copy inputs
bearing multi-dimensional dynamics, which can arise potentially in
similar ways to the motor/premotor and collicular regions related to
other motor behavior where earlier studies showed the existence of
neural manifolds17–19,21,51. Furthermore, this study highlights the cere-
bellar function in processing and learning to modify the trial-to-trial
variability in movement and neural activity. This capability is crucial in
rapid, online motor control, but has remained elusive due to studies
usually analyzing only trial-averaged body and neural dynamics. Based
on the observations reported in this study, we conclude that the cer-
ebellar neural circuit performs optimal computations for fast and
flexibly varying
sensorimotor control, indispensable
in natural
environments. Electrophysiological recordings, identification of Purkinje cells
and mossy fibers in the oculomotor vermis Electrophysiological recordings, identification of Purkinje cells
and mossy fibers in the oculomotor vermis All electrophysiological recordings of PCs (n = 151) and mossy fibers
(n = 117) from the OMV were performed using glass-coated tungsten
microelectrodes (impedance: 1–2 MΩ), manufactured by Alpha Omega
Engineering, Nazareth, Israel. To target the OMV, as predicted by the
MRI scans, the position of electrodes along the rostrocaudal (i.e, Y-
axis) and lateral (i.e, X-axis) axis were manually adjusted with the help
of a custom-made microdrive, temporarily mounted on the recording
chamber during each experimental session. The depth of the electrode
was controlled using a modular multi-electrode manipulator (Elec-
trode Positioning System and Multi-Channel Processor, Alpha Omega
Engineering). The exact location of the OMV was confirmed based on
careful inspection of online audio-visual feedback of the electrode
signals, reflecting multi-unit granule cells activity, that exhibited
strong modulations in response to fast eye movements. For PC recordings, extracellular potentials sampled at 25 KHz
were high (300 Hz–3 KHz) and low (30–400 Hz) band-pass filtered to
obtain action potentials and LFP signals, respectively. Individual PC
units were identified based on the presence of two types of action
potential signals, high-frequency simple spikes (SSs) and low-
frequency complex spikes (CSs), the latter characterized by a poly-
phasic wave morphology in the action potential trace paralleled by
large deflections in the LFP signals. The fact that both signals originate
from the same unit was confirmed online by the suppression of SS
discharge for 10–20 ms when aligned to the occurrence of a CS55–57. Although the final characterization of CSs was based on an offline
neural networks approach58, we relied on the performance of Alpha
Omega Engineering´s Multi Spikes Detector for detecting SSs online. Note that we did not analyze the LFP signals since they are only weakly
correlated to the firing rate code for movement kinematics and seem
to represent other types of information14, which are beyond the scope
of this paper. In order to record from mossy fibers (MFs) in the granular layer,
we adjusted the upper cut-off frequency of the high band-pass filter to
5 KHz while keeping the lower cut-off frequency the same as 300 Hz. The identification of MFs was based on their strong directionally
selective response to saccades, firing up to several hundred spikes
per second in the preferred direction and seldomly in the opposite
direction. Classification of mossy fiber responses Unlike the bidirectional SS discharge of PCs, well-isolated MF units
exhibited a strong and clear preference for saccades made in one of
the two horizontal directions. This property allowed us to pre-
determine the preferred direction of the MF unit under investigation
and use that direction as the rewarded direction in which the cen-
trifugal saccades were made. A majority (115 out of 117) MF units
investigated in this study exhibited a much stronger (“burst-type”)
discharge during the peri-saccadic period in their preferred direction
(=centrifugal direction) as compared to the opposite, non-preferred
direction (=centripetal direction) in which very few or almost no
spikes fired, resulting in weak modulations. Therefore, MF responses
only in the centrifugal direction were considered for classification and
all analyses. In the other two units, we did not observe a peri-
saccadic burst. Overall, we observed two main types of burst modulations: the eye
position-related tonic discharge preceded by a saccade-related burst,
i.e., the “burst-tonic” type, and the saccade-related burst discharges
that remained mostly silent outside the peri-saccadic period, i.e.,
“phasic” type. In order to identify the “burst-tonic” responses, we first
identified those units in which the difference between the average fir-
ing rate in the post-saccadic period (150 to 250 ms from saccade onset)
and the pre-saccadic period (−250 to −150 ms from saccade onset) was
larger than 1.5 × standard deviation (SD) of the average firing rate
during the pre-saccadic period. Next, we compared the slope values of
the linear regression fits applied on the pre-and post-saccadic firing
responses, and only those cases in which no significant difference
between the slopes was observed, were labeled as “burst-tonic”
responses (n = 24; Fig. 2a,b; see BT). In other words, if the post-saccadic
MF activity was not only larger than the pre-saccadic activity but also
remained elevated after the saccade-related burst discharge, the unit’s
response was classified as a “burst-tonic” type. The “phasic bursts,” on
the other hand, were further categorized into “long-lead burst” types
and “short-lead burst” types, based on the timing of each MF unit’s
burst modulation onset relative to saccade onset25. For this, modula-
tion onsets were detected whenever the averaged MF response crossed
a threshold (defined as 3 × SD of baseline activity during −400 to −200
ms from saccade onset). Classification of mossy fiber responses To this end, all MF units in which the burst
modulation led the saccade onset by more than 15 ms were labeled as
“long-lead burst” types (n = 60; Fig. 2a, b; see LLB), whereas those that
started firing less than 15 ms before the saccade onset were classified as
“short-lead burst” (SLB) types (n = 27; Fig. 2a, b; see SLB). The value
15 ms was chosen, based on the observed SD value of modulation
onsets of “long-lead burst” MF units identified by Ohstuka and Noda25. Given that the timing of the detected modulation onsets was a
crucial factor in separating these two categories, in addition to the
clarity of their firing patterns, spike data were not smoothened using a
Gaussian kernel, as in the case of SSs. Based on this criteria, four units
(in addition to two non-bursting units) could not be categorized into
any of the three categories as in those cases the onset of burst mod-
ulation occurred after (i.e., lagged) saccade onset. The timing of the
modulation offsets was detected whenever the averaged MF response
dropped below the threshold value (defined as 3 × SD of baseline
activity during 200–400 ms from saccade end) during the post-
saccadic period. Electrophysiological recordings, identification of Purkinje cells
and mossy fibers in the oculomotor vermis Unlike the relatively longer duration SSs (mean duration:
1.5 ms), MF units exhibited much shorter duration (mean duration:
0.6 ms), mostly mono- and biphasic shaped waveforms while occa-
sionally exhibiting a negative after-wave16,24,25,59,60. Additionally, MFs
exhibited a wide range of inter-spike intervals16 (mean ± sd:
82.7 ± 86 ms) as compared to those of PC SSs (mean ± sd:
19.5 ± 2.6 ms). Methods Animals, preparation, and surgical procedures
Two healthy male rhesus macaques (Macaca mulatta; monkey K and
monkey E, age: 10 years and 8 years, respectively), purchased from the
German Primate Center in Göttingen, were used for the purpose of this
study. All data presented in this study were collected from these two
animals using procedures that strictly adhered to the rules defined by
the German as well as the European law and guidelines that were
approved by the local authority (Regierungspräsidium Tübingen,
veterinary license N7/18 and N4/14) and National Institutes of Health’s
Guide for the Care and Use of Laboratory Animals. All training, experi-
mental and surgical procedures were supervised by the veterinary
service of Tübingen University. As a first step, the animals were subjected to chair training which
began in the animal facility where animals were encouraged to Nature Communications| (2023) 14:2548 11 https://doi.org/10.1038/s41467-023-37981-0 Article made a saccade from the peripheral target back to the central location
(i.e., centripetal saccade, see dashed arrows in Fig. 1a). In other words,
the appearance of the central fixation dot served as a go-cue for cen-
tripetal saccades, although these saccades were not rewarded. Depending on the motivation of the monkeys to perform the task, as
well as the duration for which a PC could be kept well isolated, the
number of trials varied in each session (median = 307 trials) with each
trial lasting for 1200 ms. While the fatigue-inducing fast and repetitive
nature of the paradigm allowed us to capture both trial-by-trial and
gradually declining changes in the peak velocity of centrifugal and
centripetal saccades, the natural endpoint variability in saccades, on
the other hand, observed as over- or undershoots resulting in inward
(Fig. 1a, see yellow arrows) or outward errors (Fig. 1a, see green
arrows), allowed us to measure the CS’s preferred and anti-preferred
direction of error for an individual PC. All experimental parameters
were designed and controlled using in-house Linux-based software,
NREC (http://nrec.neurologie.uni-tuebingen.de). Estimation of manifolds To find the dimensionally reduced approximation of the population
rate model, R(t,z) in Eq. 1, given by R0 and ∂zR, we followed the fol-
lowing steps: First, R0 and ∂zR were converted to (N,T) matrices by
discretizing time where T is the length in time in milliseconds. Second,
we performed PCA on R0, which contains the mean firing rates of
individual units at z = z0 at every time point. We obtained a dimen-
sionally reduced representation, a manifold, PK such that R0 ≈WPK
where W is some (N,K) dimensional matrix (K < N). We determined K by
finding the number of dimensions (principal components) capturing
>85% of the total variability and confirmed it by the cross-validation
analysis. Finally, we estimated the linear approximation of how the
kinematics-dependent component, ∂zR, would change the PCA result
of the firing rates if z deviates from z0. Our analytic estimation showed
that it is enough to consider a change in PK as, p
p p
We describe our classification procedure as follows. As the first
step, we used a threshold-based criteria to label each SS response with
one of the four types based on the polarity of the response modula-
tion. For this, we identified all maximum (peaks) and minimum
(troughs) SS firing rates (detected using the MATLAB function “find-
peaks,” minimum peak distance = 10 ms, minimum peak prominence =
2 spikes/s) during the peri-saccadic period. The modulation was con-
sidered significant if the peaks and troughs crossed an upper and a
lower threshold (defined as ±5 × SD of baseline activity during the −250
to −100 ms from saccade onset), respectively. The SS response was
classified as a “burst” or a “pause” type if we encountered only a
monophasic increase or decrease in SS firing during the peri-saccadic
period. Responses were categorized into “burst-pause” or a “pause-
burst” types if the first modulation in the biphasic responses showed
an increase (followed by decrease) or a decrease (followed by increase)
in SS firing, respectively. Next, we ran a principal component analysis
(PCA) on the 302 SS responses (centrifugal and centripetal direc-
tions combined) to obtain a 2D plot (Fig. 3a) of their first two principal
components (explaining 62.2% of the total variance) that seemed to
appear as overlapping clusters organized in a circular pattern, cen-
tered around the origin. Estimation of manifolds For better discrimination of these clusters, we
relied on the SS response labels (identified in the first step) to obtain
decision boundaries by resorting to linear discriminant analysis (LDA). As shown in Fig. 3a (dashed lines), the first decision boundary sepa-
rated the “burst” (blue cluster) from “burst-pause” (green cluster)
types, as well as the “pause” (orange cluster) from the “pause-burst”
(red cluster) types. On the other hand, the second decision boundary
separated the “burst” from “pause-burst” types, and the “pause” from
the “burst-pause” types. As compared to the threshold-based labeling
of these response patterns, the LDA approach was clearly better in
separating these response types (Supplementary Fig. 2c, d). PK ! PK +
X
z
δz ∂zPK, ∂zPK = Wy ∂zR
+ ∂zW
y R0 WPK
ð2Þ ð2Þ to predict the PCA results of R(t,z) with sufficient accuracy. ∂zW is a
matrix obtained in the second step and describes how the higher
dimensional (>K) components move into the K-dimensional subspace
when kinematic parameters change and † represents conjugate
transpose. See Supplementary Methods for details. Classification of simple spike responses SS responses of individual PCs were broadly categorized into
four types—burst, pause, burst-pause and pause-burst—based on their
pattern of firing during the perisaccadic period of −50 to 150 ms from
the end of primary saccades (note: all primary saccades between 13 and
17 degrees of amplitude were detected using a velocity threshold of
30 deg/s).To this end, we estimated the mean spike density function of
the SS discharge of individual PCs by first convolving the time of each Nature Communications| (2023) 14:2548 12 Article Article https://doi.org/10.1038/s41467-023-37981-0 SS event detected within a trial with a normalized Gaussian kernel
(SD = 5 ms) and then averaging across all trials. where R0 and ∂zR are the kinematics-independent and kinematics-
dependent part, respectively, and δz=z−z0 is the deviation of z from the
mean value of z, z0. We used the multivariate linear regression of the
firing rate data with respect to the kinematic parameters (Supplemen-
tary Fig. 3a) for each unit to find the model components for all unit
data (Supplementary Fig. 3b, c). See Supplementary Methods for
details. We found that in almost 50% of PCs the SS firing patterns were
entirely different for saccades made in the centrifugal and centripetal
directions. For instance, a PC could demonstrate a sharp peri-saccadic
increase (or burst) in SS firing for a rightward centripetal saccade,
whereas in the opposite direction (i.e., left centrifugal) the same PC
could exhibit a sudden drop (or pause) in SS firing. Therefore, only for
the purpose of demonstrating these different response categories and
their corresponding modulations with respect to changes in saccade
kinematics (shown in Fig. 3) we considered the response of each PC
separately for each tested direction. Consequently, every PC con-
tributed to each response category at least once if the firing patterns
were different in the centrifugal and centripetal directions, and twice if
they were same (i.e., n = 302; 151 PCs × 2 directions). Whereas the
quality of our results shown in Fig. 3 may have benefited from such a
treatment, the impact of potentially unknown variables cannot be
completely ruled out. To avoid this risk, we only consider the SS
activity of saccades made in centrifugal (left or right) direction for all
analyses, that appear later for the calculation of SS manifolds for the
pseudo-population of PCs. Analysis of manifolds Given a manifold of MFs or PCs for a given kinematic variable, we
computed the manifold size and rotation speed in 2D (Figs. 4–5). We
defined the manifold size as the area enclosed within the 2D circular
trajectory, computed by numerically integrating the areas of triangles
defined by two neighboring data points and the origin (0,0). For the
rotation speed, we first computed the phase of rotation θ at each data
point (x,y) by θ = tan−1(Δy/Δx) where (Δx, Δy) = (x−x0, y−y0) and (x0, y0)
is a reference point defined by [(maximum of x coordinate data)/2, 0]. Then, we estimated the time T3/4 from the trial beginning t = −250 ms,
where θ ≈−180° (by definition), to the point θ = 90° (rotation of 3/4
cycles), finally finding the average rotation speed by 270°/T3/4. We
summarized how the manifold size and rotation speed vary with the
kinematic parameters by computing the normalized slope angle in the
manifold size and rotation speed plane (Figs. 4p, q and 5c). To do so,
we first normalized the manifold size and rotation speed data for all
cases by the standard deviations of the control case, which was the
correlated variation in Fig. 4p, q and post-no-CS case in Fig. 5c. The
slope angle was computed in each case in the normalized coordinates. We also performed the comparison/alignment analysis of multiple
manifolds using the canonical correlation analysis21,26. See Supple-
mentary Methods for details. Rate models for individual MFs and PCs We constructed the firing rate model of individual MFs and PCs by
using a linear combination of kinematics-independent and kinematics-
dependent components. Given the baseline-subtracted dynamic firing
rate of the nth unit, Rn(t,z), where t is the time from saccade onset and
z is a vector of the specific movement kinematic parameter (e.g.,
z = [PV] or [duration], or a pair of kinematic parameters, i.e., z = [PV,
duration]), we modeled the firing rate vector of a “pseudo-population”
containing N number of neurons, R(t,z) = [R1(t,z); R2(t,z);…; RN(t,z)], as EðTÞ = ∣∣Y TX∣∣2 +
X
z
X
z0
Cov½z,z0ð∂zY T∂zXÞ: ð∂z0Y T∂z0XÞ, References 23. Markanday, A., Inoue, J., Dicke, P. W. & Thier, P. Cerebellar complex
spikes multiplex complementary behavioral information. PLoS Biol. 19, e3001400 (2021). 1. McLaughlin, S. C. Parametric adjustment in saccadic eye move-
ments. Percept. Psychophys. 2, 359–362 (1967). 1. McLaughlin, S. C. Parametric adjustment in saccadic eye move-
ments. Percept. Psychophys. 2, 359–362 (1967). 24. Kase, M., Miller, D. C. & Noda, H. Discharges of Purkinje cells
and mossy fibres in the cerebellar vermis of the monkey
during saccadic eye movements and fixation. J. Physiol. 300,
539–555 (1980). 2. Golla, H. et al. Reduced saccadic resilience and impaired saccadic
adaptation due to cerebellar disease. Eur. J. Neurosci. 27,
132–144 (2008). 3. Markanday, A., Messner, J. & Thier, P. A loss of a velocity‐duration
trade‐off impairs movement precision in patients with cerebellar
degeneration. Eur. J. Neurosci. 48, 1976–1989 (2018). 25. Ohtsuka, K. & Noda, H. Burst discharges of mossy fibers in the
oculomotor vermis of macaque monkeys during saccadic eye
movements. Neurosci. Res. 15, 102–114 (1992). 4. Prsa, M., Dicke, P. W. & Thier, P. The absence of eye muscle fatigue
indicates that the nervous system compensates for non-motor
disturbances of oculomotor function. J. Neurosci. 30,
15834–15842 (2010). 26. Sussillo, D., Churchland, M. M., Kaufman, M. T. & Shenoy, K. V. A
neural network that finds a naturalistic solution for the production
of muscle activity. Nat. Neurosci. 18, 1025–1033 (2015). 27. Marr, D. A theory of cerebellar cortex. J. Physiol. 202,
437–470 (1969). 5. Barash, S. et al. Saccadic dysmetria and adaptation after lesions of
the cerebellar cortex. J. Neurosci. 19, 10931–10939 (1999). 28. Albus, J. S. A theory of cerebellar function. Math. Biosci. 10,
25–61 (1971). 6. Catz, N., Dicke, P. W. & Thier, P. Cerebellar-dependent motor
learning is based on pruning a Purkinje cell population response. Proc. Natl Acad. Sci. USA 105, 7309–7314 (2008). 29. Ito, M. Neural design of the cerebellar motor control system. Brain
Res. 40, 81–84 (1972). 7. Hopp, J. J. & Fuchs, A. F. The characteristics and neuronal substrate
of saccadic eye movement plasticity. Prog. Neurobiol. 72,
27–53 (2004). 30. Ito, M., Sakurai, M. & Tongroach, P. Climbing fibre induced
depression of both mossy fibre responsiveness and glutamate
sensitivity of cerebellar Purkinje cells. J. Physiol. 324, 113–134 (1982). 8. Prsa, M. & Thier, P. The role of the cerebellum in saccadic adaptation
as a window into neural mechanisms of motor learning. Eur. J. Neurosci. Reporting summary Further information on research design is available in the Nature
Portfolio Reporting Summary linked to this article. 19. Elsayed, G. F., Lara, A. H., Kaufman, M. T., Churchland, M. M. &
Cunningham, J. P. Reorganization between preparatory and
movement population responses in motor cortex. Nat. Commun. 7,
1–15 (2016). Data availability All source data files are provided with this paper and can be down-
loaded from https://doi.org/10.5281/zenodo.7732421. Source data are
provided with this paper. 20. Vyas, S., O’Shea, D. J., Ryu, S. I. & Shenoy, K. V. Causal role of
motor preparation during error-driven learning. Neuron 106,
329–339.e324 (2020). Article https://doi.org/10.1038/s41467-023-37981-0 Article Article Performances of all the LFFN models were measured by this least-
square error. To prevent overfitting we used the LASSO regression61
where the hyperparameter was chosen by AIC minimization. For the
manifold-transformation inLFFN(Fig. 6e), we reused T from the MF-to-
PC LFFN model but replaced the input variables by those approxi-
mated by the dMF-dimensional MF manifold. The communication
subspace model (Supplementary Fig. 8d, e) was obtained by the rank-
reduced regression34 with the error function in Eq. 3. See Supplemen-
tary Methods for details. 11. Xu-Wilson, M., Chen-Harris, H., Zee, D. S. & Shadmehr, R. Cerebellar
contributions to adaptive control of saccades in humans. J. Neu-
rosci. 29, 12930–12939 (2009). 12. Thier, P., Dicke, P. W., Haas, R. & Barash, S. Encoding of movement
time by populations of cerebellar Purkinje cells. Nature 405,
72–76 (2000). 13. Herzfeld, D. J., Kojima, Y., Soetedjo, R. & Shadmehr, R. Encoding of
action by the Purkinje cells of the cerebellum. Nature 526,
439–442 (2015). 14. Hong, S. et al. Multiplexed coding by cerebellar Purkinje neurons. Elife 5, e13810 (2016). Statistical analysis 15. Herzfeld, D. J., Kojima, Y., Soetedjo, R. & Shadmehr, R. Encoding of
error and learning to correct that error by the Purkinje cells of the
cerebellum. Nat. Neurosci. 21, 736–743 (2018). In most data analyses, we evaluated a mean and standard error of mean
(SEM) by the jackknife resampling except for two quantities. In testing
the prediction of the population-averaged firing rate by models
(Supplementary Figs. 3e, g and 4b, d), we separated trials into two
equal-sized sets, trained the model by only one of them (train data),
and tested it on the other data set (test data). In Fig. 6g, we used the
bootstrap procedure that randomly sampled the goodness of fit for
individual time points and computed their averages with 500 repeti-
tions to give the bootstrap mean and SEM. 16. Prsa, M., Dash, S., Catz, N., Dicke, P. W. & Thier, P. Characteristics of
responses of Golgi cells and mossy fibers to eye saccades and
saccadic adaptation recorded from the posterior vermis of the
cerebellum. J. Neurosci. 29, 250–262 (2009). 17. Churchland, M. M. et al. Neural population dynamics during
reaching. Nature 487, 51–56 (2012). 18. Kaufman, M. T., Churchland, M. M., Ryu, S. I. & Shenoy, K. V. Cortical
activity in the null space: permitting preparation without move-
ment. Nat. Neurosci. 17, 440–448 (2014). Code availability 21. Gallego, J. A., Perich, M. G., Miller, L. E. & Solla, S. A. Neural mani-
folds for the control of movement. Neuron 94, 978–984 (2017). y
All underlying codes to reproduce the results and figures of this paper
are available at https://doi.org/10.5281/zenodo.7732421. 22. Ebitz, R. B. & Hayden, B. Y. The population doctrine in cognitive
neuroscience. Neuron 109, 3055–3068 (2021). Linear feed-forward network models (LFFN) Linear feed forward network models (LFFN)
The LFFN models had movement kinematics-independent and
dependent components for output variables (Y, ∂zY) and input
(X, ∂zX), such as PC and MF firing rates in Fig. 6a, b. We assumed that
the movement variable z follows the Gaussian distribution and esti-
mated the weight matrix T to minimize the least-square error, R t,z
ð
Þ = R0 tð Þ +
X
z
δz ∂zR tð Þ EðTÞ = ∣∣Y TX∣∣2 +
X
z
X
z0
Cov½z,z0ð∂zY T∂zXÞ: ð∂z0Y T∂z0XÞ,
ð3 ð1Þ ð3Þ Nature Communications| (2023) 14:2548 13 https://doi.org/10.1038/s41467-023-37981-0 34. Semedo, J. D., Zandvakili, A., Machens, C. K., Byron, M. Y. & Kohn, A. Cortical areas interact through a communication subspace. Neuron
102, 249–259.e244 (2019). 55. Bell, C. C. & Grimm, R. Discharge properties of Purkinje cells
recorded on single and double microelectrodes. J. Neurophysiol. 32, 1044–1055 (1969). 35. Ohtsuka, K. & Noda, H. Discharge properties of Purkinje cells in the
oculomotor vermis during visually guided saccades in the macaque
monkey. J. Neurophysiol. 74, 1828–1840 (1995). 56. Latham, A. & Paul, D. Spontaneous activity of cerebellar Purkinje
cells and their responses to impulses in climbing fibres. J. Physiol. 213, 135–156 (1971). 57. McDevitt, C. J., Ebner, T. J. & Bloedel, J. R. The changes in Purkinje
cell simple spike activity following spontaneous climbing fiber
inputs. Brain Res. 237, 484–491 (1982). 36. Hepp, K. & Henn, V. Spatio-temporal recoding of rapid eye move-
ment signals in the monkey paramedian pontine reticular formation
(PPRF). Exp. Brain Res. 52, 105–120 (1983). 58. Markanday, A. et al. Using deep neural networks to detect complex
spikes of cerebellar Purkinje cells. J. Neurophysiol. 123,
2217–2234 (2020). 37. Thielert, C. D. & Thier, P. Patterns of projections from the pontine
nuclei and the nucleus reticularis tegmenti pontis to the posterior
vermis in the rhesus monkey: a study using retrograde tracers. J. Comp. Neurol. 337, 113–126 (1993). 59. Miles, F., Fuller, J., Braitman, D. & Dow, B. Long-term adaptive
changes in primate vestibuloocular reflex. III. Electrophysiological
observations in flocculus of normal monkeys. J. Neurophysiol. 43,
1437–1476 (1980). 38. Thier, P. & Möck, M. The oculomotor role of the pontine nuclei and
the nucleus reticularis tegmenti pontis. Prog. Brain Res. 151,
293–320 (2006). 39. Ramat, S., Leigh, R. J., Zee, D. S. & Optican, L. M. What clinical
disorders tell us about the neural control of saccadic eye move-
ments. Brain 130, 10–35 (2007). 60. Van Kan, P. L., Gibson, A. R. & Houk, J. C. Movement-related inputs
to intermediate cerebellum of the monkey. J. Neurophysiol. 69,
74–94 (1993). 40. Tziridis, K., Dicke, P. W. & Thier, P. The role of the monkey dorsal
pontine nuclei in goal-directed eye and hand movements. J. Neu-
rosci. 29, 6154–6166 (2009). 61. Hastie, T., Tibshirani, R. & Friedman, J. H. The Elements of Statistical
Learning: Data Mining, Inference, and Prediction 2nd edn
(Springer, 2009). 41. Dicke, P. W., Barash, S., Ilg, U. J. & Thier, P. Acknowledgements A.M., J.I. and P.T. were supported by DFG Research Unit 1847 “The
Physiology of distributed computing underlying higher brain functions
in non-human primates.” S.H. and E.D.S. are supported by the Okinawa
Institute of Science and Technology Graduate University. We acknowl-
edge support from the Open Access Publication Fund of the Eberhard
Karls University Tübingen. 42. Yamada, J. & Noda, H. Afferent and efferent connections of the
oculomotor cerebellar vermis in the macaque monkey. J. Comp. Neurol. 265, 224–241 (1987). 43. Keller, E. L. & Crandall, W. Neuronal responses to optokinetic stimuli
in pontine nuclei of behaving monkey. J. Neurophysiol. 49,
169–187 (1983). Author contributions 44. Lanore, F., Cayco-Gajic, N. A., Gurnani, H., Coyle, D. & Silver, R. A. Cerebellar granule cell axons support high-dimensional repre-
sentations. Nat. Neurosci. 24, 1142–1150 (2021). The study was conceptualized by A.M., S.H., E.D.S., and P.T. P.T. per-
formed all surgical procedures and A.M. designed and conducted all
experiments. A.M. recorded and pre-processed all behavioral and
electrophysiological data under P.T.’s supervision. A.M. and S.H. pre-
pared all figures. A.M. performed statistical analysis for Figs. 1 and 2 and
Supplementary Fig. 1; J.I. for Fig. 3 and Supplementary Fig. 2c, d. S.H. performed statistical analysis for Figs. 4–6 and Supplementary Figs. 2a,
b–9. A.M., S.H., E.D.S., and P.T. wrote the manuscript. A.M., S.H., J.I.,
E.D.S., and P.T. revised the manuscript. 45. Jelitai, M., Puggioni, P., Ishikawa, T., Rinaldi, A. & Duguid, I. Dendritic
excitation-inhibition balance shapes cerebellar output during
motor behaviour. Nat. Commun. 7, 13722 (2016). 46. Jörntell, H. & Ekerot, C.-F. Properties of somatosensory synaptic
integration in cerebellar granule cells in vivo. J. Neurosci. 26,
11786–11797 (2006). 47. Knogler, L. D., Markov, D. A., Dragomir, E. I., Štih, V. & Portugues, R. Sensorimotor representations in cerebellar granule cells in larval
zebrafish are dense, spatially organized, and non-temporally pat-
terned. Curr. Biol. 27, 1288–1302 (2017). https://doi.org/10.1038/s41467-023-37981-0 Single-neuron evidence
for a contribution of the dorsal pontine nuclei to both types of
target-directed eye movements, saccades and smooth-pursuit. Eur. J. Neurosci. 19, 609–624 (2004). Funding Open Access funding enabled and organized by Projekt DEAL. Open Access funding enabled and organized by Projekt DEAL. 48. Wagner, M. J. et al. Shared cortex-cerebellum dynamics in the
execution and learning of a motor task. Cell 177,
669.e4–682.e4 (2019). Competing interests Competing interests
The authors declare no competing interests. 49. Sokolov, A. A., Miall, R. C. & Ivry, R. B. The cerebellum: adaptive
prediction for movement and cognition. Trends Cogn. Sci. 21,
313–332 (2017). References 33, 2114–2128 (2011). 31. Junker, M. et al. Learning from the past: a reverberation of past
errors in the cerebellar climbing fiber signal. PLoS Biol. 16,
e2004344 (2018). 9. Straube, A., Fuchs, A. F., Usher, S. & Robinson, F. R. Characteristics
of saccadic gain adaptation in rhesus macaques. J. Neurophysiol. 77, 874–895 (1997). 32. Soetedjo, R., Kojima, Y. & Fuchs, A. F. Complex spike activity in the
oculomotor vermis of the cerebellum: a vectorial error signal for
saccade motor learning? J. Neurophysiol. 100, 1949–1966 (2008). 10. Takagi, M., Zee, D. S. & Tamargo, R. J. Effects of lesions of the
oculomotor vermis on eye movements in primate: saccades. J. Neurophysiol. 80, 1911–1931 (1998). 33. Tanaka, H., Ishikawa, T. & Kakei, S. Neural evidence of the cere-
bellum as a state predictor. Cerebellum 18, 349–371 (2019). 14 Nature Communications| (2023) 14:2548 Article https://doi.org/10.1038/s41467-023-37981-0 Nature Communications| (2023) 14:2548 Additional information 50. Tanaka, H., Ishikawa, T., Lee, J. & Kakei, S. The cerebro-cerebellum
as a locus of forward model: a review. Front. Syst. Neurosci. 14,
19 (2020). Correspondence and requests for materials should be addressed to
Peter Thier. Correspondence and requests for materials should be addressed to
Peter Thier. 51. Lee, J. & Sabatini, B. L. Striatal indirect pathway mediates explora-
tion via collicular competition. Nature 599, 645–649 (2021). Peter Thier. Peer review information Nature Communications thanks Shinji Kakei
and Atsushi Nambu for their contribution to the peer review of this work. Reprints and permissions information is available at
http://www.nature.com/reprints
Publisher’s note Springer Nature remains neutral with regard to jur-
isdictional claims in published maps and institutional affiliations. 52. Bechert, K. & Koenig, E. A search coil system with automatic field
stabilization, calibration, and geometric processing for eye move-
ment recording in humans. Neuro Ophthalmol. 16, 163–170 (1996). Peer review information Nature Communications thanks Shinji Kakei
and Atsushi Nambu for their contribution to the peer review of this work. 53. Judge, S. J., Richmond, B. J. & Chu, F. C. Implantation of magnetic
search coils for measurement of eye position: an improved method. Vis. Res. 20, 535–538 (1980). 54. Arnstein, D., Junker, M., Smilgin, A., Dicke, P. W. & Thier, P. Micro-
saccade control signals in the cerebellum. J. Neurosci. 35,
3403–3411 (2015). Nature Communications| (2023) 14:2548 15 https://doi.org/10.1038/s41467-023-37981-0 Article Open Access This article is licensed under a Creative Commons
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FORUM PAPER FORUM PAPER Abstract This paper considers the implications of the UK leaving the European Union (EU) for
‘The City’ of London and the wider UK financial sector and for the EU’s Capital
Markets Union (CMU) project. The extent of the impact of Brexit through job losses in
London and gains in EU financial centres and the relocation of financial sector business
will depend on the degree of ‘hardness’ or ‘softness’ of Brexit and indeed whether an
exit treaty deal is struck or ‘no-Brexit’ follows a second referendum. At the time of
writing (in November 2018) the likely denouement was far from clear. For the EU’s
flagship CMU project, the loss of the core London capital markets will require the
construction of a more fragmented system based in a number of cities within the EU. In
this digital age, the various hubs can perhaps be fully networked whilst better serving
distinct regional needs. Andy Mullineux1 Andy Mullineux1 Published online: 12 January 2019
# The Author(s) 2019 * Andy Mullineux
A.W.Mullineux@bham.ac.uk 1
University of Birmingham, Edgbaston, Birmingham B15 2TT, UK International Economics and Economic Policy (2019) 16:17–25
https://doi.org/10.1007/s10368-018-00425-y International Economics and Economic Policy (2019) 16:17–25
https://doi.org/10.1007/s10368-018-00425-y International Economics and Economic Policy (2019) 16:17–25
https://doi.org/10.1007/s10368-018-00425-y 1 ‘Hard’, ‘Soft’ or No ‘Brexit’? Following the historic vote (in the June 2016 referendum in the United Kingdom (of
Great Britain and Northern Ireland) to leave the European Union (EU) in June 2016, a
‘straw poll’ taken at the 34th GdR (European Money Banking and Finance) Sympo-
sium, Paris Nanterre 5th July 2017 revealed that a significant majority believed there
would be ‘No Brexit’. The next most popular option was a ‘Soft Brexit’. By February 2018, Prime Minister Theresa May (PM) and the Chancellor Philip
Hammond (HM Treasury) seemed to favor remaining in a customs union for goods but
not for services (80% of the UK economy and 40% of exports to the EU) and hoped to
do a special deal for financial services including ‘mutual recognition’ of regulations for
the sector. In July 2018, a modified and more detailed version of the proposal (for a
‘facilitated customs arrangement’), was seemingly accepted (at Chequers, the country
House of the Prime Minister) by the ‘Cabinet’ of ministers of the United Kingdom
(UK) government. The aspiration for ‘mutual recognition’ (rejected by the EU’s
negotiating team led by Michel Barnier and undermined by divisions within The City,
was replaced by ‘enhanced, extended or expanded equivalence’ of regulations for the 18 A. Mullineux financial sector. However, subsequent to the publication of a ‘White Paper’ proposing
legislation to Parliament, there were prominent resignations from the government by
‘Brexiters’ (who seek a ‘hard’, or possibly a ‘no-deal’ Brexit) and pro-Brexiter
modifications were made to the proposals to gain Parliamentary approval. These
proposals formed the basis of the final round of pre-Brexit (March 2019) and (currently
20 months from March 2019 ‘transition period’) negotiations, even though the separa-
tion of goods from services, given the significant interactions between the sectors, did
not seem wise. The UK’s ‘Chequers’ proposals are a variant of a ‘customs union’ option and related
to the ‘Canada model’ in excluding services; and hence access by financial companies
based in the UK the UK to the ‘Single Market’ in financial services through
‘passporting’, and in treating the UK as a ‘third country’. As such, it represents a
soft(ish) Brexit. A broader trade deal involving some service sectors and more en-
hancements to ‘equivalence’ for the financial sector would create a softer Brexit. 1 ‘Hard’, ‘Soft’ or No ‘Brexit’? The degree of hardness or softness relates not just to the trading arrangements, but
also to restrictions to free movement of people between the UK and the EU, the size of
the UK contribution to the EU budget, and the extent of the jurisdiction of the European
Court of Justice (ECJ) in dispute resolution. The UK could attempt to ‘buy’ more
access to EU markets by adopting a variant of the ‘Norway model’, which involves
membership of the European Economic Area (EEA) and making contributions to the
EU budget in return for privileged access for financial services etc. Ultimately, the
degree of ‘hardness’ depends on the agreed trade-offs between budgetary contributions,
immigration restrictions, free trade in goods and/or services and the jurisdiction of the
ECJ. The difficulty in reaching an agreement between the EU and UK on these complex
matters, about which both sides have ‘red lines’, including the desire by the EU to
maintain its four ‘freedoms’ (of movement of capital, citizens, good and services) is
compounded by the need to reach a ‘backstop agreement’ to resolve the Irish border
problem. The EU is insisting on maintaining a ‘free’ border between Northern Ireland
(NI) and Eire, and the UK wants to avoid a border with the EU in the Irish Sea; and not
to create a precedent for Scotland to seek enhanced independence within the UK. The
government relies for its majority of the votes in Parliament on members of the
Democratic Unionist Party (DUP) of NI, who want to remain in the UK and for them
any border checks between NI and the rest of the UK is a ‘red line’. However, many
(‘Republican’, as opposed to ‘Loyalist’) people in NI want to remain as close to the EU
and the Republic of Ireland as possible. If his issue cannot be resolved amicably a flare
up of the historic ‘troubles’ could result. One possibility might be to agree the general Brexit parameters in Autumn 2018 and
then to work on detailed resolution of outstanding issues, including those relating to
Ireland, subsequently and before the end of a (possibly extended) transition period. Other options include a failure to reach an agreement (the ‘no deal’ option) or
parliamentary rejection of the agreed deal (or ‘no deal’), perhaps leading to a second
referendum with a revised question outlining options put to voters. 1 ‘Hard’, ‘Soft’ or No ‘Brexit’? The Brexiters’
opposition to any sort of customs union derives from the concern that it would severely
restrict options to develop trade deals not involving the EU. At the time of writing, early November 2018, the negotiations between the EU and
the UK had reached an impasse and the PM mooted an extended transition period ‘Brexit’: ‘The City’ and EU capital markets 19 through to sometime in 2021. This would extend the period of uncertainty and was not
well received either by hard ‘Brexiters’, or by some ‘Remainers’; or indeed by business
representatives, who expressed frustration with the government. Opinion polls indicat-
ed that there had been some shift by the public towards remaining, but there was no
clear majority either way. Any extension of the transition period would also involve
further UK contributions to the subsequent financial year’s budget of the EU and would
thus open up further negotiations and be anathema to the herd Brexiters. The proba-
bility of a ‘no deal’ Brexit seemed to have increased substantially, but a soft(ish) Brexit
(or even ‘no-Brexit’) was still possible. The outcome of the ‘Brussels’ negotiations is
expected to be known and voted upon by Parliament before Christmas 2018. In the meantime, the banks and other financial firms have been setting up offices in
various EU cities and moving staff to them, given that ‘passporting’ will be ended,
unless there is no-Brexit after all. In the no-deal case, we can expect more staff and
functions to be moved because ‘enhanced equivalence’ will be off the table. The banks have anyway been required by their supervisors at the European Central
bank and the bank of England to prepare for the no deal eventuality in March 2019. It
was reported in the Financial Times (p.17, Weekend 27/28 October 2018) that the
Royal Bank of Scotland (RBS) had attributed a £100 m impairment under the new
(IFRS9) accounting standard as a forward provision against losses resulting from Brexit
and other (world trade related) uncertainties. RBS would also maintain higher capital
and liquidity ratios than required by the regulators) as a buffer against Brexit. 2 Who’s ‘City’ is it anyway? Before the Brexit vote in June 2016, there were already concerns within the ‘Eurozone’
about the location of euro denominated clearing business (central counterparty clearin
houses, or CCPs) in London. The Bank of England successfully challenged (ironically in the ECJ) an ECB
initiative to relocate euro clearing inside the ‘Eurozone’. The desire to relocate euro clearing inside the Eurozone reflects growing acknowl-
edgement that the liquidity of ‘clearing houses’ (Central Counterparty Clearing houses,
or CCPs) requires central bank underpinning. The Frankfurt-based ECB, as issuer of
euro, would need to provide it as the Bank of England is not an issuer of euro within the
EU and certainly would not be post Brexit. Further, ‘The City’ is a truly international (European and ‘Global’) financial centre. As a European financial centre, it should expect EU financial regulators to have some
jurisdiction and, as a global financial centre, the regulatory authorities of banks and
other financial institutions in countries with well-developed financial sectors expect to
be consulted about regulatory changes initiated in London. Since the 2007–2009 financial crisis, asset management in London has grown
substantially and so the key EU regulators are European Securities Management
Authority (ESMA) and the European Banking Authority (EBA, which is to move from
London to Paris) and the key external supervisor of banking is the ECB. The UK financial regulatory authorities (the Prudential Regulation Authority
(PRA) and the Financial Conduct Authority (FCA)) anyway conform to the
BASELIII/IV proposals of the Basle Committee of Banking Supervisors (BCSB) 20 A. Mullineux and proposals of the Financial Stability Board (FSB), which was until recently
chaired by Mark Carney, Governor of the Bank of England. The FSB has coordi-
nated banking and wider financial sector regulation initiatives since the 2007–9
financial crisis. 3 Regulatory conformity post Brexit New EU regulations relating to banking and asset management include: the second
Marketing of Financial Instruments (MFID II); the second Payments Services Directive
(PSD2); and the General Data Protection Regulation (GDPR). These regulations are in
the process of progressive implementation. The UK has tended to ‘gold plate’ financial regulation (as has Switzerland, another
potential post-Brexit model, especially for the financial sector) and the UK’s Retail
Distribution Review, implemented form 2012, shares a number of the subsequent
MFID II requirements. The UK’s Competition and Markets Authority (CMA) has required UK banks to
implement ‘Open Banking’ from January 2018, when the GDPR was also implemented
in the UK. Open Banking, and related remedies addressing competition issues in retail
banking, cover the PSD2 requirements, but with significant enhancements. On February 5th, the Deputy Governor of the Bank of England (Sam Woods) stated
that there would be no “bonfire of banking regulations” in order to improve the
‘competitiveness’ of The City (relative to the EU) after Brexit - regulatory standards
would be maintained “at least as high as today”. In other words, there would be no
return to ‘regulation with a light touch’, which had preceded the financial crisis. 4 Brexit and the UK economy The substantial post Brexit depreciation of the pound sterling benefited exports,
particularly of goods, and enhanced dollar denominated capital earnings from overseas. The ‘pound’ subsequently fluctuated against the dollar, but remains well below pre-
Brexit levels. There has been no substantial ‘rebalancing’ of the economy to reduce its
reliance on financial services, but tourism has benefitted considerably. In the run up to the financial crisis, the contribution of the financial sector to UK
GDP growth was significantly overestimated, perhaps by as much as 50%, according to
Office of National Statistics(ONS) and Bank of England estimates. In banking, some of
the overestimation was the result of the practice of pre-booking of anticipated profits to
be earnt in the future, which, in the event of the crisis, they were not. Nevertheless,
government enjoyed substantial tax revenue from the sector prior to the crisis, which
may have encouraged regulatory forbearance. The post crisis shortfall ameliorated first
by a post crisis special ‘Bank Levy’ and subsequently by an 8% corporation tax
supercharge, or bank profit ‘supertax’ in an attempt to make banks make a ‘true and
fair contribution’ during the post crisis period of ‘fiscal austerity’. Initial Treasury scenarios of the impact of the Brexit vote on the economy proved
too pessimistic as consumer expenditure (and debt) increased, whilst real wages and
productivity growth remained stagnant. Monetary policy ‘normalisation’, which the ‘Brexit’: ‘The City’ and EU capital markets 21 Bank of England has begun tentatively pursuing by raising interest rates, can be
expected to curb the growth in consumption. In February 2018, ‘leaked’ Treasury projections (from its upgraded post Brexit
referendum model of the economy) continued to show substantial loss of growth under
various Brexit scenarios; increasing with the degree of hardness of Brexit (and includ-
ing negative effects of reduced immigration). These projections were dismissed by hard
Brexiters, as ‘Project Fear II’; a re-run of the Treasury’s seemingly over-pessimistic pre
Brexit projections from its old model. 5 Brexit and the financial sector To the extent that Brexit reduces growth in the UK (and the EU) it will impact
negatively on the banking, and the wider financial sectors’, business with the ‘real’
economy (the firm, or business, and household sectors). The negative impact of Brexit on the business sector is compounded by the
uncertainty surrounding the Brexit negotiations. With a clear outcome still not in sight
over two years after the referendum, investment proposals have been abandoned or
postponed. The proposed ‘Transition Period’ after March 2019 (itself two years after Article 50
was triggered) is a ‘double edged sword’; reducing short term uncertainty, but increas-
ing long term uncertainty; as long as there is no clear final outcome. Current uncertainty
over the length of the (possibly extended) transition periods compounds uncertainty
further. Unless a good ‘second best’ solution can be negotiated (and accepted by Parlia-
ment), with substantial concessions agreed to assure financial stability in the EU, and
beyond, along with continued EU access to cheap and efficient financial, particularly
capital market, services provided by The City; the loss of ‘passporting’ from the UK
will have substantial further negative effects. It will also complicate, hinder, and
possibly derail the EU’s flagship Capital Markets Union (CMU) project. 6 After the single market If the ‘third best’ solution of regulatory and supervisory ‘equivalence’, without signif-
icant enhancements, prevails, then significant relocation from London to other EU
financial centres, to preserve passporting within the EU, is likely. Given the continuing
uncertainty, some job relocation has already been announced by banks and is now
underway. With more substantial the enhancements (now much less likely), less
relocation is likely to occur (estimates range from 3500 to 12,000 short-term job
losses). Because equivalence rules do not currently exist for all parts of the financial sector,
some mutual agreements will be required. Third country financial centres such as New
York and Singapore must self-certify the equivalence of their rules to those of the EU,
but the EU has the right of veto and this may inhibit regulatory reform in the UK. Early indications are that Frankfurt is most attractive to banks, but Dublin, is most
attractive to insurers; whilst Paris has made a strong, and seemingly successful, pitch 22 A. Mullineux for asset management; whilst unit trusts (UCITS-Undertakings for Collective
Investments in Transferable Securities) might be attracted to Luxembourg and,
to a lesser extent, Dublin. Amsterdam and Madrid are also pitching and any
fragmentation of capital markets after Brexit may favour country and regional
capital cities. The City thrived at the expense of Wall Street following the introduction in the US
of the Sarbanes-Oxley Act (2004), which tightened corporate governance, in its pre-
crisis ‘light touch’ regulation period. However, under President Trump, a relaxation of
US financial regulations is underway. Hence, The City may also lose out to Wall Street;
which now holds most of the investment banking cards, with UBS, Deutsche, and
Barclays scaling back their investment banking operations. 8 The final outcome for The City? The politicians will ultimately decide (unless there is a second well-defined referen-
dum) and there are numerous potential trade-offs between the EU and the UK (and the
DUP) ‘red lines’, as outlined above. With some blurring of the ‘red lines’, there is
possibility of ‘horse trading’ across them; involving the financial and non-financial
sectors and the degree of freedom of movement people between the EU27 and the UK
and other matters. At present (November 2018), however, the Irish border issues
discussed above are proving hard to resolve given the desire to negotiate a common
solution for the whole of the UK (Great Britain (including Scotland) and Northern
Ireland) and the EU (including the Republic of Ireland). President Trump’s call for a doubling of contributions by EU countries to NATO
makes the UK a significantly more important strategic security partner with the EU27. This may strengthen the UK’s bargaining position. The EU27 currently benefits from access to The City’s capital markets and there is
some risk to financial stability of an abrupt change, so this too strengthens the UK’s
hand. A bigger risk for the EU is the derailment of its CMU project. Under the no-deal scenario, President Trump’s negative attitude towards the WTO
trade dispute resolution makes reliance on WTO trade rules precarious and his bi-lateral
trade policy makes the prospect of a good trade deal with the US uncertain. Anyway,
the EU is itself pursuing bilateral trade deals with a number of the countries with which
the UK hopes to conclude deals. It already has a deal with Canada, and is currently
negotiating with Japan, for example. 7 Damage to the UK financial sector Special attention would be paid to the establishment of ‘Brexit’: ‘The City’ and EU capital markets 23 ‘letterbox entities’ in the EU27 and outsourcing and delegations to third countries (such as
the UK) would only be allowed under strict conditions. NCAs should ensure that ‘sub-
stance requirements’ are met, assuring that key activities and functions are inside the EU. ‘letterbox entities’ in the EU27 and outsourcing and delegations to third countries (such as
the UK) would only be allowed under strict conditions. NCAs should ensure that ‘sub-
stance requirements’ are met, assuring that key activities and functions are inside the EU. This has again raised the question of whether euro clearing can remain in London! US regulators, and lobbyists from the US, UK, and Asia, and some from the EU27 (e.g. Luxembourg), have pushed back against restrictions on delegation, but France has been
pursuing a compromise allowing delegated outsourcing, but no letterboxes within the
EU. This seems to have prevailed, so the current delegation arrangements benefitting
the The City seem like to remain, at least initially. However, US regulatory authorities
are keeping a watchful eye on changes to the treatment of US based financial
institutions operating in London and have already signalled unease about EU regulatory
oversight of euro clearing extending to The City. 7 Damage to the UK financial sector In terms of value added as percentage of GDP, the UK financial sector contributed 6%,
compared to around 3.5% in Germany and France, but this may be a substantial
overestimate. The UK’s share of financial activities across the EU ranged from 82%
(interest rate OTC derivatives), 78% (forex trading), 49% (hedge fund assets), 50%
(funds management). Being more capital market oriented, and thus potentially a key
component of the EU’s Capital Market Union project, London’s share of EU bank
lending is around 26%. The share of financial services to UK GDP is allegedly 23%,
but may be half that. London’s importance in OTC derivatives globally is 39%, second
only to New York (41%) and well ahead of Paris (5%) - figures from Patrick Artus,
NATIXIS (as presented at the aforementioned conference in Paris-Nanterre in Ju-
ly 2017). Brexit and the City', Newsletter, Issue No 179, October 2017, p 15-16, Royal
Economic Society (http://www.res.org.uk/view/resNewsletter.html). y
p
g
So what are the likely effects of Brexit on The City? The UK (London and
Edinburgh) hosts 2250 firms using MFID passports covering investment banking,
trading and fund management and 212 firms under AIFMD (Alternative Investment
Fund Managers Directive) passports for hedge fund and private equity fund manage-
ment, as well as the three major credit rating agencies. London conducts 80% of the
clearing of euro denominated derivatives ‘passported’ under the EMIR (European
Market Infrastructure Regulations). Further, the EU’s ‘single passport’ regime involves
numerous additional regulations (e.g. for UCITS). ‘Third country rules’ (TCR) are likely to apply to the UK, if the EU were to
recognise the UK’s post Brexit regulatory regime as ‘equivalent’ to the EU’s. But,
existing TCR agreements (e.g. with Switzerland) do not grant full access to the ‘single
market’ in financial services. The share of UK financial sector business linked to the EU is approximately 25%,
whilst international business not linked to the EU is approximately 30% and domestic
business, 45%. The overall impact of Brexit would thus be proportional to the EU 25%
plus damage to the UK economy affecting the domestic 45%. What might be the consequences of Brexit for The City’s asset management sector? ESMA issued an ‘opinion’ in May 2017 on ‘delegation’ stating that there would be no
automatic recognition of existing authorisations granted by the NCAs (National Com-
petent Authorities) of the EU27. 9 The denouement for the UK and the EU27 The City is a well-established global financial centre, and is currently the most
important financial centre in the EU. It has well known advantages (time zone, legal
system, language, and London as an attractive city). It may well, in the longer run, re-
align its international business, following some loss of business to other European
centres, and continue to thrive; but there is also likely to be a continued ‘tilt to Asia’ and
a re-assertion of Wall Street as the global financial centre! 24 A. Mullineux As regards the EU27, the biggest risk, apart from increased costs of some financial
products and services currently produced efficiently inside the Single Market for
financial services in The City of London, and increase risk of financial instability
during the immediate post Brexit transition period, is damage to its flagship CMU
project. The project launched under Lord (Jonathon) Hill, as European Commissioner for
Financial Stability, Financial Services and Capital Markets Union in November 2014. Lord Hill resigned from the position after the Brexit referendum. The CMU project was
conceived after the 2007–9 financial crisis and the subsequent 2010–2012 Eurozone
crisis in recognition of the heavy dependence of the EU (particularly the EU27) on its
fragmented banking sector; which was proved by these crises to be fragile. This contrasted markedly with the US (and to a lesser extend the UK) in which debt
(bond) and equity capital markets are much further developed and provide a much
greater share of finance to the business sector. The prompt recovery of the US financial
sector and the country’s ability to deal with the post-crisis bank bad debt problems
quickly and effectively contrasted with the EU where the capital markets were under-
developed outside The City and significant bank bad debt problems remain, even as
Brexit is being negotiated. Ongoing negotiations between the EU and Italy over its budget have illustrated that
the ‘doom loop’, which was a feature of the Eurozone crisis, has not been resolved. The
Italian government relies on selling bonds to Italian banks and other financial institu-
tions, whose value depends of the credit standing of the government. A number of
Italian banks have high bad debt ratios and rely on holding government bonds as safe
coupon bearing assets. 9 The denouement for the UK and the EU27 As government risk ratings and bond yields rise, the value of the
bond portfolios fall, making it more likely that the government may have to save help
the banks. The rise in such contingent government liabilities further raises the risk
premium on government bonds, and so on. In response to the Eurozone crisis, the EU devised a Banking Union project for the
Eurozone member countries. The project involves establishing a common bank super-
visory system, a common bank resolution regime with supporting institutions and a
common deposit guarantee scheme as well as a European Stablility Mechanism (ESM). This is all in place except the establishment of a single risk-related deposit insurance
scheme, which will involve taxpayers in one country (say Germany) potentially
guaranteeing depositors in banks in another country (say Italy) and thus quasi fiscal
transfers between countries. French proposals for developing the ESM to form a
European Monetary Fund (EMF), to underpin stability and sustain growth also involve
greater fiscal pooling and potential transfers between member states. With the Banking
Union incomplete, the risks of damage to banks from Brexit are perhaps higher than
they would otherwise be. The CMU aims to achieve a ‘better’ allocation of capital in the EU and to reduce
reliance on banking. This would take advantage the free movement of capital pillar of
the EU and potentially reduce the fragmentation of small and medium-sized enterprise
(SME) financing by banks serving their local markets at differential locally prevailing
(risk-related) rates. The better allocation will in part reflect enhanced corporate gover-
nance mechanisms and good stewardship practices rewarding good policies with regard
to the environmental impact, social goals and good governance practices and the UN
Sustainable Development Goals (SDGs), as well as profitability and productivity and ‘Brexit’: ‘The City’ and EU capital markets 25 growth enhancement. To be successful, consistency would need to be achieved in the
application of bankruptcy laws with some sort of bankruptcy protection along the lines
of the US ‘Chapter 11’ procedures. Further ‘benchmark’ (ideally zero risk) bonds and
bills for the capital markets would need to be established. There are numerous
proposals concerning how such ‘Eurozone bonds’ might be created through joint
issuance by participating states. So far, opposition has tended to come from states with
stronger credit ratings, such as Germany. Publisher’s note
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English
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Thermo Compression of Thermoplastic Agar-Xanthan Gum-Carboxymethyl Cellulose Blend
|
Polymers
| 2,021
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cc-by
| 12,154
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Smarak Bandyopadhyay 1 1
Centre of Polymer Systems, University Institute, Tomas Bata University in Zlin, Tr. T. Bati 5678,
76001 Zlin, Czech Republic; dsanetrnik@utb.cz (D.S.); nabanita@utb.cz (N.S.); saha@utb.cz (P.S.)
2
Footwear Research Centre, University Institute, Tomas Bata University in Zlin, Nad Ovcirnou IV,
3685 Zlin, Czech Republic; tsaha@utb.cz
3
Faculty of Technology, Tomas Bata University in Zlin, Vavreˇckova 275, 76001 Zlin, Czech Republic
*
Correspondence: bandyopadhyay@utb.cz 1
Centre of Polymer Systems, University Institute, Tomas Bata University in Zlin, Tr. T. Bati 5678,
76001 Zlin, Czech Republic; dsanetrnik@utb.cz (D.S.); nabanita@utb.cz (N.S.); saha@utb.cz (P.S.)
2
Footwear Research Centre, University Institute, Tomas Bata University in Zlin, Nad Ovcirnou IV,
3685 Zlin, Czech Republic; tsaha@utb.cz
3
Faculty of Technology, Tomas Bata University in Zlin, Vavreˇckova 275, 76001 Zlin, Czech Republic
*
Correspondence: bandyopadhyay@utb.cz 1
Centre of Polymer Systems, University Institute, Tomas Bata University in Zlin, Tr. T. Bati 5678,
76001 Zlin, Czech Republic; dsanetrnik@utb.cz (D.S.); nabanita@utb.cz (N.S.); saha@utb.cz (P.S.)
2
Footwear Research Centre, University Institute, Tomas Bata University in Zlin, Nad Ovcirnou IV,
3685 Zlin, Czech Republic; tsaha@utb.cz
3
Faculty of Technology, Tomas Bata University in Zlin, Vavreˇckova 275, 76001 Zlin, Czech Republic
*
Correspondence: bandyopadhyay@utb.cz 1
Centre of Polymer Systems, University Institute, Tomas Bata University in Zlin, Tr. T. Bati 5678,
76001 Zlin, Czech Republic; dsanetrnik@utb.cz (D.S.); nabanita@utb.cz (N.S.); saha@utb.cz (P.S.) Abstract: There is a gap in the literature for the preparation of agar-xanthan gum-carboxymethyl
cellulose-based films by thermo compression methods. The present work aims to fill this gap by
blending the polysaccharides in a plastograph and preparation of films under high pressure and
temperature for a short duration of time. The pivotal aim of this work is also to know the effect
of different mixing conditions on the physical, chemical, mechanical and thermal properties of the
films. The films are assessed based on results from microscopic, infrared spectroscopic, permeability
(WVTR), transmittance, mechanical, rheological and thermogravimetric analysis. The results revealed
that the mixing volume and mixing duration had negative effects on the films’ transparency. WVTR
was independent of the mixing conditions and ranged between 1078 and 1082 g/m2· d. The mixing
RPM and mixing duration had a positive effect on the film tensile strength. The films from the blends
mixed at higher RPM for a longer time gave elongation percentage up to 78%. Blending also altered
the crystallinity and thermal behavior of the polysaccharides. Smarak Bandyopadhyay 1 The blend prepared at 80 RPM for
7 min and pressed at 140 ◦C showed better percent elongation and light barrier properties.
Citation: Bandyopadhyay, S.; Sáha,
T.; Sanétrník, D.; Saha, N.; Sáha, P. Thermo Compression of
Thermoplastic Agar-Xanthan
Gum-Carboxymethyl Cellulose Blend. Polymers 2021, 13, 3472. https://
doi.org/10.3390/polym13203472
Academic Editors:
Victor Tcherdyntsev and
Brigita Tomšiˇc
Received: 15 September 2021
Accepted: 5 October 2021
Published: 10 October 2021
Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Citation: Bandyopadhyay, S.; Sáha,
T.; Sanétrník, D.; Saha, N.; Sáha, P. Thermo Compression of
Thermoplastic Agar-Xanthan
Gum-Carboxymethyl Cellulose Blend. Polymers 2021, 13, 3472. https://
doi.org/10.3390/polym13203472
Academic Editors:
Victor Tcherdyntsev and
Brigita Tomšiˇc
Received: 15 September 2021
Accepted: 5 October 2021
Published: 10 October 2021 Citation: Bandyopadhyay, S.; Sáha,
T.; Sanétrník, D.; Saha, N.; Sáha, P. Thermo Compression of
Thermoplastic Agar-Xanthan
Gum-Carboxymethyl Cellulose Blend. Polymers 2021, 13, 3472. https://
doi.org/10.3390/polym13203472 Keywords: thermo compression; blend; films; agar; xanthan gum; carboxymethyl cellulose; plasto-
graph; food packaging; rheology; XRD; DTG Keywords: thermo compression; blend; films; agar; xanthan gum; carboxymethyl cellulose; plasto-
graph; food packaging; rheology; XRD; DTG polymers polymers rticle
Thermo Compression of Thermoplastic Agar-Xanthan
Gum-Carboxymethyl Cellulose Blend dhyay 1,*
, Tomáš Sáha 2, Daniel Sanétrník 1, Nabanita Saha 1,2,3
and Petr Sáha 1,2,3 1. Introduction Environmental pollution concerns have raised awareness and research regarding
biodegradable polysaccharide-based food packaging material in the last decade [1,2]. Polysaccharide molecules are not only easily available and cheap, but they also form a
continuous network by hydrogen bonding [3]. Among all the polysaccharides, agar [3],
xanthan gum (XG) and carboxymethyl cellulose (CMC) [1] are reported widely as edible
food packaging materials. Agar is a phycocolloid extracted from the cell wall of Gelidium
sp. and Gracilaria sp. of Rhodophyceae red algae [4]. The molecular arrangement of agar is
a combination of agarose and agaropectic. Agarose is formed by α-(1, 3) and β-(1, 4) glyco-
sidic bonds between D-galactose and 3–6, anhydro-L-galactose; contrarily, agaropectin is
slightly branched and sulfated [3]. Agarose is the gelling agent while agaropectin is the non-
gelling agent removed during the industrial production of commercial agar. XG is a hetero
polysaccharide produced by gram (-ve) Xanthomonas campestris during fermentation [5]. The chemical structure of XG consists of a d-glucopyranose glucan backbone linked with a
β-(1, 4) glycosidic bond and α-(1, 3) trisaccharide side chain of mannose, glucuronic acid,
and terminal mannose [6]. CMC is obtained by substitution (carboxymethylation) of –OH
groups by sodium monochloroacetate in an alkaline medium [1]. The advantage of using
CMC over native cellulose is the solubility in cold water due to its degree of substitution. The US food and drug administration (FDA) has also approved all the above-mentioned
hydrocolloids as generally recognized as safe (GRAS). Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article
distributed
under
the
terms
and
conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/). https://www.mdpi.com/journal/polymers Polymers 2021, 13, 3472. https://doi.org/10.3390/polym13203472 Polymers 2021, 13, 3472 2 of 13 A review of the literature showed no reports utilizing all three components (agar,
XG and CMC) in a single blend for food packaging. When searching in Web of Science
(WoS) with the keywords “agar” + “xanthan” + “CMC” + “blends”, there were only two
articles found. One used them in gluten-free breads [7] and the other reported them as
an interaction study with other food hydrocolloids [8]. 2. Materials and Methods
2.1. Materials The Agar used in this study was bought from HiMedia Laboratories Pvt. Ltd., Mumbai,
India. The Xanthan gum from Xanthomonas campestris was procured from Sigma Life
Science, Missouri, MI, USA, while the Sodium (6.5–8.5%) Carboxymethyl Cellulose was
obtained from Sinopharm Chemical Reagent Co., Ltd., Ningbo, China. The Polyethylene
Glycol 3000 (referred later as PEG) and Glycerol anhydrous GR were supplied by Fluka
Chemie GmbH, Buchs, Switzerland and Lach-Ner s.r.o, Neratovice, Czechia respectively. 1. Introduction Starch-based films are reported
to have increased mechanical strength when blended with agar and XG by the solvent
casting method [9]. The mixing of CMC with agar and gelatin exhibited improvements in
barrier and mechanical properties [10]. Additionally, the addition of natural colorants to
CMC-Agar blends gave a better water vapour barrier and strength to the films [11]. The
addition of XG to the gelatin-CMC blend gave films with lower tensile strength but higher
puncture resistivity [12]. Moreover, all the films made from the above composites use
solvent casting methods. The work of Sousa et al. [13] has reported preparation of thermo
compressed agar films with choline chloride and urea, but the films at higher temperature
showed opacity. To the best of our knowledge, no work has been reported yet related to
agar, XG and CMC films by thermal pressing methods. g
y
p
g
The preparation of films by solution or solvent casting methods are well suited for
laboratory scale production, but for industrial scaling-up utilization of instrumentation, it
is a must. Moreover, methods like blown extrusion, compression or injection moulding
of the agar, XG and CMC blends are also not reported, as far as we can tell. The casting
methods require high energy and large amounts of time, thus creating space for tools
designed for synthetic polymers. The extrusion, blowing, injection or thermo compression
of the agar-based blends will not only make the throughput high but also energy efficient. In particular, thermo compression is advantageous for processing films because of its
simplicity [14]. To mention in brief, when making films with thermo compression, the
process starts and ends with simple mixing and pressing machine. In comparison to casting
processes, these machines have a high throughput, reproducibility and save time. p
g
g p
p
y
Thus the aim of this study is to develop biodegradable transparent agar-based films
by thermo compression. Furthermore, the effect of the blending conditions on the physical,
chemical, mechanical and thermal properties of the films are also investigated. 2.2. Preparation of Agar Based Thermoplastic Mixture The components for mixing were divided into two parts: the solid (referred later as
MS) and the liquid. The MS comprised of Agar (57.71%), XG (28.84%), CMC (7.69%), PEG
(5.76%) and the liquid part were made of Glycerol and water mixed in a 3:1 ratio. The
MS had a volume of approximately 1.44 cm3 per gram, while the liquid portion had a
volume of approximately 0.92 cm3 per gram. This composition is chosen after much trial
and error to fit the best mixing volume in the plastograph (data not shown in this article). The MS was premixed by shaking in a glass jar 30% filled and later mixed with the liquid
portion in a Brabender R2400 Plastograph with W50 mixer (Brabender GmbH & Co KG,
Duisburg, Germany). The volume of the mixer bowl was 55 cm3 and the mixing conditions
are mention in Table 1. Polymers 2021, 13, 3472 3 of 13 Table 1. The mixing conditions of the heat pressed films. Table 1. The mixing conditions of the heat pressed films. Table 1. The mixing conditions of the heat pressed films. Components
Film A
Film B
Film C
Film D
Film E
Film F
Film G
RPM
100
100
100
100
80
80
80
MS, g
26
20
20
10
20
20
10
Liquid, mL
20
15
10
10
30
15
10
Time, min
10
7
5
5
7
7
5
Total mixing
volume, cm3
50.02
42.74
38.13
23.67
56.54
42.74
23.67
The feel of the final blend by touch and its colour is mentioned in Table 2. Later, they
were stored in plastic zip lock bags until further used for pressing. The feel of the final blend by touch and its colour is mentioned in Table 2. Later, they
were stored in plastic zip lock bags until further used for pressing. The feel of the final blend by touch and its colour is mentioned in Table 2. Later, they
were stored in plastic zip lock bags until further used for pressing. Table 2. The feel, visual appearance (colour) of the blends after mixing in a plastograph. Table 2. The feel, visual appearance (colour) of the blends after mixing in a plastograph. 2.3. Film Production by Thermo-Compression of the Mixture Thermal compression of 3.5 g from each blend was done between polytetrafluoroethy-
lene (PTFE) coated fiberglass of 0.15 mm thickness. The steel frame used as a mold had
dimensions of 130 mm × 130 mm × 4.1266 ± 0.007 mm, while the finally produced films
had a length and breadth of 125 mm × 125 mm, with varying thicknesses as reported
in Table 1. The films were prepared by pressing the blend for 3 min without pressure at
140 ◦C, then finally pressing for another 6 min at 140 ◦C with a constant pressure of 300 kN. The pressing temperature is kept way below the maximum degradation temperature (Tm)
of the individual components. The mixing time and pressure are selected from trial and
error experiments (data not shown), with the best conditions selected for this study. The
films were cooled under the same pressure in a cooling hydraulic press and then peeled off
of the PTFE foils. The appearance of the films is shown in Figure 1. where, col(X) is the column having Co K α - 2θ value; L1 = 1.7891 (Co K alpha wavelength),
L2 = 1.5418 (Cu K alpha wavelength). 2.2. Preparation of Agar Based Thermoplastic Mixture Blends for Films:
A
B
C
D
E
F
G
Softness/Hardness 1
4
5
6
2
0
3
1
Visual appearance/Colour 2
5
4
2
1
3
4
0
Remarks 3
-
-
-
-
Films formed from this
blend were sticky
-
Films formed were less
sticky than E
1 0 = Maximum soft; 6 = Maximum hard; 2 0 = Maximum white; 5 = Maximum brown; 3—Normal films
without stickiness. 2.3. Film Production by Thermo-Compression of the Mixture 2.4. Characterization of the Films Scanning electron microscopy analysis was done using FEI™(Nova Nano SEM,
Oregon, Hillsboro, OR, USA). The surface of the films was gold-sputtered for 60 s at 30 mA. The images were captured at 10,000 magnification and 5 kV. g
p
g
The Fourier transfer infrared (FTIR) spectroscopy and X-ray diffraction (XRD) was
done following the exact method in our previous study [15]. The only change in XRD is
the inclusion of the formula to convert Cobalt K alpha to Copper K alpha in OriginPro 8.5
(OriginLab Corporation, Northampton, MA, USA): Cu K α = 114.59156*asin(L2/L1*sin(0.00872664*col(X))) where, col(X) is the column having Co K α - 2θ value; L1 = 1.7891 (Co K alpha wavelength),
L2 = 1.5418 (Cu K alpha wavelength). 4 of 13
4 of 14 Polymers 2021, 13, 3472
Polymers 2021 13 3472 Figure 1. The films (A–G) after heat pressing placed over Univerzita Tomáše Bati ve Zlíně logo to show real transpar-
Figure 1. The films (A–G) after heat pressing placed over Univerzita Tomáše Bati ve Zlínˇe logo to show real transparency. films (A–G) after heat pressing placed over Univerzita Tomáše Bati ve Zlíně logo to show real transpar-
ms (A–G) after heat pressing placed over Univerzita Tomáše Bati ve Zlínˇe logo to show real transparency. Figure 1. The films (A–G) after heat pressing placed over Univerzita Tomáše Bati ve Zlíně logo to show
Figure 1. The films (A–G) after heat pressing placed over Univerzita Tomáše Bati ve Zlínˇe logo to show re ency. 2.4. Characterization of the Films
Scanning electron microscopy analysis was done using FEI™ (Nova Nano SEM, Or-
egon, Hillsboro, OR, USA). The surface of the films was gold-sputtered for 60 s at 30 mA. The images were captured at 10,000 magnification and 5 kV. The Fourier transfer infrared (FTIR) spectroscopy and X-ray diffraction (XRD) was
done following the exact method in our previous study [15]. The only change in XRD is
the inclusion of the formula to convert Cobalt K alpha to Copper K alpha in OriginPro 8.5
(OriginLab Corporation, Northampton, MA, USA):
Cu K α = 114 59156*asin(L2/L1*sin(0 00872664*col(X)))
The water vapour transmission rate (WVTR) of the materials was evaluated by the
desiccant method following ASTM E96. Pre-dried silica beads at 150 ◦C [16] of 10 g weight
were filled up to 1/3rd in a 50 mL glass beaker. 2.4. Characterization of the Films The orifice of the beaker was covered with
films and sealed with paraffin wax tape. The exposed area of the beaker and weight of the
complete experiment setup (beaker with silica and film, referred further as cell) was noted. The cell was then placed inside a humidity chamber at 90% RH and 30 ◦C. A beaker with
100 mL water was also placed inside the chamber to note down the decrease in the water
volume, absorbed by the cells each day. Three control cells were also placed without film
cover, only having the 10 g silica beads. All the setups were triplicated for each film and
the experiment was conducted for 6 days. Change in weight was recorded at 24 h intervals. The WVTR is calculated on the data for 24 h, using the formula [17]: ving Co K α - 2θ value; L1 = 1.789
h)
WVTR = (W24 −W0)/T × A (
p
g
)
The water vapour transmission rate (WVTR) of the materials was evaluated by the
desiccant method following ASTM E96. Pre-dried silica beads at 150 °C [16] of 10 g weight
where W24 is the weight of the bottle after 24 h, W0 is the weight of the bottle at the start of
the experiment, T is the time in days and A is the area in m2. g
[
]
g
g
were filled up to 1/3rd in a 50 mL glass beaker. The orifice of the beaker was covered with
films and sealed with paraffin wax tape. The exposed area of the beaker and weight of the
complete experiment setup (beaker with silica and film, referred further as cell) was noted. The water vapour absorption rate (WVAR) of the films is the representation of the
data from the WVTR setup after 24 h. WVAR is the slope plot between the w% (change in
weight of the cell from the initial weight, expressed in %) and time. p
p
p (
,
)
The cell was then placed inside a humidity chamber at 90% RH and 30 °C. A beaker with
100 mL water was also placed inside the chamber to note down the decrease in the water
volume, absorbed by the cells each day. Three control cells were also placed without film
The light transmittance and film transparency was measured following the method of
Alias et al. [18]. Transparency = A294/t where A294 is the Amax or absorbance at 294 nm and t is the thickness of the films in mm. where A294 is the Amax or absorbance at 294 nm and t is the thickness of the films in mm. The data of UV-Vis and measurement of thickness is an average of 5 replications. Additionally, the real degree of transparency is inversely proportional to the value of
transparency obtained from the above equation. The mechanical analysis was done as per the methods reported earlier in our study [20]. The cross-head speed was 10 mm/min and 10 kgf static load was used. The only change is
the dimension of the samples to 15 mm × 2 mm. The rheological analysis was done with modifications from our earlier report [15]. To
mention in brief, the amplitude sweep was done with a strain range of 0.01–100% and
angular frequency of 10 rad/s. The frequency sweeps were performed at 0.05% strain and
angular frequency range from 0.01 to 100 rad/s. The slope of the curve is reported with
25 points per decade for amplitude sweep and 5 points per decade for frequency sweep. The experiment was conducted with a rough surface of 20 mm diameter parallel plate
geometry at 25 ◦C. Thermogravimetric analysis was performed as per our previous work [15]. Under
a nitrogen environment (flow rate: 100 mL/min), the samples were heated at a rate of
10 ◦C/min between 25 and 600 ◦C. 2.5. Statistical Analysis OriginPro 8.5 (OriginLab Corporation, Northampton, MA, USA) was used for statisti-
cal analysis, represent the result as Mean ± Standard Deviation with 5% error margin. The
winTest Analysis 4.7.0 (Testometric Co. Ltd., Rochdale, UK) was also used for calculating
the coefficient of variation (C. of V.). Design Expert ver 11 (Star-Ease Inc. Minneapolis, MN,
USA) was used for two level factorial ANOVA analysis and optimization of WVTR data. 3. Results and Discussions 3.1. Morphology and Structure of Films 2.4. Characterization of the Films The films were cut into small pieces (4 cm × 1 cm) to fit inside the cuvette
for reading with Cary 300 UV-visible spectrophotometer (Agilent, Santa Clara, CA, USA). Polymers 2021, 13, 3472 5 of 13 All the films were first scanned from 200 to 800 nm wavelengths to select the peak for
maximum absorption (Amax). Later, the film transparency was calculated at 294 nm using
formula [19]: All the films were first scanned from 200 to 800 nm wavelengths to select the peak for
maximum absorption (Amax). Later, the film transparency was calculated at 294 nm using
formula [19]: Transparency = A294/t 3.1. Morphology and Structure of Films The peak at 3369 cm−1 is due to the O-H stretching [29]. The shift in the
peak of the individual polysaccharides from 1033–1068 cm−1 to 1041–1043 cm−1 and the
addition of new peaks at 1105–1112 cm−1 in the blended films may suggest the formation
of new interactions due to the addition of glycerine. The blend is a perfect amalgamation
of all the individual components as it does not replicate the exact peaks as in the compo-
nents, but shows different peaks with changed intensity due to the formation of new phys-
ical and chemical interactions [30]. Figure 2. Surface SEM images of the heat pressed films (A–G). Figure 2. Surface SEM images of the heat pressed films (A–G). The FTIR spectra in Figure 3 shows the characteristic peaks for all the individ
components of the films, namely PEG and Glycerine [23–25] at 1099 cm−1 (C-H + O
stretching), 1103 cm−1 (C-C + C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching), 1
cm−1 (C-H bending), 1464 cm−1 (C-H bending) and 2878 cm−1 (C-H stretching); Agar [26
1068 cm−1 (C-O-C stretching); XG [27] at 1033 cm−1 (C-O stretching); CMC [28] at 1058 c
(C-O stretching). The peak at 3369 cm−1 is due to the O-H stretching [29]. The shift in
peak of the individual polysaccharides from 1033–1068 cm−1 to 1041–1043 cm−1 and
addition of new peaks at 1105–1112 cm−1 in the blended films may suggest the forma
of new interactions due to the addition of glycerine. The blend is a perfect amalgama
of all the individual components as it does not replicate the exact peaks as in the com
nents, but shows different peaks with changed intensity due to the formation of new ph
ical and chemical interactions [30]. igure 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG and
Glycerine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. Figure 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG and
Glycerine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. Figure 2. Surface SEM images of the heat pressed films (A–G). Figure 2. Surface SEM images of the heat pressed films (A–G). Figure 2. Surface SEM images of the heat pressed films (A–G). 3.1. Morphology and Structure of Films The SEM images of the film’s surface are shown in Figure 2. All the films have only
suggestive evidence of the components mixed well without showing any phase separation
but the reticulated structure may be attributed to the presence of Agar in the films [21]. The structure is devoid of any pores on the surface and shows a homogeneous compact
structure, formed may be due to the strong interaction among the newly formed bonds
in all the films as evident from Figure 2. Glycerol has probably contributed to developing
new intra and inter hydrogen bonds among the hydroxyl groups of the polysaccharide
components by entering the interior of the polysaccharide components’ chains, breaking
them and creating new ones [22]. The FTIR spectra in Figure 3 shows the characteristic peaks for all the individual
components of the films, namely PEG and Glycerine [23–25] at 1099 cm−1 (C-H + O-H
stretching), 1103 cm−1 (C-C + C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching),
1343 cm−1 (C-H bending), 1464 cm−1 (C-H bending) and 2878 cm−1 (C-H stretching);
Agar [26] at 1068 cm−1 (C-O-C stretching); XG [27] at 1033 cm−1 (C-O stretching); CMC [28]
at 1058 cm−1 (C-O stretching). The peak at 3369 cm−1 is due to the O-H stretching [29]. The
shift in the peak of the individual polysaccharides from 1033–1068 cm−1 to 1041–1043 cm−1
and the addition of new peaks at 1105–1112 cm−1 in the blended films may suggest the
formation of new interactions due to the addition of glycerine. The blend is a perfect
amalgamation of all the individual components as it does not replicate the exact peaks as
in the components, but shows different peaks with changed intensity due to the formation
of new physical and chemical interactions [30]. Polymers 2021, 13, 3472
Polymers 2021, 13, 3472 6 of 13
6 of 14 Figure 2. Surface SEM images of the heat pressed films (A–G). The FTIR spectra in Figure 3 shows the characteristic peaks for all the individual
components of the films, namely PEG and Glycerine [23–25] at 1099 cm−1 (C-H + O-H
stretching), 1103 cm−1 (C-C + C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching), 1343
cm−1 (C-H bending), 1464 cm−1 (C-H bending) and 2878 cm−1 (C-H stretching); Agar [26] at
1068 cm−1 (C-O-C stretching); XG [27] at 1033 cm−1 (C-O stretching); CMC [28] at 1058 cm−1
(C-O stretching). 3.1. Morphology and Structure of Films The peak at
peak of the individual polys
addition of new peaks at 1105
of new interactions due to the
of all the individual compone
nents, but shows different pea
ical and chemical interactions ure 3 shows the characteristic peaks for all the indivi
mely PEG and Glycerine [23–25] at 1099 cm−1 (C-H +
C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching),
(C-H bending) and 2878 cm−1 (C-H stretching); Agar [2
XG [27] at 1033 cm−1 (C-O stretching); CMC [28] at 1058
3369 cm−1 is due to the O-H stretching [29]. The shift in
accharides from 1033–1068 cm−1 to 1041–1043 cm−1 and
–1112 cm−1 in the blended films may suggest the forma
addition of glycerine. The blend is a perfect amalgama
nts as it does not replicate the exact peaks as in the com
ks with changed intensity due to the formation of new p
[30]. (C H
XG [
3369
ccha
–111
add re 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG
erine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. Figure 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG and
Glycerine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. The XRD peaks of the blends are shown in Figure 4, which is similar to the peak
e constituents, but not the same. The peak at 2θ = 19 is a near average from the con
nts Agar at 19 [31], XG at 19.64 [32], CMC at 19.7 [33] and PEG at 19.23 [34] whereas
23.4 may be because of PEG at 23.3 [34] or 23.4 [35] but with less intensity due to
xing with polysaccharides. The other characteristic peaks of Agar at 14 and 27.2 [
G at 16.42 and 20.10 [32]; CMC at 18.4, 22.7, 25.3 and 28.4 [33]; PEG at 13.6 and 27.3
e missing due to decrease in the crystallinity of the final blend. The reduction in
ystalline property of the biopolymer blends which has occurred may be due to the m
The XRD peaks of the blends are shown in Figure 4, which is similar to the peaks of the
constituents, but not the same. 3.1. Morphology and Structure of Films The peak at 2θ = 19 is a near average from the constituents
Agar at 19 [31], XG at 19.64 [32], CMC at 19.7 [33] and PEG at 19.23 [34] whereas 2θ = 23.4
may be because of PEG at 23.3 [34] or 23.4 [35] but with less intensity due to the mixing
with polysaccharides. The other characteristic peaks of Agar at 14 and 27.2 [31]; XG at 16.42
and 20.10 [32]; CMC at 18.4, 22.7, 25.3 and 28.4 [33]; PEG at 13.6 and 27.3 [34] are missing
due to decrease in the crystallinity of the final blend. The reduction in the crystalline
property of the biopolymer blends which has occurred may be due to the mixing of the
components [31]. 3.1. Morphology and Structure of Films The blend is a perfect amalgamatio
of all the individual components as it does not replicate the exact peaks as in the comp
nents, but shows different peaks with changed intensity due to the formation of new phy
ical and chemical interactions [30]. re 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG an
erine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. Figure 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG and
Glycerine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. The FTIR spectra in Figure 3 shows the characteristic peaks for all the individu
components of the films, namely PEG and Glycerine [23–25] at 1099 cm−1 (C-H + O
stretching), 1103 cm−1 (C-C + C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching), 13
cm−1 (C-H bending), 1464 cm−1 (C-H bending) and 2878 cm−1 (C-H stretching); Agar [26]
1068 cm−1 (C-O-C stretching); XG [27] at 1033 cm−1 (C-O stretching); CMC [28] at 1058 cm
(C-O stretching). The peak at 3369 cm−1 is due to the O-H stretching [29]. The shift in t
peak of the individual polysaccharides from 1033–1068 cm−1 to 1041–1043 cm−1 and t
addition of new peaks at 1105–1112 cm−1 in the blended films may suggest the formati
of new interactions due to the addition of glycerine. The blend is a perfect amalgamati
of all the individual components as it does not replicate the exact peaks as in the comp
nents, but shows different peaks with changed intensity due to the formation of new phy
ical and chemical interactions [30]. re 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG a
erine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. Figure 3. FTIR spectra of heat pressed films (A–G) and the individual components (CMC, Xanthan Gum, Agar, PEG and
Glycerine) divided into two segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength 2000 to 4000 cm−1. The FTIR spectra in Fig
components of the films, nam
stretching), 1103 cm−1 (C-C + C
cm−1 (C-H bending), 1464 cm−
1068 cm−1 (C-O-C stretching);
(C-O stretching). 3.1. Morphology and Structure of Films The FTIR spectra in Figure 3 shows the characteristic peaks for all the individ
components of the films, namely PEG and Glycerine [23–25] at 1099 cm−1 (C-H + O
stretching), 1103 cm−1 (C-C + C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching), 1
cm−1 (C-H bending), 1464 cm−1 (C-H bending) and 2878 cm−1 (C-H stretching); Agar [26
1068 cm−1 (C-O-C stretching); XG [27] at 1033 cm−1 (C-O stretching); CMC [28] at 1058 c
(C-O stretching). The peak at 3369 cm−1 is due to the O-H stretching [29]. The shift in
peak of the individual polysaccharides from 1033–1068 cm−1 to 1041–1043 cm−1 and
addition of new peaks at 1105–1112 cm−1 in the blended films may suggest the format
of new interactions due to the addition of glycerine. The blend is a perfect amalgamat
of all the individual components as it does not replicate the exact peaks as in the com
nents, but shows different peaks with changed intensity due to the formation of new ph
ical and chemical interactions [30]. . stic peaks for all the indivi
3–25] at 1099 cm−1 (C-H +
(O-H + C-O-H stretching),
m−1 (C-H stretching); Agar [2
retching); CMC [28] at 1058 f the h . gure ue to
m 10 The
id Figure 2. Surface SEM images of the heat pressed films (A–G). Figure 2. Surface SEM images of the heat pressed films (A–G). and chemical interactions [30]. The FTIR spectra in Figure 3 shows the characteristic peaks for all the individu
components of the films, namely PEG and Glycerine [23–25] at 1099 cm−1 (C-H + O-
stretching), 1103 cm−1 (C-C + C-O-C stretching), 1279 cm−1 (O-H + C-O-H stretching), 134
cm−1 (C-H bending), 1464 cm−1 (C-H bending) and 2878 cm−1 (C-H stretching); Agar [26]
1068 cm−1 (C-O-C stretching); XG [27] at 1033 cm−1 (C-O stretching); CMC [28] at 1058 cm
(C-O stretching). The peak at 3369 cm−1 is due to the O-H stretching [29]. The shift in th
peak of the individual polysaccharides from 1033–1068 cm−1 to 1041–1043 cm−1 and th
addition of new peaks at 1105–1112 cm−1 in the blended films may suggest the formatio
of new interactions due to the addition of glycerine. heat pressed films (A–G) and the individual components (C
wo segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength
g of the components[31].
3.2. Mechanical and Rheological Properties of the Films The ε of the films A, B, D and F are better than the ε reported
by different authors for pure casted films of Agar at 10% [36], 31% [37] and 45.2% [38]; XG
at 56% [39]; CMC films at 50% [1] with glycerine as a plasticizer. The tensile strength of
films A, B and F are nearly 40% of the strength of commercial cellulose acetate films [40]. The effect of mixing RPM and time on the mechanical properties is depicted by the
variation in strength and elongation percentage of the films. The blends with a 4:3 ratio
between MS and liquid, mixed at a higher RPM for a longer period of time, had improved
tensile characteristics, perhaps due to good adhesion among the polysaccharides in the
polymer matrix at the interface thus resulting in reinforcements [2]. Components
Film A
Film B
Film C
Film D
Film E
Film F
Film G
E, MPa 1
9.91 ± 3.50
35.4
7.50 ± 3.13
41.81
183.22 ± 64.5
35.23
8.62 ± 4.23
49.13
4.12 ± 0.88
21.44
8.76 ± 3.27
37.36
5.46 ± 0.99
18.21
σ, MPa 1
0.59 ± 0.21
36.58
0.59 ± 0.08
14.43
0.49 ± 0.03
6.97
0.33 ± 0.04
12.95
0.10 ± 0.03
27.5
0.61 ± 0.04
8.01
0.07 ± 0.02
33.1
ε, % 1
73.75 ± 19.05
25.8
78.40 ± 14.75
18.8
16.40 ± 9.36
57.08
62.85 ± 14.05
22.3
32.39 ± 13.14
40.5
73.40 ± 21.20
28.8
28.38 ± 2.31
8.13
1 Mean ± Std. Dev. C. of V. e 3. Mechanical properties of the heat pressed films (E = Young s Modulus, σ = Tensile strength
= Elongation at break). mponents
Film A
Film B
Film C
Film D
Film E
Film F
Film G
E, MPa1
9.91 ±
3.50 35.4
7.50 ±
3.13 41.81
183.22 ±
64.5 35.23
8.62 ±
4.23 49.13
4.12 ±
0.88 21.44
8.76 ±
3.27 37.36
5.46 ±
0.99 18.21
The effect of mixing RPM and time on the mechanical properties is depicted by the
variation in strength and elongation percentage of the films. The blends with a 4:3 ratio
between MS and liquid, mixed at a higher RPM for a longer period of time, had improved
tensile characteristics, perhaps due to good adhesion among the polysaccharides in the
polymer matrix at the interface thus resulting in reinforcements [2]. heat pressed films (A–G) and the individual components (C
wo segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength
g of the components[31].
3.2. Mechanical and Rheological Properties of the Films wo segments: (1) wavelength 800 to 2000 cm (2) wavelength 2000 to 4000 cm . The XRD peaks of the blends are shown in Figure 4, which is similar to the peaks of
the constituents, but not the same. The peak at 2θ = 19 is a near average from the constit-
uents Agar at 19 [31], XG at 19.64 [32], CMC at 19.7 [33] and PEG at 19.23 [34] whereas 2θ
= 23.4 may be because of PEG at 23.3 [34] or 23.4 [35] but with less intensity due to the
The mechanical properties of the films were assayed by tensile testing at room temper-
ature, reported in Table 3. The ε of the films A, B, D and F are better than the ε reported by
different authors for pure casted films of Agar at 10% [36], 31% [37] and 45.2% [38]; XG at
56% [39]; CMC films at 50% [1] with glycerine as a plasticizer. The tensile strength of films
A, B and F are nearly 40% of the strength of commercial cellulose acetate films [40]. 7 of 13
4 Polymers 2021, 13, 3472
ers 2021, 13, 3472 Figure 4. X-ray diffraction patterns of heat pressed films (A–G). 3.2. Mechanical and Rheological Properties of the Films
Figure 4. X-ray diffraction patterns of heat pressed films (A–G). Table 3. Mechanical properties of the heat pressed films (E = Young’s Modulus, σ = Tensile strength and ε = Elongation re 4. X-ray diffraction patterns of heat pressed films (A–G). Figure 4. X-ray diffraction patterns of heat pressed films (A–G). 3.2. Mechanical and Rheological Properties of the Films
Table 3. Mechanical properties of the heat pressed films (E = Young’s Modulus, σ = Tensile strength and ε = Elongation
t b
k) 3.2. Mechanical and Rheological Properties of the Films
The mechanical properties of the films were assayed by tensile testing
Table 3. Mechanical properties of the heat pressed films (E = Young’s Modulus, σ = Tensile strength and
at break). 3.2. Mechanical and Rheological Properties of the Films
nical properties of the heat pressed films (E = Young’s Modulus, σ = Tensile strength and ε = Elongation The mechanical properties of the films were assayed by tensile testing at room tem-
perature, reported in Table 3. heat pressed films (A–G) and the individual components (C
wo segments: (1) wavelength 800 to 2000 cm−1 (2) wavelength
g of the components[31].
3.2. Mechanical and Rheological Properties of the Films σ, MPa1
0.59 ±
0.21 36.58
0.59 ±
0.08 14.43
0.49 ±
0.03 6.97
0.33 ±
0.04 12.95
0.10 ±
0.03 27.5
0.61 ±
0.04 8.01
0.07 ±
0.02 33.1
ε, %1
73.75 ±
19.05 25.8
78.40 ±
14.75 18.8
16.40 ±
9.36 57.08
62.85 ±
14.05 22.3
32.39 ±
13.14 40.5
73.40 ±
21.20 28.8
28.38 ±
2.31 8.13
n ± Std. Dev. C. of V. The amplitude sweep was done to determine the linear viscoelastic region (LVE re-
, reported in Figure 5A. Consequently, the amplitude sweep (Figure 5B) was done
n the LVE region to avoid any sample deformation during measurements The stor
The amplitude sweep was done to determine the linear viscoelastic region (LVE
region), reported in Figure 5A. Consequently, the amplitude sweep (Figure 5B) was done
within the LVE region to avoid any sample deformation during measurements. The storage
modulus of all the films is above the loss modulus for the entire frequency zone, thus
suggesting the elastic behaviour of the material over viscosity. The MS content and mixing
time had an effect on the viscoelastic properties of the films. As with a decrease in the solid
portion and increase in mixing time, the viscoelasticity of the films changes from higher
to lower. The reason behind the change may be due to the formation of better inter and
intra hydrogen bonding among the polysaccharides [15] when mixed at high quantity for a
lower time. As the elasticity and viscosity of the film C are greater than other films, so the
same is reflected in the loss factor. modulus of all the films is above the
ti
th
l
ti b h
i
f th
3.3. Physical Properties of the Films (A) Amplitude sweep with Storage modulus G’ (■) and Loss modulus (□);
(B) Frequency sweep with Storage modulus G’ (■), Loss modulus (□) and Loss factor (▲) (The reader is requested to refer
to the web version for better interpretation). Figure 5. Rheological analysis of the heat pressed films, marked with distinct colors: A (Red), B (Orange), C (Dark Yellow),
D (Green), E (Violet), F (Navy), and G (Blue). (A) Amplitude sweep with Storage modulus G’ (■) and Loss modulus (□);
(B) Frequency sweep with Storage modulus G’ (■), Loss modulus (□) and Loss factor (▲) (The reader is requested to refer
to the web version for better interpretation). Figure 5. Rheological analysis of the heat pressed films, marked with distinct colors: A (Red), B (Orange), C (Dark Yellow),
D (Green), E (Violet), F (Navy), and G (Blue). (A) Amplitude sweep with Storage modulus G’ (■) and Loss modulus (□);
(B) Frequency sweep with Storage modulus G’ (■), Loss modulus (□) and Loss factor (▲) (The reader is requested to refer
to the web version for better interpretation). Figure 5. Rheological analysis of the heat pressed films, marked with distinct colors: A (Red), B (Orange), C (Dark Yellow),
D (Green), E (Violet), F (Navy), and G (Blue). (A) Amplitude sweep with Storage modulus G’ (■) and Loss modulus (□);
(B) Frequency sweep with Storage modulus G’ (■), Loss modulus (□) and Loss factor (▲) (The reader is requested to refer
to the web version for better interpretation). 3.3. Physical Properties of the Films
Water vapour permeability is an important parameter for assessing the quality of
food packaging material. WVTR decides the fate of the packaging material for packing
suitable food products. In reports by other authors, WVTR of pure Agar and CMC cast
films are reported to be 1130 g/m2.d [41] and 1098 g/m2.d [42], respectively. Additionally, the addition of XG in higher amounts to hydrocolloids has been re-
ported to reduce the water permeability of the films due to blocking of the free –OH
groups (which binds with water vapour molecules) with new hydrogen bonds [9]. Our
results show similar trends when the XG is mixed with Agar and CMC (Table 4). Table 4. Water vapour transmission rate, transparency, water content and thickness of the heat
pressed films. modulus of all the films is above the
ti
th
l
ti b h
i
f th
3.3. Physical Properties of the Films esting the elastic behaviour of the material over viscosity. The MS content and mixing
had an effect on the viscoelastic properties of the films. As with a decrease in the
portion and increase in mixing time, the viscoelasticity of the films changes from
er to lower. The reason behind the change may be due to the formation of better inter
ntra hydrogen bonding among the polysaccharides [15] when mixed at high quantity
Water vapour permeability is an important parameter for assessing the quality of food
packaging material. WVTR decides the fate of the packaging material for packing suitable
food products. In reports by other authors, WVTR of pure Agar and CMC cast films are
reported to be 1130 g/m2.d [41] and 1098 g/m2.d [42], respectively. ntra hydrogen bonding among the polysaccharides [15] when mixed at high quantity
p
g
g
p
y
Additionally, the addition of XG in higher amounts to hydrocolloids has been reported
to reduce the water permeability of the films due to blocking of the free –OH groups (which Polymers 2021, 13, 3472
Polymers 2021, 13, 3472 8 of 13
8 of 14 binds with water vapour molecules) with new hydrogen bonds [9]. Our results show
similar trends when the XG is mixed with Agar and CMC (Table 4). for a lower time. As the elasticity and viscosity of the film C are greater than other films,
so the same is reflected in the loss factor. binds with water vapour molecules) with new hydrogen bonds [9]. Our results show
similar trends when the XG is mixed with Agar and CMC (Table 4). for a lower time. As the elasticity and viscosity of the film C are greater than other films,
so the same is reflected in the loss factor. binds with water vapour molecules) with new hydrogen bonds [9]. Our results show
similar trends when the XG is mixed with Agar and CMC (Table 4). for a lower time. As the elasticity and viscosity of the film C are greater than other films,
so the same is reflected in the loss factor. Figure 5. Rheological analysis of the heat pressed films, marked with distinct colors: A (Red), B (Orange), C (Dark Yellow),
D (Green), E (Violet), F (Navy), and G (Blue). modulus of all the films is above the
ti
th
l
ti b h
i
f th
3.3. Physical Properties of the Films Film A
Film B
Film C
Film D
Film E
Film F
Film G
WVTR, g/m2.d 1 1119.6 a ±
15 8
1105.3 a ±
75 19
1082.8 a ±
21 06
1143.5 a ±
37 2
1178.1 a ±
104 6
1094.9 a ±
66 8
1153.8 a ±
10 3
Table 4. Water vapour transmission rate, transparency, water content and thickness of the heat pressed films. Film A
Film B
Film C
Film D
Film E
Film F
Film G
WVTR,
g/m2.d 1
1119.6 a ±
15.8 1.41
1105.3 a ±
75.19 6.80
1082.8 a ±
21.06 1.94
1143.5 a ±
37.2 3.25
1178.1 a ±
104.6 8.88
1094.9 a ±
66.8 6.10
1153.8 a ±
10.3 0.90
Transparency 1
16.18 ± 1.33
8.26
16.14 ± 1.39
8.62
13.80 ± 0.43
3.12
12.01 ± 0.99
8.24
14.91 ± 0.98
6.57
16.98 ± 3.41
20.08
11.95 ± 0.42
3.52
Moisture % 1
6.34 ± 0.1 1.65
7.24 ±5.11
70.65
5.84 ±0.39
6.73
10.05 ± 1.8
8.69
10.83 ± 0.57
5.29
6.26 ± 0.29
4.73
7.69 ± 0.62
8.06
Thickness,
mm 1
0.095 ± 0.008
8.32
0.099 ± 0.008
8.37
0.141 ± 0.005
3.25
0.125 ± 0.009
7.56
0.099 ± 0.007
6.69
0.085 ± 0.022
26.3
0.107 ± 0.004
3.45
1 Mean ± Std. Dev. C. of V.; a Statistically insignificant at p = 0.05. 3.3. Physical Properties of the Films
ble 4. Water vapour transmission rate, transparency, water content and thickness of the heat pressed films. 3.3. Physical Properties of the Films
Table 4. Water vapour transmission rate, transparency, water content and thickness of th 15.8 1.41
75.19 6.80 21.06 1.94
37.2 3.25
104.6 8.88
66.8 6.10
10.3 0.90
Transparency 1
16.18 ±
1.33 8.26
16.14 ±
1.39 8.62
13.80 ±
0.43 3.12
12.01 ±
0.99 8.24
14.91 ±
0.98 6.57
16.98 ±
3.41 20.08
11.95 ±
0.42 3.52
Statistically, the variability in mixing conditions had no effect on the vapour perme-
ability. As shown in Figure 6, since the LSD bars overlaps with each other, the WVTR
values do not have any statistically significant difference. The permeability obtained has a
range from 1078 to 1082 g/m2.d1 (Table 4). modulus of all the films is above the
ti
th
l
ti b h
i
f th
3.3. Physical Properties of the Films Moisture % 1
6.34 ± 0.1
1.65
7.24 ±5.11
70.65
5.84 ±0.39
6.73
10.05 ± 1.8
8.69
10.83 ±
0.57 5.29
6.26 ± 0.29
4.73
7.69 ± 0.62
8.06
Thus, all the films show better WVTR than individual Agar and CMC films. The
improvement in the barrier properties may be also due to the presence of polysaccharides
at higher concentrations which results in thicker compacted matrix arrangement with high
solid concentration/area [9]. Thickness, mm 1 0.095 ±
0.008 8.32
0.099 ±
0.008 8.37
0.141 ±
0.005 3.25
0.125 ±
0.009 7.56
0.099 ±
0.007 6.69
0.085 ±
0.022 26.3
0.107 ±
0.004 3.45
PEG and Glycerol may not have affected the WVTR when the polysaccharides are
present in higher concentrations (≈75%) in the films, as not being able to open the strong
interactions in the network structure of the blend in a continuous phase [41]. Thickness, mm 1 0.095 ±
0.008 8.32
0.099 ±
0.008 8.37
0.141 ±
0.005 3.25
0.125 ±
0.009 7.56
0.099 ±
0.007 6.69
0.085 ±
0.022 26.3
0.107 ±
0.004 3.45
PEG and Glycerol may not have affected the WVTR when the polysaccharides are
present in higher concentrations (≈75%) in the films, as not being able to open the strong
interactions in the network structure of the blend in a continuous phase [41]. 9 of 13
arides at
with high Polymers 2021, 13, 3472 Figure 6. Optimization graph from two level factorial analysis for the WVTR of the films, showing the desirability and
LSD bars interactions
Figure 6. Optimization graph from two level factorial analysis for the WVTR of the films, showing the desirability and LSD
bars interactions. Figure 6. Optimization graph from two level factorial analysis for the WVTR of the films, showing the desirability and
Figure 6. Optimization graph from two level factorial analysis for the WVTR of the films, showing the desirability and LSD
b Figure 6. Optimization graph from two level factorial analysis for the WVTR of the films, showing the desirability and
LSD bars interactions
Figure 6. Optimization graph from two level factorial analysis for the WVTR of the films, showing the desirability and LSD
bars interactions. PEG and Glycerol may not have affected the WVTR when the polysaccharides are
present in higher concentrations (≈75%) in the films, as not being able to open the strong
interactions in the network structure of the blend in a continuous phase [41]. modulus of all the films is above the
ti
th
l
ti b h
i
f th
3.3. Physical Properties of the Films Figure 7, shows the WVAR or moisture absorption capacity of the films in high hu
mid conditions. It is evident from the graph that the films keep on absorbing moistur
from the environment until 120 h, in contrast to the control with only silica beads reached
saturation after 24 h. In real applications, Agar-XG-CMC films can also lower the wate
activity (AW) in the package and prevent microbial spoilage. As suggested by Nur Hazirah
Figure 7, shows the WVAR or moisture absorption capacity of the films in high humid
conditions. It is evident from the graph that the films keep on absorbing moisture from the
environment until 120 h, in contrast to the control with only silica beads reached saturation
after 24 h. In real applications, Agar-XG-CMC films can also lower the water activity (AW)
in the package and prevent microbial spoilage. As suggested by Nur Hazirah et al. [12] from
their study, films with higher barrier properties than conventional packaging materials may
be used where WVTR is not essential for the foods packed in it or a secondary packaging
can be given with desirable barrier properties. Additionally, moisture absorbing films can
also be used as a moisture triggered active packaging material [43]. 10 of 14 et al. [12] from their study, films with higher barrier properties than conventional pack-
aging materials may be used where WVTR is not essential for the foods packed in it or a
secondary packaging can be given with desirable barrier properties. Additionally, mois-
ture absorbing films can also be used as a moisture triggered active packaging materia
[43]. re 7. Water vapour absorption rate of the heat pressed films A–G in 90% RH humidity chamber. Ultraviolet-C (UV-C: 100 to 280 nm) is recommended and used for the sterilization
ood against bacteria and viruses [44,45]. As shown in Figure 8, all the films show max-
Figure 7. Water vapour absorption rate of the heat pressed films A–G in 90% RH humidity chamber. Ultraviolet-C (UV-C: 100 to 280 nm) is recommended and used for the sterilization
of food against bacteria and viruses [44,45]. As shown in Figure 8, all the films show
i
b
ti
ith
l
th b t
280
d 300
t d b e 7. Water vapour absorption rate of the heat pressed films A–G in 90% RH humidity chamber. Figure 7. modulus of all the films is above the
ti
th
l
ti b h
i
f th
3.3. Physical Properties of the Films Water vapour absorption rate of the heat pressed films A–G in 90% RH humidity chamber. Ultraviolet-C (UV-C: 100 to 280 nm) is recommended and used for the sterilization
od against bacteria and viruses [44,45]. As shown in Figure 8, all the films show max-
m absorption with wavelengths between 280 and 300 nm, so as suggested by Calle et
4], wavelengths in the range 250 to 280 nm can be used to sterilize food contents when
ed with Agar-XG-CMC films
Ultraviolet-C (UV-C: 100 to 280 nm) is recommended and used for the sterilization
of food against bacteria and viruses [44,45]. As shown in Figure 8, all the films show
maximum absorption with wavelengths between 280 and 300 nm, so as suggested by
Calle et al. [44], wavelengths in the range 250 to 280 nm can be used to sterilize food
contents when packed with Agar-XG-CMC films. 10 of 13
ans Polymers 2021, 13, 3472 igure 8. Absorbance of the heat pressed films (A–G) from wavelength 200 nm to 800 nm. Figure 8. Absorbance of the heat pressed films (A–G) from wavelength 200 nm to 800 nm. ure 8. Absorbance of the heat pressed films (A–G) from wavelength 200 nm to 800 nm. Figure 8. Absorbance of the heat pressed films (A–G) from wavelength 200 nm to 800 nm. Since the transparency of the films was calculated on absorbance, the value of trans-
parency mentioned in Table 3 is inversely proportional to the actual degree of UV trans-
parency. The mixing time has an effect on the transparency of the films; lowering mixing
time irrespective of RPM gives films with better transparency and lower transparency with
increasing time. Mixing the blend for a longer time may result in oxidative degradation of
the polymeric chains which in turn affects the colour of the blend and overall transparency. Film C has the best barrier against UV and Film E for visible light. 3.4. Thermal Properties of the Films Figure 9A–G shows the TG and DTG curves of the Agar-XG-CMC-based films from
room temperature to 600 ◦C. The degradation occurs in three to four steps. In the first
phase below 100 ◦C, the evaporation of water vapour takes place, resulting in 20% mass
loss. The second phase marked by Tm in DTG from 150 ◦C to 160 ◦C in films D (Figure 9D),
E (Figure 9E) and G (Figure 9G) are due to reminiscent from the excess plasticizers
PEG + glycerol [46,47] which may not have bonded with the hydrocolloids. The films
with ≥50% liquid share during mixing show the second degradation peak between 150 and
160 ◦C. The change in mass of all the films is negligible from the start of the second phase
until the start of the third phase but the third phase with Tm from 227.7 ◦C to 230.2 ◦C
ends with degradation of 80% mass. The fourth phase is marked with Tm from 377.1 ◦C
to 381.08 ◦C. The Tm in the third and the fourth phase may be due to the amalgamation
of the pure polysaccharides with Tm reported for Agar at 300 ◦C [48], XG at 290 ◦C [49]
and Na-CMC at 280.89 ◦C [50]. Thus, it is also evident that the mixing and compression
temperatures are kept far below the degradation temperatures. 11 of 13
Na-CMC
peratures Polymers 2021, 13, 3472 Figure 9 TGA and DTG signals of heat pressed films (A–G)
Figure 9. TGA and DTG signals of heat pressed films (A–G). A
d
l
f h
d f l
A
Figure 9. TGA and DTG signals of heat pressed films (A–G). Institutional Review Board Statement: Not applicable. 4 C
l
i
4. Conclusions Acknowledgments: The first author is thankful to Tomáš Sedláˇcek, Roman Kolaˇrík, of Centre of
Polymer Systems, University Institute, Tomas Bata University in Zlin for helping us with the use of
Rheometer, AntonPaar. The graphical abstract was created with BioRender.com. Conflicts of Interest: The authors declare no conflict of interest. Informed Consent Statement: Not applicable. Acknowledgments: The first author is thankful to Tomáš Sedláˇcek, Roman Kolaˇrík, of Centre of
Polymer Systems, University Institute, Tomas Bata University in Zlin for helping us with the use of
Rheometer, AntonPaar. The graphical abstract was created with BioRender.com. Conflicts of Interest: The authors declare no conflict of interest. References 1. Wilpiszewska, K.; Antosik, A.K.; Schmidt, B.; Janik, J.; Rokicka, J. Hydrophilic Films Based on Carboxymethylated Derivatives of
Starch and Cellulose. Polymers 2020, 12, 2447. [CrossRef] 2. Ncube, L.K.; Ude, A.U.; Ogunmuyiwa, E.N.; Zulkifli, R.; Beas, I.N. Environmental Impact of Food Packaging Materials: A Review
of Contemporary Development from Conventional Plastics to Polylactic Acid Based Materials. Materials 2020, 13, 4994. [CrossRef]
3. Mostafavi, F.S.; Zaeim, D. Agar-Based Edible Films for Food Packaging Applications—A Review. Int. J. Biol. Macromol. 2020, 159,
1165–1176. [CrossRef] 4. Martínez-Sanz, M.; Gómez-Mascaraque, L.G.; Ballester, A.R.; Martínez-Abad, A.; Brodkorb, A.; López-Rubio, A. Production of
Unpurified Agar-Based Extracts from Red Seaweed Gelidium Sesquipedale by Means of Simplified Extraction Protocols. Algal
Res. 2019, 38, 101420. [CrossRef] oorthy, N.S.H.N.; Maiti, S. Xanthan Gum Derivatives: Review of Synthesis, Properties and Diverse Applica
0, 10, 27103–27136. [CrossRef] 5. Patel, J.; Maji, B.; Moorthy, N.S.H.N.; Maiti, S. Xanthan Gum Derivatives: Review of Synthesis, Pro
tions. RSC Adv. 2020, 10, 27103–27136. [CrossRef] 6. Chaturvedi, S.; Kulshrestha, S.; Bhardwaj, K.; Jangir, R. A Review on Properties and Applications of Xanthan Gum. In Microbial
Polymers: Applications and Ecological Perspectives; Vaishnav, A., Choudhary, D.K., Eds.; Springer: Singapore, 2021; pp. 87–107. ISBN
9789811600456. I.; Kelkar, S.; Campanella, O.H.; Sumnu, G.; Sahin, S.; Okos, M. Characterization of Structure of Gluten-Free
Ray Microtomography. Food Hydrocoll. 2014, 36, 37–44. [CrossRef] 7. Demirkesen, I.; Kelkar, S.; Campanella, O.H.; Sumnu, G.; Sahin, S.; Okos, M. Characterization of Str
by Using X-Ray Microtomography. Food Hydrocoll. 2014, 36, 37–44. [CrossRef] 8. Marimuthu, M.; Ilansuriyan, P.; Yap, T.N. Munisamy Shanmugam Interaction of Semi-Refined Carrageenan (E407a) with Nano
Quanta of Some Food Hydrocolloids and Their Physiochemical, Functional and Rheological Properties. J. Microbiol. Biotechnol. Food Sci. 2021, 2021, 1049–1053. 9. Nagar, M.; Sharanagat, V.S.; Kumar, Y.; Singh, L. Development and Characterization of Elephant Foot Yam Starch–Hydrocolloids
Based Edible Packaging Film: Physical, Optical, Thermal and Barrier Properties. J. Food Sci. Technol. 2020, 57, 1331–1341. [CrossRef] [PubMed] [
] [
]
10. Yaradoddi, J.S.; Banapurmath, N.R.; Ganachari, S.V.; Soudagar, M.E.M.; Mubarak, N.M.; Hallad, S.; Hugar, S.; Fayaz, H. Biodegrad-
able Carboxymethyl Cellulose Based Material for Sustainable Packaging Application. Sci. Rep. 2020, 10, 21960. [CrossRef]
11. Roy, S.; Kim, H.-J.; Rhim, J.-W. Effect of Blended Colorants of Anthocyanin and Shikonin on Carboxymethyl Cellulose/Agar-Based
Smart Packaging Film. Int. J. Biol. Macromol. 2021, 183, 305–315. [CrossRef] [PubMed] 10. References Yaradoddi, J.S.; Banapurmath, N.R.; Ganachari, S.V.; Soudagar, M.E.M.; Mubarak, N.M.; Hallad, S.; Hugar, S.; Fayaz, H. Biodegrad-
able Carboxymethyl Cellulose Based Material for Sustainable Packaging Application. Sci. Rep. 2020, 10, 21960. [CrossRef] 11. Roy, S.; Kim, H.-J.; Rhim, J.-W. Effect of Blended Colorants of Anthocyanin and Shikonin on Carboxymethyl Cellulose/Agar-Based
Smart Packaging Film. Int. J. Biol. Macromol. 2021, 183, 305–315. [CrossRef] [PubMed]
h
b
ff
f
h
h
h
l
d
h
l
f
l 11. Roy, S.; Kim, H.-J.; Rhim, J.-W. Effect of Blended Colorants of Anthocyanin and Shikonin on Ca
Smart Packaging Film. Int. J. Biol. Macromol. 2021, 183, 305–315. [CrossRef] [PubMed] Smart Packaging Film. Int. J. Biol. Macromol. 2021, 183, 305–315. [CrossRef] [PubMed] g
g
irah, M.A.S.P.; Isa, M.I.N.; Sarbon, N.M. Effect of Xanthan Gum on the Physical and Mechanical Properties
methyl Cellulose Film Blends Food Packag Shelf Life 2016 9 55 63 [CrossRef] g
g
12. Nur Hazirah, M.A.S.P.; Isa, M.I.N.; Sarbon, N.M. Effect of Xanthan Gum on the Physical and Mechan Carboxymethyl Cellulose Film Blends. Food Packag. Shelf Life 2016, 9, 55–63. [CrossRef] 13. Sousa, A.M.M.; Souza, H.K.S.; Liu, L.; Gonçalves, M.P. Alternative Plasticizers for the Production of Thermo-Compressed Agar
Films. Int. J. Biol. Macromol. 2015, 76, 138–145. [CrossRef] [PubMed] J
[
] [
]
14. Lopez, O.; Garcia, M.A.; Villar, M.A.; Gentili, A.; Rodriguez, M.S.; Albertengo, L. Thermo-Compression of Biodegradable
Thermoplastic Corn Starch Films Containing Chitin and Chitosan. LWT Food Sci. Technol. 2014, 57, 106–115. [CrossRef] 15. Bandyopadhyay, S.; Saha, N.; Saha, P. Characterization of Bacterial Cellulose Produced Using Media Containing Waste Apple
Juice. Appl. Biochem. Microbiol. 2018, 54, 649–657. [CrossRef] pp
16. Chen, Y. Packaging Selection for Solid Oral Dosage Forms. In Developing Solid Oral Dosage Forms; Elsevier: Amsterdam,
The Netherlands, 2017; pp. 637–651. ISBN 978-0-12-802447-8. pp
Cheng, M. Preparation and Characterization of Potato Starch Film with Various Size of Nano-SiO2. Polymers
ssRef] [PubMed] pp
17. Zhang, R.; Wang, X.; Cheng, M. Preparation and Characterization of Potato Starch Film with Various
2018, 10, 1172. [CrossRef] [PubMed] 18. Alias, S.A.; Mhd Sarbon, N. Rheological, Physical, and Mechanical Properties of Chicken Skin Gelatin Films Incorporated with
Potato Starch. NPJ Sci. Food 2019, 3, 26. [CrossRef] J
, ,
[
]
19. Bao, S.; Xu, S.; Wang, Z. Antioxidant Activity and Properties of Gelatin Films Incorporated with Tea Polyphenol-Loaded Chitosan
Nanoparticles. J. Sci. Food Agric. 2009, 89, 2692–2700. [CrossRef] J
, ,
[
]
19. 4 C
l
i
4. Conclusions 4. Conclusions
The transparency of the films was negatively dependent on the mixing volume and
mixing time respectively. The mixing conditions had no effect on the WVTR. The tensile
strength of the films was positively dependent on the mixing RPM and mixing time. The
crystallinity and thermal behaviour of the individual polysaccharides changed due to
blending. The films in our study showed more elongation when prepared by blending
followed with thermal pressing than casting of the individual components as reported by
The transparency of the films was negatively dependent on the mixing volume and
mixing time respectively. The mixing conditions had no effect on the WVTR. The tensile
strength of the films was positively dependent on the mixing RPM and mixing time. The
crystallinity and thermal behaviour of the individual polysaccharides changed due to
blending. The films in our study showed more elongation when prepared by blending
followed with thermal pressing than casting of the individual components as reported
by previous works. A direct comparison between blending and casting cannot be drawn
unless they are done with the same composition; thus, this is a scope for future research. Moreover, it can be concluded that since different blending conditions have an effect on the
properties of the films, industry prototypes of agar blends can be developed with blending
techniques. The improvement in the elongation at break suggests the use of these materials,
especially film F, as a primary wrapping material for less moisture sensitive foods. The
suggested blending conditions of Agar blends for future use may be mixing at 80 RPM for
7 min with 4:3 ratio between solid to liquid and 84% working volume, 16% free volume. Author Contributions: Conceptualization, S.B.; methodology, S.B.; software, S.B.; validation, S.B.;
formal analysis, S.B. and D.S.; investigation, S.B.; resources, N.S. and P.S.; data curation, S.B.; writing—
original draft preparation, S.B.; writing—review and editing, S.B. and T.S.; visualization, S.B.; super-
vision, N.S. and P.S.; project administration, T.S.; funding acquisition, T.S. All authors have read and
agreed to the published version of the manuscript. Funding: This work is supported by the Ministry of Education, Youth and Sports of the Czech
Republic—DKRVO (RP/CPS/2020/005) and DKRVO (RP/CPS/2020/003). Institutional Review Board Statement: Not applicable. 12 of 13 12 of 13 Polymers 2021, 13, 3472 Informed Consent Statement: Not applicable. References Bao, S.; Xu, S.; Wang, Z. Antioxidant Activity and Properties of Gelatin Films Incorporated with Tea Polyphenol-Loaded Chitosan
N
ti l
J S i F
d A
i
2009 89 2692 2700 [C
R f] 19. Bao, S.; Xu, S.; Wang, Z. Antioxidant Activity and Properties of Gelatin Films Incorporated with Tea
Nanoparticles. J. Sci. Food Agric. 2009, 89, 2692–2700. [CrossRef] p
g
20. Bandyopadhyay, S.; Saha, N.; Zandraa, O.; Pummerová, M.; Sáha, P. Essential Oil Based PVP-CMC-BC-GG Functional Hydrogel
Sachet for ‘Cheese’: Its Shelf Life Confirmed with Anthocyanin (Isolated from Red Cabbage) Bio Stickers. Foods 2020, 9,
307. [CrossRef] [
]
21. Pagano, C.; Puglia, D.; Luzi, F.; Michele, A.D.; Scuota, S.; Primavilla, S.; Ceccarini, M.R.; Beccari, T.; Iborra, C.A.V.; Ramella,
D.; et al. Development and Characterization of Xanthan Gum and Alginate Based Bioadhesive Film for Pycnogenol Topical Use
in Wound Treatment. Pharmaceutics 2021, 13, 324. [CrossRef] 22. Wu, Y.; Geng, F.; Chang, P.R.; Yu, J.; Ma, X. Effect of Agar on the Microstructure and Performance of Potato Starch Film. Carbohydr. Polym. 2009, 76, 299–304. [CrossRef] 22. Wu, Y.; Geng, F.; Chang, P.R.; Yu, J.; Ma, X. Effect of Agar on the Microstructure and Performance of Pota
Polym. 2009, 76, 299–304. [CrossRef] 13 of 13 13 of 13 Polymers 2021, 13, 3472 23. Chieng, B.W.; Ibrahim, N.; Yunus, W.; Hussein, M. Effects of Graphene Nanopletelets on Poly(Lactic Acid)/Poly(Ethylene Glycol)
Polymer Nanocomposites. Polymers 2013, 6, 93–104. [CrossRef] y
p
y
24. Kamyar, S.; Ahmad, M.; Jazayeri, S.D.; Sedaghat, S.; Shabanzadeh, P.; Jahangirian, H. (kamran); Mahdavi, M.; Abdollahi, Y. Synthesis and Characterization of Polyethylene Glycol Mediated Silver Nanoparticles by the Green Method. Int. J. Mol. Sci. 2012,
13, 6639–6650. [CrossRef] [
]
25. Kachel, M.; Matwijczuk, A.; Gago´s, M. Analysis of the Physicochemical Properties of Post-Manufacturing Waste Derived from
Production of Methyl Esters from Rapeseed Oil. Int. Agrophysics 2017, 31, 1–8. [CrossRef] 26. Usha Rani, G.; Konreddy, A.K.; Mishra, S.; Sen, G. Synthesis and Applications of Polyacrylamide Grafted Agar as a Matrix for
Controlled Drug Release of 5-ASA. Int. J. Biol. Macromol. 2014, 65, 375–382. [CrossRef] g
27. Chis,, A.; Fetea, F.; Taoutaou, A.; Socaciu, C. Application of FTIR Spectroscopy for a Rapid Determination of Some Hydrolytic
Enzymes Activity on Sea Buckthorn Substrate. Rom. Biotechnol. Lett. 2010, 15, 5738–5744. 28. Bandyopadhyay, S.; Saha, N.; Brodnjak, U.V.; Saha, P. Bacterial Cellulose Based Greener Packaging Material: A Bioadhesive
Polymeric Film. Mater. Res. References Express 2018, 5, 115405. [CrossRef] 29. Shamsuri, A.; Daik, R. Utilization of an Ionic Liquid/Urea Mixture a
Films. Materials 2013, 6, 682–698. [CrossRef] [PubMed] 29. Shamsuri, A.; Daik, R. Utilization of an Ionic Liquid/Urea Mixture as a Physical Coupling Agent for Agarose/Talc Composite
Films. Materials 2013, 6, 682–698. [CrossRef] [PubMed] ef, M.M.; Yahaya, A.H. Preparation and Characterization of Chitosan/Agar Blended Films: Part 1. Chemical
hology. E-J. Chem. 2012, 9, 1431–1439. [CrossRef] 30. El-hefian, E.A.; Nasef, M.M.; Yahaya, A.H. Preparation and Characterization of Chitosan/Agar Blen
Structure and Morphology. E-J. Chem. 2012, 9, 1431–1439. [CrossRef] 31. Sharma, K.; Kumar, V.; Swart, C.; Chaudhary, B.; Swart, H. Synthesis, Characterization and Anti-Microbial Activity of Superab-
sorbents Based on Agar-Poly(Methacrylic Acid-Glycine). J. Bioact. Compat. Polym. 2016, 32. [CrossRef] g
y(
y
y
) J
p
y
32. Sharma, V.; Pathak, K. Modified Xanthan Gum as Rapidly Disintegrating Hydrophilic Excipient for Time-Controlled Disintegrat-
ing Tablets of Roxithromycin. Indian J. Pharm. Educ. Res. 2013, 47, 79–87. [CrossRef] g
y
y
y
32. Sharma, V.; Pathak, K. Modified Xanthan Gum as Rapidly Disintegrating Hydrophilic Excipient for Time-Controlled Disintegrat- 32. Sharma, V.; Pathak, K. Modified Xanthan Gum as Rapidly Disintegrating Hydrophilic Exc
ing Tablets of Roxithromycin. Indian J. Pharm. Educ. Res. 2013, 47, 79–87. [CrossRef] p
y
g
g
y
p
ing Tablets of Roxithromycin. Indian J. Pharm. Educ. Res. 2013, 47, 79–87. [CrossRef] g
y
33. Basu, P.; Uttamchand, N.K.; Arunachalam, R.; Devi, S.; Inderchand, M. Characterization and Evaluation of Carboxymethyl Cellulose-
Based Films for Healing of Full-Thickness Wounds in Normal and Diabetic Rats. ACS Omega 2018, 3, 12622–12632. [CrossRef] d, N.K.; Arunachalam, R.; Devi, S.; Inderchand, M. Characterization and Evaluation of Carboxymethyl Cellulose 33. Basu, P.; Uttamchand, N.K.; Arunachalam, R.; Devi, S.; Inderchand, M. Characterization and Evaluation of
Based Films for Healing of Full-Thickness Wounds in Normal and Diabetic Rats ACS Omega 2018 3 12622 Basu, P.; Uttamchand, N.K.; Arunachalam, R.; Devi, S.; Inderchand, M. Characterization and Evaluation of Car 33. Basu, P.; Uttamchand, N.K.; Arunachalam, R.; Devi, S.; Inderchand, M. Characterization and Evaluation of Carboxymethyl Cellulose
Based Films for Healing of Full-Thickness Wounds in Normal and Diabetic Rats. ACS Omega 2018, 3, 12622–12632. [CrossRef] Based Films for Healing of Full-Thickness Wounds in Normal and Diabetic Rats. ACS Omega 2018, 3, 12622–12 34. Ahmad, M.; Tay, M.; Kamyar, S.; Hussein, M.; Lim, J. Green Synthesis and Characterization of Silver/Chitosan/Polyethylene
Glycol Nanocomposites without Any Reducing Agent. Int. J. References Physicochemical and Morphological Properties of Plasticized
–Agar Biodegradable Films. Int. J. Biol. Macromol. 2014, 69, 176–184. [CrossRef] [PubMed] Madera Santana, T.J.; Freile Pelegrín, Y.; Azamar Barrios, J.A. Physicochemical and Morphological Pro
Poly(Vinyl Alcohol)–Agar Biodegradable Films. Int. J. Biol. Macromol. 2014, 69, 176–184. [CrossRef] [PubM
´
´ y(Vinyl Alcohol)–Agar Biodegradable Films. Int. J. Biol. Macromol. 2014, 69, 176–184. [CrossRef] [PubMed
´
´ 42. Łopusiewicz, Ł.; Kwiatkowski, P.; Drozłowska, E.; Trocer, P.; Kostek, M.; ´Sliwi´nski, M.; Polak-´Sliwi´nska, M.; Kowalczyk, E.;
Sienkiewicz, M. Preparation and Characterization of Carboxymethyl Cellulose-Based Bioactive Composite Films Modified with
Fungal Melanin and Carvacrol. Polymer 2021, 13, 499. [CrossRef] [PubMed] g
y
43. Bahmid, N.A.; Dekker, M.; Fogliano, V.; Heising, J. Development of a Moisture-Activated Antimicrobial
Mustard Seeds and Its Application on Meat in Active Packaging System. Food Packag. Shelf Life 2021, 3 43. Bahmid, N.A.; Dekker, M.; Fogliano, V.; Heising, J. Development of a Moisture-Activated Antimicrobial Film Containing Ground
Mustard Seeds and Its Application on Meat in Active Packaging System. Food Packag. Shelf Life 2021, 30, 100753. [CrossRef]
44. Calle, A.; Fernandez, M.; Montoya, B.; Schmidt, M.; Thompson, J. UV-C LED Irradiation Reduces Salmonella on Chicken and Mustard Seeds and Its Application on Meat in Active Packaging System. Food Packag. Shelf Life 2021, 30, 100753. [CrossRef]
44. Calle, A.; Fernandez, M.; Montoya, B.; Schmidt, M.; Thompson, J. UV-C LED Irradiation Reduces Salmonella on Chicken and
Food Contact Surfaces. Foods 2021, 10, 1459. [CrossRef] [PubMed] 44. Calle, A.; Fernandez, M.; Montoya, B.; Schmidt, M.; Thompson, J. UV-C LED Irradiation Reduces Sal
Food Contact Surfaces. Foods 2021, 10, 1459. [CrossRef] [PubMed] 45. Debnath, S. Low Cost Homemade System to Disinfect Food Items from SARS-CoV-2. J. Med. Syst. 2020, 44, 126. [CrossRef] [PubMed]
46
C
d
J R F
it
l
N A Shi
i M K Th
l D
iti
f P l
th l
Gl
l 20
d E
ti l Oil i
G 45. Debnath, S. Low Cost Homemade System to Disinfect Food Items from SARS-CoV-2. J. Med. Syst. 2020, 44, 126. [CrossRef] [PubMed]
46. Conder, J.R.; Fruitwala, N.A.; Shingari, M.K. Thermal Decomposition of Polyethylene Glycol 20m and Essential Oils in Gas—
Liquid Chromatography and the Effect of Traces of Oxygen. J. Chromatogr. A 1983, 269, 171–178. [CrossRef] 46. Conder, J.R.; Fruitwala, N.A.; Shingari, M.K. Thermal Decomposition of Polyethylene Glycol 20m and Essential Oils in Gas—
Liquid Chromatography and the Effect of Traces of Oxygen. J. Chromatogr. References Mol. Sci. 2011, 12, 4872–4884. [CrossRef] 34. Ahmad, M.; Tay, M.; Kamyar, S.; Hussein, M.; Lim, J. Green Synthesis and Characterization of Silver/Chitosan/Polyethylene
Glycol Nanocomposites without Any Reducing Agent. Int. J. Mol. Sci. 2011, 12, 4872–4884. [CrossRef] 35. Barron, M.; Young, T.; Johnston, K.; Williams, R. Investigation of Processing Parameters of Spray Freezing into Liquid to Prepare
Polyethylene Glycol Polymeric Particles for Drug Delivery. AAPS PharmSciTech 2003, 4, E12. [CrossRef] 35. Barron, M.; Young, T.; Johnston, K.; Williams, R. Investigation of Processing Parameters of Spray Freezi
Polyethylene Glycol Polymeric Particles for Drug Delivery. AAPS PharmSciTech 2003, 4, E12. [CrossRef ,
;
g,
; J
,
;
,
g
g
p
y
g
Polyethylene Glycol Polymeric Particles for Drug Delivery. AAPS PharmSciTech 2003, 4, E12. [CrossRef] Guo, Y.; Zhang, B.; Zhao, S.; Qiao, D.; Xie, F. Plasticized Starch/Agar Composite Films: Processing, M 36. Guo, Y.; Zhang, B.; Zhao, S.; Qiao, D.; Xie, F. Plasticized Starch/Agar Composite Films: Process
Mechanical Properties and Surface Hydrophilicity. Coatings 2021, 11, 311. [CrossRef] 36. Guo, Y.; Zhang, B.; Zhao, S.; Qiao, D.; Xie, F. Plasticized Starch/Agar Composite Films: P
Mechanical Properties and Surface Hydrophilicity. Coatings 2021, 11, 311. [CrossRef] ,
;
g,
;
,
; Q
,
;
,
g
p
Mechanical Properties and Surface Hydrophilicity. Coatings 2021, 11, 311. [CrossRef] 37. Rusli, A.; Mulyati, M.T.; Metusalach, M.; Salengke, S. Physical and Mechanical Properties of Agar Based Edible Film with Glycerol
Plasticizer. Int. Food Res. J. 2016, 24, 1669–1675. [CrossRef] 38. Rhim, J.-W. Physical-Mechanical Properties of Agar/κ-Carrageenan Blend Film and Derived Clay Nanocomposite Film. J. Food
Sci. 2012, 77, N66–N73. [CrossRef] [PubMed] 39. Setoyama, M.; Yamamoto, K.; Kadokawa, J. Preparation of Cellulose/Xanthan Gum Composite Films and Hydrogels Using Ionic
Liquid. J. Polym. Environ. 2014, 22, 298–303. [CrossRef] q
40. Cazón, P.; Velazquez, G.; Ramírez, J.A.; Vázquez, M. Polysaccharide-Based Films and Coatings for Food Packaging: A Review. Food Hydrocoll. 2017, 68, 136–148. [CrossRef] y
41. Madera-Santana, T.J.; Freile-Pelegrín, Y.; Azamar-Barrios, J.A. Physicochemical and Morphologi
Poly(Vinyl Alcohol)–Agar Biodegradable Films. Int. J. Biol. Macromol. 2014, 69, 176–184. [CrossRef
´
´ J.; Freile-Pelegrín, Y.; Azamar-Barrios, J.A. Physicochemical and Morphological Properties of Plasticized
A
Bi d
d bl Fil
I t J Bi l M
l 2014 69 176 184 [C
R f] [P bM d] adera-Santana, T.J.; Freile-Pelegrín, Y.; Azamar-Barrios, J.A. Physicochemical and Morphological Proper J.; Freile Pelegrín, Y.; Azamar Barrios, J.A. References A 1983, 269, 171–178. [CrossRef] 47. Ochoa-Yepes, O.; Di Giogio, L.; Goyanes, S.; Mauri, A.; Famá, L. Influence of Process (Extrusion/Thermo-Compression,
Casting) and Lentil Protein Content on Physicochemical Properties of Starch Films. Carbohydr. Polym. 2019, 208, 221–231. [CrossRef] [PubMed] 48. Ouyang, Q.-Q.; Hu, Z.; Li, S.-D.; Quan, W.-Y.; Wen, L.-L.; Yang, Z.-M.; Li, P.-W. Thermal Degradation of Agar: Mechanism and
Toxicity of Products. Food Chem. 2018, 264, 277–283. [CrossRef] [PubMed] y
49. Srivastava, A.; Mishra, V.; Singh, P.; Srivastava, A.; Kumar, R. Comparative Study of Thermal Degra
Copolymers of Polysaccharides and Vinyl Monomers. J. Therm. Anal. Calorim. 2012, 107, 211–223. [Cro 50. de Britto, D.; Assis, O.B.G. Thermal Degradation of Carboxymethylcellulose in Different Salty Forms. Thermochim. Acta 2009, 494,
115–122. [CrossRef]
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https://openalex.org/W3012487926
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https://journals.iucr.org/s/issues/2020/03/00/mo5212/mo5212.pdf
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English
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Measurement and compensation of misalignment in double-sided hard X-ray Fresnel zone plates
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Journal of synchrotron radiation
| 2,020
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cc-by
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Measurement and compensation of misalignment
in double-sided hard X-ray Fresnel zone plates ISSN 1600-5775 ISSN 1600-5775 Viktoria Yurgens,a*‡ Frieder Koch,a Mario Scheel,b Timm Weitkampb and
Christian Davida aPaul Scherrer Institute, 5232 Villigen PSI, Switzerland, and bSynchrotron SOLEIL, 91192 Gif-sur-Yvette, France. *Correspondence e-mail: viktoria.yurgens@psi.ch Received 2 September 2019
Accepted 7 February 2020 Double-sided Fresnel zone plates are diffractive lenses used for high-resolution
hard X-ray microscopy. The double-sided structures have significantly higher
aspect ratios compared with single-sided components and hence enable more
efficient imaging. The zone plates discussed in this paper are fabricated on each
side of a thin support membrane, and the alignment of the zone plates with
respect to each other is critical. Here, a simple and reliable way of quantifying
misalignments by recording efficiency maps and measuring the absolute
diffraction efficiency of the zone plates as a function of tilting angle in two
directions is presented. The measurements are performed in a setup based on a
tungsten-anode microfocus X-ray tube, providing an X-ray energy of 8.4 keV
through differential measurements with a Cu and an Ni filter. This study
investigates the sources of the misalignments and concludes that they can be
avoided by decreasing the structure heights on both sides of the membrane
and by pre-programming size differences between the front- and back-side
zone plates. Edited by A. Momose, Tohoku University, Japan ‡ Present address: University of Basel,
Klingelbergstrasse 82, 4056 Basel, Switzerland Keywords: X-ray optics; Fresnel zone plate;
diffraction efficiency; microfocus X-ray source. Keywords: X-ray optics; Fresnel zone plate;
diffraction efficiency; microfocus X-ray source. research papers research papers Measurement and compensation of misalignment
in double-sided hard X-ray Fresnel zone plates research papers 2002; Snigireva et al., 2007; Gleber et al., 2014). The approach
bears the challenge of maintaining the mechanical alignment
of the stacked zone plates during operation within a fraction
of the outermost zone width. This problem can be avoided by
making double-sided zone plates (Mohacsi et al., 2015), where
the zone plates are fabricated as a monolithic device, on each
side of a thin support membrane. An additional approach to
achieving small linewidths at high aspect ratios is provided by
a technique called line-doubling (Jefimovs et al., 2007; Vila-
Comamala et al., 2011). In this method, template structures are
fabricated from a low-atomic-number material, e.g. hydrogen
silsesquioxane (HSQ), which has a very small effect on the
transmission of hard X-rays. These structures are then coated
with a heavy metal, for example Ir, by atomic layer deposition
(ALD). The interaction with X-rays is then dominated by the
metal deposited on the side-walls of the template structures,
which double the effective number of lines. onal. In Fig. 1(e), the zone plates are concentric, but there is
a scaling difference of 2dr between the zone plate radii,
resulting in a concentric circular fringe. Curved and non-
centric fringes are visible in Fig. 1(f), where the zone plates
have a scaling difference of 2dr and are offset by 2dr along
the diagonal. This illustrates that straight fringes result from
offsets between the zone plates, whereas curved fringes always
indicate the presence of a scaling difference. In this paper, we present an X-ray tube-based setup that
yields absolute measurements of first-order diffraction effi-
ciency of Fresnel zone plates, as well as maps of the zone plate
diffraction efficiency. The setup is used to measure misalign-
ments, to find ways to compensate for them in the fabrication
and, finally, to minimize their effect in finished zone plates. The step to a laboratory-based setup is crucial to provide
quick feedback to the fabrication process that would be
impossible to obtain on a regular basis at a synchrotron. Fig. 1(a) shows a schematic of a double-sided and line-
doubled structure. Together, these two methods make it
possible to fabricate FZPs with much higher aspect ratios
compared with what is possible for single-sided zone plates. However, one needs to ensure that the alignment between the
two zone plates is within a fraction of the outermost zone
width, since larger misalignments will impair the optical
performance. research papers In regions on a double-sided zone plate where
the two sides have a radial displacement by one zone width,
the local efficiency will vanish. 1. Introduction Fresnel zone plates (FZPs) are diffractive lenses used as
focusing elements in a range of soft and hard X-ray imaging
applications in synchrotrons all over the world. In their most
common form, they are circular gratings consisting of a series
of concentric rings, or ‘zones’, with gradually decreasing
widths towards the periphery. The zones are spaced such that
light transmitted through the zone plate interferes construc-
tively at an intended focal distance. The interference occurs
due to a relative phase or amplitude difference induced in
beams emerging from neighbouring zones (CXRO; Kirz,
1974). The diffraction efficiency of a zone plate, defined as the
fraction of the incoming intensity diffracted into a certain
diffraction order, is one of its most important characteristics
(Buralli & Morris, 1992). The maximum diffraction efficiency
is reached when the zone plate structure introduces a phase
shift close to to the incoming X-ray wave. For hard X-rays,
this requires that the zones must be several micrometres thick,
even when the zone plate is fabricated out of heavy materials
(Snigirev & Snigireva, 2008). At the same time, in order to be
able to perform high-resolution imaging, the outermost zone
width dr needs to be very small, in many cases down to tens of
nanometres. The resulting extreme aspect ratios are very
difficult to fabricate. A way of overcoming the aspect ratio limitations in the
fabrication is to stack two or more zone plates on top of each
other, so that they work as a single zone plate with a zone
height equal to the total height of the structures (Maser et al., 583 https://doi.org/10.1107/S1600577520001757 J. Synchrotron Rad. (2020). 27, 583–589 research papers 584
Yurgens et al.
Improving misalignment in double-sided hard X-ray Fresnel zone plates 2. Zone plate fabrication Arrays of double-sided, line-doubled zone plates were
produced on 250 nm-thick silicon nitride membranes. The
zone plates were designed with a 100 mm diameter and an
outermost zone width of 50 nm to yield a focal length of
34 mm at an X-ray energy of 8.4 keV. The structures were
made from an HSQ template covered with Ir by plasma-
enhanced ALD; the width of the HSQ template structures as
well as the Ir layer thickness were designed for optimum
diffraction efficiency (Marschall et al., 2017). The complete
processing, including the patterning of a set of alignment
markers around each zone plate, was performed first on the
back-side of the membranes. Subsequently, the same processes
were repeated on the front-side, using the markers on the
back-side for alignment. If strong misalignments are present, the efficiency distri-
bution over the zone plate area – here referred to as the
efficiency map – will contain moire´ fringes. Such fringes are
visual artefacts arising from the interference in the overlay of
ordered patterns, in our case the two zone plates. The fringes
can be used to determine the relative offsets and distortions of
the two zone plates (Vladimirsky, 1988). The chips were spin-coated with undiluted HSQ FOx-16
resist at 1000 rpm for 60 s, resulting in approximately 600 nm-
thick HSQ layers on the back-side of the membrane and
between 800 nm and 2 mm-thick layers on the front-side. A
low rotation speed was used in order to obtain HSQ layers
that were as thick as possible. The difference in height at the
same rotation speed originates from the different structures
of the silicon chip on its two sides due to the etching of the
membrane. On the back-side, the etched side-walls of the
carrier wafer affect the resist spread during spin-coating,
causing a strong height gradient over about 400 mm, which
is unusable for structuring. Only the central part of the
membrane can therefore be used for the zone plate fabrication
on the back-side. The tension due to the curved surface of the
resist flowing over the sidewall is also likely to be responsible
for the lower overall height on the back-side compared with
the front when using identical spinning parameters. The layer
thicknesses were measured on finished Ir-coated structures
in a scanning electron microscope (SEM) under a 45 tilting
angle. Figs. 2. Zone plate fabrication 1(c)–1(f) show how different moire´ interference
patterns emerge from the overlay of two zone plate sketches
such as the one in Fig. 1(b). Figs. 1(c) and 1(d) show examples
of linear offsets in different directions: in the former, the zone
plates are offset with respect to each other by 2dr in the
horizontal direction, and in the latter by 4dr along the diag- Figure 1
(a) Schematic of a double-sided line-doubled Fresnel zone plate. The
HSQ template structures are indicated in light grey and the Ir deposited
on top is marked in dark grey. Adapted from Mohacsi et al. (2015). (b) Sketch of a Fresnel zone plate. (c)–(f) Different ways of overlaying
two zone plates such as the one in (b), illustrating various types of
moire´ fringes. Figure 1 (a) Schematic of a double-sided line-doubled Fresnel zone plate. The
HSQ template structures are indicated in light grey and the Ir deposited
on top is marked in dark grey. Adapted from Mohacsi et al. (2015). (b) Sketch of a Fresnel zone plate. (c)–(f) Different ways of overlaying
two zone plates such as the one in (b), illustrating various types of
moire´ fringes. (a) Schematic of a double-sided line-doubled Fresnel zone plate. The
HSQ template structures are indicated in light grey and the Ir deposited
on top is marked in dark grey. Adapted from Mohacsi et al. (2015). (b) Sketch of a Fresnel zone plate. (c)–(f) Different ways of overlaying
two zone plates such as the one in (b), illustrating various types of
moire´ fringes. Patterning of the HSQ layers was performed using a Vistec
EBPG 5000+ electron-beam lithography system, operated at
an acceleration voltage of 100 kV, a beam current of 4 nA and J. Synchrotron Rad. (2020). 27, 583–589 research papers yielded almost half the bandwidth in comparison due to the
smaller difference between the absorption edge energies of
Cu and Ni, and therefore isolated the lines of interest more
effectively. The resulting monochromaticity was E/E = 7.5
103. The filtered beam illuminated the zone plate placed
117 mm downstream of the source, and the first diffraction
order was isolated using a 10 mm pinhole placed in the focal
plane 48 mm downstream of the zone plate. 3. X-ray tube setup design By
subtracting the number of counts in the
region labelled ‘outside of ZP’ from
the number of counts in the region
labelled ‘1st, 0th, 1st’, one is effec-
tively subtracting the slightly elevated
number of photons diffracted into the
zeroth order in the centre of the zone
plate as well as the counts in the nega-
tive first order, and obtaining the first
order counts. Reference measurements
to account for the incoming photons
were made by removing the 10 mm
pinhole and replacing the zone plate by
a 100 mm pinhole. All measurements
were differential, meaning that they
were performed once with the Cu filter
and once with the Ni filter, with the final
result given after subtraction of the two
signals. Dividing the first-order counts
by the number of counts in the refer-
ence measurements finally gave the
efficiency of the zone plate. Figure 2
(a) Schematic of the X-ray tube-based setup. (b) Measured tungsten X-ray tube spectrum without
filtering (blue, dashed) and after differential filtering with a 12 mm Cu and a 12.85 mm Ni filter
(black). The main emission lines of tungsten are indicated; after filtering, only the L1,2 line with an
approximate X-ray energy of 8.4 keV remains. The separate sublines cannot be resolved by the
spectrometer. (c) Measured tungsten X-ray tube spectrum when filtered with a 12 mm Cu filter
(orange) and a 12.85 mm Ni filter (green). Subtracting the two spectra yields the final spectrum in
(b). The insets show a closer view of the region of interest for the filtering, where it is apparent that
the filter thicknesses have been matched so that the curves overlap for energies outside the L1,2
line. Fi
2 Figure 2 g
(a) Schematic of the X-ray tube-based setup. (b) Measured tungsten X-ray tube spectrum without
filtering (blue, dashed) and after differential filtering with a 12 mm Cu and a 12.85 mm Ni filter
(black). The main emission lines of tungsten are indicated; after filtering, only the L1,2 line with an
approximate X-ray energy of 8.4 keV remains. The separate sublines cannot be resolved by the
spectrometer. (c) Measured tungsten X-ray tube spectrum when filtered with a 12 mm Cu filter
(orange) and a 12.85 mm Ni filter (green). Subtracting the two spectra yields the final spectrum in
(b). 3. X-ray tube setup design Reference measurements
to account for the incoming photons
were made by removing the 10 mm
pinhole and replacing the zone plate by
a 100 mm pinhole. All measurements
were differential, meaning that they
were performed once with the Cu filter
and once with the Ni filter, with the final
result given after subtraction of the two
signals. Dividing the first-order counts
by the number of counts in the refer-
ence measurements finally gave the
efficiency of the zone plate. ube spectrum without
a 12.85 mm Ni filter
the L1,2 line with an
t be resolved by the
th a 12 mm Cu filter
the final spectrum in
ere it is apparent that
gies outside the L1,2 The efficiency measurements were performed by scanning
the zone plate in a plane perpendicular to the optical axis and
recording the photons diffracted into the first order with the
PCH. Scans were performed with a step length of 1 mm over a
range covering three times the zone plate diameter; the counts
were integrated for 10 s at each point. Line-doubled zone
plates suffer from an increased contribution of the zeroth
order in the centre, which makes it difficult to determine the
number of first-order counts in the peak
in the resulting scans. However, since
the central part of the zone plate mainly
consists of low-Z HSQ, the zeroth-order
counts at that position can be well
approximated
by
the
number
of
photons passing through the silicon
nitride membrane outside of the zone
plate. This is why a broad scanning
range was chosen (see Fig. 3). By
b
i
h
b
f
i
h asurements were performed by scanning
ane perpendicular to the optical axis and
ns diffracted into the first order with the
formed with a step length of 1 mm over a
times the zone plate diameter; the counts
10 s at each point. Line-doubled zone
n increased contribution of the zeroth
which makes it difficult to determine the
number of first-order counts in the peak
in the resulting scans. However, since
the central part of the zone plate mainly
consists of low-Z HSQ, the zeroth-order
counts at that position can be well
approximated
by
the
number
of
photons passing through the silicon
nitride membrane outside of the zone
plate. This is why a broad scanning
range was chosen (see Fig. 3). 3. X-ray tube setup design 3. X-ray tube setup design The setup, schematically illustrated in Fig. 2(a), was based on a
Hamamatsu L10101 microfocus X-ray tube with a tungsten
anode operated at 40 kV acceleration voltage and 150 mA
current, resulting in a spot size of approximately 10 mm. A
close-to-monochromatic beam was isolated from its spectrum
by performing measurements first with a 12 mm Cu filter, then
with a 12.85 mm Ni filter, and subtracting the signals [see
Figs. 2(b) and 2(c)]. The filter thicknesses were chosen to
match the absorption of Cu and Ni outside the transmitted
window of energies. In the resulting effective spectrum, only
the tungsten L1 and L2 line doublet remained, with X-ray
energies of 8.398 keV and 8.335 keV and a relative intensity
ratio of 9:1 (CXRO, Center For X-ray Optics; http://zone
plate.lbl.gov/theory). The two-filter scheme is similar to the
one employed by Chen et al. (2008), which filters out the same
tungsten lines by using a Co and a Cu filter. Our scheme y
(
)
The efficiency measurements were performed by scanning
the zone plate in a plane perpendicular to the optical axis and
recording the photons diffracted into the first order with the
PCH. Scans were performed with a step length of 1 mm over a
range covering three times the zone plate diameter; the counts
were integrated for 10 s at each point. Line-doubled zone
plates suffer from an increased contribution of the zeroth
order in the centre, which makes it difficult to determine the
number of first-order counts in the peak
in the resulting scans. However, since
the central part of the zone plate mainly
consists of low-Z HSQ, the zeroth-order
counts at that position can be well
approximated
by
the
number
of
photons passing through the silicon
nitride membrane outside of the zone
plate. This is why a broad scanning
range was chosen (see Fig. 3). By
subtracting the number of counts in the
region labelled ‘outside of ZP’ from
the number of counts in the region
labelled ‘1st, 0th, 1st’, one is effec-
tively subtracting the slightly elevated
number of photons diffracted into the
zeroth order in the centre of the zone
plate as well as the counts in the nega-
tive first order, and obtaining the first
order counts. 2. Zone plate fabrication The emerging
light was projected onto a MO¨ NCH03 direct-conversion
hybrid Si pixel detector (Ramilli et al., 2017; Bergamaschi et
al., 2018) placed 1135 mm downstream from the pinhole and
yielding a projection of the efficiency distribution of the zone
plate. In the diffraction efficiency measurements, a Hama-
matsu Photon Counting Head H10682-210 (PCH) was placed
behind the pinhole and counted the transmitted flux. For the
conversion of X-rays to visible photons, a 5.5 mm-thick poly-
vinyl toluene scintillator (BC400, Saint-Gobain) was used. a dose of 15 000 mC cm2. The development was carried out in
a 1:3 mixture of the developer AZ A351 with water for a
duration of 15 min; the structures were rinsed in water and
subsequently dried by critical-point drying in a Leica EM
CPD300 system. The Ir deposition was achieved using a
Picosun R200 ALD tool. Yurgens et al.
Improving misalignment in double-sided hard X-ray Fresnel zone plates
585 4. Results Fig. 4 shows a comparison between imaging performed with
the X-ray tube and at a synchrotron beamline. Figs. 4(a)–4(c)
show normalized diffraction efficiency maps of three double-
sided line-doubled zone plates from the same chip labelled A,
B and C, recorded in the X-ray tube setup at an energy of
8.4 keV with a 1400 s exposure time. The drift in the relative
position of the pinhole and zone plates was negligible,
enabling prolonged exposure times. Figs. 4(d)–4(f) show
normalized maps made of the same zone plates at the
ANATOMIX beamline of Synchrotron SOLEIL (Weitkamp
et al., 2017; Scheel et al., 2018) at an X-ray energy of 10 keV
with a 2 s exposure time. The measurement geometry at the
beamline was similar to that presented in Fig. 2, but with
a parallel beam impinging on the zone plate and a 25 mm
pinhole instead of the smaller one used with the laboratory As a test of the influence of the height differences, and to
determine the sign of the scaling error, two double-sided chips
were prepared with identical layouts but different front-side
structure heights. The layouts consisted of a three-by-three
grid of zone plates, all identical on the back-side with a 100 mm
diameter and 50 nm outermost zone width, but different on
the front-side where the zone plate diameters were varied
from 0.5% to +0.5% in one direction and diagonal offsets in
steps of 100 nm were introduced in the other. The chips were
spin-coated at 2500 rpm on the back-side, giving structure
heights of 550 nm, and at 1500 rpm and 2500 rpm on the front-
side, giving structure heights of 1200 nm (chip 1) and 750 nm
(chip 2), respectively. Figure 4
(a)–(c) Diffraction efficiency maps recorded with the X-ray tube setup
at an X-ray energy of 8.4 keV and an exposure time of 1400 s. (d)–(f)
Diffraction efficiency maps of the same three zone plates made at the
ANATOMIX beamline of Synchrotron SOLEIL at an X-ray energy of
10 keV with an exposure time of 2 s. The zeroth-order counts in the
centre of the maps have been subtracted. Fig. 5(a) shows the efficiency maps of the zone plates on
chip 1, the sample with a large height difference between the
front- and the back-side structures. research papers research papers research papers
Figure 3
Schematic of the counts recorded on the PCH as a function of zone plate
position along one of the scanning directions. Shaded regions in the
background illustrate how the zone plate (in red) diffracts the incoming
light into the distinct diffraction orders. The red dashed line indicates the
resulting regions with different count levels within and outside of the
zone plate. Figure 3 setup, with an indirect scintillator-coupled detector (pco.4000
with 1 detector optics) 4 m downstream of the zone plate. The synchrotron images show higher resolution, revealing
subtle details in the efficiency maps and a signal-to-noise ratio
6.5 times higher than the X-ray tube images, but the important
information about the alignment given by the moire´ patterns is
clearly also obtained from the maps made with an X-ray tube
as the source. The efficiencies obtained for zone plates A, B and C at
8.4 keV were 5.6%, 3.0% and 5.3%, respectively. The large
differences between the zone plate efficiencies can be
explained by the moire´ patterns in the three cases, showing
that A is a double-sided zone plate with little misalignment, B
is a double-sided zone plate with good alignment but a scaling
difference between the zone plate on the front- and back-side,
and C is a double-sided zone plate with both a size difference
and an offset between its halves. The comparably high effi-
ciency of C can be explained by its total structure height being
close to ideal for the measured energy. Figure 3 g
Schematic of the counts recorded on the PCH as a function of zone plate
position along one of the scanning directions. Shaded regions in the
background illustrate how the zone plate (in red) diffracts the incoming
light into the distinct diffraction orders. The red dashed line indicates the
resulting regions with different count levels within and outside of the
zone plate. These zone plates, made on the same chip with the same
design parameters, showed vastly different alignment results. The only substantial difference between zone plates on the
same chip is height, since the slow HSQ spin-coating leads to
strong variations in the layer thickness over the membrane. research papers General fabrication trends were seen where zone plates
showing curved moire´ fringes like C or strong concentric
fringes like B had front-side zone plate heights of approxi-
mately 1.4 mm, whereas zone plates with a good alignment like
A had front-side heights of only 900 nm, all compared with
back-side heights of approximately 600 nm. This indicated a
structure–height-related alignment and scaling problem. In
the case of the scaling problem, the question arose whether
the front- or the back-side zone plates had a larger diameter
than their counterparts. 3. X-ray tube setup design The insets show a closer view of the region of interest for the filtering, where it is apparent that
the filter thicknesses have been matched so that the curves overlap for energies outside the L1,2
line. 585 J. Synchrotron Rad. (2020). 27, 583–589 research papers J. Synchrotron Rad. (2020). 27, 583–589 4. Results The
larger the difference in height between
the zone plates on the two sides of the
membrane, the stronger the effect. We
noted that the electron beam system
measured smaller distances between the
alignment markers on the back-side
compared with what was written, and
correspondingly rescaled the structure
on the front-side before writing it. Due
to the somewhat different measured
positions of the markers, offsets were
likewise introduced. In addition, since
the system uses three markers for the
alignment, it obtains one scaling factor
for each of the two directions spanning
the membrane plane, meaning that in
some cases even slightly elliptical zone
plates were patterned on the front-side. Possible
changes
to
the
alignment
ithm of the electron beam system are being investigated. e misalignments in double-sided structures were studied
er by means of zone plate tilting. Fig. 6(a) illustrates that,
mall offsets of the front-side zone plate by a distance loff
regard to the back-side zone plate, there is a tilting angle
which the centres of mass of the zones on the opposing
of the membrane are aligned again. Such an angle should
mize the efficiency, compensate for the misalignment and
ve the moire´ fringes in the corresponding direction. ugh simple geometrical considerations with the thickness
e silicon nitride membrane tmembr, the heights on the
height between
ciency maps of
back-side zone
side are varied
ried along the
are made. Figure 5 g
(a) Diffraction efficiency maps of the zone plates on chip 1 with a large difference in height between
the back-side zone plate ZP1 and the front-side zone plate ZP2. (b) Diffraction efficiency maps of
the zone plates on chip 2 with a small difference in height between the front- and back-side zone
plates. The relative sizes (diameters) of the zone plates on the back-side and front-side are varied
along the vertical axis in the grids and the diagonal offsets between them are varied along the
horizontal axis. The red dashed line indicates the direction along which the offsets are made. zone plate A1 has three, A2 has one and A3 has two but with a
shifted centre – one can conclude, by simple interpolation, that
a case between the latter two, with the back-side zone plate
being 0.2% larger in diameter than the front-side, would
compensate for the size difference between the zone plates. Fig. 4. Results 5(b) shows the efficiency maps of chip 2, the sample
with a small height difference between the front- and back-
side structures. The alignment is generally much better than
for chip 1 and there are no indications of scaling issues in row 2
where no intentional size differences have been made. In
column A, the moire´ fringes are purely concentric, indicating a
good alignment. Zone plates A1 and A3 are symmetric around
zone plate A2 in terms of the number of fringes, indicating
that A2 is the best case and showing that the optimal double-
sided zone plate for these structure heights is obtained when
the front- and back-side zone plates are fabricated to be the
same size. Figure 6
(a) Schematic of a front-side zone offset a distance loff with respect to the
corresponding back-side zone. Tilting angle will realign the centres of
mass of the two zones and should maximize the diffraction efficiency of
the total structure. (b) Zone plates with different degrees of misalign-
ment, chosen for the tilting measurements. The diagonal fringes on zone
plate F indicate a strong misalignment along both the x and the y
directions. We can conclude that it is more difficult to guarantee a good
alignment between the parts of a double-sided zone plate
when the structure heights on the front-side are much higher
than on the back-side. When such a case arises, one must find
ways to compensate for the offset issues appearing, which is
difficult since these typically vary for every zone plate. In
order to compensate for the scaling issues for a sample such as
chip 1 with an average front-side structure height of 1.2 mm
and a back-side structure height of 550 nm, the zone plates
on the back-side should be designed to be 0.2% larger in
diameter than the corresponding front-side zone plates. When
the structure heights on the back-side and front-side are more
similar, such as on chip 2, no compensation is needed. Figure 6
(a) Schematic of a front-side zone offset a distance loff with respect to the
corresponding back-side zone. Tilting angle will realign the centres of
mass of the two zones and should maximize the diffraction efficiency of
the total structure. (b) Zone plates with different degrees of misalign-
ment, chosen for the tilting measurements. 4. Results These and all of the
following diffraction efficiency maps presented in this paper
were made at the X-ray tube setup with a total acquisition
time of 700 s. The case with no intentional offset or size
difference, A2, shows the least fringes. The maps confirm the
expected trends; the number of fringes increases with the
offset, and their direction corresponds to the diagonal offset. By counting the number of dark moire´ fringes in column A – Figure 4
(a)–(c) Diffraction efficiency maps recorded with the X-ray tube setup
at an X-ray energy of 8.4 keV and an exposure time of 1400 s. (d)–(f)
Diffraction efficiency maps of the same three zone plates made at the
ANATOMIX beamline of Synchrotron SOLEIL at an X-ray energy of
10 keV with an exposure time of 2 s. The zeroth-order counts in the
centre of the maps have been subtracted. g
(a)–(c) Diffraction efficiency maps recorded with the X-ray tube setup
at an X-ray energy of 8.4 keV and an exposure time of 1400 s. (d)–(f)
Diffraction efficiency maps of the same three zone plates made at the
ANATOMIX beamline of Synchrotron SOLEIL at an X-ray energy of
10 keV with an exposure time of 2 s. The zeroth-order counts in the
centre of the maps have been subtracted. J. Synchrotron Rad. (2020). 27, 583–589 586
Yurgens et al. Improving misalignment in double-sided hard X-ray Fresnel zone plates research papers Figure 5
(a) Diffraction efficiency maps of the zone plates on chip 1 with a large difference in height between
the back-side zone plate ZP1 and the front-side zone plate ZP2. (b) Diffraction efficiency maps of
the zone plates on chip 2 with a small difference in height between the front- and back-side zone
plates. The relative sizes (diameters) of the zone plates on the back-side and front-side are varied
along the vertical axis in the grids and the diagonal offsets between them are varied along the
horizontal axis. The red dashed line indicates the direction along which the offsets are made. on the back-side structures before the
frontside
patterning,
the
elevated
temperatures in the process could lead
to a decrease in size which subsequently
affects the front-side alignment. The
larger the difference in height between
the zone plates on the two sides of the
membrane, the stronger the effect. J. Synchrotron Rad. (2020). 27, 583–589 4. Results We
noted that the electron beam system
measured smaller distances between the
alignment markers on the back-side
compared with what was written, and
correspondingly rescaled the structure
on the front-side before writing it. Due
to the somewhat different measured
positions of the markers, offsets were
likewise introduced. In addition, since
the system uses three markers for the
alignment, it obtains one scaling factor
for each of the two directions spanning
the membrane plane, meaning that in
some cases even slightly elliptical zone
plates were patterned on the front-side. Possible
changes
to
the
alignment
algorithm of the electron beam system are being investigated. The misalignments in double-sided structures were studied
further by means of zone plate tilting. Fig. 6(a) illustrates that,
for small offsets of the front-side zone plate by a distance loff
with regard to the back-side zone plate, there is a tilting angle
for which the centres of mass of the zones on the opposing
sides of the membrane are aligned again. Such an angle should
maximize the efficiency, compensate for the misalignment and
remove the moire´ fringes in the corresponding direction. Through simple geometrical considerations with the thickness
of the silicon nitride membrane tmembr, the heights on the
ence in height between
ion efficiency maps of
nt- and back-side zone
d front-side are varied
m are varied along the
offsets are made. on the back-side structures before the
frontside
patterning,
the
elevated
temperatures in the process could lead
to a decrease in size which subsequently
affects the front-side alignment. The
larger the difference in height between
the zone plates on the two sides of the
membrane, the stronger the effect. We
noted that the electron beam system
measured smaller distances between the
alignment markers on the back-side
compared with what was written, and
correspondingly rescaled the structure
on the front-side before writing it. Due
to the somewhat different measured
positions of the markers, offsets were
likewise introduced. In addition, since
the system uses three markers for the
alignment, it obtains one scaling factor
for each of the two directions spanning
the membrane plane, meaning that in
some cases even slightly elliptical zone
plates were patterned on the front-side. on the back-side structures before the
frontside
patterning,
the
elevated
temperatures in the process could lead
to a decrease in size which subsequently
affects the front-side alignment. Yurgens et al.
Improving misalignment in double-sided hard X-ray Fresnel zone plates
587 4. Results g
g
In order to determine the misalignment in the double-sided
zone plates along the x direction, they were rotated around the
y axis. The rotation angle around the x axis was kept at 0. The
angle range 3 to 3 was chosen according to predictions
made from the moire´ patterns in the diffraction efficiency
maps at zero rotation and known front- and back-side zone
plate heights. The resulting images and efficiencies are
presented in Fig. 7. As expected, all three zone plates show the
highest diffraction efficiency at the rotation angle with the
least and best centred moire´ fringes. This angle and the known
structure height yield an x-offset for zone plates D, E and F of
8 nm, 25 nm and 33 nm, respectively. Using the optimal angle
around y and rotating around x, the same procedure yielded a
y-offset of 17 nm, 17 nm and 66 nm for the three zone plates. The calculated offsets in x and y correspond well to the
diffraction efficiency maps taken at 0 tilt angle. Two full-
fringe periods over the aperture correspond to an offset of
100 nm, and in the case of zone plate F with a calculated
misalignment in x of 33 nm and in y of 66 nm, we see slightly
less than one period in x and more than one in y. The other
zone plates show fewer fringes and correspondingly less
misalignment. As a consequence of optimal tilting, the
diffraction efficiencies of the zone plates increase; the increase
in efficiency is small for zone plate D with the best alignment
(6.3% to 6.4%), but is more substantial for zone plates E and F In order to determine the misalignment in the double-sided
zone plates along the x direction, they were rotated around the
y axis. The rotation angle around the x axis was kept at 0. The
angle range 3 to 3 was chosen according to predictions
made from the moire´ patterns in the diffraction efficiency
maps at zero rotation and known front- and back-side zone
plate heights. The resulting images and efficiencies are
presented in Fig. 7. As expected, all three zone plates show the
highest diffraction efficiency at the rotation angle with the
least and best centred moire´ fringes. 588
Yurgens et al.
Improving misalignment in double-sided hard X-ray Fresnel zone plates 4. Results The diagonal fringes on zone
plate F indicate a strong misalignment along both the x and the y
directions. A possible origin of the scaling and alignment issues is the
shrinking of the HSQ after the electron beam exposure,
possibly induced by the Ir deposition. Since the Ir is deposited 587 J. Synchrotron Rad. (2020). 27, 583–589 research papers Figure 7
Diffraction efficiency maps of three different zone plates for different rotation angles around the y axis (top) and the corresponding diffraction
efficiencies (bottom). White dots mark the maps where the moire´ fringes in the x direction are minimized; the optimal angles correspond well with the
maxima of the approximate fits made in the efficiency curves. Figure 7
Diffraction efficiency maps of three different zone plates for different rotation angles around the y axis (top) and the corresponding diffraction
efficiencies (bottom). White dots mark the maps where the moire´ fringes in the x direction are minimized; the optimal angles correspond well with the
maxima of the approximate fits made in the efficiency curves. with larger misalignments (B: 5.7% to 6.4%; C: 4.5% to 5.9%). Consequently, a well aligned zone plate will suffer perfor-
mance loss when not carefully aligned perpendicular to the
optical axis. back-side and front-side hback and hfront, and the optimal tilting
angle , we can calculate the offset from loff = (hfront/2 + tmembr
+ hback/2)tan. Fig. 6(b) shows diffraction efficiency maps of
three zone plates D, E and F, on which these measurements
were performed. The structures were spin-coated at a speed of
2500 rpm on both the back-side and the front-side, giving
structure heights of 550 nm and 750 nm, respectively, and a
specific set of zone plates was chosen to represent different
degrees of misalignment. As a concluding measurement, a mesh-like scan was
performed on zone plate D, where the diffraction efficiency
was recorded for a range of tilting angles in x and y simulta-
neously. The result is presented in Fig. 8. There is a clear peak
in the two-dimensional plot, centred around (rot x, rot y) =
(1, 0.5 ), corresponding well to the optimal values found
in the previous measurements. This type of scan gives a more
exact result for the optimal tilting position of a zone plate but
is also more time-consuming. Funding information ANATOMIX is an Equipment of Excellence (EQUIPEX)
funded by the ‘Investments for the Future’ program of the
French National Research Agency (ANR), project ‘Nano-
imagesX’ (grant No. ANR-11-EQPX-0031). Another obvious advantage of zone plate tilting is that the
moire´ fringes are reduced; zone plates with visible fringes
produce overlapping twin images and are thus not usable for
imaging. However, we need to discuss how the tilting of a zone
plate affects its function as a diffractive lens in an imaging
application: a tilted zone plate will appear elliptical as seen
from the sample, giving a difference between the focal lengths
along the minor and the major axes of this ellipse and causing
astigmatism. This effect is negligible as long as the difference
in focal length is well within the depth of field (DOF), given by
DOF = 2(dr)2/ (Thomson et al., 2009). In the case of our
zone plate, the DOF is 1/1000 of the focal length, allowing for
a relative difference between the ellipse axes of 1/2000. This
limit is reached at a tilt angle of 1.8. While this value is large
enough to allow for unperturbed optical performance at the
optimum tilt angles displayed in Fig. 8, it should be pointed out
that zone plates with smaller dr or zone plates used at a lower
photon energy can have a substantially smaller DOF and
therefore only tolerate smaller tilt angles. 4. Results This angle and the known
structure height yield an x-offset for zone plates D, E and F of
8 nm, 25 nm and 33 nm, respectively. Using the optimal angle
around y and rotating around x, the same procedure yielded a
y-offset of 17 nm, 17 nm and 66 nm for the three zone plates. An advantage of the combination of tilting and efficiency
mapping is the fact that one can distinguish between issues in Figure 8
Zone plate diffraction efficiency as a function of tilting angle around
x and y. The calculated offsets in x and y correspond well to the
diffraction efficiency maps taken at 0 tilt angle. Two full-
fringe periods over the aperture correspond to an offset of
100 nm, and in the case of zone plate F with a calculated
misalignment in x of 33 nm and in y of 66 nm, we see slightly
less than one period in x and more than one in y. The other
zone plates show fewer fringes and correspondingly less
misalignment. As a consequence of optimal tilting, the
diffraction efficiencies of the zone plates increase; the increase
in efficiency is small for zone plate D with the best alignment
(6.3% to 6.4%), but is more substantial for zone plates E and F Figure 8
Zone plate diffraction efficiency as a function of tilting angle around
x and y. J. Synchrotron Rad. (2020). 27, 583–589 588 research papers helpful discussions and support regarding the electron beam
system. the fabrication and issues in the alignment. A dark region in a
diffraction efficiency map could indicate a fabrication problem
such as undeveloped or destroyed zones or zones with an
incorrect Ir duty cycle, but could also be a moire´ fringe. The
two cases will behave differently under tilting – the former will
stay even when rotating the zone plate, whereas the latter will
change just as described for the tilting tests. 5. Conclusions The X-ray tube-based setup provides a quantitative and
absolute measure of the efficiency of hard X-ray Fresnel zone
plates. The obtained diffraction efficiency maps, which are
fully comparable with maps measured at a hard X-ray
synchrotron beamline, present important information about
the spatial distribution of the efficiency and give crucial indi-
cations of misalignment, providing insight and continuous
feedback on the zone plate fabrication process. In this way, the
setup provides straightforward means of quality control and
study of Fresnel zone plates without relying on access to
synchrotron beamlines. Using the information obtained with
the setup and by tilting zone plates in two directions, a method
has been found to both measure and compensate for the
misalignments occurring in the fabrication of double-sided
line-doubled zone plates. Within limits, the performance of
zone plates initially unsuitable for imaging applications can be
recovered by using them at an optimal inclination. Mohacsi, I., Vartiainen, I., Guizar-Sicairos, M., Karvinen, P.,
Guzenko, V. A., Mu¨ller, E., Fa¨rm, E., Ritala, M., Kewish, C. M.,
Somogyi, A. & David, C. (2015). Opt. Express, 23, 776–786. Ramilli, M., Bergamaschi, A., Andrae, M., Bru¨ckner, M., Cartier, S.,
Dinapoli, R., Fro¨jdh, E., Greiffenberg, D., Hutwelker, T., Lopez-
Cuenca, C., Mezza, D., Mozzanica, A., Ruat, M., Redford, S.,
Schmitt, B., Shi, X., Tinti, G. & Zhang, J. (2017). J. Instrum. 12,
C01071. Scheel, M., Perrin, J., Koch, F., Yurgens, V., Le Roux, V., Giorgetta,
J.-L., Desjardins, K., Menneglier, C., Zhang, S., Engblom, C.,
Abiven, Y.-M., Cauchon, G., Bourgoin, C., Lestrade, A., Moreno,
T., Polack, F., David, C. & Weitkamp, T. (2018). Microsc. Microanal. 24(S2), 246–247. Snigirev, A. & Snigireva, I. (2008). C. R. Phys. 9, 507–516. S i i
I
S i i
A
K h
V
Y
ki
V
G i Snigireva, I., Snigirev, A., Kohn, V., Yunkin, V., Grigoriev, M.,
Kuznetsov, S., Vaughan, G. & Di Michiel, M. (2007). Phys. Status
Solidi A, 204, 2817–2823. Thomson, A., Atwood, D., Gullikson, E., Howells, M., Kim, K.-J.,
Kirz, J., Kortright, J., Lindau, I., Liu, Y., Pianetta, P., Robinson, A.,
Scofield, J., Underwood, J., Williams, G. & Winick, H. (2009). X-ray
Data Booklet. Lawrence Berkeley National Laboratory, University
of California, USA. References Bergamaschi, A., Andra¨, M., Barten, R., Borca, C., Bru¨ckner, M.,
Chiriotti, S., Dinapoli, R., Fro¨jdh, E., Greiffenberg, D., Huthwelker,
T., Kleibert, A., Langer, M., Lebugle, M., Lopez-Cuenca, C.,
Mezza, D., Mozzanica, D., Raabe, J., Redford, S., Ruder, C.,
Scagnoli, V., Schmitt, B., Shi, X., Staub, U., Thattil, D., Tinti, G., Vaz,
C. F., Vetter, S., Vila-Comamala, J. & Zhang, J. (2018). Synchrotron
Radiat. News 31, 11–15. Buralli, D. A. & Morris, G. M. (1992). Appl. Opt. 31, 4389–4396. Chen, S., Lyon, A., Kirz, J., Seshadri, S., Feng, Y., Feser, M., Sassolini,
S., Duewer, F., Zeng, X. & Huang, C. (2008). J. X-ray Sci. Technol. 16, 235–241. Chen, S., Lyon, A., Kirz, J., Seshadri, S., Feng, Y., Feser, M., Sassolini,
(
) S., Duewer, F., Zeng, X. & Huang, C. (2008). J. X-ray Sci. Technol. 16, 235–241. Gleber, S.-C., Wojcik, J., Liu, J., Roehrig, C., Cummings, M., Vila-
Comamala, J., Li, K., Lai, B., Shu, D. & Vogt, S. (2014). Opt. Express, 22, 28142. p
,
,
Jefimovs, K., Vila-Comamala, J., Pilvi, T., Raabe, J., Ritala, M. &
D
id C (2007) Ph
R
L
99 264801 Jefimovs, K., Vila-Comamala, J., Pilvi, T., Raabe, J., Ritala, M. &
David, C. (2007). Phys. Rev. Lett. 99, 264801. Jefimovs, K., Vila-Comamala, J., Pilvi, T., Raabe, J., Ritala, M. &
David, C. (2007). Phys. Rev. Lett. 99, 264801. Kirz, J. (1974). J. Opt. Soc. Am. 64, 301–309. M
h ll F Vil C
l
J G
k
V A & D
id C (2017) David, C. (2007). Phys. Rev. Lett. 99, 264801. Kirz, J. (1974). J. Opt. Soc. Am. 64, 301–309. Marschall, F., Vila-Comamala, J., Guzenko, V. A. & David, C. (2017). Microelectron. Eng. 177, 25–29. Maser, J., Lai, B., Yun, W., Shasti, S. D., Cai, Z., Rodrigues, W., Xua, S. & Trackhtenberg, E. (2002). Proc. SPIE, 4783, 74–81. Yurgens et al.
Improving misalignment in double-sided hard X-ray Fresnel zone plates
5 Acknowledgements Vila-Comamala, J., Gorelick, S., Fa¨rm, E., Kewish, C. M., Diaz, A.,
Barrett, R., Guzenko, V. A., Ritala, M. & David, C. (2011). Opt. Express, 19, 175–184. The authors are grateful to J. Vila-Comamala for providing the
spectrometer used for this work. They are also grateful to the
SLS Detectors Group of the Paul Scherrer Institute for
providing the MO¨ NCH03 detector, and to A. Bergamaschi for
the detector support. Special thanks go to V. A. Guzenko for p
Vladimirsky, Y. (1988). J. Vac. Sci. Technol. B, 6, 2142–2146. Weitkamp, T., Scheel, M., Giorgetta, J.-L., Joyet, V., Le Roux, V.,
Cauchon, G., Moreno, T., Polack, F., Thompson, A. & Samama, J.-P. (2017). J. Phys. Conf. Ser. 849, 012037. 589 J. Synchrotron Rad. (2020). 27, 583–589 Yurgens et al. Improving misalignment in double-sided hard X-ray Fresnel zone plates
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English
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TEMPORAL AND SPATIAL DIMENSIONS OF GROUP ENTREPRENEURSHIP: THE CASE OF A CRAFT FAIR AS A COMMUNITY OF PRACTICE
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Cadernos EBAPE.BR
| 2,021
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cc-by
| 12,885
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Resumo Este artigo propõe uma análise das dimensões temporais e espaciais da prática empreendedora em grupo e da sua aprendizagem, habilitação
e capacitação para construí-las na estrutura social em que tal prática se situa. Para tanto, examinamos, sob a perspectiva da teoria social
da aprendizagem, um empreendimento coletivo autogerido que precisa conquistar e construir seu lugar e momento com visibilidade, em
termos simbólicos, econômicos e materiais, e enfrentar as condições adversas da estrutura social e a concorrência. No caso, escolhemos
uma feira conduzida pelas próprias artesãs que oferece e vende os artesanatos delas ocupando espaço público e enfrentando a vizinhança
de shopping centers. Adotamos uma metodologia qualitativa para estudo em profundidade. Concluímos que a territorialização pode ser uma
atividade ou prática que define posicionamento e relações e, ao mesmo tempo que estabelece limites e fronteiras, cria conexões e novas
possibilidades. Esse tipo de participação promove a aprendizagem do grupo – ou da comunidade – que o habilita a construir o espaço social
e a estabelecer um lugar no contexto. Palavras-chave: Comunidade de prática. Territorialização. Aprendizagem. Feira de artesanato. Abstract This article proposes an analysis of the temporal and spatial dimensions of group entrepreneurship, covering aspects such as learning,
qualification, and training to build the social structure dimensions around entrepreneurial practices. The study adopts the social
learning theory to examine a self-managed collective enterprise working to gain space and momentum, expanding its visibility in symbolic,
economic, and material terms, while facing adverse conditions of social structure and competition. The study analyzes a craft fair the
artisans conduct themselves. The fair offers and sells handicrafts, occupying public space and facing the competition of shopping malls
established in the same region. We adopted a qualitative methodology for in-depth study. We conclude that territorialization can be an
activity or practice that defines positioning and relationships and, at the same time establishes limits and borders, creates connections
and new possibilities. This type of participation promotes group or community learning, enabling the construction of social space and
establishing a place for the fair in the context. Keywords: Community of practice. Territorialization. Learning. Craft fair. Temporal and spatial dimensions of group
entrepreneurship: the case of a craft fair as
a community of practice Ariane Latoski ¹
Eloy Eros da Silva Nogueira ¹ ¹ Universidade Positivo / Doctorate Program in Administration, Curitiba – PR, Brazil INTRODUCTION INTRODUCTION The notion of ‘community of practice’ has received increasing attention in studies on learning and organizational knowledge in
Brazil. These studies reflect the interest and efforts to establish a basic conceptual framework on this issue (Ferrarini, Camargo
& Bulgacov, 2014; Mendes & Urbina, 2015). ‘Community of practice’ is associated with the theory of situated learning, which
proposes that knowledge and learning are achieved through acting in a given material and social context (Brown & Duguid,
1991; Lave, 2011; Lave & Wenger, 1991; Wenger, 2011). This notion brings the perspective that learning takes place in the
context of our own experience of participation in the world, a phenomenon of our social nature. In this concept, participation
represents the relationships between the social structure and the situated condition of experience in the actions that produce
and reproduce such social structure (Giddens, 2003; Wenger, 2011). These relationships have continuities and discontinuities,
possibilities, improvisations, and interactions. Wenger (2011) seeks a more precise conceptualization of ‘community of
practice,’ identifying its borders and limits, what is internal and external, and its location and historical conditions. The author
considers that the practice creates not only limits but also constitutes a connection. Wenger’s (2011) geography of practice
suggests that the community is a portion of the social structure (Wenger, 2011) and that learning is an engine to develop
the practice due to its structuring character. However, as Lervik, Fahy and Eastertby-Smith (2010) and Fahy, Easterby-Smith
and Lervik (2014) pointed out, the temporal and spatial dimensions seem to have received less attention in organizational
studies, especially those dedicated to learning and organizational knowledge. These theories on practice describe the context
as the place in which the practice finds its essential elements, and as the social structure where the practice has its sense
and meaning and realizes the social world. Time and space are usually seen as elements from natural reality – part of the
world – and people can experience, but not create them. This article reflects on this issue from a different point of view. The assumption here is that we can investigate time and space as elements that constitute – and are constituted by – social
relations and practices. Previous reflections (Bachelard, 1978; Bourdieu, 2013; Certeau, 2014; Giddens, 2003; Harvey, 2017;
Lefebvre, 1974) suggest that the ability to influence or build spatial-temporal orders is a form of social power. INTRODUCTION The practice
and the community have limits and boundaries; their existence presupposes a defined space and time, in relationship with
other practices and communities. The territory emerges from the action on time and space (Harvey, 2017; Mendes & Cavedon,
2015) and brings its political, material, and symbolic dimensions to establish relations and positions with other entities of
the social structure or in the context. Territorialization, therefore, is part of the life of the community of practice and may have implications for situated learning,
given its structuring nature. This article proposes an initial analysis of the possibility that the practice of the community would need the dedication of
energy and action over space and time, in order to differ from the dominant social structure. The study also explores the
implications of this possibility for learning and community capacity building from the perspective of the social learning theory. The research is a case study of a craft fair. The fair is an activity of artisans that happen in a public place, and, therefore,
brings the dimension of learning about making crafts, together with the action of creating and conquering a place within the
collective social space. Resumen Este artículo propone un análisis de las dimensiones temporal y espacial de la práctica empresarial grupal y de su aprendizaje, calificación
y formación para construirlas en la estructura social en la que se ubica dicha práctica. Para ello, examinamos, desde la perspectiva de la
teoría del aprendizaje social, una empresa colectiva autogestionada que necesita conquistar y construir su lugar y momento con visibilidad,
en términos simbólicos, económicos y materiales, y enfrentar las condiciones adversas de la estructura social y de la competencia. En este
caso, optamos por una feria dirigida por las propias artesanas que ofrecen y venden sus artesanías, en un espacio público, en medio a los
centros comerciales. Adoptamos una metodología cualitativa para un estudio en profundidad. Concluimos que la territorialización puede ser
una actividad o práctica que define posicionamientos y relaciones y, al mismo tiempo que establece límites y fronteras, crea conexiones y
nuevas posibilidades. Este tipo de participación promueve el aprendizaje del grupo ‒o de la comunidad‒ que le permite construir un espacio
social y establecer un lugar en el contexto. Palabras clave: Comunidad de práctica. Territorialización. Aprendizaje. Feria artesanal. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021
ISSN 1679-3951
Article submitted on September 30, 2019 and accepted for publication on February 13, 2020. [Translated version] Note: All quotes in English translated by this article’s translator. DOI: http://dx.doi.org/10.1590/1679-395120190129x Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Situated learning in groups ad community of practice The concept of ‘community of practice’ has been used to understand the development of learning and as a tool to promote
knowledge transfer and sharing (Nicolini, Scarbrough & Gracheva, 2015). Wenger, Mcdermott and Snyder (2002) developed an argument that enables analyzing social learning in workgroups where
there are substantive changes, especially technological ones, and whose assessment applied to current times seems to provide
questions and contributions about collective entrepreneurial action and competence, in a social context under intense and
accelerated transition due to technology. Wenger et al. (2002) considered that cultivating communities of practice in strategic areas of a company is a way of systematically
managing knowledge, as the advance of science and technology creates a paradox: at the same time as the growing complexity Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice of knowledge requires greater specialization and collaboration, the half-life of knowledge makes it challenging to keep up
with the rapid pace of change. al. (2002) present three elements that provide a practical model to guide community development 1. Domain – community development relies on the task of negotiating a shared domain. A community must ask itself:
what are topics and issues that really matter? 2. Community – the community needs attention, organization, and education. What roles will pe 3. Practice – any community with continuous interactions among people will develop some kind o 3. Practice – any community with continuous interactions among people will develop some kind of practice over time. Wh t k
l d
ill b
h
d d
l
d d
t d? Wh t t
f l
i
ti iti
ill b
i
d? g
,
p
,
yp
gii
g
In addition, when seeking to describe the dynamics that support the existence of a community of practice, Wenger (1998)
proposed that ‘domain,’ ‘community,’ and ‘practice’ are present in three dimensions: 1. Shared repertoire; 2. Joint enterprise; 3. Mutual engagement. Figure 1 represents how the elements are intertwined. Figure 1 represents how the elements are intertwined. 1 represents how the elements are intertwined. Figure 1
The three dimensions of a community
Source: Gouvêa, Paranhos and Motta (2008, p. 5, our translation). Situated learning in groups ad community of practice Figure 1 Figure 1
The three dimensions of a community The three dimensions of a community Source: Gouvêa, Paranhos and Motta (2008, p. 5, our translation). In communities of practice, common knowledge, through mutual engagement, demonstrates the social and negotiated nature
character between the tacit and the explicit in people’s lives and the work environment. This feeling of identity and belonging
creates, in the informal structures of the organization (Gropp, 2007), an environment that facilitates organizational learning,
where knowledge and innovation occur. In communities of practice, common knowledge, through mutual engagement, demonstrates the social and negotiated nature
character between the tacit and the explicit in people’s lives and the work environment. This feeling of identity and belonging
creates, in the informal structures of the organization (Gropp, 2007), an environment that facilitates organizational learning,
where knowledge and innovation occur. For Lave and Wenger (1991), the participation in the practices of a community can be described based on a peripheral and
legitimated initial position from which the inclusion starts. It is an inclusion associated with the degree of knowledge acquired
by the practice in a movement toward completeness, going through different stages of group belonging (Gropp, 2005). Note that these theories focus on a practice that occurs in an organizational environment or working conditions. The elements
that constitute the learning process and the community of practice are in line with these environments and conditions. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 3-17 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice
Ar
Eloy Eros da Sil Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice However, this research focuses on a collective enterprise in which a craft fair that happens in a public place is its most
visible face. Craftwork does not exhaust the field of knowledge that the artisans must master. Situated learning in groups ad community of practice As a group, their actions must
systematically (and not accidentally or occasionally) address those who are not part of their primary field of knowledge –
craftwork –, at a time and place that the group must build and define, considering the context. However, this research focuses on a collective enterprise in which a craft fair that happens in a public place is its most
visible face. Craftwork does not exhaust the field of knowledge that the artisans must master. As a group, their actions must
systematically (and not accidentally or occasionally) address those who are not part of their primary field of knowledge –
craftwork –, at a time and place that the group must build and define, considering the context. Space and time in social practices Spaces (and their times) are complex social constructions, dialectically based on socially produced values and meanings
encompassing three aspects: a) perceptions and daily practices; b) representations and theorizations; and c) the spatial
imaginary of the time lived. The collective social space is related to spatial practice (Giddens, 1985, 2003; Hagerstrand, 1975;
Lefebvre, 1974). Bourdieu (1997, 2013) states that social space is inscribed in the objectivity of spatial structures and simultaneously in
subjective structures (schemes of action, thought, and perception). The distribution of goods, relationships, and positions
combine these structures, their meanings, and values, in competing, overlapping, or contained fields. The physical space has
inscribed the hierarchies defined by the social spaces. This is the symbolic reality, revealed in the territories and perpetuated
by social practices. Occupying a physical space does not mean enjoying the social space or appropriating it effectively. The
neo-occupant may lack the tacit or the corresponding habit; however, this may be acquired over time. For Bachelard (1978), space and time are two sides of historical becoming and social reproduction schemes: materiality
crystallizes the meanings that are attributed to time. Harvey (2017), in turn, proposes that the processes of reproduction and transformation of society are related to the
conceptions of space and time. These conceptions are the basis for maintaining power through these social processes. The author’s analytical model incorporates three dialectically interrelated spheres in which spatial practice takes place:
a) effective flows and interactions; b) representations in the concepts, offering intelligibility (to spatiality and temporality);
and c) negotiations and reinterpretations of new meanings and representations for spatial practices. These spheres potentially combine a) the modes of signification and reproduction, b) modes of appropriation and use of
spaces, and c) the ways of dominating the possibilities of change in the production of spaces. The work by Lefebvre (1974) inspired Lervik et al.(2010) and Fahy et al. (2014) to develop an analytical framework that takes
advantage of the triadic conception of space (conceived, perceived, and lived) to study the socially constructed space. They
transpose this dialectical triadic vision to study time (conceived temporal structures, established temporal practices, and lived
experience of these structures and practices in specific contexts and situations). The authors verify how temporal structures
influence and may synchronize organizational actions and interactions among its members and with others, and how actors
can appropriate them to gain power. Social learning, territorialization, practice, and culture The authors demonstrated the importance of mutual monitoring among
the vendors themselves, in order to occupy and use the public space, contrasting the commercialization and the determination
of places and borders, in addition to the search for power and positions, either through representativeness and associations
or through negotiations with third parties (particularly public authorities). Zioli, Rodrigues, Gaffuri and Ichikawa (2018) observe that daily practices not only compete to reproduce the social space, its
places, and positions but create ruptures and allow divergent territorialization. In the case presented here, the daily practices
are a strategic procedure of the social movement that intends, step by step, to achieve a place and a position – albeit uncertain –
in the face of the reactions of the status quo. It is about resilience and resistance, combined with change and no-change. Resistance is a practice that occurs in everyday life, in the very modes of existence in the common social space, and in the
ways of making use of such space (Vasconcelos & Domingues, 2018). For Haesbaert (2015), territorialization is the appropriation of space in which three dimensions stand out, not necessarily
with equal importance: a) political; b) symbolic; and c) economic. It has a relational and temporal nature as it results from
social processes in material space. Saquet (2015) understands territorialization as space and time in movement: social relations produce territory in temporalities. Different sets of social relations and temporalities converge, overlap, and compete for space, characterizing multiple aspects
of the dynamics of territorialization. Mendes and Cavedon (2013, 2014, 2015) and Mendes (2011) stress the cultural and economic dimensions of the general and
informal commerce, whose temporality and territorialization provide survival and social integration to intermediaries
and street vendors, and slowly, through successive installations over the months, a place (physical, economic, and symbolic)
in the local social space. Territorialization is the action over time and space; it is a social construction, with symbolic and
political dimensions, in multiple itineraries, encounters and disagreements, experiences. In a report on movements of territorialization and deterritorialization, Pereira and Carrieri (2005) concluded that the symbolic
space, territoriality, and deterritorialization are close to the concepts of organizations, practices, identity, cultural meanings,
and power relations. In symbolic spaces such as the territory, there are ambiguity and relational aspects that allow us to
enter the cultural traits. Social learning, territorialization, practice, and culture The central question is not limited to learning a particular craft, to become a reproducer of practice, but involves how the
learner can become a practitioner, develop an identity in this universe of spatially and temporally determined activities
(Brown & Duguid, 1991). Social learning, territorialization, practice, and culture Producing craftwork is a non-industrial activity in a non-scale economy. The artisan dominates the technology or technique,
and the process of imprinting a personal and direct identity on the product, even when it comes to crafts made in groups or
collectively. As highlighted by Davel, Cavedon and Fischer (2012), the artisan incorporates aesthetics, physical dexterity, mastery of
technique, and planning and operation skills in their work. The visibility and invisibility of the artist and artisan and their art are related to the dimension of the work associated with the
social time-space where it is developed (Chiesa, Gois, De Luca & Cavedon, 2015) and, thus, can be appreciated or criticized. The visibility and invisibility of the artist and artisan and their art are related to the dimension of the work associated with the
social time-space where it is developed (Chiesa, Gois, De Luca & Cavedon, 2015) and, thus, can be appreciated or criticized. When studying the case of lacemakers in the municipality of Alcaçuz, in the Northeast of Brazil, from the perspective of social
learning theory, Ferreira, Helal and Paiva (2016) demonstrated how the artisans acquired their skills and tacit knowledge
within the community (in that case, their families), daily life, and practice. Moreover, the ability to make craftwork was not
restricted to mastering the technique, but depended mainly on social meanings shared and associated with their identity and
the construction of their place in the social space. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Carrieri, Pereira and Correia (2018) and Alves, Farias and Pereira (2018) analyzed popcorn street vendors also in the municipality
of Alcaçuz, focusing on their activities in the territory. The authors demonstrated the importance of mutual monitoring among
the vendors themselves, in order to occupy and use the public space, contrasting the commercialization and the determination
of places and borders, in addition to the search for power and positions, either through representativeness and associations
or through negotiations with third parties (particularly public authorities). Carrieri, Pereira and Correia (2018) and Alves, Farias and Pereira (2018) analyzed popcorn street vendors also in the municipality
of Alcaçuz, focusing on their activities in the territory. METHODOLOGY The research used interviews, dialogue, and observation of ways of doing, documents, and artifacts. The study focused on
the experience of a group of female artisans, describing and following their activities and practices. Also, the work seeks
to identify the group’s activities and practices temporally and spatially, the conditions of its existence, and discovering the
meanings and relationships around the practices. The researchers visited the craft fair to observe, describe, and map the
geography of the urban space and the immediate neighborhood. Other places and times of the artisans’ activities were also
visited (Gherardi, 2012; Nicolini, 2013; Stoddard, 2010; Van-Maanen, 2009; Van-Maanen & Barley, 1982; Van-Maanen & Kolb,
1982; Van-Manen, 2007). The interviews allowed to approach, map, and understand the respondents’ lives, through their respective narratives, which
brings beliefs, values, attitudes, and motivations in a specific context (Bauer & Gaskell, 2002). The life story technique was adopted for the narrative interviews, with words and meanings specific to the artisans’ experience
and way of life. According to this technique, the interviewee can tell their story in a particular place and time, and the personal
experiences shared to form a plot (Bauer & Gaskell, 2002; Josselson, 2011; Webster & Mertova, 2007). Box 1 illustrates the procedure adopted in the narrative interview used in this study. Box 1 illustrates the procedure adopted in the narrative interview used in this study. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 5-17 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira Box 1
Basic phases of the narrative interview
Phases
Rules
1. Preparation
Exploring the field
Formulating exmanent questions
2. Initiation
Formulating initial topic for narration Emprego de Using visual aids
3. Main narration
No interruptions
Only non-verbal encouragement to continue story-telling
Wait for the coda
4. Questioning phase
Only ‘What happened then?’
No opinion and attitude questions
No arguing on contradictions
No why-questions
Exmanent into immanent questions
5. Concluding talk
Stop recording
Why-questions allowed
Memory protocol immediately after the interview
Source: Jovchelovitch and Bauer (2002). Box 1
Basic phases of the narrative interview Box 1 Basic phases of the narrative interview Source: Jovchelovitch and Bauer (2002). METHODOLOGY There are three procedures for analyzing the trajectories collected during the narrative interview: a) thematic analysis
(conversion of data through the transcription of recorded interviews); b) Schultze’s (2010) six-step proposal (first, the detailed
transcription of verbal material; second, the differentiation between indexical and non-indexical material; third, the use of
indexical material to order events; fourth, the non-indexical dimensions of the text are investigated as knowledge analysis –
opinions and reflections; fifth, the grouping and comparison of individual trajectories; and sixth, the identification of collective
trajectories); and c) structuralist analysis (formal elements of the narrative) (Jovchelovitch & Bauer, 2002). Other instruments were also used in the field research, such as participant observation and document analysis. ents were also used in the field research, such as participant observation and document analysis. Box 2
Description of research procedures
Number of hours
(Event, observation in the field,
participation in meetings)
70 hours
Number of interviews
15
Analyzed Documents
Municipal Law 14,786, February 23, 2016, Curitiba
(state of Paraná – PR, Brazil)
Regimento da Feira Economia Solidária do Portão
(Regiment of the Solidarity Economy Fair of Portão)
Observation and participation
Fair meeting at Tecsol – Solidarity Economy Incubator
of the Federal Technological University of Paraná
(UTFPR), Curitiba, PR
Assembly and disassembly of the craft fair
Solidarity Economy Exhibition at UTFPR
Collected Material
Photos
Folders
Source: Elaborated by the authors. Box 2
Description of research procedures Description of research procedures Source: Elaborated by the authors. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice The artisans were identified by the initial letters of their names: A.M., E.D.1; E.D. 2; M.A. 1; M.A. 2; AT.; PAN.; S.I. (see Box 3 below). The artisans were identified by the initial letters of their names: A.M., E.D.1; E.D. 2; M.A. 1; M.A. 2; AT.; PAN.; S.I. (see Box 3 below). Each interview was transcribed and allocated a number in the data set sequence. The excerpts of the interviews presented
in this article contain the number that identifies them with the lines of the transcribed text. For example, I1, 2-3 – interview
number 1, lines 2 and 3; I10, 12-14 – interview number 10, lines 12 to 14. General description of activities: location, positioning, and territorialization General description of activities: location, positioning, and territorialization The women arrive early to set up the stalls. As they arrive, they concentrate on the space for assembling the stalls and wait
for the parking lot to open to pick up the structures to set up the stalls, chairs, tables, plastic tarpaulins, stall protection, and
portable stalls. This activity is divided into tasks, according to the physical and health possibilities of the artisans. Some are
unable to carry weight, so they prepare and pack the goods, which will be exhibited at the fair. Everyone assembles the stall structures. Only after the structures are ready, the artisans start to organize each stall – at least
three artisans per stall. At that moment, each artisan arranges their own space, checking the layout of products, the visibility
of prices, the display of new products, the production of posters. Each vendor organizes their space in their way. [...] Everyone assembles and dismantles the stalls together (I2, 2-3). The artisans still do not have all legal documentation to operate, which is a challenge for them. They are aware of the situation
and work together to overcome the problem. Every day at the fair, the artisans cannot avoid the fact that they have to struggle
with the difference marked by the conception of the solidarity economy in comparison to the massive commercial activity of
the neighboring shopping malls, in addition to dealing with passersby’s ignorance regarding the popular economy. […] A client comes and asks for a soda, then we have to explain that this is a solidarity economy craft
fair, we don’t work with brands, we produce everything ourselves (I3, 5-6). […] A client comes and asks for a soda, then we have to explain that this is a solidarity economy craft
fair, we don’t work with brands, we produce everything ourselves (I3, 5-6). [...] We are winners, almost two years ago, we are the leading actors in our own space (I7, 3-4). [...] We are winners, almost two years ago, we are the leading actors in our own space (I7, 3-4). [...] We have grown, we got an accountant, information, papers, and [we are] almost finalizing the
legalization of our fair (I5, 10-11; I9, 7-9). [...] We have grown, we got an accountant, information, papers, and [we are] almost finalizing the
legalization of our fair (I5, 10-11; I9, 7-9). METHODOLOGY The researchers worked in immersion for approximately six months (July to December). Observation and participation took
place during the artisans’ work meetings, accompanying them in their commute, their research and production projects,
and whole days at the craft fair (from before the assembly of the infrastructure until the end of the day, the disassembly and
storage of equipment and products). The field notes were kept in a diary, used as a source to describe the elements of the
case. The dialogues and interviews were transcribed and qualitatively analyzed through content analysis possible. This analysis
supported the identification of themes and contents of the group’s and the enterprise’s experiences. [...] I tell the story of my own product, seek innovation, and ask friends who travel to bring me different
seeds [raw material] for my craftwork (I3, 13-14). The craft fair as an element of ‘organizing,’ a complex set of coordinated activities As a practice, the craft fair is not limited to the moment when it is set up in the public space, with the stalls and the exhibition
and marketing activities. The fair demands a series of other precedent and following activities, all necessary and contributing
to the success and quality of the event. [...] Everyone at the fair has to make their products. This is the rule of the solidarity economy. If I don’t
have products, my group will help me so I can work. Each artisan represents an enterprise of at least
three people (I13, 3-5). The fair’s work extends to different times and places, in addition to requiring huge dedication from the artisans. This concerns
purchases of raw materials, preparation and processing of products, research, and study of materials and techniques. This research identified and mapped the extent of these activities and the conditions of the artisans to manage them. They
coordinate and lead the processes as an action group, with purpose and dynamic capabilities. In this regard, according to
Gropp and Tavares (2007), the following aspects stand out: The fair’s work extends to different times and places, in addition to requiring huge dedication from the artisans. This concerns
purchases of raw materials, preparation and processing of products, research, and study of materials and techniques. This research identified and mapped the extent of these activities and the conditions of the artisans to manage them. They
coordinate and lead the processes as an action group, with purpose and dynamic capabilities. General description of activities: location, positioning, and territorialization The daily observations of the event and the interviewees’ testimonies converge to demonstrate that, for the artisans, the
enterprise is a mission and a way to position themselves in society proactively. These are descriptive elements of their sense
of existence, which they recognize has been built, understood, and made real in their lives in the day-to-day clashes, to
guarantee their survival, among themselves and with passersby, in order to overcome indifference. [...] I tell the story of my own product, seek innovation, and ask friends who travel to bring me different
seeds [raw material] for my craftwork (I3, 13-14). 7-17 Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice The artisans are determined to set up the craft fair twice a week continuously, and for the entire day, come rain or shine. They
are always attentive to the situation of their peers and ready to assist when necessary. They also show a kind and welcoming
attitude toward visitors, who are not seen as potential buyers, but as their “students” or “children,” with whom they share
what they consider to be their most precious gift. [...] A 9-year-old girl came and said she had a school project to complete, so I told her the story behind
the wall hangings I produce. She got the highest grade (I3, 16-17). Most artisans are between 55 and 60 years old, with an average age of 53. Only 30% are newcomers. Most have been at
the craft fair for over two years. In other words, they are mature women who undertake solidarity enterprise and exchange
experiences with the younger ones, who gather and mobilize the crat fair participants for meetings, sharing experiences of
life and solidarity economy. [...] We have a regiment with the principle of solidarity economy and the craft fair (I5, 6-7). [...] We have a regiment with the principle of solidarity economy and the craft fair (I5, 6-7). [...] I help in the administration; I do the cash-book. To raise funds, we hold bazaars and exchange clubs
(I1, 9-10). [...] Every Wednesday, before the fair opens to the public, we have coffee and say a prayer, to start our
day well (I1, 4-5). The craft fair as an element of ‘organizing,’ a complex set of coordinated activities In this regard, according to
Gropp and Tavares (2007), the following aspects stand out: •
The division of time and temporalities occurs in two ways: direct – in the moments they are together – and indirect –
concerning the projects and activities carried out in moments and places other than the fair; •
The division of time and temporalities occurs in two ways: direct – in the moments they are together – and indirect –
concerning the projects and activities carried out in moments and places other than the fair; •
There are different specialized knowledge to help the enterprises to thrive and to carry out the activities of selling,
setting up the stalls, managing the fair as an event, and planning the collective activities; •
In addition to their sense of existence, the social situation and identity found in associative self-management
are the elements that distinguish them from others. Through this associative dynamic, the artisans work
together to set up the craft fair, contribute to a collective fund when there is commercialization. The dynamic
is present in the way of conducting the meetings, setting the agenda, open spaces for opinions, and vote in
decision-making processes. It is also noteworthy that there are competing temporalities related to various activities, such as those of research, design,
preparation of production conditions, and production itself. These times depend on the craft technique’s characteristics, the
product, and the artisans’ profile and working conditions. In addition, there is time for personal preparation of the craft fair
participant, their displacement, organizing the stall, and the permanence in the public space. Box 3 correlates the activities that involve the practice with the places (spaces) and times available f he activities that involve the practice with the places (spaces) and times available for that purpose. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 8-17 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira Box 3
Fairs and activities
Fair
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
Artisan
N. A. R. F. ECOSOL -
4 hours
R. F. - 4 hours
P - 7 hours
F - 9 hours
P - 5 hours
P - 7 hours
P. I - 2 hours
T. E. A. P - 2 hours
P - 5 hours
C. M. The craft fair as an element of ‘organizing,’ a complex set of coordinated activities - 3 hours
F - 9 hours
P - 5 hours
P - 7 hours
Artisan
P. A. R. F. ECOSOL -
4 hours
R. F. - 4 hours;
C. M. - 2 hours
P. I - 2 hours
P - 6 hours
F - 9 hours
P - 6 hours
P - 6 hours
P - 6 hours
P - 6 hours
Artisan
M. A. 1
R. F. ECOSOL -
4 hours
R. F. - 4 hours
C. M. - 2 hours
P - 5 hours
C. M. - 2
hours
F - 9 hours
P - 5 hours
P. I - 3 hours
P - 5 hours
P - 5 hours
P - 5 hours
Artisan
M. A. 2
R. F. ECOSOL -
4 hours
R. F. - 4 hours
C. M. - 2 hours
P - 5 hours
F - 9 hours
P - 5 hours
R. G. P. - 3 hours
P - 5 hours
F - 9 hours
P. M. P. - 4 hours
[G. P. C. - 4 hours,
once a month]
Artisan
S. I
R. F. ECOSOL -
4 hours
R. F. - 4 hours;
C. M. - 3 hours
P - 4 hours
F - 9 hours
C. M. - 3 hours
P - 4 hours
F - 9 hours
C. F. F. - 2 hours
C. F. Fs. - 1 hour
Artisan
E. D. 2
R. F. ECOSOL -
4 hours
R. F. - 4 hours;
C. M. - 2 hours
P. M. P. -
4 hours
P - 6 hours
P. I - 1 hour
P. M. P. -
4 hours
P - 6 hours
P. I - 1 hour
P - 10 hours
P - 10 hours
F - 9 hours
P - 5 hours
Artisan
A. M. R. F. ECOSOL -
4 hours
R. F. - 4 hours
P - 5 hours
P - 5 hours
R. G. P. -
3 hours
P - 5 hours
C. M. - 3 hours
F - 9 hours
P. I. R. - 1 hour
P. I - 1 hour
Artisan
E. D. 1
R. F. ECOSOL -
4 hours
R. F. - 4 hours
P - 3 hours
C. M. The craft fair as an element of ‘organizing,’ a complex set of coordinated activities -
3 hours
P - 5 hours
F - 8 hours
P - 5 hours
P - 5 hours
F - 9 hours
Key: Box 3
Fairs and activities Box 3
Fairs and activities
Fair
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
Artisan
N. A. R. F. ECOSOL -
4 hours
R. F. - 4 hours
P - 7 hours
F - 9 hours
P - 5 hours
P - 7 hours
P. I - 2 hours
T. E. A. P - 2 hours
P - 5 hours
C. M. - 3 hours
F - 9 hours
P - 5 hours
P - 7 hours
Artisan
P. A. R. F. ECOSOL -
4 hours
R. F. - 4 hours;
C. M. - 2 hours
P. I - 2 hours
P - 6 hours
F - 9 hours
P - 6 hours
P - 6 hours
P - 6 hours
P - 6 hours
Artisan
M. A. 1
R. F. ECOSOL -
4 hours
R. F. - 4 hours
C. M. - 2 hours
P - 5 hours
C. M. - 2
hours
F - 9 hours
P - 5 hours
P. I - 3 hours
P - 5 hours
P - 5 hours
P - 5 hours
Artisan
M. A. 2
R. F. ECOSOL -
4 hours
R. F. - 4 hours
C. M. - 2 hours
P - 5 hours
F - 9 hours
P - 5 hours
R. G. P. - 3 hours
P - 5 hours
F - 9 hours
P. M. P. - 4 hours
[G. P. C. - 4 hours,
once a month]
Artisan
S. I
R. F. ECOSOL -
4 hours
R. F. - 4 hours;
C. M. - 3 hours
P - 4 hours
F - 9 hours
C. M. - 3 hours
P - 4 hours
F - 9 hours
C. F. F. - 2 hours
C. F. Fs. - 1 hour
Artisan
E. D. 2
R. F. ECOSOL -
4 hours
R. F. - 4 hours;
C. M. - 2 hours
P. M. P. -
4 hours
P - 6 hours
P. I - 1 hour
P. M. P. -
4 hours
P - 6 hours
P. I - 1 hour
P - 10 hours
P - 10 hours
F - 9 hours
P - 5 hours
Artisan
A. M. R. F. ECOSOL -
4 hours
R. F. The craft fair as an element of ‘organizing,’ a complex set of coordinated activities The artisans produce daily to have a variety of products and increase sales since the fair is not attractive to customers if there
are only a few products. Customers always seek a variety of options that include colors, models, sizes, and formats. [...] I launched a baby changing bag with a mat, baby wipes, and cream. I’m starting a line of footb
and gym bags (I4, 6-7). [...] I launched a baby changing bag with a mat, baby wipes, and cream. I’m starting a line of football
and gym bags (I4, 6-7). [...] A client arrives and asks for a specific design, then they send the design via WhatsApp, and I
embroider the design in the product. I have a new towel embroidered for ‘Festa Junina’ [traditional
Brazilian party that happens in June] (I8, 12-13). [...] A client arrives and asks for a specific design, then they send the design via WhatsApp, and I
embroider the design in the product. I have a new towel embroidered for ‘Festa Junina’ [traditional
Brazilian party that happens in June] (I8, 12-13). [...] Sometimes, there is a lack of money to buy material. Then we have to find substitute material, we
discuss and research (I5, 9-10). [...] Sometimes, there is a lack of money to buy material. Then we have to find substitute material, we
discuss and research (I5, 9-10). The period of resting also involves activities related to the fair, either researching materials or techniques on the internet, or
traveling and working while on the way, and when they are on the beach, they also produce (a moment the artisans consider
therapeutic). There is no set calendar for the production of festivities; each stall and its group decided what they will produce, but that
does not stop them from observing the commercial calendar. The craft fair as an element of ‘organizing,’ a complex set of coordinated activities - 4 hours
P - 5 hours
P - 5 hours
R. G. P. -
3 hours
P - 5 hours
C. M. - 3 hours
F - 9 hours
P. I. R. - 1 hour
P. I - 1 hour
Artisan
E. D. 1
R. F. ECOSOL -
4 hours
R. F. - 4 hours
P - 3 hours
C. M. -
3 hours
P - 5 hours
F - 8 hours
P - 5 hours
P - 5 hours
F - 9 hours
Key:
C. F. F. – Financial control of the fair
C. F. Fs. – Control of artisans’ frequency
C. M. – Purchase of merchandise, prime-material
F – Fair
G. P. C. – Group produce collectively
P – Production
P. I. – Research to innovate the products on the internet
P. I. R. – Research of innovation in journals/magazines
P. M. P. – Prepare material to produce
R. F. ECOSOL – Meeting of the Forum of Solidarity Economy
R. F. – Fair meeting
R. G. P. – Meeting of the production team
T. E. – Exchange of craft and product experiences
Source: Elaborated by the authors. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira It is demonstrated that the majority of artisans worked daily with activities linked to the fair, whether through production,
participation in meetings, researching product innovations, purchasing materials, training, and events in universities,
as required. On average, they dedicate 36 hours/week to the fair. Given the above, it appears that there is not only the time
for the fair itself but a conjunction of correlated activities, which extend to other environments, with several hours not related
to the activity during the sales at the craft fair. It is demonstrated that the majority of artisans worked daily with activities linked to the fair, whether through production,
participation in meetings, researching product innovations, purchasing materials, training, and events in universities,
as required. On average, they dedicate 36 hours/week to the fair. Given the above, it appears that there is not only the time
for the fair itself but a conjunction of correlated activities, which extend to other environments, with several hours not related
to the activity during the sales at the craft fair. RESULTS AND ANALYSIS 2021 Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice The artisans have a unique way of selling their products, based on their historical and cultural context. This element is another
that differentiates the craft fair from other businesses. The artisans have a unique way of selling their products, based on their historical and cultural context. This element is another
that differentiates the craft fair from other businesses. They self-identify as practitioners of the solidarity economy. When transposing the craft fair to the symbolic space, it appears to encompass other concepts, such as a) the activities
carried out to constitute the practice; b) the identity the artisans adopt when saying “we are a fair of solidarity economy;”
c) the relational aspects they develop with those who are directly and indirectly connected with the fair; and d) the power
relationships that they must put into practice when in contact with the public, from the legal aspects to market systems,
in addition to the artisan’s interaction with each other through the established rules. The concept of the territory allows understanding the history of the social actors as part of an organization. As the craft fair is
considered as something so precious, it somehow contributes to the artisans’ mental and physical health. This aspect shows
the identification processes and the registration of the person’s history within the organization. Territorialization is part of the community and the learning process. The relationship the artisans develop with third parties,
such as police officers, students, passersby, and homeless people, extends and involves the other characters in the craft
fair’s territorialization. Some of the artisans say that customers visiting the fair discuss fashion trends, suggest products, and
exchange experiences. However, the observations and content of the artisans’ reports confirm and recognize the power and influence of being a
neighbor of shopping malls. These elements define a specific spatial and social organization that creates a reality and imposes
a socialization process for its users, as suggested by Lengler and Cavedon (2018). Despite being private spaces created for the
community, two malls close to the craft fair have reconfigured the public space and the neighborhood in symbolic, economic,
and political terms. In addition, these shopping malls changed the very behavior of those who transit or live in the region. RESULTS AND ANALYSIS For example, the fact that they are immense buildings required small businesses to be more distant from the malls in order
to gain more visibility (a measure that was not considered necessary in the case of nearby commercial galleries). However, the presence of these massive players did not intimidate the artisans, who had to recognize them and develop skills to
establish conviviality with the neighbors. The occupation of space is not only material, but also symbolic, and phenomenological. Territorialization occurs in the form of occupation and disposition of the fair (its positioning in the public social space). The
economic, political, cultural, and symbolic dimensions are intertwined. The fair does not violate the order defined in that
place but creates an enclave, and it is inserted in the social space. Each day of the fair, artisans need to physically reconstruct
the symbolic space, starting to exist in that place and assuming a position in front of others, especially their neighbors. This reality differs from the traditional view of ‘community of practice,’ located in a pre-existing space, or situated in a context
and social structure from which derives its matrix or foundation. In the case studied, it is possible to observe the opposite. This community must have, among the activities of its practice, those dedicated to bringing its locus, its space, its territory
into existence, competing, or facing the dominant conditions in the social space. Here, the concepts of territory – planned,
negotiated, lived – may be differentiated. RESULTS AND ANALYSIS These artisans work individually and collectively in this craft fair. They are, at the same time, ‘employers’ and ‘employees,’
conducting the activities in the process of self-management, and showing solidarity with each other and attention to their
customers. The research revealed the artisans’ weekly challenge of having to work for five days in order to carry out two full
days of craft fair (Wednesday and Saturday) and, simultaneously, having to take care of their families. The craft fair does not happen automatically, nor is it facilitated based on the repetition of the same procedures. The existence
of such endeavor flows dynamically, because, in addition to cultivating the attitude of seeking innovation, the artisans have
to deal with unforeseen situations and the competition (from other products, ideas, and communication strategies that
attract the consumers’ attention). Therefore, there are internal and external elements leading to the group’s learning. It is
worth mentioning that the group is stable, and new members enter only after a careful admission process conducted by the
artisans. Different forms of participation – in planning, producing, or commercialization, for instance – may describe
the learning process, which is marked by the mutuality observed in the flow of the parallel and joint activities. The artisans
form a community of practice, as they are engaged, develop, and maintain an enterprise daily, which reconstructs a shared
repertoire (constituted from a group experience, but inspired by the popular economy). They delineate the rules that guide
the enterprise’s operation and the decision-making process, and the production occurs collectively according to each of the
artisans’ initiative. In this sense, ‘belonging’ and ‘differentiation’ are important elements. There is something that happens when they are
together, in terms of learning, knowledge, and structuring of actions. There is companionship among them, translated into
gestures, attitudes, and actions such as taking care of each other’s stall, recommending a peer to a customer looking for
a specific product, or even talking to a colleague that seems very quiet. All of these gestures denote ties that strengthen
affective relationships and friendship. However, there are rules of coexistence and a strong feeling of a collective commitment. Even though each artisan and
each stall represent a small enterprise, the craft fair as a whole constitutes a more significant endeavor engaging
and uniting the group. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. MAIN FINDINGS The craft fair is a collective enterprise, and its core activity is the event that represents a place for a location where the artisans
exhibit and commercialize their products. The craft fair is a collective enterprise, and its core activity is the event that represents a place for a location where the artisans
exhibit and commercialize their products. The fair represents space and time of joint knowledge, a community context, and an environment of identity – the solidarity
economy system – for those who form the event. There are elements to analyze the group of artisans as a community of practice, and their collective entrepreneurial action
as a practice from the perspective of social learning theory. There are elements to analyze the group of artisans as a community of practice, and their collective entrepreneurial action
as a practice from the perspective of social learning theory. These artisans are a community of practice since they share a set of problems and interact with each other on an ongoing
basis, creating products, and developing a tacit understanding. Such a community is not restricted to the moment and space
of the event ‘craft fair.’ The enterprise is embodied in the collection of activities happening in several times and places. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice It represents the collective construction of these women. Their coexistence and experience are elements that host and nurture
a culture not restricted to the fair, reaching their families and homes. It represents the collective construction of these women. Their coexistence and experience are elements that host and nurture
a culture not restricted to the fair, reaching their families and homes. This phenomenon is also immaterial, due to the way the activities are organized, their coordination, direction, intertwining. There is no manual that artisans consult for guidance on their actions and existence. Nor is there a constituted place for them
to play their roles. The case suggests that, as an organization, there is more action than structure. It is possible to observe the
existence of rules, although fewer than the ones of organizations in general, and almost all of them unwritten. MAIN FINDINGS Still regarding
this immateriality, stands out the expansion of the enterprise’s activities such as a) the strategy of collectively purchasing
raw material; b) research on how to innovate the product; c) search for suppliers; d) production; e) participation in the fair’s
meetings; f) activities of the fair’s incubator; and g) participation in training sessions about solidarity economy. All these
activities converging to the practice called here ‘craft fair.’ The artisans somehow face the confrontation of power. This aspect does not refer only to fulfilling the legal requirements
regarding documents and regulations, but under the economic and cultural perspectives (the dominance of the current
consumerism and capitalist system) and also under the spatial perspective, with the two large neighboring malls. However, the artisans won a place. For the local community and the neighborhood, the craft fair is part of the landscape and is
embedded in the pace of local events. There are customers who, before going to work, stop by the food stall to buy snacks or
to visit the other stalls. Other actors pass by the fair, such as street vendors, city inspectors, homeless people, police officers,
students, and employees of the neighborhood’s cultural center. The artisans end up developing a relationship with these
actors. They approach and try, as far as possible, to help them when, for example, a) they give coffee and bread to homeless
people; and b) they make baskets with their products to celebrate festivities, particularly Easter and Christmas, offering them
to employees of the neighborhood cultural center, as a way of thanking them for socializing throughout the year. The group is
receptive to students or anyone who wants to know something about solidarity economy and the craft fair. In the community
of practice, there is temporalization and a calendar for production that precedes commercialization and territorialization. In the artisans’ point of view, according to what was observed and achieved in the various strategies adopted in this research,
the relationship they established in the territorialization combine symbolic distances and possibilities of interaction. Figure 2
represents these elements as a circular gradient of positions in the configuration of this territory. Figure 2
Circular gradient of territorialization as a group practice, interactions, and positioning
Nodes, group or community of practice, internal
relationships, group feeling. The other and the thing to which one interacts directly,
face-to-face: visitor, mall, store, police officer. MAIN FINDINGS 2021 Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Observation and analysis enabled the identification of the following experiences and configurations of space and time, which
end up designing the form of participation:ii Observation and analysis enabled the identification of the following experiences and configurations of space and time, which
end up designing the form of participation: Observation and analysis enabled the identification of the following experiences and configurations of space and time, which
end up designing the form of participation: 1. The time and space for transportation;
2. The time and space to set up;
3. The space and time of the event;
4. The time and space of support and the public event;
5. The space and time of the community meeting and practice;
6. The time and space for reflection and consolidation of knowledge;
7. The time and space of the fair visitor (kairós); and
8. The time and space of production. The activities focused on territorialization are a fundamental part of the practice for this type of enterprise. They imply learning
according to the model proposed by the social theory of group or community practice. Table 4 synthesizes these data and
conclusions, considering as a starting point, the main axes of the social theory of practice, as proposed by Wenger (2011, pp. 20-30). The activities focused on territorialization are a fundamental part of the practice for this type of enterprise. They imply learning
according to the model proposed by the social theory of group or community practice. Table 4 synthesizes these data and
conclusions, considering as a starting point, the main axes of the social theory of practice, as proposed by Wenger (2011, pp. 20-30). MAIN FINDINGS The other and the thing for which one positions: peers,
third parties. The contextual place: the urban space, the reference orb,
the background. Source: Elaborated by the authors. The artisans take ownership of the public space, build, symbolize, attribute meaning, and engage third parties who pass by. They manage to shape their own space, so they have a pace, a proposal, a symbolic value, which is essentially the combination
of the craftwork and solidarity economy. They organize actions and activities, establish their pace and times. Figure 2
Circular gradient of territorialization as a group practice, interactions, and positioning
Nodes, group or community of practice, internal
relationships, group feeling. The other and the thing to which one interacts directly,
face-to-face: visitor, mall, store, police officer. The other and the thing for which one positions: peers,
third parties. The contextual place: the urban space, the reference orb,
the background. Source: Elaborated by the authors. Figure 2 Figure 2
Circular gradient of territorialization as a group practice, interactions, and positioning Figure 2
Circular gradient of territorialization as a group practice, interactions, and positioning Source: Elaborated by the authors. Source: Elaborated by the authors. The artisans take ownership of the public space, build, symbolize, attribute meaning, and engage third parties who pass by. They manage to shape their own space, so they have a pace, a proposal, a symbolic value, which is essentially the combination
of the craftwork and solidarity economy. They organize actions and activities, establish their pace and times. The artisans take ownership of the public space, build, symbolize, attribute meaning, and engage third parties who pass by. They manage to shape their own space, so they have a pace, a proposal, a symbolic value, which is essentially the combination
of the craftwork and solidarity economy. They organize actions and activities, establish their pace and times. The artisans take ownership of the public space, build, symbolize, attribute meaning, and engage third parties who pass by. They manage to shape their own space, so they have a pace, a proposal, a symbolic value, which is essentially the combination
of the craftwork and solidarity economy. They organize actions and activities, establish their pace and times. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. MAIN FINDINGS Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice
E Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice When connecting the case to the concepts presented in the theoretical framework presented in a previous section of this
article, it is possible to argue that territorialization does not mean only the creation of a physical space or a place in that
part of the neighborhood. The territorialization is not completed in the group’s positioning in the local geography and in
that landscape dominated by two large shopping malls. When connecting the case to the concepts presented in the theoretical framework presented in a previous section of this
article, it is possible to argue that territorialization does not mean only the creation of a physical space or a place in that
part of the neighborhood. The territorialization is not completed in the group’s positioning in the local geography and in
that landscape dominated by two large shopping malls. Territorialization is an essential element in the reconstruction of the artisans’ identities and learning process. The weekly
construction of the craft fair is the materialization of the scenery and dramatization, the participation and experience of cultural
elements, and their feelings and meanings. In this set of actions, understood as a practice, roles and identities are always being
reconstructed and reconfirmed. There is a vital link between territorialization and identities because the following aspects
have been defined through participation: a) the negotiated experience of who they are as a group and as social agents, what
they are doing there, and what for; b) the artisans’ learning trajectory, c) their commitments and responsibilities, and d) their
affiliations. The phenomenon is the result of the awareness and knowledge exercised in daily life, referring to the way the
territorialization and the identities become real as part of “us” (a group) – in the face of the others and become a ‘thing’ –
also referring to the way they are gathered, represent, and communicate their history and their connections and affiliations
(cultural and symbolic elements). MAIN FINDINGS Box 4
Elements of territorialization as practice and learning
Main axes of the
social theory
Implication for
community
learning
Territorialization
content
Meanings based
on analyzed data
Examples: mentions
and parts of interviews
Community
• Affiliation
• Social structure
Position
(economic, political, symbolic,
cultural) in relationship with:
• others
• peers
• context
• Relationship with
• Interact with
• Be an entrepreneur
“you are the meaning of
our existence, our work, our
enterprise.”
Practice
• How to do
• Coordinating
spaces and times
• Dynamic capacity of
self-management and of managing
interactions
(also implies learning)
• Boundaries
• Build
• Negotiate
• Occupy
• Confront
• Seduce
• Coopt
• Contract
• Set up the fair
• Produce the craftwork
• Act artistically
“They realize that we are
simple people with no
resources.”
“Each of us makes their own
craftwork, but everything
here is planned collectively
every detail.”
Meaning
• Experience
• Meaning of work
• Contrast with the social structure
and space
• Ideals
• Living and learning in a group
• Explain – to yourself
and others – what is it
you do, why you do, and
what is it for. • Understand the others
• Perceive the differences
“This is our work, my
friend. It is the popular and
solidarity economy!”
“I live and offer these people
a new form of living, a new
economy.”
Identity
• Becoming
• Process
• Flow
• Sense that the group is a subject
and content, with increasing
ownership of the situation
• Group members understood as
subjects with increasing ownership
of the situation. • Identify and overcome
problems
• Define who we are and
our place
“We manage to sort out our
challenges. We kill a lion
every day and week!” Box 4
Elements of territorialization as practice and learning Source: Elaborated by the authors. MAIN FINDINGS Finally, territorialization and identities refer to the way the artisans cultivate their political
existence, through acts of choice, purpose, positioning, negotiation, and the future. Identity is not explained only by the occupational nature of the group’s work, as they are artisans. Observations and data
point out that identity is closely linked to values and the meanings attributed to their knowledge, as well as to the women’s
interpretations of popular and solidarity economy. All these aspects are related to the fact that they are in that specific
territory, in that community. The artisans could be faced as co-operators or spectators. This symbolic element of the craftwork corresponds to the artisans’ interpretations and constitutes political acts. The artisans
are aware that others compete in the social space, with divergent values regarding individual production, different concepts
of what is a handmade product. However, the craftwork and the organization of the craft fair are part of the artisans’ trajectory of reflection, experience, and
learning. Through these activities of production and territorialization, the artisans learn and negotiate social and cultural
meanings, exercise their differences at the same time as maintaining their group identity. FINAL CONSIDERATIONS The set of group activities and the notion of ‘organizing’ observed in practice demonstrates how space and time influence the
modes of participation and present essential elements of the women’s learning and domain of their enterprise and relationships. Finally, this article sought to clarify the possibility of dialogue between the concepts of ‘community of practice’ and
entrepreneurial group action, and the concepts of social space and territorialization. Further studies may explore in-depth
the spatial-temporal conditions of such phenomena and the implications of these concepts for learning. FINAL CONSIDERATIONS This study explored how the mapping of spatial-temporal elements, based on a perspective of situated learning, offers new
insights about group enterprise as a practice, and about the knowledge shared among and through organizational communities. The research also contributes to understanding the processes of building identities and power relations inherent in forms of
group participation and learning. The study assumes that space and time constitute social practices, and are constituted by social practices and relationships. The
way the group (community) is positioned in the social space and interacts with the elements and external agents to build its
locus is composed of a set of activities that dialog with the practice’s social and historical context. These activities constitute
a practice of positioning and territorialization in the social space (which is different from the perspective that the context
unilaterally facilitates and hinders learning and sharing). The ability to build the space-time order is a form of social power. In this case, it proved to be a challenge for the group’s
enterprise, and for the content of situated and community learning. It is difficult for artisans to modify the spatial and temporal conditions of their work, but these conditions characterize limitations
and opportunities for group learning. The face-to-face meetings that take place at the craft fair, for example, facilitate visualizing
the group work, whereas the artisans work at home reflects a group activity of production, carried out at a distance. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice
Eloy Eros da Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice
Ariane Latoski
Eloy Eros da Silva Nogueira Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice The craft fair continues to be the main time and place where the artisans maintain and reinforce their identities (at the
individual and collective level), the sense of belonging to their group (community), and where they master their practice
while sharing a meaning for the joint activities. We thank the support from the Universidade Positivo, for the scholarship of the National Postdoctoral Program / CAPES –
PNPD according the Edital No. 005/2016 – PMDA. ACKNOWLEDGMENTS We thank the support from the Universidade Positivo, for the scholarship of the National Postdoctoral Program / CAPES –
PNPD according the Edital No. 005/2016 – PMDA. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira REFERENCES Gropp, B. M. C. (2007). De cascão a lagartixa: uma abordagem etnográfica
de comunidades de prática em aprendizagem organizacional. In J. Alves, C., Farias, G., & Pereira, H. G. (2018). Cotidiano e identificação:
o ser trabalhador pipoqueiro belo-horizontino. In Anais do 42º
Encontro da Associação Nacional dos Programas de Pós-Graduação
em Administração, Maringá, PR. Gropp, B. M. C. (2007). De cascão a lagartixa: uma abordagem etnográfica
de comunidades de prática em aprendizagem organizacional. In J. A. Valente, K. Mazzone, & M. C. Baranauskas (Org.), Aprendizagem
na era das tecnologias digitais (v. 30235, pp. 203-222). São Paulo,
SP: Cortez. A. Valente, K. Mazzone, & M. C. Baranauskas (Org.), Aprendizagem
na era das tecnologias digitais (v. 30235, pp. 203-222). São Paulo,
SP: Cortez. Bachelard, G. (1978). A filosofia do não; Novo espírito científico:
a poética do espaço (Coleção Os Pensadores). São Paulo, SP: Abril
Cultural. Gropp, B. M. C., & Tavares, M. G. P. (2007). Comunidade de prática:
gestão de conhecimento nas empresas. São Paulo, SP: Trevisan. Bourdieu, P. (1997). Efeitos do lugar. In P. Bourdieu (Org.), Miséria
do mundo (pp. 159-166). Petrópolis, RJ: Vozes. Haesbaert, R. (2015). O mito da desterritorialização. Rio de Janeiro,
RJ: Bertrand Brasil. Bourdieu, P. (2013). Espaço físico, espaço social e espaço físico
apropriado. Estudos Avançados, 27(79), 133-144. Hagerstrand, T. (1975). Space, time and human conditions. In A. Karlqvist, L. Lundqvist, & F. Snickars (Eds.), Dynamic allocation of
urban space (pp. 3-14). Lexington, MA: Lexington. Brown, J. S., & Duguid, P. (1991). Organizational learning and
communities of practice: toward a unified view of working, learning,
and innovation. Organization Science, 2(1), 40-57. Harvey, D. (2017). Condição pós-moderna. São Paulo, SP: Loyola. Humes, L. L., & Reinhard, N. (2006). A adoção do software livre na
Universidade de São Paulo. RAUSP Management Journal, 41(3), 14-39. Carrieri, A., Pereira, H. G., & Correia, G. F. A. (2018). ACKNOWLEDGMENTS A pipoca e seu
território nos arranjos organizativos de trabalhadores ambulantes
belo-horizontinos. In Anais do 42º Encontro da Associação Nacional
dos Programas de Pós-Graduação em Administração, Maringá, PR. Josselson, R. (2011). Narrative research: constructing, deconstructing
and reconstructing story. In F. J. Wertz, K. Charmaz, L. M. McMullen,
R. Josselson, R. Anderson, & E. McSpadden (Org.), Five ways of doing
qualitative analysis (pp. 224-242). New York, NY: Guilford. Certeau, M. (2014). A invenção do cotidiano. Petrópolis, RJ: Vozes. Jovchelovitch, S., & Bauer, M. W. (2002). Entrevista narrativa. In M. W. Bauer, & G. Gaskell (Eds.), Pesquisa qualitativa com texto, imagem
e som: um manual prático (pp. 90-113). Petrópolis, RJ: Vozes. Chiesa, C. D., Gois, P. H., De Luca, G. & Cavedon, N. R. (2015). Tramando
arames, pedras e fios: espaço e estigma no trabalho de um artista. Ciências Sociais Unisinos, 51(1), 32-41. Lave, J. (2011). Apprenticeship in critical ethnographic practice. Chicago, IL: University of Chicago Press. Davel, E., Cavedon, N. R., & Fischer, T. (2012). A vitalidade artesanal
da gestão contemporânea. Revista Interdisciplinar de Gestão Social,
1(3), 11-19. Lave, J., & Wenger, E. (1991). Situated learning: legitimate peripheral
participation. Cambridge, UK: Cambridge University Press. Fahy, K. M., Easterby-Smith, M., & Lervik, J. E. (2014). The power of
spatial and temporal orderings in organizational learning. Management
Learning, 45(2), 123-144. Lefebvre, H. (1974). La production de l’espace. Paris, France: Anthropos. Lengler, J. F. B., & Cavedon, N. R. (2018). Do “templo do consumo” à
representação mitológica: um olhar etnográfico desconstrutivo sobre
os ritos no shopping center. In Anais do 42º Encontro da Associação
Nacional dos Programas de Pós-Graduação em Administração,
Maringá, PR. Ferrarini, N. L., Camargo, D., & Bulgacov, Y. L. M. (2014). Comunidades
de práticas sociais e o debate sobre a formação do psicólogo. International Journal of developmental and educational Psichology
INFAD, 2(1), 299-306. Ferreira, T. B., Helal, D. H., & Paiva, K. C. M. (2016). Artesanato,
aprendizagem social e comunidade de prática: um estudo com rendeiras
em Alcaçuz (RN). Revista Brasileira de Gestão e Desenvolvimento
Regional, 12(1), 33-61. Lervik, J. E., Fahy, K. M., & Eastertby-Smith, M. (2010). Temporal
dynamics of situated learning in organizations. Management Learning,
41(3), 285-301. Mendes, L. (2011). As culturas organizacionais territorializadas
na atividade de camelô em Três Lagoas (Doctoral Dissertation). Universidade Federal do Rio Grande do Sul, Porto Alegre, RS. Gherardi, S. (2012). How to conduct a practice-based study: problems
and methods. Cheltenham, UK: Edward Elgar. ACKNOWLEDGMENTS Giddens, A. (1985). Time, space and regionalisation. In D. Gregory,
& J. Urry (Ed.), Social relations and spatial structures (critical human
geography) (pp. 265-295). Basingstoke, UK: Palgrave. Mendes, L., & Cavedon, N. R. (2013). As culturas organizacionais
territorializadas. Revista de Ciências da Administração, 15(35), 108-123. Mendes, L., & Cavedon, N. R. (2014). O mercado de camelôs e as
contribuições ao desenvolvimento local de uma cidade. Interações,
15(2), 341-352. Giddens, A. (2003). A constituição da sociedade. São Paulo, SP:
Martins Fontes. Gouvêa, M. T. A., Paranhos, C., & Motta, C. L. R. (2008). Promovendo
o aprendizado organizacional por meio das comunidades de prática. Boletim Técnico do Senac, 34(3), 49-62. Mendes, L., & Cavedon, N. R. (2015). Território como ordem e caos:
relação de poder entre camelôs, poder público e comerciantes. BASE:
Revista de Administração e Contabilidade da UNISINOS, 12(1), 15-26. Gropp, B. M. C. (2005). Uma abordagem etnográfica em comunidades
de prática (Masther Thesis). Pontifícia Universidade Católica de São
Paulo, São Paulo, SP. Mendes, L., & Urbina, L. M. S. (2015). Análise sobre a produção
acadêmica brasileira em comunidades de prática. Revista de
Administração Contemporânea, 19(3), 305-327. Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021 Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Temporal and spatial dimensions of group entrepreneurship:
the case of a craft fair as a community of practice Ariane Latoski
Eloy Eros da Silva Nogueira Ariane Latoski Eloy Eros da Silva Nogueira In S. B. Bacharach (Ed.), Research in organizational sociology
(v. 3, pp. 1323-1382). Greenwich, CT: JAI Press. Nicolini, D. (2013). Practice theory, work & organization: an introduction. Oxford, UK: Oxford University Press. Nicolini, D. (2013). Practice theory, work & organization: an introduction. Oxford, UK: Oxford University Press. Nicolini, D., Scarbrough, H., & Gracheva, J. (2015). Communities of
practice and situated learning in healthcare. In E. Ferlie, K. Montgomery, Van-Manen, M. (2007). Phenomenology of practice. Phenomenology
& Practice, 1(1), 11-30. Nicolini, D., Scarbrough, H., & Gracheva, J. (2015). Communities of
practice and situated learning in healthcare. In E. Ferlie, K. Montgomery,
& A. R. Pedersen (Ed.), Oxford handbook of health care management
(pp. 255-278). Oxford, UK: Oxford University Press. i
& A. R. Pedersen (Ed.), Oxford handbook of health care management
(pp. 255-278). Oxford, UK: Oxford University Press. Vasconcelos, M. E. S. ACKNOWLEDGMENTS M., & Domingues, F. F. (2018). Ser quem eu
quiser na Liberdade: práticas de resistência na ocupação da Praça
da Liberdade em Belo Horizonte-MG. In Anais do 42º Encontro
da Associação Nacional dos Programas de Pós-Graduação em
Administração, Maringá, PR. Pereira, D. C., & Carrieri, A. P. (2005). Movimentos de desterritorialização
e reterritorilização na transformação das organizações. Revista de
Administração de Empresas, 4(1), 13-43. Saquet, M. A. (2015). Abordagens e concepções de território. São
Paulo, SP: Outras Expressões. Webster, L., & Mertova, P. (2007). Using narrative inquiry as research
method: an introduction to using critical event narrative analysis in
research on learning and teaching. London, UK: Routledge. Schultze, F. (2010). Pesquisa biográfica e entrevista narrativa. In
V. Weller, & N. Pfaff (Org.), Metodologias da pesquisa qualitativa
em educação: teoria e prática (pp. 211-222). Petrópolis, RJ: Vozes. Wenger, E. (1998). Communities of practice: learning, meaning, and
identity. Cambridge, UK: Cambridge University Press. Stoddard, R. H. (2010). Field techniques and research methods in
geography. Dubuque, IA: KendalUHunt. Wenger, E. (2011). Comunidades de práctica: aprendizaje, significado
e identidad. Buenos Aires, Argentina: Paidós. Van-Maanen, J. (2009). A song for my supper: more tales of the field. Organizational Research Methods, 13(1), 240-255. Wenger, E., McDermott, R., & Snyder, W. (2002). Cultivating
communities of practice: a guide to managing knowledge. Boston,
MA: Harvard Business School Press. Van-Maanen, J., & Barley, S. R. (1982). Occupational communities:
culture and control in organizations. In B. Staw, & L. Cummings (Ed.),
Research in organizational behavior (v. 6, pp. 287-366). Greenwich,
CT: JAI Press. Zioli, E. G. O., Rodrigues, F. S., Gaffuri, E. L., & Ichikawa, E. Y. (2018). As
práticas cotidianas e os processos de territorialização de assentados
no Município de Querência do Norte-RN. In Anais do 42º Encontro
da Associação Nacional dos Programas de Pós-Graduação em
Administração, Maringá, PR. Van-Maanen, J., & Kolb, D. (1982). The professional apprentice:
observation on fieldwork roles in two organizational settings. Van-Maanen, J., & Kolb, D. (1982). The professional apprentice:
observation on fieldwork roles in two organizational settings. Ariane Latoski
ORCID: https://orcid.org/0000-0002-5208-6921
Associate Researcher at the Universidade Positivo in the Doctoral Program in Administration; Post-Doctorate in the Master and Doctorate Program in
Administration at Universidade Positivo. E-mail: ariane.latoski1@gmail.com
Eloy Eros da Silva Nogueira
ORCID: https://orcid.org/0000-0002-5234-496X
Professor and associated Researcher of the Research Group on Practices, Subjectivity, and Organizations, of the Master and Doctorate Program in
Administration at Universidade Positivo. ACKNOWLEDGMENTS E-mail: esn.ipe777@gmail.com Associate Researcher at the Universidade Positivo in the Doctoral Program in Administration; Post-Doctorate in the Master and Doctorate Program in
Administration at Universidade Positivo. E-mail: ariane.latoski1@gmail.com Eloy Eros da Silva Nogueira
ORCID: https://orcid.org/0000-0002-5234-496X
Professor and associated Researcher of the Research Group on Practices, Subjectivity, and Organizations, of the Master and Doctorate Program in
Administration at Universidade Positivo. E-mail: esn.ipe777@gmail.com ORCID: https://orcid.org/0000 0002 5234 496X
Professor and associated Researcher of the Research Group on Practices, Subjectivity, and Organizations, of the Master and Doctorate Program in
Administration at Universidade Positivo. E-mail: esn.ipe777@gmail.com Professor and associated Researcher of the Research Group on Practices, Subjectivity, and Organizations, of the Master
Administration at Universidade Positivo. E-mail: esn.ipe777@gmail.com Cad. EBAPE.BR, v. 19, nº 1, Rio de Janeiro, Jan./Mar. 2021
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https://openalex.org/W1877167531
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https://europepmc.org/articles/pmc4591280?pdf=render
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English
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Retinoic Acid Receptors Control Spermatogonia Cell-Fate and Induce Expression of the SALL4A Transcription Factor
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PLOS genetics
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cc-by
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OPEN ACCESS ¤a Current Address: Institut de Recherche en Santé Environnement et Travail (IRSET), U1085 INSERM,
Université de Rennes 1, Rennes, France
¤b Current Address: Immunology Research Centre, School of Biochemistry and Immunology, Trinity
Biomedical Sciences Institute, Trinity College Dublin, Ireland
* norbert@igbmc.fr Citation: Gely-Pernot A, Raverdeau M, Teletin M,
Vernet N, Féret B, Klopfenstein M, et al. (2015)
Retinoic Acid Receptors Control Spermatogonia Cell-
Fate and Induce Expression of the SALL4A
Transcription Factor. PLoS Genet 11(10): e1005501. doi:10.1371/journal.pgen.1005501 Retinoic Acid Receptors Control
Spermatogonia Cell-Fate and Induce
Expression of the SALL4A Transcription
Factor Aurore Gely-Pernot1,2,3,4¤a, Mathilde Raverdeau1,2,3,4¤b, Marius Teletin1,2,3,4,5,
Nadège Vernet1,2,3,4, Betty Féret1,2,3,4, Muriel Klopfenstein1,2,3,4, Christine Dennefeld1,2,3,4,
Irwin Davidson1,2,3,4, Gérard Benoit6, Manuel Mark1,2,3,4,5, Norbert B. Ghyselinck1,2,3,4* a1111 1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique
Fonctionnelle et Cancer, Illkirch, France, 2 Centre National de la Recherche Scientifique (CNRS), UMR7104,
Illkirch, France, 3 Institut National de la Santé et de la Recherche Médicale (INSERM), U964, Illkirch, France,
4 Université de Strasbourg (UNISTRA), Illkirch Cedex, France, 5 Hôpitaux Universitaires de Strasbourg
(HUS), Strasbourg, France, 6 Centre de Génétique et de Physiologie Moléculaire et Cellulaire (GCPhiMC),
UMR5534 CNRS, Université de Lyon 1, Villeurbanne, France Abstract Editor: Paula E. Cohen, Cornell University, UNITED
STATES All-trans retinoic acid (ATRA) is instrumental to male germ cell differentiation, but its mecha-
nism of action remains elusive. To address this question, we have analyzed the phenotypes
of mice lacking, in spermatogonia, all rexinoid receptors (RXRA, RXRB and RXRG) or all
ATRA receptors (RARA, RARB and RARG). We demonstrate that the combined ablation of
RXRA and RXRB in spermatogonia recapitulates the set of defects observed both upon
ablation of RAR in spermatogonia. We also show that ATRA activates RAR and RXR
bound to a conserved regulatory region to increase expression of the SALL4A transcription
factor in spermatogonia. Our results reveal that this major pluripotency gene is a target of
ATRA signaling and that RAR/RXR heterodimers are the functional units driving its expres-
sion in spermatogonia. They add to the mechanisms through which ATRA promote expres-
sion of the KIT tyrosine kinase receptor to trigger a critical step in spermatogonia
differentiation. Importantly, they indicate also that meiosis eventually occurs in the absence
of a RAR/RXR pathway within germ cells and suggest that instructing this process is either
ATRA-independent or requires an ATRA signal originating from Sertoli cells. STATES
Received: January 29, 2015
Accepted: August 14, 2015
Published: October 1, 2015
Copyright: © 2015 Gely-Pernot et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. Copyright: © 2015 Gely-Pernot et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited. Data Availability Statement: All relevant data are
within the paper and its Supporting Information files. RESEARCH ARTICLE Data Availability Statement: All relevant data are
within the paper and its Supporting Information files. Funding: This work was supported by grants from
CNRS, INSERM, UNISTRA, Agence Nationale pour
la Recherche (ANR 09-BLAN-0282; 10-BLAN-1239;
13-BSV2-0017), Fondation pour la Recherche
Médicale (FDT20110922849; DEQ20071210544) and
European community (FP7-PEOPLE-2012-IEF Marie
Curie action, project #331687). It was also supported
in part by the grant ANR-10-LABX-0030-INRT under
the frame program Investissements d'Avenir labeled
ANR-10-IDEX-0002-02. The funders had no role in Author Summary
Differentiation of spermatozoa from immature germ cells, called spermatogonia, critically
depends on retinoic acid (ATRA), the active metabolite of vitamin A that acts though Introduction Spermatogenesis is a tightly regulated, cyclical, cell differentiation process, taking place in the
seminiferous epithelium of the testis and yielding mature spermatozoa from stem cells. Sper-
matogonia in the single cell state, known as A single (As) spermatogonia, have traditionally be
considered as the main spermatogonia stem cells in the mouse. Upon division, As spermatogo-
nia give rise either to two new single cells or to a pair of daughter cells called A paired (Apr)
spermatogonia that do not complete cytokinesis and remain connected through an intercellular
bridge. The Apr spermatogonia divide further to form syncytial chains of 4 to 16 A aligned
(Aal) spermatogonia [1]. Collectively, As, Apr and Aal (referred to as “undifferentiated sper-
matogonia”) are present throughout the seminiferous epithelial cycle and retain stem cell prop-
erties. Subsequently, Aal cells differentiate without mitotic division into A1 spermatogonia. Five
cell divisions follow A1 formation, forming successively A2, A3 A4, In (intermediate) and B
spermatogonia. Collectively, A1 to B spermatogonia (referred to as “differentiating spermato-
gonia”) express the prototypic marker KIT [2,3] and differentiate at given stages of the seminif-
erous epithelium cycle, each step of differentiation being associated with a mitotic division [4]. In rodent, all-trans retinoic acid (ATRA), the biologically active form of vitamin A (retinol)
is instrumental to spermatogonia differentiation as assessed from vitamin A deficiency studies. In mice fed a vitamin A-deficient (VAD) diet from weaning onwards, all spermatogonia pro-
gressively arrest at the Aal-A1 transition, yielding seminiferous tubules that contain only Aal
spermatogonia and Sertoli cells. Systemic administration of ATRA to VAD mice reinitiates
spermatogenesis from mitotically-arrested Aal spermatogonia, resulting in their massive differ-
entiation into spermatogonia expressing KIT, the marker of the Aal-A1 transition [2], and
resuming their proliferation/differentiation [5,6]. The molecular mechanism through which
ATRA controls Kit expression is however not yet fully elucidated. Characterizing this mecha-
nism is important not only in the field of reproduction, but also for a better understanding of
the biology of testicular germ cell tumors as KIT is also frequently deregulated in seminomas
[7]. In cells, ATRA binds to and activates nuclear receptors (RARA, RARB and RARG), which
are ligand-dependent transcriptional regulators. They usually function in the form of heterodi-
mers with rexinoid receptors (RXRA, RXRB and RXRG) to control expression of ATRA-target
genes through binding to specific sites located in genomic regulatory regions and called retinoic
acid response elements (RARE) [8]. Retinoid-Induced Male Germ Cell Differentiation study design, data collection and analysis, decision to
publish, or preparation of the manuscript. study design, data collection and analysis, decision to
publish, or preparation of the manuscript. binding to nuclear receptors called RXR and RAR. To understand the mechanism by
which ATRA control germ cell differentiation, we generated mice simultaneously lacking
all RXR or all RAR specifically in spermatogonia. From their phenotypic analysis, we dem-
onstrate that meiosis does not require a RAR/RXR-dependent pathway in germ cells and
propose that this process is either ATRA-independent or requires an ATRA signal origi-
nating from somatic cells. We also show that RXR, in the form of dimers with RAR, can
drive spermatogonia differentiation through binding to a regulatory region located in the
Sall4 gene. This finding is significant, as the transcription factor encoded by Sall4 is known
to regulate the expression of KIT, a key tyrosine kinase receptor which is frequently dereg-
ulated in testicular cancer. Competing Interests: The authors have declared
that no competing interests exist. Author Summary Author Summary Differentiation of spermatozoa from immature germ cells, called spermatogonia, critically
depends on retinoic acid (ATRA), the active metabolite of vitamin A that acts though 1 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Results and Discussion The ATRA signal is generally transduced by RAR/RXR heterodimers, notably during mouse
embryonic development [15]. However, it can also be relayed by RAR independently of RXR,
as it is the case in Sertoli cells [12]. Analysis by reverse transcription (RT) coupled to quantita-
tive PCR (qPCR) of mRNA extracted from fluorescent-activated cell sorting (FACS) purified
spermatogonia [13] showed that Rxra and Rxrb mRNA were present in these cells. Thus, con-
trary to our previous thoughts [10] but in agreement with IHC analyses [11], RXR are actually
present in spermatogonia and could well be necessary for their ATRA-induced differentiation. To test for this possibility, we generated mutant mice lacking all three RXR isotypes in undiffer-
entiated spermatogonia and their descendants (hereafter called Rxra;b;gSpg–/– mutants) using
Tg(Stra8-cre)1Reb transgene [16]. In this transgenic line, Cre-mediated ablation occurs as early
as post-natal day 3 (PN3), as assessed using a reporter assay (S1 Fig) and in agreement with
previous reports [14,16]. The crosses also generated control males devoid of the Cre transgene
and carrying loxP-flanked alleles of Rxra, Rxrb and Rxrg. They did not display testis defects
and were hereafter referred to as control mice. Retinoid-Induced Male Germ Cell Differentiation RXR isotypes, the situation is contrasted. Our in situ hybridization (ISH) analyses failed to
detect any of them in spermatogonia in the normal mouse testis [10], while another study evi-
denced RXRA in spermatogonia by immunohistochemistry (IHC) [11]. Thus, either RXR is
absent and therefore dispensable for RAR functioning in spermatogonia, as it is the case in Ser-
toli cells [12], or RXRA is required but its expression level in spermatogonia too low to be
detected by ISH. To discriminate between these two possibilities, we have generated mice lacking all RXR iso-
types specifically in spermatogonia from PN5 onwards and analyzed their phenotype. We
demonstrate that ablation of all Rxr genes arrests differentiation of some spermatogonia at the
Aal-A1 transition and recapitulates the full set of defects characteristic of the vitamin A defi-
ciency-induced testis degeneration. We further show that efficient ablation of the 3 Rar genes
in spermatogonia using the same genetic approach resembles ablation of the 3 Rxr genes. Importantly, some A1 spermatogonia still differentiate in these mutants, indicating the exis-
tence of a mechanism allowing the Aal to A1 transition independently of RAR/RXR in germ
cells. Along these lines, both meiotic and post-meiotic cells devoid of RAR or RXR are also pro-
duced, in contrast to the situation when ATRA synthesis is impaired [13]. We propose that
paracrine signals emanating from and transduced in Sertoli cells by ATRA-activated RARA
stimulate some Aal spermatogonia to become A1 and trigger entry into meiosis. We finally pro-
vide evidence that RXR and RAR bind to the same Sall4 regulatory region to control ATRA-
dependent expression of SALL4A in the RAR/RXR-dependent spermatogonia. As SALL4A is
known to impair ZBTB16-mediated Kit repression [14], our study provides novel insights into
the molecular mechanism by which ATRA could control KIT expression, and thereby the dif-
ferentiation of Aal into A1 spermatogonia in vivo. Introduction In the adult mouse testis, RARG cell-autonomously trans-
duces an ATRA signal required for spermatogonia differentiation. Accordingly, the testes
abnormalities observed upon deletion of Rarg either in the whole organism or specifically in
spermatogonia in sexually mature males are similar to those present in VAD males [9]. As to PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 2 / 23 Loss of RXR in undifferentiated spermatogonia yields age-related testis
degeneration The different generations of germ cells form cellular associations of fixed composition called
epithelial stages. In control testes only the twelve normal epithelial stages (I–XII) [17] were
identified (Fig 1A). In contrast, analysis of 12-week-old Rxra;b;gSpg–/– mutant testes (n = 5),
revealed that, aside from normal epithelial stages (Fig 1C), 36.3 ± 9.6% of the tubule sections
exhibited a degenerated seminiferous epithelium (Fig 1B) either lacking a large proportion of
germ cells (T3) or containing only spermatogonia and Sertoli cells (T4). In addition, 3 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation Fig 1. Ablation of RXR in spermatogonia induces age-related testis degeneration. (A,B) Periodic acid-
Schiff stains illustrating overviews and (C-H) details of germ cell associations in the seminiferous epithelium
of 12 week-old control and Rxra;b;gSgp–/– testes, as indicated. Normal gem cell associations at epithelial
stage VII (C) coexist with abnormal associations mimicking, to some extent, this epithelial stage, but lacking:
pachytene spermatocytes (D,H), preleptotene spermatocytes (E,G) and round spermatids (F,H). (I,J)
Hematoxylin and eosin stain showing overviews of 12 month-old control and Rxra;b;gSgp–/– testes:
seminiferous tubules containing only spermatogonia and Sertoli cells represent the end-stage of
degeneration in the mutant testes. PR and P, preleptotene and pachytene spermatocytes, respectively; St7
and St16, step 7 and 16 spermatids, respectively; T2, tubule sections lacking generation(s) of germ cells
around their entire circumference; T3, tubule sections with disorganization of the germ cell layer; T4, tubule
sections containing only spermatogonia and Sertoli cells. Germ cell populations present in a given
seminiferous tubule cross-section are highlighted by colored bars: red, preleptotene spermatocytes; green,
pachytene spermatocytes; blue, step 7 (round) spermatids; purple, step 16 (elongated, mature) spermatids. Roman numerals indicate the stages of the seminiferous epithelium cycle. Scale bar, 80 μm (A,B and I,J) and
30 μm (C-H). Fig 1. Ablation of RXR in spermatogonia induces age-related testis degeneration. (A,B) Periodic acid-
Schiff stains illustrating overviews and (C-H) details of germ cell associations in the seminiferous epithelium
of 12 week-old control and Rxra;b;gSgp–/– testes, as indicated. Normal gem cell associations at epithelial
stage VII (C) coexist with abnormal associations mimicking, to some extent, this epithelial stage, but lacking:
pachytene spermatocytes (D,H), preleptotene spermatocytes (E,G) and round spermatids (F,H). PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Loss of RXR in undifferentiated spermatogonia yields age-related testis
degeneration Mean percentages of
tubule sections showing normal cellular associations (white bars), abnormal associations resembling the
VAD situation with either one or two generations of germ cells lacking (grey bars), and degenerated
epithelium containing only spermatogonia and Sertoli cells (black bars) in testes of 12 month-old mice (n = 5)
with the indicated genotype. Mice lacking Rxrg and either Rxra (Rxra;gSgp–/– mutants) or Rxrb (Rxrb;gSgp–/–
mutants) are marginally affected. In contrast, mice simultaneously lacking Rxra and Rxrb (Rxra;bSgp–/–
mutant) displayed a high proportion of affected tubule sections. Additional ablation of Rxrg does not worsen
the pathological phenotype (Rxra;bSgp–/– mutant). This indicates that RXRG is dispensable, whereas RXRA
and RXRB are both required and exert redundant functions in spermatogonia. doi:10.1371/journal.pgen.1005501.g002 doi:10.1371/journal.pgen.1005501.g002 upon the simultaneous ablation of Rxra and Rxrb (Fig 2). This indicates that both RXRA and
RXRB exert redundant functions in spermatogonia, while RXRG is dispensable. One year-old
controls (n = 4) displayed only normal germ cell associations, whereas mutants (n = 4) dis-
played tubule sections containing only Sertoli cells and spermatogonia (Fig 1I and 1J). The lat-
ter expressed molecular markers of undifferentiated spermatogonia such as Gfra1 and Zbtb16
[3,18], but not of differentiating spermatogonia such as Kit and Stra8 [2,19] (Fig 3A–3H). Loss of RXR in undifferentiated spermatogonia yields age-related testis
degeneration (I,J)
Hematoxylin and eosin stain showing overviews of 12 month-old control and Rxra;b;gSgp–/– testes:
seminiferous tubules containing only spermatogonia and Sertoli cells represent the end-stage of
degeneration in the mutant testes. PR and P, preleptotene and pachytene spermatocytes, respectively; St7
and St16, step 7 and 16 spermatids, respectively; T2, tubule sections lacking generation(s) of germ cells
around their entire circumference; T3, tubule sections with disorganization of the germ cell layer; T4, tubule
sections containing only spermatogonia and Sertoli cells. Germ cell populations present in a given
seminiferous tubule cross-section are highlighted by colored bars: red, preleptotene spermatocytes; green,
pachytene spermatocytes; blue, step 7 (round) spermatids; purple, step 16 (elongated, mature) spermatids. Roman numerals indicate the stages of the seminiferous epithelium cycle. Scale bar, 80 μm (A,B and I,J) and
30 μm (C-H). doi:10.1371/journal.pgen.1005501.g001 17.8 ± 3.4% of the tubule sections lacked, around their entire circumference, either one or two
generations of germ cells, yielding abnormal variants of the epithelial stages (T2). The missing
germ cell layers included: preleptotene spermatocytes (Fig 1E and 1G), pachytene spermato-
cytes (Fig 1D and 1H), and/or round spermatids (Fig 1F and 1H). Thus, germ cell differentia-
tion appeared altered in Rxra;b;gSpg–/– mutants. Analysis of other combinations of compound
mutants at the age of 12 weeks revealed that the pathological phenotype was generated solely PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 4 / 23 Retinoid-Induced Male Germ Cell Differentiation Fig 2. RXRA and RXRB are both instrumental to spermatogonia differentiation. Mean percentages of
tubule sections showing normal cellular associations (white bars), abnormal associations resembling the
VAD situation with either one or two generations of germ cells lacking (grey bars), and degenerated
epithelium containing only spermatogonia and Sertoli cells (black bars) in testes of 12 month-old mice (n = 5)
with the indicated genotype. Mice lacking Rxrg and either Rxra (Rxra;gSgp–/– mutants) or Rxrb (Rxrb;gSgp–/–
mutants) are marginally affected. In contrast, mice simultaneously lacking Rxra and Rxrb (Rxra;bSgp–/–
mutant) displayed a high proportion of affected tubule sections. Additional ablation of Rxrg does not worsen
the pathological phenotype (Rxra;bSgp–/– mutant). This indicates that RXRG is dispensable, whereas RXRA
and RXRB are both required and exert redundant functions in spermatogonia. doi:10.1371/journal.pgen.1005501.g002 Fig 2. RXRA and RXRB are both instrumental to spermatogonia differentiation. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Ablation of all Rar in spermatogonia yields age-related testis
degeneration resembling that induced by loss of RXR The histological defects displayed by Rxra;b;gSpg–/– mutants appeared to be much more severe
than those observed when Rarg and Rara genes are deleted using the Tg(Neurog3-cre)24Syos
transgene [9]. This raised the possibility that RXR isotypes could be instrumental to some
aspects of spermatogonia differentiation, independently of RARG and RARA. To test for this
hypothesis, we analyzed the outcome of deleting Rar genes in spermatogonia by means of the
same Tg(Stra8-cre)1Reb transgene. Accordingly, mice carrying loxP-flanked alleles of Rara,
Rarb and Rarg were crossed with Tg(Stra8-cre)1Reb mice to generate Rara;b;gSpg–/– mutants and
their controls. In 12 week-old Rara;b;gSpg–/– mutants (n = 5), 24.5 ± 10.1% of the seminiferous tubule sec-
tions were abnormal, amongst which 11.5 ± 5%, identified as variants of the normal epithelial
stages, lacked one or two generations of germ cells and 12.9 ± 7.3% exhibited a seminiferous
epithelium either with a complete disorganization of the germ cell layers or with spermatogo-
nia and Sertoli cells only (S2 Fig). In one-year-old mutants (n = 3), the seminiferous epithelium PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 5 / 23 Retinoid-Induced Male Germ Cell Differentiation Fig 3. Ablation of RXR blocks spermatogonia are at the undifferentiated stage. In situ hybridization with
anti-sense probes for Gfra1, Zbtb16, Kit and Stra8 on histological sections of 12 month-old control (A-D),
Rxra;b;gSpg–/–(E-H) and Rara;b;gSpg–/–(I-L) testes. Undifferentiated spermatogonia expressing Gfra1 and
Zbtb16 are found in both control and mutant testes. In contrast differentiating spermatogonia expressing Kit
and Stra8 are found in control (C,D) but not in mutant (G,H,K,L) testes. T1, tubule sections showing normal
germ cell associations; T4, tubule sections containing only spermatogonia and Sertoli cells; L, Leydig cells. Scale bar: 80 μm. d i 10 1371/j
l
1005501 003 Fig 3. Ablation of RXR blocks spermatogonia are at the undifferentiated stage. In situ hybridization with
anti-sense probes for Gfra1, Zbtb16, Kit and Stra8 on histological sections of 12 month-old control (A-D),
Rxra;b;gSpg–/–(E-H) and Rara;b;gSpg–/–(I-L) testes. Undifferentiated spermatogonia expressing Gfra1 and
Zbtb16 are found in both control and mutant testes. In contrast differentiating spermatogonia expressing Kit
and Stra8 are found in control (C,D) but not in mutant (G,H,K,L) testes. T1, tubule sections showing normal
germ cell associations; T4, tubule sections containing only spermatogonia and Sertoli cells; L, Leydig cells. Scale bar: 80 μm. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Ablation of all Rar in spermatogonia yields age-related testis
degeneration resembling that induced by loss of RXR doi:10.1371/journal.pgen.1005501.g003 consisted only in Sertoli cells and spermatogonia, which expressed genes that are typical of
undifferentiated spermatogonia (i.e., Gfra1 and Zbtb16), but not of differentiating spermatogo-
nia (i.e., Kit and Stra8) (Fig 3I–3L). Altogether, these data indicate that age-matched Rara;b;
gSpg–/– and Rxra;b;gSpg–/– mutants display similar, if not identical, phenotypes, including a slow
and progressive loss of differentiating germ cells and the presence of spermatogonia blocked at
an undifferentiated, Aal, stage (i.e., ZBTB16-positive, KIT-negative [2,3]) in aged mutants, both
of which are features of the VAD testis [20]. To further document the similarities between the phenotypes induced by Rxr and Rar loss-
of-functions, we examined the effect of Rxr ablation on germ cell apoptosis. Terminal deoxynu-
cleotidyl-transferase dUTP nick end-labeling (TUNEL) assays indicated that apoptosis of pre-
leptotene spermatocytes was not increased in testes of 8 week-old Rxra;b;gSpg–/– mutants,
relative to age-matched controls (Fig 4A and 4B). Actually, we did not detect a single TUNEL-
positive preleptotene spermatocyte in controls and in Rxra;b;gSpg–/– mutants (n = 3 males for
each genotype; n > 200 preleptotene spermatocytes per testis). Therefore, similarly to the situa-
tion in mice lacking Rara and Rarg in spermatogonia [9], cell-death cannot account for the
missing germ cell layers observed in Rxra;b;gSpg–/– mutant testes. We next examined the effect of Rxr ablation on the pace of preleptotene spermatocyte dif-
ferentiation, because any delay or an arrest of this process may lead: (i) to the disappearance of
pachytene spermatocytes through their normal differentiation into round, step 7, spermatids 6 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation Fig 4. Ablation of RXR in spermatogonia blocks their division, but does not affect meiosis. (A,B)
TUNEL assays on histological sections from 8 week-old control and Rxra;b;gSpg–/– testis as indicated. Red
signals correspond to apoptotic cells and nuclei are counterstained with DAPI (in blue). (C-F)
Immunohistochemical detection of BrdU (red signals). After administration, incorporated BrdU has been
similarly transferred to spermatids at 17 days (C,D) or to pachytene spermatocytes at 9 days (E,F) both in
control and mutant seminiferous tubules. In contrast, spermatogonia retaining BrdU are observed only in
mutants (E,F). PR and P, preleptotene and pachytene spermatocytes, respectively; S, Sertoli cells; SG,
spermatogonia; St7 and St16, step 7 and 16 spermatids, respectively; Z, zygotene spermatocytes. Roman
numerals refer to the stages of the seminiferous epithelium cycle. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Differentiation of A1 spermatogonia and meiosis still can occur when
RAR and RXR are absent in germ cells Given the central role assigned to ATRA in spermatogonia differentiation and in male meiosis
[13,21], it was surprising that differentiation of only some spermatogonia was impaired, and
that meiosis always proceeded normally in the absence of either Rar or Rxr. To exclude the pos-
sibility that Cre-mediated excision was mosaic, thereby resulting in the absence of RAR or
RXR in some, but not all, differentiating germ cells, we analyzed their expression in Rara;b;
gSpg–/– and Rxra;b;gSpg–/– testes. RT-qPCR analysis of whole testis RNA showed that the amount
of Rarg transcripts was markedly reduced (4-fold) in Rara;b;gSpg–/– mutants, as early as PN5
(S3 Fig). Consistent with this finding, IHC analyses indicated a total absence of RARG in germ
cells of Rara;b;gSpg–/– mutants, at PN5 and at PN60 (S3 Fig). In fact 100% of spermatogonia
and of preleptotene spermatocytes were devoid of RARG in Rara;b;gSpg–/– mutants. Efficient
loss of RARA and RARB in these mutants can be assessed neither by RT-qPCR because they
are not, or only weakly, expressed in spermatogonia nor by IHC analyses because reliable anti-
bodies are not available [9,10]. However, efficient ablation of loxP-flanked Rara and Rarb
alleles was assessed at the genomic level, using FACS-purified germ cell populations [22]. PCR
analysis demonstrated that excised (null, L–), but not conditional (L2) alleles, were detected in
genomic DNA isolated from spermatogonia, spermatocytes and spermatids of PN60 mice
bearing the Tg(Stra8-cre)1Reb transgene (S3 Fig). Together, these data indicate that ablation of
all 3 Rar genes was efficient in all germ cells, as early as PN5. As the outcome of ablating all
RAR in spermatogonia appears very close to that induced upon Rarg knockout (Rarg–/–
mutants) [9], our data suggest that RARG is the major functional RAR isotype in spermatogo-
nia. Similar results were obtained in Rxra;b;gSpg–/– mutants, with Rxra transcript amounts
markedly reduced (4- to 5-fold) as early as PN5 (S3 Fig). Assuming that the excision of Rar and Rxr genes was complete from PN5 onwards, the
impact of RAR or RXR loss-of-functions during the pubertal development of the testis was
evaluated at PN20, i.e., when the first post-meiotic cells appear. At this developmental stage,
control, Rxra;b;gSpg–/– and Rara;b;gSpg–/– mutant testes (n = 4 for each genotype) were indistin-
guishable: in both situations, late pachytene and diplotene spermatocytes represented the most
advanced germ cell in the vast majority of tubule sections (Fig 5A). Retinoid-Induced Male Germ Cell Differentiation in mice lacking Rara and Rarg in spermatogonia [9], the duration of meiosis is not altered in
Rxra;b;gSpg–/– mutant testes. In this context, it seems logical to assume that ablation of Rxr
genes induces germ cell depletion solely through altering the spermatogonia proliferation/dif-
ferentiation process. Accordingly, BrdU was detected in Rxra;b;gSpg–/– testes, 9 days after its
incorporation, in cells displaying histological features of spermatogonia (Fig 4E and 4F). BrdU
was never detected in spermatogonia of control testes at this time-point after injection because
its amount becomes diminished by half in each daughter cell upon cell-division, yielding a pro-
gressive decrease of the signal over time and its absence 9 days after BrdU incorporation. This
observation indicates that some of the spermatogonia that had incorporated BrdU in the Rxra;
b;gSpg–/– testes did not divide further or divided more slowly than in control testes, as it is the
case for spermatogonia lacking Rar [9] and in VAD testis [20]. Our study shows therefore that
the outcomes of ablating RAR or RXR in spermatogonia are identical at the histological level. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Ablation of all Rar in spermatogonia yields age-related testis
degeneration resembling that induced by loss of RXR In mutant testes, one asterisk and two
asterisks indicate tubule sections without pachytene spermatocytes and without round spermatids,
respectively. Scale bar: 160 μm (A,B), 40 μm (C,D) and 25 μm (E,F). Fig 4. Ablation of RXR in spermatogonia blocks their division, but does not affect meiosis. (A,B)
TUNEL assays on histological sections from 8 week-old control and Rxra;b;gSpg–/– testis as indicated. Red
signals correspond to apoptotic cells and nuclei are counterstained with DAPI (in blue). (C-F)
Immunohistochemical detection of BrdU (red signals). After administration, incorporated BrdU has been
similarly transferred to spermatids at 17 days (C,D) or to pachytene spermatocytes at 9 days (E,F) both in
control and mutant seminiferous tubules. In contrast, spermatogonia retaining BrdU are observed only in
mutants (E,F). PR and P, preleptotene and pachytene spermatocytes, respectively; S, Sertoli cells; SG,
spermatogonia; St7 and St16, step 7 and 16 spermatids, respectively; Z, zygotene spermatocytes. Roman
numerals refer to the stages of the seminiferous epithelium cycle. In mutant testes, one asterisk and two
asterisks indicate tubule sections without pachytene spermatocytes and without round spermatids,
respectively. Scale bar: 160 μm (A,B), 40 μm (C,D) and 25 μm (E,F). doi:10.1371/journal.pgen.1005501.g004 doi:10.1371/journal.pgen.1005501.g004 doi:10.1371/journal.pgen.1005501.g004 after one cycle of the seminiferous epithelium (i.e., 8.6 days), then (ii) to the disappearance of
step 7 spermatids through their normal transformation into mature, step 16, spermatids after
completion of a second cycle. Thus, we evaluated the duration of meiotic phase of spermato-
genesis after 5-bromo-2'-deoxyuridine (BrdU) incorporation into S-phase nuclei. In adult tes-
tis, BrdU is mainly incorporated into B spermatogonia and preleptotene spermatocytes [20]. We fate-mapped the BrdU-labeled descendants of these cells 9 and 17 days after injection of
the tracer. At the latter time-point, the most advanced, BrdU-positive, cell-type was step 7 sper-
matids in both control and Rxra;b;gSpg–/– testes (n = 3 for each genotype; 8 week-old) and there
was no retained labeling in any spermatocyte (Fig 4C and 4D). Thus, similarly to the situation PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 7 / 23 (A) Percentages of seminiferous tubule cross-sections in which preleptotene/leptotene
(PR+L), zygotene and early pachytene (Z+eP), late pachytene (P) and diplotene (D) spermatocytes or round
spermatids (RS) represent the most advanced germ cell-types in control (white bars), Rxra/b/gSpg–/–(black
bars) and Rara/b/gSpg–/–(grey bars) testes at post-natal day 20 (PN20). The bars represent mean ± s.e.m. (n = 4–5). (B-D) Histological sections of seminiferous from post-natal day 25 (PN25) control, Rara/b/gSpg–/–
and RaraSer–/–/Rarg–/– mice stained with hematoxylin and eosin. Note the absence of spermatocytes (C) or of
all meiotic and post meiotic germ cells (D) in the mutant testes. (E-J) Detection of spermatogonia expressing
KIT (red signal in E, F, H and J) and RARG (red signal in G and I) in control and Rara/b/gSpg–/– testes at 6
weeks of age. ZBTB16 (green nuclear signal in E, F, H and J) identifies spermatogonia. Alexa Fluor Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of
spermatogenesis. (A) Percentages of seminiferous tubule cross-sections in which preleptotene/leptotene
(PR+L), zygotene and early pachytene (Z+eP), late pachytene (P) and diplotene (D) spermatocytes or round
spermatids (RS) represent the most advanced germ cell-types in control (white bars), Rxra/b/gSpg–/–(black
bars) and Rara/b/gSpg–/–(grey bars) testes at post-natal day 20 (PN20). The bars represent mean ± s.e.m. (n = 4–5). (B-D) Histological sections of seminiferous from post-natal day 25 (PN25) control, Rara/b/gSpg–/–
and RaraSer–/–/Rarg–/– mice stained with hematoxylin and eosin. Note the absence of spermatocytes (C) or of
all meiotic and post meiotic germ cells (D) in the mutant testes. (E-J) Detection of spermatogonia expressing
KIT (red signal in E, F, H and J) and RARG (red signal in G and I) in control and Rara/b/gSpg–/– testes at 6
weeks of age. ZBTB16 (green nuclear signal in E, F, H and J) identifies spermatogonia. Alexa Fluor Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of
spermatogenesis. (A) Percentages of seminiferous tubule cross-sections in which preleptotene/leptotene
(PR+L), zygotene and early pachytene (Z+eP), late pachytene (P) and diplotene (D) spermatocytes or round
spermatids (RS) represent the most advanced germ cell-types in control (white bars), Rxra/b/gSpg–/–(black
bars) and Rara/b/gSpg–/–(grey bars) testes at post-natal day 20 (PN20). The bars represent mean ± s.e.m. (n = 4–5). Differentiation of A1 spermatogonia and meiosis still can occur when
RAR and RXR are absent in germ cells These results indicate that
the spermatocytes present at PN20 in the mutants testes, appeared in due time, likely because
the spermatogonia from which they derived started to differentiate before PN3, at a time when
Rar or Rxr genes were not yet knocked out. More importantly, they also indicate that all prelep-
totene spermatocytes initiated meiosis normally (around PN8), at a time when they were
devoid of RAR or RXR since ablation was obvious from PN5 in their precursors (see above). 8 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of
spermatogenesis. (A) Percentages of seminiferous tubule cross-sections in which preleptotene/leptotene
(PR+L), zygotene and early pachytene (Z+eP), late pachytene (P) and diplotene (D) spermatocytes or round
spermatids (RS) represent the most advanced germ cell-types in control (white bars), Rxra/b/gSpg–/–(black
bars) and Rara/b/gSpg–/–(grey bars) testes at post-natal day 20 (PN20). The bars represent mean ± s.e.m. (n = 4–5). (B-D) Histological sections of seminiferous from post-natal day 25 (PN25) control, Rara/b/gSpg–/–
and RaraSer–/–/Rarg–/– mice stained with hematoxylin and eosin. Note the absence of spermatocytes (C) or of
all meiotic and post meiotic germ cells (D) in the mutant testes. (E-J) Detection of spermatogonia expressing
KIT (red signal in E, F, H and J) and RARG (red signal in G and I) in control and Rara/b/gSpg–/– testes at 6
weeks of age. ZBTB16 (green nuclear signal in E, F, H and J) identifies spermatogonia. Alexa Fluor
Retinoid-Induced Male Germ Cell Differentiation Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of
spermatogenesis. (A) Percentages of seminiferous tubule cross-sections in which preleptotene/leptotene
(PR+L), zygotene and early pachytene (Z+eP), late pachytene (P) and diplotene (D) spermatocytes or round
spermatids (RS) represent the most advanced germ cell-types in control (white bars), Rxra/b/gSpg–/–(black
bars) and Rara/b/gSpg–/–(grey bars) testes at post-natal day 20 (PN20). The bars represent mean ± s.e.m. (n = 4–5). (B-D) Histological sections of seminiferous from post-natal day 25 (PN25) control, Rara/b/gSpg–/–
and RaraSer–/–/Rarg–/– mice stained with hematoxylin and eosin. Note the absence of spermatocytes (C) or of
all meiotic and post meiotic germ cells (D) in the mutant testes. (E-J) Detection of spermatogonia expressing
KIT (red signal in E, F, H and J) and RARG (red signal in G and I) in control and Rara/b/gSpg–/– testes at 6
weeks of age. ZBTB16 (green nuclear signal in E, F, H and J) identifies spermatogonia. Alexa Fluor Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of Fig 5. Ablation of either RXR or RAR in spermatogonia does not alter the first round of
spermatogenesis. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation 488-conjugated peanut agglutinin (in E and F) labels the acrosomal system of spermatids, allowing precise
identification of the stage of the seminiferous epithelium cycle. (G and H) and (I and J) represent consecutive
histological sections. All sections were counterstained with 40,6-diamidino-2-phenylindole (DAPI) to label
nuclei (blue signal). A1, A1 spermatogonia, based on their presence in seminiferous tubule sections that
contain both preleptotene spermatocytes (KIT-positive and ZBTB16-negative) and step8 spermatids. Int,
intermediate spermatogonia, based on cell density co-expression of KIT and ZBTB16, and peanut
hemagglutinin staining of acrosomes on consecutive sections. PR, P, preleptotene and pachytene
spermatocytes, respectively; SG, spermatogonia, St7 and St8, step 7 and step8 round spermatids. Scale
bars: 30 μm (B-D), 20 μm (E and F) and 55 μm (G-J). doi:10.1371/journal.pgen.1005501.g005 Analyzing the seminiferous epithelium later during pubertal development revealed the occur-
rence of abnormal cellular associations at PN25: few tubule sections in mutant testes displayed
spermatogonia associated with round spermatids but without the intervening layers of prelep-
totene and pachytene spermatocytes (Fig 5B and 5C). This observation confirms the initial
wave of A1 spermatogonia differentiation was not affected (yielding step 7 spermatids at
PN25), and suggests the second wave was arrested (or delayed) in few tubules at some point
before meiosis, leading to the absence of spermatocytes at PN25. However, the presence of nor-
mal cellular associations in the majority of tubule sections indicates that both A1 spermatogo-
nia differentiation and meiosis occurred, despite absence of RAR or RXR in germ cells (see
above). In keeping with this, KIT-positive A1 spermatogonia were found at stages VII-VIII of
the seminiferous epithelium cycle in Rara;b;gSpg–/– mutants at PN60, similarly to the situation
in control mice (Fig 5E and 5F). The reason why ablation of RAR or RXR in germ cells affects only a fraction of A1 sper-
matogonia is unclear. In some cases the A1 transition appears to take place in due time, yielding
normal cell associations, while in other instances no A1 are formed and Aal spermatogonia
have to wait one (or several) epithelial cycles to become A1, yielding seminiferous tubule seg-
ments with missing generations of spermatocytes and spermatids. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 (B-D) Histological sections of seminiferous from post-natal day 25 (PN25) control, Rara/b/gSpg–/–
and RaraSer–/–/Rarg–/– mice stained with hematoxylin and eosin. Note the absence of spermatocytes (C) or of
all meiotic and post meiotic germ cells (D) in the mutant testes. (E-J) Detection of spermatogonia expressing
KIT (red signal in E, F, H and J) and RARG (red signal in G and I) in control and Rara/b/gSpg–/– testes at 6
weeks of age. ZBTB16 (green nuclear signal in E, F, H and J) identifies spermatogonia. Alexa Fluor PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 9 / 23 RARG/RXR heterodimers bind to Sall4 and induce expression of
SALL4A in spermatogonia The similarities between Rar and Rxr gene ablations indicate that RAR and RXR exert conver-
gent functions in spermatogonia, and support the possibility that ATRA signaling in these cells
involves RAR/RXR heterodimers. They also indicate that RXR in spermatogonia are unlikely
to play a role other than controlling differentiation in conjunction with RAR. To test whether
RAR and RXR were actually recruited to an endogenous gene promoter in spermatogonia in
vivo, we performed immunoprecipitation (IP) of these nuclear receptors using chromatin from
PN5 wild-type testes, followed by qPCR analysis of the recovered DNA fragments, and assessed
binding to Stra8, which is proposed as a RAR target-gene in spermatogonia [21]. Both anti-
RAR and anti-RXR antibodies were able to precipitate, with similar efficiencies, the DNA
sequences containing the RAR binding sites of the Stra8 promoter (S4 Fig). These data further
support the notion that RAR/RXR heterodimers can be the functional units transducing the
ATRA-signal in spermatogonia. However, although STRA8 promotes spermatogonia differen-
tiation, it is not strictly required for this process [19,25,26] and its expression does not appears
to be dependent upon RAR/RXR-signaling (see above). Thus, effectors acting downstream of
ATRA and distinct from STRA8 likely account for the Aal to A1 spermatogonia transition. To gain insights into the genetic cascade controlled by RAR/RXR heterodimers and aside
from STRA8, we set up an experiment aimed at identifying ATRA-controlled genes in sper-
matogonia. To this purpose, we used Aldh1a1-3Ser−/−mutants as a model, in which all retinal-
dehyde dehydrogenase activity is ablated in Sertoli cells. These mutants were chosen because
(i) their spermatogonia differentiation is blocked at the Aal stage, (ii) Aal spermatogonia express
RARG [9] and (iii) Aal spermatogonia are poised to differentiate into A1 spermatogonia upon
activation of ATRA signaling [13]. We treated organotypic cultures of Aldh1a1-3Ser−/−testes
with the RARG-selective agonist BMS961 (n = 5) or with its vehicle (n = 5) for 6 hours and
extracted mRNA. Microarray expression profiling identified only a few transcripts that were
differentially expressed upon activation of RARG, amongst which Sall4. This gene encodes two
isoforms named SALL4A and SALL4B [27]. They are zinc-finger transcription factors, which
participate in regulatory networks and are critical for cell fate decisions and lineage specifica-
tion [28,29]. Retinoid-Induced Male Germ Cell Differentiation substance in vertebrates [23], then our finding necessarily implies that the ATRA-dependent
pathway instructing preleptotene spermatocytes is not autocrine in nature, as previously pro-
posed [13], but instead operates in Sertoli cells. In this context, ATRA would control the syn-
thesis by Sertoli cells of yet unknown, intermediate, secreted factor(s) acting on spermatocytes
to trigger meiosis. Alternatively, the possibility exists that meiotic initiation does not require
ATRA in male germ cells, as it was shown to be the case in female germ cells [24]. Discriminat-
ing between these two possibilities awaits further investigations. Regardless of the scenario, our
findings indicate that expression of Stra8 does not require a RAR/RXR-dependent signaling
pathway in preleptotene spermatocytes, even though this receptor heterodimer can efficiently
bind to RARE in the Stra8 promoter [13,24]. Moreover, spermatogonia
do not transition at random because, as a result of stage-dependent cell divisions [4], extensive
rows of differentiating, KIT-positive, RARG-negative, spermatogonia were observed at stages
I-VI of the seminiferous epithelium cycle in Rara;b;gSpg–/– mutants, as it is the case in control
males (Fig 5G–5I). An unknown signal, distinct from ATRA, may operate as a backup only in
the context of Rara;b;gSpg–/– and Rxra;b;gSpg–/– mutants to promote spermatogonia differentia-
tion. Alternatively, two populations of Aal spermatogonia may normally exist in the seminifer-
ous epithelium at stages VII-VIII, one requiring RAR/RXR to transition, the other one being
committed to become A1, independently of RAR/RXR heterodimers. As A1 spermatogonia
were less and less often generated with aging and no longer observed in old Rara;b;gSpg–/– and
Rxra;b;gSpg–/– mutants, the second population may become depleted with time resulting in a
complete arrest of spermatogenesis. Given the pivotal role of ATRA and the precise timing in
spermatogonia differentiation at stage VII-VIII of the seminiferous epithelium cycle [4],
instructing the transition in this second population may also require ATRA. We propose that
an ATRA signal transduced by RARA in Sertoli cells stimulates some Aal spermatogonia to
become A1 even though no RAR/RXR pathway is functional within these latter cells. In keeping
with this proposal, it worth noting that the seminiferous epithelium of mice lacking both
RARA in Sertoli cells and RARG in spermatogonia (RaraSer–/–;Rarg–/– mutants) was found to
consist only in Sertoli cells and undifferentiated spermatogonia (Fig 5D), as it is the case when
ATRA synthesis is specifically abolished in Sertoli cells [13]. More surprisingly, following the Aal to A1 transition, germ cell differentiation progressed at
a normal pace despite the lack of RAR or RXR inside these cells. This indicates that initiation
(and progression) of meiosis can proceed even in the absence of a functional ATRA signaling
pathway in spermatocytes. If one considers that ATRA is as a mandatory meiosis-inducing PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 10 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation analysis of protein extracts from Aldh1a1-3Ser−/−testes revealed that SALL4A protein level was
increased by BMS961-activated RARG (Fig 6B, compare lane 1 to 2); this increase was pre-
vented in mice additionally carrying a Rarg knock-out (Fig 6B, compare lane 3 to 4) and was
not observed in BMS961-treated Rara;b;gSpg–/– mutants (Fig 6B, compare lane 5 to 6). In addi-
tion, Sall4a mRNA levels were significantly decreased in whole testis of Rara;b;gSpg–/– and
Rxra;b;gSpg–/– mutants at PN60, while Sall4b and Zbtb16 mRNA levels were unchanged (Fig
6C). The finding that Sall4b mRNA level was not altered is in keeping with previous reports
showing that SALL4B is expressed at a constant level in spermatogonia [31,32]. Altogether our
results indicate that (i) Sall4a expression is decreased in testes of mice lacking RAR or RXR in
spermatogonia (Rara;b;gSpg–/– and Rxra;b;gSpg–/– testes); (ii) SALL4A is detected at a low level
in the seminiferous epithelium of mice deficient in ATRA (Aldh1a1-3Ser−/−testes), but at a
high level when RARG is activated by BMS961 in these mice (Aldh1a1-3Ser−/−testes treated
with BMS961), except when RARG is lacking (Aldh1a1-3Ser−/−;Rarg−/−testes, treated with
BMS961); and (iii) SALL4A is not detected in testes of adult mice lacking RAR in spermatogo-
nia even in the presence of the RARG agonist (Rara;b;gSpg–/– testes, treated with BMS961). Altogether, these data indicate that Sall4a expression is controlled by ATRA-activated RARG
in spermatogonia. Using data sets locating RAR-occupied sites genome-wide in several cell-types [33,34], we
identified a 700 bp-long RAR-binding region located in the first intron of Sall4 (RARE, Fig
7A). This DNA fragment contained a RAR binding sequence called IR1, consisting of inverted
repeats (two core motifs 5’-RGKTSA-3’ oriented head-to-tail) separated by 1 bp (Fig 7B), as
well as two additional sites called DR1 and DR0 (direct repeats of the core motif separated by 1
and 0 bp, respectively). We performed triplicate IP experiments with anti-RAR and anti-RXR
antibodies using chromatin extracted from PN5 wild-type mouse testes as substrate. At this
developmental stage, Sall4a expression was dependent upon RARG (Fig 7C, left panel). We
analyzed the immuno-precipitated chromatin fragments by qPCR and evidenced robust bind-
ing of both RAR and RXR in vivo, in a 106bp-long region restricted to chr2:168,591,142–
168,591,247 (NCBI37/mm9) in Sall4 (RARE, Fig 7C, right panel). To further confirm interac-
tion of IR1 with RAR/RXR heterodimers, we performed electrophoretic mobility shift assays
(EMSA) (Fig 7D). PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 RARG/RXR heterodimers bind to Sall4 and induce expression of
SALL4A in spermatogonia In the mouse testis, their expression is restricted to spermatogonia [30,31] and
mice deficient for Sall4 in these cell-type display testis defects that resemble those observed in
Rxra;b;gSpg–/– and Rara;b;gSpg–/– mutants, namely loss of differentiating, KIT-positive, sper-
matogonia and of meiotic cells [14]. Thus Sall4 gene appears particularly relevant to ATRA-
induced spermatogonia differentiation. We confirmed by RT-qPCR that Sall4a mRNA steady state level was increased upon
BMS961 administration in Aldh1a1-3Ser−/−testes, without the need for intermediate protein
synthesis as this increase occurred in the presence of cycloheximide (Fig 6A). Western-blot PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 11 / 23 Retinoid-Induced Male Germ Cell Differentiation Fig 6. Sall4a expression in undifferentiated spermatogonia is controlled by ligand-activated RARG. (A) Relative expression of Sall4a mRNA quantified by RT-qPCR in Aldh1a1-3Ser−/−testes cultured in the
absence (−) or in the presence (+) of cycloheximide (CHX) and treated for 6 hours with vehicle (white bar) and
BM961 (grey bars). Error bars represent s.e.m. (n = 5); * p < 0.05. (B) Western blot analysis of protein
extracts from testes of mutants as indicated treated with BMS961 (+) or with vehicle (−), using anti-SALL4 or
anti-ACTIN antibodies. NS points to an unspecific signal. (C) Relative expression of Sall4a, Sall4b and
Zbtb16 mRNA quantified by RT-qPCR in whole testes from control (white bars), Rara;b;gSpg−/−(grey bars)
and Rxra;b;gSpg−/−(black bars) mice at PN60. Error bars represent s.e.m. (n = 5); * p < 0.05. doi:10.1371/journal.pgen.1005501.g006 Fig 6. Sall4a expression in undifferentiated spermatogonia is controlled by ligand-activated RARG. (A) Relative expression of Sall4a mRNA quantified by RT-qPCR in Aldh1a1-3Ser−/−testes cultured in the
absence (−) or in the presence (+) of cycloheximide (CHX) and treated for 6 hours with vehicle (white bar) and
BM961 (grey bars). Error bars represent s.e.m. (n = 5); * p < 0.05. (B) Western blot analysis of protein
extracts from testes of mutants as indicated treated with BMS961 (+) or with vehicle (−), using anti-SALL4 or
anti-ACTIN antibodies. NS points to an unspecific signal. (C) Relative expression of Sall4a, Sall4b and
Zbtb16 mRNA quantified by RT-qPCR in whole testes from control (white bars), Rara;b;gSpg−/−(grey bars)
and Rxra;b;gSpg−/−(black bars) mice at PN60. Error bars represent s.e.m. (n = 5); * p < 0.05. doi:10.1371/journal.pgen.1005501.g006 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 12 / 23 (A) UCSC Genome Browser snapshot of
the Sall4 locus in NCBI37/mm9 assembly, including tracks for anti-RAR ChIP-seq [34], RefSeq genes and mammalian conservation (from top to bottom). RARE points to the RAR-binding region identified according to Moutier et al. [34]. (B) Alignments of the DNA sequences from the indicated species and
corresponding to the region containing the RAR-binding region in mouse Sall4. The dotted arrows indicate orientations of the core motifs. Stars and grey
boxes highlight the DNA residues and the RAR binding sequences that are conserved in all 6 species, respectively. (C) Left panel: relative expression of
Sall4a mRNA quantified by RT-qPCR in whole testes from control (white bars) and Rarg−/−(grey bars) mice at PN5. Error bars represent s.e.m. (n = 9); *
p < 0.05. Right panel: schematic representation of Sall4 locus and analysis of DNA recovered from testis chromatin immunoprecipitated using antibodies
directed against RNApol2, all RAR or all RXR isotypes (RAR or RXR, respectively). The untranslated exon and the transcription start site (TSS) are depicted
by an open box and a broken arrow, respectively. The locations of primers used are indicated at −11 kb and in the RAR-binding region (RARE). Mean fold
enrichment of three experiments at RARE binding site (grey bars) is relative to the amount of DNA recovered at −11 kb (set at 1, white bars). Error bars
represent s.e.m. (n = 4 to 5); * p < 0.05. (D) EMSA showing that RARG/RXRA heterodimers (Het) bind to the 32P-labelled IR1 of Sall4 (lane 4). Binding is
competed when increasing amounts of unlabeled IR1 are added to reaction (lanes 5–7), but not when a mutated form IR1 is added (IR1m, lanes 8–10). 32P-IR1 probe indicates unbound DNA. (E) EMSA showing that RARG/RXRA heterodimers (Het) bound to the DR5 of Rarb (lane 3) are competed both when
unlabeled DR5 (lane 4) or increasing amounts of IR1 (lanes 5–7) are added to reaction. 32P-DR5 probe indicates unbound DNA. doi:10.1371/journal.pgen.1005501.g007 doi:10.1371/journal.pgen.1005501.g007 Retinoid-Induced Male Germ Cell Differentiation Fig 7. RARG/RXRA heterodimers bind to Sall4 in testis chromatin, on an IR1 motif located in the first intron. (A) UCSC Genome Browser snapshot of
the Sall4 locus in NCBI37/mm9 assembly, including tracks for anti-RAR ChIP-seq [34], RefSeq genes and mammalian conservation (from top to bottom). RARE points to the RAR-binding region identified according to Moutier et al. [34]. (B) Alignments of the DNA sequences from the indicated species and
corresponding to the region containing the RAR-binding region in mouse Sall4. The dotted arrows indicate orientations of the core motifs. Stars and grey
boxes highlight the DNA residues and the RAR binding sequences that are conserved in all 6 species, respectively. (C) Left panel: relative expression of
Sall4a mRNA quantified by RT-qPCR in whole testes from control (white bars) and Rarg−/−(grey bars) mice at PN5. Error bars represent s.e.m. (n = 9); *
p < 0.05. Right panel: schematic representation of Sall4 locus and analysis of DNA recovered from testis chromatin immunoprecipitated using antibodies
directed against RNApol2, all RAR or all RXR isotypes (RAR or RXR, respectively). The untranslated exon and the transcription start site (TSS) are depicted
by an open box and a broken arrow, respectively. The locations of primers used are indicated at −11 kb and in the RAR-binding region (RARE). Mean fold
enrichment of three experiments at RARE binding site (grey bars) is relative to the amount of DNA recovered at −11 kb (set at 1, white bars). Error bars
represent s.e.m. (n = 4 to 5); * p < 0.05. (D) EMSA showing that RARG/RXRA heterodimers (Het) bind to the 32P-labelled IR1 of Sall4 (lane 4). Binding is
competed when increasing amounts of unlabeled IR1 are added to reaction (lanes 5–7), but not when a mutated form IR1 is added (IR1m, lanes 8–10). 32P-IR1 probe indicates unbound DNA. (E) EMSA showing that RARG/RXRA heterodimers (Het) bound to the DR5 of Rarb (lane 3) are competed both when
unlabeled DR5 (lane 4) or increasing amounts of IR1 (lanes 5–7) are added to reaction. 32P-DR5 probe indicates unbound DNA. Fig 7. RARG/RXRA heterodimers bind to Sall4 in testis chromatin, on an IR1 motif located in the first Fig 7. RARG/RXRA heterodimers bind to Sall4 in testis chromatin, on an IR1 motif located in the first intron. They revealed that RARG isotype in combination with RXRA isotype (lane
4), but neither RARG nor RXRA alone (lanes 2 and 3, respectively), bound the radiolabelled
IR1 sequence. Binding was competed by increasing amounts of unlabeled IR1 (lanes 5–7), but
not by IR1m bearing point-mutations in the first core motif (lanes 8–10). They also showed
that unlabeled IR1 efficiently competed binding of RARG/RXRA heterodimers to the radiola-
beled, canonical, RAR binding site of Rarb gene (called DR5, Fig 7E). The data suggested there-
fore that RARG/RXRA heterodimers could enhance expression of SALL4A through binding to
an IR1 motif located in Sall4 intron. This motif appeared moderately well-conserved in mouse,
rat, human and primate genomes (Fig 7B), but single mismatches do not necessarily abrogate
RAR/RXR binding, even when located at highly conserved positions [33]. The DR1 and DR0
were also able to bind RARG/RXRA heterodimers (S5 Fig). Their sequences were even well-
conserved across the species than that of IR1 (Fig 7B). Thus the RAR binding region in Sall4
belongs to the category of “composite elements”, the functionality of which has already been
demonstrated [34]. Interestingly, SALL4A is also expressed in human spermatogonia [35]. Moreover, Fertilysin (N,N’-1,8-octanediylbis[2,2-dichloro-acetamide], also called WIN
18,446), which acts by inhibiting ATRA synthesis [36], reversibly inhibits spermatogenesis in
men by inducing an arrest of germ cell differentiation at the spermatogonia stage [37,38],
which resembles the phenotype we describe here in the mouse. Thus it is possible that RAR/
RXR heterodimers also drive SALL4A expression in human spermatogonia. 13 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 A model for the effects of ATRA on KIT expression A hallmark of the transition to a differentiating state in spermatogonia is the expression of KIT
receptor at the surface of A1 spermatogonia [5]. However, it is unclear what regulatory steps
control the expression of this crucial cell surface receptor. Several studies have shown that
undifferentiated spermatogonia are primed to turns on KIT and initiate differentiation upon
activation of an ATRA signal [2]. This ATRA signal acts indirectly on Kit because its mRNA is
not induced by BMS961, as assessed from our microarray expression profiling (see above) and PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 14 / 23 Retinoid-Induced Male Germ Cell Differentiation no RAR binding site is found in Kit [39]. From our present study, we propose that ATRA
enhances the level of Sall4a mRNA, allowing thereby an increase of the amount of SALL4A in
spermatogonia. In agreement with this proposal, SALL4A appears at PN3-PN4 in wild-type
spermatogonia [31,32], coinciding with the onset of endogenous ATRA signaling [40] and dif-
ferentiation of the first KIT-positive spermatogonia [41]. SALL4A in high amount could (i)
sequester ZBTB16, resulting in the release of the ZBTB16-mediated repression of Kit expres-
sion [14]; (ii) interact with DNMT3A and/or DNMT3B [42], allowing the epigenetic shift
which is instrumental to A1 transition to take place properly [43]; and (iii) act on yet unknown
other components of the differentiation program required in spermatogonia to transition to
the A1 state. In agreement with our proposal, Hobbs et al. [14] reported that the total amount of SALL4
protein detected in spermatogonia is higher at the A1 stage (i.e., in the ZBTB16-high, KIT-posi-
tive cell population) than at the Aal stage (i.e., in the ZBTB16-high, KIT-negative cell popula-
tion). It is however not possible to show by IHC that Aal spermatogonia expressing SALL4A
upon ATRA signaling activation differentiate into A1 spermatogonia and express KIT because,
contrary to what has been stated in a previous report [31], antibodies to SALL4 do not distin-
guish between SALL4A and SALL4B. As SALL4B is expressed in spermatogonia and in their
precursors from embryonic day 17.5 onwards [31,32], these antibodies are unsuitable to detect
a specific increase in the expression of the sole SALL4Aisoform. A comprehensive model summarizing the combination of transcriptional, post-transcrip-
tional and non-genomic effects of ATRA pathways possibly controlling KIT expression and
the commitment of Aal spermatogonia towards the A1 fate is proposed (Fig 8). The interest of
better understanding the control of KIT expression in spermatogonia is not restricted to game-
togenesis, but extends to testicular cancer. In fact, seminoma cells frequently bear somatic
mutations activating KIT, or overexpress KIT or SALL4 [7,44,45]. Therefore, pharmacological
modulation of mechanisms that regulate KIT expression in spermatogonia, such as antagoniz-
ing ATRA action, might have important applications for future therapeutic strategies. Isolation of germ cell populations by flow cytometry and organotypic
cultures Germ cell populations were purified from testes of Aldh1a1-3ser-/-, Rara;b;gSpg–/– and Rxra;b;
gSpg–/– mice by FACS and characterized as described previously [13,22]. Organotypic cultures
of testes from Aldh1a1-3ser-/- mice were also as described previously, except that the RARG-
selective agonist BMS961 at 10–7M (Tocris Bioscience) was used to activate RAR signaling
instead of BMS753 [13]. Retinoid-Induced Male Germ Cell Differentiation Fig 8. Proposed model for the regulation of Kit expression by ATRA during the transition from Aal to A1 spermatogonia. (A) Spermatogonia at an
undifferentiated state. ATRA is not available to activate RARG/RXRA heterodimer and transcription of Sall4 is low. Transcription of Kit is also low because
ZBTB16 is bound to its promoter [48]. In addition, translation of Kit mRNA already present in cells [2,49,50] is prevented by the Mirc1, Mirc3 and miR221/222
small interfering RNAs (brown comb) [50,51]. (B) Spermatogonia at a differentiating state upon ATRA action. (i) At the Aal-A1 transition, one possible way for
ATRA (yellow triangle) to regulate Kit expression is to activate RARG/RXRA heterodimer, which increases Sall4a expression (high, our study). (ii) SALL4A in
large amount can then sequesters ZBTB16 [14], clearing Kit promoter and relieving the repression of Kit transcription normally exerted by ZBTB16 [48]. (iii)
ATRA is also proposed to increase the level of SOHLH1, which can replace ZBTB16 on regulatory regions to increase Kit expression (high) [52]. Sohlh1 is
however not a direct target of RARG as RAR-binding sites are not found in this gene [34] and its expression is not induced by BMS961 (our study). (iv)
Alternatively, SALL4A can also interact with DNMT3A/B to facilitate the epigenetic shift required for A1 differentiation [42,43]. (v) In parallel, ATRA can further
induce KIT protein through decreasing expression of microRNA such as Mirc1, Mirc3 and miR221/222 that prevent Kit mRNA translation. How ATRA
regulate miRNA expression is however unknown, as RARE have not been identified in the vicinity of their promoters [34,50,51]. ATRA can also function as a
rapid, non-genomic, agent by (vi) increasing the loading of Kit mRNA on polysomes (grey ovals) and its translation [41] and (vii) inducing phosphorylation of
KIT (orange stars) and of downstream KIT-effectors, reinforcing commitment towards the A1 spermatogonia fate [53]. Fig 8. Proposed model for the regulation of Kit expression by ATRA during the transition from Aal to A1 spermatogonia. (A) Spermatogonia at an
undifferentiated state. ATRA is not available to activate RARG/RXRA heterodimer and transcription of Sall4 is low. Transcription of Kit is also low because
ZBTB16 is bound to its promoter [48]. In addition, translation of Kit mRNA already present in cells [2,49,50] is prevented by the Mirc1, Mirc3 and miR221/222
small interfering RNAs (brown comb) [50,51]. (B) Spermatogonia at a differentiating state upon ATRA action. (i) At the Aal-A1 transition, one possible way for
ATRA (yellow triangle) to regulate Kit expression is to activate RARG/RXRA heterodimer, which increases Sall4a expression (high, our study). (ii) SALL4A in
large amount can then sequesters ZBTB16 [14], clearing Kit promoter and relieving the repression of Kit transcription normally exerted by ZBTB16 [48]. (iii)
ATRA is also proposed to increase the level of SOHLH1, which can replace ZBTB16 on regulatory regions to increase Kit expression (high) [52]. Sohlh1 is
however not a direct target of RARG as RAR-binding sites are not found in this gene [34] and its expression is not induced by BMS961 (our study). (iv)
Alternatively, SALL4A can also interact with DNMT3A/B to facilitate the epigenetic shift required for A1 differentiation [42,43]. (v) In parallel, ATRA can further
induce KIT protein through decreasing expression of microRNA such as Mirc1, Mirc3 and miR221/222 that prevent Kit mRNA translation. How ATRA
regulate miRNA expression is however unknown, as RARE have not been identified in the vicinity of their promoters [34,50,51]. ATRA can also function as a
rapid, non-genomic, agent by (vi) increasing the loading of Kit mRNA on polysomes (grey ovals) and its translation [41] and (vii) inducing phosphorylation of
KIT (orange stars) and of downstream KIT-effectors, reinforcing commitment towards the A1 spermatogonia fate [53]. doi:10.1371/journal.pgen.1005501.g008 Mice and treatments Mice were on a mixed C57BL/6-129/Sv (50–50%) genetic background. They were housed in a
licensed animal facility (agreement #A67-218-37). All experiments were approved by the local
ethical committee (Com’Eth, accreditations #2012–080 and #2012–081), and were supervised
by N.B.G. or M.M. who are qualified in compliance with the European Community guidelines
for laboratory animal care and use (2010/63/UE). To inactivate Rar- or Rxr-coding genes in
spermatogonia, mice carrying loxP-flanked alleles (L2) of Rara, Rarb and Rarg or of Rxra, Rxrb
and Rxrg [12, and references therein] were crossed with mice bearing the Tg(Stra8-cre)1Reb
transgene [16]. In F1, RxraL2/L2;RxrbL2/L2;RxrgL2/L2 females were crossed with males bearing
one copy of the transgene (Stra8tg/0). The resulting males (Stra8-Cretg/0;Rxra+/L2;Rxrb+/L2;Rxrg-
+/L2) were backcrossed on RxraL2/L2;RxrbL2/L2;RxrgL2/L2 females to generate mutant males in F2
(Stra8-Cretg/0;RxraL2/L2;RxrbL2/L2;RargL2/L2), and their control littermates (Rxra+/L2;Rxrb+/L2;
Rxrg+/L2 and RxraL2/L2;RxrbL2/L2;RxrgL2/L2 males). The same approach was used to inactivate
Rara, Rarb and Rarg in spermatogonia. Aldh1a1-3ser-/- mutants were generated as described
previously [13]. Mice lacking RARA in Sertoli cells in a RARG-null genetic background were
obtained by crossing RaraSer–/–[12] and Rarg–/– mice [9] together. BMS961 (50 mg/kg body
weight, Tocris Bioscience) dissolved in dimethylsulfoxide was administered to the mice by
intra peritoneal injections. BrdU (Sigma-Aldrich) was dissolved in phosphate buffered saline
and injected by intra peritoneal at 50 mg/kg body weight. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 15 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation rabbit anti-STRA8 (Ab49602, Abcam), rabbit anti-RARG1 (D3A4 #8965, Cell Signaling Tech-
nology), goat anti-ZBTB16 (AF2944, R&D Systems) and rabbit anti-KIT (D13A2 #3074, Cell
Signaling Technology) antibodies diluted 1:200 to 1:500. Detection of bound primary antibod-
ies was achieved by incubating the section with Cy3-conjugated goat anti-rabbit IgG (Jackson
ImmunoResearch) or Alexa Fluor 488-conjugated donkey anti-goat IgG (Life Technologies). ISH using digoxigenin-labeled probes for detection of Gfra1, Kit, Stra8 and Zbtb16 expression
was performed as described [9,10,20]. The sections were all counterstained with 0.001% (vol/
vol) 4,6-diamidino-2-phenylindole dihydrochloride (DAPI) and mounted in Vectashield (Vec-
tor Laboratories). The pattern of Cre expression driven by Tg(Stra8-cre)1Reb [16] was assessed
through testing excision in mice carrying the Gt(ROSA)26Sortm1Sor reporter transgene [46]. In
these mice, E. coli beta-galactosidase is synthesized only in cells that have experienced Cre-
mediated deletion of an intervening stop sequence. Analysis of beta-galactosidase activity was
as described [10]. these mice, E. coli beta-galactosidase is synthesized only in cells that have experienced Cre-
mediated deletion of an intervening stop sequence. Analysis of beta-galactosidase activity was
as described [10]. Histology, detection of apoptotic and proliferating cells,
immunohistochemistry (IHC) and in situ hybridization (ISH) For histology, testis samples were fixed in Bouin’s fluid for 16 hours and embedded in paraffin. Histological sections (5 μm-thick) were stained with hematoxylin and eosin or with periodic
acid-Shiff (PAS). The percentage of affected seminiferous tubules was established on PAS-
stained histological sections by counting cross-sections of tubules (n > 400 per testis). For all
other methods, testes were fixed for 16 hours in 4% (wt/vol) buffered paraformaldehyde (PFA). For detection of apoptotic cells, TUNEL assays were performed using the In Situ Cell-Death
Detection kit, Fluorescein (Roche Diagnostics). BrdU incorporation was detected by using an
anti-BrdU antibody (Roche Molecular Biochemicals) and immunofluorescence labeling as
described [9]. For IHC, 10 μm-thick frozen sections were incubated overnight at 4°C with PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 16 / 23 Gene names, accession numbers, forward (upper line) and reverse (lower line) primers, their positions in the sequences and sizes of the amplified
fragments are indicated. nt: nucleotide. doi:10.1371/journal.pgen.1005501.t001 Retinoid-Induced Male Germ Cell Differentiation Rplp0 or Gapdh transcripts, whose expressions are not changed by retinoid administration. Data were expressed as fold induction relative to vehicle or control conditions. To prepare
chromatin, PN5 testes were fixed with 0.4% PFA (wt/vol) for 15 minutes, before being soni-
cated to shear DNA to an average size of 500 bp. For each reaction, 100 μg of chromatin was
first incubated with 18 μg of ChIP grade anti-RAR (sc-773; Santa Cruz biotechnology), anti-
RXR (sc-774; Santa Cruz biotechnology) or anti-RNA polymerase II (RNApol2; sc-9001; Santa
Cruz biotechnology) antibodies and then with protein G-Sepharose. Beads were washed, and
eluted DNA–protein complexes were reverse cross-linked and purified. ChIP was performed in
triplicate, using distinct chromatin extracts. The recovered immuno-precipitated DNA was
analyzed by triplicate qPCR and was compared with input DNA. Quantitation was determined
by the enrichment of the binding site compared with a site located upstream the TSS (–11kb),
and were expressed as mean fold-enrichment (n = 3). The sequences of the oligonucleotides
used are indicated in Table 2. Statistical significance was assessed by Student t tests or by one-
way ANOVA followed by the post hoc Newman-Keuls test for comparison by pairs. Analysis of RNA and chromatin Total RNA was prepared using TRIzol reagent (Life Technologies). Reverse transcription of
total RNA followed by PCR amplification of cDNA was performed using QuantiTect Reverse
Transcription (Qiagen) and LightCycler 480 SYBR Green I Master (Roche Diagnostics) kits,
respectively. Primers were as indicated in Table 1. Triplicates of at least three samples were
used in each experimental condition. The transcript levels were normalized relative to that of Table 1. Primers used in quantitative RT-PCR. Gene
Accession no. Primers
Position (nt)
Size (nt)
Gapdh
NM_001289726.1
5’-AAGGTCATCCATGACAACTT-3’
570–657
88
5’-GGCCATCCACAGTCTTCTGG-3’
Rara
NM_001177
5’-AGCACCAGCTTCCAGTCAGT-3’
569–733
165
5’-AGTGGTAGCCGGATGATTTG-3’
Rarb
NM_011243
5’-GCTGGGTCGTCGTTTTCTAA-3’
1167–1282
135
5’-GAAACAGGCCTTCTCAGTGC-3’
Rarg
NM_011244.4
5’-CTCGGGTCTATAAGCCATGC-3’
746–805
60
5’-CCCCATAGTGGTAGCCAGAA-3’
Rplp0
NM_007475
5’-ACCCTGAAGTGCTCGACATC-3’
720–908
208
5’-AGGAAGGCCTTGACCTTTTC-3’
Rxra
NM_001290481.1
5’-GATATCAAGCCGCCACTAGG-3’
384–534
151
5’-TTGCAGCCCTCACAACTGTA-3’
Rxrb
NM_001205
5’-GGGCTGCAAGGGTTTCTTCA-3’
186–348
163
5’-CTCCTGAACCGCCTCCCTTT-3’
Rxrg
NM_009107
5’-TGTGGTCAACAGTGTCAGCA-3’
6–190
185
5’-AGAAGCCTTTGCAACCTTCA-3’
Sall4a
NM_175303.4
5’-AGTGTCACCTGCCAATAGCC-3’
2560–2726
167
5’-TGCCAGGCACTTCAACTTT-3’
Sall4b
NM_201395.3
5’-CTCGACCAGTCCAAGAAAGG-3’
1232–1394
163
5’-TGCCAGGCACTTCAACTTT-3’
Zbtb16
NM_001033324.2
5’-AACGGTTCCTGGACAGTTTG-3’
1563–1734
172
5’-CCACACAGCAGACAGAAGA-3’
Gene names, accession numbers, forward (upper line) and reverse (lower line) primers, their positions in the sequences and sizes of the amplified
fragments are indicated. nt: nucleotide. Table 1. Primers used in quantitative RT-PCR. Table 1. Primers used in quantitative RT-PCR. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 17 / 23 Gene, forward (upper line) and reverse (lower line) primers and their use are indicated. IR0, inverted repeats separated by 0 nucleotide; DR0, DR1, DR2,
DR4 and DR5, direct repeats separated by 0, 1, 2, 4 and 5 nucleotides, respectively. doi:10.1371/journal.pgen.1005501.t002 Supporting Information S1 Fig. The Tg(Stra8-cre)1Reb transgene allows gene ablation in spermatogonia from post-
natal day 3 (PN3) onward. The pattern of Cre-mediated gene excision was assessed through
testing DNA excision in mice also carrying the Gt(ROSA)26Sortm1Sor reporter transgene. In these
mice, E. coli beta-galactosidase is synthesized only in cells that have experienced Cre-mediated
deletion of an intervening stop sequence (Soriano, 1999). (A-C,E,F) X-Gal staining and (D)
STRA8 IHC on testis sections in mice bearing both Tg(Stra8-cre)1Reb and Gt(ROSA)26Sortm1Sor
transgenes. At PN3 (i.e., shortly after the onset of spermatogenesis), beta-galactosidase activity
(red signal) is already initiated in about 50% of the spermatogonia and in all seminiferous cord
(A,B), whereas spermatogonia expressing endogenous STRA8 are exceptional. At PN5, beta-
galactosidase-positive spermatogonia become widespread (C), and staining for STRA8 on con-
secutive sections (D) shows that its activity is initiated within a subset of spermatogonia that
outnumbers those expressing the endogenous Stra8. At PN20, beta-galactosidase activity is
observed in all spermatocytes and spermatids (E,F). These data indicate that excision of the
reporter transgene occurs in undifferentiated spermatogonia as early as PN3 and is complete in
all germ cells from PN5 onwards, in accordance with previous reports [14,16]. The Tg(Stra8--
cre)1Reb thus appears to be a suitable tool to study the role of RXR and RAR in spermatogonia. Note that (i) both the cytosolic and the juxta-nuclear, punctate (green arrowheads), beta-
galactosidase activities indicate Cre-mediated excision of LacZ; (ii) in A, B and F, the staining
resulting from beta-galactosidase activity was converted to a red false color, and the DAPI
nuclear stain was converted to a bright-field image and then to a blue false color using Photo-
shop software; (iii) a processing artifact of consecutive sections has induced a distortion mak-
ing the distances between the seminiferous cords wider in panel D than in panel C; and (iv)
X-Gal-positive cells are never detected in testes of age-matched Gt(ROSA)26Sortm1Sor mice that
do not harbor the Tg(Stra8-cre)1Reb transgene. The box in A indicates the region displayed at a
higher magnification in B. Legend: C, seminiferous cords; G spermatogonia; PR and P, prelep-
totene and pachytene spermatocytes, respectively; R, round spermatids. Scale bar: 80 μm (A
and C-F) and 25 μm (B). S2 Fig. Ablation of all RAR in spermatogonia induces age-related testis degeneration. (A-B) Section from 12 week-old control and Rara;b;gSpg–/– testes. (C-H) Germ cell associations
in the seminiferous epithelium of Rara;b;gSpg–/– mutants. Western blotting Protein extracts were prepared in 50 mM Tris-HCl (pH7.5) buffer containing 150 mM NaCl,
0.5% (wt/vol) sodium deoxycholate, 1% (vol/vol) NP40, 0.2% (vol/vol) sodium dodecyl sulfate
(SDS), and protease inhibitor mixture (Roche diagnostics). They were resolved by 4–16% (wt/
vol) gradient SDS polyacrylamide gel electrophoresis (Expedeon) and transferred to nitrocellu-
lose membranes (Protran) using standard protocols. The membranes were incubated with
anti-SALL4 antibodies (Ab29112; Abcam) diluted 1:500 and IgG were detected using goat anti-
mouse coupled to horseradish peroxidase as secondary antibodies (diluted 1:5000) followed by
chemiluminescence according to the manufacturer’s protocol (GE Healthcare). The blots were
subsequently incubated 2 times for 10 minutes at room temperature in 0.2M glycine pH 2.2
containing 0.1% (wt/vol) SDS and 0.1% (wt/vol) Tween 20, and were further probed with anti-
actin antibodies (sc-58673; Santa Cruz biotechnology) diluted 1:500 to verify for equivalent
loading in all the lanes. Retinoid-Induced Male Germ Cell Differentiation Electrophoretic mobility shift assays They were performed as described previously [47]. Briefly, the oligonucleotides were annealed
and labeled with [γ-32P]ATP (Amersham Bioscience). For competition assays, unlabeled oli-
gonucleotides were added in the incubation mixture in 1- to 1000-fold molar excess. The
sequences of the oligonucleotides used are described in Table 2. Table 2. Primers used for ChIP and EMSA assays. Gene
Primer
Assay
IR1
5’-ATGAGGTAGAAGGTCACTGAACTTTGATAAACTCG-3’
EMSA
5’-CGAGTTTATCAAAGTTCAGTGACCTTCTACCTCAT-3’
mutated IR1
5’-ATGAGGTAGAAAGGCGCTGAACTTTGATAAACTCG-3’
EMSA
5’-CGAGTTTATCAAAGTTCAGCGCCTTTCTACCTCAT-3’
DR0
5’-GCAGGCGGGCTGAGGGTTAACCCTTTTGTT-3’
EMSA
5’-AACAAAAGGGTTAACCCTCAGCCCGCCTGC-3’
DR1
5’-CATCGCAGGACCAGGGGAGGGGTCAGGGCC-3’
EMSA
5’-GGCCCTGACCCCTCCCCTGGTCCTGCGATG-3’
Rarb DR5
5’-CGGGTAGGGTTCACCGAAAGTTCACTCGCA-3’
EMSA
5’-TGCGAGTGAACTTTCGGTGAACCCTACCCG-3’
Sall4
5’-AGCAATGACCTTCCAGTTGC-3’
ChIP
5’-TGGGATCCTACTTTTCCCAAA-3’
Sall4 –11kb
5’-TTGATCGGACAGCTTTTGTG-3’
ChIP
5’-GGGACTGGAGGGAGAAAAAG-3’
Stra8 –3kb
5’-GGCAGCAGGCCACCAATAAA-3’
ChIP
5’-TAGGCTTGGTTCCCCGTGTG-3’
Stra8 DR2
5’-AGGTCATCTTGCTCCTTCCA-3’
ChIP
5’-ATCACAGCCCTGTCACTGC-3’
Stra8 DR4
5’-GTGAGGTAGATCCCGGATTG-3’
ChIP
5’-GACCTGAGGTGAGCTGCTTC-3’
Gene, forward (upper line) and reverse (lower line) primers and their use are indicated. IR0, inverted repeats separated by 0 nucleotide; DR0, DR1, DR2,
DR4 and DR5, direct repeats separated by 0, 1, 2, 4 and 5 nucleotides, respectively. d i 10 1371/j
l
1005501 t002 Table 2. Primers used for ChIP and EMSA assays. doi:10.1371/journal.pgen.1005501.t002 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 18 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation H), preleptotene spermatocytes (E,G) and round spermatids (F,H). (I,J) Section from
12 month-old control and Rara;b;gSpg–/– testes: seminiferous tubules containing only spermato-
gonia and Sertoli cells represent the end-stage of degeneration in the mutant testes (J). PR and
P, preleptotene and pachytene spermatocytes, respectively; St7 and St16, step 7 and 16 sperma-
tids, respectively; T2, tubules sections lacking generation(s) of germ cells around their entire
circumference; T3, tubules sections with complete disorganization of the germ cell layer; T4,
tubules sections containing only spermatogonia and Sertoli cells. Germ cell populations present
in a given tubule cross-section are highlighted by colored bars: red, preleptotene spermatocytes;
green, pachytene spermatocytes; blue, step 7 (round) spermatids; purple, step 16 (elongated,
mature) spermatids. Roman numerals indicate the stages of the seminiferous epithelium cycle. Periodic acid-Schiff (A-H) and hematoxylin and eosin (I-J) stains. Scale bar, 80 μm (A-B and
I-J) and 30 μm (C-H). (
) H), preleptotene spermatocytes (E,G) and round spermatids (F,H). (I,J) Section from
12 month-old control and Rara;b;gSpg–/– testes: seminiferous tubules containing only spermato-
gonia and Sertoli cells represent the end-stage of degeneration in the mutant testes (J). PR and
P, preleptotene and pachytene spermatocytes, respectively; St7 and St16, step 7 and 16 sperma-
tids, respectively; T2, tubules sections lacking generation(s) of germ cells around their entire
circumference; T3, tubules sections with complete disorganization of the germ cell layer; T4,
tubules sections containing only spermatogonia and Sertoli cells. Germ cell populations present
in a given tubule cross-section are highlighted by colored bars: red, preleptotene spermatocytes;
green, pachytene spermatocytes; blue, step 7 (round) spermatids; purple, step 16 (elongated,
mature) spermatids. Roman numerals indicate the stages of the seminiferous epithelium cycle. Periodic acid-Schiff (A-H) and hematoxylin and eosin (I-J) stains. Scale bar, 80 μm (A-B and
I-J) and 30 μm (C-H). (
) S3 Fig. Ablation of Rar and Rxr genes in spermatogonia with Tg(Stra8-cre)1Reb transgene is
efficient from PN3 onward. (A) Relative expression of Rarg and Rxra mRNA quantified by
RT-qPCR in whole testes from control (white bars), Rara;b;gSpg−/−(grey bars) and Rxra;b;gSpg
−/−(black bars) mice at PN5 (upper panel) and PN60 (lower panel). Error bars represent s.e.m. (n = 5); p < 0.05. (B) PCR analysis of genomic DNA extracted from FACS-purified germ cells
in heterozygote control mice (left panel) and Rara;b;gSpg−/−mutant mice (right panel) at PN60. Supporting Information Normal gem cell associations at epi-
thelial stage VII (C) coexist with abnormal associations lacking: pachytene spermatocytes (D, 19 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 References 1. de Rooij DG. Proliferation and differentiation of spermatogonial stem cells. Reproduction 2001;
121:347–354. PMID: 11226060 1. de Rooij DG. Proliferation and differentiation of spermatogonial stem cells. Reproduction 2001;
121:347–354. PMID: 11226060 2. Schrans-Stassen BH, van de Kant HJ, de Rooij DG, van Pelt AM. Differential expression of c-kit in
mouse undifferentiated and differentiating type A spermatogonia. Endocrinology 1999; 140:5894–
5900. PMID: 10579355 2. Schrans-Stassen BH, van de Kant HJ, de Rooij DG, van Pelt AM. Differential expression of c-kit in
mouse undifferentiated and differentiating type A spermatogonia. Endocrinology 1999; 140:5894–
5900. PMID: 10579355 3. Suzuki H, Sada A, Yoshida S, Saga Y. The heterogeneity of spermatogonia is revealed by their topol-
ogy and expression of marker proteins including the germ cell-specific proteins Nanos2 and Nanos3. Dev Biol. 2009; 336:222–231. doi: 10.1016/j.ydbio.2009.10.002 PMID: 19818747 4. de Rooij DG. Stem cells in the testis. Int J Exp Pathol. 1998; 79:67–80. PMID: 9709376 5. van Pelt AM, de Rooij DG. Retinoic acid is able to reinitiate spermatogenesis in vitamin A-deficient rats
and high replicate doses support the full development of spermatogenic cells. Endocrinology. 1991;
128:697–704. PMID: 1989855 6. de Rooij DG, Russell LD. All you wanted to know about spermatogonia but were afraid to ask. J Androl. 2000; 21:776–798. PMID: 11105904 7. Rossi P. Transcriptional control of KIT gene expression during germ cell development. Int J Dev Biol. 2013; 57:179–184. doi: 10.1387/ijdb.130014pr PMID: 23784828 8. Chambon P. The nuclear receptor superfamily: a personal retrospect on the first two decades. Mol
Endocrinol. 2005; 19:1418–1428. PMID: 15914711 9. Gely-Pernot A, Raverdeau M, Célébi C, Dennefeld C, Feret B, Klopfenstein M, et al. Spermatogonia dif-
ferentiation requires retinoic acid receptor γ. Endocrinology 2012; 153:438–449. doi: 10.1210/en.2011-
1102 PMID: 22045663 10. Vernet N, Dennefeld C, Rochette-Egly C, Oulad-Abdelghani M, Chambon P, Ghyselinck NB, et al. Reti-
noic acid metabolism and signaling pathways in the adult and developing mouse testis. Endocrinology
2006; 147:96–110. PMID: 16210368 11. Gaemers IC, van Pelt AM, van der Saag PT, Hoogerbrugge JW, Themmen AP, de Rooij DG. Differen-
tial expression pattern of retinoid X receptors in adult murine testicular cells implies varying roles for
these receptors in spermatogenesis. Biol Reprod. 1998; 58:1351–1356. PMID: 9623592 12. Vernet N, Dennefeld C, Guillou F, Chambon P, Ghyselinck NB, Mark M. Prepubertal testis development
relies on retinoic acid but not rexinoid receptors in Sertoli cells. EMBO J. 2006; 25:5816–5825. PMID:
17124491 13. Acknowledgments We thank common services and platforms of IGBMC, and Cathie ERB for helpful advices on
EMSA. Author Contributions Conceived and designed the experiments: AGP MR MT NV MM NBG. Performed the experi-
ments: AGP MR MT BF MK CD MM NBG. Analyzed the data: AGP MR BF MK CD MM
NBG. Contributed reagents/materials/analysis tools: ID GB. Wrote the paper: AGP NV MM
NBG. Retinoid-Induced Male Germ Cell Differentiation (lanes 6–8), DR0 (lanes 9–11) and IR1 (lanes 12–14) are added to reaction. 32P-DR5 probe
indicates unbound DNA. (TIF) (lanes 6–8), DR0 (lanes 9–11) and IR1 (lanes 12–14) are added to reaction. 32P-DR5 probe
indicates unbound DNA. (TIF) PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 This experiment proves efficient excision of the Rara, Rarb and Rarg alleles in all germ cells
populations isolated from the mutant testes, as assessed by the absence of Rara L2 alleles and
the trace amounts of Rarb or Rarg L2 alleles, which might be attributed to a low, contaminat-
ing, number of somatic cells. SG, PR, Z/P, P and RS, purified germ cell populations containing
spermatogonia, preleptotene/leptotene spermatocytes, zygotene/early pachytene spermato-
cytes, late pachytene/diplotene spermatocytes and round spermatids, respectively. L2 and L–,
conditional (loxP-flanked) and null (excised) alleles, respectively. CTL– and CTL+, negative
(no DNA added) and positive (L2/L2 or L–/L–DNA added) control PCR reactions, respec-
tively. (C-F) Immunohistochemical detection of spermatogonia expressing RARG (red nuclear
signal) in control and Rara;b;gSpg–/– testes at PN5 and PN60. ZBTB16 expression (green nuclear
signal) identifies spermatogonia. Spermatogonia nuclei co-expressing RARG and ZBTB16
appear in yellow. VII, stage VII of the seminiferous epithelium cycle; SG, spermatogonia. PR,
preleptotene spermatocytes; asterisks indicate non-specific fluorescence in Leydig cells. Scale
bars: 55 μm (C and D) and 40 μm (E and F). S4 Fig. Both RAR and RXR are bound to Stra8 promoter in mouse testis. Schematic repre-
sentation of Stra8 locus and analysis by qPCR of DNA recovered from PN5 wild-type testis
chromatin immunoprecipitated using antibodies directed against RNApol2, all RAR isotypes
(RAR) or all RXR isotypes (RXR) at the Stra8 locus. The untranslated exons and the two tran-
scription start sites (TSS1 and TSS2) are depicted by open boxes and broken arrows, respec-
tively. The locations of primers used for qPCR are indicated at −3 kb and in Stra8. Mean fold
enrichment of three experiments at DR4 (grey bars) and DR2 (black bars) binding sites is rela-
tive to the amount of DNA recovered at −3 kb (set at 1, white bars). Error bars represent s.e.m
(n = 5); p < 0.05. (TIF) S5 Fig. RARG/RXRA heterodimers bind to the DR1, DR0 and IR1 motifs of Sall4 RAR-
binding region. EMSA showing that RARG/RXRA heterodimers (Het) bound to the DR5 of
Rarb (lane 3) are competed both when unlabeled DR5 (lane 5) or increasing amounts of DR1 20 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation 15. Mark M, Ghyselinck NB, Chambon P. Function of retinoid nuclear receptors: lessons from genetic and
pharmacological dissections of the retinoic acid signaling pathway during mouse embryogenesis. Annu
Rev Pharmacol Toxicol. 2006; 46:451–480. PMID: 16402912 16. Sadate-Ngatchou PI, Payne CJ, Dearth AT, Braun RE. Cre recombinase activity specific to postnatal,
premeiotic male germ cells in transgenic mice. Genesis 2008; 46:738–742. doi: 10.1002/dvg.20437
PMID: 18850594 17. Russell LD, Ettlin RA, SinhaHikim AP, Clegg ED. Histological and histopathological evaluation of the
testis. Clearwater, FL: Cache River Press, 1990. 18. Naughton CK, Jain S, Strickland AM, Gupta A, Milbrandt J. Glial cell-line derived neurotrophic factor-
mediated RET signaling regulates spermatogonial stem cell fate. Biol Reprod. 2006; 74:314–321. PMID: 16237148 19. Mark M, Jacobs H, Oulad-Abdelghani M, Dennefeld C, Féret B, Vernet N, et al. STRA8-deficient sper-
matocytes initiate, but fail to complete, meiosis and undergo premature chromosome condensation. J
Cell Sci. 2008; 121:3233–3242. doi: 10.1242/jcs.035071 PMID: 18799790 20. Ghyselinck NB, Vernet N, Dennefeld C, Giese N, Nau H, Chambon P, et al. Retinoids and spermato-
genesis: lessons from mutant mice lacking the plasma retinol binding protein. Dev Dyn. 2006;
235:1608–1622. PMID: 16586441 21. Hogarth CA, Griswold MD. The key role of vitamin A in spermatogenesis. J Clin Invest. 2010;
120:956–962. doi: 10.1172/JCI41303 PMID: 20364093 22. Getun IV, Torres B, Bois PR. Flow cytometry purification of mouse meiotic cells. J Vis Exp. 2011; 50:
e2602. 23. Griswold MD, Hogarth CA, Bowles J, Koopman P. Initiating meiosis: the case for retinoic acid. Biol
Reprod. 2012; 86:35. doi: 10.1095/biolreprod.111.096610 PMID: 22075477 24. Kumar S, Chatzi C, Brade T, Cunningham TJ, Zhao X, Duester G. Sex-specific timing of meiotic initia-
tion is regulated by Cyp26b1 independent of retinoic acid signalling. Nat Commun. 2011; 2:151. PMID:
21224842 25. Anderson EL, Baltus AE, Roepers-Gajadien HL, Hassold TJ, de Rooij DG, van Pelt AM, Page DC. Stra8 and its inducer, retinoic acid, regulate meiotic initiation in both spermatogenesis and oogenesis in
mice. Proc Natl Acad Sci USA 2008; 105:14976–14980. doi: 10.1073/pnas.0807297105 PMID:
18799751 26. Endo T, Romer KA, Anderson EL, Baltus AE, de Rooij DG, Page DC. Periodic retinoic acid-STRA8 sig-
naling intersects with periodic germ-cell competencies to regulate spermatogenesis. Proc Natl Acad
Sci USA 2015; 112:E2347–E2356. doi: 10.1073/pnas.1505683112 PMID: 25902548 27. Rao S, Zhen S, Roumiantsev S, McDonald LT, Yuan GC, Orkin SH. Differential roles of Sall4 isoforms
in embryonic stem cell pluripotency. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 References Raverdeau M, Gely-Pernot A, Féret B, Dennefeld C, Benoit G, Davidson I, et al. Retinoic acid induces
Sertoli cell paracrine signals for spermatogonia differentiation but cell autonomously drives spermato-
cyte meiosis. Proc Natl Acad Sci USA 2012; 109:16582–16587. doi: 10.1073/pnas.1214936109 PMID:
23012458 14. Hobbs RM, Fagoonee S, Papa A, Webster K, Altruda F, Nishinakamura R, et al. Functional antagonism
between Sall4 and Plzf defines germline progenitors. Cell Stem Cell 2012; 10:284–298. doi: 10.1016/j. stem.2012.02.004 PMID: 22385656 21 / 23 PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Retinoid-Induced Male Germ Cell Differentiation restriction to premeiotic germ cells. Cells Tissues Organs 2012; 196:206–220. doi: 10.1159/
000335031 PMID: 22572102 restriction to premeiotic germ cells. Cells Tissues Organs 2012; 196:206–220. doi: 10.1159/
000335031 PMID: 22572102 36. Paik J, Haenisch M, Muller CH, Goldstein AS, Arnold S, Isoherranen N, et al. Inhibition of retinoic acid
biosynthesis by the bisdichloroacetyldiamine WIN 18,446 markedly suppresses spermatogenesis and
alters retinoid metabolism in mice. J Biol Chem 2014; 289:15104–15117. doi: 10.1074/jbc.M113. 540211 PMID: 24711451 37. Heller CG, Moore DJ, Paulsen CA. Suppression of spermatogenesis and chronic toxicity in men by a
new series of bis(dichloroacetyl) diamines. Toxicol Appl Pharmacol. 1961; 3:1–11. PMID: 13713106 38. Heller CG, Flageolle BY, Matson LJ. Histopathology of the human testes as affected by bis(dichloroa-
cetyl)diamines. Exp Mol Pathol Suppl. 1963; 2:107–114. PMID: 14089658 39. Hayashi S, Kunisada T, Ogawa M, Nishikawa S. Identification of the control regions for mouse c-kit
gene transcription induced by retinoic acid. DNA Res. 1995; 2:211–218. PMID: 8770562 40. Snyder EM, Small C, Griswold MD. Retinoic acid availability drives the asynchronous initiation of sper-
matogonial differentiation in the mouse. Biol Reprod. 2010; 83:783–790. doi: 10.1095/biolreprod.110. 085811 PMID: 20650878 41. Busada JT, Chappell VA, Niedenberger BA, Kaye EP, Keiper BD, Hogarth CA, et al. Retinoic acid regu-
lates Kit translation during spermatogonial differentiation in the mouse. Dev Biol. 2015; 397:140–149. doi: 10.1016/j.ydbio.2014.10.020 PMID: 25446031 42. Yang J, Corsello TR, Ma Y. Stem cell gene SALL4 suppresses transcription through recruitment of
DNA methyltransferases. J Biol Chem. 2012; 287:1996–2005. doi: 10.1074/jbc.M111.308734 PMID:
22128185 43. Shirakawa T, Yaman-Deveci R, Tomizawa S, Kamizato Y, Nakajima K, Sone H, et al. An epigenetic
switch is crucial for spermatogonia to exit the undifferentiated state toward a Kit-positive identity. Devel-
opment 2013; 140:3565–3576. doi: 10.1242/dev.094045 PMID: 23903187 44. Coffey J, Linger R, Pugh J, Dudakia D, Sokal M, Easton DF, et al. Somatic KIT mutations occur pre-
dominantly in seminoma germ cell tumors and are not predictive of bilateral disease: report of 220
tumors and review of literature. Genes Chromosomes Cancer 2008; 47:34–42. PMID: 17943970 45. Cao D, Li J, Guo CC, Allan RW, Humphrey PA. SALL4 is a novel diagnostic marker for testicular germ
cell tumors. Am J Surg Pathol. 2009; 33:1065–1077. doi: 10.1097/PAS.0b013e3181a13eef PMID:
19390421 46. Soriano P. Generalized lacZ expression with the ROSA26 Cre reporter strain. Nat Genet. 1999;
21:70–71. PMID: 9916792 47. Hwang JJ, Chambon P, Davidson I. PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 Mol Cell Biol. 2010; 30:5364–5380. doi: 10.1128/MCB.00419-10
PMID: 20837710 28. Elling U, Klasen C, Eisenberger T, Anlag K, Treier M. Murine inner cell mass-derived lineages depend
on Sall4 function. Proc Natl Acad Sci USA 2006; 103:16319–21634. PMID: 17060609 29. Sakaki-Yumoto M, Kobayashi C, Sato A, Fujimura S, Matsumoto Y, Takasato M, et al. The murine
homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell prolifera-
tion, and cooperates with Sall1 in anorectal, heart, brain and kidney development. Development 2006;
133:3005–3013. PMID: 16790473 30. Shima JE, McLean DJ, McCarrey JR, Griswold MD. The murine testicular transcriptome: characterizing
gene expression in the testis during the progression of spermatogenesis. Biol Reprod. 2004;
71:319–330. PMID: 15028632 31. Gassei K, Orwig KE. SALL4 expression in gonocytes and spermatogonial clones of postnatal mouse
testes. PLoS One 2013; 8:e53976. doi: 10.1371/journal.pone.0053976 PMID: 23326552 32. Liao HF, Chen WS, Chen YH, Kao TH, Tseng YT, Lee CY, et al. DNMT3L promotes quiescence in post-
natal spermatogonial progenitor cells. Development 2014; 141:2402–2413. doi: 10.1242/dev.105130
PMID: 24850856 33. Delacroix L, Moutier E, Altobelli G, Legras S, Poch O, Choukrallah MA, et al. Cell-specific interaction of
retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. Mol
Cell Biol. 2010; 30:231–244. doi: 10.1128/MCB.00756-09 PMID: 19884340 34. Moutier E, Ye T, Choukrallah MA, Urban S, Osz J, Chatagnon A, et al. Retinoic acid receptors recog-
nize the mouse genome through binding elements with diverse spacing and topology. J Biol Chem. 2012; 287:26328–265341. doi: 10.1074/jbc.M112.361790 PMID: 22661711 35. Eildermann K, Aeckerle N, Debowski K, Godmann M, Christiansen H, Heistermann M, et al. Develop-
mental expression of the pluripotency factor sal-like protein 4 in the monkey, human and mouse testis: PLOS Genetics | DOI:10.1371/journal.pgen.1005501
October 1, 2015 22 / 23 Characterization of the transcription activation function and the
DNA binding domain of transcriptional enhancer factor-1. EMBO J. 1993; 12:2337–2348. PMID:
8389695 48. Filipponi D, Hobbs RM, Ottolenghi S, Rossi P, Jannini EA, Pandolfi PP, et al. Repression of kit expres-
sion by Plzf in germ cells. Mol Cell. Biol. 2007; 27:6770–6781. PMID: 17664282 49. Prabhu SM, Meistrich ML, McLaughlin EA, Roman SD, Warne S, Mendis S, Itman C, Loveland KL. Expression of c-Kit receptor mRNA and protein in the developing, adult and irradiated rodent testis. Reproduction. 2006; 131:489–499. PMID: 16514192 50. Yang QE, Racicot KE, Kaucher AV, Oatley MJ, Oatley JM. MicroRNAs 221 and 222 regulate the undif-
ferentiated state in mammalian male germ cells. Development 2013; 140:280–290. doi: 10.1242/dev. 087403 PMID: 23221369 51. Tong MH, Mitchell DA, McGowan SD, Evanoff R, Griswold MD. Two miRNA clusters, Mir-17-92 (Mirc1)
and Mir-106b-25 (Mirc3), are involved in the regulation of spermatogonial differentiation in mice. Biol
Reprod. 2012; 86:72. doi: 10.1095/biolreprod.111.096313 PMID: 22116806 52. Barrios F, Filipponi D, Campolo F, Gori M, Bramucci F, Pellegrini M, et al. SOHLH1 and SOHLH2 con-
trol Kit expression during postnatal male germ cell development. J Cell Sci. 2012; 125:1455–1464. doi:
10.1242/jcs.092593 PMID: 22328502 53. Pellegrini M, Filipponi D, Gori M, Barrios F, Lolicato F, Grimaldi P, et al. ATRA and KL promote differen-
tiation toward the meiotic program of male germ cells. Cell Cycle 2008; 7:3878–3888. PMID: 19098446 23 / 23
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The role of cities in reducing the cardiovascular impacts of environmental pollution in low- and middle-income countries
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BMC medicine
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Abstract Background: As low- and middle-income countries urbanize and industrialize, they must also cope with pollution
emitted from diverse sources. Main text: Strong and consistent evidence associates exposure to air pollution and lead with increased risk of
cardiovascular disease occurrence and death. Further, increasing evidence, mostly from high-income countries,
indicates that exposure to noise and to both high and low temperatures may also increase cardiovascular risk. There is considerably less research on the cardiovascular impacts of environmental conditions in low- and middle-
income countries (LMICs), where the levels of pollution are often higher and the types and sources of pollution
markedly different from those in higher-income settings. However, as such evidence gathers, actions to reduce
exposures to pollution in low- and middle-income countries are warranted, not least because such exposures are
very high. Cities, where pollution, populations, and other cardiovascular risk factors are most concentrated, may be
best suited to reduce the cardiovascular burden in LMICs by applying environmental standards and policies to
mitigate pollution and by implementing interventions that target the most vulnerable. The physical environment of
cities can be improved though municipal processes, including infrastructure development, energy and
transportation planning, and public health actions. Local regulations can incentivize or inhibit the polluting Main text: Strong and consistent evidence associates exposure to air pollution and lead with increased risk of
cardiovascular disease occurrence and death. Further, increasing evidence, mostly from high-income countries,
indicates that exposure to noise and to both high and low temperatures may also increase cardiovascular risk. There is considerably less research on the cardiovascular impacts of environmental conditions in low- and middle-
income countries (LMICs), where the levels of pollution are often higher and the types and sources of pollution
markedly different from those in higher-income settings. However, as such evidence gathers, actions to reduce
exposures to pollution in low- and middle-income countries are warranted, not least because such exposures are
very high. Cities, where pollution, populations, and other cardiovascular risk factors are most concentrated, may be
best suited to reduce the cardiovascular burden in LMICs by applying environmental standards and policies to
mitigate pollution and by implementing interventions that target the most vulnerable. The physical environment of
cities can be improved though municipal processes, including infrastructure development, energy and
transportation planning, and public health actions. Local regulations can incentivize or inhibit the polluting
behaviors of industries and individuals. The role of cities in reducing the
cardiovascular impacts of environmental
pollution in low- and middle-income
countries Jill Baumgartner1,2,3*, Michael Brauer4,5 and Majid Ezzati3,6,7 Abstract Environmental monitoring can be combined with public health warning
systems and publicly available exposure maps to inform residents of environmental hazards and encourage the
adoption of pollution-avoiding behaviors. Targeted individual or neighborhood interventions that identify and treat
high-risk populations (e.g., lead mitigation, portable air cleaners, and preventative medications) can also be
leveraged in the very near term. Research will play a key role in evaluating whether these approaches achieve their
intended benefits, and whether these benefits reach the most vulnerable. p
g
p
p
g
p
gy
transportation planning, and public health actions. Local regulations can incentivize or inhibit the polluting
behaviors of industries and individuals. Environmental monitoring can be combined with public health warning
systems and publicly available exposure maps to inform residents of environmental hazards and encourage the
adoption of pollution-avoiding behaviors. Targeted individual or neighborhood interventions that identify and treat
high-risk populations (e.g., lead mitigation, portable air cleaners, and preventative medications) can also be
leveraged in the very near term. Research will play a key role in evaluating whether these approaches achieve their
intended benefits, and whether these benefits reach the most vulnerable. Conclusion: Cities in LMICs can play a defining role in global health and cardiovascular disease prevention in the
next several decades, as they are well poised to develop innovative, multisectoral approaches to pollution
mitigation, while also protecting the most vulnerable. Keywords: Developing countries, Heavy metals, Household air pollution, Inequalities, Noise, Urban * Correspondence: jill.baumgartner@mcgill.ca
1Institute for Health and Social Policy, McGill University, Montreal, QC,
Canada 2Department of Epidemiology, Biostatistics, and Occupational Health, McGill
University, 1110 Pine Avenue West, Montreal, QC H3A 1A3, Canada
Full list of author information is available at the end of the article 2Department of Epidemiology, Biostatistics, and Occupational Health, McGill
University, 1110 Pine Avenue West, Montreal, QC H3A 1A3, Canada
Full list of author information is available at the end of the article 2Department of Epidemiology, Biostatistics, and Occupational Health, McGill
University, 1110 Pine Avenue West, Montreal, QC H3A 1A3, Canada
Full list of author information is available at the end of the article Baumgartner et al. BMC Medicine (2020) 18:39
https://doi.org/10.1186/s12916-020-1499-y Baumgartner et al. BMC Medicine (2020) 18:39
https://doi.org/10.1186/s12916-020-1499-y Background tanneries are a priority economic growth sector and
leather is a major export [16]. However, wastewater dis-
charged from the hundreds of local tanneries is a major
source of air and surface water contamination in the re-
gion [17], and of high exposure to heavy metals and other
chemicals among workers and local residents [18]. Often
historically overlooked in the development–environment
equation are the health and welfare impacts of pollution
[19], which can themselves impose very large economic
and social costs [20]. Conversely, economic development
and urban living brings many environmental benefits,
including increased access to clean drinking water, im-
proved sanitation, and access to clean household energy. Exposure to environmental pollutants has emerged as an
important but significantly understudied risk factor for
the development of cardiovascular diseases (CVD) [1],
which form the leading cause of death globally. Up to
90% of the estimated global CVD burden is borne by
populations in low- and middle-income countries (LMICs),
threatening public health and economic development [2]. Air pollution and lead exposures accounted for an esti-
mated 10% of all deaths and 17% of cardiovascular deaths
in 2017, as reported by the Global Burden of Disease study. Air pollution alone was responsible for 12 and 17% of all
CVD deaths in the rapidly developing countries of China
and India, respectively, along with nearly a million prema-
ture CVD deaths in these two countries alone [3]. While
the proportional CVD risks of pollution are much lower
than those of behavioral risk factors (e.g., tobacco use,
harmful use of alcohol, and unhealthy diet) [4], the popula-
tion impacts of pollution are enormous given the number
of people exposed [5]. Over 90% of the world’s population
lives in places where air pollution surpasses levels stated by
World Health Organization (WHO) guidelines [6] and
hundreds of millions of people are exposed to high levels of
lead and other heavy metals in their food and water [7]. The high prevalence of exposure suggests a large potential
for pollution mitigation to reduce CVD. Spatial patterns of environmental pollution and of the
diseases that result from it vary greatly between and
within cities, and depend on numerous factors, including
population density, land use practices, the location of
economic activities, the occupation of urban residents,
availability of transportation networks, energy sources,
sanitation, and access to healthcare services. Background It is histor-
ically well documented that the urban poor tend to have
unsafe housing and poor sanitation, particularly in
LMICs. Most recent evidence documents how the urban
poor also tend to live closer to industry and other
polluting activities, and often bear the highest burden of
pollution. Lower-income neighborhoods in Accra are
the most densely populated areas and have the highest
air pollution [21, 22], an outcome driven by higher levels
of household biomass burning, unpaved roads (and thus
exposure to dust), and more traffic than in higher-
income neighborhoods [23]. Studies from Beijing, China,
observed worse air quality in neighborhoods where resi-
dents have lower incomes and less education [24, 25],
findings that are consistent with studies in North Ameri-
can cities [26, 27]. Residents of the Kibera slums in
Nairobi, Kenya, use urban agriculture to improve their
food security, but the locally sourced soil used to grow
their food is contaminated with heavy metals, including
lead, cadmium, and arsenic from nearby industries [28]. Cities in LMICs can play a defining role in pollution
reduction and global CVD prevention in the next several
decades. Worldwide, cities contain 55% of the popula-
tion, a proportion that is expected to increase to 68% by
2050, with an estimated 83% of the global urban popula-
tion living in LMICs [8]. The health benefits of living in
urban as opposed to rural areas are well documented
[9], where urban dwellers benefit from improved access
to healthcare and other public services [10]. However,
cities also concentrate industry, traffic, and waste at
unprecedented scales, which can lead to high levels of
population exposures to contaminated soil, water, and
air [1, 11]. Further, the management and mitigation of
environmental pollution in LMICs is challenged by the
widespread diffusion of multiple pollutants from mul-
tiple sources and sectors and a lack of technology, finan-
cial resources, and protective environmental regulations. In the sections below, we summarize the evidence
associating chronic exposure to pollution and the devel-
opment of CVD, focusing on the most well-studied
pollutants, including air pollution, heavy metals, noise,
as well as ambient temperature. We identify key know-
ledge gaps and discuss the unique role of cities in mitigat-
ing exposures to pollution and reducing its CVD impacts. Background An often cited justification for these environmental
trends is that high levels of pollution are a largely inevit-
able outcome of economic development [12, 13] and
urbanization [14], with some evidence of this trend also
at lower levels of development. In Accra, Ghana, for ex-
ample, informal electronic waste recycling employs thou-
sands of residents and plays a pivotal role in the local
economy, but is also a source of high exposure to heavy
metals (i.e., lead, mercury, cadmium), flame retardants,
and other pollutants among workers as well as adults and
children living near waste sites [15]. In Dhaka, Bangladesh, © The Author(s). 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Page 2 of 11 Page 2 of 11 Page 2 of 11 Baumgartner et al. BMC Medicine (2020) 18:39 Baumgartner et al. BMC Medicine (2020) 18:39 Baumgartner et al. BMC Medicine Main text
Air pollution Air pollution is a complex mixture of particulate matter
and gases that are emitted from diverse sources, includ-
ing industry, household solid fuel stoves, motor vehicles,
and agriculture. Fine particulate matter < 2.5 μm in
diameter (PM2.5) can be deeply inhaled into the lungs, Baumgartner et al. BMC Medicine (2020) 18:39 Page 3 of 11 Page 3 of 11 Baumgartner et al. BMC Medicine and is the air pollutant with the largest population
health impacts [29]. Cities in LMICs are most impacted
by air pollution due to concentrated poverty, rapid
industrialization, a lack of environmental regulations,
and often limited enforcement of existing regulations. Urban air pollution in LMIC cities is up to 17 times
higher than in Europe and North America [30, 31], and
many residents are additionally exposed to indoor and
neighborhood air pollution from household solid fuel
burning [30, 32]. Exposure to PM2.5 from solid fuel
stoves is higher than that to outdoor PM2.5 in most
high-income countries [33], yet there is substantial overlap
between indoor (solid fuel) and urban PM2.5 exposures in
LMICs. In a systematic review, average daily exposures to
PM2.5 ranged from 40 to 186 μg/m3 among solid fuel stove
users in Latin America, sub-Saharan Africa, and Asia [33],
which overlaps considerably with the outdoor PM2.5 levels
in the world’s 500 most polluted cities (range: 27–173 μg/
m3), over 85% of which are in LMICs [30]. association was observed for wood-stove users [46]. Most recently, a multi-country cohort study observed an
increased risk of CVD hospitalizations, fatal and non-
fatal events, and CVD mortality (range of HRs: 1.04–
1.10) among users of solid fuel cookstoves [43]. These
studies are supported by studies of subclinical CVD end-
points showing higher levels of inflammatory markers,
blood pressure, and arterial stiffness in women using
solid fuel stoves and with higher PM2.5 exposures, with
larger associations in older age [42, 47–49]. Similarly,
switching from biomass to gas stoves is associated with
blood pressure reductions [50]. Nevertheless,
the limited epidemiological
evidence
from LMICs is a significant knowledge gap in under-
standing the global health benefits of mitigating air
pollution in these regions. Whether the exposure–re-
sponse functions can be generalized to LMICs remains
an area of debate [30, 51]. Main text
Air pollution The exposure–response asso-
ciations in LMICs are likely to be affected by differences
in the underlying population health profiles [30], and
may also be impacted by differences in the chemical
composition of PM2.5 from different sources [52–54] as
well as co-exposures to other CVD risk factors. Greater
evidence from large, prospective studies in LMICs could
fill this knowledge gap. Exposure to PM2.5 can induce inflammatory and oxida-
tive stress responses, which are underlying mechanisms
for CVD and other diseases [29, 34, 35]. Epidemiological
and toxicological evidence indicates that PM2.5 is causally
associated with the development of CVD [35]. Short-
term exposure to PM2.5 in both high-income countries
and LMICs is consistently associated with an increased
risk of hospital admissions and incidence of myocardial
infarction and stroke [29, 36, 37]. Additionally, al-
though evidence is mostly from high-income countries,
long-term exposure to PM2.5 over years can increase
CVD risk by an even larger magnitude [29, 35]. Even in
low PM2.5 settings (yearly averages < 9 μg/m3), increases
in PM2.5 are associated with progression in coronary
calcification [38], increased risk of ischemic heart dis-
ease [39, 40], and CVD mortality [40], indicating that
any level of exposure can increase CVD risk. Lead, cadmium, and arsenic BMC Medicine (2020) 18:39 Baumgartner et al. BMC Medicine [67, 68], and lead was associated with a reduced heart
rate variability and with abnormalities of cardiac structure
and function in adults with low exposures in Europe,
Korea, and the US [64]. Based on this evidence, lead
accounted for an estimated 998,000 cardiovascular deaths
in 2017, mostly due to cerebrovascular disease and ische-
mic heart disease, as well as for 5.6% of the global CVD
burden [3]. urbanization and urban densification [84], and a growing
body of evidence links chronic exposure to noise with a
greater risk of CVD [85]. Studies from high-income coun-
tries observed associations between exposure to transpor-
tation noise (road traffic, aircrafts, railways) with increased
risk of CVD and metabolic diseases. Road traffic noise was
associated with myocardial infarction in case–control and
longitudinal studies, with the associations increasing after
excluding participants with hearing impairment [85, 86]. Experimental and panel studies have consistently observed
active positive associations between noise and subclinical
markers, including blood pressure, heart rate, and the
release of stress hormones [85, 87]. Cadmium is less researched despite millions of people
globally being chronically exposed to high levels of cad-
mium in their drinking water and food [69]. Among 12
prospective studies in high-income regions with low-to-
moderate levels of cadmium, there was supportive evidence
of an association with an increased risk of coronary heart
disease, stroke, and peripheral arterial disease [70, 71]. No
studies have been conducted in LMICs, even though blood
and urine levels of cadmium in their general populations
can be several orders of magnitude higher than in North
America and Europe [59, 72, 73]. As traffic is also a source of air pollution, which is
itself a risk factor for CVD, the question of whether the
effect of noise was confounded by air pollution was also
evaluated. A systematic review on this topic concluded
that the correlations between PM2.5 and noise were low
to moderate (range of correlations: 0.16–0.72) and that
confounding of cardiovascular effects by noise or air pol-
lution were small (< 10%) [88]. However, all reviewed
studies were conducted in high-income countries. In a
large German cohort, long-term exposure to PM2.5 and
traffic noise were both independently associated with
markers of atherosclerosis [89]. Ambient temperature A number of studies have shown associations between
increased cardiovascular mortality and both high and
low ambient temperature. A recent study of 340 cities
and metropolitan areas from 22 countries (9 of which
were classified as developing economies) estimated that
0.54% (95% CI: 0.49–0.58%) and 6.05% (95% CI: 5.59–
6.36%) of mortality in those cities were respectively at-
tributable to heat and cold [95]. Among the relatively
few studies conducted in LMICs, high and low tempera-
tures were associated with increased cardiovascular risk
in India [96], many cities across China [97, 98], and mul-
tiple countries in Latin America and sub-Saharan Africa
[99–103]. In these studies, low temperatures contributed Lead, cadmium, and arsenic Studies on the CVD impacts of cadmium [70, 71] as
well as lead [64] in LMICs are limited to a handful of
small studies with subclinical outcomes. Blood lead
levels were associated with higher blood pressure in
adults living in China [74] and Brazil [75], and among
industrial workers in Kenya [76]. Higher levels of serum
lead and cadmium were correlated with greater carotid-
intimal media thickness in a small cross-sectional study
of Turkish adults with renal disease [77]. Among those
living in a cadmium-contaminated area in Thailand, high
exposure to cadmium was associated with dyslipidemia,
oxidative stress, and chronic kidney disease [78]. There are no studies of noise and CVD in LMICs,
where the levels and sources of noise are considerably
different from those in higher-income settings [90]. The
few available exposure studies in LMICs measured
traffic-related noise and indicated relatively high levels
of exposure. Average daytime and night-time sound
levels were respectively in the range of 51–108 dB and
44–82 dB in urban areas of Ghana, Turkey, India,
Pakistan, and Nigeria [91–94]. By comparison, the WHO
Environmental Noise Guidelines recommend the main-
tenance of traffic noise levels below 53 dB and 45 dB in
the daytime and nighttime, respectively, as noise above
these levels is associated with adverse effects on sleep and
health, including CVD [84]. y
By comparison, the cardiovascular impacts of arsenic
exposure in LMICs are better researched [79–81]. Over
100 million people globally are chronically exposed to
arsenic levels above 50 μg/L, primarily though drinking
water and food crops grown in arsenic-contaminated soil
[82]. Systematic reviews identified over 10 studies from
high exposure areas in Taiwan, Bangladesh, Chile, China,
inner Mongolia, and Pakistan that consistently found
associations between high levels of arsenic in drinking
water (> 100 μg/L) and CVD mortality (pooled relative
risk: 1.32 [79]), ischemic heart disease, and peripheral ar-
terial disease [80]. Cross-sectional studies in highly
exposed populations in Taiwan and Bangladesh showed
associations between arsenic and hypertension, though
an exposure–response study of arsenic and blood pres-
sure in a lower-exposure region of Mexico did not [83]. This latter study reflects the inconsistent evidence from
high-income
countries
associating
low-to-moderate
exposures to arsenic with CVD outcomes [79–81]. Lead, cadmium, and arsenic Epidemiological and experimental evidence across a range
of exposures indicate that chronic exposure to heavy
metals and metalloids, including lead, arsenic, and cad-
mium, are associated with CVD development [1, 55, 56],
though most evidence is from high-income countries with
low-to-moderate levels of exposure. The full extent of
heavy metal exposure in LMICs is unknown due to few
countries having biomonitoring programs in place, though
evidence from individual studies indicates substantially
higher exposures than in high-income countries [57–59]. The impacts and magnitude of long-term exposure in
LMICs are less understood. A recent systematic review
identified just 17 studies of long-term exposure to
outdoor PM2.5 and cardiometabolic disease in LMICs
[41]. However, most (65%) of these studies were from
China and none were conducted in North or sub-Saharan
Africa, which represent nearly a fifth of the world’s popu-
lation. Overall, long-term exposure to PM2.5 was positively
associated with cardiovascular mortality (effect estimate
range: 0.2–6.1% per 10 μg/m3) and with CVD-related hos-
pitalizations and emergency room visits (effect estimate
range: 0.3–19.6% per 10 μg/m3) [41]. Lead was one of the first pollutants to receive global
attention following elucidation of its neuro-cognitive
effects in children [58]. Despite remarkable global de-
creases in blood lead levels following bans on leaded
gasoline in many countries [60, 61], pockets of high
exposure persist among people living near industry and
in areas with less environmental regulation [58, 62, 63]. Studies in high-income countries associate blood lead
levels with cardiovascular mortality and clinical out-
comes, including coronary heart disease, stroke, and per-
ipheral arterial disease, with associations evident at
blood lead levels as low as 5 μg/dL [1, 7, 64, 65]. For ref-
erence, an estimated 120 million people had blood lead
levels between 5 and 10 μg/dL and approximately the
same number had levels > 10 μg/dL in 2000, the majority
of whom were living in LMICs [66]. A link between lead
and higher blood pressure is reasonably well-established Several studies separately evaluated the CVD impacts
of solid fuel stove use [42–45]. In China, solid fuel stove
use was associated with a greater risk of CVD mortality
(range of hazard ratios (HRs): 1.20–1.29) [44]. In Iran,
the use of kerosene stoves was positively associated with
CVD
mortality
(HR:
1.11)
in
adults,
though
no Baumgartner et al. BMC Medicine (2020) 18:39 Page 4 of 11 Page 4 of 11 Baumgartner et al. Noise Exposure to environmental noise from transportation
and other sources (e.g., people, industry) increases with Page 5 of 11 Baumgartner et al. BMC Medicine (2020) 18:39 Page 5 of 11 to higher attributable risks of CVD and all-cause mortal-
ity than higher temperatures, supporting findings from
high-income countries [104]. In South Africa, for ex-
ample, the estimated attributable mortality was 3.0% for
low and 0.4% for high temperatures [99]. to higher attributable risks of CVD and all-cause mortal-
ity than higher temperatures, supporting findings from
high-income countries [104]. In South Africa, for ex-
ample, the estimated attributable mortality was 3.0% for
low and 0.4% for high temperatures [99]. have already demonstrated a capacity to more readily re-
spond to environmental issues in the face of global and
national-level inaction [111]. For decades, the focus on the
global response to climate change was on countries, which
have proven largely unsuccessful in producing comprehen-
sive agreements or taking action. By contrast, cities around
the world have prepared risk assessments, setting air pollu-
tion reduction targets, and pledging to act [112]. Compared with high-income settings, populations in
LMICs are more likely to live in homes and environments
that do not adequately protect against the heat or cold. The
role that housing and other urban characteristics play in
modifying the direct effects of temperature on CVD is
poorly understood, particularly for LMICs [103], but lim-
ited evidence indicates that these factors may impact vul-
nerability. Seasonal differences in blood pressure were
smaller in regions with central heating in a multi-provincial
study in China [105], and support randomized trials show-
ing that indoor heating reduces blood pressure [106, 107]. Studies in Europe found associations between excess winter
deaths from CVD and poor housing conditions, including
lack of central heating and poor insulation [108, 109]. A re-
cent evaluation of 340 cities observed that the effects of
heat on mortality were higher in cities with greater inequal-
ity, worse air quality, fewer green spaces, and lower avail-
ability of health services [95]. Cities are sources of innovation for solutions for reducing
pollution because they are most directly impacted by its
health and economic impacts. The physical environment of
cities can be improved though various municipal processes,
including urban planning, infrastructure development, en-
ergy and transportation planning, and public health. Noise In cit-
ies in Brazil and Colombia, implementation of extensive
bus rapid transit systems with features including at-level
boarding, prepayment, and articulated busses led to reduc-
tions in traffic congestion, travel time, and energy con-
sumption at a fraction of the cost of proposed alternatives,
including road and highway expansion [113–115]. Beijing
introduced rationing policies to reduce traffic congestion,
including driving restrictions (i.e., certain vehicles cannot
be used at certain times) [116] and a vehicle quota system
that restricted the number of license plates allocated to resi-
dents [117]. Congestion charging and low emission zones
are being considered by officials in Delhi and Beijing and
have been implemented in a growing number of cities, in-
cluding Milan, Stockholm, Singapore, and London, where
there is evidence of lowered traffic emissions [118] and im-
proved road safety and journey times [119]. There
is
an urgency to better understand the
temperature–CVD relationships in LMICs, and how
features of housing and other urban characteristics can mod-
ify these associations when considering the near-term oppor-
tunities for intervention. Many LMIC cities are undergoing
major growth and revitalization of their infrastructure and
physical form amidst urban densification and expansion, pro-
viding opportunities to develop new regulations and norms
for building construction and to implement well-informed
policies and government programs to upgrade existing infra-
structure and reduce vulnerability to temperature. Citywide implementation of air quality and temperature
indices combined with public health warning systems can
be cost-effectively used to inform residents of poor air
quality and weather events (e.g., high or low temperatures,
flooding, drought), and to encourage the adoption of pol-
lution- or weather-avoiding behaviors [120, 121]. While
most common in North America and Europe, major cities
in China and a growing number of cities in India have
implemented early-warning systems that notify residents
of poor air quality and alert health professionals to pre-
pare for air pollution-related hospitalizations. In 2014,
Ahmedabad, India, was the first city in South Asia to im-
plement a heatwave early warning system [122], with pre-
liminary evidence indicating lower summertime mortality
rates after its implementation and larger declines at the
highest temperatures [123]. Societal and governmental interventions Technology and infrastructure • Cleaner vehicles, e.g., lower or no emissions vehicles, investment in public transportation, reduce the sulfur content of motor fuels
• Less polluting industrial sources and transport, e.g., implementation of emissions filters and better equipment (i.e., diesel particle traps, catalytic
converters) • Cleaner vehicles, e.g., lower or no emissions vehicles, investment in public transportation, reduce the sulfur content of motor fuels • Cleaner vehicles, e.g., lower or no emissions vehicles, investment in public transportation, reduce the sulfur content of motor fuels
• Less polluting industrial sources and transport, e.g., implementation of emissions filters and better equipment (i.e., diesel particle traps, catalytic
converters) • Less polluting industrial sources and transport, e.g., implementation of emissions filters and better equipment (i.e., diesel particle traps, catalytic
converters) • More efficient energy generation – lower emission fuels or renewable sources (e.g., wind, solar) for energy generation • Increased investments in cycling and public transport infrastructure to encourage active transport Increasing the distance between populations and pollution • Zoning laws, e.g., requiring new residential areas, schools, daycares and elder care facilities to be located at certain distances from major
roadways or polluting industries • Zoning laws, e.g., requiring new residential areas, schools, daycares and elder care facilities to be located at certain distances from major
roadways or polluting industries • Shifting polluting industry away from city centers, restrict trucks from city centers
Education • Shifting polluting industry away from city centers, restrict trucks from city centers
Education • Air quality monitoring combined with public health warning systems • Air quality monitoring combined with public health warning systems • Publicity campaigns to increase public awareness and compliance alongside pollution prevention initiatives • Media campaigns to mitigate lobbying activities by industries involved in power and transport
Regulation and policy • Congestion charging schemes • Congestion charging schemes • Residential wood or coal burning bans or regulations • Emissions standards The role of cities in mitigating pollution and related CVD
burden Age-adjusted cardiovascular disease mortality rates have
generally been decreasing and are the main driver of
decline in the non-communicable disease mortality rates
in LMICs, though the pace of decline varies substantially
across countries [110]. Given the rather large (14.6%) es-
timated attributable fractions of CVD burden described
above for environmental risks, developing and applying
population-wide strategies to mitigate environmental
risks in LMIC cities, where pollution and people are most
concentrated, could help accelerate this CVD decline. Evidence-based clinical approaches can also be lever-
aged [124]. Healthcare professionals can develop a suite of
targeted community-tailored intervention packages for
their service populations. Populations with or at risk of
CVD and who live in highly polluted cities may benefit
from the targeted use of therapies known to prevent CVD
events, including antiplatelet agents, statins, and treat-
ments for hypertension and diabetes [125]. The relative Historically, environmental pollution has received less at-
tention in global and national health agendas compared
with infectious diseases like HIV/AIDS, tuberculosis, and
malaria [20]. Cities are central to pollution mitigation ef-
forts because they sit at the interface of local action and of
national and international pollution commitments like the
UN Sustainable Development Goals. Importantly, cities Baumgartner et al. BMC Medicine (2020) 18:39 Baumgartner et al. BMC Medicine (2020) 18:39 Page 6 of 11 Past experiences with pollution mitigation in high-income
countries can inform evidence-based policies and regula-
tions in LMICs (Table 1). Policies on emissions-based air
pollution control (e.g., regulations that promote cleaner ve-
hicle technologies, power generation, or industrial processes)
have been most effective [131]. Zoning laws that separate
people and pollution sources (e.g., low or no emission zones;
requiring schools, daycares, or elder care facilities to be cer-
tain distances from major roadways) are less common, but
can also be effective given the large (up to 70%) decrease in
traffic-related PM2.5 within 150 m of a freeway [132]. Redu-
cing the infiltration of outdoor pollutants into the indoor
environment through improvements in mechanical ventila-
tion or building design can further reduce indoor exposure
but cannot address outdoor exposure [131]. By comparison,
the
air
quality
benefits
of
technologies
that
remove
pollutants from ambient air are negligible – cities in China,
India, Korea, and the Netherlands experimented with out-
door air filtration units that were ultimately deemed costly,
ineffective, and impractical. The role of cities in mitigating pollution and related CVD
burden Green infrastructure (i.e., urban effectiveness of these approaches in highly polluted com-
pared with less-polluted areas is unclear, but they are po-
tential short-term public health interventions. effectiveness of these approaches in highly polluted com-
pared with less-polluted areas is unclear, but they are po-
tential short-term public health interventions. Local regulations can be used to incentivize or inhibit
the polluting behaviors of industries and individuals. As
part of a multi-sectoral approach to reduce regional air
pollution, the Beijing government banned household
coal heaters in millions of homes and simultaneously
offered large subsidies for electric heaters and electricity
[126]. National bans on leaded gasoline substantially
reduced lead exposures in many countries (up to 90%),
although lead remains a public health concern in several
places [60, 62, 63, 127]. Concentrated poverty combined
with a deteriorated housing stock contributes to pockets
of high exposure to lead paint in US cities; in response,
several affected cities introduced new lead prevention
policies and programs, including education, housing
inspections in high-risk areas, and local ordinances that
require abatement for rental properties [128], with some
evidence of success [129, 130]. Table 1 Strategies and technologies to mitigate exposure to air pollution (adapted from Burns et al. [131] an Individual or household interventions Improving indoor air quality Hazardous waste from electronics LMICs continue to receive a large proportion of global hazardous waste, including used lead-acid batteries and discarded electronics. A portion of
this waste is often inappropriately disposed of into uncontrolled landfills and another portion is recycled, often in informal settings that involve
rudimentary processing and disposal methods [138]. These practices contaminate the local environment as well as exposure workers and nearby
residents to heavy metals, flame retardants, and other pollutants [139]. has undoubtedly contributed to high levels of exposure in
many LMIC settings, particularly in urban areas, these high
levels of pollution are not unavoidable outcomes of these
shifts. The health and economic benefits of managing and
mitigating pollution are increasingly well recognized, and
the behavior of prioritizing economic growth over en-
vironmental protection is shifting. Rapidly growing cit-
ies in LMICs will play a defining role in global health
and CVD prevention in the next several decades as they
are well poised to develop innovative, multisectoral ap-
proaches to pollution mitigation while also protecting
the most vulnerable. trees, green walls and roofs, and other urban vegetation) has
been promoted to improve air quality and beautify land-
scapes in several cities, including London [133], despite lim-
ited and conflicting emprical evidence of a benefit. Urban
vegetation may provide a very small and highly localized air
quality benefit in very specific settings, but it does not
effectively remove pollution and can actually lead to de-
terioration of air quality under various meteorological
and urban planning conditions [134]. Case studies from
LMIC cities can further help to inform evidence-based
solutions, including those that address sources like agri-
cultural burning and household solid fuel stoves. Ensuring that new environmental policies and regulations
do not simply shift polluting industries into poor communi-
ties and further increase urban environmental inequality
(Table 2) will require careful monitoring and extensive dia-
log and consultation between researchers, officials, and
other stakeholder groups. On a global scale, lower costs of
labor and production in transitioning economies have
attracted new industry, leading to higher levels of air and
water pollution [140]. Similar trends have occurred within
countries; for example, efforts to reduce urban air pollution
in China and India by simply transferring polluting indus-
tries to peri-urban and rural areas continued to generate re-
gional air pollution and may have worsened exposures for
rural populations who are already more vulnerable and have
less access to healthcare [141]. Improving indoor air quality • Switch to cleaner-burning fuels for fireplaces and cooking stoves • Use of mechanical ventilation and/or reducing use of natural ventilation to reduce infiltration of polluted outdoor air into homes and buildings
• Installation of portable air cleaners in homes • Installation of portable air cleaners in homes Behavioral change • Avoid commutes during rush hour or avoid busy roads during active transport • Avoid commutes during rush hour or avoid busy roads during active transport • Transition to healthier lifestyles (e.g., exercise, healthy diet) to reduce risk of comorbid conditions that increase vulnerability to the health
impacts of air pollution; preventative medications and screening programs • Transition to healthier lifestyles (e.g., exercise, healthy diet) to reduce risk of comorbid conditions that increase vulnerability to the health
impacts of air pollution; preventative medications and screening programs Page 7 of 11 Baumgartner et al. BMC Medicine Baumgartner et al. BMC Medicine (2020) 18:39 Table 2 Exporting pollution to low- and middle-income countries (LMICs)
Higher polluting cars and fuels African cities are urbanizing and motorizing more rapidly than any other continent. Most countries in sub-Saharan Africa import many more used
cars than new ones. Nearly all cars imported into Kenya were previously owned, for example, shipped mainly from Japan and Europe, where they
may not meet their stringent environmental standards [135]. Used cars offer a more affordable way for residents to become more mobile but also
tend to emit higher levels of pollution [136]. Lower quality diesel fuel, common in many LMICs, further increases pollution emissions from these older
cars [137]. Competing interests Competing interests
The authors declare that they have no competing interests. Consent for publication
Not applicable. Consent for publication
Not applicable. Consent for publication
Not applicable. Ethics approval and consent to participate
Not applicable. Ethics approval and consent to participate
Not applicable. Acknowledgements
W
h
k B i
R bi Acknowledgements
We thank Brian Robinson for comments on an early draft. Authors’ contributions
JB wrote the manuscript with input from MB and ME. All authors read and
approved the final manuscript. Funding g
This work was supported by the Pathways to Equitable Healthy Cities grant
from the Wellcome Trust [209376/Z/17/Z]. g
This work was supported by the Pathways to Equitable Healthy Cities grant
from the Wellcome Trust [209376/Z/17/Z]. Hazardous waste from electronics In Beijing, poorer homes in
regions where a coal ban was implemented had difficulty in
shouldering the additional electricity costs and had colder
indoor temperatures [126], which are themselves risk factors
for higher blood pressure and CVD mortality [105, 142]. References Yusuf S, Joseph P, Rangarajan S, Islam S, Mente A, Hystad P, Brauer M, Kutty
VR, Gupta R, Wielgosz A. Modifiable risk factors, cardiovascular disease, and
mortality in 155 722 individuals from 21 high-income, middle-income, and
low-income countries (PURE): a prospective cohort study. Lancet. 2019. https://doi.org/10.1016/S0140-6736(19)32008-2. 30. Health Effects Institute. State of Global Air 2019. Special Report. Boston:
Health Effects Institute; 2019. 31. Anenberg SC, Achakulwisut P, Brauer M, Moran D, Apte JS, Henze DK. Particulate matter-attributable mortality and relationships with carbon
dioxide in 250 urban areas worldwide. Sci Rep. 2019;9(1):1–6. 5. Rose G. Sick individuals and sick populations. Int J Epidemiol. 2001;30(3):
427–32. 6. World Health Organization. Ambient air pollution: a global assessment of
exposure and burden of disease. Geneva: WHO; 2016. 32. Arku RE, Birch A, Shupler M, Yusuf S, Hystad P, Brauer M. Characterizing
exposure to household air pollution within the prospective urban rural
epidemiology (PURE) study. Environ Int. 2018;114:307–17. 7. Tong S, Schirnding YE, Prapamontol T. Environmental lead exposure: a
public health problem of global dimensions. Bull World Health Organ. 2000;
78:1068–77. 33. Carter E, Norris C, Dionisio K, Balakrishnan K, Checkley W, Clark M, Ghosh S,
Jack D, Kinney P, Marshall J, et al. Assessing exposure to household air
pollution: a systematic review and pooled analysis of carbon monoxide as a
surrogate measure of particulate matter. Environ Health Perspect. 2017;
125(7):076002. 8. United Nations. Department of Economic and Social Affairs, Population Division. World Population Prospects 2019; 2019. 9. Dye C. Health and urban living. Science. 2008;319(5864):766–9. 10. Krefis AC, Augustin M, Schlünzen KH, Oßenbrügge J, Augustin J. How does
the urban environment affect health and well-being? A systematic review. Urban Sci. 2018;2(1):21. 34. Pope CA 3rd, Dockery DW. Health effects of fine particulate air pollution:
lines that connect. J Air Waste Manage Assoc. 2006;56:709–42. 35. Rajagopalan S, Al-Kindi SG, Brook RD. Air pollution and cardiovascular
disease: JACC state-of-the-art review. J Am Coll Cardiol. 2018;72(17):2054–70. 11. Ezzati M, Webster CJ, Doyle YG, Rashid S, Owusu G, Leung GM. Cities for
global health. BMJ. 2018;363:k3794. 36. Mustafić H, Jabre P, Caussin C, Murad MH, Escolano S, Tafflet M, Périer M-C,
Marijon E, Vernerey D, Empana J-P. Main air pollutants and myocardial
infarction: a systematic review and meta-analysis. JAMA. 2012;307(7):713–21. 12. Rosenberg J. Toxic memo. Harvard Magazine. 2001. https://www. harvardmagazine.com/2001/05/toxic-memo.html. Accessed 17 Jan 2020. 13. Grossman GM, Krueger AB. Economic growth and the environment. Quart J
Econ. 1995;110(2):353–77. Author details
1 The UN Sustainable Development Goals and the WHO
Global Action Plans target a one-third reduction in prema-
ture mortality from non-communicable diseases by 2030. There is substantial evidence from high-income countries
and growing evidence from LMICs that reducing population
exposures to environmental pollution may accelerate pro-
gress in decreasing the global burden of CVD and meeting
this target. Though rapid industrialization and urbanization 1Institute for Health and Social Policy, McGill University, Montreal, QC,
Canada. 2Department of Epidemiology, Biostatistics, and Occupational
Health, McGill University, 1110 Pine Avenue West, Montreal, QC H3A 1A3,
Canada. 3Department of Epidemiology and Biostatistics, School of Public
Health, Imperial College London, London, UK. 4School of Population and
Public Health, The University of British Columbia, Vancouver, BC, Canada. 5Institute for Health Metrics and Evaluation, University of Washington, Seattle,
WA, USA. 6MRC Center for Environment and Health, Imperial College
London, London, UK. 7WHO Collaborating Centre for NCD Surveillance and
Epidemiology, Imperial College London, London, UK. Page 8 of 11 Page 8 of 11 Baumgartner et al. BMC Medicine (2020) 18:39 (2020) 18:39 Baumgartner et al. BMC Medicine (2020) 18:39 Received: 23 October 2019 Accepted: 21 January 2020 References 37. Shah AS, Lee KK, McAllister DA, Hunter A, Nair H, Whiteley W, Langrish JP,
Newby DE, Mills NL. Short term exposure to air pollution and stroke:
systematic review and meta-analysis. BMJ. 2015;350:h1295. 14. McMichael AJ. The urban environment and health in a world of increasing
globalization: issues for developing countries. Bull World Health Organ. 2000;78:1117–26. 38. Kaufman JD, Adar SD, Barr RG, Budoff M, Burke GL, Curl CL, Daviglus ML,
Roux AVD, Gassett AJ, Jacobs DR Jr. Association between air pollution and
coronary artery calcification within six metropolitan areas in the USA (the
multi-ethnic study of atherosclerosis and air pollution): a longitudinal cohort
study. Lancet. 2016;388(10045):696–704. 15. Daum K, Stoler J, Grant RJ. Toward a more sustainable trajectory for E-waste
policy: a review of a decade of E-waste research in Accra, Ghana. Int J
Environ Res Public Health. 2017;14(2):135. 16. Khan W, Hossin ME, Akbor MJ. Leather industry in Bangladesh: a systematic
literature review. Asian Business Rev. 2015;5(3):111–8. 39. Crouse DL, Peters PA, van Donkelaar A, Goldberg MS, Villeneuve PJ, Brion O,
Khan S, Atari DO, Jerrett M, Pope CA III. Risk of nonaccidental and
cardiovascular mortality in relation to long-term exposure to low
concentrations of fine particulate matter: a Canadian national-level cohort
study. Environ Health Perspect. 2012;120(5):708–14. 17. Whitehead P, Bussi G, Peters R, Hossain M, Softley L, Shawal S, Jin L,
Rampley C, Holdship P, Hope R. Modelling heavy metals in the Buriganga
River system, Dhaka, Bangladesh: impacts of tannery pollution control. Sci
Total Environ. 2019;697:134090. 40. Pinault LL, Weichenthal S, Crouse DL, Brauer M, Erickson A, van Donkelaar A,
Martin RV, Hystad P, Chen H, Finès P. Associations between fine particulate
matter and mortality in the 2001 Canadian census health and environment
cohort. Environ Res. 2017;159:406–15. 18. Hasan MM, Hosain S, Poddar P, Chowdhury AA, Katengeza EW, Roy UK. Heavy metal toxicity from the leather industry in Bangladesh: a case study
of human exposure in Dhaka industrial area. Environ Monitor Assess. 2019;
191(9):530. 41. Jaganathan S, Jaacks LM, Magsumbol M, Walia GK, Sieber NL, Shivasankar R,
Dhillon PK, Hameed SS, Schwartz J, Prabhakaran D. Association of long-term
exposure to fine particulate matter and cardio-metabolic diseases in low-
and middle-income countries: a systematic review. Int J Environ Res Public
Health. 2019;16(14):2541. 19. Cropper ML, Freeman AM III. Valuing environmental health effects. Washington DC: Resources for the Future; 1990. 20. Landrigan PJ, Fuller R. References 1. Cosselman KE, Navas-Acien A, Kaufman JD. Environmental factors in
cardiovascular disease. Nat Rev Cardiol. 2015;12(11):627. 25. Zhao X, Cheng H, He S, Cui X, Pu X, Lu L. Spatial associations between
social groups and ozone air pollution exposure in the Beijing urban area. Environ Res. 2018;164:173–83. 2. Roth GA, Abate D, Abate KH, Abay SM, Abbafati C, Abbasi N, Abbastabar H,
Abd-Allah F, Abdela J, Abdelalim A. Global, regional, and national age-sex-
specific mortality for 282 causes of death in 195 countries and territories,
1980–2017: a systematic analysis for the global burden of disease study
2017. Lancet. 2018;392(10159):1736–88. 2. Roth GA, Abate D, Abate KH, Abay SM, Abbafati C, Abbasi N, Abbastabar H,
Abd-Allah F, Abdela J, Abdelalim A. Global, regional, and national age-sex-
specific mortality for 282 causes of death in 195 countries and territories,
1980–2017: a systematic analysis for the global burden of disease study
2017. Lancet. 2018;392(10159):1736–88. 26. Hajat A, Hsia C, O’Neill MS. Socioeconomic disparities and air pollution
exposure: a global review. Current Environ Health Rep. 2015;2(4):440–50. 27. Huang L, Rao C, van der Kuijp TJ, Bi J, Liu Y. A comparison of individual
exposure, perception, and acceptable levels of PM2.5 with air pollution
policy objectives in China. Environ Res. 2017;157:78–86. 3. Stanaway JD, Afshin A, Gakidou E, Lim SS, Abate D, Abate KH, Abbafati C,
Abbasi N, Abbastabar H, Abd-Allah F. Global, regional, and national
comparative risk assessment of 84 behavioural, environmental and
occupational, and metabolic risks or clusters of risks for 195 countries and
territories, 1990–2017: a systematic analysis for the global burden of disease
study 2017. Lancet. 2018;392(10159):1923–94. 28. Gallaher CM, Mwaniki D, Njenga M, Karanja NK, WinklerPrins AM. Real or
perceived: the environmental health risks of urban sack gardening in Kibera
slums of Nairobi. Kenya EcoHealth. 2013;10(1):9–20. 29. Brook RD, Rajagopalan S, Pope CA 3rd, Brook JR, Bhatnagar A, Diez-Roux AV,
Holguin F, Hong Y, Luepker RV, Mittleman MA. Particulate matter air
pollution and cardiovascular disease: an update to the scientific statement
from the American Heart Association. Circulation. 2010;121(21):2331. 4. Yusuf S, Joseph P, Rangarajan S, Islam S, Mente A, Hystad P, Brauer M, Kutty
VR, Gupta R, Wielgosz A. Modifiable risk factors, cardiovascular disease, and
mortality in 155 722 individuals from 21 high-income, middle-income, and
low-income countries (PURE): a prospective cohort study. Lancet. 2019. https://doi.org/10.1016/S0140-6736(19)32008-2. 4. Received: 23 October 2019 Accepted: 21 January 2020 sources of particle pollution: mobile monitoring and GIS analysis in four
Accra communities. Environ Health Perspect. 2010;118(5):607–13. sources of particle pollution: mobile monitoring and GIS analysis in four
Accra communities. Environ Health Perspect. 2010;118(5):607–13. 24. Huang G, Zhou W, Qian Y, Fisher B. Breathing the same air? Socioeconomic
disparities in PM2.5 exposure and the potential benefits from air filtration. Sci
Total Environ. 2019;657:619–26. References Arku RE, Ezzati M, Baumgartner J, Fink G, Zhou B, Hystad P, Brauer M. Elevated blood pressure and household solid fuel use in premenopausal
women: analysis of 12 demographic and health surveys (DHS) from 10
countries. Environ Res. 2018;160:499–505. 70. Tellez-Plaza M, Jones MR, Dominguez-Lucas A, Guallar E, Navas-Acien A. Cadmium exposure and clinical cardiovascular disease: a systematic review. Current Atherosclerosis Rep. 2013;15(10):356. 48. Baumgartner J, Carter E, Schauer JJ, Ezzati M, Daskalopoulou SS, Valois M-F,
Shan M, Yang X. Household air pollution and measures of blood pressure,
arterial stiffness and central haemodynamics. Heart. 2018;104(18):1515–21. 71. Tinkov AA, Filippini T, Ajsuvakova OP, Skalnaya MG, Aaseth J, Bjørklund G,
Gatiatulina ER, Popova EV, Nemereshina ON, Huang P-T. Cadmium and
atherosclerosis: a review of toxicological mechanisms and a meta-analysis of
epidemiologic studies. Environmental Res. 2018;162:240–60. 49. Young BN, Clark ML, Rajkumar S, Benka-Coker ML, Bachand A, Brook RD,
Nelson TL, Volckens J, Reynolds SJ, L'Orange C. Exposure to household air
pollution from biomass cookstoves and blood pressure among women in
rural Honduras: a cross-sectional study. Indoor Air. 2019;29(1):130–42. 72. Zhang W-L, Du Y, Zhai M-M, Shang Q. Cadmium exposure and its health
effects: a 19-year follow-up study of a polluted area in China. Sci Total
Environ. 2014;470:224–8. 73. Ikeda M, Zhang Z-W, Shimbo S, Watanabe T, Nakatsuka H, Moon C-S,
Matsuda-Inoguchi N, Higashikawa K. Urban population exposure to lead
and cadmium in east and south-East Asia. Sci Total Environ. 2000;249(1–3):
373–84. 50. Onakomaiya D, Gyamfi J, Iwelunmor J, Opeyemi J, Oluwasanmi M, Obiezu-
Umeh C, Dalton M, Nwaozuru U, Ojo T, Vieira D. Implementation of clean
cookstove interventions and its effects on blood pressure in low-income
and middle-income countries: systematic review. BMJ Open. 2019;9(5):
e026517. 74. Lu Y, Liu X, Deng Q, Duan Y, Dai H, Li Y, Xiao T, Ning X, Fan J, Zhou L. Continuous lead exposure increases blood pressure but does not alter
kidney function in adults 20-44 years of age in a lead-polluted region of
China. Kidney Blood Press Res. 2015;40(3):207–14. 51. Pope CA III, Cohen AJ, Burnett RT. Cardiovascular disease and fine
particulate matter: lessons and limitations of an integrated exposure–
response approach. Circulation Res. 2018;122(12):1645–7. 52. Secrest MH, Schauer JJ, Carter E, Baumgartner J. Particulate matter chemical
component concentrations and sources in settings of household solid fuel
use. Indoor Air. 2017;27(6):1052–66. 75. References Pollution, health and development: the need for a
new paradigm. Rev Environ Health. 2016;31(1):121–4. 21. Dionisio KL, Arku RE, Hughes AF, Vallarino J, Carmichael H, Spengler JD,
Agyei-Mensah S, Ezzati M. Air pollution in Accra neighborhoods: spatial,
socioeconomic, and temporal patterns. Environ Sci Technol. 2010;44(7):
2270–6. 42. Fatmi Z, Coggon D. Coronary heart disease and household air pollution
from use of solid fuel: a systematic review. Br Med Bull. 2016;118(1):91. 43. Hystad P, Duong M, Brauer M, Larkin A, Arku R, Kurmi OP, Fan WQ, Avezum
A, Azam I, Chifamba J. Health effects of household solid fuel use: findings
from 11 countries within the prospective urban and rural epidemiology
study. Environ Health Perspect. 2019;127(5):057003. 22. Zhou Z, Dionisio KL, Arku RE, Quaye A, Hughes AF, Vallarino J, Spengler JD,
Hill A, Agyei-Mensah S, Ezzati M. Household and community poverty,
biomass use, and air pollution in Accra. Ghana Proc Natl Acad Sci. 2011;
108(27):11028–33. 44. Yu K, Qiu G, Chan K-H, Lam K-BH, Kurmi OP, Bennett DA, Yu C, Pan A, Lv J,
Guo Y. Association of solid fuel use with risk of cardiovascular and all-cause
mortality in rural China. JAMA. 2018;319(13):1351–61. 23. Dionisio KL, Rooney MS, Arku RE, Friedman AB, Hughes AF, Vallarino J,
Agyei-Mensah S, Spengler JD, Ezzati M. Within neighborhood patterns and Page 9 of 11 Page 9 of 11 Page 9 of 11 Baumgartner et al. BMC Medicine (2020) 18:39 (2020) 18:39 Baumgartner et al. BMC Medicine (2020) 18:39 45. Yamamoto S, Phalkey R, Malik A. A systematic review of air pollution as a
risk factor for cardiovascular disease in South Asia: limited evidence from
India and Pakistan. Int J Hygiene Environ Health. 2014;217(2–3):133–44. 67. Pirkle JL, Schwartz J, Landis JR, Harlan WR. The relationship between blood
lead levels and blood pressure and its cardiovascular risk implications. Am J
Epidemiol. 1985;121(2):246–58. 46. Mitter SS, Vedanthan R, Islami F, Pourshams A, Khademi H, Kamangar F,
Abnet CC, Dawsey SM, Pharoah PD, Brennan P. Household fuel use and
cardiovascular disease mortality: Golestan cohort study. Circulation. 2016;
133(24):2360–9. 68. Nawrot T, Thijs L, Den Hond E, Roels H, Staessen JA. An epidemiological re-
appraisal of the association between blood pressure and blood lead: a
meta-analysis. J Human Hypertens. 2002;16(2):123. 69. Järup L, Åkesson A. Current status of cadmium as an environmental health
problem. Toxicol Appl Pharmacol. 2009;238(3):201–8. 47. References de Almeida Lopes ACB, Silbergeld EK, Navas-Acien A, Zamoiski R, da Cunha
Martins Jr A, Camargo AEI, Urbano MR, Mesas AE, Paoliello MMB. Association between blood lead and blood pressure: a population-based
study in Brazilian adults. Environ Health. 2017;16(1):27. 53. Baumgartner J, Zhang Y, Schauer JJ, Huang W, Wang Y, Ezzati M. Highway
proximity and black carbon from cookstoves as a risk factor for higher blood
pressure in rural China. Proc Natl Acad Sci U S A. 2014;111(36):13229–34. 76. Were FH, Moturi MC, Gottesfeld P, Wafula GA, Kamau GN, Shiundu PM. Lead
exposure and blood pressure among workers in diverse industrial plants in
Kenya. J Occup Environ Hyg. 2014;11(11):706–15. 54. Bell ML. Assessment of the health impacts of particulate matter
characteristics. Res Rep Health Effects Inst. 2012;161:5–38. 77. Ari E, Kaya Y, Demir H, Asicioglu E, Keskin S. The correlation of serum trace
elements and heavy metals with carotid artery atherosclerosis in maintenance
hemodialysis patients. Biol Trace Element Res. 2011;144(1–3):351–9. 55. Solenkova NV, Newman JD, Berger JS, Thurston G, Hochman JS, Lamas GA. Metal pollutants and cardiovascular disease: mechanisms and consequences
of exposure. Am Heart J. 2014;168(6):812–22. 78. Tangvarasittichai S, Niyomtam S, Pingmuangkaew P, Nunthawarasilp P. Dyslipidemia in the elevated cadmium exposure population. Int J Toxicol
Pharmacol Res. 2015;7:92–8. 56. Chowdhury R, Ramond A, O’Keeffe LM, Shahzad S, Kunutsor SK, Muka T,
Gregson J, Willeit P, Warnakula S, Khan H. Environmental toxic metal
contaminants and risk of cardiovascular disease: systematic review and
meta-analysis. BMJ. 2018;362:k3310. 79. Moon K, Guallar E, Navas-Acien A. Arsenic exposure and cardiovascular
disease: an updated systematic review. Curr Atheroscler Rep. 2012;14(6):
542–55. 57. Brinkel J, Khan M, Kraemer A. A systematic review of arsenic exposure and
its social and mental health effects with special reference to Bangladesh. Int
J Environ Res Public Health. 2009;6(5):1609–19. 80. Kuo C-C, Moon KA, Wang S-L, Silbergeld E, Navas-Acien A. The association
of arsenic metabolism with cancer, cardiovascular disease, and diabetes: a
systematic review of the epidemiological evidence. Environ Health Perspect. 2017;125(8):087001. 58. Kordas K, Ravenscroft J, Cao Y, McLean E. Lead exposure in low and middle-
income countries: perspectives and lessons on patterns, injustices,
economics, and politics. Int J Environ Res Public Health. 2018;15(11):2351. 81. Abhyankar LN, Jones MR, Guallar E, Navas-Acien A. Arsenic exposure and
hypertension: a systematic review. Environ Health Perspect. 2011;120(4):494–500. 59. Horton LM, Mortensen ME, Iossifova Y, Wald MM, Burgess P. References What do we
know of childhood exposures to metals (arsenic, cadmium, lead, and
mercury) in emerging market countries? Int J Pediatr. 2013;2013:872596. 82. Naujokas MF, Anderson B, Ahsan H, Aposhian HV, Graziano JH, Thompson C
Suk WA. The broad scope of health effects from chronic arsenic exposure:
update on a worldwide public health problem. Environ Health Perspect. 2013;121(3):295–302. 60. Thomas VM, Socolow RH, Fanelli JJ, Spiro TG. Effects of reducing lead in
gasoline: an analysis of the international experience. Environ Sci Technol. 1999;33(22):3942–8. 83. Mendez MA, González-Horta C, Sánchez-Ramírez B, Ballinas-Casarrubias L,
Cerón RH, Morales DV, Terrazas FAB, Ishida MC, Gutiérrez-Torres DS,
Saunders RJ. Chronic exposure to arsenic and markers of cardiometabolic
risk: a cross-sectional study in Chihuahua, Mexico. Environ Health Perspect. 2015;124(1):104–11. 61. Landrigan PJ. The worldwide problem of lead in petrol. Bull World Health
Organ. 2002;80(10):768. 62. Mathee A, Röllin H, von Schirnding Y, Levin J, Naik I. Reductions in blood
lead levels among school children following the introduction of unleaded
petrol in South Africa. Environ Res. 2006;100(3):319–22. 84. World Health Organization. Environmental noise guidelines for the
European region. Geneva: WHO; 2018. 63. Nichani V, Li W-I, Smith MA, Noonan G, Kulkarni M, Kodavor M, Naeher LP. Blood lead levels in children after phase-out of leaded gasoline in Bombay,
India. Sci Total Environ. 2006;363(1–3):95–106. 85. Münzel T, Gori T, Babisch W, Basner M. Cardiovascular effects of
environmental noise exposure. Eur Heart J. 2014;35(13):829–36. 64. Navas-Acien A, Guallar E, Silbergeld EK, Rothenberg SJ. Lead exposure and
cardiovascular disease — a systematic review. Environ Health Perspect. 2006;115(3):472–82. 86. Babisch W, Beule B, Schust M, Kersten N, Ising H. Traffic noise and risk of
myocardial infarction. Epidemiology. 2005;16:33–40. 87. Van Kempen E, Babisch W. The quantitative relationship between road
traffic noise and hypertension: a meta-analysis. J Hypertens. 2012;30(6):
1075–86. 65. Fewtrell L, Prüss-Üstün A, Landrigan P, Ayuso-Mateos J. Estimating the global
burden of disease of mild mental retardation and cardiovascular diseases from
environmental lead exposure. Environmental Res. 2004;94(2):120–33. 88. Tétreault L-F, Perron S, Smargiassi A. Cardiovascular health, traffic-related air
pollution and noise: are associations mutually confounded? A systematic
review. Int J Public Health. 2013;58(5):649–66. 66. Fewtrell L, Kaufman R, Prüss-Üstün A. Lead. Assessing the Environmental
Burden of Diseases at National and Local Levels. Environmental Burden of
Disease Series, No. 2. 2003. https://www.who.int/quantifying_ehimpacts/
publications/en/leadebd2.pdf. Accessed 20 Jan 2020. 89. References Lower ambient temperature
was associated with an increased risk of hospitalization for stroke and acute
myocardial infarction in young women. J Clin Epidemiol. 2004;57(7):749–57. 126. Barrington-Leigh C, Baumgartner J, Carter E, Robinson BE, Tao S, Zhang Y. An evaluation of air quality, home heating and well-being under Beijing’s
programme to eliminate household coal use. Nat Energy. 2019;4(5):416. 127. Thomas V. The elimination of lead in gasoline. Ann Rev Energy Environ. 1995;20(1):301–24. 103. Green H, Bailey J, Schwarz L, Vanos J, Ebi K, Benmarhnia T. Impact of heat
on mortality and morbidity in low and middle income countries: a review
of the epidemiological evidence and considerations for future research. Environ Res. 2019;171:80–91. 128. Magavern S. Policies to reduce lead exposure: lessons from Buffalo and
Rochester. Int J Environ Res Public Health. 2018;15(10):2197. 104. Gasparrini A, Guo Y, Hashizume M, Lavigne E, Zanobetti A, Schwartz J,
Tobias A, Tong S, Rocklöv J, Forsberg B. Mortality risk attributable to high
and low ambient temperature: a multicountry observational study. Lancet. 2015;386(9991):369–75. 129. Korfmacher KS, Ayoob M, Morley R. Rochester’s lead law: evaluation of a
local environmental health policy innovation. Environ Health Perspect. 2011;
120(2):309–15. 130. Korfmacher KS, Hanley ML. Are local laws the key to ending childhood lead
poisoning? J Health Politics Policy Law. 2013;38(4):757–813. 105. Lewington S, LiMing L, Sherliker P, Yu G, Millwood I, Zheng B, Whitlock G,
Ling Y, Collins R, Junshi C. Seasonal variation in blood pressure and its
relationship with outdoor temperature in 10 diverse regions of China: the
China Kadoorie biobank. J Hypertens. 2012;30(7):1383–91. 131. Burns J, Boogaard H, Polus S, Pfadenhauer LM, Rohwer AC, van Erp AM, Turley
R, Rehfuess E. Interventions to reduce ambient particulate matter air pollution
and their effect on health. Cochrane Database Syst Rev. 2019;5:CD010919. 106. Saeki K, Obayashi K, Iwamoto J, Tanaka Y, Tanaka N, Takata S, Kubo H,
Okamoto N, Tomioka K, Nezu S. Influence of room heating on ambulatory
blood pressure in winter: a randomised controlled study. J Epidemiol
Commun Health. 2013;67(6):484–90. 132. Health Effects Institute. Panel on the health effects of traffic-related air
pollution: traffic-related air pollution: a critical review of the literature on
emissions, exposure, and health effects. Boston: Health Effects Institute; 2010. 133. Greater London Authority. Using Green Infrastructure to Protect People
from Air Pollution. 2019. https://www.london.gov.uk/WHAT-WE-DO/
environment/environment-publications/using-green-infrastructure-protect-
people-air-pollution. Accessed 17 Jan 2020. 107. References The effects of congestion charging on road
traffic casualties: a causal analysis using difference-in-difference estimation. Accid Anal Prev. 2012;49:366–77. 96. Fu SH, Gasparrini A, Rodriguez PS, Jha P. Mortality attributable to hot and
cold ambient temperatures in India: a nationally representative case-
crossover study. PLoS Med. 2018;15(7):e1002619. 97. Yang J, Zhou M, Ou C-Q, Yin P, Li M, Tong S, Gasparrini A, Liu X, Li J, Cao L. Seasonal variations of temperature-related mortality burden from
cardiovascular disease and myocardial infarction in China. Environ Pollution. 2017;224:400–6. 120. Wen X-J, Balluz L, Mokdad A. Association between media alerts of air quality
index and change of outdoor activity among adult asthma in six states,
BRFSS, 2005. J Commun Health. 2009;34(1):40–6. 121. Wang F, Zhao H, Zhang X, Niu C, Ma J. Understanding individual-level
protective responses to air pollution warning: a case study of Beijing, China. Human Ecol Risk Assess. 2019;25(6):1473–87. 98. Yang J, Yin P, Zhou M, Ou C-Q, Guo Y, Gasparrini A, Liu Y, Yue Y, Gu S, Sang
S. Cardiovascular mortality risk attributable to ambient temperature in
China. Heart. 2015;101(24):1966–72. 122. Knowlton K, Kulkarni S, Azhar G, Mavalankar D, Jaiswal A, Connolly M, Nori-
Sarma A, Rajiva A, Dutta P, Deol B. Development and implementation of
South Asia’s first heat-health action plan in Ahmedabad (Gujarat, India). Int J
Environ Res Public Health. 2014;11(4):3473–92. 99. Scovronick N, Sera F, Acquaotta F, Garzena D, Fratianni S, Wright CY,
Gasparrini A. The association between ambient temperature and mortality
in South Africa: a time-series analysis. Environ Res. 2018;161:229–35. 123. Hess JJ, Lm S, Knowlton K, Saha S, Dutta P, Ganguly P, Tiwari A, Jaiswal A,
Sheffield P, Sarkar J. Building resilience to climate change: pilot evaluation
of the impact of India’s first heat action plan on all-cause mortality. J
Environ Public Health. 2018;2018:7973519. 100. Amegah AK, Rezza G, Jaakkola JJ. Temperature-related morbidity and
mortality in sub-Saharan Africa: a systematic review of the empirical
evidence. Environ Int. 2016;91:133–49. 101. McMichael AJ, Wilkinson P, Kovats RS, Pattenden S, Hajat S, Armstrong B,
Vajanapoom N, Niciu EM, Mahomed H, Kingkeow C. International study of
temperature, heat and urban mortality: the ‘ISOTHURM’project. Int J
Epidemiol. 2008;37(5):1121–31. 124. Hadley MB, Baumgartner J, Vedanthan R. Developing a clinical approach to
air pollution and cardiovascular health. Circulation. 2018;137(7):725–42. 125. Brauer M, Mancini GBJ. Where there’s smoke. BMJ. 2014;348:g40. 102. Chang CL, Shipley M, Marmot M, Poulter N. References Kälsch H, Hennig F, Moebus S, Möhlenkamp S, Dragano N, Jakobs H,
Memmesheimer M, Erbel R, Jöckel K-H, Hoffmann B. Are air pollution and Page 10 of 11 Baumgartner et al. BMC Medicine (2020) 18:39 (2020) 18:39 Baumgartner et al. BMC Medicine (2020) 18:39 112. C40 Cities: The Power of C40 Cities. 2016. https://www.c40.org/researches/
c40-cities-the-power-to-act. Accessed 20 Jan 2020. traffic noise independently associated with atherosclerosis: the Heinz
Nixdorf recall study. Eur Heart J. 2013;35(13):853–60. 90. Al-harthy I, Tamura A. Sound environment evaluation and categorization of
audible sounds. JASJ. 1999;20(5):353–64. 113. Rabinovitch J, Hoehn JP. A Sustainable Urban Transportation System: The
“Surface Metro” in Curitiba, Brazil. Environ Nat Resour Policy Train Proj. 1995. https://doi.org/10.22004/ag.econ.11886. 91. Mehdi MR, Kim M, Seong JC, Arsalan MH. Spatio-temporal patterns of road
traffic noise pollution in Karachi, Pakistan. Environ Int. 2011;37(1):97–104. 114. Parra D, Gomez L, Pratt M, Sarmiento OL, Mosquera J, Triche E. Policy and
built environment changes in Bogotá and their importance in health
promotion. Indoor Built Environ. 2007;16(4):344–8. 92. Anomohanran O. Evaluation of environmental noise pollution in Abuja, the
capital city of Nigeria. Int J Res Rev Appl Sci. 2013;14(2):470–6. promotion. Indoor Built Environ. 2007;16(4):344–8. capital city of Nigeria. Int J Res Rev Appl Sci. 2013;14(2):470–6. 115. Cain A, Darido G, Baltes MR, Rodriguez P, Barrios JC. Applicability of
TransMilenio bus rapid transit system of Bogotá, Colombia, to the United
States. Transport Res Record. 2007;2034(1):45–54. 93. Doygun H, Gurun DK. Analysing and mapping spatial and temporal
dynamics of urban traffic noise pollution: a case study in Kahramanmaraş,
Turkey. Environ Monitor Assess. 2008;142(1–3):65–72. 94. Banerjee D, Chakraborty S, Bhattacharyya S, Gangopadhyay A. Evaluation
and analysis of road traffic noise in Asansol: an industrial town of eastern
India. Int J Environ Res Public Health. 2008;5(3):165–71. 116. Viard VB, Fu S. The effect of Beijing's driving restrictions on pollution and
economic activity. J Public Econ. 2015;125:98–115. 117. Yang J, Liu Y, Qin P, Liu AA. A review of Beijing′ s vehicle registration lottery:
short-term effects on vehicle growth and fuel consumption. Energy Policy. 2014;75:157–66. 95. Sera F, Armstrong B, Tobias A, Vicedo-Cabrera AM, Åström C, Bell ML, Chen
B-Y, Coelho MSZS, Correa PM, Cruz JC. How urban characteristics affect
vulnerability to heat and cold: a multi-country analysis. Int J Epidemiol. 2019;48(4):1101–12. 118. Beevers SD, Carslaw DC. The impact of congestion charging on vehicle
emissions in London. Atmospheric Environ. 2005;39(1):1–5. 119. Li H, Graham DJ, Majumdar A. References FDI and the capital intensity of “dirty” sectors: a missing
piece of the pollution haven puzzle. Rev Dev Econ. 2005;9(4):530–48. 141. Bai X. Industrial relocation in Asia a sound environmental management
strategy? Environ Sci Policy Sustain Dev. 2002;44(5):8–21. 141. Bai X. Industrial relocation in Asia a sound environmental management
strategy? Environ Sci Policy Sustain Dev. 2002;44(5):8–21. 142. Yang L, Li L, Lewington S, Guo Y, Sherliker P, Bian Z, Collins R, Peto R, Liu Y,
Yang R. Outdoor temperature, blood pressure, and cardiovascular disease
mortality among 23 000 individuals with diagnosed cardiovascular diseases
from China. Eur Heart J. 2015;36(19):1178–85. References Wang Q, Li C, Guo Y, Barnett AG, Tong S, Phung D, Chu C, Dear K, Wang X,
Huang C. Environmental ambient temperature and blood pressure in adults:
a systematic review and meta-analysis. Sci Total Environ. 2017;575:276–86. 108. Healy JD. Excess winter mortality in Europe: a cross country analysis
identifying key risk factors. J Epidemiol Commun Health. 2003;57(10):784–9. 134. Abhijith K, Kumar P, Gallagher J, McNabola A, Baldauf R, Pilla F, Broderick B,
Di Sabatino S, Pulvirenti B. Air pollution abatement performances of green
infrastructure in open road and built-up street canyon environments – a
review. Atmospheric Environ. 2017;162:71–86. 109. Aylin P, Morris S, Wakefield J, Grossinho A, Jarup L, Elliott P. Temperature,
housing, deprivation and their relationship to excess winter mortality in
Great Britain, 1986–1996. Int J Epidemiol. 2001;30(5):1100–8. 135. Ogot M, Nyang’aya J, Nkatha R. Characteristics of the in-service vehicle fleet
in Kenya. Draft Report. 2018. https://www.changing-transport.org/wp-
content/uploads/Characteristics_of_the_In-Service_vehicle_fleet_in_Kenya. pdf. Accessed 17 Jan 2020. 110. Bennett JE, Stevens GA, Mathers CD, Bonita R, Rehm J, Kruk ME, Riley LM,
Dain K, Kengne AP, Chalkidou K. NCD countdown 2030: worldwide trends
in non-communicable disease mortality and progress towards sustainable
development goal target 3.4. Lancet. 2018;392(10152):1072–88. 136. National Research Council and National Academy of Engineering. Personal
cars and China. Washington, DC: The National Academies Press; 2003. https://doi.org/10.17226/10491 111. Rosenzweig C, Solecki W, Hammer SA, Mehrotra S. Cities lead the way in
climate–change action. Nature. 2010;467(7318):909. Page 11 of 11 Baumgartner et al. BMC Medicine (2020) 18:39 Baumgartner et al. BMC Medicine (2020) 18:39 137. Climate and Clean Air Coalition: Cleaning Up the Global On-Road Diesel
Fleet: A Global Strategy to Introduce Low-Sulfur Fuels and Cleaner Diesel
Vehicles. 2016. www.ccacoalition.org/en/initiatives/diesel. Accessed 17 Jan
2020. 138. Wang R, Xu Z. Recycling of non-metallic fractions from waste electrical and
electronic equipment (WEEE): a review. Waste Manag. 2014;34(8):1455–69. 139. Ericson B, Landrigan P, Taylor MP, Frostad J, Caravanos J, Keith J, Fuller R. The global burden of lead toxicity attributable to informal used lead-acid
battery sites. Ann Global Health. 2016;82(5):686–99. 139. Ericson B, Landrigan P, Taylor MP, Frostad J, Caravanos J, Keith J, Fuller R. The global burden of lead toxicity attributable to informal used lead-acid
battery sites. Ann Global Health. 2016;82(5):686–99. y
140. Cole MA, Elliott RJ. FDI and the capital intensity of “dirty” sectors: a missing
piece of the pollution haven puzzle. Rev Dev Econ. 2005;9(4):530–48. 140. Cole MA, Elliott RJ. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
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MicroRNA 27b promotes cardiac fibrosis by targeting the FBW7/Snail pathway
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AGING 2019, Vol. 11, No. 24 www.aging-us.com AGING 2019, Vol. 11, No. 24 ABSTRACT Our study aspires to understand the impact of miR-27b on myocardial fibrosis as well as its functional
mechanism. 12 days post the ligation of coronary artery in rats, the expression of miR-27b in the peri-infarction
region was elevated. Treating cultivated rat neonatal cardiac fibroblasts (CFs) with angiotensin II (AngII) also
enhanced the miR-27b expression. Forced expression of miR-27b promoted the proliferation and collagen
production in rat neonatal CFs, as revealed by cell counting, MTT assay, and quantitative reverse transcription-
polymerase chain reaction. FBW7 was found to be the miR-27b’s target since the overexpression of miR-27b
reduced the transcriptional level of FBW7. The enhanced expression of FBW7 protein abrogated the effects of
miR-27b in cultured CFs, while the siRNA silence of FBW7 promoted the pro-fibrosis activity of AngII. As to the
mechanism, we found that the expression of FBW7 led to the degradation of Snail, which is an important
regulator of cardiac epithelial-mesenchymal transitions. Importantly, inhibition of miR-27b abrogated the
coronary artery ligation (CAL) induced cardiac fibrosis in vivo, suggesting that it might be a potential target for
the treatment of fibrosis associated cardiac diseases. Published: December 23, 2019 Copyright: Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License
(CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and
source are credited. Qiang Fu1,*, Zhihong Lu2,*, Xiao Fu3, Shitang Ma4, Xiaochun Lu5 1Department of Cardiovascular Surgery, The General Hospital of Tianjin Medical University, Tianjin, China
2Department of Anatomy and Histology and Embryology, School of Basic Medical Sciences, Tianjin Medical
University, Tianjin, China
3Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University,
Tianjin, China
4College of Life and Health Sciences, Anhui Science and Technology University, Chuzhou, Anhui, China
5Department of Cardiology, The 2nd Medical Centre, PLA General Hospital, Beijing, China
*Equal contribution and Co-first authors Correspondence to: Shitang Ma, Xiaochun Lu; email: mast@ahstu.edu.cn, abeoc@163.com
Keywords: MicroRNA 27b, cardiac fibrosis, FBW7, Snail
Received: July 19, 2019
Accepted: November 8, 2019
Published: December Published: December 23, 2019 INTRODUCTION ECM, and upon activation they directly result in
hypertrophic
cardiomyocytes
through
paracrine
principles, aggravating the impairment in heart
functioning [3, 4]. Fibroblasts in cardiac fibrosis are
thought to be derived from epithelial-mesenchymal
transition (EMT) of the epicardium-derived cells
(EPDC) and promote their differentiation into fibroblast
phenotype under the influence of growth factors,
including TGF-β [5, 6]. Coupling of TGF-β with its
cell-surface receptors signals, the Smad pathway
mediates the transcriptional processes of some central
fibrosis genes, such as fibronectin, collagens [7]. Although the use of TGF-β as a molecular target has The fibrotic formation is an important pathological
characteristic linked to many types of cardiac disorders,
such as myocardial infarction, myocardial ischemia,
hypertrophic cardiomyopathies, and cardiac failure [1]. The fundamental of fibrotic formation is the adverse
collection of collagen and extracellular matrix (ECM)
proteins, which damage normal cardiac function and
cause arrhythmia [2]. The fibrotic ECM leads to
elevated rigidity and triggers pathological signals in
cardiocytes, which result in heart failure. Fibroblasts
primarily cause the deposition of the extra fibrotic AGING 11865 www.aging-us.com was found to be elevated in the peri-infarct area (PIA)
of rat heart compared to that of the control/sham-
operated animals, as shown in Figure 1A. In contrast to
the cells of the control group, the CFs from the neonatal
rats after serum treatment showed increased miR-27
expression, as shown in Figure 1B. Additionally, Figure
1C reveals that miR-27b expression was enhanced after
treating CFs with AngII (100 nM), a commonly used
stimulus to induced cardiac fibrosis [13]. Besides, the
CFs exhibited about 2-fold higher miR-27b expression
relative to the cardiac monocytes (CMs) (Figure 1D). Furthermore, serum or AngII treatment did not
significantly increase the miR-27b level in CMs
(Supplementary Figure 1A, 1B), suggesting the specific
role of miR-27b in CFs. To further confirm the
regulation of miR-27b, we study its expression in acute
ischemic stroke patients. Compared to the healthy
controls, the acute ischemic stroke patients showed an
expected rise in the miR-27b level in their circulating
plasma (Figure 1E). Therefore, miR-27b was presumed
to be involved in cardiac fibrosis. been seen as a promising anti-fibrosis treatment, its
impact on the cardiovascular system is ambiguous. Therefore, more efforts should be made to identify
novel therapeutic targets for cardiac fibrosis. INTRODUCTION MicroRNAs (miRNAs/miRs) have recently been under
the spotlight to be one of the influential factors
mediating gene expression, and essentially have an
impact on the pathogenic mechanism underlying
various
diseases,
including
myocardial
fibrosis
[6, 8]. The miRNAs are highly conserved small
noncoding RNAs that enable gene silencing by post-
transcriptional mRNA degradation and suppression of
the expressed protein [9]. miRNAs are formed in a
strictly regulated process within the nucleus and are
subsequently moved to the cell cytoplasm for
processing the next step [9]. Several studies have
indicated the significant contribution of miRNAs during
the initiation and progression of diseases by regulating
certain signaling pathways. The up-regulation of miR-
21 stimulates the development of fibrosis [8], while
enhanced overexpression of miR-29, miR-30, miR-
133, or miR-590 [10] restrained the fibrotic reactions of
cardiac fibroblasts (CFs). A recent study showed that
overexpression of miR-27b in cardiocytes triggers
cardiac hypertrophy and other disorders in animals [11]. However, the role and underlying mechanism for the
infarction induced and miR-27b mediated cardiac
fibrosis remains obscure. Moreover, a recent study
reported that miR-27b also takes effects in mediating
cancer cell EMT, and promotes cancer invasion and
metastasis [12]. We, therefore, hypothesized that miR-
27b might also promote EMT in cardiac fibrosis. MiR-27b promotes CF proliferation To evaluate the role of miR-27b in cardiac fibrosis, the
effect of miR-27b on neonatal CFs proliferation was
evaluated by cell counting and MTT assay. The
proliferation of CFs showed a steep rise upon treatment
with AngII (100 nmol/L), as shown in Figure 2A–2C. Transfection of the miR-27 antagonist (miR-27i, 50
nmol/L) eliminated the AngII induced CF proliferation,
working as miR-27’s specific inhibitor (Figure 2A–2C). Similarly, mRNA expression of collagen I, collagen III,
and pro-matrix metalloproteinase (MMP)-9 increased
after treatment with 100 nmol/L of AngII (Figure 2D),
which was abolished after transfecting the cells with 50
nmol/L miR-27i (Figure 2D). Then transfection with
miR-27b was performed to study its role in the
proliferation of CFs. The results showed that both the
growth and proliferation were promoted by the
enhanced miR-27b expression (Figure 2E, 2F). Accordingly, collagen I, collagen III, and MMP-9
showed higher mRNA levels upon enhanced miR-27b
expression (Figure 2G). Therefore, miR-27 was
presumed to have a key impact on the CF cell
proliferation and ECM expression. Our experiments investigated the cardiac infarction
induced fibrosis, and found the capability of miR-27b,
which is a frequently upregulated miRNA in hyper-
trophic and postinfarct hearts, to promote the CF
generation in rats. We also observed that miR-27b
inhibition by adenovirus transfection alleviated cardiac
interstitial fibrosis and improved left ventricular
compliance of rats subjected to coronary artery ligation. Our research suggested that manipulating the expression
of miR-27b could be a potential treatment direction
towards curing heart fibrotic disease. MiR-27b increases in cardiac fibrosis patients and
infarcted heart of rats The collagen I and III, and MMP-9 are reported to have
crucial modulatory effects on cardiac fibrosis. We
investigated the expression of their upstream factors,
including Twist, TGF-β, SMAD3/4, and Snail, in CFs
upon AngII treatment [7, 14]. Our results showed that
AngII treatment in CFs induced the expression of Twist, To investigate the role of miR-27 in the cardiac fibrosis,
its expression in rat post-infarct cardiac tissues and
cultured CFs was first detected under the conditions
with significant CF proliferation. At 2, 6, and 12 d post-
coronary artery ligation (CAL), the miR-27 expression AGING 11866 www.aging-us.com Figure 1. The miR-27b expression (A–C) The miR-27b expression in PIA of infarcted heart at different time points (A) and 10 % serum-treated
CFs of rats (B) or angiotensin II (AngII, 100 nM; C) at designated time points. (D) The miR-27b expression in CMs and CFs. Data were
represented as mean ± SEM (n=4). (E) The miR-27b expression in plasma specimens of healthy participants (n=16) and cardiac fibrosis
patients (n=19). *, p<0.05; **, p<0.01; ***, p<0.001. Figure 1. The miR-27b expression (A–C) The miR-27b expression in PIA of infarcted heart at different time points (A) and 10 % serum-treated
CFs of rats (B) or angiotensin II (AngII, 100 nM; C) at designated time points. (D) The miR-27b expression in CMs and CFs. Data were
represented as mean ± SEM (n=4). (E) The miR-27b expression in plasma specimens of healthy participants (n=16) and cardiac fibrosis
patients (n=19). *, p<0.05; **, p<0.01; ***, p<0.001. igure 2. miR-27b expression promoted cardiac fibrosis (A–C) Supplementation of antagomiR-27b (miR-27i) inhibited the CF proliferation in
eonatal rats. (A) Counting of cell numbers. (B) MTT analysis. (C) BrdU assay. (D) Collagen I, III, and MMP-9 mRNA levels in CFs treated with
AngII in combination with miR27i. (E, F) Supplementation of miR-27b stimulated the proliferation of neonatal rats CF. (E) MTT test. (F) BrdU
ssay. (G) Collagen I, III, and MMP-9 mRNA levels in miR-27b-treated CFs. Data were represented as mean ± SEM (n=4). *, p<0.05; **, p<0.01. Figure 2. miR-27b expression promoted cardiac fibrosis (A–C) Supplementation of antagomiR-27b (miR-27i) inhibited the CF proliferation in
neonatal rats. (A) Counting of cell numbers. (B) MTT analysis. (C) BrdU assay. (D) Collagen I, III, and MMP-9 mRNA levels in CFs treated with
AngII in combination with miR27i. (E, F) Supplementation of miR-27b stimulated the proliferation of neonatal rats CF. (E) MTT test. MiR-27b increases in cardiac fibrosis patients and
infarcted heart of rats (F) BrdU
assay. (G) Collagen I, III, and MMP-9 mRNA levels in miR-27b-treated CFs. Data were represented as mean ± SEM (n=4). *, p<0.05; **, p<0.01. AGING 11867 www.aging-us.com TGF-β, and Snail, as well as the phosphorylation of
SMAD3/4 (Figure 3A, Supplementary Figure 2A). However, miR-27b antagonist treatment specifically
suppressed the induction of Snail, without influencing
the
AngII-induced
TGF-β,
Twist
expression,
or
phosphorylation of SMAD3/4 (Figure 3B, Supplementary
Figure 2B). It was further demonstrated that miR-27b
transfection in CFs specifically induced Snail, and not
Twist, TGF- β, p-SMAD3/4 (Figure 3C, Supplementary
Figure 2C). These results suggest that the expression of
Snail might contribute to miR-27b mediated cardiac
fibrosis. To validate this hypothesis, the CFs were
transfected with Snail siRNA. We found that depletion of Snail suppressed the cell growth and proliferation induced
by AngII or miR-27b (Figure 3D, 3E). Moreover, the
absence of Snail also abrogated the expression of collagen
I and III, and MMP-9 induced by AngII or miR-27b in
CFs (Figure 3F). Therefore, our results suggest that Snail
mediated the proliferative effect of miR-27b as well as the
cellular matrix growth in CFs. The miR-27b enhances the expression of Snail by
targeting FBW7 In the next step, we tried to explore the mechanism
underlying miR-27b mediated induction of Snail. Figure 3. Snail mediated proliferative effects of miR-27b on CFs. (A–C) TGF-β, Twist, SMAD3/4, p-SMAD3/4, and Snail expression
levels in CFs treated with AngII (A), AngII combined with miR-27i (B), and miR-27b (C). (D, E) The effect of silencing Snail on CFs cell
proliferation induced by AngII or miR-27b was analyzed by MTT test (D) and BrdU assay (E). (F) Collagen I, III, and MMP-9’s mRNA levels in CFs
subjected to treatment in (D). Data were represented as mean ± SEM (n=4). *, p<0.05. Figure 3. Snail mediated proliferative effects of miR-27b on CFs. (A–C) TGF-β, Twist, SMAD3/4, p-SMAD3/4, and Snail expression
levels in CFs treated with AngII (A), AngII combined with miR-27i (B), and miR-27b (C). (D, E) The effect of silencing Snail on CFs cell
proliferation induced by AngII or miR-27b was analyzed by MTT test (D) and BrdU assay (E). (F) Collagen I, III, and MMP-9’s mRNA levels in CFs
subjected to treatment in (D). Data were represented as mean ± SEM (n=4). *, p<0.05. AGING 11868 www.aging-us.com We firstly investigated the transcriptional control of
Snail, and found that AngII substantially enhanced the
mRNA levels of Snail (Figure 4A). However, the
AngII mediated induction of Snail was clearly un-
influenced in the presence of the miR-27b antagonist
(Figure 4A). Supplementation of miR-27b in CFs also
failed to show any obvious variation in the mRNA
expression of Snail (Figure 4B). These results
suggested that miR-27b did not target Snail at its
transcriptional level. We therefore investigated the
role of miR-27b in its protein expression. DNA
translation inhibition by cycloheximide (CHX) led to
degradation of Snail within 6 h (Figure 4C). However,
miR-27b transfection in CFs inhibited the degradation
of Snail (Figure 4C). The ubiquitination of Snail was
also observed in CFs when pretreated with protease
inhibitor (MG132, 5 µM) (Figure 4D). As expected,
miR-27b supplementation also compromised the ubiquitination of Snail (Figure 4D), suggesting that
miR-27b mediated the induction of Snail by inhibiting
its ubiquitination and degradation. The bioinformatics tool TargetScan (http://genes.mit. edu/targetscan/) was employed for the screening of the
potential miR-27b target mRNAs involved in protein
ubiquitination, so as to study the possible impact of
miR-27b on Snail ubiquitination. FBW7 was identified
in this process, where mRNA 3′-UTR regions were
composed of seed sequences and flanking nucleotides
matching miR-27b (Figure 4E). The miR-27b enhances the expression of Snail by
targeting FBW7 Consistently, FBW7 overexpression also suppressed the
proliferative effect of miR-27b on CFs (Figure 5E, 5F). Furthermore, antagomiR-27b treatment rescued the
expression of FBW7, which was hindered by AngII
treatment, but suppressed the induction of Snail (Figure
5G). Silencing of FBW7 by its siRNA also abolished the
suppressive effect of antagomiR-27b on the expression of
Snail (Figure 5G), and promoted cell proliferation (Figure
5H, 5I). Cumulatively, our results suggest that miR-27b
mediates the induction of Snail by targeting FBW7
regulation. (Supplementary Figure 3B). Therefore, these results
collectively suggested that miR-27b directly targeted the
3’-UTR of FBW7, and suppressed its expression. We
transfected the CFs with FBW7 plasmid along with miR-
27b so as to verify the effect of FBW7 on the miR-27b
mediated proliferation of CFs and matrix production. Our
results indicated that FBW7 expression in CFs suppressed
the induction of Snail, collagen I and III, and MMP-9,
mediated
by
miR-27b
transfection
(Figure
5D). Consistently, FBW7 overexpression also suppressed the
proliferative effect of miR-27b on CFs (Figure 5E, 5F). Furthermore, antagomiR-27b treatment rescued the
expression of FBW7, which was hindered by AngII
treatment, but suppressed the induction of Snail (Figure
5G). Silencing of FBW7 by its siRNA also abolished the
suppressive effect of antagomiR-27b on the expression of
Snail (Figure 5G), and promoted cell proliferation (Figure
5H, 5I). Cumulatively, our results suggest that miR-27b
mediates the induction of Snail by targeting FBW7
regulation. overexpression
of
FBW7
also
increased
the
ubiquitination of Snail (Figure 4H). Therefore, FBW7
was found to have an intermediary role in the Snail
protein degradation in the CFs. The miR-27b enhances the expression of Snail by
targeting FBW7 Next, we investigated
the effect of FBW7 on the degradation and
ubiquitination of Snail and found that in the absence of
any treatment, FBW7 can interact with Snail in the CFs
(Figure 4F). Enhanced expression of FBW7 in CFs
abolished the protective effect of miR-27b on the
degeneration of Snail (Figure 4G). Furthermore, miR-27b modulated the expression of Snail by inhibiting its degradation (A, B) The mRNA level of Snail in CFs treated w
bined with miR-27i (A) or miR2-7b (B). (C) The effect of miR-27b on the expression of Snail in CFs treated with cycloheximide (CHX
ndicated time points. (D) Roles of miR-27b in Snail ubiquitination. (E) Characterization of the messenger RNA (mRNA) of FBW7, whi
miR-27b binding site (BS) in its 3′-untranslated region (UTR). (F) The interaction of FBW7 and Snail in CFs. (G) The effect of FBW
sion on the expression of Snail in CFs treated with cycloheximide (CHX, 1 μg/ml) at indicated time points. (H) The effect of FBW
sion on the ubiquitination of Snail. Arrow indicates the GFP-FBW7. Data were represented as mean ± SEM (n=4). N, p>0.05. Figure 4. miR-27b modulated the expression of Snail by inhibiting its degradation (A, B) The mRNA level of Snail in CFs treated with
AngII combined with miR-27i (A) or miR2-7b (B). (C) The effect of miR-27b on the expression of Snail in CFs treated with cycloheximide (CHX, 1
μg/ml) at indicated time points. (D) Roles of miR-27b in Snail ubiquitination. (E) Characterization of the messenger RNA (mRNA) of FBW7, which
depicted miR-27b binding site (BS) in its 3′-untranslated region (UTR). (F) The interaction of FBW7 and Snail in CFs. (G) The effect of FBW7
overexpression on the expression of Snail in CFs treated with cycloheximide (CHX, 1 μg/ml) at indicated time points. (H) The effect of FBW7
overexpression on the ubiquitination of Snail. Arrow indicates the GFP-FBW7. Data were represented as mean ± SEM (n=4). N, p>0.05. AGING 11869 www.aging-us.com (Supplementary Figure 3B). Therefore, these results
collectively suggested that miR-27b directly targeted the
3’-UTR of FBW7, and suppressed its expression. We
transfected the CFs with FBW7 plasmid along with miR-
27b so as to verify the effect of FBW7 on the miR-27b
mediated proliferation of CFs and matrix production. Our
results indicated that FBW7 expression in CFs suppressed
the induction of Snail, collagen I and III, and MMP-9,
mediated
by
miR-27b
transfection
(Figure
5D). FBW7 acts as the target of miR-27b in cardiac
fibrosis In order to verify the role of FBW7 as the downstream
target miR-27b, its mRNA levels were investigated under
different circumstances of miR-27b activation. The
transfection of miR-27b or treatment of AngII in the CFs
substantially suppressed the transcript levels of FBW7
(Figure 5A, 5B). The mRNA expression of FBW7 was
lowered at 2, 6, and 12 days post-CAL in the PIA of rats
heart, when compared with sham-operated animals
(Figure 5C). Consistently, miR-27b transfection or AngII
treatment also suppressed the luciferase activity of FBW7
(Supplementary Figure 3A, 3B). Inhibition of miR-27b by
its antagonist recovered the luciferase reporter activity igure 5. FBW7 was the miR-27b target in cardiac fibrosis (A–C) The mRNA levels of FBW7 in serum-treated CFs (A), AngII (B), or miR-
7b (C). (D) Snail expression in CFs transfection with miR-27b and/or peGFP-FBW7 plasmids. (E, F) The proliferation of CFs treated in (D) were
nalyzed by MTT test (E), and BrdU assay (F). (G) CFs transfected with miR-27i and/or FBW7 siRNA were subjected to AngII treatment as
ndicated. Snail expression was analyzed using WB. (H, I) The proliferation of CFs treated in (G) was analyzed by MTT test (H), and BrdU assay
). Data were represented as mean ± SEM (n=4). *, p<0.05; **, p<0.01. Figure 5. FBW7 was the miR-27b target in cardiac fibrosis (A–C) The mRNA levels of FBW7 in serum-treated CFs (A), AngII (B), or miR-
27b (C). (D) Snail expression in CFs transfection with miR-27b and/or peGFP-FBW7 plasmids. (E, F) The proliferation of CFs treated in (D) were
analyzed by MTT test (E), and BrdU assay (F). (G) CFs transfected with miR-27i and/or FBW7 siRNA were subjected to AngII treatment as
indicated. Snail expression was analyzed using WB. (H, I) The proliferation of CFs treated in (G) was analyzed by MTT test (H), and BrdU assay
(I). Data were represented as mean ± SEM (n=4). *, p<0.05; **, p<0.01. AGING 11870 www.aging-us.com Inhibition of miR-27b suppresses interstitial fibrosis
of the infarcted heart evaluate the deposition of ECM. In comparison to the
sham-operated control groups, the MI groups showed
obviously elevated interstitial fibrotic area and collagen
accumulation (Figure 6B, 6C). Administration of
antagomir-27b significantly alleviated the collagen I
deposition and the fibrotic area (Figure 6B, 6C). Additionally, the peri-infarct myocardium shows a
reduction in collagen I, collagen III, and MMP-9,
indicating that antagomir-27b mitigated the peri-infarct
ECM deposition (Figure 6D). FBW7 acts as the target of miR-27b in cardiac
fibrosis In addition, the variations
of FBW7 and Snail expression in MI heart PIA were
reversed upon antagomir-27b treatment (Figure 6E). Therefore, our in vivo data also supports the significant
effect of miR-27b on cardiac fibrosis after MI. DISCUSSION To investigate the function of miR-27b in the
cardiac fibrosis after cardiac infarct, CFs treated with
AngII were used as an in vitro model of cardiac
fibrosis [16], and experiments in rats CAL induced
cardiac infarct were used as an in vivo model. Collagen
generation and CF proliferation were enhanced post
upregulation of miR-27b due to cardiac infarction. The
present investigation showed that miR-27b inhibition
impaired cardiac function of the MI hearts by
suppressing the cardiac fibrosis in CAL heart. Additionally, miR-27b was observed to stimulate
cardiac fibrosis via suppression of FBW7-mediated
Snail degradation (Supplementary Figure 4). The miRNA dysregulation is a commonly observed
phenomenon in a wide range of diseases [17] and their
pathogenesis. In ischemic heart disease, dilated cardiac
myopathy, aortic stenosis, and many other heart-related
diseases, the cardiac tissues often show decreased miR-
101 expression [18]. Compared with CMs, CFs showed a
higher abundance of miR-30c (antifibrotic miRNA)
[19]. The levels of the profibrotic miRNA, miR-21, are
increased selectively in fibroblasts of the failing heart
[20]. In this study, we observed that miR-27b was
upregulated in cardiac tissue after infarct. Furthermore,
we provided the first direct evidence to prove that miR-
27b overexpression is sufficient to induce cardiac fibrosis
and proliferation both in vitro and in vivo. It is
noteworthy that miR-27b is frequently upregulated in
pressure-overloaded
hypertrophic
hearts
[11,
21]. Nevertheless, no clear results have been achieved
pertaining to the role exerted by miR-27b on cardiac
fibrosis. Here, the loss-of-function and gain-of-function
routes were employed to investigate the in vivo and in
vitro impact on cardiac fibrosis, both pathologically and
physiologically. Notably, the overloaded pressure-induced
fibrosis effects were clearly abated by miR-27b inhibition
in vivo, which is of clinical significance to these diseases. As to the mechanism of miR-27b mediated Snail
expression, we found that FBW7 is the E3 ligase of
Snail, which is targeted by miR-27b. It has been
reported that miR-27 negatively controls the expression
of the FBW7, which targets the cell cycle regulator,
cyclin E [25]. Moreover, miR-27b is overexpressed and
targets FBW7 in human hepatocellular carcinoma,
which is associated with poor clinical outcome
[26]. The overexpression of miR-27b led to obvious
FBW7 suppression in CFs and infarcted hearts, proven
by the high expression of miR-27b in infarcted hearts
and proliferative CFs, and its potential key role in
cardiac fibrosis. DISCUSSION DISCUSSION and thus regulates fibroblast survival and growth factor
secretion [8]. Also, miR-30 and miR-133 directly
participate in the downregulation of Hey inducer
(connective tissue growth factor) ECM synthesis to
exert control over the extent of interstitial fibrosis [19]. The present study demonstrates that miR-27b could
target FBW7 and suppress Snail degradation, which
promotes CF proliferation and ECM synthesis, resulting
in cardiac fibrosis. In the mice group with carbon
tetrachloride and ureteral obstruction treatments, the
liver and kidney fibrosis are strongly associated with a
zinc finger transcription factor (Snail) which is
frequently seen to be expressed in the mesenchymal
cells [22, 23]. In the heart, Snail has been shown to be
expressed in cardiac fibroblasts and contribute to
fibrosis, especially in mesenchymal (non-epithelial)
cells in the heart following injury [24]. Snail is also
involved in the expression of crosslinking genes and
modifications in the extracellular collagen. Collagens I
and III are the primary collagens secreted by the cardiac
fibroblasts/myofibroblasts in the infarcted myocardium
in response to pro-fibrotic factors. TGF-β, a potent
stimulator of collagen production by cardiac fibroblasts,
is induced in response to cardiovascular injury. It has
been reported that antifibrosis treatment can be
achieved by targeting TGF-β. However, due to the
additional functions of TGF-β in different fibrotic
pathologies such as post-MI remodeling (leading to
heart failure progress) and postangioplasty restenosis,
no evidence was obtained for its role in the
cardiovascular system [1]. In contrast, Snail regulates
the fibrosis pathway more specifically by promoting
fibroblast proliferation and ECM production in fibrotic
disorders. It was also reported that Snail absent cardiac
fibroblasts have reduced collagen I mRNA expression
and collagen deposition in response to TGF-β,
suggesting that manipulating the expression of Snail is
an alternative means to treat cardiac fibrosis. Our data
indicated that miR-27b promoted the expression of
Snail without the involvement of the TGF-β/SMAD
pathway, which makes miR-27b inhibition to be a
promising mode of treatment for cardiac fibrosis. Cardiac fibrosis might be associated with unfavorable
cardiovascular outcomes, since it plays a key role in
cardiac remodeling [15]. As reported previously,
overexpression of miR-27b in primary cultured
cardiomyocytes promoted hypertrophic cell growth by
targeting the peroxisome proliferator-activated receptor-
γ (PPAR-γ) [11]. Nevertheless, no clear evidence was
shown for the mechanism of miR-27b in cardiac
fibrosis. Inhibition of miR-27b suppresses interstitial fibrosis
of the infarcted heart To test whether miR-27b inhibition was truly beneficial
for cardiac diseases, we injected antagomir-27b (miR-
27i) into rat subjected to coronary artery ligation (CAL)
induced myocardial infarction (MI). First, we tested the
effect of antagomir-27b in vivo and found that mature
miR-27b was significantly downregulated in hearts by
antagomir-27b administration (Figure 6A). One of the
main factors affecting the cardiac compliance MI
depression and myocardial stiffness aggravation is
interstitial fibrosis. Masson trichrome and Laminin
staining were conducted on the tissue sections to ure 6. Antagomir-27b attenuated cardiac fibrosis in rat model of MI (A) Real-time PCR results of miR-27b levels in miR-27i or saline-
ted specimens (3 weeks post-injection). (B, C) Analytical results of miR-27i-treated peri-infarct area of rat heart (3 weeks post-treatment). Typical heart sections after treatments of Masson trichrome staining, laminin and collagen I immunostaining. Scale bar, 20 µm. (C) The
centage of tissue area represented the deposition of collagen I, where the automated image analyzer was used for its quantification. (D)
ntitative reverse transcription–PCR results of collagen I, collagen III, and MMP-9 mRNA levels. (E) FBW7 and Snail expression in rat heart. a were represented as mean ± SEM (n=6). *, p<0.05; **, p<0.01. Figure 6. Antagomir-27b attenuated cardiac fibrosis in rat model of MI (A) Real-time PCR results of miR-27b levels in miR-27i or saline-
treated specimens (3 weeks post-injection). (B, C) Analytical results of miR-27i-treated peri-infarct area of rat heart (3 weeks post-treatment). (B) Typical heart sections after treatments of Masson trichrome staining, laminin and collagen I immunostaining. Scale bar, 20 µm. (C) The
percentage of tissue area represented the deposition of collagen I, where the automated image analyzer was used for its quantification. (D)
Quantitative reverse transcription–PCR results of collagen I, collagen III, and MMP-9 mRNA levels. (E) FBW7 and Snail expression in rat heart. Data were represented as mean ± SEM (n=6). *, p<0.05; **, p<0.01. AGING 11871 www.aging-us.com DISCUSSION This also revealed the involvement of The alteration in the key signaling pathways during the
pathological process of fibrosis is the usual reason for
the miRNA-mediated fibrotic regulation at the molecule
level. Interestingly, miR-21 augments extracellular
signal-regulated
kinase–mitogen-activated
protein
kinase activity through inhibition of sprouty homolog 1 AGING 11872 www.aging-us.com FBW7 in cardiac fibrosis. FBW7 could suppress tumors
by its important function in cell-cycle progression,
proliferation, and cell division in multiple cancers [27,
28]. FBW7 expression resulted in cell growth arrest,
increased
chemo-sensitivity,
and
inhibition
of
Epithelial-mesenchymal Transition (EMT), which led to
suppressed
lung
cancer
development
[29]. Mechanically, FBW7 directly interacts with Snail, the
transcription factor in EMT, and degrades its expression
through ubiquitylation alternation in NSCLC [29, 30]. A number of previous reports have illustrated the role of
FBW7 role in degrading Snail and enhancing EMT. However, no definite results have been acquired for
their potential role in EMT progression of cardiac
fibrosis. Our study revealed for the first time that FBW7
also contributes to inhibition of ECM formation in
cardiac fibrosis by targeting Snail degradation. artery (LAD) was ligated via a 5–0 silk thread, which
led to infarct of the left ventricular free wall. Heart
infarct was validated through significant S-T up-
regulation in ECG and defective cyanotic cardiac
muscle. The control surgery constituted a fake stitch in
the left cardiac pericardium. The rats got free access to
water and food post-operation. Modified antisense oligonucleotides (antagomir) were
synthesized on order (GenePharma). Treatments were
initiated 3 days post-surgery, and rats were injected
with 0.2 ml saline, antagomir-27b, one shot a day, for
three days through the tail veins [8]. Blood samples of patients with cardiac fibrosis We enrolled 19 patients with cardiac fibrosis and 16
healthy participants in the General Hospital of Tianjin
Medical University. The inclusion criteria involved
the diagnosis of cardiac fibrosis based on clinical
information. Blood was collected from each of the
participants for assessment. Transfection of cells The exponentially growing CFs were seeded into 6-well
plates (2 × 105 cells/well), followed by 24 h incubation. The transfection was performed using DharmaFECT 1 of
Life
Technologies,
Germany,
based
on
the
manufacturer’s instructions. Firstly, in the Opti-MEM
(Invitrogen, U.S.A.), the transfection agent was added to
75 nM mimics and incubated for 20 min, which was
further mixed with the serum-free medium. After 1 day,
hypertrophy-enhancing medium containing DMEM/high
glucose, 1% Insulin-Transferrin-Selenium (ITS)+3, 50
µg/ml ascorbate-2-phosphate, 40 µg/ml L-proline, and 1
nM triiodothyronine (Sigma–Aldrich, U.S.A.) was used
to replace the serum-free medium. Isolated and cultivated CFs of newborn rats Cardiac fibroblasts from newborn rats were processed as
follows: over ten hearts extracted from SD rats aged 1–3
days were cut and immersed in 0.25% trypsin solution. The cell suspension was subjected to centrifugation and
then resuspended in DMEM mixed with fetal bovine
serum (10%), streptomycin (100 μg/ml), and penicillin
(100 U/ml). The resuspension was plated onto culture
flasks for 90 min, after which the fibroblasts were
preferentially able to adhere to the flask bottom. This was
followed by the removal of weakly adherent cells (or
non-adherent cells), and media replacement. The cells
were grown till confluency and passaged using trypsin. The incubation of cells was carried out with air (95%)
and CO2 (5%) under the humidified condition at 37°C. In
the FBS containing media, the cardiac fibroblasts (CFs;
passage no. 2–4) were grown up to suboptimal
confluency and used for experiments. To conclude, the present study succeeded in identifying
miR-27b as a novel pro-fibrotic miRNA, raising an
interesting prospect for its use as a potential candidate
for targeted therapy. The infarcted hearts of rat showed
alleviated fibrosis growth after miR-27b was inhibited
in vivo, where the FBW7/Snail pathway was inhibited. Therefore, antagomiR-27b can be exogenously applied
for interceding cardiac fibrosis and its related
pathological mechanisms. Animals and cardiac infarction model Disease-free Sprague-Dawley (SD) male rats weighing
~200-250 g were utilized for our research and cultivated
for one week beforehand in standard in-house
conditions of 21 ± 1°C, humidity range of 55–60%, and
free access to water and food. All experimental tests of
our study were conducted in accordance with the rules
of the Institutional Animal Care and Use Committee in
the General Hospital of Tianjin Medical University, PR
China. To induce myocardial infarction (MI), the rats
were anesthetized with 100 mg/kg ketamine-xylazine
and subsequently subjected to artificial respiration by
inserting the polyethylene pipe via the mouth. The
thoracotomy on the left part was conducted in the 4th
intercostal section. Meanwhile, the pericardium was left
open to expose the heart. Next, the left descending In the present study, miR-27b and its antisense
oligonucleotides (antagomiR-27b) [31] were synthesized
by GenePharma of Shanghai GenePharma Co, Ltd. The
siRNA for FBW7 (L-115782-00-0005) and Snail (L-
093687-02-0005)
were
purchased
from
ON-
TARGETplus SMARTpool of Dharmacon (Lafayette, AGING 11873 www.aging-us.com CO, USA). The negative control was a scrambled siRNA
purchased from Dharmaco. The primer pair (forward, 5′-
ccggtcgacatgacacaaaagtggacaaca -3′; reverse, 5′-tttcatgtcc
acatcaaagtccaagcttgag-3′) was used for the amplification
of FBW7 mRNA (XM_002729089) encoding the
protein. This was followed by cloning the FBW7 cDNA
sequence to the cytomegalovirus promoter-containing
pEGFP-N1 vector, and the negative control was an empty
pEGFP-N1 plasmid. loading control in the western blotting experiment for
normalization. Real-time PCR Based on the manufacturer’s instructions, we isolated
the total RNA including miRNAs from the cultured
fibroblasts and cardiac tissues using NucleoSpin®
miRNA
kit
(Macherey–Nagel,
Germany). The
miRCURY LNATM Universal RT microRNA PCR of
Exiqon A/S, Vedbaek, Denmark, was used for reverse
transcription. On an ABI 7500 fast real-time polymerase
chain reaction system (Applied Biosystems, Foster City,
CA), the RNA levels of FBW7, Snail, MMP-9, collagen
I, and collagen III were detected using SYBR Green I
incorporation method [18]. On the other hand, TaqMan
MicroRNA Assay Kit (Applied Biosystems) was used
to detect the miR-27b levels, where the internal control
was U6. Additionally, PCR
primers
used
for
amplification of miR-27b are: 5′-TTTCTCGAGGAA
GATGCTCACCAGCCCTTTA-3′ (miR-27b sense) and
5′-TTTTCTAGAGCATCATCTTGCCAGCGACT-3′
(miR-27b antisense) [11]. In the present study, a previously described method
was used to perform immunohistochemical staining
[11]. Probing with anti-collagen I and anti-collagen III
antibodies (1:200 dilutions for both) were conducted
on the tissue sections for 2 h at 37°C. This was
followed by PBS washing for three times and the
addition of the corresponding secondary antibody. After 2 h of incubation at 37°C, the samples were
subjected to PBS washing prior to the addition of 3, 3′
Diaminobenzidine (DAB) for 5 min, followed by
hematoxylin counterstaining. Then the graded series of
alcohol was prepared for dehydration, and xylene was
employed for stepping. Subsequently, the samples
were mounted with neutral gums. An inverted
microscope (Nikon Eclipse TS 100, Japan), was used
for the observation of brown granules in the cells, with
a random selection of 6 fields. Masson’s trichrome staining and
immunohistochemistry Fixation was carried out for 24 h in phosphate-buffered
saline (PBS) using formalin (10%). The cardiac tissues
were dehydrated with alcohol, followed by paraffin
(4%) embedding. HE and Masson’s trichrome staining
was conducted on the sliced sections (5 μm) of the
tissues. The extent of myocardial fibrosis was assessed
by detecting the collagen volume fraction (CVF) using
Image-Pro Plus software. Finally, the mean CVF values
were obtained by blinding one investigator to the group
assignment. WB analysis The total protein was extracted from the cultured CFs,
and the levels were compared by immunoblotting the
proteins based on their expression in the left ventricular
peri-infarct area (PIA) of rats [32]. Antibodies used for
probing were anti-FBW7, anti-Snail, anti-SMAD3/4,
anti-phosphor-SMAD3/4 (Abcam, Cambridge, UK),
anti-Twist, anti-TGF-β, anti-ubiquitin, and anti-actin
antibody (Sigma-Aldrich Corp. St. Louis, MO, USA). The
corresponding
secondary
antibodies
were
purchased from Stressgen Biotechnologies Corporation,
Victoria, BC, Canada. Signals were used for detection
using the Enhanced Chemiluminescence (ECL) kit (GE
Healthcare, UK). Densitometry was employed to
quantify the protein levels. β-actin was used as the Luciferase reporter assay The 3′UTR of the FBW7 luciferase reporter plasmid
(pRL-TK 3′FBXW7 UTR) were obtained from
Addgene (#26649). For the luciferase reporter assay,
293 cells were seeded in a 24-well plate and incubated
for 24 hours before transfection. Next, luciferase
constructs and miR-27b, or its antagonist were co-
transfected into 293 cells using Lipofectamine 2000. Cells were collected at 48 hours after transfection, and
measured using the Dual-Luciferase Reporter System
(Promega, WI, USA), according to manufacturer’s
protocols. Four
independent
experiments
were
performed, and data were presented as mean ± SD. Evaluation of cell viability CytoTox 96® Non-Radioactive Cytotoxicity Assay
(lactate dehydrogenase; LDH; Promega Cor, Madison,
WI, USA) was employed to assess the viability of CFs
based on thiazolyl blue tetrazolium bromide containing
0.5 mg/ml MTT (Applichem Inc., Omaha, NE, USA)
based on the manufacturer’s protocol. Statistical analysis The t-test was used for statistical analyses, along with
the
one-way
analysis
of
variance
(ANOVA). Additionally, the Bonferroniʼs test was conducted for
pairwise multiple comparison. Data were represented as AGING 11874 www.aging-us.com 9.
Lorenzen J, Kumarswamy R, Dangwal S, Thum T.
MicroRNAs in diabetes and diabetes-associated
complications. RNA Biol. 2012; 9:820–27.
https://doi.org/10.4161/rna.20162
PMID:22664916 9. Lorenzen J, Kumarswamy R, Dangwal S, Thum T. MicroRNAs in diabetes and diabetes-associated
complications. RNA Biol. 2012; 9:820–27. https://doi.org/10.4161/rna.20162
PMID:22664916 https://doi.org/10.1016/j.cardiores.2006.10.002
PMID:17109837 mean ± SEM,
and
a
significant
difference
was
considered when P < 0.05. 8. Thum T, Gross C, Fiedler J, Fischer T, Kissler S,
Bussen M, Galuppo P, Just S, Rottbauer W, Frantz S,
Castoldi M, Soutschek J, Koteliansky V, et al. MicroRNA-21 contributes to myocardial disease by
stimulating MAP kinase signalling in fibroblasts. Nature. 2008; 456:980–84. CONFLICTS OF INTEREST The authors declare that they have no conflicts of
interests https://doi.org/10.1172/JCI31487
PMID:17332879 3. Gray MO, Long CS, Kalinyak JE, Li HT, Karliner JS. Angiotensin II stimulates cardiac myocyte hypertrophy
via paracrine release of TGF-beta 1 and endothelin-1
from fibroblasts. Cardiovasc Res. 1998; 40:352–63. https://doi.org/10.1016/S0008-6363(98)00121-7
PMID:9893729 3. Gray MO, Long CS, Kalinyak JE, Li HT, Karliner JS. Angiotensin II stimulates cardiac myocyte hypertrophy
via paracrine release of TGF-beta 1 and endothelin-1
from fibroblasts. Cardiovasc Res. 1998; 40:352–63. https://doi.org/10.1093/cvr/cvp130
PMID:19398468 2. Wynn TA. Common and unique mechanisms regulate
fibrosis in various fibroproliferative diseases. J Clin
Invest. 2007; 117:524–29. 11. Wang J, Song Y, Zhang Y, Xiao H, Sun Q, Hou N, Guo S,
Wang Y, Fan K, Zhan D, Zha L, Cao Y, Li Z, et al. Cardiomyocyte overexpression of miR-27b induces
cardiac hypertrophy and dysfunction in mice. Cell Res. 2012; 22:516–27. REFERENCES 10 Shan H, Zhang Y, Lu Y, Zhang Y, Pan Z, Cai B, Wang N,
Li X, Feng T, Hong Y, Yang B. Downregulation of miR-
133 and miR-590 contributes to nicotine-induced
atrial remodelling in canines. Cardiovasc Res. 2009;
83:465–72. 1. van Rooij E, Olson EN. Searching for miR-acles in
cardiac fibrosis. Circ Res. 2009; 104:138–40. https://doi.org/10.1161/CIRCRESAHA.108.192492
PMID:19179664 https://doi.org/10.1038/cr.2011.132
PMID:21844895 12. Liu L, Hu J, Yu T, You S, Zhang Y, Hu L. miR-27b-
3p/MARCH7 regulates invasion and metastasis of
endometrial cancer cells through Snail-mediated
pathway. Acta Biochim Biophys Sin (Shanghai). 2019;
51:492–500. https://doi.org/10.1093/abbs/gmz030
PMID:31006800 4. Jiang ZS, Jeyaraman M, Wen GB, Fandrich RR, Dixon
IM, Cattini PA, Kardami E. High- but not low-molecular
weight FGF-2 causes cardiac hypertrophy in vivo;
possible involvement of cardiotrophin-1. J Mol Cell
Cardiol. 2007; 42:222–33. 13. Schnee JM, Hsueh WA. Angiotensin II, adhesion, and
cardiac fibrosis. Cardiovasc Res. 2000; 46:264–68. https://doi.org/10.1016/S0008-6363(00)00044-4
PMID:10773230 https://doi.org/10.1161/CIRCRESAHA.114.302533
PMID:24577967 6. Thum T, Lorenzen JM. Cardiac fibrosis revisited by
microRNA therapeutics. Circulation. 2012; 126:800–02. https://doi.org/10.1161/CIRCULATIONAHA.112.12501
3 PMID:22811579 https://doi.org/10.1038/nature07511 This work was supported by the National Science
Foundation of China (31501056), National Research
Center of Engineering and Technology of Quality and
Safety
(2017NTQS0403)
and
National
Science
Foundation of China (No. 30600236). https://doi.org/10.1016/j.yjmcc.2006.09.002
PMID:17045289 5. Zhou B, von Gise A, Ma Q, Hu YW, Pu WT. Genetic fate
mapping demonstrates contribution of epicardium-
derived cells to the annulus fibrosis of the mammalian
heart. Dev Biol. 2010; 338:251–61. https://doi.org/10.1016/j.ydbio.2009.12.007
PMID:20025864 5. Zhou B, von Gise A, Ma Q, Hu YW, Pu WT. Genetic fate
mapping demonstrates contribution of epicardium-
derived cells to the annulus fibrosis of the mammalian
heart. Dev Biol. 2010; 338:251–61. 14. Rienks M, Papageorgiou AP, Frangogiannis NG,
Heymans S. Myocardial extracellular matrix: an
ever-changing and diverse entity. Circ Res. 2014;
114:872–88. 6.
Thum T, Lorenzen JM. Cardiac fibrosis revisited by
microRNA therapeutics. Circulation. 2012; 126:800–02.
https://doi.org/10.1161/CIRCULATIONAHA.112.12501
3 PMID:22811579 15. Chin CW, Messika-Zeitoun D, Shah AS, Lefevre G,
Bailleul S, Yeung EN, Koo M, Mirsadraee S, Mathieu T,
Semple SI, Mills NL, Vahanian A, Newby DE, Dweck MR. A clinical risk score of myocardial fibrosis predicts
adverse outcomes in aortic stenosis. Eur Heart J. 2016;
37:713–23. 7. Bujak M, Frangogiannis NG. The role of TGF-beta
signaling
in
myocardial
infarction
and
cardiac
remodeling. Cardiovasc Res. 2007; 74:184–95. AGING 11875 www.aging-us.com PMID:18309113 17. Divakaran V, Mann DL. The emerging role of
microRNAs in cardiac remodeling and heart failure. Circ
Res. 2008; 103:1072–83. https://doi.org/10.1161/CIRCRESAHA.108.183087
PMID:18988904 25. Chen KD, Huang KT, Lin CC, Weng WT, Hsu LW, Goto S,
Nakano T, Lai CY, Kung CP, Chiu KW, Wang CC, Cheng
YF, Ma YY, Chen CL. MicroRNA-27b Enhances the
Hepatic Regenerative Properties of Adipose-Derived
Mesenchymal Stem Cells. Mol Ther Nucleic Acids. 2016; 5:e285. 18. Pan Z, Sun X, Shan H, Wang N, Wang J, Ren J, Feng S,
Xie L, Lu C, Yuan Y, Zhang Y, Wang Y, Lu Y, Yang B. MicroRNA-101 inhibited postinfarct cardiac fibrosis
and improved left ventricular compliance via the FBJ
osteosarcoma oncogene/transforming growth factor-
β1 pathway. Circulation. 2012; 126:840–50. https://doi.org/10.1161/CIRCULATIONAHA.112.09452
4 PMID:22811578 https://doi.org/10.1038/mtna.2015.55
PMID:26836372 26. Sun XF, Sun JP, Hou HT, Li K, Liu X, Ge QX. MicroRNA-
27b exerts an oncogenic function by targeting Fbxw7 in
human hepatocellular carcinoma. Tumour Biol. 2016;
37:15325–32. https://doi.org/10.1007/s13277-016-5444-9
PMID:27704356 19. Duisters RF, Tijsen AJ, Schroen B, Leenders JJ, Lentink
V, van der Made I, Herias V, van Leeuwen RE,
Schellings MW, Barenbrug P, Maessen JG, Heymans S,
Pinto YM, Creemers EE. miR-133 and miR-30 regulate
connective tissue growth factor: implications for a role
of microRNAs in myocardial matrix remodeling. Circ
Res. 2009;104:170–8. 27. Davis RJ, Welcker M, Clurman BE. Tumor suppression
by the Fbw7 ubiquitin ligase: mechanisms and
opportunities. Cancer Cell. 2014; 26:455–64. https://doi.org/10.1016/j.ccell.2014.09.013
PMID:25314076 https://doi.org/10.1016/j.canlet.2018.01.047 30. Yang H, Lu X, Liu Z, Chen L, Xu Y, Wang Y, Wei G, Chen Y. FBXW7 suppresses epithelial-mesenchymal transition,
stemness
and
metastatic
potential
of
cholangiocarcinoma cells. Oncotarget. 2015; 6:6310–25. https://doi.org/10.18632/oncotarget.3355
PMID:25749036 22. Rowe RG, Lin Y, Shimizu-Hirota R, Hanada S, Neilson
EG, Greenson JK, Weiss SJ. Hepatocyte-derived Snail1
propagates liver fibrosis progression. Mol Cell Biol. 2011; 31:2392–403. https://doi.org/10.1161/CIRCRESAHA.108.182535 https://doi.org/10.1161/CIRCRESAHA.108.182535 28. Tong J, Tan S, Nikolovska-Coleska Z, Yu J, Zou F, Zhang
L. FBW7-Dependent Mcl-1 Degradation Mediates the
Anticancer Effect of Hsp90 Inhibitors. Mol Cancer Ther. 2017; 16:1979–88. https://doi.org/10.1158/1535-7163.MCT-17-0032
PMID:28619760 28. Tong J, Tan S, Nikolovska-Coleska Z, Yu J, Zou F, Zhang
L. FBW7-Dependent Mcl-1 Degradation Mediates the
Anticancer Effect of Hsp90 Inhibitors. Mol Cancer Ther. 2017; 16:1979–88. 20. Roy S, Khanna S, Hussain SR, Biswas S, Azad A, Rink C,
Gnyawali S, Shilo S, Nuovo GJ, Sen CK. MicroRNA
expression in response to murine myocardial infarction:
miR-21 regulates fibroblast metalloprotease-2 via
phosphatase and tensin homologue. Cardiovasc Res. 2009; 82:21–29. https://doi.org/10.1093/cvr/cvp015 PMID:19147652 29. Zhang Y, Zhang X, Ye M, Jing P, Xiong J, Han Z, Kong J, Li
M, Lai X, Chang N, Zhang J, Zhang J. FBW7 loss
promotes epithelial-to-mesenchymal transition in non-
small cell lung cancer through the stabilization of Snail
protein. Cancer Lett. 2018; 419:75–83. https://doi.org/10.1016/j.canlet.2018.01.047
PMID:29355657 https://doi.org/10.1093/eurheartj/ehv525
PMID:26491110 López-Novoa JM, Nieto MA. Snail1-induced partial
epithelial-to-mesenchymal
transition
drives
renal
fibrosis in mice and can be targeted to reverse
established disease. Nat Med. 2015; 21:989–97. https://doi.org/10.1038/nm.3901 PMID:26236989 16. Fujita K, Maeda N, Sonoda M, Ohashi K, Hibuse T,
Nishizawa H, Nishida M, Hiuge A, Kurata A, Kihara S,
Shimomura I, Funahashi T. Adiponectin protects
against angiotensin II-induced cardiac fibrosis through
activation of PPAR-alpha. Arterioscler Thromb Vasc
Biol. 2008; 28:863–70. 24. Lee SW, Won JY, Kim WJ, Lee J, Kim KH, Youn SW, Kim
JY, Lee EJ, Kim YJ, Kim KW, Kim HS. Snail as a potential
target molecule in cardiac fibrosis: paracrine action of
endothelial cells on fibroblasts through snail and CTGF
axis. Mol Ther. 2013; 21:1767–77. https://doi.org/10.1038/mt.2013.146 PMID:23760445 https://doi.org/10.1093/cvr/cvp015 PMID:19147652 21. Wang Y, Chen S, Gao Y, Zhang S. Serum MicroRNA-27b
as a Screening Biomarker for Left Ventricular
Hypertrophy. Tex Heart Inst J. 2017; 44:385–89. https://doi.org/10.14503/THIJ-16-5955
PMID:29276436 ischemia/reperfusion
injury.
PLoS
One.
2017;
12:e0172178.
https://doi.org/10.1371/journal.pone.0172178
PMID:28222148 ischemia/reperfusion
injury. PLoS
One. 2017;
12:e0172178. https://doi.org/10.1371/journal.pone.0172178
PMID:28222148 https://doi.org/10.1128/MCB.01218-10
PMID:21482667 31. Ji J, Zhang J, Huang G, Qian J, Wang X, Mei S. Over-
expressed microRNA-27a and 27b influence fat
accumulation and cell proliferation during rat hepatic 23. Grande MT, Sánchez-Laorden B, López-Blau C, De
Frutos CA, Boutet A, Arévalo M, Rowe RG, Weiss SJ, AGING 11876 www.aging-us.com stellate cell activation. FEBS Lett. 2009; 583:759–66.
https://doi.org/10.1016/j.febslet.2009.01.034
PMID:19185571 32. Ma J, Shui S, Han X, Guo D, Li T, Yan L. microRNA-200a
silencing protects neural stem cells against cerebral 32. Ma J, Shui S, Han X, Guo D, Li T, Yan L. microRNA-200a
silencing protects neural stem cells against cerebral AGING 11877 www.aging-us.com SUPPLEMENTARY MATERIALS Supplementary Figure 1. The miR-27b expression in CMs. The miR-27b expression in CFs treated with 10 % serum of rats (A) or
angiotensin II (AngII, 100 nM; B) at designated time points. Supplementary Figure 1. The miR-27b expression in CMs. The miR-27b expression in CFs treated with 10 % serum of rats (A) or
angiotensin II (AngII, 100 nM; B) at designated time points. Supplementary Figure 2. The western blot densitometry of several proteins as shown in Figure 3A–3C. Supplementary Figure 2. The western blot densitometry of several proteins as shown in Figure 3A–3C. AGING 11878 www.aging-us.com Supplementary Figure 3. miR-27b targets FBW7 3’-UTR. (A) The 3′-UTR of FBW7 luciferase reporter activity upon miR-27b co-
transfection. (B) The 3′-UTR of FBW7 luciferase reporter activity upon AngII treatment with or without co-transfection of miR-27i. Supplementary Figure 3. miR-27b targets FBW7 3’-UTR. (A) The 3′-UTR of FBW7 luciferase reporter activity upon miR-27b co-
transfection. (B) The 3′-UTR of FBW7 luciferase reporter activity upon AngII treatment with or without co-transfection of miR-27i. Supplementary Figure 4. A model of action. Supplementary Figure 4. A model of action. AGING 11879 www.aging-us.com
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Erratum Erratum ISSN 1984-2961 (Electronic)
www.cbpv.org.br/rbpv ISSN 1984-2961 (Electronic)
www.cbpv.org.br/rbpv 1-1
Braz J Vet Parasitol 2020; 29(2): e2001 | https://doi.org/10.1590/S1984-29612020021
This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited. Braz J Vet Parasitol 2020; 29(2): e2001 | https://doi.org/10.1590/S1984-29612020021 This is an Open Access article distributed under the terms of the Creative Commons Attribution License,
distribution, and reproduction in any medium, provided the original work is properly cited. Erratum In the article “First case report of nematode parasitic myelopathy in a wild feline in Brazil” (https://doi.org/10.1590/
s1984-29612019099) published in issue 1, volume 29, 2020, the Brazilian Journal of Veterinary Parasitology, on
page 1, which reads: Cláudia Ceruti Dazzi Cláudia Ceruti Dazzi Read up:
Cláudia Cerutti Dazzi Read up:
Cláudia Cerutti Dazzi 1-1 Braz J Vet Parasitol 2020; 29(2): e2001 | https://doi.org/10.1590/S1984-29612020021
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plementary Material S1. IPA pathway report of EMP1 plementary Material S1. IPA pathway report of EMP1 Supplementary Material S1. IPA pathway report of EMP1 ntary Material S2. EMP1 pathway map as drawn by IPA, Ingenuity Systems Supplementary Material S3. IPA pathway report of SND1 Supplementary Material S3. IPA pathway report of SND1
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Does Spotify Create Attachment?
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Does Spotify Create Attachment?
Algorithmic Playlists, Intermediation
and the Artist-Fan Relationship
By Adrian Leisewitz & George Musgrave By Adrian Leisewitz & George Musgrave This work is licensed under a Creative Commons
Attribution 4.0 International License Introduction Understanding the economic impact of streaming on musicians with a focus on
issues such as equitability and economic sustainability has risen to prominence
not only in academic discussions (Hesmondhalgh 2020, 2021; Hesmondhalgh,
et.al 2021) and the professional music industries (Music Ally 2019, Dredge 2020),
but in political and public policy circles too. The UK Government’s Digital,
Media, Culture and Sport (DCMS) Committee recently launched ‘The Economics
of Music Streaming’ (GOV 2020) inquiry, propelled by the #BrokenRecord
campaign on social media. As part of this inquiry, the committee sought to move
beyond economics alone, and instead engage with questions around the nature of
the relationship between streaming platforms and consumers, asking: “Have new
features associated with streaming platforms, such as algorithmic curation of music
or company playlists, influenced consumer habits, tastes, etc?” (ibid). Mulligan
(2019, in Griffiths 2019) argues that, indeed, they have influenced consumer
habits. He suggests that while music is being consumed more, less music is being
discovered ‘meaningfully’ and criticises the abilities of these new technologies
to transform casual listeners into fans; a phenomenon which appears alarming
given that these “dedicated aficionados” (Negus 2019: 375) are seen as important
income generators to artists, who – especially in a post Covid-19 environment –
are likely to be in financially precarious situations (ibid, Musicians’ Union 2012:
4, Dredge 2020). In other words, a critique is developing amongst commentators
within the professional music industries and beyond that streaming services
might not give context to songs (Jopling 2019, Mulligan 2019 in Griffiths, 2019),
and might therefore fail to generate fans outside of their own realms (Chartmetric
2018, Music Ally 2019). Arguments such as this have particular resonance for
artists working in genres such as rap and pop where being embedded within
digital methods of promotion such as Spotify playlists or TikTok can be crucial to
musical careers1.h This paper seeks to measure the extent to which algorithmically generated
playlists create ‘attachment’ between consumers of music and producers of music. By conceptualising streaming platforms as cultural intermediaries (Bourdieu 1984),
we argue that whilst cultural and economic scholars suggest that intermediation
results in attachment on behalf of consumers (Callon et.al 2002: 205, Smith
Maguire & Matthews 2012: 554), the term itself has not been robustly defined
beyond repeat purchases, nor has the phenomenon been examined empirically
in the context of streaming. Abstract This paper seeks to measure the extent to which algorithmically generated
playlists, conceptualised herein as cultural intermediaries (Bourdieu 1984),
create ‘attachment’ between consumers of music and producers of music. This
was undertaken following debates in the professional music press problematising
the ability of streaming platforms to create relationships between artists and
listeners and, in a wider discussion, to generate sustainable income for musicians
(Chartmetric 2018, Mulligan 2019 in Griffiths 2019, Music Ally 2019). We develop
the idea from cultural and economic scholars that intermediation results in
‘attachment’ on behalf of consumers (Callon et.al 2002, Smith Maguire & Matthews
2012) by formulating a definition of the term informed by insights from consumer
psychology and applying this framework to a 115-question survey completed by
listeners to Spotify’s ‘Discover Weekly’ Playlist for a one-week period. The findings
suggest that the playlist was able to generate almost no attachment for those
who were considered poorly-involved new music consumers, and only minor
to mid-levels of attachment for those participants considered heavily-involved
new music consumers. We therefore propose that this specific algorithmically
curated playlist might influence low-cost audience attachment behaviours while
its overall impact on the economic success of artists may be limited. This paper
contributes towards academic debates concerning the role and impact of cultural
intermediaries and lends early empirical support to discussions within the
professional music industries and wider public policy (GOV 2020) concerning the
uncertain ability of playlists to influence the artist-fan relationship. In addition, by
developing a more methodologically precise definition of ‘attachment’, it is hoped
that the framework provided by this modest study can act as a guide for other
researchers to explore the concept of intermediation and attachment with larger
sample sizes on alternative playlist types and on other digital platforms. Keywords: streaming, cultural intermediaries, attachment, playlists, Spotify Leisewitz, Adrian & Musgrave, George: “Does Spotify Create Attachment? Algorithmic
Playlists, Intermediation and the Artist-Fan Relationship”, Culture Unbound, Volume
14, Issue 1, 2022: 75–100. Published by Linköping University Electronic Press: http://
www.cultureunbound.ep.liu.se This work is licensed under a Creative Commons
Attribution 4.0 International License Does Spotify Create Attachment? Introduction Drawing on the work of consumer psychologists to
formulate a working definition of attachment, and applying this framework to a
survey of listeners to Spotify’s ‘Discover Weekly’ Playlist for a one-week period,
we present results which suggest that the playlist was able to generate close to
no attachment for those considered poorly-involved consumers and only minor 76 Does Spotify Create Attachment? 76 76 to mid-levels of attachment for those participants considered heavy new music
consumers. In this modest study we therefore propose that ‘Discover Weekly’ –
an algorithmically curated playlist – demonstrates an ability to influence only
low-cost audience attachment behaviours, suggesting a limited overall impact on
the economic success of artists. By synthesising consumer psychology, economic and cultural studies
literature to analyse the influence of algorithmic playlists through the prism
of attachment, this paper provides a deeper understanding of the impact of
taste-making on consumer behaviour. It also seeks to refine our understanding
of the results of cultural intermediation, which have been conceptualised with
varying levels of precision in existing academic discussions on the topic (Bourdieu
1984, Featherstone 1993, Callon et.al 2002: 205, Negus 2002, Hesmondhalgh
2006, Smith Maguire & Matthews 2012: 554, Powers 2015). Finally, we seek to
contribute towards debates concerning streaming services’ ability (or lack thereof)
to generate sustainable income for artists (Dredge 2020), and thereby highlight the
necessity of a holistic music marketing approach which seeks to build long-term
artist-fan relationships both within and outside of the playlist realm. Streaming Platforms as Cultural Intermediaries In his original conceptualisation, Bourdieu (1984) suggested that cultural
intermediaries, stemming from higher social backgrounds, are afforded influence
by virtue of their understanding of ‘legitimate culture’ and control over mass
media, enabling them to exert influence over middle class taste. Building on
Bourdieu’s (1984: 359) notion of cultural intermediaries encompassing all
occupations involved in “providing symbolic goods and services”, the range of
who might be considered as such has included designers (du Gay et al. 1997) or
even accountants involved in cultural production (Negus 2002). This approach,
however, was critiqued by Hesmondhalgh (2006: 226), who argues that this new
definition of cultural intermediaries equates to Bourdieu’s (1984: 359) definition
of the new petite bourgeoisie, which he had originally defined as a super-group
of the former (ibid). Whilst debates over who might be classified as a cultural
intermediary is thus subject to much debate (Featherstone 1993, du Gay et.al
1997, Negus 2002, Hesmondhalgh 2006, Smith Maguire & Matthews 2010, Prior
2013, Smith Maguire 2014), Smith Maguire & Matthews (2012: 2014), and Powers
(2015) suggest that cultural intermediaries today can be defined by their activities,
rather than social groups or occupations. This appears to unite Bourdieu’s (1984)
ideas with the interpretations made by Featherstone (1993) and Negus (2002) inter
alia, by focussing on “what they do, rather than what they are” (Smith Maguire
2014: 17). Does Spotify Create Attachment? 77 77 What do cultural intermediaries do, then? A definition which serves to
synthesise Bourdieu’s ideas with current literature is that; equipped with an
understanding of the cultural landscape and expertise, cultural intermediaries
select and recognise certain cultural goods as legitimate, thus increasing their
value in the form of recognition (symbolic capital) through discourse (Bourdieu
1991: 72, Negus & Pickering 2004: 18-19, Smith Maguire & Matthews 2012: 552,
Smith Maguire & Matthews 2014: 3). Indeed, cultural intermediaries have been
ascribed a significant role for the success of new music due to their perceived
ability to provide culture with value (Fairchild 2014, Musgrave 2017). Smith
Maguire (2014: 22) further concludes that cultural intermediaries need a deep
understanding of their own audiences (ideally by being part of them themselves)
in order to shape their views – a claim supported by Kuipers (2012: 600) and Moor
(2008: 424). Callon et al. Streaming Platforms as Cultural Intermediaries (2002: 205) argue that the more intermediaries frame a
good in accordance with a consumers’ values, the more consumers are inclined
to become detached from another good and attached to the good in question. This process, referred to by Callon et al. (2002: 205) as “requalification”, entails
a (re)-positioning of a good to meet the values of a consumer. It is questionable
whether the specific process of detachment applies to cultural goods such as music
however, given music’s status as a club (or toll) good which is non-rivalrous in its
consumption (Tschmuck, 2017), the ways in which consumers can hold multiple
parasocial relationships with human brands such as musicians in much the same
way we can have multiple friends and companions (see Thomson 2006: 105), and,
as per Torres (2019: 20) drawing on Latour and Stark (1999: 27): “There is not a
way of erasing the mark of that song that we hate now”. Nonetheless, the principle
of attachment through qualification chimes with the aforementioned processes
of providing value through singularisation and presentation. It may therefore be
concluded that the more intermediaries understand their audiences, the more
they are able to successfully impose their own values. This may not only serve
to underline the importance of audience understanding, but also explains one of
the results of their work. As suggested by Smith Maguire & Matthews (2012: 554)
cultural intermediaries’ framing of cultural goods results in an ‘attachment’ on
behalf of their audiences, and this attachment could possibly have a sustainable
impact on the economic success of goods. However, while Callon et.al (2002)
suggest that attachment for consumer goods can result in repeat purchases of
the same good, Smith Maguire & Matthews (2012) do not develop the idea of
attachment nor define the term. Thus, while ‘attachment’ has been employed
within cultural sociology to describe a sense of “fandom”, passion, or the
development of taste (Gomart and Hennion, 1999; Hennion, 2010), alongside a
phenomenological perspective too in the work of Redman (2008), an empirical
interrogation of the term in the context of intermediation debates remains Does Spotify Create Attachment? 78 78 78 78 underdeveloped (see Thomson 2006, and Loroz & Braig 2015 on attachment to
‘human brands’ for notable related examples). Is it reasonable to categorise streaming services as cultural intermediaries? In the first instance, streaming services play an increasingly important role in
new music discovery (Lindsay 2016, Datta et.al 2018). Streaming Platforms as Cultural Intermediaries Many have discussed the
ability of streaming services (primarily Spotify) to perform an act of presentation
through their recommendation systems (Mulligan 2014, Morris 2015, Kjus 2016,
Webster et.al 2016, Barna 2017, Eriksson and Johansson 2017, Snickars 2017,
Aguiar & Waldfogel 2018, Bonini & Gandini 2019: 8). Most of the streaming
services’ recommendations appear in the form of playlists, and Mulligan (2014)
suggests that playlists have become the most significant method of music
consumption. Indeed, as noted by Prey (2020: 2): “Spotify has become the focus
of promotional efforts across the recording industry. Much of this focus is on
playlists”. In addition, Spotify’s editorial teams are made of up music professionals
with knowledge of local cultures (Fleischer and Snickars 2017) and playlist
curators for streaming platforms have music industry backgrounds (Gross and
Musgrave 2020: 81) and utilise a network of industry actors to stay informed on
current music news (Bonini & Gandini 2019). Editorial teams at Spotify therefore
have the knowledge necessary to deem musical goods as legitimate, and with a
certain understanding of their audience necessary to exert an influence over
their taste, as least in principle (Fleischer & Snickars 2017: 139-140). Algorithmic
recommendations are suggested to be based on listeners’ taste profiles created
by data collected on the platform (Popper 2015, Eriksson & Johannson 2017:
177). Depending on the user’s intensity of use on the streaming site, they can
thus generate a more or less refined image of what music the listener may like
(Popper 2015). Finally, various writers have suggested that algorithms which
generate recommendations have a deeper understanding of the cultural field due
to their abilities to match similar songs based on similar audiences and playlists
that contain the track, skim the internet for discourse on certain artists/releases,
and identify tastemakers and analyse their preferences (Morris 2015, Webster
et.al 2016, Snickars 2017: 208, Tiffany 2017, Bonini & Gandini 2019: 6). Webster
et.al (2016) further argue that in these cases, cultural knowledge is generated by a
collaboration of human and algorithmic work i.e., the algorithm makes decisions
or recommendations based on human input, such as discourse on online blogs. Algorithms therefore collect and condense the knowledge of various human
actors in order to make recommendations. Does Spotify Create Attachment? Streaming Platforms as Cultural Intermediaries We therefore suggest that, drawing
on Smith Maguire’s (2014: 17) focus on “what [cultural] intermediaries’ do”, it
is thus reasonable to conclude that algorithmically curated playlists perform
the aforementioned activities of cultural intermediaries by: (i) the framing of
cultural goods as legitimate, (by selecting relevant music from an abundance of Does Spotify Create Attachment? 79 79 79 options), and (ii) seeking to provide goods with symbolic capital on the basis of
their knowledge of the cultural field (generated by both humans and algorithms). Indeed, given that they condense knowledge from various (human) sources as
well as having an in-depth understanding of their audiences (i.e., due to user
data), algorithmically curated playlists might arguably have superior abilities to act
as cultural intermediaries compared to a singular human actor. Considering this,
as well as their aforementioned importance in the contemporary music industries,
it may prove particularly insightful to interrogate algorithmically curated playlists’
efficacy as cultural intermediaries. l fi
However, to what extent do playlists exert the kind of influence over consumers
suggested, but not developed, in the work of Callon et.al (2002) and Smith Maguire
& Matthews (2012: 554)? That is, do algorithmically generated playlists engender
‘attachment’? The first challenge this presents is that the term does not receive
sufficient terminological interrogation in the academic literature. Aguiar and
Waldvogel (2018: 25-27), for example, found that being included on a humanly
curated playlist resulted in large numbers of streams for songs over a period of
100 days, thus suggesting that these recommendation systems could also lead to
increased consumer engagement. However, they further found that being on such
a playlist had no effect on song consumption outside of the platform (ibid: 17-18). Additionally, music industry media has critiqued an increased focus on playlists
due to an observation of many artists receiving high numbers of streams for those
songs that had been included on playlists but failing to generate purchases of their
products outside of the platform (Music Ally 2019). In short, given the existing
scholastic and media landscape, it is extremely difficult to answer the question as
to whether playlists generate ‘attachment’ i.e., to explore the efficacy of algorithmic
playlists at, in the words of the DCMS, “influencing consumer habits, tastes, etc”
(GOV 2020). In order to address this, the second step in this paper involves the
development of a more systematic working definition of attachment. Defining ‘Attachment’ In the absence of a clear definition of attachment from cultural and economic
scholars – particularly in terms of providing an empirical architecture to examine
the term in the context of intermediation - the most obvious starting point is the
field where the term has enjoyed the most meaningful interrogation: psychology. Developmental and evolutionary psychology scholars have discussed attachment
as an emotional bond based on a desire for proximity between individuals and
other individuals. As a consequence of feeling distressed when this connection
is withdrawn, individuals can demonstrate “attachment behaviours” in order
to maintain close proximity (Bowlby 1982: 668, 671, Hazan & Shaver 1994: 4). Does Spotify Create Attachment? 80 80 Consumer psychology scholars have built on these findings to suggest that these
patterns are reflected by consumers with emotional bonds to brands and products
too (Thomson et.al 2005: 81, 88, Schifferstein & Zwartkruis-Pelgrim 2008, Park
et.al 2010: 10). According to Thomson et.al (2005: 88) this can manifest in a
higher willingness to pay premium prices i.e., that the emotional bond is so strong
that consumers would rather pay above average prices than lose proximity to a
good. Whilst this method of contingent valuation has been widely used – notably
in environmental economics (Bateman & Willis 2000) – studies suggest the
construct is impacted by factors such as income (Horowirz & McConnell 2003),
necessitating some degree of caution. l Park et.al (2010) further argue that strong attachment is reflected by a higher
willingness to enact difficult behaviours in order to maintain a relationship with a
brand. This entails the willingness to regularly purchase a brands’ newest products,
promote it at personal expense, and waiting to purchase a product of said brand in
the future instead of purchasing a non-brand product immediately (ibid: 11). Given
the nature of new music being a product i.e., physically and digitally reproducible
sound recordings, and music artists being referred to as brands (Temple 2018),
it appears reasonable to apply these theoretical constructs to musical goods and
artists. Applied in this way, the ‘products’ might be concert tickets, merchandise
or physical releases (Forde 2018, Music Ally 2019). Furthermore, Park et.al (2010:
10-11) empirically connect brand attachment to actual purchase behaviour, thus
corroborating the idea set forth by Callon et al. (2002) that attachment results
in consumption. As such, Thomson et al. (2005) and Park et al. Defining ‘Attachment’ (2010) provide
us with a series of well-defined behavioural indicators of attachment; a higher
willingness to pay premium prices, and a higher willingness to enact difficult
behaviour in order to maintain a relationship with a brand. Alongside these behavioural dimensions of attachment, scholars in this area
also delineate three cognitive dimensions of attachment. Firstly, consumers who
show such an intense emotional bond to a product or brand are found to be likely
to see these as a part of their own identity (Schultz et.al 1989, Ball & Tasaki 1992:
158, Fournier 1998: 366, Schifferstein & Zwartkruis-Pelgrim 2008: 7, Park et.al
2010: 6). Secondly, Park et.al (2010: 2) suggest that highly attached consumers’
thoughts and memories towards attachment objects are likely to come to their
mind easily and automatically. Thirdly, Thomson et.al (2005: 79) argue that the
aforementioned anxiety of separation (Bowlby 1982: 671) increases with strong
attachment to brands, which is corroborated by Schifferstein & Zwartkruis-Pelgrim
(2008: 11). Finally, Schifferstein & Zwartkruis-Pelgrim (2008: 7) and Thomson
et.al (2005: 88) further suggest that strongly attached consumers are more likely
to feel positive emotions, such as enjoyment, affection, connection and passion. However, Park et.al (2010: 3) argue that analysing attachment through the prism Does Spotify Create Attachment? 81 81 81 of emotions may not serve to provide an accurate determination of attachment
strength, due to these being of an individual nature and thus difficult to
conceptualise. As such, this literature provides us additionally with three cognitive
indicators of strong attachment. i Refining the idea of attachment posed by Smith Maguire & Matthews
(2012) and Callon et al. (2002), it thus appears reasonable to assume that if
cultural intermediaries are able to influence the above behavioural and cognitive
indicators, their work might be described as resulting in attachment, thus arguably
influencing the success of new music. The question we seek to answer in this paper
is: to what extent are algorithmically generated playlists successful at generating
attachment defined in this way? Does Spotify Create Attachment? Methodology The study of digital streaming services is a new and emerging area of academic
inquiry ripe for methodological innovation, as per the work of Snickars (2017)
for example. Building on this, we sought to develop a new model to measure
the concept of attachment in two stages. Firstly, given that the intensity of music
consumption can vary greatly between individuals, a maximum variation sampling
approach was adopted in order to find two different kinds of music consumer. The
first were those heavily involved in new music discovery who might therefore be
likely to show what we call a high willingness to form attachment (HWTFA). This
consumer would be similar in some respects to those music consumers described
by the BPI (2017: 63) as “heavy spenders” or the IFPI (2019: 13) as “music fanatics”,
as they already show increased attachment behaviours towards musical goods they
like. The second were those who rarely sought to discover new music who might
therefore show what we call a low willingness to form attachment (LWTFA). This
consumer would be similar in some respects to those described by the IFPI (2019:
13) as considering music an “unimportant” part of their lives. Furthermore, as
Popper (2015) suggests, algorithmic recommendations become more refined the
more a consumer interacts with them. It is therefore further reasonable to see
heavy Discover Weekly users as more likely to form attachment than those who
rarely use the playlist. In this respect, music consumers are not homogenous, and
the sampling method employed in this study sought to reflect the wide variety of
potential engagement styles (and therefore potential attachment strengths), such
as those captured in the categorisations provided by the BPI and IFPI. A small initial sample of nine volunteer participants who self-identified as
users of Spotify’s algorithmically curated playlist ‘Discover Weekly’ were drawn
from a postgraduate Music Business Masters cohort alongside respondents to
an open call on social media (via an Instagram post on the researcher’s personal Does Spotify Create Attachment? 82 82 account) based on purposive sampling methods. These respondents took part
in a pre-survey to determine their relative willingness to form attachment based
on their responses to a Music Consumption Involvement task based on the
aforementioned attributes of consumers with either HWTFA or LWTFA (see
Appendix 1). From this, two consumers (one male, one female) were identified
as having HWTFA based on a Music Consumption Involvement score of >6. Methodology One was drawn from the postgraduate Music Business Masters cohort and one
from the open call. A further two consumers drawn from the open call (one male,
one female) were identified as having LWTFA based on a Music Consumption
Involvement score of <4.2 The participants were asked to use the ‘Discover Weekly’
playlist as the only tool for new music discovery for the duration of one week,
starting on a Monday given that the playlist is updated each week on this day
(Ditto 2018). They were further requested to block out all other ways to discover
new music e.g., radio, other streaming playlists, YouTube, Instagram livestreams,
etc. in order to increase the validity of their replies and reduce bias through
other influences. On the following Monday, participants were sent an online
questionnaire aiming to determine their levels of attachment after one week of
intermediary interaction. The questionnaire was devised in order to measure both behavioural
indicators of attachment i.e., higher willingness to pay premium prices, and higher
willingness to enact difficult behaviours, and cognitive indicators of attachment i.e.,
self-connection/identification, memories and thoughts, and separation anxiety. By synthesising and adapting the psychology and consumer psychology literature
discussed above, an online survey of 115 questions was created to measure
both indicators (see Appendix 2). Questions 1-7 were designed as classification
questions. Questions 8-30 aimed to determine the participants’ attachment
strength toward the most liked and previously unknown song on the playlist,
and questions 31-61 aimed to determine the extent to which the participants
became attached to musician performing the song. Our attachment construct
was therefore comprised of 54 questions. Finally, these questions were repeated
and adapted to measure attachment levels to the participants’ favourite songs and
artists outside ‘Discover Weekly’, in order to maximise validity. All replies were
coded to fit a 7-point Likert scale and each of the aforementioned five constructs
(two behavioural indicators and three cognitive indicators) were analysed by
calculating their respective arithmetic means. Attachment indices were calculated
over all replies in order to determine the participants’ total attachment strength,
with a score of 7 suggesting high attachment according to that variable, and a
score of 1 indicating an absence of attachment according to that variable. In this
sense, our construct sought to measure attachment strength which, according
to Thomson (2006: 105), “may provide a parsimonious and unidimensional Does Spotify Create Attachment? Methodology 83 83 83 indicator of “relationship quality” or strength”. Methodological details regarding
calculations have been included as endnotes for the purpose of clarification. Findings The findings presented below should be interpreted as offering initial data into the
relationships between cultural intermediaries, consumption and attachment, and
as an exercise in exploring the applicability and utility of our multi-dimensional
attachment construct. The small sample size does not provide sufficient strength
to make strong statistical inferences, but the differences observed between the
two groups of consumers in their attachment index scores suggests the tool is
accurately capturing differences in consumer responses and thus highlights
interesting and important areas for further research. Table 1. Overall Attachment Index3 4 Table 1. Overall Attachment Index3 4 Table 1. Overall Attachment Index3 4 Table 1. Overall Attachment Index3 4 An analysis of both behavioural and cognitive attachment indicators seen in Table
1 above suggests that the ‘Discover Weekly’ playlist was able to generate close to
no attachment for LWTFA participants. This lack of attachment was observed
both towards the individual songs, and the musician performing the song, as
will be delineated below. In addition, the playlist was only able to generate minor
to mid-levels of attachment for HWTFA participants towards both songs and
musicians. Whilst repeat listens of single tracks were relatively likely for these
consumers, the chances of repeat purchases were considerably lower. Does Spotify Create Attachment? 84 Consumers with Low Willingness to Form Attachment (LWTFA)
Table 2. LWTFA - Behavioural Indicators5
Table 3. LWTFA - Cognitive Indicators
Theconsumerswehavecategorisedashavingalowwillingnesstoformattachm Consumers with Low Willingness to Form Attachment (LWTFA) Consumers with Low Willingness to Form Attachment (LWTFA) Table 3. LWTFA - Cognitive Indicators Table 3. LWTFA - Cognitive Indicators The consumers we have categorised as having a low willingness to form attachment
(LWTFA) demonstrated an average index score of 1.43 for behavioural indicators
of attachment, whereby a score of 1 suggests no attachment and a score of 7
suggests deep and meaningful attachment. This suggests that they are very
unlikely to demonstrate attachment behaviours in the form of higher willingness
to pay a premium price (1.25) or willingness to enact difficult behaviours (1.45)
based on their interaction with the ‘Discover Weekly’ playlist as a tool for new
music discovery. These low behavioural indexes were exhibited both towards
their favourite song on the ‘Discover Weekly’ playlist (1.43), and towards that
songs’ musician (1.42). In addition, LWTFA consumers had an overall index
score of 1.04 for cognitive indicators of attachment. Does Spotify Create Attachment? Findings This again suggests that they
are very unlikely to display emotional signs of attachment in the form of feelings
of self-connection (1.10), triggering of memories (1.00), or separation distress
(1.00). Again, these low levels were exhibited both towards their favourite song
on the ‘Discover Weekly’ playlist (1.08), and towards the songs’ musician (1.00).hi These findings suggest that the playlist generated close to no attachment Does Spotify Create Attachment? 85 85 for those participants who were less-involved music consumers. Whilst repeat
listens were not entirely ruled out by respondents, behaviours linked to additional
monetary expenditure were extremely unlikely. A cognitive indicator score of close
to 1 suggests that almost no formative dimension of attachment could be observed
amongst these participants too. Certainly, these results may be linked to the
participants’ predispositions of not being likely to become attached to new music. Consumers with High Willingness to Form Attachment (HWTFA)
Table 4. HWTFA - Behavioural Indicators
Table 5. HWTFA - Cognitive Indicatorsh Consumers with High Willingness to Form Attachment (HWTFA)
Table 4. HWTFA - Behavioural Indicators
Table 5. HWTFA - Cognitive Indicators
The consumers we have categorised as having a high willingness to form attachm
(HWTFA) demonstrated an average index score of 3.71 for behavioural indica
of attachment, whereby 4 is a neutral value. This suggests that they demonst
weak to moderate attachment behaviours in the form of willingness to pa Consumers with High Willingness to Form Attachment (HWTFA)
Table 4. HWTFA - Behavioural Indicators
Table 5. HWTFA - Cognitive Indicators
The consumers we have categorised as having a high willingness to form attachm
(HWTFA) demonstrated an average index score of 3.71 for behavioural indicat
of attachment, whereby 4 is a neutral value. This suggests that they demonst
weak to moderate attachment behaviours in the form of willingness to pa
premium price (3.23) or willingness to enact difficult behaviours (3.80) ba
on their interaction with the ‘Discover Weekly’ playlist as a tool for new mu
discovery. These moderate levels of behavioural attachment were exhibited b
towards their favourite song on the playlist (3.88), and towards their favou Consumers with High Willingness to Form Attachment (HWTFA)
Table 4. HWTFA - Behavioural Indicators Consumers with High Willingness to Form Attachment (HWTFA) Table 5. HWTFA - Cognitive Indicators Table 5. Findings HWTFA - Cognitive Indicators The consumers we have categorised as having a high willingness to form attachment
(HWTFA) demonstrated an average index score of 3.71 for behavioural indicators
of attachment, whereby 4 is a neutral value. This suggests that they demonstrate
weak to moderate attachment behaviours in the form of willingness to pay a
premium price (3.23) or willingness to enact difficult behaviours (3.80) based
on their interaction with the ‘Discover Weekly’ playlist as a tool for new music
discovery. These moderate levels of behavioural attachment were exhibited both
towards their favourite song on the playlist (3.88), and towards their favourite Does Spotify Create Attachment? 86 musician from the playlist (3.53). In addition, HWTFA consumers demonstrated
an attachment average index score of 3.58 for cognitive indicators of attachment. This again suggests that they display moderate levels of formative signs of
attachment in the form of feels of self-connection (3.30), and automatic thoughts
and memories (4.13), although they scored much lower regarding separation
distress (2.63). Again, these relatively low cognitive indicators for attachment
were exhibited both towards their favourite song on the ‘Discover Weekly’ playlist
(3.77), and towards the songs’ musician (3.38). Both HWTFA participants showed slightly increased levels of attachment to
both the songs on the playlist as well as their artists. Furthermore, both participants
either saved the track and another track of the same artist or stated they would be
likely to save the track and another track of the same artist. Whilst this shows
certain behaviours to maintain the bond, the connection does not appear to be
strong enough for definite purchase intentions outside of the Spotify platform. Whilst initial interest was generated, reflected by a mid-strength emotional bond
of sufficient strength for considerations of consumption, sustainable behaviour
outside of the playlist remains unlikely. Overall, for these consumers, the
playlist was able to generate slightly elevated indicators of attachment which can
reasonably be interpreted as an initial interest; that is, the audience likes the song
and may listen to more music the artist releases. However, at the current levels of
attachment, it appears likely that consumption would be limited to the Spotify
platform. Does Spotify Create Attachment? Playlists and Attachment hi The findings summarised in tables 1 to 5 above suggest that Spotify’s ‘Discover
Weekly’ playlist generated slightly elevated indicators of attachment for consumers
who were already highly involved in new music consumption. It may be the case
that given the refinement of algorithmic playlists based upon intensity of usage,
that the HWTFA group showed more attachment because they had previously
shown engagement with Spotify and thus generated more data for the algorithm
to analyse and therefore serve them better. However, for those less involved in
new music consumption the playlist almost entirely failed to generate attachment. It slightly influenced attachment behaviours for those with a high willingness to
form attachment, both in regard to the song they liked most as well as its artist. Whilst saving the track or listening to another song was considered likely, more
difficult actions to maintain a bond with the artist (such as regularly purchasing
a concert ticket or a vinyl) were unlikely and moderated by price. Thus, amongst
our sample, the playlist demonstrated the potential to build a fundament for
consumption in the future, but only if their audience is strongly receptive; a key Does Spotify Create Attachment? 87 87 87 finding needing further research. However, playlist interaction alone appeared
insufficient for definite and sustainable consumption intentions. Furthermore,
these findings suggest that interaction with the ‘Discover Weekly’ playlist for the
participants in this study did not necessarily result in attachment at all, cognitively
or in behavioural intentions, if consumers are not already engaged in new music
seeking behaviours, and thus already likely to become attached to new music. Discussion The findings of this study into the ability of an algorithmic playlist to create
attachment, and thus influence the relationship between consumers and recorded
music itself, are important in two ways. The first relates to scholastic debates
concerning intermediation. The finding that Spotify’s ‘Discover Weekly’ playlist
might have a generally poor - at best moderate - ability to generate attachment,
defined according to the behavioural and cognitive dimensions of the construct
provided by consumer psychologists (Schultz et.al 1989, Ball & Tasaki 1992: 158,
Fournier 1998: 366, Thomson et.al 2005, Schifferstein & Zwartkruis-Pelgrim 2008:
7, Park et.al 2009, Park et.al 2010) problematises how we understand the impact
of intermediation. Given our suggestion that algorithmically generated playlists
- such as ‘Discover Weekly’ - can be considered cultural intermediaries given
their singularising and presenting of both new songs and musicians to audiences,
and providing those that are chosen to be shared with symbolic capital, the fact
that the specific intermediation presented herein resulted in generally poor levels
of attachment can be read in various ways. On the one hand, it may be seen as
challenging the idea that intermediation engenders attachment as per Callon et.al
(2002) and Smith Maguire & Matthews (2012: 554). On the other, it might provide
a mechanism for thinking critically about the effectiveness of Spotify at being an
effective intermediary (although, of course, intermediaries do not solely aim to
create attachment). That is, intermediaries are effective (at least in part) when
consumers trust them to select and present products or brands towards which
consumers might (under certain conditions) go on to form attachments. This has
been seen to be the case, for example, amongst larger, trusted broadcasters in the
competitive television space (Seabright and Weeds 2006) and in the effectiveness
of Oprah Winfrey in reducing consumer seeking costs in the crowded book market
(Thompson 2010; Loroz and Braig 2015). Interestingly then, intermediation
necessitates a relationship – and a form of attachment – with the intermediary
itself. The variance of attachment strengths between the two sample groups
further suggests that the impact of Discover Weekly is not solely dependent on the
work of the intermediary i.e., the content of the playlist, but also on the individual
predispositions of consumers. In this respect, attachment as the outcome of Does Spotify Create Attachment? Discussion 88 88 intermediation is achieved via the interaction between the intermediary and their
content, alongside the active consumer and their habits, traits and interests (a
position perhaps aligned with Gomart and Hennion’s (2010) notion of the active
listener). That being said, it is not clear to what extent the fact that the playlist
was algorithmically generated resulted in poor attachment i.e. whether playlists
which are curated by influential tastemakers such as those seen on competitor
streaming platforms such as Apple Music or Tidal, or even compared to other
forms of tastemaker curated playlists on radio stations for example, might be more
successful at creating attachment. This is an area for further research in the form
of comparative studies and we hope the methodology developed herein might
assist in these. Secondly, the suggestion that algorithms-as-intermediaries might not have
the power to create strong artist-fan relationships evidenced in a low likelihood
of actions of long-term consumption, has ramifications for how we understand
musical careers and might inform professional practice from music marketing
to artist management. Our findings lend tentative empirical corroboration to
the criticisms of those in the music industry media and beyond who argue that
playlists struggle to create meaningful relationships outside of their realm (Aguiar
& Waldvogel 2018, Chartmetric 2018, Mulligan 2019 cited in Griffiths 2019, Music
Ally 2019). The attachment index scores for highly-involved new music consumers
suggest that while the cognitive signs of attachment were not (yet) strong enough
for repeat purchases, repeat listens were likely for some consumers. In this sense,
our findings suggest that ‘Discover Weekly’ may generate some attachment
behaviours by influencing low-cost consumption when presented to the right
audience. However, any long-term behaviours involving monetary expenditure
were unlikely amongst our sample, thus making it reasonable to assume that
playlist placement alone cannot serve to enable an artists’ sustainable financial
success. Indeed, the ability of streaming more generally to provide sustainable
income to artists is an area currently facing intense scrutiny (Hesmondhalgh
et.al, 2021). Further research across a range of algorithmic playlists with a more
statistically significant sample size is needed to explore the ability (or not) of
playlists of this kind to build relationships strong enough for repeat purchase
intentions and strong bonds of cognitive attachment. Discussion Weak bonds of attachment
would make them a questionable tool for sustainable music marketing, and thus
musicians and their teams might want to consider the longer-term benefits of
seeking (algorithmic) playlist placement. Of course, playlist placement represents
just one element in the matrix of precarious artistic careers, and our findings point
towards the necessity of holistic music marketing approaches which aim to build
long-term relationships with consumers both within and outside of the streaming
realm. Certainly, a wide variety of musicians operating in multiple genres and with Does Spotify Create Attachment? 89 89 diverse contractual arrangements adopt a range of income diversification strategies
beyond playlist placement, from distribution, publishing, live performances,
merchandise, and more recently the newly emerging NFT (non-fungible token)
market. However, as Prey (2020: 3) notes: “to build and sustain a career in the
music industry, musicians and record labels have become increasingly dependent
on landing on Spotify-curated playlists”. Our findings encourage critical questions
about this as a long-term and sustainable method of promotion. Schofield (2019)
suggests that dedicated music fans may opt to support artists through platforms
considered to provide more artist-friendly monetisation, such as Bandcamp or
Patreon. Indeed, in doing so, consumers satisfy both a need for a greater level of
engagement with the product and a sense of community that Spotify does not
provide, and in fairness does not claim to provide. diverse contractual arrangements adopt a range of income diversification strategies
beyond playlist placement, from distribution, publishing, live performances,
merchandise, and more recently the newly emerging NFT (non-fungible token)
market. However, as Prey (2020: 3) notes: “to build and sustain a career in the
music industry, musicians and record labels have become increasingly dependent
on landing on Spotify-curated playlists”. Our findings encourage critical questions
about this as a long-term and sustainable method of promotion. Schofield (2019)
suggests that dedicated music fans may opt to support artists through platforms
considered to provide more artist-friendly monetisation, such as Bandcamp or
Patreon. Indeed, in doing so, consumers satisfy both a need for a greater level of
engagement with the product and a sense of community that Spotify does not
provide, and in fairness does not claim to provide. Does Spotify Create Attachment? Conclusion This paper has presented a small study to try and further our empirical
understanding of the nature of the relationship between consumers of music and
playlists on streaming platforms, in the context of public policy discussions in the
United Kingdom which have sought to better understand this relationship. Our
findings, based on a sample of users of Spotify’s ‘Discover Weekly’ algorithmically
generated playlist, suggest that whilst the playlist offered artists a platform and
generated a small level of initial interest amongst those consumers actively
looking for new music, there was a negligible impact on more passive consumers
of music. Following our development of a more terminologically precise
and methodologically robust definition of attachment - accounting for both
behavioural and cognitive dimensions of the construct by drawing on findings
from consumer psychology – our findings suggest that after employing the playlist
for one week as a method of new music discovery, there was no attachment
demonstrated amongst consumers with a low willingness to form attachment, and
only limited to moderate attachment amongst consumers with a high willingness
to form attachment.i Certainly, there are a number of limitations to the findings presented herein
which are crucial to acknowledge. In the first instance, ‘Discover Weekly’ is only
one algorithmically generated playlist, and therefore it is unclear as to whether
these findings would be observed across other similar playlists. Likewise, as
suggested, these findings would be enriched by follow-up studies exploring the
same concept using curated playlists. Perhaps most saliently, the sample size is
small, driven not least in part by the extensive participant involvement required
to complete our multi-dimensional survey, and relatively homogenous vis-à-vis
its composition. In this respect, our findings cannot meaningfully claim to be Does Spotify Create Attachment? 90 90 90 statistically significant, and in order to confidently determine the extent to which
algorithmically curated playlists generate attachment, a survey with a more
representative sample is therefore recommended. In addition, upon reflection, a
qualitative dimension in the form of follow up interviews to better interrogate our
respondents’ use of Discover Weekly might have been insightful, not least to allow
us to explore issues around the quality of the attachment formed, how this was
experienced, and how this might change or develop over time. Authors Adrian Leisewitz is a marketing practitioner within the cultural industries with
an expertise in music streaming. Having completed an MA in Music Business
Management at the University of Westminster, his research interests lie in cultural
intermediation, cultural value, and the intersections of/tensions between culture,
commerce and technology George Musgrave FRSA is an academic based at both the University of
Westminster and Goldsmiths (University of London). His research concerns
the psychological experiences and working conditions of creative careers, with a
current focus on mental health and wellbeing in the music industries. He is also a
musician who has signed major recording and publishing deals (Sony/EMI/ATV). Conclusion Furthermore, while
the sample was carefully chosen to consist of both heavily and poorly involved
music consumers, many users exist in between these extremes, and it is important
to understand these consumers too. Again, a larger sample size may serve to
reduce this risk in further research. In addition, as aforementioned, the contingent
valuation approach centred on the concept of ‘willingness to pay’ can suffer from
an income effect in that those with low incomes may express a low ‘willingness to
pay’ despite being lovers and fans of a particular musician or song. It is also key
to note that respondents in this study were using Discover Weekly in what might
be thought of laboratory settings as opposed to more naturalistic usage where the
playlist would form part of a wider media environment. This was done in order
to isolate the impact of Discover Weekly but removes the possibility that results
might differ with normal day-to-day use. Finally, in order to guarantee consistency
within replies, this research and its findings are constrained to a specific case; that
is, they depict attachment levels to one song and artist, generated by one playlist,
on one streaming platform, after one week of interaction. Whilst all of these
factors were carefully chosen to be the most representative and to provide the
richest possible information, further research is needed. That being said, perhaps the most important contribution of this paper after
the findings of the study itself, is the methodological approach adopted and its
capacity for subsequent adoption by other researchers in this area. That is, whilst
the findings of the study have limitations, the methodology offers a new model of
how to investigate attachment. We hope further application can be made of our
survey – the construction of which can be seen in Appendix 2 - devised in order to
measure the concept of attachment which has suffered from relative terminological
ambiguity and imprecision in the context of intermediation to date. In developing
this toolkit, we hope other scholars might build on the concepts explored herein
in order that we might obtain a richer and more rounded picture of how, if at
all, streaming services influence the relationship between musicians and music
listeners. Does Spotify Create Attachment? 91 91 Bibliography Aguiar, Luis and Waldfogel, Joel (2018): “Platforms, Promotion, and Product
Discovery: Evidence from Spotify Playlists,” JRC Technical Reports, JRC Digital
Economy Working Paper (2018–04): 1-44. h Ball, Dwayne and Tasaki, Lori (1992): “The Role and Measurement of Attachment
in Consumer Behavior,” Journal of Consumer Psychology, 1:2, 155–172. h Barna, Emilia (2017): “The perfect guide in a crowded musical landscape:
Online music platforms and curatorship,” First Monday. No issue number: No
pagination. Bateman, Ian J. and Willis, Kenneth G. (2001) Valuing Environmental Preferences:
Theory and Practice of the Contingent Valuation Method in the US, EU and
developing Countries, Oxford: Oxford University Press. Bourdieu, Pierre (1984): Distinction: A Social Critique of the Judgement of Taste,
London: Routledge. Bourdieu, Pierre (1990): Photography: A Middle-brow Art, Cambridge: Stanford
University Press. Bourdieu, Pierre (1991): Language and symbolic power, Cambridge: Polity in
association with Basil Blackwell. hi Bourdieu, Pierre (1993): The field of cultural production: essays on art and literature,
Cambridge: Polity Press. Bowlby, John (1982): “Attachment and loss: Retrospect and prospect,” American
Journal of Orthopsychiatry, 52:4, 664–678. Bonini, Tiziano and Gandini, Alessandro (2019): “First Week Is Editorial, Second
Week Is Algorithmic: Platform Gatekeepers and the Platformization of Music
Curation,” Social Media + Society, 5:4, 1-11. Does Spotify Create Attachment? 92 BPI. (2017): 2017 All about the music: recorded music in the UK: facts, figures and
analysis. London: BPI Limited.h Callon, Michel, Méadel, Cécile and Rabeharisoa, Vololona (2002): “The economy
of qualities,” Economy and Society, 31:2, 194–217. Chartmetric. (2018): “How Spotify Playlist Curators Turn Listeners Into Followers,”
Beats & Bytes, 31 May 2018:https://blog.chartmetric.com/how-spotifys-gate-
keepers-are-turning-listeners-into-fans-or-not/ (accessed 2 August 2020). Datta, Hannes, Knox, George and Bronnenberg, Bart J. (2018): “Changing
Their Tune: How Consumers’ Adoption of Online Streaming Affects Music
Consumption and Discovery,” Marketing Science, 37:1, 5–21. Ditto Music. (2018): “How to get on Spotify’s Discover Weekly & Release Radar,”
Dittomusic.com, 9 May 2018: https://www.dittomusic.com/blog/how-to-get-
your-music-on-discover-weekly-and-release-radar (accessed 25 July 2020). Dredge, Stuart (2020): “#BrokenRecord: ‘It’s about saying we all recognise that this
is problematic’,” Music Ally, 18 May 2018: https://musically.com/2020/05/18/
brokenrecord-its-about-saying-we-all-recognise-that-this-is-problematic/
(Accessed 1 August 2020). Eriksson, Maria and Johansson, Anna (2017): “Tracking Gendered Streams,”
Culture Unbound: Journal of Current Cultural Research, 9:2, 163–183.h Culture Unbound: Journal of Current Cultural Research, 9:2, 163 183. du Gay, Paul et al. (1997): Doing Cultural Studies: The Story of the Sony Walkman. du Gay, Paul et al. (1997): Doing Cultural Studies: The Story of the Sony Walkman. London: SAGE London: SAGE. Bibliography Fairchild, Charles (2014): “Popular Music,” Smith Maguire, Jennifer and Matthews, h Fairchild, Charles (2014): “Popular Music,” Smith Maguire, Jennifer and Matthews, h Julian, (eds): The Cultural Intermediaries Reader, London: SAGE, 125-133. Julian, (eds): The Cultural Intermediaries Reader, London: SAGE, 125-133. Featherstone, M. (1993): Consumer Culture and Postmodernism. London: SAGE
Publications Ltd. Julian, (eds): The Cultural Intermediaries Reader, London: SAGE, 125-133. Featherstone, M. (1993): Consumer Culture and Postmodernism. London: SAGE Julian, (eds): The Cultural Intermediaries Reader, London: SAGE, 125 133. Featherstone, M. (1993): Consumer Culture and Postmodernism. London: SAGE h
Featherstone, M. (1993): Consumer Culture and Postmodernism. London: SAGE
Publications Ltd. Fleischer, R. (2017): “If the Song has No Price, is it Still a Commodity? Rethinking
the Commodification of Digital Music,” Culture Unbound: Journal of Current
Cultural Research, 9:2, 146–162. Fleischer, Rasmus and Snickars, Pelle (2017): “Discovering Spotify – A Thematic
Introduction,” Culture Unbound: Journal of Current Cultural Research, 9:2,
130–145. Forde, Eamonn (2018). “The secrets of successful D2C sales: ‘It is about scale
and speed’,” Music Ally, 29 April 2018: https://musically.com/2018/04/29/se-
crets-successful-d2c-sales/ (accessed 30 July 2020).h Fournier, Susan (1998): “Consumers and Their Brands: Developing Relationship
Theory in Consumer Research,” Journal of Consumer Research, 24:4, 343–373. h
Gallhofer, Irmtraud and Saris, Willem (2014): Design, evaluation, and analysis of
questionnaires for survey research, 2nd ed. Hoboken, New Jersey: Wiley Griffiths, Emma (2019): “Music Industry Analysts on the Trends to Watch in 2020
– Synchblog,” Synchtank, 19 December 2019: https://www.synchtank.com/ Does Spotify Create Attachment? 93 93 blog/music-industry-analysts-on-the-trends-to-watch-in-2020/ (accessed 2
August 2020). Gross, Sally Anne and Musgrave, George (2020): Can Music Make You Sick? Measuring the Price of Musical Ambition. London: University of Westminster
Press. Gomart, Emilie and Hennion, Antoine (1999). “A Sociology of Attachment: Music
Amateurs, Drug Users,” The Sociological review (Keele), 47, 220-247. GOV (2020): “Call for evidence – Economics of music streaming,” UK Parliament:
https://committees.parliament.uk/call-for-evidence/273/economics-of-mu-
sic-streaming/ (accessed 5 December 2020). Hazan, Cindy and Shaver, Philip (1994): “Attachment as an Organizational
Framework for Research on Close Relationships,” Psychological Inquiry, 5:1,
1–22. Hennion, Antoine (2010): “Loving Music: from a Sociology of Mediation to a
Pragmatics of Taste,” Comunicar (Huelva, Spain), 17:34, 25-33. Hesmondhalgh, David (2006): “Bourdieu, the media and cultural production,”
Media, Culture & Society, 28:2, 211–231. Hesmondhalgh, David (2020). “Is music streaming bad for musicians? Problems
of evidence and argument,” New Media & Society, 00:0, 1–23. Bibliography f Hesmondhalgh, David (2021): “Streaming’s Effects on Music Culture: Old
Anxieties and New Simplifications,” Cultural Sociology, June 2021
Hesmondhalgh, David, Osborne, R, Sun, Hyojung and Barr, Kenny (2021) Music Creators Earnings in the Digital Era, London: Intellectual Property Office
Horowitz, John K. and McConnell, Kenneth, E. (2003) Willingness to accept,
willingness to pay and the income effect, Organization, 51:4, 537-545. Horowitz, John K. and McConnell, Kenneth, E. (2003) Willingness to accept,
willingness to pay and the income effect, Organization, 51:4, 537-545. IFPI (2019): Music Listening 2019. London: IFPI. Jopling, Keith (2019): “Playlist innovation. MIDiA Research,” 4 March 2019:
https://www.midiaresearch.com/blog/whats-next-for-playlist-innovation/
(accessed 22 May 2020).h Kjus, Yngvar (2016): “Musical exploration via streaming services: The Norwegian
experience,” Popular Communication, 14:3, 127–136.h Kuipers, Giselinde (2012): “The cosmopolitan tribe of television buyers:
Professional ethos, personal taste and cosmopolitan capital in transnational
cultural mediation,” European Journal of Cultural Studies, 15:5, 581–603. Latour, Bruno and Stark, Monique Girard (1999) Factures/Fractures: From the
Concept of Network to the Concept of Attachment, RES: Anthropology and
Aesthetics, 36, 20-31. Lindsay, Charlie (2016): “An Exploration into How the Rise of Curation Within
Streaming Services Has Impacted How Music Fans in the UK Discover New
Music,” Journal of Promotional Communications, 4:1, 114-141. Does Spotify Create Attachment? 94 Loroz, Peggy Sue and Braig, Bridgette M. (2015) Consumer Attachments to
Human Brands: The “Oprah Effect”, Psychology & Marketing, 32:7, 751-763h Moor, Liz (2008): “Branding consultants as cultural intermediaries,” The
Sociological Review, 56:3, 408–428. Morris, Jeremy Wade (2015): “Curation by code: Infomediaries and the data
mining of taste,” European Journal of Cultural Studies, 18:4–5, 446–463.hh Mulligan, Mark (2014): “What Future For The Album In The On-Demand Age?,”
Music Industry Blog, 15 July 2014: https://musicindustryblog.wordpress. com/2014/07/15/what-future-for-the-album-in-the-on-demand-age/
(accessed 22 May 2020). Mulligan, Mark (2019): “Spotify, the Decline of Playlists and the Rise of Podcasts,”
MIDiA Research, 11 April 2019: https://www.midiaresearch.com/blog/spotify-
the-decline-of-playlists-and-the-rise-of-podcasts/ (accessed 22 May 2020].h Musgrave, George (2017): “Collaborating to Compete: The Role of Cultural
Intermediaries in Hypercompetition,” International Journal of Music Business
Research, 6:2, 41–68. h Music Ally. (2019): “The Dry Streams Paradox,” Music Ally, 14 April 2019: https://
musically.com/2019/04/24/the-dry-streams-paradox/ (accessed 26 May 2020).i Music Ally. (2021): “Atlantic hails TikTok’s rile in first UK drill number one,” Music
Ally, 10 May 2021: https://musically.com/2021/05/10/atlantic-hails-tiktoks-
role-in-first-uk-drill-number-one/ (accessed 26 September 2021).h i
Musicians’ Union. (2012): The Working Musician. London: Musicians’ Union. Bibliography Negus, Keith (2019): “From creator to data: the post-record music industry and
the digital conglomerates,” Media, Culture & Society, 41:3, 367–384.h Negus, Keith (2002): “The Work of Cultural Intermediaries and the Enduring
Distance Between Production and Consumption,” Cultural Studies, 16:4,
501–515. Negus, Keith and Pickering, Michael (2004). “Creativity, Communication and
Cultural Value.” London: SAGE. Park, C. Whan et al. (2010): “Brand Attachment and Brand Attitude Strength:
Conceptual and Empirical Differentiation of Two Critical Brand Equity
Drivers,” Journal of Marketing, 74:6, 1–17. Popper, Ben (2015): “Tastemaker: How Spotify’s Discover Weekly cracked human
curation at internet scale,” The Verge, 30 September 2015: https://www.theverge. com/2015/9/30/9416579/spotify-discover-weekly-online-music-curation-in-
terview (accessed 21 May 2020). Powers, Devon (2015). “Intermediaries and Intermediation,” Bennett, Andy,
Waksman, Steve (eds): The SAGE Handbook of Popular Music, London: SAGE
Publications Ltd, 120–134. Prey, Robert (2020) Locating Power in Platformization: Music Streaming Playlists
and Curatorial Power, Social Media + Society, 1-11. Does Spotify Create Attachment? 95 Prior, Nick (2013): “Bourdieu and the Sociology of Music Consumption: A Critical
Assessment of Recent Developments,” Sociology Compass, 7:3, 181–193. Redman, Peter (2008). Attachment: Sociology and social worlds, Manchester:
Manchester University Press.f Schifferstein, Hendrik N. J. and Zwartkruis-Pelgrim, Elly P. H. (2008):
“Consumer-Product Attachment,” International Journal of Design, 2:3, 1–13.i Schofield, Jack (2019). “Which is the best streaming service for supporting artists?,”
The Guardian, 31 October 2019: http://www.theguardian.com/technology/
askjack/2019/oct/31/best-streaming-service-mp3-pays-artists
(accessed
25
October 2020).h Schultz, Susan E., Kleine, Robert E., and Kernan, Jerome B. (1989): “‘These
Are a Few of My Favorite Things’; Toward an Explication of Attachment as a
Consumer Behavior Construct,” ACR North American Advances, 16:no issue
number, no pagination. Seabright, Paul and Weeds, Helen (2007) “Competition and market power in
broadcasting: where are the rents?” Paul Seabright & Jurgen von Hagen (eds):
The Economic Regulation of Broadcasting Markets: Evolving Technology and
Challenges for Policy, Cambridge: Cambridge University Press, 47-80. Smith Maguire, Jennifer and Matthews, Julian (2010): “Cultural Intermediaries
and the Media,” Sociology Compass, 4:7, 405–416. Smith Maguire, Jennifer and Matthews, Julian (2012): “Are we all cultural
intermediaries now? An introduction to cultural intermediaries in context,”
European Journal of Cultural Studies, 15:5, 551–562. Smith Maguire, Jennifer (2014). “Bourdieu on Cultural Intermediaries,” Smith
Maguire, Jennifer and Matthews, Julian (eds): The Cultural Intermediaries
Reader, London: SAGE, 15-24. Snickars, P. (2017): “More of the Same - On Spotify Radio,” Culture Unbound:
Journal of Current Cultural Research, 9:2, 184–211. Temple, Ian (2018): “Don’t Be Boring: A Musician’s Guide to Branding,” AWAL. Bibliography com, 6 June 2018: https://www.awal.com/blog/musician-branding (accessed 15
April 2020). Thompson, John B. (2013): Merchants of Culture: The Publishing Business in the
Twenty-First Century, 2nd ed., Cambridge: Polity Press.h Thomson, Matthew (2006) Human Brands: Investigating Antecedents to
Consumers’ Strong Attachments to Celebrities, Journal of Marketing, 70:3,
104-119. Thomson, Matthew, MacInnis, Deborah J. and Park, C. Whan (2005): “The Ties
That Bind: Measuring the Strength of Consumers’ Emotional Attachments to
Brands,” Journal of Consumer Psychology, 15:1, 77–91. Does Spotify Create Attachment? 96 Tiffany, Kaitlyn (2017): “Following Spotify playlist curators around New York’s
live music scene,” The Verge, 13 November 2017: https://www.theverge. com/2017/11/13/16617900/spotify-playlist-curation-nyc-live-shows-fresh-
finds-indie-latin-new-music (accessed 21 May 2020). Torres, Victor Miguel Avila (2019) How Music Matters: Exploring the Music
Experience, its attachments and its technologies, doctoral dissertation, University
of York. Tschmuck, Peter (2017) The Economics of Music, Newcastle: Agenda Publishing.h Verboord, Marc (2014): “The impact of peer-produced criticism on cultural
evaluation: A multilevel analysis of discourse employment in online and offline
film reviews,” New Media & Society, 16:6, 921–940. i
Webster, Jack et al. (2016): “Towards a theoretical approach for analysing music
recommender systems as sociotechnical cultural intermediaries,” Proceedings
of the 8th ACM Conference on Web Science - WebSci ’16. 2016. Hannover,
Germany: ACM Press, 137–145. i
Webster, Jack et al. (2016): “Towards a theoretical approach for analysing music
recommender systems as sociotechnical cultural intermediaries,” Proceedings
of the 8th ACM Conference on Web Science - WebSci ’16. 2016. Hannover,
Germany: ACM Press, 137–145. Does Spotify Create Attachment?
97 Does Spotify Create Attachment? Appendix 1. Music Consumption Involvement task Table 1: Music Consumption Involvement Task (Replies on a 1-7 Likert Scale)6 Table 1: Music Consumption Involvement Task (Replies on a 1-7 Likert Scale)6 Does Spotify Create Attachment? Attachment to Favourite Song on Playlisth To what extent are you prepared to spend money, time an 25. Did you save this track to your library in any form? 30. What price (in £) are you willing to pay for this song? Classification Questions Which genres describe your musical taste? Multiple answers possibl 4. How big of a role does music play in your life? (As a consumer)t 5. How often do you use Spotify’s Discover Weekly? 6. On average, how much money (in £) do you spend on recorded music per year? (excluding streaming
subscriptions)l 7. To what extent did the songs on the playlist reflect your musical taste? Attachment to Favourite Song on Playlisth Attachment to Favourite Song on Playlist
8. This song reminds me of who I am. 9. If I were describing myself, this song would likely be something I would mention. 10. I feel personally connected to this song. 11. If someone ridiculed this song, I would feel irritated. 12. If someone praised this song, I would feel somewhat praised myself. 13. This song gives me the feeling that I am loved and cared for. 14. This song reminds me of persons who are important to me. 15. This song symbolises a bond with friends or family
16. This song reminds me of important things I’ve done or places I’ve been. 17. My thoughts and feelings toward the song are often automatic, coming to mind seemingly on their own. 18. My thoughts and feelings toward the song come to my mind naturally and instantly. 19. I would feel distressed if this song was made unavailable on all platforms. 20. I could easily imagine a life without this song
21. How likely are you to listen to this song when you are distressed or fearful? 22. How likely are you to listen to this song to reduce stress? 23. To what extent are you prepared to spend money, time and energy to promote this song? 24. How likely are you to defend this song when others speak poorly of it? 25. Did you save this track to your library in any form? 26. If no, how likely will you save this track to your library in any form? 27. Did you purchase this track outside of Spotify in any form? (this includes as part of an album)
28. If no, how likely will you purchase this track outside of Spotify in any form? (this includes as part of an
album)
29. This song is one of many in a digital download store. What do you estimate is the average price (in £)
for songs in this store? 30 What price (in £) are you willing to pay for this song? 8. This song reminds me of who I am. 8. This song reminds me of who I am. h
g
9. If I were describing myself, this song would likely be something I would mention. 10. I feel personally connected to this song. 11. If someone ridiculed this song, I would feel irritated. 12. Attachment to Favourite Song on Playlisth If someone praised this song, I would feel somewhat praised myself. 13. This song gives me the feeling that I am loved and cared for. 14. This song reminds me of persons who are important to me. 15. This song symbolises a bond with friends or family
16. This song reminds me of important things I’ve done or places I’ve been. 17. My thoughts and feelings toward the song are often automatic, coming to mind seemingly on their own. 18. My thoughts and feelings toward the song come to my mind naturally and instantly. 19. I would feel distressed if this song was made unavailable on all platforms. 20. I could easily imagine a life without this song
21. How likely are you to listen to this song when you are distressed or fearful? 22. How likely are you to listen to this song to reduce stress? 23. To what extent are you prepared to spend money, time and energy to promote this song? 24. How likely are you to defend this song when others speak poorly of it? 25. Did you save this track to your library in any form? 26. If no, how likely will you save this track to your library in any form? 27. Did you purchase this track outside of Spotify in any form? (this includes as part of an album)
28. If no, how likely will you purchase this track outside of Spotify in any form? (this includes as part of an
album)
29. This song is one of many in a digital download store. What do you estimate is the average price (in £)
for songs in this store? 30 What price (in £) are you willing to pay for this song? h
9. If I were describing myself, this song would likely be something I would mention. 13. This song gives me the feeling that I am loved and cared for.h h
14. This song reminds me of persons who are important to me.h h
15. This song symbolises a bond with friends or family 19. I would feel distressed if this song was made unavailable on all 20. I could easily imagine a life without this song 21. How likely are you to listen to this song when you are distr 22. How likely are you to listen to this song to reduce stress? 23. Appendix 2. Attachment Questionnaire7 Classification Questions
1. Gender
2. How old are you? 3. Which genres describe your musical taste? Multiple answers possible. 4. How big of a role does music play in your life? (As a consumer)
5. How often do you use Spotify’s Discover Weekly? 6. On average, how much money (in £) do you spend on recorded music per year? (excluding streaming
subscriptions)
7. To what extent did the songs on the playlist reflect your musical taste? Attachment to Song’s Artisth What price (in £) are you willing to pay for a vinyl record of this artist? 58. This artist is one of many artists playing concerts. What do you think is the average price (in £) of
similar sized artists’ concerts? 59. What price (in £) are you willing to pay for a concert ticket to see this artist? 60. This artist is one of many artists selling a merchandise t-shirt. What do you think is the average price
(in £) of these t-shirts? 61 What price (in £) are you willing to pay for this artist’s merchandise t-shirt? 48. Have you purchased any music of this artist outside of Spotify? 49. If no, how likely will you purchase any music of this artist outside of Spotify? 50. To what extent will you listen to all new music this artist releases? 51. To what extent will you purchase all new music this artist releases? 52. To what extent do you intend to go to all concerts this artist plays in your area? 53. To what extent do you intend to buy all new merchandise this artist releases? 54. To what extent are you prepared to spend money, time and energy to promote this artist? 55. How likely are you to defend this artist when others speak poorly of them? 56. This artist is one of many artists selling a vinyl record. What do you think is the average price (in £) of
these records? 57. What price (in £) are you willing to pay for a vinyl record of this artist? 58. This artist is one of many artists playing concerts. What do you think is the average price (in £) of
similar sized artists’ concerts? 59. What price (in £) are you willing to pay for a concert ticket to see this artist? 60. This artist is one of many artists selling a merchandise t-shirt. What do you think is the average price
(in £) of these t-shirts? 61. What price (in £) are you willing to pay for this artist’s merchandise t-shirt? Attachment to Song’s Artisth 31. This artist is part of me and who I am. 31. This artist is part of me and who I am. h
32. If I were describing myself, this artist would likely be something I would mention. 32. If I were describing myself, this artist would likely be somethin 33. I feel personally connected to this artist. 34. If someone ridiculed this artist, I would feel irritated. 35. If someone praised this artist, I would feel somewhat praised myself.h 36. This artist gives me the feeling that I am loved and cared for.h h
g
g
37. This artist reminds me of persons who are important to me.h h
37. This artist reminds me of persons who are important to me.h h
37. This artist reminds me of persons who are important to me.h h
38. This artist symbolises a bond with friends or family. h
39. This artist reminds me of important things I’ve done or places I’ve beent h
40. My thoughts and feelings toward the artist are often automatic, coming to mind seemingly on their own. t
41. My thoughts and feelings toward the artist come to my mind naturally and instantly. 42. I would feel distressed if this artist stopped performing. y
g
44. How likely are you to listen to this artist when you are distressed or fearful? y
y
y
p
y
y
47. If no, how likely will you save any other track of this artist to your library? 98 98 Does Spotify Create Attachment? 48. Have you purchased any music of this artist outside of Spotify? 49. If no, how likely will you purchase any music of this artist outside of Spotify? 50. To what extent will you listen to all new music this artist releases? 51. To what extent will you purchase all new music this artist releases? 52. To what extent do you intend to go to all concerts this artist plays in your area? 53. To what extent do you intend to buy all new merchandise this artist releases? 54. To what extent are you prepared to spend money, time and energy to promote this artist? 55. How likely are you to defend this artist when others speak poorly of them? 56. This artist is one of many artists selling a vinyl record. What do you think is the average price (in £) of
these records? 57. Attachment to Favourite Artisth 62. This artist is part of me and who I am. 63. If I were describing myself, this artist would likely be someth 63. If I were describing myself, this artist would likely be something I would mention 64. I feel personally connected to this artist. 64. I feel personally connected to this artist. 65. If someone ridiculed this artist, I would feel irritated. 65. If someone ridiculed this artist, I would feel irritated. 66. If someone praised this artist, I would feel somewhat praised m 67. This artist gives me the feeling that I am loved and cared for.h h
68. This artist reminds me of persons who are important to me.h h
69. This artist symbolises a bond with friends or family. h
69. This artist symbolises a bond with friends or family. h
y
y
70. This artist reminds me of important things I’ve done or places I’ve beent h
71. My thoughts and feelings toward the artist are often automatic, coming to mind seemingly on their own. h
h
d f
l
d h
d
ll
d
l h
71. My thoughts and feelings toward the artist are often automatic, coming to mind seemingly on their own. 72. My thoughts and feelings toward the artist come to my mind naturally and instantly. t
2. My thoughts and feelings toward the artist come to my mind nat 73. I would feel distressed if this artists’ music got taken off all plat 74. I could easily imagine a life without this artist. 75. How likely are you to listen to this artist when you are distressed or fearful? 75. How likely are you to listen to this artist when you are dist 76. How likely are you to listen to this artist to reduce stress? 77. Have you saved any track of this artist to your Spotify librar 9. Have you purchased any music of this artist outside of Spotify? y
p
y
p
y
80. If you ticked no, how likely will you purchase any music of this artist outside of Spotify? 1. To what extent will you listen to all new music this artist releases To what extent will you purchase all new music this artist releases? Attachment to Favourite Song from Favourite Artisth This song gives me the feeling that I am loved and cared for. 99. This song reminds me of persons who are important to me. 100. This song symbolises a bond with friends or family
101. This song reminds me of important things I’ve done or places I’ve been. 102. My thoughts and feelings toward the song are often automatic, coming to mind seemingly on their own. 103. My thoughts and feelings toward the song come to my mind naturally and instantly. 104. I would feel distressed if this song was made unavailable on all platforms. 105. I could easily imagine a life without this song
106. How likely are you to listen to this song when you are distressed or fearful? 107. How likely are you to listen to this song to reduce stress? 108. To what extent are you prepared to spend money, time and energy to promote this song? 109. How likely are you to defend this song when others speak poorly of it? 110. Did you save this track to your library in any form? 111. If no, how likely will you save this track to your library in any form? 112. Did you purchase this track outside of Spotify in any form? (this includes as part of an album)
113. If no, how likely will you purchase this track outside of Spotify in any form? (this includes as part of
an album)
114. This song is one of many in a digital download store. What do you estimate is the average price (in £)
for songs in this store? 115. What price (in £) are you willing to pay for this song? 95. I feel personally connected to this song. 96. If someone ridiculed this song, I would feel irritated. 114. This song is one of many in a digital download store. What do you estimate is the average price (in £)
for songs in this store? g
115. What price (in £) are you willing to pay for this song? 1 At the time of writing we note that the track ‘Body’ by Russ Millions and Tion Wayne recently went to
Number 1 in the UK music chart propelled by its performance on TikTok (Music Ally, 2021) 2 No participant was found to have an average score of 2 or less. Attachment to Favourite Song from Favourite Artisth g
93. This song reminds me of who I am. h
g
94. If I were describing myself, this song would likely be something I would mention. h
94. If I were describing myself, this song would likely be something I would mention. Does Spotify Create Attachment? 99 99 95. I feel personally connected to this song. 96. If someone ridiculed this song, I would feel irritated. 97. If someone praised this song, I would feel somewhat praised myself. 98. This song gives me the feeling that I am loved and cared for. 99. This song reminds me of persons who are important to me. 100. This song symbolises a bond with friends or family
101. This song reminds me of important things I’ve done or places I’ve been. 102. My thoughts and feelings toward the song are often automatic, coming to mind seemingly on their own. 103. My thoughts and feelings toward the song come to my mind naturally and instantly. 104. I would feel distressed if this song was made unavailable on all platforms. 105. I could easily imagine a life without this song
106. How likely are you to listen to this song when you are distressed or fearful? 107. How likely are you to listen to this song to reduce stress? 108. To what extent are you prepared to spend money, time and energy to promote this song? 109. How likely are you to defend this song when others speak poorly of it? 110. Did you save this track to your library in any form? 111. If no, how likely will you save this track to your library in any form? 112. Did you purchase this track outside of Spotify in any form? (this includes as part of an album)
113. If no, how likely will you purchase this track outside of Spotify in any form? (this includes as part of
an album)
114. This song is one of many in a digital download store. What do you estimate is the average price (in £)
for songs in this store? 115 What price (in £) are you willing to pay for this song? 95. I feel personally connected to this song. 96. If someone ridiculed this song, I would feel irritated. 97. If someone praised this song, I would feel somewhat praised myself. 98. Attachment to Favourite Song from Favourite Artisth Nevertheless, as this research is focussed
on Discover Weekly users, it is reasonable to assume that all participants are at least moderately involved
in new music consumption. Furthermore, the IFPI (2019: 13) suggests that only 2.5% of consumers consi-
der music as “unimportant” to them, thus decreasing the chances of drawing these in a sample. Therefore,
a below centre (i.e. <4) score could reasonably be seen as sufficient. This enabled the inclusion of two parti-
cipants with scores of 2.96 and 2.97 as those less likely to become attached to previously unknown music. 3 Each score represents an own calculation based on reply results. Table used for presentation purposes,
not for calculation. 4 Index calculated as the arithmetic mean over all replies (from each participant) and not as arithme-
tic mean of each construct, hence more weight toward constructs consisting of more questions. This
calculation was chosen due to the fact that the questions were adapted from previous scholars’ results of
statistical verification, while the constructs were developed as a summary for this examination. For the sake
of presentation, both participants of each consumer group were summarized into one indicator for each
construct and attachment object. 5 “Overall” score calculated as: (arithmetic mean results song + arithmetic mean results artist)/2 6 Question 6 was asked as an open-ended question. The Likert scale for average spend on recorded music
per year was indexed according to those consumers considered “heavy spenders” by the BPI (2017: 63),
spending more than £62 a year on recorded music. Any participant spending equal to, or more than £62
on recorded music per year was indexed as a 7, with all replies below £62 being proportionally given a
value between 1 and 6. 7 The 54 questions seen in questions 8-61 represent the attachment construct Does Spotify Create Attachment? 100
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https://openalex.org/W2083944100
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https://europepmc.org/articles/pmc3987017?pdf=render
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English
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Comparing the Selection and Placement of Best Management Practices in Improving Water Quality Using a Multiobjective Optimization and Targeting Method
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International journal of environmental research and public health/International journal of environmental research and public health
| 2,014
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cc-by
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Int. J. Environ. Res. Public Health 2014, 11, 2992-3014; doi:10.3390/ijerph110302992 Int. J. Environ. Res. Public Health 2014, 11, 2992-3014; doi:10.3390/ijerph110302992 International Journal of
Environmental Research and
Public Health
ISSN 1660-4601
www.mdpi.com/journal/ijerph International Journal of
Environmental Research and
Public Health
ISSN 1660-4601
www.mdpi.com/journal/ijerph Article 1. Introduction Nonpoint source (NPS) pollution from agricultural watersheds has become one of the major water
quality concerns [1,2]. For example, more than 70% of the delivered nitrogen (N) and phosphorus (P) in
the Mississippi River Basin are contributed from the adjacent agricultural lands and these increased
nutrient fluxes are linked to seasonal hypoxia in the northern Gulf of Mexico [3]. Excessive fertilizer
usage on tea fields in Taiwan was identified as the major source of ammonia, which can lead to
eutrophication [4]. Agricultural practices not only determine the level of food production, but also the
state of the global environment, including water quality, soil quality, and species composition [5]. Intensive agricultural practices are considered sources of significant amounts of nutrients, especially
nitrogen (N) and phosphorus (P), pesticides, fecal bacteria and sediment to receiving water
bodies [6,7], reducing the ability of ecosystems to provide goods and services [5]. Usually in an
agricultural watershed with concentrated animal production operations, improper usage of manure with
commercial fertilizers could result in excessive nutrient losses from the fields to the receiving water
bodies [8,9]. Sediment losses from top soil containing relatively large amounts of nutrients can
threaten water quality and decrease the productive capacity of the land [10]. The adverse impacts from agricultural areas can be controlled by implementing best management
practices (BMPs) to reduce source or retard pollutant transports in a watershed. Many studies have
used simulation models to evaluate BMP effectiveness and determine the optimum BMPs to improve
water quality at the farm level [11] and at a watershed level [12–16]. However, considering resource
constraints, it is not possible to implement BMPs in every candidate location in a watershed. Besides,
certain critical areas in a watershed may contribute disproportionally large amounts of pollutants in
a watershed. Pionke et al. [17] concluded that up to 90% of the annual phosphorus loads were
contributed by approximately 10% of the watershed in the Brown catchment (Pennsylvania, USA)
Therefore, several methods have been developed to select and place cost-effective BMPs in
a watershed. Those methods can be categorized into plan- or performance-based methods [18]. Plan-based methods are mainly used to assign BMPs based on the identification of critical areas in
a watershed. However, interactions among BMPs on pollutant reduction are typically not considered in
plan-based methods. The performance-based method incorporates simulation models to evaluate
the cost-effectiveness of selected BMP combinations based on their individual performance and cost. Li-Chi Chiang 1, Indrajeet Chaubey 2,*, Chetan Maringanti 3 and Tao Huang Li-Chi Chiang 1, Indrajeet Chaubey 2,*, Chetan Maringanti 3 and Tao Huang 1 1 Department of Civil and Disaster Prevention Engineering, National United University,
Miaoli 36003, Taiwan; E-Mails: lchiang@nuu.edu.tw (L.-C.C.); r99622021@ntu.edu.tw (T.H.)
2 Department of Earth, Atmospheric, and Planetary Sciences; Department of Agricultural and
Biological Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette,
IN 47907, USA; E-Mail: ichaubey@purdue.edu 1 Department of Civil and Disaster Prevention Engineering, National United University,
Miaoli 36003, Taiwan; E-Mails: lchiang@nuu.edu.tw (L.-C.C.); r99622021@ntu.edu.tw (T.H.)
2 Department of Earth, Atmospheric, and Planetary Sciences; Department of Agricultural and
Biological Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette,
IN 47907, USA; E-Mail: ichaubey@purdue.edu 2 Department of Earth, Atmospheric, and Planetary Sciences; Department of Agricultural and
Biological Engineering, Purdue University, 550 Stadium Mall Drive, West Lafayette,
IN 47907, USA; E-Mail: ichaubey@purdue.edu 3 Risk Modeling Unit, Zurich Financial Services Ltd., Mythenquai 2, Zurich 8002, Switzerland;
E-Mail: chetan.maringanti@zurich.com 3 Risk Modeling Unit, Zurich Financial Services Ltd., Mythenquai 2, Zurich 8002, Switzerland;
E-Mail: chetan.maringanti@zurich.com * Author to whom correspondence should be addressed; E-Mail: ichaubey@purdue.edu;
Tel.: +1-765-494-3258; Fax: +1-765-496-1210. Received: 16 December 2013; in revised version: 3 March 2014 / Accepted: 3 March 2014 /
Published: 11 March 2014 Abstract: Suites of Best Management Practices (BMPs) are usually selected to be
economically and environmentally efficient in reducing nonpoint source (NPS) pollutants
from agricultural areas in a watershed. The objective of this research was to compare the
selection and placement of BMPs in a pasture-dominated watershed using multiobjective
optimization and targeting methods. Two objective functions were used in the optimization
process, which minimize pollutant losses and the BMP placement areas. The optimization
tool was an integration of a multi-objective genetic algorithm (GA) and a watershed model
(Soil and Water Assessment Tool—SWAT). For the targeting method, an optimum BMP
option was implemented in critical areas in the watershed that contribute the greatest
pollutant losses. A total of 171 BMP combinations, which consist of grazing management,
vegetated filter strips (VFS), and poultry litter applications were considered. The results
showed that the optimization is less effective when vegetated filter strips (VFS) are not
considered, and it requires much longer computation times than the targeting method to
search for optimum BMPs. Although the targeting method is effective in selecting and 2993 Int. J. Environ. Res. Li-Chi Chiang 1, Indrajeet Chaubey 2,*, Chetan Maringanti 3 and Tao Huang Public Health 2014, 11 placing an optimum BMP, larger areas are needed for BMP implementation to achieve
the same pollutant reductions as the optimization method. placing an optimum BMP, larger areas are needed for BMP implementation to achieve
the same pollutant reductions as the optimization method. Keywords: best management practice; nonpoint source pollution; multiobjective optimization;
genetic algorithm; Soil and Water Assessment Tool 1. Introduction Targeting is a plan-based method to place BMPs in critical source areas which contribute
a disproportionate amount of NPS pollutants. Many studies have been conducted to identify critical
source areas and to estimate the improvement of water quality due to implementation of selected
BMPs in those critical regions [18–21]. Because spatial interactions among BMPs are not considered
in establishing a targeting strategy, a BMP that is selected based on certain targeting strategy Int. J. Environ. Res. Public Health 2014, 11 2994 may or may not be the most cost-effective BMP for the watershed. In contrast, optimization is
a performance-based method that considers the effectiveness and cost of various BMPs, evaluates
numerous BMP scenarios and incorporates the impacts of BMP interactions in assessing the
cost-effectiveness of BMP scenarios. Many studies have combined the genetic algorithm (GA) and NPS
prediction models to optimize the BMP selection and placement in a watershed [22–27]. Most of the
previous work has focused on using a single objective function which combines both BMP effectiveness
and cost [23], sequentially optimizing two objective functions separately [24,25] or optimizing two
objective functions of BMP effectiveness and cost simultaneously [22]. Zare et al. [28] applied
the Non-dominated Sorting Genetic Algorithm II (NSGA-II) optimization technique to derive
the optimal tradeoff curve simultaneously between three objectives: reducing cost of BMP
implementation, maintaining runoff quality, and minimizing runoff volume. Cost of BMPs was
estimated based on the volume (Rain barrel and Bio-retention) or the areas (Porous pavement). Optimization studies related to selection of BMPs have traditionally used cost minimization as
an objective function. Cost as an optimization function does not ensure that the watershed areas under
BMPs are also minimized. Many researchers have indicated that a relatively small portion of
a watershed contributes a larger amount of pollutants. BMPs are generally targeted in those high-risk
watershed areas. To enhance the effectiveness of BMPs, achieving the same pollutant reductions with
less areas should be considered. In order to compare the watershed areas that needs to have BMPs
under targeting and optimization options to produce similar water quality benefits, we used
the watershed area as one of the objective functions in this study. 1. Introduction Therefore, the overall goal of this
study was to compare the selection and placement of optimal BMPs using an optimization model with
various BMP options and a targeting method for achieving a high level pollutant reduction with BMP
implementation in a small portion of the pasture lands. The hypotheses we tested were as follows
(1) selection and placement of BMPs from different sets of BMP options using a genetic algorithm (GA)
optimization tool can result in different water quality improvements; (2) Limiting the BMP options to the
BMPs which have a greater pollutant reduction rate can assist the optimization tool to allocate BMPs
more effectively. We used the multiobjective optimization model developed by Maringanti et al. [22]. This optimization model incorporates a BMP tool which replaces the requirement of dynamic linkage
with a hydrologic model (Soil and Water Assessment Tool, SWAT) in the BMP optimization
architecture. The BMP tool is a database that contains quantitative information of BMP effectiveness in
reducing pollutant losses for given land use. The two objective functions optimized in this study were
minimizing the pollutant loads and minimizing the areas for BMP implementation in the watershed. 2.2. SWAT Model Development The Soil and Water Assessment Tool (SWAT, version SWAT 2009), was used to estimate
the effectiveness of various BMP combinations in reducing pollutant losses in a previous study [32]. The SWAT 2009 has the abilities to simulate dynamic land use changes and has improved routines for
simulating vegetated filter strips. The model can predict long-term impacts of land use and
management on water, sediment and agricultural chemical yields at different scales in a mixed land use
watershed [33,34]. More than 250 peer-reviewed journal articles have been published demonstrating
the SWAT applications on sensitivity analyses, model calibration, hydrologic analyses, pollutant load
assessment, and climate change impacts on hydrology and pollutant losses [35]. The key GIS input
files to SWAT for this study included a 30 m digital elevation model (DEM) [36], 28.5 m land
use/land cover [37], and Soil Survey Geographic (SSURGO) soil data at a scale of 1:24,000 [38]. The watershed was delineated into several subbasins based on DEM and the outlets selected within the
watershed. Subsequently, the subbasins were partitioned into homogeneous units (hydrologic response
units, HRUs) by setting threshold percentages of land use and soil type [30,39]. In this study,
a threshold for a land use and soil type covering an area of 0% and 0%, respectively, within any given
subbasin was applied in order to capture all the land use changes that occurred during the study period. This resulted in a total number of 1,465 HRUs in the watershed. Weather data (daily precipitation,
minimum and maximum temperature) were obtained from Fayetteville Weather Station located
approximately 25 km from the watershed. Other weather variables needed by the model (solar
radiation, wind speed and relative humidity) were estimated using the weather generator built into
the SWAT model. The SWAT model has the ability to define specific types of manure and fertilizers by building
fertilizer and manure components, such as fractions of mineral N (P), organic N (P), and a ratio of
ammonium nitrate to mineral N in the SWAT fertilizer database. The pasture management
information, including amount of litter and fertilizer application, timing of manure and fertilizer
application, grazing intensity and dates were obtained from a detailed review of historical nutrient
management plans and interviews with 63 out of 75 farmers in the watershed [40]. The baseline
scenario consists of actual nutrient management and grazing management applied in the watershed
during 1992–2004. Int. J. Environ. Res. Public Health 2014, 11 Int. J. Environ. Res. Public Health 2014, 11 2996 2.1. Study Site This study was conducted in the Lincoln Lake CEAP watershed, a 32 km2 agricultural watershed
within the Illinois River basin located in Northwest Arkansas and Eastern Oklahoma (Figure 1). The average slope in the watershed is 6%. The elevation ranges from 365 to 487 m with a mean
elevation of 429 m. The major soil series in the watershed are Enders gravelly loam,
Hector-Mountainburg gravelly fine sandy loam, Captina silt loam and Linker loam, which account for 2995 Int. J. Environ. Res. Public Health 2014, 11 23%, 21%, 13% and 12% of the entire area, respectively. An average annual precipitation of 1,231 mm
was observed during 1990–2002 with the highest average monthly precipitation (158.3 mm) in April and
the lowest average monthly precipitation (74 mm) in January. The average maximum and minimum
temperature during 1990–2002 were 20.1 °C and 8.7 °C, respectively. Excessive nutrient losses due to
improper litter application and grazing activity on pasture lands has been one of the main environmental
issues in the watershed. The measured total phosphorus (TP) concentration at the Illinois River near
the Arkansas-Oklahoma border was about 0.4 mg/L [29]. Moores Creek and Beatty Branch are the two major tributaries in the Lincoln Lake watershed
representing 21 and 11 km2 of the watershed area, respectively. The watershed has a mixed land use
with pasture, forest, urban residential, urban commercial and water representing 35.8%, 48.6%, 11.9%,
1.5% and 2.2% of the watershed area, respectively (Figure 1). The pasture land use area has decreased
from 43% to 36% primarily due to increasing urbanization in the watershed since 1994 [30]. Pasture
fields in the watershed have numerous poultry, beef, and dairy cattle production facilities. Excessive
litter and manure application for perennial forage grass production in the watershed have been shown
to increase surface and ground water pollution due to increasing losses of sediment, nutrients and
pathogens [31]. Since 1994, BMPs implemented in the watershed have increased from 1% to 34% of
the watershed area, representing 53% of total pasture areas in the watershed in 2004. Figure 1. Location of Beatty Branch, Moores Creek, land-use distribution and the gauging
stations in the Lincoln Lake watershed. Figure 1. Location of Beatty Branch, Moores Creek, land-use distribution and the gauging
stations in the Lincoln Lake watershed. Figure 1. Location of Beatty Branch, Moores Creek, land-use distribution and the gauging
stations in the Lincoln Lake watershed. 2.3. BMP Scenarios The watershed BMPs considered in this study were grouped into three categories: grazing and
pasture management, vegetated filter strips, and nutrient management. These scenarios were based on
detailed interactions with the watershed stakeholders and history of past BMPs implemented in
the watershed [40]. Three grazing intensities were considered: (1) no grazing; (2) optimum grazing;
and (3) overgrazing. The overgrazing application started on 30 September and lasted for 213 days until
30 April of the next year. The optimum grazing assumed that within 30 days the cattle should graze
through the whole watershed and would stay for approximately 4–6 days in each pasture HRU [42]. This approach was similar to grazing operations reported in other watersheds located near the study
area [43]. Vegetated filter strips (VFS) have been proven to be an effective management practice for trapping
sediment and nutrients in field runoff [44–46], and reducing the transport of sediment and nutrients to
down-gradient area [47,48]. Based on the worst condition of sediment delivery simulated in
the previous study [49] and a method to design and estimate sediment removal from VFS by the
Natural Resources Conservation Service [50], buffer strips with VFS ratios of 42 and 76 were
simulated in this study. Nutrient management scenarios evaluated in this study included poultry litter application rates, litter
characteristics, and application timing. The litter application rates evaluated were 1, 1.5 and 2 tons/acre
in spring (applied on 30 April) and summer (31 August) to support growth of warm season grasses,
and 2, 2.5 and 3 tons/acre in fall (15 October) to support growth of cool season grasses. For all
application rates and timings evaluated in this study, two types of poultry litter were selected—normal
poultry litter and alum-amended litter. A total of 171 BMP combinations were simulated using the SWAT2009 model with dynamic land
use changes during 1990–2007 in a previous study [32] and the performances of those BMP
combinations in terms of pollutant reduction rates were further calculated for this study. It should be
noted that the latest SWAT2009 model, which was publicly released in January 2010, has incorporated
dynamic land use changes and modified simulation of vegetated filter strips. The model application
simulating the impacts of dynamic land use changes concurrent with installation of conservation
practices in the Lincoln Lake watershed can be found in Chiang et al. [32]. 2.3. BMP Scenarios In order to evaluate
the performance of the optimization models with different sets of BMP options, those 171 BMPs were
grouped by litter application in spring (SP, a total of 54 BMPs) and summer (SU, a total of 54 BMPs),
no grazing (NG, a total of 57 BMPs), optimum grazing (OG, a total of 57 BMPs), no buffer strips
(VFS0, a total of 57 BMPs) and buffer strips with a ratio of 42 (VFS42, a total of 57 BMPs). Int. J. Environ. Res. Public Health 2014, 11 Int. J. Environ. Res. Public Health 2014, 11 2997 2.2. SWAT Model Development The average litter application and approximate dates of application were
2,500 kg/ha applied on 30 April and 31 August. The manure excreted from grazing management
ranged from 0.01–14.2 kg/(ha·day) for grazing days ranging from 11–365 days in the watershed during
1992–2004. Those management practices were implemented throughout the entire pasture area in the
watershed. Detailed information of types of fertilizer and manure, the SWAT fertilizer database, and
management practices and schedules for SWAT management files can be found in Chiang et al. [32]. Model calibration and validation were performed for monthly stream flow, total sediment (TS),
total nitrogen (TN) and total phosphorus (TP) using the measured flow and water quality data collected
at the Upper Moores Creek for the period January 1996–February 1999, January 2000–December 2003
and January 2006–December 2007. A total of 10 SWAT parameters were calibrated using Nash-Sutcliffe
efficiency (NSE) [41] and coefficient of determination (R2) as the model performance criteria. Detailed
information of calibrated SWAT parameters and performance of the SWAT model can be found in
Chiang et al. [32]. 2.4. Multiobjective Genetic Algorithm Model A genetic algorithm (GA) is a search technique to find solutions for optimization problems. Genetic
algorithms are based on techniques inspired by evolutionary biology such as inheritance, selection,
crossover and mutation. An algorithm is started with a set of solutions (chromosomes), called
a population. The initial population of chromosomes is randomly generated for the given population
size (Figure 2). Inheritance is the ability of the modeled object to mate, mutate and propagate 2998 Int. J. Environ. Res. Public Health 2014, 11 the population as evolved solutions to a problem. A GA follows an iterated procedure (Figure 2). First,
evaluate objective functions by computing a fitness value for each number of the population. Second,
select a pair of chromosomes (parents) for mating (reproduction). During the selection process,
the existing solutions from one population are taken into the mating pool and used to form a new
population (children) based on their fitness; the higher the fitness of solutions are the more chance they
have to reproduce. Third, the solutions in the mating pool then undergo the genetic operations:
crossover and mutation. Crossover is a process that the new generation (child solutions) shares many
of the positive characteristics of the parents, while mutation is a process that a bit in the solutions of a
population is selected randomly and altered from its original state. The generational process is repeated
until a termination condition (e.g., a solution is found that satisfies minimum criteria) has been reached. Figure 2. Overview of the GA method. Multiobjective optimization problems have been evaluated in the hydrology/water quality field,
where optimal decisions need to be taken between two or more conflicting objectives. Single-objective
optimization yields a single optimal solution, while a multiobjective optimization produces a family of
near-optimal solutions known as Pareto-optimal set. Deb et al. [51] concluded that the nondominated
sorted genetic algorithm (NSGA-II) can search a larger number of variables and better spread of
solutions than the strength Pareto evolutionary algorithm (SPEA-2) [52]. In this study, a total of
461 pasture HRUs are the variables for which the BMPs are to be searched to meet the two objective
functions: (1) minimization of pollutant loading and (2) minimization of the pasture area that has
BMPs implemented. The greater the pasture areas that have BMP, the less the polluatant loading. 2.4. Multiobjective Genetic Algorithm Model where pol is the number of pollutants of concern (pol = 1 for TN and pol = 2 for TP), Ppol, hru is the unit
pollutant load from a HRU, Rpol, bmp is the pollutant reduction efficiency of BMP, A is the area of HRU. A BMP tool was used to provide pollutant effectiveness for each BMP that can be implemented at
a HRU scale in the watershed [22]. In a previous study, the SWAT model was run for those 171 BMP
scenarios for dynamic land use and management practices during 1992–2007 with the corresponding
historical weather [32]. The pollutant reduction efficiency was estimated by calculating the percentage
reduction in the pollutant load for a BMP scenario compared with the baseline pollutant load. In order
to narrow the search space for a given land use, seven allele sets of different BMP groups for pasture
lands were created. Those allele sets for pasture lands are: a set of 171 simulated BMPs applicable to
pasture HRUs (All), and other six sets of BMPs that contain no grazing (NG), optimum grazing (OG),
spring litter application (SP), summer litter application (SU), no buffer strips (VFS0) and buffer strips
with a VFS ratio of 42 (VFS42). During the optimization process, the algorithm first searches one
BMP in the allele set for a pasture HRU. The estimation of the pollutant loading for the placement of
that BMP in the selected pasture HRU is obtained from the BMP tool. An aggregated pollutant index
(API), which is a product of the area-weighted pollutant reduction rates for TN and TP, and the total
pasture lands that have BMP implemented were calculated for an estimation at the watershed scale. Four parameters for a GA optimization are population size, number of generations, crossover rate
and mutation probability. Population size determines the number of solutions considered for
the evolutionary process. Crossover rate and mutation probability are critical in the optimization
process in terms of creating a new set of child population which might be stronger than the parent
population and eliminating the weaker individuals. The optimization process continues until a given
number of iterations known as generations. Generally, the larger the population size, the more spread
the solution space. Increasing the number of generations can also improve the performance of GA. However, it also increases the computing time to reach the near-optimal solution. 2.4. Multiobjective Genetic Algorithm Model The two objective functions are mathematically expressed as follows, where f(x) denotes total
pollution load and g(x) denotes the percentage of pasture area with BMPs implemented in total pasture
lands. It should be noted that total nitrogen (TN) and total phosphorus (TP) losses were the two
pollutants of concern for BMP implementation in this watershed: Figure 2. Overview of the GA method. Multiobjective optimization problems have been evaluated in the hydrology/water quality field,
where optimal decisions need to be taken between two or more conflicting objectives. Single-objective
optimization yields a single optimal solution, while a multiobjective optimization produces a family of
near-optimal solutions known as Pareto-optimal set. Deb et al. [51] concluded that the nondominated
sorted genetic algorithm (NSGA-II) can search a larger number of variables and better spread of
solutions than the strength Pareto evolutionary algorithm (SPEA-2) [52]. In this study, a total of
461 pasture HRUs are the variables for which the BMPs are to be searched to meet the two objective
functions: (1) minimization of pollutant loading and (2) minimization of the pasture area that has
BMPs implemented. The greater the pasture areas that have BMP, the less the polluatant loading. The two objective functions are mathematically expressed as follows, where f(x) denotes total
pollution load and g(x) denotes the percentage of pasture area with BMPs implemented in total pasture
lands. It should be noted that total nitrogen (TN) and total phosphorus (TP) losses were the two
pollutants of concern for BMP implementation in this watershed: Int. J. Environ. Res. Public Health 2014, 11 2999 min[ ( )
( )]
[ ,
]
f x
g x
f
P N
(1)
,
,
1
1
,
1
(
(1
)
)
(
)
HRU
POL
HRU
n
n
pol hru
pol bmp
hru
hru
n
pol
pol hru
hru
hru
P
R
A
P
A
(2)
1
HRU
n
hru
hru
A
(3) min[ ( )
( )]
[ ,
]
f x
g x
f
P N
(1) (2) (3) where pol is the number of pollutants of concern (pol = 1 for TN and pol = 2 for TP), Ppol, hru is the unit
pollutant load from a HRU, Rpol, bmp is the pollutant reduction efficiency of BMP, A is the area of HRU. 2.6. Targeting Method The targeting method was chosen as a comparison of the selection and placement of BMPs from
the GA optimization tool. The pasture HRUs were first ranked by the TN or TP losses. A single BMP
scenario that has the greatest TN or TP reduction rate is implemented on the top ranked HRUs which
accounted for 20%, 40%, 60%, 80% and 100% of the total pasture area. The pollutant losses from
the entire pasture lands were calculated by summing up the pollutant losses from the HRUs that have
the selected BMP scenario implemented and the current pollutant losses from the rest of pasture
HRUs, and then divided by the total pasture area. One of the differences between GA optimization
method and targeting method is that GA requires much longer computing time for a larger population
size (>5,000) to get a wide range in solution space (i.e., large number of choices for various pollutant
reductions and areas under BMP combinations). Contrarily, the targeting method can provide a quicker
solution by placing a BMP option on any pasture area that has relatively high TN or TP losses. In order
to compare the performance of the optimization tool and the targeting method, the optimal percentage
of BMP-implemented area that is identified by GA optimization was used to target the top ranked
pasture HRUs which account for the same percentage of the area and calculate the pollutant losses
from the pasture lands. 2.5. Sensitivity Analysis and Estimation of GA Parameters A sensitivity analysis of four GA parameters for different allele sets (BMP options) was performed
to determine the influence of the parameters on the Pareto-optimal front and to identify the optimal
parameter values. In order to evaluate the individual influence of a GA parameter on the Pareto-optimal
front, one parameter (population size, number of generation, crossover and mutation probability) was
changed at a time and the other parameters remained as default values (Table 1). The goodness of
the Pareto-optimal front is determined subjectively as the closer the front gets to the origin, the better
the solution is to minimize the two objective functions. When the front with a specific parameter value 3000 Int. J. Environ. Res. Public Health 2014, 11 is closer to the origin, that value is then used for the optimization process. The aggregated pollutant
index (API) and the percentage of pasture lands with BMPs implemented were estimated from
equations (2) and (3). These two values are plotted against each other during the sensitivity analysis to
obtain the optimal parameter values that have the Pareto-optimal front closest to the origin. Table 1. Default and optimal GA parameters for different allele sets selected from
sensitivity analysis. Parameter
Population
Number of
Generations
Crossover
Probability
Mutation
Probability
Default
100
1,000
0.9
0.0001
Optimal for different allele sets
171 BMPs (All)
5,000
40,000
0.9
0.001
NG BMPs
3,000
40,000
0.5
0.001
OG BMPs
5,000
40,000
0.9
0.001
SP BMPs
3,000
40,000
0.7
0.001
SU BMPs
3,000
40,000
0.9
0.001
VFS0 BMPs
5,000
40,000
0.7
0.001
VFS42 BMPs
3,000
40,000
0.5
0.001
Targeting Method 3.1. Sensitivity and Estimation of GA Parameters The optimal GA parameters were selected using the sensitivity analysis of the optimal front. A total
of seven sets of sensitivity analyses were performed for 171 BMPs. The sensitivity of GA parameters
for the optimization model with a set of 171 BMP options (All), namely, population size, number of Int. J. Environ. Res. Public Health 2014, 11 3001 generations, crossover probability, and mutation probability, are shown in Table 1. Two GA
parameters, population size and number of generations, can influence the computing time of the
optimization. For example, when the population size increased from 100 to 5,000, the computation
time increased from 10 min to 12 h for 1,000 generations. Similarly, the computation time increased
from 10 min to 1 h when number of generation increased from 100 to 5,000. The maximum population
size tested in this study was 5,000, with which the GA optimization tool could result in the most spread
in the solution space in terms of the percentage of BMP-implemented pasture area for all different sets
of BMP options. The sensitivity analysis results of the VFS42 BMP options (VFS42) and 171 BMP
options (All) were selected for comparison (Figures 3 and 4). It is because buffer strips are the most
effective BMP in reducing pollutant losses and considerably greater pollutant reduction is expected if
buffer strips with a VFS ratio of 42 are considered in the suite of BMP options. Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). As the population size increased from 10 to 5,000, more individuals were present during each
evolution and there was a higher probability of obtaining a better offspring. Therefore, an improvement
of the Pareto-optimal front that is getting closer to the origin was observed during the increases of
population size. For the 171 BMP options, when population size further increased to 5,000 the
individuals in the solution space had more freedom in terms of more spread of solutions compared to
other population sizes (Figure 3a). Therefore, a population size of 5,000 was selected as an optimal value
for the models with the sets of 171 BMP, OG BMP and VFS0 BMP options (Table 1). However, when
only the BMPs with buffer strips of a VFS ratio of 42 were considered, an increase in population size
from 3,000 to 5,000 did not show a considerable improvement in the Pareto-optimal front (Figure 4a). It As the population size increased from 10 to 5,000, more individuals were present during each
evolution and there was a higher probability of obtaining a better offspring. Therefore, an improvement
of the Pareto-optimal front that is getting closer to the origin was observed during the increases of
population size. For the 171 BMP options, when population size further increased to 5,000 the
individuals in the solution space had more freedom in terms of more spread of solutions compared to
other population sizes (Figure 3a). Therefore, a population size of 5,000 was selected as an optimal value
for the models with the sets of 171 BMP, OG BMP and VFS0 BMP options (Table 1). However, when
only the BMPs with buffer strips of a VFS ratio of 42 were considered, an increase in population size
from 3,000 to 5,000 did not show a considerable improvement in the Pareto-optimal front (Figure 4a). It As the population size increased from 10 to 5,000, more individuals were present during each
evolution and there was a higher probability of obtaining a better offspring. Therefore, an improvement
of the Pareto-optimal front that is getting closer to the origin was observed during the increases of
population size. For the 171 BMP options, when population size further increased to 5,000 the
individuals in the solution space had more freedom in terms of more spread of solutions compared to
other population sizes (Figure 3a). Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). Therefore, a population size of 5,000 was selected as an optimal value
for the models with the sets of 171 BMP, OG BMP and VFS0 BMP options (Table 1). However, when
only the BMPs with buffer strips of a VFS ratio of 42 were considered, an increase in population size
from 3,000 to 5,000 did not show a considerable improvement in the Pareto-optimal front (Figure 4a). It As the population size increased from 10 to 5,000, more individuals were present during each
evolution and there was a higher probability of obtaining a better offspring. Therefore, an improvement
of the Pareto-optimal front that is getting closer to the origin was observed during the increases of
population size. For the 171 BMP options, when population size further increased to 5,000 the
individuals in the solution space had more freedom in terms of more spread of solutions compared to
other population sizes (Figure 3a). Therefore, a population size of 5,000 was selected as an optimal value
for the models with the sets of 171 BMP, OG BMP and VFS0 BMP options (Table 1). However, when
only the BMPs with buffer strips of a VFS ratio of 42 were considered, an increase in population size
from 3,000 to 5,000 did not show a considerable improvement in the Pareto-optimal front (Figure 4a). It 3002 Int. J. Environ. Res. Public Health 2014, 11 should be noted that during sensitivity analysis, only one GA parameter of concern was changed and
the other three parameters were fixed at their default values. Therefore, a population size of 5,000
might require more generations (>1,000) for the individuals to show a considerable change in
the objective functions. However, as the number of generations increases, the computing time would
also increase. Therefore, a population size of 3,000 was selected as an optimal value for the models
with the sets of NG BMP, SP BMP, SU BMP and VFS42 BMP options. Figure 4. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of VFS42 BMP options. Figure 4. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of VFS42 BMP options. Similar to the population size, an increase in the number of generations can lead the Pareto-optimal
ront closer to the origin and a better optimal solution can be found. Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). The larger the number of
enerations is, the better the fittest individuals for reproduction can be selected. The Pareto-optimal
ront greatly improved when the number of generations increased from 100 to 1,000, while there was
o considerable change between 10,000 and 40,000 generations (Figures 3b and 4b). A similar result
was observed for the models with other sets of BMP options. It was noticed that the Pareto-optimal
ront considerably improved as the number of generations increased. However, a model run with
combination of the population size of 3,000 or 5,000 and the 40,000 generations will take much more
omputation time. Therefore, 10,000 generations were used in the final optimization model for all sets
f BMP options. Similar to the population size, an increase in the number of generations can lead the Pareto-optimal
front closer to the origin and a better optimal solution can be found. The larger the number of
generations is, the better the fittest individuals for reproduction can be selected. The Pareto-optimal
front greatly improved when the number of generations increased from 100 to 1,000, while there was
no considerable change between 10,000 and 40,000 generations (Figures 3b and 4b). A similar result
was observed for the models with other sets of BMP options. It was noticed that the Pareto-optimal
front considerably improved as the number of generations increased. However, a model run with
a combination of the population size of 3,000 or 5,000 and the 40,000 generations will take much more
computation time. Therefore, 10,000 generations were used in the final optimization model for all sets
of BMP options. Similar to the population size, an increase in the number of generations can lead the Pareto-optimal
front closer to the origin and a better optimal solution can be found. The larger the number of
generations is, the better the fittest individuals for reproduction can be selected. The Pareto-optimal
front greatly improved when the number of generations increased from 100 to 1,000, while there was
no considerable change between 10,000 and 40,000 generations (Figures 3b and 4b). A similar result
was observed for the models with other sets of BMP options. It was noticed that the Pareto-optimal
front considerably improved as the number of generations increased. However, a model run with
a combination of the population size of 3,000 or 5,000 and the 40,000 generations will take much more
computation time. Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). Therefore, 10,000 generations were used in the final optimization model for all sets
of BMP options. Unlike the population size and the number of generations, an increase in crossover probability did
not always result in a better Pareto-optimal front. For example, the solutions of the model with the
171 BMP options improved when the crossover probability increased from 0.1 to 0.4, but the front
moved away from the origin when it further increased to 0.5 and 0.7 (Figure 3c). The optimal solution
was found when the crossover probability was 0.9, indicating that the higher crossover probability Int. J. Environ. Res. Public Health 2014, 11 Int. J. Environ. Res. Public Health 2014, 11 3003 leads to faster convergence. The same optimal crossover probability (0.9) was found for the models
with the sets of OG BMP and SU BMP options, while other models had different optimal values
(0.5 and 0.7) (Table 1). No consistent pattern in the shift of the Pareto-optimal front was found for the mutation probability. For both the models with sets of 171 BMP and VFS42 BMP options, a slightly higher mutation
probability (0.001) than the default value (0.0001) made the Pareto-optimal front move toward
the origin (Figures 3d and 4d). Further increases in the mutation probability (0.01 and 0.1) resulted in
a dramatic deterioration in the performance. Similar results were found in other models with different
sets of BMP options, and the optimal value for mutation probability (0.001) was used in the final BMP
optimization model for the models with all different sets of BMP options. An interesting result was observed when comparing the Pareto-optimal fronts for these models with
different BMP options using their optimal GA parameters (Table 1 and Figure 5). Generally,
the Pareto-optimal front of the model with VFS0 BMP options was the farthest from the origin,
indicating that the solutions obtained from the BMPs with no buffer strips were greatly limited in
finding an optimal solution in terms of minimizing the BMP-implemented area and minimizing
the nutrient losses. The best performance of the Pareto-optimal front was observed for the model with
the VFS42 BMP option, followed by two models with NG and OG BMP options, and the other two
models with SP and SU BMP options. 3.2. Performance of the Optimization Tool and the Targeting Method After assessing the sensitivity analysis for the GA parameters, various final values of the GA
parameters were applied to each model to search for the optimal BMP solutions (Table 1). The optimized
results were then compared to the solutions obtained using the targeting method (Figure 6). The average
annual area-weighted baseline loadings from the pasture lands were 4.55 kg/ha and 1.66 kg/ha for total
nitrogen (TN) and total phosphorus (TP), respectively. The optimization provided 3,000–5,000
solutions during each generation depending on the BMP options were considered. All
the solutions in the last generation (10,000th) were presented in the Pareto-optimal front (Figure 6),
and the optimal solution was found as median of the range of the pollutant loads and
BMP-implemented area for each BMP option (Table 2). For the optimization model with the 171 BMP
option, the optimal solution resulted in nutrient losses of 3.39 kg/ha (25.54% reduction) and 0.74 kg/ha
(55.12% reduction) for TN and TP, respectively when various BMPs are implemented in 77% of
the entire pasture areas. The optimal solution for the model with the NG BMP options showed that
greater nutrient reductions would be found if BMPs are installed in more than 77% of the pasture
areas. Generally, there is no significant difference among the solutions for the models with 171 BMP
options and different grazing options (Figure 6). However, even more pasture areas having BMPs with
only spring or summer litter application implemented, less nutrient reductions could be found in
the watershed compared with the 171 BMP option. When only summer litter application was
considered, much less TN reduction would be achieved compared to the solutions with SP BMP
options. Similarly, the optimal solution for the model with the VFS0 BMP option was 3.75 kg/ha and
1.11 kg/ha of TN and TP loads, respectively, with various BMPs implemented in 82% of the pasture
areas. It showed that even if more pasture lands have BMPs implemented, less pollutant reduction
would be achieved if buffer strips were not among the BMP options considered. Those observations
were consistent with the observation in the sensitivity analyses for different models (Figure 5) that
the Pareto-optimal fronts of the models with sets of VFS0 and SU BMP options were away from
the origin, indicating that the low pollutant reduction rates of the selected BMPs themselves can affect
the overall reduction obtained from the optimization. Int. J. Environ. Res. Public Health 2014, 11 Int. J. Environ. Res. Public Health 2014, 11 3004 Figure 3. Pareto-optimal fronts for the sensitivity analysis of genetic algorithm (GA)
parameters for the optimization model with a set of 171 BMP options (All). This can be explained as buffer strip is the most effective
management practice in reducing pollutant losses and most of the nutrient losses come from land
application than grazing management. Figure 5. Comparison of the Pareto-optimal fronts for models with different BMP options
using their optimal GA parameters. 3.2. Performance of the Optimization Tool and the Targeting Method A total of 461 pasture HRUs were ranked by the pollutant losses. The BMPs that resulted in
the greatest TN reduction rate are the BMP combination of buffer strips (VFS ratio = 42 or 76) and no
litter application. However, use of fertilizer or manure to support plant growth is needed and generally
found in the watershed. Except the no litter application, the litter types, application timing and amount
can be optimized. Therefore, an optimal suite of BMPs (scenario 81) to reduce TN losses, which has
the TN reduction rate of 28.33%, is a combination of buffer strips (VFS ratio = 42), optimum grazing
and 1 ton/acre litter application in spring. While the optimal suite of BMPs (scenario 59) to reduce TP
losses with a TP reduction rate of 62.15% is the combination of buffer strips (VFS ratio = 42), no
grazing and 1 ton/acre alum-treated litter application in spring. By using the targeting method, the least
annual TN and TP losses from pasture area that would be seen were 3.26 kg/ha and 0.63 kg/ha if the
optimal suites of BMPs were adopted in all pasture lands (Figure 6). When 50% of the pasture
lands have the optimal BMPs implemented, the TN and TP loads could reduce to 3.65 kg/ha
(19.15% reduction) and 0.96 kg/ha (41.98% reduction), respectively. While a greater reduction in
the pollutant losses can be obtained from BMP optimization, the computation time requirement for the 3005 Int. J. Environ. Res. Public Health 2014, 11 optimization is considerably longer, when using a 3,000–5,000 population size and 10,000 generations,
than the targeting method, which is simply a ranking of pollutant losses from HRUs. However, the
targeting method does not compare interactions among BMPs, and adoption of a single suit of BMPs
throughout the pasture lands may not be practical due to various land characteristics or farmers’
choices of BMPs. Table 2. Solutions which are medians of the range of pollutant loads and BMP-implemented
area for different optimization models. 3.2. Performance of the Optimization Tool and the Targeting Method The distribution of those optimal BMPs were presented into three maps with different
legend categories, which are grazing management, litter application timing and buffer strips. The blue
areas denote no BMPs were selected for those areas, which account for 23% of the total pasture area. Among those selected BMPs, no BMPs with fall litter application and no buffer strips were selected by
the optimization tool. It was observed that no grazing management, no litter application and buffer
strips with a VFS ratio of 42 were frequently selected by the optimization tool, indicating this BMP
combination can reduce nutrient losses more effectively than other BMP combinations. From
the perspective of a watershed manager, those extreme management practices can reduce the greatest
pollutant losses without considering the crop yields. If this optimal solution is adopted in
the watershed, TN and TP losses can be expected to reduce by 25.5% and 55.1%, respectively. However, various BMP combinations can be designed as BMP options for optimization tool to assess
the pollutant reduction by optimal practical or farmers-preferable management practices. Figure 6. Cont. 3.3. Comparison of Selection and Placement of BMPs Figure 6. Cont. 3 3 C
i
f S l
ti
d Pl
t f BMP Figure 6. Cont. 3.3. Comparison of Selection and Placement of BMPs The optimal solution for the model with 171 BMP options was distributed throughout the watershed
(Figure 7). The distribution of those optimal BMPs were presented into three maps with different
legend categories, which are grazing management, litter application timing and buffer strips. The blue
areas denote no BMPs were selected for those areas, which account for 23% of the total pasture area. Among those selected BMPs, no BMPs with fall litter application and no buffer strips were selected by
the optimization tool. It was observed that no grazing management, no litter application and buffer
strips with a VFS ratio of 42 were frequently selected by the optimization tool, indicating this BMP
combination can reduce nutrient losses more effectively than other BMP combinations. From
the perspective of a watershed manager, those extreme management practices can reduce the greatest
pollutant losses without considering the crop yields. If this optimal solution is adopted in
the watershed, TN and TP losses can be expected to reduce by 25.5% and 55.1%, respectively. 3.2. Performance of the Optimization Tool and the Targeting Method BMP Options
TN Load
(kg/ha)
BMP
Area(%)
TP Load
(kg/ha)
BMP
Area(%)
ALL
3.39
0.77
0.74
0.77
NG
3.36
0.82
0.70
0.82
OG
3.41
0.75
0.74
0.75
SP
3.51
0.78
0.75
0.78
SU
3.77
0.74
0.79
0.74
VFS0
3.75
0.82
1.11
0.82
VFS42
3.38
0.77
0.77
0.77
Note: ALL denotes all 171 BMP options; NG denotes the BMP options containing only BMPs with no
grazing management; OG denotes the BMP options containing only BMPs with optimum grazing
management; SP denotes the BMP options containing only BMPs with spring litter application; SU denotes
the BMP options containing only BMPs with summer litter application; VFS0 denotes the BMP options
containing only BMPs with no buffer strips; VFS42 denotes the BMP options containing only BMPs with
buffer strips with a VFS ratio of 42. 2. Solutions which are medians of the range of pollutant loads and BMP-implemented
or different optimization models. Table 2. Solutions which are medians of the range of pollutant loads and BMP-implemented
area for different optimization models. BMP Options
TN Load
(kg/ha)
BMP
Area(%)
TP Load
(kg/ha)
BMP
Area(%)
ALL
3.39
0.77
0.74
0.77
NG
3.36
0.82
0.70
0.82
OG
3.41
0.75
0.74
0.75
SP
3.51
0.78
0.75
0.78
SU
3.77
0.74
0.79
0.74
VFS0
3.75
0.82
1.11
0.82
VFS42
3.38
0.77
0.77
0.77
Note: ALL denotes all 171 BMP options; NG denotes the BMP options containing only BMPs with no Note: ALL denotes all 171 BMP options; NG denotes the BMP options containing only BMPs with no
grazing management; OG denotes the BMP options containing only BMPs with optimum grazing
management; SP denotes the BMP options containing only BMPs with spring litter application; SU denotes
the BMP options containing only BMPs with summer litter application; VFS0 denotes the BMP options
containing only BMPs with no buffer strips; VFS42 denotes the BMP options containing only BMPs with
buffer strips with a VFS ratio of 42. Figure 6. Comparison of the Pareto-optimal fronts of different optimization models after
the final generation and the solutions obtained from the targeting method for total nitrogen
(TN) and total phosphorus (TP) reduction. 3006 Int. J. Environ. Res. Public Health 2014, 11 Int. J. Environ. Res. Public Health 2014, 11
3006
Figure 6. Cont. 3.3. Comparison of Selection and Placement of BMPs
The optimal solution for the model with 171 BMP options was distributed throughout the watershed
(Figure 7). Int. J. Environ. Res. Public Health 2014, 11 Int. J. Environ. Res. Public Health 2014, 11 In order to compare the performance of optimization models with different BMP options, various
solutions that meet either the optimal pollutant reduction or BMP-implemented area by the model with
171 BMP options were selected (Table 3 and Figure 9). Both solutions from the models with NG and
OG BMP options were able to reduce TN losses to 3.39 kg/ha, which was the same as the optimal TN
reduction of the model with 171 BMP options (Figure 9a,b). Those BMP combinations were grouped
by no BMP, no buffer strips, buffer strips with a ratio of 42 and with a ratio of 76. The selected NG
BMPs were implemented on 80% of the pasture lands, while the selected OG BMPs were implemented
on 77% of the pasture lands, which is the same as the optimal BMP-implemented area for the model
with 171 BMP options. When only BMP combinations that consist of litter application in spring were selected for the
optimization model, more pasture lands (89%) are needed to achieve the same pollutant reduction from
the optimization model with the 171 BMP options (Figure 9c). It was observed that even all the pasture
lands have BMPs that consist of litter application in summer, the pollutant losses with 3.54 kg/ha of
TN load and 0.66 kg/ha of TP load were relatively higher than the pollutant reduction from the optimal
solution of the model with 171 BMP options (Figure 9d). It indicated that BMPs with the litter
application in summer should be avoided. Similarly, when only the BMPs with no buffer strips were
evaluated, less effectiveness of those BMPs could be expected even if they were adopted on all pasture
lands (Figure 9e). The higher pollutant loads resulted by implementing VFS0 BMPs throughout
the pasture lands than by implementing VFS42 BMPs indicated that buffer strips are most effective
management practices to reduce pollutant losses. The effectiveness of buffer strips with a ratio of
42 indicated that fewer pasture areas (75%) are needed to have BMPs implemented to improve water
quality (Figure 9f). Table 3. Solutions from other models which at least meet the same pollutant reduction of
the model with 171 BMP options. Table 3. Solutions from other models which at least meet the same pollutant reduction of
the model with 171 BMP options. Int. J. Environ. Res. Public Health 2014, 11 BMP
options
TN Load (kg/ha)
BMP Area(%)
TP Load (kg/ha)
BMP Area(%)
Baseline
4.55
0.00
1.66
0.00
ALL
3.39
0.77
0.74
0.77
NG
3.39
0.80
0.72
0.80
OG
3.39
0.77
0.73
0.77
SP
3.39
0.89
0.68
0.89
SU
3.54
1.00
0.66
1.00
VFS0
3.62
1.00
1.07
1.00
VFS42
3.39
0.75
0.78
0.75
Conclusions 3.2. Performance of the Optimization Tool and the Targeting Method However, various BMP combinations can be designed as BMP options for optimization tool to assess
the pollutant reduction by optimal practical or farmers-preferable management practices. Compared to the distribution of the BMP-implemented area from the optimization tool, a slightly
different distribution of the selected BMP in the watershed by using the targeting tool was observed
(Figure 8). It should be noted that the total percentage of original pasture lands that have BMP
implemented is the same as the solution from the optimization tool. The BMP combination (BMP 81)
that has the greatest TN reduction rate was selected as the optimal BMP combination to reduce TN
losses. Likewise, the BMP combination (BMP 59) was selected as the optimal BMP combination to
reduce TP losses. The blue areas denote no BMPs were selected for those areas. It was observed that
the distributions of targeted area for reducing TN and TP losses were different, indicating that a proper
BMP combination needs to be adopted to reduce both pollutants of concern. 3007 Int. J. Environ. Res. Public Health 2014, 11 Figure 7. Distribution of BMPs selected by the optimization model with the 171 BMP
options on 77% of the pasture lands in the watershed. Figure 8. Distribution of BMPs selected by the targeting method on 77% of the pasture
lands in the watershed. Figure 8. Distribution of BMPs selected by the targeting method on 77% of the pasture
lands in the watershed. 3008 4. Conclusions Many studies have been conducted to optimize the selection and placement of BMPs to
economically reduce pollutant loads from watersheds by using plan- or performance-based methods. The objectives of this study were to: (1) compare the selection and placement of BMPs using a genetic
algorithm (GA) optimization and a targeting method; (2) evaluate the impacts of various BMP options 3009 Int. J. Environ. Res. Public Health 2014, 11 Figure 9. Distribution of selected BMPs from different optimization models to meet the
same pollutant reduction of the model with the 171 BMP options. Figure 9. Distribution of selected BMPs from different optimization models to meet the
same pollutant reduction of the model with the 171 BMP options. same pollutant reduction of the model with the 171 BMP options. Int. J. Environ. Res. Public Health 2014, 11 3010 on the optimal solutions from optimization. Two objective functions were used to minimize the TN and
TP losses and the BMP-implemented pasture area. It was found that optimization required much longer
computation time than the targeting method to obtain a more spread of solutions. The solutions
obtained from the optimization tool were optimal for both reducing TN and TP losses by placing
BMPs in the same pasture areas, while the targeting method focused on reducing one individual
pollutant loading at a time by placing a single suite of BMPs in different areas, which may not be
practical due to various land characteristics or farmers’ choices of BMPs. Overall, when using
the targeting method more pasture areas are needed to have BMPs implemented in order to achieve
the same pollutant reductions that result from the optimal BMPs selected by optimization. A total of 171 BMP scenarios were grouped by no grazing (NG), optimum grazing (OG), spring
litter application (SP), summer litter application (SU), no buffer strips (VFS0) and buffer strips with
a VFS ratio of 42 (VFS42) as various sets of BMP options for evaluating their impacts on the optimal
solutions from the optimization model. The results showed that limiting the BMP options to certain
BMPs, such as buffer strips with a VFS ratio of 42, could result in greater pollutant reductions within
smaller pasture areas managed with BMPs. Author Contributions Li-Chi Chiang and Indrajeet Chaubey designed research; Li-Chi Chiang conducted research,
analyzed data and drafted this manuscript under Indrajeet Chaubey’s supervision; Chetan Maringanti
developed the GA model for the research and assisted the analyses; Tao Huang managed the
manuscript and provided some useful comments; Li-Chi Chiang had the primary responsibility for the
final content. All authors have read and approved the final manuscript. 4. Conclusions However, when only summer litter application or no buffer
strips are considered during optimization and the optimal BMPs are implemented in the entire pasture
areas, they still resulted in greater pollutant losses than the solutions from the model with 171 BMP
options. Therefore, it is essential to carefully select the BMP options for optimization in order to obtain
more effective solutions in minimizing pollutant losses and BMP-implemented area in a watershed. Moreover, for a more comprehensive evaluation of selection and placement of BMPs in a watershed,
other pollutants of concerns, and cost and maintenance of selected BMPs options should be taken into
consideration when applying this evaluation framework. Conflicts of Interest The authors declare no conflict of interest. 1.
Harmel, R.D.; Torbert, H.A.; Haggard, B.E.; Haney, R.; Dozier, M. Water quality impacts of
converting to a poultry litter fertilization strategy. J. Environ. Qual. 2004, 33, 2229–2242.
2.
Yu, C.; Northcott, W.J.; McIsaac, G.F. Development of an artificial neural network for hydrologic
and water quality modeling of agricultural watersheds Trans ASAE 2004 47 285 290 1.
Harmel, R.D.; Torbert, H.A.; Haggard, B.E.; Haney, R.; Dozier, M. Water quality impacts of
converting to a poultry litter fertilization strategy. J. Environ. Qual. 2004, 33, 2229–2242. References 1. Harmel, R.D.; Torbert, H.A.; Haggard, B.E.; Haney, R.; Dozier, M. Water quality impacts of
converting to a poultry litter fertilization strategy. J. Environ. Qual. 2004, 33, 2229–2242. 2. Yu, C.; Northcott, W.J.; McIsaac, G.F. Development of an artificial neural network for hydrologic
and water quality modeling of agricultural watersheds. Trans. ASAE 2004, 47, 285–290. Int. J. Environ. Res. Public Health 2014, 11 3011 3. Alexander, R.B.; Smith, R.A.; Schwarz, G.E.; Boyer, E.W.; Nolan, J.V.; Brakebill, J.W. Differences in phosphorus and nitrogen delivery to the Gulf of Mexico from the Mississippi river
basin. Environ. Sci. Technol. 2008, 42, 822–830. 4. Chiueh, P.T.; Shang, W.T.; Lo, S.L. An integrated risk management model for source water
protection areas. Int. J. Environ. Res. Public Health 2012, 9, 3724–3739. 5. Tilman, D.; Cassman, K.G.; Matson, P.A.; Naylor, R.; Polasky, S. Agricultural sustainability and
intensive production practices. Nature 2002, 418, 671–677. 6. Gillingham, A.G.; Thorrold, B.S. A review of New Zealand research measuring phosphorus in
runoff from pasture. J. Environ. Qual. 2000, 29, 88–96. 7. Monaghan, R.M.; Paton, R.J.; Smith, L.C.; Drewry, J.J.; Littlejohn, R.P. The impacts of nitrogen
fertilization and increased stocking rate on pasture yield, soil physical condition and nutrient
losses in drainage from a cattle-grazed pasture. New Zeal. J. Agr. Res. 2005, 48, 227–240. 8. Sharpley, A.N.; Chapra, S.C.; Wedepohl, R.; Sims, J.T.; Daniel, T.C.; Reddy, K.R. Managing
agricultural phosphorus for protection of surface waters: Issues and options. J. Environ. Qual. 1994, 23, 437–451. 9. Edwards, D.R.; Daniel, T.C. Potential runoff quality effects of poultry manure slurry applied to
fescue plots. Trans. ASAE 1992, 35, 1827–1832. 10. U.S. Environmental Protection Agency (USEPA). National Management Measures to Control
Nonpoint Source Pollution from Agriculture: EPA 841-B-03–004; U.S. Environmental Protection
Agency: Washington, DC, USA, 2003. 11. Santhi, C.; Srinivasan, R.; Arnold, J.G.; Williams, J.R. A modeling approach to evaluate
the impacts of water quality management plans implemented in a watershed in texas. Environ. Model. Softw. 2006, 21, 1141–1157. 12. Arabi, M.; Govindaraju, R.S.; Hantush, M.M. A probabilistic approach for analysis of uncertainty
in the evaluation of watershed management practices. J. Hydrol. 2007, 333, 459–471. 13. Chiang, L.C.; Chaubey, I.; Hong, N.M.; Lin, Y.P.; Huang, T. Implementation of BMP strategies
for adaptation to climate change and land use change in a pasture-dominated watershed. Int. J. Environ. Res. Public Health 2012, 9, 3654–3684. 14. Green, C.H.; Arnold, J.G.; Williams, J.R.; Haney, R.; Harmel, R.D. References Soil and water assessment
tool hydrologic and water quality evaluation of poultry litter application to small-scale subwatersheds
in texas. Trans. ASABE 2007, 50, 1199–1209. 15. Rodríguez, H.G.; Popp, J.; Maringanti, C.; Chaubey, I. Selection and placement of best
management practices used to reduce water quality degradation in lincoln lake watershed. Water Resour. Res. 2011, 47, 1–13. 16. Vaché, K.B.; Eilers, J.M.; Santelmann, M.V. Water quality modeling of alternative agricultural
scenarios in the us corn belt. J. Am. Water Resour. Assoc. 2002, 38, 773–787. 17. Pionke, H.B.; Gburek, W.J.; Sharpley, A.N. Hydrologic and Chemical Controls on Phosphorous
Loss from Catchments; CAB International Press: Cambridge, UK, 1997; pp. 225–242. 18. Veith, T.L.; Wolfe, M.L.; Heatwole, C.D. Cost-effective BMP placement: Optimization vs. targeting. Trans. ASAE 2004, 47, 1585–1594. Int. J. Environ. Res. Public Health 2014, 11 3012 19. Behera, S.; Panda, R.K. Evaluation of management alternatives for an agricultural watershed in
a sub-humid subtropical region using a physical process based model. Agric. Ecosyst. Environ. 2006, 113, 62–72. 20. Tripathi, M.P.; Panda, R.K.; Raghuwanshi, N.S. Development of effective management plan for
critical subwatersheds using SWAT model. Hydrol. Process. 2005, 19, 809–826. 21. Giri, S.; Nejadhashemi, A.P.; Woznicki, S.A. Evaluation of targeting methods for implementation of
best management practices in the Saginaw river watershed. J. Environ. Manage. 2012, 103, 24–40. 22. Maringanti, C.; Chaubey, I.; Popp, J. Development of a multiobjective optimization tool for
the selection and placement of best management practices for nonpoint source pollution control. Water Resour. Res. 2009, 45, doi:10.1029/2008WR007094. 23. Srivastava, P.; Hamlett, J.M.; Robillard, P.D.; Day, R.L. Watershed optimization of best
management practices using annagnps and a genetic algorithm. Water Resour. Res. 2002, 38, 1–14. 24. Veith, T.L.; Wolfe, M.L.; Heatwole, C.D. Optimization procedure for cost effective BMP
placement at a watershed scale. JAWRA 2003, 39, 1331–1343. 25. Gitau, M.W.; Veith, T.L.; Gburek, W.J. Farm-level optimization of BMP placement for cost-effective
pollution reduction. Trans. ASAE 2004, 47, 1923–1931. 26. Arabi, M.; Govindaraju, R.S.; Hantush, M.M. Cost-effective allocation of watershed management
practices using a genetic algorithm. Water Resour. Res. 2006, 42, 1–8. 27. Shen, Z.; Chen, L.; Xu, L. A topography analysis incorporated optimization method for
the selection and placement of best management practices. PLoS One 2013, 8, doi:10.1371/
journal.pone.0054520. 28. Oraei Zare, S.; Saghafian, B.; Shamsai, A. Multi-objective optimization for combined quality–
quantity urban runoff control. HESS 2012, 16, 4531–4542. 29. Green, W.R.; Haggard, B.E. References Phosphorus and Nitrogen Concentrations and Loads at Illinois River
South of Siloam Springs, Arkansas, 1997–1999; Branch of Information Services, U.S. Geological
Survey: Denver, CO, USA, 2001. 30. Gitau, M.W.; Chaubey, I. Regionalization of SWAT model parameters for use in ungauged
watersheds. Water 2010, 2, 849–871. 31. Edwards, D.R.; Daniel, T.C.; Scott, H.D.; Murdoch, J.F.; Habiger, M.J.; Burks, H.M. Stream quality
impacts of best management practices in a northwestern arkansas basin. Water Resour. Bull. 1996,
32, 499–509. 32. Chiang, L.; Chaubey, I.; Gitau, M.W.; Arnold, J.G. Differentiating impacts of land use changes from
pasture management in a ceap watershed using swat model. Trans. ASABE 2010, 53, 1569–1584. 33. Arnold, J.G.; Srinivasan, R.; Muttiah, R.S.; Williams, J.R. Large area hydrologic modeling and
assessment part I: Model development. J. Am. Water Resour. Assoc. 1998, 34, 73–89. 34. Huang, J.; Zhou, P.; Zhou, Z.; Huang, Y. Assessing the influence of land use and land cover
datasets with different points in time and levels of detail on watershed modeling in the north river
watershed, china. Int. J. Environ. Res. Public Health 2012, 10, 144–157. 35. Gassman, P.W.; Reyes, M.R.; Green, C.H.; Arnold, J.G. The soil and water assessment tool:
Historical development, applications, and future research directions. Trans. ASABE 2007, 50,
1211–1250. Int. J. Environ. Res. Public Health 2014, 11 3013 36. U.S. Geological Survey Geographic Data Download. Available online: http://edc2.usgs.gov/
geodata/index.php (accessed on 3 July 2007). 36. U.S. Geological Survey Geographic Data Download. Available online: http://edc2.usgs.gov/
geodata/index.php (accessed on 3 July 2007). 37. Land Use/Land Cover Data. Available online: http://www.cast.uark.edu/cast/geostor/ (accessed on
3 July 2007). 37. Land Use/Land Cover Data. Available online: http://www.cast.uark.edu/cast/geostor/ (accessed on
3 July 2007). 38. Soil Survey Geographic (SSURGO Database). Available online: http://soildatamart.nrcs.usda.gov/
(accessed on 3 July 2007). 39. Neitsch, S.L.; Arnold, J.G.; Kiniry, J.R.; Williams, J.R. Soil and Water Assessment Tool
Theoretical Documentation: Version 2005; Grassland, Soil and Water Research Laboratory,
Agricultrue Research Service: Temple, TX, USA, 2005. 40. Pennington, J.H.; Steele, M.A.; Teague, K.A.; Kurz, B.; Gbur, E.; Popp, J.; Rodríguez, G.;
Chaubey, I.; Gitau, M.; Nelson, M.A. Breaking ground a cooperative approach to collecting
information on conservation practices from an initially uncooperative population. J. Soil Water
Conserv. 2008, 63, 206–211. 41. Nash, J.E.; Sutcliffe, J.V. River flow forecasting through conceptual models part I—A discussion
of principles. J. Hydrol. 1970, 10, 282–290. 42. Forage and Pasture Forage Management Guides. Self-Study Guide 5: Utilization of Forages by
Beef Cattle. References Available online: http://www.aragriculture.org/forage_pasture/Management_Guide/
Forages_Self_Help_Guide5.htm (accessed on 3 July 2007). 43. White, K.L.; Chaubey, I. Sensitivity analysis, calibration, and validations for a multisite and
multivariable swat model. J. Am. Water Resour. Assoc. 2005, 41, 1077–1089. 44. Lowrance, R.; Dabney, S.; Schultz, R. Improving water and soil quality with conservation buffers. J. Soil Water Conserv. 2002, 57, 36–43. 45. Conservation Buffers to Reduce Pesticide Losses. Available online: http://pesticidestewardship. org/drift/Documents/Conservbuffers.pdf (accessed on 5 March 2014). 46. Naiman, R.J.; Decamps, H.; Pollock, M. The role of riparian corridors in maintaining regional
biodiversity. Ecol. Appl. 1993, 3, 209–212. 47. Park, Y.S.; Park, J.H.; Jang, W.S.; Ryu, J.C.; Kang, H.; Choi, J.; Lim, K.J. Hydrologic response
unit routing in SWAT to simulate effects of vegetated filter strip for South-Korean conditions
based on VFSMOD. Water 2011, 3, 819–842. 48. Park, Y.S.; Engel, B.A.; Shin, Y.; Choi, J.; Kim, N.-W.; Kim, S.-J.; Kong, D.S.; Lim, K.J. Development of web gis-based VFSMOD system with three modules for effective vegetative
filter strip design. Water 2013, 5, 1194–1210. 49. Chaubey, I.; Chiang, L.; Gitau, M.W.; Mohamed, S. Effectiveness of best management practices
in improving water quality in a pasture-dominated watershed. J. Soil Water Conserv. 2010, 65,
424–437. 50. U.S. Department of Agriculture, Natural Resources Conservation Service (USDA-NRCS). Using
RUSLE2 for the Design and Predicted Effectiveness of Vegetative Filter Strips (VFS) for Sediment;
USDA-NRCS: Washington, DC, USA, 2007. 51. Deb, K.; Pratap, A.; Agarwal, S.; Meyarivan, T. A fast and elitist multiobjective genetic algorithm:
NSGA-II. IEEE Trans. Evolut. Comput. 2002, 6, 182–197. Int. J. Environ. Res. Public Health 2014, 11 3014 52. Zitzler, E.; Thiele, L. Multiobjective evolutionary algorithms: A comparative case study and
the strength pareto approach. IEEE Trans. Evolut. Comput. 1999, 3, 257–271. 52. Zitzler, E.; Thiele, L. Multiobjective evolutionary algorithms: A comparative case study and
the strength pareto approach. IEEE Trans. Evolut. Comput. 1999, 3, 257–271. 52. Zitzler, E.; Thiele, L. Multiobjective evolutionary algorithms: A comparative case study and
the strength pareto approach. IEEE Trans. Evolut. Comput. 1999, 3, 257–271. © 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and conditions of the Creative Commons Attribution license
(http://creativecommons.org/licenses/by/3.0/). © 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and conditions of the Creative Commons Attribution license
(http://creativecommons.org/licenses/by/3.0/).
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Techno.COM, Vol. 21, No. 1, Februari 2022: 116-126
SIKARTUN: Sistem Informasi Karang Taruna Berbasis
Web Menggunakan Metode FDD dan XP
SIKARTUN: Web-Based Karang Taruna Information System Using FDD and XP
Method
Navita Putri Purwanti1, Septi Andryana2, Aris Gunaryati3
1
Program Studi Sistem Informasi, Universitas Nasional
2,3
Program Studi Informatika, Universitas Nasional
1
E-mail: navitaputrip@gmail.com, 2septi.andryana@civitas.unas.ac.id,
3
aris.gunaryati@civitas.unas.ac.id
Abstrak
Karang Taruna menjadi topik pilihan pada penelitian ini terkait dengan peran pentingnya
sebagai wadah kegiatan dan pengembangan generasi muda. Salah satu elemen penting dari
organisasi ini adalah informasi dan komunikasi. Umumnya organisasi ini belum memiliki sarana
informasi digital seperti website dan hanya menggunakan sarana informasi dari mulut ke mulut.
Hal ini mengakibatkan keterlambatan, duplikasi dan ketidakakuratan dalam penyampaian
informasi. Objek penelitian ini adalah Karang Taruna RT 005 RW 009 Kelurahan Pondok
Labu, Kecamatan Cilandak, Jakarta Selatan. Penelitian ini menerapkan metode gabungan FDD
(Feature Driven Development) dan XP (Extreme Programming) dalam pengembangan website
SIKARTUN atau Sistem Informasi Karang Taruna agar mempermudah penyampaian informasi
tersebut. Desain aplikasi website menggunakan framework CodeIgniter dan Bootsrap, serta
bahasa dan database yang digunakan adalah PHP dan MySQL. Hasil penelitian ini, SIKARTUN
memiliki kinerja yang baik berdasarkan oleh pengujian Google Lighthouse dan Usabilitiy.
Kata kunci: Karang Taruna, Sistem Informasi, Feature Driven Development, XP (Extreme
Programming)
Abstract
Karang Taruna became the topic of choice in this study related to its important role as a forum
for activities and development of the younger generation. One of the important elements of this
organization is information and communication. Generally, these organizations do not have
digital information facilities such as websites and only use word of mouth information. This
results in delays, duplication and inaccuracies in the delivery of information. The object of this
research is Karang Taruna RT 005 RW 009 Pondok Labu Village, Cilandak District, South
Jakarta. This study applies a combined method of FDD (Feature Driven Development) and XP
(Extreme Programming) in the development of the SIKARTUN website or Karang Taruna
Information System in order to facilitate the delivery of this information. The website
application design uses the CodeIgniter and Bootstrap frameworks, and the language and
database used are PHP and MySQL. The results of this study, SIKARTUN has a good
performance based on Google Lighthouse and Usability testing.
Keywords: Youth Organization, Information Systems, Feature Driven Development, XP
(Extreme Programming)
1. PENDAHULUAN
Karang Taruna ialah sebuah organisasi sosial bersifat formal yang berguna untuk tempat
pengembangan jiwa sosial keremajaan. Sebagai organisasi pemuda yang sarat dengan kegiatan,
informasi dan komunikasi merupakan dua hal yang paling penting sebagai penunjang
kelangsungan organisasi ini. Umumnya organisasi ini belum memiliki sarana informasi digital
116
Techno.COM, Vol. 21, No. 1, Februari 2022: 116-126
seperti website dan hanya menggunakan sarana informasi dari mulut ke mulut. Hal ini
mengakibatkan keterlambatan, duplikasi dan ketidakakuratan dalam penyampaian informasi.
Pada saat ini, kondisi objek penelitian di Karang Taruna RT 005 RW 009 Kelurahan Pondok
Labu, Kecamatan Cilandak, Jakarta Selatan belum memiliki website sebagai sarana informasi.
Sarana yang digunakan sebelumnya melalui chatting dan mulut ke mulut. Hal ini
mengakibatkan keterlambatan dan memerlukan waktu cukup lama dalam proses penyampaian
informasi kepada warga terkait hal penting pada Karang Taruna. Selain itu, setiap kegiatan yang
diselenggarakan oleh Karang Taruna tidak terkelola dengan baik sebagai mana mestinya,
diantaranya dicatat di buku maupun note di HP. Masalah terakhir, tidak adanya wadah
dokumentasi, setiap foto atau bukti yang dilakukan oleh Karang Taruna tersimpan di HP orangorang tertentu yang ini tidak dapat di lihat oleh yang lainnya. Maka, dibutuhkan sebuah sistem
informasi agar masalah dapat teratasi. Memberikan informasi akurat dan relevan mengenai
Karang Taruna adalah cara terbaik untuk menjaga sosialisasi agar tetap terjalin[1].
Pada penelitian ini terdapat beberapa referensi yang terkait dengan topik. Jurnal pertama
dengan metode waterfall pemodelan UML (Unified Modeling Language) membantu
menyelesaikan tahapan secara berurutan, sehingga proses rancangan lebih teliti. Kekurangan
terdapat pada metode waterfall yaitu menjadi tidak fleksibel apabila ada revisi pada sistem yang
dibangun[2]. Jurnal kedua membuat website pengelolaan Karang Taruna dengan metode
pengumpulan data observasi, wawancara dan studi pustaka telah sesuai harapan dengan hasil
yang divalidasi guna memudahkan user dalam menggunakan website. Kekurangan terdapat
pada pengujian black box yang dapat memungkinkan pengulangan tes yang telah dilakukan[3].
Jurnal ketiga menggunakan bahasa pemrograman PHP dan database MySQL dengan hasil bisa
digunakan pada computer secara online karena lebih efektif. Kekurangan terdapat pada gambar
yang disajikan tidak terlihat jelas[4]. Jurnal keempat menggunakan metode XP (Extreme
Programming) dan framework Bootstrap bisa mengatasi masalah yang ada dengan lebih efektif
dan efisien. Kekurangan terdapat pada penulisan jurnal yang ejaannya kurang benar[5]. Selain
itu, penelitian ini juga terdapat pembanding website yaitu pada website Karang Taruna
Sardonoharjo dan website Karang Taruna Kabupaten Pati yang hanya terdapat sedikit fitur. Dari
referensi tersebut terkhusus dari kekurangan yang telah dijelaskan, maka pada penelitian ini
menggunakan metode gabungan yaitu metode FDD (Feature Driven Development) dan metode
XP (Extreme Programming) guna menghasilkan kualitas sistem yang mudah dipahami, fitur
lebih lengkap dan cepat dalam pembuatan sistem serta mengusulkan menu tambahan dan
tampilan web yang berbeda dari website pembanding untuk Sistem Informasi Karang Taruna
yang akan dibuat guna memudahkan user dalam mengakses web dan metode testing dengan
menggunakan Google Lighthouse serta Usability.
Penelitian ini bertujuan untuk membuat atau membangun sistem informasi berbasis web
berdasarkan fakta atau masalah yang terjadi pada Karang Taruna RT 005 RW 009 Kelurahan
Pondok Labu, Kecamatan Cilandak, Jakarta Selatan dengan dinamakan (SIKARTUN) atau
Sistem Informasi Karang Taruna agar efisien. Sistem Informasi ini berfungsi sebagai wadah
informasi, diantaranya yang dapat mengolah data ialah admin (kepengurusan Karang Taruna),
sebagai tempat dokumentasi kegiatan berupa foto, fitur berita untuk informasi seputar kegiatan,
tabel berkas sebagai wadah surat-surat yang dapat dilihat user, kalender untuk pengingat
kegiatan yang akan diselenggarakan. User dapat melihat informasi melalui web, mendownload
file berkas dan kontak yang terhubung dengan WhatsApp guna komunikasi. Dalam merancang
sistem informasi ini, pertama peneliti menggunakan metode FDD (Feature Driven
Development) dari tahap build an overall model hingga design by feature agar sistem yang
dibangun dapat mudah dipahami dan dapat diperiksa secara efektif, selanjutnya menggunakan
metode XP (Extreme Programming) pada coding dan testing guna menghasilkan peningkatan
kualitas dari sistem menjadi fleksibel. Dengan sistem ini dapat memudahkan warga mencari
informasi.
Penelitian ini terdapat beberapa studi literatur yang diantaranya yaitu Sistem Informasi
menurut Kadir (2014) adalah sistem informasi menggunakan komputer atau sama dengan
Sistem Informasi Berbasis Komputer[4]. Karang Taruna adalah organisasi kepemudaan sebagai
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wadah pengembangan jiwa sosial remaja yang tumbuh atas rasa kesadaran dan tanggung jawab
sosial[4]. Metode FDD (Feature Driven Development) ialah metode pendekatan agile yang
mengacu kepada pembuatan sistem agar mudah dipahami, diimplementasi, teknik problem
solving dan juga pelaporan yang dapat dikontrol oleh stakeholders[6]. Metode Extreme
Programming (XP) ialah metode pengembangan software untuk meningkatkan kualitas pada
software[5]. Codeigniter merupakan framework PHP yang bertujuan untuk mempercepat
pengembangan aplikasi web yang dilakukan oleh developer[7].
2. METODE PENELITIAN
2.1 Metode FDD (Feature Driven Development)
Metode pertama yang dilakukan oleh peneliti adalah metode FDD. Metode ini dimulai
pada build an overall model hingga design by feature. Metode FDD ialah metode pendekatan
agile yang mengacu kepada pembuatan sistem agar mudah dipahami, diimplementasi, teknik
problem solving dan juga pelaporan yang dapat dikontrol oleh stakeholders[6]. Karena itu,
peneliti memilih metode ini agar sistem yang dibangun dapat mudah dipahami dan dapat
diperiksa secara efektif.
Berikut adalah tahapan pada metode FDD yang akan dilakukan oleh peneliti:
1. Build an Overall Model
Pada tahap pertama, mengumpulkan informasi yang akan diteliti dengan cara studi
literatur melalui jurnal, observasi dengan mengamati masalah dan wawancara
dengan pengurus Karang Taruna.
2. Build a Feature List
Pada tahap kedua, mengidentifikasikan fitur untuk di list sesuai dengan kebutuhan
pada sistem yang akan dibangun.
3. Plan by Feature
Pada tahap ketiga, menentukan perencanaan yang akan dibuat supaya berjalan
dengan baik sesuai dengan fitur yang dibutuhkan.
4. Design by Feature
Pada tahap keempat, membuat desain use case guna menunjukkan alur kerja sistem.
5. Build by Feature
Pada tahap terakhir, membangun sistem menggunakan bahasa pemrograman PHP,
database MySQL, framework CodeIgniter serta Bootsrap dan software text editor
Visual Studio Code.
2.2 Metode XP (Extreme Programming)
Setelah metode FDD, yang digabungkan pada metode XP yaitu pada Coding dan
Testing. Metode XP merupakan metode pengembangan perangkat lunak dengan peningkatan
kualitas sistem lebih cepat[5]. Karena itu, peneliti memilih metode ini agar system menjadi
fleksibel. Berikut adalah tahapan gambaran metode XP (Extreme Programming):
Gambar 2. Tahapan Metode XP
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Berikut ini yaitu tahapan pada metode Extreme Programming (XP):
1. Planning
Tahap ini yaitu perencanaan yang dimulai dengan identifikasi masalah pada
penelitian.
2. Design
Tahap ini yaitu membuat pemodelan sistem. Pemodelan yang digunakan ialah use
case diagram dan rancangan sistem website.
3. Coding
Tahap ini yaitu penerapan pemodelan sistem menggunakan Bahasa pemrograman
PHP dan text editor yaitu Visual Studio Code.
4. Testing
Tahap ini yaitu mengecek apakah sistem terjadi kesalahan atau tidak. Menggunakan
tools Google Lighthouse dan Usability.
2.3 Flowchart Metode Penelitian
Flowchart Metode Penelitian ini merupakan alur dari metode penelitian yang dibuat[9].
Gambar 3. Flowchart Metode Penelitian
1. Identifikasi Masalah
Identifikasi masalah yaitu menelaah suatu masalah sebelum di rumuskan, ini
merupakan hal penting supaya tidak terjadi kesalahan pada langkah selanjutnya.
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2. Tujuan Penelitian
Tujuan penelitian dilakukan peneliti dengan cara Observasi dan Wawancara untuk
mengetahui data dan fakta masalah yang akan diteliti pada jurnal.
3. Studi Literatur
Studi literatur yaitu suatu studi atau referensi yang berguna untuk pemahaman yang
lebih pada data yang akan diteliti supaya penelitian relevan. Peneliti mencari
referensi berupa jurnal yang bereputasi dan terakreditasi.
4. Pengumpulan Data
Pengumpulan data yaitu mengumpulkan data yang telah di dapat sebelum dilakukan
perancangan system. Data disesuaikan dengan saat wawancara.
5. Perancangan Sistem
Perancangan SIKARTUN dilakukan oleh peneliti menggunakan bahasa
pemrograman PHP, database yaitu MySQL, desain aplikasi dengan framework
CodeIgniter dan Bootsrap serta software untuk coding menggunakan Visual Studio
Code.
6. Implementasi dan Testing
Implementasi dan testing dilakukan supaya sistem berjalan dengan lancar tanpa ada
kesalahan dan sesuai dengan rencana. Dengan mengecek kembali coding, apabila
terdapat kesalahan di perbaiki. Jika sudah tidak ada kesalahan lanjut ke tahap
berikutnya.
7. Kesimpulan
Terakhir yaitu kesimpulan, ini dilakukan saat sistem sudah berjalan dengan baik
atau tidak ada kesalahan.
2.4 Flowchart Rancangan SIKARTUN
SIKARTUN merupakan Sistem Informasi Karang Taruna berbasis web pada Karang
Taruna RT 005 RW 009 Kelurahan Pondok Labu, Kecamatan Cilandak, Jakarta Selatan yang
berguna sebagai wadah informasi seputar kegiatan Karang Taruna. Aplikasi ini dibuat dengan
user friendly (mudah digunakan) dan desain web yang responsive[7]. Gambaran flowchart pada
rancangan ini sebagai berikut :
Gambar 4. Flowchart Rancangan SIKARTUN
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2.5 Desain Rancangan SIKARTUN
Rancangan antarmuka ini dibuat untuk memenuhi kebutuhan informasi. Fungsi dari
Sistem Informasi Karang Taruna (SIKARTUN) yaitu untuk wadah informasi seputar Karang
Taruna dan mempermudah dalam penggunaannya melalui website[3]. Berikut adalah gambaran
desain sistem:
Gambar 5. Desain Rancangan SIKARTUN
2.6 Use Case Diagram SIKARTUN
Dalam penelitian ini, peneliti menggunakan pemodelan UML (Unified Modelling
Language) yaitu Use Case Diagram untuk SIKARTUN. Pada hal ini, hanya Admin yang dapat
login ke web SIKARTUN. Admin login untuk mengolah data yang termasuk di dalamnya
seperti mengedit, menambahkan, menghapus data seputar Karang Taruna. Dan User
diperuntukan hanya melihat informasi yang ada pada website SIKARTUN[2]. Gambarannya
seperti berikut :
Gambar 6. Use Case Diagram SIKARTUN
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3. HASIL DAN PEMBAHASAN
3.1 Implementasi Sistem
Implementasi sistem merupakan tahap penerapan sistem yang telah direncanakan dan
dirancang. Tujuan implementasi adalah untuk menjelaskan penggunaan sistem kepada user agar
merespon apa yang ditampilkan pada sistem sesuai dengan kebutuhan.
Gambar 7. Tampilan Home SIKARTUN
Website SIKARTUN yang dibuat pada penelitian ini terdiri dari 6 fitur, diantaranya
yaitu Home, Tentang, Kegiatan, Berita, Kontak dan Login untuk Admin.
Gambar 8. Tampilan Galeri SIKARTUN
Tampilan Galeri ini untuk bukti kegiatan Karang Taruna berupa foto. Wadah
dokumentasi ini dibuat untuk memenuhi kebutuhan website yang telah direncanakan. User dapat
melihat galeri pada menu home dan atau kegiatan.
Gambar 9. Tampilan Kalender SIKARTUN
Tampilan Kalender dibuat untuk memenuhi kebutuhan pada perencanaan sebelumnya
yang berfungsi untuk pengingat setiap kegiatan yang akan diselenggarakan oleh Karang Taruna.
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User dapat melihat kalender kegiatan pada menu home dan atau kegiatan.
Gambar 10. Tampilan Berkas SIKARTUN
Tampilan Berkas berfungsi untuk tempat berkas-berkas Karang Taruna dalam setiap
penyelenggaraan acara yang dapat di download oleh user dan sebagai aspek Sistem Informasi.
User dapat melihat serta mendownload file berkas pada menu kegiatan.
Gambar 11. Tampilan Berita SIKARTUN
Tampilan Berita berfungsi sebagai wadah informasi seputar Karang Taruna yang terbaru
dan sebagai aspek Sistem Informasi. User dapat melihat berita pada menu home dan atau berita.
Gambar 12. Tampilan Kontak SIKARTUN
Tampilan Kontak berfungsi sebagai tempat user dapat menghubungi pihak Karang
Taruna apabila diperlukan dan terdapat FAQ untuk pertanyaan pada user dan juga sebagai aspek
Sistem Informasi. User dapat melihat kontak pada menu kontak.
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Gambar 13. Tampilan Halaman Login Admin
Tampilan halaman login untuk admin yang mengolah data pada website SIKARTUN.
Gambar 14. Tampilan Dashboard Admin
Tampilan dashboard admin untuk mengolah data, berupa Admin multi-user, Berita,
Galeri, Berkas, Jadwal (Kalender), Definisi dan Sejarah, Visi, Misi dan Struktur Organisasi.
3.2 Pengujian tools Google Lighthouse
Pengujian atau testing pada sistem dimaksudkan untuk mengecek sistem yang dibuat
sudah berjalan dengan lancar atau belum dan sesuai dengan kebutuhan. Pengujian sistem pada
penelitian ini menggunakan Google Lighthouse yang berguna untuk menguji kinerja atau
kualitas sistem[10]. Parameter yang diuji diantaranya Performance yaitu menilai kinerja web,
Accessibility yaitu memeriksa masalah yang umum terjadi, Best Practices yaitu memeriksa kode
situs web yang dibuat sudah berjalan baik atau belum dan SEO yaitu memeriksa web dalam
melakukan praktik apakah mudah ditemukan pada mesin pencarian. Hasil parameter yang diuji
diukur dengan skor penilaian sesuai yang ada pada Google Lighthouse. Berikut adalah tabel
skor penilaian dan hasil pengujiannya:
Tabel 1 Skor Penilaian SIKARTUN
Status
Kurang Baik
Cukup Baik
Sangat Baik
Skor
0-49
50-89
90-100
Warna Status
Tabel 2 Pengujian SIKARTUN pada Google Lighthouse
No
1
2
3
4
5
6
Menu SIKARTUN
Home
Tentang
Kegiatan
Berita
Kontak
Login Admin
Performance
97
98
93
96
99
99
124
Accessibility
86
89
90
88
98
97
Best Practices
93
93
93
93
93
87
SEO
70
80
70
80
89
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Keterangan dari tabel 3.2 yaitu pengujian telah sukses dilakukan yang berarti kinerja
atau kualitas SIKARTUN yang dibuat dikategorikan baik dengan rata-rata Performance 97,
Accessibility 91.3, Best Practice 92 dan SEO 79.67 maka dapat digunakan oleh user.
3.3 Usability Testing SIKARTUN
Pengujian ini dimaksudkan untuk mengecek sistem sudah sesuai dengan kebutuhan atau
belum melalui tiga komponen diantaranya kecepatan load pada web, mendownload file pada
berkas dan terhubung pada WhatsApp dan terdapat pertanyaan untuk website lain sebagai
pembanding SIKARTUN serta jumlah user yang diuji 20 orang dan 10 pertanyaan melalui
kuesioner[11]. Interaksi website dengan user pada berkas yang dapat didownload dan menu
Kontak, user dapat mengklik nomor WhatsApp untuk terhubung. Skala untuk hasil testing
dengan skor 5-7 berarti dikategorikan telah sesuai dan efisien. Hasil didapat sistem bekerja
dengan baik atau telah sesuai serta efisien berdasar jumlah nilai rata-rata dan skor skala. Berikut
adalah tabel skala penilaian dan hasil dari testing sistem kepada user:
Tabel 3 Skala Penilaian Usability SIKARTUN
Keterangan
Kurang Baik / Sesuai
Cukup Baik / Sesuai
Sangat Baik / Sesuai
Rumus Nilai Rata-rata
Skor: Jumlah Responden x Persentase
Skor
1-3
4
5-7
Isi Tabel Skor = Jumlah Responden
Tabel 4 Usability Testing SIKARTUN
No
Pertanyaan
Skor 1-3
1
Bagaimana kecepatan loading pada
website SIKARTUN?
2
Apakah file berkas pada menu Kegiatan di
website SIKARTUN dapat di download?
3
Apakah Anda dapat terhubung ke
WhatsApp pada menu Kontak
SIKARTUN?
4
Apakah website SIKARTUN menarik
dilihat daripada website pembanding?
5
Apakah tampilan website SIKARTUN
mudah dikenali daripada website
pembanding?
6
Apakah menu dan isi dari website
SIKARTUN lebih lengkap daripada
website pembanding?
7
Apakah Anda puas dengan informasi yang
disajikan pada website SIKARTUN?
8
Apakah fitur yang terdapat pada
SIKARTUN sesuai dengan fungsinya?
9
Menurut Anda, apakah website
SIKARTUN mudah digunakan?
10
Menurut Anda, Apakah website
SIKARTUN telah efisien sebagai wadah
informasi?
Jumlah Nilai Rata-rata
Jumlah Nilai Rata-rata / Jumlah Pertanyaan
Pembulatan / Skala
1
1
Skor 4
Skor 5-7
Nilai Rata-rata
2
18
6,55
2
18
5,85
1
19
6,55
1
18
6,55
2
18
6,6
1
19
4,75
1
18
5,9
1
19
8,15
2
18
8,2
1
19
7,3
66,4
6,64
7
4. KESIMPULAN DAN SARAN
Berdasarkan apa yang sudah dijelaskan pada penelitian ini, maka kesimpulan yaitu
sudah sesuai dengan harapan bahwa dibutuhkan sistem informasi yang berguna untuk
penyampaian informasi terkait organisasi Karang Taruna memiliki hasil kinerja website sukses
dan baik berdasar pengujian pada Google Lighthouse dan Usability. Sistem informasi ini dapat
digunakan oleh user untuk melihat informasi, mendownload file berkas, kontak yang terhubung
dengan WhatsApp dan admin website untuk mengolah data di mana admin merupakan anggota
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kepengurusan Karang Taruna. Kelebihan pada penelitian ini adalah sistem informasi yang
dibuat user friendly (mudah digunakan) dengan web yang responsive dan terdapat fitur lebih
lengkap dari website yang menjadi pembanding. Disamping adanya kelebihan juga ada
kekurangan, diharapkan pada penelitian selanjutnya sistem dapat dikembangkan oleh developer
dengan lebih baik dan peneliti menyarankan menambahkan fitur arsip dokumentasi pada setiap
bidang kepengurusan dan fitur e-voting untuk pemilihan pengurus Karang Taruna.
DAFTAR PUSTAKA
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
H. Almaimoni et al., “Developing and Implementing WEB-based Online Destination
Information Management System for Tourism,” International Journal of Applied
Engineering Research, vol. 13, no. 10, pp. 7541–7550, 2018, [Online]. Available:
http://www.ripublication.com
F. Akbar and S. Setiaji, “RANCANG BANGUN SISTEM INFORMASI KARANG
TARUNA MENGGUNAKAN METODE WATERFALL,” JURNAL KHATULISTIWA
INFORMATIKA, vol. VIII, no. 1, 2020, [Online]. Available: www.bsi.ac.id
Pamungkas Regen T and Tofan Rapiyanta P, “Sistem Informasi Pengelolaan Kegiatan
Karang Taruna (SIPEKATAR) Naralatu Agantuka Berbasis Website,” Prosiding
Nasional Rekayasa Teknologi Industri dan Informatika, pp. 324–331, 2019.
I. Nur Amanda, A. Hafiz Ramadani, and C. Responden, “RANCANG BANGUN
SISTEM INFORMASI MEDIA KEGIATAN PADA LEMBAGA KARANG TARUNA
KECAMATAN SEPATAN TIMUR,” JIKA (Jurnal Informatika), pp. 104–108, 2021.
H. Ismatullah and Q. Jafar Adrian, “IMPLEMENTASI PROTOTYPE DALAM
PERANCANGAN SISTEM INFORMASI IKATAN KELUARGA ALUMNI SANTRI
BERBASIS WEB,” Jurnal Informatika dan Rekayasa Perangkat Lunak (JATIKA), vol.
2,
no.
2,
pp.
213–220,
2021,
[Online].
Available:
http://jim.teknokrat.ac.id/index.php/informatika
A. Rifai and Y. Prabawati Yuniar, “Penerapan Metode Waterfall Dalam Perancangan
Sistem Informasi Ujian Pada SMK Indonesia Global Berbasis Web,” JURNAL
KHATULISTIWA INFORMATIKA, vol. VII, no. 1, 2019.
N. Cahya, A. Triayudi, and B. Benrahman, “Implementasi Framework Codeigniter Pada
Perancangan Chatbot Interaktif Menerapkan Metode Waterfall,” JURNAL MEDIA
INFORMATIKA BUDIDARMA, vol. 5, no. 1, pp. 273–279, Jan. 2021, doi:
10.30865/mib.v5i1.2623.
Putri R M, Renaldi F, and Santikarama I, “Pembangunan Sistem Informasi Monitoring
Pengelolaan Kegiatan Karang Taruna Kecamatan Padalarang,” Seminar Nasional
Aplikasi Teknologi Informasi (SNATi), 2019.
R. Firmansyah, S. Andryana, and B. Benrahman, “Sistem Informasi Laporan Asset
Fakultas Teknologi Komunikasi dan Informatika Universitas Nasional,” JURNAL
MEDIA INFORMATIKA BUDIDARMA, vol. 4, no. 3, pp. 574–581, Jul. 2020, doi:
10.30865/mib.v4i3.2150.
P. H. Pangestu, R. Tulloh, and R. Adiati, “PERANCANGAN DAN IMPLEMENTASI
APLIKASI PELAYANAN KESEHATAN PUSKESMAS BERBASIS WEB
MENGGUNAKAN FRAMEWORK LARAVEL (STUDI KASUS PUSKESMAS
MULYAHARJA) Design and Implementation of Web Based Publlic Health Center
Application Using Laravel Framework (Case Study Of Mulyaharja Publlic Health
Center),” e-Proceeding of Applied Science, vol. 7, no. 5, pp. 1818–1835, 2021.
S. Kasus et al., “EVALUASI USABILITY TERHADAP SISTEM PROMOSI
PARIWISATA BERBASIS ANDROID DAN WEB (Studi Kasus: Objek Pariwisata di
Provinsi Bengkulu),” Jurnal Rekursif, vol. 7, no. 2, 2019, [Online]. Available:
http://ejournal.unib.ac.id/index.php/rekursif/
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https://openalex.org/W2944170856
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https://bmccancer.biomedcentral.com/track/pdf/10.1186/s12885-019-5658-5
|
English
| null |
Establishment of a rat ovarian peritoneal metastasis model to study pressurized intraperitoneal aerosol chemotherapy (PIPAC)
|
BMC cancer
| 2,019
|
cc-by
| 7,109
|
Van de Sande et al. BMC Cancer (2019) 19:424
https://doi.org/10.1186/s12885-019-5658-5 Van de Sande et al. BMC Cancer (2019) 19:424
https://doi.org/10.1186/s12885-019-5658-5 Open Access Establishment of a rat ovarian peritoneal
metastasis model to study pressurized
intraperitoneal aerosol chemotherapy
(PIPAC) Leen Van de Sande1,2
, Wouter Willaert1,2, Sarah Cosyns1,2, Kaat De Clercq2,3, Molood Shariati4,
Katrien Remaut2,4 and Wim Ceelen1,2,5* Abstract Background: pressurized intraperitoneal aerosol chemotherapy (PIPAC), with or without electrostatic precipitation
(ePIPAC), was recently introduced in the treatment of peritoneal metastases (PM) from ovarian cancer (OC). Preliminary clinical data are promising, but several methodological issues as well the anticancer efficacy of PIPAC
remain unaddressed. Here, we propose a rat ePIPAC model that allows to study these issues in a clinically relevant,
reproducible, and high throughput model. Methods: laparoscopy and PIPAC were established in healthy Wistar rats. Aerosol properties were measured using
laser diffraction spectrometry based granulometric analyses. Electrostatic precipitation was accomplished using a
commercially available generator (Ultravision™). A xenograft model of ovarian PM was created in athymic rats using
intraperitoneal (IP) injection of SKOV-3 luciferase positive cells. Tumor growth was monitored weekly by in vivo
bioluminescence imaging. Results: PIPAC and electrostatic precipitation were well tolerated using a capnoperitoneum of 8 mmHg. All rats
survived the (e)PIPAC procedure and no gas or aerosol leakage was observed over the entire procedure. With an
injection pressure of 20 bar, granulometry showed a mean droplet diameter (D(v,0.5)) of 47 μm with a flow rate of
0.5 mL/s, and a significantly lower diameter (30 μm) when a flow rate of 0.8 mL/s was used. Experiments using IP
injection of SKOV-3 luciferase positive cells showed that after IP injection of 20 × 106 cells, miliary PM was observed
in all animals. PIPAC was feasible and well supported in these tumor bearing animals. Conclusions: we propose a reproducible and efficient rodent model to study PIPAC and ePIPAC in OC xenografts
with widespread PM. This model allows to characterize and optimize pharmacokinetic and biophysical parameters,
and to evaluate the anti-cancer efficacy of (e)PIPAC treatment. Keywords: PIPAC, ePIPAC, Ovarian cancer, Peritoneal metastases, Laparoscopic surgery, Intraperitoneal drug
delivery, Rat xenograft Keywords: PIPAC, ePIPAC, Ovarian cancer, Peritoneal metastases, Laparoscopic surgery, Intraperitoneal drug
delivery, Rat xenograft * Correspondence: Wim.Ceelen@UGent.be Correspondence: Wim.Ceelen@UGent.be
1Laboratory of Experimental Surgery, Department of Human Structure and
Repair, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
Full list of author information is available at the end of the article * Correspondence: Wim.Ceelen@UGent.be
1Laboratory of Experimental Surgery, Department of Human Structure and
Repair, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
Full list of author information is available at the end of the article Ex vivo simulation of PIPAC A 12 mm balloon trocar (Kii, advanced fixation sleeve,
Applied Medical, Amersfoort, The Netherlands) was
inserted in a closed 100 mL ethylene vinyl acetate (EVA)
bag. CO2 was insufflated to establish a constant pressure
of 8 mmHg. Twenty mL of undiluted royal blue ink
(Pelikan nv, Groot-Bijgaarden, Belgium) was nebulized
into the EVA bag with a flow rate of 0.8 mL/s and a
maximal upstream injection pressure of 20 bar. The
nebulizer was fixed either perpendicularly to the surface
of the EVA bag, or in a slightly tilted position. Several in vitro experimental PIPAC models have been
described. The cytotoxic efficacy of PIPAC was investi-
gated in vitro using proliferation assays of human colon
cancer cells [13]. An in vitro model consisting of aerosol
generation in a plastic box that contains human periton-
eum with PM was used to study tissue penetration of
doxorubicin, as well as the effect of treatment parame-
ters such as nebulizer position, pressure, and drug dose
[14, 15]. Schnelle et al. developed an interesting ex vivo
model that consists of an inverted bovine urinary
bladder, resulting in a serosa-lined cavity that can be
used to study PIPAC [16]. Solass and coworkers demon-
strated the technical proof of principle of PIPAC in a pig
model [17]. However, the pig model is cumbersome, Background labour intensive, and expensive, and does not allow to
study anticancer properties in xenografted or syngeneic
PM. Here, we report the first small animal model of
PIPAC and ePIPAC that allows to study several import-
ant endpoints such as tissue penetration and anti-cancer
efficacy in PM of human origin. g
Selected
patients
with
peritoneal
metastases
(PM)
benefit from cytoreductive surgery (CRS) combined with
hyperthermic intraperitoneal chemoperfusion (HIPEC)
[1, 2]. However, many patients present with irresectable
disease, which has a dismal prognosis. Survival in
patients with irresectable PM from colon cancer is 15
months, from gastric cancer 4 months, and from pancre-
atic cancer only 6 weeks [3–5]. Systemic chemotherapy
is relatively inefficient in PM due to poor vascularity of
peritoneal tumor nodules [6, 7]. Pressurized intraperito-
neal aerosol chemotherapy (PIPAC) is a novel locoregio-
nal treatment modality which involves intraperitoneal
(IP) delivery of chemotherapy as an aerosol during
laparoscopic surgery [7, 8]. Chemotherapy is aerosolized
in the abdominal cavity using a high-pressure injector
and
a
nebulizer
(Capnopen®). This
method
allows
aerosolized chemotherapy to interact directly with tumor
tissue. In addition, the elevated intra-abdominal pressure
may enhance tumor tissue drug penetration [9]. © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Van de Sande et al. BMC Cancer (2019) 19:424 Van de Sande et al. BMC Cancer (2019) 19:424 Page 2 of 10 Page 2 of 10 Granulometric analyses y
Volume-weighted particle size distribution (PSD) of
aerosol droplets was performed in triplicate by laser
diffraction
(Mastersizer
S
long
bench,
Malvern
Instruments, Worcestershire, United Kingdom). The size
of aerosol droplets was measured in an open laser beam
(water vs. air, refractive index of 1.33 and 1.00 respect-
ively) using a 300F lens (0.5–900 μm) over a time
horizon of 10 to 20 s after initiation of injection. Saline
was nebulized using a commercially available nebulizer
(Capnopen®, Capnomed, Zimmern, Germany) and a
high-pressure
injector
(Injektron™
82 M,
Medtron,
Saarbrücken, Germany). The outlet of the nebulizer was
perpendicularly secured at a distance of 35 mm to the
beam and 100 mm to the lens. The laser diffraction mea-
surements were performed as soon as the high-pressure
injector achieved the desired injection conditions, i.e. 10
s after initiating the injection. Results are expressed by
median of volume distribution, D(v,0.5), i.e. the size at
which 50 vol% of the droplets were either finer or
coarser
than
the
predicted
value,
with
standard
deviation. y
g p
Despite the significant potential of PIPAC and the
preliminary clinical data already available, many techno-
logical and anti-cancer properties of the technique re-
main to be elucidated. In recent clinical practice, PIPAC
was combined with electrostatic aerosol precipitation
using the Ultravision™system [10]. This device, originally
developed to clear smoke from the laparoscopic operat-
ing field by an electrostatic force, uses a stainless-steel
microfilament brush (Ionwand™) which is inserted into
the abdominal cavity [11]. A high DC voltage (7.5–9.5
kV, ≤10 μA) is applied to the Ionwand, resulting in a
corona discharge and a stream of negatively charged
ions, which attach to suspended particles. These now
negatively charged aerosol particles are attracted to the
positive charge of the return electrode. In theory, the
combination of electrostatic precipitation with PIPAC,
termed ePIPAC, can result in increased tissue uptake of
the aerosolized chemotherapy. However, this theoretical
advantage remains to be confirmed in well-designed
preclinical as well as clinical studies [12]. Animals Adult Wistar Hannover rats (n = 3 preliminary experi-
ment; n = 6 in vivo experiment; Envigo, Horst, The
Netherlands) and adult athymic nude rats (n = 9; Envigo,
Horst, The Netherlands) were allowed to acclimatize to
the surroundings for at least three days and were kept in
standard housing conditions with water and food ad
libitum and a 12 h light/dark cycle. After the experi-
ments, all rats were euthanized with a lethal injection of
T-61 (0.3 mL/kg, IV) into the tail vein. The experiments
were approved by the Animal Ethical Committee of the Van de Sande et al. BMC Cancer (2019) 19:424 Page 3 of 10 Faculty of Medicine of Ghent University, Belgium (ECD
17–50 and ECD 18–30). Faculty of Medicine of Ghent University, Belgium (ECD
17–50 and ECD 18–30). closed with a two-layered running suture (Vicryl Plus 4–0
Ethicon, Johnson & Johnson international, Sint-Stevens-
Woluwe, Belgium) and analgesia was administered (Keto-
profen, 5 mg/kg, SC). Electrostatic precipitation The experimental procedure of PIPAC in the rat was
based on clinical treatment protocols [18, 19]. Adult
Wistar Hannover rats (n = 6) were anesthetized with
sevoflurane
(8 vol%
induction,
4 vol%
maintenance). Animals were placed in a class II laminar flow hood
(Airstream, Esco Global, Barnsley, United Kingdom) in a
supine position and fixed at all four extremities. The
abdomen was shaved and disinfected. Next, a 5 mm and
a 12 mm balloon trocar were inserted and a constant
capnoperitoneum pressure of 8 mmHg was established
(Olympus UHI-3 insufflator, Olympus Surgical Tech-
nologies Europe, Hamburg, Germany). Each trocar was
secured by a tripod. The nebulizer was then connected
to the high-pressure injector through a high-pressure
line and inserted into the abdominal cavity using the 12
mm trocar. Afterwards, a 5 mm laparoscope was intro-
duced into the abdominal cavity using the 5 mm trocar. The tightness of the abdomen was documented via
absence of CO2 flow. Next, the high-pressure injector
was activated. Injection parameters were set at a flow
rate of 0.8 mL/s and a maximal upstream injection
pressure of 20 bar. When used with the nebulizer, the
high-pressure injector needs up to 10 s to achieve the
desired conditions (flow rate and injection pressure). Therefore, the high-pressure injector was set to inject
8 mL of air during these first 10 s, before nebulizing
20 mL of saline at the desired conditions. The capno-
peritoneum pressure of 8 mmHg was maintained for
30 min. Thereafter, the aerosol was evacuated through
a closed aerosol waste system containing a 99.999%
ULPA-carbon filter. Finally, trocars were removed, and the
laparoscopic procedure was terminated. The abdomen was In three adult Wistar Hannover rats, the use of Ultravi-
sion™technology (Alesi Surgical, Cardiff, United King-
dom) was added to the PIPAC-setup. The system was
activated at the start of aerosol generation and the elec-
tric current was maintained for 30 min. The Ultravision™
system integrates the following components: a generator
unit (voltage 7500–9500 V, current ≤10 μA), an active
cable terminating in an atraumatic stainless-steel brush
electrode (Ionwand) that is responsible for the electro-
static charging of aerosol particles, and a return elec-
trode with a solid return plate. To obtain a closed
electrical circuit, the solid return plate was fixed under a
metal plate. During the ePIPAC procedure, the rat was
positioned on this metal plate (Fig. 1). Influence of physical parameters on aerosol formation Influence of physical parameters on aerosol formation
A maximal upstream injection pressure of 20 bar and a
fixed flow rate of 0.5 mL/s were associated with a
D(v,0.5) of 47 ± 2 μm (Fig. 2a). Decreasing the maximal
upstream injection pressure to 10 bar, resulted in an
increased D(v,0.5) of 51 ± 1 μm (p = 0.127). However,
when the maximal upstream injection pressure was further
decreased to 5 bar, D(v,0.5) remained 51 ± 2 μm (p = 0.127). Analysis of different flow rates (0.5 and 0.8 mL/s) at a
fixed maximal upstream injection pressure of 20 bar,
showed a strong impact on the volume-weighted PSD
curves (Fig. 2b). Applying a flow rate of 0.5 mL/s, D(v,0.5)
was 47 ± 2 μm. Increasing the flow rate to 0.8 mL/s re-
sulted in a decreased D(v,0.5) of 30 ± 3 μm (p = 0.05). Influence of physical parameters on aerosol formation
A maximal upstream injection pressure of 20 bar and a
fixed flow rate of 0.5 mL/s were associated with a
D(v,0.5) of 47 ± 2 μm (Fig. 2a). Decreasing the maximal
upstream injection pressure to 10 bar, resulted in an
increased D(v,0.5) of 51 ± 1 μm (p = 0.127). However,
when the maximal upstream injection pressure was further
decreased to 5 bar, D(v,0.5) remained 51 ± 2 μm (p = 0.127). To assess whether it was possible to perform (e)PIPAC
in tumor bearing rats, this procedure was performed
with saline on day 28 in the athymic nude rats of group
3. All athymic nude rats survived this procedure. On day
29, the rats of group 3 were sacrificed and autopsy was
done. Diffuse PM with widespread small tumor nodules
could be demonstrated (Fig. 5). Tumor nodules were
embedded in paraffin before standard H&E staining was
conducted. H&E staining confirmed the presence of
tumor cells in the nodules (Fig. 6). Analysis of different flow rates (0.5 and 0.8 mL/s) at a
fixed maximal upstream injection pressure of 20 bar,
showed a strong impact on the volume-weighted PSD
curves (Fig. 2b). Applying a flow rate of 0.5 mL/s, D(v,0.5)
was 47 ± 2 μm. Increasing the flow rate to 0.8 mL/s re-
sulted in a decreased D(v,0.5) of 30 ± 3 μm (p = 0.05). μ
Bimodal volume-weighted PSD curves were observed
when nebulization of saline was done in a closed environ-
ment using a plastic box (Fig. 2c). Influence of physical parameters on aerosol formation Aerosol formation in
patient-like conditions, i.e. nebulization of 200 mL saline
with a maximal upstream injection pressure of 20 bar and
a flow rate of 0.5 mL/s in a plastic box of 5 L, showed a
D(v,0.5) of 35 ± 1 μm. After nebulization with rat-like con-
ditions,
i.e. nebulization of 20 mL with a maximal
upstream injection pressure of 20 bar and a flow rate of
0.8 mL/s in a plastic box of 100 mL, a D(v,0.5) of 25 ±
3 μm (p = 0.05) was detected. Rat ovarian PM model Differences between D(v,0.5) values were compared
using the non-parametric Mann-Whitney U test since
data were not normally distributed. A p-value of ≤0.05
was considered to indicate statistical significance. In vivo BLI of tumor-bearing rats is illustrated in Fig. 4. In the first (5 × 106 SKOV-3 Luc IP2 cells) and second
group (10 × 106 SKOV-3 Luc IP2 cells), no diffuse PM
was observed. After four weeks, two rats had only one
tumor nodule and in the other specimens no tumor
growth occurred. However, in the third group (20 × 106
SKOV-3 Luc IP2 cells) miliary PM was observed with a
tumor induction rate of 100% (3/3). Rat ovarian PM model Experimental PIPAC procedure p
p
Once the ideal injection parameters for (e)PIPAC were
determined, PIPAC with saline was tested in healthy
Wistar Hannover rats (n = 3). The feasibility of repeated
PIPAC applications was successfully tested in these
preliminary experiments. The three rats underwent three
consecutive PIPAC procedures with an interval of four
weeks. The rats tolerated multiple PIPAC applications
very well and were in good health after the third PIPAC
application. Thereafter, PIPAC (n = 3) and ePIPAC (n =
3) was performed in healthy adult Wistar Hannover rats. Procedures were executed as planned in both groups. The nebulizer enabled rapid and effective nebulization
of saline in the abdominal cavity without extracorporeal
leakage of aerosolized droplets over the entire setup. All
rats survived the procedures. After four weeks, PIPAC and ePIPAC with saline were
performed according to the abovementioned experimen-
tal procedures. The rats were euthanized 24 h after
(e)PIPAC with a lethal injection of T-61 (0.3 mL/kg, IV)
into the tail vein. Peritoneal tumors were excised and
embedded in paraffin for standard hematoxylin and
eosin (H&E) staining. Rat ovarian PM model SKOV-3 Luc IP2 cells, a human ovarian carcinoma cell
line created by double in vivo selection of SKOV-3 Luc
cells, were used to create a rat xenograft model [20]. The cells (kindly donated by Olivier De Wever, Labora-
tory of Experimental Cancer Research, Ghent University)
were cultured at 37 °C in a 10% CO2 containing atmos-
phere in McCoy’s 5A medium (ThermoFisher Scientific
Bvba, Merelbeke, Belgium) supplemented with 10% fetal
bovine serum, penicillin and streptomycin (Thermo-
Fisher Scientific Bvba, Merelbeke, Belgium). Athymic nude rats (n = 9) were injected IP with 5 ×
106 (n = 3), 10 × 106 (n = 3) or 20 × 106 (n = 3) SKOV-3
Luc IP2 cells in a volume of 5 mL saline. The rats under-
went a daily subcutaneous injection of cyclosporine (3
mg) starting three days prior to, and until four weeks Fig. 1 A ePIPAC setup in a healthy Wistar Hannover rat. 12 mm balloon trocar with nebulizer and closed aerosol waste system (a), 5 mm balloon
trocar with laparoscope and CO2 insufflator (b), Ionwand (c), electrical conductor between return electrode (underneath metal plate) and
generator unit (d). B Intra-abdominal view of the Ionwand in a healthy Wistar Hannover rat Fig. 1 A ePIPAC setup in a healthy Wistar Hannover rat. 12 mm balloon trocar with nebulizer and closed aerosol waste system (a), 5 mm balloon
trocar with laparoscope and CO2 insufflator (b), Ionwand (c), electrical conductor between return electrode (underneath metal plate) and
generator unit (d). B Intra-abdominal view of the Ionwand in a healthy Wistar Hannover rat Van de Sande et al. BMC Cancer (2019) 19:424 Page 4 of 10 Van de Sande et al. BMC Cancer (2019) 19:424 Page 4 of 10 after tumor cell inoculation to ensure tumor growth. Tumor
growth
was
monitored
by
weekly
in
vivo
bioluminescent imaging (BLI) (IVIS Lumina II, PerkinEl-
mer, Zaventem, Belgium). Imaging was performed 12
min after IP injection of D-luciferin (120 mg/kg; Perki-
nElmer, Zaventem, Belgium). The exposure time was
one second and the binning (resolution setting) was set
to medium. after tumor cell inoculation to ensure tumor growth. Tumor
growth
was
monitored
by
weekly
in
vivo
bioluminescent imaging (BLI) (IVIS Lumina II, PerkinEl-
mer, Zaventem, Belgium). Imaging was performed 12
min after IP injection of D-luciferin (120 mg/kg; Perki-
nElmer, Zaventem, Belgium). The exposure time was
one second and the binning (resolution setting) was set
to medium. Discussion To simulate a nebulization in a rat’s abdominal cavity, 20 mL of
saline was nebulized in a plastic box (V = 100 mL) with a flow rate of 0.8 mL/s and a maximal upstream injection pressure of 20 bar (red graph). 200 mL of saline was nebulized in a plastic box (V = 5 L) with a flow rate of 0.5 mL/s and a maximal upstream injection pressure of 20 bar (blue
graph) as a comparison with the nebulization in human. The plastic boxes were bilaterally pierced to transvers laser light and a third perforation
was made at the top of the boxes to insert the nebulizer medicine, only very small (< 5 μm) particles reach the
alveoles and exert a meaningful therapeutic effect. [29–31] It should be noted that smaller particles carry
less drug mass, and that the anatomical restrictions
that apply to the respiratory tree do not apply to the
peritoneal cavity. For instance, large (> 10 μm) inhaled
particles tend to be deposited in the larynx or upper
airways, which is undesirable, but in PIPAC treatment
size considerations seem to be less important. Never-
theless, the current and ideal PIPAC droplet size, and
the biophysical parameters that affect it, should be
further
characterized. In
our
model,
analysis
of
volume-weighted
PSD
curves
demonstrated
that
D(v,0.5) is 47 μm when a flow rate of 0.5 mL/s and a
maximal upstream injection pressure of 20 bar are
used (Fig. 2a). Increasing the flow rate to 0.8 mL/s re-
sulted in a statistically significant decrease of D(v,0.5)
to 30 μm, an observation in accordance with experi-
ence from nozzles used in inlet fogging of gas turbine
engines [32]. Interestingly, after nebulization of saline
in a plastic box, a bimodal volume-weighted PSD
distribution curves was observed, possibly explained
by aggregation of the injected aerosol droplets. biophysical, pharmacokinetic, and anticancer properties
and parameters that are relevant in PIPAC remain rela-
tively unknown. To date, four models were reported for
(e)PIPAC research: in vitro using cancer cells, an ex vivo
box model, an ex vivo bovine urinary bladder model and
an in vivo pig model [13–17, 24, 25]. We report a stan-
dardized rat model that allows to study biophysical,
pharmacokinetic, and anticancer properties of PIPAC
and electrostatic precipitation combined with PIPAC. The first step was to ascertain that the model generates
an aerosol that is comparable to the clinical situation. Discussion The prognosis of patients with irresectable PM is poor,
with a median survival ranging from several weeks to
months [3–5]. Recently, PIPAC has been introduced in
clinical practice [21]. During PIPAC, chemotherapy is
delivered as an aerosol, generated by a nebulizer (Cap-
nopen®) connected to a high-pressure injector. This
novel approach may overcome two major limitations of
conventional liquid based IP chemotherapy: incomplete
coverage the peritoneal surfaces and poor tissue drug
penetration [22, 23]. The increased intra-abdominal
pressure during PIPAC by means of the capnoperito-
neum may overcome the high interstitial fluid pressure
in tumor tissue, and therefore improve tissue penetra-
tion [9]. Also, IP delivery of therapeutic agents as an
aerosol result in a more homogeneous distribution
compared to liquid instillation [12, 17, 21]. However, the Adequacy of stain distribution throughout the entire
EVA bag was clearly superior with a slightly tilted
nebulizer position (Fig. 3). Specifically, the top of the
EVA bag was stained when the nebulizer was secured in
a tilted position, while this was not the case when it was
placed perpendicularly. Van de Sande et al. BMC Cancer (2019) 19:424 Page 5 of 10 Fig. 2 (See legend on next page.) Fig. 2 (See legend on next page.) Van de Sande et al. BMC Cancer (2019) 19:424 Page 6 of 10 (See figure on previous page.)
Fig. 2 PSD curves of nebulized saline showing the distribution density (left curves) and cumulative distribution (right curves). Mean droplet
diameters were measured (n = 3 for each confirmation) in a range of 0.5 to 900 μm. The error bars show one time the standard deviation. a
Volume-weighted PSD curves showing the influence of maximal upstream injection pressure on D(v,0.5). 20 mL of saline was nebulized in open
space at a fixed flow rate of 0.5 mL/s and a maximal upstream injection pressure of 20 bar (blue graph), 10 bar (red graph) or 5 bar (black graph). b Volume-weighted PSD curves illustrating the influence of flow rate on D(v,0.5). 20 mL of saline was nebulized in open space at a fixed maximal
upstream injection pressure of 20 bar and a flow rate of 0.5 mL/s (blue graph) or 0.8 mL/s (red graph). c Volume-weighted PSD curves
demonstrating the influence of the volume of the peritoneal cavity on D(v,0.5). Discussion One rat demonstrated tumor clearance, two rats had only one tumor
nodule and in the other specimens no tumor growth occurred. In the third group diffuse PM was observed with a tumor induction rate of 100% Fig. 4 In vivo BLI of athymic nude rats inoculated with 5 × 106 (group 1), 10 × 106 (group 2) or 20 × 106 (group 3) SKOV-3 Luc IP2 cells (n = 3 in
each group). In the first and second group no diffuse PM was observed. One rat demonstrated tumor clearance, two rats had only one tumor
nodule and in the other specimens no tumor growth occurred. In the third group diffuse PM was observed with a tumor induction rate of 100% explained by a longer travelling distance of the injected
aerosol droplets compared to the perpendicular position. competent animals would allow to study PIPAC in combin-
ation with immunotherapy. A syngeneic rat OC model,
based on IP injection of NuTu-19 cells in female Fischer
344 rats, has been described [36], and may represent an in-
teresting future addition to the xenograft model that we
propose. Also, the use of immune competent animals al-
lows to study how PIPAC treatment affects the peritoneal
immune environment, a relevant parameter in the biology
of post-therapy recurrence. aerosol droplets compared to the perpendicular position. For the in vivo experiments, the pneumoperitoneum
pressure was set at 8 mm of Hg, since it is well known
that an intra-abdominal pressure of 12 mmHg is poorly
tolerated in rats [33, 34]. Preliminary results showed ex-
cellent tolerance of both PIPAC and electrostatic pre-
cipitation. With experience, the total procedure time
(from start to end of anesthesia) was ±100 min. The
ovarian cancer xenograft model, resulting in widespread
military PM, was successfully established after increasing
the number of SKOV-3 Luc IP2 cells to 20 × 106 and with
concurrent administration of cyclosporin. The required
number of cells may appear high, but it is known that athy-
mic rats have a lower degree of immune deficiency com-
pared to athymic mice [35]. This model now offers the
opportunity to study the anticancer effects of (e)PIPAC ei-
ther alone or in combination with systemic treatment. Discussion In
clinical practice, the recommended settings are: nebuliza-
tion of a volume of 150 to 200 mL, maximal upstream
injection pressure of 20 bar, flow rate of 0.5 mL/s and a
capnoperitoneum pressure of 12 mmHg [21]. The result-
ing aerosol droplet size is reported to be in the range of
30–40 μm [26]. In vitro granulometric analyses performed
by Göhler et al. showed that the Capnopen® generated
aerosol consists of a bimodal volume-weighted PSD with a
D(v,0.5) of 25 μm [27]. The authors argue, based on theor-
etical assumptions and calculations, that the ideal droplet
size to obtain a gas-like behaviour should be 1.2 μm (for
Stokes numbers of Stk = 1) [27]. The droplet size of the
aerosol is indeed important for its physical behaviour in
the peritoneal cavity (diffusion versus sedimentation or
inertial impaction), but may also affect tissue penetration
of the administered cytotoxic agent [27, 28]. In pulmonary Next, we studied homogeneity of aerosol distribution
using a dye. It was observed that distribution of
undiluted royal blue ink is improved when the nebulizer
was held in a slightly tilted position; this could be Fig. 3 Distribution pattern of 20 mL undiluted royal blue ink. The injection parameters were set on a flow rate of 0.8 mL/s, a maximal upstream
injection pressure of 20 bar and an intracavitary pressure of 8 mmHg. a Blue ink distribution was limited to the bottom of the EVA bag when the
nebulizer was perpendicularly secured. b Complete staining of the EVA bag was observed when the nebulizer was placed in a tilted position Fig. 3 Distribution pattern of 20 mL undiluted royal blue ink. The injection parameters were set on a flow rate of 0.8 mL/s, a maximal upstream
injection pressure of 20 bar and an intracavitary pressure of 8 mmHg. a Blue ink distribution was limited to the bottom of the EVA bag when the
nebulizer was perpendicularly secured. b Complete staining of the EVA bag was observed when the nebulizer was placed in a tilted position Page 7 of 10 Van de Sande et al. BMC Cancer (2019) 19:424 Fig. 4 In vivo BLI of athymic nude rats inoculated with 5 × 106 (group 1), 10 × 106 (group 2) or 20 × 106 (group 3) SKOV-3 Luc IP2 cells (n = 3 in
each group). In the first and second group no diffuse PM was observed. Conclusion Received: 5 December 2018 Accepted: 30 April 2019 Competing interests Competing interests
The authors declare that they have no competing interests. Acknowledgements The authors thank their lab technician Evelien Dierick for conducting H&E
stainings. We also thank the staff of Infinity IBiTech-MEDISIP (Christian Van
Hove and Benedicte Descamp) and Laboratory of Pharmaceutical Technol-
ogy (Valérie Vanhoorne and Chris Vervaet) for providing their devices. MS is
an ERS from the International Training Network ‘Nanomed’. Wim Ceelen is a
senior clinical investigator from the Fund for Scientific Research – Flanders
(FWO). g
j
5. Thomassen I, Lemmens VEPP, Nienhuijs SW, Luyer MD, Klaver YL, de Hingh
IHJT. Incidence, prognosis, and possible treatment strategies of peritoneal
carcinomatosis of pancreatic origin: a population-based study. Pancreas. 2013;42:72–5. https://doi.org/10.1097/MPA.0b013e31825abf8c. 5. Thomassen I, Lemmens VEPP, Nienhuijs SW, Luyer MD, Klaver YL, de Hingh
IHJT. Incidence, prognosis, and possible treatment strategies of peritoneal
carcinomatosis of pancreatic origin: a population-based study. Pancreas. 2013;42:72–5. https://doi.org/10.1097/MPA.0b013e31825abf8c. 6. Winner KK, Steinkamp MP, Lee RJ, Swat M, Muller CY, Moses ME, Jiang Y,
Wilson BS. Spatial modeling of drug delivery routes for treatment of
disseminated ovarian cancer. Cancer Res. 2016;76:1320–34. https://doi.org/
10.1158/0008-5472.CAN-15-1620. 6. Winner KK, Steinkamp MP, Lee RJ, Swat M, Muller CY, Moses ME, Jiang Y,
Wilson BS. Spatial modeling of drug delivery routes for treatment of
disseminated ovarian cancer. Cancer Res. 2016;76:1320–34. https://doi.org/
10.1158/0008-5472.CAN-15-1620. Discussion Since
immunotherapy offers considerable promise in ovarian can-
cer, the availability of a syngeneic OC model in immune The major limitation of our model is related to the
large difference in size between the rat and the human
peritoneal cavity. This requires scaling of the effects
found, and some clinical apparatus and methods may
work differently when used in a rat. As an example,
when using the clinically used electrostatic generator for
ePIPAC in a rat, the shorter distance between electrode
and grounding plate will result in a much stronger elec-
trical field (volt/meter). In the future, we will study ePI-
PAC using a custom made apparatus that allows to vary
voltage, current, and polarity. Page 8 of 10 Van de Sande et al. BMC Cancer (2019) 19:424 Fig. 5 Tumor nodules (white arrows) in athymic nude rats inoculated intraperitoneally with 20 × 106 SKOV-3 Luc IP2 cells. a Laparoscopic image
of the right upper abdomen. b Post-mortem view of the upper abdomen. c Intestines and mesentery Fig. 5 Tumor nodules (white arrows) in athymic nude rats inoculated intraperitoneally with 20 × 106 SKOV-3 Luc IP2 cells. a Laparoscopic image
of the right upper abdomen. b Post-mortem view of the upper abdomen. c Intestines and mesentery Fig. 6 H&E stainings of peritoneal implants at the parietal peritoneum (a) and mesentery (b), 40x magnification. In the right upper corner, a close
up of the H&E staining is shown, 400x magnification. The typical morphology of cancer cells can be detected Fig. 6 H&E stainings of peritoneal implants at the parietal peritoneum (a) and mesentery (b), 40x magnification. In the right upper corner, a close
up of the H&E staining is shown, 400x magnification. The typical morphology of cancer cells can be detected Fig. 6 H&E stainings of peritoneal implants at the parietal peritoneum (a) and mesentery (b), 40x magnification. In the right upper corner, a close
up of the H&E staining is shown, 400x magnification. The typical morphology of cancer cells can be detected Van de Sande et al. BMC Cancer (2019) 19:424 Van de Sande et al. BMC Cancer (2019) 19:424 Page 9 of 10 Page 9 of 10 Funding
N
f
di No funding was received. 7. Tempfer CB. Pressurized intraperitoneal aerosol chemotherapy as an
innovative approach to treat peritoneal carcinomatosis. Med Hypotheses. 2015;85:480–4. https://doi.org/10.1016/j.mehy.2015.07.001. Received: 5 December 2018 Accepted: 30 April 2019 We report the first reproducible small animal model of
PIPAC and ePIPAC in human ovarian PM bearing rats. This model will allow to study essential technology re-
lated aspects, pharmacokinetics and tissue penetration,
and the activity of aerosolized anticancer therapies. Abbreviations BLI: Bioluminiscent imaging; CRS: Cytoreductive surgery; D(v,0.5): Median of
volume distribution; ePIPAC: Electrostatic aerosol precipitation with PIPAC;
EVA: Ethylene vinyl acetate; H&E: Hematoxylin and eosin;
HIPEC: Hyperthermic intraperitoneal chemoperfusion; IP: Intraperitoneal;
OC: Ovarian cancer; PIPAC: Pressurized intraperitoneal aerosol chemotherapy;
PM: Peritoneal metastases; PSD: Particle size distribution; Stk: Stokes number BLI: Bioluminiscent imaging; CRS: Cytoreductive surgery; D(v,0.5): Median of
volume distribution; ePIPAC: Electrostatic aerosol precipitation with PIPAC;
EVA: Ethylene vinyl acetate; H&E: Hematoxylin and eosin; 3. Klaver YLB, Simkens LHJ, Lemmens VEPP, Koopman M, Teerenstra S,
Bleichrodt RP, de Hingh IHJT, Punt CJA. Outcomes of colorectal cancer
patients with peritoneal carcinomatosis treated with chemotherapy with
and without targeted therapy. Eur J Surg Oncol. 2012;38:617–23. https://doi.org/10.1016/j.ejso.2012.03.008. HIPEC: Hyperthermic intraperitoneal chemoperfusion; IP: Intraperitoneal;
OC: Ovarian cancer; PIPAC: Pressurized intraperitoneal aerosol chemotherapy;
PM P i
l
PSD P
i l
i
di
ib
i
S k S
k
b PM: Peritoneal metastases; PSD: Particle size distribution; Stk: Stokes number 4. Thomassen I, van Gestel YR, van Ramshorst B, Luyer MD, Bosscha K,
Nienhuijs SW, Lemmens VE, de Hingh IH. Peritoneal carcinomatosis of
gastric origin: a population-based study on incidence, survival and risk
factors. Int J Cancer. 2014;134:622–8. https://doi.org/10.1002/ijc.28373. Publisher’s Note 14. Solass W, Herbette A, Schwarz T, Hetzel A, Sun J-S, Dutreix M, Reymond MA. Therapeutic approach of human peritoneal carcinomatosis with Dbait in
combination with capnoperitoneum: proof of concept. Surg Endosc. 2012;
26:847–52. https://doi.org/10.1007/s00464-011-1964-y. Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Authors’ contributions LVDS designed the ex vivo and in vivo experiments, KDC designed the
granulometric experiments. LVDS and KDC conducted the granulometric
experiments. LVDS performed the ex vivo simulation of PIPAC. LVDS and
WW made the (e)PIPAC rat model. LVDS and MS performed cell culturing. LVDS made the rat ovarian PM model. LVDS performed data analysis. LVDS,
WW, SC, KR and WC discussed the results. LVDS has drafted the manuscript
and WW, SC, KR, WC substantively revised it. All authors read and approved
the final manuscript. 9. Esquis P, Consolo D, Magnin G, Pointaire P, Moretto P, Ynsa MD, Beltramo J-
L, Drogoul C, Simonet M, Benoit L, Rat P, Chauffert B. High intra-abdominal
pressure enhances the penetration and antitumor effect of intraperitoneal
cisplatin on experimental peritoneal carcinomatosis. Ann Surg. 2006;244:
106–12. https://doi.org/10.1097/01.sla.0000218089.61635.5f. 10. Reymond M, Demtroeder C, Solass W, Winnekendonk G, Tempfer C. Electrostatic precipitation pressurized IntraPeritoneal aerosol chemotherapy
(ePIPAC): first in-human application. Pleura and Peritoneum. 2016;1:109–16. https://doi.org/10.1515/pp-2016-0005. 11. Ansell J, Warren N, Wall P, Cocks K, Goddard S, Whiston R, Stechman M,
Scott-Coombes D, Torkington J. Electrostatic precipitation is a novel way of
maintaining visual field clarity during laparoscopic surgery: a prospective
double-blind randomized controlled pilot study. Surg Endosc. 2014;28:2057–
65. https://doi.org/10.1007/s00464-014-3427-8. 11. Ansell J, Warren N, Wall P, Cocks K, Goddard S, Whiston R, Stechman M,
Scott-Coombes D, Torkington J. Electrostatic precipitation is a novel way of
maintaining visual field clarity during laparoscopic surgery: a prospective
double-blind randomized controlled pilot study. Surg Endosc. 2014;28:2057–
65. https://doi.org/10.1007/s00464-014-3427-8. Availability of data and materials The datasets used and/or analyses during the study available from the
corresponding author on reasonable request. 8. Grass F, Vuagniaux A, Teixeira-Farinha H, Lehmann K, Demartines N, Hübner
M. Systematic review of pressurized intraperitoneal aerosol chemotherapy
for the treatment of advanced peritoneal carcinomatosis. Br J Surg. 2017;
104:669–78. https://doi.org/10.1002/bjs.10521. References 1. Al Rawahi T, Lopes AD, Bristow RE, Bryant A, Elattar A, Chattopadhyay S,
Galaal K. Surgical cytoreduction for recurrent epithelial ovarian cancer. Cochrane Database Syst Rev. 2013;(2):CD008765. https://doi.org/10.1002/14651858.CD008765.pub3. 2. 2. Oseledchyk A, Zivanovic O. Intraoperative Hyperthermic intraperitoneal
chemotherapy in patients with advanced ovarian Cancer. Oncology
(Williston Park, NY). 2015;29:695–701. 2. Oseledchyk A, Zivanovic O. Intraoperative Hyperthermic intraperitoneal
chemotherapy in patients with advanced ovarian Cancer. Oncology
(Williston Park, NY). 2015;29:695–701. Consent for publication
Not applicable. Not applicable. 13. Khosrawipour V, Diaz-Carballo D, Ali-Haydar A, Khosrawipour T, Falkenstein
TA, Wu D, Zieren J, Giger-Pabst U. Cytotoxic effect of different treatment
parameters in pressurized intraperitoneal aerosol chemotherapy (PIPAC) on
the in vitro proliferation of human colonic cancer cells. World J Surg Oncol. 2017;15:43. https://doi.org/10.1186/s12957-017-1109-4. Ethics approval The study protocol was approved by the Animal Ethical Committee of the
Faculty of Medicine, Ghent University, Belgium (ECD 17–50 and ECD 18–30). The human cell lines did not require ethics approval from our institution as
they were purchased from legal commercial product. 12. Kakchekeeva T, Demtröder C, Herath NI, Griffiths D, Torkington J, Solaß W,
Dutreix M, Reymond MA. In vivo feasibility of electrostatic precipitation as
an adjunct to pressurized intraperitoneal aerosol chemotherapy (ePIPAC). Ann Surg Oncol. 2016;23:592–8. https://doi.org/10.1245/s10434-016-5108-4. Author details
1 2018;44:991–
6. https://doi.org/10.1016/j.ejso.2018.02.014. 20. De Vlieghere E, Carlier C, Ceelen W, Bracke M, De Wever O. Data on in vivo
selection of SK-OV-3 Luc ovarian cancer cells and intraperitoneal tumor
formation with low inoculation numbers. Data Brief. 2016;6:542–9. https://doi.org/10.1016/j.dib.2015.12.037. 21. Solass W, Kerb R, Mürdter T, Giger-Pabst U, Strumberg D, Tempfer C, Zieren
J, Schwab M, Reymond MA. Intraperitoneal chemotherapy of peritoneal
Carcinomatosis using pressurized aerosol as an alternative to liquid solution:
first evidence for efficacy. Ann Surg Oncol. 2014;21:553–9. https://doi.org/10.1245/s10434-013-3213-1. 22. Dedrick RL, Flessner MF. Pharmacokinetic problems in peritoneal drug
administration: tissue penetration and surface exposure. J Natl Cancer Inst. 1997;89:480–7. https://doi.org/10.1093/jnci/89.7.480. 23. Tempfer CB, Hilal Z, Dogan A, Petersen M, Rezniczek GA. Concentrations of
cisplatin and doxorubicin in ascites and peritoneal tumor nodules before
and after pressurized intraperitoneal aerosol chemotherapy (PIPAC) in
patients with peritoneal metastasis. Eur J Surg Oncol. 2018;44:1112–7. https://doi.org/10.1016/j.ejso.2018.04.020. 24. Khosrawipour V, Khosrawipour T, Kern AJP, Osma A, Kabakci B, Diaz-Carballo
D, Förster E, Zieren J, Fakhrian K. Distribution pattern and penetration depth
of doxorubicin after pressurized intraperitoneal aerosol chemotherapy
(PIPAC) in a postmortem swine model. J Cancer Res Clin Oncol. 2016;142:
2275–80. https://doi.org/10.1007/s00432-016-2234-0. 25. Tempfer C, Giger-Pabst U, Hilal Z, Dogan A, Rezniczek GA. Pressurized
intraperitoneal aerosol chemotherapy (PIPAC) for peritoneal carcinomatosis:
systematic review of clinical and experimental evidence with special
emphasis on ovarian cancer. Arch Gynecol Obstet. 2018;298:234–57. https://doi.org/10.1007/s00404-018-4784-7. 26. Reymond MA, Solass W. PIPAC: pressurized IntraPeritoneal aerosol
chemotherapy – Cancer under pressure. Berlin: Walter de Gruyter GmbH &
Co KG; 2014. 26. Reymond MA, Solass W. PIPAC: pressurized IntraPeritoneal aerosol
chemotherapy – Cancer under pressure. Berlin: Walter de Gruyter GmbH &
Co KG; 2014. 27. Göhler D, Khosrawipour V, Khosrawipour T, Diaz-Carballo D, Falkenstein TA,
Zieren J, Stintz M, Giger-Pabst U. Technical description of the microinjection
pump (MIP®) and granulometric characterization of the aerosol applied for
pressurized intraperitoneal aerosol chemotherapy (PIPAC). Surg Endosc. 2016:1–7. https://doi.org/10.1007/s00464-016-5174-5. 28. Try C, Moulari B, Béduneau A, Fantini O, Pin D, Pellequer Y, Lamprecht A. Size dependent skin penetration of nanoparticles in murine and porcine
dermatitis models. Eur J Pharm Biopharm. 2016;100:101–8. https://doi.org/10.1016/j.ejpb.2016.01.002. 29. Dalby RN, Eicher J, Zierenberg B. Development of Respimat® soft mist™
inhaler and its clinical utility in respiratory disorders. Med Devices (Auckl). 2011;4:145–55. https://doi.org/10.2147/MDER.S7409. 30. Labiris NR, Dolovich MB. Pulmonary drug delivery. Part I: physiological
factors affecting therapeutic effectiveness of aerosolized medications. Br J
Clin Pharmacol. 2003;56:588–99. https://doi.org/10.1046/j.1365-2125.2003.01892.x. 31. 35.
Mashimo T, Takizawa A, Kobayashi J, Kunihiro Y, Yoshimi K, Ishida S, Tanabe
K, Yanagi A, Tachibana A, Hirose J, Yomoda J, Morimoto S, Kuramoto T,
Voigt B, Watanabe T, Hiai H, Tateno C, Komatsu K, Serikawa T. Generation
and characterization of severe combined immunodeficiency rats. Cell Rep.
2012;2:685–94. https://doi.org/10.1016/j.celrep.2012.08.009. Author details
1 15. Khosrawipour V, Khosrawipour T, Falkenstein TA, Diaz-Carballo D, Foerster E,
Osma A, Adamietz IA, Zieren J, Fakhrian K. Evaluating the effect of micropump
(c) position, internal pressure and doxorubicin dosage on efficacy of
pressurized intra-peritoneal aerosol chemotherapy (PIPAC) in an ex vivo model. Anticancer Res. 2016;36:4595–600. https://doi.org/10.21873/anticanres.11008. 1Laboratory of Experimental Surgery, Department of Human Structure and
Repair, Ghent University, Ghent, Belgium. 2Cancer Research Institute Ghent
(CRIG), Ghent University, Ghent, Belgium. 3Laboratory of Pharmaceutical
Technology, Department of Pharmaceutics, Ghent University, Ghent, Belgium. 4Laboratory for General Biochemistry and Physical Pharmacy, Department of
Pharmaceutics, Ghent University, Ghent, Belgium. 5Department of GI Surgery,
Ghent University Hospital, route 1275, C. Heymanslaan 10, B-9000 Ghent,
Belgium. p
g
16. Schnelle D, Weinreich F-J, Kibat J, Reymond MA. A new ex vivo model for
optimizing distribution of therapeutic aerosols: the (inverted) bovine urinary
bladder. Pleura and Peritoneum. 2017;2:37–41. https://doi.org/10.1515/pp-2017-0006. 16. Schnelle D, Weinreich F-J, Kibat J, Reymond MA. A new ex vivo model for
optimizing distribution of therapeutic aerosols: the (inverted) bovine urinary
bladder. Pleura and Peritoneum. 2017;2:37–41. https://doi.org/10.1515/pp-2017-0006. Page 10 of 10 Page 10 of 10 Page 10 of 10 Van de Sande et al. BMC Cancer (2019) 19:424 Van de Sande et al. BMC Cancer (2019) 19:424 17. Solaß W, Hetzel A, Nadiradze G, Sagynaliev E, Reymond MA. Description of a
novel approach for intraperitoneal drug delivery and the related device. Surg Endosc. 2012;26:1849–55. https://doi.org/10.1007/s00464-012-2148-0. 18. Alyami M, Gagniere J, Sgarbura O, Cabelguenne D, Villeneuve L, Pezet D,
Quenet F, Glehen O, Bakrin N, Passot G. Multicentric initial experience with
the use of the pressurized intraperitoneal aerosol chemotherapy (PIPAC) in
the management of unresectable peritoneal carcinomatosis. EJSO. 2017;43:
2178–83. https://doi.org/10.1016/j.ejso.2017.09.010. 19. Nowacki M, Alyami M, Villeneuve L, Mercier F, Hubner M, Willaert W, Ceelen
W, Reymond M, Pezet D, Arvieux C, Khomyakov V, Lay L, Gianni S, Zegarski
W, Bakrin N, Glehen O. Multicenter comprehensive methodological and
technical analysis of 832 pressurized intraperitoneal aerosol chemotherapy
(PIPAC) interventions performed in 349 patients for peritoneal
carcinomatosis treatment: an international survey study. EJSO. 2018;44:991–
6. https://doi.org/10.1016/j.ejso.2018.02.014. 19. Nowacki M, Alyami M, Villeneuve L, Mercier F, Hubner M, Willaert W, Ceelen
W, Reymond M, Pezet D, Arvieux C, Khomyakov V, Lay L, Gianni S, Zegarski
W, Bakrin N, Glehen O. Multicenter comprehensive methodological and
technical analysis of 832 pressurized intraperitoneal aerosol chemotherapy
(PIPAC) interventions performed in 349 patients for peritoneal
carcinomatosis treatment: an international survey study. EJSO. 36.
Azaïs H, Queniat G, Bonner C, Kerdraon O, Tardivel M, Jetpisbayeva G,
Frochot C, Betrouni N, Collinet P, Mordon S. Fischer 344 Rat: a preclinical
model for epithelial ovarian Cancer folate-targeted therapy. Int J Gynecol
Cancer. 2015;25:1194–200. https://doi.org/10.1097/IGC.0000000000000497. 34.
Schmandra TC, Kim ZG, Gutt CN. Effect of insufflation gas and
intraabdominal pressure on portal venous flow during pneumoperitoneum
in the rat. Surg Endosc. 2001;15:405–8.
https://doi.org/10.1007/s004640000331. 34.
Schmandra TC, Kim ZG, Gutt CN. Effect of insufflation gas and
intraabdominal pressure on portal venous flow during pneumoperitoneum
in the rat. Surg Endosc. 2001;15:405–8.
https://doi.org/10.1007/s004640000331.
35.
Mashimo T, Takizawa A, Kobayashi J, Kunihiro Y, Yoshimi K, Ishida S, Tanabe
K, Yanagi A, Tachibana A, Hirose J, Yomoda J, Morimoto S, Kuramoto T,
Voigt B, Watanabe T, Hiai H, Tateno C, Komatsu K, Serikawa T. Generation
and characterization of severe combined immunodeficiency rats. Cell Rep.
2012;2:685–94. https://doi.org/10.1016/j.celrep.2012.08.009.
36.
Azaïs H, Queniat G, Bonner C, Kerdraon O, Tardivel M, Jetpisbayeva G,
Frochot C, Betrouni N, Collinet P, Mordon S. Fischer 344 Rat: a preclinical
model for epithelial ovarian Cancer folate-targeted therapy. Int J Gynecol
Cancer. 2015;25:1194–200. https://doi.org/10.1097/IGC.0000000000000497. Author details
1 Carvalho TC, Peters JI, Williams RO. Influence of particle size on regional
lung deposition – what evidence is there? Int J Pharm. 2011;406:1–10. https://doi.org/10.1016/j.ijpharm.2010.12.040. 32. Chaker MA. Key Parameters for the Performance of Impaction-Pin Nozzles
Used in Inlet Fogging of Gas Turbine Engines 2005;4:91–97. doi:https://doi.org/10.1115/GT2005-68346. 33. Niu X, Song X, Su A, Zhao S, Li Q. Low-pressure capnoperitoneum reduces
stress responses during pediatric laparoscopic high ligation of indirect
inguinal hernia sac. Medicine (Baltimore). 2017;96:e6563. https://doi.org/10.1097/MD.0000000000006563.
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Autophagy and intermittent fasting: the connection for cancer therapy?
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Clinics
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Autophagy: definition and mechanisms autophagy) is the best-characterized process; in this process,
cytoplasmic constituents are engulfed within double-mem-
brane vesicles called autophagosomes, which subsequently
fuse with lysosomes to form autolysosomes, where the
cargo are degraded or recycled (3,7). The degradation
products include sugars, nucleosides/nucleotides, amino
acids and fatty acids that can be redirected to new
metabolic routes for cellular maintenance (8-10). The 2016 Nobel Prize in Physiology or Medicine was
awarded to Yoshinori Ohsumi for his initial elucidation of
the morphological and molecular mechanisms of autophagy
in the 1990s (1,2). Autophagy is an evolutionarily conserved
lysosomal catabolic process by which cells degrade and recycle
intracellular endogenous (damaged organelles, misfolded or
mutant proteins and macromolecules) and exogenous (viruses
and bacteria) components to maintain cellular homeostasis
(3,4). The specificity of the cargo and the delivery route to
lysosomes distinguishes the three major types of autop-
hagy. Mircroautophagy involves the direct engulfment of
cargo in endosomal/lysosomal membrane invaginations
(5). Chaperone-mediated autophagy (CMA) recycles solu-
ble proteins with an exposed amino acid motif (KFERQ)
that is recognized by the heat shock protein hsc70; these
proteins are internalized by binding to lysosomal recep-
tors (LAMP-2A) (6). Macroautophagy (herein referred to as Autophagy occurs at basal levels under physiological
conditions and can also be upregulated in response to
stressful stimuli such as hypoxia, nutritional deprivation,
DNA damage, and cytotoxic agents (11,12). The molecular
machinery that mediates the autophagic process is evolutio-
narily conserved in higher eukaryotes and regulated by
specific genes (ATG genes), which were initially character-
ized in yeast (13,14). Each stage is controlled by different
protein complexes regulated by the activation or inactivation
of several stress-responsive pathways, such as those invol-
ving mammalian target of rapamycin (mTOR—nutrient),
AMP-activated protein kinase (AMPK—energy) and hypoxia-
inducible factors (HIFs—stress) (3,15). Regarding initialization,
the activation of the ULK1 complex (ULK1/2, Atg13, FIP200
and Atg101) signals for autophagosome nucleation under the
control of the PI3K III complex (PI3KIII, Beclin-1, Atg14/
Barkor, Vps15 and Ambra-1), whose activation induces PIP3
(phosphatidyl inositol 3 phosphate) production, which in
turn recruits other Atg proteins to form the phagophore
(16). REVIEW ARTICLE REVIEW ARTICLE Autophagy and intermittent fasting: the connection
for cancer therapy? Fernanda Antunes,I Adolfo Garcia Erustes,I Ange´lica Jardim Costa,I Ana Carolina Nascimento,I
Claudia Bincoletto,I Rodrigo Portes Ureshino,II Gustavo Jose´ Silva Pereira,I Soraya Soubhi SmailiI,*
I Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de Sao Paulo (EPM-UNIFESP), Sao Paulo, SP, BR. II Departamento de
Ciencias Biologicas, Universidade Federal de Sao Paulo, Diadema, SP, BR. Antunes F, Erustes AG, Costa AJ, Nascimento AC, Bincoletto C, Ureshino RP, et al. Autophagy and intermittent fasting: the connection for cancer therapy? Clinics. 2018;73(suppl 1):e814s Nascimento AC, Bincoletto C, Ureshino RP, et al. Autophagy and intermittent fasting: the connection for cancer therapy? *Corresponding author. E-mail: soraya.smaili23@gmail.com Cancer is a leading cause of death worldwide, and its incidence is continually increasing. Although anticancer
therapy has improved significantly, it still has limited efficacy for tumor eradication and is highly toxic to healthy
cells. Thus, novel therapeutic strategies to improve chemotherapy, radiotherapy and targeted therapy are an
important goal in cancer research. Macroautophagy (herein referred to as autophagy) is a conserved lysosomal
degradation pathway for the intracellular recycling of macromolecules and clearance of damaged organelles
and misfolded proteins to ensure cellular homeostasis. Dysfunctional autophagy contributes to many diseases,
including cancer. Autophagy can suppress or promote tumors depending on the developmental stage and
tumor type, and modulating autophagy for cancer treatment is an interesting therapeutic approach currently
under intense investigation. Nutritional restriction is a promising protocol to modulate autophagy and enhance
the efficacy of anticancer therapies while protecting normal cells. Here, the description and role of autophagy
in tumorigenesis will be summarized. Moreover, the possibility of using fasting as an adjuvant therapy for
cancer treatment, as well as the molecular mechanisms underlying this approach, will be presented. KEYWORDS: Apoptosis; Autophagy; Fasting; Cancer; Therapy. Autophagy: definition and mechanisms Finally, studies have demonstrated that autophagy is com-
monly induced as a survival mechanism against antitumor
treatments, such as chemotherapy, radiotherapy and targeted
therapy, contributing to treatment resistance (48,49). stressors, including hypoxia, nutritional and growth factor
deprivation and damaging stimuli, thus allowing tumor
adaptation, proliferation, survival and dissemination (40). Autophagy, by degrading macromolecules and defective
organelles, supplies metabolites and upregulates mitochon-
drial function, supporting tumor cell viability even in
constantly stressful environments (11,29). Studies have demon-
strated that autophagy increases in hypoxic regions of solid
tumors, favoring cell survival. The inhibition of autophagy
leads to an intense induction of cell death in these regions
(41,42). Moreover, tumors frequently have mutations or
deletions in the tumor suppressor protein p53, which also
favors autophagy induction to recycle intracellular compo-
nents for tumor growth (43). Although the basal autophagy
rate is generally low in normal cells under physiological
conditions, some tumors show a high level of basal auto-
phagy, reinforcing the prosurvival role of autophagy in
cancer
(40,44). RAS-transformed
cancer
cells
undergo
autophagy upregulation to supply metabolic needs and
maintain functional mitochondria, which in turn favors
tumor establishment (45-47). Autophagy also has a supportive
role in metastasis by interfering with epithelial-mesenchymal
transition constituents to favor tumor cell dissemination (30). Finally, studies have demonstrated that autophagy is com-
monly induced as a survival mechanism against antitumor
treatments, such as chemotherapy, radiotherapy and targeted
therapy, contributing to treatment resistance (48,49). Throughout the past decade, autophagy has attracted
considerable attention as a potential target of pharmacolo-
gical agents or dietary interventions that inhibit or activate
this process for several human disorders, including infections
and inflammatory diseases (22), neurodegeneration (23),
metabolic and cardiovascular diseases (24), obesity (25) and
cancer (26,27). Autophagy and cancer gy
The role of autophagy in cancer is complex, and its
function may vary according to several biological factors,
including tumor type, progression stage and genetic land-
scape, along with oncogene activation and tumor suppressor
inactivation (26,28). Thus, autophagy can be related either to
the prevention of tumorigenesis or to the enabling of cancer
cell adaptation, proliferation, survival and metastasis (29,30). The initial indication that autophagy could have an impor-
tant role in tumor suppression came from several studies
exploring the essential autophagy gene BECN1, which
encodes the Beclin-1 protein, in different cellular models. Liang et al. (31) demonstrated that BECN1 was frequently
monoallelically deleted in ovarian, breast and testicular
cancer. Moreover, mice harboring allelic loss of BECN1 had
a partial autophagy deficiency and were prone to the devel-
opment of hepatocarcinoma and lung tumors at an advanced
age (32,33). However, BECN1 is located adjacent to the well-
known tumor suppressor gene BRCA1, which is commonly
deleted in hereditary breast cancer. These deletions are
generally extensive and affect BRCA1 along with several
other genes, including BECN1, suggesting that the deletion
of BRCA1, not the deletion of BECN1, is the driver mutation
in breast cancer (34). However, autophagy impairment due
to a mosaic deletion of ATG5 induces benign liver tumors,
demonstrating that different tissues have different responses
to autophagy impairment (35). Furthermore, the activation of
oncogenes (e.g., PI3KCA) and inactivation of tumor sup-
pressors (e.g., PTEN and LKB1) are associated with auto-
phagy inhibition and tumorigenesis (36). In general, studies
from animal models note that the tumor suppressor func-
tion of autophagy is associated with cell protection from
oxidative stress, DNA damage, inflammation and the accu-
mulation of dysfunctional organelles. Collectively, these
phenomena are important factors that could trigger genomic
instabilities leading to tumor development (29,37,38). How-
ever, the loss of function of autophagy genes has not yet been
identified and demonstrated in humans, raising doubts
about the relevance of autophagy to tumor initiation in
different types of cancer (26). In addition, the autophagic
machinery is not a common target of somatic mutations,
indicating that autophagy may have a fundamental role in
the survival and progression of tumor cells (39). O
h
i
bli h d
h
i
f
i
f Autophagy: definition and mechanisms Subsequently, two ubiquitin-like conjugation systems
mediate the recruitment of ATG12–ATG5 and microtubule-
associated protein light chain 3 (LC3) proteins to the Copyright & 2018 CLINICS – This is an Open Access article distributed under the
terms of the Creative Commons License (http://creativecommons.org/licenses/by/
4.0/) which permits unrestricted use, distribution, and reproduction in any
medium or format, provided the original work is properly cited. No potential conflict of interest was reported. No potential conflict of interest was reported. Received for publication on May 30, 2018. Accepted for publication
on September 25, 2018 Received for publication on May 30, 2018. Accepted for publication
on September 25, 2018 Commemorative Edition: 10 years of ICESP Commemorative Edition: 10 years of ICESP 1 Fasting-mediated autophagy in cancer therapy
Antunes F et al. CLINICS 2018;73(suppl 1):e814s CLINICS 2018;73(suppl 1):e814s phagophore, allowing its expansion and closure to form the
mature autophagosome (17). This process leads to the
conversion of the soluble protein LC3-I via conjugation to
phosphatidylethanolamine to form an LC3-II membrane-
associated form in the cytosol, specifically in the inner and
outer membranes of the autophagosome (18,19). Further-
more, LC3-II can interact with adaptor proteins such as p62
(also known as sequestosome-1/SQSTM1), which directs
cargo delivery to autophagosomes for further degradation
in lysosomes, the final step of autophagy (20,21). stressors, including hypoxia, nutritional and growth factor
deprivation and damaging stimuli, thus allowing tumor
adaptation, proliferation, survival and dissemination (40). Autophagy, by degrading macromolecules and defective
organelles, supplies metabolites and upregulates mitochon-
drial function, supporting tumor cell viability even in
constantly stressful environments (11,29). Studies have demon-
strated that autophagy increases in hypoxic regions of solid
tumors, favoring cell survival. The inhibition of autophagy
leads to an intense induction of cell death in these regions
(41,42). Moreover, tumors frequently have mutations or
deletions in the tumor suppressor protein p53, which also
favors autophagy induction to recycle intracellular compo-
nents for tumor growth (43). Although the basal autophagy
rate is generally low in normal cells under physiological
conditions, some tumors show a high level of basal auto-
phagy, reinforcing the prosurvival role of autophagy in
cancer
(40,44). RAS-transformed
cancer
cells
undergo
autophagy upregulation to supply metabolic needs and
maintain functional mitochondria, which in turn favors
tumor establishment (45-47). Autophagy also has a supportive
role in metastasis by interfering with epithelial-mesenchymal
transition constituents to favor tumor cell dissemination (30). How does dietary restriction modulate autophagy
and cancer therapy? y
In preclinical studies, dietary restriction (DR) has been
shown to extend the lifespan and reduce the development of
age-related diseases such as diabetes, cancer, and neurode-
generative and cardiovascular diseases (63). DR promotes
metabolic and cellular changes in organisms from prokar-
yotes to humans that allow adaptation to periods of limited
nutrient availability (64). The main changes include decrea-
sed blood glucose levels and growth factor signaling and the
activation of stress resistance pathways affecting cell growth,
energy metabolism, and protection against oxidative stress,
inflammation and cell death (64,65). Nutrient starvation also
activates autophagy in most cultured cells and organs, such
as the liver and muscle, as an adaptive mechanism to
stressful conditions (11,66). Table 1 - Completed and current clinical trials investigating the effects of fasting as adjunct therapy to anti-cancer treatment. als investigating the effects of fasting as adjunct therapy to anti-cancer treatment. Studies demonstrate that dietary interventions can reduce
tumor incidence and potentiate the effectiveness of chemo-
and radiotherapy in different tumor models, highlight-
ing dietary manipulation as a possible adjunct to standard
cancer therapies (63,65). Among the many diet regimens
that have been assessed, caloric restriction (CR) and fasting
are the methods under intense investigation in oncology
(63,65,67). CR is defined as a chronic reduction in the daily
caloric intake by 20-40% without the incurrence of malnutri-
tion and with the maintenance of meal frequency (68). In
contrast, fasting is characterized by the complete deprivation
of food but not water, with intervening periods of normal
food intake. Based on the duration, fasting can be classified
as (i) intermittent fasting (IF—e.g., alternate day fasting
(X16 hours) or 48 hours of fasting/week) or (ii) periodic
fasting (PF—e.g., a minimum of 3 days of fasting every 2 or
more weeks) (65). In this article, we do not review CR studies
that have been reviewed elsewhere (63,68,69); instead, we
focus on studies using IF protocols as an adjuvant to cancer
treatment in animals and humans. Autophagy and cancer therapeutics Cancer/Phase
Treatment
Outcome/Status
Reference
Breast Cancer, Hormone-resistant Prostate
Cancer, Recurrent Prostate Cancer
Chemotherapy + low-calorie diet
Currently recruiting participants
NCT01802346
Advanced Metastatic Prostate Cancer
Chemotherapy + fasting and nutritional therapy
Currently recruiting participants
NCT02710721
HER2 Negative Breast Cancer
Chemotherapy + fasting mimicking diet
Currently recruiting participants
NCT02126449
Breast Cancer
Chemotherapy + short-term fasting (IF)
IF associated with chemotherapy was well tolerated,
reduced hematological toxicity in HER2-negative BC
patients and also induced a faster recovery of DNA
damage in PBMCs (peripheral blood mononuclear cells)
NCT01304251 (96)
Gynecological cancer disease (ovarian
and breast cancer)
Chemotherapy + short-term fasting
Completed, no results reported
NCT01954836
Breast cancer
Chemotherapy + short-term fasting
Completed, no results reported
NCT02379585
Malignant Neoplasm
Short-term fasting prior to systemic chemotherapy
Active
NCT01175837
Malignant Neoplasm
Chemotherapy + fasting
Completed, no results reported
NCT00757094 provided reliable therapeutic benefits to patients (59). Cur-
rently, protocols targeting autophagy induction instead of
autophagy blockade are under intense investigation in
oncology (28,50,60). Nevertheless, no drug currently licen-
sed by any regulatory agency was developed for autophagy
modulation, although several approved agents indeed
modulate autophagy to some extent (61,62). Table 1 - Completed and current clinical trials investigating the effects of fasting as adjunct therapy to anti-cancer treatment. NCT01802346 Reference Autophagy and cancer therapeutics Because autophagy can inhibit tumor development or
favor tumor growth, progression, invasion and treatment
resistance, researchers proposed that autophagy modulation
could be a new therapeutic strategy in the treatment of some
malignancies (28,49,50). g
Recently, we published a review on autophagy and cancer,
suggesting that some challenges, such as the incomplete
understanding of the relationship between autophagy, tumor
resistance, and cell death, as well as the identification of new
druggable targets, need to be overcome with the aim of
pharmacologically modulating autophagy for cancer treat-
ment (51). Some of these suggestions are based on the current
literature and on previous studies published by our group
demonstrating that combining different agents such as selu-
metinib and cytarabine with autophagy inhibitors (bafilo-
mycin A1, chloroquine or 3-methyladenine) enhanced the
activity of selumetinib and cytarabine against colorectal
cancer cells (52) and leukemia cells (53), respectively. Auto-
phagy was also observed in melanoma cells under treatment
with palladium complex drugs (54), indicating the importance
of investigating the relationship between autophagy and
apoptosis during new drug development. Additionally,
other studies demonstrated that inhibiting autophagy by
chloroquine in combination with sorafenib in an in vitro
model of glioblastoma (55) and in combination with temo-
zolomide in melanoma patients augmented antitumor
treatment efficacy (56). The inhibition of autophagy was
also demonstrated to potentiate the response to radio-
therapy in ovarian (57) and esophageal cancer (58). The
efficacy of autophagy in favoring cell death has been
demonstrated in many other cancer models, such as breast
cancer, leukemia, prostate cancer, and myeloma (48,49). However, to date, clinical trials have not demonstrated that
autophagy inhibition associated with anticancer therapy Once the tumor is established, the main function of
autophagy is to provide a means to cope with cellular 2 CLINICS 2018;73(suppl 1):e814s Fasting-mediated autophagy in cancer therapy
Antunes F et al. Table 1 - Completed and current clinical trials investigating the effects of fasting as adjunct therapy to anti-cancer treatment. How does dietary restriction modulate autophagy
and cancer therapy? This group also showed
that the impairment of tumor growth was dependent on the
cellular immune system as well as on autophagy; IF +
chemotherapy could not impair tumor growth in either
athymic nu/nu mice or tumor cells after autophagy deficiency
was induced by Atg5 knockdown. y
p
g
g
py
Although the results of combining IF with anticancer
drugs are encouraging, the molecular mechanisms are not
completely clear. Lee et al. (81) demonstrated that IF (48-hour
fasting) reduced the glucose and IGF-1 levels by 60% and
70%, respectively, in a breast cancer animal model. In a colon
cancer model, IF inhibited tumor growth without causing
permanent weight loss and decreased M2 polarization of
tumor-associated macrophages in mice. In vitro data showed
autophagy induction and CD73 downregulation, followed
by a decrease in extracellular adenosine and the inhibition of
M2 polarization due to the inactivation of JAK1/STAT3 (82). Although the results of combining IF with anticancer
drugs are encouraging, the molecular mechanisms are not
completely clear. Lee et al. (81) demonstrated that IF (48-hour
fasting) reduced the glucose and IGF-1 levels by 60% and
70%, respectively, in a breast cancer animal model. In a colon
cancer model, IF inhibited tumor growth without causing
permanent weight loss and decreased M2 polarization of
tumor-associated macrophages in mice. In vitro data showed
autophagy induction and CD73 downregulation, followed
by a decrease in extracellular adenosine and the inhibition of
M2 polarization due to the inactivation of JAK1/STAT3 (82). When IF cycles were combined with chemotherapy, tumor
growth was slowed and overall survival was prolonged in
breast cancer, melanoma and neuroblastoma animal models
(70). The in vitro data showed that this therapeutic combina-
tion resulted in increased Akt and S6 kinase phosphorylation, p
When IF cycles were combined with chemotherapy, tumor
growth was slowed and overall survival was prolonged in
breast cancer, melanoma and neuroblastoma animal models
(70). The in vitro data showed that this therapeutic combina-
tion resulted in increased Akt and S6 kinase phosphorylation, The combination of IF and tyrosine kinase inhibitors such
as erlotinib, gefitinib, lapatinib, crizotinib and regorafenib
promoted the sustained inhibition of the MAPK pathway,
leading to antiproliferative effects in breast, colorectal and Figure 1 - Presumable molecular mechanisms induced by fasting and anticancer treatment to promote intracellular changes and
autophagy induction in tumor cells. How does dietary restriction modulate autophagy
and cancer therapy? Table 1 - Completed and current clinical trials investigating the effects of fasting as ad Recently, studies in in vitro and in vivo models have shown
that intermittent fasting improved the chemotherapeutic
response to cisplatin, doxorubicin, cyclophosphamide (70),
oxaliplatin (71), sorafenib (72), mitoxantrone (73), gemcita-
bine (74), etoposide (75), temozolomide (76) and tyrosine
kinase inhibitors (77) in models of glioma, neuroblastoma,
melanoma, fibrosarcoma and breast cancer, colon cancer,
pancreatic cancer, hepatocellular cancer and lung cancer. IF
has also been shown to improve the radiosensitivity of
glioma (76) and breast cancer (78) in mice. Interestingly,
fasting in combination with cytotoxic agents elicited differ-
ential responses in normal and cancer cells, a phenomenon
known as differential stress resistance (DSR). For DSR,
normal cells prioritize maintenance pathways and inactivate
growth factor signaling when nutrients are absent. In con-
trast, cancer cells, due to oncogene activation, do not inhibit
stress resistance pathways, thus becoming vulnerable to
cytotoxic treatment (70,75). IF, by reducing the circulating
glucose levels, protected mice from doxorubicin toxicity and Cancer/Phase 3 Fasting-mediated autophagy in cancer therapy
Antunes F et al. CLINICS 2018;73(suppl 1):e814s CLINICS 2018;73(suppl 1):e814s particularly promoted cardioprotection mediated in part
by EGFR1-dependent transcriptional regulation of atrial
natriuretic peptide and B-type natriuretic peptide in heart
tissue (79). As demonstrated by Tinkum et al. (80), IF also
facilitated DNA repair activation mechanisms and preserved
small intestinal (SI) stem cell viability as well SI architecture
and barrier function after exposure to high-dose etoposide,
suggesting that fasting can be applied to reduce side effects
and toxicity in patients undergoing chemotherapy. caspase-3 cleavage and apoptosis induction in cancer cells but
not in normal cells (70). Other studies demonstrated that the
combination of IF and oxaliplatin also reduced tumor growth
and glucose uptake in vivo and resulted in downregulated
aerobic glycolysis followed by augmented oxidative phos-
phorylation, leading to increased oxidative stress, decreased
ATP synthesis and cell death in colon cancer cell models (71). Furthermore, Our group also demonstrated that nutritional
deprivation enhanced the sensitivity of both wild type and
BRAFV600E human melanoma cells to cisplatin treatment
followed by ROS production and mitochondrial perturbation
leading to apoptosis without autophagy involvement in the
cell death process (83). Pietrocola et al. (73) showed that IF
improved the chemotherapeutic response to mitoxantrone
and oxaliplatin in murine fibrosarcoma, reducing tumor
growth in immunocompetent mice. ’ REFERENCES 1. Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-
defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993;333(1-2):
169-74, http://dx.doi.org/10.1016/0014-5793(93)80398-E. 2. Takeshige K, Baba M, Tsuboi S, Noda T, Ohsumi Y. Autophagy in yeast
demonstrated with proteinase-deficient mutants and conditions for
its induction. J Cell Biol. 1992;119(2):301-11, http://dx.doi.org/10.1083/
jcb.119.2.301. j
3. Galluzzi L, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM,
Cecconi F, et al. Molecular definitions of autophagy and related processes. EMBO J. 2017;36(13):1811-36, http://dx.doi.org/10.15252/embj.201796697. (
)
p
g
j
4. Levine B, Klionsky DJ. Development by self-digestion: molecular mech-
anisms and biological functions of autophagy. Dev Cell. 2004;6(4):463-77,
http://dx.doi.org/10.1016/S1534-5807(04)00099-1. Another novel pharmacological therapeutic strategy cur-
rently being investigated to treat cancer is the combination of
caloric restriction mimetics (CRMs) with cytotoxic agents. CRMs are compounds that have different chemical structures
and mimic the biochemical and functional effects of CR, such
as the activation of AMPK and inhibition of mTOR leading to
autophagy induction, the depletion of acetyl-CoA and ATP,
and the reduced utilization of glucose, without eliciting the
discomfort of CR (88). Several studies demonstrated the
tumor-suppressive effects of CRM agents, for example, 2-
deoxy-glucose (89), metformin (90,91), mTOR inhibitors (92),
resveratrol (73,93), hydroxycitrate (73), spermidine (73,94)
and natural compounds such as curcumin (95), in combination
with antitumor treatments in different cancer models. The
possible connections between fasting and anticancer therapy
potentiation in tumor cells are summarized in Figure 1. p
g
(
)
5. Mijaljica D, Prescott M, Devenish RJ. Microautophagy in mammalian
cells: revisiting a 40-year-old conundrum. Autophagy. 2011;7(7):673-82,
http://dx.doi.org/10.4161/auto.7.7.14733. p
g
6. Kaushik S, Cuervo AM. Chaperone-mediated autophagy: a unique way to
enter the lysosome world. Trends Cell Biol. 2012;22(8):407-17, http://dx. doi.org/10.1016/j.tcb.2012.05.006. g
j
7. Mizushima N, Komatsu M. Autophagy: renovation of cells and tissues. Cell. 2011;147(4):728-41, http://dx.doi.org/10.1016/j.cell.2011.10.026. 8. Kimmelman AC, White E. Autophagy and Tumor Metabolism. Cell
Metab. 2017;25(5):1037-43, http://dx.doi.org/10.1016/j.cmet.2017.04.004. ( )
p
g
j
9. Saxton RA, Sabatini DM. mTOR Signaling in Growth, Metabolism,
and Disease. Cell. 2017;168(6):960-76, http://dx.doi.org/10.1016/j.cell. 2017.02.004. 10. Settembre C, De Cegli R, Mansueto G, Saha PK, Vetrini F, Visvikis O, et al. TFEB controls cellular lipid metabolism through a starvation-induced
autoregulatory loop. Nat Cell Biol. 2013;15(6):647-58, http://dx.doi.org/
10.1038/ncb2718. 11. Kroemer G, Mariño G, Levine B. Autophagy and the integrated stress
response. Mol Cell. 2010;40(2):280-93, http://dx.doi.org/10.1016/j.molcel. 2010.09.023. 12. Kaur J, Debnath J. Autophagy at the crossroads of catabolism and ana-
bolism. Nat Rev Mol Cell Biol. 2015;16(8):461-72, http://dx.doi.org/
10.1038/nrm4024. How does dietary restriction modulate autophagy
and cancer therapy? I) Fasting may oppose the Warburg effect (glucose breakdown by glycolysis even in the presence of
oxygen), favoring oxidative phosphorylation in tumor cells and resulting in increased ROS production and reduced levels of lactate and
possibly ATP. The increase in the ADP/ATP ratio can activate the AMPK pathway, leading to autophagy induction. Moreover, the
sustained stressful environment can result in cell death induction. II) Several tumors harbor mutations that favor MAPK pathway
hyperactivation, which enables tumor cell growth, survival and proliferation. Therapies targeting this pathway, as well as fasting, may
result in the downregulation of this pathway alongside a reduction in AKT and mTOR activation, resulting in autophagy induction and
cell death. III) Furthermore, fasting potentiates the detrimental effects of chemotherapy, such as DNA damage, thus activating the cell
death machinery, deregulating pro- and antiapoptotic proteins, and inducing mitochondrial alterations and caspase activation, which
in turn culminates in apoptosis. Figure 1 - Presumable molecular mechanisms induced by fasting and anticancer treatment to promote intracellular changes and
autophagy induction in tumor cells. I) Fasting may oppose the Warburg effect (glucose breakdown by glycolysis even in the presence of
oxygen), favoring oxidative phosphorylation in tumor cells and resulting in increased ROS production and reduced levels of lactate and
possibly ATP. The increase in the ADP/ATP ratio can activate the AMPK pathway, leading to autophagy induction. Moreover, the
sustained stressful environment can result in cell death induction. II) Several tumors harbor mutations that favor MAPK pathway
hyperactivation, which enables tumor cell growth, survival and proliferation. Therapies targeting this pathway, as well as fasting, may
result in the downregulation of this pathway alongside a reduction in AKT and mTOR activation, resulting in autophagy induction and
cell death. III) Furthermore, fasting potentiates the detrimental effects of chemotherapy, such as DNA damage, thus activating the cell
death machinery, deregulating pro- and antiapoptotic proteins, and inducing mitochondrial alterations and caspase activation, which
in turn culminates in apoptosis. 4 Fasting-mediated autophagy in cancer therapy
Antunes F et al. Fasting-mediated autophagy in cancer therapy
Antunes F et al. CLINICS 2018;73(suppl 1):e814s lung cancer cell models, as well as to the inhibition of
tumor growth in an in vivo model of lung cancer (77). How does dietary restriction modulate autophagy
and cancer therapy? The combination of IF and the multi-tyrosine kinase inhibitor
sorafenib exhibited an additive effect in inhibiting hepato-
carcinoma cell proliferation and glucose uptake as well as
downregulating the MAPK pathway and the gene expres-
sion of BIRC5, DKK1, TRIB3 and VEGF, which are com-
monly altered in hepatocarcinoma cells (72). In pancreatic
cancer, fasting increased the uptake of gemcitabine due to
enhanced levels of its transporter (hENT1), thus potentiating
cell death. In a xenograft pancreatic cancer model, fasting
cycles and gemcitabine treatment induced a reduction in
tumor growth of more than 40% (74). are required to better understand the molecular mechanisms
evoked by fasting, aiming to identify the context in which
fasting may be beneficial as an adjunct to cancer treatment. Moreover, further knowledge may also lead to the develop-
ment of novel pharmacological protocols that replicate
effects similar to those of fasting and are more suitable for
different oncologic patients. ’ ACKNOWLEDGMENTS The authors are grateful for the financial support given by the Fundac¸ão de
Amparo à Pesquisa do Estado de São Paulo (FAPESP) (08/11515-3 and
13/20073-2 by Smaili SS), Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq) and Coordenac¸ão de Aperfeic¸oamento
de Pessoal de Ensino Superior (CAPES). g
(
)
A small pilot study comprising 10 patients diagnosed with
breast, prostate, esophageal or lung cancer in advanced
stages suggested that periods of intermittent fasting before
and after chemotherapy reduces the self-reported side effects
of therapy, especially those associated with the gastrointest-
inal system, as well as weakness and fatigue. Additionally,
no negative effect on the chemotherapy response or persis-
tent weight loss was observed (84,85). In another clinical
trial, the combination of IF and platinum-based chemother-
apy promoted pathologic complete or partial radiographic
responses in the majority of patients affected by different
stages and types of tumors, such as ovarian, uterine, breast
and urothelial cancer. A reduction in leukocyte DNA damage,
in addition to decreased levels of circulating IGF-1, has also
been reported (86). Both studies established the feasibility of IF
in humans and suggested that combining IF with cytotoxic
agents in the clinical context is safe and may be well-tolerated
by patients, although this regimen may be psychologically
uncomfortable for some individuals (84-87). Currently, other
clinical trials involving IF combined with chemotherapy in
cancer patients are underway; these trials are summarized in
Table 1. The results of these trials will be essential for a better
evaluation of the clinical potential and application of this new
therapeutic strategy. ’ AUTHOR CONTRIBUTIONS Antunes F contributed to the design of the study, wrote most of the study
and edited the manuscript. Erustes AG, Costa AJ, Nascimento AC and
Trindade CB wrote the manuscript. Ureshino RP, Pereira GJ and Smaili
SS wrote, designed and coordinated the study and edited and reviewed the
final version of the manuscript. All authors reviewed and approved the final
version of the manuscript. CLINICS 2018;73(suppl 1):e814s Galluzzi L, Bravo-San Pedro JM, Levine B, Green DR, Kroemer G. Phar-
macological modulation of autophagy: therapeutic potential and persist-
ing obstacles. Nat Rev Drug Discov. 2017;16(7):487-511, http://dx.doi. org/10.1038/nrd.2017.22. g
25. Lavallard VJ, Meijer AJ, Codogno P, Gual P. Autophagy, signaling and
obesity. Pharmacol Res. 2012;66(6):513-25, http://dx.doi.org/10.1016/
j.phrs.2012.09.003. g
50. Fulda S. Autophagy in Cancer Therapy. Front Oncol. 2017;7:128, http://
dx.doi.org/10.3389/fonc.2017.00128. j p
26. Amaravadi R, Kimmelman AC, White E. Recent insights into the function
of autophagy in cancer. Genes Dev. 2016;30(17):1913-30, http://dx.doi. org/10.1101/gad.287524.116. g
51. Bincoletto C, Bechara A, Pereira GJ, Santos CP, Antunes F, Peixoto da-
Silva J, et al. Interplay between apoptosis and autophagy, a challenging
puzzle: new perspectives on antitumor chemotherapies. Chem Biol
Interact. 2013;206(2):279-88, http://dx.doi.org/10.1016/j.cbi.2013.09.018. g
g
27. Galluzzi L, Pietrocola F, Bravo-San Pedro JM, Amaravadi RK, Baehrecke
EH, Cecconi F, et al. Autophagy in malignant transformation and cancer
progression. EMBO J. 2015;34(7):856-80, http://dx.doi.org/10.15252/
embj.201490784. 52. Grasso S, Pereira GJ, Palmeira-Dos-Santos C, Calgarotto AK, Martínez-
Lacaci I, Ferragut JA, et al. Autophagy regulates Selumetinib (AZD6244)
induced-apoptosis in colorectal cancer cells. Eur J Med Chem. 2016;122:
611-8, http://dx.doi.org/10.1016/j.ejmech.2016.06.043. j
28. Levy JM, Towers CG, Thorburn A. Targeting autophagy in cancer. Nat
Rev Cancer. 2017;17(9):528-42, http://dx.doi.org/10.1038/nrc.2017.53. p
g
29. White E. Deconvoluting the context-dependent role for autophagy in
cancer. Nat Rev Cancer. 2012;12(6):401-10, http://dx.doi.org/10.1038/
nrc3262. p
g
j j
53. Palmeira dos Santos C, Pereira GJ, Barbosa CM, Jurkiewicz A, Smaili SS,
Bincoletto C. Comparative study of autophagy inhibition by 3MA and CQ
on Cytarabine-induced death of leukaemia cells. J Cancer Res Clin Oncol. 2014;140(6):909-20, http://dx.doi.org/10.1007/s00432-014-1640-4. 30. Sharifi MN, Mowers EE, Drake LE, Collier C, Chen H, Zamora M, et al. Autophagy Promotes Focal Adhesion Disassembly and Cell Motility of
Metastati Tumor Cells through the Direct Interaction of Paxillin with LC3. Cell Rep. 2016;15(8):1660-72, http://dx.doi.org/10.1016/j.celrep.2016.04.065. 54. Gigli R, Pereira GJ, Antunes F, Bechara A, Garcia DM, Spindola DG, et al. The biphosphinic paladacycle complex induces melanoma cell death
through lysosomal-mitochondrial axis modulation and impaired auto-
phagy. Eur J Med Chem. 2016;107:245-54, http://dx.doi.org/10.1016/
j.ejmech.2015.11.008. 31. Liang XH, Jackson S, Seaman M, Brown K, Kempkes B, Hibshoosh H,
et al. Induction of autophagy and inhibition of tumorigenesis by beclin 1. Nature. 1999;402(6762):672-6, http://dx.doi.org/10.1038/45257. j j
55. Liu X, Sun K, Wang H, Dai Y. Inhibition of Autophagy by Chloroquine
Enhances the Antitumor Efficacy of Sorafenib in Glioblastoma. Cell Mol
Neurobiol. 2016;36(7):1197-208,
http://dx.doi.org/10.1007/s10571-015-
0318-z. (
)
p
g
32. CLINICS 2018;73(suppl 1):e814s Qu X, Yu J, Bhagat G, Furuya N, Hibshoosh H, Troxel A, Rosen J, et al. Promotion of tumorigenesis by heterozygous disruption of the beclin 1
autophagy gene. J Clin Invest. 2003;112(12):1809-20, http://dx.doi.org/
10.1172/JCI20039. 33. Yue Z, Jin S, Yang C, Levine AJ, Heintz N. Beclin 1, an autophagy gene
essential for early embryonic development, is a haploinsufficient tumor
suppressor. Proc Natl Acad Sci U S A. 2003;100(25):15077-82, http://dx. doi.org/10.1073/pnas.2436255100. 56. Rangwala R, Leone R, Chang YC, Fecher LA, Schuchter LM, Kramer A,
et al. Phase I trial of hydroxychloroquine with dose-intense temozolomide
in patients with advanced solid tumors and melanoma. Autophagy. 2014;10(8):1369-79, http://dx.doi.org/10.4161/auto.29118. g
p
34. Laddha SV, Ganesan S, Chan CS, White E. Mutational landscape of the
essential autophagy gene BECN1 in human cancers. Mol Cancer Res. 2014;12(4):485-90, http://dx.doi.org/10.1158/1541-7786.MCR-13-0614. p
g
57. Liang B, Kong D, Liu Y, Liang N, He M, Ma S, et al. Autophagy inhibition
plays the synergetic killing roles with radiation in the multi-drug resistant
SKVCR ovarian cancer cells. Radiat Oncol. 2012;7:213, http://dx.doi.org/
10.1186/1748-717X-7-213. 35. Takamura A, Komatsu M, Hara T, Sakamoto A, Kishi C, Waguri S, et al. Autophagy-deficient mice develop multiple liver tumors. Genes Dev. 2011;25(8):795-800, http://dx.doi.org/10.1101/gad.2016211. 58. Chen Y, Li X, Guo L, Wu X, He C, Zhang S, et al. Combining radiation
with autophagy inhibition enhances suppression of tumor growth and
angiogenesis in esophageal cancer. Mol Med Rep. 2015;12(2):1645-52,
http://dx.doi.org/10.3892/mmr.2015.3623. p
g
g
36. He C, Levine B. The Beclin 1 interactome. Curr Opin Cell Biol. 2010;
22(2):140-9, http://dx.doi.org/10.1016/j.ceb.2010.01.001. p
g
59. Gewirtz DA. The Challenge of Developing Autophagy Inhibition as a
Therapeutic Strategy. Cancer Res. 2016;76(19):5610-4, http://dx.doi.org/
10.1158/0008-5472.CAN-16-0722. p
g
j
37. Mathew R, Kongara S, Beaudoin B, Karp CM, Bray K, Degenhardt K, et al. Autophagy suppresses tumor progression by limiting chromosomal
instability. Genes Dev. 2007;21(11):1367-81, http://dx.doi.org/10.1101/
gad.1545107. 60. Galluzzi L, Bravo-San Pedro JM, Demaria S, Formenti SC, Kroemer G. Activating autophagy to potentiate immunogenic chemotherapy and
radiation therapy. Nat Rev Clin Oncol. 2017;14(4):247-58, http://dx.doi. org/10.1038/nrclinonc.2016.183. g
38. Mathew R, White E. Autophagy, stress, and cancer metabolism: what
doesn’t kill you makes you stronger. Cold Spring Harb Symp Quant Biol. 2011;76:389-96, http://dx.doi.org/10.1101/sqb.2012.76.011015. g
61. Vakifahmetoglu-Norberg H, Xia HG, Yuan J. Pharmacologic agents tar-
geting autophagy. J Clin Invest. 2015;125(1):5-13, http://dx.doi.org/
10.1172/JCI73937. p
g
q
39. Lebovitz CB, Robertson AG, Goya R, Jones SJ, Morin RD, Marra MA, et al. CLINICS 2018;73(suppl 1):e814s CLINICS 2018;73(suppl 1):e814s BNIP3, and BNIP3L. Cell Death Differ. 2008;15(10):1572-81, http://dx.doi. org/10.1038/cdd.2008.84. 17. Mizushima N, Noda T, Yoshimori T, Tanaka Y, Ishii T, George MD, et al. A protein conjugation system essential for autophagy. Nature. 1998;
395(6700):395-8, http://dx.doi.org/10.1038/26506. g
43. Tasdemir E, Maiuri MC, Galluzzi L, Vitale I, Djavaheri-Mergny M,
D’Amelio M, et al. Regulation of autophagy by cytoplasmic p53. Nat Cell
Biol. 2008;10(6):676-87, http://dx.doi.org/10.1038/ncb1730. (
)
p
g
18. Ichimura Y, Kirisako T, Takao T, Satomi Y, Shimonishi Y, Ishihara N,
et al. A ubiquitin-like system mediates protein lipidation. Nature. 2000;408(6811):488-92, http://dx.doi.org/10.1038/35044114. 44. Corazzari M, Rapino F, Ciccosanti F, Giglio P, Antonioli M, Conti B, et al. Oncogenic BRAF induces chronic ER stress condition resulting in
increased basal autophagy and apoptotic resistance of cutaneous mela-
noma. Cell Death Differ. 2015;22(6):946-58, http://dx.doi.org/10.1038/
cdd.2014.183. p
g
19. Yang Z, Klionsky DJ. Mammalian autophagy: core molecular machinery
and signaling regulation. Curr Opin Cell Biol. 2010;22(2):124-31, http://
dx.doi.org/10.1016/j.ceb.2009.11.014. g
j
20. Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of
ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007;282(33):
24131-45, http://dx.doi.org/10.1074/jbc.M702824200. 45. Lock R, Kenific CM, Leidal AM, Salas E, Debnath J. Autophagy-depen-
dent production of secreted factors facilitates oncogenic RAS-driven
invasion. Cancer Discov. 2014;4(4):466-79, http://dx.doi.org/10.1158/
2159-8290.CD-13-0841. q
p
gg
g
y
p
gy
24131-45, http://dx.doi.org/10.1074/jbc.M702824200. p
g
j
21. Puissant A, Fenouille N, Auberger P. When autophagy meets cancer
through p62/SQSTM1. Am J Cancer Res. 2012;2(4):397-413. 46. Lock R, Roy S, Kenific CM, Su JS, Salas E, Ronen SM, et al. Autophagy
facilitates glycolysis during Ras-mediated oncogenic transformation. Mol Biol Cell. 2011;22(2):165-78, http://dx.doi.org/10.1091/mbc.e10-06-
0500. g
p
22. Cadwell K. Crosstalk between autophagy and inflammatory signalling
pathways: balancing defence and homeostasis. Nat Rev Immunol. 2016;
16(11):661-75, http://dx.doi.org/10.1038/nri.2016.100. 47. Guo JY, Chen HY, Mathew R, Fan J, Strohecker AM, Karsli-Uzunbas G,
et al. Activated Ras requires autophagy to maintain oxidative metabolism
and tumorigenesis. Genes Dev. 2011;25(5):460-70, http://dx.doi.org/
10.1101/gad.2016311. p
g
23. Menzies FM, Fleming A, Caricasole A, Bento CF, Andrews SP, Ashkenazi
A, et al. Autophagy and Neurodegeneration: Pathogenic Mechanisms
and Therapeutic Opportunities. Neuron. 2017;93(5):1015-34, http://dx. doi.org/10.1016/j.neuron.2017.01.022. g
48. Chen N, Karantza V. Autophagy as a therapeutic target in cancer. Cancer
Biol Ther. 2011;11(2):157-68, http://dx.doi.org/10.4161/cbt.11.2.14622. g
j
24. Bravo-San Pedro JM, Kroemer G, Galluzzi L. Autophagy and Mitophagy
in Cardiovascular Disease. Circ Res. 2017;120(11):1812-24, http://dx.doi. org/10.1161/CIRCRESAHA.117.311082. 49. ’ REFERENCES p
g
In this review, we highlighted the concepts of autophagy,
especially in relation to tumorigenesis, as well as the poten-
tial of autophagy as a therapeutic target in the treatment of
different malignancies. We also pointed out the possibility of
using dietary manipulation as an autophagy modulator as
well as a cost-effective intervention to increase therapeutic
response in the challenging oncologic arena. Furthermore,
fasting may protect normal cells from the toxicity of anti-
cancer agents, reducing side effects in patients and increasing
the detrimental effects of chemotherapy, radiotherapy and
targeted therapy on tumor cells. However, additional studies 13. Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in
autophagosome formation. Annu Rev Cell Dev Biol. 2011;27:107-32,
http://dx.doi.org/10.1146/annurev-cellbio-092910-154005. 14. Klionsky DJ, Cregg JM, Dunn WA Jr, Emr SD, Sakai Y, Sandoval IV, et al. A unified nomenclature for yeast autophagy-related genes. Dev Cell. 2003;5(4):539-45, http://dx.doi.org/10.1016/S1534-5807(03)00296-X. ( )
p
g
(
)
15. Antonioli M, Di Rienzo M, Piacentini M, Fimia GM. Emerging Mechan-
isms in Initiating and Terminating Autophagy. Trends Biochem Sci. 2017;42(1):28-41, http://dx.doi.org/10.1016/j.tibs.2016.09.008. p
g
j
16. Lin MG, Hurley JH. Structure and function of the ULK1 complex in
autophagy. Curr Opin Cell Biol. 2016;39:61-8, http://dx.doi.org/10.1016/
j.ceb.2016.02.010. 5 Fasting-mediated autophagy in cancer therapy
Antunes F et al. CLINICS 2018;73(suppl 1):e814s 65. Mattson MP, Longo VD, Harvie M. Impact of intermittent fasting on
health and disease processes. Ageing Res Rev. 2017;39:46-58, http://dx. doi.org/10.1016/j.arr.2016.10.005. cancer cells in response to fasting and improve chemotherapeutic index. Cancer
Res. 2010;70(4):1564-72,
http://dx.doi.org/10.1158/0008-5472. CAN-09-3228. cancer cells in response to fasting and improve chemotherapeutic index. Cancer
Res. 2010;70(4):1564-72,
http://dx.doi.org/10.1158/0008-5472. CAN-09-3228. 82. Sun P, Wang H, He Z, Chen X, Wu Q, Chen W, et al. Fasting inhibits
colorectal cancer growth by reducing M2 polarization of tumor-associated
macrophages. Oncotarget. 2017;8(43):74649-60, http://dx.doi.org/10.18632/
oncotarget.20301. g
j
66. Mizushima N, Yamamoto A, Matsui M, Yoshimori T, Ohsumi Y. In vivo
analysis of autophagy in response to nutrient starvation using transgenic
mice expressing a fluorescent autophagosome marker. Mol Biol Cell. 2004;15(3):1101-11, http://dx.doi.org/10.1091/mbc.e03-09-0704. g
83. Antunes F, Corazzari M, Pereira G, Fimia GM, Piacentini M, Smaili S. Fasting boosts sensitivity of human skin melanoma to cisplatin-induced
cell death. Biochem Biophys Res Commun. 2017;485(1):16-22, http://dx. doi.org/10.1016/j.bbrc.2016.09.149. 67. Simone BA, Champ CE, Rosenberg AL, Berger AC, Monti DA, Dicker AP,
et al. Selectively starving cancer cells through dietary manipulation:
methods and clinical implications. Future Oncol. 2013;9(7):959-76, http://
dx.doi.org/10.2217/fon.13.31. g
j
84. Safdie FM, Dorff T, Quinn D, Fontana L, Wei M, Lee C, et al. Fasting and
cancer treatment in humans: A case series report. Aging (Albany NY). 2009;1(12):988-1007, http://dx.doi.org/10.18632/aging.100114. g
68. Speakman JR, Mitchell SE. Caloric restriction. Mol Aspects Med. 2011;
32(3):159-221, http://dx.doi.org/10.1016/j.mam.2011.07.001. 69. Kopeina GS, Senichkin VV, Zhivotovsky B. Caloric restriction - A pro-
mising anti-cancer approach: From molecular mechanisms to clinical
trials. Biochim Biophys Acta Rev Cancer. 2017;1867(1):29-41, http://dx. doi.org/10.1016/j.bbcan.2016.11.002. p
g
g
g
85. Raffaghello L, Safdie F, Bianchi G, Dorff T, Fontana L, Longo VD. Fasting
and differential chemotherapy protection in patients. Cell Cycle. 2010;
9(22):4474-6, http://dx.doi.org/10.4161/cc.9.22.13954. (
)
p
g
86. Dorff TB, Groshen S, Garcia A, Shah M, Tsao-Wei D, Pham H, et al. Safety
and feasibility of fasting in combination with platinum-based chemo-
therapy. BMC Cancer. 2016;16:360, http://dx.doi.org/10.1186/s12885-
016-2370-6. g
j
70. Lee C, Raffaghello L, Brandhorst S, Safdie FM, Bianchi G, Martin-
Montalvo A, et al. Fasting cycles retard growth of tumors and sensitize
a range of cancer cell types to chemotherapy. Sci Transl Med. 2012;4(124):
124ra27, http://dx.doi.org/10.1126/scitranslmed.3003293. 71. Bianchi G, Martella R, Ravera S, Marini C, Capitanio S, Orengo A, et al. Fasting induces anti-Warburg effect that increases respiration but reduces
ATP-synthesis to promote apoptosis in colon cancer models. Oncotarget. 2015;6(14):11806-19, http://dx.doi.org/10.18632/oncotarget.3688. 87. Fasting-mediated autophagy in cancer therapy
Antunes F et al. Michalsen A, Hoffmann B, Moebus S, Bäcker M, Langhorst J, Dobos GJ. Incorporation of fasting therapy in an integrative medicine ward: eva-
luation of outcome, safety, and effects on lifestyle adherence in a large
prospective cohort study. J Altern Complement Med. 2005;11(4):601-7,
http://dx.doi.org/10.1089/acm.2005.11.601. p
g
g
72. Lo Re O, Panebianco C, Porto S, Cervi C, Rappa F, Di Biase S, et al. Fasting
inhibits hepatic stellate cells activation and potentiates anti-cancer activity
of Sorafenib in hepatocellular cancer cells. J Cell Physiol. 2018;233(2):1202-
12, http://dx.doi.org/10.1002/jcp.25987. 88. Madeo F, Pietrocola F, Eisenberg T, Kroemer G. Caloric restriction
mimetics: towards a molecular definition. Nat Rev Drug Discov. 2014;
13(10):727-40, http://dx.doi.org/10.1038/nrd4391. p
g
89. Dwarakanath B, Jain V. Targeting glucose metabolism with 2-deoxy-D-
glucose for improving cancer therapy. Future Oncol. 2009;5(5):581-5,
http://dx.doi.org/10.2217/fon.09.44. p
g
j p
73. Pietrocola F, Pol J, Vacchelli E, Rao S, Enot DP, Baracco EE, et al. Caloric
Restriction Mimetics Enhance Anticancer Immunosurveillance. Cancer
Cell. 2016;30(1):147-60, http://dx.doi.org/10.1016/j.ccell.2016.05.016. ( )
p
g
j
74. D’Aronzo M, Vinciguerra M, Mazza T, Panebianco C, Saracino C, Pereira
SP, et al. Fasting cycles potentiate the efficacy of gemcitabine treatment in
in vitro and in vivo pancreatic cancer models. Oncotarget. 2015;6(21):
18545-57, http://dx.doi.org/10.18632/oncotarget.4186. p
g
90. Miranda VC, Braghiroli MI, Faria LD, Bariani G, Alex A, Bezerra Neto JE,
et al. Phase 2 Trial of Metformin Combined With 5-Fluorouracil in Patients
With Refractory Metastatic Colorectal Cancer. Clin Colorectal Cancer. 2016;15(4):321-328.e1, http://dx.doi.org/10.1016/j.clcc.2016.04.011. p
g
g
75. Raffaghello L, Lee C, Safdie FM, Wei M, Madia F, Bianchi G, et al. Star-
vation-dependent differential stress resistance protects normal but not
cancer cells against high-dose chemotherapy. Proc Natl Acad Sci U S A. 2008;105(24):8215-20, http://dx.doi.org/10.1073/pnas.0708100105. p
g
j
91. Liu Y, He C, Huang X. Metformin partially reverses the carboplatin-
resistance in NSCLC by inhibiting glucose metabolism. Oncotarget. 2017;
8(43):75206-16, http://dx.doi.org/10.18632/oncotarget.20663. p
g
g
92. Chiarini F, Evangelisti C, McCubrey JA, Martelli AM. Current treatment
strategies for inhibiting mTOR in cancer. Trends Pharmacol Sci. 2015;
36(2):124-35, http://dx.doi.org/10.1016/j.tips.2014.11.004. p
g
p
76. Safdie F, Brandhorst S, Wei M, Wang W, Lee C, Hwang S, et al. Fasting
enhances the response of glioma to chemo- and radiotherapy. PLoS One. 2012;7(9):e44603, http://dx.doi.org/10.1371/journal.pone.0044603. p
g
j
p
93. Xu J, Liu D, Niu H, Zhu G, Xu Y, Ye D, et al. Resveratrol reverses
Doxorubicin resistance by inhibiting epithelial-mesenchymal transition
(EMT) through modulating PTEN/Akt signaling pathway in gastric
cancer. CLINICS 2018;73(suppl 1):e814s Cross-cancer profiling of molecular alterations within the human auto-
phagy interaction network. Autophagy. 2015;11(9):1668-87, http://dx.doi. org/10.1080/15548627.2015.1067362. 62. Ha J, Kim J. Novel pharmacological modulators of autophagy: an upda-
ted patent review (2012-2015). Expert Opin Ther Pat. 2016;26(11):1273-89,
http://dx.doi.org/10.1080/13543776.2016.1217996. g
40. White E. The role for autophagy in cancer. J Clin Invest. 2015;125(1):42-6,
http://dx.doi.org/10.1172/JCI73941. p
g
63. O’Flanagan CH, Smith LA, McDonell SB, Hursting SD. When less may be
more: calorie restriction and response to cancer therapy. BMC Med. 2017;
15(1):106, http://dx.doi.org/10.1186/s12916-017-0873-x. p
g
41. Degenhardt K, Mathew R, Beaudoin B, Bray K, Anderson D, Chen G,
et al. Autophagy promotes tumor cell survival and restricts necrosis,
inflammation, and tumorigenesis. Cancer Cell. 2006;10(1):51-64, http://
dx.doi.org/10.1016/j.ccr.2006.06.001. p
g
64. Longo VD, Mattson MP. Fasting: molecular mechanisms and clinical
applications. Cell Metab. 2014;19(2):181-92, http://dx.doi.org/10.1016/
j.cmet.2013.12.008. g
j
42. Papandreou I, Lim AL, Laderoute K, Denko NC. Hypoxia signals
autophagy in tumor cells via AMPK activity, independent of HIF-1, 6 Fasting-mediated autophagy in cancer therapy
Antunes F et al. J Exp Clin Cancer Res. 2017;36(1):19, http://dx.doi.org/10.1186/
s13046-016-0487-8. p
g
j
p
77. Caffa I, D’Agostino V, Damonte P, Soncini D, Cea M, Monacelli F, et al. Fasting potentiates the anticancer activity of tyrosine kinase inhibitors by
strengthening MAPK signaling inhibition. Oncotarget. 2015;6(14):11820-32,
http://dx.doi.org/10.18632/oncotarget.3689. 94. Wang C, Ruan P, Zhao Y, Li X, Wang J, Wu X, et al. Spermidine/spermine
N1-acetyltransferase regulates cell growth and metastasis via AKT/
b-catenin signaling pathways in hepatocellular and colorectal carcinoma
cells. Oncotarget. 2017;8(1):1092-109. p
g
g
78. Saleh AD, Simone BA, Palazzo J, Savage JE, Sano Y, Dan T, et al. Caloric
restriction augments radiation efficacy in breast cancer. Cell Cycle. 2013;
12(12):1955-63, http://dx.doi.org/10.4161/cc.25016. p
g
79. Di Biase S, Shim HS, Kim KH, Vinciguerra M, Rappa F, Wei M, et al. Fasting regulates EGR1 and protects from glucose- and dexamethasone-
dependent sensitization to chemotherapy. PLoS Biol. 2017;15(3):e2001951,
http://dx.doi.org/10.1371/journal.pbio.2001951. g
95. Mou S, Zhou Z, He Y, Liu F, Gong L. Curcumin inhibits cell proliferation
and promotes apoptosis of laryngeal cancer cells through Bcl-2 and PI3K/
Akt, and by upregulating miR-15a. Oncol Lett. 2017;14(4):4937-42, http://
dx.doi.org/10.3892/ol.2017.6739. 80. Tinkum KL, Stemler KM, White LS, Loza AJ, Jeter-Jones S, Michalski BM,
et al. Fasting protects mice from lethal DNA damage by promoting small
intestinal epithelial stem cell survival. Proc Natl Acad Sci U S A. 2015;
112(51):E7148-54, http://dx.doi.org/10.1073/pnas.1509249112. g
96. de Groot S, Vreeswijk MP, Welters MJ, Gravesteijn G, Boei JJ, Jochems A,
et al. The effects of short-term fasting on tolerance to (neo) adjuvant
chemotherapy in HER2-negative breast cancer patients: a randomized
pilot study. BMC Cancer. 2015;15:652, http://dx.doi.org/10.1186/s12885-
015-1663-5. p
g
p
81. Lee C, Safdie FM, Raffaghello L, Wei M, Madia F, Parrella E, et al. Reduced levels of IGF-I mediate differential protection of normal and 7
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https://zenodo.org/records/3949508/files/Development%20of%20typical%20state%20software%20patterns%20for%20Cortex%C2%ADM%20microcontrollers%20in%20real%20time.pdf
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Development of typical "state" software patterns for CortexM microcontrollers in real time
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Eastern-European journal of enterprise technologies
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cc-by
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Information and controlling system Information and controlling system UDC 004.451:004.354-022
DOI: 10.15587/1729-4061.2020.205377 UDC 004.451:004.354-022
DOI: 10.15587/1729-4061.2020.205377 UDC 004.451:004.354-022 Вiдомi технiчнi системи реального часу (real-time technical
systems RTTS), вимагають високої швидкостi програмних
рiшень. Крiм того, для них потрiбно забезпечити унiфiкацiю
вихiдного коду, якiсть супроводу програмного забезпечення
та математичне моделювання. Все це потрiбно реалiзува
ти з вiдносно невисокою вартiстю програмного i апаратно
го рiшення. Апаратну частину можна реалiзувати на основi
розповсюджених мiкроконтролерiв архiтектури Cortex-M DEVELOPMENT OF
TYPICAL "STATE"
SOFTWARE PATTERNS
FOR CORTEX-M
MICROCONTROLLERS
IN REAL TIME розповсюджених мiкроконтролерiв архiтектури Cortex M. Програмна частина даних мiкроконтролерiв може бути
реалiзована на основi операцiйної системи реального часу
(ОСРЧ) (real-time operation systems RTOS). В ходi дослiд
жень було виявлено два недолiки. Першим є те, що викори
стання ОСРЧ призводить до обмеження швидкостi. Другим
недолiком є труднощi унiфiкацiї, пiдтримки вихiдного коду
(Source)i математичного моделювання. Для усунення недолiкiв розробленi типовi програмнi
патерни Стан для допомiжного контролера у колi виконав
чих механiзмiв або датчикiв на основi мiкроконтролерiв архi
тектури Сortex-М в режимi реального часу, в процедурнiй
парадигмi. Особливiстю таких патернiв є висока швидкiсть
програмного рiшення (software)у порiвняннi з рiшеннями на
основi ОСРЧ. Copyright © 2020, P. Katin, V. Chmelov, V. Shemaev
This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0)
P . K a t i n
PhD, Associate Professor*
E-mail: p.katin@kpi.ua
V . C h m e l o v
PhD, Associate Professor**
E-mail: viacheslavchmelov@gmail.com
V . S h e m a e v
Doctor Military Sciences, Professor*
Е-mail: shemaev@niss.gov.ua
*Department of Automation and Control
in Technical Systems***
**Department of Radio Engineering Devices
and Systems***
***National Technical University of Ukraine
"Igor Sikorsky Kyiv Polytechnic Institute"
Peremohy ave., 37, Kyiv, Ukraine, 03056 Copyright © 2020, P. Katin, V. Chmelov, V. Shemaev
This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0)
P . K a t i n
PhD, Associate Professor*
E-mail: p.katin@kpi.ua
V . C h m e l o v
PhD, Associate Professor**
E-mail: viacheslavchmelov@gmail.com
V . S h e m a e v
Doctor Military Sciences, Professor*
Е-mail: shemaev@niss.gov.ua
*Department of Automation and Control
in Technical Systems***
**Department of Radio Engineering Devices
and Systems***
***National Technical University of Ukraine
"Igor Sikorsky Kyiv Polytechnic Institute"
Peremohy ave., 37, Kyiv, Ukraine, 03056 Розробленi патерни дозволяють унiфiкувати вихiдний
код (Source) для мiкроконтролерiв архiтектури Сortex-М
рiзних виробникiв, покращити супроводження програмного
забезпечення (software)i адаптувати його до математичної
моделi кiнцевого автомата (mathematical model finite state
machine). Результати пройшли випробування на мiкрокон
тролерi STM32F103 з використанням бiблiотеки Cortex
microcontroller software interface system (CMSIS). Це дозво
ляє поширити отримане рiшення на МК iнших виробникiв,
що пiдтверджує практичну цiннiсть розроблених патернiв щ
р
у
р
у ц
р
р
р
Ключовi слова: реальний час, керуючий контролер, кiнце
вий автомат, мiкроконтролер Cortex-M, шаблон Стан The European aviation standard ED-12B is analogous to
DO-178B. There are many options to categorize software for micro
controllers. DEVELOPMENT OF
TYPICAL "STATE"
SOFTWARE PATTERNS
FOR CORTEX-M
MICROCONTROLLERS
IN REAL TIME We shall use one of the variants for the informal
classification of real-time operating systems (RTOS) for mi
crocontrollers (MC). It was proposed by the Massachusetts
Institute of Technology (MIT). This classification takes
into consideration the software for real-time technical
systems (RTTS) based on microcontrollers and micro
processors [1, 2]. According to this classification, there are
4 classes of hard-real time operating systems: Many modern real-time software and hardware technical
systems (RTTS) are built on the basis of a master controller. More complex systems typically consist of a main con
troller based on the Cortex-A (Cortex-M) architecture
microcontrollers and auxiliary controllers (based on the
Cortex-M MCs or simpler 8-, 16-bit MCs). In most cases,
the auxiliary controller in a circuit of actuator and sensor
controllers (ASCs) may be subject to higher requirements
for the speed of computation and the unification of MCs
from different manufacturers. The software solution is
subject to requirements for the ease of source code main
tenance. In addition, the issue of mathematical modeling
is important. g y
– the pattern template based on Polled Loop Systems; – the pattern template of software based on the micro
controller interruption system (Interrupt Driven); – the simple patterns of real-time operating systems based
on a multi-tasking core, such as SafeRTOS, the IEC 61508
standard-certified, μC/OS-II, RTXC Quadr, and others; – the simple patterns of real-time operating systems based
on a multi-tasking core, such as SafeRTOS, the IEC 61508
standard-certified, μC/OS-II, RTXC Quadr, and others; At present, one of the acceptable solutions for the cre
ation of ASC hardware is the Cortex-M architecture MCs
due to their relatively high power and low price. The price of
these 32-bit Cortex-M architecture microcontrollers is com
parable to some 8-bit MCs for similar purposes while and
the speed of operation is much greater. Using the Cortex-M
architecture makes it possible to unify the source code for
the MCs from different manufacturers. – a full-featured operating system (Full Featured RTOS)
maintaining the POSIX standard (portable operating sys
tem interface). For a given option, there are typical RTOS
standards such as POSIX 1003.1a, the POSIX 1003.1b stan
dard, the POSIX 1003.1c standard. Aviation engineering
employs the RTOS of the DO-178B, ARINC-653 standards. – a full-featured operating system (Full Featured RTOS)
maintaining the POSIX standard (portable operating sys
tem interface). DEVELOPMENT OF
TYPICAL "STATE"
SOFTWARE PATTERNS
FOR CORTEX-M
MICROCONTROLLERS
IN REAL TIME The solution was obtained
on the basis of a Cortex-A MC. At the same time, the issue
of achieving an acceptable cost of the ASC prototype was
not resolved. This is due to the high cost of the Cortex-M
architecture MCs. The infrastructure management solutions built on In
ternet technology are outlined in [8]. The implementation
of high-speed software remains a problematic issue. This is
due to that Internet technologies are a limiting factor in a
hard-real-time mode. One can achieve greater performance speed of the ASC
software, compared to a multi-tasking RTOS, by using the
Polled Loop Systems or on the basis of the microcontroller
Interrupt Driven system [1, 2]. However, developing the
software without patterns makes it difficult to unify, to
maintain the code, and to model mathematically. Therefore,
it is a relevant task to develop typical State design patterns
for the Cortex-M architecture MCs to address the above
shortcomings related to unification, maintenance, and math
ematical modeling. The software that makes it possible to reach high speeds
for image processing is described in [9]. The authors do not
address the mathematical notation and software for for
malizing and switching the RTTS states within the State
pattern. A solution to the problem is to develop typical State
templates (patterns) for the Cortex-M architecture MCs. Work [10] reveals the implementation of the software
based on the State pattern in the object-oriented program
ming (OOP) variant. The downside of this solution is the
redundant code and computational requirements, which is
not always acceptable for ASC. Therefore, the possibility of
eliminating the above flaw is to develop a pattern in a sim
pler, procedural version. The Cortex-M architecture microcontrollers, for which
patterns are designed, are produced by many manufacturers
and are now widely used in equipment. Using the Universal
Cortex-Microcontroller Software Interface System (CMSIS)
libraries makes it possible to adapt the obtained patterns to
a large number of Cortex-M architecture microcontrollers
from many manufacturers. That makes it possible to apply
the resulting solution for a broad range of Cortex-M ar
chitecture MCs and thus ensure unification. Therefore, it
seems expedient to explore a given field of research as the
developed patterns could be widely used in practice to cre
ate the ASC software libraries based on a wide range of the
Cortex-M architecture MCs. DEVELOPMENT OF
TYPICAL "STATE"
SOFTWARE PATTERNS
FOR CORTEX-M
MICROCONTROLLERS
IN REAL TIME For a given option, there are typical RTOS
standards such as POSIX 1003.1a, the POSIX 1003.1b stan
dard, the POSIX 1003.1c standard. Aviation engineering
employs the RTOS of the DO-178B, ARINC-653 standards. 29 3/9 ( 105 ) 2020 3/9 ( 105 ) 2020 The ASC software can be implemented on the basis of
the first three classes of RTOS, namely, based on the Polled
Loop Systems, based on the Interrupt Driven microcon
troller system, or on the basis of simple real-time operating
systems based on a multi-tasking core [1, 2]. The use of a
full-featured RTOS [1, 2] for ASC is not acceptable due to
additional unreasonable costs. Study [4] reports the results of achieving the maximum
switching speed by using an 8-bit microcontroller. However,
such hardware implies the difficulty of unifying the source
code of the software. The reason for this is that the archi
tecture of 8-bit MCs is typically not universal for several
manufacturing firms. The general results of RTTS testing based on high-speed
controllers are described in [5]. At the same time, there are
no specific implementations of the software and hardware of
RTTS controllers. We shall consider the pros and cons of using a multi-
tasking-core-based RTOS as a base for the ASC software
compared to other solutions [1, 2]. The advantage of a multi-
tasking-core-based RTOS is the relative simplicity of soft
ware development and project support. The results of the development of a controller using the
Cortex-M architecture for scalable solutions are reported
in [6]. However, the issue of mathematical modeling remains
unresolved, which complicates the possibility of mathemati
cal analysis of the ASC software. At the same time, we can note two drawbacks of the ASC
software based on the RTOS that maintains multi-tasking. The first is the relative speed limit of the software compared
to solutions based on the Polled Loop Systems or based on
the Microcontroller Interrupt Driven system. The second
drawback is the need to study the source code of the RTOS
for the presence of hidden errors, to test the RTOS for sys
tems requiring great reliability (aircraft, missile technology,
medicine, etc.). Relatively simple solutions based on the
Polled Loop Systems or the Interrupt Driven systems are
easier to find hidden programming errors. A system of food production by evaporating the raw ma
terials was implemented in [7]. DEVELOPMENT OF
TYPICAL "STATE"
SOFTWARE PATTERNS
FOR CORTEX-M
MICROCONTROLLERS
IN REAL TIME A study of the software implementation of the State pat
tern in OOP for low-power microcontrollers in a generalized
form was conducted in [11]. At the same time, the problem
of universalization of the received solutions for a wide range
of MCs was not solved. A solution to this problem at present
is the development of the State pattern for the universal
Cortex-M architecture MCs. A study of the software implementation of the finite
state machine in OOP was carried out in [12]. The issues of
the mathematical modeling of the software remained unre
solved. One solution is to bring the developed pattern to the
mathematical model of the finite state machine. 4. 1. The hardware of the Cortex-M-based high-speed
controller prototype 4. 1. The hardware of the Cortex-M-based high-speed
controller prototype Chapter 2 shows that there are options for building the
RTTS prototypes based on a single MC. The generalized
diagram of such a system is shown in Fig. 1. It depicts the
software and hardware components of a real-time technical
system. It can be implemented on the basis of MC of any
architecture and power, depending on the tasks. This can
employ a complex control system that requires the power of
Cortex-A MC, for example, to control a video camera. A variant of solving the tasks related to the software of
the ASC prototype, outlined in [9‒17], concerning the issues
of increasing the software speed, unification, maintenance,
and mathematical modeling, is the development of typical
software State templates (patterns) for the Cortex-M ar
chitecture MCs. These patterns can be implemented in the
Polled Loop System variant or through the microcontroller
Interrupt Driven system. This system includes sensors, actuators, it enables com
munication with a personal computer. The software shown
in Fig. 1 implies a procedural paradigm. 2. Literature review and problem statement Materials and methods for implementing the hardware
of an auxiliary high-speed controller 4. Materials and methods for implementing the hardware
of an auxiliary high-speed controller 3. The aim and objectives of the study The more complex RTTSs include actuators, sensors,
information transfer systems, etc. The most generalized
scheme of such RTTSs is shown in Fig. 2. Unlike Fig. 1,
it has an auxiliary ASC (there may be several of them). It
manages auxiliary systems and can be built on the basis of
the Cortex-M architecture MCs, or the simpler ones, 8-,
16-bit MCs of other architecture. A given ASC is designed
to process sensor signals and control actuators and subsys
tems. All these subsystems and elements imply the increased
performance speed, so there are higher requirements for
ASC in terms of the software speed. The ASC controller is
almost autonomous but can receive control signals from the
main controller. The aim of this study is to develop a software solution to
increase the speed of the ASC prototype compared to RTOS. At the same time, the result to be obtained should ensure
the unification of the source code, facilitate the maintenance
process, as well as the mathematical modeling of the software. To accomplish the aim, the following tasks have been set: – to develop and implement a typical State software pat
tern for ASC based on Cortex-M in a procedural paradigm,
maximally adapted for the mathematical model of the finite
state machine; – to analyze the shortcomings of a typical pattern; in or
der to eliminate them, design a State pattern for ASC based RTOS System controller
Video
camera
Sensor 1
Sensor
adapter 1
Sensor 2
Sensor
adapter 2
Sensor N
Sensor
adapter N
Microphone
Personal computer
Control gear 1
Control
adapter 1
Control
gear N
Control
adapter 1
Control adapter
N
Control gear 2
Microcontroller
Operating system
Sensor OS functions
Control gear functions
Functions for personal computer
interaction
Feedback 1
Feedback 2
Fig. 1. A generalized RTTS scheme based on a single controller
Fig. 2. 4. Materials and methods for implementing the hardware
of an auxiliary high-speed controller One of the solutions to the above issues concerning the
hardware of the ASC prototype, outlined in [3‒8] is the use
of relatively inexpensive general-purpose Cortex-M archi
tecture MCs. 4. 1. The hardware of the Cortex-M-based high-speed
controller prototype 2. Literature review and problem statement It is shown in [1, 2] that in most cases a real-time operat
ing system from any of the 4 classes must be described along
with the hardware and cannot be considered separately
from the physical environment and the processes it manages. The authors revealed the hardware and software problems
related to increasing the speed of software, standardizing,
maintaining, and mathematical modeling. The most high-speed version of the State pattern hardware
implementation is offered in [13]. However, at the highest po
tential speed, a given solution cannot be quickly reprogrammed
and reconfigured, which is its main drawback. The most ac
ceptable option is to develop a software pattern for MC. The mathematical theory of the description of the finite
state machine is set out in [14] but there are no software
examples, nor any connection to practical tasks. Paper [3] explores the possibility of increasing the speed of
the software by increasing the number of MC computational
cores. At the same time, the task of increasing the speed of
performance at minimal cost remains unresolved. This is due
to that the cost of multi-core MCs is much higher than the
cost of single-core MCs. An option to solve this problem is to
use a relatively inexpensive and universal MC architecture. The general descriptions of the finite state machine soft
ware templates are outlined in [15]. However, there are no
examples of practical software solutions. The State patterns designs and their software implemen
tation were developed in [16]. In this case, the solutions are 30 Information and controlling system given in the OOP version, which entails the shortcomings
specified for [11]. A solution to this problem is to develop a
universal State pattern for a wide range of MCs. on Cortex-M in the form of a linked list (a typical construct
of the C language), to maximally adapt the pattern for the
mathematical model of the finite state machine; A solution using RTOS is proposed in [17]. At the same
time, there is a potential drawback ‒ reducing the software
speed by switching the RTOS context. To address this
shortcoming, one can use solutions based on the Polled Loop
Systems or based on the microcontroller Interrupt Driven
system. – to objectively assess the speed of the software based on
the developed patterns compared to a multi-tasking-core-
based RTOS [1, 2]. 4. 3. The aim and objectives of the study RTTS scheme with the main and auxiliary ASC microcontroller
RTOS System controller
Video
camera
Sensor 1
Sensor
adapter 1
Sensor 2
Sensor N
Microphone
Personal сomputer
Control gear
1
Control gear 1
Control
gear N
Control gear 1
Control adapter
N
Control gear 2
Microcontroller CORTEX - A
Soft real-time operating system
Sensor OS functions
Control gear functions
Functions for personal computer interaction
Microcontroller
CORTEX-M
Нard real-time
operating system
Feedback 1
Feedback 2
Feedback 3
Sensor
adapter 2
Sensor
adapter 1 RTOS System controller
Video
camera
Sensor 1
Sensor
adapter 1
Sensor 2
Sensor
adapter 2
Sensor N
Sensor
adapter N
Microphone
Personal computer
Control gear 1
Control
adapter 1
Control
gear N
Control
adapter 1
Control adapter
N
Control gear 2
Microcontroller
Operating system
Sensor OS functions
Control gear functions
Functions for personal computer
interaction
Feedback 1
Feedback 2
Fig 1 A generalized RTTS scheme based on a single controller Fig. 1. A generalized RTTS scheme based on a single controller Fig. 1. A generalized RTTS scheme based on a single controller
Fig. 2. RTTS scheme with the main and auxiliary ASC microcontroller
RTOS System controller
Video
camera
Sensor 1
Sensor
adapter 1
Sensor 2
Sensor N
Microphone
Personal сomputer
Control gear
1
Control gear 1
Control
gear N
Control gear 1
Control adapter
N
Control gear 2
Microcontroller CORTEX - A
Soft real-time operating system
Sensor OS functions
Control gear functions
Functions for personal computer interaction
Microcontroller
CORTEX-M
Нard real-time
operating system
Feedback 1
Feedback 2
Feedback 3
Sensor
adapter 2
Sensor
adapter 1 g
g
g
Fig. 2. RTTS scheme with the main and auxiliary ASC microcontroller
RTOS System controller
Video
camera
Sensor 1
Sensor
adapter 1
Sensor 2
Sensor N
Microphone
Personal сomputer
Control gear
1
Control gear 1
Control
gear N
Control gear 1
Control adapter
N
Control gear 2
Microcontroller CORTEX - A
Soft real-time operating system
Sensor OS functions
Control gear functions
Functions for personal computer interaction
Microcontroller
CORTEX-M
Нard real-time
operating system
Feedback 1
Feedback 2
Feedback 3
Sensor
adapter 2
Sensor
adapter 1 Video
camera Feedback 1 Fig. 2. 3. The aim and objectives of the study RTTS scheme with the main and auxiliary ASC microcontroller 31 3/9 ( 105 ) 2020 Eastern-European Journal of Enterprise Technologies ISSN 1729-3774 To compare other variants of the finite state machines,
we shall write (1) and (2) in the form of a classic representa
tion as a totality The hardware (material part) of ASC can utilize low-cost
Cortex-M, such as the STM32F40x or STM32F10x series. MCs from other manufacturers are also possible. These
MCs demonstrate the high performance speed and are less
costly even compared to 16- or 8-bit MCs. At the same
time, the practice of programming the Cortex-M microcon
trollers in the C language is much easier than that of 16- or
8-bit MCs. The RTTS software in Fig. 2 includes the main
controller’s software and the high-speed ASC software. The developed typical State software patterns are designed
exactly for ASC. (
)
(
)
(
)
1
1
0
,
,
,
,
,
,
. i
i
i+
i
f x
z
x
,z
+
ϕ
X Y Z
Z
(3) (3) Thus, (3) includes all the classic elements of the mathe
matical model of a finite state machine. A given formula pro
vides an opportunity to implement a mathematical model in
the form of a State software pattern for ASC in a procedural
paradigm in the classic version of the Polled Loop Systems
or based on the microcontroller Interrupt Driven system
according to the classification given in [1, 2]. As previously stated, the cost of the Cortex-M MCs is ap
proaching the cost of low-power microcontrollers. Therefore,
the ASC hardware can be built on the basis of the Cortex-M
architecture MCs. The software for ASC can be built on the
basis of the State template or based on a multitasking RTOS
according to the classification given in [1, 2]. The Full Fea
tured RTOS operating systems [1, 2] based on the Cortex-M
MCs are not used to build ASC due to unreasonable cost
increases. 4. 2. A mathematical model for formalizing the State
pattern There are several options for describing the model of
the finite state machine. The basic description of the finite
state machine chosen for the development of a State design
pattern was the variant proposed in [19] in the form of sets
and recurrent formulae. This option is more appropriate to
describe nearly implemented software. To improve the readability of the obtained results, the
typical formatting of the C programming language was slight
ly modified. During the development, we identified a global
CurrentState variable. It stores the current value of the ASC
state. Thus, below is the classical software implementation of
mathematical model (3). It is implemented in the procedural
variant. The developed header file that demonstrates the
idea of a typical State software pattern for ASC based on
Cortex-M in the procedural paradigm is shown further. The finite state machine is set by the following recurrent
formulae: (
)
(
)
+
+
+
+
=
= φ
1
1
1
1
,
,
;
,
,
,
i
i
i
i
i
i
i
i
z
f x
z y
y
x
z y
(1) (
)
(
)
+
+
+
+
=
= φ
1
1
1
1
,
,
;
,
,
,
i
i
i
i
i
i
i
i
z
f x
z y
y
x
z y (1) where the sequence х0, х1, х2,…, хn, using the
terminology from [19], forms the input word
and can be considered as a set X; the sequence
of values z0, z1, z2,…, zk, using the terminology
from [19], forms the word of states and can be
considered as a set of Z states; the sequence of
values y0, y1, y2,…, yl, using the terminology
from [19], forms an output word and can be con
sidered as a set of outputs Y. The pair (х0, y0)
is termed the original state for the finite state
machine. 5. 1. Software implementation of the typical State
software pattern in the form of the software for ASC in
the procedural paradigm In the development of the patterns, the standard 32-bit
microcontroller STM32F103 was used as the ASC hardware. The clock frequency of the microcontroller was 72 MHz. Power voltage was 3.3 V. The indoor temperature during
testing was within 20‒25 °C. The more precise characteris
tics of the microcontroller are given in [18]. The first step implies the software that represents a
typical State software pattern for the ACS based on Cortex-
M-based in the procedural paradigm of the classic variant
of the polled loop in real time. A special feature is that it is
maximally adapted to the mathematical model of a finite
state machine (3). The software development method is to use the Keil en
vironment, the CMSIS typical libraries, and to evaluate the
resulting solutions at debugging. Next, we show the result of the development of a header
file for the software, which demonstrates the presence of all
three sets in formula (3). A given file demonstrates exclu
sively the idea of the developed State software pattern in the
procedural paradigm, in the variant of Polled Loop Systems
in accordance with the classification of RTOS given in [1, 2]. Although STM32F103 is not the most powerful MC,
the software tested on STM32F103 can be easily adapted
to similar and improved MCs. The software can be stan
dardized for the Cortex-M architecture MCs and for other
vendors through the CMSIS libraries. The pattern can be implemented in the peripheral inter
ruption function or a system timer of the Cortex-M series,
that is, in the microcontroller Interrupt Driven variant or in
a polled loop variant [1, 2]. A given solution makes it possible
to reach the maximum speed of computations for ASC as it
does not contain additional software delays, caused by the
operation of the RTOS core elements. 5. Results of the development of State software pattern
for a controller 5. 1. Software implementation of the typical State
software pattern in the form of the software for ASC in
the procedural paradigm 4. 2. A mathematical model for formalizing the State
pattern To form the set of output signals, the structure struct
Y_OutSignal is used, whose elements are the indicators on the
function, which corresponds to the set of output signals (3). The functions void FSM_simple(void) and void FSM_
switch(void) correspond to the transition functions of the
mathematical model of a finite state machine (3). #include “stm32f10x.h”
#include “stm32f10x_tim.h”
#include “stm32f10x_gpio.h”
#include “stm32f10x_rcc.h” #include “stm32f10x.h”
#include “stm32f10x_tim.h”
#include “stm32f10x_gpio.h”
#include “stm32f10x_rcc.h” If necessary, a developer can increase the
number of functions and states to the required
value. Development practice has shown that the
use of enumerators is convenient for a relatively
small number of states. The implementation file
and the test run variant file can be built inde
pendently using a well-known model solution. void init_state_structsPK(void);
void init_state_structsPK_better(void);
void init_state_structs(void); Thus, a given header file demonstrates the
developed typical State software pattern for an
ASC based on Cortex-M in the procedural para
digm in the variant of a polled loop system. The
solution is maximally close to the mathematical
model of the finite state machine. void _FSM_linked(void);
void FSM_to_step_PK(void); enum Z_State
{// state
STATE_S = ‘*’,STATE_RES = ‘#’,STATE_0 = ‘0’,STATE_9 = ‘9’,
STATE_8 = ‘8’,STATE_7 = ‘7’,STATE_6 = ‘6’,STATE_5 = ‘5’,
STATE_4 = ‘4’, STATE_3 = ‘3’, STATE_2 = ‘2’,STATE_1 = ‘1’
}; 4. 2. A mathematical model for formalizing the State
pattern struct Y_OutSignal
{// output signal
char (*ptr_state_0)(void);
char (*ptr_state_1)(void);
char (*ptr_state_2)(void);
} O
Si
l
{h
dl
0 h struct Y_OutSignal
{// output signal
char (*ptr_state_0)(void);
char (*ptr_state_1)(void);
char (*ptr_state_2)(void);
} O tSi
l
{h
dl
t t
0 h
dl
t t
1 h
dl
t t
2} struct Y_OutSignal
{// output signal
char (*ptr_state_0)(void);
char (*ptr_state_1)(void);
char (*ptr_state_2)(void);
} O
S
l
{h
dl
0 The source code demonstrates only the
very idea of using a linked list in the de
velopment of a typical State pattern in the
form of software for ASC based on Cor
tex-M. Therefore, the software is as simpli
fied as possible. In the developed example,
the transition from state to state is carried
out in sync, without a random input signal. This is done with the aim of explaining the
idea of a typical State pattern in the form of
software for ASC based on Cortex-M in the
form of a linked list (the typical construct of
the C language). } OutSignal= {handle_state_0,handle_state_1, handle_state_2}; } OutSignal= {handle_state_0,handle_state_1, handle_state_2}; char handle_state_0(void); char (*ptr_state_0)(void);
char handle_state_1(void); char (*ptr_state_1)(void);
char handle_state_2(void); char (*ptr_state_2)(void); char handle_state_0(void); char (*ptr_state_0)(void); char handle_state_1(void); char (*ptr_state_1)(void); char handle_state_2(void); char (*ptr_state_2)(void); char handle_state_2(void); char (*ptr_state_2)(void); void init_state(enum Z_States INIT_STATE,enum X_InputSignal _0_INP);
uint32_t _FSM_simple(void);
void _FSM_switch(void);
enum X_InputSignal input_from_external(void); In the header file, we use the enumerator enum Z_State
to describe the set of states, forming the finite set of the
internal ASC states, which corresponds to (3). If necessary,
a developer can increase this number to the required value. The example includes a modification of the model for
matting of the C language to improve the readability of the
software solution. The software was tested for the microcon
troller stm32f103. The enumerator enum X_InputSignal is also used to
describe the set of input signals, which corresponds to the
set of inputs (3). As one can see from the header file below, the code
contains all the elements of the finite state machine (3). In
this variant, the sets are implemented as structures, which
slightly increases the volume of the source code. The rela
tionship between the solution obtained in a given header file
and mathematical model (3) is detailed in chapter 5. 1, with
minor changes. 4. 2. A mathematical model for formalizing the State
pattern If functions (1) are not dependent
on Y [19], (1) is transformed to the form where the sequence х0, х1, х2,…, хn, using the
terminology from [19], forms the input word
and can be considered as a set X; the sequence
of values z0, z1, z2,…, zk, using the terminology
from [19], forms the word of states and can be
considered as a set of Z states; the sequence of
values y0, y1, y2,…, yl, using the terminology
from [19], forms an output word and can be con
sidered as a set of outputs Y. The pair (х0, y0)
is termed the original state for the finite state
machine. If functions (1) are not dependent
on Y [19], (1) is transformed to the form #include “stm32f10x.h”
#include “stm32f10x_tim.h”
#include “stm32f10x_gpio.h”
#include “stm32f10x_rcc.h”
#define _KEYPAD_NO_PRESSED 0xFF enum X_InputSignal InputsSig;
enum Z_States
{// state from keyboard
STATE_S = '*',STATE_RES = '#',STATE_0 = '0',STATE_9 = '9',
STATE_8 = '8',STATE_7 = '7',STATE_6 = '6',STATE_5 = '5',
STATE_4 = '4', STATE_3 = '3', STATE_2 = '2',STATE_1 = '1'}; enum Z_States
{// state from keyboard
STATE_S = '*',STATE_RES = '#',STATE_0 = '0',STATE_9 = '9',
STATE_8 = '8',STATE_7 = '7',STATE_6 = '6',STATE_5 = '5',
STATE_4 = '4', STATE_3 = '3', STATE_2 = '2',STATE_1 = '1'}; (
)
(
)
+
+
+
+
=
= φ
1
1
1
1
,
;
,
. i
i
i
i
i
i
z
f x
z
y
x
z
(2) (
)
(
)
+
+
+
+
=
= φ
1
1
1
1
,
;
,
. i
i
i
i
i
i
z
f x
z
y
x
z (2) 32 Information and controlling system enum X_InputSignal
{// input signals from keyboard
SIG_STATE_S = '*',SIG_STATE_RES = '#',SIG_STATE_0 = '0',
SIG_STATE_9 = '9',SIG_STATE_8 = '8',SIG_STATE_7 = '7',
SIG_STATE_6 = '6',SIG_STATE_5 = '5',SIG_STATE_4 = '4',
SIG_STATE_3 = '3',SIG_STATE_2 = '2',SIG_STATE_1 = '1', }; language. A special feature of the solution
is a link between the pattern and mathe
matical model (3) and the elimination of
the specified flaw by using the mechanism
of a linked list (the typical construct of the
C language). In the developed solution for Cortex-M,
a linked list is used that eliminates the long
polling cycle in a brute force algorithm and
implements the functions of transition and
output (2). 5. 2. Software implementation of the typi
cal State pattern for the Cortex-M microcon
troller in the form of a linked list typedef struct Z_State_struct
{// state from keyboard
int STATE_S; int STATE_RES; int STATE_0; int STATE_9;
int STATE_8; int STATE_7; int STATE_6; int STATE_5 ;
int STATE_4; int STATE_3; int STATE_2; int STATE_1 ;
}z_state; typedef struct X_InputSignal_struct
{// input signals from keyboard
int SIG_STATE_S; int SIG_STATE_RES; int SIG_STATE_0; int SIG_STATE_9;
int SIG_STATE_8; int SIG_STATE_7; int SIG_STATE_6; int SIG_STATE_5 ;
int SIG_STATE_4; int SIG_STATE_3; int SIG_STATE_2; int SIG_STATE_1 ;
}x_state; typedef struct X_InputSignal_struct
{// input signals from keyboard
int SIG_STATE_S; int SIG_STATE_RES; int SIG_STATE_0; int SIG_STATE_9;
int SIG_STATE_8; int SIG_STATE_7; int SIG_STATE_6; int SIG_STATE_5 ;
int SIG_STATE_4; int SIG_STATE_3; int SIG_STATE_2; int SIG_STATE_1 ;
}x_state; // Y_OutSignal
void handle_state_0(void); //void (*ptr_state_0)(void);
void handle_state_1(void); //void (*ptr_state_1)(void);
void handle_state_2(void); //void (*ptr_state_2)(void);
void handle_state_3(void); //void (*ptr_state_3)(void);
void handle_state_4(void); //void (*ptr_state_4)(void);
void handle_state_5(void); //void (*ptr_state_5)(void); The pattern can be tested
in the peripheral interruption
processing function or the
Cortex-M series MC system
timer based on the microcon
troller Interrupt Driven archi
tecture [1, 2]. The basic idea behind the de
velopment of a model State pat
tern in the form of software for
ASC based on Cortex-M in the
form of a linked list is shown later
in the implementation file. The
feature that distinguishes a given
solution from the classic pattern
with an infinite polling cycle is
that the structure state_infoPK
contains all the elements of (3)
and is part of a linked list. The
linked list makes it possible to
navigate it without the cumber
some switch design. #include “FSM.h”
#include “tm1637.h”
#include “delay.h”
#include <stdio.h> /* printf, scanf, NULL */
#include <stdlib.h> /* malloc, free, rand */
uint32_t CurrentStateInit =’0’; #include “FSM.h”
#include “tm1637.h”
#include “delay.h”
#include <stdio.h> /* printf, scanf, NULL */
#include <stdlib.h> /* malloc, free, rand */
uint32_t CurrentStateInit =’0’; #include “FSM.h”
#include “tm1637.h”
#include “delay.h”
#include <stdio.h> /* printf, scanf, NULL */
#include <stdlib.h> /* malloc, free, rand */
uint32_t CurrentStateInit =’0’; const struct Z_State_struct Z_States={‘*’,’#’, ‘0’, ‘9’, ‘8’, ‘7’,’6’,’5’, ‘4’,’3’, ‘2’, ‘1’};
const struct X_InputSignal_struct X_InputList={‘*’,’#’, ‘0’, ‘9’, ‘8’, ‘7’,’6’,’5’, ‘4’,’3’}; int Z_CurrentState; int Z_CurrentState;
int X_CurrentInput; int X_CurrentInput; enum Z_State CurrentState; enum X_InputSignal InputsSig; Next, the source code includes
a function to initiate the entire
linked list init_state_structsPK,
which creates the sets of states
and all elements of the mathemat
ical model of the finite state ma-
chine (3). 5. 2. Software implementation of the typi
cal State pattern for the Cortex-M microcon
troller in the form of a linked list Developed in chapter 5. 1, the typical State
software pattern for a Cortex-M-based ACS in
the procedural paradigm in the classic variant
of the polled loop systems has one drawback. It can occur at a large number of states in the
form of a long polled cycle in a state-busting al
gorithm, such as a switch operator. This makes
it more difficult to read the code at a large num
ber of states and to maintain it. Next, a code is
offered that represents the result of the develop
ment of the State pattern in the C programming enum X_InputSignal
{// input signals from keyboard _
p
g
{// input signals from keyboard
SIG_STATE_S = ‘*’,SIG_STATE_RES = ‘#’,SIG_STATE_0 = ‘0’,
SIG_STATE_9 = ‘9’,SIG_STATE_8 = ‘8’,SIG_STATE_7 = ‘7’,
SIG_STATE_6 = ‘6’,SIG_STATE_5 = ‘5’,SIG_STATE_4 = ‘4’,
SIG_STATE_3 = ‘3’,SIG_STATE_2 = ‘2’,SIG_STATE_1 = ‘1’,
// add signals
SIG_NO_ST_0 = ‘/’,SIG_NO_ST_1 = ‘|’,SIG_NO_ST_2 = ‘+’,
}; 33 33 Eastern-European Journal of Enterprise Technologies ISSN 1729-3774 Eastern-European Journal of Enterprise Technologies ISSN 1729-3774 3/9 ( 105 ) 2020 State pattern for ASC based
on Cortex-M in the form of
a linked list (the typical con-
struct of the C programming
language). The overall imple-
mentation of the template
is maximally adapted to the
mathematical model of the fi
nite state machine (3). Pat
tern testing in a given ex
ample is performed at launch
based on the polled loop sys
tem in accordance with the
RTOS classification [1, 2]. void init_state_structsPK(void)
{ void init_state_structsPK(void) {
head = (my_node_t*)malloc(sizeof(my_node_t)); head = (my_node_t*)malloc(sizeof(my_node_t)); The first feature of the procedure is the
units to estimate the time of the software
operation. The software operation time was
evaluated using the capabilities of the Keil
programming environment. In this case, we
measured not the time of operation between
the steps of the software but the number of
clocks recorded in the Cycle Count register
(DWT_CYCCNT) register. Hereafter, we
term this value the number of cycles. A given
value can be determined in a step-by-step
debugging in the Keil programming environ
ment. Such a capability of the programming
environment is demonstrated in Fig. 3, where
the arrow shows the value of the States count
er, which records the number of cycles during
step-by-step debugging. if (head == NULL){while(1);}
head->val = 0;
head->Y_handle=Y_handle_state_0; head->next = (my_node_t *) malloc(sizeof(my_node_t)); head->next->val = 1;
head->next->Y_handle=Y_handle_state_1; head->next->Y_handle=Y_handle_state_1; head->next->next = (my_node_t *) malloc(sizeof(my_node_t)); head->next->next->val = 2; head->next->next->val = 2; head->next->next->Y_handle=Y_handle_state_2; head->next->next->next = (my_node_t *) malloc(sizeof(my_node_t)); head->next->next->next->val = 3; head->next->next->next->Y_handle=Y_handle_state_3; This approach provides an opportunity to
summarize the results of the evaluation of the
software speed on the Cortex-M MCs from
other manufacturers. Since the Cortex-M
MCs may have different clock rates, the time
estimate obtained for a single MC cannot be
summarized on MCs from different manufac
turers. And the estimate of the number of cy
cles makes it possible to compare the speed for
different software solutions and summarize it
for the Cortex-M MCs by different manufac
turers supporting the CMSIS libraries in the
Keil environment. 5. 2. Software implementation of the typi
cal State pattern for the Cortex-M microcon
troller in the form of a linked list A given solution is de
monstrative and requires further
refinement for registration in the
form of a library for ASC. _
_
_ (
)
{TM1637_clearDisplay(); TM1637_display(0,Z_States.STATE_0);}
void Y handle state 1(void) {TM1637_clearDisplay(); TM1637_display(0,Z_States.STATE_0);}
void Y handle state 1(void) _
_
_ (
)
{TM1637_clearDisplay(); TM1637_display(0,Z_States.STATE_1);} {TM1637_clearDisplay(); TM1637_display(0,Z_States.STATE_1);} Y_handle_state_2(void) {TM1637_clearDisplay(); TM1637_display(0,2);} void Y_handle_state_2(void) {TM1637_clearDisplay(); TM1637_display(0,2);} void Y_handle_state_3(void) {TM1637_clearDisplay(); TM1637_display(1,3);} void Y_handle_state_4(void) {TM1637_clearDisplay(); TM1637_display(1,4);} void Y_handle_state_6(void) {TM1637_clearDisplay(); TM1637_display(2,6);} void Y_handle_state_7(void) {TM1637_clearDisplay(); TM1637_display(2,7);}
d
h
dl
d
l
l
d
l void Y_handle_state_8(void) {TM1637_clearDisplay(); TM1637_display(3,8);} Transfer and output functions
are designed as a FSM_to_step_
PK() function, which makes it pos
sible to navigate the list without
using a simple busting algorithm,
which significantly reduces the
source code of the demo software. void Y_handle_state_9(void) {TM1637_clearDisplay(); TM1637_display(3,9);}
….. void Y_handle_state_9(void) {TM1637_clearDisplay(); TM1637_display(3,9);} typedef struct state_infoPK
{ int val;
struct Z_State_struct z_state;// enums is not suitable there
struct X_InputSignal_struct x_state;
void (*Y_handle)(void);
struct state_infoPK *next;
} my_node_t;
my_node_t *head = NULL;
void FSM_to_step_PK(void)
{
my_node_t * current = head; { int val;
struct Z_State_struct z_state;// enums is not suitable there
struct X_InputSignal_struct x_state;
void (*Y_handle)(void);
struct state_infoPK *next;
} my_node_t;
my_node_t *head = NULL;
void FSM_to_step_PK(void)
{
d
t *
t
h
d uct Z_State_struct z_state;// enums is not suitable the The software example given
in the source code below shows
the State pattern testing using
a linked list and demonstrates
that one does not need a polling
cycle to switch the state. The file
contains an entry point to the
software. It is designed solely to
demonstrate the idea and the fea
sibility of implementing a typical struct X_InputSignal_struct x_state; 34 Information and controlling system of the developed pattern and the RTOS-
based solutions. while (current != NULL) {
current->Y_handle();
current = current->next;
delay_ms(250); }} For the purpose of comparison, a proce
dure of speed estimation was devised based
on the calculation of clocks under the mode
of step-by-step debugging of MC in the Keil
programming environment. void init_state_structsPK_better(void) {
head = (my_node_t*)malloc(sizeof(my_node_t));
int size_str = sizeof(head); {
head = (my_node_t*)malloc(sizeof(my_node_t)); int size_str = sizeof(head); _
(
);
if (head == NULL){while(1);}
(*head).val = 0;
(*head).Y_handle=Y_handle_state _
(
)
if (head == NULL){while(1);} (
)
(*head).Y_handle=Y_handle_state_0; (*(head)).next = (my_node_t *) malloc(sizeof(my_node_t));
(*(head+size_str)).val = 1;
(*(head+size str)).Y handle=Y handle state 1; } (*(head)).next = (my_node_t *) malloc(sizeof(my_node_t));
h
d
l (*(head+size_str)).val = 1; ( (
))
(*(head+size_str)).Y_handle=Y_handle_state_1; } The STM32F10 microcontroller was used for testing. The software was developed in the Keil environment. The next feature of the procedure is the choice of RTOS. The real-time CMSIS-RTOS Variant 1.03 operating system
was chosen for comparison. It belongs to a multi-tasking-
core-based RTOS according to the classification given
in [1, 2]. For the ASC technical solution, the full-featured
RTOS, according to the classification given in [1, 2], is not
intended to be used. That is why we chose the CMSIS-RTOS
Variant 1.03. This choice is also due to the fact that the de
veloper of a given RTOS is the Keil developer. This allows
us to argue that the RTOS works properly, it has optimal
characteristics and is adapted to the Cortex-M architecture
MC for most manufacturers. This makes it possible to extend
the results for other multi-tasking RTOS according to the
classification given in [1, 2]. #include “delay.h”
#include “FSM.h”
#include “tm1637.h”
int main()
{
TM1637_init();
TM1637_brightness(BRIGHTEST);
TM1637_clearDisplay();
init_state_structsPK();
FSM_to_step_PK();
while(1)
{
delay_ms(250);
FSM_to_step_PK();}} #include “delay.h”
#include “FSM.h”
#include “tm1637.h”
int main()
{
TM1637_init();
TM1637_brightness(BRIGHTEST);
TM1637_clearDisplay();
init_state_structsPK();
FSM_to_step_PK();
while(1)
{
delay_ms(250);
FSM_to_step_PK();}} {
TM1637_init();
b
h The third feature of the procedure is to select the loca
tion of the software’s stop points during the step-by-step
run and measure the number of cycles recorded in the Cycle
Count (DWT_CYCCNT) register to compare different
software solutions. The main element of the comparison
for RTOS-based software and that based on the developed
pattern is the estimate of the number of cycles. Moreover,
the RTOS measured the number of cycles between exiting
one function of one thread and entering another function of
another thread when switching threads. {
delay_ms(250);
FSM_to_step_PK();}} 5. 3. Results of estimating the speed of the developed
patterns compared to the real-time operating system void test_thread1(void const *argument) void test_thread1(void const *argument) Such an approach makes it possible to most accurately
assess the difference in the operation time of practical soft
ware solutions based on RTOS and that on the basis of the
developed pattern. in the process of thread switching. The third step summarized the results obtained, which
are given in Table 1. They are shown in relative cycles
(States). Statistical treatment of the results was not carried
out because during repeated repetitions of debugging, more
than 50 times, the same number of cycles were produced. A
given solution can be generalized for other Cortex-M archi
tecture MCs by other manufacturers. The Sec field (Fig. 3)
was used for approximate time assessment. Fig. 3. States register in the Keil programming environment
(Registers work window) The cycle counter value was similarly compared when
switching between the states of the developed patterns,
namely: Fig. 3. States register in the Keil programming environment
(Registers work window) – software implementation of the typical State software
pattern for ASC based on Cortex-M in the procedural
paradigm in the classic variant of the polled loop systems,
line 2, Table 1; There was no statistical estimate of the number of
cycles (States, Fig. 3) because in multiple experiments the
States’ value for the same stop points did not change. This is
the peculiarity of a hard time mode RTOS. – software implementation of the typical State pattern
for the Cortex-M microcontroller in the form of a linked list,
line 3, Table 1. Both patterns are brought to the mathemati
cal model of the finite state machine in accordance with the
developed solution. This is followed by an example of a procedure to deter
mine the number of cycles between exiting one function
of one thread and entering another function of a different
thread when one switches threads for CMSIS-RTOS Vari
ant 1.03. The results of comparing the relative speed of the soft
ware based on RTOS and that based on the developed pat
terns are summarized in Table 1. At the initial stage, we selected the 32-bit microcontrol
ler STM32F103 of the Cortex-M architecture. To implement
the procedure, we used a demo source code, shown below. It
represents the demonstration of the parallel execution of the
two threads. void test_thread1(void const *argument) The values given in column 3 are closer to development
practice because they show the actual number of cycles in
the course of exiting one function (state or thread) and en
tering another function (state or thread). A given value in
RTOS is much higher than the value of switching between
the states. Because the periphery was set up the same in
all three cases at debugging, one of the main sources of
delay is the switch time between these func
tions. Therefore, a given procedure makes it pos
sible to correctly compare the software speed. In the first step, stop points were set in the function
void test_thread1(void const *argument) and in void test_
thread1(void const *argument). The second step was to determine the number of States
in the step-by-step debugging. The number of States was
determined between the stop points in the first function
void test_thread1(void const *argument)
all three cases at debugging, one of the main sources of
delay is the switch time between these func
tions. Therefore, a given procedure makes it pos
sible to correctly compare the software speed. Table 1
The results of comparing the relative speed of
software solutions
No. Software solution
The number
of States at
debugging
Estimated
time of
delay (ap
proximate)
1. Real-time operating
system CMSIS-RTOS
Variant 1.03
564
7×10-5 s
2. Software implementa
tion of the typical State
pattern in the form of
software for ASC in the
procedural paradigm
42
5×10-6 s
3. Software implementa
tion of the typical State
pattern for a Cortex-M
microcontroller in the
form of a linked list
59
7×10-6 s
6. Discussion of the developed State software patterns
The reported solutions provide an opportunity to im
plement the software for ASC based on a Cortex-M MC in
#include “STM32F10x.h”
#include <cmsis_os.h>
#include “STM32F10x_rcc.h”
osThreadId test_ID1; //Identifiers of threads 1 and 2
osThreadId test_ID2;
void test_thread1(void const *argument)
{__NOP(); }//Function that is implemented in thread 1
void test_thread2(void const *argument)
{__NOP();}//Function that is implemented in thread 2
osThreadDef(test_thread2, osPriorityNormal,1, 0); //Macros settings
osThreadDef(test_thread1, osPriorityNormal,1, 0);
int main(void) {
//MC periphery configuration (not shown)
osKernelInitialize(); //Initializing the CMSIS-RTOS Variant 1.03
// Creation of threads 1 and 2
test_ID2 = osThreadCreate(osThread(test_thread2), NULL);
test_ID1 = osThreadCreate(osThread(test_thread1), NULL);
osKernelStart(); //Launch the core CMSIS-RTOS Variant 1.03
while (1) { ; }
} #include “STM32F10x.h”
#include <cmsis_os.h>
#include “STM32F10x_rcc.h”
osThreadId test_ID1; //Identifiers of threads 1 and 2
osThreadId test_ID2; void test_thread1(void const *argument) 5. 3. Results of estimating the speed of the developed
patterns compared to the real-time operating system As previously stated, the typical State software pat
terns for Cortex-M to implement the ASC software make
it possible to reach a faster software performance speed
compared to RTOS-based solutions. This is because the
patterns do not contain additional software delays, caused
by the work of the RTOS core elements. To confirm this,
the comparison was performed between the software speed In the developed pattern, we measured the number of
cycles between exiting one function of one state and enter
ing another function of another state as one moves from one 35 3/9 ( 105 ) 2020 3/9 ( 105 ) 2020 Eastern-European Journal of Enterprise Technologies ISSN 1729-3774 and in the second function state to another. In both cases, an empty __NOP() operator
is employed to properly assess the function. and in the second function Table 1 The results of comparing the relative speed of
software solutions The results of comparing the relative speed of
software solutions
No. Software solution
The number
of States at
debugging
Estimated
time of
delay (ap
proximate)
1. Real-time operating
system CMSIS-RTOS
Variant 1.03
564
7×10-5 s
2. Software implementa
tion of the typical State
pattern in the form of
software for ASC in the
procedural paradigm
42
5×10-6 s
3. Software implementa
tion of the typical State
pattern for a Cortex-M
microcontroller in the
form of a linked list
59
7×10-6 s void test_thread1(void const *argument)
{__NOP(); }//Function that is implemented in thread 1
void test_thread2(void const *argument)
{__NOP();}//Function that is implemented in thread 2
osThreadDef(test_thread2, osPriorityNormal,1, 0); //Macros settings
osThreadDef(test_thread1, osPriorityNormal,1, 0); osThreadDef(test_thread2, osPriorityNormal,1, 0); //Macros settings
osThreadDef(test_thread1, osPriorityNormal,1, 0); int main(void) {
//MC periphery configuration (not shown)
osKernelInitialize(); //Initializing the CMSIS-RTOS Variant 1.03
// Creation of threads 1 and 2
test_ID2 = osThreadCreate(osThread(test_thread2), NULL);
test_ID1 = osThreadCreate(osThread(test_thread1), NULL);
osKernelStart(); //Launch the core CMSIS-RTOS Variant 1.03
while (1) { ; }
} int main(void) {
//MC periphery configuration (not shown)
osKernelInitialize(); //Initializing the CMSIS-RTOS Variant 1.03
// Creation of threads 1 and 2
test_ID2 = osThreadCreate(osThread(test_thread2), NULL);
test_ID1 = osThreadCreate(osThread(test_thread1), NULL);
osKernelStart(); //Launch the core CMSIS-RTOS Variant 1.03
while (1) { ; }
} The second step was to determine the number of States
in the step-by-step debugging. The number of States was
determined between the stop points in the first function 6. Discussion of the developed State software patterns In
this case, the pattern makes it possible to use the transition
over the elements of the linked list instead of busting states,
which significantly reduces the volume of the source code as
the number of states increases. The peculiarity of the first solution of the State software
pattern for use in ASC is that the software template is max
imally adapted to the mathematical model of the finite state
machine (3). This allows mathematical analysis. The feature of the second solution is to use a linked list
when implementing the finite state machine. As one can see
from Table 1, the number of cycles (States) in the variant
with a linked list increases slightly, while the potential
readability of the code and its brevity significantly improves. The pattern has been maximally adapted to the mathe
matical model of the finite state machine. The adaptation to
the model of the finite state machine implies that the pattern
includes all elements of the mathematical model of the finite
state machine, namely: a set of internal states, the sets of
input signals, output signals, input functions and output
functions. These elements have appropriate designations in
the source code and can be used for mathematical analysis. An additional focus of this study is to refine the State
patterns for the typical libraries and actual software solu
tions as the proposed variant is a demonstration of the
technology. In addition, it is necessary to investigate other
potential possibilities to increase the speed of the software
related to the hardware features of Cortex-M MCs. The resulting solutions should be used in the following
cases: y
3. The developed State patterns for use in ASC provide a
higher speed compared to the RTOS-based software. 3. The developed State patterns for use in ASC provide a
higher speed compared to the RTOS-based software. – the limitations of using the built-in memory of a mi
crocontroller, for example, the core of an operating system
takes up Read-Only Memory (ROM) and Random-Access
Memory (RAM); To objectively evaluate the developed patterns com
pared to solutions based on RTOS, a procedure has been
developed and applied that makes it possible to assess the
performance speed of different software and is based on the
calculation of the number of cycles recorded in the Cycle
Count (DWT_CYCCNT) register in the programming en
vironment. 6. Discussion of the developed State software patterns The reported solutions provide an opportunity to im
plement the software for ASC based on a Cortex-M MC in void test_thread1(void const *argument) 36 Information and controlling system methods during development. Applying a given pattern pro
vides faster speed of the software solution than the solutions
based on RTOS. the procedural paradigm in the State pattern variant. As it
follows from Table 1, the number of cycles when switching
between the states of the obtained patterns is about 10 times
less than the number of switches between the RTOS threads
in CMSIS-RTOS Variant 1.03. The testing was carried
out at the same functionality and hardware base. Thus, the
switch rate between the states of the resulting patterns is
about 10 times greater than the switch rate between the
RTOS threads in CMSIS-RTOS Variant 1.03. The mea
surements are given in relative units and make it possible to
generalize a given solution for Cortex-M MCs from different
manufacturers. the procedural paradigm in the State pattern variant. As it
follows from Table 1, the number of cycles when switching
between the states of the obtained patterns is about 10 times
less than the number of switches between the RTOS threads
in CMSIS-RTOS Variant 1.03. The testing was carried
out at the same functionality and hardware base. Thus, the
switch rate between the states of the resulting patterns is
about 10 times greater than the switch rate between the
RTOS threads in CMSIS-RTOS Variant 1.03. The mea
surements are given in relative units and make it possible to
generalize a given solution for Cortex-M MCs from different
manufacturers. 2. A drawback in the developed State software pattern
for use in ASC has been revealed. It can occur at a large
number of states in the software in the form of a long polling
cycle in the brute force algorithm, such as using a switch op
erator. This requires a description of the entire functionality
of the software in the busting operator, increasing the length
of the programming code. To address this shortcoming, a State pattern has been
developed for ACS based on Cortex-M in the form of a
linked list (the typical construct of the C language). A given
pattern also ensures a faster software performance compared
to those based on RTOS; it has been built on the basis of
the Cortex M architecture microcontroller libraries. 6. Discussion of the developed State software patterns Our analysis has shown that the number of cycles
at switching between the state functions of the developed
patterns is about 10 times less than the number of cycles
when switching between the thread functions in RTOS. Consequently, the developed patterns make it possible to in
crease the speed of ASC operation by about 10 times, which
is a positive result of the current study. The increase in speed
is due to the lack of computational costs in the patterns that
occur in RTOS and are related to the operation of its core. – the speed of patterns performance should be greater
than it is allowed by an RTOS; – the patterns should be used with a relatively large
number of sensors and actuators under the ACS control in
the RTTS structure. 1. Real Time Operating Systems Lecture (2001). MIT. Available at: http://web.mit.edu/16.070/www/year2001/RTOS27.pdf
2. Real Time Operating Systems. Part II (2001). MIT. Available at: http://web.mit.edu/16.070/www/year2001/RTOS28.pdf
3. Saini, P., Bansal, A., Sharma, A. (2015). Time Critical Multitasking For Multicore Microcontroller Using Xmos® Kit. International
Journal of Embedded Systems and Applications, 5 (1), 01–18. doi: https://doi.org/10.5121/ijesa.2015.5101
4. Sadgrove, M. (2011). Microcontroller interrupts for flexible control of time critical tasks in experiments with laser cooled atoms.
Available at: https://arxiv.org/pdf/1104.0064.pdf
5. Execution time analysis. Rapita Systems. Available at: https://www.rapitasystems.com/products/features/execution-time-analysis
6. Chen, Z., Chen, J., Zhou, S. (2019). Embedded electronic scale measuring system based on STM32 single chip microcomputer. 2019
Chinese Automation Congress (CAC). doi: https://doi.org/10.1109/cac48633.2019.8997317 7. Conclusions P bli h d b Addi
W l
P
f
i
l 416 A
il bl
h
//
l
/
/ df/D
i
P
df ,
,
,
, J
,
,
, J ,
,
(
)
g
j
Published by Addison-Wesley Professional, 416. Available at: http://www.uml.org.cn/c++/pdf/DesignPatterns.pdf Katin, P. (2017). Development of variant of software architecture implementation for low-power general purpose microcont 1. Katin, P. (2017). Development of variant of software architecture implementation for low-power general purpose microc
by finite state machines. EUREKA: Physics and Engineering, 3, 49–54. doi: https://doi.org/10.21303/2461-4262.2017.0 11. Katin, P. (2017). Development of variant of software architecture implementation for low-power general purpose microcontrollers
by finite state machines. EUREKA: Physics and Engineering, 3, 49–54. doi: https://doi.org/10.21303/2461-4262.2017.00361 11. Katin, P. (2017). Development of variant of software architecture implementation for low power general purpose microcontrollers
by finite state machines. EUREKA: Physics and Engineering, 3, 49–54. doi: https://doi.org/10.21303/2461-4262.2017.00361 12. Solodovnikov, A. (2016). Developing method for assessing functional complexity of software information system. EUREKA: Phys
ics and Engineering, 5, 3–9. doi: https://doi.org/10.21303/2461-4262.2016.00157 12. Solodovnikov, A. (2016). Developing method for assessing functional complexity of software information system. EUREKA: Phys
ics and Engineering, 5, 3–9. doi: https://doi.org/10.21303/2461-4262.2016.00157 13. Dietrich, С., Hoffmann, M., Lohmann, D. (2015). Back to the Roots: Implementing the RTOS as a Specialized State Machine. The
11th Annual Workshop on Operating Systems Platforms for Embedded Real-Time Applications, 7–12. Available at: https://people. mpi-sws.org/~bbb/events/ospert15/pdf/ospert15-p7.pdf 13. Dietrich, С., Hoffmann, M., Lohmann, D. (2015). Back to the Roots: Implementing the RTOS as a Specialized State Machine. The
11th Annual Workshop on Operating Systems Platforms for Embedded Real-Time Applications, 7–12. Available at: https://people. mpi-sws.org/~bbb/events/ospert15/pdf/ospert15-p7.pdf 14. Beynon, W. M. (1980). On the structure of free finite state machines. Theoretical Computer Science, 11 (2), 167–180. doi: https://
doi.org/10.1016/0304-3975(80)90044-4 14. Beynon, W. M. (1980). On the structure of free finite state machines. Theoretical Computer Science, 11 (2), 167–180. doi: https://
doi.org/10.1016/0304-3975(80)90044-4 15. Adamczyk, P. The Anthology of the Finite State Machine Design Patterns. Available at: http://citeseerx.ist.psu.edu/viewdoc/
download?doi=10.1.1.95.838&rep=rep1&type=pdf 15. Adamczyk, P. The Anthology of the Finite State Machine Design Patterns. Available at: http://citeseerx.ist.psu.edu/viewdoc/
download?doi=10.1.1.95.838&rep=rep1&type=pdf 16. Andresen, K., Møller-Pedersen, B., Runde, R. K. (2015). Combined Modelling and Programming Support for Composite States and
Extensible State Machines. Proceedings of the 3rd International Conference on Model-Driven Engineering and Software Develop
ment. doi: https://doi.org/10.5220/0005237302310238 16. Andresen, K., Møller-Pedersen, B., Runde, R. K. (2015). 7. Conclusions 1. A State software pattern has been developed for use
in ASC. Unlike well-known solutions, it is built on the basis
of the libraries of the Cortex M architecture microcontrol
lers and is maximally adapted to the mathematical model of
the finite state machine. This makes the resulting solution
easy to adapt to a wide range of Cortex-M MCs from differ
ent manufacturers, ensuring code unification and simplify
ing the maintenance process. The maximum adaptability to
a mathematical model allows using mathematical modeling When developing the source code for patterns, we have
demonstrated solely the basic idea of using a linked list for
implementing the pattern of a finite state machine. There
fore, it is necessary to develop a software implementation op
tion in the form of software infrastructure and a full-fledged
library for practical use in ASC. References 37 3/9 ( 105 ) 2020 Eastern-European Journal of Enterprise Technologies ISSN 1729-3774 7. Bessmertnyy, R. S., Katin, P. Y. (2019). Use of high-performance microcontroller for improving economic efficiency of jem produc
tion. Standartyzatsiya. Sertyfikatsiya. Yakist, 3 (115), 69–77. 7. Bessmertnyy, R. S., Katin, P. Y. (2019). Use of high-performance microcontroller for improving economic efficiency of jem
tion. Standartyzatsiya. Sertyfikatsiya. Yakist, 3 (115), 69–77. 8. Zhu, W., Wang, Z., Zhang, Z. (2020). Renovation of Automation System Based on Industrial Internet of Things: A C
Sewage Treatment Plant. Sensors, 20 (8), 2175. doi: https://doi.org/10.3390/s20082175 9. Kasthuri Arachchi, S. P., Shih, T. K., Hakim, N. L. (2020). Modelling a Spatial-Motion Deep Learning Framework to Classify Dy
namic Patterns of Videos. Applied Sciences, 10 (4), 1479. doi: https://doi.org/10.3390/app10041479 9. Kasthuri Arachchi, S. P., Shih, T. K., Hakim, N. L. (2020). Modelling a Spatial-Motion Deep Learning Framework to Classify Dy
namic Patterns of Videos. Applied Sciences, 10 (4), 1479. doi: https://doi.org/10.3390/app10041479 10. Gamma, E., Helm, R., Johnson, R., Vlissides, J., Booch, G. (1994). Design Patterns: Elements of Reusable Object-Oriented Software
Published by Addison-Wesley Professional, 416. Available at: http://www.uml.org.cn/c++/pdf/DesignPatterns.pdf 10. Gamma, E., Helm, R., Johnson, R., Vlissides, J., Booch, G. (1994). Design Patterns: Elements of Reusable Object-Oriented Software. P bli h d b Addi
W l
P
f
i
l 416 A
il bl
h
//
l
/
/ df/D
i
P
df 10. Gamma, E., Helm, R., Johnson, R., Vlissides, J., Booch, G. (1994). Design Patterns: Elements of Reusable Object-Oriented Software. 7. Conclusions Combined Modelling and Programming Support for Composite States and
Extensible State Machines. Proceedings of the 3rd International Conference on Model-Driven Engineering and Software Develop
ment. doi: https://doi.org/10.5220/0005237302310238 17. Prasanna, Ch. S. L., Venkateswara Rao, M. (2012). Implementation of a Scalable µC/OS-II Based Multitasking Monitoring System. International Journal of Computer Science And Technology, 3 (2), 86–89. Available at: http://ijcst.com/vol32/1/prasanna.pdf 17. Prasanna, Ch. S. L., Venkateswara Rao, M. (2012). Implementation of a Scalable µC/OS-II Based Multitasking Monitoring System. International Journal of Computer Science And Technology, 3 (2), 86–89. Available at: http://ijcst.com/vol32/1/prasanna.pdf 18. RM0008 Reference manual STM32F101xx, STM32F102xx, STM32F103xx, STM32F105xx and STM32F107xx advanced Arm®-
based 32-bit MCUs. Available at: https://www.st.com/resource/en/reference_manual/cd00171190-stm32f101xx-stm32f102xx-
stm32f103xx-stm32f105xx-and-stm32f107xx-advanced-arm-based-32-bit-mcus-stmicroelectronics.pdf 18. RM0008 Reference manual STM32F101xx, STM32F102xx, STM32F103xx, STM32F105xx and STM32F107xx advanced Arm®-
based 32-bit MCUs. Available at: https://www.st.com/resource/en/reference_manual/cd00171190-stm32f101xx-stm32f102xx-
stm32f103xx-stm32f105xx-and-stm32f107xx-advanced-arm-based-32-bit-mcus-stmicroelectronics.pdf 19. Bloh, A. Sh. (1975). Graf shemy i ih primenenie. Minsk: Visheyshaya shkola, 294. 19. Bloh, A. Sh. (1975). Graf shemy i ih primenenie. Minsk: Visheyshaya shkola, 294. 38
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Correlation between polio immunization coverage and overall morbidity and mortality for COVID-19: an epidemiological study
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Environmental science and pollution research international
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Correlation between polio immunization coverage and overall
morbidity and mortality for COVID-19: an epidemiological study Marwa Adel Afify1
& Rakan M. Alqahtani2 & Mohammed Abdulrahman Mohammed Alzamil3 &
Faten Abdulrahman Khorshid4 & Sumayyah Mohammad Almarshedy5 & Sana Ghazi Alattas6 & Talal Nabeel Alrawaf7 &
May Bin-Jumah8 & Mohamed M. Abdel-Daim9,10 & Mohammad Almohideb11 Marwa Adel Afify1
& Rakan M. Alqahtani2 & Mohammed Abdulrahman Mohammed Alzamil3 &
Faten Abdulrahman Khorshid4 & Sumayyah Mohammad Almarshedy5 & Sana Ghazi Alattas6 & Talal Nabeel Alrawaf7 &
May Bin-Jumah8 & Mohamed M. Abdel-Daim9,10 & Mohammad Almohideb11 Received: 30 October 2020 /Accepted: 4 February 2021
# The Author(s) 2021
/ Published online: 2 March 2021 Abstract We conducted the current analysis to determine the potential role of polio vaccination in the context of the spread of
COVID-19. Data were extracted from the World Health Organization’s (WHO) Global Health Observatory data repos-
itory regarding the polio immunization coverage estimates and correlated to the overall morbidity and mortality for
COVID-19 among different countries. Data were analyzed using R software version 4.0.2. Mean and standard deviation
were used to represent continuous variables while we used frequencies and percentages to represent categorical vari-
ables. The Kruskal-Wallis H test was used for continuous variables since they were not normally distributed. Moreover,
the Spearman rank correlation coefficient (rho) was used to determine the relationship between different variables. There
was a significantly positive correlation between the vaccine coverage (%) and both of total cases per one million
populations (rho = 0.37; p-value < 0.001) and deaths per one million populations (rho = 0.30; p-value < 0.001). Moreover, there was a significant correlation between different income groups and each of vaccine coverage (%) (rho
= 0.71; p-value < 0.001), total cases per one million populations (rho = 0.50; p-value < 0.001), and deaths per one
million populations (rho = 0.39; p-value < 0.001). All claims regarding the possible protective effect of Polio vaccina-
tion do not have any support when analyzing the related data. Polio vaccination efforts should be limited to eradicate the
disease from endemic countries; however, there is no evidence to support the immunization with live-attenuated vaccines
for the protection against COVID-19. Keywords Polio . Immunization . COVID-19 . Correlation https://doi.org/10.1007/s11356-021-12861-6
Environmental Science and Pollution Research (2021) 28:34611–34618 https://doi.org/10.1007/s11356-021-12861-6
Environmental Science and Pollution Research (2021) 28:34611–34618 RESEARCH ARTICLE Statistical analysis Mean and standard deviation (SD) were used to represent
continuous variables while we used frequencies and percent-
ages to represent categorical variables. The skewness and
Kurtosis tests were used for testing the normal distribution
of continuous variables. The Kruskal-Wallis H test was used
for continuous variables since they were not normally distrib-
uted (Shapiro-Wilk p-value < 0.001 for all variables) (Chan
and Walmsley 1997). Moreover, the Spearman rank correla-
tion coefficient (rho) was used to determine the relationship
between different variables (de Winter et al. 2016; Kumar
et al. 2018). Data were analyzed using R software version
4.0.2 using the packages (Rcmdr) and (corrr). The statistical
significance was considered when the p-value was < 0.05. Oral poliovirus vaccine (OPV) and inactivated poliovi-
rus vaccine (IPV) have been used to eradicate poliovirus. In addition to the protective properties of live-attenuated
vaccines against specific microorganisms, various vaccines
have been shown to induce non-specific immune effects. Recent epidemiological data suggest that the use of live-
attenuated vaccines (for example, Bacillus Calmette-
Guérin (BCG), measles vaccine, and OPV) may result in
the induction of non-specific effects in the immune system
(Blok et al. 2015; De Bree et al. 2018; Higgins et al. 2014;
Jensen et al. 2016) and may protect against other types of
viruses (Aaby and Benn 2017; Higgins et al. 2016; Upfill-
Brown et al. 2017). These non-specific effects are mediat-
ed via various immunological mechanisms, including the
induction of the innate immune system (trained immunity)
and heterologous lymphocyte effects. In turn, trained im-
munity promotes the long-term upregulation of innate im-
mune cells via epigenetic and metabolic programming (De
Bree et al. 2018). Even though the exact mechanisms be-
hind this phenomenon—trained immunity and non-specific
immune effects—are not yet clearly understood, we con-
ducted the current analysis to determine the potential role
of polio vaccination in the context of the spread of
COVID-19 until specific vaccines and antiviral therapy
are designed and approved. Responsible Editor: Philippe Garrigues * Marwa Adel Afify
marwa.adel.pharmacy2@gmail.com
* Mohamed M. Abdel-Daim
abdeldaim.m@vet.suez.edu.eg * Marwa Adel Afify
marwa.adel.pharmacy2@gmail.com * Marwa Adel Afify
marwa.adel.pharmacy2@gmail.com marwa.adel.pharmacy2@gmail.com
* Mohamed M. Abdel-Daim
abdeldaim.m@vet.suez.edu.eg
Rakan M. Alqahtani
arakan@ksu.edu.sa
Mohammed Abdulrahman Mohammed Alzamil
Mohammed.alzamil@yahoo.com
Faten Abdulrahman Khorshid
Fatenkhorshid@yahoo.com
Sumayyah Mohammad Almarshedy
dr.sumayyahalmarshedy@hotmail.com * Mohamed M. Abdel-Daim
abdeldaim.m@vet.suez.edu.eg * Mohamed M. Abdel-Daim
abdeldaim.m@vet.suez.edu.eg * Mohamed M. Abdel-Daim
abdeldaim.m@vet.suez.edu.eg
Rakan M. Alqahtani
arakan@ksu.edu.sa
Mohammed Abdulrahman Mohammed Alzamil
Mohammed.alzamil@yahoo.com
Faten Abdulrahman Khorshid
Fatenkhorshid@yahoo.com
Sumayyah Mohammad Almarshedy
dr.sumayyahalmarshedy@hotmail.com Extended author information available on the last page of the article Environ Sci Pollut Res (2021) 28:34611–34618 34612 Data collection Data were extracted from the World Health Organization’s
(WHO) Global Health Observatory data repository regarding
the polio immunization coverage estimates (González et al. 2003). The coverage was estimated as “the percentage of chil-
dren ages 12–23 months who received three doses of the polio
vaccine before the survey” (Li et al. 2016b). Data of COVID-
19 total cases per one million populations and deaths per one
million populations, for all possible countries, were obtained
from the Internet continuously updated repository
“Worldometers” on 28 October 2020 (Karimi et al. 2020). Finally, the data were then merged according to the country
to restore only countries having reported immunization
coverage. Introduction As of December 2019, a significant number of patients
with “unknown viral pneumonia” connected to a local
Seafood Wholesale Market were identified in Wuhan
City, China (Huang et al. 2020). A novel coronavirus
strain (SARS-CoV-2) was recognized as the cause of
the 2019 coronavirus disease (COVID-19). SARS-CoV-
2 has exhibited an unprecedented spreading potential, af-
fecting more than 210 countries all over the globe. However, there are dramatic differences in patterns of
disease spread and how it behaves in various countries. For example, as of 17 March 2020, the UK and Italy
have strikingly high mortality rates of 13.41% (total
cases = 108.692) and 13.19% (total cases = 172.434),
respectively, despite the deployment of extensive restric-
tions on social interactions in these countries. On the
other hand, the USA, which accounts for 29.5% of the
total confirmed cases of COVID-19 globally, has a low
mortality rate of 5.27%, which is the case in many other
countries (Glass et al. 2004). These differences have been
hypothesized to be attributable to the variations in cultur-
al norms and healthcare infrastructure. Herein, we pro-
pose an alternative theory, suggesting that the differences
in the number of COVID-19 cases and the associated
mortality rates might be explained, in part, by the varia-
tions in the coverage rates of universal polio vaccination
policy in different countries all over the world. Results Initially, we analyzed the correlation between polio vaccina-
tion coverage (%) and COVID-19 statistics in different coun-
tries (Tables 1 and 2). There was a significant positive corre-
lation between the vaccine coverage (%) and both of total
cases per one million populations (rho = 0.37; p-value <
0.001) and deaths per one million populations (rho = 0.30;
p-value < 0.001) (Figs. 1 and 2). On further analysis of the
effect of starting year of vaccination policy, there was a pos-
itive correlation with total cases per one million populations
(rho = 0.07; p-value = 0.375) and a negative one with deaths
per one million populations (rho = −0.02; p-value = 0.788);
however, these correlations were not statistically significant
(Figs. 3 and 4). We furtherly did a stratification of data according to the
World Bank income group (Table 2); in general, there was a
significant correlation between different income groups and Environ Sci Pollut Res (2021) 28:34611–34618 34613 Table 1
Correlation matrix between different variables Table 1
Correlation matrix between different variables
Variable
Correlation
Polio immunization coverage
World bank
income group
Tot Cases/1 M
population
Deaths/1 M
population
Starting Year
Polio
immunization
coverage
World bank
income group
Spearman's rho
0.71
p-value
< 0.001*
Tot Cases/1 M
population
Spearman's rho
0.37
0.50
p-value
< 0.001*
< 0.001*
Deaths/1 M
population
Spearman's rho
0.30
0.39
0.69
p-value
< 0.001*
< 0.001*
< 0.001*
Starting Year
Spearman's rho
0.05
-0.07
0.07
-0.02
p-value
0.541
0.371
0.375
0.788
*Statistically significant p-value < 0.05 attention and support for its complete eradication (Mshelia et al. 2020). Following the intensive efforts of the Global Polio
Eradication Initiative (GPEI), which was launched in 1988 to
reach the goal of complete polio eradication, the incidence of
this disease was successfully reduced to 99% (Glass et al. 2004). Meanwhile, the current policy of GPEI in eradicating
poliovirus is the Polio Endgame Strategy, which was set to take
place between 2019 and 2023, with three major goals: polio
eradication, integration, and certification and containment
(World Health Organization 2019). However, soon enough af-
ter the emergence of a new coronavirus strain (COVID-19), all
universal polio vaccination campaigns were suspended by the
GPEI program until the 2nd half of 2020 in an attempt to reduce
the risk of increasing transmission of COVID-19 through
healthcare providers and laboratory personnel (Li et al. 2016a). Results Therefore, we conducted the current analysis to deter-
mine whether poliovirus vaccination with OPV or IPV has a
protective role against COVID-19. each of the vaccine coverage (%) (rho = 0.71; p-value <
0.001), total cases per one million populations (rho = 0.50;
p-value < 0.001), and deaths per one million populations (rho
= 0.39; p-value < 0.001) (Table 1). In the same context, there
was a significant difference among different income groups in
terms of polio immunization coverage (X2 = 90.96; p-value <
0.001), total cases per one million populations (X2 = 117.05;
p-value < 0.001), and deaths per one million populations (X2 =
75.76; p-value < 0.001) (Figs. 5 and 6). Moreover, the
pairwise comparisons between each pair of World Bank
groups showed a significant difference among the aforemen-
tioned three aspects, except for “lower-middle” and “low”
income groups which were comparable (p-value < 0.05)
(Supplementary Tables). Discussion Live-attenuated RNA virus vaccines such as mumps, mea-
sles, polio, or rubella viruses are known to result in the induc-
tion of long-term immune response in terms of both cell-
mediated and humoral immunity following one or two doses Oral poliovirus vaccine (OPV) and inactivated poliovirus vac-
cine (IPV) are the two major types of vaccines that protect
individuals against poliovirus. Polio is now recognized as the
main vaccine-preventable disease after receiving the required Table 2
Data stratified according to the World Bank income groups
World Bank income group
Polio immunization coverage (%)
Tot cases/1M pop
Deaths/1M pop
Mean
Standard deviation
Mean
Standard deviation
Mean
Standard deviation
High income
92.00
10.00
612.59
1023.01
11.80
11.76
Upper middle income
84.00
18.00
8569.45
8068.06
214.62
136.79
Lower middle income
71.00
26.00
3118.89
3739.36
84.64
136.79
Low income
60.00
27.00
13,871.58
13,037.06
256.36
291.62 Table 2
Data stratified according to the World Bank income groups Environ Sci Pollut Res (2021) 28:34611–34618 34614 0
20000
40000
60000
40
60
80
100
Polio_Immunization_Coverage
Total_Cases_Per_1M_Pop
Fig. 1 The correlation between
polio immunization coverage (%)
and new cases per one million
populations 100 earlier reported higher mortality rates and higher total numbers
of COVID-19 cases (per one million population) compared to
countries that implemented polio vaccination policies at later a
date. This indicates that the earlier the universal polio vaccina-
tion policy was deployed, the greater the number of COVID-19
cases as well as the greater the number of mortality cases per
one million populations. of these vaccines (Escriou et al. 2014). However, the question
of whether the universal coverage of such vaccines might
protect against or slow the spread of COVID-19 infection
remains to be answered. We conducted the current study as an attempt to identify the
potential correlation between the coverage rates of universal
poliovirus vaccines and the number of mortality cases as well
as new cases of COVID-19 in different countries all over the
globe to provide possible explanations for the variations in
trends of disease spread all over the world. Overall, we noted
that countries that had higher polio vaccine coverage rates were
associated with higher COVID-19 disease burden in terms of
mortality rates and the total number of COVID-19-confirmed
cases per one million populations. Noteworthy, this finding was
highly significant, indicating that polio vaccination does not
protect against COVID-19 or slow its spread. Discussion Moreover, coun-
tries that implemented the universal polio vaccination policies Countries were divided into low, low-middle, upper-mid-
dle, and high-income countries based on the World Bank clas-
sification. We noted that low-income countries had the lowest
mean poliovirus (3rd dose) vaccination coverage rates of 60%
compared to the 92% mean coverage rate of high-income
countries. Surprisingly, these low-income countries had much
lower mortality cases compared to high-income countries
(mean deaths per 1 million populations: 0.66 vs 89.16). In
the same context, the total number of COVID-19 cases was
dramatically lower in low-income countries compared to 0
400
800
1200
40
60
80
100
Polio_Immunization_Coverage
Deaths_Per_1M_Pop
Fig. 2 The correlation between
polio immunization coverage (%)
and deaths per one million
populations 0
400
800
1200
40
60
80
100
Polio_Immunization_Coverage
Deaths_Per_1M_Pop Fig. 2 The correlation between
polio immunization coverage (%)
and deaths per one million
populations Deaths_Per_1M_Pop Environ Sci Pollut Res (2021) 28:34611–34618 Environ Sci Pollut Res (2021) 28:34611–34618 34615 0
20000
40000
60000
1980
1990
2000
2010
Starting_Year
Total_Cases_Per_1M_Pop
Fig. 3 The correlation between
starting year polio immunization
policy and new cases per one
million populations Fig. 3 The correlation between
starting year polio immunization
policy and new cases per one
million populations burden in each country accordingly. In their analysis, the au-
thors found that 55 middle-high and high-income countries
with a current BCG vaccination policy had much fewer mor-
tality cases per million populations when compared with five
middle-high and high-income countries, where no universal
BCG vaccination policies exist (mean mortality rate: 0.78 vs
16.39). In the same context, middle-high and high-income
countries with no universal BCG vaccination policy have a
fourfold increase in the number of COVID-19 cases per mil-
lion populations. The authors also observed a significant cor-
relation between the timing of universal BCG vaccination
policy implementation and the number of mortality cases; they
found that the earlier the vaccination policy was implemented,
the fewer death cases were reported, indicating a possible
protective effect of early BCG vaccination. high-income ones (mean: 16.43 vs 1493.04 new cases per one
million populations). These differences were noted to be high-
ly significant, indicating that coverage of polio vaccination
policies is not correlated with a protective effect against
COVID-19 infection. Discussion However, it should be noted that a con-
siderable proportion of low-income countries did not report
the rates of mortality or report no deaths due to COVID-19,
while nearly half low-income countries reported mortality
rates < 1 per one million populations. Therefore, the afore-
mentioned differences based on the income of countries could
be attributed to the underreporting of these countries. On 28 March 2020, Miller et al. (2020) conducted a similar
analysis to determine if a potential correlation between uni-
versal Bacillus Calmette-Guérin (BCG) vaccination policies
in different countries and the morbidity, as well as mortality
associated with COVID-19 infection, exists and whether BCG
vaccination is protective against or indicative of the disease To date, there is no evidence that OPV protects against
COVID-19 infection. Multiple experimental studies that have 0
500
1000
1980
1990
2000
2010
Starting_Year
Deaths_Per_1M_Pop
Fig. 4 The correlation between
starting year polio immunization
policy and deaths per one million
populations 0
500
1000
1980
1990
2000
2010
Starting_Year
Deaths_Per_1M_Pop 34616 Environ Sci Pollut Res (2021) 28:34611–34618 Environ Sci Pollut Res (2021) 28:34611–34618 Income:
Low
Income:
Lower-middle
Income:
Upper-middle
Income:
High
40
60
80
100
40
60
80
100
40
60
80
100
40
60
80
100
0
20000
40000
60000
Polio_Immunization_Coverage
Total_Cases_Per_1M_Pop
Fig. 5 The correlation between
polio immunization coverage (%)
and new cases per one million
populations (stratified by World
Bank income group) been conducted over the years have reported that OPV has
non-specific effects on the immune system; all of which can
potentially protect against COVID-19 in theory (Aaby and
Benn 2017; Upfill-Brown et al. 2017). However, these effects
have not been well-characterized, and their clinical relevance
is not yet known. These reported effects may not be essentially
limited to OPV, as various live vaccines have also been re-
ported to exhibit non-specific protective effects in the immune
system as well, such as the BCG vaccine against tuberculosis
(Miller et al. 2020). The underlying mechanism of potential
immune protection, through the use of these vaccines, needs
to be elucidated further. The major advantage in this matter is
that clinical studies can be initiated right away, as the vaccines
in question are licensed and have excellent safety profiles. Polio vaccination efforts should be limited to eradicate the
disease from endemic countries; however, there is no evidence to support the immunization with live-attenuated vaccines for
the protection against COVID-19. Discussion been conducted over the years have reported that OPV has
non-specific effects on the immune system; all of which can
potentially protect against COVID-19 in theory (Aaby and
Benn 2017; Upfill-Brown et al. 2017). However, these effects
have not been well-characterized, and their clinical relevance
is not yet known. These reported effects may not be essentially
limited to OPV, as various live vaccines have also been re-
ported to exhibit non-specific protective effects in the immune
system as well, such as the BCG vaccine against tuberculosis
(Miller et al. 2020). The underlying mechanism of potential
immune protection, through the use of these vaccines, needs
to be elucidated further. The major advantage in this matter is
that clinical studies can be initiated right away, as the vaccines
in question are licensed and have excellent safety profiles. Polio vaccination efforts should be limited to eradicate the
disease from endemic countries; however, there is no evidence Our analysis does not account for a direct association be-
tween increased universal poliovirus vaccination coverage
rates and increased rates of new COVID-19 cases and mortal-
ity rates per 1 million populations among analyzed countries. Many significant role-playing factors could have attributed to
such results; however, we could not identify these factors due
to the limited data available in this matter. We also could not
analyze whether a certain type of polio vaccine (OPV or IPV)
was the main contributor to our results because these data
were not available. Notably, underreporting in low-income
countries is a potential limitation to our findings. Therefore,
our results should be interpreted with caution. Although the
data regarding the immunization data quality—in low- and
middle-income countries—are limited in the literature, Income:
Low
Income:
Lower-middle
Income:
Upper-middle
Income:
High
406080100
406080100
406080100
406080100
-500
0
500
1000
Polio_Immunization_Coverage
Deaths_Per_1M_Pop
Fig. 6 The correlation between
polio immunization coverage (%)
and deaths per one million
populations (stratified by World
Bank income group) Income:
Low
Income:
Lower-middle
Income:
Upper-middle
Income:
High
406080100
406080100
406080100
406080100
-500
0
500
1000
Polio_Immunization_Coverage
Deaths_Per_1M_Pop Fig. 6 The correlation between
polio immunization coverage (%)
and deaths per one million
populations (stratified by World
Bank income group) Fig. Supplementary Information The online version contains supplementary
material available at https://doi.org/10.1007/s11356-021-12861-6. Acknowledgements This research was funded by the Deanship of
Scientific Research at Princess Nourah Bint Abdulrahman University
through the Fast-track Research Funding Program. Authors contribution MAA: contributed to the conception, analysis, and
writing of the draft; approved the final version of the manuscript; and
agreed to be responsible for the quality and accuracy of all parts of the
work. Conflict of interest
The authors declare no conflict of interest. Conflict of interest
The authors declare no conflict of interest. Open Access This article is licensed under a Creative Commons
Attribution 4.0 International License, which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as
long as you give appropriate credit to the original author(s) and the
source, provide a link to the Creative Commons licence, and indicate if
changes were made. The images or other third party material in this article
are included in the article's Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not included in the
article's Creative Commons licence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a
copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Discussion 6 The correlation between
polio immunization coverage (%)
and deaths per one million
populations (stratified by World
Bank income group) Deaths_Per_1M_Pop Environ Sci Pollut Res (2021) 28:34611–34618 34617 MBG: contributed to supervision, conception, interpretation of data,
and writing of the draft; approved the final version of the manuscript; and
agreed to be responsible for the quality and accuracy of all parts of the
work. coverage values were found to be inflated and adjusted in the
official reports (Harrison et al. 2020). In addition, many other
logistic deficiencies were reported including healthcare
worker-related factors, the fragmentation of health informa-
tion system, bad data management, and targets’ overreliance
(Harrison et al. 2020). Akin to that are the problems in the
costs and cost-effectiveness of the immunization coverage in
low- and middle-income countries (Munk et al. 2019). MMA: contributed to supervision, conception, interpretation of data,
and writing of the draft; approved the final version of the manuscript; and
agreed to be responsible for the quality and accuracy of all parts of the
work. MA: designed the work and analysis, revised the draft, approved the
final version of the manuscript, and agreed to be responsible for the
quality and accuracy of all parts of the work. Funding This research was funded by the Deanship of Scientific
Research at Princess Nourah Bint Abdulrahman University through the
Fast-track Research Funding Program. Conclusion In conclusion, our analysis provides novel insight into the
potential correlation between the coverage rates of universal
poliovirus vaccination policies and the mortality rates/new
cases of COVID-19 infection. Countries with increased polio-
virus vaccination coverage rates are significantly correlated
with increased mortality rates and the number of new cases
of COVID-19 per one million population. In the same context,
high-income countries had significantly higher mortality rates
and an increased number of new cases of COVID-19 per 1
million populations. Finally, countries that implemented po-
liovirus vaccination policies earlier had significantly more
mortality cases and an increased number of new cases of
COVID-19 per 1 million inhabitants. Data availability Data are available on request. Ethics approval and consent to participate
Not applicable Consent for publication
Not applicable References Virology
452:32–41 in the perspectives of skin injury. Dermatol Res Pract:4512840. https://doi.org/10.1155/2018/45128406 Glass WG, Subbarao K, Murphy B, Murphy PM (2004) Mechanisms of
host defense following severe acute respiratory syndrome-
coronavirus (SARS-CoV) pulmonary infection of mice. J Immunol
(Baltimore, Md : 1950) 173:4030–4039. https://doi.org/10.4049/
jimmunol.173.6.4030 Li K et al (2016a) Middle East respiratory syndrome coronavirus causes
multiple organ damage and lethal disease in mice transgenic for
human dipeptidyl peptidase 4. J Infect Dis 213:712–722. https://
doi.org/10.1093/infdis/jiv499 Li Z, He W, Lan Y, Zhao K, Lv X, Lu H, Ding N, Zhang J, Shi J, Shan C,
Gao F (2016b) The evidence of porcine hemagglutinating encepha-
lomyelitis virus induced nonsuppurative encephalitis as the cause of
death in piglets. PeerJ 4:e2443. https://doi.org/10.7717/peerj.2443 González JM, Gomez-Puertas P, Cavanagh D, Gorbalenya AE, Enjuanes
L (2003) A comparative sequence analysis to revise the current
taxonomy of the family Coronaviridae. Arch Virol 148:2207–
2235. https://doi.org/10.1007/s00705-003-0162-1 Miller A, Reandelar MJ, Fasciglione K, Roumenova V, Li Y, Otazu GH
(2020) Correlation between universal BCG vaccination policy and
reduced morbidity and mortality for COVID-19: an epidemiological
study medRxiv Harrison K, Rahimi N, Carolina Danovaro-Holliday M (2020) Factors
limiting data quality in the expanded programme on immunization
in low and middle-income countries: a scoping review. Vaccine 38:
4652–4663 Mshelia SE, Blackmore C, Archer R, Booth A (2020) Factors affecting
the successful implementation of Global Polio Eradication Initiative
(GPEI) in low- and middle-income countries. J Glob Health 10:
010322. https://doi.org/10.7189/jogh.10.010322 Higgins J, Soares-Weiser K, Reingold A (2014) Systematic review of the
non-specific effects of BCG, DTP and measles containing vaccines. Higgins JP et al (2016) Association of BCG, DTP, and measles contain-
ing vaccines with childhood mortality: systematic review. bmj 355:
i5170 Munk C, Portnoy A, Suharlim C, Clarke-Deelder E, Brenzel L, Resch
SC, Menzies NA (2019) Systematic review of the costs and effec-
tiveness of interventions to increase infant vaccination coverage in
low- and middle-income countries. BMC Health Serv Res 19:741 Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu
X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu
M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q,
Wang J, Cao B (2020) Clinical features of patients infected with
2019 novel coronavirus in Wuhan, China. References RMA: designed the work, the acquisition, and the interpretation of
data; revised the draft; approved the final version of the manuscript; and
agreed to be responsible for the quality and accuracy of all parts of the
work. Aaby P, Benn CS (2017) Beneficial nonspecific effects of oral polio
vaccine (OPV): implications for the cessation of OPV? Press US,
Oxford University Blok BA, Arts RJ, van Crevel R, Benn CS, Netea MG (2015) Trained
innate immunity as underlying mechanism for the long-term, non-
specific effects of vaccines. J Leukoc Biol 98:347–356 MAMA: contributed to the conception, interpretation of data, and
writing of the draft; approved the final version of the manuscript; and
agreed to be responsible for the quality and accuracy of all parts of the
work. Chan Y, Walmsley RP (1997) Learning and understanding the Kruskal-
Wallis one-way analysis-of-variance-by-ranks test for differences
among three or more independent groups. Phys Ther 77:1755–
1762. https://doi.org/10.1093/ptj/77.12.1755 FAK: designed the work, the acquisition, the interpretation of data,
and the writing of the draft; approved the final version of the manuscript;
and agreed to be responsible for the quality and accuracy of all parts of the
work 1762. https://doi.org/10.1093/ptj/77.12.1755 De Bree L, Koeken VA, Joosten LA, Aaby P, Benn CS, van Crevel R,
Netea MG Non-specific effects of vaccines: current evidence and
potential implications. In: Seminars in immunology, 2018. Elsevier,
pp 35-43 SMA: designed the work and analysis, revised the draft, approved the
final version of the manuscript, and agreed to be responsible for the
quality and accuracy of all parts of the work. de Winter JC, Gosling SD, Potter J (2016) Comparing the Pearson and
Spearman correlation coefficients across distributions and sample
sizes: a tutorial using simulations and empirical data. Psychol
Methods 21:273–290. https://doi.org/10.1037/met0000079 SGA: contributed to the conception, interpretation of data, and writing
of the draft; approved the final version of the manuscript; and agreed to be
responsible for the quality and accuracy of all parts of the work. TNA: designed the work and analysis, revised the draft, approved the
final version of the manuscript, and agreed to be responsible for the
quality and accuracy of all parts of the work. Escriou N, Callendret B, Lorin V, Combredet C, Marianneau P, Février
M, Tangy F (2014) Protection from SARS coronavirus conferred by 34618 Environ Sci Pollut Res (2021) 28:34611–34618 live measles vaccine expressing the spike glycoprotein. References Lancet 395:497–506 Worl Health Organization, Initiative GPE (2019) Polio endgame strategy
2019-2023: eradication, integration, certification and containment. World Health Organization Jensen KJ, Benn CS, van Crevel R Unravelling the nature of non-specific
effects of vaccines—a challenge for innate immunologists. In:
Seminars in immunology, 2016. vol 4. Elsevier, pp 377-383 Upfill-Brown A, Taniuchi M, Platts-Mills JA, Kirkpatrick B, Burgess SL,
Oberste MS, Weldon W, Houpt E, Haque R, Zaman K, Petri WA Jr
(2017) Nonspecific effects of oral polio vaccine on diarrheal burden
and etiology among Bangladeshi infants. Clin Infect Dis 65:414–
419 Karimi N, Sharifi Razavi A, Rouhani N (2020) Frequent convulsive
seizures in an adult patient with COVID-19: a case report Iran. Red Crescent Med J 22:e102828. https://doi.org/10.5812/ircmj. 102828 Publisher’s note Springer Nature remains neutral with regard to jurisdic-
tional claims in published maps and institutional affiliations. Kumar N, Kumar P, Badagabettu SN, Lewis MG, Adiga M, Padur AA
(2018) Determination of Spearman correlation coefficient (r) to
evaluate the linear association of dermal collagen and elastic fibers Affiliations Marwa Adel Afify1
& Rakan M. Alqahtani2 & Mohammed Abdulrahman Mohammed Alzamil3 &
Faten Abdulrahman Khorshid4 & Sumayyah Mohammad Almarshedy5 & Sana Ghazi Alattas6 & Talal Nabeel Alrawaf7 &
May Bin-Jumah8 & Mohamed M. Abdel-Daim9,10 & Mohammad Almohideb11 Marwa Adel Afify1
& Rakan M. Alqahtani2 & Mohammed Abdulrahman Mohammed Alzamil3 &
Faten Abdulrahman Khorshid4 & Sumayyah Mohammad Almarshedy5 & Sana Ghazi Alattas6 & Talal Nabeel Alrawaf7 &
May Bin-Jumah8 & Mohamed M. Abdel-Daim9,10 & Mohammad Almohideb11 1
Potion CRO, Integrative Medicine Company, Al Malqa,
Riyadh 13524, Saudi Arabia
6
Biological Sciences Department, King Abdulaziz University,
Jeddah, Saudi Arabia 6
Biological Sciences Department, King Abdulaziz University,
Jeddah, Saudi Arabia ing Khalid University Hospital,
Ri
dh S
di A bi
7
Al Yamamah Hospital, Riyadh, Saudi Arabia 7
Al Yamamah Hospital, Riyadh, Saudi Arabia 2
Department of Critical Care (95), King Khalid University Hospital,
King Saud University Medical City, Riyadh, Saudi Arabia
7
Al Yamamah Hospital, Riyadh
8
Biology Department, College o 2
Department of Critical Care (95), King Khalid University Hospital,
King Saud University Medical City, Riyadh, Saudi Arabia 8
Biology Department, College of Science, Princess Nourah Bint
Abdulrahman University, Riyadh, Saudi Arabia 3
Prince Sultan Medical Military City (PSMMC), Riyadh, Saudi
Arabia 9
Department of Zoology, Science College, King Saud University,
Riyadh 11451, Saudi Arabia 4
Department of Biological Sciences, Faculty of Science, King
Abdulaziz University, Jeddah 21589, Saudi Arabia 10
Pharmacology Department, Faculty of Veterinary Medicine, Suez
Canal University, Ismailia 41522, Egypt 5
Division of Adult Neurology, Department of Internal Medicine,
College of medicine, University of Hail, Hail, Saudi Arabia 11
College of Medicine, King Saud bin Abdulaziz University for
Health Sciences, Riyadh, Saudi Arabia
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Bibliometric Analysis of Dental Informatics via Pubmed
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Journal of Health Information and Libraries Australasia Journal of Health Information and Libraries Australasia Cameron P Smith Tasmanian School of Medicine, College of Health and Medicine, University of
Tasmania, Hobart, Tasmania
cpsmith0@utas.edu.au Mr Cameron Smith obtained a combined undergraduate degree in Business and
Science and completed a Master of Public Health in 2019 at the University of
Tasmania. During his master’s program, he conducted a research thesis under the
supervision of Dr Silvana Bettiol in dental health informatics. After graduation,
Cameron joined the Tasmanian Department of Education. Currently, he is pursuing
his Master of Education degree. Shahrukh Khan Melbourne Dental School, The University of Melbourne, Melbourne, Victoria
shah.khan@unimelb.edu.au | https://orcid.org/0000-0002-6695-4013
Dr Shahrukh Khan is a qualified dentist who obtained his PhD from the University of
Tasmania in 2020. He completed a Graduate Diploma of Digital Health from the
University of Melbourne in 2021. Dr Khan’s work in the field of oral health in Australia
has been instrumental in bringing attention to the challenges faced by rural and
remote communities in accessing dental care services. Silvana S Bettiol Tasmanian School of Medicine, College of Health and Medicine, University of
Tasmania, Hobart, Tasmania s.bettiol@utas.edu.au | https://orcid.org/0000-0002-4355-4498
Dr Silvana Bettiol is a Senior Lecturer and researcher in public health and
communicable disease at the University of Tasmania. With 30 years experience in
teaching and learning and pedagogy development, she has demonstrated a strong
commitment to education and advancing knowledge in her field. Her current
research interests focus on the social determinants of health and advocates for policy
and practice changes in dental public health and community health. Acknowledgements: We thank the Tasmanian School of Medicine, Master of public
health team members for their valuable feedback. Statement of Conflicts of Interest: The authors declare no conflicts of interest. Funding Source: Not funded externally. Key words: dental informatics, health informatics, bibliometric analysis Key words: dental informatics, health informatics, bibliometric analysis 9 4(1), Apr 2023 4(1), Apr 2023 9 Journal of Health Information and Libraries Australasia Abstract Introduction: This study examines the main characteristics of dental informatics
research using bibliometric analysis of articles in the online journal database
PubMed, to identify the main trends of research in dental informatics. The study aims
to identify trends, geographic distribution of papers and authors, rates of
collaboration, and performances of journals and institutions. Methods: Information on dental informatics was extracted solely from the PubMed
online journal database from January 1989 to September 2019. A three-phase search
approach was employed. Bibliometrics was used to examine the growth and progress
of dental informatics over time. Results: A total of n=236 papers on dental informatics were identified, with an
average of 7.9 papers per year. The trend of papers published increased over time
with 41 countries represented in this study. There were only 15 countries which had
10 or more representatives, seven of which came from Europe. North America
produced the most research in dental informatics, with 149 paper affiliations and ten
were cross regional, in 61% of the total papers. Discussion: The topic of dental informatics began in the mid to late 1980s, with the
most productive years in the last decade, reaching a high point in the mid 2010s. There was a low level of international collaboration, and few conducted across
different continents. Conclusion: There is steady increase in the pace of research in dental informatics,
with growing interest in exploring various implementation methods. Collaboration
has become a product of a globalised world, with the potential to share data and
exchange ideas using cutting-edge technologies. As these trends continue, the field
of dental informatics may see further growth and development, with more
technology available to provide communication and share data points and methods
becoming widespread. Introduction The recent advances in computing have given rise to the discipline of health
informatics and health information technology (HIT) that has grown steadily over the
past few decades, coinciding with the vast increase in power that computing has
been able to achieve in a relatively short amount of time (Eysenbach, 2000; Gandhi,
Khanna & Ramaswamy, 2016). The literature indicates there is a great and growing
diversity in sub-disciplines of health informatics, including medical informatics and
clinical informatics. 10 4(1), Apr 2023 Journal of Health Information and Libraries Australasia One of the more recent areas of technology integration in healthcare has come in
dentistry. Progress in dentistry relies heavily on progress in information technology. The term "dental informatics" was coined by Zimmerman et al., in 1968. Dental
informatics is a subfield of health informatics that focuses on the application of
computer and information science to improve dental care, research, education, and
management (Chhabra et al., 2016). It encompasses a wide range of areas, including
electronic health records, clinical decision support systems, telemedicine, imaging
technologies, and data analytics. By leveraging technology and data, dental
informatics seeks to improve patient outcomes, enhance the efficiency and
effectiveness of dental practices, and advance the field of dentistry as a whole. Among the more recent breakthroughs in dental informatics are diagnostic tools,
computer-aided design and manufacturing, digital acquisition of 2D or 3D images,
and computer-assisted surgery (Islam et al., 2018; Schleyer, 2003; Benoit et al., 2022). Due to the high importance of dental health, there is a constant need to improve
patient care, as well as training and education for future dental practitioners (Masic
2012). With the progress of IT has come a reduction in the size of medical devices, as
increased power has also coincided with a decrease in computer size (Hovenga et
al.,2010). Many computing advances have been made over the last decade, with the
technological landscape now being dominated by both user-carried smart devices, as
well as non-invasive implantable devices (Hovenga et al., 2010). Similarly, during the
COVID-19 pandemic, there was a growing realisation of the potential usefulness of
Information Technology (IT) tools in providing remote clinical services and educating
patients, where appropriate (Golinelli et al., 2020). Introduction This was also seen in dentistry,
where there was a changing view of the workforce during the pandemic as dental
health practitioners contributed to the public health practice of testing, monitoring,
tracking cases and staffing in healthcare services. It was also an opportunity to reflect
on competencies of dental practitioners in the HIT and the interoperability of
electronic medical and dental records (London & Boroumand, 2022). Currently, the most used technology is electronic patient records. Maintaining
accurate records is a vital responsibility from both a professional and legal
standpoint. Nevertheless, investigations globally demonstrate that standard
requirements for clinical record keeping face barriers, including countries and
regions such as the UK, Australia, and Scandinavia (Sittig et al., 2020; Sheikh et al.,
2021; Rexhepi et al., 2021). Any application of dental informatics should prove its
practical value by enhancing the standard of care and accessibility, improving
management, promoting efficiency and safety, empowering and enabling patients,
facilitating medical research, and promoting sustainability. Healthcare in itself is a highly resource heavy sector, and due to its importance, there
is a constant need for the resources to be available for use (Grosskopf et al., 2006). 11 4(1), Apr 2023 4(1), Apr 2023 Journal of Health Information and Libraries Australasia There is also a large amount of waste produced from healthcare, most of which
comes from either single use objects or hazardous medical waste (Kane et al., 2018). With the steady push for more sustainable healthcare measures as guided by the
United Nations’ sustainable development goals (SDG) the integration of digital
technologies to limit the amount of resources needed by healthcare sectors,
including dental care (McCombs & Darby, 2010; Singaraju et al., 2012; Khanna et al.,
2022) is evident and supported by the World Dental Federation (FDI). The economic,
social and ecological imperative at the heart of innovation is fundamental to societal
transformation which support the SDG. It is important to identify where the primary research is being conducted in the
rapidly growing field of dental informatics (Masic, 2012; van Noort, 2012). Research
into the current and potential impacts of health informatics has gained significant
interest, exploring the history and limitations of the field prior to the digital age. With
the emergence of digital technology, there is vast potential in health informatics to
not only improve human health but also reduce the environmental impact of
healthcare services through minimizing carbon footprints and resource consumption. Introduction Despite the documented uses of informatics in other areas of healthcare, there
appears to be a scarcity of research on dental informatics, highlighting the need for
more investigation in this domain. This study adopts a bibliometric analysis in order to map out the knowledge
structure of health informatics research, a technique proven to be valuable in the
evaluation of social science research performance (Van Rann, 2003). This paper also
reports a historical review to trace back the evolution of the health informatics
concept. The study aims to provide an illustration and updated analysis of the research that
has been conducted in the field of dental informatics, trends in publication, quality,
and quantity. With this information we map and evaluate the relevant literature for
the purpose of identifying potential research gaps, and knowledge base, exploring
the forefront of trends in its development, and exhibiting the boundaries of existing
academic work. PubMed was chosen for this source as it is an online literature
database and source of information for scientific research spanning the field of
biomedicine and health. The NCBI PubMed (Canese & Weis, 2013) database is very
important in biomedical literature and data mining (Frisch et al., 2009; Rani et al.,
2015). There are more than 35 million citations in PubMed®, representing the largest
collection of biomedical literature (National Library of Medicine, n.d.) We examine the main contributors to the research in terms of countries, institutions
and individual authors of papers. Country-specific contributions, degree of local and
international research and the impact of the published research. This is revealed by 4(1), Apr 2023 12 4(1), Apr 2023 Journal of Health Information and Libraries Australasia the cooperation network among various countries, institutions and even individuals
in the dental health informatics field. the cooperation network among various countries, institutions and even individuals
in the dental health informatics field. Phase one The first phase was the initial search for literature. The data were obtained through a
keyword search of Dental Informatics and Mesh terms used included dental
Informatics, economics, education, ethics history, instrumentation, legislation and
jurisprudence, methods, organization and administration, standards, statistics and
numerical data, and trends. As the main purpose of this study was to analyse the
trends of dental informatics, this is determined as a sufficient method of data
extraction. Articles were downloaded into an EndNote database, and then vetted for
their relevancy within the study in the second phase. Phase two The second phase included vetting the articles for relevancy to the subject. This
involved analysing the articles to determine their relevancy in the field of dental
informatics. This was completed by reading the titles and abstracts of the articles, as
well as analysing the keywords section for the mention of ‘dental informatics’. Inclusion criteria considered were articles only in the English language and that they
were submitted and uploaded to the PubMed database as late as September 2019. Methods Bibliometrics was used to examine the growth and progress of dental informatics
over time. All data was extracted exclusively from the PubMed online journal
database over a period of 20 years (Jan 1989 to September 2019). The search was conducted in three phases: Phase three The third phase involved excluding publications from magazine articles, editorials,
conference notes and other non-peer reviewed material. After this final stage, 236
articles were remaining for the examination. All the data used for analysis was manually collected from the articles contained
within PubMed. These articles were accessed in electronic form from PubMed, the
publisher’s database or through the University of Tasmania. Two databases were
created in Microsoft Excel 2013 in congruence with the third vetting stage for articles
which were entered into the study. The first database contained information based on the articles overall general
information, from which the following information was recorded: • Author/s • Year of publication 13 4(1), Apr 2023 Journal of Health Information and Libraries Australasia • Journal of publication
• Institution of research affiliation
• International collaboration
• Geographic region of author/s
• Number of contribution authors • Journal of publication
• Institution of research affiliation
• International collaboration
• Geographic region of author/s
• Number of contribution authors The second database contained information about the contributing authors within
the overall dataset, from which the following information was recorded: • Author name
• Institutional affiliation
• Country
• Region
• Number of contributing articles To ensure a succinct and accurate analysis, a coding scheme was developed for each
of these factors. There were certain factors that did not necessarily need to be coded. For instance, the journal of publication is already listed, and thus could be easily
analysed. These data were then coded manually and systematically. As listed above,
each paper was given an individual entry into the first database, and then each
author was given an individual entry into the second database, irrespective of
whether they had authored multiple papers in the first database. This equated to 236
entries in database one, and 671 entries in database two. For this study, the data within the two created datasets were analysed by using the
same Microsoft Excel 2013 program. The two datasets were analysed in isolation of
each other, with characteristics of both being compared throughout the analysis of
the results in the following chapter. During the data analysis, tables and charts were
developed using Excel to categorically illustrate the finding of the analysis. Results There was a total of n=236 papers on dental informatics in this study published
between 1986-2018. Figure 1 shows the number of papers published by year. Overall,
this is an average of 7.9 papers per year. The trend of papers has increased over time,
with very slight increases in the first decade of its inception in scientific papers. Whilst there were a few outlier years where productivity doubled and tripled from
the previous years, shown in the years 1999, 2002, 2003, 2007 and 2016, the level of
output in journals was stable in the first 20 years. North America produced the most research in dental informatics, with 149 paper
affiliations (ten of which were cross regional), in 61% of the total papers. Table 1
shows the distribution of the 236 papers in relation to their regional affiliation. This
also provided cross-regional partnership numbers and a total number of paper
affiliations by region. Figure 2 shows the total distribution of papers produced by 4(1), Apr 2023 4(1), Apr 2023 14 Journal of Health Information and Libraries Australasia
( )
regions over time. As exemplified by the North American and European regions,
there is linear growth in the amount of research into dental informatics as time has
progressed. Figure 1: Time span of published papers. Table 1: Top ten most published journals. Ranking
Name of Journal Used
No. of papers
% of total papers
1
Journal of Dental Education
44
18.6%
2
Journal of the American
Dental Association
17
7.20%
3
Studies in Health Technologies
and Informatics
14
5.93%
4
International Journal of
Computerized Dentistry
11
4.66%
5
Advances in Dental Research
8
3.39%
6
British Dental Journal
8
3.39%
7
Dental Clinics of North
America
7
2.97%
8
European Journal of Dental
Education
7
2.97%
9
Journal of the American
Medical Informatics Society
6
2.54%
10
American Journal of
Orthodontics and Dentofacial
Orthopedics
4
1.70%
0
2
4
6
8
10
12
14
16
18
20
1986
1989
1990
1991
1992
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
No. of Published Paper
Year of Publication Journal of Health Information and Libraries Australasia regions over time. As exemplified by the North American and European regions,
there is linear growth in the amount of research into dental informatics as time has
progressed. Results Figure 1: Time span of published papers. 0
2
4
6
8
10
12
14
16
18
20
1986
1989
1990
1991
1992
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
No. of Published Paper
Year of Publication Figure 1: Time span of published papers. Table 1: Top ten most published journals. Ranking
Name of Journal Used
No. of papers
% of total papers
1
Journal of Dental Education
44
18.6%
2
Journal of the American
Dental Association
17
7.20%
3
Studies in Health Technologies
and Informatics
14
5.93%
4
International Journal of
Computerized Dentistry
11
4.66%
5
Advances in Dental Research
8
3.39%
6
British Dental Journal
8
3.39%
7
Dental Clinics of North
America
7
2.97%
8
European Journal of Dental
Education
7
2.97%
9
Journal of the American
Medical Informatics Society
6
2.54%
10
American Journal of
Orthodontics and Dentofacial
Orthopedics
4
1.70% 15 Journal of Health Information and Libraries Australasia Figure 2: Total number of papers produce by Journal over time. 0
5
10
15
20
25
30
35
40
45
50
Total no. of Papers Published
Year of Publication
J Dent Educ
J Am Dent Assoc
Stud Health Technol Inform
Int J Conput Dent Figure 2: Total number of papers produce by Journal over time. Table 2 illustrates further the amount of collaboration between institutes through the
decades. This increased in the last decade compared to previous years, with an
emphasis on cross institutional collaboration as opposed to working within the
realms of a single institute. In terms of the number of authors on the papers
themselves, there is a high level of colleague collaboration. Whilst the highest
proportion of papers feature only one author, there are a large proportion of articles
that featured two, three and four authors. Figure 3 shows the proportion of papers
by the number of authors featured in the paper. Eight papers featured ten or more
authors and one paper contained 26 individual authors. Table 2: Top ten most productive countries by papers authors. Ranking
Country
No. Results of papers
% of total papers
1
United States
144 (15)
61.2%
2
United Kingdom
18 (6)
7.63%
3
Germany
15 (6)
6.36%
4
Australia
8 (1)
3.39%
5
Brazil
8 (3)
3.39%
6
China
6 (3)
2.54%
7
Greece
6 (3)
2.54%
8
Italy
6 (5)
2.54%
9
Thailand
5 (1)
2.12%
10
Sweden
5 (2)
2.12% Table 2: Top ten most productive countries by papers authors. 16 Journal of Health Information and Libraries Australasia Table 3: Distribution of papers by region
Region
No. Papers
produced
No papers
collaborated
Total paper
affiliation
% Papers
affiliated
Africa
2
1
3
1.22%
Asia
17
4
21
8.54%
Europe
47
11
58
23.6%
Middle East
4
-
4
1.63%
North
America
139
10
149
60.6%
Oceania
7
1
8
3.25%
South
America
8
3
11
4.47%
Figure 3: Total number of papers produced by region over time. Of the 671 individual authors, almost half of them came from North America, with
320 (48.9%) coming from North American Institutions. There were 195 authors from
European nations, and 80 from Asian nations (27.6% and 12.2% respectfully). Figure 4
shows the shows the total number of authors by region. 0
20
40
60
80
100
120
140
160
1986
1989
1990
1991
1992
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
Total No. of Papers Produced
Year of Publication
Africa
Asia
Europe
Middle East
North America
Oceania
South America Table 3: Distribution of papers by region
Region
No. Papers
produced
No papers
collaborated
Total paper
affiliation
% Papers
affiliated
Africa
2
1
3
1.22%
Asia
17
4
21
8.54%
Europe
47
11
58
23.6%
Middle East
4
-
4
1.63%
North
America
139
10
149
60.6%
Oceania
7
1
8
3.25%
South
America
8
3
11
4.47% Table 3: Distribution of papers by region
Region
No. Papers
produced
No papers
collaborated
Total paper
affiliation
% Papers
affiliated
Africa
2
1
3
1.22%
Asia
17
4
21
8.54%
Europe
47
11
58
23.6%
Middle East
4
-
4
1.63%
North
America
139
10
149
60.6%
Oceania
7
1
8
3.25%
South
America
8
3
11
4.47% Figure 3: Total number of papers produced by region over time. Results 0
20
40
60
80
100
120
140
160
1986
1989
1990
1991
1992
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
Total No. of Papers Produced
Year of Publication
Africa
Asia
Europe
Middle East
North America
Oceania
South America Figure 3: Total number of papers produced by region over time. Of the 671 individual authors, almost half of them came from North America, with
320 (48.9%) coming from North American Institutions. There were 195 authors from
European nations, and 80 from Asian nations (27.6% and 12.2% respectfully). Figure 4
shows the shows the total number of authors by region. 17 4(1), Apr 2023 4(1), Apr 2023 17 Journal of Health Information and Libraries Australasia Journal of Health Information and Libraries Australasia Journal of Health Information and Libraries Australasia
Figure 4: Number of papers produced over time, comparing levels of collaboration. 0
2
4
6
8
10
12
14
16
1986
1989
1990
1991
1992
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
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2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
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No. of Papers Published
Year of Publication
Collaborated
Didn't Collaborate gure 4: Number of papers produced over time, comparing levels of collaboratio As mentioned in the previous section, there were 41 countries represented in this
study. There were only 15 countries which had 10 or more representatives, seven of
which came from Europe. Unsurprisingly, the United States had the highest number
of authors, over 50, with 309 (46.1%) from this country. The other top five nations by
representation were the only participants to have over 20 authors, with the UK (43),
Germany (34), China (29) and Brazil (23) represented by two thirds of the total
number of authors (64.2%). Discussion The results revealed that research on the topic of dental informatics began in the mid
to late 1980s but did not really take off until the turn of the millennia. The most
productive years were in the last decade, reaching a high point in the mid 2010s. (Cesnik & Kidd 2010; Kim et al., 2011). The term ‘health/medical informatics’ was
thought of as a concept when the idea that information technology could harness a
power for high levels of data storage in the 1960s was starting to become a reality
(Fitzmaurice et al., 2002; Tachakra et al., 2003). It was not until the 1980s when the
potential of information technology in medicine was realised, primarily though the
implementation of computer-aided design and computer-aided manufacturing
(CAD-CAM) (Qi et al., 2015; Tapie et al., 2015). Computer processing powers had a
mostly linear growth from the 1980s and 1990s, but over the course of the last 15-20
years, this growth in processing power has become more logarithmic (Fitzmaurice, et
al., 2002; Tachakra et al., 2003). In this growth in power, there is a higher capacity to
use IT for medical purposes. The growth of medical-related computer software,
development of programs such as electronic records and mass amounts of data
storage have coincided with the growth in computer power (Pavis & Morris 2015). 4(1), Apr 2023 4(1), Apr 2023 18 Journal of Health Information and Libraries Australasia In terms of geographic distribution of papers and authors, North America featured in
145 papers, or 61.4% of all papers. European authors were present on 47 papers, or
around 24%. This demonstrates that America’s dental informatics researchers are at
the forefront of the current and historical research into dental informatics (Singhal et
al., 2018). It also indicates a high level of investment into the development and
implementation of dental informatics in the United States (Acharya et al., 2017;
Washington et al., 2017; Singhal et al., 2018; Wu, 2020). The introduction of the
widespread use of HIT in North America has also been aided by the HITECH Act. This
has been established to ensure that electronic health records are implemented
throughout the United States, with the supporting technology also provided. This has
diverted over USD$19 billion into the integration of HIT into American health
facilities (Hoggle, 2012; Washington et al.,2017). Discussion This investment may also act as a drawcard for influential members of the scientific
community, which can garner increased funding for projects in this field, and thus
increase knowledge and research in the field of dental informatics (Molloy et al,
2011; Wu, 2020). This becomes increasingly apparent when analysing the most
prevalent authors within this study, all of which come from the United States, with
the top three authors employed by the same institution. Historically, the United
states have always been at the forefront of computer technology advancement, and
thus it would also make sense that they have developed a high level of research into
medical informatics, including dental informatics (Tibbo, 2003; Leidner & Kayworth,
2006; Ozbolt & Saba, 2008; Acharya et al., 2017). Worldwide research is generally
thought to have global emphasis and local impacts, but this is not always the case. Developed countries make up the bulk of global research in all areas (Bean et al.,
2004; Duque et al., 2005). Whilst tools such as electronic dental records have already
improved the efficiency and quality of dental care that patients are receiving, there
are barriers to entry of dental informatics in developing countries, who cannot afford
the infrastructure for electronics within health systems (Sood et al., 2008; Ahlan &
Ahmad, 2014; Qi et al., 2015; Gonzalez-Brambila et al., 2016). This study found a low level of international collaboration, with only 25 papers
featuring international collaboration. Of these, 12 papers were conducted across
different continents. Collaboration has become a product of a globalised world, with
more technology available to provide communication and share data points and
methods becoming widespread (Godoy-Ruiz et al., 2016). In most fields this has
generally led to the ability to pool viewpoints, resources, and workloads to produce
answers to complex questions (Davidson et al., 1979; Chen et al., 2019). Whilst benefits of cross-national and cross-regional collaboration are noted, there
are limitations to the possibility of collaboration. Possible reasons can include the
length of time to develop relationships between institutions and researchers; barriers 19 4(1), Apr 2023 Journal of Health Information and Libraries Australasia in research protocols; barriers in resource gathering; failure of integration of HIT
systems; as well as possible security concerns that may occur in implementation of
HIT systems (Davidson et al., 1979; Freshwater et al., 2006; Lee et al.,2010; Chinchilla-
Rodríguez et al., 2012). Discussion It is also an issue for countries who do not have adequate
infrastructure to develop HIT systems of their own (Wagner, Park & Leydesdorff,
2015; Nolan et al., 2017). It has been noted that there are considerable difficulties in
not only implementing HIT infrastructure, but also maintaining it, with necessary
resources like healthcare professionals, hospitals and clinics and readily available
access to important structures like the internet being sparse in developing regions
(Fraser et al., 2005; Sood et al.,2008). Low-income countries that have attempted to
implement HIT have seen improvements in healthcare efficiency, with successes in
Brazil and India (Fraser et al., 2005; Sood et al., 2008; Radhakrishna et al., 2014; Bassi
et al., 2018). Whilst the level of international collaboration was low, there was an overwhelming
presence in institutional collaboration. Almost half of the total papers in this study, as
well as the majority of papers in the last decade, have had cross-institutional
involvement. As mentioned, this normally occurs across institutions within the same
countries (Ductor 2015). It can be perceived that multiple authors on papers would
lead to a higher quality study, as the greater the number of minds working on a
project would garner greater and more diverse knowledge on subjects (Edwards et
al., 2010; Zare-Farashbandi et al.,2014). Health informatics has been viewed as the modern way forward in terms of
advancement in records management, but more importantly sustainability and
improved efficiency in healthcare. The current understandings of the power of using
HIT have already been implemented to good effect in developed countries, with the
framework for further implementation already underway. This bibliometric study
aimed to analyse the current rates of research into dental informatics and may be
used to establish where the main bases of knowledge lie on the subject. This study
has assembled a collection of characteristics of all current dental informatics within
PubMed from 1986 up to 2018. These characteristics highlight the distribution of
papers in terms of region, country, and journal, as well as discussion of the most
prevalent minds in the field of dental informatics through the analysis of production
of papers, institution of origin and the rates of collaboration. This study also provides
the basis of new research for future topics of research within the field of dental
informatics as it evolves from its current state. Limitations Bibliometrics is a quantitative method that is often used to evaluate research
performance, identify trends, and inform decision-making, but it provides only one
part of the picture. High citations may not always indicate quality but may be
refuting its results. They should always be used in conjunction with other data 20 4(1), Apr 2023 Journal of Health Information and Libraries Australasia including funding received, awards granted and peer review. The process used in this
study may be limited by manual process rather than use of statistical software,
human error and incomplete data processing may have occurred. Conclusion Dental informatics is still in its infancy. The rates of research are increasing yearly,
with more methods of dental informatics implementation being researched. Health
informatics in general has been successful in achieving sustainability, with increased
efficiency and reduced resource waste being linked with HIT. Whilst rates of HIT
uptake in developed countries is high, it is still quite low in developing countries. Future research is needed to investigate more cost effective and successful methods
of dental informatics implementation, to enhance the sustainability of dental
healthcare. References Hovenga, EJS, Kidd, MR, Garde, S & Cossio, CHL 2010,
Health Informatics: An Overview, IOS Press, Washington, DC. Hovenga, E. J. Hovenga, EJS, Kidd, MR, Garde, S & Cossio, CHL (Ed.). (2010). Health
informatics: an overview. Hovenga, EJS, Kidd, MR, Garde, S & Cossio, CHL 2010,
Health Informatics: An Overview, IOS Press, Washington, DC. Golinelli, D., Boetto, E., Carullo, G., Nuzzolese, A. G., Landini, M. P., & Fantini, M. P. (2020). Adoption of digital technologies in health care during the COVID-19
pandemic: systematic review of early scientific literature. Journal of medical Internet
research, 22(11), e22280. https://doi.org/10.2196/22280. Golinelli, D., Boetto, E., Carullo, G., Nuzzolese, A. G., Landini, M. P., & Fantini, M. P. (2020). Adoption of digital technologies in health care during the COVID-19
pandemic: systematic review of early scientific literature. Journal of medical Internet
research, 22(11), e22280. https://doi.org/10.2196/22280. London, S. D., Fontelo, P., Boroumand, S., & Dye, B. A. (2022). COVID-19 provides an
opportunity for integration of dentistry into the health informatics system. The
Journal of the American Dental Association, 153(1), 3-8. https://doi.org/10.1016/j.adaj.2021.11.003. London, S. D., Fontelo, P., Boroumand, S., & Dye, B. A. (2022). COVID-19 provides an
opportunity for integration of dentistry into the health informatics system. The
Journal of the American Dental Association, 153(1), 3-8. https://doi.org/10.1016/j.adaj.2021.11.003. Sittig, D. F., Wright, A., Coiera, E., Magrabi, F., Ratwani, R., Bates, D. W., & Singh, H. (2020). Current challenges in health information technology–related patient
safety. Health informatics journal, 26(1), 181-189. https://doi.org/10.1177/1460458218814893. Sittig, D. F., Wright, A., Coiera, E., Magrabi, F., Ratwani, R., Bates, D. W., & Singh, H. (2020). Current challenges in health information technology–related patient
safety. Health informatics journal, 26(1), 181-189. https://doi.org/10.1177/1460458218814893. Sheikh, A., Anderson, M., Albala, S., Casadei, B., Franklin, B. D., Richards, M., ... &
Mossialos, E. (2021). Health information technology and digital innovation for
national learning health and care systems. The Lancet Digital Health, 3(6), e383-e396. https://doi.org/10.1016/S2589-7500(21)00005-4. Sheikh, A., Anderson, M., Albala, S., Casadei, B., Franklin, B. D., Richards, M., ... &
Mossialos, E. (2021). Health information technology and digital innovation for
national learning health and care systems. The Lancet Digital Health, 3(6), e383-e396. https://doi.org/10.1016/S2589-7500(21)00005-4. Rexhepi, H., Moll, J., Huvila, I., & Åhlfeldt, R. M. (2021). Do you want to receive bad
news through your patient accessible electronic health record? A national survey on
receiving bad news in an era of digital health. Health Informatics Journal, 27(3),
14604582211035817. Rexhepi, H., Moll, J., Huvila, I., & Åhlfeldt, R. Kane, G. M., Bakker, C. A., & Balkenende, A. R. (2018). Towards design strategies for
circular medical products. Resources, Conservation and Recycling, 135, 38-47. References References
Eysenbach, G. (2000). Consumer health informatics. BMJ, 320(7251), 1713-
1716. https://doi.org/10.1136/bmj.320.7251.1713 Gandhi, P., Khanna, S., & Ramaswamy, S. (2016). Which industries are the most digital
(and why). Harvard Business Review, 1, 45-48. Zimmerman, J. L., Ball, M. J., & Petroski, S. P. (1986). Computers in dentistry. Dental
Clinics of North America, 30(4), 739-743. Lam, R., Kruger, E., & Tennant, M. (2014). How a modified approach to dental coding
can benefit personal and professional development with improved clinical
outcomes. Journal of Evidence Based Dental Practice, 14(4), 174-182. https://doi.org/10.1016/j.jebdp.2013.12.002 Lam, R., Kruger, E., & Tennant, M. (2014). How a modified approach to dental coding
can benefit personal and professional development with improved clinical
outcomes. Journal of Evidence Based Dental Practice, 14(4), 174-182. https://doi.org/10.1016/j.jebdp.2013.12.002 Chhabra, K. G., Mulla, S. H., Deolia, S. G., Chhabra, C., Singh, J., & Marwaha, B. S. (2016). Dental informatics in India: time to embrace the change. Journal of clinical
and diagnostic research: JCDR, 10(3), ZE12. https://doi.org/10.7860/JCDR/2016/16970.7453 Islam, M. M., Poly, T. N., & Li, Y. C. J. (2018). Recent advancement of clinical
information systems: opportunities and challenges. Yearbook of medical
informatics, 27(01), 083-090. chleyer, T. K. (2003). Dental informatics: A work in progress. Advances in dental
esearch, 17(1), 9-15. https://doi.org/10.1177/154407370301700104 Schleyer, T. K. (2003). Dental informatics: A work in progress. Advances in dental
research, 17(1), 9-15. https://doi.org/10.1177/154407370301700104 Schleyer, T. K. (2003). Dental informatics: A work in progress. Advances in dental
research, 17(1), 9-15. https://doi.org/10.1177/154407370301700104 21 4(1), Apr 2023 4(1), Apr 2023 Journal of Health Information and Libraries Australasia Benoit, B., Frédéric, B., & Jean-Charles, D. (2022). Current state of dental informatics
in the field of health information systems: a scoping review. BMC oral health, 22(1), 1-
17. Hovenga, E. J. Hovenga, EJS, Kidd, MR, Garde, S & Cossio, CHL (Ed.). (2010). Health
informatics: an overview. Hovenga, EJS, Kidd, MR, Garde, S & Cossio, CHL 2010,
Health Informatics: An Overview, IOS Press, Washington, DC. Benoit, B., Frédéric, B., & Jean-Charles, D. (2022). Current state of dental informatics
in the field of health information systems: a scoping review. BMC oral health, 22(1), 1-
17. Benoit, B., Frédéric, B., & Jean-Charles, D. (2022). Current state of dental informatics
in the field of health information systems: a scoping review. BMC oral health, 22(1), 1-
17. Hovenga, E. J. Hovenga, EJS, Kidd, MR, Garde, S & Cossio, CHL (Ed.). (2010). Health
informatics: an overview. References M. (2021). Do you want to receive bad
news through your patient accessible electronic health record? A national survey on
receiving bad news in an era of digital health. Health Informatics Journal, 27(3),
14604582211035817. Grosios, K., Gahan, P. B., & Burbidge, J. (2010). Overview of healthcare in the
UK. EPMA Journal, 1, 529-534. https://doi.org/10.1177/14604582211035817. Grosios, K., Gahan, P. B., & Burbidge, J. (2010). Overview of healthcare in the
UK. EPMA Journal, 1, 529-534. https://doi.org/10.1177/14604582211035817. Grosskopf, S., Self, S., & Zaim, O. (2006). Estimating the efficiency of the system of
healthcare financing in achieving better health. Applied Economics, 38(13), 1477-
1488. Kane, G. M., Bakker, C. A., & Balkenende, A. R. (2018). Towards design strategies for
circular medical products. Resources, Conservation and Recycling, 135, 38-47. 22 22 4(1), Apr 2023 Journal of Health Information and Libraries Australasia McCombs, G. B., & Darby, M. L. (2010). New discoveries and directions for medical,
dental and dental hygiene research: low temperature atmospheric pressure
plasma. International journal of dental hygiene, 8(1), 10-
15. https://doi.org/10.1111/j.1601-5037.2009.00386.x McCombs, G. B., & Darby, M. L. (2010). New discoveries and directions for medical,
dental and dental hygiene research: low temperature atmospheric pressure
plasma. International journal of dental hygiene, 8(1), 10-
15. https://doi.org/10.1111/j.1601-5037.2009.00386.x Singaraju, S., Prasad, H., & Singaraju, M. (2012). Evolution of dental informatics as a
major research tool in oral pathology. Journal of Oral and Maxillofacial
Pathology, 16(1), 83-87. https://doi.org/10.4103/0973-029X.92979 Khanna, R. K., Cecchetti, A. A., Bhardwaj, N., Muto, B. S., & Murughiyan, U. (2022). Understanding Emergency Room Visits for Nontraumatic Oral Health Conditions in a
Hospital Serving Rural Appalachia: Dental Informatics Study. JMIR Formative
Research, 6(12), e31433. Masic, F. (2012). Information systems in dentistry. Acta Inform Med, 20 (1), 47-55. https://doi.org/10.5455/aim.2012.20.47-55. Van Noort, R. (2012). The future of dental devices is digital. Dental materials, 28(1), 3-
12. https://doi.org/10.1016/j.dental.2011.10.014 Van Raan, A. (2003). The use of bibliometric analysis in research performance
assessment and monitoring of interdisciplinary scientific developments. TATuP-
Zeitschrift für Technikfolgenabschätzung in Theorie und Praxis, 12(1), 20-29. Canese, K., & Weis, S. (2013). PubMed: the bibliographic database. The NCBI
handbook, 2(1). Frisch, M., Klocke, B., Haltmeier, M., & Frech, K. (2009). LitInspector: literature and
signal transduction pathway mining in PubMed abstracts. Nucleic acids
research, 37(suppl_2), W135-W140. Rani, J., Shah, A. R., & Ramachandran, S. (2015). pubmed. mineR: An R package with
text-mining algorithms to analyse PubMed abstracts. References Journal of biosciences, 40, 671-
682 https://doi org/10 1007/s12038 015 9552 2 Rani, J., Shah, A. R., & Ramachandran, S. (2015). pubmed. mineR: An R package with
text-mining algorithms to analyse PubMed abstracts. Journal of biosciences, 40, 671-
682. https://doi.org/10.1007/s12038-015-9552-2. 682. https://doi.org/10.1007/s12038-015-9552-2. 682. https://doi.org/10.1007/s12038-015-9552-2. National Library of Medicne. (n.d.). Pubmed Overview. https://pubmed.ncbi.nlm.nih.gov/about/ Cesnik, B., & Kidd, M. R. (2010). History of health informatics: a global
perspective. Studies in health technology and informatics, 151, 3-3. Kim, J., Jung, H., & Bates, D. W. (2011). History and Trends of. Healthcare Informatics
Research, 17(1), 3-17. 23 4(1), Apr 2023 Journal of Health Information and Libraries Australasia Fitzmaurice, J. M., Adams, K., & Eisenberg, J. M. (2002). Three decades of research on
computer applications in health care: medical informatics support at the Agency for
Healthcare Research and Quality. Journal of the American Medical Informatics
Association, 9(2), 144-160. https://doi.org/10.1197/jamia.m0867. Fitzmaurice, J. M., Adams, K., & Eisenberg, J. M. (2002). Three decades of research on
computer applications in health care: medical informatics support at the Agency for
Healthcare Research and Quality. Journal of the American Medical Informatics
Association, 9(2), 144-160. https://doi.org/10.1197/jamia.m0867. Tachakra, S., Wang, X. H., Istepanian, R. S., & Song, Y. H. (2003). Mobile e-health: the
unwired evolution of telemedicine. Telemedicine Journal and E-health, 9(3), 247-257. https://doi.org/10.1089/153056203322502632. Schleyer, T. K., Thyvalikakath, T. P., Spallek, H., Dziabiak, M. P., & Johnson, L. A. (2012). From information technology to informatics: the information revolution in dental
education. Journal of dental education, 76(1), 142-153. Qi, S., Yan, Y., Luo, E., & Hu, J. (2015). The development of dental informatics and
dental information technology in China: A systematic study. Journal of Dental
Sciences, 10(2), 176-184. https://doi.org/10.1016/j.jds.2014.07.003 Tapiea, L., Lebonb, N., Mawussic, B., Chabouisd, H. F., Durete, F., & Attalf, J. P. (2015). Understanding dental CAD/CAM for restorations–the digital workflow from a
mechanical engineering viewpoint. International journal of computerized
dentistry, 18(1), 21-44. Pavis, S., & Morris, A. D. (2015). Unleashing the power of administrative health data:
the Scottish model. Public health research & practice, 25(4), e2541541. https://doi.org/10.17061/phrp2541541. Singhal, A., McKernan, S. C., & Sohn, W. (2018). Dental public health practice,
infrastructure, and workforce in the United States. Dental Clinics, 62(2), 155-175. Acharya, A., Schroeder, D., Schwei, K., & Chyou, P. H. (2017). Update on electronic
dental record and clinical computing adoption among dental practices in the United
States. Clinical Medicine & Research, 15(3-4), 59-74. https://doi.org/10.1016/j.cden.2017.11.001. Ahmad, B. I. E. (2014). User acceptance of health information technology (HIT) in
developing countries: a conceptual model. Procedia Technology, 16, 1287-1296.
https://doi.org/10.1016/j.protcy.2014.10.145 References Washington, V., DeSalvo, K., Mostashari, F., & Blumenthal, D. (2017). The HITECH era
and the path forward. New England Journal of Medicine, 377(10), 904-906. https://doi.org/10.1056/NEJMp1703370. Wu, Y., & Wu, Y. (2020). Geographical Concentration of Funding of Academic
Research. America's Leaning Ivory Tower: The Measurement of and Response to
Concentration of Federal Funding for Academic Research, 11-28. Springer Wu, Y., & Wu, Y. (2020). Geographical Concentration of Funding of Academic
Research. America's Leaning Ivory Tower: The Measurement of and Response to
Concentration of Federal Funding for Academic Research, 11-28. Springer 24 4(1), Apr 2023 4(1), Apr 2023 Journal of Health Information and Libraries Australasia International Publishing, Cham, pp. 11-28, https://doi.org/10.1007/978-3-030-18704-
0_2. Hoggle, L. (2012). The Health Information Technology for Economic and Clinical
Health (HITECH) Act and Nutrition Inclusion in Medicare/Medicaid Electronic Health
Records: leveraging policy to support nutrition care. Journal of the Academy of
Nutrition and Dietetics, 112(12), 1935-1940. https://doi.org/10.1016/j.jand.2012.10.005. Molloy, R., Smith, C. L., & Wozniak, A. (2011). Internal migration in the United
States. Journal of Economic perspectives, 25(3), 173-196. Tibbo, H. (2003). Primarily history in America: How US historians search for primary
materials at the dawn of the digital age. The American Archivist, 66(1), 9-50. Leidner, D. E., & Kayworth, T. (2006). A review of culture in information systems
research: Toward a theory of information technology culture conflict. MIS quarterly,
357-399. Ozbolt, J. G., & Saba, V. K. (2008). A brief history of nursing informatics in the United
States of America. Nursing outlook, 56(5), 199-205. https://doi.org/10.1016/j.outlook.2008.06.008. Bean, F. D., Leach, M., & Lowell, B. L. (2004). Immigrant job quality and mobility in the
United States. Work and occupations, 31(4), 499-518. https://doi.org/10.1177/0730888404268902 https://doi.org/10.1177/0730888404268902 Sood, S. P., Nwabueze, S. N., Mbarika, V. W., Prakash, N., Chatterjee, S., Ray, P., &
Mishra, S. (2008, January). Electronic medical records: A review comparing the
challenges in developed and developing countries. In Proceedings of the 41st Annual
Hawaii International Conference on System Sciences (HICSS 2008) (pp. 248-248). IEEE. Duque, R. B., Ynalvez, M., Sooryamoorthy, R., Mbatia, P., Dzorgbo, D. B. S., & Shrum,
W. (2005). Collaboration paradox: Scientific productivity, the Internet, and problems
of research in developing areas. Social studies of science, 35(5), 755-785. https://doi.org/10.1177/0306212705053048 Duque, R. B., Ynalvez, M., Sooryamoorthy, R., Mbatia, P., Dzorgbo, D. B. S., & Shrum,
W. (2005). Collaboration paradox: Scientific productivity, the Internet, and problems
of research in developing areas. Social studies of science, 35(5), 755-785. https://doi.org/10.1177/0306212705053048 Ahmad, B. I. E. (2014). User acceptance of health information technology (HIT) in
developing countries: a conceptual model. Procedia Technology, 16, 1287-1296. https://doi.org/10.1016/j.protcy.2014.10.145 25 25 4(1), Apr 2023 4(1), Apr 2023 Journal of Health Information and Libraries Australasia Gonzalez-Brambila, C. N., Reyes-Gonzalez, L., Veloso, F., & Perez-Angón, M. A. (2016). The scientific impact of developing nations. PLoS One, 11(3), e0151328. https://doi.org/10.1371/journal.pone.0151328 Gonzalez-Brambila, C. N., Reyes-Gonzalez, L., Veloso, F., & Perez-Angón, M. A. (2016). The scientific impact of developing nations. PLoS One, 11(3), e0151328. https://doi.org/10.1371/journal.pone.0151328 Gonzalez-Brambila, C. N., Reyes-Gonzalez, L., Veloso, F., & Perez-Angón, M. A. (2016). The scientific impact of developing nations. PLoS One, 11(3), e0151328. https://doi.org/10.1371/journal.pone.0151328 Godoy-Ruiz, P., Cole, D. C., Lenters, L., & McKenzie, K. (2016). Developing
collaborative approaches to international research: Perspectives of new global health
researchers. Global Public Health, 11(3), 253-275. https://doi.org/10.1080/17441692.2014.999814 Godoy-Ruiz, P., Cole, D. C., Lenters, L., & McKenzie, K. (2016). Developing
collaborative approaches to international research: Perspectives of new global health
researchers. Global Public Health, 11(3), 253-275. https://doi.org/10.1080/17441692.2014.999814 Davidson Frame, J., & Carpenter, M. P. (1979). International research
collaboration. Social studies of science, 9(4), 481-497. https://doi.org/10.1177/030631277900900405 Chen, J. C., Dolan, M., & Lin, B. (2004). Improve processes on healthcare: current
issues and future trends. International journal of electronic healthcare, 1(2), 149-164. https://doi.org/10.1504/IJEH.2004.005862. Chen, J. C., Dolan, M., & Lin, B. (2004). Improve processes on healthcare: current
issues and future trends. International journal of electronic healthcare, 1(2), 149-164. https://doi.org/10.1504/IJEH.2004.005862. Freshwater, D., Sherwood, G., & Drury, V. (2006). International research collaboration:
Issues, benefits and challenges of the global network. Journal of Research in
Nursing, 11(4), 295-303. Freshwater, D., Sherwood, G., & Drury, V. (2006). https://doi.org/10.1177/0730888404268902 International research collaboration:
Issues, benefits and challenges of the global network. Journal of Research in
Nursing, 11(4), 295-303. Lee, B., Kwon, O., & Kim, H. J. (2011). Identification of dependency patterns in
research collaboration environments through cluster analysis. Journal of Information
Science, 37(1), 67-85. https://doi.org/110.1177/0165551510392147 Lee, B., Kwon, O., & Kim, H. J. (2011). Identification of dependency patterns in
research collaboration environments through cluster analysis. Journal of Information
Science, 37(1), 67-85. https://doi.org/110.1177/0165551510392147 Chinchilla‐Rodríguez, Z., Benavent‐Pérez, M., de Moya‐Anegón, F., & Miguel, S. (2012). International collaboration in Medical Research in Latin America and the
Caribbean (2003–2007). Journal of the American Society for Information Science and
Technology, 63(11), 2223-2238. https://doi.org/10.1002/asi.22669 Chinchilla‐Rodríguez, Z., Benavent‐Pérez, M., de Moya‐Anegón, F., & Miguel, S. (2012). International collaboration in Medical Research in Latin America and the
Caribbean (2003–2007). Journal of the American Society for Information Science and
Technology, 63(11), 2223-2238. https://doi.org/10.1002/asi.22669 Wagner, C. S., Park, H. W., & Leydesdorff, L. (2015). The continuing growth of global
cooperation networks in research: A conundrum for national governments. PloS
one, 10(7), e0131816. https://doi.org/10.1371/journal.pone.0131816 Nolan, L. B., Lucas, R., Choi, Y., Fabic, M. S., & Adetunji, J. A. (2017). The contribution
of demographic and health survey data to population and health policymaking:
evidence from three developing countries. Etude de la Population
Africaine, 31(1S2). https://doi.org/10.11564/31-1-998 Fraser, H. S., Biondich, P., Moodley, D., Choi, S., Mamlin, B. W., & Szolovits, P. (2005). Implementing electronic medical record systems in developing countries. Informatics
in primary care, 13(2). https://doi.org/10.14236/jhi.v13i2.585. 26 4(1), Apr 2023 4(1), Apr 2023 Journal of Health Information and Libraries Australasia Radhakrishna, K., Goud, B. R., Kasthuri, A., Waghmare, A., & Raj, T. (2014). Electronic
health records and information portability: a pilot study in a rural primary healthcare
center in India. Perspectives in health information Management, 11(Summer). Radhakrishna, K., Goud, B. R., Kasthuri, A., Waghmare, A., & Raj, T. (2014). Electronic
health records and information portability: a pilot study in a rural primary healthcare
center in India. Perspectives in health information Management, 11(Summer). Radhakrishna, K., Goud, B. R., Kasthuri, A., Waghmare, A., & Raj, T. (2014). Electronic
health records and information portability: a pilot study in a rural primary healthcare
center in India. Perspectives in health information Management, 11(Summer). Bassi, A., John, O., Praveen, D., Maulik, P. K., Panda, R., & Jha, V. (2018). Current status
and future directions of mHealth interventions for health system strengthening in
India: systematic review. https://doi.org/10.1177/0730888404268902 JMIR mHealth and uHealth, 6(10), e11440. https://doi.org/10.2196/11440. Bassi, A., John, O., Praveen, D., Maulik, P. K., Panda, R., & Jha, V. (2018). Current status
and future directions of mHealth interventions for health system strengthening in
India: systematic review. JMIR mHealth and uHealth, 6(10), e11440. https://doi.org/10.2196/11440. Ductor, L. (2015). Does co‐authorship lead to higher academic productivity?. Oxford
Bulletin of Economics and Statistics, 77(3), 385-407. https://doi.org/10.1111/obes.12070 Edwards, A., Hollin, I., Barry, J., & Kachnowski, S. (2010). Barriers to cross--institutional
health information exchange: a literature review. Journal of healthcare information
management: JHIM, 24(3), 22-34. Zare-Farashbandi, F., Geraei, E., & Siamaki, S. (2014). Study of co-authorship network
of papers in the Journal of Research in Medical Sciences using social network
analysis. Journal of research in medical sciences: the official journal of Isfahan
University of Medical Sciences, 19(1), 41. 27 4(1), Apr 2023 4(1), Apr 2023 4(1), Apr 2023
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